EP4058578A2 - Immunostimulatory bacteria delivery platforms and their use for delivery of therapeutic products - Google Patents

Immunostimulatory bacteria delivery platforms and their use for delivery of therapeutic products

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Publication number
EP4058578A2
EP4058578A2 EP20820673.0A EP20820673A EP4058578A2 EP 4058578 A2 EP4058578 A2 EP 4058578A2 EP 20820673 A EP20820673 A EP 20820673A EP 4058578 A2 EP4058578 A2 EP 4058578A2
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EP
European Patent Office
Prior art keywords
sting
bacterium
1bbl
immunostimulatory
immunostimulatory bacterium
Prior art date
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Pending
Application number
EP20820673.0A
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German (de)
English (en)
French (fr)
Inventor
Christopher D. Thanos
Laura Hix GLICKMAN
Alexandre Charles Michel IANNELLO
Chris Rae
Haixing Kehoe
Bret Nicholas PETERSON
Chingnam CHEUNG
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Actym Therapeutics Inc
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Actym Therapeutics Inc
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Publication date
Application filed by Actym Therapeutics Inc filed Critical Actym Therapeutics Inc
Publication of EP4058578A2 publication Critical patent/EP4058578A2/en
Pending legal-status Critical Current

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    • A61K39/00114—Interleukins [IL]
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    • A61K2039/80—Vaccine for a specifically defined cancer
    • A61K2039/82—Colon

Definitions

  • Provisional Application Serial No.62/962,162 filed on January 16, 2020, entitled “TUMOR-SPECIFIC IMMUNOSTIMULATORY BACTERIA DELIVERY PLATFORM,” to Applicant Actym Therapeutics, Inc., and inventors Laura Hix Glickman, Christopher D. Thanos, Alexandre Charles Michel Iannello, Chris Rae, and Haixing Kehoe. Benefit of priority also is claimed to co-pending U.S. Provisional Application Serial No.62/934,503, filed on November 12, 2019, entitled “TUMOR-SPECIFIC IMMUNOSTIMULATORY BACTERIA DELIVERY PLATFORM,” to Applicant Actym Therapeutics, Inc., and inventors Laura Hix Glickman, Christopher D.
  • Provisional Application Serial No.62/962,140 filed on January 16, 2020, entitled “IMMUNOSTIMULATORY BACTERIA ENGINEERED TO COLONIZE TUMORS, TUMOR-RESIDENT IMMUNE CELLS, AND THE TUMOR MICROENVIRONMENT,” to Applicant Actym Therapeutics, Inc., and inventors Christopher D. Thanos, Laura Hix Glickman, Justin Skoble, Alexandre Charles Michel Iannello, and Haixing Kehoe. This application also is related to co-pending U.S.
  • This application also is related to International Application No. PCT/US2018/041713, filed on July 11, 2018 and published as WO 2019/014398 on January 17, 2019, and to co-pending U.S. Patent Application Serial No.16/033,187, filed on July 11, 2018 and published as U.S.
  • This application also is related to U.S. Provisional Application Serial Nos. 62/811,521, filed on February 27, 2019, and 62/828,990, filed on April 03, 2019.
  • the immunostimulatory bacteria provided in each of these applications can be modified as described in this application, and such bacteria are incorporated by reference herein.
  • FIELD OF THE INVENTION Provided are attenuated immunostimulatory bacteria with genomes that are modified to, for example, reduce toxicity and improve the anti-tumor activity, such as by increasing accumulation in the tumor microenvironment, particularly in tumor- resident myeloid cells, by improving resistance to complement inactivation, by reducing immune cell death, by promoting adaptive immunity, and by enhancing T- cell function.
  • the increase in colonization of phagocytic cells improves the delivery of encoded therapeutic products to the tumor microenvironment and tumors, and permits, among other routes, systemic administration of the immunostimulatory bacteria.
  • the genome modifications result in immunostimulatory bacteria that accumulate in the tumor microenvironment and in tumor-resident immune cells, where they express the encoded therapeutic products.
  • the immunostimulatory bacteria provided herein encoded one or a plurality of complementary products that stimulate or induce or result in a robust anti-cancer response in the subject.
  • immunostimulatory bacteria that contain a plasmid encoding a therapeutic product or combinations of therapeutic products, under control of a eukaryotic promoter.
  • the genomes of the bacteria contain modifications, such as one, two, or more modifications, selected from among: a) deletion or disruption or inactivation of all or of a sufficient portion of a gene or genes, whereby the bacterium has been modified to generate penta-acylated lipopolysaccharide (LPS), wherein: the genome of the immunostimulatory bacterium is modified by deletion or disruption of all or of a sufficient portion of a gene or genes, whereby the bacterium has been modified to generate penta-acylated lipopolysaccharide; and/or hexa-acylated lipopolysaccharide is substantially reduced, by at least 10-fold, compared to the wild-type bacterium, or is absent; b) deletion or disruption or inactivation of all or of a sufficient portion of a gene or genes, whereby the bacterium has attenuated recognition by Toll-like Receptors (TLRs): TLR2, TLR4, and TLR5; c) deletion or disruption or
  • the immunostimulatory bacteria contain modifications, including deletions, insertions, and replacements, of a), d), and f), or modifications c) and d), or modifications a), c), d), e), and f), or modifications a), c), d), e), f), and i), or modifications a), d) f), and i), or modifications c), d), and i), or modifications f) and i), or modifications a)-i), or modifications a), b), d), and f), or modifications a), b), c), and d), and other combinations of a)-i).
  • the immunostimulatory bacteria also can comprise or further comprise deletion of or disruption of the genes encoding the flagella, whereby the bacterium is flagellin- (fliC-/fljB-) and does not produce flagella, wherein the wild- type bacterium has flagella.
  • the immunostimulatory bacteria can be auxotrophic for purines, such as auxotrophic for adenosine, or auxotrophic for adenosine, adenine, and/or ATP.
  • the immunostimulatory bacteria also can be purI-.
  • the immunostimulatory bacteria also can be pagP-.
  • the immunostimulatory bacteria also can be asd- (aspartate-semialdehyde dehydrogenase-), such as where the bacterium is asd- by virtue of disruption or deletion of all or a portion of the endogenous gene encoding aspartate-semialdehyde dehydrogenase (asd), whereby endogenous asd is not expressed.
  • the bacteria can encode aspartate-semialdehyde dehydrogenase (asd) on the plasmid under control of a bacterial promoter.
  • the immunostimulatory bacteria also can be msbB-, or can be pagP-/msbB-.
  • the immunostimulatory bacteria can be asd-, purI-, msbB-, flagellin- (fliC-/fljB-), and pagP-, or they can be asd- , csgD-, purI-, msbB-, flagellin- (fliC-/fljB-), and pagP-.
  • the immunostimulatory bacteria are ansB-, asd-, csgD-, purI-, msbB-, flagellin- (fliC-/fljB-), and pagP-.
  • immunostimulatory bacteria that contain a plasmid encoding a therapeutic product under control of a eukaryotic promoter, or that encode a plurality of products under control of a plurality of eukaryotic promoters or a single promoter.
  • the genome of the immunostimulatory bacteria is modified by deletion of a sufficient portion of, or by the disruption of genes, whereby the bacterium is one or more of ansB-, asd-, csgD-, purI-, msbB-, flagellin- (fliC-/fljB-), and pagP-.
  • the immunostimulatory bacteria provided herein also include those that have the genes lppA (lpp1) and/or lppB (lpp2), which encode major outer membrane lipoproteins Lpp1 (LppA) and Lpp2 (LppB), respectively, deleted or disrupted, to eliminate or substantially reduce expression of the encoded lipoprotein(s).
  • the bacteria are lppA- and lppB-.
  • immunostimulatory bacteria that contain a plasmid encoding an anti-cancer therapeutic under control of eukaryotic regulatory sequences, and that are lppA- and lppB-.
  • the immunostimulatory bacteria can be ansB-, asd-, csgD-, purI-, msbB-, flagellin- (fliC-/fljB-), pagP-, lppA-, and lppB-.
  • the therapeutic product is an anti-cancer therapeutic or a therapeutic used in cancer therapy.
  • the encoded product(s) can be operably linked to nucleic acid encoding a secretion signal, whereby, when expressed, the therapeutic product is secreted, such as secreted from a tumor-resident immune cell.
  • any of the immunostimulatory bacteria also can have one or more genes or operons involved in Salmonella pathogenicity island 1 (SPI-1) invasion deleted or inactivated, whereby the immunostimulatory bacteria do not invade or infect epithelial cells.
  • the one or more genes/operons are selected from among avrA, hilA, hilD, invA, invB, invC, invE, invF, invG, invH, invI, invJ, iacP, iagB, spaO, spaQ, spaR, spaS, orgA, orgB, orgC, prgH, prgI, prgJ, prgK, sicA, sicP, sipA, sipB, sipC, sipD, sirC, sopB, sopD, sopE, sopE2, sprB, and sptP.
  • the plasmid in the immunostimulatory bacteria can be present in low copy number or medium copy number.
  • the plasmid can contain a medium-to-low copy number origin of replication, such as a low copy number origin of replication. In some embodiments, the plasmid is present in higher copy number.
  • medium copy number is less than 150 or less than about 150, and more than 20 or about 20, or is between 20 or 25 and 150; and low copy number is less than 25, or less than 20, or less than about 25, or less than about 20 copies.
  • low to medium copy number is less than about 150 copies, or less than 150 copies; low copy number is less than about 25 copies, or less than 25 copies.
  • nucleic acid constructs which are nucleic acid molecules that encode products, such as proteins, that are designed to be introduced into a cell or into a plasmid for expression of the encoded product.
  • the constructs contain nucleic acid encoding a plurality of anti-cancer products as a polycistronic sequence under control of a single promoter.
  • the promoter can be a eukaryotic promoter.
  • polycistronic sequences such as enhancers, and nucleic acid encoding protein trafficking signals, such as secretion signals, and other regulatory sequences, such as terminators, including bacterial terminators to prevent read-through from bacterial promoters on the constructs, and particular configurations of elements and the order of the product- encoding nucleic acid open reading frames and/or genes, are provided and described herein.
  • the polycistronic sequence can include signals or encoded signals, such as peptides, that result in expression of discrete products encoded by the polycistronic construct. Exemplary of such peptides are the 2A family of viral peptides.
  • the constructs include such peptides or other signal between each open reading frame encoding each product.
  • the 2A peptide include one or more of T2A, P2A, E2A, or F2A.
  • Included among the anti-cancer products are any that are used for treatment of cancer or to promote or aid or stimulate or help an anti-cancer response in a subject.
  • the anti-cancer products are proteins.
  • the encoded products include one or more immunostimulatory protein(s) that confer(s )or contributes to an anti-tumor immune response in a tumor microenvironment.
  • Exemplary encoded products is/are immunostimulatory protein(s) that confer(s) or contribute(s) to an anti-tumor immune response in the tumor microenvironment, such as, for example, any selected from among one or more of: IL-2, IL-7, IL-12p70 (IL-12p40 + IL-12p35), IL-15, IL-2 that has attenuated binding to IL-2Ra, IL-15/IL-15R alpha chain complex, IL-18, IL-21, IL-23, IL-36 ⁇ , IL-2 modified so that it does not bind to IL-2Ra, CXCL9, CXCL10, CXCL11, interferon- ⁇ , interferon- ⁇ , interferon- ⁇ , CCL3, CCL4, CCL5, proteins that are involved in or that effect or potentiate recruitment/persistence of T-cells, co- stimulatory proteins, such as, CD40, CD40 ligand (CD40L), CD28, OX40, OX40 ligand (O
  • an immunostimulatory protein that confers or contributes to an anti-tumor immune response in the tumor microenvironment that is selected from among one or more of: IFN- ⁇ , IFN- ⁇ , GM-CSF, IL-2, IL-7, IL-12, IL- 15, IL-18, IL-21, IL-23, IL-12p70 (IL-12p40 + IL-12p35), IL-15/IL-15R alpha chain complex, IL-36 gamma, IL-2 that has attenuated binding to IL-2Ra, IL-2 that is modified so that it does not bind to IL-2Ra, CXCL9, CXCL10 (IP-10), CXCL11, CCL3, CCL4, CCL5, molecules involved in the potential recruitment and/or persistence of T-cells, CD40, CD40 ligand (CD40L), OX40, OX40 ligand (OX40L), 4-1BB, 4-1BB ligand (4-1BBL), 4-1BBL with
  • the construct can contain nucleic acid encoding 4-1BBL with a deleted, or partially deleted cytoplasmic domain, or a partially deleted cytoplasmic domain and optionally including amino acid modifications, whereby the resulting 4-1BBL assumes the proper orientation when expressed in a cell (see, SEQ ID NOs:389-392 and detailed description below providing exemplary modified 4- 1BBL variants with truncated cytoplasmic domains, where residues are replaced with positively charged residues (i.e., K and L) to confer proper orientation when expressed in a cell.
  • the cytoplasmic domain is truncated sufficiently to eliminate or reduce immunosuppressive reverse signaling.
  • Constructs also can contain nucleic acid encoding any of the following products and combinations of products: one or more of IL-12, or IL-15, or IL12p70, or IL-15/IL-15R alpha chain complex; a cytokine and a STING pathway agonist; a cytokine, a sting pathway agonist, and either a co-stimulatory molecule or an immune checkpoint inhibitor; a cytokine and a STING pathway agonist, and a TGF-beta polypeptide antagonist; a cytokine, a STING pathway agonist, a TGF-beta polypeptide antagonist, and either a co-stimulatory molecule (receptor or ligand) or an immune checkpoint inhibitor, wherein a STING pathway agonist is any product that increases type I interferon expression via activation of the STING pathway.
  • constructs that encode a Stimulator of Interferon Genes (STING) polypeptide, or a variant thereof or chimera thereof, as described in detail herein.
  • STING Stimulator of Interferon Genes
  • the constructs include those that encode a combination of therapeutic products, selected from among the following combinations: an anti-CTLA-4 antibody and a STING polypeptide, IL-15 and a STING polypeptide, 4-1BBL and a STING polypeptide, A TGF-beta decoy receptor or polypeptide antagonist, and a STING polypeptide, IL-12 and STING polypeptide an anti-CTLA-4 antibody, IL-15, and a STING polypeptide, 4-1BBL, IL-15, and a STING polypeptide, TGF-beta decoy receptor or polypeptide antagonist, and IL-15, and a STING polypeptide, an anti-CTLA-4 antibody, and IL-12, and a STING polypeptide, 4-1BBL, IL-12
  • constructs include those that encode a combination of therapeutic products selected from among: IL-2 and IL-12p70; IL-2 and IL-21; IL-2, IL-12p70, and a STING gain-of-function (GOF) variant; IL-2, IL-21, and a STING GOF variant; IL-2, IL-12p70, a STING GOF variant, and 4-1BBL (including 4-1BBL ⁇ cyt), where ⁇ cyt is a deleted cytoplasmic domain; IL-2, IL-21, a STING GOF variant, and 4-1BBL (including 4-1BBL ⁇ cyt); IL-15/IL-15R ⁇ , and a STING GOF variant; IL-15/IL-15R ⁇ , a STING GOF variant, and 4-1BBL (including 4-1BBL ⁇ cyt); IL-15/IL-15R ⁇ and IL-12p70; IL-15/IL-15R ⁇ and IL-21; IL-15/IL-15R ⁇ , IL
  • Exemplary of the STING polypeptides are those in which the STING polypeptide is modified to result in increased or constitutive expression of a type I interferon, or is a chimeric polypeptide comprising a human STING polypeptide with a C-terminal tail from a different species that has lower NF- ⁇ B signaling activity than the NF- ⁇ B signaling activity of human STING, and where, for example: the TRAF6 binding site in the CTT optionally is deleted; and the human STING protein has the sequence set forth in any of SEQ ID NOs:305-309.
  • encoded products include those where the encoded therapeutic proteins comprise IL- 12p70 and a chimeric human STING polypeptide with a CTT from Georgian devil and an amino acid replacement that results in increased or constitutive expression of type I interferon, or is a STING polypeptide with an amino acid replacement that results in increased or constitutive expression of type I interferon, where a mutation that results in increased or constitutive expression of type I interferon is a gain-of- function mutation.
  • Exemplary are STING proteins or polypeptides with replacements described in the detailed description, such as where the amino replacement in the STING polypeptide corresponds to R284G or N154S/R284G with reference, for alignment, to any of SEQ ID NOs: 305-309, which set forth human STING proteins.
  • These constructs can additional encode IL-36 ⁇ and/or an immune checkpoint inhibitor antibody.
  • antibodies include an antigen-binding portions thereof, and any of the various forms of antibodies, such as, but not limited to, scFvs, and scFv-Fc (generally IgG Fc), where the presence of the Fc multimerizes the resulting product so that it has two chains.
  • Immune checkpoints targeted include, but are not limited to, CTLA-4 or PD-1 or PD-L1, and antibody forms of include scFV and is an scFV-Fc two-chain polypeptides.
  • plasmids that contain the constructs described above and throughout the disclosure herein. Plasmids include a bacterial plasmid, where the construct is operatively linked to eukaryotic transcriptional regulatory sequences.
  • compositions such as pharmaceutical compositions, that contain the mixture of anti-cancer protein products encoded by the construct or plasmid as the only anti-cancer proteins in the compositions. Hence, among these are provided compositions that contain complementary combinations of therapeutic proteins; the mixtures include unique combinations of agents.
  • immunostimulatory bacteria that contain any of the constructs and/or plasmids.
  • the constructs and plasmids can be provided in or otherwise introduced into any of the immunostimulatory bacteria provided herein, including any discussed above and below.
  • the constructs and plasmids also can be introduced into suitable bacteria known in the art, such as bacteria described in publications, such as International Application Publication Nos. WO2020/172461 and WO2020/172462, and U.S. Patent Nos.10,449,237, 10,286,051, and 9,616,114.
  • the immunostimulatory bacteria provided herein include genome modifications, such as deletions, disruptions, alterations, such as changing the orientation of all or part of the gene, so that functional gene products in not expressed.
  • the immunostimulatory bacteria provided those that are modified so that the resulting bacteria are msbB-/purI-.
  • the bacteria are msbB- and purI-, whereby the full length of at least the coding portion of the msbB- and/or purI- genes are/is deleted.
  • the genome of the bacteria also can be modified so that bacteria lack flagella. This is effected in bacteria that normally express flagella.
  • bacteria for example the genes in Salmonella or equivalent genes in other species to fliC-/fljB- can be deleted or other modified so that functional gene product is not expressed.
  • the bacteria also can be modified so that they are adenosine auxotrophs, and/or are msbB-/pagP-.
  • immunostimulatory bacteria and pharmaceutical compositions containing them where the bacteria do not express L- asparaginase II, whereby the bacteria ansB-.
  • immunostimulatory bacteria that contain a plasmid encoding a therapeutic product under control of a eukaryotic promoter, where the genome of the immunostimulatory bacterium is modified by deletion or disruption of all or of a sufficient portion of a gene or genes, whereby the bacterium does not activate the synthesis of secreted asparaginase.
  • Exemplary of such bacteria are those in which the asparaginase is L-asparaginase II encoded by the gene ansB. It shown herein that in parental strain VNP20009, which is msbB- and purI-, the genes are not completely deleted.
  • the genome of the bacterium is modified so that the full length of at least the coding portion of the msbB- and purI- genes is deleted. These strains are more fit, grow faster and/or to a greater extent than the parental strain.
  • the bacteria can be modified so that the native asd gene product is inactive or not expressed.
  • the asd gene is encoded on a plasmid under control of a prokaryotic promoter, such as an inducible promoter.
  • the strains include modifications so that bacteria that lack flagella, and are pagP-, ansB-, and csgD-. In addition the bacteria are purI- and asd-.
  • strains include modified parental strains that already are msbB- and purI-, and/or have other modifications, particularly those that modify the LPS, that also are ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB/ ⁇ csgD.
  • the strains also can be an adenosine or adenosine and adenine auxotroph.
  • Encoded therapeutic products include nucleic acids and proteins.
  • the plasmid can encode two or more therapeutic products. Exemplary products include, but are not limited to, a cytokine, a protein that constitutively induces a type I interferon (IFN), and a co-stimulatory receptor or ligand. Further exemplary combinations are described below.
  • the co-stimulatory molecule lacks all or a portion of the cytoplasmic domain for expression on an antigen-presenting cell (APC), whereby the truncated molecule is capable of constitutive immuno-stimulatory signaling to a T-cell through co-stimulatory receptor engagement, and is unable to counter-regulatory signal to the antigen-presenting cell (APC), due to the deleted or truncated or otherwise modified cytoplasmic domain or portion thereof.
  • Other products include enzymes that activate therapeutic proteins, such as those that activate prodrugs.
  • the immunostimulatory bacteria provided herein encode anti-cancer therapeutics, including combinations of therapeutic products that combine to provide a robust anti-cancer response.
  • proteins encoded are each of the products listed above and below, and combinations of products from different classes. Included are the co-stimulatory proteins, such as 4- 1BBL, particularly those with truncated or deleted cytoplasmic domains to eliminate immunosuppressive reverse signaling, and also any compensatory mutations to ensure that the resulting protein is correctly oriented in the cell membrane when expressed in a cell.
  • co-stimulatory proteins such as 4- 1BBL, particularly those with truncated or deleted cytoplasmic domains to eliminate immunosuppressive reverse signaling, and also any compensatory mutations to ensure that the resulting protein is correctly oriented in the cell membrane when expressed in a cell.
  • Other products include STING pathway agonists to induce or result in constitutive expression of type I interferons. These products include STING protein and, particularly, the modified and chimeric STING proteins provided and described herein.
  • cytokines such as IL-12, IL-15, IL-21, L-12p70 (IL-12p40 + IL- 12p35), IL-2 that has attenuated binding to IL-2Ra, IL-15/IL-15R alpha chain complex, and others, such as IL-18, IL-21, IL-23, IL-36 ⁇ , also are encoded on the plasmids.
  • STING pathway agonist proteins such as STING
  • antibodies such as checkpoint inhibitor antibodies, including anti-CTLA-4 antibodies, can be encoded on the plasmids.
  • the antibodies can be scFvs and also scFvs-Fc two-chain forms, as well as other forms. Additionally, among other products, TGF-beta antagonists and TGF-beta receptor decoys can be included.
  • the encoded therapeutic products can be operatively linked to nucleic acid encoding regulatory sequences recognized by a eukaryotic host, such as, for example, secretion signals to effect secretion from a cell comprising the bacterium or plasmid. In embodiments where the immunostimulatory bacteria encode two or more products, expression of each product can be under control of a separate promoter.
  • two or more products can be expressed under control of a single promoter, and each product is separated by nucleic acid encoding, for example, an internal ribosomal entry site (IRES), or a 2A peptide, to effect separate expression of each encoded therapeutic product.
  • IRS internal ribosomal entry site
  • exemplary 2A peptides are T2A, F2A, E2A, or P2A, which can flank nucleic acids encoding the therapeutic products, to effect separate expression of the therapeutic products expressed under control of a single promoter.
  • the therapeutic products are expressed under control of a eukaryotic promoter, such as an RNA polymerase II promoter, or an RNA polymerase III promoter.
  • RNA polymerase II promoter that is a viral promoter, or a mammalian RNA polymerase II promoter, such as, but not limited to, as a cytomegalovirus (CMV) promoter, an SV40 promoter, an Epstein-Barr virus (EBV) promoter, a herpes virus promoter, an adenovirus promoter, an elongation factor-1 (EF-1) alpha promoter, a UBC promoter, a PGK promoter, a CAGG promoter, an adenovirus 2 or 5 late promoter, an EIF4A1 promoter, a CAG promoter, or a CD68 promoter.
  • CMV cytomegalovirus
  • EBV Epstein-Barr virus
  • EF-1 elongation factor-1
  • the plasmids further can include other eukaryotic regulatory sequences, such as terminators and/or promoters selected from among SV40, human growth hormone (hGH), bovine growth hormone (BGH or bGH), MND (a synthetic promoter that contains the U3 region of a modified MoMuLV LTR with myeloproliferative sarcoma virus enhancer), chicken beta- globulin, and rbGlob (rabbit globulin) genes, to control expression of the therapeutic product(s).
  • Other regulatory sequences include a polyA tail, a Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE), and a Hepatitis B virus Posttranscriptional Regulatory Element (HPRE).
  • the encoded therapeutic products include any described herein and in the original claims, such as nucleic acid encoding a protein that is part of a cytosolic DNA/RNA sensor pathway that leads to expression of type I interferon (IFN), or a variant thereof.
  • Type I IFNs include interferon- ⁇ and interferon- ⁇ .
  • Variants include those that, when expressed in a subject, lead to constitutive expression of type I IFN.
  • GEF gain-of-function
  • cytosolic nucleic acids nucleotides, dinucleotides, or cyclic dinucleotides to result in expression of type I IFN.
  • exemplary of these proteins is a protein selected from among STING, RIG-I, MDA-5, IRF-3, IRF-7, TRIM56, RIP1, Sec5, TRAF3, TRAF2, TRAF6, STAT1, LGP2, DDX3, DHX9, DDX1, DDX9, DDX21, DHX15, DHX33, DHX36, DDX60, and SNRNP200, and variants thereof that have increased activity, or that result in constitutive expression of type I interferon (IFN).
  • IFN type I interferon
  • Variants include a variant of STING, RIG-I, IRF-3, or MDA5, in which one or more serine (S) or threonine (T) residue(s) that is/are phosphorylated as a consequence of viral infection, is/are replaced with an aspartic acid (D), whereby the resulting variant is a phosphomimetic that constitutively induces type I IFN, and any known to those of skill in the art and/or described herein.
  • Variants include, for example, those wherein the mutations are selected as follows: a) in STING, with reference to SEQ ID NOs: 305-309, one or more selected from among: S102P, V147L, V147M, N154S, V155M, G166E, C206Y, G207E, S102P/F279L, F279L, R281Q, R284G, R284S, R284M, R284K, R284T, R197A, D205A, R310A, R293A, T294A, E296A, R197A/D205A, S272A/Q273A, R310A/E316A, E316A, E316N, E316Q, S272A, R293A/T294A/E296A, D231A, R232A, K236A, Q273A, S358A/E360A/S366A, D231A/R232A/K236A/
  • the immunostimulatory bacteria also can encode an immunostimulatory protein that confers or contributes to an anti-tumor immune response in the tumor microenvironment.
  • immunostimulatory protein that confers or contributes to an anti-tumor immune response in the tumor microenvironment.
  • immunostimulatory proteins include, but are not limited to, a cytokine, a chemokine, or a co-stimulatory molecule.
  • IL-2 IL-2, IL-7, IL-12p70 (IL-12p40 + IL-12p35), IL-15, IL-36 gamma, IL-2 that has attenuated binding to IL-2Ra, IL-15/IL-15R alpha chain complex, IL-18, IL-21, IL-23, IL-2 modified so that it does not bind to IL-2Ra, CXCL9, CXCL10, CXCL11, interferon- ⁇ , interferon- ⁇ , interferon- ⁇ , CCL3, CCL4, CCL5, proteins that are involved in or that effect or potentiate the recruitment and/or persistence of T-cells, CD40, CD40 ligand (CD40L), CD28, OX40, OX40 ligand (OX40L), 4-1BB, 4-1BB ligand (4-1BBL), members of the B7-CD28 family, CD47 antagonists, an anti-IL-6 antibody or IL-6 binding de
  • the co- stimulatory molecule selected from among CD40, CD40 ligand, CD28, OX40, OX40 ligand, 4-1BB, and 4-1BB ligand, can be truncated, such that the molecule lacks a cytoplasmic domain (or a portion thereof) for expression on an antigen-presenting cell (APC); and the truncated gene product is capable of constitutive immunostimulatory signaling to a T-cell through co-stimulatory receptor engagement, and is unable to counter-regulatory signal to the antigen-presenting cell (APC), due to the deleted cytoplasmic domain, or partially deleted or truncated cytoplasmic domain, to eliminate the immunosuppressive reverse signaling.
  • APC antigen-presenting cell
  • TGF-beta polypeptide antagonists such as an anti-TGF-beta antibody or antibody fragment, an anti-TGF-beta receptor antibody or antibody fragment, a soluble TGF-beta antagonist polypeptide, or a TGF-beta binding decoy receptor.
  • the plasmids can encode a therapeutic antibody or antigen-binding fragment thereof, such as, for example, a Fab, Fab’, F(ab’)2, single-chain Fv (scFv), scFv-Fc, Fv, dsFv, nanobody, diabody fragment, or a single-chain antibody.
  • the immunostimulatory bacteria provided herein contain a plasmid that encodes two or more therapeutic proteins selected from among: a) an immunostimulatory protein that confers or contributes to an anti-tumor immune response in the tumor microenvironment; b) one or more of a protein that is part of a cytosolic DNA/RNA sensor pathway that leads to expression of type I interferon (IFN), or a variant thereof that has increased activity to increase expression of type I IFN, or a variant thereof that results in constitutive expression of a type I IFN; and c) an anti-cancer antibody or antigen-binding portion thereof.
  • IFN type I interferon
  • the immunostimulatory protein can be a co-stimulatory molecule that is one that lacks a cytoplasmic domain or a sufficient portion thereof, for expression on an antigen- presenting cell (APC), whereby the truncated co-stimulatory molecule is capable of constitutive immunostimulatory signaling to a T-cell through co-stimulatory receptor engagement, and is unable to counter-regulatory signal to the antigen presenting cell (APC).
  • APC antigen-presenting cell
  • the immunostimulatory bacteria encode at least two therapeutic products selected from among a cytokine, a protein that constitutively induces a type I IFN, a co-stimulatory molecule, and an anti-cancer antibody or antigen-binding portion thereof, which can be under control of a single promoter.
  • expression of the nucleic acid encoding at least two or all of the products is under control of a single promoter, and the nucleic acid encoding each product is separated by nucleic acid encoding 2A polypeptides, whereby, upon translation, each product is separately expressed.
  • each product can be operatively linked to nucleic acid encoding a sequence that directs secretion of the expressed product from a cell.
  • immunostimulatory bacteria that encode two or more therapeutic products, wherein at least one product is selected from a), and at least one is selected from b), and a) is IL-2, IL-7, IL-12p70 (IL-12p40 + IL-12p35), IL-15, IL-23, IL-36 gamma, IL-2 that has attenuated binding to IL-2Ra, IL-15/IL-15R alpha chain complex, IL-18, IL-2 modified so that it does not bind to IL-2Ra, CXCL9, CXCL10, CXCL11, interferon- ⁇ , interferon- ⁇ , CCL3, CCL4, CCL5, proteins that are involved in or that effect or potentiate the recruitment and/or persistence of T cells, CD40, CD40 Ligand (CD40L), OX40, O
  • TGF-beta inhibitory antibody a TGF-beta binding decoy receptor
  • an anti-IL-6 antibody an IL-6 binding decoy receptor
  • exemplary of combinations of encoded therapeutic products are any of the following combinations of therapeutic products: IL-2 and IL-12p70; IL-2 and IL-21; IL-2, IL-12p70, and a STING GOF variant; IL-2, IL-21, and a STING GOF variant; IL-2, IL-12p70, a STING GOF variant, and 4-1BBL (including 4-1BBL ⁇ cyt, where ⁇ cyt is a deleted cytoplasmic domain, and 4-1BBL with a truncated cytoplasmic domain (4-1BBLcyt trunc)); IL-2, IL-21, a STING GOF variant, and 4-1BBL (including 4-1BBL ⁇ cyt, and 4-1BBL with a truncated cytoplasmic domain (4-1BBLc
  • the 4-1BBL molecule can be a full- length protein (see, e.g., SEQ ID NOs:389 and 393, for human and mouse 4-1BBL, respectively); a 4-1BBL variant with the cytoplasmic domain deleted (4-1BBL ⁇ cyt; see e.g., SEQ ID NOs:390 and 394, for human and murine 4-1BBL ⁇ cyt, respectively); a 4-1BBL variant with a truncated (i.e., not fully deleted) cytoplasmic domain (4-1BBLcyt trunc; see, e.g., SEQ ID NOs:391-392 and SEQ ID NOs:395-396, for exemplary human and mouse 4-1BBLcyt trunc variants); or a 4-1BBL molecule with a modified cytoplasmic domain, in which one or more Ser residues, which act as phosphorylation sites, are replaced at an appropriate locus or loci, such as
  • an anti-CTLA-4 antibody can include an anti-CTLA-4 antibody fragment, such as an anti-CTLA-4 scFv (see, e.g., SEQ ID NOs:403 and 404, for exemplary human and mouse anti-CTLA-4 scFv fragments, respectively), or an anti-CTLA-4 scFv-Fc (see, e.g., SEQ ID NOs:402 and 405, for exemplary human and mouse anti-CTLA-4 scFv- Fc fragments, respectively).
  • an anti-CTLA-4 antibody fragment such as an anti-CTLA-4 scFv (see, e.g., SEQ ID NOs:403 and 404, for exemplary human and mouse anti-CTLA-4 scFv fragments, respectively), or an anti-CTLA-4 scFv-Fc (see, e.g., SEQ ID NOs:402 and 405, for exemplary human and mouse anti-CTLA-4 scFv- Fc fragments,
  • the immunostimulatory bacteria provided herein encode the modified non-human STING proteins, non-human STING proteins, and chimeras, as described herein.
  • STING proteins that are encoded by the immunostimulatory bacteria are provided herein and described throughout. Provided herein are: 1.
  • Non-human STING proteins where the non-human STING protein is one that has lower NF- ⁇ B activation than the human STING protein, and, optionally, higher type I interferon activation activity compared to the wild-type (WT) human STING protein.
  • WT wild-type
  • These non-human STING proteins are modified to include a mutation or mutations so that they have increased activity, or act constitutively in the absence of cytosolic nucleic acid signaling.
  • the mutations are typically amino acid mutations that occur in interferonopathies in humans, such as those described above for human STING.
  • the corresponding mutations are introduced into the non-human species STING proteins, where corresponding amino acid residues are identified by alignment.
  • the TRAF6 binding site in the C-terminal tail (CTT) of the STING protein is deleted, reducing NF- ⁇ B signaling activity.
  • CTT C-terminal tail
  • the TRAF6 binding site is optionally deleted in these chimeras.
  • the modified STING proteins of 2 that also include the mutations of 1. 4.
  • Delivery vehicles such as immunostimulatory bacteria, any provided herein or known to those of skill in the art, including, for example, exosomes, nanoparticles, minicells, cells, liposomes, lysosomes, oncolytic viruses, and other viral vectors, that encode the modified STING proteins of any of 1-3. 5.
  • Delivery vehicles such as immunostimulatory bacteria, any provided herein or known to those of skill in the art, including, for example, exosomes, nanoparticles, minicells, cells, liposomes, lysosomes, oncolytic viruses, and other viral vectors, that encode unmodified STING from a non-human species whose STING protein has reduced NF- ⁇ B signaling activity compared to that of human STING, and optionally, increased type I interferon stimulating/signaling activity compared to that of human STING.
  • Cells non-zygotes, if human
  • cells used for cell therapy such as T-cells and stem cells, and cells used to produce the STING proteins of any of 1-3. 7.
  • compositions that contain the STING proteins of any of 1- 3, or the delivery vehicles of 4 and 5, or the cells of 6. 8. Uses and methods of treatment of cancer by administering any of 1-7, as described herein for the immunostimulatory bacteria. Assays and methods to assess NF- ⁇ B activity (signaling activity), and type I interferon stimulating activity or interferon- ⁇ stimulating activity of STING are described herein, and also are known to those of skill in the art. Methods include those described, for example, in de Oliveira Mann et al.
  • the non-human STING proteins can be, but are not limited to, STING proteins from the following species: Colombian devil (Sarcophilus harrisii; SEQ ID NO:349), marmoset (Callithrix jacchus; SEQ ID NO:359), cattle (Bos taurus; SEQ ID NO:360), cat (Felis catus; SEQ ID NO:356), ostrich (Struthio camelus australis; SEQ ID NO:361), crested ibis (Nipponia nippon; SEQ ID NO:362), coelacanth (Latimeria chalumnae; SEQ ID NOs:363-364), boar (Sus scrofa; SEQ ID NO:365), bat (Rousettus aegyptiacus; SEQ ID NO:366), manatee (Trichechus manatus latirostris; SEQ ID NO:367), ghost shark (Callorhinchus milii; S
  • the immunostimulatory bacteria provided herein, by virtue of the ability to infect myeloid cells, such as tumor-resident and tissue-resident macrophages, and to retain viability for at least a limited time, and/or that deliver plasmids that encode therapeutic products that result in expression of type I IFN and/or other immune-stimulating products, such as gain-of-function (GOF) variants that do not require cytosolic nucleic acids, nucleotides, dinucleotides, or cyclic dinucleotides to result in expression of type I IFN, can convert macrophages that have the M2 phenotype into M1 or M1-like, with immunosuppressive properties reduced or eliminated, and immune-stimulating, anti-t
  • GAF gain-of-function
  • immunostimulatory bacteria that contain a plasmid encoding a therapeutic product, where infection of a macrophage, including human macrophages, by the bacterium, converts an M2 macrophage to an M1 phenotype or M1-like phenotype macrophage.
  • immunostimulatory bacteria that contain a plasmid encoding a therapeutic product whose expression in a macrophage results in the conversion of, or converts, M2 macrophages, such as human M2 macrophages, to an M1 or M1-like phenotype.
  • the immunostimulatory bacteria with such properties include any of the bacteria provided herein that contain genome modifications that result in infection of tumor-resident (in subjects with cancer), and tissue-resident myeloid cells.
  • Exemplary of the therapeutic products are those that are part of a cytosolic DNA/RNA sensor pathway that leads to expression of type I interferon (IFN), particularly constitutive expression.
  • IFN type I interferon
  • the immunostimulatory bacteria include any that can be modified as described herein, including the species listed herein, such as Salmonella species and strains.
  • immunostimulatory bacteria in which an encoded therapeutic product, such as a protein, is linked to a moiety that confers an improved pharmacological property, such a pharmacokinetic or pharmacodynamic property, such as increased serum half-life.
  • an encoded therapeutic product comprises an Fc domain, or a half-life extending moiety, such as human serum albumin, or a portion thereof.
  • Half-life extension modalities or methods include, for example, PEGylation, modification of glycosylation, sialylation, PASylation (modification with polymers of PAS amino acids that are about 100-200 residues in length), ELPylation (see, e.g., Floss et al.
  • HAPylation modification with a glycine homopolymer
  • fusion to human serum albumin fusion to GLK, fusion to CTP, GLP fusion, fusion to the constant fragment (Fc) domain of a human immunoglobulin (IgG)
  • IgG human immunoglobulin
  • transferrin fusion to non-structured polypeptides, such as XTEN (also referred to as rPEG, which is a genetic fusion of non-exact repeat peptide sequences, containing A, E, G, P, S, and T; see, e.g., Schellenberger et al. (2009) Nat.
  • immunostimulatory bacteria where the encoded therapeutic product comprises the B7 protein transmembrane domain, or where the therapeutic product is GPI-anchored by virtue of an endogenous or added GPI anchor.
  • the encoded therapeutic product can comprise a fusion to collagen.
  • the immunostimulatory bacteria in any and all embodiments can be any suitable species. Where reference is made to particular genes and gene modifications, the genes and modifications are those that correspond to the genes and modifications referenced with respect to Salmonella, as an exemplary species.
  • Species and strains include, for example, a strain of Rickettsia, Klebsiella, Bordetella, Neisseria, Aeromonas, Francisella, Corynebacterium, Citrobacter, Chlamydia, Haemophilus, Brucella, Mycobacterium, Mycoplasma, Legionella, Rhodococcus, Pseudomonas, Helicobacter, Vibrio, Bacillus, and Erysipelothrix.
  • Rickettsia rickettsiae Rickettsia prowazekii, Rickettsia tsutsugamuchi, Rickettsia mooseri, Rickettsia sibirica, Bordetella bronchiseptica, Neisseria meningitidis, Neisseria gonorrhoeae, Aeromonas eucrenophila, Aeromonas salmonicida, Francisella tularensis, Corynebacterium pseudotuberculosis, Citrobacter freundii, Chlamydia pneumoniae, Haemophilus somnus, Brucella abortus, Mycobacterium intracellulare, Legionella pneumophila, Rhodococcus equi, Pudomonas aeruginosa, Helicobacter mustelae, Vibrio cholerae, Bacillus subtilis, Erysipelothrix
  • the bacteria can be attenuated, or rendered of low toxicity or non-toxic, by virtue of the modifications described herein.
  • Exemplary of bacteria are species of Salmonella, such as a Salmonella typhimurium strain.
  • the immunostimulatory bacteria provided herein include those that endogenously encode and express, or are modified to encode and express, a gene encoding resistance to complement killing (rck), such as a Salmonella rck gene.
  • Therapeutic E. coli are modified to encode rck so that they can be administered systemically.
  • delivery vehicles, cells, pharmaceutical compositions, methods, uses, and treatments of cancer particularly in humans.
  • companion diagnostics and methods for selection of subjects for treatment, and methods for monitoring treatment are also provided.
  • Figure 1 depicts the alignment of wild-type human and Kenyan devil STING proteins.
  • Figure 2 depicts the alignment of wild-type human and marmoset STING proteins.
  • Figure 3 depicts the alignment of wild-type human and cattle STING proteins.
  • Figure 4 depicts the alignment of wild-type human and cat STING proteins.
  • Figure 5 depicts the alignment of wild-type human and ostrich STING proteins.
  • Figure 6 depicts the alignment of wild-type human and crested ibis STING proteins.
  • Figure 7 depicts the alignment of wild-type human and coelacanth (SEQ ID NO:345) STING proteins.
  • Figure 8 depicts the alignment of wild-type human and zebrafish STING proteins.
  • Figure 9 depicts the alignment of wild-type human and boar STING proteins.
  • Figure 10 depicts the alignment of wild-type human and bat STING proteins.
  • Figure 11 depicts the alignment of wild-type human and manatee STING proteins.
  • Figure 12 depicts the alignment of wild-type human and ghost shark STING proteins.
  • Figure 13 depicts the alignment of wild-type human and mouse STING proteins.
  • Figure 14 depicts an exemplary construct containing the asd expression cassette, including the bacterial promoter and any other bacterial regulatory sequence(s), placed in the opposite orientation of the cassette encoding the payload(s) under control of the eukaryotic promoter, and including bacterial terminators flanking the nucleic acid encoding the payload(s), and in the orientation to terminate any readthrough transcripts, from the prokaryotic promoter.
  • DEFINITIONS B OVERVIEW OF IMMUNOSTIMULATORY BACTERIA FOR CANCER THERAPY 1. Bacterial Cancer Immunotherapy 2. Prior Therapies that Target the Tumor Microenvironment a. Limitations of Autologous T-Cell Therapies b.
  • Adenosine Auxotrophy Plasmid Maintenance and Delivery a. asd Deletion b. endA Deletion/Disruption 4. Flagellin Knockout Strains 5. Engineering Bacteria to Promote Adaptive Immunity and Enhance T-Cell Function L-asparaginase II (ansB) Deletion/Disruption 6. Deletions/Disruptions in Salmonella Genes Required for Curli Fimbriae Expression 7. Improving Resistance to Complement Rck Expression 8. Deletions of Genes Required for Lipoprotein Expression in Salmonella and Other Gram-Negative Bacteria 9.
  • Constitutively Active Proteins that Stimulate the Immune Response and/or Type I IFN, Non-Human STING Proteins, Chimeras, and Modified Forms a. Constitutive STING Expression and Gain-of- Function Mutations b. Constitutive IRF3 Expression and Gain-of-Function Mutations c. Non-Human STING Proteins, and Variants Thereof with Increased or Constitutive Activity, and STING Chimeras, and Variants Thereof with Increased or Constitutive Activity d. Other Gene Products that Act as Cytosolic DNA/RNA Sensors and Constitutive Variants Thereof i. RIG-I ii. MDA5/IFIH1 iii. IRF7 e. Other Type I IFN Regulatory Proteins 4.
  • Antibodies and Antibody Fragments a. TGF- ⁇ b. Bispecific scFvs and T-Cell Engagers c. Anti-PD-1/Anti-PD-L1 Antibodies d. Anti-CTLA-4 Antibodies e. Additional Exemplary Checkpoint Targets 5. Combinations of Immunomodulatory Proteins can have Synergistic Effects and/or Complementary Effects 6. Immunostimulatory Bacteria that Deliver Combination Therapies E. CONSTRUCTING EXEMPLARY PLASMIDS ENCODING THERAPEUTIC PRODUCTS FOR BACTERIAL DELIVERY 1. Constitutive Promoters for Heterologous Expression of Proteins 2. Multiple Therapeutic Product Expression Cassettes a. Single Promoter Constructs b.
  • Regulatory Elements a. Post-Transcriptional Regulatory Elements b. Polyadenylation Signal Sequences and Terminators c. Enhancers d. Secretion Signals e. Improving Bacterial Fitness 4. Origin of Replication and Plasmid Copy Number 5. CpG Motifs and CpG Islands 6. Plasmid Maintenance/Selection Components 7. DNA Nuclear Targeting Sequences F. PHARMACEUTICAL PRODUCTION, COMPOSITIONS, AND FORMULATIONS 1. Manufacturing a. Cell Bank Manufacturing b. Drug Substance Manufacturing c. Drug Product Manufacturing 2. Compositions 3. Formulations a. Liquids, Injectables, Emulsions b. Dried Thermostable Formulations 4.
  • compositions for Other Routes of Administration 5. Dosages and Administration 6. Packaging and Articles of Manufacture
  • G. METHODS OF TREATMENT AND USES 1. Diagnostics for Patient Selection for Treatment and for Monitoring Treatment a. Patient Selection b. Diagnostics to Assess or Detect Activity of the Immunostimulatory Bacteria are Indicative of the Effectiveness of Treatment 2. Tumors 3. Administration 4. Monitoring H. EXAMPLES A. DEFINITIONS Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which the invention(s) belong. All patents, patent applications, published applications and publications, GenBank sequences, databases, websites and other published materials referred to throughout the entire disclosure herein, unless noted otherwise, are incorporated by reference in their entirety.
  • therapeutic bacteria are bacteria that effect therapy, such as anti-cancer or anti-tumor therapy, when administered to a subject, such as a human.
  • immunostimulation bacteria are therapeutic bacteria that, when introduced into a subject, accumulate in immunoprivileged tissues and cells, such as tumors, the tumor microenvironment and tumor-resident immune cells, and replicate and/or express products that are immunostimulatory or that result in immunostimulation.
  • the immunostimulatory bacteria are attenuated in the host by virtue of reduced toxicity or pathogenicity and/or by virtue of encoded products that reduce toxicity or pathogenicity, as the immunostimulatory bacteria cannot replicate and/or express products (or have reduced replication/product expression), except primarily in immunoprivileged environments.
  • Immunostimulatory bacteria provided herein are modified to encode a product or products or exhibit a trait or property that renders them immunostimulatory.
  • Such products, properties and traits include, but are not limited to, for example, at least one of: an immunostimulatory protein, such as a cytokine, chemokine, or co-stimulatory molecule; a cytosolic DNA/RNA sensor or gain-of-function or constitutively active variant thereof (e.g., STING, IRF3, IRF7, MDA5, RIG-I); RNAi, such as siRNA (shRNA and microRNA), or CRISPR, that targets, disrupts, or inhibits a checkpoint gene, such as TREX1, PD- 1, CTLA-4 and/or PD-L1; antibodies and fragments thereof, such as an anti-immune checkpoint antibody, an anti-IL-6 antibody, an anti-VEGF antibody, or a TGF- ⁇ inhibitory antibody; other antibody constructs such as bi-specific T-cell engagers (BiTEs®); soluble TGF- ⁇ receptors that act as decoys for binding TGF- ⁇ , or TGF- ⁇ antagonizing poly
  • Immunostimulatory bacteria also can include a modification that renders the bacterium auxotrophic for a metabolite that is immunosuppressive or that is in an immunosuppressive pathway, such as adenosine.
  • the strain designations VNP20009 see, e.g., International PCT Application Publication No. WO 99/13053, see, also U.S. Patent No.6,863,894
  • YS1646 and 41.2.9 are used interchangeably, and each refer to the strain deposited with the American Type Culture Collection (ATCC) and assigned Accession No. 202165.
  • VNP20009 is a modified attenuated strain of Salmonella typhimurium, which contains deletions in msbB and purI, and was generated from wild-type strain ATCC #14028.
  • the strain designations YS1456 and 8.7 are used interchangeably and each refer to the strain deposited with the American Type Culture Collection (ATCC) and assigned Accession No.202164 (see, U.S. Patent No. 6,863,894).
  • ATCC American Type Culture Collection
  • recitation that a bacterium is “derived from” a particular strain means that such strain can serve as a starting material and can be modified to result in the particular bacterium.
  • an “expression cassette” refers to a nucleic acid construct that includes regulatory sequences for gene expression, operatively linked to nucleic acid encoding open reading frames (ORFs) that encode payloads, such as therapeutic products, or other proteins.
  • ORFs open reading frames
  • 2A peptides are 18–22 amino-acid (aa)-long viral oligopeptides that mediate cleavage of polypeptides during translation in eukaryotic cells.
  • the designation “2A” refers to a specific region of the viral genome, and different viral 2As have generally been named after the virus they were derived from.
  • F2A foot-and-mouth disease virus 2A
  • E2A equine rhinitis A virus
  • P2A porcine teschovirus-12A
  • T2A Thosea asigna virus 2A.
  • F2A foot-and-mouth disease virus 2A
  • E2A equine rhinitis A virus
  • P2A porcine teschovirus-12A
  • T2A Thosea asigna virus 2A.
  • SEQ ID NOs:327-330 SEQ ID NOs:327-330.
  • These peptides generally share a core sequence motif of DxExNPGP, and occur in a large number of viral families. They help break apart polyproteins by causing the ribosome to fail at making a peptide bond.
  • the 2A peptides provide for multicistronic vectors, in which a plurality of proteins are expressed from a single open reading frame (ORF).
  • the 2A peptides include those that are naturally occurring, and any modified forms thereof, such as any having at 97%, 98%, or 99% sequence identity with any naturally- occurring 2A peptide, including those disclosed herein, that result in single polypeptides being transcribed and translated from a transcript comprising a plurality (2 or more) of open reading frames.
  • an “interferonopathy” refers to a disorder associated with an upregulation of interferon by virtue of a mutation in a gene product involved in a pathway that regulates or induces expression of interferon.
  • the activity of the products normally is regulated by a mediator, such as cytosolic DNA or RNA or nucleotides; when the protein product is mutated, the activity is constitutive.
  • Type I interferonopathies include a spectrum of conditions, including the severe forms of Aicardi-Goutines Syndrome (AGS), and the milder Familial Chilblain Lupus (FCL). Nucleic acid molecules encoding mutated products with these properties can be produced in vitro, such as by selecting for mutations that result in a gain-of-function in the product, compared to the product of an allele that has normal activity, or has further gain-of-function compared to the disease-associated gain-of-function mutants described herein.
  • a “gain-of-function mutation” is one that increases the activity of a protein compared to the same protein that does not have the mutation. For example, if the protein is a receptor, it will have increased affinity for a ligand; if it is an enzyme, it will have increased activity, including constitutive activity.
  • an “origin of replication” is a sequence of DNA at which replication is initiated on a chromosome, or plasmid, or in a virus. For small DNA, including bacterial plasmids and small viruses, a single origin is sufficient. The origin of replication determines the vector copy number, which depends upon the selected origin of replication.
  • the copy number is between about 15-20 copies/cell, and if derived from the high-copy-number plasmid pUC, it can be 500-700 copies/cell.
  • medium copy number of a plasmid in cells is about or is 150 or less than 150, and low copy number is 5-30, such as 20 or less than 20. Low to medium copy number is less than 150 copies/cell. High copy number is greater than 150 copies/cell.
  • a “CpG motif” is a pattern of bases that includes an unmethylated central CpG (“p” refers to the phosphodiester link between consecutive C and G nucleotides), surrounded by at least one base flanking (on the 3' and the 5' side of) the central CpG.
  • a CpG oligodeoxynucleotide is an oligodeoxynucleotide that is at least about ten nucleotides in length and includes an unmethylated CpG. At least the C of the 5' CG 3' is unmethylated.
  • a “RIG-I binding sequence” refers to a 5’triphosphate (5’ppp) structure directly, or that which is synthesized by RNA pol III from a poly(dA-dT) sequence, which, by virtue of interaction with RIG-I, can activate type I IFN via the RIG-I pathway.
  • the RNA includes at least four A ribonucleotides (A-A-A-A); it can contain 4, 5, 6, 7, 8, 9, 10, or more.
  • the RIG-I binding sequence is introduced into a plasmid in the bacterium for transcription into the polyA.
  • cytokines are a broad and loose category of small proteins ( ⁇ 5–20 kDa) that are important in cell signaling.
  • Cytokines include chemokines, interferons, interleukins, lymphokines, and tumor necrosis factors. Cytokines are cell signaling molecules that aid cell to cell communication in immune responses, and stimulate the movement of cells towards sites of inflammation, infection and trauma. As used herein, “chemokines” refer to chemoattractant (chemotactic) cytokines that bind to chemokine receptors and include proteins isolated from natural sources as well as those made synthetically, as by recombinant means or by chemical synthesis.
  • chemokines refer to chemoattractant (chemotactic) cytokines that bind to chemokine receptors and include proteins isolated from natural sources as well as those made synthetically, as by recombinant means or by chemical synthesis.
  • chemokines include, but are not limited to, IL-8, IL-10, GCP-2, GRO- ⁇ , GRO- ⁇ , GRO- ⁇ , ENA-78, PBP, CTAP III, NAP-2, LAPF-4, MIG (CXCL9), CXCL10 (IP-10), CXCL11, PF4, SDF-1 ⁇ , SDF-1 ⁇ , SDF-2, MCP-1, MCP-2, MCP-3, MCP-4, MCP-5, MIP-1 ⁇ (CCL3), MIP-1 ⁇ (CCL4), MIP-1 ⁇ (CCL9), MIP-2, MIP-2 ⁇ , MIP-3 ⁇ , MIP-3 ⁇ , MIP-4, MIP-5, MDC, HCC-1, ALP, lungkine, Tim-1, eotaxin-1, eotaxin-2, I-309, SCYA17, TRAC, RANTES (CCL5), DC-CK-1, lymphotactin, and fractalkine, and others known to those of skill in the art.
  • MIG C
  • Chemokines are involved in the migration of immune cells to sites of inflammation, as well as in the maturation of immune cells and in the generation of adaptive immune responses.
  • an “immunostimulatory protein” is a protein that exhibits or promotes an anti-tumor immune response in the tumor microenvironment.
  • cytokines such as, but not limited to, IFN- ⁇ , IFN- ⁇ , GM-CSF, IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IL- 23, IL-12p70 (IL-12p40 + IL-12p35), IL-15/IL-15R alpha chain complex, IL-36 gamma, IL-2 that has attenuated binding to IL-2Ra, IL-2 that is modified so that it does not bind to IL-2Ra, CXCL9, CXCL10 (IP-10), CXCL11, CCL3, CCL4, CCL5, molecules involved in the potential recruitment and/or persistence of T-cells, CD40, CD40 ligand (CD40L), OX40, OX40 ligand (OX40L), 4-1BB, 4-1BB ligand (4- 1BBL), 4-1BBL with a deleted cytoplasmic domain (4-1B
  • immunostimulatory proteins are truncated co-stimulatory molecules, such as, for example, 4-1BBL, CD80, CD86, CD27L, B7RP1 and OX40L, each with a full or partial cytoplasmic domain deletion, for expression on an antigen presenting cell (APC).
  • APC antigen presenting cell
  • truncated gene products such as those with deletions or partial deletions of the cytoplasmic domain, are capable of constitutive immunostimulatory signaling to a T-cell through co-stimulatory receptor engagement, but are unable to counter-regulatory signal to the APC, due to a truncated or deleted cytoplasmic domain.
  • cytoplasmic domain deletion is a deletion in all, or a portion of, the amino acid residues that comprise the cytoplasmic, or intracellular, domain of the protein, where the deletion is sufficient to effect constitutive immunostimulatory signaling to a T-cell through co-stimulatory receptor engagement, and is sufficient to inhibit counter-regulatory signaling to the APC.
  • the cytoplasmic domain of human 4-1BBL also known as TNFSF9 comprises amino acid residues 1-28 of SEQ ID NO:342.
  • the cytoplasmic domain of human CD80 comprises amino acid residues 264-288 of the protein; the cytoplasmic domain of human CD86 comprises amino acid residues 269-329 of the protein; the cytoplasmic domain of human CD27L (also known as CD70) comprises amino acid residues 1-17 of the protein; the cytoplasmic domain of human B7RP1 (also known as ICOSLG or ICOS ligand) comprises amino acid residues 278-302 of the protein; and the cytoplasmic domain of human OX40L (also known as TNFSF4 or CD252) comprises amino acid residues 1-23 of the protein.
  • a “decoy receptor” is a receptor that can specifically bind to specific growth factors or cytokines efficiently, but is not structurally able to signal or activate the intended receptor complex.
  • the decoy receptor acts as an inhibitor by binding to a ligand and preventing it from binding to its cognate receptor.
  • TGF- ⁇ family receptors include the cell-surface serine/threonine kinase receptors type I (T ⁇ RI or TGF ⁇ R1) and type II (T ⁇ RII or TGF ⁇ R2), which form heteromeric complexes in the presence of dimerized ligands, as well as the type III receptor betaglycan (T ⁇ RIII or TGF ⁇ R3).
  • Soluble decoy receptors for TGF- ⁇ which prevent the binding of TGF- ⁇ to its receptors, include the soluble extracellular domains (the TGF- ⁇ binding regions) of T ⁇ RI, T ⁇ RII, or T ⁇ RIII ( ⁇ glycan), which can be fused with other molecules, such as an Fc domain.
  • BAMBI bone morphogenetic protein (BMP) and activin membrane-bound inhibitor
  • BMP bone morphogenetic protein
  • activin membrane-bound inhibitor is structurally related to type I receptors and acts as a decoy that inhibits receptor activation.
  • a dominant negative TGF ⁇ R2 (DN-TGF ⁇ R2), which comprises the extracellular domain of TGF ⁇ R2 and the transmembrane region, but which lacks the cytoplasmic domain required for signaling, also can be used as a TGF- ⁇ decoy receptor (see, e.g., International Application Publication No. WO 2018/138003).
  • a co-stimulatory molecule agonist is a molecule that, upon binding to the co-stimulatory molecule, activates it or increases its activity.
  • the agonist can be an agonist antibody.
  • CD40 agonist antibodies include, for example, CP-870,893, dacetuzumab, ADC-1013 (mitazalimab), and Chi Lob 7/4.
  • a cytosolic DNA/RNA sensor pathway is one that is initiated by the presence of DNA, RNA, nucleotides, dinucleotides, cyclic nucleotides and/or cyclic dinucleotides or other nucleic acid molecules, that leads to production of type I interferon.
  • the nucleic acid molecules in the cytosol occur from viral or bacterial or radiation or other such exposure, leading to activation of an immune response in a host.
  • a “type I interferon pathway protein” is a protein that induces an innate immune response, such as the induction of type I interferon.
  • cytosolic DNA/RNA sensor is a protein that is part of a cytosolic DNA/RNA sensor pathway that leads to expression of an immune response mediator, such as type I interferon.
  • cytosolic DNA is sensed by cGAS, leading to the production of cGAMP and subsequent STING/TBK1/IRF3 signaling, and type I IFN production.
  • Bacterial cyclic dinucleotides (such as bacterial cyclic di-AMP) also activate STING.
  • STING is an immunomodulatory protein that induces type I interferon.5’- triphosphate RNA and double stranded RNA are sensed by RIG-I and either MDA-5 alone, or MDA-5/LGP2. This leads to polymerization of mitochondrial MAVS (mitochondrial antiviral-signaling protein), and also activates TANK-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3). The proteins in such pathways are immunostimulatory and lead to expression of innate immune response mediators, such as type I interferon.
  • the immunomodulatory proteins in the DNA/RNA sensor pathways can be modified so that they have increased activity, or act constitutively in the absence of cytosolic nucleic acids, to lead to the immune response, such as the expression of type I interferon.
  • the “carboxy-terminal tail” or “C-terminal tail” (CTT) of the innate immune protein STING refers to the C-terminal portion of a STING protein that, in a wild-type STING protein, is tethered to the cGAMP-binding domain by a flexible linker region.
  • the CTT includes an IRF3 binding site, a TBK1 binding site, and a TRAF6 binding site.
  • STING promotes the induction of interferon beta (IFN- ⁇ ) production via the phosphorylation of the STING protein C-terminal tail (CTT) by TANK-binding kinase 1 (TBK1).
  • CTT carboxy-terminal tail
  • TRAF6 catalyzes the formation of K63-linked ubiquitin chains on STING, leading to the activation of the transcription factor NF- ⁇ B and the induction of an alternative STING-dependent gene expression program. Deletion or disruption of the TRAF6 binding site in the CTT can reduce activation of NF- ⁇ B signaling.
  • Substitution of the human STING CTT (or portions thereof), with the CTT (or corresponding portion thereof) from the STING protein of a species with low NF- ⁇ B activation, can decrease NF- ⁇ B activation by the resulting modified human STING protein.
  • the STING CTT is an unstructured stretch of ⁇ 40 amino acids that contains sequence motifs required for STING phosphorylation and recruitment of IRF3 (see, de Oliveira Mann et al. (2019) Cell Reports 27:1165-1175).
  • Human STING residue S366 has been identified as a primary TBK1 phosphorylation site that is part of an LxIS motif shared among innate immune adaptor proteins that activate interferon signaling (see, de Oliveira Mann et al.
  • the human STING CTT contains a second PxPLR motif that includes the residue L374, which is required for TBK1 binding; the LxIS and PxPLR sequences are conserved among vertebrate STING alleles (see, de Oliveira Mann et al. (2019) Cell Reports 27:1165-1175).
  • Exemplary STING CTT sequences, and the IRF3, TBK1 and TRAF6 binding sites, are set forth in the following table:
  • a “STING pathway agonist” is any product that increases type I interferon (IFN) expression via activation of the STING pathway.
  • agonists are the gain-of-function STING polypeptide variants provided herein, as well as gain-of-function variants of other cytosolic DNA/RNA sensors and type I IFN pathway proteins, such as variants of IRF-3, IRF-7, MDA5, and RIG-I, that increase or render expression of type I IFN constitutive, via the STING pathway.
  • a bacterium that is modified so that it “induces less cell death in tumor-resident immune cells” or “induces less cell death in immune cells” is one that is less toxic than the bacterium without the modification, or one that has reduced virulence compared to the bacterium without the modification.
  • modifications are those that eliminate pyroptosis in phagocytic cells and that alter lipopolysaccharide (LPS) profiles on the bacterium.
  • LPS lipopolysaccharide
  • modifications include disruption of or deletion of flagellin genes, pagP, or one or more components of the SPI-1 pathway, such as hilA, rod protein (e.g., prgJ), needle protein (e.g., prgI), and QseC.
  • a bacterium that is “modified so that it preferentially infects tumor-resident immune cells” or “modified so that it preferentially infects immune cells” has a modification in its genome that reduces its ability to infect cells other than immune cells.
  • modifications that disrupt the type 3 secretion system or type 4 secretion system or other genes or systems that affect the ability of a bacterium to invade a non-immune cell.
  • modifications include disruption/deletion of an SPI-1 component, which is needed for infection of cells, such as epithelial cells, but does not affect infection of immune cells, such as phagocytic cells, by Salmonella.
  • a “modification” is in reference to modification of a sequence of amino acids of a polypeptide, or a sequence of nucleotides in a nucleic acid molecule, and includes deletions, insertions, and replacements of amino acids or nucleotides, respectively.
  • RNA interference is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules to inhibit translation, and thereby expression, of a targeted gene.
  • RNA molecules that act via RNAi are referred to as inhibitory by virtue of their silencing of the expression of a targeted gene. Silencing expression means that expression of the targeted gene is reduced, or suppressed, or inhibited.
  • gene silencing via RNAi is said to inhibit, suppress, disrupt, or silence expression of a targeted gene.
  • a targeted gene contains sequences of nucleotides that correspond to the sequences in the inhibitory RNA, whereby the inhibitory RNA silences expression of target mRNA.
  • inhibiting, suppressing, disrupting, or silencing a targeted gene refers to processes that alter expression, such as translation, of the targeted gene, whereby activity or expression of the product encoded by the targeted gene is reduced. Reduction includes a complete knock-out or a partial knockout, whereby, with reference to the immunostimulatory bacteria provided herein and administration herein, treatment is effected.
  • siRNAs small interfering RNAs
  • ds double- stranded RNA
  • mRNA messenger RNA
  • siRNAs prevent the production of specific proteins based on the nucleotide sequences of their corresponding mRNAs.
  • RNAi RNA interference
  • siRNA silencing siRNA knockdown.
  • RNA interference RNA interference
  • shRNA short-hairpin RNA or small-hairpin RNA
  • RNAi RNA interference
  • TME tumor microenvironment
  • ECM extracellular matrix
  • Conditions that exist include, but are not limited to, increased vascularization, hypoxia, low pH, increased lactate concentration, increased pyruvate concentration, increased interstitial fluid pressure, and altered metabolites or metabolism, such as higher levels of adenosine, which are indicative of a tumor.
  • bactofection refers to the bacteria-mediated transfer of genes or plasmid DNA into eukaryotic cells, such as mammalian cells.
  • human type I interferons IFNs
  • All type I IFNs bind to a specific cell surface receptor complex, such as the IFN- ⁇ receptor.
  • Type I interferons include IFN- ⁇ and IFN- ⁇ , among others.
  • Myeloid cells are the primary producers of IFN- ⁇ and IFN- ⁇ , which have antiviral activity that is involved mainly in innate immune responses.
  • IFN- ⁇ Two types of IFN- ⁇ are IFN- ⁇ 1 (IFNB1) and IFN- ⁇ 3 (IFNB3).
  • IFNB1 IFN- ⁇ 1
  • IFNB3 IFN- ⁇ 3
  • M1 macrophage phenotype and M2 macrophage phenotype refer to the two broad groups into which macrophage phenotype is divided: M1 (classically activated macrophages) and M2 (alternatively activated macrophages).
  • M1 macrophages The role of M1 macrophages is to secrete pro-inflammatory cytokines and chemokines, and to present antigens, so that they participate in the positive immune response and function as an immune monitor.
  • the main pro-inflammatory cytokines they produces are IL-6, IL-12 and TNF-alpha.
  • M2 macrophages primarily secrete arginase-I, IL-10, TGF- ⁇ , and other anti-inflammatory cytokines, which have the function of reducing inflammation, and contributing to tumor growth and immunosuppressive function.
  • a macrophage with an M1-like phenotype secretes pro- inflammatory cytokines, and does not have the immunosuppressive activity(ies) of an M2 macrophage.
  • M2 macrophage Conversion of an M2 macrophage into a macrophage with an M1 or M1-like phenotype converts an M2 macrophage into one that is not immunosuppressive, but participates in an anti-tumor response.
  • M1 phenyotypic markers include, but are not limited to, one or more of CD80, CD86, CD64, CD16, and CD32.
  • nitric oxide synthase (iNOS) in M1 also can serve as a phenotypic marker.
  • CD163 and CD206 are major markers for the identification of M2 macrophages.
  • Other surface markers for M2-type cells also include CD68.
  • nucleic acid or encoded RNA targets a gene means that it inhibits or suppresses or silences expression of the gene by any mechanism.
  • nucleic acid includes at least a portion complementary to the targeted gene, where the portion is sufficient to form a hybrid with the complementary portion.
  • “deletion,” when referring to a nucleic acid or polypeptide sequence refers to the deletion of one or more nucleotides or amino acids compared to a sequence, such as a target polynucleotide, or polypeptide, or a native, or wild- type sequence.
  • insertion when referring to a nucleic acid or amino acid sequence, describes the inclusion of one or more additional nucleotides or amino acids, within a target, native, wild-type or other related sequence.
  • a nucleic acid molecule that contains one or more insertions compared to a wild-type sequence contains one or more additional nucleotides within the linear length of the sequence.
  • additional nucleic acid and amino acid sequences describe addition of nucleotides or amino acids onto either termini compared to another sequence.
  • substitution refers to the replacing of one or more nucleotides or amino acids in a native, target, wild-type or other nucleic acid or polypeptide sequence with an alternative nucleotide or amino acid, without changing the length (as described in numbers of nucleotides or residues) of the molecule.
  • one or more substitutions in a molecule does not change the number of nucleotides or amino acid residues of the molecule.
  • Amino acid replacements compared to a particular polypeptide can be expressed in terms of the number of the amino acid residue along the length of the polypeptide sequence.
  • nucleotides or amino acid positions “correspond to” nucleotides or amino acid positions in a disclosed sequence refers to nucleotides or amino acid positions identified upon alignment with the disclosed sequence to maximize identity using a standard alignment algorithm, such as the GAP algorithm.
  • a standard alignment algorithm such as the GAP algorithm.
  • alignment of a sequence refers to the use of homology to align two or more sequences of nucleotides or amino acids. Typically, two or more sequences that are related by 50% or more identity are aligned.
  • An aligned set of sequences refers to 2 or more sequences that are aligned at corresponding positions and can include aligning sequences derived from RNAs, such as ESTs and other cDNAs, aligned with a genomic DNA sequence.
  • polypeptides or nucleic acid molecules can be aligned by any method known to those of skill in the art. Such methods typically maximize matches, and include methods, such as using manual alignments, and by using the numerous alignment programs available (e.g., BLASTP) and others known to those of skill in the art.
  • BLASTP the numerous alignment programs available
  • aligning the sequences of polypeptides or nucleic acids one skilled in the art can identify analogous portions or positions, using conserved and identical amino acid residues as guides. Further, one skilled in the art also can employ conserved amino acid or nucleotide residues as guides to find corresponding amino acid or nucleotide residues between and among human and non-human sequences.
  • Corresponding positions also can be based on structural alignments, for example by using computer simulated alignments of protein structure. In other instances, corresponding regions can be identified. One skilled in the art also can employ conserved amino acid residues as guides to find corresponding amino acid residues between and among human and non-human sequences.
  • a “property” of a polypeptide such as an antibody, refers to any property exhibited by a polypeptide, including, but not limited to, binding specificity, structural configuration or conformation, protein stability, resistance to proteolysis, conformational stability, thermal tolerance, and tolerance to pH conditions. Changes in properties can alter an “activity” of the polypeptide.
  • a change in the binding specificity of the antibody polypeptide can alter the ability to bind an antigen, and/or various binding activities, such as affinity or avidity, or in vivo activities of the polypeptide.
  • an “activity” or a “functional activity” of a polypeptide, such as an antibody refers to any activity exhibited by the polypeptide. Such activities can be empirically determined. Exemplary activities include, but are not limited to, the ability to interact with a biomolecule, for example, through antigen-binding, DNA binding, ligand binding, or dimerization, or enzymatic activity, for example, kinase activity, or proteolytic activity.
  • activities include, but are not limited to, the ability to specifically bind a particular antigen, affinity of antigen-binding (e.g., high or low affinity), avidity of antigen- binding (e.g., high or low avidity), on-rate, off-rate, effector functions, such as the ability to promote antigen neutralization or clearance, virus neutralization, and in vivo activities, such as the ability to prevent infection or invasion of a pathogen, or to promote clearance, or to penetrate a particular tissue or fluid or cell in the body.
  • affinity of antigen-binding e.g., high or low affinity
  • avidity of antigen- binding e.g., high or low avidity
  • effector functions such as the ability to promote antigen neutralization or clearance, virus neutralization
  • in vivo activities such as the ability to prevent infection or invasion of a pathogen, or to promote clearance, or to penetrate a particular tissue or fluid or cell in the body.
  • Activity can be assessed in vitro or in vivo using recognized assays, such as ELISA, flow cytometry, surface plasmon resonance, or equivalent assays to measure on-rate or off-rate, immunohistochemistry and immunofluorescence histology and microscopy, cell-based assays, and binding assays (e.g., panning assays).
  • recognized assays such as ELISA, flow cytometry, surface plasmon resonance, or equivalent assays to measure on-rate or off-rate, immunohistochemistry and immunofluorescence histology and microscopy, cell-based assays, and binding assays (e.g., panning assays).
  • binding e.g., panning assays
  • Binding includes, but is not limited to, non-covalent bonds, covalent bonds (such as reversible and irreversible covalent bonds), and includes interactions between molecules such as, but not limited to, proteins, nucleic acids, carbohydrates, lipids, and small molecules, such as chemical compounds, including drugs.
  • antibody refers to immunoglobulins and immunoglobulin fragments, whether natural, or partially or wholly synthetically, such as recombinantly produced, including any fragment thereof containing at least a portion of the variable heavy chain and light region of the immunoglobulin molecule that is sufficient to form an antigen-binding site and, when assembled, to specifically bind an antigen.
  • an antibody includes any protein having a binding domain that is homologous or substantially homologous to an immunoglobulin antigen-binding domain (antibody combining site).
  • an antibody refers to an antibody that contains two heavy chains (which can be denoted H and H’) and two light chains (which can be denoted L and L’), where each heavy chain can be a full-length immunoglobulin heavy chain or a portion thereof sufficient to form an antigen-binding site (e.g., heavy chains include, but are not limited to, VH chains, VH-CH1 chains, and VH-CH1-CH2- C H 3 chains), and each light chain can be a full-length light chain or a portion thereof sufficient to form an antigen-binding site (e.g., light chains include, but are not limited to, VL chains and VL-CL chains).
  • antibodies typically include all or at least a portion of the variable heavy (V H ) chain and/or the variable light (V L ) chain.
  • the antibody also can include all or a portion of the constant region.
  • the term antibody includes full-length antibodies and portions thereof including antibody fragments, such as anti-CTLA-4 antibody fragments.
  • Antibody fragments include, but are not limited to, Fab fragments, Fab’ fragments, F(ab’)2 fragments, Fv fragments, disulfide-linked Fvs (dsFv), Fd fragments, Fd’ fragments, single-chain Fvs (scFvs), scFv-Fc fragments (in which the VH domain in the scFv is linked to an Fc, such as a human IgG1 Fc, for example), single-chain Fabs (scFabs), diabodies, anti-idiotypic (anti-Id) antibodies, or antigen- binding fragments of any of the above.
  • Fab fragments fragments, Fab’ fragments, F(ab’)2 fragments, Fv fragments, disulfide-linked Fvs (dsFv), Fd fragments, Fd’ fragments, single-chain Fvs (scFvs), scFv-Fc fragments (in which the VH domain in the
  • Antibody also includes synthetic antibodies, recombinantly produced antibodies, multi-specific antibodies (e.g., bispecific antibodies), human antibodies, non-human antibodies, humanized antibodies, chimeric antibodies, and intrabodies.
  • Antibodies provided herein include members of any immunoglobulin class (e.g., IgG, IgM, IgD, IgE, IgA and IgY), any subclass (e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2), or sub-subclass (e.g., IgG2a and IgG2b).
  • Antibodies for human therapy generally are human antibodies or are humanized.
  • antibody fragment(s) refers to (i) monovalent and monospecific antibody derivatives that contain the variable heavy and/or light chains, or functional fragments of an antibody and lack an Fc part; and (ii) BiTEs® (tandem scFvs), DARTs, diabodies, and single-chain diabodies (scDbs).
  • an antibody fragment includes a/an: Fab, Fab’, scFab, scFv, scFv-Fc, Fv fragment, nanobody (see, e.g., antibodies derived from Camelus bactriamus, Camelus dromedarius, or Lama paccos) (see, e.g., U.S.
  • nucleic acid refers to at least two linked nucleotides or nucleotide derivatives, including a deoxyribonucleic acid (DNA) and a ribonucleic acid (RNA), joined together, typically by phosphodiester linkages.
  • nucleic acid also include analogs of nucleic acids, such as peptide nucleic acid (PNA), phosphorothioate DNA, and other such analogs and derivatives, or combinations thereof. Nucleic acids also include DNA and RNA derivatives containing, for example, a nucleotide analog or a “backbone” bond other than a phosphodiester bond, for example, a phosphotriester bond, a phosphoramidate bond, a phosphorothioate bond, a thioester bond, or a peptide bond (peptide nucleic acid).
  • PNA peptide nucleic acid
  • Nucleic acids also include DNA and RNA derivatives containing, for example, a nucleotide analog or a “backbone” bond other than a phosphodiester bond, for example, a phosphotriester bond, a phosphoramidate bond, a phosphorothioate bond, a thioester bond, or a peptide bond (peptid
  • RNA or DNA made from nucleotide analogs, and single-stranded (sense or antisense) and double-stranded nucleic acids.
  • Deoxyribonucleotides include deoxyadenosine, deoxycytidine, deoxyguanosine, and deoxythymidine.
  • the uracil base is uridine.
  • an isolated nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid molecule.
  • isolated nucleic acid molecule such as a cDNA molecule
  • exemplary isolated nucleic acid molecules provided herein include isolated nucleic acid molecules encoding an antibody or antigen-binding fragments provided herein.
  • operably linked or “operatively linked,” with reference to nucleic acid sequences, regions, elements, or domains, means that the nucleic acid regions are functionally related to each other. It refers to a juxtaposition whereby the components so described are in a relationship permitting them to function in their intended manner.
  • a promoter is operably linked to a coding sequence if the promoter effects or affects its transcription or expression.
  • a nucleic acid encoding a leader peptide can be operably linked to a nucleic acid encoding a polypeptide, whereby the nucleic acids can be transcribed and translated to express a functional fusion protein, wherein the leader peptide effects secretion of the fusion polypeptide.
  • the nucleic acid encoding a first polypeptide is operably linked to a nucleic acid encoding a second polypeptide, and the nucleic acids are transcribed as a single mRNA transcript, but translation of the mRNA transcript can result in one of two polypeptides being expressed.
  • an amber stop codon can be located between the nucleic acid encoding the first polypeptide and the nucleic acid encoding the second polypeptide, such that, when introduced into a partial amber suppressor cell, the resulting single mRNA transcript can be translated to produce either a fusion protein containing the first and second polypeptides, or can be translated to produce only the first polypeptide.
  • a promoter can be operably linked to nucleic acid encoding a polypeptide, whereby the promoter regulates or mediates the transcription of the nucleic acid.
  • synthetic with reference to, for example, a synthetic nucleic acid molecule or a synthetic gene or a synthetic peptide, refers to a nucleic acid molecule, or gene, or polypeptide molecule that is produced by recombinant methods and/or by chemical synthesis methods.
  • residues of naturally occurring ⁇ -amino acids are the residues of those 20 ⁇ -amino acids found in nature which are incorporated into a protein by the specific recognition of the charged tRNA molecule with its cognate mRNA codon in humans.
  • a “polypeptide” refers to two or more amino acids covalently joined.
  • the terms “polypeptide” and “protein” are used interchangeably herein.
  • a “peptide” refers to a polypeptide that is from 2 to about or 40 amino acids in length.
  • an “amino acid” is an organic compound containing an amino group and a carboxylic acid group. A polypeptide contains two or more amino acids.
  • amino acids contained in the antibodies and immunostimulatory proteins provided include the twenty naturally-occurring amino acids (see Table below), non-natural amino acids, and amino acid analogs (e.g., amino acids wherein the ⁇ -carbon has a side chain).
  • amino acids which occur in the various amino acid sequences of polypeptides appearing herein, are identified according to their well-known, three-letter or one-letter abbreviations (see Table below).
  • the nucleotides, which occur in the various nucleic acid molecules and fragments, are designated with the standard single-letter designations used routinely in the art.
  • amino acid residue refers to an amino acid formed upon chemical digestion (hydrolysis) of a polypeptide at its peptide linkages.
  • the amino acid residues described herein are generally in the “L” isomeric form. Residues in the “D” isomeric form can be substituted for any L-amino acid residue, as long as the desired functional property is retained by the polypeptide.
  • NH2 refers to the free amino group present at the amino terminus of a polypeptide.
  • COOH refers to the free carboxy group present at the carboxyl terminus of a polypeptide.
  • amino acid residues represented herein by a formula have a left to right orientation in the conventional direction of amino-terminus to carboxyl- terminus.
  • amino acid residue is defined to include the amino acids listed in the above Table of Correspondence, as well as modified, non-natural, and unusual amino acids.
  • a dash at the beginning or end of an amino acid residue sequence indicates a peptide bond to a further sequence of one or more amino acid residues, or to an amino-terminal group such as NH2, or to a carboxyl-terminal group such as COOH.
  • suitable conservative substitutions of amino acids are known to those of skill in the art and generally can be made without altering a biological activity of a resulting molecule.
  • “naturally occurring amino acids” refer to the 20 L-amino acids that occur in polypeptides.
  • the term “non-natural amino acid” refers to an organic compound that has a structure similar to a natural amino acid, but that has been modified structurally to mimic the structure and reactivity of a natural amino acid.
  • Non-naturally occurring amino acids thus include, for example, amino acids or analogs of amino acids other than the 20 naturally occurring amino acids and include, but are not limited to, the D-stereoisomers of amino acids.
  • non-natural amino acids are known to those of skill in the art, and include, but are not limited to, 2-Aminoadipic acid (Aad), 3-Aminoadipic acid (bAad), ⁇ -alanine/ ⁇ -Amino-propionic acid (Bala), 2-Aminobutyric acid (Abu), 4-Aminobutyric acid/piperidinic acid (4Abu), 6-Aminocaproic acid (Acp), 2-Aminoheptanoic acid (Ahe), 2- Aminoisobutyric acid (Aib), 3-Aminoisobutyric acid (Baib), 2-Aminopimelic acid (Apm), 2,4-Diaminobutyric acid (Dbu), Desmosine (Des), 2,2'-Diaminopimelic acid (Dpm), 2,3-Diaminopropionic acid (Dpr), N-Ethylglycine (EtGly), N-Ethylasparagine (EtAsn
  • a DNA construct is a single- or double-stranded, linear or circular DNA molecule that contains segments of DNA combined and juxtaposed in a manner not found in nature. DNA constructs exist as a result of human manipulation, and include clones and other copies of manipulated molecules.
  • a DNA segment is a portion of a larger DNA molecule having specified attributes.
  • a DNA segment encoding a specified polypeptide is a portion of a longer DNA molecule, such as a plasmid or plasmid fragment, which, when read from the 5’ to 3’ direction, encodes the sequence of amino acids of the specified polypeptide.
  • polynucleotide means a single- or double-stranded polymer of deoxyribonucleotides or ribonucleotide bases read from the 5’ to the 3’ end.
  • Polynucleotides include RNA and DNA, and can be isolated from natural sources, synthesized in vitro, or prepared from a combination of natural and synthetic molecules.
  • the length of a polynucleotide molecule is given herein in terms of nucleotides (abbreviated “nt”), or base pairs (abbreviated “bp”).
  • nt nucleotides
  • bp base pairs
  • heterologous nucleic acid is nucleic acid that encodes products (i.e., RNA and/or proteins) that are not normally produced in vivo by the cell in which it is expressed, or nucleic acid that is in a locus in which it does not normally occur, or that mediates or encodes mediators that alter expression of endogenous nucleic acid, such as DNA, by affecting transcription, translation, or other regulatable biochemical processes.
  • Heterologous nucleic acid, such as DNA also is referred to as foreign nucleic acid.
  • heterologous nucleic acid includes exogenously added nucleic acid that is also expressed endogenously.
  • Heterologous nucleic acid is generally not endogenous to the cell into which it is introduced, but has been obtained from another cell, or prepared synthetically, or is introduced into a genomic locus in which it does not occur naturally, or its expression is under the control of regulatory sequences or a sequence that differs from the natural regulatory sequence or sequences.
  • heterologous nucleic acid examples include, but are not limited to, nucleic acid that encodes a protein in a DNA/RNA sensor pathway or a gain-of- function or constitutively active variant thereof, or an immunostimulatory protein, such as a cytokine, chemokine or co-stimulatory molecule, that confers or contributes to anti-tumor immunity in the tumor microenvironment.
  • an immunostimulatory protein such as a cytokine, chemokine or co-stimulatory molecule
  • Other products such as antibodies and fragments thereof, BiTEs®, decoy receptors, antagonizing polypeptides and RNAi, that confer or contribute to anti-tumor immunity in the tumor microenvironment, also are included.
  • the heterologous nucleic acid generally is encoded on the introduced plasmid, but it can be introduced into the genome of the bacterium, such as a promoter that alters expression of a bacterial product.
  • Heterologous nucleic acid, such as DNA includes nucleic acid that can, in some manner, mediate expression of DNA that encodes a therapeutic product, or it can encode a product, such as a peptide or RNA, that in some manner mediates, directly or indirectly, expression of a therapeutic product.
  • cell therapy involves the delivery of cells to a subject to treat a disease or condition.
  • the cells which can be allogeneic or autologous to the subject, are modified ex vivo, such as by infection of cells with immunostimulatory bacteria provided herein, so that they deliver or express products when introduced to a subject.
  • genetic therapy involves the transfer of heterologous nucleic acid, such as DNA, into certain cells, such as target cells, of a mammal, particularly a human, with a disorder or condition for which such therapy is sought.
  • the nucleic acid, such as DNA is introduced into the selected target cells in a manner such that the heterologous nucleic acid, such as DNA, is expressed, and a therapeutic product(s) encoded thereby is (are) produced.
  • Genetic therapy can also be used to deliver nucleic acid encoding a gene product that replaces a defective gene or supplements a gene product produced by the mammal or the cell in which it is introduced.
  • the introduced nucleic acid can encode a therapeutic compound, such as a growth factor or inhibitor thereof, or a tumor necrosis factor or inhibitor thereof, such as a receptor thereof, that is not normally produced in the mammalian host or that is not produced in therapeutically effective amounts or at a therapeutically useful time.
  • the heterologous nucleic acid, such as DNA, encoding the therapeutic product can be modified prior to introduction into the cells of the afflicted host in order to enhance or otherwise alter the product or expression thereof.
  • Genetic therapy can also involve delivery of an inhibitor or repressor or other modulator of gene expression.
  • expression refers to the process by which polypeptides are produced by transcription and translation of polynucleotides.
  • the level of expression of a polypeptide can be assessed using any method known in art, including, for example, methods of determining the amount of the polypeptide produced from the host cell. Such methods can include, but are not limited to, quantitation of the polypeptide in the cell lysate by ELISA, Coomassie blue staining following gel electrophoresis, Lowry protein assay, and Bradford protein assay.
  • a “host cell” is a cell that is used to receive, maintain, reproduce and/or amplify a vector. A host cell also can be used to express the polypeptide encoded by the vector.
  • a “vector” is a replicable nucleic acid from which one or more heterologous proteins can be expressed when the vector is transformed into an appropriate host cell.
  • Reference to a vector includes those vectors into which a nucleic acid encoding a polypeptide or fragment thereof can be introduced, typically by restriction digest and ligation.
  • Reference to a vector also includes those vectors that contain nucleic acid encoding a polypeptide, such as a modified anti-CTLA-4 antibody.
  • the vector is used to introduce the nucleic acid encoding the polypeptide into the host cell for amplification of the nucleic acid, or for expression/display of the polypeptide encoded by the nucleic acid.
  • the vectors typically remain episomal, but can be designed to effect integration of a gene or portion thereof into a chromosome of the genome.
  • vectors that are artificial chromosomes such as yeast artificial chromosomes and mammalian artificial chromosomes. Selection and use of such vehicles are well-known to those of skill in the art.
  • a vector also includes “virus vectors” or “viral vectors.”
  • Viral vectors are engineered viruses that are operatively linked to exogenous genes to transfer (as vehicles or shuttles) the exogenous genes into cells.
  • an “expression vector” includes vectors capable of expressing DNA that is operatively linked with regulatory sequences, such as promoter regions, that are capable of effecting expression of such DNA fragments. Such additional segments can include promoter and terminator sequences, and optionally can include one or more origins of replication, one or more selectable markers, an enhancer, a polyadenylation signal, and the like. Expression vectors are generally derived from plasmid or viral DNA, or can contain elements of both.
  • an expression vector refers to a recombinant DNA or RNA construct, such as a plasmid, a phage, recombinant virus or other vector that, upon introduction into an appropriate host cell, results in expression of the cloned DNA.
  • Appropriate expression vectors are well- known to those of skill in the art and include those that are replicable in eukaryotic cells and/or prokaryotic cells and those that remain episomal or those which integrate into the host cell genome.
  • “primary sequence” refers to the sequence of amino acid residues in a polypeptide, or the sequence of nucleotides in a nucleic acid molecule.
  • sequence identity refers to the number of identical or similar amino acids or nucleotide bases in a comparison between a test and a reference poly- peptide or polynucleotide. Sequence identity can be determined by sequence alignment of nucleic acid or protein sequences to identify regions of similarity or identity. For purposes herein, sequence identity is generally determined by alignment to identify identical residues. The alignment can be local or global. Matches, mismatches and gaps can be identified between compared sequences. Gaps are null amino acids or nucleotides inserted between the residues of aligned sequences so that identical or similar characters are aligned. Generally, there can be internal and terminal gaps.
  • sequence identity can be determined with no penalty for end gaps (e.g., terminal gaps are not penalized).
  • sequence identity can be determined without taking into account gaps, as the number of identical positions/length of the total aligned sequence x 100.
  • a “global alignment” is an alignment that aligns two sequences from beginning to end, aligning each letter in each sequence only once. An alignment is produced, regardless of whether or not there is similarity or identity between the se- quences. For example, 50% sequence identity based on “global alignment” means that in an alignment of the full sequence of two compared sequences each of 100 nucleo- tides in length, 50% of the residues are the same.
  • global align- ment also can be used in determining sequence identity even when the length of the aligned sequences is not the same. The differences in the terminal ends of the se- quences will be taken into account in determining sequence identity, unless the “no penalty for end gaps” is selected. Generally, a global alignment is used on sequences that share significant similarity over most of their length. Exemplary algorithms for performing global alignment include the Needleman-Wunsch algorithm (Needleman et al. (1970) J. Mol. Biol.48:443-453).
  • Exemplary programs for performing global alignment are publicly available and include the Global Sequence Alignment Tool available at the National Center for Biotechnology Information (NCBI) website (ncbi.nlm.nih.gov/), and the program available at deepc2.psi.iastate.edu/aat/align/align.html.
  • a “local alignment” is an alignment that aligns two sequences, but only aligns those portions of the sequences that share similarity or identity. Hence, a local alignment determines if sub-segments of one sequence are present in another sequence. If there is no similarity, no alignment will be returned. Local alignment algorithms include BLAST or the Smith-Waterman algorithm (Adv. Appl. Math.2:482 (1981)).
  • sequence identity can be determined by standard alignment algorithm programs used with default gap penalties established by each supplier.
  • Default parameters for the GAP program can include: (1) a unary comparison matrix (containing a value of 1 for identities and 0 for non-identities) and the weighted comparison matrix of Gribskov et al. (1986) Nucl.
  • nucleic acid molecules have nucleotide sequences, or any two polypeptides have amino acid sequences that are at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% “identical,” or other similar variations reciting a percent identity, can be determined using known computer algorithms based on local or global alignment (see, e.g., wikipedia.org/wiki/Sequence_alignment_software, providing links to dozens of known and publicly available alignment databases and programs).
  • the full-length sequence of each of the compared polypeptides or nucleotides is aligned across the full-length of each sequence in a global alignment. Local alignment also can be used when the sequences being compared are substantially the same length. Therefore, as used herein, the term “identity” represents a comparison or alignment between a test and a reference polypeptide or polynucleotide. In one non- limiting example, “at least 90% identical to” refers to percent identities from 90% to 100% relative to the reference polypeptide or polynucleotide.
  • Identity at a level of 90% or more is indicative of the fact that, assuming for exemplification purposes a test and reference polypeptide or polynucleotide length of 100 amino acids or nucleotides are compared, no more than 10% (i.e., 10 out of 100) of amino acids or nucleotides in the test polypeptide or polynucleotide differ from those of the reference polypeptide or polynucleotide. Similar comparisons can be made between a test and reference polynucleotide.
  • differences can be represented as point mutations randomly distributed over the entire length of an amino acid sequence, or they can be clustered in one or more locations of varying length up to the maximum allowable, e.g., 10/100, amino acid differences (approximately 90% identity). Differences also can be due to deletions or truncations of amino acid residues. Differences are defined as nucleic acid or amino acid substitutions, insertions, or deletions. Depending on the length of the compared sequences, at the level of homologies or identities above about 85-90%, the result can be independent of the program and gap parameters set; such high levels of identity can be assessed readily, often without relying on software.
  • a “disease or disorder” refers to a pathological condition in an organism resulting from a cause or condition, including, but not limited to, infections, acquired conditions, and genetic conditions, and that is characterized by identifiable symptoms.
  • “treating” a subject with a disease or condition means that the subject’s symptoms are partially or totally alleviated, or remain static following treatment.
  • “treatment” refers to any effects that ameliorate symptoms of a disease or disorder. Treatment encompasses prophylaxis, therapy and/or cure. Treatment also encompasses any pharmaceutical use of any immunostimulatory bacterium or composition provided herein.
  • prophylaxis refers to prevention of a potential disease and/or a prevention of worsening of symptoms or of progression of a disease.
  • prevention or prophylaxis, and grammatically equivalent forms thereof refers to methods in which the risk or probability of developing a disease or condition is reduced.
  • a “pharmaceutically effective agent” includes any therapeutic agent or bioactive agent, including, but not limited to, for example, anesthetics, vasoconstrictors, dispersing agents, and conventional therapeutic drugs, including small molecule drugs and therapeutic proteins.
  • a “therapeutic effect” means an effect resulting from treatment of a subject that alters, typically improves or ameliorates, the symptoms of a disease or condition, or that cures a disease or condition.
  • a “therapeutically effective amount” or a “therapeutically effective dose” refers to the quantity of an agent, compound, material, or composition containing a compound that is at least sufficient to produce a therapeutic effect following administration to a subject. Hence, it is the quantity necessary for preventing, curing, ameliorating, arresting, or partially arresting a symptom of a disease or disorder.
  • therapeutic efficacy refers to the ability of an agent, compound, material, or composition containing a compound to produce a therapeutic effect in a subject to whom the agent, compound, material, or composition containing a compound has been administered.
  • a “prophylactically effective amount” or a “prophylactically effective dose” refers to the quantity of an agent, compound, material, or composition containing a compound that, when administered to a subject, will have the intended prophylactic effect, e.g., preventing or delaying the onset or reoccurrence, of disease or symptoms, reducing the likelihood of the onset or reoccurrence, of disease or symptoms, or reducing the incidence of viral infection.
  • a prophylactically effective amount can be administered in one or more administrations.
  • amelioration of the symptoms of a particular disease or disorder by a treatment refers to any lessening, whether permanent or temporary, lasting or transient, of the symptoms, that can be attributed to or associated with administration of the composition or therapeutic.
  • an “anti-cancer agent” or “an anti-cancer therapeutic” refers to any agent or therapeutic that is destructive or toxic, either directly or indirectly, to malignant cells and tissues.
  • anti-cancer agents include agents that kill cancer cells or otherwise inhibit or impair the growth of tumors or cancer cells.
  • exemplary anti-cancer agents are chemotherapeutic agents, and immunotherapeutic agents.
  • therapeutic activity refers to the in vivo activity of a therapeutic product, such as a polypeptide, a nucleic acid molecule, and other therapeutic molecules. Generally, the therapeutic activity is the activity that is associated with treatment of a disease or condition.
  • the term “subject” refers to an animal, including a mammal, such as a human being. As used herein, a patient refers to a human subject.
  • animal includes any animal, such as, but not limited to, primates, including humans, gorillas and monkeys; rodents, such as mice and rats; fowl, such as chickens; ruminants, such as goats, cows, deer, and sheep; and pigs and other animals.
  • Non-human animals exclude humans as the contemplated animal.
  • the polypeptides provided herein are from any source, animal, plant, prokaryotic and fungal. Most polypeptides are of animal origin, including mammalian origin.
  • a “composition” refers to any mixture. It can be a solution, suspension, liquid, powder, paste, aqueous, non-aqueous, or any combination thereof.
  • a “combination” refers to any association between or among two or more items.
  • the combination can be two or more separate items, such as two compositions or two collections, a mixture thereof, such as a single mixture of the two or more items, or any variation thereof.
  • the elements of a combination are generally functionally associated or related.
  • “combination therapy” refers to administration of two or more different therapeutics.
  • the different therapeutic agents can be provided and administered separately, sequentially, intermittently, or can be provided in a single composition.
  • a “kit” is a packaged combination that optionally includes other elements, such as additional reagents and instructions for use of the combination or elements thereof, for a purpose including, but not limited to, activation, administration, diagnosis, and assessment of a biological activity or property.
  • a “unit dose form” refers to physically discrete units suitable for human and animal subjects and packaged individually, as is known in the art.
  • a “single dosage formulation” refers to a formulation for direct administration.
  • a “multi-dose formulation” refers to a formulation that contains multiple doses of a therapeutic agent and that can be directly administered to provide several single doses of the therapeutic agent.
  • the doses can be administered over the course of minutes, hours, weeks, days, or months.
  • Multi-dose formulations can allow dose adjustment, dose-pooling and/or dose-splitting. Because multi-dose formulations are used over time, they generally contain one or more preservatives to prevent microbial growth.
  • an “article of manufacture” is a product that is made and sold. As used throughout this application, the term is intended to encompass any of the compositions provided herein contained in articles of packaging.
  • a “fluid” refers to any composition that can flow. Fluids thus encompass compositions that are in the form of semi-solids, pastes, solutions, aqueous mixtures, gels, lotions, creams, and other such compositions.
  • an isolated or purified polypeptide or protein e.g., an isolated antibody or antigen-binding fragment thereof
  • a biologically-active portion thereof e.g., an isolated antigen-binding fragment
  • an isolated or purified polypeptide or protein is substantially free of cellular material or other contaminating proteins from the cell or tissue from which the polypeptide or protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized.
  • Preparations can be determined to be substantially free if they appear free of readily detectable impurities as determined by standard methods of analysis, such as thin layer chromatography (TLC), gel electrophoresis and high performance liquid chromatography (HPLC), that are used by those of skill in the art to assess such purity, or are sufficiently pure such that further purification does not detectably alter the physical and chemical properties, such as enzymatic and biological activities, of the substance.
  • TLC thin layer chromatography
  • HPLC high performance liquid chromatography
  • a “cellular extract” or “lysate” refers to a preparation or fraction which is made from a lysed or disrupted cell.
  • a “control” refers to a sample that is substantially identical to the test sample, except that it is not treated with a test parameter, or, if it is a plasma sample, it can be from a normal volunteer not affected with the condition of interest. A control also can be an internal control.
  • the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise.
  • reference to a polypeptide, comprising “an immunoglobulin domain” includes polypeptides with one or a plurality of immunoglobulin domains.
  • the term “or” is used to mean “and/or” unless explicitly indicated to refer to alternatives only, or the alternatives are mutually exclusive.
  • ranges and amounts can be expressed as “about” a particular value or range. “About” also includes the exact amount. Hence, “about 5 amino acids” means “about 5 amino acids” and also “5 amino acids.”
  • “optional” or “optionally” means that the subsequently described event or circumstance does or does not occur, and that the description includes instances where said event or circumstance occurs and instances where it does not.
  • an optionally variant portion means that the portion is variant or non-variant.
  • bacteria have several advantages over other therapies such as oncolytic viruses.
  • Some bacterial species can be engineered to be orally and systemically (intravenously; IV) administered, they propagate readily in vitro and in vivo, and they can be stored and transported in a lyophilized state.
  • Bacterial chromosomes readily can be manipulated as they lack exons, and the complete genomes for numerous strains have been fully characterized (Felgner et al. (2016) mBio 7(5):e01220-16).
  • bacteria are cheaper and easier to produce than viruses, and proper delivery of engineered bacteria can be favorable over viral delivery because they do not permanently integrate into host cell genomes, they preferentially infect myeloid cells over epithelial cells, and they can be rapidly eliminated by antibiotics if necessary, rendering them safe.
  • immunostimulatory bacteria that are modified to exploit these advantageous properties.
  • the bacteria provided herein are modified so that they infect and accumulate in the tumor microenvironment, particularly in tumor-resident immune cells (myeloid cells), such as tumor-associated macrophages (TAMs), dendritic cells (DCs), and myeloid-derived suppressor cells (MDSCs), and also are designed to express and deliver high levels of therapeutic proteins and combinations, particularly complementary combinations, thereof.
  • myeloid cells tumor-resident immune cells
  • TAMs tumor-associated macrophages
  • DCs dendritic cells
  • MDSCs myeloid-derived suppressor cells
  • the immunostimulatory bacteria provided herein have advantageous properties that are superior to existing bacterial therapies, and also cell therapies, oncolytic virus therapies, and prior bacterial therapies.
  • the immunostimulatory bacteria provided herein while they can be administered by any suitable route, are suitable for systemic, such as intravenous, administration. As shown and described herein, the immunostimulatory bacteria provided herein can target major immune pathways.
  • the bacteria provided herein are designed and engineered to maintain the beneficial scaffold properties of bacteria, and to have a viral-like immune signature. This is advantageous for use as an anti-cancer therapeutic.
  • the following table summarizes some of the immune and scaffold properties of bacteria and viruses; the immunostimulatory bacteria provided herein retain the feasibility of the bacterial scaffold, but result in a viral-like immune response in a treated subject (discussed in more detail in section C below).
  • the flagella contribute to TRL5-mediated inflammation
  • the LPS results in TLR4-mediated inflammatory responses
  • the adhesive curli fimbriae result in TLR2-mediated inflammatory responses.
  • the genomes of the immunostimulatory bacteria provided herein are modified so that the bacteria lack flagella and adhesive curli fimbriae, and have modified LPS, resulting in the reduction or elimination of TLR4-mediated inflammatory responses.
  • the immunostimulatory bacteria provided herein induce a viral-like anti-tumor immune response. Elimination or modification of these components confers other advantageous properties, such as those discussed in detail below.
  • the immunostimulatory bacteria deliver therapeutic products, such as anti- cancer therapeutics, and particularly, complementary combinations of products.
  • the immunostimulatory bacteria provided herein deliver encoded genetic payloads in a tumor-specific manner to tumor-resident myeloid cells.
  • an anti-cancer therapeutic product an immunostimulatory bacterium, that delivers a genetic payload encoding one or a plurality of therapeutic products.
  • a truncated co-stimulatory molecule receptor or ligand; e.g., 4- 1BBL, CD80, CD86, CD27L, B7RP1, OX40L
  • APC antigen presenting cell
  • the truncated gene product is capable of constitutive immunostimulatory signaling to a T-cell through co-stimulatory receptor engagement, and is unable to counter-regulatory signal to the APC due to a truncated or deleted cytoplasmic domain.
  • the immunostimulatory bacteria can encode and express one or more of IL-2, IL-7, IL-12p70 (IL-12p40 + IL-12p35), IL-12, IL-15, IL-15/IL-15R ⁇ chain complex, IL-18, IL-21, IL-23, IL-36 ⁇ , interferon- ⁇ , interferon- ⁇ , IL-2 that has attenuated binding to IL-2Ra, IL-2 that is modified so that it does not bind to IL-2Ra, CXCL9, CXCL10, CXCL11, CCL3, CCL4, CCL5, cytosolic DNA/RNA sensors or type I IFN pathway proteins, such as gain-of-function or constitutively active STING, IRF3, IRF7, MDA5, or RIG-I variants (that induce type I IFN), inhibitors of TGF-beta, such as TGF- ⁇ inhibitory antibodies, TGF-beta polypeptide antagonists, and TGF-beta binding decoy receptors, antibodies and
  • the immunostimulatory bacteria also can encode and express a truncated co-stimulatory molecule (e.g., 4-1BBL, CD80, CD86, CD27L, B7RP1, OX40L), with a partial or complete cytoplasmic domain deletion, for expression on an antigen-presenting cell (APC), where the truncated gene product is capable of constitutive immuno- stimulatory signaling to a T-cell through co-stimulatory receptor engagement, and is unable to counter-regulatory signal to the APC, due to a deleted or truncated cytoplasmic domain. Combinations of such therapeutic products and agents can be expressed in a single therapeutic composition.
  • a truncated co-stimulatory molecule e.g., 4-1BBL, CD80, CD86, CD27L, B7RP1, OX40L
  • APC antigen-presenting cell
  • the immunostimulatory bacteria exhibit tumor-specific localization and enrichment, and provide intravenous (IV) administration for activation of anti- tumor immune pathways that are otherwise toxic if systemically activated.
  • the immunostimulatory bacteria provided herein are genetically designed to be safe and to target tumors, the tumor microenvironment, and/or tumor-resident immune cells.
  • the immunostimulatory bacteria provided herein include a combination of genomic modifications and other modifications, as well as encoded therapeutic products, that function in concert to provide immunostimulatory bacteria that accumulate in tumor-resident immune cells and that persist sufficiently long to deliver therapeutic products, particularly combinations that induce or promote anti- cancer immune stimulation in tumors and the tumor microenvironment, without toxic side-effects, or with limited toxic side-effects.
  • the immunostimulatory bacteria When delivered systemically, such as intravenously (IV), the immunostimulatory bacteria enrich in tumors, including in metastatic lesions; they provide efficient genetic transfer of immune payloads, specifically to tumor-resident myeloid cells, including tumor-associated macrophages (TAMs), myeloid-derived suppressor cells (MDSCs), and dendritic cells (DCs); they induce powerful, local immune responses, destroying tumors and vaccinating against future recurrence; and, when therapy is finished, they are naturally eliminated, such as by phagocytosis and destruction by the infected cells, or they can be destroyed rapidly by a course of antibiotics.
  • TAMs tumor-associated macrophages
  • MDSCs myeloid-derived suppressor cells
  • DCs dendritic cells
  • the immunostimulatory bacteria provided herein exhibit preferential accumulation in the tumor microenvironment and/or in tumor-resident immune cells due to a designed purine/adenosine auxotrophy, and exhibit an inability to replicate inside of phagocytic cells.
  • Immunostimulatory bacteria that avoid inactivation by serum complement allow for the delivery of a variety of immunotherapeutic agents and therapeutic products at high concentrations, directly within the tumor microenvironment, while minimizing toxicity to normal tissues, and are provided herein.
  • the immunostimulatory bacteria provided herein include modifications of the genome that render them msbB-/pagP-, which alters the lipid A in LPS, resulting in penta-acylation (wild-type lipid A has 6-7 fatty acid chains), reducing the TLR4 affinity; are adenonsine/adenine auxotrophs, such as purI-; are asparaginase II- (ansB-), which improves T-cell quality; are csgD-, which, among other properties, removes curli fimbriae; and include other optional genomic modifications, such as insertions, deletions, disruptions, and any other modification, so that the encoded product(s) is(are) not produced in active form, as discussed in detail herein.
  • the immunostimulatory bacteria include a plasmid that encodes one or more therapeutic products, particularly anti-cancer products, under control of a eukaryotic promoter.
  • the immunostimulatory bacteria provided herein, that deliver therapeutic products (such as constitutively active STING variants and other immunomodulatory proteins and products), to the tumor-resident myeloid cells promote adaptive immunity and enhance T-cell function.
  • the immunostimulatory bacteria lead to a complete remodeling of the immunosuppressive tumor microenvironment, towards an adaptive anti-tumor phenotype, and away from a bacterial phenotype, which is characterized by the promotion of innate immunity and the suppression of adaptive immunity.
  • the immunostimulatory bacteria provided herein include genomic modifications whereby they target or accumulate in tumor-resident immune cells, particularly tumor-resident myeloid cells, such as macrophages, MDSCs (myeloid derived suppressor cells), and DCs (dendritic cells), in which they deliver payloads of encoded therapeutic products expressed under control of regulatory sequences recognized by the hose cell (eukaryotic) transcriptional/translational machinery.
  • the encoded products are expressed in the myeloid cells, and, as appropriate, delivered into the tumor microenvironment.
  • the bacteria generate anti-tumor immunity, and also can deliver anti-tumor products that directly treat tumors, and products that can activate prodrugs.
  • Immunostimulatory bacteria provided herein can exhibit at least about 100,000-fold greater tumor infiltration and enrichment compared to unmodified bacteria.
  • the immunostimulatory bacteria are consumed by tumor-resident immune cells, and deliver the plasmid encoding therapeutic products, which are expressed and produced in the immune cells and tumor microenvironment, to generate anti-tumor immunity.
  • Bacterial Cancer Immunotherapy Many solid tumor types have evolved a profoundly immunosuppressive microenvironment that renders them highly refractory to approved checkpoint therapies, such as anti-CTLA-4, anti-PD-1 and anti-PD-L1 therapies.
  • Tumors initiate multiple mechanisms to evade immune surveillance, reprogram anti-tumor immune cells to suppress immunity, exclude and inactivate anti- tumor T-cells, and develop emerged resistance to the targeted cancer therapies (see, e.g., Mahoney et al. (2015) Nat. Rev. Drug Discov.14(8):561-584). Solving this problem will require immunotherapies that can properly inflame these tumors, and generate anti-tumor immunity that can provide long-lasting tumor regressions. In addition, intratumoral therapies are intractable and will be quite limiting in a metastatic disease setting.
  • CAR-T cells chimeric antigen receptors T-cells
  • Ig variable extracellular domain specific for a particular tumor antigen This confers upon the cells the antigen-recognition properties of antibodies, with the cytolytic properties of activated T-cells (see, e.g., Sadelain et al. (2015) J. Clin.
  • Tumors can mutate rapidly to downregulate the targeted tumor antigens for solid tumors, including the antigen CD19, thereby fostering immune escape (see, e.g., Mardiana et al. (2019) Sci. Transl. Med.11(495):eaaw2293).
  • Solid tumor targets that are not expressed in healthy tissue are a major impediment to CAR-T therapy. Beyond that, CAR-T therapies suffer from other impediments to accessing solid tumor microenvironments, due to the lack of sufficient T-cell chemokine gradients, which are required for proper T-cell infiltration into tumors.
  • OVs Viral Vaccine Platforms
  • Oncolytic viruses have natural and engineered properties to induce tumor cell lysis, recruit T-cells to the tumor, and deliver genetic material that can be read by tumor cells to produce immunomodulatory proteins.
  • T-VEC Talimogene laherparepvec
  • T-VEC is a modified herpes simplex virus encoding anti-melanoma antigens and the cytokine GM-CSF (granulocyte-macrophage colony-stimulating factor), that is intratumorally administered. It is FDA-approved for metastatic melanoma (see, e.g., Bastin et al. (2016) Biomedicines 4(3):21).
  • T-VEC has demonstrated clinical benefit for some melanoma patients, and with fewer immune toxicities than the immune checkpoint antibodies or the FDA-approved systemic cytokines, such as IL-2 and interferon- alpha (see, e.g., Kim et al. (2006) Cytokine Growth Factor Rev.17(5):349-366; and Paul et al. (2015) Gene 567(2):132-137).
  • Oncolytic viruses possess a number of limitations as anti-cancer therapies. First, oncolytic viruses are rapidly inactivated by the human complement system in blood. It has proven difficult to deliver enough virus through systemic administration to have a desired therapeutic effect.
  • Intratumoral delivery is limiting in a metastatic setting (where lesions are spread throughout the body), is intractable for most solid tumor types (e.g., lung and visceral lesions), and requires interventional, guided radiology for injection, which limits repeat dosing.
  • Viruses can be difficult to manufacture at commercial scale and to store.
  • Oncolytic viruses are inherently immunogenic and rapidly cleared from human blood, and T-cells that traffic into the tumor have a much higher affinity for viral antigens over weaker tumor neoantigens (see, e.g., Aleksic et al. (2012) Eur. J. Immunol. 42(12):3174-3179). Thus, in addition to the recognized technical limitations of the platform, OVs thus far have limited capacity to stimulate durable anti-tumor immunity.
  • Bacterial Cancer Therapies A number of bacterial species have demonstrated preferential replication within solid tumors when injected from a distal site in preclinical animal studies. These include, but are not limited to, species of Salmonella, Bifodobacterium, Clostridium, and Escherichia.
  • the tumor-homing properties of the bacteria can mediate an anti- tumor response.
  • This tumor tissue tropism reduces the size of tumors to varying degrees.
  • One contributing factor to the tumor tropism of these bacterial species is the ability to replicate in anoxic and hypoxic environments.
  • a number of these naturally tumor-tropic bacteria have been further engineered to increase the potency of the anti- tumor response (reviewed in Zu et al. (2014) Crit. Rev. Microbiol.40(3):225–235; and Felgner et al. (2017) Microbial Biotechnology 10(5):1074–1078).
  • Patent Nos.7,344,710 and 3,936,354 Mycobacterium (see, e.g., U.S. Patent Publication Nos.2015/0224151 and 2015/0071873), Bifidobacterium (see, e.g., Dang et al. (2001); and Kimura et al. (1980) Cancer Res.40:2061-2068), Lactobacillus (see, e.g., Dang et al. (2001)), Listeria monocytogenes (see, e.g., Le et al. (2012) Clin. Cancer Res.18(3):858-868; Starks et al. (2004) J. Immunol.173:420-427; and U.S.
  • Patent Publication No. 2006/0051380 and Escherichia coli (see, e.g., U.S. Patent No.9,320,787), have been studied as possible agents for anti-cancer therapy.
  • the immunostimulatory bacteria provided herein include genome modifications that address problems with prior bacteria developed for treating tumors. The modifications improve the targeting or accumulation of bacteria in the tumor microenvironment, and in particular, are designed so that the bacteria infect tumor- resident immune cells and not healthy tissues, thereby decreasing toxicity and improving delivery of encoded products.
  • the immunostimulatory bacteria also are designed to deliver therapeutic products, including combinations thereof, designed to eliminate immune suppressive effects of tumors, enhance a host’s anti-tumor response, and provide anti-tumor products. i.
  • Listeria Listeria monocytogenes a live attenuated intracellular bacterium capable of inducing potent CD8 + T-cell priming to expressed tumor antigens in mouse models of cancer, has also been explored as a bacterial cancer vector (see, e.g., Le et al. (2012) Clin. Cancer Res.18(3):858-868). In a clinical trial of the L.
  • monocytogenes also has shown limited immune responses to the encoded tumor antigens due to the requirement for bacteria to be lysed after phagocytosis, a pre- requisite to efficient plasmid transfer, which has not been demonstrated to occur by L. monocytogenes in human macrophages.
  • Salmonella Species Salmonella enterica serovar Typhimurium (S. typhimurium) is exemplary of a bacterial species for use as an anti-cancer therapeutic. S.
  • typhimurium is a Gram- negative facultative anaerobe, which preferentially accumulates in hypoxic and necrotic areas due to the availability of nutrients from tissue necrosis, the leaky tumor vasculature, and their increased likelihood to survive in the immunosuppressed tumor microenvironment (see, e.g., Baban et al. (2010) Bioengineered Bugs 1(6):385-394).
  • a facultative anaerobe S. typhimurium is able to grow under aerobic and anaerobic conditions, and is therefore able to colonize both small tumors that are less hypoxic, and large tumors that are more hypoxic.
  • S. typhimurium transmission through the fecal-oral route causes localized gastrointestinal infections.
  • the bacterium can also enter the bloodstream and lymphatic system, infecting systemic tissues such as the liver, spleen and lungs.
  • Systemic administration of wild-type S. typhimurium overstimulates TNF- ⁇ and IL-6, leading to a cytokine cascade and septic shock, which, if left untreated, can be fatal.
  • pathogenic bacterial strains such as S. typhimurium, must be attenuated to prevent systemic infection, without completely suppressing their ability to effectively colonize tumor tissues.
  • S. typhimurium is an intracellular pathogen that is rapidly taken up by phagocytic myeloid cells such as macrophages, or it can directly invade non- phagocytic cells, such as epithelial cells, through its Salmonella pathogenicity island 1 (SPI-1)-encoded type III secretion system (T3SS1).
  • SPI-1 Salmonella pathogenicity island 1
  • T3SS1 Salmonella pathogenicity island 1
  • S. typhimurium has been described as anti-tumor agents to elicit direct tumoricidal effects and/or to deliver tumoricidal molecules (see, e.g., Clairmont et al. (2000) J. Infect. Dis.181:1996-2002; Bermudes, D. et al. (2002) Curr.
  • S. typhimurium strain SL7207 is an aromatic amino acid auxotroph (aroA- mutant), and strains A1 and A1-R are leucine-arginine auxotrophs.
  • Mutations that attenuate bacteria also include, but are not limited to, mutations in genes that alter the biosynthesis of lipopolysaccharide (LPS), such as rfaL, rfaG, rfaH, rfaD, rfaP, rFb, rfa, msbB, htrB, firA, pagL, pagP, lpxR, arnT, eptA, and lpxT; mutations that introduce a suicide gene, such as sacB, nuk, hok, gef, kil, or phlA; mutations that introduce a bacterial lysis gene, such as hly and cly; mutations in genes that encode virulence factors, such as IsyA, pag, prg, iscA, virG, plc, and act; mutations in genes that modify the stress response, such as recA, htrA, htpR, hsp, and
  • Attenuating mutations are gene deletions to prevent spontaneous compensatory mutations that might result in reversion to a virulent phenotype.
  • PhoP/PhoQ operon system is a typical bacterial two-component regulatory system, composed of a membrane-associated sensor kinase (PhoQ), and a cytoplasmic transcriptional regulator (PhoP)
  • PhoP/PhoQ operon system is a typical bacterial two-component regulatory system, composed of a membrane-associated sensor kinase (PhoQ), and a cytoplasmic transcriptional regulator (PhoP)
  • PhoP/PhoQ is required for virulence; its deletion results in poor survival of this bacterium in macrophages, and a marked attenuation in mice and humans (see, e.g., Miller, S. I. et al. (1989) Proc. Natl. Acad. Sci. U.S.A.86:5054- 5058; Groisman, E. A. et al. (1989) Proc. Natl. Acad. Sci. U.S.A.86:7077-7081; Galan, J. E. and Curtiss, R. III. (1989) Microb.
  • PhoP/PhoQ deletion strains have been employed as vaccine delivery vehicles (see, e.g., Galan, J. E. and Curtiss, R. III. (1989) Microb. Pathog.6:433-443; Fields, P. I. et al. (1986) Proc. Natl. Acad. Sci. U.S.A.83:5189-5193; and Angelakopoulos, H. and Hohmann, E. L. (2000) Infect. Immun.68:2135-2141).
  • typhimurium that have been attenuated for therapy are, for example, the leucine-arginine auxtroph A-1 (see, e.g., Zhao et al. (2005) Proc. Natl. Acad. Sci. U.S.A.102(3):755-760; Yu et al. (2012) Scientific Reports 2:436; U.S. Patent No.8,822,194; and U.S. Patent Publication No.2014/0178341), and its derivative AR-1 (see, e.g., Yu et al. (2012) Scientific Reports 2:436; Kawaguchi et al. (2017) Oncotarget 8(12):19065-19073; Zhao et al.
  • the leucine-arginine auxtroph A-1 see, e.g., Zhao et al. (2005) Proc. Natl. Acad. Sci. U.S.A.102(3):755-760; Yu et al. (2012) Scientific Reports 2:436; U.S. Patent No
  • Patent Publication Nos.2012/0009153, 2016/0369282 and 2016/0184456), and its obligate anaerobe derivative YB1 see, e.g., International Application Publication No. WO 2015/032165; Yu et al. (2012) Scientific Reports 2:436; and Leschner et al. (2009) PLoS ONE 4(8):e6692; the aroA- /aroD- mutant S. typhimurium strain BRD509, a derivative of the SL1344 (wild-type) strain (see, e.g., Yoon et al. (2017) Eur. J. Cancer 70:48-61); the asd-/cya-/crp- mutant S.
  • the immunostimulatory bacteria such as the Salmonella strains exemplified herein, are attenuated by virtue of modifications, that can include some of those described above, but also have other modifications and properties described herein that enhance the effectiveness as a cancer therapeutic.
  • Attenuated strains of S. typhimurium possess the innate ability to deliver DNA following phagocytosis and degradation (see, e.g., Weiss et al. (2003) Int. J. Med. Microbiol.41(7):3413-3414). They have been used as vectors for gene therapy.
  • S. typhimurium strains have been used to deliver and express a variety of genes, including those that encode cytokines, angiogenesis inhibitors, toxins, and prodrug-converting enzymes (see, e.g., U.S. Patent Publication No.2007/0298012; Loeffler et al. (2008) Cancer Gene Ther.15(12):787-794; Loeffler et al.
  • S. typhimurium has been modified to deliver the tumor-associated antigen (TAA) survivin (SVN) to antigen presenting cells (APCs) to prime adaptive immunity (see, e.g., U.S. Patent Publication No.2014/0186401; and Xu et al. (2014) Cancer Res.74(21):6260-6270).
  • TAA tumor-associated antigen
  • APCs antigen presenting cells
  • SVN is an inhibitor of apoptosis protein (IAP), which prolongs cell survival and provides cell cycle control, and is overexpressed in all solid tumors and poorly expressed in normal tissues.
  • IAP apoptosis protein
  • This technology uses SPI-2 and its type III secretion system to deliver the TAAs into the cytosol of APCs, which then are activated to induce TAA-specific CD8 + T-cells and anti-tumor immunity (see, e.g., Xu et al. (2014) Cancer Res.74(21):6260-6270). Similar to the Listeria-based TAA vaccines, this approach has shown promise in mouse models, but has not demonstrated effective tumor antigen-specific T-cell priming in humans. In addition to the delivery of DNA that encodes proteins, S. typhimurium also has been used for the delivery of small interfering RNAs (siRNAs) and short hairpin RNAs (shRNAs) for cancer therapy. For example, attenuated S.
  • siRNAs small interfering RNAs
  • shRNAs short hairpin RNAs
  • typhimurium has been modified to express certain shRNAs, such as those that target the immunosuppressive gene indolamine dioxygenase (IDO).
  • IDO immunosuppressive gene indolamine dioxygenase
  • Silenced IDO expression in a murine melanoma model resulted in tumor cell death and significant tumor infiltration by neutrophils (see, e.g., Blache et al. (2012) Cancer Res.72(24):6447-6456; International Application Publication No. WO 2008/091375; and U.S. Patent No.9,453,227).
  • Co- administration of this vector with a hyaluronidase showed positive results in the treatment of murine pancreatic ductal adenocarcinoma (see, e.g., Manuel et al.
  • typhimurium strain SL7207 has been used for the delivery of shRNA targeting CTNNB1, the gene that encodes ⁇ -catenin (see, e.g., Guo et al. (2011) Gene Therapy 18:95-105; and U.S. Patent Publication Nos. 2009/0123426 and 2016/0369282).
  • the S. typhimurium strain VNP20009 has been used for the delivery of shRNA targeting STAT3 (see, e.g., Manuel et al. (2011) Cancer Res.71(12):4183-4191; U.S. Patent Publication Nos.2009/0208534, 2014/0186401 and 2016/0184456; and International Application Publication Nos.
  • siRNAs targeting the autophagy genes Atg5 and Beclin1 have been delivered to tumor cells using S. typhimurium strains A1- R and VNP20009 (see, e.g., Liu et al. (2016) Oncotarget 7(16):22873-22882). It has been found, however, that these strains do not effectively stimulate an anti-tumor immune response, nor effectively colonize tumors for delivery of therapeutic doses of encoded products. Improvement of such strains is needed so that they more effectively stimulate an anti-tumor immune response, such as the immunostimulatory bacteria provided herein. Further and alternative modifications of various bacteria have been described in published International PCT Application No.
  • VNP20009 Exemplary of a therapeutic bacterium that can be used as a starting strain for modification as described herein is the strain designated as VNP20009 (ATCC # 202165, YS1646). This virus was a clinical candidate. VNP20009 (ATCC # 202165, YS1646) was at least 50,000-fold attenuated for safety by deletion of the msbB and purI genes (see, e.g., Clairmont et al. (2000) J. Infect.
  • VNP20009 also is auxotrophic for the immunosuppressive nucleoside adenosine.
  • Adenosine can accumulate to pathologically high levels in the tumor and contribute to an immunosuppressive tumor microenvironment (see, e.g., Peter Vaupel and Arnulf Mayer, Oxygen Transport to Tissue XXXVII, Advances in Experimental Medicine and Biology 876 chapter 22, pp.177-183).
  • VNP20009 When VNP20009 was administered into mice bearing syngeneic or human xenograft tumors, the bacteria accumulated preferentially within the extracellular components of tumors at ratios exceeding 300-1000 to 1, and demonstrated tumor growth inhibition, as well as prolonged survival compared to control mice (see, e.g., Clairmont et al. (2000) J. Infect. Dis.181:1996-2002). VNP20009 demonstrated success in tumor targeting and tumor growth suppression in animal models, while eliciting very little toxicity (see, e.g., Broadway et al. (2014) J. Biotechnology 192:177-178; Loeffler et al. (2007) Proc. Natl. Acad. Sci.
  • the immunostimulatory bacteria provide numerous improvements and advantages that strain VNP20009 lacks.
  • the immunostimulatory bacteria deliver encoded genetic payloads in a tumor-specific manner, to tumor- resident myeloid cells.
  • the immunostimulatory bacteria by virtue of genomic modifications, such as deletions or disruptions of genes, and other modifications of the genome, exhibit reduced TLR2-, TLR4-, and TLR5-mediated inflammation, for example, by virtue of the elimination of the flagella, the modifications of the LPS, and the elimination of the curl fimbriae and reduced biofilm formation.
  • the immunostimulatory bacteria enhance T-cell function, such as by virtue of the elimination of the expression of L-asparaginase II, and facilitate, provide, permit, and support plasmid maintenance.
  • the bacteria accumulate in (or target) only, or substantially only, myeloid cells, particularly tumor-resident myeloid cells, providing highly efficient plasmid delivery after phagocytosis.
  • the immunostimulatory bacteria provided herein colonize the tumor microenvironment, and can be administered systemically.
  • the immunostimulatory bacteria provided herein exhibit at least 15-fold improved LD 50 compared to VNP20009. Thus, a much higher dose, if needed, of the immunostimulatory bacteria provided herein can be administered without toxic effects, compared to VNP20009 (see, the table below in the section F.5.
  • immunostimulatory bacteria modified as described herein including elimination of flagella, LPS modifications, and other modifications, preferentially accumulate in or target myeloid cells, particularly tumor- resident myeloid cells.
  • the Examples demonstrate that the immunostimulatory bacteria accumulate in such cells following systemic, such as intravenous, administration.
  • the Examples also describe and show plasmid transfer from the immunostimulatory bacteria into tumor-resident myeloid cells, and durable protein expression following bacterial cell death, thereby delivering therapeutic products, including products that result in an anti-cancer response and phenotype. iv.
  • Wild-Type Strains Accumulation of VNP20009 in tumors results from a combination of factors including: the inherent invasiveness of the parental strain, ATCC 14028, its ability to replicate in hypoxic environments, and its requirement for high concentrations of purines that are present in the interstitial fluid of tumors. As described herein, it is not necessary to use an attenuated strain, such as VNP20009, as a starting bacterial strain. By virtue of the modifications described herein, the bacteria are rendered non-toxic or attenuated.
  • the parental strain, ATCC 14028, or another wild-type strain can be used as a starting strain, and modified as described herein. 3.
  • Bacteria have numerous advantageous properties for use as anti-cancer therapeutics, compared to, for example, oncolytic viruses. These include the ease with which they can be propagated, manufactured, stored, and eliminated from a host when treatment is completed. Viruses, however, also have advantageous properties, including the host response.
  • the response to a bacterial infection is an innate inflammatory response, which is not advantageous for an anti-cancer therapeutic.
  • the response to a viral infection is similar to an anti-cancer response.
  • a limitation of bacteria as a microbial anti-cancer platform derives from the specific immune program that is initiated upon sensing of bacteria, even intracellular bacteria, by the immune system, compared to viral-sensing pathways, which are more akin to anti-cancer pathways.
  • the sensing programs that recognize viruses permit the generation of highly effective vaccines and durable adaptive immunity.
  • Vaccinating against bacteria has been met with limited success.
  • the FDA-approved vaccine for typhoid fever against Salmonella typhi is only 55% effective (see, e.g., Hart et al. (2016) PLoS ONE 11(1):e0145945), despite S.
  • PAMPs Pathogen- Associated Molecular Patterns
  • PRRs host cell Pattern Recognition Receptors
  • TLRs Toll-Like Receptors
  • TLRs recognize a variety of ligands, including lipopolysaccharide (TLR4), lipoproteins (TLR2), flagellin (TLR5), unmethylated CpG motifs in DNA (TLR9), double-stranded RNA (TLR3), and single-stranded RNA (TLR7 and TLR8) (see, e.g., Akira et al. (2001) Nat. Immunol.2(8):675-680; and Kawai and Akira (2005) Curr. Opin. Immunol.17(4):338-344).
  • DNA and RNA-based viruses can be sensed either in host cytosolic compartments after phagocytosis, or directly in the cytosol.
  • Type I interferons are the signature cytokines induced by host recognition of single-stranded and double-stranded DNA and RNA, either of viral origin, or from the uptake of damaged host cell DNA.
  • the synthetic dsRNA analog polyinosinic:polycytidylic acid (poly(I:C)) is an agonist for endosomal TLR3 and a powerful inducer of type I IFN, and its more stable version, poly ICLC (such as that sold under the trademark Hiltonol®), has been in clinical development (see, e.g., Caskey et al. (2011) J. Exp. Med.208(12):2357-2366).
  • single- stranded RNA (ssRNA) in the endosome is sensed by TLR7 and TLR8 (only in humans), and its known synthetic ligands, resiquimod and imiquimod, are FDA- approved topical cancer immunotherapies.
  • dsRNA double-stranded RNA
  • RNA helicases such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation- associated gene 5 (MDA-5), leading to induction of type I IFN (see, e.g., Ireton and Gale (2011) Viruses 3(6):906-919).
  • the cytosolic sensor for dsDNA is mediated through Stimulator of Interferon Genes (STING), an ER-resident adaptor protein that is the central mediator for sensing cytosolic dsDNA from infectious pathogens or aberrant host cell damage (see, e.g., Barber (2011) Immunol. Rev.243(1):99-108).
  • STING signaling activates the TANK-binding kinase 1 (TBK1)/interferon regulatory factor 3 (IRF3) axis, and the NF- ⁇ B signaling axis, resulting in the induction of IFN- ⁇ and other pro-inflammatory cytokines and chemokines that strongly activate innate and adaptive immunity (see, e.g., Burdette et al.
  • cytosolic dsDNA through STING requires cyclic GMP-AMP synthase (cGAS), a host cell nucleotidyl transferase that directly binds dsDNA, and in response, synthesizes a cyclic dinucleotide (CDN) second messenger, cyclic GMP- AMP (cGAMP), which binds and activates STING (see, e.g., Sun et al. (2013) Science 339(6121):786-791; and Wu et al. (2013) Science 339(6121):826-830).
  • CDN cyclic dinucleotide
  • cGAMP cyclic GMP- AMP
  • STING also can bind to bacterially-derived CDNs, such as c-di-AMP produced from intracellular L. monocytogenes, or c-di-GMP from S. typhimurium.
  • cGAS produces a non-canonical CDN that can activate human STING alleles that are non-responsive to bacterially-derived canonical CDNs.
  • the internucleotide phosphate bridge in the cGAMP synthesized by cGAS is joined by a non-canonical 2’-3’ linkage.
  • viral-sensing PRRs and TLRs such as STING, RIG-I, TLR3 and TLR7/8, induce type I IFN, and the cytokines and chemokines that lead to effective T- cell mediated adaptive immunity.
  • type I IFN signaling is required to induce T-cell trafficking chemokines, such as CXCL10, and also to activate DC cross-presentation of tumor antigens to prime CD8 + T-cells (see, e.g., Diamond et al. (2011) J. Exp. Med.208(10):1989–2003; and Fuertes et al. (2011) J. Exp. Med. 208(10):2005–2016).
  • host surveillance of bacteria such as S.
  • TLR2 myeloid differentiation primary response protein 88
  • TLR4 MyD88-myeloid differentiation primary response protein 88
  • TRIF Toll/interleukin-1 receptor (TIR)-domain- containing adapter-inducing interferon- ⁇ ) adaptor molecules to mediate induction of the NF- ⁇ B-dependent pro-inflammatory cytokines TNF- ⁇ and IL-6 (see, e.g., Pandey et al. (2015) Cold Spring Harb. Perspect. Biol.7(1):a016246).
  • typhimurium was shown to activate the NLRP3 inflammasome pathway, resulting in the cleavage of caspase-1 and the induction of the pro-inflammatory cytokines IL-1 ⁇ and IL-18 that lead to pyroptotic cell death. Engagement of TLR2, TLR4 and TLR5, and inflammasome activation, induces chemokines and cytokines that lead to bacterial clearance by neutrophils and macrophages. Evidence that S. typhimurium is cleared by T-cells is limited, and antibodies that are generated against it are non-neutralizing (see, e.g., McSorley (2014) Immunol. Rev.260(1):168-182). Further, S.
  • typhimurium has mechanisms to directly suppress T-cell function, impairing any potential anti- tumor T-cell response from being generated (see, e.g., Kullas et al. (2012) Cell Host Microbe.12(6)791-798).
  • bacterial cancer therapies such as S. typhimurium, lead to recruitment and clearance by neutrophils and macrophages, which are not the T-cells that are required to generate adaptive anti-tumor immunity. It is described herein that these differences can explain why prior bacterial anti-cancer vaccines, even those harboring host tumor antigens, are poor T-cell priming vectors in humans. These problems are among those addressed by the immunostimulatory bacteria provided herein.
  • the immunostimulatory bacteria provided herein are engineered to have advantageous properties that were previously only provided by viral therapeutics, and also, to retain the advantageous properties of bacterial therapeutics.
  • the bacteria provided herein can be systemically administered, can localize to tumors, tumor-resident immune cells, and/or the tumor microenvironment, overcome immunosuppression, and properly activate anti-tumor immunity, while also limiting the autoimmune-related toxicities of existing systemic immunotherapies.
  • the immunostimulatory bacteria provided herein effectively localize to tumor-resident immune cells, and encode therapeutic anti-cancer products, and can encode a plurality of such products.
  • the bacteria provided herein can encode complementary therapeutic products.
  • bacteria such as strains of Salmonella and other species
  • bacteria can be modified as described herein to have reduced inflammatory effects, and thus, to be less toxic. As a result, for example, higher dosages can be administered.
  • the immunostimulatory bacteria provided herein are modified to have increased colonization of the tumor microenvironment, tumor-resident immune cells, and tumors.
  • an anti-cancer therapeutic product that delivers a genetic payload encoding a truncated co-stimulatory molecule (receptor or ligand; e.g., 4-1BBL, CD80, CD86, CD27L, B7RP1, OX40L), with a full or truncated or partial cytoplasmic domain deletion, for expression on an antigen presenting cell (APC), where the truncated gene product is capable of constitutive immuno-stimulatory signaling to a T-cell through co-stimulatory receptor engagement, and is unable to counter-regulatory signal to the APC due to a deleted or truncated cytoplasmic domain.
  • receptor or ligand e.g., 4-1BBL, CD80, CD86, CD27L, B7RP1, OX40L
  • APC antigen presenting cell
  • the co-stimulatory molecules also can be modified to include residues (such as positive residues) in the truncated cytoplasmic domain, to ensure that they are expressed in the correct orientation in the cell membrane (the Examples below describe this in more detail; see, e.g., Example 19).
  • residues such as positive residues
  • the bacterial strains provided herein are engineered to deliver therapeutic products.
  • the bacterial strains herein deliver immunostimulatory proteins, including cytokines, chemokines and co-stimulatory molecules, as well as modified gain-of- function cytosolic DNA/RNA sensors that can constitutively evoke or induce type I IFN expression, and other therapeutic products, such as, but not limited to, antibodies and fragments thereof, TGF- ⁇ and IL-6 binding decoy receptors, TGF- ⁇ polypeptide antagonists, bispecific T-cell engagers (BiTEs®), RNAi, and complementary combinations thereof, that promote an anti-tumor immune response in the tumor microenvironment.
  • immunostimulatory proteins including cytokines, chemokines and co-stimulatory molecules, as well as modified gain-of- function cytosolic DNA/RNA sensors that can constitutively evoke or induce type I IFN expression
  • other therapeutic products such as, but not limited to, antibodies and fragments thereof, TGF- ⁇ and IL-6 binding decoy receptors, TGF- ⁇ polypeptide antagonists, bispecific T-cell
  • the bacterial strains also include genomic modifications that reduce pyroptosis of phagocytic cells, thereby providing for a more robust immune response, and/or reduce or eliminate the ability to infect/invade epithelial cells, but retain the ability to infect/invade phagocytic cells, so that they accumulate more effectively in tumors, the tumor microenvironment and in tumor-resident immune cells.
  • the bacterial strains also can be modified to be resistant to inactivation by complement factors in human serum.
  • the bacterial strains also can be modified to encode therapeutic products, including, alone or in combinations, for example, cytokines, chemokines, co-stimulatory molecules, constitutively active inducers of type I IFN, and monoclonal antibodies (and fragments thereof) to immune checkpoints, and also to other such targets.
  • therapeutic products including, alone or in combinations, for example, cytokines, chemokines, co-stimulatory molecules, constitutively active inducers of type I IFN, and monoclonal antibodies (and fragments thereof) to immune checkpoints, and also to other such targets.
  • enhancements including modifications to the bacterial genome, or to the immunostimulatory bacteria, that, for example, reduce toxicity and improve the anti-tumor activity, such as by increasing accumulation in tumor-resident myeloid cells, improving resistance to complement inactivation, reducing immune cell death, promoting adaptive immunity, and enhancing T-cell function.
  • the modifications are described with respect to Salmonella, particularly S. typhimurium; it is understood that the skilled person can effect similar enhancements/modifications in other bacterial species and other Salmonella strains.
  • LPS lipopolysaccharide
  • O antigen or O polysaccharide
  • the lipopolysaccharide (LPS) of Gram-negative bacteria is the major component of the outer leaflet of the bacterial membrane. It is composed of three major parts, lipid A, a non-repeating core oligosaccharide, and the O antigen (or O polysaccharide).
  • O antigen is the outermost portion on LPS and serves as a protective layer against bacterial permeability, however, the sugar composition of O antigen varies widely between strains.
  • the lipid A and core oligosaccharide vary less, and are more typically conserved within strains of the same species.
  • Lipid A is the portion of LPS that contains endotoxin activity. It is typically a disaccharide decorated with multiple fatty acids. These hydrophobic fatty acid chains anchor the LPS into the bacterial membrane, and the rest of the LPS projects from the cell surface. The lipid A domain is responsible for much of the toxicity of Gram-negative bacteria. Typically, LPS in the blood is recognized as a significant pathogen associated molecular pattern (PAMP), and induces a profound pro-inflammatory response. LPS is the ligand for a membrane-bound receptor complex comprising CD14, MD2, and TLR4.
  • PAMP pathogen associated molecular pattern
  • TLR4 is a transmembrane protein that can signal through the MyD88 and TRIF pathways to stimulate the NF- ⁇ B pathway and result in the production of pro-inflammatory cytokines, such as TNF- ⁇ and IL-6, the result of which can be endotoxic shock, which can be fatal.
  • LPS in the cytosol of mammalian cells can bind directly to the CARD domains of caspases 4, 5, and 11, leading to autoactivation and pyroptotic cell death (see, e.g., Hagar et al. (2015) Cell Research 25:149-150). The composition of lipid A and the toxigenicity of lipid A variants is well documented.
  • a monophosphorylated lipid A is much less inflammatory than lipid A with multiple phosphate groups.
  • the number and length of the acyl chains on lipid A also can have a profound impact on the degree of toxicity.
  • Canonical lipid A from E. coli has six acyl chains, and this hexa-acylation is potently toxic.
  • S. typhimurium lipid A is similar to that of E. coli; it is a glucosamine disaccharide that carries four primary and two secondary hydroxyacyl chains (see, e.g., Raetz et al. (2002) Annu. Rev. Biochem. 71:635-700).
  • msbB Deletion of The enzyme lipid A biosynthesis myristoyltransferase, encoded by the msbB gene in S. typhimurium, catalyzes the addition of a terminal myristoyl group to the lipid A domain of lipopolysaccharide (LPS) (see, e.g., Low et al. (1999) Nat. Biotechnol.17(1):37-41). Deletion of msbB thus alters the acyl composition of the lipid A domain of LPS, the major component of the outer membranes of Gram- negative bacteria. For example, deletion of msbB in the S.
  • LPS lipopolysaccharide
  • typhimurium strain VNP20009 results in the production of a predominantly penta-acylated lipid A, which is less toxic than native hexa-acylated lipid A, and allows for systemic delivery without the induction of toxic shock (see, e.g., Lee et al. (2000) International Journal of Toxicology 19:19-25).
  • This modification significantly reduces the ability of the LPS to induce septic shock, attenuating the bacterial strain, and thus, increasing the therapeutic index of Salmonella-based immunotherapeutics (see, e.g., U.S. Patent Publication Nos.2003/0170276, 2003/0109026, 2004/0229338, 2005/0255088, and 2007/0298012).
  • msbB mutants that do no express the msbB product are unable to replicate intracellularly, as exemplified herein (see, e.g., Example 2), which is a requirement for Salmonella virulence (see, e.g., Leung et al. (1991) Proc. Natl. Acad. Sci. U.S.A.88:11470-11474).
  • Other LPS mutations, including replacements, deletions, or insertions, that alter LPS expression can be introduced into the bacterial strains provided herein, including the Salmonella strains, that dramatically reduce virulence, and thereby provide for lower toxicity, and permit the administration of higher doses.
  • genes encoding homologs or orthologs of lipid A biosynthesis myristoyltransferase in other bacterial species, also can be deleted or disrupted to achieve similar results.
  • These genes include, but are not limited to, for example, lpxM, encoding myristoyl-acyl carrier protein-dependent acyltransferase in E. coli; and msbB, encoding lipid A acyltransferase in S. typhi.
  • b. pagP Deletion As described above, msbB mutants of S.
  • typhimurium cannot undergo the terminal myristoylation of LPS, and produce predominantly penta-acylated lipid A that is significantly less toxic than hexa-acylated lipid A.
  • the modification of lipid A with palmitate is catalyzed by the enzyme lipid A palmitoyltransferase (PagP).
  • PagP lipid A palmitoyltransferase
  • Transcription of the pagP gene is under control of the PhoP/PhoQ system which is activated by low concentrations of magnesium, e.g., inside the SCV.
  • the acyl content of S. typhimurium lipid A is variable, and with wild-type bacteria, it can be hexa- or penta-acylated. The ability of S.
  • typhimurium to palmitate its lipid A increases resistance to antimicrobial peptides that are secreted into phagolysosomes.
  • expression of pagP results in a lipid A that is hepta-acylated.
  • msbB mutant in which the terminal acyl chain of the lipid A cannot be added
  • the induction of pagP results in a hexa-acylated lipid A (see, e.g., Kong et al. (2011) Infection and Immunity 79(12):5027–5038).
  • Hexa-acylated lipid A has been shown to be the most pro-inflammatory.
  • LPS is a potent TLR4 agonist that induces TNF- ⁇ and IL-6.
  • the dose-limiting toxicities in the I.V. VNP20009 clinical trial (see, e.g., Toso et al. (2002) J. Clin. Oncol.20(1):142-152), at 1E9 CFUs/m 2 , were cytokine mediated (fever, hypotension), with TNF- ⁇ levels > 100,000 pg/ml, and IL-6 levels > 10,000 pg/ml in serum at 2 hours.
  • the LPS still can be toxic at high doses, possibly due to the presence of hexa-acylated lipid A.
  • a pagP-/msbB- strain which cannot produce hexa- acylated lipid A, and produces only penta-acylated lipid A, resulting in lower induction of pro-inflammatory cytokines, is better tolerated at higher doses, and will allow for dosing in humans at or above 1E9 CFUs/m 2 .
  • Higher dosing leads to increased colonization of tumors, tumor-resident immune cells, and the tumor microenvironment, enhancing the therapeutic efficacy of the immunostimulatory bacteria. Because of the resulting change in bacterial membranes and structure, the host immune response, such as complement activity, is altered so that the bacteria are not eliminated upon systemic administration.
  • pagP-/msbB- mutant strains have increased resistance to complement inactivation, and enhanced stability in human serum.
  • immunostimulatory bacteria exemplified by live attenuated Salmonella strains, such as the exemplary strain of S. typhimurium, that only can produce LPS with penta-acylated lipid A, that contain a deletion of the msbB gene, and that further are modified by deletion or disruption of pagP.
  • deletion of msbB expression prevents the terminal myristoylation of lipid A
  • deletion of pagP expression prevents palmitoylation.
  • a strain modified to produce LPS with penta-acylated lipid A results in lower levels of pro-inflammatory cytokines, improved stability in the blood, resistance to complement fixation, increased sensitivity to antimicrobial peptides, enhanced tolerability, and increased anti-tumor immunity when further modified to express heterologous genetic payloads that stimulate the immune response in the tumor microenvironment.
  • Corresponding genes, encoding homologs and orthologs of lipid A palmitoyltransferase (PagP) in other bacterial species also can be deleted or disrupted to achieve similar results. These genes include, but are not limited to, for example, pagP, encoding Lipid IVA palmitoyltransferase in E.
  • the immunostimulatory bacteria provided herein can be attenuated by rendering them auxotrophic for one or more essential nutrients, such as purines (for example, adenine), nucleosides (for example, adenosine), amino acids (for example, aromatic amino acids, arginine and leucine), adenosine triphosphate (ATP), or other nutrients as known and described in the art. a.
  • purines for example, adenine
  • nucleosides for example, adenosine
  • amino acids for example, aromatic amino acids, arginine and leucine
  • ATP adenosine triphosphate
  • purI Deletion/Disruption Phosphoribosylaminoimidazole synthetase an enzyme encoded by the purI gene (synonymous with the purM gene), is involved in the biosynthesis pathway of purines. Disruption or deletion or inactivation of the purI gene thus renders the bacteria auxotrophic for purines.
  • purI- mutants are enriched in the tumor environment and have significant anti-tumor activity (see, e.g., Pawelek et al. (1997) Cancer Research 57:4537-4544). It was previously described that this colonization results from the high concentration of purines present in the interstitial fluid of tumors as a result of their rapid cellular turnover.
  • the purI- bacteria are unable to synthesize purines, they require an external source of adenine, and it was thought that this would lead to their restricted growth in the purine- enriched tumor microenvironment (see, e.g., Rosenberg et al. (2002) J. Immunotherapy 25(3):218-225). While the VNP20009 strain was initially reported to contain a deletion of the purI gene (see, e.g., Low et al.
  • VNP20009 a chromosomal inversion
  • the entire purI gene is contained within two parts of the VNP20009 chromosome that is flanked by insertion sequences, one of which has an active transposase. While disruption of the purI gene limits replication to the tumor tissue/microenvironment, it still permits intracellular replication and virulence.
  • each of the msbB and the purI genes is required to limit growth to the extracellular space in tumor tissue, and prevent intracellular replication.
  • Provided herein are strains in which the coding portion of these genes are completely deleted to eliminate any possible reversion to wild-type by recombination.
  • nutrient auxotrophy can be introduced into the immunostimulatory bacteria by deletions/mutations in genes such as aro, gua, thy, nad and asd, for example. Nutrients produced by the biosynthesis pathways involving these genes are often unavailable in host cells, and as such, bacterial survival is challenging.
  • Attenuation of Salmonella and other bacterial species can be achieved by deletion of the aroA gene, which is part of the shikimate pathway, connecting glycolysis to aromatic amino acid biosynthesis (see, e.g., Felgner et al. (2016) mBio 7(5):e01220-16).
  • Deletion of aroA results in bacterial auxotrophy for aromatic amino acids and subsequent attenuation (see, e.g., U.S. Patent Publication Nos.2003/0170276, 2003/0175297, 2012/0009153, and 2016/0369282; and International Application Publication Nos. WO 2015/032165 and WO 2016/025582).
  • S. typhimurium strain SL7207 is an aromatic amino acid auxotroph (aroA- mutant); strains A1 and A1-R are leucine-arginine auxotrophs; and VNP20009/YS1646 is a purine auxotroph (purI- mutant).
  • VNP20009/YS1646 is also auxotrophic for the immunosuppressive nucleoside adenosine, and for ATP (see, e.g., Example 1).
  • purM encoding phosphoribosyl- formylglycinamidine cyclo-ligase in S. typhi
  • purA encoding adenylosuccinate synthetase
  • purQ encoding phosphoribosylformylglycinamidine synthase II
  • purS encoding phosphoribosylformylglycinamidine synthase subunit PurS in L.
  • Adenosine Auxotrophy Metabolites derived from the tryptophan and adenosine triphosphate (ATP)/adenosine pathways are major drivers in forming an immunosuppressive environment within the tumor/tumor microenvironment (TME).
  • Adenosine which exists in the free form inside and outside of cells, is an effector of immune function. Adenosine decreases T-cell receptor induced activation of NF- ⁇ B, and inhibits IL-2, IL-4, and IFN- ⁇ . Adenosine decreases T-cell cytotoxicity, increases T-cell anergy, and increases T-cell differentiation to Foxp3 + or Lag3 + regulatory T-cells (T-reg cells, T- regs, or Tregs). On natural killer (NK) cells, adenosine decreases IFN- ⁇ production, and suppresses NK cell cytotoxicity.
  • NK natural killer
  • Adenosine blocks neutrophil adhesion and extravasation, decreases phagocytosis, and attenuates levels of superoxide and nitric oxide. Adenosine also decreases the expression of TNF- ⁇ , IL-12, and MIP-1 ⁇ (CCL3) on macrophages, attenuates major histocompatibility complex (MHC) Class II expression, and increases levels of IL-10 and IL-6. Adenosine immunomodulation activity occurs after its release into the extracellular space of the tumor and activation of adenosine receptors (ADRs) on the surface of target immune cells, cancer cells, or endothelial cells.
  • ADRs adenosine receptors
  • Extracellular adenosine is produced by the sequential activities of membrane associated ectoenzymes CD39 (ecto-nucleoside triphosphate diphosphohydrolase1, or NTPDase1) and CD73 (ecto-5’-nucleotidase), which are expressed on tumor stromal cells, together producing adenosine by phosphohydrolysis of ATP or ADP produced from dead or dying cells.
  • CD39 converts extracellular ATP (or ADP) to 5’-AMP, which is converted to adenosine by CD73.
  • Tumor hypoxia can result from inadequate blood supply and disorganized tumor vasculature, impairing delivery of oxygen (see, e.g., Carroll and Ashcroft (2005) Expert. Rev. Mol. Med.7(6), DOI: 10.1017/S1462399405009117).
  • Hypoxia which occurs in the tumor micro- environment, also inhibits adenylate kinase (AK), which converts adenosine to AMP, leading to very high extracellular adenosine concentrations.
  • AK adenylate kinase
  • the extracellular concentration of adenosine in the hypoxic tumor microenvironment has been measured at 10-100 ⁇ M, which is up to about 100-1000 fold higher than the typical extracellular adenosine concentration of approximately 0.1 ⁇ M (see, e.g., Vaupel et al. (2016) Adv. Exp. Med. Biol.876:177-183; and Antonioli et al. (2013) Nat. Rev. Can.13:842-857). Since hypoxic regions in tumors are distal from microvessels, the local concentration of adenosine in some regions of the tumor can be higher than in others.
  • adenosine also can control cancer cell growth and dissemination by effects on cancer cell proliferation, apoptosis, and angiogenesis.
  • adenosine can promote angiogenesis, primarily through the stimulation of A 2A and A 2B receptors. Stimulation of the receptors on endothelial cells can regulate the expression of intercellular adhesion molecule 1 (ICAM-1) and E-selectin on endothelial cells, maintain vascular integrity, and promote vessel growth (see, e.g., Antonioli et al. (2013) Nat. Rev. Can.13:842-857).
  • IAM-1 intercellular adhesion molecule 1
  • E-selectin E-selectin
  • Activation of one or more of A2A, A2B, or A3 on various cells by adenosine can stimulate the production of the pro-angiogenic factors, such as vascular endothelial growth factor (VEGF), interleukin-8 (IL-8) or angiopoietin 2 (see, e.g., Antonioli et al. (2013) Nat. Rev. Can.13:842-857).
  • VEGF vascular endothelial growth factor
  • IL-8 interleukin-8
  • angiopoietin 2 see, e.g., Antonioli et al. (2013) Nat. Rev. Can.13:842-857.
  • Adenosine also can directly regulate tumor cell proliferation, apoptosis, and metastasis through interaction with receptors on cancer cells.
  • Adenosine also can trigger apoptosis of cancer cells, and various studies have correlated this activity to activation of the extrinsic apoptotic pathway through A 3 , or the intrinsic apoptotic pathway through A 2A and A 2B (see, e.g., Antonioli et al. (2013)).
  • Adenosine can promote tumor cell migration and metastasis, by increasing cell motility, adhesion to the extracellular matrix, and expression of cell attachment proteins and receptors to promote cell movement and motility.
  • the extracellular release of adenosine triphosphate (ATP) occurs from stimulated immune cells, and damaged, dying, or stressed cells.
  • the NLR family pyrin domain-containing 3 (NLRP3) inflammasome when stimulated by this extracellular release of ATP, activates caspase-1 and results in the secretion of the cytokines IL-1 ⁇ and IL-18, which in turn activate innate and adaptive immune responses (see, e.g., Stagg and Smyth (2010) Oncogene 29:5346–5358).
  • ATP can accumulate to concentrations exceeding 100 mM in tumor tissue, whereas levels of ATP found in healthy tissues are very low ( ⁇ 1-5 ⁇ M) (see, e.g., Song et al. (2016) Am. J. Physiol. Cell Physiol.310(2):C99–C114). ATP is catabolized into adenosine by the enzymes CD39 and CD73. Activated adenosine acts as a highly immunosuppressive metabolite via a negative-feedback mechanism and has a pleiotropic effect against multiple immune cell types in the hypoxic tumor microenvironment (see, e.g., Stagg and Smyth (2010) Oncogene 29:5346–5358).
  • Adenosine receptors A 2A and A 2B are expressed on a variety of immune cells and are stimulated by adenosine to promote cAMP-mediated signaling changes, resulting in immunosuppressive phenotypes of T- cells, B-cells, NK cells, dendritic cells (DCs), mast cells, macrophages, neutrophils, and natural killer T (NKT) cells.
  • adenosine levels can accumulate to over one hundred times their normal concentration in pathological tissues, such as solid tumors, which have been shown to overexpress ecto-nucleotidases, such as CD73.
  • Adenosine also has been shown to promote tumor angiogenesis and development.
  • Immunostimulatory bacteria such as Salmonella typhi
  • Salmonella typhi can be made auxotrophic for adenosine by, for example, deletion of the tsx gene (see, e.g., Bucarey et al. (2005) Infection and Immunity 73(10):6210–6219) or by deletion of purD (see. e.g., Husseiny (2005) Infection and Immunity 73(3):1598–1605).
  • a purD gene knockout was shown to be auxotrophic for adenosine (see, e.g., Park et al. (2007) FEMS Microbiol. Lett.276:55– 59).
  • S. typhimurium strain VNP20009 is auxotrophic for adenosine due to its purI modification; hence, further modification to render it auxotrophic for adenosine is not required.
  • embodiments of the immunostimulatory bacterial strains, as provided herein are auxotrophic for adenosine.
  • auxotrophic bacteria selectively replicate in the tumor microenvironment, further increasing accumulation and replication of the administered bacteria in tumors, and decreasing the levels of adenosine in and around tumors, thereby reducing or eliminating the immunosuppression caused by the accumulation of adenosine.
  • Exemplary of such bacteria is a modified strain of S. typhimurium containing purI-/msbB- mutations to provide adenosine auxotrophy.
  • the purI gene can be disrupted as it has been in VNP20009, or it can contain a deletion of all or a portion of the purI gene, which ensures that there cannot be a reversion to a wild-type gene.
  • strain VNP20009 the purI- gene was inactivated by inversion. Similarly, the msbB gene in VNP20009 was not completely deleted. As exemplified herein, strains in which the purI and msbB genes have been completely deleted to eliminate any risk of reversion, demonstrate superior fitness as assessed by growth of cultures in vitro. Immunostimulatory bacteria modified by rendering them auxotrophic for one or more essential nutrients, such as purines (for example, adenine), nucleosides (for example, adenosine), amino acids (for example, aromatic amino acids, arginine, and leucine), or adenosine triphosphate (ATP), are employed.
  • purines for example, adenine
  • nucleosides for example, adenosine
  • amino acids for example, aromatic amino acids, arginine, and leucine
  • ATP adenosine triphosphate
  • the bacteria are rendered auxotrophic for adenosine, and optionally, for ATP, and preferentially accumulate in tumor microenvironments (TMEs).
  • TMEs tumor microenvironments
  • adenosine auxotrophy eliminates the immunosuppression from adenosine that accumulates in the tumor microenvironment of certain cancers.
  • This DAP auxotrophy can be used for plasmid selection and maintenance of plasmid stability in vivo, without the use of antibiotics, when the asd gene is complemented in trans on a plasmid in the bacterium.
  • Non- antibiotic-based plasmid selection systems are advantageous and allow for 1) use of administered antibiotics as a rapid clearance mechanism in the event of adverse symptoms, and 2) for antibiotic-free scale up of production, where such use is commonly avoided.
  • the asd gene complementation system provides for such non- antibiotic-based plasmid selection (see, e.g., Galán et al. (1990) Gene 94(1):29-35).
  • the use of the asd gene complementation system to maintain plasmids in the tumor microenvironment is expected to increase the potency of S.
  • immunostimulatory proteins e.g., cytokines, chemokines, co-stimulatory molecules
  • cytosolic DNA/RNA sensors that induce type I IFN, such as STING and IRF3, and gain-of-function/constitutively active mutants thereof; antibodies and fragments thereof (e.g., checkpoint inhibitors, or anti-IL-6 or anti-VEGF antibodies); bi-specific T-cell engagers (sold under the trademark BiTEs®); interfering RNAs; and other therapeutic products as discussed elsewhere herein and known in the art; and complementary combinations of all of the preceding therapeutic products.
  • typhimurium is to exploit the DAP auxotrophy to produce an autolytic (or suicidal) strain, for delivery of therapeutic products/macromolecules to infected cells without the ability to persistently colonize host tumors.
  • Deletion of the asd gene makes the bacteria auxotrophic for DAP when grown in vitro or in vivo.
  • An example described herein provides an asd deletion strain that is auxotrophic for DAP and that contains a plasmid suitable for delivery of immunomodulatory proteins, that does not contain an asd complementing gene, resulting in a strain that is defective for replication in vivo.
  • This strain is propagated in vitro in the presence of DAP, and grows normally, and then is administered as an immunotherapeutic agent to a mammalian host where DAP is not present.
  • the suicidal strain is able to invade host cells, but is not be able to replicate due to the absence of DAP in mammalian tissues, lysing automatically and delivering its cytosolic contents (e.g., plasmids or proteins).
  • cytosolic contents e.g., plasmids or proteins.
  • Corresponding genes, encoding homologs or orthologs of aspartate- semialdehyde dehydrogenase (asd) in other bacterial species also can be deleted or disrupted to achieve similar results.
  • genes include, but are not limited to, for example, asd, encoding aspartate-semialdehyde dehydrogenase in E. coli; asd (STY4271), encoding aspartate-semialdehyde dehydrogenase in S. typhi; asd (lmo1437), encoding aspartate-semialdehyde dehydrogenase in L.
  • endA Deletion/Disruption
  • the endA gene (see, for example, SEQ ID NO:250) encodes an endonuclease (DNA-specific endonuclease I; see, for example, SEQ ID NO:251) that mediates degradation of double-stranded DNA (dsDNA) in the periplasm of Gram-negative bacteria. Most common strains of laboratory E.
  • endA- as a mutation in the endA gene allows for higher yields of plasmid DNA. This gene is conserved among species.
  • the endA gene of the engineered immunostimulatory bacteria is deleted or mutated to prevent its endonuclease activity. Exemplary of such mutations is an E208K amino acid substitution (see, e.g., Durfee et al. (2008) J. Bacteriol.190(7):2597-2606), or a corresponding mutation in the species of interest.
  • endA, including residue E208 is conserved among bacterial species, including Salmonella.
  • the E208K mutation can be used to eliminate endo- nuclease activity in other species, including Salmonella species.
  • Flagellin Knockout Strains Flagella are organelles on the surface of bacteria that are composed of a long filament that is attached, via a hook, to a rotary motor that can rotate in a clockwise or counterclockwise manner to provide a means for locomotion.
  • Flagella for example, in S. typhimurium, are important for chemotaxis and for establishing an infection via the oral route, due to the ability to mediate motility across the mucous layer in the gastrointestinal tract. While flagella have been demonstrated to be required for chemotaxis to and colonization of tumor cylindroids in vitro (see, e.g., Kasinskas and Forbes (2007) Cancer Res.67(7):3201-3209), and motility has been shown to be important for tumor penetration (see, e.g., Toley and Forbes (2012) Integr. Biol.
  • flagella are not required for tumor colonization in animals when the bacteria are administered intravenously (see, e.g., Stritzker et al. (2010) International Journal of Medical Microbiology 300:449–456).
  • Each flagellar filament is composed of tens of thousands of flagellin subunits.
  • the S. typhimurium chromosome contains two genes, fliC and fljB, that encode antigenically distinct flagellin monomers. Mutants defective for both fliC and fljB are nonmotile and avirulent when administered via the oral route of infection, but maintain virulence when administered parenterally.
  • Flagellin is a major pro-inflammatory determinant of Salmonella (see, e.g., Zeng et al. (2003) J. Immunol.171:3668-3674), and is directly recognized by TLR5 on the surface of cells, and by NLCR4 in the cytosol (see, e.g., Lightfield et al. (2008) Nat. Immunol.9(10):1171–1178). Both pathways lead to pro-inflammatory responses resulting in the secretion of cytokines, including IL-1 ⁇ , IL-18, TNF- ⁇ , and IL-6.
  • Salmonella-based cancer immunotherapy attempts have been made to make Salmonella-based cancer immunotherapy more potent by increasing the pro-inflammatory response to flagellin by engineering the bacteria to secrete Vibrio vulnificus flagellin B, which induces greater inflammation than flagellin encoded by fliC and fljB (see, e.g., Zheng et al. (2017) Sci. Transl. Med. 9(376):eaak9537).
  • Salmonella bacteria such as S. typhimurium, are engineered to lack both flagellin subunits fliC and fljB, to reduce TLR5-mediated pro-inflammatory signaling.
  • Other bacteria that contain flagella can be similarly engineered to eliminate flagella.
  • a Salmonella strain lacking msbB and/or pagP which results in reduced TNF-alpha induction, is combined with fliC and fljB knockouts.
  • These bacterial modifications, msbB-, pagP-, fliC-, and fljB- can be combined with an immunostimulatory plasmid, optionally containing CpGs, encoding therapeutic products, such as immunomodulatory proteins, alone or in combinations thereof.
  • the resulting bacteria have reduced pro-inflammatory signaling, but robust anti-tumor activity.
  • a fliC and fljB double mutant was constructed in the asd-deleted strain of S. typhimurium, VNP20009.
  • VNP20009 which is attenuated for virulence by disruption of purI/purM, contains a modification of the msbB gene (a partial deletion) that results in production of a lipid A subunit that is less toxigenic than wild-type lipid A. This results in reduced TNF- ⁇ production in a mouse model after intravenous administration, compared to strains with wild-type lipid A.
  • the resulting strain is exemplary of strains that are attenuated for bacterial inflammation by modification of lipid A to reduce TLR2/4 signaling, and deletion of expression of the flagellin subunits to reduce TLR5 recognition and inflammasome induction.
  • Pathogenesis in certain bacterial species involves a cluster of genes referred to as Salmonella pathogenicity islands (SPIs). Salmonella invades non-phagocytic intestinal epithelial cells using a type 3 secretion system (T3SS) encoded by the Salmonella pathogenicity island 1 (SPI-1), which forms a needle-like structure that injects effector proteins directly into the cytosol of host cells.
  • SPIs Salmonella pathogenicity islands
  • SPI-1 mediates invasion of epithelial cells.
  • SPI-1 genes include, but are not limited to: avrA, hilA, hilD, invA, invB, invC, invE, invF, invG, invH, invI, invJ, iacP, iagB, spaO, spaP, spaQ, spaR, spaS, orgA, orgB, orgC, prgH, prgI, prgJ, prgK, sicA, sicP, sipA, sipB, sipC, sipD, sirC, sopB, sopD, sopE, sopE2, sprB, and sptP.
  • Deletion of one or more of these genes reduces or eliminates the ability of the bacterium to infect epithelial cells, but does not affect their ability to infect or invade phagocytic cells, including phagocytic immune cells.
  • deletion of both the fliC and fljB genes significantly reduced expression of SPI-1 genes, such as hilA, hilD, invA, invF and sopB, thereby reducing the ability to invade non-phagocytic cells (see, e.g., Elhadad et al. (2015) Infect. Immun.83(9):3355-3368).
  • flagellin in addition to the SPI-1 type 3 secretion system (T3SS), is necessary for triggering pyroptosis in macrophages, and can be detected by the macrophage NLRC4 inflammasome. Elimination of flagellin subunits decreases pyroptosis in macrophages.
  • S. typhimurium with deletions in fliC and fljB results in significantly reduced IL-1 ⁇ secretion compared to the wild-type strain, whereas cellular uptake and intracellular replication of the bacterium remains unaffected. This demonstrates that flagellin plays a significant role in inflammasome activation. Additionally, S.
  • the genome of the immunostimulatory bacteria herein can be modified to delete or mutate the flagellin genes fliC and fljB in S. typhimurium, leading to decreased cell death of tumor-resident immune cells, such as macrophages, and enhancing the anti-tumor immune response of the immunostimulatory bacteria.
  • Deletion of the flagellin subunits allows for greater tolerability in the host, limits uptake into only phagocytic cells and decreases their pyroptotic cell death, and directs the immunostimulatory response towards delivery of therapeutic products, such as immunomodulatory proteins, to the TME, particularly tumor-resident myeloid cells.
  • the resulting immunostimulatory bacteria elicit an anti-tumor response and promote an adaptive immune response to the tumor.
  • Corresponding genes, encoding flagellin in other bacterial species also can be deleted to achieve similar results.
  • genes include, but are not limited to, for example, fliC, encoding flagellar filament structural protein, and fliE, encoding flagellar basal-body protein FliE in E. coli; fliC, encoding flagellin, and flgB, encoding flagellar basal-body rod protein FlgB, in S. typhi; flaA encoding flagellin, fliE, encoding flagellar hook-basal body protein FliE, and flgB, encoding flagellar basal-body rod protein FlgB, in L.
  • L-asparaginase II is an enzyme that catalyzes conversion of L-asparagine to ammonia and aspartic acid.
  • Several bacterial strains such as E. coli and S. typhimurium, utilize L-asparaginase to scavenge fructose-asparagine as a carbon and nitrogen source (see, e.g., Sabag-Daigle et al. (2016) Appl. Environ. Microbiol. 84(5):e01957-17).
  • T-cells such as in acute lymphoblastic leukemia (ALL) require asparagine as they lack the enzymes to synthesize it.
  • Administration of L- asparaginases has been a frontline therapy for ALL since the early 1970’s (see, e.g., Batool et al. (2016) Appl. Biochem. Biotechnol.178(5):900-923).
  • Production of L- asparaginase II by S. typhimurium is both necessary and sufficient for T-cell inhibition, as it directly induces T-cell receptor (TCR) downregulation, decreases T- cell cytokine production, and inhibits tumor cytolytic function (see, e.g., Kullas et al.
  • L-asparaginase II has been used as an anti-cancer therapeutic for cancers in which T-cell suppression is a therapeutic modality.
  • L-asparaginase activity in the immunostimulatory bacteria enhances the function of T-cells in the tumor micro- environment. Elimination of L-asparaginase activity can be effected by modifying the bacterial genome to eliminate expression of active enzyme. Modifications include insertions, deletions, inversions, and replacements of nucleic acids, so that the resulting encoded enzyme is not active, or not expressed, or is eliminated.
  • deletion of all or of a part of the gene that encodes L-asparaginase II, ansB, or disruption thereof, to eliminate expression of the encoded enzyme in the immunostimulatory bacteria enhances the function of T-cells in a bacterially- colonized tumor microenvironment.
  • Inhibition of L-asparaginase II activity is accomplished by deletion of all or of a part of, or interruption/disruption of, the gene ansB in the immunostimulatory bacteria, whereby L-asparaginase II is not produced.
  • immunostimulatory bacteria whose genomes are modified so that L-asparaginase II is not produced.
  • Immunostimulatory bacteria provided herein are employed to colonize tumor-resident immune cells to enhance the anti-tumor immune response; included among the genome modifications are deletions, insertions, disruptions, and/or other modifications that eliminate expression of L-asparaginase II.
  • the genome of the immunostimulatory bacteria herein can be modified to delete ansB, or to disrupt it or otherwise modify it, to result in inactive encoded L-asparaginase II, or to eliminate the asparginase, preventing T-cell suppression and enhancing anti-tumor T-cell function in vivo. It is shown herein that strains in which ansB is intact induce profound T-cell immunosuppression in T-cells infected with the strain.
  • ansB do not induce immunosuppression, thus, solving another problem in the art in using bacteria to deliver encoded therapeutic products to tumors.
  • immunostimulatory bacteria that combine deletions or disruptions of the ansB gene, whereby functional encoded enzyme is not expressed, with other modifications described herein that result in increased accumulation in the tumor microenvironment and/or in tumor-resident immune cells, provide a superior therapeutic immunostimulatory bacteria.
  • Bacteria and fungi are capable of forming multicellular structures called biofilms.
  • Bacterial biofilms are encased within a mixture of secreted and cell wall- associated polysaccharides, glycoproteins, and glycolipids, as well as extracellular DNA, known collectively as extracellular polymeric substances. These extracellular polymeric substances protect the bacteria from multiple insults, such as cleaning agents, antibiotics, and antimicrobial peptides. Bacterial biofilms allow for colonization of surfaces, and are a cause of significant infection of prosthetics, such as injection ports and catheters. Biofilms also can form in tissues during the course of an infection, which leads to increases in the duration of bacterial persistence and shedding, and limits the effectiveness of antibiotic therapies. Chronic persistence of bacteria in biofilms is associated with increased tumorigenesis, for example in S.
  • CsgA is recognized as a PAMP by TLR2 and induces production of IL-8 from human macrophages (see, e.g., Tukel et al.
  • csgD indirectly increases cellulose production by activating the adrA gene that encodes for di-guanylate cyclase.
  • the small molecule cyclic di-guanosine monophosphate (c-di-GMP), generated by adrA, is a ubiquitous secondary messenger that occurs in almost all bacterial species.
  • Increases in c-di- GMP enhance expression of the cellulose synthase gene bcsA, which in turn increases cellulose production via stimulation of the bcsABZC and bcsEFG operons, leading to cellulose biofilm formation.
  • bacteria such as S.
  • typhimurium can form biofilms in solid tumors as protection against phagocytosis by host immune cells.
  • Bacterial mutants such as Salmonella mutants, that cannot form biofilms, are taken up more rapidly by host phagocytic cells and are more readily cleared from infected tumors (see, e.g., Crull et al. (2011) Cellular Microbiology 13(8):1223-1233).
  • This increase in intracellular localization within phagocytic cells can reduce the persistence of extracellular bacteria, and, as shown herein, can enhance the effectiveness of plasmid delivery of therapeutic products, such as immunomodulatory proteins and other anti-cancer therapeutics, as described herein. Reduction in the capability of immunostimulatory bacteria, such as S.
  • biofilms can be achieved through deletion or disruption of genes involved in biofilm formation, such as, for example, csgD, csgA, csgB, adrA, bcsA, bcsB, bcsZ, bcsE, bcsF, bcsG, dsbA, or dsbB (see, e.g., Anwar et al. (2014) PLoS ONE 9(8):e106095).
  • genes involved in biofilm formation such as, for example, csgD, csgA, csgB, adrA, bcsA, bcsB, bcsZ, bcsE, bcsF, bcsG, dsbA, or dsbB (see, e.g., Anwar et al. (2014) PLoS ONE 9(8):e106095).
  • genes encoding homologs and orthologs of csgD, and other genes that are required for curli fimbriae and biofilm formation in other bacterial species, also can be deleted or disrupted or otherwise modified to achieve similar results.
  • genes include, but are not limited to, for example, csgD, encoding DNA-binding transcriptional dual regulator CsgD in E. coli; csgD (STY1179), encoding regulatory protein CsgD in S. typhi; and lcp, encoding the Listeria cellulose binding protein that is involved in biofilm formation in L. monocytogenes.
  • Modification of the bacterial genome results in elimination of curli fimbriae and inflammatory cyclic dinucleotides (CDNs), and removes cellulose secretion.
  • CDNs inflammatory cyclic dinucleotides
  • bacterial strains such as S.
  • typhimurium strains that are engineered to be auxotrophic for adenosine; and are reduced in their ability to induce pro-inflammatory cytokines by modification of the LPS and/or deletion of flagellin; and/or that do not express L-asparaginase II to improve T-cell function; and/or that contain deletions of genes required for biofilm formation; and/or that are further modified to maintain significant plasmid copy number per cell, at least low to medium copy number or higher, in the absence of antibiotic selection; and that deliver genetic expression cassettes encoding therapeutic products, promote robust anti-tumor immune responses.
  • the plasmids include regulatory sequences to promote secretion of the encoded therapeutic products into the tumor microenvironment. 7.
  • the complement system is the first line of immune defense against invading pathogens that directly activate the lectin pathway or the alternative pathway (AP) cascades in the human host.
  • the complement system involves more than 30 soluble and cell-membrane bound proteins that function in the innate immune response to recognize and kill pathogens, such as bacteria, virus-infected cells, and parasites, and also play a role in the antibody-mediated immune response.
  • pathogens such as bacteria, virus-infected cells, and parasites
  • Activation of the complement cascade leads to opsonization of foreign microbes, release of chemotactic peptides, and finally, to disruption of bacterial cell membranes.
  • Three homologous glycoproteins in the complement system, C3, C4 and C5 play a central role in complement function and interact with other complement components.
  • C3b and C4b generated from C3 and C4, respectively, are important components of convertases that promote activation of the complement cascade.
  • the cleavage fragments of C5 are C5a, which induces migration of phagocytes into the infection site, and C5b, which initiates the formation of the membrane attack complex and bacterial lysis (see, e.g., Ramu et al. (2007) FEBS Letters 581:1716-1720).
  • pathogens have developed strategies to prevent deleterious consequences of complement activation.
  • members of the Ail/Lom family of outer membrane proteins provide protection from complement-dependent killing for a number of pathogenic bacteria.
  • Ail/Lom family which include Ail (attachment invasion locus) of Yersinia species, e.g., Y. enterocolitica and Y. pseudotuberculosis, Rck (resistance to complement killing) and PagC of Salmonella species, and OmpX of Escherichia coli, are outer membrane proteins that share significant amino acid sequence similarity and identity, and have similar membrane topologies. While members of this family of proteins exhibit diverse functions, several of them, including Ail of Y. enterocolitica and Y. pseudotuberculosis, as well as Rck of S.
  • enterica function, at least in part, to protect bacteria from complement-mediated lysis (see, e.g., Bartra et al. (2008) Infection and Immunity 76:612–622).
  • Another bacterial product that aids in avoiding or mitigating complement is the surface protease, designated PgtE (outer membrane serine protease) in Salmonella, and other members of the omptin family.
  • PgtE outer membrane serine protease
  • the surface protease PgtE of S. enterica belongs to the omptin family of enterobacterial outer membrane aspartate proteases. PgtE and other omptins require rough LPS to be active, but are sterically inhibited by the O-antigen.
  • PgtE proteolytically activates the mammalian plasma proenzyme plasminogen to plasmin, inactivates the main physiological inhibitor of plasmin, alpha 2-antiplasmin, and mediates bacterial adhesion to extracellular matrices of human cells. This way, PgtE mediates the degradation of extracellular matrix components and generates potent, localized proteolytic activity, which can promote migration of Salmonella across extracellular matrices. PgtE also degrades alpha-helical antimicrobial peptides which can be important during intracellular growth of Salmonella.
  • the omptin Pla of Yersinia pestis is a close ortholog of PgtE and shares functions with PgtE. Pla cleaves C3, and PgtE increases serum resistance of Salmonella by cleaving complement components C3b, C4b, and C5.
  • the gene pgtE, and orthologs thereof from other bacterial species, can be included in the immunostimulatory bacteria herein to increase resistance to complement. It is shown herein that the effects of complement in human serum explain the failure of therapeutic immunostimulatory bacteria, such as the Salmonella strain VNP20009, which had been shown to effectively colonize tumors in rodent models.
  • VNP20009 Systemic administration of VNP20009 resulted in colonization of mouse tumors (see, e.g., Clairmont et al. (2000) J. Infect. Dis.181:1996-2002; and Bermudes et al. (2001) Biotechnol. Genet. Eng. Rev.18:219-33); whereas systemic administration of VNP20009 in human patients resulted in very little colonization.
  • very little VNP20009 was detected in human tumors after a 30 minute intravenous infusion (see, Toso et al. (2002) J. Clin. Oncol.20:142- 52).
  • VNP20009 Patients that entered into a follow-up study evaluating a longer, four hour infusion of VNP20009, also demonstrated a lack of detectable VNP20009 after tumor biopsy (see, Heimann et al. (2003) J. Immunother.26:179–180). Following intratumoral administration, colonization of a derivative of VNP20009 was detected (see, Nemunaitis et al. (2003) Cancer Gene Ther.10:737-744). Direct intratumoral administration of VNP20009 to human tumors resulted in much higher tumor colonization, indicating that human tumors can be colonized at a high level, and that the difference in tumor colonization between mice and humans occurs only after systemic administration. It is shown and described herein, that, while not previously known to occur in wild-type S.
  • VNP20009 is inactivated by human complement, which explains the low tumor colonization observed in humans upon systemic administration of VNP20009.
  • Strains provided herein exhibit resistance to complement. They can be modified to express Rck and other proteins involved in mediating complement resistance or avoidance, such as Ail of Yersinia enterocolitica, or PgtE of Salmonella typhimurium, or, if they natively express such a protein, they can be modified to overexpress Rck and/or other such proteins.
  • Rck can be introduced into bacteria, such as E. coli, that lack a homolog.
  • Rck Expression Rck (resistance to complement killing) is a 17 kDa outer membrane protein encoded by the large virulence plasmid of Salmonella species, such as S. enteritidis and S. typhimurium, that induces adhesion to and invasion of epithelial cells.
  • the Rck protein has been shown to protect S. enterica from complement by inhibiting C9 polymerization and subsequent assembly of a functional membrane attack complex.
  • An rck mutant exhibited a 2-3 fold decrease in epithelial cell invasion compared to the wild-type strain, while rck overexpression in wild-type leads to increased invasion.
  • the Rck protein induces cell entry by a receptor-mediated process, promoting local actin remodeling, and weak and closely adherent membrane extensions.
  • Salmonella can enter cells by two distinct mechanisms: the Trigger mechanism mediated by the T3SS-1 complex, and a Zipper mechanism induced by rck (see, e.g., Manon et al. (2012), Salmonella, Chapter 17, eds. Annous and Gurtler, Rijeka, pp. 339-364).
  • rck a Zipper mechanism induced by rck
  • Expression of rck on the Salmonella virulence plasmid confers a high level of resistance to neutralization by human complement, by preventing the formation of the membrane attack complex.
  • S. typhimurium virulence plasmid containing rck was expressed in a highly serum-sensitive strain of E. coli, Rck was able to restore complement resistance.
  • the immunostimulatory bacteria provided herein retain, or are provided with, Rck to confer resistance to human complement. It is shown herein that immunostimulatory bacteria, such as E. coli, can be modified by encoding rck on a plasmid in the bacteria to thereby confer resistance to complement. Immunostimulatory bacteria provided herein encode rck, either endogenously, or can be modified to encode it in order to increase resistance to complement. Methods for conferring resistance to complement also are provided. For example, the therapeutic E. coli species described in U.S. Patent Application Publication Nos.2018/0325963 and 2018/0273956, and U.S.
  • Patent Nos.9,889,164 and 9,688,967 can be improved by modifying the bacteria therein, such as by introducing nucleic acid encoding the Salmonella rck gene on a plasmid therein, to thereby improve or provide resistance to complement.
  • Bacteria that are resistant to complement can be systemically administered, and sufficient bacteria can survive to be therapeutically effective.
  • Nucleic acids encoding the Salmonella rck gene are introduced into bacteria, such as therapeutic E. coli, to thereby confer or increase complement resistance.
  • Other orthologs and homologs of rck from other bacterial species similarly can be expressed in the immunostimulatory bacteria.
  • Ail is an Rck homolog from Yersinia enterocolitica, which enhances complement resistance under heterologous expression.
  • PgtE is an S. typhimurium surface protease that has also been shown to enhance complement resistance under heterologous expression.
  • the LPS and Braun (murein) lipoprotein (Lpp) are major components of the outer membrane of Gram-negative enteric bacteria that function as potent stimulators of inflammatory and immune responses.
  • Braun (murein) lipoprotein (Lpp) is one of the most abundant components of the outer membrane in S. typhimurium, and leads to TLR2 induction of pro-inflammatory cytokines, such as TNF ⁇ , IL-6 and IL-8 (in humans).
  • lppA SEQ ID NO:387
  • lppB SEQ ID NO:388
  • lppA and lppB genes Two functional copies of the lipoprotein gene (SEQ ID NO:387) and lppB (SEQ ID NO:388)), that are located on the bacterial chromosome of Salmonella, contribute to bacterial virulence.
  • Deletion of the lppA and lppB genes, and elimination of lipoprotein expression reduces virulence and decreases pro-inflammatory cytokine production (see, e.g., Sha et al. (2004) Infect. Immun.72(7):3987-4003; Fadl et al. (2005) Infect. Immun.73(2):1081-1096).
  • Deletion of the Lpp genes would be expected to reduce infection of cells, and, thus, decrease plasmid delivery and expression of the encoded therapeutic products or proteins.
  • deletion of these genes did reduce tumor colonization, the amount of plasmid delivered to the targeted cells, the tumor-resident immune cells, particularly macrophages, significantly was increased.
  • deletion or disruption of these genes resulted in decreased virulence due to the inability to survive in infected macrophages, but resulted in enhanced plasmid delivery of the immunostimulatory bacteria, thereby increasing expression of encoded therapeutic genes in the targeted cells, i.e., the tumor-resident immune cells, particularly macrophages. 9.
  • bacterial strains such as S. typhimurium strains, that are engineered to be adenosine auxotrophic, and are reduced in their ability to induce pro- inflammatory cytokines by modification of the LPS and/or deletion of flagellin, and/or are modified by deletion or elimination of L-asparaginase II expression to improve T-cell function, and/or are modified by deletion or disruption of genes required for biofilm formation, and/or that demonstrate enhanced human serum survival due to increased rck expression, are further modified to deliver therapeutic products, such as immunomodulatory proteins, and promote robust anti-tumor immune responses.
  • the table below summarizes the bacterial genotypes/modifications, their functional effects, and some of the effects/benefits achieved herein.
  • Strains provided herein are ⁇ FLG, and/or ⁇ pagP, and/or ⁇ ansB, and/or ⁇ csgD. Additionally, the strains are one or more of ⁇ purI ( ⁇ purM), ⁇ msbB, and ⁇ asd (in the bacterial genome). In particular, the strains are ⁇ purI ( ⁇ purM), ⁇ msbB, ⁇ pagP, and ⁇ ansB, and ⁇ asd. The strains also can be lppA- and/or lppB-, particularly lppA-/lppB- .
  • the plasmid is modified to encode therapeutic products under control of host-recognized promoters (e.g., eukaryotic promoters, such as RNA polymerase II promoters, including those from eukaryotes, and animal viruses).
  • host-recognized promoters e.g., eukaryotic promoters, such as RNA polymerase II promoters, including those from eukaryotes, and animal viruses.
  • the plasmids can encode asd to permit bacterial replication in vivo, and can encode nucleic acids with other beneficial functions (such as CpGs), and can encode gene products, as described elsewhere herein.
  • the immunostimulatory bacteria provided herein can be modified to eliminate the ability to infect epithelial cells, such as by elimination of the flagella.
  • Elimination of the ability to infect epithelial cells, as described elsewhere herein, also can be achieved by inactivating SPI-1-dependent invasion, through inactivation or knockout of one or more genes involved in the SPI-1 pathway.
  • genes include, but are not limited to, one more of: avrA, hilA, hilD, invA, invB, invC, invE, invF, invG, invH, invI, invJ, iacP, iagB, spaO, spaP, spaQ, spaR, spaS, orgA, orgB, orgC, prgH, prgI, prgJ, prgK, sicA, sicP, sipA, sipB, sipC, sipD, sirC, sopB, sopD, sopE, sopE2, sprB, and sptP.
  • the immunostimulatory bacteria can contain knockouts or deletions in genes to inactivate products involved in SPI-1-independent infection/invasion, such as one or more of the genes fljB, fliC, rck, pagN, hlyE, pefI, srgD, srgA, srgB, and srgC, and/or the immunostimulatory bacteria can contain knockouts or deletions to inactivate products of genes that induce cell death of tumor- resident immune cells, such as genes that encode proteins that are directly recognized by the inflammasome, including fljB, fliC, prgI (needle protein), and prgJ (rod protein).
  • the rck gene is desirable because it protects against inactivation against complement.
  • Bacteria that do not endogenously encode rck can be modified to encode a heterologous rck gene.
  • the immunostimulatory bacteria are derived from suitable bacterial strains.
  • Bacterial strains can be attenuated strains, or strains that are attenuated by standard methods, or that, by virtue of the modifications provided herein, are attenuated in that their ability to colonize is limited primarily to immunoprivileged tissues and organs, particularly tumor-resident immune cells, the TME, and tumor cells, including solid tumors.
  • Bacteria include, but are not limited to, for example, strains of Salmonella, Shigella, Listeria, E.
  • species include Shigella sonnei, Shigella flexneri, Shigella dysenteriae, Listeria monocytogenes, Salmonella typhi, Salmonella typhimurium, Salmonella gallinarum, and Salmonella enteritidis.
  • Suitable bacterial species include Rickettsia, Klebsiella, Bordetella, Neisseria, Aeromonas, Francisella, Corynebacterium, Citrobacter, Chlamydia, Haemophilus, Brucella, Mycobacterium, Mycoplasma, Legionella, Rhodococcus, Pseudomonas, Helicobacter, Vibrio, Bacillus, and Erysipelothrix.
  • Exemplary of the immunostimulatory bacteria provided herein are species of Salmonella.
  • Exemplary of bacteria for modification as described herein are wild-type strains of Salmonella, such as the strain that has all of the identifying characteristics of the strain deposited in the American Type Culture Collection (ATCC) as accession #14028.
  • Engineered strains of Salmonella typhimurium such as strain YS1646 (ATCC catalog # 202165, also referred to as VNP20009; see, also, International PCT Application Publication No. WO 99/13053), is engineered with plasmids to complement an asd gene knockout and to allow for antibiotic-free plasmid maintenance. The strains then are modified to delete the flagellin genes, and/or to delete pagP.
  • the combination of flagella knockout and pagP deletion renders the strain highly resistant to human serum complement.
  • the strains also are rendered auxotrophic for purines, particularly adenosine, and are asd- and msbB-.
  • strains in which purI and msbB are completely deleted are more fit (grow faster) that strain VNP20009, in which these genes are not deleted, but are modified to eliminate expression.
  • the asd gene can be provided on a plasmid for in vivo replication in the eukaryotic host.
  • the strains also have a modification, such as a deletion, disruption, or other modification, in the ansB gene, preventing them from producing immunosuppressive L-asparaginase II, and improving tumor T-cell function.
  • the strains also are modified to eliminate biofilm production, such as by a csgD deletion, which renders them unable to produce curli fimbriae, cellulose, and c- di-GMP, reducing unwanted inflammatory responses, and preventing them from forming biofilms.
  • any of the nucleic acid encoding therapeutic products can be included on the plasmid.
  • the plasmid generally is present in low to medium copy number, as described elsewhere herein.
  • Therapeutic products include gain-of-function mutants of cytosolic DNA/RNA sensors, that can constitutively evoke/induce type I IFN expression, and other immunostimulatory proteins, such as cytokines, chemokines, and co-stimulatory molecules, that promote an anti-tumor immune response in the tumor microenvironment, and other such products described herein.
  • the plasmids also can encode antibodies, and fragments thereof, e.g., single chain antibodies, that target immune checkpoints and other cancer targets, such as VEGF, IL-6, and TGF- ⁇ , and other molecules, such as bispecific T-cell engagers, or BiTEs®.
  • the plasmids also can encode IL-6 binding decoy receptors, TGF-beta binding decoy receptors, and TGF- beta polypeptide antagonists.
  • the plasmid can encode one or a plurality of therapeutic products/genetic payloads (i.e., multiplexed), for delivery of anti-cancer therapeutic products to the tumor/tumor microenvironment.
  • the products can be operatively linked to trafficking signals, such as signals for secretion.
  • the products also can be designed for expression on a cell surface, such as in tumor- resident myeloid cells. 10.
  • Conversion of M2 Phenotype Macrophages into M1 and M1-Like Phenotype Macrophages As described herein, the immunostimulatory bacteria provided herein accumulate in and/or target macrophages. Macrophages are phagocytic immune cells; they play a role in clearing senescent and apoptotic cells, as well as in the phagocytosis of immune-related complexes and pathogens, and in the maintenance of homeostasis. The phenotype and function of macrophages can be polarized by the microenvironment.
  • M1-type classically activated macrophage
  • M2-type alternatively activated macrophage
  • the role of M1 macrophages is to secrete pro-inflammatory cytokines and chemokines, and to present antigens, and thus, to participate in the positive immune response and function as an immune monitor.
  • M1 macrophages produce pro- inflammatory cytokines, including IL-6, IL-12, and TNF- ⁇ .
  • M2 macrophages secrete arginase 1, IL-10, TGF- ⁇ , and other anti-inflammatory cytokines, which have the function of reducing inflammation, and contributing to tumor growth and immunosuppressive function.
  • M1 or M1-like phenotype is advantageous.
  • M2 macrophages can be converted into M1 macrophages or into macrophages with an M1-like phenotype.
  • Immunostimulatory bacteria provided herein, which infect macrophages, can convert M2 macrophages into an M1 or M1-like phenotype.
  • M1 macrophage phenotypic markers include CD80 (also known as B7, B7.1, or BB1), CD86 (also known as B7.2), CD64 (also known as high affinity immunoglobulin gamma Fc receptor I ), CD16, and CD32 (also known as low affinity immunoglobulin gamma Fc receptor IIb).
  • nitric oxide synthase (iNOS) in M1 macrophages also can serve as a phenotypic marker.
  • CD163 and CD206 are markers for the identification of M2 macrophages.
  • Arginase 1 (Arg1) and DECTIN-1 also are ideal phenotypic indicators for the identification of M2 macrophages. Thus, the conversion can be monitored or assessed by virtue of expression of these markers.
  • Tumor-associated macrophages (TAMs) are associated with an immunos- uppressive M2 phenotype. Immunostimulatory bacteria provided herein can convert such macrophages into an M1 or M1-like phenotype.
  • the immunostimulatory bacteria provided herein that encode a therapeutic product that leads to expression of type I interferon (IFN), can effect such conversion. This is a property unique to the immunostimulatory bacteria provided herein, and exploits the ability of the bacteria that include genomic modifications that result in the infection of macrophages.
  • the encoded therapeutic products include those that are part of a cytosolic DNA/RNA sensor pathway, such as the STING variants (described in detail herein).
  • the encoding immunostimulatory bacteria can effect conversion to an M1 phenotype (or an M1-like phenotype) upon infection of the tumor-resident macrophages, and expression of the therapeutic product(s). This ability to convert macrophage phenotypes is demonstrated and exemplified in Example 12 below.
  • a modified STING protein by immunostimulatory bacteria provided herein that infect macrophages and express the STING protein converts the phenotype of M1 macrophages to M2 macrophages.
  • Immunostimulatory bacteria provided herein that include genome modifications as descrbied herein, such as the elimination of flagella and LPS modification, convert infected M2 macrophages into those that induce cytokine profiles of M1 macrophages.
  • Immunostimulatory bacteria that express a variant STING protein that results in constitutive type I IFN expression in human primary M2 macrophages convert these cells to M1-like (having phenotypic markers and/or expression profiles typical of M1 macrophages) type I IFN producing cells.
  • the Examples demonstrate this change from an M2 to an M1-like or M1 phenotype.
  • the immunostimulatory bacteria provided herein are modified so that they accumulate in the tumor microenvironment, and in tumor-resident myeloid cells, where therapeutic products, under the control of eukaryotic promoters, are expressed.
  • the bacteria encode therapeutic products, particularly anti-cancer products, including products that stimulate the immune system and/or that reverse or mitigate the immunosuppressive effects of tumors.
  • the bacteria can encode a plurality of products, where expression of each product is under control of a separate promoter, or they are under control of one promotor, and can include sequences that result in expression of the discrete products, and, where appropriate, include regulatory sequences to ensure secretion of the encoded products into the tumor microenvironment.
  • the immunostimulatory bacteria express encoded therapeutic products on the plasmid. As discussed, the plasmid can encode one product or a plurality thereof.
  • Each product can be under control of a different eukaryotic promoter, or multiple encoded products can be expressed under control of a single promoter, such as by including 2A self-cleaving peptides between the coding portions, such as T2A (SEQ ID NO:327), P2A (SEQ ID NO:328), E2A (SEQ ID NO:329), and F2A (SEQ ID NO:330).
  • the encoded products include those described herein, and they can be anti-cancer immune stimulating products whose activities are complementary.
  • the immunostimulatory bacteria provided herein permit the combinatorial administration of multiple immunomodulatory products or payloads (multiplexed payloads) that would otherwise be too toxic if systemically administered.
  • Exemplary of multiplexed payloads include one or more cytokine(s), an immunostimulatory protein to stimulate or induce expression of type I IFN, such as STING or a variant thereof that has increased activity or that is constitutively active, and a co-stimulatory molecule, such as an engineered 4-1BBL co-stimulatory molecule.
  • cytokine(s) an immunostimulatory protein to stimulate or induce expression of type I IFN, such as STING or a variant thereof that has increased activity or that is constitutively active
  • a co-stimulatory molecule such as an engineered 4-1BBL co-stimulatory molecule.
  • a modified 4-1BBL polypeptide, and encoding nucleic acid that exhibits improved expression and activity when encoded on a plasmid in the immunostimulatory bacteria provided herein that deliver the plasmids to myeloid cells for expression under control of the host transcriptional and translational machinery.
  • the immunostimulatory bacteria provided herein have strong anti-tumor effects, including provision of cures, such as after IV dosing with the multiplexed payloads or single agent payloads.
  • the immunostimulatory bacteria when systemically administered, infiltrate and enrich in solid tumors, the TME, and tumor- resident myeloid cells, in which the encoded therapeutic products are expressed and then locally delivered to the tumor microenvironment.
  • the bacteria Upon consumption (phagocytosis) by tumor-resident myeloid cells, the bacteria deliver a genetic payload-encoding plasmid, which allows for ectopic, single or multiplexed payload expression in a tumor-specific manner.
  • the immunostimulatory bacteria herein can be modified to encode one or more of an immunostimulatory protein that promotes, induces, or enhances an anti- tumor response.
  • an immunostimulatory protein that promotes, induces, or enhances an anti- tumor response.
  • the order in which the encoding nucleic acids are arranged on the plasmid can improve overall expression, and modifications to the plasmids can improve the fitness of the bacteria that contain the plasmids encoding the proteins.
  • the immunostimulatory protein can be encoded on a plasmid in the bacterium, under the control of a eukaryotic promoter, such as a promoter recognized by RNA polymerase II, for expression in a eukaryotic subject, particularly the subject for whom the immunostimulatory bacterium is to be administered, such as a human.
  • a eukaryotic promoter such as a promoter recognized by RNA polymerase II
  • the nucleic acid encoding the immunostimulatory protein(s) can include, in addition to the eukaryotic promoter, other regulatory signals for expression or trafficking in the cells, such as for secretion or expression on the surface of a cell.
  • Immunostimulatory proteins are those that, in the appropriate environment, such as a tumor microenvironment (TME), can promote, or participate in, or enhance, an anti-tumor response by the subject to whom the immunostimulatory bacterium is administered.
  • Immunostimulatory proteins include, but are not limited to, cytokines, chemokines, and co-stimulatory molecules.
  • cytokines such as, but not limited to, IL-2, IL-7, IL-12, IL-15, IL-18, IL-21, IL-23, IL-12p70 (IL-12p40 + IL- 12p35), IL-15/IL-15R alpha chain complex, IL-36 ⁇ , GM-CSF, IFN ⁇ , IFN ⁇ , IL-2 that has attenuated binding to IL-2Ra, and IL-2 that is modified so that it does not bind to IL-2Ra; chemokines, such as, but not limited to, CCL3, CCL4, CCL5, CXCL9, CXCL10, and CXCL11; and/or co-stimulatory molecules, such as, but not limited to, CD40, CD40L, OX40, OX40L, 4-1BB, 4-1BBL, 4-1BBL with the cytoplasmic domain truncated or deleted (4-1BBL ⁇ cyt), members of the TNF/TNFR superfamily (e.g.,
  • immunostimulatory proteins that are used for the treatment of tumors, or that can promote, enhance or otherwise increase or evoke an anti-tumor response, known to those of skill in the art, are contemplated for encoding in the immunostimulatory bacteria provided herein.
  • the immunostimulatory bacteria can deliver a genetic payload encoding a truncated co-stimulatory molecule (e.g., 4-1BBL, CD80, CD86, CD27L, B7RP1, and OX40L), with a full or partial cytoplasmic domain deletion, for expression on an APC, where the truncated gene product is capable of constitutive immuno-stimulatory signaling to a T-cell through co-stimulatory receptor engagement, and is unable to counter-regulatory signal to the APC due to a deleted or truncated cytoplasmic domain.
  • a truncated co-stimulatory molecule e.g., 4-1BBL, CD80, CD86, CD27L, B7RP1, and OX40L
  • the modified truncated cytoplasmic domain for example, of 4-1BBL, contains particular residues to ensure proper orientation of the protein domains, which increases expression of the protein.
  • This is exemplified with respect to 4-1BBL as described in the Examples and as follows; the same modifications, including replacement of residues in the truncated cytoplasmic domain to ensure proper orientation in the membrane, can be applied to any of the co-stimulatory molecules, as well as other transmembrane polypeptides.
  • the full-length sequence of human 4-1BBL (SEQ ID NO:389 see also, Uniprot P41273) is: where the ctoplasmic domain corresponds to amino acids 1-28 (italicized), the transmembrane domain corresponds to amino acids 29-49 (bold), and the extracellular domain corresponds to amino acids 50-254 (underlined).
  • the human 4-1BBL ⁇ cyt sequence (see, SEQ ID NO:390) is: which is the same as the full-length protein, but lacking the cytoplasmic domain, so that the transmembrane domain corresponds to amino acid residues 2-22 (bold), and the extracellular domain corresponds to amino acid residues 23-227 (underlined).
  • An exemplary human 4-1BBL, with a truncated cytoplasmic domain is as follows (see, SEQ ID NO:391): where the truncated cytoplasmic domain corresponds to residues RLVP (in italics), with the initiating M, the transmembrane domain corresponds to residues 6-26 (bold), and the extracellular domain corresponds to residues 27-231 (underlined).
  • positively charged amino acids such as R and K, tend to be positioned in the cytoplasm (inside/cytoplasmic domain), which orients the transmembrane domain so that N-terminus is inside.
  • the 4-1BBL variant with the truncated cytoplasmic domain can be modified to include positive residues, to ensure the proper orientation of the protein in the cell membrane upon expression.
  • Exemplary of possible modifications of 4-1BBL are those in which residues are replaced with positively charged residues, or a c-myc tag is included. The skilled person can envision other similar replacements/additions to achieve the same result.
  • Exemplary modified human 4-1BBL variants with a truncated cytoplasmic domain include the following, in which extra positive residues (Arginine (R), Lysine (K), italicized) are included in the cytoplasmic domain region, as follows, so that the resulting protein, when expressed in a cell, is properly oriented (has the correct configuration and not the “inside out” configuration). See, SEQ ID NOs:391 and 392, respectively: Truncated cytoplasmic domain: This adds a positive charge back to the N-terminus (R), which favors a configuration in which the N-terminus is correctly oriented inside the cytoplasm. In another example a MYC tag is added.
  • Truncated cytoplasmic domain with a MYC tag For sequences of full-length mouse 4-1BBL, and exemplary sequences of mu4-1BBL ⁇ cyt (murine 4-1BBL with a deletion of the cytoplasmic domain), mu4- 1BBL with a truncated cytoplasmic domain, and mu4-1BBL with a truncated cytoplasmic domain and a MYC tag, see Example 19 below; see, also, SEQ ID NOs:393-396, respectively. Additional or alternative amino acid replacements can be included in the co- stimulatory molecules to ensure proper orientation of the expressed protein in the membrane.
  • co-stimulatory molecules e.g., 4-1BBL, CD80, CD86, CD27L, B7RP1, and OX40L
  • co-stimulatory molecules for expression on an APC
  • co-stimulatory molecules also can be modified by introducing amino acid modifications, such as insertions, deletions, and/or replacements, to the cytoplasmic domain, such that the modified gene product is capable of constitutive immuno-stimulatory signaling to a T- cell through co-stimulatory receptor engagement, and is unable to counter-regulatory signal to the APC due to the modifications to the cytoplasmic domain.
  • the immunosuppressive reverse (intracellular) signaling can be eliminated by modifying the cytoplasmic domain phosphorylation sites, such as by replacing one or more Ser residues, at an appropriate locus or loci, with a residue that reduces or eliminates reverse signaling.
  • the immunosuppressive reverse (intracellular) signaling can be eliminated by modifying the cytoplasmic domain phosphorylation sites, including Ser5 and Ser8, with reference to the sequence of full-length human 4-1BBL (SEQ ID NO:389).
  • the serine residues in the cytoplasmic domain can be replaced by any other residue that reduces or eliminates reverse signaling.
  • Additional or alternative amino acid replacements can be included in the co- stimulatory molecules to eliminate immunosuppressive intracellular (reverse) signaling.
  • the skilled person readily can prepare other similar modifications to eliminate immunosuppressive reverse signaling, while still maintaining the co- stimulatory molecule’s ability to activate constitutive immuno-stimulatory signaling to a T-cell through co-stimulatory receptor engagement. a.
  • the immunostimulatory bacteria herein are engineered to express cytokines to stimulate the immune system, including, but not limited to, IL- 2, IL-7, IL-12, IL-12p70 (IL-12p40 + IL-12p35), IL-15 (and the IL-15:IL-15R alpha chain complex), IL-18, IL-21, IL-23, IL-36 ⁇ , IL-2 that has attenuated binding to IL- 2Ra, IL-2 that is modified so that it does not bind to IL-2Ra, IFN- ⁇ , and IFN- ⁇ .
  • Cytokines stimulate immune effector cells and stromal cells at the tumor site, and enhance tumor cell recognition by cytotoxic cells.
  • the immunostimulatory bacteria can be engineered to express chemokines, such as, for example, CCL3, CCL4, CCL5, CXCL9, CXCL10, and CXCL11.
  • chemokines such as, for example, CCL3, CCL4, CCL5, CXCL9, CXCL10, and CXCL11.
  • IL-2 Interleukin-2 (IL-2) which was the first cytokine approved for the treatment of cancer, is implicated in the activation of the immune system by several mechanisms, including the activation and promotion of cytotoxic T lymphocyte (CTL) growth, the generation of lymphokine-activated killer (LAK) cells, the promotion of Treg cell growth and proliferation, the stimulation of tumor-infiltrating lymphocytes (TILs), and the promotion of T-cell, B cell and NK cell proliferation and differentiation.
  • CTL cytotoxic T lymphocyte
  • LAK lymphokine-activated killer
  • Treg cell growth and proliferation the stimulation of tumor-infiltrating lymphocytes
  • TILs tumor
  • IL-2 Recombinant IL-2 (rIL-2) is FDA-approved for the treatment of metastatic renal cell carcinoma (RCC) and metastatic melanoma (see, e.g., Sheikhi et al. (2016) Iran J. Immunol.13(3):148-166).
  • IL-7 IL-7 which is a member of the IL-2 superfamily, is implicated in the survival, proliferation and homeostasis of T-cells. Mutations in the IL-7 receptor have been shown to result in the loss of T-cells, and the development of severe combined immunodeficiency (SCID), highlighting the critical role that IL-7 plays in T-cell development.
  • SCID severe combined immunodeficiency
  • IL-7 is a homeostatic cytokine that provides continuous signals to resting na ⁇ ve and memory T-cells, and which accumulates during conditions of lymphopenia, leading to an increase in both T-cell proliferation and T-cell repertoire diversity.
  • IL-7 is selective for expanding CD8 + T-cells over CD4 + FOXP3 + regulatory T-cells.
  • Recombinant IL-7 has been shown to augment antigen-specific T-cell responses following vaccination, and adoptive cell therapy in mice.
  • IL-7 also can play a role in promoting T-cell recovery following chemotherapy of hematopoietic stem cell transplantation.
  • IL-7 has been shown to possess antitumor effects in tumors such as gliomas, melanomas, lymphomas, leukemia, prostate cancer, and glioblastoma, and the in vivo administration of IL-7 in murine models resulted in decreased cancer cell growth.
  • IL-7 also has been shown to enhance the antitumor effects of IFN- ⁇ in rat glioma tumors, and to induce the production of IL-1 ⁇ , IL-1 ⁇ and TNF- ⁇ by monocytes, which results in the inhibition of melanoma growth. Additionally, administration of recombinant IL-7 following the treatment of pediatric sarcomas resulted in the promotion of immune recovery (see, e.g., Lin et al. (2017) Anticancer Research 37:963-968).
  • IL-12p70 IL-12p40 + IL-12p35
  • Bioactive IL-12 IL-12p70
  • IL-12p70 which promotes cell-mediated immunity, is a heterodimer, composed of p35 and p40 subunits, whereas IL-12p40 monomers and homodimers act as IL-12 antagonists.
  • IL-12 which is secreted by antigen-presenting cells, promotes the secretion of IFN- ⁇ from NK and T-cells, inhibits tumor angiogenesis, results in the activation and proliferation of NK cells, CD8 + T-cells and CD4 + T-cells, enhances the differentiation of na ⁇ ve CD4 + T-cells into Th1 cells, and promotes antibody-dependent cell-mediated cytotoxicity (ADCC) against tumor cells.
  • IL-12 has been shown to exhibit anti-tumor effects in murine models of melanoma, colon carcinoma, mammary carcinoma, and sarcoma (see, e.g., Kalinski et al. (2001) Blood 97:3466-3469; Sheikhi et al.
  • IL-15 and IL-15:IL-15R ⁇ IL-15 is structurally similar to IL-2, and while both IL-2 and IL-15 provide early stimulation for the proliferation and activation of T-cells, IL-15 blocks IL-2 induced apoptosis, which is a process that leads to the elimination of stimulated T- cells and induction of T-cell tolerance, limiting memory T-cell responses and potentially limiting the therapeutic efficacy of IL-2 alone.
  • IL-15 also supports the persistence of memory CD8 + T-cells for maintaining long-term anti-tumor immunity, and has demonstrated significant anti-tumor activity in pre-clinical murine models via the direct activation of CD8 + effector T-cells in an antigen-independent manner.
  • IL-15 is responsible for the development, proliferation and activation of effector natural killer (NK) cells (see, e.g., Lee, S. and Margolin, K. (2011) Cancers 3:3856-3893; and Han et al. (2011) Cytokine 56(3):804-810).
  • NK effector natural killer
  • IL-15 and IL-15 receptor alpha are coordinately expressed by antigen-presenting cells, such as monocytes and dendritic cells, and IL-15 is presented in trans by IL-15R ⁇ to the IL-15R ⁇ C receptor complex expressed on the surfaces of CD8 + T-cells and NK cells.
  • Soluble 1L-15:IL15-R ⁇ complexes have been shown to modulate immune responses via the IL-15R ⁇ C complex, and the biological activity of IL-15 has been shown to be increased 50-fold by administering it in a preformed complex of IL-15 and soluble IL-15R ⁇ , which has an increased half-life compared to IL-15 alone.
  • IL-18 IL-18 induces the secretion of IFN- ⁇ by NK and CD8 + T-cells, enhancing their toxicity.
  • IL-18 also activates macrophages and stimulates the development of Th1 helper CD4 + T-cells.
  • IL-18 has shown promising anti-tumor activity in several preclinical mouse models.
  • IL-18 recombinant IL-18
  • rIL-18 recombinant IL-18
  • IL-18 anti-tumor effects were mediated by IFN- ⁇ , and involved antiangiogenic mechanisms.
  • IL-18 with other cytokines, such as IL-12, or with co-stimulatory molecules, such as CD80, enhances the IL-18-mediated anti-tumor effects.
  • IL-18 can be combined with other anti-cancer therapeutic agents, such as monoclonal antibodies, cytotoxic drugs, or vaccines (see, e.g., Fabbi et al. (2015) J. Leukoc. Biol.97:665-675; and Lee, S. and Margolin, K. (2011) Cancers 3:3856-3893).
  • Chemokines are a family of small cytokines that mediate leukocyte migration to areas of injury or inflammation, and are involved in mediating immune and inflammatory responses.
  • Chemokines are classified into four subfamilies, based on the position of cysteine residues in their sequences, namely XC-, CC-, CXC-, and CX3C-chemokine ligands, or XCL, CCL, CXCL, and CX3CL.
  • the chemokine ligands bind to their cognate receptors and regulate the circulation, homing and retention of immune cells, with each chemokine ligand-receptor pair selectively regulating a certain type of immune cell.
  • Different chemokines attract different leukocyte populations, and form a concentration gradient in vivo, with attracted immune cells moving through the gradient towards the higher concentration of chemokine (see, e.g., Argyle D.
  • Chemokines can improve the anti- tumor immune response by increasing the infiltration of immune cells into the tumor, and facilitating the movement of antigen-presenting cells (APCs) to tumor-draining lymph nodes, which primes na ⁇ ve T-cells and B cells (see, e.g., Lechner et al. (2011) Immunotherapy 3(11):1317-1340).
  • the immunostimulatory bacteria herein can be engineered to encode chemokines, including, but not limited to, CCL3, CCL4, CCL5, CXCL9, CXCL10, and CXCL11.
  • CCL3, CCL4, CCL5 CCL3, CCL4, and CCL5 share a high degree of homology, and bind to CCR5 (CCL3, CCL4 and CCL5) and CCR1 (CCL3 and CCL5) on several cell types, including immature DCs and T-cells, in both humans and mice.
  • Therapeutic T-cells have been shown to induce chemotaxis of innate immune cells to tumor sites, via the tumor-specific secretion of CCL3, CCL4, and CCL5 (see, e.g., Dubinett et al. (2010) Cancer J.16(4):325-335).
  • CCL3 is chemotactic for both neutrophils and monocytes; specifically, CCL3 can mediate myeloid precursor cell (MPC) mobilization from the bone marrow, and has MPC regulatory and stimulatory effects.
  • MPC myeloid precursor cell
  • DCs transfected with the tumor antigen human melanoma-associated gene (MAGE)-1 that were recruited by CCL3 exhibited superior anti-tumor effects, including increased lymphocyte proliferation, cytolytic capacity, and survival, and decreased tumor growth, in a mouse model of melanoma.
  • MAGE tumor antigen human melanoma-associated gene
  • CCL3 has been used as an adjuvant for the treatment of cancer.
  • CCL3 has also shown success as an adjuvant in systemic cancers, whereby mice vaccinated with CCL3 and IL-2 or granulocyte-macrophage colony-stimulating factor (GM-CSF), in a model of leukemia/lymphoma, exhibited increased survival (see, e.g., Schaller et al. (2017) Expert Rev. Clin. Immunol.13(11):1049-1060).
  • CCL3 and CCL4 play a role in directing CD8 + T-cell infiltration into primary tumor sites in melanoma and colon cancers.
  • CCL4 Tumor production of CCL4 leads to the accumulation of CD103 + DCs; suppression of CCL4 through a WNT/ ⁇ -catenin- dependent pathway prevented CD103 + DC infiltration of melanoma tumors (see, e.g., Spranger et al. (2015) Nature 523(7559):231-235).
  • CCL3 was also shown to enhance CD4 + and CD8 + T-cell infiltration to the primary tumor site in a mouse model of colon cancer (see, e.g., Allen et al. (2017) Oncoimmunology 7(3):e1393598).
  • CCL3 or CCL5 The binding of CCL3 or CCL5 to their receptors (CCR1 and CCR5), moves immature DCs, monocytes, and memory and T effector cells from the circulation into sites of inflammation or infection.
  • CCL5 expression in colorectal tumors contributes to T lymphocyte chemoattraction and survival.
  • CCL3 and CCL5 have been used alone or in combination therapy to induce tumor regression and immunity in several preclinical models. For example, studies have shown that the subcutaneous injection of Chinese hamster ovary cells genetically modified to express CCL3, resulted in tumor inhibition and neutrophilic infiltration.
  • CCL5 a recombinant oncolytic adenovirus expressing CCL5 (Ad-RANTES-E1A) resulted in primary tumor regression, and blocked metastasis in a mammary carcinoma murine model (see, e.g., Lechner et al. (2011) Immunotherapy 3(11):1317-1340).
  • CCL5 induced an “antiviral response pattern” in macrophages.
  • CXCR3-mediated migration of lymphocytes at the invasive margin of liver metastases in colorectal cancer CCL5 is produced.
  • Blockade of CCR5 the CCL5 receptor, results in tumor death, driven by macrophages producing IFN and reactive oxygen species.
  • CCR5 inhibition induces a phenotypic shift from an M2 to an M1 phenotype.
  • CCR5 blockade also leads to clinical responses in colorectal cancer patients (see, e.g., Halama et al. (2016) Cancer Cell 29(4):587-601).
  • CCL3, CCL4, and CCL5 can be used for treating conditions, including lymphatic tumors, bladder cancer, colorectal cancer, lung cancer, melanoma, pancreatic cancer, ovarian cancer, cervical cancer, or liver cancer (see, e.g., U.S. Patent Publication No. US 2015/0232880; and International Application Publication Nos.
  • CXCL9, CXCL10, CXCL11 CXCL9 (MIG), CXCL10 (IP10), and CXCL11 (ITAC) are induced by the production of IFN- ⁇ .
  • chemokines bind CXCR3, preferentially expressed on activated T-cells, and function both angiostatically, and in the recruitment and activation of leukocytes.
  • Prognosis in colorectal cancer is strongly correlated to tumor-infiltrating T-cells, particularly Th1 and CD8 + effector T-cells; high intratumoral expression of CXCL9, CXCL10 and CXCL11 is indicative of good prognosis.
  • high intratumoral expression of CXCL9, CXCL10 and CXCL11 is indicative of good prognosis.
  • CXCL9, CXCL10 and CXCL11 were significantly higher numbers of CD3 + T-cells, CD4 + T-helper cells, and CD8 + cytotoxic T-cells.
  • CXCL9 and CXCL10 levels were increased at the invasive margin, and correlated with effector T-cell density.
  • CXCL9 functions as a chemoattractant for tumor-infiltrating lymphocytes (TILs), activated peripheral blood lymphocytes, natural killer (NK) cells, and Th1 lymphocytes.
  • TILs tumor-infiltrating lymphocytes
  • NK natural killer cells
  • Th1 lymphocytes Th1 lymphocytes.
  • CXCL9 also is critical for T-cell-mediated suppression of cutaneous tumors.
  • CXCL9 when combined with systemic IL-2, CXCL9 has been shown to inhibit tumor growth via the increased intratumoral infiltration of CXCR3 + mononuclear cells.
  • a combination of the huKS1/4-IL-2 fusion protein with CXCL9 gene therapy achieved a superior anti- tumor effect and prolonged lifespan through the chemoattraction and activation of CD8 + and CD4 + T lymphocytes (see, e.g., Dubinett et al. (2010) Cancer J.16(4):325- 335; and Ruehlmann et al. (2001) Cancer Res.61(23):8498-8503).
  • CXCL10 produced by activated monocytes, fibroblasts, endothelial cells, and keratinocytes, is chemotactic for activated T-cells, and can act as an inhibitor of angiogenesis in vivo.
  • Expression of CXCL10 in colorectal tumors has been shown to contribute to cytotoxic T lymphocyte chemoattraction and longer survival.
  • the administration of immunostimulatory cytokines, such as IL-12 has been shown to enhance the anti-tumor effects generated by CXCL10.
  • DC dendritic cell
  • Interferons (which can be produced by plasmacytoid dendritic cells; these cells are associated with primary melanoma lesions and can be recruited to a tumor site by CCL20) can act on tumor DC subsets, for example, CD103 + DCs, which have been shown to produce CXCL9/10 in a mouse melanoma model, and have been associated with CXCL9/10 in human disease.
  • CXCL10 also has shown higher expression in human metastatic melanoma samples relative to primary melanoma samples.
  • adjuvant IFN- ⁇ melanoma therapy upregulates CXCL10 production, whereas the chemotherapy agent cisplatin induces CXCL9 and CXCL10 (see, e.g., Dubinett et al. (2010) Cancer J.16(4):325-335; Kuo et al. (2016) Front. Med. (Lausanne) 5:271; Li et al. (2007) Scand. J. Immunol.65(1):8-13; and Muenchmeier et al. (2013) PLoS One 8(8):e72749).
  • CXCL10/11 and CXCR3 expression has been established in human keratinocytes derived from basal cell carcinomas (BCCs).
  • CXCL11 also is capable of promoting immunosuppressive indoleamine 2,3-dioxygenase (IDO) expression in human basal cell carcinoma, as well as enhancing keratinocyte proliferation, which could reduce the anti-tumor activity of any infiltrating CXCR3 + effector T-cells (see, e.g., Kuo et al. (2016) Front. Med. (Lausanne) 5:271).
  • CXCL9, CXCL10 and CXCL11 can be encoded in oncolytic viruses for treating cancer (see, e.g., U.S. Patent Publication No.2015/0232880; and International Application Publication No. WO 2015/059303).
  • Pseudotyped oncolytic viruses or a genetically engineered bacterium encoding the gene for CXCL10 also can be used to treat cancer (see, e.g., International Application Publication Nos. WO 2018/006005 and WO 2018/129404).
  • Co-Stimulatory Molecules Co-stimulatory molecules enhance the immune response against tumor cells, and co-stimulatory pathways are inhibited by tumor cells to promote tumorigenesis.
  • the immunostimulatory bacteria herein can be engineered to express co-stimulatory molecules, such as, for example, CD40, CD40L, 4-1BB, 4-1BBL, 4-1BBL with a deletion of the cytoplasmic domain (4-1BBL ⁇ cyt), 4-1BBL with a truncated cytoplasmic domain, OX40 (CD134), OX40L (CD252), other members of the TNFR superfamily (e.g., CD27, CD27 ligand, GITR, CD30, Fas receptor, TRAIL-R, TNF-R, HVEM, and RANK), B7, CD80, CD86, ICOS, ICOS ligand (B7RP1), and CD28.
  • co-stimulatory molecules such as, for example, CD40, CD40L, 4-1BB, 4-1BBL, 4-1BBL with a deletion of the cytoplasmic domain (4-1BBL ⁇ cyt), 4-1BBL with a truncated cytoplasm
  • the immunostimulatory bacteria can encode and express truncated co- stimulatory molecules (e.g., 4-1BBL, CD80, CD86, CD27L, B7RP1, OX40L), with a full or partial (complete, or truncated, or modified to ensure proper orientation when expressed in a cell) cytoplasmic domain deletion, for expression on an antigen presenting cell (APC).
  • truncated co- stimulatory molecules e.g., 4-1BBL, CD80, CD86, CD27L, B7RP1, OX40L
  • the gene product with a truncated cytoplasmic domain provides constitutive immunostimulatory signaling to a T-cell through co-stimulatory receptor engagement, and is unable to counter-regulatory signal to the APC due to a truncated or deleted (or otherwise modified as described herein) cytoplasmic domain.
  • the truncation is sufficient to provide the signaling, and to be unable to counter-regulatory signal to the APC.
  • the complete or partial deletion of the cytoplasmic domain of a co-stimulatory molecule potentiates the activation of the co-stimulatory molecule, without the immunosuppressive reverse signaling.
  • the partial deletion (or truncation) of the cytoplasmic domain is a sufficient deletion to achieve these effects, without affecting the expression of the co-stimulatory molecule, or the orientation of the expressed co-stimulatory molecule.
  • the co-stimulatory molecules also can be modified to eliminate or reduce the immunosuppressive intracellular/reverse signaling by modifications to the amino acids in the cytoplasmic domain, including insertions, deletions, and/or replacements.
  • the co-stimulatory molecules are modified by modification, such as by replacement, of cytoplasmic domain phosphorylation sites.
  • the immunostimulatory bacteria herein also can be engineered to express agonistic antibodies against co-stimulatory molecules (e.g., 4-1BB) to enhance the anti-tumor immune response.
  • co-stimulatory molecules e.g. 4-1BB
  • TNF Receptor Superfamily The TNF superfamily of ligands (TNFSF) and their receptors (TNFRSF) are involved in the proliferation, differentiation, activation and survival of tumor and immune effector cells.
  • Stimulatory antibodies against molecules such as 4-1BB, OX40 and GITR also can be encoded by the immunostimulatory bacteria to stimulate the immune system.
  • agonistic anti-4-1BB monoclonal antibodies have been shown to enhance anti-tumor CTL responses
  • agonistic anti-OX40 antibodies have been shown to increase anti-tumor activity in transplantable tumor models.
  • agonistic anti-GITR antibodies have been shown to enhance anti-tumor responses and immunity (see, e.g., Lechner et al.
  • CD40 and CD40L CD40 which is a member of the TNF receptor superfamily, is expressed by APCs and B cells, while its ligand, CD40L (CD154), is expressed by activated T- cells. Interaction between CD40 and CD40L stimulates B cells to produce cytokines, resulting in T-cell activation and tumor cell death. Studies have shown that anti-tumor immune responses are impaired with reduced expression of CD40L on T-cells, or CD40 on dendritic cells.
  • CD40 is expressed on the surface of several B-cell tumors, such as follicular lymphoma, Burkitt lymphoma, lymphoblastic leukemia, and chronic lymphocytic leukemia, and its interaction with CD40L has been shown to increase the expression of B7-1/CD80, B7-2/CD86, and human leukocyte antigen (HLA) class II molecules in the CD40 + tumor cells, as well as enhance their antigen-presenting abilities.
  • Transgenic expression of CD40L in a murine model of multiple myeloma resulted in the induction of CD4 + and CD8 + T-cells, local and systemic anti-tumor immune responses, and reduced tumor growth.
  • Anti-CD40 agonistic antibodies also induced anti-tumor T-cell responses (see, e.g., Marin-Acevedo et al. (2016) Journal of Hematology & Oncology 11:39; Dotti et al. (2002) Blood 100(1):200-207; and Murugaiyan et al. (2007) J. Immunol.178:2047-2055).
  • 4-1BB and 4-1BBL 4-1BB (CD137) is an inducible co-stimulatory receptor that is expressed primarily by T-cells and NK cells; it binds its ligand 4-1BBL that is expressed on APCs, including DCs, B-cells, and monocytes, to trigger immune cell proliferation and activation.4-1BB results in longer and more widespread responses of activated T- cells.
  • Anti-4-1BB agonists and 4-1BBL fusion proteins have been shown to increase immune-mediated anti-tumor activity, for example, against sarcoma and mastocytoma tumors, mediated by CD4 + Th1 and tumor-specific CTL activity (see, e.g., Lechner et al.
  • 4-1BBL is negatively regulated by its cytoplasmic signaling domain.
  • reverse signaling of the 4-1BBL cytoplasmic domain induces surface translocation of 4-1BBL to bind to form a signaling complex with TLR4.
  • This induces high levels of TNF- ⁇ , comparable to LPS activation of TLR4, that leads to immunosuppression of the adaptive immune response (see, e.g., Ma et al. (2013) Sci. Signaling 295(6):1-11).
  • 4-1BBL a member of the TNF superfamily, is expressed in B-cells, dendritic cells, activated T-cells and macrophages.4-1BBL binds to its receptor, 4-1BB, and provides a co-stimulatory signal for T-cell activation and expansion.
  • the human 4- 1BBL gene encodes a 254 amino acid type II transmembrane protein containing a 28 amino acid cytoplasmic domain, a 21 amino acid transmembrane protein domain, and a 205 amino acid extracellular domain (see, SEQ ID NO:389).
  • cytoplasmic domain of 4-1BBL corresponding to amino acid residues 1-28 of SEQ ID NO:342 or 389
  • the portion that is deleted is sufficient to potentiate the activation of 4-1BBL, but without the immunosuppressive reverse signaling.
  • the truncated cytoplasmic domain can include amino acids or replacements to ensure proper orientation of the expressed protein in the cell membrane (similar modifications can be effected in others of the membrane- spanning proteins in which the cytoplasmic domain is truncated or deleted).
  • nucleic acid molecules encoding a 4-1BBL variant that lacks the cytoplasmic domain, or that has a truncated cytoplasmic domain, to eliminate the immunosuppressive reverse signaling.
  • An example of such nucleic acid and encoded protein is described in the Examples (see, e.g., SEQ ID NOs: 391 and 395).
  • the receptors also can be cytoplasmically truncated or deleted.
  • OX40 and OX40L OX40 are members of the TNF receptor superfamily that is expressed on activated effector T-cells, while its ligand, OX40L is expressed on APCs, including DCs, B cells and macrophages, following activation by TLR agonists and CD40-CD40L signaling.
  • OX40-OX40L signaling results in the activation, potentiation, proliferation and survival of T-cells, as well as the modulation of NK cell function and inhibition of the suppressive activity of Tregs. Signaling through OX40 also results in the secretion of cytokines (IL-2, IL-4, IL-5, and IFN- ⁇ ), boosting Th1 and Th2 cell responses.
  • cytokines IL-2, IL-4, IL-5, and IFN- ⁇
  • TILs tumor-infiltrating lymphocytes
  • B7-CD28 Family CD28 is a co-stimulatory molecule expressed on the surface of T-cells that acts as a receptor for B7-1 (CD80) and B7-2 (CD86), which are co-stimulatory molecules expressed on antigen-presenting cells.
  • CD28-B7 signaling is required for T-cell activation and survival, and for the prevention of T-cell anergy, and results in the production of interleukins, such as IL-6.
  • T-cell priming requires two signals: (1) T-cell receptor (TCR) recognition of MHC-presented antigens, and (2) co-stimulatory signals resulting from the ligation of T-cell CD28 with B7-1 (CD80) or B7-2 (CD86) expressed on APCs.
  • TCR T-cell receptor
  • CTLA-4 receptors are induced, which then outcompete CD28 for binding to B7-1 and B7-2 ligands.
  • Antigen presentation by tumor cells is poor due to their lack of expression of co-stimulatory molecules, such as B7-1/CD80 and B7-2/CD86, resulting in a failure to activate the T-cell receptor complex.
  • upregulation of these molecules on the surfaces of tumor cells can enhance their immunogenicity.
  • Immunotherapy of solid tumors and hematologic malignancies has been successfully induced by B7, for example, via tumor cell expression of B7, or soluble B7-immunoglobulin fusion proteins.
  • the viral-mediated tumor expression of B7, in combination with other co-stimulatory ligands, such as ICAM-3 and LFA-3, has been successful in preclinical and clinical trials for the treatment of chronic lymphocytic leukemia and metastatic melanoma.
  • co-stimulatory ligands such as ICAM-3 and LFA-3
  • soluble B7 fusion proteins have demonstrated promising results in the immunotherapy of solid tumors as single agent immunotherapies (see, e.g., Lechner et al. (2011) Immunotherapy 3(11):1317-1340; and Dotti et al.
  • the plasmids in the immunostimulatory bacteria provided herein can include nucleic acids that encode molecules, such as enzymes, that activate, such as by cleavage of a portion of, therapeutic products, such as prodrugs, including chemotherapeutic prodrugs, particularly toxins, that are activated by enzymatic cleavage.
  • the inactive prodrug can be administered systemically, and is inactive.
  • the plasmid-encoded activating molecule such as an enzyme, is expressed in the tumor microenvironment after delivery of the immunostimulatory bacteria provided herein, so that the inactive prodrug is activated in the tumor microenvironment, where it exerts its anti-tumor effect.
  • prodrugs including certain nucleosides, and toxin conjugates.
  • Many such prodrugs and enzymes are known (see, e.g., Malekshah et al., (2016) Curr. Pharmacol. Rep.2:299-308).
  • Type I interferons include IFN- ⁇ and IFN- ⁇ , and are pleiotropic cytokines with antiviral, anti-tumor, and immunoregulatory activities.
  • IFN- ⁇ is produced by most cell types; IFN- ⁇ primarily is produced by hematopoietic cells, particularly plasmacytoid dendritic cells.
  • Type I IFNs are produced following the sensing of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). They are involved in the innate immune response against pathogens, mainly viral, and are potent immunomodulators that promote antigen presentation, mediate dendritic cell (DC) maturation, activate cytotoxic T lymphocytes (CTLs), natural killer (NK) cells and macrophages, and activate the adaptive immune system by promoting the development of high-affinity antigen-specific T-cell and B-cell responses and immunological memory.
  • PAMPs pathogen-associated molecular patterns
  • PRRs pattern recognition receptors
  • Type I IFNs exhibit anti-proliferative and pro-apoptotic effects on tumors and have anti-angiogenic effects on tumor neovasculature. They induce the expression of MHC class I molecules on tumor cell surfaces, increase the immunogenicity of tumor cells, and activate cytotoxicity against them. Type I IFN has been used as a therapeutic for the treatment of cancers and viral infections.
  • IFN- ⁇ (sold under the trademark Intron®/Roferon®-A) is approved for the treatment of hairy cell leukemia, malignant melanoma, AIDS-related Kaposi’s sarcoma, and follicular non- Hodgkin’s lymphoma; it also is used in the treatment of chronic myelogenous leukemia (CML), renal cell carcinoma, neuroendocrine tumors, multiple myeloma, non-follicular non-Hodgkin’s lymphoma, desmoid tumors, and cutaneous T-cell lymphoma, although use is limited due to systemic immunotoxicity (see, e.g., Ivashkiv and Donlin (2014) Nat. Rev.
  • Type I interferons in tumors and the tumor microenvironment is among the immune responses that the immunostimulatory bacteria herein are designed to evoke. Inducing or evoking type I interferon provides anti-tumor immunity for the treatment of cancer. a. Constitutive STING Expression and Gain-of-Function Mutations The induction of type I IFNs, proinflammatory cytokines and chemokines is necessary for mounting an immune response that prevents or inhibits infection by viral pathogens.
  • the immunostimulatory bacteria provided herein encode proteins that constitutively induce type I IFNs. Among these proteins are those that occur in individuals with various diseases or disorders that involve the over-production of immune response modulators. For example, over-production or excessive production, or defective negative regulation of type I IFNs and pro-inflammatory cytokines, can lead to undesirable effects, such as inflammatory and autoimmune diseases. Disorders involving the overproduction, generally chronic, of type I IFNs, are referred to as interferonopathies (see, e.g., Lu and MacDougall (2017) Front. Genet.8:118; and Konno et al. (2016) Cell Reports 23:1112-1123).
  • Aicardi-Goutiéres syndrome Aicardi-Goutiéres syndrome (AGS), STING-associated vasculopathy with onset in infancy (SAVI), Singleton-Merten syndrome (SMS), atypical SMS, familial chilblain lupus (FCL), systemic lupus erythematosus (SLE), bilateral striatal necrosis (BSN), cerebrovascular disease (CVD), dyschromatosis symmetrica hereditaria (DSH), spastic paraparesis (SP), X- linked reticulate pigmentary disorder (XLPDR), proteasome-associated auto- inflammatory syndrome (PRAAS), intracranial calcification (ICC), Mendelian susceptibility to mycobacterial disease (MSMD), and spondyloenchondrodysplasia (SPENCD) (see, e.g., Rodero et al.
  • the sustained activation of interferon signaling can be due to: 1) loss-of- function mutations leading to increased cytosolic DNA (e.g., mutations in TREX1 and SAMHD1), or increased cytosolic RNA/DNA hybrids (e.g., mutations in RNASEH2A, RNASEH2B, RNASEH2C, and POLA1); 2) loss-of-function mutations resulting in a defect in RNA editing and abnormal sensing of self-nucleic acid RNA species in the cytosol (e.g., mutations in ADAR1); 3) gain-of-function mutations leading to constitutive activation of cytosolic IFN signaling pathways/increased sensitivity to cytosolic nucleic acid ligands (e.g., a mutations in TREX1 and SAMHD1), or increased cytosolic RNA/DNA hybrids (e.g., mutations in RNASEH2A, RNASEH2B, RNASEH2C
  • GEF gain-of-function
  • TMEM173 STING Alleles Stimulator of interferon genes is encoded by the transmembrane protein 173 (TMEM173) gene, which is a ⁇ 7 kb-long gene.
  • TMEM173 gene is characterized by significant heterogeneity and population stratification of alleles.
  • the most common human TMEM173 allele is referred to as R232 (referencing the amino acid present at residue 232; see, e.g., SEQ ID NOs:305-309, setting forth the sequences of various human TMEM173 alleles ) . More than half the American population is not R232/R232.
  • the second most common allele is R71H-G230A- R293Q (HAQ).
  • AQ G230A-R293Q
  • Q Q293
  • R232H named REF after the reference STING allele first identified and catalogued in the database by Glen Barber.
  • R232/R232 is the most common genotype in Europeans
  • HAQ/R232 is the most common genotype in East Asians. Africans have no HAQ/HAQ genotypes, but have the Q allele, and ⁇ 4% of Africans are AQ/AQ, which is absent in other ethnic populations (see, e.g., Patel and Jin (2016) Genes & Immunity, doi:10.1038/s41435- 018-0029-9).
  • the REF, AQ and Q alleles are highly refractory to bacterially-derived CDNs, such as 3’3’ c-di-GMP (see, e.g., Corrales et al. (2015) Cell Reports 11:1018- 1030).
  • STING Gain-of-Function Mutations Several activating or gain-of-function (GOF) mutations in TMEM173, the gene for STING, inherited and de novo, have been linked to the rare auto- inflammatory disease SAVI (STING-associated vasculopathy with onset in infancy). SAVI is an autosomal dominant disease and is characterized by systemic inflammation, interstitial lung disease, cutaneous vasculitis, and recurrent bacterial infection.
  • SAVI with de novo TMEM173 mutations typically is characterized by an early-onset ( ⁇ 8 weeks) and severe phenotype, while familial mutations result in late- onset (teens to adults) and milder clinical symptoms.
  • Inherited TMEM173 activating mutations include G166E and V155M, whereas de novo mutations include N154S, V155M, V147M, V147L, C206Y, R284G, R281Q and S102P/F279L (see, e.g., Patel and Jin (2019) Genes & Immunity 20:82-89).
  • TMEM173 mutations that have been identified include R284M, R284K, R284T, E316Q, and R375A (see, e.g., U.S. Patent Publication No.2018/0311343).
  • R284S Another gain-of-function mutation in TMEM173 is R284S, which results in a highly constitutively active STING, and was found to trigger innate immune signaling in the absence of activating CDNs, leading to chronic production of pro-inflammatory cytokines (see, e.g., Konno et al. (2016) Cell Reports 23:1112-1123).
  • TMEM173 mutations such as N154S, V155M and V147L, and/or any of the mutations listed in the table below, singly or in any combination with these and any other such mutations, such as N154S/R284G, result in a gain-of-function STING that is constitutively active and does not require, or is hypersensitive to, ligand stimulation, leading to chronic activation of the STING-interferon pathway. This has been demonstrated (see, e.g., Liu et al. (2014) N. Engl. J. Med.371:507-518).
  • Stimulation with cGAMP resulted in a response in a dose-dependent manner in cells with non- mutated TMEM173, and resulted in a minimal response only at the highest cGAMP concentration, in cells expressing the loss-of-function mutant (see, e.g., Liu et al. (2014) N. Engl. J. Med.371:507-518). These results show that the activating TMEM173 mutations result in constitutive activation of STING, even in the absence of stimulation by cGAMP.
  • G207E is another gain-of-function STING mutation that causes alopecia, photosensitivity, thyroid dysfunction, and SAVI-features.
  • the G207E mutation causes constitutive activation of inflammation-related pathways in HEK cells, as well as aberrant interferon signature and inflammasome activation in patient peripheral blood mononuclear cells (PBMCs).
  • PBMCs peripheral blood mononuclear cells
  • mutants identified were hyperactive mutants R196A/D204A, S271A/Q272A, R309A/E315A, E315A, E315N, E315Q, and S271A (corresponding to R197A/D205A, S272A/Q273A, R310A/E316A, E316A, E316N, E316Q, and S272A, respectively, with reference to the sequence of human STING as set forth in SEQ ID NOs:305-309), that spontaneously induced IFN at low levels of transfection and did not respond to c-di-GMP, and the mutants R374A, R292A/T293A/E295A/E299A, D230A, R231A, K235A, Q272A
  • the immunostimulatory bacteria increase the production of type I IFN-mediated cytokines and chemokines in the tumor microenvironment, potentiating the anti-tumor immune response and improving the therapeutic efficacy of the immunostimulatory bacteria.
  • the gene encoding STING is referred to as TMEM173, the gene encoding MDA5 is IFIH1, and the gene encoding RIG-I is DDX58.
  • TMEM173 the gene encoding MDA5
  • RIG-I is DDX58.
  • STING/TMEM173 SEQ ID NOs:305-309
  • MDA5/IFIH1 SEQ ID NO:310
  • RIG-I/DDX58 SEQ ID NO:311
  • IRF3 SEQ ID NO:312
  • IRF7 SEQ ID NO:313
  • a phosphorylation site or sites such as S324/L325/S326 ⁇ S324A/L325/S326A in STING, and other replacements to eliminate a phosphorylation site to reduce nuclear factor- ⁇ B (NF- ⁇ B) signaling in STING, or other proteins that employ such signaling, also can be introduced.
  • the resulting proteins can be encoded in the immunostimulatory bacteria provided herein.
  • the proteins are encoded on plasmids in the immunostimulatory bacteria.
  • Administering nucleic acids encoding wild-type STING can induce an immune response; the administration of gain-of-function STING mutants, with constitutive activity as provided herein, in tumor-targeted immunostimulatory bacteria, leads to a more potent immune response and more effective anti-cancer therapeutic.
  • the enhanced immune response by the tumor-targeted administration of constitutively active STING, or other such modified DNA/RNA sensors, such as gain- of-function mutants of MDA5, RIG-I, IRF3, or IRF7, as provided herein, provides a therapeutically more effective anti-cancer treatment.
  • modifying the immunostimulatory bacteria so that they do not infect epithelial cells, but retain the ability to infect phagocytic cells, including tumor-resident immune cells effectively targets the immunostimulatory bacteria to the tumor microenvironment, improving therapeutic efficiency and preventing undesirable systemic immune responses.
  • These tumor-targeted bacteria are engineered to encode gain-of-function STING, MDA5, RIG-I, IRF3, or IRF7 mutants, which are constitutively active, for example, even in the absence of ligand stimulation, providing a potent type I IFN response to improve the anti-cancer immune response in the tumor microenvironment.
  • the administration of constitutively activated STING can provide an alternative means to boost STING signaling for the immunotherapeutic treatment of cancer.
  • the tumor-targeting immunostimulatory bacteria provided herein can be modified to encode STING/TMEM173 (SEQ ID NOs: 305-309) with gain-of-function mutations, selected from S102P, V147L, V147M, N154S, V155M, G166E, R197A, D205A, R197A/D205A, C206Y, G207E, D231A, R232A, K236A, R238A, D231A/R232A/K236A/R238A, S272A, Q273A, S272A/Q273A, F279L, S102P/F279L, R281Q, R284G, R284S, R284M, R284K, R284T, R293A, T294A, E296A, R293
  • IRF3 interferon regulatory factor 3, or IRF-3)
  • IRF7 or IRF-7
  • IRF3 and IRF7 are key activators of type I IFN genes. Following virus-induced C-terminal phosphorylation (by TBK1), activated IRF3 and IRF7 form homodimers, translocate from the cytoplasm to the nucleus, and bind to IFN-stimulated response elements (ISREs) to induce type I IFN responses.
  • IRF3 is expressed constitutively in unstimulated cells, and exists as an inactive cytoplasmic form, while IRF7 is not constitutively expressed in cells, and is induced by IFN, lipopolysaccharide, and virus infection.
  • Overexpression of IRF3 significantly increases the virus-mediated expression of type I IFN genes, resulting in the induction of an antiviral state.
  • IRF3 activation also has been shown to up-regulate the transcription of the CC-chemokine RANTES (CCL5) following viral infection (see, e.g., Lin et al. (1999) Mol. Cell Biol.19(4):2465-2474).
  • Residues S385, S386, S396, S398, S402, T404, and S405 in the C-terminal domain of IRF3 are phosphorylated after virus infection, inducing a conformational change that results in the activation of IRF3.
  • IRF3 activation is induced, not only by viral infection, but also by lipopolysaccharide (LPS) and poly(I:C).
  • LPS lipopolysaccharide
  • poly(I:C) poly(I:C)
  • IRF3(S396D) enhances the transactivation of IFN ⁇ 1, IFN- ⁇ , and RANTES promoters by 13-, 14-, and 11-fold, respectively, compared to wild-type IRF3.
  • Another mutant, IRF3(S396D/S398D) enhances the transactivation of IFN ⁇ 1, IFN- ⁇ , and RANTES promoters by 13-, 12-, and 12-fold, respectively, compared to wild-type IRF3.
  • IRF3(5D) Another constitutively active mutant of IRF3 is IRF3(5D), in which the serine or threonine residues at positions 396, 398, 402, 404, and 405 are replaced by phosphomimetic aspartic acid residues (IRF3(S396D/S398D/S402D/T404D/S405D)).
  • Similar gain-of-function mutations, leading to constitutive activity of immune response mediators, such as induction of type I interferon can be achieved by mutating serine residues to phosphomimetic aspartic acid in other proteins, such as RIG-I, MDA5, and STING, that are in immune response signaling pathways.
  • IRF3(5D) displays constitutive DNA binding and transactivation activities, dimer formation, association with the transcription coactivators p300 (also called EP300, or E1A binding protein p300)/ CBP (also known as CREB-binding protein, or CREBBP), and nuclear localization. Its transactivation activity is not induced further by virus infection.
  • IRF3(5D) is a very strong activator of IFN- ⁇ and ISG-15 gene expression; IRF3(5D) alone stimulates IFN- ⁇ expression as strongly as virus infection, and enhances transactivation of IFN ⁇ 1, IFN- ⁇ , and RANTES promoters by 9-fold, 5.5-fold, and 8-fold, respectively, compared to wild-type IRF3 (see, e.g., Lin et al. (2000) J. Biol. Chem.275(44):34320-34327; Lin et al. (1998) Mol. Cell Biol. 18(5):2986-2996; and Servant et al. (2003) J. Biol. Chem.278(11):9441-9447).
  • dsDNA cytosolic double-stranded DNA
  • IFN type I interferon
  • ER endoplasmic reticulum
  • IRF3 transcription factor interferon regulatory factor 3
  • the TANK binding kinase 1 (TBK1)/IRF3 axis results in the induction of type I IFNs, and the activation of dendritic cells (DCs) and cross-presentation of tumor antigens to activate CD8 + T cell-mediated anti-tumor immunity.
  • STING signaling also activates the nuclear factor kappa-light-chain-enhancer of activated B cell (NF- ⁇ B) signaling axis, resulting in a pro-inflammatory response, but not in the activation of the DCs and CD8 + T cells that are required for anti-tumor immunity.
  • STING Upon recognition of 2’3’ cGAMP, STING translocates from the endoplasmic reticulum through the Golgi apparatus, allowing the recruitment of TANK-binding kinase 1 (TBK1) and activation of the transcription factors IRF3 and NF- ⁇ B.
  • the carboxyl-terminal tail (C-terminal tail or CTT) region of STING is necessary and sufficient to activate TBK1 and stimulate the phosphorylation of IRF3; it also is involved in NF- ⁇ B signaling.
  • the CTT is an unstructured stretch of approximately 40 amino acids that contains sequence motifs required for STING phosphorylation and recruitment of IRF3.
  • IRF3 and NF- ⁇ B downstream signaling is attributed to specific sequence motifs within the C-terminal tail (CTT) of STING that are conserved among vertebrate species.
  • CTT C-terminal tail
  • Modular motifs in the CTT which include IRF3-, TBK1- and TRAF6-binding modules, control the strength and specificity of cell signaling and immune responses.
  • the IRF3 and NF- ⁇ B downstream responses can be affected, and sometimes opposite.
  • the STING CTT elements dictate and finely tune the balance between the two signaling pathways, resulting in different biological responses. In human and mouse immune cells, for example, STING-dependent IRF3 activation results predominantly in a type I interferon response.
  • STING signaling in human cells also drives a pro-inflammatory response through canonical and possibly non-canonical NF- ⁇ B pathways via TRAF6 recruitment.
  • Human STING residue S366 (see, e.g., SEQ ID NOs:305-309) is a primary TBK1 phosphorylation site that is part of an LxIS motif in the CTT, which is required for IRF3 binding, while a second PxPLR motif, including residue L374, is required for TBK1 binding.
  • the LxIS and PxPLR motifs are highly conserved in all vertebrate STING alleles. In other species, STING signaling results predominantly in the activation of the NF- ⁇ B signaling axis.
  • the zebrafish CTT which is responsible for hyperactivation of NF- ⁇ B signaling, contains an extension with a highly conserved PxExxD motif at the extreme C-terminus that is not present in human and other mammalian STING alleles; this motif shares similarity with tumor necrosis factor receptor-associated factor 6 (TRAF6) binding sites. While the role of TRAF6 in human STING signaling is non- essential, TRAF6 recruitment is essential for zebrafish STING-induced NF- ⁇ B activation.
  • TRAF6 tumor necrosis factor receptor-associated factor 6
  • a human-zebrafish STING chimera in which human STING was engineered to contain the zebrafish STING CTT module DPVETTDY, induced more than 100-fold activation of NF- ⁇ B activation, indicating that this region is necessary and sufficient to direct enhanced NF- ⁇ B signal activation.
  • the addition of the zebrafish CTT also resulted in an increased STING interferon response (see, de Oliveira Mann et al. (2019) Cell Reports 27:1165-1175).
  • modified STING proteins that have reduced NF- ⁇ B signaling, and/or optionally, increased IRF3 signaling, so that when the STING protein is delivered to and expressed in the TME, the resulting response is an increased anti-tumor/anti-viral response, compared to the unmodified STING protein.
  • STING proteins from species that have low or no NF- ⁇ B signaling activity are provided in delivery vehicles, including any of the immunostimulatory bacteria described herein or known to those of skill in the art, as well as in other delivery vehicles, such as viral vectors, including oncolytic vectors, minicells, exosomes, liposomes, and in cells, such as T-cells that are used in cell therapy and used to deliver vehicles, such as bacteria and oncolytic vectors.
  • the non-human STING proteins can be, but are not limited to, STING proteins from the following species: Colombian devil (Sarcophilus harrisii; SEQ ID NO:349), marmoset (Callithrix jacchus; SEQ ID NO:359), cattle (Bos taurus; SEQ ID NO:360), cat (Felis catus; SEQ ID NO:356), ostrich (Struthio camelus australis; SEQ ID NO:361), crested ibis (Nipponia nippon; SEQ ID NO:362), coelacanth (Latimeria chalumnae; SEQ ID NOs:363-364), boar (Sus scrofa; SEQ ID NO:365), bat (Rousettus aegyptiacus; SEQ ID NO:366), manatee (Trichechus manatus latirostris; SEQ ID NO:367), ghost shark (Callorhinchus milii; S
  • the non-human STING proteins readily activate immune signaling in human cells, indicating that the molecular mechanism of STING signaling is shared in vertebrates (see, de Oliveira Mann et al. (2019) Cell Reports 27:1165-1175).
  • the non-human STING proteins contain any of the constitutive STING activation and gain-of-function mutations, at corresponding loci in the non-human STING corresponding to those in human STING, described above (see, Example 17 below, which provides exemplary alignments and corresponding mutations in various species; see, also, Figures 1-13).
  • chimeras of STING proteins are provided.
  • the CTT region, or portion(s) thereof that confers or participates in NF- ⁇ B signaling/activity, of a first species STING protein is replaced with the corresponding CTT or portion(s) thereof from a second species, whose STING protein has lower or very little, less than human, NF- ⁇ B signaling activity.
  • the first species is human
  • the replacing CTT or portion(s) thereof is from the STING of a species such as Georgian devil, marmoset, cattle, cat, ostrich, boar, bat, manatee, crested ibis, coelacanth, and ghost shark, which have much lower NF- ⁇ B activity.
  • the chimeras can further include the human constitutive STING activation and gain-of-function mutations in corresponding loci, to increase or render type I interferon activity constitutive.
  • the TRAF6 binding motif can be deleted to further decrease or eliminate activity that is not desirable in an anti-tumor therapeutic.
  • non-human STING proteins, chimeras, and mutants are provided in delivery vehicles, such as any described herein or known to those of skill in the art, including oncolytic viral vectors, cells, such as stem cells and T-cells that are used in cell therapies, exosomes, minicells, liposomes, and the immunostimulatory bacteria provided herein, which accumulate in tumor-resident immune cells, and deliver encoded proteins to the tumor microenvironment and to tumors.
  • the non-human STING proteins, modified STING proteins, and STING chimeras are for use as therapeutics for the treatment of tumors as described herein, or for use in other methods known to those of skill in the art.
  • Pharmaceutical compositions containing the STING proteins, delivery vehicles, and encoding nucleic acids also are provided.
  • RLRs retinoic acid-inducible gene I (RIG-I)-like receptors
  • RIG-I retinoic acid-inducible gene I
  • MDA5 melanoma differentiation-associated protein 5
  • RLRs are cytoplasmic sensors of viral dsRNA and nucleic acids secreted by bacteria, and include RIG-I, MDA5, and LGP2 (laboratory of genetics and physiology 2).
  • a ligand such as a viral dsRNA
  • RIG-I and MDA5 activate the mitochondrial antiviral- signaling adaptor protein, or MAVS, which recruits tumor necrosis factor (TNF) receptor-associated factors (TRAFs), to assemble a signaling complex at the outer membranes of the mitochondria.
  • TRAFs tumor necrosis factor receptor-associated factors
  • Downstream signaling components further are recruited by TRAFs, resulting in the phosphorylation and activation of IRF3 (interferon regulatory factor 3), IRF7, NF- ⁇ B (nuclear factor kappa-light-chain- enhancer of activated B cells), and AP-1 (activator protein 1).
  • IFNs As a result, the expression of IFNs, proinflammatory cytokines, and other genes involved in pathogen clearance, is induced (see, e.g., Lu and MacDougall (2017) Front. Genet.8:118). Like STING, the constitutive activation of MDA5 and RIG-I due to gain-of-function mutations leads to the induction of type I IFNs, which can be leveraged to enhance the anti-tumor immune response in the immunostimulatory bacteria. i.
  • RIG-I Retinoic acid-inducible gene I (RIG-I), also known as DDX58 (DEXD/H-box helicase 58), is another protein whose constitutive activation has been linked to the development of interferonopathies, such as atypical Smith-Magenis syndrome.
  • RIG-I like MDA5/IFIH1, is a member of the RIG-I-like receptor (RLR) family, and is a 925- residue cytosolic pattern recognition receptor that functions in the detection of viral dsRNA.
  • RIG-I initiates an innate immune response to viral RNA through independent pathways that promote the expression of type I and type III IFNs and proinflammatory cytokines (see, e.g., Jang et al.
  • Atypical Smith-Magenis syndrome without hallmark dental anomalies, but with variable phenotypes, including glaucoma, aortic calcification, and skeletal abnormalities, has been found to be caused by mutations in the DEXD/H-box helicase 58 gene (DDX58), which encodes retinoic acid-inducible gene I (RIG-I).
  • DDX58 DEXD/H-box helicase 58 gene
  • RIG-I retinoic acid-inducible gene
  • Elevated amounts of mutated DDX58 were associated with a significant increase in the basal levels of NF- ⁇ B reporter gene activity, and this activity was further increased by stimulation with the dsRNA analog poly(I:C).
  • the RIG-I mutations also induced IRF3 phosphorylation and dimerization at the basal level, and led to increased expression of IFNB1, interferon-stimulated gene 15 (ISG15), and chemokine (C-C motif) ligand 5 (CCL5) in both basal, and poly(I:C) transfected HEK293FT cells.
  • Tumor-targeting immunostimulatory bacteria can be modified to encode RIG-I/DDX58 (see, e.g., SEQ ID NO:311) with gain-of-function mutations such as, but not limited to, E373A and C268F, singly and in combination. ii.
  • MDA5/IFIH1 Another interferonopathy gene is the IFN-induced with helicase C domain- containing protein 1 (IFIH1), also known as melanoma differentiation-associated protein 5 (MDA5), which is a member of the RIG-I-like family of cytoplasmic DExD/H box RNA receptors.
  • IFIH1 IFN-induced with helicase C domain- containing protein 1
  • MDA5 melanoma differentiation-associated protein 5
  • MDA5 melanoma differentiation-associated protein 5
  • TNF tumor necrosis factor
  • TRF7 tumor necrosis factor 7
  • NF- ⁇ B tumor necrosis factor kappa-light-chain-enhancer of activated B cells
  • AP-1 activator protein 1
  • Gain-of-function (GOF) IFIH1 variants occur in subjects with autoimmune disorders, including Aicardi-Goutiéres syndrome (AGS) and Singleton-Merten syndrome (SMS), which are characterized by prominent vascular inflammation.
  • AGS is an inflammatory disease particularly affecting the brain and skin, and is characterized by an upregulation of interferon-induced transcripts.
  • AGS typically occurs due to mutations in any of the genes encoding DNA exonuclease TREX1, the three non-allelic components of the RNase H2 endonuclease complex, the deoxynucleoside triphosphate triphosphohydrolase SAMHD1, and the double- stranded RNA editing enzyme ADAR1.
  • Singleton-Merten syndrome is an autosomal- dominant disorder characterized by abnormalities in the blood vessels (e.g., calcification), teeth (e.g., early-onset periodontitis, root resorption), and bones (e.g., osteopenia, acro-osteolysis, osteoporosis).
  • Interferon signature genes are upregulated in Singleton-Merten syndrome patients, which was linked to GOF mutations in IFIH1 (see, e.g., Rice et al. (2014) Nat. Genet.46(5):503-509; and Rutsch et al.
  • IFN- ⁇ reporter stimulatory activity of wild-type IFIH1, and six IFIH1 GOF mutants identified in AGS patients was compared in HEK293T cells, which express low levels of endogenous viral RNA receptors.
  • Wild-type IFIH1 was induced upon binding of the long (> 1 kb) dsRNA analog polyinosinic-polycytidylic acid (poly(I:C)), but not by a short 162 bp dsRNA, and had minimal activity in the absence of exogenous RNA.
  • the IFIH1 mutants displayed a significant induction of IFN signaling in response to the short 162 bp dsRNA, in addition to robust signaling in response to poly(I:C).
  • the mutants also displayed a 4-10 fold higher level of baseline signaling activity in the absence of exogenous ligand (see, e.g., Rice et al. (2014) Nat. Genet.46(5):503-509).
  • Another gain-of-function IFIH1 mutation, R822Q was identified as causing Singleton-Merten syndrome by triggering type I IFN production, and leading to early arterial calcification, as well as dental inflammation and resorption.
  • HEK293T cells which have the lowest endogenous IFIH1 expression levels were used to overexpress wild-type and R822Q MDA5.
  • Wild-type IFIH1 expression led to an increase in the expression of IFNB1 (interferon, beta 1, fibroblast) in a dose-dependent manner, whereas the mutated IFIH1 led to approximately 20-fold more IFNB1 expression.
  • R822Q IFIH1 resulted in higher levels of IFNB1 expression than wild-type IFIH1, indicating that R822Q IFIH1 is hyperactive to non-self dsRNA.
  • interferon signature genes such as IFI27, IFI44L, IFIT1, ISG15, RSG15, RSAD2, and SIGLEC1
  • IFI27, IFI44L, IFIT1, ISG15, RSG15, RSAD2, and SIGLEC1 were also higher expression of interferon signature genes, which was in agreement with the higher expression level of IFNB1 by R822Q IFIH1 (see, e.g., Rutsch et al. (2015) Am. J. Hum. Genet.96:275-282).
  • the interferon signature observed in patients with another IFIH1 GOF mutation, A489T is indicative of a type I interferonopathy; IFIH1 A489T is associated with increased interferon production and phenotypes resembling chilblain lupus, AGS and SMS (see, e.g., Bursztejn et al. (2015) Br. J. Dermatol.173(6):1505- 1513).
  • the A489T variant not only resulted in IFN induction following stimulation with the long dsRNA analog poly(I:C), but also with short dsRNA.
  • T331I and T331R Two additional gain-of-function mutations in IFIH1, T331I and T331R, were identified in patients with SMS phenotypes, who presented with a significant upregulation of IFN-induced transcripts.
  • the T331I and T331R variants resulted in increased expression of IFN- ⁇ , even in the absence of exogenous dsRNA ligand, consistent with the observed constitutive activation of MDA5 (see, e.g., Lu and MacDougall (2017) Front. Genet. 8:118).
  • A946T is another IFIH1 GOF mutation that leads to the increased production of type I IFN, promoting inflammation and increasing the risk of autoimmunity.
  • the A946T mutation in IFIH1 results in additive effects when combined with the TMEM173 R232 allele and G207E GOF mutation in STING, leading to a severe early-onset phenotype with features similar to SAVI (see, e.g., Keskitalo et al. (2016) preprint, available from doi.org/10.1101/394353).
  • G821S is a GOF mutation in IFIH1 which has been shown to lead to spontaneously developed lupus-like autoimmune symptoms in a mouse model (see, e.g., Rutsch et al. (2015) Am. J. Hum. Genet.
  • the tumor-targeting immunostimulatory bacteria provided herein can be modified to encode MDA5/IFIH1 (see, e.g., SEQ ID NO:310) with gain-of-function mutations selected from T331I, T331R, R337G, L372F, D393V, A452T, A489T, G495R, R720Q, R779H, R779C, G821S, R822Q, and A946T, singly or in any combination. iii.
  • IRF7 Constitutively active forms of IRF7 (or IRF-7) include mutants in which different C-terminal serines are substituted by phosphomimetic Asp, including IRF7(S477D/S479D), IRF7(S475D/S477D/S479D), and IRF7(S475D/S476D/S477D/S479D/S483D/S487D).
  • IRF7(S477D/S479D) is a strong transactivator for IFNA and RANTES gene expression, and stimulates gene expression, even in the absence of virus infection.
  • IRF7(S475D/S477D/S479D), and IRF7(S475D/S476D/S477D/S479D/S483D/S487D) do not further augment the transactivation activity of IRF7(S477D/S479D), but the transactivation activity of all three mutants is stimulated further by virus infection.
  • the mutant IRF7( ⁇ 247-467), which localizes to the nucleus in uninfected cells, is a very strong constitutive form of IRF7; it activates transcription more than 1500-fold higher than wild-type IRF7 in unstimulated and virus-infected cells (see, e.g., Lin et al. (2000) J. Biol. Chem.
  • the immunostimulatory bacteria provided herein can encode and express constitutively active IRF7 mutants, including those with replacements at residues 475- 477, 479, 483, and 487, and those with amino acid deletions.
  • the immunostimulatory bacteria encode these proteins on plasmids under the control of promoters and any other desired regulatory signals recognized by mammalian hosts, including humans. e. Other Type I IFN Regulatory Proteins Other proteins involved in the recognition of DNA/RNA that activate type I IFN responses can be mutated to generate constitutive type I IFN expression.
  • the unmodified and/or modified proteins can be encoded in the immunostimulatory bacteria provided herein, to be used to deliver the protein to the tumor microenvironment, such as to tumor-resident immune cells, to increase expression of type I IFN.
  • proteins include, but are not limited to, proteins designated TRIM56, RIP1, Sec5, TRAF2, TRAF3, TRAF6, STAT1, LGP2, DDX3, DHX9 (DDX9), DDX1, DDX21, DHX15, DHX33, DHX36, DDX60, and SNRNP200.
  • Gain-of-function variants can be produced, such as by screening and/or by mutagenesis.
  • Site-directed mutagenesis can be performed in vitro to identify mutations with enhanced activity, that lead to higher level and/or constitutive type I IFN expression.
  • Intact genomic DNA can be obtained from non-related patients experiencing auto-immune and auto-inflammatory symptoms, and from healthy individuals, to screen for and identify other products whose expression leads to increased or constitutive type I IFN expression.
  • Whole exome sequencing can be performed, and introns and exons can be analyzed, such that proteins with mutations in the pathways associated with the increased or constitutive expression of type I interferon are identified.
  • cDNA molecules encoding the full-length gene, with and without the identified mutation(s) are transfected into a reporter cell line that measures expression of type I interferon.
  • a reporter cell line can be generated where the expression of luciferase is placed under control of the promoter for IFN- ⁇ .
  • a gain-of-function mutant that is constitutively active will promote the expression of IFN- ⁇ , whereas the unstimulated wild-type protein will not.
  • Stimulation can be by virus infection, bacterial infection, bacterial nucleic acids, LPS, dsRNA, poly(I:C), or by increasing exogenous levels of the protein’s ligand (e.g., CDNs).
  • Identified proteins also include those that enhance an immune response to an antigen(s) of interest in a subject.
  • the immune response comprises a cellular or humoral immune response characterized by one or more of: (i) stimulating type I interferon pathway signaling; (ii) stimulating NF- ⁇ B pathway signaling; (iii) stimulating an inflammatory response; (iv) stimulating cytokine production; (v) stimulating dendritic cell development, activity, or mobilization; (vi) any other responses indicative of a product whose expression enhances an immune response; and (vii) a combination of any of (i)-(vi). 4.
  • TGF- ⁇ Transforming growth factor beta (TGF- ⁇ ) is a pleiotropic cytokine with numerous roles in embryogenesis, wound healing, angiogenesis, and immune regulation. It exists in three isoforms in mammalian cells, TGF- ⁇ 1, TGF- ⁇ 2, and TGF- ⁇ 3; TGF- ⁇ 1 is the most predominant in immune cells (see, e.g., Esebanmen et al. (2017) Immunol.
  • TGF- ⁇ s role as an immunosuppressant is arguably its most dominant function. Its activation from a latent form in the tumor microenvironment, in particular, has profound immunosuppressive effects on DCs and their ability to tolerize antigen-specific T-cells. TGF- ⁇ also can directly convert Th1 CD4 + T-cells to immunosuppressive Tregs, further promoting tumor tolerance (see, e.g., Travis et al. (2014) Annu. Rev. Immunol.32:51-82). Based on its tumor- specific immunosuppressive functions, and irrespective of its known cancer cell growth and metastasis-promoting properties, inhibition of TGF- ⁇ is a cancer therapy target.
  • TGF- ⁇ signaling has been demonstrated in several human tumor types, including colorectal cancer (CRC), hepatocellular carcinoma (HCC), pancreatic ductal adenocarcinoma (PDAC), and non-small-cell lung cancer (NSCLC) (see, e.g., Colak et al. (2017) Trends Cancer 3(1):56-71).
  • CRC colorectal cancer
  • HCC hepatocellular carcinoma
  • PDAC pancreatic ductal adenocarcinoma
  • NSCLC non-small-cell lung cancer
  • Systemic inhibition of TGF- ⁇ can lead to unacceptable autoimmune toxicities, and its inhibition should be localized to the tumor microenvironment.
  • One way to accomplish this is to create a soluble TGF- ⁇ receptor that acts as a decoy for binding TGF- ⁇ (see, e.g., Zhang et al. (2008) J. Immunol.181:3690-3697).
  • a tumor-targeting immunostimulatory bacteria containing a TGF- ⁇ ⁇ receptor decoy, provided herein, can bind and remove TGF- ⁇ from the tumor microenvironment, thereby breaking tumor immune tolerance and stimulating anti-tumor immunity.
  • TGF-beta binding decoy receptors include anti-TGF-beta antibodies or antibody fragments, anti-TGF-beta receptor antibodies or antibody fragments, and soluble TGF-beta antagonist polypeptides.
  • immunostimulatory bacteria that accumulate in the tumor microenvironment, in tumors, and in particular, in tumor-resident immune cells, that contain plasmids encoding TGF-beta polypeptide antagonists, including, for example, TGF-beta binding decoy receptors (TGF- ⁇ ⁇ receptor decoys), anti-TGF-beta antibodies or antibody fragments, anti-TGF-beta receptor antibodies or antibody fragments, and soluble TGF-beta antagonist polypeptides.
  • TGF-beta binding decoy receptors TGF- ⁇ ⁇ receptor decoys
  • anti-TGF-beta antibodies or antibody fragments anti-TGF-beta receptor antibodies or antibody fragments
  • soluble TGF-beta antagonist polypeptides soluble TGF-beta antagonist polypeptides.
  • the antibody fragments can include any known in the art, or described herein, such as, but not limited to, scFvs and scFv-Fc
  • Bi-specific scFvs and T-Cell Engagers The use of scFvs has been improved by increasing the valency of binding to the target, often through the use of one or more scFv fragments (bi-specific, tri- specific, etc.), joined together by a long linker.
  • Bi-specific T-cell engager (sold under the trademark BiTE®) constructs are a class of artificial bispecific monoclonal antibodies that are utilized in cancer immunotherapy, and are formed by linking two single-chain variable fragments (scFvs), such that one scFv binds CD3 on the surface of cytotoxic T-cells, and the other binds a specific tumor-associated antigen.
  • BiTEs® thus target T-cells to tumor cells, stimulating T-cell activation, cytokine production, and tumor cell cytotoxicity, independently of MHC class I or co-stimulatory molecules.
  • Two examples of BiTEs® have been approved by the FDA, including catumaxomab, which is directed against the tumor antigen EpCAM, and CD3, and is used in the treatment of malignant ascites, and blinatumomab, a BiTE® antibody against CD19 and CD3, which is used for the treatment of relapsed, refractory acute lymphoblastic leukemia (ALL) (see, e.g., Ahamadi-Fesharaki et al. (2019) Mol. Ther. Oncolytics 14:38-56).
  • ALL refractory acute lymphoblastic leukemia
  • BiTEs® target other antigens, including carcinoembryonic antigen (CEA), prostate-specific membrane antigen (PSMA), EGFR, EphA2, Her2, ADAM17/TACE, prostate stem cell antigen (PSCA), and melanoma-associated chondroitin sulfate proteoglycan (MCSP).
  • CCA carcinoembryonic antigen
  • PSMA prostate-specific membrane antigen
  • EGFR epigallocate protein
  • PSCA prostate stem cell antigen
  • MCSP melanoma-associated chondroitin sulfate proteoglycan
  • MCSP melanoma-associated chondroitin sulfate proteoglycan
  • a BiTE® antibody also can be expressed from a plasmid following delivery by an immunostimulatory bacterium.
  • PD-1 is an immune-inhibitory receptor that is involved in the negative regulation of immune responses.
  • PD-L1 programmed death-ligand 1
  • APCs antigen-presenting cells
  • PD-1 PD-1 on T-cells
  • APCs antigen-presenting cells
  • CD8 + T-cell effector function inducing T-cell tolerance.
  • the expression of PD-L1 is often associated with tumor aggressiveness and reduced survival in certain human cancers (see, e.g., Gao et al. (2009) Clin. Cancer Res.15(3):971-979).
  • Antibodies designed to block immune checkpoints can prevent T-cell anergy and break immune tolerance. Only a fraction of treated patients, however, exhibit clinical benefit, and those that do, often present with autoimmune-related toxicities (see, e.g., Ribas (2015) N. Engl. J. Med.373(16):1490-1492; and Topalian et al. (2012) N. Engl. J. Med.366(26):2443-2454).
  • an immunostimulatory bacterium containing a plasmid encoding an antibody or antibody fragment, such as an scFv or scFv-Fc, and others known in the art or described herein, against PD-1 or against PD-L1, will synergize with activation of immune cells to potentiate anti-tumor immunity. d.
  • CTLA-4 cytotoxic T-lymphocyte-associated protein 4
  • CD152 cluster of differentiation 152
  • CTLA-4 is another immune-inhibitory receptor that functions as an immune checkpoint, and downregulates immune responses.
  • CTLA-4 is constitutively expressed in regulatory T-cells (Tregs, or Tregs), and contributes to their inhibitory function, but is upregulated in conventional T-cells only after activation.
  • Tregs regulatory T-cells
  • CTLA-4 functions as an immune checkpoint by transmitting inhibitory signals to T- cells.
  • CTLA-4 is homologous to the T-cell co-stimulatory protein, CD28, and both molecules bind to CD80 (also known as B7-1 or B7.1) and CD86 (also known as B7- 2 or B7.2) ligands on antigen-presenting cells (APCs).
  • CD80 also known as B7-1 or B7.1
  • CD86 also known as B7- 2 or B7.2
  • APCs antigen-presenting cells
  • the binding of CTLA-4 to the ligands transmits an inhibitory signal to T-cells, whereas the binding of CD28 transmits a stimulatory signal.
  • CTLA-4 receptors are induced, which then outcompete CD28 receptors on T-cells, for binding to CD80 and CD86 ligands on the surfaces of APCs.
  • CTLA-4 binds to CD80 and CD86 with greater affinity and avidity than CD28, thus enabling it to outcompete CD28 for its ligands, resulting in the transmittal of inhibitory signals to T-cells, and an immune inhibitory response.
  • T-cell activation through the T-cell receptor and CD28 leads to increased expression of CTLA-4.
  • Optimal T-cell priming requires co-stimulatory signals resulting from the ligation of T-cell CD28 with CD80 and/or CD86. The blockade of CTLA-4 from binding to these ligands thus enhances T-cell priming, and allows for the induction of an anti-tumor immune response.
  • the immunostimulatory bacterial strains provided herein contain plasmids encoding anti-CTLA-4 antibodies, including fragments thereof, such as, but not limited to, anti-CTLA-4 scFvs (see, e.g., SEQ ID NO:403 for an exemplary human anti-CTLA-4 scFv fragment), and anti-CTLA-4 scFv-Fcs (see, e.g., SEQ ID NO:402, for an exemplary human anti-CTLA-4 scFv-Fc fragment; see, also, Example 20).
  • anti-CTLA-4 scFvs see, e.g., SEQ ID NO:403 for an exemplary human anti-CTLA-4 scFv fragment
  • anti-CTLA-4 scFv-Fcs see, e.g., SEQ ID NO:402 for an exemplary human anti-CTLA-4 scFv-Fc fragment; see, also, Example 20.
  • Exemplary immune checkpoint targets for which an scFv, or any other recombinant antibody fragment against them can be prepared, or are exemplified herein include, but are not limited to, those listed in the table below: 5.
  • Combinations of Immunomodulatory Proteins can have Synergistic Effects and/or Complementary Effects
  • Cytokines are powerful modulators of the anti-tumor immune response. Cytokine combinations are known to have profound synergistic effects on different immune compartments involving T-cells, NK cells, and myeloid cells (including dendritic cells and macrophages).
  • Cytokines are known to play major roles in antigen priming by dendritic cells, survival and proliferation of innate immune cells and antigen-specific T-cells, and the cytotoxic activity of NK and T-cells. Cytokine combinations must be properly chosen to maximize biological responses and enhance anti-tumor immunity. For example, in a murine model of hepatitis, IFN- ⁇ alone was found to enhance the CD8 + T-cell cytolytic function of virally infected cells, while IL- 15 alone enhanced the proliferation of activated lymphocytes. Together, they maximally suppressed hepatitis B (HBV) infection (see e.g., Di Scala et al. (2016) J. Virol.90(19):8563-8574).
  • HBV hepatitis B
  • combinations of the cytokines IL-15 + IL-18, and IL-15 + IL-21 were able to enhance the production of IFN- ⁇ from human NK and T-cells (see, e.g., Strengell et al. (2003) J. Immunol.170(11):5464-5469).
  • IL-2 + IL-18 synergized to enhance IFN- ⁇ production and increase cytolytic function of CD4 + T-cells, CD8 + T cells, and NK lymphocytes (see, e.g., Son et al. (2001) Cancer Res.61(3):884-888).
  • IL-12 and IL-18 were found to synergize to promote antigen-CD3 T-cell ligation-independent production of IFN- ⁇ from human T-cells (see, e.g., Tominaga et al. (2000) Int. Immunol.12(2):151-160). Combinations of cytokines are powerful enhancers of T-cell function, but the FDA- approved anti-cancer cytokines are too toxic to be dosed systemically and are thus rarely used, and combinations of systemically-administered cytokines only compound the toxicity (see, e.g., Conlon et al. (2019) J. Interferon Cytokine Res.39(1):6-21).
  • immunostimulatory bacteria provided herein solve these problems.
  • immunostimulatory bacteria containing plasmids encoding multiple therapeutic products, such as immunomodulatory proteins, that allow for tumor- specific delivery of cytokine combinations, and/or combinations with other therapeutic products, such as the inducers of type I interferon discussed herein, and others, including co-stimulatory molecules, chemokines, and antibodies and fragments thereof.
  • These immunostimulatory bacteria achieve powerful and synergistic immuno-activation without the systemic toxicities and pharmacokinetic (PK) liabilities associated with direct IV administration of the cytokines and other therapeutic products.
  • PK pharmacokinetic
  • Combinations of therapeutic products that can be encoded on the plasmids in the immunostimulatory bacteria provided herein include, but are not limited to, for example, two or more cytokines; one or more cytokines and an inducer of type I IFN (e.g., STING, IRF3, IRF7, MDA5, RIG-I, and constitutively active, GOF variants thereof), and/or a co-stimulatory molecule (e.g., 4-1BBL, 4-1BBL ⁇ cyt, and other variants of 4-1BBL discussed herein); a TGF- ⁇ decoy receptor and one or more cytokines; a TGF- ⁇ decoy receptor and an inducer of type I IFN; a TGF- ⁇ decoy receptor, one or more cytokines, and/or an inducer of type I IFN, and/or a co- stimulatory molecule; an antibody (e.g., against an immune checkpoint, such as CTLA-4) and one or more cytokines
  • the multiple therapeutic product expression cassettes can include single promoter constructs and/or dual/multiple promoter constructs, as well as post-transcriptional regulatory elements, and other regulatory elements, such as enhancers, polyadenylation signals, terminators, signal peptides, etc.
  • the nucleic acid sequences can be codon optimized to increase protein expression, and generally, are under control of a eukaryotic promoter. Particular constructs and details thereof are described elsewhere herein.
  • immunostimulatory bacteria include those that contain plasmids encoding immunostimulatory proteins (e.g., cytokines, chemokines, co- stimulatory molecules), and/or gene products with gain-of-function mutations that increase immune responses in the tumor microenvironment (e.g., cytosolic DNA/RNA sensors that induce type I IFN), and/or antibodies and fragments thereof, and/or other therapeutic products that enhance the anti-tumor response, such as TGF- ⁇ and/or IL-6 decoy receptors, and/or TGF- ⁇ antagonizing polypeptides.
  • immunostimulatory proteins e.g., cytokines, chemokines, co- stimulatory molecules
  • gene products with gain-of-function mutations that increase immune responses in the tumor microenvironment
  • cytosolic DNA/RNA sensors that induce type I IFN e.g., cytosolic DNA/RNA sensors that induce type I IFN
  • antibodies and fragments thereof e.g., antibodies and fragments thereof, and/
  • immunostimulatory bacteria that encode the cytokines, gain-of-function products/type I IFN pathway proteins, and/or chemokines, and/or co-stimulatory molecules, and/or antibodies and fragments thereof, such as single-chain antibodies, and other therapeutic products discussed herein, include the immunostimulatory bacteria that preferentially infiltrate the tumor microenvironment, tumors, and tumor-resident immune cells.
  • the immunostimulatory bacteria also include those in which the genome is modified so that they induce less cell death in tumor-resident immune cells, whereby the immunostimulatory bacteria accumulate in tumor-resident myeloid cells, to achieve high level ectopic expression of multiplexed genetic payloads in the target cells, and deliver the therapeutic products/immunomodulatory proteins to the tumor microenvironment (TME), to stimulate the immune response against the tumor.
  • TEE tumor microenvironment
  • the immunostimulatory bacteria provided herein include up to about 8 or 8 modifications as described herein, including, but not limited to, adenosine auxotrophy, csgD-, pagP-, msbB-, flagellin- (fliC-/fljB-), purI-, ansB-, asd-, and any other modifications described herein or known to improve targeting to, or accumulation in, the tumor microenvironment and/or tumor-resident myeloid cells, or to improve safety and tolerability (allowing for a higher dose), reduce the immunosuppressive cytokine profile, improve T-cell quality and function, limit replication in healthy tissues, eliminate biofilms, and improve the anti-tumor immune response, or to impart any of the desirable and advantageous properties discussed elsewhere herein.
  • adenosine auxotrophy csgD-, pagP-, msbB-, flagellin- (fliC-/fljB-), purI-, ansB-, asd-
  • the immunostimulatory bacteria further can encode other therapeutic products, such as a tumor antigen from the subject’s tumor, to enhance the response against the particular tumor.
  • a tumor antigen from the subject for example, a tumor antigen from the subject’s tumor.
  • Any of the immunostimulatory bacteria provided herein and described above and below can be modified to encode the therapeutic products, such as cytokines, chemokines, co-stimulatory molecules, and gain-of-function type I IFN pathway product(s).
  • the therapeutic products are encoded on a plasmid under control of a promoter recognized by the host, and any other desired regulatory sequences recognized in a eukaryotic, such as a human, or other animal, or mammalian, subject.
  • the nucleic acid encoding the product is under the control of an RNA polymerase II promoter.
  • any of the bacteria described herein for modification such as any of the strains of Salmonella, Shigella, E. coli, Bifidobacteriae, Rickettsia, Vibrio, Listeria, Klebsiella, Bordetella, Neisseria, Aeromonas, Francisella, Cholera, Corynebacterium, Citrobacter, Chlamydia, Haemophilus, Brucella, Mycobacterium, Mycoplasma, Legionella, Rhodococcus, Pseudomonas, Helicobacter, Bacillus, and Erysipelothrix, or an attenuated strain thereof, or a modified strain thereof, can be modified by introducing a plasmid containing, or encoding on a plasmid in the bacteria, nucleic acid encoding the therapeutic product(s) under control of an RNA polymerase promoter recognized by the host.
  • the therapeutic products are expressed in the infected subject’s cells.
  • the immunostimulatory bacteria include those that are modified, as described herein, to accumulate in, or to preferentially infect, tumors, the TME and/or tumor-resident myeloid cells.
  • immunostimulatory bacteria that encode gain-of-function products leading to the expression of, or the constitutive expression of, type I interferon (IFN), such as IFN-beta, and/or other therapeutic products as discussed herein further are modified to have reduced ability or no ability to infect epithelial cells, but are able to infect phagocytic cells, including tumor-resident immune cells, and/or the immunostimulatory bacteria are modified so that they do not kill the infected phagocytic cells.
  • IFN type I interferon
  • genes involved in the SPI-1 pathway, and flagella activate the inflammasome in phagocytic cells (immune cells), triggering pyroptosis.
  • Knocking out SPI-1 genes and genes that encode flagella decreases or eliminates pyroptosis of phagocytic cells, and also, eliminates infection of epithelial cells, resulting in increased infection of phagocytic cells.
  • immunostimulatory bacteria that accumulate in phagocytic cells, particularly tumor-resident immune cells, such as, for example, myeloid-derived suppresser cells (MDSCs), tumor-associated macrophages (TAMs), and dendritic cells (DCs), in which they express the genetic payloads/therapeutic products encoded on plasmids that are controlled by eukaryotic promoters, such as those recognized by RNA polymerase II, and include other eukaryotic regulatory signals, as discussed herein.
  • Expressed therapeutic products include those that evoke immune responses, such as through pathways that increase or induce type I interferons, which increase the host response in the tumor microenvironment.
  • the immunostimulatory bacteria also can encode immunostimulatory proteins, such as IL-2 and/or other cytokines, and/or other immunostimulatory proteins and therapeutic products, as discussed herein, further enhancing the immune response in the tumor microenvironment.
  • the immunostimulatory bacteria can encode products, referred to as cytosolic DNA/RNA sensors, that evoke immune responses when exposed to nucleic acids, such as RNA, DNA, nucleotides, dinucleotides, cyclic nucleotides, cyclic dinucleotides, and other such molecules, in the cytosol of cells.
  • the immunostimulatory bacteria herein encode modified therapeutic products that constitutively evoke immune responses, and do not require the presence of the DNA/RNA in the cytosol.
  • the therapeutic products contemplated herein include modified forms of these cytosolic DNA/RNA sensors, that have constitutive activity or increased activity (i.e., gain-of-function products), such that type I interferon(s) is/are expressed or produced in the absence of nucleotides, dinucleotides, cyclic nucleotides, cyclic dinucleotides, and other such ligands, in the cytosol of cells.
  • expression of these modified products in cells, particularly in tumor cells, including tumor-resident immune cells leads to constitutive expression of type I interferons, including interferon- ⁇ , in the tumor microenvironment.
  • the immunostimulatory bacteria that express these gain-of-function products accumulate in or preferentially infect tumor cells/the TME/tumor-resident immune cells, the therapeutic products are expressed in the tumor microenvironment, resulting in increased immune responses in the tumor microenvironment.
  • Exemplary gene products that can be encoded in the immunostimulatory bacteria and other vehicles include, but are not limited to, proteins that sense or are involved in innate pathways that recognize cytosolic DNA/RNA and activate type I interferon production.
  • Proteins involved in innate DNA/RNA recognition that activate type I interferon include, but are not limited to: STING, RIG-I, MDA5, IRF3, IRF7, TRIM56, RIP1/RIPK1, Sec5/EXOC2, TRAF2, TRAF3, TRAF6, STAT1, LGP2/DHX58, DDX3/DDX3X, DHX9/DDX9, DDX1, DDX21, DHX15/DDX15, DHX33/DDX33, DHX36/DDX36, DDX60, and SNRNP200.
  • Gain-of-function mutations in any of these proteins that result in constitutive type I interferon expression are known, or can be identified, and the mutants can be delivered by the immunostimulatory bacteria to the tumor microenvironment, such as by infection of phagocytic cells, or by targeting and binding to tumor cells.
  • the gain-of-function mutations include those identified from individuals with disorders resulting from constitutive type I interferon expression. Exemplary of gain- of-function products are those that occur in subjects with interferonopathies.
  • mutations can be identified by screening, to generate gain-of-function products as well.
  • the nucleic acids encoding the therapeutic products further can be modified to improve properties for expression.
  • Modifications include, for example, codon optimization to increase transcriptional efficiency in a mammalian, particularly human, subject, such as reduction of GC content or CpG dinucleotide content, removal of cryptic splicing sites, adding or removing (generally removing) CpG islands to improve expression in eukaryotic cells, and replacement of TATA box and/or terminal signals to increase transcriptional efficiency.
  • Codons can be optimized for increasing translation efficiency by altering codon usage bias, decreasing GC content, decreasing mRNA secondary structure, removing premature PolyA sites, removing RNA instability motifs (ARE), reducing stable free energy of mRNA, modifying internal chi sites and ribosomal binding sites, and reducing RNA secondary structures.
  • codon optimization to increase transcriptional efficiency in a mammalian, particularly human, subject, such as reduction of GC content or CpG dinucleotide content, removal of cryptic splicing sites, adding or removing (generally removing) CpG islands to improve expression in
  • type I interferon induction pathways mediated by host recognition of cytosolic nucleic acids, such as single-stranded and double-stranded RNA, cyclic di-nucleotides (CDNs), and other such forms of nucleic acids, induce type I IFN.
  • CDNs cyclic di-nucleotides
  • TLR Toll-Like Receptor
  • RNA helicases including retinoic acid- inducible gene I (RIG-I), melanoma differentiation-associated gene 5 (MDA5), and through IFN- ⁇ promoter stimulator 1 (IPS-1) adaptor protein-mediated phosphorylation of the IRF3 transcription factor, leading to induction of IFN- ⁇ (see, e.g., Ireton and Gale (2011) Viruses 3(6):906-919).
  • IPS-1 IFN- ⁇ promoter stimulator 1
  • proteins in these pathways can be modified, or can exist as variants, that result in constitutive expression of type I interferons (also referred to as interferon type 1), which include IFN- ⁇ and IFN- ⁇ .
  • modified STING polypeptides provided herein, which include those with mutations that result in constitutive expression of the type I interferons so that the interferons are expressed in the absence of induction, and also, chimeric STING proteins, such as those in which the a C- terminal tail (CTT) portion is replaced with a CTT portion from a STING protein from a second species, wherein the STING protein of the second species has lower NF- ⁇ B signaling activity than the NF- ⁇ B signaling activity of human STING, and the TRAF6 binding site in the CTT optionally is deleted.
  • CTT C- terminal tail
  • Immunostimulatory Bacteria that Deliver Combination Therapies The immunostimulatory bacteria herein can be used to provide more than one therapeutic product, particularly those that are for anti-cancer therapy. In general, the products are complementary products to enhance and re-program the anti-tumor immune response.
  • the immunostimulatory bacteria by virtue of the genomic modifications described herein, particularly the combination of several or all of asd-, flagellin- (fliC-/fljB-), pagP-, csgD-, purI-, adenosine auxotrophy, msbB-, ansB-, and any other modifications described elsewhere herein or known to those of skill in the art, accumulate in the tumor microenvironment (TME) and infect tumor-resident immune cells (myeloid cells).
  • TEE tumor microenvironment
  • myeloid cells myeloid cells
  • the immunostimulatory bacteria contain plasmids, encoding complementary therapeutic products, under control of a promoter or promoters recognized by the host, and any other desired regulatory sequences recognized in a eukaryotic, such as a human, or other animal, or mammalian, subject, to effect expression of the encoded products, and, also, secretion of the products.
  • the immunostimulatory bacteria accumulate in the TME, particularly in tumor-resident immune cells, including myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages (TAMs), and dendritic cells (DCs), where the encoded therapeutic products are expressed and then secreted into the tumor microenvironment to achieve an anti-tumor effect.
  • MDSCs myeloid-derived suppressor cells
  • TAMs tumor-associated macrophages
  • DCs dendritic cells
  • the anti-tumor effect can be enhanced by virtue of interactions of the various products with the host immune system.
  • the immunostimulatory bacteria containing plasmids encoding therapeutic products, with a single promoter and open reading frame (ORF)
  • ORF open reading frame
  • the immunostimulatory bacteria can express two (or more) proteins through the use of viral internal ribosomal entry sites (IRES), which are cap-independent, or through translational read-through of 2A peptides (e.g., T2A, P2A, E2A, or F2A), and subsequent self- cleavage into equally expressed co-proteins.
  • IRS viral internal ribosomal entry sites
  • the genetic payloads/therapeutic products can be expressed using dual or multiple promoter constructs, where each protein is expressed under the control of a separate promoter.
  • the nucleic acids encoding the therapeutic products are under the control of RNA polymerase II promoters.
  • promoters include, but are not limited to EF-1 ⁇ , CMV, SV40, UBC, CBA, PGK, GUSB, GAPDH, EIF41A, CAG, CD68, and synthetic MND promoters.
  • the plasmids can contain other regulatory elements, such as post- transcriptional regulatory elements (PREs; e.g., WPRE, HPRE), polyadenylation signal sequences, terminators, enhancers, secretion signals (also known as signal peptides/sequences, leader peptides/sequences), DNA nuclear targeting sequences (DTS), and other regulatory elements, described elsewhere herein or known to those of skill in the art, that can enhance or increase the expression and/or secretion of the encoded therapeutic products.
  • PREs post- transcriptional regulatory elements
  • the genetic payloads or therapeutic products encoded on the plasmids include immunostimulatory proteins, such as cytokines, chemokines, and co-stimulatory molecules; cytosolic DNA/RNA sensors that induce type I IFN and gain-of- function/constitutively active mutants/variants thereof; antibodies and fragments thereof; bi-specific T-cell engagers (BiTEs®); soluble TGF- ⁇ receptors that act as decoys for binding TGF- ⁇ , or TGF- ⁇ antagonizing polypeptides; IL-6 binding decoy receptors; interfering RNAs (e.g., siRNA, shRNA, miRNA); and other therapeutic products as discussed below and elsewhere herein, and as known in the art; and complementary combinations of all of the preceding therapeutic products.
  • immunostimulatory proteins such as cytokines, chemokines, and co-stimulatory molecules
  • cytosolic DNA/RNA sensors that induce type I IFN and gain-of- function/constitutively
  • the cytokines can be encoded on the plasmid within the immunostimulatory bacteria, with a membrane anchoring motif, such as a transmembrane domain, and a collagen-binding domain.
  • the immunostimulatory proteins, including cytokines, chemokines, and co- stimulatory molecules, that can be encoded on the plasmids include, but are not limited to, IL-2, IL-7, IL-12p70 (IL-12p40 + IL-12p35), IL-15, IL-15/IL-15R ⁇ chain complex, IL-18, IL-21, IL-23, IL-36 gamma, interferon- ⁇ , interferon- ⁇ , IL-2 that has attenuated binding to IL-2Ra, IL-2 that is modified so that it does not bind to IL-2Ra, CXCL9, CXCL10, CXCL11, CCL3, CCL4, CCL5, proteins that are involved in or that effect or potentiate the recruitment and/or persistence
  • the immunostimulatory proteins also include truncated co- stimulatory molecules, such as, for example, 4-1BBL, CD80, CD86, CD27L, B7RP1 and OX40L, with a full-length cytoplasmic domain, or with a truncated, or partial, or partial with modifications to ensure proper orientation, cytoplasmic domain deletion, for expression on an antigen-presenting cell (APC), where the truncated gene product is capable of constitutive immunostimulatory signaling to a T-cell through co- stimulatory receptor engagement, and is unable to counter-regulatory signal to the APC due to a deleted cytoplasmic domain.
  • APC antigen-presenting cell
  • the cytosolic DNA/RNA sensors, that induce or activate type I IFN production include, but are not limited to, STING, RIG-I, MDA5, IRF3, IRF5, and IRF7, and gain-of-function (GOF) or constitutively active variants thereof.
  • Other proteins involved in the recognition of DNA/RNA that activate type I IFN responses, that can be mutated to generate constitutive type I IFN expression and can be encoded on the plasmids include, but are not limited to, TRIM56, RIP1, Sec5, TRAF2, TRAF3, TRAF6, STAT1, LGP2, DDX3, DHX9, DDX1, DDX21, DHX15, DHX33, DHX36, DDX60, and SNRNP200.
  • therapeutic products that can be encoded on the plasmids delivered by the immunostimulatory bacteria herein, or that can be co-administered with the bacteria, that enhance or increase the anti-tumor response, include, but are not limited to, antibodies and fragments thereof, for example, TGF- ⁇ inhibitory antibodies; anti- IL-6 antibodies; antibodies against checkpoint inhibitors, such as PD-1, PD-L1, and CTLA-4; and antibodies against, or inhibitors of, VEGF, CD73, CD38, Siglec-15, EGFR, Her2, Mesothelin, and BCMA.
  • TGF- ⁇ inhibitory antibodies include, but are not limited to, antibodies and fragments thereof, for example, TGF- ⁇ inhibitory antibodies; anti- IL-6 antibodies; antibodies against checkpoint inhibitors, such as PD-1, PD-L1, and CTLA-4; and antibodies against, or inhibitors of, VEGF, CD73, CD38, Siglec-15, EGFR, Her2, Mesothelin, and BCMA.
  • bispecific T-cell engagers BiTEs®
  • IL-6 binding decoy receptors TGF-beta binding decoy receptors
  • TGF-beta polypeptide antagonists TGF-beta polypeptide antagonists
  • Any of these antibodies, inhibitors, or decoy receptors can be co-administered with the immunostimulatory bacteria herein.
  • PARP poly (ADP)-ribose polymerase) inhibitors, histone deacetylase (HDAC) inhibitors and/or chemotherapy, also can be co-administered with any of the therapeutic products listed above, alone or in any combination.
  • Exemplary of complementary combinations of therapeutic products that can be encoded on the plasmids in the immunostimulatory bacteria herein include, but are not limited to: IL-2 and IL-12p70; IL-2 and IL-21; IL-2, IL-12p70, and a STING GOF variant; IL-2, IL-21, and a STING GOF variant; IL-2, IL-12p70, a STING GOF variant, and 4-1BBL (including 4-1BBL ⁇ cyt); and IL-2, IL-21, a STING GOF variant, and 4-1BBL (including 4-1BBL ⁇ cyt); IL-15/IL-15R ⁇ and a STING GOF variant; IL-15/IL-15R ⁇ , a STING GOF variant, and 4-1BBL (including 4-1BBL ⁇ cyt); IL-15/IL-15R ⁇ and a STING GOF variant; IL-15/IL-15R ⁇ , a STING GOF variant, and 4-1B
  • the 4-1BBL molecule can be a full- length protein (see, e.g., SEQ ID NOs:389 and 393, for human and mouse 4-1BBL, respectively); a 4-1BBL variant with the cytoplasmic domain deleted (4-1BBL ⁇ cyt; see e.g., SEQ ID NOs:390 and 394, for human and murine 4-1BBL ⁇ cyt, respectively); a 4-1BBL variant with a truncated (i.e., not fully deleted) cytoplasmic domain (4-1BBLcyt trunc; see, e.g., SEQ ID NOs:391-392 and SEQ ID NOs:395-396, for exemplary human and mouse 4-1BBLcyt trunc variants); or a 4-1BBL molecule with a modified cytoplasmic domain, in which one or more Ser residues, which act as phosphorylation sites, are replaced at an appropriate locus or loci, such as
  • an anti-CTLA-4 antibody can include an anti-CTLA-4 antibody fragment, such as an anti-CTLA-4 scFv (see, e.g., SEQ ID NOs:403 and 404, for exemplary human and mouse anti-CTLA-4 scFv fragments, respectively), or an anti-CTLA-4 scFv-Fc (see, e.g., SEQ ID NOs:402 and 405, for exemplary human and mouse anti-CTLA-4 scFv- Fc fragments, respectively).
  • an anti-CTLA-4 antibody fragment such as an anti-CTLA-4 scFv (see, e.g., SEQ ID NOs:403 and 404, for exemplary human and mouse anti-CTLA-4 scFv fragments, respectively), or an anti-CTLA-4 scFv-Fc (see, e.g., SEQ ID NOs:402 and 405, for exemplary human and mouse anti-CTLA-4 scFv- Fc fragments,
  • a TGF- ⁇ receptor decoy can be replaced by other TGF-beta polypeptide antagonists, that can bind and remove TGF- ⁇ from the tumor microenvironment, including, for example, anti-TGF-beta antibodies or antibody fragments, anti-TGF-beta receptor antibodies or antibody fragments, and soluble TGF-beta antagonist polypeptides.
  • TGF-beta polypeptide antagonists that can bind and remove TGF- ⁇ from the tumor microenvironment, including, for example, anti-TGF-beta antibodies or antibody fragments, anti-TGF-beta receptor antibodies or antibody fragments, and soluble TGF-beta antagonist polypeptides.
  • TGF- ⁇ decoy receptor can be replaced with a TGF- ⁇ antagonizing polypeptide.
  • TGF- ⁇ decoy receptors are any that act as decoys for binding TGF- ⁇ to remove it, or are TGF- ⁇ antagonizing polypeptides (e.g., anti-TGF-beta antibodies or antibody fragments, and anti-TGF-beta receptor antibodies or antibody fragments).
  • the STING protein or other DNA/RNA sensor that induces or activates type I IFN production, can be a GOF/constitutively active variant, or can be the wild-type protein, including the modified STING polypeptides and chimeric STING polypeptides described and provided herein.
  • any of the complementary combinations above also can be administered in combination with any one or more of: an anti-PD-1 antibody, an anti-CTLA-4 antibody, an anti-PD-L1 antibody, an anti-IL-6 antibody, an anti-Siglec-15 antibody, an anti-VEGF antibody, an anti-CD73 antibody, an anti-CD38 antibody, an anti-EGFR antibody, an anti-Her2 antibody, an anti-Mesothelin antibody, an anti- BCMA antibody, and antibody fragments thereof, as well as PARP inhibitors, HDAC inhibitors, or chemotherapy, and combinations thereof.
  • the plasmids and immunostimulatory bacteria provided herein encode combinations of therapeutic payloads. These include combinations of nucleic acid encoding any or all of the products listed in the table above.
  • Combinations of complementary payloads were assessed, and exemplary combinations and their effects are described in the Examples.
  • combinations of the payloads can induce a strong secretion of CXCL10 by bone marrow dendritic cells (BMDCs).
  • BMDCs bone marrow dendritic cells
  • Combining IL-36 ⁇ with IL-12p70 and STING R284G tazCTT led to higher secretion of CXCL10 and IFN- ⁇ by BMDCs (see, Example 26).
  • cytokines IL-12p70, IL-15, IL-21, and IL-36 ⁇
  • 4-1BB engagement activate T-cells to secrete high levels of IFN- ⁇ , with and without TCR stimulation by an anti-CD3 ⁇ agonistic antibody, for CD4 + and CD8 + T-cells.
  • STING variants described herein as well as IL-12 can increase antigen specific activation of human CD8 + T-cells.
  • Example 24 also showed, in a mouse (mu) model of colorectal carcinoma, that immunostimulatory bacterial strains, expressing IL-15, or the combination of 4-1BBL ⁇ cyt + IL-12 more potently inhibit tumor growth inhibition that the same strains expressing 4-1BBL( ⁇ cyt) or IL-12 alone, and result in a high complete response rate (50% cure rate). Other combinations also were tested and shown to have potent anti-tumor activity in vivo.
  • Combinations of payloads can include a co-stimulatory molecule, such as an OX40L polypeptide, or a 4-1BBL polypeptide, or one of the cytoplasmic deleted or truncated variants thereof, and/or the modified forms thereof described and exemplified herein; or an anti-immune checkpoint antibody or fragment thereof, such as an anti-CTLA-4 scFv-Fc or an anti-CTLA-4 scFv (see, Example 20 and SEQ ID NOs:402 and 403, respectively); one or more cytokines/chemokines, such as IL-12, IL-15, IL-18, IL-21, IL-23, IL-36 ⁇ , IFN- ⁇ , IFN- ⁇ 2, and CXCL10; TGF- ⁇ binding decoy receptors and other TGF-beta polypeptide antagonists, such as, for example, a human soluble TGF ⁇ receptor II fused with a human IgG1 Fc (hu sTGF ⁇
  • these payloads/products/polypeptides can be encoded as a polycistronic construct, under the control of a single promoter (i.e., a single promoter system) and, as required, other regulatory sequences, and also can include 2A polypeptides or other such polypeptides that result in the translation of individual products.
  • the payloads also can be expressed on plasmids containing two separate open reading frames (ORFs), each under the control of a different promoter (i.e., a dual promoter system).
  • ORFs open reading frames
  • Exemplary combinations of payloads, in the order they are encoded on a plasmid, and including the 2A peptide that is encoded in the polycistronic construct are set forth in the following table.
  • *4-1BBL the modified 4-1BBL with the cytoplasmic truncation and residue modifications to render the remaining cytoplasmic domain more positive to retain correct orientation with respect to the cell membrane.
  • **Chimeric STING STING with the West Devil CTT and the replacements R284G/N154S.
  • sTGF ⁇ RIIFc # type II receptor betaglycan.
  • the properties of the immunostimulatory bacteria provided herein, such as the accumulation in tumor-resident myeloid cells, and in the TME, and the combinations of products/payloads that can be expressed, can be selected to cover the cancer immunity cycle.
  • a skilled person can identify other product payload combinations and other orders of the products as encoded on a polycistronic construct, that have immune-activating and/or immune suppressing effects, to enhance the anti-tumor activities of the immunostimulatory bacteria provided herein.
  • the immunostimulatory bacteria herein can be modified to encode one or more therapeutic products, including immunomodulatory proteins, that promote, or induce, or enhance an anti-tumor response.
  • the therapeutic product can be encoded on a plasmid in the bacterium, under the control of a eukaryotic promoter, such as a promoter recognized by RNA polymerase II, for expression in a eukaryotic subject, particularly the subject for whom the immunostimulatory bacterium is to be administered, such as a human.
  • a eukaryotic promoter such as a promoter recognized by RNA polymerase II
  • the nucleic acid encoding the therapeutic product(s) can include, in addition to the eukaryotic promoter, other regulatory signals for expression or trafficking in the cells, such as for secretion or expression on the surface of a cell.
  • Immunostimulatory proteins are those that, in the appropriate environment, such as a tumor microenvironment (TME), can promote, or participate in, or enhance an anti-tumor response in the subject to whom the immunostimulatory bacterium is administered.
  • Immunostimulatory proteins include, but are not limited to, cytokines, chemokines, and co-stimulatory molecules.
  • cytokines such as, but not limited to, IL-2, IL-7, IL-12, IL-12p70 (IL-12p40 + IL-12p35), IL-15, IL-15/IL-15R ⁇ chain complex, IL-18, IL-21, IL-23, IL-36 ⁇ , IL-2 that has attenuated binding to IL- 2Ra, IL-2 that is modified so that it does not bind to IL-2Ra, IFN- ⁇ , and IFN- ⁇ ; chemokines, such as, but not limited to, CCL3, CCL4, CCL5, CXCL9, CXCL10, and CXCL11; proteins that are involved in, or that effect or potentiate the recruitment and/or persistence of T-cells; and/or co-stimulatory molecules, such as, but not limited to, CD40, CD40L, OX40, OX40L, 4-1BB, 4-1BBL, 4-1BBL with a deletion of the cytoplasmic domain (4-1BBL ⁇ c
  • immunostimulatory proteins that are used for treatment of tumors or that can promote, enhance, or otherwise increase or evoke an anti-tumor response, known to those of skill in the art, are contemplated for encoding in the immunostimulatory bacteria provided herein.
  • Other therapeutic products, encoded by the immunostimulatory bacteria herein, include cytosolic DNA/RNA sensors that induce or activate type I interferon production, including STING, MDA5, RIG-I, IRF3, and IRF7, as well as gain-of- function and constitutively active variants thereof.
  • the constitutively active STING variants include those with the mutations V147L, N154S, V155M, C206Y, R281Q, and/or R284G, such as N154S/R284G, and others described herein and known in the art
  • the constitutively active IRF3 variants include those with the mutations S396D, S398D, S402D, T404D, and/or S405D, and others described herein and known in the art.
  • therapeutic products encoded by the immunostimulatory bacteria herein, include antibodies and antibody fragments, including single chain fragment variables (scFvs), Fab fragments, Fab’ fragments, F(ab’)2 fragments, Fv fragments, disulfide-linked Fvs (dsFvs), Fd fragments, Fd’ fragments, single-chain Fabs (scFabs), diabodies, anti-idiotypic (anti-Id) antibodies, synthetic antibodies, recombinantly produced antibodies, multi-specific antibodies (e.g., bi-specific antibodies), human antibodies, non-human antibodies, humanized antibodies, chimeric antibodies, and intrabodies, or antigen-binding fragments of any of the above.
  • scFvs single chain fragment variables
  • Fab fragments fragments
  • Fab’ fragments fragments
  • F(ab’)2 fragments fragments
  • dsFvs disulfide-linked Fvs
  • FdsFvs Fd fragments
  • Fd single
  • the antibodies can be directed against immune checkpoints, such as PD- 1, PD-L1, CTLA-4, IDO 1 and 2, CTNNB1 ( ⁇ -catenin), SIRP ⁇ , VISTA, and TREX- 1, and others known in the art or described herein, or against other targets such as TGF- ⁇ , VEGF, HER2, EGFR, STAT3, and IL-6, and other such targets whose inhibition improves the anti-tumor response.
  • the immunostimulatory bacteria also can encode RNAi, such as siRNA (shRNA and miRNA) against immune checkpoints, such as TREX1, and other targets whose inhibition, suppression, or disruption improves the anti-tumor response.
  • the immunostimulatory bacteria herein are engineered to encode and express one or more cytokines to stimulate the immune system, including, but not limited to, IL-2, IL-7, IL-12 (IL-12p70 (IL-12p40 + IL-12p35)), IL- 15 (and the IL-15:IL-15R alpha chain complex), IL-18, IL-21, IL-23, IL-36 gamma, IFN-alpha, and IFN-beta.
  • Cytokines stimulate immune effector cells and stromal cells at the tumor site, and enhance tumor cell recognition by cytotoxic cells.
  • the immunostimulatory bacteria can be engineered to encode and express chemokines, such as, for example, one or more of CCL3, CCL4, CCL5, CXCL9, CXCL10 and CXCL11.
  • chemokines such as, for example, one or more of CCL3, CCL4, CCL5, CXCL9, CXCL10 and CXCL11.
  • Complementary combinations of any of the therapeutic products can be encoded and delivered to the tumor microenvironment, to enhance the anti-tumor efficacy of the immunostimulatory bacteria.
  • Plasmids provided herein are designed to encode a therapeutic product, such as an immunostimulatory protein, that, when expressed in a mammalian subject, confers or contributes to anti-tumor immunity in the tumor microenvironment; the immunostimulatory protein or other therapeutic product is encoded on a plasmid in the bacterium under control of a eukaryotic promoter, such as a promoter that is recognized by RNA polymerase II (RNAP II). Generally the promoter is a constitutive promoter, such as a late eukaryotic virus promoter.
  • Exemplary promoters include, but are not limited to, a cytomegalovirus (CMV) promoter, an elongation factor-1 alpha (EF-1 ⁇ ) promoter, a ubiquitin C (UBC) promoter, a simian virus 40 (SV40) early promoter, a phosphoglycerate kinase 1 (PGK) promoter, a chicken ⁇ - actin (CBA) promoter and its derivative promoters CAGG or CAG, a ⁇ -glucuronidase (GUSB) promoter, the MND promoter (a synthetic promoter that contains the U3 region of a modified MoMuLV (Moloney murine leukemia virus) LTR with myeloproliferative sarcoma virus enhancer and deleted negative control region), a eukaryotic initiation factor 4A-I (EIF4A1) promoter, a CD68 promoter, and a GAPDH promoter, among others (see, e.g., Powell e
  • the CAG promoter consists of: (C) the cytomegalovirus (CMV) early enhancer element; (A) the promoter, the first exon, and the first intron of chicken beta-actin gene; and (G) the splice acceptor of the rabbit beta-globin gene.
  • C cytomegalovirus
  • A the promoter, the first exon, and the first intron of chicken beta-actin gene
  • G the splice acceptor of the rabbit beta-globin gene.
  • MND is a synthetic promoter that contains the U3 region of a modified MoMuLV (Moloney murine leukemia virus) LTR with myeloproliferative sarcoma virus enhancer and deleted negative control region (murine leukemia virus-derived MND promoter (myeloproliferative sarcoma virus enhancer, negative control region deleted, dl587rev primer-binding site substituted); see, e.g., Li et al. (2010) J. Neurosci. Methods 189:56-64). Two or more of these promoters can be encoded in multiple open reading frames (ORFs) on the plasmid.
  • ORFs open reading frames
  • promoters including, but not limited to, CMV, contain multiple cAMP response element binding protein (CREB) sites.
  • CREB cAMP response element binding protein
  • the plasmids can include multiple promoters, including bacterial promoters, such as for expression of asd, and eukaryotic promoters for expression of therapeutic products.
  • Internal ribosome entry site (IRES) sequences have been used to separate two coding sequences under control of a single promoter, however, the expression level of the second protein can be reduced compared to the first protein, and the length of the IRES sequence can be prohibitive in certain cases, such as when using viruses with small packaging capacities.
  • the discovery of short ( ⁇ 18-22 amino acid long), virus-derived peptide sequences, known as 2A peptides, that mediate a ribosome-skipping event, enables the generation of multiple separate peptide products, at similar levels, from a single mRNA.
  • the 2A peptide coding sequence is included between the polypeptide- encoding transgenes (see, e.g., Daniels et al.
  • IRES and 2A peptides use different mechanisms for co-expression of multiple genes in one transcript.
  • the gene directly downstream of the promoter is translated by the canonical cap-dependent mechanism, and those downstream of the IRES are translated by a cap-independent mechanism, which has a lower translation efficiency than the cap-dependent mechanism, resulting in unbalanced expression, with lower expression of the IRES-driven gene (see, e.g., Chng et al. (2015) mAbs 7(2):403-412).
  • 2A linked genes are translated in one open reading frame (ORF).
  • the cleavage of proteins separated by a 2A sequence occurs co-translationally, in an unconventional process, where a peptide bond often fails to form (i.e., the peptide bond is “skipped”) between the C-terminal glycine and proline in the 2A peptide. Despite this, translation proceeds, and two distinct proteins are produced in equal amounts. A short stretch, coding for approximately 20 amino acids, of the 2A peptide sequence, is sufficient to cause the bond-skipping. If the bond skipping does not occur, however, a fusion protein is generated that will not subsequently cleave (see, e.g., Daniels et al. (2014) PLoS One 9(6):e100637).
  • T2A SEQ ID NO:327
  • P2A SEQ ID NO:328
  • E2A SEQ ID NO:329
  • F2A SEQ ID NO:330
  • Cleavage efficiency and enhanced protein expression can often be improved through the use of upstream viral cleavage sequences, such as, but not limited to, the peptide furin cleavage sequence, RRKR, as well as by inserting GSG and SGS peptide linkers, a V5 epitope tag (GKPUPNPLLGLDST), or a 3xFlag epitope tag immediately preceding the 2A peptide (see, e.g., Chng et al. (2015) mAbs 7(2):403-412).
  • upstream viral cleavage sequences such as, but not limited to, the peptide furin cleavage sequence, RRKR, as well as by inserting GSG and SGS peptide linkers, a V5 epitope tag (GKPUPNPLLGLDST), or a 3xFlag epitope tag immediately preceding the 2A peptide (see, e.g., Chng et al. (2015) mAbs 7(2):403-
  • the immunostimulatory bacteria herein containing plasmids encoding therapeutic products, such as immunomodulatory proteins, with a single promoter and ORF, can express two or more proteins through the use of viral internal ribosomal entry sites (IRES), which are cap-independent, or through translational read-through of 2A peptides, and subsequent self-cleavage into equally expressed co-proteins.
  • IRS viral internal ribosomal entry sites
  • the plasmids can contain other regulatory elements, as discussed below and elsewhere herein.
  • an exemplary construct is CMV-muIL-2 CO_T2A_muIFN- ⁇ 2-WPRE, where codon optimized murine IL-2 is co-expressed with murine IFN- ⁇ 2, using a CMV promoter, and a T2A peptide. Additionally, a Woodchuck Hepatitis Virus (WHP) Posttranscriptional Regulatory Element (WPRE) is included, to enhance expression.
  • WP Woodchuck Hepatitis Virus
  • WPRE Woodchuck Hepatitis Virus
  • a 2A sequence is flanked by the first two proteins, which are expressed under the control of a first promoter, e.g., CMV, and a third protein is encoded under the control of a second promoter, e.g., EF-1 ⁇ .
  • a first promoter e.g., CMV
  • a second promoter e.g., EF-1 ⁇ .
  • Exemplary of such a construct is CMV-muIL-15R ⁇ /IL-15sc_T2A_muSTING-R283G + EF-1 ⁇ -muIL-18- WPRE, where murine 15R ⁇ /IL-15sc and murine STING with the replacement R283G are co-expressed under control of a CMV promoter, using T2A, and murine IL-18 is expressed separately under control of an EF-1 ⁇ promoter.
  • This exemplary construct also includes a WPRE for enhanced expression.
  • the genetic payloads/therapeutic products can be expressed using dual or multiple promoter constructs, where each protein is expressed under the control of a separate promoter.
  • plasmids encoding therapeutic products can contain multiple promoters, each controlling an individual intact ORF with proper stop codon processing (i.e., dual/multiple promoter constructs); or multiple proteins can be expressed in a single ORF through the use of 2A peptides (i.e., single promoter constructs); or the plasmid can contain a mixture of single and dual/multiple promoter constructs, to express three or more proteins, as described above. 3. Regulatory Elements a.
  • regulatory elements may be employed that enhance the transcription and translation of the protein(s) of interest.
  • the post-transcriptional regulatory element (PRE) of woodchuck hepatitis virus (WPRE) when inserted in the 3’ untranslated region of the ORF, can enhance expression levels several fold (see, e.g., Zufferey et al. (1999) J. Virol. 73(4):2886-2892).
  • other such elements including, but not limited to, the Hepatitis B Virus PRE (HPRE), also can enhance expression.
  • the combination of these can be used at the 3’ ends of multiple ORFs to improve expression of multiple proteins on a single plasmid.
  • the PREs WPRE and HPRE are hepadnaviral cis-acting RNA elements that can increase the accumulation of cytoplasmic mRNA by promoting mRNA exportation from the nucleus, and can enhance post-transcriptional processing and stability.
  • b. Polyadenylation Signal Sequences and Terminators Other elements on the plasmid that can enhance protein expression include polyadenylation signal sequences and terminators. Polyadenylation is the post- transcriptional addition of a poly(A) tail to the 3’ end of an mRNA transcript, which is part of the process that produces mature mRNA for translation.
  • a terminator is a sequence that defines the end of a transcript, creating a free 3’ end, and initiates the release of the newly synthesized mRNA from the transcriptional machinery. The free 3’ end is then available for the addition of the poly(A) tail. Terminators are found downstream of the gene to be transcribed, and typically occur directly after any 3’ regulatory elements, such as the polyadenylation or poly(A) signal.
  • simian virus 40 SV40
  • human growth hormone hGH
  • bovine growth hormone BGH or bGH
  • rabbit beta-globin rbGlob
  • sequences such as the simian virus 40 poly A (SV40pA) or the bovine growth hormone poly A (bGHpA) signals, result in several-fold increased expression both in vitro and in vivo (see, e.g., Powell et al. (2015) Discov. Med.19(102):49–57).
  • Enhancers and enhancers are found upstream of the multiple cloning site (MCS) in a plasmid, and cooperate to determine the rate of transcription. Enhancers are sequences that bind activator proteins, in order to loop the DNA, and bring a specific promoter to the initiation complex, thus increasing the rate of transcription.
  • MCS multiple cloning site
  • the immunostimulatory bacteria herein contain plasmids that can comprise enhancer(s) to enhance the expression of the therapeutic products/proteins encoded on the plasmids. d.
  • a secretion signal also known as a signal sequence or peptide, a leader sequence or peptide, or a localization signal or sequence, is a short peptide at the N- terminus of a newly synthesized protein that is to be secreted.
  • Signal peptides promote a cell to translocate a protein, usually to the cellular membrane. The efficiency of protein secretion is strongly determined by the signal peptide.
  • the immunostimulatory bacteria herein contain plasmids that can comprise a signal peptide/secretion signal peptide, to facilitate and/or increase the expression or secretion of the encoded therapeutic product(s). e.
  • the plasmids in the immunostimulatory bacteria that encode the therapeutic products include genes and regulatory elements that are provided for expression of bacterial genes, and also for expression of complex polycistronic eukaryotic payloads.
  • the switch between such evolutionarily divergent organisms introduces challenges for proper functioning in prokaryotes and eukaryotes.
  • the bacteria are cultured in vitro, then administered to a eukaryotic subject, where the plasmids are delivered to cells, particularly to tumor-resident myeloid cells, in cancer subjects, where the payloads are expressed, processed and trafficked.
  • transcriptional leakiness from the eukaryotic promoter, such as the CMV promoter, in bacteria, combined with large eukaryotic genes and regulatory sequences, can result in reduced bacterial fitness that manifests as low injection stock viability, and reduced growth rate in broth culture.
  • the delivery plasmid was systematically modified to improve bacterial fitness, and to maintain or improve eukaryotic expression.
  • the possible exemplary negative impacts and solutions include, for example, the following: 1) cryptic bacterial promoter sequences encoded within the CMV promoter enhancer region were identified using PromoterHunter (available online at phisite.org/promoterhunter/; see, e.g., Klucar et al. (2010) Nucleic Acids Res.
  • the results, detailed in the Examples show that, when the expression cassette was reversed on the plasmid and the BBa_B0015 bacterial terminator was inserted after the coding region, and the T4 bacterial terminator was inserted downstream of the CMV promoter (see, e.g., Figure 14), there was an increase in the bacterial cell viability, a reduced doubling time, growth to a higher stationary OD 600 , and increased expression of the encoded payload in vitro, compared to the plasmid without the modifications.
  • the BBa_B0015 terminator is a composite terminator, in which a terminator derived from E.
  • plasmids in which the eukaryotic promoter, such as a viral promoter, is in the opposite orientation from the bacterial promoter, such as the bacterial promoter controlling expression of the exogenous asd gene on the plasmid.
  • the exogenous asd cassette (includes the regulatory sequences for expression and the exogenous asd gene, encoded on the plasmid in the asd- bacteria) is in the opposite orientation from the eukaryotic regulatory sequences and operatively linked payload-encoding nucleic acid.
  • constructs also include bacterial terminators flanking the payload expression cassette that includes the eukaryotic promoter, which reduces readthrough from bacterial promoters.
  • Figure 14 provides an exemplary construct configuration.
  • bacterial fitness if desired, can be improved by one or more of several strategies, including orienting expression cassettes including eukaryotic promoters in the opposite direction from those under the control of bacterial promoters, and the inclusion of bacterially-recognized terminators to terminate bacterial expression at strategic loci.
  • Plasmids are autonomously-replicating, extra-chromosomal, circular double- stranded DNA molecules that are maintained within bacteria by means of a replication origin. Copy number influences the plasmid stability. High copy number generally results in greater stability of the plasmid when the random partitioning occurs at cell division.
  • a high copy number of plasmids generally decreases the growth rate, thus possibly allowing for bacterial cells with few plasmids to dominate the culture, since they grow faster. This can be ameliorated by using gene attenuation and gene dosing strategies, that limit the expression of certain genes on the plasmid that can be toxic to the bacteria when present in high copy numbers.
  • the origin of replication also determines the plasmid’s compatibility, i.e., its ability to replicate in conjunction with another plasmid within the same bacterial cell. Plasmids that utilize the same replication system cannot co-exist in the same bacterial cell; they are said to belong to the same compatibility group.
  • Origins of replication contain sequences that are recognized as initiation sites of plasmid replication via DNA-dependent DNA polymerases (see, e.g., del Solar et al. (1998) Microbiol. Mol. Biol. Rev.62(2):434-464).
  • bacterial plasmid origins of replication include, but are not limited to, pMB1 derived origins, which have very high copy derivatives, such as pUC, and lower copy derivatives, such as pBR322, as well as ColE1, p15A, and pSC101, and other origins, which have low copy numbers.
  • pMB1 derived origins which have very high copy derivatives, such as pUC
  • pBR322 lower copy derivatives
  • ColE1, p15A, and pSC101 and other origins, which have low copy numbers.
  • Such origins are well-known to those of skill in the art.
  • the pUC19 origin results in copy numbers of 500-700 copies per cell.
  • the pBR322 origin has a known copy number of 15-20 copies per cell. These origins only vary by a single base pair.
  • the ColE1 origin copy number is 15-20, and derivatives, such as pBluescript, have copy numbers ranging from 300- 500.
  • the pSC101 origins confer a copy number of approximately 5.
  • Other low copy number vectors from which origins of replication can be obtained include, for example, pWSK29, pWKS30, pWSK129, and pWKS130 (see, e.g., Wang et al. (1991) Gene 100:195-199).
  • Medium to low copy number is less than 150, or less than 100.
  • Low copy number is less than 20, 25, or 30.
  • less than medium copy number is less than 150 copies
  • less than low copy number is less than about 25 or less than 25 copies
  • copy number refers to the average copies of plasmid per bacterium in a preparation.
  • Those of skill in the art can identify plasmids with low, medium, or high copy numbers. For example, one method to determine experimentally if the copy number is high or low is to perform a miniprep.
  • a high-copy plasmid should yield between 3-5 ⁇ g DNA per 1 ml LB culture; a low-copy plasmid will yield between 0.2-1 ⁇ g DNA per ml of LB culture.
  • Sequences of bacterial plasmids are well known (see, e.g., snapgene.com/resources/plasmid_files/basic_cloning_vectors/pBR322/).
  • Exemplary origins of replication, and their plasmid copy numbers are summarized in the table below.
  • High copy plasmids are selected for heterologous expression of proteins in vitro, because the gene dosage is increased relative to chromosomal genes, there are higher specific yields of protein, and for therapeutic bacteria, higher therapeutic dosages of encoded therapeutics. It is shown, herein, however, that for delivery of plasmids encoding therapeutic products (e.g., immunomodulatory proteins), such as by S.
  • therapeutic products e.g., immunomodulatory proteins
  • a high copy plasmid might be advantageous.
  • the requirement for bacteria to maintain the high copy plasmids can be a problem if the expressed molecule is toxic to the organism.
  • the metabolic requirements for maintaining these plasmids can come at a cost of replicative fitness in vivo.
  • Optimal plasmid copy number for delivery of therapeutic products can depend on the mechanism of attenuation of the strain engineered to deliver the plasmid. If needed, the skilled person, in view of the disclosure herein, can select an appropriate copy number for a particular immunostimulatory species and strain of bacteria. 5.
  • CpG Motifs and CpG Islands Unmethylated cytidine-phosphate-guanosine (CpG) motifs are prevalent in bacterial, but not in vertebrate, genomic DNA. Pathogenic DNA and synthetic oligodeoxynucleotides (ODNs) containing CpG motifs activate host defense mechanisms, leading to innate and acquired immune responses.
  • ODNs oligodeoxynucleotides
  • the unmethylated CpG motifs contain a central unmethylated CG dinucleotide plus flanking regions.
  • four distinct classes of CpG ODNs have been identified, based on differences in structure, and the nature of the immune response they induce.
  • K-type ODNs (also referred to as B-type) contain from 1 to 5 CpG motifs, typically on a phosphorothioate backbone.
  • D-type ODNs (also referred to as A-type) have a mixed phosphodiester/phosphorothioate backbone and have a single CpG motif, flanked by palindromic sequences that permit the formation of a stem-loop structure, as well as poly G motifs at the 3’ and 5’ ends.
  • C-type ODNs have a phosphorothioate backbone, and contain multiple palindromic CpG motifs that can form stem loop structures or dimers.
  • P-Class CpG ODNs have a phosphorothioate backbone, and contain multiple CpG motifs with double palindromes that can form hairpins at their GC-rich 3’ ends (see, e.g., Scheiermann et al. (2014) Vaccine 32(48):6377-6389).
  • the CpGs are encoded in the plasmid DNA; they can be introduced as a motif, or in a gene.
  • Toll-like receptors TLRs are key receptors for sensing pathogen-associated molecular patterns (PAMPs) and activating innate immunity against pathogens (see, e.g., Akira et al. (2001) Nat.
  • TLR9 recognizes hypomethylated CpG motifs in the DNA of prokaryotes that do not occur naturally in mammalian DNA (see, e.g., McKelvey et al. (2011) J. Autoimmun.36:76-86). Recognition of CpG motifs, upon phagocytosis of pathogens into endosomes in immune cell subsets, induces IRF7-dependent type I interferon signaling, and activates innate and adaptive immunity. Immunostimulatory bacteria, such as Salmonella species, such as S. typhimurium strains, carrying plasmids containing CpG islands or motifs, are provided herein.
  • bacterial plasmids that contain hypomethylated CpG islands can elicit innate and adaptive anti-tumor immune responses that, in combination with the therapeutic products encoded on the plasmid, such as immunostimulatory proteins and constitutively active variants of STING, IRF3, and other cytosolic DNA/RNA sensors, can have synergistic or enhanced anti- tumor activity.
  • the asd gene (SEQ ID NO:48) encodes a high frequency of hypomethylated CpG islands.
  • CpG motifs can be included in combination with any of the therapeutic products, described or apparent from the description herein, in the immunostimulatory bacteria, to thereby enhance or improve anti-tumor immune responses in a treated subject.
  • Immunostimulatory CpGs can be included in the plasmids, by including a nucleic acid, typically from a bacterial gene, that encodes a gene product, and also, by adding a nucleic acid that encodes CpG motifs.
  • the plasmids herein can include CpG motifs. Exemplary CpG motifs are known (see, e.g., U.S. Patent Nos.8,232,259, 8,426,375, and 8,241,844).
  • oligonucleotides that are between 10 and 100, 10 and 20, 10 and 30, 10 and 40, 10 and 50, or 10 and 75, base pairs long, with the general formula: (CpG)n, where n is the number of repeats. Generally, at least one or two repeats are used; non-CG bases can be interspersed.
  • CpG motifs for inducing an immune response by modulating TLRs, particularly TLR9.
  • the use of an asd deletion mutant, complemented with a functional asd gene on the plasmid allows for plasmid selection in vitro without the use of antibiotics, and allows for plasmid maintenance in vivo.
  • the asd gene complementation system provides for such selection/maintenance (see, e.g., Galán et al. (1990) Gene 94(1):29-35).
  • the use of the asd gene complementation system to maintain plasmids in the tumor microenvironment increases the potency of S.
  • DNA nuclear targeting sequences such as the SV40 DTS, mediate the translocation of DNA sequences through the nuclear pore complex. The mechanism of this transport is reported to be dependent on the binding of DNA binding proteins that contain nuclear localization sequences. The inclusion of a DTS on a plasmid to increase nuclear transport and expression has been demonstrated (see, e.g., Dean, D.A. et al. (1999) Exp.
  • Rho-independent or class I transcriptional terminators such as the T1 terminator of the rrnB gene of E. coli, contain sequences of DNA that form secondary structures that cause dissociation of the transcription elongation complex.
  • Transcriptional terminators are included in the plasmid in order to prevent expression of heterologous proteins by the S. typhimurium transcriptional machinery.
  • Plasmids used for transformation of Salmonella contain all or some of the following attributes: 1) one or more constitutive promoters for heterologous expression of proteins; 2) one or more human immunomodulatory expression cassettes; 3) a bacterial origin of replication and optimized plasmid copy number; 4) immunostimulatory CpG islands; 5) an asd gene selectable marker for plasmid maintenance and selection; 6) DNA nuclear targeting sequences; and 7) transcriptional terminators.
  • attributes 1) one or more constitutive promoters for heterologous expression of proteins; 2) one or more human immunomodulatory expression cassettes; 3) a bacterial origin of replication and optimized plasmid copy number; 4) immunostimulatory CpG islands; 5) an asd gene selectable marker for plasmid maintenance and selection; 6) DNA nuclear targeting sequences; and 7) transcriptional terminators.
  • PHARMACEUTICAL PRODUCTION, COMPOSITIONS, AND FORMULATIONS Provided herein are methods for manufacturing, and pharmaceutical compositions and formulations, containing any of the immunostimulatory bacteria provided herein and pharmaceutically acceptable excipients or additives.
  • the pharmaceutical compositions can be used in the treatment of diseases, such as hyperproliferative diseases or conditions, such as a tumor or cancer.
  • the immunostimulatory bacteria can be administered as a single agent therapy, or can be administered in a combination therapy with a further agent(s) or treatment(s).
  • Combination therapy includes combining therapy with the immunostimulatory bacteria and/or other delivery vehicles provided herein, with any other anti-cancer therapy or treatment, including, but not limited to, immunotherapies, such as CAR-T therapy and checkpoint inhibitors, radiation, surgery, chemotherapeutic agents, such as nucleoside analogs and platinum compounds, and cellular therapies.
  • immunotherapies such as CAR-T therapy and checkpoint inhibitors
  • radiation surgery
  • chemotherapeutic agents such as nucleoside analogs and platinum compounds
  • cellular therapies include, but not limited to, immunotherapies, such as CAR-T therapy and checkpoint inhibitors, radiation, surgery, chemotherapeutic agents, such as nucleoside analogs and platinum compounds, and cellular therapies.
  • the compositions can be formulated for single dosage administration, or for multiple dosage administration.
  • the agents can be formulated for direct administration.
  • the compositions can be provided as a liquid or dried formulation. 1. Manufacturing a.
  • the active ingredient of the immunotherapeutic described herein is composed of engineered self-replicating bacteria, the selected composition will be expanded into a series of cell banks that will be maintained for long-term storage and as the starting material for manufacturing of the drug substance.
  • Cell banks are produced under current good manufacturing practices (cGMP) in an appropriate manufacturing facility per the Code of Federal Regulations (CFR) 21 part 211, or other relevant regulatory authority.
  • cGMP current good manufacturing practices
  • CFR Code of Federal Regulations
  • a master cell bank is produced by sequential serial single colony isolation of the selected bacterial strain, to ensure no contaminants are present in the starting material.
  • a sterile culture vessel containing sterile media can be complex media, e.g., LB or MSB, or defined media, e.g., M9 supplemented with appropriate nutrients) is inoculated with a single well-isolated bacterial colony and the bacteria are allowed to replicate, e.g., by incubation at 37 °C with shaking. The bacteria are then prepared for cryopreservation by suspension in a solution containing a cryoprotective agent or agents.
  • cryoprotective agents include: proteins, such as human or bovine serum albumin, gelatin, and immunoglobulins; carbohydrates, including monosaccharides (e.g., galactose, D-mannose, sorbose, etc.) and their non-reducing derivatives (e.g., methylglucoside), disaccharides (trehalose, sucrose, and others), cyclodextrins, and polysaccharides (e.g., raffinose, maltodextrins, dextrans, etc.); amino-acids (e.g., glutamate, glycine, alanine, arginine or histidine, tryptophan, tyrosine, leucine, phenylalanine, etc.); methylamines, such as betaine; polyols, such as trihydric or higher sugar alcohols, e.g., glycerin, erythritol, glycerol, arabi
  • Cryopreservation solutions can include one or more cryoprotective agents in a solution that also can contain salts (e.g., sodium chloride, potassium chloride, magnesium sulfate), and/or buffering agents, such as sodium phosphate, tris(hydroxymethyl)aminomethane (TRIS), 4-(2-hydroxyethyl)-1- piperazineethanesulfonic acid (HEPES), and other such buffering agents known to those of skill in the art.
  • salts e.g., sodium chloride, potassium chloride, magnesium sulfate
  • buffering agents such as sodium phosphate, tris(hydroxymethyl)aminomethane (TRIS), 4-(2-hydroxyethyl)-1- piperazineethanesulfonic acid (HEPES), and other such buffering agents known to those of skill in the art.
  • Suspension of the bacteria in cryopreservation solution can be achieved either by addition of a concentrated cryoprotective agent or agents to the culture material to achieve a final concentration that preserves viability of the bacteria during the freezing and thawing process (e.g., 0.5% to 20% final concentration of glycerol), or by harvesting the bacteria (e.g., by centrifugation) and suspending in a cryopreservative solution containing the appropriate final concentration of cryoprotective agent(s).
  • the suspension of bacteria in cryopreservation solution is then filled into appropriate sterile vials (plastic or glass) with a container closure system that is capable of maintaining closure integrity under frozen conditions (e.g., butyl stoppers and crimp seals).
  • the vials of master cell bank are then frozen (either slowly by means of a controlled rate freezer, or quickly by means of placing directly into a freezer).
  • the MCB is then stored frozen at a temperature that preserves long- term viability (e.g., at or below -60 oC).
  • Thawed master cell bank material is thoroughly characterized to ensure identity, purity, and activity per regulation by the appropriate authorities.
  • Working cell banks (WCBs) are produced much the same way as the master cell bank, but the starting material is derived from the MCB.
  • MCB material can be directly transferred into a fermentation vessel containing sterile media and expanded as above.
  • the bacteria are then suspended in a cryopreservation solution, filled into containers, sealed, and frozen at or below -20 oC.
  • WCBs can be produced from MCB material, and WCB material can be used to make additional cell banks (e.g., a manufacturer’s working cell bank (MWCB)).
  • WCBs are stored frozen, and are characterized to ensure identity, purity, and activity.
  • WCB material is typically the starting material used in the production of the drug substance of biologics such as engineered bacteria.
  • Drug Substance Manufacturing Drug substance is manufactured using aseptic processes under cGMP, as described above.
  • Working cell bank material is typically used as starting material for manufacturing of drug substance under cGMP, however, other cell banks can be used (e.g., MCB or MWCB).
  • Aseptic processing is used for production of all cell therapies, including bacterial cell-based therapies.
  • the bacteria from the cell bank are expanded by fermentation; this can be achieved by production of a pre-culture (e.g., in a shake flask), or by direct inoculation of a fermenter. Fermentation is accomplished in a sterile bioreactor or flask that can be single-use disposable, or re-usable. Bacteria are harvested by concentration (e.g., by centrifugation, continuous centrifugation, or tangential flow filtration). Concentrated bacteria are purified from media components and bacterial metabolites by exchange of the media with buffer (e.g., by diafiltration). The bulk drug product is formulated and preserved as an intermediate (e.g., by freezing or drying), or is processed directly into a drug product.
  • a pre-culture e.g., in a shake flask
  • Fermentation is accomplished in a sterile bioreactor or flask that can be single-use disposable, or re-usable.
  • Bacteria are harvested by concentration (e.g., by centr
  • Drug substance is tested for identity, strength, purity, potency, and quality.
  • Drug Product Manufacturing is defined as the final formulation of the active substance contained in its final container. Drug product is manufactured using aseptic processes under cGMP. Drug product is produced from drug substance. Drug substance is thawed or reconstituted if necessary, then formulated at the appropriate target strength. Because the active component of the drug product is live, engineered bacteria, the strength is determined by the number of colony forming units (CFUs) contained within the suspension. The bulk product is diluted in a final formulation appropriate for storage and use, as described below. Containers are filled and sealed with a container closure system, and the drug product is labeled.
  • CFUs colony forming units
  • compositions are prepared in view of approvals for a regulatory agency or other agency, and/or prepared in accordance with generally recognized pharmacopeia for use in animals and in humans.
  • the compositions can be prepared as solutions, suspensions, powders, or sustained release formulations.
  • the compounds are formulated into pharmaceutical compositions using techniques and procedures well-known in the art (see, e.g., Ansel, Introduction to Pharmaceutical Dosage Forms, Fourth Edition, 1985, page 126). The formulation should suit the mode of administration.
  • compositions can be formulated for administration by any route known to those of skill in the art, including intramuscular, intravenous, intradermal, intralesional, intraperitoneal, subcutaneous, intratumoral, epidural, nasal, oral, vaginal, rectal, topical, local, otic, inhalational, buccal (e.g., sublingual), and transdermal administration, or by any suitable route. Other modes of administration also are contemplated. Administration can be local, topical, or systemic, depending upon the locus of treatment.
  • Local administration to an area in need of treatment can be achieved by, for example, but not limited to, local infusion during surgery, topical application, e.g., in conjunction with a wound dressing after surgery, by injection, by means of a catheter, by means of a suppository, or by means of an implant.
  • Compositions also can be administered with other biologically active agents, either sequentially, intermittently, or in the same composition. Administration also can include controlled release systems, including controlled release formulations and device controlled release, such as by means of a pump. The most suitable route in any given case depends on a variety of factors, such as the nature of the disease, the progress of the disease, the severity of the disease, and the particular composition which is used. Pharmaceutical compositions can be formulated in dosage forms appropriate for each route of administration.
  • compositions can be formulated into any suitable pharmaceutical preparations for systemic, local, intraperitoneal, oral, or direct administration.
  • the compositions can be formulated for administration subcutaneously, intramuscularly, intratumorally, intravenously, or intradermally.
  • Administration methods can be employed to decrease the exposure of the active agent to degradative processes, such as immunological intervention via antigenic and immunogenic responses. Examples of such methods include local administration at the site of treatment, or continuous infusion.
  • the immunostimulatory bacteria can be formulated into suitable pharmaceutical preparations, such as solutions, suspensions, tablets, dispersible tablets, pills, capsules, powders, sustained release formulations, or elixirs, for oral administrations, as well as transdermal patch preparations, and dry powder inhalers.
  • the compounds are formulated into pharmaceutical compositions using techniques and procedures well-known in the art (see, e.g., Ansel, Introduction to Pharmaceutical Dosage Forms, Fourth Edition, 1985, page 126).
  • the mode of formulation is a function of the route of administration.
  • the compositions can be formulated in dried (lyophilized or other forms of vitrification) or liquid form. Where the compositions are provided in dried form, they can be reconstituted just prior to use by addition of an appropriate buffer, for example, a sterile saline solution.
  • Formulations a. Liquids, Injectables, Emulsions The formulation generally is made to suit the route of administration.
  • Parenteral administration generally characterized by injection or infusion, either subcutaneously, intramuscularly, intratumorally, intravenously, or intradermally, is contemplated herein.
  • Preparations of bacteria for parenteral administration include suspensions ready for injection (direct administration), frozen suspensions that are thawed prior to use, dry soluble products, such as lyophilized powders, ready to be combined with a resuspension solution just prior to use, and emulsions.
  • Dried thermostable formulations such as lyophilized formulations, can be used for storage of unit doses for later use.
  • the pharmaceutical preparation can be in a frozen liquid form, for example, a suspension.
  • the drug product can be provided as a concentrated preparation to be thawed and diluted to a therapeutically effective concentration before use.
  • the pharmaceutical preparations also can be provided in a dosage form that does not require thawing or dilution for use.
  • Such liquid preparations can be prepared by conventional means with pharmaceutically acceptable additives, as appropriate, such as suspending agents (e.g., sorbitol, cellulose derivatives, or hydrogenated edible fats); emulsifying agents (e.g., lecithin or acacia); non-aqueous vehicles (e.g., almond oil, oily esters, or fractionated vegetable oils); and preservatives suitable for use with microbial therapeutics.
  • suspending agents e.g., sorbitol, cellulose derivatives, or hydrogenated edible fats
  • emulsifying agents e.g., lecithin or acacia
  • non-aqueous vehicles e.g., almond oil, oily esters, or fractionated vegetable oils
  • the pharmaceutical preparations can be presented in dried form, such as lyophilized or spray-dried, for reconstitution with water or other sterile suitable vehicle before use.
  • suitable excipients are, for example, water, saline, dextrose, or glycerol.
  • the solutions can be either aqueous or non-aqueous.
  • suitable carriers include physiological saline or phosphate buffered saline (PBS), and other buffered solutions used for intravenous hydration.
  • PBS physiological saline or phosphate buffered saline
  • solutions containing thickening agents such as glucose, polyethylene glycol, and polypropylene glycol, oil emulsions, and mixtures thereof, can be appropriate to maintain localization of the injectant.
  • compositions can include carriers or other excipients.
  • pharmaceutical compositions provided herein can contain any one or more of a diluents(s), adjuvant(s), antiadherent(s), binder(s), coating(s), filler(s), flavor(s), color(s), lubricant(s), glidant(s), preservative(s), detergent(s), or sorbent(s), and a combination thereof, or a vehicle with which a modified therapeutic bacteria is administered.
  • pharmaceutically acceptable carriers or excipients used in parenteral preparations include aqueous vehicles, non-aqueous vehicles, isotonic agents, buffers, antioxidants, local anesthetics, suspending and dispersing agents, emulsifying agents, sequestering or chelating agents, and other pharmaceutically acceptable substances.
  • Formulations, including liquid preparations can be prepared by conventional means with pharmaceutically acceptable additives or excipients.
  • Pharmaceutical compositions can include carriers, such as a diluent, adjuvant, excipient, or vehicle, with which the compositions are administered. Examples of suitable pharmaceutical carriers are described in “Remington’s Pharmaceutical Sciences” by E. W. Martin.
  • compositions will contain a therapeutically effective amount of the compound or agent, generally in purified form or partially purified form, together with a suitable amount of carrier, so as to provide the form for proper administration to the patient.
  • suitable amount of carrier can be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin, such as peanut oil, soybean oil, mineral oil, and sesame oil. Water is a typical carrier. Saline solutions and aqueous dextrose and glycerol solutions also can be employed as liquid carriers, particularly for injectable solutions.
  • Compositions can contain, along with an active ingredient: a diluent, such as lactose, sucrose, dicalcium phosphate, or carboxymethylcellulose; a lubricant, such as magnesium stearate, calcium stearate, and talc; and a binder, such as starch, natural gums, such as gum acacia, gelatin, glucose, molasses, polyvinylpyrrolidine, celluloses and derivatives thereof, povidone, crospovidone, and other such binders known to those of skill in the art.
  • a diluent such as lactose, sucrose, dicalcium phosphate, or carboxymethylcellulose
  • a lubricant such as magnesium stearate, calcium stearate, and talc
  • a binder such as starch, natural gums, such as gum acacia, gelatin, glucose, molasses, polyvinylpyrrolidine, celluloses and derivatives thereof, povidone,
  • Suitable pharmaceutical excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, and ethanol.
  • suitable excipients are, for example, water, saline, dextrose, glycerol, or ethanol.
  • a composition if desired, also can contain other minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, pH buffering agents, stabilizers, solubility enhancers, and other such agents, such as, for example, sodium acetate, sorbitan monolaurate, triethanolamine oleate, and cyclodextrins.
  • Pharmaceutically acceptable carriers used in parenteral preparations include aqueous vehicles, non-aqueous vehicles, antimicrobial agents, isotonic agents, buffers, antioxidants, local anesthetics, suspending and dispersing agents, emulsifying agents, sequestering or chelating agents, and other pharmaceutically acceptable substances.
  • aqueous vehicles include Sodium Chloride Injection, Ringer’s Injection, Isotonic Dextrose Injection, Sterile Water Injection, and Dextrose and Lactated Ringer’s Injection.
  • Non-aqueous parenteral vehicles include fixed oils of vegetable origin, cottonseed oil, corn oil, sesame oil, and peanut oil.
  • Isotonic agents include sodium chloride and dextrose.
  • Buffers include phosphate and citrate.
  • Antioxidants include sodium bisulfate.
  • Local anesthetics include procaine hydrochloride.
  • Suspending and dispersing agents include sodium carboxymethylcellulose, hydroxypropyl methylcellulose, and polyvinylpyrrolidone.
  • Emulsifying agents include, for example, polysorbates, such Polysorbate 80 (TWEEN 80). Sequestering or chelating agents of metal ions, such as EDTA, can be included.
  • Pharmaceutical carriers also include polyethylene glycol and propylene glycol, for water miscible vehicles, and sodium hydroxide, hydrochloric acid, citric acid, or lactic acid, for pH adjustment. Non-anti-microbial preservatives can be included.
  • the pharmaceutical compositions also can contain other minor amounts of non-toxic auxiliary substances, such as wetting or emulsifying agents, pH buffering agents, stabilizers, solubility enhancers, and other such agents, such as, for example, sodium acetate, sorbitan monolaurate, triethanolamine oleate, and cyclodextrins.
  • Implantation of a slow-release or sustained-release system such that a constant level of dosage is maintained (see, e.g., U.S. Patent No.3,710,795), also is contemplated herein.
  • the percentage of active compound contained in such parenteral compositions is highly dependent on the specific nature thereof, as well as the activity of the compound and the needs of the subject. b.
  • the bacteria can be dried.
  • Dried thermostable formulations such as lyophilized or spray dried powders and vitrified glass, can be reconstituted for administration as solutions, emulsions, and other mixtures.
  • the dried thermostable formulations can be prepared from any of the liquid formulations, such as the suspensions, described above.
  • the pharmaceutical preparations can be presented in lyophilized or vitrified form, for reconstitution with water or other suitable vehicle, before use.
  • the thermostable formulation is prepared for administration by reconstituting the dried compound with a sterile solution.
  • the solution can contain an excipient which improves the stability or other pharmacological attribute of the active substance or reconstituted solution, prepared from the powder.
  • thermostable formulation is prepared by dissolving an excipient, such as dextrose, sorbitol, fructose, corn syrup, xylitol, glycerin, glucose, sucrose, or other suitable agent, in a suitable buffer, such as citrate, sodium, or potassium phosphate, or other such buffer known to those of skill in the art. Then, the drug substance is added to the resulting mixture, and stirred until it is mixed. The resulting mixture is apportioned into vials for drying. Each vial will contain a single dosage, containing 1x10 5 to 1x10 11 CFUs per vial. After drying, the product vial is sealed with a container closure system that prevents moisture or contaminants from entering the sealed vial.
  • an excipient such as dextrose, sorbitol, fructose, corn syrup, xylitol, glycerin, glucose, sucrose, or other suitable agent
  • a suitable buffer such as citrate, sodium, or potassium phosphate,
  • the dried product can be stored under appropriate conditions, such as at -20 °C, 4 °C, or room temperature. Reconstitution of this dried formulation with water or a buffer solution provides a formulation for use in parenteral administration. The precise amount depends upon the indication treated and selected compound. Such amount can be empirically determined. 4. Compositions for Other Routes of Administration Depending upon the condition treated, other routes of administration in addition to parenteral, such as topical application, transdermal patches, and oral and rectal administration, also are contemplated herein. The suspensions and powders described above can be administered orally, or can be reconstituted for oral administration. Pharmaceutical dosage forms for rectal administration are rectal suppositories, capsules, and tablets and gel capsules for systemic effect.
  • Rectal suppositories include solid bodies for insertion into the rectum which melt or soften at body temperature, releasing one or more pharmacologically or therapeutically active ingredients.
  • Pharmaceutically acceptable substances in rectal suppositories are bases or vehicles and agents to raise the melting point.
  • bases include cocoa butter (theobroma oil), glycerin-gelatin, carbowax (polyoxyethylene glycol), and appropriate mixtures of mono-, di-, and triglycerides of fatty acids. Combinations of the various bases can be used.
  • Agents to raise the melting point of suppositories include spermaceti and wax. Rectal suppositories can be prepared either by the compressed method, or by molding.
  • the typical weight of a rectal suppository is about 2 to 3 grams.
  • Tablets and capsules for rectal administration are manufactured using the same pharmaceutically acceptable substance and by the same methods as for formulations for oral administration.
  • Formulations suitable for rectal administration can be provided as unit dose suppositories. These can be prepared by admixing the drug substance with one or more conventional solid carriers, for example, cocoa butter, and then shaping the resulting mixture.
  • compositions can take the form of, for example, tablets or capsules prepared by conventional means with pharmaceutically acceptable excipients, such as binding agents (e.g., pregelatinized maize starch, polyvinyl pyrrolidone, or hydroxypropyl methylcellulose); fillers (e.g., lactose, microcrystalline cellulose, or calcium hydrogen phosphate); lubricants (e.g., magnesium stearate, talc, or silica); disintegrants (e.g., potato starch or sodium starch glycolate); or wetting agents (e.g., sodium lauryl sulfate).
  • binding agents e.g., pregelatinized maize starch, polyvinyl pyrrolidone, or hydroxypropyl methylcellulose
  • fillers e.g., lactose, microcrystalline cellulose, or calcium hydrogen phosphate
  • lubricants e.g., magnesium stearate, talc, or silica
  • disintegrants
  • Formulations suitable for buccal (sublingual) administration include, for example, lozenges containing the active compound in a flavored base, usually sucrose and acacia or tragacanth; and pastilles containing the compound in an inert base, such as gelatin and glycerin, or sucrose and acacia. Topical mixtures are prepared as described for local and systemic administration.
  • the resulting mixtures can be solutions, suspensions, emulsions, or the like, and are formulated as creams, gels, ointments, emulsions, solutions, elixirs, lotions, suspensions, tinctures, pastes, foams, aerosols, irrigations, sprays, suppositories, bandages, dermal patches, or any other formulations suitable for topical administration.
  • the compositions can be formulated as aerosols for topical application, such as by inhalation (see, e.g., U.S. Patent Nos.4,044,126, 4,414,209, and 4,364,923, which describe aerosols for the delivery of a steroid useful for treatment of lung diseases).
  • formulations for administration to the respiratory tract, can be in the form of an aerosol or solution for a nebulizer, or as a microfine powder for insufflation, alone or in combination with an inert carrier such as lactose.
  • the particles of the formulation will typically have diameters of less than 50 microns, or less than 10 microns.
  • the compounds can be formulated for local or topical application, such as for topical application to the skin and mucous membranes, such as in the eye, in the form of gels, creams, and lotions, and for application to the eye, or for intracisternal or intraspinal application.
  • Topical administration is contemplated for transdermal delivery, and also for administration to the eyes or mucosa, or for inhalation therapies.
  • Nasal solutions of the active compound alone, or in combination with other pharmaceutically acceptable excipients also can be administered.
  • Formulations suitable for transdermal administration are provided. They can be provided in any suitable format, such as discrete patches adapted to remain in intimate contact with the epidermis of the recipient for a prolonged period of time. Such patches contain the active compound in an optionally buffered aqueous solution of, for example, 0.1 to 0.2 M concentration, with respect to the active compound.
  • Formulations suitable for transdermal administration also can be delivered by iontophoresis (see, e.g., Tyle, P.
  • compositions also can be administered by controlled release formulations and/or delivery devices (see e.g., U.S. Patent Nos.3,536,809; 3,598,123; 3,630,200; 3,845,770; 3,916,899; 4,008,719; 4,769,027; 5,059,595; 5,073,543; 5,120,548; 5,591,767; 5,639,476; 5,674,533; and 5,733,566). 5. Dosages and Administration The compositions can be formulated as pharmaceutical compositions for single dosage or multiple dosage administration.
  • the immunostimulatory bacteria can be included in an amount sufficient to exert a therapeutically useful effect in the absence of undesirable side effects on the patient treated.
  • concentration of the pharmaceutically active compound is adjusted so that an injection provides an effective amount to produce the desired pharmacological effect.
  • the therapeutically effective concentration can be determined empirically by testing the immunostimulatory bacteria in known in vitro and in vivo systems, such as by using the assays described herein or known in the art. For example, standard clinical techniques can be employed. In vitro assays and animal models can be employed to help identify optimal dosage ranges.
  • the precise dose which can be determinied empirically, can depend on the age, weight, body surface area, and condition of the patient or animal, the particular immunostimulatory bacteria administered, the route of administration, the type of disease to be treated, and the seriousness of the disease.
  • the precise dosage and duration of treatment is a function of the disease being treated, and can be determined empirically using known testing protocols, or by extrapolation from in vivo or in vitro test data. Concentrations and dosage values also can vary with the severity of the condition to be alleviated.
  • compositions can be administered hourly, daily, weekly, monthly, yearly, or once.
  • dosage regimens are chosen to limit toxicity.
  • the attending physician would know how to and when to terminate, interrupt, or adjust therapy to lower dosage due to toxicity, or bone marrow, liver, or kidney, or other tissue dysfunctions. Conversely, the attending physician would also know how to and when to adjust treatment to higher levels if the clinical response is not adequate (precluding toxic side effects).
  • the immunostimulatory bacteria are included in the composition in an amount sufficient to exert a therapeutically useful effect.
  • the amount is one that achieves a therapeutic effect in the treatment of a hyperproliferative disease or condition, such as cancer.
  • An exemplary dose can be about 1 x 10 9 CFU/m 2 .
  • higher doses can be administered.
  • Unit dosage forms are typically formulated and administered in unit dosage forms or multiple dosage forms.
  • Each unit dose contains a predetermined quantity of therapeutically active compound sufficient to produce the desired therapeutic effect, in association with the required pharmaceutical carrier, vehicle, or diluent.
  • Unit dosage forms include, but are not limited to, tablets, capsules, pills, powders, granules, parenteral suspensions, oral solutions or suspensions, and oil-in-water emulsions, containing suitable quantities of the compounds or pharmaceutically acceptable derivatives thereof.
  • Unit dose forms can be contained in vials, ampoules and syringes, or individually packaged tablets or capsules.
  • Unit dose forms can be administered in fractions or multiples thereof.
  • a multiple dose form is a plurality of identical unit dosage forms packaged in a single container to be administered in segregated unit dose form.
  • multiple dose forms include vials, bottles of tablets or capsules, or bottles of pints or gallons.
  • multiple dose form is a multiple of unit doses that are not segregated in packaging.
  • dosage forms or compositions containing active ingredient in the range of 0.005% to 100%, with the balance made up from non-toxic carrier can be prepared.
  • Pharmaceutical compositions can be formulated in dosage forms appropriate for each route of administration.
  • the unit-dose parenteral preparations are packaged in an ampoule, a vial, or a syringe with a needle.
  • compositions provided herein can be formulated for any route known to those of skill in the art, including, but not limited to, subcutaneous, intramuscular, intravenous, intradermal, intralesional, intraperitoneal, epidural, vaginal, rectal, local, otic, or transdermal administration, or any route of administration. Formulations suited for such routes are known to one of skill in the art. Compositions also can be administered with other biologically active agents, either sequentially, intermittently, or in the same composition.
  • compositions can be administered by controlled release formulations and/or delivery devices (see, e.g., U.S. Patent Nos.3,536,809; 3,598,123; 3,630,200; 3,845,770; 3,847,770; 3,916,899; 4,008,719; 4,687,660; 4,769,027; 5,059,595; 5,073,543; 5,120,548; 5,354,556; 5,591,767; 5,639,476; 5,674,533; and 5,733,566).
  • Various delivery systems are known and can be used to administer selected compositions, are contemplated for use herein, and such particles can be easily made. 6.
  • packaging and Articles of Manufacture Also provided are articles of manufacture containing packaging materials, any pharmaceutical composition provided herein, and a label that indicates that the compositions are to be used for treatment of diseases or conditions as described herein.
  • the label can indicate that the treatment is for a tumor or for cancer.
  • Combinations of immunostimulatory bacteria described herein and another therapeutic agent also can be packaged in an article of manufacture.
  • the article of manufacture contains a pharmaceutical composition containing the immunostimulatory bacteria composition and no further agent or treatment.
  • the article of manufacture contains another further therapeutic agent, such as a different anti-cancer agent.
  • the agents can be provided together or separately, for packaging as articles of manufacture.
  • the articles of manufacture provided herein contain packaging materials.
  • Packaging materials for use in packaging pharmaceutical products are well-known to those of skill in the art. See, for example, U.S. Patent Nos.5,323,907, 5,052,558, and 5,033,252, each of which is incorporated herein in its entirety.
  • Examples of pharmaceutical packaging materials include, but are not limited to, blister packs, bottles, tubes, inhalers, pumps, bags, vials, containers, syringes, bottles, and any packaging material suitable for a selected formulation and intended mode of administration and treatment.
  • Exemplary of articles of manufacture are containers, including single chamber and dual chamber containers.
  • the containers include, but are not limited to, tubes, bottles, and syringes.
  • the containers can further include a needle for intravenous administration.
  • kits can include a pharmaceutical composition described herein, and an item for administration provided as an article of manufacture. The compositions can be contained in the item for administration, or can be provided separately to be added later.
  • kits can, optionally, include instructions for application, including dosages, dosing regimens, and instructions for modes of administration.
  • Kits also can include a pharmaceutical composition described herein and an item for diagnosis.
  • G. METHODS OF TREATMENT AND USES The methods provided herein include methods of administering or using the immunostimulatory bacteria, for treating subjects having a disease or condition whose symptoms can be ameliorated or lessened by administration of such bacteria, such as cancer.
  • the disease or condition is a tumor or a cancer.
  • methods of combination therapies with one or more additional agents for treatment such as an anti-cancer agent or an anti-hyaluronan agent, also are provided.
  • the bacteria can be administered by any suitable route, including, but not limited to, parenteral, systemic, topical, and local, such as intra-tumoral, intravenous, rectal, oral, intramuscular, mucosal, and other routes. Because of the modifications of the bacteria described herein, problems associated with systemic administration are solved. Formulations suitable for each route of administration are provided. The skilled person can establish suitable regimens and doses, and can select routes of administration. 1. Diagnostics for Patient Selection for Treatment and for Monitoring Treatment a. Patient Selection Biomarkers can be used to identify patients who are likely to respond to therapy with the immunostimulatory bacteria provided herein.
  • the Adenosine Signature and the Myeloid Signature can be assessed by NanoString gene expression panels, and T-cell infiltration of tumors can be assessed by the Immunoscore® test, which is an in vitro diagnostic test used for predicting the risk of relapse in early stage colon cancer patients, by measuring the host immune response at a tumor site. Patients whose tumors or body fluids indicate an immune responsiveness or an immune response are more likely to respond to the treatment with the immunostimulatory bacteria provided herein.
  • Other biomarkers include tumor-infiltrating lymphocytes (TILs), CD73, CD39, TNAP (tissue-nonspecific alkaline phosphatase), CD38, CD68, PD-L1, and FoxP3.
  • tumors that can be treated with the immunostimulatory bacteria provided herein are T-cell excluded, exhibit high levels of purines/adenosine, and are unresponsive to PD-1/PD-L1 targeted therapies.
  • Gene expression profiles which can be determined using various NanoString gene expression panels, can be analyzed, for example, to identify the “adenosine signature” of tumors. High concentrations of adenosine are found in certain tumors, including colorectal carcinoma (CRC), non-small cell lung cancer (NSCLC), and pancreatic cancer, among others.
  • CRC colorectal carcinoma
  • NSCLC non-small cell lung cancer
  • pancreatic cancer among others.
  • the “Adenosine Signature” is nearly identical to the “Myeloid Signature” that is associated with poor response to atezolizumab (anti-PD- L1) monotherapy in renal cell carcinoma (RCC) patients, which is indicative of the role of adenosine in tumor escape from anti-PD-L1 therapy (see, e.g., McDermott et al. (2016) Nature Medicine 24:749-757).
  • Tumor-myeloid and tumor-adenosine NanoString signature panels are available and can be used for the selection of patients. Macrophages limit T-cell infiltration into solid tumors and suppress their function, for example, in triple negative breast cancer (see, e.g., Keren et al.
  • Immunoscore® a method to estimate the prognosis of cancer patients, based on the immune cells that infiltrate the cancer and surround it, can be used to measure T-cell exclusion or T-cell infiltration. Immunoscore® incorporates the effects of the host immune response into cancer classification and improves prognostic accuracy.
  • T-cell poor/uninflamed tumors can be treated, because the immunostimulatory bacteria provided herein induce T-cell infiltration in cold tumors.
  • Such tumors represent a high, unmet need population that is refractory to checkpoint inhibition.
  • Extracellular adenosine is produced by the sequential activities of membrane associated ectoenzymes, CD39 (ecto-nucleoside triphosphate diphosphohydrolase 1, or NTPDase1) and CD73 (ecto-5’-nucleotidase), which are expressed on tumor stromal cells, together producing adenosine by phosphohydrolysis of ATP or ADP that is produced from dead or dying cells.
  • CD39 converts extracellular ATP (or ADP) to 5’-AMP, which is converted to adenosine by CD73.
  • Expression of CD39 and CD73 on endothelial cells is increased under the hypoxic conditions of the tumor microenvironment, thereby increasing levels of adenosine.
  • CD39 and CD73 can be used as biomarkers that indicate adenosine-rich tumors that can be targeted with the immunostimulatory bacteria provided herein.
  • CD38 also known as cyclic ADP ribose hydrolase, is a glycoprotein that is found on the surface of many immune cells, including CD4 + T-cells, CD8 + T-cells, B lymphocytes, and natural killer cells.
  • CD38 which is a marker of cell activation, is associated with impaired immune responses, and has been linked to leukemias, myelomas, and solid tumors. Additionally, increased expression of CD38 is an unfavorable diagnostic marker in chronic lymphocytic leukemia and is associated with increased disease progression. CD38 also is used as a target for daratumumab (Darzalex®), which has been approved for the treatment of multiple myeloma. CD68 is highly expressed by monocytes, circulating macrophages, and by tissue macrophages (e.g., Kupffer cells, microglia).
  • CD38, CD68, and FoxP3 also can be used as biomarkers for the selection of patients that are likely to respond to therapy with the immunostimulatory bacteria herein.
  • Biomarkers can be used to monitor the immunostimulatory bacteria following treatment. Biomarkers occur in tumor samples and/or in body fluid samples, such as blood, plasma, urine, saliva, and other fluids.
  • peripheral blood biomarkers are used to evaluate the immune status of patients prior to and during treatment, to determine changes in the immune status, which correlate with the effectiveness of treatment.
  • a change to, or an increase in, anti-tumor immune response status indicates that treatment with the immunostimulatory bacteria is having an effect.
  • Immunomodulatory activity of the immunostimulatory bacteria provided herein, for example, in dose escalation and expansion studies, can be assessed.
  • Examination of biomarkers reveals prognostic and predictive factors relating to disease (e.g., a tumor) status and its treatment, which can aid in monitoring treatment. Evaluating the tumor microenvironment, for example, provides insights into the mechanism of tumor responses to immunotherapies.
  • Serum biomarkers to detect immunomodulatory activity of the immunostimulatory bacteria include, but are not limited to, CXCL10 (IP-10), CXCL9, interferon- ⁇ , interferon- ⁇ , proinflammatory serum cytokines (e.g., IL-6, TNF- ⁇ , MCP-1/CCL1), and IL-18 binding protein.
  • CXCL10 and CXCL9 are chemokines that are necessary for CD8 + T-cell activation and trafficking to tumors, for example, in response to immunotherapies.
  • an anti-PD-1 immune checkpoint inhibitor for the treatment of previously treated patients with metastatic renal cell carcinoma (mRCC), immune pharmacodynamic effects that were shared by the majority of patients, irrespective of the dose administered, were identified.
  • Assessment of the IFN- ⁇ regulated serum chemokines CXCL9 and CXCL10 was performed using a multiplex panel based on Luminex technology (Myriad® Rules-Based Medicine (RBM)), and the results demonstrated that increased CXCL9 and CXCL10 serum levels, as well as increased transcription in the tumor, correlated with clinical response.
  • IL-18 participates in protective immune responses to intracellular bacteria, fungi and viruses, and has demonstrated anti-tumor activity in preclinical models of lung cancer, breast cancer, sarcoma, and melanoma.
  • the biological activity of IL-18 is modulated in a negative feedback loop by IL-18 binding protein (IL-18BP), induced through IFN- ⁇ .
  • IL-18BP IL-18 binding protein
  • serum levels of IL-18BP are predictive of clinical IFN- ⁇ activity.
  • rhIL-18 recombinant human IL-18
  • IL-18BP can be used as a biomarker for tumor immune responses.
  • Tumors The immunostimulatory bacteria, combinations, uses, and methods provided herein are applicable to treating all types of tumors, including cancers, particularly solid tumors, including lung cancer, bladder cancer, non-small cell lung cancer, gastric cancers, head and neck cancers, ovarian cancer, liver cancer, pancreatic cancer, kidney cancer, breast cancer, colorectal cancer, and prostate cancer.
  • the methods also can be used for treating hematological cancers.
  • Tumors and cancers subject to treatment by the immunostimulatory bacteria, compositions, combinations, uses, and methods provided herein include, but are not limited to, those that originate in the immune system, skeletal system, muscles and heart, breast, pancreas, gastrointestinal tract, central and peripheral nervous system, renal system, reproductive system, respiratory system, skin, connective tissue systems, including joints, fatty tissues, and the circulatory system, including blood vessel walls.
  • tumors that can be treated with the immunostimulatory bacteria provided herein include carcinomas, gliomas, sarcomas (including liposarcoma), adenocarcinomas, adenosarcomas, and adenomas.
  • Tumors of the skeletal system include, for example, sarcomas and blastomas, such as osteosarcoma, chondrosarcoma, and chondroblastoma.
  • Muscle and heart tumors include tumors of both skeletal and smooth muscles, e.g., leiomyomas (benign tumors of smooth muscle), leiomyosarcomas, rhabdomyomas (benign tumors of skeletal muscle), rhabdomyosarcomas, and cardiac sarcomas.
  • Tumors of the gastrointestinal tract include, e.g., tumors of the mouth, esophagus, stomach, small intestine, and colon, and colorectal tumors, as well as tumors of gastrointestinal secretory organs, such as the salivary glands, liver, pancreas, and the biliary tract.
  • Tumors of the central nervous system include tumors of the brain, retina, and spinal cord, and can also originate in associated connective tissue, bone, blood vessels, or nervous tissue. Treatment of tumors of the peripheral nervous system are also contemplated.
  • Tumors of the peripheral nervous system include malignant peripheral nerve sheath tumors.
  • Tumors of the renal system include those of the kidneys, e.g., renal cell carcinoma, as well as tumors of the ureters and bladder.
  • Tumors of the reproductive system include tumors of the cervix, uterus, ovary, prostate, testes, and related secretory glands.
  • Tumors of the immune system include both blood-based and solid tumors, including lymphomas, e.g., both Hodgkin’s and non-Hodgkin’s lymphomas.
  • Tumors of the respiratory system include tumors of the nasal passages, bronchi, and lungs.
  • Tumors of the breast include, e.g., both lobular and ductal carcinomas.
  • tumors that can be treated by the immunostimulatory bacteria and methods provided herein include Kaposi’s sarcoma, CNS neoplasms, neuroblastomas, capillary hemangioblastomas, meningiomas and cerebral metastases, melanoma, gastrointestinal and renal carcinomas and sarcomas, rhabdomyosarcoma, glioblastoma (such as glioblastoma multiforme), and leiomyosarcoma.
  • cancers that can be treated as provided herein include, but are not limited to, lymphoma, blastoma, neuroendocrine tumors, mesothelioma, schwannoma, meningioma, melanoma, and leukemia or lymphoid malignancies.
  • cancers include hematologic malignancies, such as Hodgkin’s lymphoma, non- Hodgkin’s lymphomas (Burkitt’s lymphoma, small lymphocytic lymphoma, chronic lymphocytic leukemia, mycosis fungoides, mantle cell lymphoma, follicular lymphoma, diffuse large B-cell lymphoma, marginal zone lymphoma, hairy cell leukemia, and lymphoplasmacytic leukemia), tumors of lymphocyte precursor cells, including B-cell acute lymphoblastic leukemia/lymphoma, and T-cell acute lymphoblastic leukemia/lymphoma, thymoma, tumors of the mature T and NK cells, including peripheral T-cell leukemias, adult T-cell leukemia/T-cell lymphomas and large granular lymphocytic leukemia, Langerhans cell histiocytosis, myeloid neoplasia
  • immunostimulatory bacteria provided herein can be administered to a subject, including a subject having a tumor or having neoplastic cells, or a subject to be immunized.
  • One or more steps can be performed prior to, simultaneously with, or after administration of the immunostimulatory bacteria to the subject, including, but not limited to, diagnosing the subject with a condition appropriate for administering immunostimulatory bacteria, determining the immunocompetence of the subject, immunizing the subject, treating the subject with a chemotherapeutic agent, treating the subject with radiation, or surgically treating the subject.
  • the subject typically has previously been diagnosed with a neoplastic condition.
  • Diagnostic methods also can include determining the type of neoplastic condition, determining the stage of the neoplastic condition, determining the size of one or more tumors in the subject, determining the presence or absence of metastatic or neoplastic cells in the lymph nodes of the subject, or determining the presence of metastases in the subject.
  • Some embodiments of the therapeutic methods for administering immunostimulatory bacteria to a subject can include a step of determining the size of the primary tumor or the stage of the neoplastic disease, and, if the size of the primary tumor is equal to or above a threshold volume, or if the stage of the neoplastic disease is at or above a threshold stage, an immunostimulatory bacterium is administered to the subject.
  • the immunostimulatory bacterium is not yet administered to the subject; such methods can include monitoring the subject until the tumor size or neoplastic disease stage reaches a threshold amount, and then administering the immunostimulatory bacterium to the subject. Threshold sizes can vary according to several factors, including rate of growth of the tumor, ability of the immunostimulatory bacterium to infect a tumor, and immunocompetence of the subject.
  • the threshold size will be a size sufficient for an immunostimulatory bacterium to accumulate and replicate in or near the tumor, without being completely removed by the host’s immune system, and will typically also be a size sufficient to sustain a bacterial infection for a time long enough for the host to mount an immune response against the tumor cells, typically about one week or more, about ten days or more, or about two weeks or more.
  • Exemplary threshold stages are any stage beyond the lowest stage (e.g., Stage I or equivalent), or any stage where the primary tumor is larger than a threshold size, or any stage where metastatic cells are detected. Any mode of administration of a microorganism to a subject can be used, provided the mode of administration permits the immunostimulatory bacteria to enter a tumor or metastasis.
  • Modes of administration can include, but are not limited to, intravenous, intraperitoneal, subcutaneous, intramuscular, topical, intratumoral, multipuncture, inhalation, intranasal, oral, intracavity (e.g., administering to the bladder via a catheter, or administering to the gut by suppository or enema), aural, rectal, and ocular administration.
  • One skilled in the art can select any mode of administration compatible with the subject and the bacteria, and that also is likely to result in the bacteria reaching tumors and/or metastases.
  • the route of administration can be selected by one skilled in the art according to any of a variety of factors, including the nature of the disease, the kind of tumor, and the particular bacteria contained in the pharmaceutical composition.
  • Administration to the target site can be performed, for example, by ballistic delivery, or as a colloidal dispersion system, or systemic administration can be performed by injection into an artery.
  • the dosage regimen can be any of a variety of methods and amounts, and can be determined by one skilled in the art according to known clinical factors.
  • a single dose can be therapeutically effective for treating a disease or disorder in which immune stimulation effects treatment.
  • Exemplary of such stimulation is an immune response, that includes, but is not limited to, one or both of a specific immune response and non-specific immune response, both specific and non-specific responses, innate response, primary immune response, adaptive immunity, secondary immune response, memory immune response, immune cell activation, immune cell proliferation, immune cell differentiation, and cytokine expression.
  • dosages for a subject can depend on many factors, including the subject’s species, size, body surface area, age, sex, immunocompetence, and general health, the particular bacteria to be administered, the duration and route of administration, the kind and stage of the disease, for example, the tumor size, and other compounds, such as drugs, being administered concurrently.
  • levels can be affected by the infectivity of the bacteria and the nature of the bacteria, as can be determined by one skilled in the art.
  • appropriate minimum dosage levels of bacteria can be levels sufficient for the bacteria to survive, grow, and replicate in a tumor or metastasis.
  • Exemplary minimum levels for administering a bacterium to a 65 kg human can include at least about 5 x 10 6 colony forming units (CFUs), at least about 1 x 10 7 CFUs, at least about 5 x 10 7 CFUs, at least about 1 x 10 8 CFUs, or at least about 1 x 10 9 CFUs.
  • appropriate maximum dosage levels of bacteria can be levels that are not toxic to the host, levels that do not cause splenomegaly of 3x or more, or levels that do not result in colonies or plaques in normal tissues or organs after about 1 day, or after about 3 days, or after about 7 days.
  • Exemplary maximum levels for administering a bacterium to a 65 kg human can include no more than about 5 x 10 11 CFUs, no more than about 1 x 10 11 CFUs, no more than about 5 x 10 10 CFUs, no more than about 1 x 10 10 CFUs, or no more than about 1 x 10 9 CFUs.
  • the methods and uses provided herein can include a single administration of immunostimulatory bacteria to a subject, or multiple administrations of immunostimulatory bacteria to a subject, or others of a variety of regimens, including combination therapies with other anti-tumor therapeutics and/or treatments.
  • cancer therapies such as administration of modified immune cells; CAR-T therapy; CRISPR therapy; checkpoint inhibitors, such as antibodies (e.g., anti-PD-1 antibodies, anti-PD-L1 antibodies, and anti-CTLA-4 antibodies, and other such immunotherapies); chemotherapeutic compounds, such as nucleoside analogs; surgery; and radiotherapy.
  • Other cancer therapies also include anti-VEGF, anti-VEGFR, anti-VEGFR2, anti-TGF- ⁇ or anti-IL-6 antibodies, or fragments thereof, cancer vaccines, and oncolytic viruses.
  • a single administration is sufficient to establish immunostimulatory bacteria in a tumor, where the bacteria can colonize, and can cause or enhance an anti-tumor response in the subject.
  • the immunostimulatory bacteria provided for use in the methods herein can be administered on different occasions, separated in time, typically by at least one day. Separate administrations can increase the likelihood of delivering a bacterium to a tumor or metastasis, where a previous administration may have been ineffective in delivering the bacterium to a tumor or metastasis. In embodiments, separate administrations can increase the locations on a tumor or metastasis where bacterial colonization/proliferation can occur, or can otherwise increase the titer of bacteria accumulated in the tumor, which can increase eliciting or enhancing a host’s anti- tumor immune response. When separate administrations are performed, each administration can be a dosage amount that is the same or different relative to other administration dosage amounts.
  • all administration dosage amounts are the same.
  • a first dosage amount can be a larger dosage amount than one or more subsequent dosage amounts, for example, at least 10x larger, at least 100x larger, or at least 1000x larger, than subsequent dosage amounts.
  • all subsequent dosage amounts can be the same, smaller amount, relative to the first administration.
  • Separate administrations can include any number of two or more administrations, including two, three, four, five, or six administrations. One skilled in the art readily can determine the number of administrations to perform, or the desirability of performing one or more additional administrations, according to methods known in the art for monitoring therapeutic methods, and other monitoring methods provided herein.
  • the methods provided herein include methods of providing to the subject one or more administrations of immunostimulatory bacteria, where the number of administrations can be determined by monitoring the subject, and, based on the results of the monitoring, determining whether or not to provide one or more additional administrations. Deciding whether or not to provide one or more additional administrations can be based on a variety of monitoring results, including, but not limited to, indication of tumor growth or inhibition of tumor growth, appearance of new metastases or inhibition of metastasis, the subject’s anti- bacterial antibody titer, the subject’s anti-tumor antibody titer, the overall health of the subject, and the weight of the subject.
  • the time period between administrations can be any of a variety of time periods.
  • the time period between administrations can be a function of any of a variety of factors, including monitoring steps, as described in relation to the number of administrations, the time period for a subject to mount an immune response, the time period for a subject to clear bacteria from normal tissue, or the time period for bacterial colonization/proliferation in the tumor or metastasis.
  • the time period can be a function of the time period for a subject to mount an immune response; for example, the time period can be more than the time period for a subject to mount an immune response, such as more than about one week, more than about ten days, more than about two weeks, or more than about a month.
  • the time period can be less than the time period for a subject to mount an immune response, such as less than about one week, less than about ten days, less than about two weeks, or less than about a month.
  • the time period can be a function of the time period for bacterial colonization/proliferation in the tumor or metastasis; for example, the time period can be more than the amount of time for a detectable signal to arise in a tumor or metastasis after administration of a microorganism expressing a detectable marker, such as about 3 days, about 5 days, about a week, about ten days, about two weeks, or about a month.
  • compositions such as suspensions and other formulations, containing the immunostimulatory bacteria provided herein.
  • Such compositions contain the bacteria and a pharmaceutically acceptable excipient or vehicle, as provided herein or known to those of skill in the art.
  • the uses and methods provided herein also can include administering one or more therapeutic compounds, such as anti-tumor compounds or other cancer therapeutics, to a subject, in addition to administering the immunostimulatory bacteria to the subject.
  • the therapeutic compounds can act independently, or in conjunction with the immunostimulatory bacteria, for tumor therapeutic effects.
  • Therapeutic compounds that can act independently include any of a variety of known chemotherapeutic compounds that can inhibit tumor growth, inhibit metastasis growth and/or formation, decrease the size of a tumor or metastasis, or eliminate a tumor or metastasis, without reducing the ability of the immunostimulatory bacteria to accumulate in a tumor, replicate in the tumor, and cause or enhance an anti-tumor immune response in the subject.
  • chemotherapeutic agents include, but are not limited to, alkylating agents, such as thiotepa and cyclophosphamide; alkyl sulfonates, such as busulfan, improsulfan, and piposulfan; androgens, such as calusterone, dromostanolone propionate, epitiostanol, mepitiostane, and testolactone; anti-adrenals, such as aminoglutethimide, mitotane, and trilostane; anti-androgens, such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; antibiotics, such as aclacinomycin, actinomycin, anthramycin, azaserine, bleomycin, cactinomycin, calicheamicin, carubicin, carminomycin, carzinophilin, chromomycin, dactinomycin
  • Therapeutic compounds that act in conjunction with the immunostimulatory bacteria include, for example, compounds that increase the immune response eliciting properties of the bacteria, e.g., by increasing expression of encoded therapeutic products, such as cytokines, chemokines, co-stimulatory molecules, proteins that constitutively induce type I IFNs, RNAi molecules that inhibit, suppress, or disrupt expression of checkpoint gene(s), a checkpoint inhibitor antibody and antibodies or fragments thereof against other targets, or compounds that can further augment bacterial colonization/proliferation.
  • encoded therapeutic products such as cytokines, chemokines, co-stimulatory molecules, proteins that constitutively induce type I IFNs, RNAi molecules that inhibit, suppress, or disrupt expression of checkpoint gene(s), a checkpoint inhibitor antibody and antibodies or fragments thereof against other targets, or compounds that can further augment bacterial colonization/proliferation.
  • a gene expression-altering compound can induce or increase transcription of a gene in a bacterium, such as an exogenous gene encoded on the plasmid, thereby provoking an immune response.
  • a gene expression-altering compound can induce or increase transcription of a gene in a bacterium, such as an exogenous gene encoded on the plasmid, thereby provoking an immune response.
  • Any of a wide variety of compounds that can alter gene expression are known in the art, including IPTG and RU486.
  • Exemplary genes whose expression can be up- regulated include those encoding proteins and RNA molecules, including toxins, enzymes that can convert a prodrug to an anti-tumor drug, cytokines, transcription regulating proteins, shRNA, siRNA, and ribozymes.
  • therapeutic compounds that can act in conjunction with the immunostimulatory bacteria to increase the colonization/proliferation or immune response eliciting properties of the bacteria are compounds that can interact with a bacterially-encoded gene product, and such interaction can result in an increased killing of tumor cells, or an increased anti-tumor immune response in the subject.
  • a therapeutic compound that can interact with a bacterially-encoded gene product can include, for example, a prodrug or other compound that has little or no toxicity, or other biological activity in its subject-administered form, but after interaction with a bacterially-encoded gene product, the compound can develop a property that results in tumor cell death, including but not limited to, cytotoxicity, the ability to induce apoptosis, or the ability to trigger an immune response.
  • prodrug-like substances include ganciclovir, 5-fluorouracil, 6-methylpurine deoxyriboside, cephalosporin-doxorubicin, 4-[(2-chloroethyl)(2-mesuloxyethyl)amino]benzoyl-L- glutamic acid, acetaminophen, indole-3-acetic acid, CB1954, 7-ethyl-10-[4-(1- piperidino)-1-piperidino]carbonyloxycamptothecin, bis-(2-chloroethyl)amino-4- hydroxyphenylaminomethanone 28, 1-chloromethyl-5-hydroxy-1,2-dihyro-3H- benz[e]indole, epirubicin-glucuronide, 5’-deoxy5-fluorouridine, cytosine arabinoside, and linamarin.
  • monitoring can further include one or more steps of monitoring the subject, monitoring the tumor, and/or monitoring the immunostimulatory bacteria administered to the subject. Any of a variety of monitoring steps can be included in the methods provided herein, including, but not limited to, monitoring tumor size, monitoring the presence and/or size of metastases, monitoring the subject’s lymph nodes, monitoring the subject’s weight or other health indicators, including blood or urine markers, monitoring anti-bacterial antibody titer, monitoring bacterial expression of a detectable gene product, and directly monitoring bacterial titer in a tumor, tissue, or organ of a subject.
  • the purpose of the monitoring can be simply for assessing the health state of the subject, or the progress of therapeutic treatment of the subject, or can be for determining whether or not further administration of the same or a different immunostimulatory bacterium is warranted, or for determining when or whether or not to administer a compound to the subject where the compound can act to increase the efficacy of the therapeutic method, or the compound can act to decrease the pathogenicity of the bacteria administered to the subject.
  • the methods provided herein can include monitoring one or more bacterially-expressed genes. Bacteria, such as those provided herein or otherwise known in the art, can express one or more detectable gene products, including but not limited to, detectable proteins.
  • measurement of a detectable gene product expressed in a bacterium can provide an accurate determination of the level of bacteria present in the subject.
  • measurement of the location of the detectable gene product for example, by imaging methods, including tomographic methods, can determine the localization of the bacteria in the subject.
  • the methods provided herein that include monitoring a detectable bacterial gene product can be used to determine the presence or absence of the bacteria in one or more organs or tissues of a subject, and/or the presence or absence of the bacteria in a tumor or metastases of a subject.
  • the methods provided herein that include monitoring a detectable bacterial gene product can be used to determine the titer of bacteria present in one or more organs, tissues, tumors, or metastases.
  • Methods that include monitoring the localization and/or titer of bacteria in a subject can be used for determining the pathogenicity of bacteria, since bacterial infection, and particularly the level of infection, of normal tissues and organs can indicate the pathogenicity of the bacteria.
  • the methods that include monitoring the localization and/or titer of the immunostimulatory bacteria in a subject can be performed at multiple time points and, accordingly, can determine the rate of bacterial replication in a subject, including the rate of bacterial replication in one or more organs or tissues of a subject; accordingly, methods that include monitoring a bacterial gene product can be used for determining the replication competence of the bacteria.
  • the methods provided herein also can be used to quantitate the amount of immunostimulatory bacteria present in a variety of organs or tissues, and tumors or metastases, and can thereby indicate the degree of preferential accumulation of the bacteria in a subject; accordingly, the bacterial gene product monitoring can be used in methods of determining the ability of the bacteria to accumulate in tumors or metastases, in preference to normal tissues or organs. Since the immunostimulatory bacteria used in the methods provided herein can accumulate in an entire tumor, or can accumulate at multiple sites in a tumor, and can also accumulate in metastases, the methods provided herein for monitoring a bacterial gene product can be used to determine the size of a tumor, or the number of metastases present in a subject.
  • Monitoring such presence of a bacterial gene product in a tumor or metastasis over a range of time can be used to assess changes in the tumor or metastasis, including growth or shrinking of a tumor, or development of new metastases, or disappearance of metastases, and also can be used to determine the rate of growth or shrinking of a tumor, or the rate of development of new metastases or disappearance of metastases, or the change in the rate of growth or shrinking of a tumor, or the change in the rate of development of new metastases or disappearance of metastases.
  • monitoring a bacterial gene product can be used for monitoring a neoplastic disease in a subject, or for determining the efficacy of treatment of a neoplastic disease, by determining the rate of growth or shrinking of a tumor, or the development of new metastases or disappearance of metastases, or the change in the rate of growth or shrinking of a tumor, or the development of new metastases or disappearance of metastases.
  • detectable proteins can be detected by monitoring, exemplary of which are any of a variety of fluorescent proteins (e.g., green fluorescent proteins), any of a variety of luciferases, transferrin, or other iron-binding proteins; or receptors, binding proteins, and antibodies, where a compound that specifically binds the receptor, binding protein or antibody can be a detectable agent, or can be labeled with a detectable substance (e.g., a radionuclide or imaging agent).
  • a detectable substance e.g., a radionuclide or imaging agent.
  • monitoring bacterial gene expression can be used for monitoring tumor and/or metastasis size.
  • Monitoring size over several time points can provide information regarding the increase or decrease in the size of a tumor or metastasis, and can also provide information regarding the presence of additional tumors and/or metastases in the subject.
  • Monitoring tumor size over several time points can provide information regarding the development of a neoplastic disease in a subject, including the efficacy of treatment of a neoplastic disease in a subject.
  • the methods provided herein also can include monitoring the antibody titer in a subject, including antibodies produced in response to administration of the immunostimulatory bacteria to a subject.
  • the bacteria administered in the methods provided herein can elicit an immune response to endogenous bacterial antigens.
  • the bacteria administered in the methods provided herein also can elicit an immune response to exogenous genes expressed by the bacteria.
  • the bacteria administered in the methods provided herein also can elicit an immune response to tumor antigens.
  • Monitoring antibody titer against bacterial antigens, bacterially-expressed exogenous gene products, or tumor antigens can be used to monitor the toxicity of the bacteria, to monitor the efficacy of treatment methods, or to monitor the level of gene product(s) or antibodies for production and/or harvesting. Monitoring antibody titer can be used to monitor the toxicity of the bacteria.
  • Antibody titer against a bacteria can vary over the time period after administration of the bacteria to the subject, where at some particular time points, a low anti-(bacterial antigen) antibody titer can indicate a lower toxicity, while at other time points, a high anti-(bacterial antigen) antibody titer can indicate a higher toxicity.
  • the bacteria used in the methods provided herein can be immunogenic, and can, therefore, elicit an immune response soon after administering the bacteria to the subject.
  • immunostimulatory bacteria against which the immune system of a subject can mount a strong immune response can be bacteria that have low toxicity when the subject’s immune system can remove the bacteria from all normal organs or tissues.
  • a high antibody titer against bacterial antigens soon after administering the bacteria to a subject can indicate low toxicity of the bacteria.
  • monitoring antibody titer can be used to monitor the efficacy of treatment methods.
  • antibody titer such as anti-(tumor antigen) antibody titer
  • a therapeutic method such as a therapeutic method to treat neoplastic disease.
  • Therapeutic methods provided herein can include causing or enhancing an immune response against a tumor and/or metastasis.
  • monitoring the anti-(tumor antigen) antibody titer it is possible to monitor the efficacy of a therapeutic method in causing or enhancing an immune response against a tumor and/or metastasis.
  • monitoring antibody titer can be used for monitoring the level of gene product(s) or antibodies for production and/or harvesting.
  • methods can be used for producing proteins, RNA molecules, or other compounds, by expressing an exogenous gene in a microorganism that has accumulated in a tumor, in the tumor microenvironment, and/or in tumor-resident immune cells.
  • Monitoring antibody titer against the protein, RNA molecule, or other compound can indicate the level of production of the protein, RNA molecule, or other compound by the tumor-accumulated microorganism, and also, can directly indicate the level of antibodies specific for such a protein, RNA molecule, or other compound.
  • the methods provided herein also can include methods of monitoring the health of a subject. Some of the methods provided herein are therapeutic methods, including neoplastic disease therapeutic methods. Monitoring the health of a subject can be used to determine the efficacy of the therapeutic method, as is known in the art.
  • the methods provided herein also can include a step of administering to a subject an immunostimulatory bacterium, as provided herein.
  • Monitoring the health of a subject can be used to determine the pathogenicity of an immunostimulatory bacterium administered to a subject.
  • Any of a variety of health diagnostic methods for monitoring disease such as neoplastic disease, infectious disease, or immune-related disease, can be monitored, as is known in the art.
  • the weight, blood pressure, pulse, breathing, color, temperature, or other observable state of a subject can indicate the health of a subject.
  • the presence, or absence, or level of one or more components in a sample from a subject can indicate the health of a subject.
  • Typical samples can include blood and urine samples, where the presence, or absence, or level of one or more components can be determined by performing, for example, a blood panel or a urine panel diagnostic test.
  • Exemplary components indicative of a subject’s health include, but are not limited to, white blood cell count, hematocrit, and c-reactive protein concentration.
  • the methods provided herein can include monitoring a therapy, where therapeutic decisions can be based on the results of the monitoring.
  • Therapeutic methods provided herein can include administering to a subject immunostimulatory bacteria, where the bacteria can preferentially accumulate in a tumor, the tumor microenvironment, or in tumor-resident immune cells, and/or in metastases, and where the bacteria can cause or enhance an anti-tumor immune response.
  • Such therapeutic methods can include a variety of steps, including multiple administrations of a particular immunostimulatory bacterium, administration of a second immunostimulatory bacterium, or administration of a therapeutic compound.
  • Determination of the amount, timing, or type of immunostimulatory bacteria or compound to administer to the subject can be based on one or more results from monitoring the subject.
  • the antibody titer in a subject can be used to determine whether or not it is desirable to administer an immunostimulatory bacterium and, optionally, a compound, the quantity of bacteria and/or compound to administer, and the type of bacteria and/or compound to administer, where, for example, a low antibody titer can indicate the desirability of administering an additional immunostimulatory bacterium, a different immunostimulatory bacterium, and/or a therapeutic compound, such as a compound that induces bacterial gene expression, or a therapeutic compound that is effective independent of the immunostimulatory bacteria.
  • the overall health state of a subject can be used to determine whether or not it is desirable to administer an immunostimulatory bacterium and, optionally, a compound, the quantity of bacterium and/or compound to administer, and the type of bacterium and/or compound to administer, where, for example, determining that the subject is healthy can indicate the desirability of administering additional bacteria, different bacteria, or a therapeutic compound, such as a compound that induces bacterial gene/genetic payload/therapeutic product expression.
  • monitoring a detectable bacterially-expressed gene product can be used to determine whether it is desirable to administer an immunostimulatory bacterium and, optionally, a compound, the quantity of bacterium and/or compound to administer, and the type of bacterium and/or compound to administer, where, for example, determining that the subject is healthy can indicate the desirability of administering additional bacteria, different bacteria, or a therapeutic compound, such as a compound that induces bacterial gene/genetic payload/therapeutic product expression.
  • Such monitoring methods can be used to determine whether or not the therapeutic method is effective, whether or not the therapeutic method is pathogenic to the subject, whether or not the bacteria have accumulated in a tumor or metastasis, and whether or not the bacteria have accumulated in normal tissues or organs.
  • monitoring can determine whether or not immunostimulatory bacteria have accumulated in a tumor or metastasis of a subject. Upon such a determination, a decision can be made to further administer additional bacteria, a different immunostimulatory bacterium, and, optionally, a compound to the subject.
  • H. EXAMPLES The following examples are included for illustrative purposes only and are not intended to limit the scope of the invention.
  • Example 1 Auxotrophic Strains of S. typhimurium
  • the Salmonella Strain YS1646 is Auxotrophic for Adenosine Strains provided herein are engineered to be auxotrophic for adenosine.
  • the Salmonella strain YS1646 is a derivative of the wild-type strain ATCC 14028, and was engineered to be auxotrophic for purines due to disruption of the purI gene (synonymous with purM) (see, e.g., Low et al. (2004) Methods Mol. Med.90:47-60).
  • Strain YS1646 was grown overnight in lysogeny broth (LB) medium, washed with M9 minimal medium, and diluted into M9 minimal medium containing no adenosine, or increasing concentrations of adenosine. Growth was measured using a SpectraMax® M3 Spectrophotometer (Molecular Devices) at 37 °C, reading the OD 600 every 15 minutes.
  • strain YS1646 only was able to replicate when adenosine was provided at concentrations ranging from 11 to 300 micromolar, and was completely unable to replicate in M9 alone, or in M9 supplemented with 130 nanomolar adenosine.
  • Engineered adenosine auxotrophic strains exemplified herein include strains in which all or portions of the purI open reading frame are deleted from the chromosome to prevent reversion to wild-type. Such gene deletions can be achieved by any method known to one of skill in the art, including the lambda red system, as described below.
  • the Salmonella Strain YS1646 is Auxotrophic for ATP In addition to the purine and adenosine auxotrophy, it was determined whether the purI-deleted strain also can scavenge ATP. ATP accumulates to high levels in the tumor microenvironment, due to leakage from dying tumor cells.
  • strain YS1646 when provided with ATP, strain YS1646 is able to replicate in minimal media, but is unable to grow when not supplemented with ATP.
  • strain YS1646 was grown overnight in LB medium, washed with M9 minimal medium, and diluted into M9 minimal medium containing no ATP, or increasing concentrations of ATP (Fisher). Growth was measured using a SpectraMax® M3 Spectrophotometer (Molecular Devices) at 37 °C, reading the OD 600 every 15 minutes. The results demonstrated that strain YS1646 is able to replicate when ATP is provided at concentrations of 0.012 mM, but not in M9 alone.
  • Example 2 Defects in Intracellular Replication are Attributed to the msbB Mutation
  • the YS1646 strain contains mutations in purI, which limits replication to sites containing high concentrations of purines, adenosine, or ATP, and mutations in msbB, which alters the lipopolysaccharide (LPS) surface coat in order to reduce TLR4- mediated pro-inflammatory signaling. It also has been established that, unlike wild- type Salmonella, strain YS1646 is unable to replicate in macrophages. Experiments were performed to determine which of these genetic mutations is responsible for conferring that phenotype within the wild-type strain, ATCC 14028.
  • mouse RAW macrophage cells (InvivoGen, San Diego, Ca.) were infected with wild-type Salmonella strains containing deletions in purI, msbB, or both, at a multiplicity of infection (MOI) of approximately 5 bacteria per cell for 30 minutes, then the cells were washed with PBS, and medium containing gentamicin was added to kill extracellular bacteria. Intracellular bacteria are not killed by gentamicin, as it cannot cross the cell membrane.
  • MOI multiplicity of infection
  • cell monolayers were lysed by osmotic shock with water, and the cell lysates were diluted and plated on LB agar to enumerate surviving colony forming units (CFUs).
  • Salmonella typhimurium strain derived from strain YS1646 (which can be purchased from ATCC, Catalog # 202165) that has been engineered to have a deletion in the asd gene.
  • the Salmonella typhimurium strain YS1646 ⁇ asd was engineered using modifications of the method of Datsenko and Wanner (Proc. Natl. Acad. Sci. U.S.A.97:6640–6645 (2000)), as described below. Introduction of the Lambda Red Helper Plasmid into Strain YS1646 The YS1646 strain was prepared to be electrocompetent as described previously (Sambrook J.
  • Construction of asd Gene Knockout Cassette The asd gene from the genome of strain YS1646 (Broadway et al. (2014) J. Biotechnology 192:177-178) was used for designing the asd gene knockout cassette.
  • the asd gene knockout cassette then was PCR amplified using primers asd-1 and asd-2 (see, Table 1), and gel purified. Deletion of asd gene
  • the YS1646 strain carrying plasmid pKD46 was electroporated with the gel- purified linear asd gene knock-out cassette. Electroporated cells were recovered in SOC medium and plated onto LB agar plates supplemented with kanamycin (20 ⁇ g/mL) and diaminopimelic acid (DAP, 50 ⁇ g/mL).
  • lambda red recombinase induces homologous recombination of the chromosomal asd gene with the kan cassette (due to the presence of homologous flanking sequences upstream and downstream of the chromosomal asd gene), and knockout of the chromosomal copy of the asd gene occurs.
  • the presence of the disrupted asd gene in the selected kanamycin-resistant clones was confirmed by PCR amplification, with primers from the YS1646 genome flanking the sites of disruption (primer asd-3), and from the multi-cloning site (primer scFv-3) (see, Table 1).
  • Kanamycin Gene Cassette Removal The kan selectable marker was removed by using the Cre/loxP site-specific recombination system.
  • the YS1646 ⁇ asd gene Kan R mutant was transformed with pJW168, a temperature-sensitive plasmid expressing the Cre recombinase (SEQ ID NO:224). Amp R colonies were selected at 30 °C; pJW168 was subsequently eliminated by growth at 42 °C.
  • a selected clone was tested for loss of kan by replica plating on LB agar plates with and without kanamycin, and confirmed by PCR verification using primers from the YS1646 genome flanking the sites of disruption (primers asd-3 and asd-4; for primer sequence, see Table 1).
  • ⁇ asd mutant was unable to grow on LB agar plates at 37 °C, but was able to grow on LB plates containing 50 ⁇ g/mL diaminopimelic acid (DAP).
  • DAP diaminopimelic acid
  • the ⁇ asd mutant growth rate was evaluated in LB liquid media; it was unable to grow in liquid LB, but was able to grow in LB supplemented with 50 ⁇ g/mL DAP, as determined by measuring absorbance at 600 nM.
  • the plasmid contained the following features: a high copy (pUC19) origin of replication, a U6 promoter for driving expression of a short hairpin, an ampicillin resistance gene flanked by HindIII restriction sites for subsequent removal, and the asd gene containing 85 base pairs of sequence upstream of the start codon (SEQ ID NO:246).
  • shRNAs targeting murine TREX1 were introduced by restriction digestion with SpeI and XhoI, and ligation and cloning into E. coli DH5- alpha cells. The resulting plasmid was designated pATI-shTREX1.
  • Electroporated cells were added to 1 mL SOC supplemented with 50 ⁇ M diaminopimelic acid (DAP), incubated for 1 hour at 37 °C, and then spread onto agar plates that do not contain DAP, to select for strains that received plasmids with a functional asd gene.
  • DAP diaminopimelic acid
  • cell banks were produced by inoculating a flask of sterile lysogeny broth (LB) with a single well isolated colony of S. typhimurium, and incubating at 37 °C with agitation at 250 RPM. After the culture was grown to stationary phase, the bacteria were washed in PBS containing 10% glycerol, and stored in aliquots frozen at less than -60 °C.
  • the plasmid pATI-shTREX1 was amplified in E. coli and purified for transformation into the YS1646 ⁇ asd strain by electroporation and clonal selection on LB Amp plates, to produce strain YS1646 ⁇ asd-shTREX1.
  • the YS1646 ⁇ asd mutants complemented with pATIU6-derived plasmids were able to grow on LB agar and liquid media in the absence of DAP.
  • the ampicillin resistance gene (Amp R ) from pATI- shTREX1 was replaced with a kanamycin resistance gene.
  • kanamycin resistance (Kan R ) gene was amplified by PCR using primers APR-001 and APR-002 (SEQ ID NO:226 and SEQ ID NO:227, respectively), followed by digestion with HindIII, and ligation into the gel purified, digested pATIU6 plasmid.
  • a single point mutation was introduced into the pATIKan plasmid at the pUC19 origin of replication, using the Q5® Site-Directed Mutagenesis Kit (New England Biolabs) and the primers APR-003 (SEQ ID NO:228) and APR-004 (SEQ ID NO:229), to change the nucleotide T at position 148 to a C.
  • This mutation makes the origin of replication homologous to the pBR322 origin of replication, which is a low copy origin of replication, in order to reduce the plasmid copy number.
  • CT26 tumor-bearing mice were treated with strain YS1646, containing a plasmid that expresses an shRNA targeting TREX1 (YS1646-shTREX1), or with an asd-deleted strain of YS1646, containing a plasmid with a functional asd gene and an shRNA targeting TREX1 (YS1646 ⁇ asd-shTREX1).
  • CT26 (Colon Tumor #26) is a tumor model that originated from exposing BALB/c mice to N-nitro-N-methylurethane (NMU), resulting in a highly metastatic carcinoma that recapitulates the aggressive, undifferentiated and checkpoint- refractory human colorectal carcinoma (see, e.g., Castle et al. (2014) BMC Genomics 15(1):190).
  • NMU N-nitro-N-methylurethane
  • the tumor is rich in myeloid cells, such as macrophages and myeloid-derived suppressor cells (MDSCs) (see, e.g., Zhao et al. (2017) Oncotarget 8(33):54775-54787).
  • myeloid cells such as macrophages and myeloid-derived suppressor cells (MDSCs)
  • MDS myeloid-derived suppressor cells
  • mice bearing 8 day-old established flank tumors were intravenously (IV) injected with three doses of 5 x10 6 CFUs of the YS1646 ⁇ asd-shTREX1 strain, or the parental YS1646-shTREX1 strain, on days 8, 15, and 23.
  • the plasmid encodes shTREX1 as an exemplary therapeutic product; any other desired therapeutic product or products can be substituted.
  • Body weights and tumors were measured twice weekly. Tumor measurements were performed using electronic calipers (Fowler, Newton, MA). Tumor volume was calculated using the modified ellipsoid formula, 1/2(length ⁇ width 2 ).
  • mice were euthanized when tumor size reached >20% of body weight or became necrotic, as per IACUC regulations.
  • tumors were homogenized, and homogenates were serially diluted and plated on LB agar plates, to enumerate the total number of colony forming units (CFUs) present, or on LB plates containing kanamycin, to enumerate the number of kanamycin resistant colonies.
  • CFUs colony forming units
  • S. typhimurium strain YS1646-shTREX1 did not have selective pressure to maintain the shRNA plasmid, and demonstrated significant plasmid loss, as the percent of kanamycin resistant (Kan R ) colonies was less than 10%.
  • the strain that used the asd gene complementation system for plasmid maintenance had nearly identical numbers of kanamycin resistant and kanamycin sensitive CFUs. These data demonstrate that the asd gene complementation system is sufficient to maintain the plasmid in the context of the tumor microenvironment in mice.
  • Enhanced Anti-Tumor Efficacy Using asd Complementation System The asd complementation system is designed to prevent plasmid loss and potentiate the anti-tumor efficacy of the therapeutic product delivery by S. typhimurium strains in vivo.
  • YS1646 ⁇ asd strains containing the shTREX1 plasmid (YS1646 ⁇ asd-shTREX1), or scrambled control (YS1646 ⁇ asd- shSCR), that contain a functional asd gene cassette, were compared for anti-tumor efficacy in a murine colon carcinoma model, to strain YS1646 containing plasmid pEQU6-shTREX1 (YS1646-shTREX1), a plasmid that lacks an asd gene cassette, and therefore, does not have a mechanism for plasmid maintenance.
  • shTREX1 is an exemplary therapeutic product.
  • mice 6-8 week-old female BALB/c mice (8 mice per group) were inoculated SC in the right flank with CT26 cells (2x10 5 cells in 100 ⁇ L PBS). Mice bearing established flank tumors were IV injected twice, on day 8 and on day 18, with 5x10 6 CFUs of YS1646 ⁇ asd-shTREX1, or YS1646-shTREX1, and compared to PBS control.
  • the YS1646-shTREX1 strain demonstrated enhanced tumor control compared to PBS (70% tumor growth inhibition (TGI), day 28) despite its demonstrated plasmid loss over time.
  • These data demonstrate that improved potency is achieved by preventing plasmid loss, using the asd complementation system, and delivery of shTREX1, as compared to YS1646 containing plasmids without the asd gene complementation system.
  • strains with asd complementation systems are superior anti-cancer therapeutics.
  • the live attenuated S. typhimurium YS1646 strain containing the asd gene deletion was further engineered to delete the fliC and fljB genes, in order to remove both flagellin subunits. This eliminates pro-inflammatory TLR5 activation, in order to reduce pro-inflammatory signaling and improve anti- tumor adaptive immunity.
  • Deletion of fliC Gene In this example, fliC was deleted from the chromosome of the YS1646 ⁇ asd strain using modifications of the method of Datsenko and Wanner (Proc. Natl. Acad.
  • a kanamycin gene cassette flanked by cre/loxP sites then was cloned into plasmid pSL0147, and the fliC gene knockout cassette was then PCR amplified with primers flic-1 (SEQ ID NO:232) and flic-2 (SEQ ID NO:233), gel purified, and then introduced into the YS1646 ⁇ asd strain carrying the temperature sensitive lambda red recombination plasmid pKD46, by electroporation. Electroporated cells were recovered in SOC + DAP medium, and plated onto LB agar plates supplemented with kanamycin (20 ⁇ g/mL) and diaminopimelic acid (DAP, 50 ⁇ g/mL).
  • Colonies were selected and screened for insertion of the knockout fragment by PCR using primers flic-3 (SEQ ID NO:234) and flic-4 (SEQ ID NO:235).
  • pKD46 then was cured by culturing the selected kanamycin resistant strain at 42 °C and screening for loss of ampicillin resistance.
  • the kanamycin resistance marker then was cured by electroporation of a temperature-sensitive plasmid expressing the Cre recombinase (pJW168), and Amp R colonies were selected at 30 °C; pJW168 was subsequently eliminated by growing cultures at 42 °C.
  • fliC knockout clones were then tested for loss of the kanamycin marker by PCR, using primers flanking the sites of disruption (flic-3 and flic-4), and evaluation of the electrophoretic mobility on agarose gels.
  • Deletion of fljB Gene The fljB gene was then deleted from the YS1646 ⁇ asd/ ⁇ fliC strain using modifications of the methods described above. Synthetic fljB gene homology arm sequences that contained 249 and 213 bases of the left hand and right hand sequence, respectively, flanking the fljB gene, were synthesized and cloned into a plasmid called pSL0148 (SEQ ID NO:231).
  • a kanamycin gene cassette flanked by cre/loxP sites then was cloned into pSL0148, and the fljB gene knockout cassette was PCR amplified with primers fljb-1 (SEQ ID NO:236) and fljb-2 (SEQ ID NO:237) (see, Table 1), gel purified, and introduced into strain YS1646 ⁇ asd/ ⁇ fliC carrying the temperature sensitive lambda red recombination plasmid pKD46, by electroporation. The kanamycin resistance gene then was cured by Cre-mediated recombination, as described above, and the temperature-sensitive plasmids were cured by growth at non- permissive temperature.
  • fliC and fljB gene knockout sequences were amplified by PCR using primers flic-3 and flic-4, or fljb-3 (SEQ ID NO:238) and fljb-4 (SEQ ID NO:239), respectively, and verified by DNA sequencing.
  • This mutant derivative of strain YS1646 was designated YS1646 ⁇ asd/ ⁇ fliC/ ⁇ fljB, or YS1646 ⁇ asd/ ⁇ FLG for short.
  • YS1646 ⁇ asd/ ⁇ FLG The YS1646-derived asd- mutant strain harboring the deletions of both fliC and fljB, herein referred to as YS1646 ⁇ asd/ ⁇ FLG, was evaluated for swimming motility by spotting 10 microliters of overnight cultures onto swimming plates (LB containing 0.3% agar and 50 mg/mL DAP). While motility was observed for the YS1646 ⁇ asd strain, no motility was evident with the YS1646 ⁇ asd/ ⁇ FLG strain. The YS1646 ⁇ asd/ ⁇ FLG strain then was electroporated with a plasmid containing an asd gene, and its growth rate in the absence of DAP was assessed.
  • the YS1646 ⁇ asd strain induced 75% maximal LDH release, while the YS1646 ⁇ asd/ ⁇ FLG strain induced 54% maximal LDH release, demonstrating that deletion of the flagellin genes reduces the S. typhimurium-induced pyroptosis of infected macrophages.
  • Flagella-Deleted Mutants Lead to Less Pyroptosis in Infected Human Monocytes
  • THP-1 human macrophage cells (ATCC Catalog # 202165) were infected with the S.
  • typhimurium strains YS1646 and YS1646 ⁇ asd/ ⁇ FLG with the ⁇ asd strain containing plasmids encoding a functional asd gene to ensure plasmid maintenance.5x10 4 cells were placed in a 96-well dish with DMEM and 10% FBS. Cells were infected with washed log-phase cultures of S. typhimurium for 1 hour at an MOI of 100 CFUs per cell, then the cells were washed with PBS, and the media was replaced with media containing 50 ⁇ g/mL gentamicin to kill extracellular bacteria, and 50 ng/mL of IFN ⁇ to convert the monocytes into a macrophage phenotype.
  • the THP-1 cells were stained with CellTiter- Glo ® reagent (Promega), and the percentage of viable cells was determined using a luminescent cell viability assay using a SpectraMax® M3 plate reader (Molecular Devices) to quantify the luminescence.
  • the cells infected with the YS1646 strain had only 38% viability, while the cells infected with the YS1646 ⁇ asd/ ⁇ FLG strain had 51% viability, indicating that the deletion of the flagellin genes induced less cell death of human macrophages, despite a very high and supraphysiological MOI.
  • Flagella is not Required for Tumor Colonization After Systemic Administration
  • 6-8 week-old female BALB/c mice (5 mice per group) were inoculated SC in the right flank with CT26 cells (2x10 5 cells in 100 ⁇ L PBS).
  • Mice bearing 10-day established flank tumors were IV injected with a single dose of 3 x10 5 CFUs of the YS1646 ⁇ asd/ ⁇ FLG-shTREX1 strain, or the parental YS1646 ⁇ asd-shTREX1 strain.
  • mice were euthanized, and tumors were homogenized and plated on LB plates to enumerate the number of colony forming units (CFUs) per gram of tumor tissue.
  • CFUs colony forming units
  • the splenic colonization of the YS1646 ⁇ asd-shTREX1 strain was calculated as a mean of 1.5 x 10 3 CFU/g of spleen tissue, whereas splenic colonization of the flagella-deleted YS1646 ⁇ asd/ ⁇ FLG-shTREX1 strain was slightly lower, at a mean of 1.2 x 10 3 CFU/g of spleen tissue.
  • Flagella-Deleted Strains Demonstrate Enhanced Adaptive Immunity in a Murine Tumor Model
  • the CT26 murine model of colon carcinoma was used, where 6-8 week-old female BALB/c mice (5 mice per group) were inoculated SC in the right flank with CT26 cells (2x10 5 cells in 100 ⁇ L PBS).
  • mice bearing established flank tumors were IV injected 11 days post tumor implantation with 5 x10 6 CFUs of the YS1646 ⁇ asd/ ⁇ FLG-shTREX1 strain, or the parental YS1646 ⁇ asd-shTREX1, or the scrambled plasmid control strain, YS1646 ⁇ asd-shSCR, and compared to PBS control. Mice were bled 7 days post dosing on Sodium Heparin coated tubes (Becton Dickinson).
  • Non-coagulated blood was then diluted in the same volume of PBS and peripheral blood mononuclear cells (PBMCs) were separated from the interphase layer of whole blood using Lympholyte®-M cell separation reagent (Cedarlane). Isolated PBMCs were washed with PBS + 2% FBS by centrifugation at 1300 RPM for 3 minutes at room temperature, and resuspended in flow buffer. One million PBMCs were seeded per well of a V-bottom 96-well plate.
  • PBMCs peripheral blood mononuclear cells
  • CD11b + Gr1 + neutrophils possibly MDSCs, although further phenotyping in an ex vivo functional assay would be required
  • CD11b + F4/80 + macrophages CD8 + T-cells
  • CD8 + T-cells that recognize the CT26 tumor rejection antigen gp70 (AH1), the product of the envelope gene of murine leukemia virus (MuLV)-related cell surface antigen (see, e.g., Castle et al. (2014) BMC Genomics 15(1):190).
  • both strains carrying type I IFN-inducing payloads were capable of overwriting the normal anti-bacterial immune response, which clears bacterial infections through neutrophils and macrophages, and does not induce adaptive T-cell-mediate immunity.
  • a YS1646 ⁇ asd/ ⁇ FLG strain constitutively expressing mCherry (a red fluorescent protein) under the bacterial rpsM promoter, was IV administered to MC38 subcutaneous flank tumor-bearing mice.
  • the MC38 (murine colon adenocarcinoma #38) model was derived similarly as the CT26 model using mutagenesis, but with dimethylhydralazine, and in a C57BL/6 mouse strain (see, e.g., Corbett et al. (1975) Cancer Res.35(9):2434-2439).
  • MC38 has a higher mutational burden than CT26, and a similar viral-derived gp70 antigen (p15E) that can be detected by CD8 + T-cells, although it is not considered a rejection antigen. While variants of MC38 have been found to be partially responsive to checkpoint therapy, most variants of the cell line are considered checkpoint refractory and T-cell excluded (see, e.g., Mariathasan et al.
  • mice 6-8 week-old female C57BL/6 mice (5 mice per group) were inoculated SC in the right flank with MC38 cells (5x10 5 cells in 100 ⁇ L PBS). Mice bearing large established flank tumors were IV injected on day 34 with 1x10 6 CFUs of the YS1646 ⁇ asd/ ⁇ FLG-mCherry strain.
  • Tumors were resected 7 days post IV-dosing, and cut into 2-3 mm pieces into gentleMACSTM C tubes (Miltenyi Biotec) filled with 2.5 mL enzyme mix (RPMI-1640 containing 10% FBS with 1 mg/mL Collagenase IV and 20 ⁇ g/mL DNase I).
  • the tumor pieces were dissociated using OctoMACSTM (Miltenyi Biotec) specific dissociation program (mouse implanted tumors), and the whole cell preparation was incubated with agitation for 45 minutes at 37 °C.
  • a second round of dissociation was performed using the OctoMACSTM (mouse implanted tumor) program, and the resulting single cell suspensions were filtered through a 70 ⁇ M nylon mesh into a 50 mL tube.
  • the nylon mesh was washed once with 5 mL of RPMI-1640 + 10% FBS, and the cells were filtered a second time using a new 70 ⁇ M nylon mesh into a new 50 mL tube.
  • the nylon mesh was washed with 5 mL of RPMI-1640 + 10% FBS, and the filtered cells were then centrifuged at 1000 RPM for 7 minutes. The resulting dissociated cells were resuspended in PBS and kept on ice before the staining process.
  • the YS1646 ⁇ asd/ ⁇ FLG strain was further modified to delete pagP.
  • the pagP gene is induced during the infectious life cycle of S. typhimurium, and encodes an enzyme (lipid A palmitoyltransferase) that modifies lipid A with palmitate.
  • a strain deleted of pagP and msbB can produce only penta-acylated lipid A, allowing for lower pro-inflammatory cytokines due to low affinity for TLR4, enhanced tolerability, and increased adaptive immunity when the bacteria are engineered to deliver plasmids encoding immunomodulatory proteins.
  • ⁇ pagP Strain Construction The pagP gene was deleted from the YS1646 ⁇ asd/ ⁇ FLG strain using modifications of the methods described in the preceding examples. Synthetic pagP gene homology arm sequences that contain 203 and 279 bases of the left hand and right hand sequence, respectively, flanking the pagP gene, were synthesized and cloned into a plasmid called pSL0191 (SEQ ID NO:331).
  • a kanamycin gene cassette flanked by cre/loxP sites then was cloned into pSL0191, and the pagP gene knockout cassette was PCR amplified with primers pagp-1 (SEQ ID NO:315) and pagp-2 (SEQ ID NO:316) (see, Table 1), gel purified, and introduced into strain YS1646 ⁇ asd/ ⁇ FLG, carrying the temperature sensitive lambda red recombination plasmid pKD46, by electroporation. The kanamycin resistance gene then was cured by Cre-mediated recombination, as described above, and the temperature-sensitive plasmids were cured by growth at non-permissive temperature.
  • the pagP gene knockout sequences were amplified by PCR using primers pagp-3 (SEQ ID NO:317) and pagp-4 (SEQ ID NO:318), and verified by DNA sequencing.
  • the resulting mutant derivative of YS1646 was designated YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP.
  • pagP Deletion Mutants have Penta-Acylated LPS and Induce Reduced Inflammatory Cytokines
  • the pagP gene also was deleted from the YS1646 ⁇ asd strain using the lambda-derived Red recombination system, as described in Datsenko and Wanner (Proc. Natl. Acad. Sci.
  • Wild-type Salmonella had a minor lipid A peak with a mass of 2034, and a major peak with a mass of 1796, corresponding to the hepta-acylated and hexa-acylated species, respectively, due to the presence of a functional msbB gene.
  • the msbB- deleted strains, YS1646 and YS1646 ⁇ asd had major peaks at 1828 and 1585, corresponding to a mixture of hexa-acylated and penta-acylated lipid A.
  • LPS from the YS1646 ⁇ asd/ ⁇ pagP strain induced 25% of the amount of TNF ⁇ , compared to wild-type LPS, and induced 7-fold less IL-6 than wild-type LPS.
  • the LPS from the YS1646 ⁇ asd/ ⁇ pagP strain induced 22-fold less IL-6 than strain YS1646, demonstrating that the penta-acylated LPS species from a ⁇ pagP mutant is significantly less inflammatory in human cells, and indicating that the ⁇ pagP mutant would be better tolerated in humans.
  • PBMCs Frozen human PBMCs, isolated from healthy human donors, were thawed in complete medium (RPMI-1640 + 1X non-essential amino acids + 5% human AB serum), and washed by centrifugation for 10 minutes at 800 RPM at room temperature. PBMCs were resuspended in PBS + 2% FBS, and monocytes were negatively isolated using a CD16 depletion kit (StemCell Technologies). Isolated untouched monocytes were then washed by centrifugation in PBS + 2% FBS and resuspended in complete medium containing 100 ng/mL human macrophage colony- stimulating factor (M-CSF) and 10 ng/mL human IL-4.
  • M-CSF human macrophage colony- stimulating factor
  • Isolated monocytes (3e5 per well) were then seeded in a 24-well plate with a final volume of 750 ⁇ L. Two days after seeding, the cell culture media was entirely aspirated and replaced with fresh complete medium containing 100 ng/mL human M-CSF and 10 ng/mL human IL-4. Two days later (on day 4), 500 ⁇ ⁇ L of complete medium containing 100 ng/mL human M-CSF and 10 ng/mL human IL-4 was added per well for 48 hours. On day 6, the cell culture media was entirely aspirated and replaced with fresh complete medium without cytokines, alone, or with media containing the log-phase cultures of the S. typhimurium strains at an MOI of 20.
  • the YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP strain elicited the lowest IL-6 levels, at 332 ⁇ 100 pg /mL, demonstrating the reduced ability of this modified LPS coating to stimulate TLR4, and the resulting dramatically reduced inflammatory IL-6 production.
  • mice were injected intravenously with a dose range of 3e5 to 3e7 CFUs of strain YS1646, or the derivative strains YS1646 ⁇ asd/ ⁇ FLG, YS1646 ⁇ asd/ ⁇ pagP, and YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP.
  • strain YS1646 Unlike strain YS1646, the derivative strains also carried a plasmid encoding murine IL-2, an FDA-approved cytokine that has demonstrated significant toxicity when systemically administered.
  • the LD50 for strain YS1646 was found to be 4.4 x 10 6 CFUs (average of two studies), in line with previously published LD 50 reports of YS1646, and a >1000-fold improvement compared to wild-type S. typhimurium (see, e.g., Clairmont et al. (2000) J. Infect. Dis.181:1996-2002).
  • the LD50 for the YS1646 ⁇ asd/ ⁇ FLG strain was determined to be 2.07 x 10 7 CFUs, demonstrating a greater than 4.5-fold reduction in virulence compared to strain YS1646.
  • the LD50 for the YS1646 ⁇ asd/ ⁇ pagP strain was determined to be 1.39 x 10 6 CFUs, demonstrating at least a 3.2-fold reduction in virulence compared to strain YS1646, which is expected, given that the strain still has highly inflammatory flagella.
  • the LD 50 for the YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP strain could not be established, as no mice died at the highest dose given, but was >6.2 x 10 7 CFUs.
  • the YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP strain therefore demonstrates a >14-fold reduction in virulence compared to parental YS1646 strain.
  • mice from the 3 x 10 6 CFU dosing group described above were kept for 40 days post IV-dosing, at which time they were bled for serum, and assessed for antibody titers to S. typhimurium, by a modified flow-based antibody titering system.
  • Overnight cultures of the YS1646 ⁇ asd/ ⁇ FLG-mCherry strain were washed and fixed with flow cytometry fixation buffer.
  • Sera from the previously-treated mice, and from na ⁇ ve control mice were seeded in a 96-well plate, and serial dilutions were performed in PBS.
  • the bacteria were resuspended in PBS, and data were acquired using the NovoCyte® flow cytometer (ACEA Biosciences, Inc.), and analyzed using the MFI FlowJoTM software (Tree Star, Inc.).
  • MFI mean fluorescence intensity
  • the limit of detection (LOD) was chosen at an MFI of 1000, as that is the MFI obtained without staining, as well as with background staining with Goat anti-Mouse Fc AF488 antibody only.
  • mice treated with 3 x 10 6 CFUs of the YS1646 strain revealed a high MFI titer of anti-S. typhimurium serum antibodies from mice treated with 3 x 10 6 CFUs of the YS1646 strain (MFI of 29196.3 ⁇ 20730), in line with previously published data that YS1646 is able to generate serum antibodies (that are non-neutralizing). Fewer antibodies were detected in the mice treated with the YS1646 ⁇ asd/ ⁇ FLG strain (MFI of 11257 ⁇ 9290), which can be due to the lack of adjuvant activity from the flagella.
  • the combined deletions of the flagella and the pagP gene enable both improved safety, as well as significantly reduced immunogenicity, which will enable repeat dosing of high CFUs in humans.
  • pagP and Flagella Deleted Strains, and their Combination Demonstrate Significantly Higher Viability in Human Serum Compared to Strain YS1646
  • Strain YS1646 exhibits limited tumor colonization in humans after systemic administration. It is shown herein that strain YS1646 is inactivated by complement factors in human blood. To demonstrate this, strains YS1646 and E. coli D10B were compared to exemplary immunostimulatory bacteria provided herein, that contain additional mutations that alter the surface of the bacteria.
  • HI heat-inactivated
  • strain YS1646 (VNP20009) has very low tumor colonization when systemically administered. It is shown herein that strain YS1646 is highly sensitive to complement inactivation in human serum, but not in mouse serum. These data explain why limited tumor colonization was observed in humans, while mouse tumors were colonized at a high level. The fljB/fliC or pagP deletions, or the combination of these mutations, partially or completely rescues this phenotype. Thus, the enhanced stability observed in human serum with the YS1646 ⁇ asd/ ⁇ pagP, YS1646 ⁇ asd/ ⁇ FLG, and YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP strains provides for increased human tumor colonization.
  • the YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP strain was further modified to delete ansB, the gene encoding bacterial L-asparaginase II.
  • Secretion of L- asparaginase II by S. typhimurium in the presence of T-cells has been shown to directly impair T-cell function, by reducing T-cell receptor (TCR) expression and impairing cytolytic cytokine production.
  • TCR T-cell receptor
  • bacterially-derived asparaginases have been successfully used to treat acute lymphoblastic leukemia (ALL) for decades. Deletion of ansB eliminates the ability of the S.
  • ⁇ ansB Strain Construction The ansB gene was deleted from the YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP strain using modifications of the methods described in the preceding examples. Synthetic ansB gene homology arm sequences that contained 236 and 251 bases of the left hand and right hand sequence, respectively, flanking the ansB gene, were synthesized and cloned into a plasmid called pSL0230 (SEQ ID NO:332).
  • a kanamycin gene cassette flanked by cre/loxP sites then was cloned into plasmid pSL0230 and the ansB gene knockout cassette was PCR amplified with primers ansb-1 (SEQ ID NO:319) and ansb-2 (SEQ ID NO:320), gel purified, and introduced into strain YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP, carrying the temperature sensitive lambda red recombination plasmid pKD46, by electroporation.
  • the kanamycin resistance gene then was cured by Cre-mediated recombination, as described above, and the temperature-sensitive plasmids were cured by growth at non-permissive temperature.
  • the ansB gene knockout sequences were amplified by PCR using primers ansb-3 (SEQ ID NO:321) and ansb-4 (SEQ ID NO:322) (see, Table 1), and verified by DNA sequencing.
  • the resulting mutant derivative of YS1646 was designated YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB.
  • the plate was incubated at 37 °C in a 5% CO 2 incubator.
  • 100 ⁇ L of the co-culture supernatants were harvested from the wells, and a murine Th1-specific cytokine bead array (CBA, BioLegend) was performed.
  • CBA Th1-specific cytokine bead array
  • T-cells were harvested and analyzed for surface T-cell receptor ⁇ (TCR ⁇ ) expression on CD4 + and CD8 + T-cells by flow cytometry, as well as for intracellular staining of IFN ⁇ , TNF ⁇ , and IL-2.
  • deletion of ansB in the YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB strain significantly restores T-cell cytolytic function, as compared to the parental YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP strain.
  • mice bearing large established flank tumors were IV injected on day 17 with 1x10 7 CFUs of the YS1646 ⁇ asd/ ⁇ FLG-mCherry strain.
  • Tumors were resected 7 days post IV dosing and cut into 2-3 mm pieces into gentleMACSTM C tubes (Miltenyi Biotec) filled with 2.5 mL enzyme mix (RPMI-1640 containing 10% FBS with 1 mg/mL Collagenase IV and 20 ⁇ g/mL DNase I).
  • the tumor pieces were dissociated using OctoMACSTM (Miltenyi Biotec) specific dissociation program (mouse implanted tumors), and the whole cell preparation was incubated with agitation for 45 minutes at 37 °C.
  • a second round of dissociation was performed using the OctoMACSTM (mouse implanted tumor) program, and the resulting single cell suspensions were filtered through a 70 ⁇ M nylon mesh into a 50 mL tube.
  • the nylon mesh was washed once with 5 mL of RPMI-1640 + 10% FBS, and the cells were filtered a second time using a new 70 ⁇ M nylon mesh, into a new 50 mL tube.
  • the nylon mesh was washed with 5 mL of RPMI-1640 + 10% FBS, and the filtered cells were then centrifuged at 1000 RPM for 7 minutes. The resulting dissociated cells were resuspended in PBS and kept on ice before the staining process.
  • Flow cytometry data were acquired using the ACEA NovoCyte® flow cytometer (ACEA Biosciences, Inc.), and analyzed using the FlowJoTM software (Tree Star, Inc.).
  • MFI mean fluorescence intensity
  • csgD deletion eliminates the possibility of cellulose-mediated biofilm formation, reduces pro-inflammatory signaling, and enhances uptake by host phagocytic cells. This increase in intracellular localization would thereby enhance the effectiveness of plasmid delivery and immunomodulatory protein production.
  • ⁇ csgD Strain Construction The csgD gene was deleted from the YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB strain, using modifications of the methods described in the preceding examples.
  • Synthetic csgD gene homology arm sequences that contained 207 and 209 bases of the left hand and right hand sequence, respectively, flanking the csgD gene, were synthesized and cloned into a plasmid called pSL0196 (SEQ ID NO:333).
  • a kanamycin gene cassette flanked by cre/loxP sites then was cloned into plasmid pSL0196, and the csgD gene knockout cassette was PCR amplified with primers csgd-1 (SEQ ID NO:323) and csgd-2 (SEQ ID NO:324), gel purified, and introduced into strain YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ansB, carrying the temperature sensitive lambda red recombination plasmid pKD46, by electroporation.
  • the kanamycin resistance gene then was cured by Cre-mediated recombination as described above, and the temperature-sensitive plasmids were cured by growth at non-permissive temperature.
  • csgD gene knockout sequences were amplified by PCR, using primers csgd-3 (SEQ ID NO:325) and csgd-4 (SEQ ID NO:326), and verified by DNA sequencing.
  • the resulting mutant derivative of parental strain YS1646 was designated YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB/ ⁇ csgD.
  • csgD-Deleted Strains Cannot Form RDAR Colonies on Congo Red Plates
  • the ability to form Rough Dry And Red (RDAR) colonies after growth on Congo Red plates is a well-validated assay for bacterial biofilm formation.
  • the Rough and Dry texture occurs through cellulose production, and the red is due to the accumulation of pigment by the curli fimbriae surface structures.
  • the YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB strain was compared to the YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB/ ⁇ csgD strain for the ability to form the RDAR phenotype after incubation on Congo Red agar plates.
  • Congo Red agar plates were prepared with soytone (10 g/L) and yeast extract (5 g/L) (modified LB without NaCl), and complemented with Congo red (40 mg/L) and Coomassie brilliant blue G-250 (20 mg/L).
  • csgD-Deleted Strains Demonstrate Superior Anti-Tumor Efficacy in a Highly Refractory Mouse Model of Triple Negative Breast Cancer The impact of the csgD deletion in models where the immunostimulatory bacterial therapy colonizes tumors, but has shown limited efficacy, was assessed.
  • EMT6 tumor cells are administered orthotopically into the mammary fat pad, as opposed to subcutaneously in the flank, the model is T-cell excluded, highly metastatic, and highly refractory to immunotherapy, including to all approved checkpoint antibodies (see, e.g., Mariathasan et al. (2016) Nature 554: 544–548).
  • 6-8 week-old female BALB/c mice (5 mice per group) were inoculated in the left mammary fat pad with EMT6 tumor cells (ATCC # CRL- 2755) (2x10 5 cells in 100 ⁇ L PBS).
  • mice bearing 13 day-old established mammary tumors were IV injected with a single dose of 1 x10 7 CFUs of the csgD- deleted strain YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB/ ⁇ csgD, or the parental YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB strain, and compared to PBS control.
  • the bacterial strains contained a plasmid expressing a constitutively active murine STING (EF-1 ⁇ muSTING R283G).
  • the tumors in the PBS-treated mice grew evenly, reaching a max tumor volume at day 35 (1199.0 ⁇ 298.1 mm 3 ).
  • TGI tumor growth inhibition
  • the two bacterial strains contained the same plasmid payload, yet only one demonstrated significant anti-tumor efficacy.
  • orthotopic EMT6 a strain with a csgD deletion was able to induce systemic anti-tumor efficacy, and result in 60% complete responses.
  • csgD-Deleted Strains Demonstrate Enhanced Intracellular Uptake In Vivo
  • an ex vivo gentamicin protection assay was performed (see, Crull et al.
  • Tumors were resected 7 days post IV dosing, weighed, and minced in RPMI supplemented with 1 mg/mL collagenase IV and 20 mg/mL DNase I, and incubated with shaking at 37 °C for 30 minutes to generate a single cell suspension. After 30 minutes, the suspension was passed through a 70 mm filter, and the recovered volume was divided into two separate, identical samples. Gentamicin (Thermo Fisher Scientific) was added at 200 mg/mL to one of each of the paired samples to kill extracellular bacteria, and the samples were incubated with shaking at 37 °C for 90 minutes.
  • Gentamicin Thermo Fisher Scientific
  • the non-gentamicin treated tumors yielded high CFUs, as expected from well-colonized tumors, and treatment with gentamicin yielded less CFUs (1276 ⁇ 2410 CFUs), and much more than in the parental YS1646 strain-treated tumors.
  • This is due to more of the csgD- deleted bacteria residing intracellularly, and thus, being protected from gentamicin.
  • Example 8 pATI-1.75 Vector Construction A plasmid (pATI-1.75) was designed and synthesized that contains the following features: a pBR322 origin of replication, the asd gene, a kanamycin resistance gene flanked by HindIII sites for curing, and a multiple cloning site for expression cassette insertion.
  • the expression cassette is composed of multiple elements, including eukaryotic promoters, open reading frames (ORFs), posttranscriptional regulatory elements, and polyadenylation signals, that are assembled in various configurations.
  • Exemplary promoters include the human cytomegalovirus (CMV) immediate early core promoter encoded directly downstream of the CMV immediate early enhancer sequence, and the core promoter for human elongation factor-1 alpha (EF- 1 ⁇ ).
  • CMV human cytomegalovirus
  • EF- 1 ⁇ human elongation factor-1 alpha
  • Open reading frames can include one or more sequences that each are translated into a protein, and can be separated into distinct polypeptides by insertion of a 2A sequence, whereby eukaryotic ribosomes fail to insert a peptide bond between Gly and Pro residues within the 2A sequence.
  • 2A sequences are the T2A peptide (SEQ ID NO:327) from the Thosea asigna virus (TaV) capsid protein, and the P2A peptide (SEQ ID NO:328) from porcine teschovirus (PTV).
  • Upstream furin cleavage sites (RRKR), and other enhancer elements, are placed upstream to facilitate cleavage to separate the expressed proteins.
  • post-transcriptional regulatory elements examples include the Woodchuck Hepatitis virus PRE (WPRE; SEQ ID NO:346), and the Hepatitis B virus PRE (HPRE; SEQ ID NO:347), which increase accumulation of the cytoplasmic mRNA of a gene by promoting mRNA nuclear export to the cytoplasm, enhancing 3’ end processing and stability.
  • PREs post-transcriptional regulatory elements
  • WPRE Woodchuck Hepatitis virus PRE
  • HPRE Hepatitis B virus PRE
  • polyadenylation signal sequences include the SV40 polyadenylation signal, and the bovine growth hormone polyadenylation signal, both of which are 3’ regulatory elements that serve to promote transcriptional termination, and contain the sequence motif recognized by the RNA cleavage complex.
  • Example 9 Designed Heterologous Protein Expression Plasmids Induce Functional Protein Production from Human Cells Optimal Expression of Cytokines Established in Human Cells
  • immunostimulatory cytokines can be expressed from designed plasmids in human cells
  • a panel of cytokines were cloned into the pATI-1.75 plasmid, under the control of the EF-1 ⁇ promoter.
  • the cytokines include, but are not limited to, murine IL-2 (muIL-2), muIL-12p70, muIL-23, and human IL-2 (huIL-2).
  • HEK293T STING Null cells (InvivoGen) were seeded in 24-well plates coated with poly-L-lysine at 200,000 cells per well, overnight at 37 °C in a 5% CO 2 incubator, to achieve 80% confluency. The following day, 200 ng of each cytokine plasmid DNA was diluted in serum-free media and added to FuGENE® transfection reagent (Promega), at the proper reagent:DNA ratios, with untransfected wells as negative controls (in duplicates).
  • muIL-2 construct was evaluated in a murine IL-2 ELISA (R&D Systems), according to the manufacturer’s instructions, and an additional version of muIL-2 with codon optimization (muIL-2 CO) also was evaluated. Concentrations of neat supernatant were tested, and yielded an average of 1680 pg/mL of muIL-2 for the muIL-2 construct, and 1812 pg/mL of muIL-2 for the muIL-2 CO construct. These data confirmed the functionality of the constructs, and demonstrated that yield could be improved with codon optimization.
  • the muIL-12p70 construct was evaluated in a murine IL-12 ELISA (R&D Systems), according to the manufacturer’s protocol. When supernatants were added neat, a mean of 400 pg/mL of secreted muIL-12p70 was measured, although this was outside the linear range. When the supernatants were diluted 5-fold, an average of 105 pg/mL of secreted muIL-12p70 was detected. For the muIL-23 plasmid, detection of protein was achieved using the murine IL-23 ELISA (BioLegend), per kit instructions. With the supernatant added neat, a mean of 966 pg/mL of muIL-23 was detected.
  • IL-2 plasmid detection of protein was achieved using the human IL-2 ELISA (Invitrogen), per kit instructions. With the supernatant added neat, an average of 1422 pg/mL of huIL-2 was detected.
  • muIL-15R ⁇ -IL-15sc construct expressed using either the EF-1 ⁇ or CMV promoters, the murine IL-15 ELISA (eBioscience, Inc.) was used, per kit instructions.
  • the muIL-15R ⁇ -IL-15sc plasmid with the EF-1 ⁇ promoter resulted in an average of 131 pg/mL
  • the muIL-15R ⁇ -IL-15sc plasmid with the CMV promoter resulted in an average of 289 pg/mL.
  • PREs post-transcriptional regulatory elements
  • WPRE Woodchuck Hepatitis virus post- transcriptional regulatory element
  • HEK293T STING Null cells were seeded in 24-well plates coated with poly-L-lysine at 200,000 cells per well, overnight at 37 °C in a 5% CO2 incubator, to achieve 80% confluency.
  • cytokine plasmid DNA was diluted in serum-free media and added to FuGENE® transfection reagent (Promega), at the proper reagent:DNA ratios, with untransfected wells as negative controls (in duplicates).
  • FuGENE® transfection reagent Promega
  • Cell culture supernatants from each sample were collected at 24 hours post-transfection and assessed for activity by a human IL-2 ELISA (Invitrogen), according to the manufacturer’s instructions. Supernatants were added neat, or were diluted 5-fold.
  • cytokines such as muIL-15R ⁇ -IL-15sc
  • CMV promoter it was determined whether expression of cytokines could similarly be enhanced in donor-derived primary human M2 macrophages, the predominant macrophage phenotype in T-cell excluded, solid human tumors. Additionally, it was determined whether post-transcriptional regulatory elements, such as WPRE, could enhance expression in these cells.
  • the promoters EF-1 ⁇ and CMV were tested for controlling expression of muIL-2, and the WPRE post-transcriptional regulatory element was tested for expression of huIL-2.
  • Frozen human PBMCs isolated from healthy human donors, were thawed in complete medium (RPMI-1640 + 1X non-essential amino acids + 5% Human AB serum), and washed by centrifugation for 10 minutes at 800 RPM at room temperature. PBMCs were resuspended in PBS + 2% FBS, and monocytes were negatively isolated using a CD16 depletion kit (StemCell Technologies).
  • the isolated monocytes were cultured for 6 days in RPMI media containing M-CSF and IL-4, to generate M2 macrophages. For this, isolated untouched monocytes were washed by centrifugation in PBS + 2% FBS, and resuspended in complete medium containing 100 ng/mL human M-CSF and 10 ng/mL human IL-4. Isolated monocytes (3e5 per well) were then seeded in a 24- well plate with a final volume of 750 microliters. Two days after the seeding, the cell culture media was entirely aspirated and replaced with fresh complete medium containing 100 ng/mL human M-CSF and 10 ng/mL human IL-4.
  • plasmid DNA containing the EF-1 ⁇ - muIL-2 construct, the CMV-muIL-2 construct, the EF-1 ⁇ -huIL-2 construct, or the EF-1 ⁇ -huIL-2 + WPRE construct, as well as untransfected control, were diluted in the provided buffer, and mixed with 0.2 ⁇ L of Viromer® RED, and incubated at room temperature for 15 minutes to allow the Viromer® complexes to form. The DNA/Viromer® RED complexes were then slowly added to each well of the 24-well plate (in duplicates), and the plate was incubated at 37 °C in a CO2 incubator for 24 hours.
  • Co-Stimulatory Receptor Ligand 4-1BBL Expressed from Human Cells Co-stimulatory molecules, such as 4-1BBL, when expressed on antigen- presenting cells (APCs), can engage 4-1BB expressed on T-cells to promote optimal T-cell function.4-1BBL is negatively regulated by its cytoplasmic signaling domain. In the late-phase of 4-1BBL ligation of macrophages to T-cells, reverse signaling of the 4-1BBL cytoplasmic domain induces surface translocation of 4-1BBL to bind and form a signaling complex with TLR4.
  • HEK-293T cells were utilized.
  • HEK293T STING Null cells (InvivoGen) were seeded in 24-well plates coated with poly-L-lysine at 200,000 cells per well, overnight at 37 °C in a CO2 incubator, to achieve 80% confluency.
  • 200 ng of plasmid DNA, encoding mu4-1BBL ⁇ cyt was diluted in serum-free media and added to FuGENE® transfection reagent (Promega), at the proper reagent:DNA ratio, with untransfected wells as a negative control (in duplicates).
  • the cells were washed twice with PBS + 2% FBS by centrifugation at 1300 RPM for 3 minutes. The cells were then resuspended in PBS + 2% FBS, and stained with a PE-conjugated murine anti-4-1BBL antibody (clone TKS-1, BioLegend) and DAPI (dead/live stain). After 30 minutes, the cells were washed twice with PBS + 2% FBS by centrifugation at 1300 RPM for 3 minutes, and resuspended in PBS + 2% FBS.
  • a PE-conjugated murine anti-4-1BBL antibody clone TKS-1, BioLegend
  • DAPI dead/live stain
  • Flow cytometry data were acquired using the ACEA NovoCyte® flow cytometer (ACEA Biosciences, Inc.) and analyzed using the FlowJoTM software (Tree Star, Inc.). As a percentage of live cells, the untransfected control cells showed a percent positive staining for murine 4-1BBL of 14.6. In comparison, 93.4% of the cells that were transfected with the plasmid encoding mu4-1BBL ⁇ cyt, were positive for surface expression of 4-1BBL. These data demonstrate that the pATI-1.75 plasmid can effectively be used to express 4-1BBL at high levels on the surface of human cells.
  • Soluble TGF ⁇ Receptor II Expressed from Human Cells Soluble mouse TGF ⁇ receptor II variants were designed by removing the cytoplasmic and transmembrane portions of the full TGF ⁇ receptor II. Additionally, either a FLAG or Fc tag was added for detection. These variants were cloned into the pATI-1.75 vector under the control of a CMV promoter and a 3’ WPRE element. The sequences were confirmed by Sanger sequencing.1.5 x 10 6 HEK293T cells were plated one day prior on 6-well plates coated with poly-L-lysine, to achieve 80% confluency.
  • Mouse T- cells were harvested from the spleen using a magnetic isolation kit (StemCell Technologies). T-cells were incubated with anti-mouse CD3 ⁇ antibody, with or without the soluble receptor, at various concentrations of mouse TGF-beta. T-cell activation was quantified using the mouse TH1 CBA kit (BioLegend), and flow cytometry labeling of CD4, CD8, 4-1BB, and CD69. These data demonstrate the ability to express heterologous molecules, such as extracellular receptors fused to an Fc domain, from the plasmid engineered for delivery by the immunostimulatory bacteria to eukaryotic, such as human, cells.
  • heterologous molecules such as extracellular receptors fused to an Fc domain
  • CD3xCD19 bispecific T-cell engager (BiTE®), containing a FLAG tag and a His tag, was cloned into the pATI-1.75 vector, under the control of a CMV promoter and with a 3’ WPRE element. The sequences were confirmed by Sanger sequencing. 1.5 x 10 6 HEK293T cells were plated one day prior on 6-well plates coated with poly- L-lysine, to achieve 80% confluency. On the day of transfection, 3 ⁇ g of DNA was diluted in serum-free media and added to FuGENE® transfection reagent (Promega) at the proper reagent:DNA ratios.
  • FuGENE® transfection reagent Promega
  • Example 10 Immunostimulatory Bacterial Strains Efficiently Deliver Plasmids and Express Cytokines in Human Cells Flagella-Deleted Strains Containing Plasmids Encoding Murine IL-2 Induce Functional IL-2 Protein Expression Following Infection in Human Monocytes
  • the flagellin genes, fljB and fliC were deleted from the YS1646 strain of S. typhimurium with the asd gene deleted, generating the strainYS1646 ⁇ asd/ ⁇ FLG. This strain was electroporated with a plasmid containing an expression cassette with the EF-1 ⁇ promoter and the murine cytokine IL-2 (muIL-2).
  • the YS1646 ⁇ asd/ ⁇ FLG strain was electroporated with an expression plasmid encoding murine IL-15 ⁇ , as a control for a non-cognate cytokine. Additional constructs were created using the CMV promoter. To determine whether these strains containing expression plasmids can infect human monocytes and induce the production of murine IL-2, THP-1 human monocytic cells were plated at 50,000 cells/well in RPMI 1640 (GibcoTM) + 10% Nu- SerumTM (Corning®), one day prior to infection.
  • the cells were infected with the various strains at an MOI of 50 for one hour in RPMI, then washed 3 times with PBS, and resuspended in RPMI + 100 ⁇ g/mL gentamicin (Sigma). Supernatants were collected 48 hours later from a 96-well plate, and assessed for the concentration of murine IL-2 by ELISA (R&D Systems). The concentration of muIL-2 detected in the YS1646 ⁇ asd/ ⁇ FLG-IL15 ⁇ control wells was very low (6.52 pg/mL), as expected, and likely reflective of some cross-reactivity to the endogenous human IL-2 receptor.
  • bactofection i.e., transfer of plasmid DNA by the immunostimulatory bacterial strains herein
  • primary human M2 macrophages for expression of muIL-2
  • Frozen human PBMCs isolated from healthy human donors, were thawed in complete medium (RPMI-1640 + 1X non-essential amino acids + 5% Human AB serum), and washed by centrifugation for 10 minutes at 800 RPM at room temperature.
  • PBMCs were resuspended in PBS + 2% FBS, and monocytes were negatively isolated using a CD16 depletion kit (StemCell Technologies).
  • Isolated untouched monocytes were then washed by centrifugation in PBS + 2% FBS, and resuspended in complete medium containing 100 ng/mL human M-CSF and 10 ng/mL human IL-4.
  • Isolated monocytes (3e5 per well) were then seeded in a 24-well plate, with a final volume of 750 microliters. Two days after the seeding, the cell culture media was entirely aspirated and replaced with fresh complete medium containing 100 ng/mL human M-CSF and 10 ng/mL human IL-4.
  • plasmid DNA from the constructs encoding muIL-2 under control of the EF-1 ⁇ promoter (EF-1 ⁇ -muIL-2), or under control of the CMV promoter (CMV-muIL-2), or untransfected control were diluted in the provided buffer, mixed with 0.2 ⁇ L of Viromer® RED transfection reagent, and incubated at room temperature for 15 minutes to allow the DNA/Viromer® RED complexes to form. The DNA/Viromer® RED complexes were then slowly added to each well of the 24-well plate containing the monocytes (in duplicates), and the plate was incubated at 37 ⁇ C in a CO 2 incubator for 24 hours.
  • RNA extraction was performed using the Qiagen RNeasy Mini Kit with the following modifications.
  • a genomic DNA elimination step using an RNase-Free DNase kit (Qiagen) was included in the kit to remove genomic DNA from the total RNA.
  • Total RNA concentration was measured using a NanoDropTM One C UV-Vis Spectrophotometer (Thermo Fisher Scientific). The purity of each sample also was assessed from the A260/A230 absorption ratio. RNA was stored at -80 °C without freeze-thawing until reverse-transcription was performed.
  • cDNA synthesis was performed using 0.4-1 ⁇ g of template RNA using a C1000 Touch Thermal Cycler (Bio-Rad) and SuperScriptTM VILOTM Master Mix (Invitrogen) in a 30 ⁇ L reaction, according to the manufacturer’s instructions.
  • qPCR quantitative polymerase chain reaction
  • Bio-Rad a C1000 Touch Thermal Cycler
  • SuperScriptTM VILOTM Master Mix Invitrogen
  • qPCR quantitative polymerase chain reaction
  • SYBR® primers for murine IL-2 (Assay ID: qMmuCED0060978) were purchased from Bio-Rad.
  • the qPCR reaction (20 ⁇ L) was conducted per protocol, using the iTaqTM Universal SYBR® Green Supermix (Bio-Rad).
  • the standard thermocycling program on the Bio-Rad CFX96TM Real-Time System consisted of a 95 °C denaturation for 30 seconds, followed by 40 cycles of 95 °C for 5 seconds and 60 °C for 30 seconds. Reactions with template-free control were included for each set of primers on each plate. All samples were run in duplicate, and the mean Cq values were calculated. Quantification of the target mRNA was normalized using Gapdh (glyceraldehyde-3-phosphate dehydrogenase) reference mRNA (Bio-Rad, Assay ID: qMmuCED0027497). ⁇ Cq was calculated as the difference between target (mu-IL2) and reference (Gapdh) gene.
  • ⁇ C q was obtained by normalizing the ⁇ C q values of the treatments, to the ⁇ C q values of the non-treatment controls. Fold increase was calculated as 2 ⁇ - ⁇ Cq. The fold increases relative to untransfected/uninfected control are shown in the table below. The results show that, with either transfection or bactofection, the CMV promoter demonstrated superior expression of muIL-2, compared to the EF-1 ⁇ promoter, in primary human M2 macrophages. While transfection using the most efficient reagent currently available gave the highest levels of muIL-2 expression, bactofection also elicited high expression levels of muIL-2, demonstrating the high efficacy of heterologous gene transfer with the bacterial platforms provided herein.
  • Example 11 Bacterial Strains Efficiently Deliver Immunomodulatory Plasmids In Vivo and Demonstrate Potent Anti-tumor Activity Flagella-Deleted Strains Containing Plasmids Encoding Murine IL-2 Induce Potent Tumor Inhibition without Toxicity in a Mouse Model of Colorectal Carcinoma
  • S. typhimurium strains containing the muIL-2 expression plasmids can induce anti-tumor efficacy without additional toxicity
  • the YS1646 ⁇ asd/ ⁇ FLG strain containing the muIL-2 plasmid was compared to PBS control for safety and efficacy in the subcutaneous flank MC38 colorectal adenocarcinoma model.
  • TGI tumor growth inhibition
  • the immunostimulatory strain expressing muIL-2 potently inhibits tumor growth inhibition, in a safe and non-toxic manner, in a model of colorectal carcinoma.
  • tumors and spleens were excised and processed for tumor extracts using the GentleMACSTM Octo Dissociator and the M tubes (Miltenyi Biotec) molecule setting in 2 mL of PBS.
  • the homogenates were spun down at 1300 RPM for 10 minutes, and the supernatant was collected and assayed using the muIL-2 CBA kit (BD Biosciences), according to the manufacturer’s instructions. Results were quantified as pg/mL of muIL-2, and standardized to per gram of tissue.
  • the PBS control tumors exhibited background levels of muIL-2 in the tumor, with a mean of 134 pg/mL per gram of tumor tissue.
  • the YS1646 ⁇ asd/ ⁇ FLG-muIL-2 treated tumors yielded a much higher mean of 389.9 pg/mL muIL-2 per gram of tumor tissue, demonstrating the ability to detect elevated muIL-2 levels due to plasmid delivery in the tumor-resident myeloid cells.
  • Attenuated Bacterial Strains Containing Plasmids Encoding Murine Co- stimulatory Receptor Ligand 4-1BBL Demonstrate Curative Effects In Vivo
  • a bacterial strain containing a plasmid encoding 4-1BBL( ⁇ cyt) (described above), under control of the CMV promoter and containing a 3’ WPRE element, was assessed in the MC38 murine model of colorectal adenocarcinoma.
  • mice 6-8 week-old female C57BL/6 mice (5 mice per group) were inoculated SC in the right flank with MC38 colorectal adenocarcinoma cells (5x10 5 cells in 100 ⁇ L PBS). Mice bearing established flank tumors were IV injected on day 10 with 1x10 7 CFUs of strain YS1646 ⁇ asd/ ⁇ FLG/ ⁇ pagP/ ⁇ ansB containing the CMV-4-1BBL( ⁇ cyt)-WPRE plasmid, or with PBS vehicle control. The therapy was very well tolerated, with only an initial weight loss of 2.2% that had fully recovered 3 days later.
  • Example 12 Identification of Gain-of-Function Mutations in Genes That Promote Constitutive Type I Interferon Production Instances of subjects presenting with severe auto-inflammatory conditions and vasculopathies of unknown etiology occur, and, often derive from mutations. The cause for these conditions has, and can be, identified. Steps to identify a mutational basis for such a pathology are as follows.
  • step one intact genomic DNA is obtained from patients experiencing symptoms, and from healthy individuals.
  • Whole exome sequencing is performed, then introns and exons are analyzed. Analysis of genes, and identification of mutations in products in the pathways associated with the expression of type I interferon (IFN), is performed. From this analysis, mutations are discovered in genes known to lead to constitutive functional activation of the encoded proteins, and subsequent persistent expression of type I IFN.
  • cDNAs encoding the full-length gene, with and without the identified mutation(s) are transfected into a reporter cell line that measures expression of type I IFN.
  • a reporter cell line can be generated where the expression of luciferase is placed under control of the promoter for IFN- ⁇ .
  • a gain-of-function (GOF) mutant that is constitutively active will promote the expression of IFN- ⁇ ⁇ whereas the unstimulated wild-type (WT) protein will not.
  • WT unstimulated wild-type
  • STING SAVI STING-associated vasculopathy with onset in infancy
  • the WT-STING stimulation of IFN- ⁇ requires the addition of increasing exogenous levels of cGAMP to directly activate WT-STING.
  • Constitutively active mutations stimulate the expression of IFN- ⁇ in a cGAMP-independent manner.
  • Exemplary gain-of-function mutations in each of STING, RIG-I, MDA5, IRF3, and IRF7 are set forth below in Example 15, and discussed elsewhere herein.
  • genes in which gain-of-function mutations can be identified in subjects or produced by in vitro mutation and screening, include, but are not limited to TRIM56, RIP1, Sec5, TRAF3, TRAF2, TRAF6, STAT1, LGP2, DDX3, DHX9, DDX1, DDX9, DDX21, DHX15, DHX33, DHX36, DDX60, and SNRNP200.
  • TRIM56 RIP1, Sec5, TRAF3, TRAF2, TRAF6, STAT1, LGP2, DDX3, DHX9, DDX1, DDX9, DDX21, DHX15, DHX33, DHX36, DDX60, and SNRNP200.
  • Expression of Functional Constitutive Type I IFN Mutants in Human Cells Human STING (allele R232) and IRF3 gain-of-function (GOF) mutants were cloned into the pATI-1.75 vector, and the sequences were confirmed by PCR.
  • the plasmids were assessed using HEK293T STING Null Reporter cells (InvivoGen), which do not contain endogenous STING. These cells express secreted embryonic alkaline phosphatase (SEAP), placed under the control of the endogenous IFN-stimulated response element (ISRE) promoter, where the coding sequence of ISRE has been replaced by the SEAP ORF using knock-in technology.
  • SEAP embryonic alkaline phosphatase
  • ISRE endogenous IFN-stimulated response element
  • Type I interferon activity can be assessed by monitoring Type I IFN-stimulated SEAP production in the cell supernatants.
  • Type I interferon activation was determined by measuring ISRE-induced SEAP activity on a SpectraMax® M3 Spectrophotometer (Molecular Devices), at an absorbance of 650 nm. As shown in the table below, all GOF mutants were able to induce type I IFN activity in a STING ligand-independent manner in human cells, compared to the wild- type and negative controls, which did not induce type I IFN activity. The highest levels of type I IFN induction were observed with the human STING R284G variant, and the human IRF3 S396D phosphomimetic variant.
  • PBMCs Frozen human PBMCs, isolated from healthy human donors, were thawed in complete medium (RPMI-1640 + 1X non-essential amino acids + 5% Human AB serum), and washed by centrifugation for 10 minutes at 800 RPM at room temperature. PBMCs were resuspended in PBS + 2% FBS, and monocytes were negatively isolated using a CD16 depletion kit (StemCell Technologies). To generate primary human M2 macrophages, isolated untouched monocytes were washed by centrifugation in PBS + 2% FBS, and resuspended in complete medium containing 100 ng/mL human M-CSF and 10 ng/mL human IL-4.
  • Isolated monocytes (3e5 per well) were then seeded in a 24-well plate with a final volume of 750 microliters. Two days after the seeding, the cell culture media was entirely aspirated and replaced with fresh complete medium containing 100 ng/mL human M-CSF and 10 ng/mL human IL-4. Two days later (on day 4), 500 ⁇ ⁇ L of complete medium containing the cytokines was added per well and incubated for 48 hours. On day 6, the cell culture media was entirely aspirated and replaced with fresh complete medium without cytokines.
  • Duplicate wells were infected at an MOI of 450, for one hour in RPMI, with the following strains: YS1646 ⁇ asd/ ⁇ FLG containing a plasmid encoding wild-type (WT) human (hu) STING; YS1646 ⁇ asd/ ⁇ FLG containing a plasmid encoding the huSTING R284G variant; YS1646 ⁇ asd/ ⁇ FLG containing a plasmid encoding WT huIRF3; YS1646 ⁇ asd/ ⁇ FLG containing a plasmid encoding the huIRF3 S396D variant; or a strain containing a plasmid control.
  • WT wild-type
  • hu human
  • the cells were then washed 3 times with PBS, and resuspended in RPMI + 100 ⁇ g/mL gentamicin (Sigma).
  • the STING agonist 3’5’ RpRp c-di-AMP (InvivoGen)
  • ADU-S100 an analog of the clinical compound ADU-S100
  • the cells were lysed with 350 ⁇ L Buffer RLT with ⁇ -ME (Qiagen), and RNA extraction was performed using the Qiagen RNeasy Mini Kit with the following modification.
  • a genomic DNA elimination step using an RNase-Free DNase kit (Qiagen), was included to remove genomic DNA from the total RNA.

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