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Definitions

• the disclosure provides replicating viral vectors (RRVs) and non-replicating viral vectors (RNVs) for adoptive cell therapy.
• the RRVs and RNVs can deliver chimeric antigen receptors to immune cells (e.g., T-Cells) in vivo.
• CAR Chimeric antigen receptor
• T cells Chimeric antigen receptor (CAR)-engineered T cells (June & Sadelain, N Engl J Med, 379:64-73, 2018) were a key part of this designation with at least two groups of researchers, beginning in 2013, reporting on eye-catching responses to CAR therapy in patients, with“pounds of leukemia that melted away,” and showing amazing recoveries from advanced cancers.
• CARs are engineered receptors that graft a defined specificity onto an immune effector cell, typically a T cell, that augments T-cell function.
• Kymriah also known as tisagenlecleucel, [www.Jhcp.novartis.com/products/kymriah/, marketed by Novartis
• Yeskarta also known as axicabtagene ciloleucel, [www.Jyescartahcp.com developed by Kite Pharmaceuticals, now marketed by Gilead
• Kite Pharmaceuticals now marketed by Gilead
• a patient s own T lymphocytes are harvested, cultured ex vivo, and genetically modified to encode a synthetic receptor that binds a tumor antigen, allowing T cells to recognize and kill antigen-expressing cancer cells after reinfusion into the patient.
• This approach has been approved for CARs recognizing the B cell marker CD 19 (S.L. Maude et al., N Engl J Med., 371 : 1507-17, 2014) and has demonstrated success clinically for CD20 and BCMA, both markers for various types of lymphoma as well as some types of normal B cells, for which deficient patients can be simply treated by infusions of gamma-globulins.
• CARs recognizing the B cell marker CD 19
• BCMA both markers for various types of lymphoma as well as some types of normal B cells, for which deficient patients can be simply treated by infusions of gamma-globulins.
• CD34 + hematopoietic stem cells gamma delta T cells and NK cells
• CD34 + hematopoietic stem cells for which there is an approved therapy (StrimvelisTM, developed by GlaxoSmithKline, now marketed by Orchard Therapeutics) in Europe for treatment of children with the genetic disease, X-linked Severe Combined Immunodeficiency Syndrome (X-SCIDS).
• the disclosure provides a way around at least some of these difficulties by using direct administration of integrating gene transfer vectors encoding therapeutic gene(s) that transduce patient’s cells directly.
• the vector is a retroviral vector
• the target is a T cell
• the transgene is a CAR or similar artificial receptor construct (e.g., 1 st , 2 nd , 3 rd etc. generation CAR constructs).
• the vector is retroviral vector
• the target is a cell that has been activated by administration of an external agent and the transgene encodes a therapeutic activity.
• a retroviral vector can be replicating (RRV) or non-replicating (RNV) and can be derived from any integrating virus such as a foamy virus, a lentivirus, an alpha, beta or gamma retrovirus or CRISPR elements and also includes non-viral integrating vector such as those based on transposons such as“Piggy-bac” (Saito et al, Cytother. 16: 1257-1269, 2014) or“Sleeping Beauty”.
• the vector is a retroviral vector
• the activating agent is granulocyte colony stimulating factor (GCSF) and the target is CD34 + cells.
• GCSF granulocyte colony stimulating factor
• the vector is a gamma retroviral non-replicating vector, the target population is naturally activated T cells, and the transgene is a T cell receptor.
• the vector is a gamma retroviral vector, the target cell population is a naturally activated cell population and the transgene encodes an immune activating agent.
• the vector is a gamma retroviral vector, the target population is naturally activated T cells, and the transgene is a CAR (e.g., 1 st , 2 nd , 3 rd generation CAR).
• the CAR comprises a binding domain that targets one or more of: CD5; CD19; CD123; CD22; CD30; CD171; CS1 (also referred to as CD2 subset 1, CRACC, SLAMF7, CD319, and 19A24); C- type lectin-like molecule-1 (CLL-1 or CLECL1); CD33; epidermal growth factor receptor variant III (EGFRviii); ganglioside G2 (GD2); ganglioside GD3 (aNeu5Ac(2-8)aNeu5Ac(2- 3)bDGalp(l-4 )bDGlcp(l-l)Cer); TNF receptor family member B cell maturation (BCMA); Tn antigen ((Tn Ag) or (GalNAca-Ser/Thr)); prostate-specific membrane antigen (PSMA); Receptor tyrosine kinase-like orphan receptor 1 (ROR1); Fms Like Tyrosine Kinase 3 (FLT3)
• glycoceramide GloboH; mammary gland differentiation antigen (NY-BR-1); uroplakin 2 (UPK2); Hepatitis A virus cellular receptor 1 (HAVCR1); adrenoceptor beta 3 (ADRB3); pannexin 3 (PANX3); G protein-coupled receptor 20 (GPR20); lymphocyte antigen 6 complex, locus K 9 (LY6K); Olfactory receptor 51E2 (OR51E2); TCR Gamma Alternate Reading Frame Protein (TARP); Wilms tumor protein (WT1); Cancer/testis antigen 1 (NY- ESO-1); Cancer/testis antigen 2 (LAGE-la); Melanoma-associated antigen 1 (MAGE-A1); ETS translocation-variant gene 6, located on chromosome 12p (ETV6-AML); sperm protein 17 (SPA17); X Antigen Family, Member 1A (XAGE1); angiopoietin-binding cell surface receptor 2 (Tie 2); mela
• prostein prostein
• survivin telomerase
• telomerase prostate carcinoma tumor antigen- 1 (PCT A-l or Galectin 8), melanoma antigen recognized by T cells 1 (MelanA or MARTI); Rat sarcoma (Ras) mutant; human Telomerase reverse transcriptase (hTERT); sarcoma translocation breakpoints;
• ML-IAP melanoma inhibitor of apoptosis
• ERG transmembrane protease, serine 2
• TMPRSS2 N-Acetyl glucosaminyl-transferase V (NA17); paired box protein Pax-3 (PAX3); Androgen receptor; Cyclin Bl; v-myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN); Ras Homolog Family Member C (RhoC); Tyrosinase-related protein 2 (TRP-2); Cytochrome P450 IB 1 (CYP1B 1); CCCTC- Binding Factor (Zinc Finger Protein)-Like (BORIS or Brother of the Regulator oflmprinted Sites), Squamous Cell Carcinoma Antigen Recognized By T Cells 3 (SART3); Paired box protein Pax-5 (PAX5); proacrosin binding protein sp32 (OY-TES1); lymphocyte-specific protein tyrosine kinase (LCK); A kinase anchor
• TGFbetaR2 Lews Ag, TCR-betal chain, TCR-beta2 chain, TCR-gamma chain, TCR-delta chain, FITC, lenizing hormone receptor (LHR), Follicle stimulating hormone receptor (FSHR), Gonadotropin Hormone receptor (CGHR or GR), CCR4, GD3, SLAMF6, SLAMF4, HIV1 envelope glycoprotein, HTLVl-Tax, CMV pp65, EBV-EBNA3c, KSHV K8.1, KSHV- gH, influenza A hemagglutinin (HA), GAD, PDL1, Guanylyl cyclase C (GCC), auto antibody to desmoglein 3 (Dsg3), auto antibody to desmoglein 1 (Dsgl), HLA, HLA-A, HLA-A2, HLA-B, HLA-C, HLA-DP, HLA-DM, HLA-DOA, HLA-DOB, HLA-DQ, HLA- DR
• FIG. 1 shows the sequence and annotation of the sequence of a plasmid construct of the disclosure.
• FIG. 2 shows the viral RNA (vRNA) sequence with the multiple cloning site highlighted/bold/underlined.
• RNA CAR coding sequence
• MCS multiple cloning site
• FIG. 3 shows various DNA sequences encoding CARs used to exemplify the invention. Note that the corresponding RNA sequence is contemplated wherein T is replaced with U in the sequences.
• FIG. 4 shows various plasmid sequences containing an scFv sequence that binds to CD 19 for the production of an CD19-RNVCAR.
• FIG. 5A-B schematically depicts exemplary RNV vectors of the disclosure.
• FIG. 6 a plot of Infection level in PBMC in Balb/c mice with RNV-GFP determined in peripheral blood mononuclear cells (PBMC) at 7 days after the first IV dose of RNV-GFP.
• FIG. 7 shows a plot of RNV -GFP infection evaluated in a subset of PBMC populations: CD1 lb + , CD4 + , CD8 + , and CD19 + in parallel samples to those taken to generate the data for FIG. 6.
• FIG. 8 shows the results of an experiment in theA20 B-cell lymphoma animal model where tumor-bearing mice injected IV with the vector, RNV-1D3CAR, at a dose of 1E7 or 1E8 TU per day for five consecutive days, starting at day 5 after A20 implantation. Mice were monitored for 37 days and survival assessed. The higher dose of RNV-1D3CAR (5E8 TU) led to an improvement in survival in A20 lymphoma tumor bearing mice compared to a vehicle treated control group (no RNV) or the lower dose of RNV-1D3CAR (5E7).
• the disclosure provides pharmaceutical preparations, vectors, cells and methods for use in adoptive cell therapy.
• the vectors of the disclosure comprise a replicating or non-replicating viral-derived vector comprising coding sequences for various chimeric antigen receptors.
• ABSM antigen binding molecule
• Non-Ig scaffold proteins are domain-derived subunit of natural proteins from human and other species or are artificial and their size range from 6-20 kDa and can be expressed from a single polypeptide. They possess surface-exposed loops or amino acids in alpha-helical or beta sheet framework that can tolerate insertion, deletion and substitutions which via randomization, phage display screening and affinity maturation processes resulted in antigen-binding scaffold proteins that can function as antagonists or agonists.
• non-Ig scaffold proteins that have been identified and developed for therapeutics as scaffold binders. Due to their size, one major challenge these proteins face are fast renal clearance leading to short half-life in circulation but this not an issue when they are incorporated into a CAR or other membrane penetrating molecule. [ 0022 ] A separate challenge is that they often have lower binding affinity (KD 1-100 nM) than monoclonal antibodies and are associated with fast dissociation rates. Genetic modification of these scaffold proteins to include dimerization domain may increase steric hindrance-mediated blocking or avidity so that in certain signaling pathways this can lead to biological functions and therapeutic effects. Multiple methods have been proposed and at least partially tested using fusion proteins containing scaffold proteins.
• compositions and methods that use binding domains that comprise combinations of heavy and/or light chain CDRs linked by scaffold domains (e.g., Adhiron scaffold; scaffolds from human stefin A - see, EP22792058B1 and
• Tables 1 and 2 provide sequences useful in the compositions and methods of the disclosure. Please note that“T” can be“U” in the following nucleic acid sequences as RNA is contemplated.
• Table 1 Amino acid sequence of some non-Ig scaffold proteins that can function as antigen-binding proteins:
• the disclosure provides viral vectors the contain a heterologous
• polynucleotide encoding for example a CAR with an antigen binding domain (e.g., antibody or antibody fragment; or non-antibody binding domain such as a non-immunoglobulin (Ig) scaffold protein, or combinations of coding sequences etc.), that can be delivered to a cell or directly to a subject.
• an antigen binding domain e.g., antibody or antibody fragment; or non-antibody binding domain such as a non-immunoglobulin (Ig) scaffold protein, or combinations of coding sequences etc.
• the viral vector can be an adenoviral vector, a measles vector, a herpes vector, a retroviral vector (including Alpha-, Beta-, Gamma-, Delta-retroviral vector, Spumavirus vector such as Simian Foamy Virus (SFV) or Human Foamy Virus (HFV), or lentiviral vector), a rhabdoviral vector such as a Vesicular Stomatitis viral vector, a reovirus vector, a Seneca Valley Virus vector, a poxvirus vector (including animal pox or vaccinia derived vectors), a parvovirus vector (including an AAV vector), an alphavirus vector or other viral vector known to one skilled in the art (see also, e.g., Concepts in Genetic Medicine, ed. Boro Dropulic and Barrie Carter, Wiley, 2008, Hoboken, NJ.; The
• the retroviral vectors of the disclosure can be derived from (i.e., the parental nucleotide sequence is obtained from) MLV, MoMLV,
• the other type of antigen binding domain can be another scFv or antibody fragemt or a non-Ig-molecule such as described here (e.g . an adenectin, a pronectin, an affimer, a hckamer, or an anti-calin).
• antibody refers to a protein, or polypeptide sequence derived from an immunoglobulin molecule which specifically binds with an antigen.
• Antibodies can be monoclonal, or polyclonal, multiple or single chain, or intact immunoglobulins, and may be derived from natural sources or from recombinant sources.
• Antibodies can be tetramers of immunoglobulin molecules. The antibody may be
• antibody fragment refers to at least one portion of an antibody, that retains the ability to specifically interact with (e.g., by binding, steric hindrance,
• antibody fragments include, but are not limited to, Fab, Fab', F(ab'h, Fv fragments, scFv antibody fragments, disulfide-linked Fvs (sdFv), a Fd fragment consisting of the VH and CHI domains, linear antibodies, single domain antibodies such as sdAb (either vL or vH), camelid vHH domains, multi-specific antibodies formed from antibody fragments such as a bivalent fragment comprising two Fab fragments linked by a disulfide bridge at the hinge region, and an isolated CDR or other epitope binding fragments of an antibody.
• An antigen binding fragment can also be incorporated into single domain antibodies, maxibodies, minibodies, nanobodies, intrabodies, diabodies, triabodies, tetrabodies, v-NAR and bis-scFv (see, e.g., Hollinger and Hudson, Nature Biotechnology 23: 1126-1136, 2005).
• Antigen binding fragments can also be grafted into scaffolds based on polypeptides such as a fibronectin type III (Fn3)(see U.S. Patent No.: 6,703,199, which describes fibronectin polypeptide mini bodies).
• antibody heavy chain refers to the larger of the two types of polypeptide chains present in antibody molecules in their naturally occurring conformations, and which normally determines the class to which the antibody belongs.
• antibody light chain refers to the smaller of the two types of polypeptide chains present in antibody molecules in their naturally occurring conformations.
• Kappa (K) and lambda (l) light chains refer to the two major antibody light chain isotypes.
• anticancer effect refers to a biological effect which can be manifested by various means, including but not limited to, a decrease in tumor volume, a decrease in the number of cancer cells, a decrease in the number of metastases, an increase in life expectancy, decrease in cancer cell proliferation, decrease in cancer cell survival, or amelioration of various physiological symptoms associated with the cancerous condition.
• Anticancer agent refers to agents that inhibit aberrant cellular division and growth, inhibit migration of neoplastic cells, inhibit invasiveness or prevent cancer growth and metastasis.
• the term includes chemotherapeutic agents, biological agent (e.g., siRNA, viral vectors such as engineered MLV, adenoviruses, herpes virus that deliver cytotoxic genes), antibodies and the like.
• antigen refers to a molecule that provokes an immune response. This immune response may involve either antibody production, or the activation of specific immunologically-competent cells, or both.
• antigens can be derived from recombinant or genomic DNA. A skilled artisan will understand that any DNA, which comprises a nucleotide sequences or a partial nucleotide sequence encoding a protein that elicits an immune response therefore encodes an "antigen" as that term is used herein.
• an antigen need not be encoded solely by a full length nucleotide sequence of a gene. It is readily apparent that the disclosure includes, but is not limited to, the use of partial nucleotide sequences of more than one gene and that these nucleotide sequences are arranged in various combinations to encode polypeptides that elicit the desired immune response. Moreover, a skilled artisan will understand that an antigen need not be encoded by a "gene" at all. It is readily apparent that an antigen can be generated synthesized or can be derived from a biological sample, or might be macromolecule besides a polypeptide. Such a biological sample can include, but is not limited to a tissue sample, a tumor sample, a cell or a fluid with other biological components.
• Non-limiting examples of target antigens include: CD5, CD19; CD123; CD22; CD30; CD171; CS1 (also referred to as CD2 subset 1, CRACC, SLAMF7, CD319, and 19A24); C-type lectin-like molecule-1 (CLL-1 or CLECL1); CD33; epidermal growth factor receptor variant III (EGFRviii); ganglioside G2 (GD2); ganglioside GD3 (aNeu5Ac(2- 8)aNeu5Ac(2-3)bDGalp(l-4 )bDGlcp(l-l)Cer); TNF receptor family member B cell maturation (BCMA); Tn antigen ((Tn Ag) or (GalNAca-Ser/Thr)); prostate-specific membrane antigen (PSMA); Receptor tyrosine kinase-like orphan receptor 1 (ROR1); Fms Like Tyrosine Kinase 3 (FLT3); Tumor-associated
• CD44v6 a glycosylated CD43 epitope expressed on acute leukemia or lymphoma but not on hematopoietic progenitors, a glycosylated CD43 epitope expressed on non-hematopoietic cancers, Carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); B7H3 (CD276); KIT (CD117); Interleukin- 13 receptor subunit alpha-2 (IL-13Ra2 or CD213A2); Mesothelin; Interleukin 11 receptor alpha (IL-llRa); prostate stem cell antigen (PSCA); Protease Serine 21 (Testisin or PRSS21); vascular endothelial growth factor receptor 2 (VEGFR2); Lewis(Y) antigen; CD24; Platelet-derived growth factor receptor beta (PDGFR-beta); Stage-specific embryonic antigen-4 (SSEA-4); CD20; Folate receptor alpha (FRa or FR1); Folate
• MUC1 Mucin 1, cell surface associated
• EGFR epidermal growth factor receptor
• NCAM neural cell adhesion molecule
• Prostase prostatic acid phosphatase (PAP); elongation factor 2 mutated (ELF2M); Ephrin B2; fibroblast activation protein alpha (FAP); insulin-like growth factor 1 receptor (IGF-I receptor), carbonic anhydrase IX (CA1X);
• Proteasome Prosome, Macropain Subunit, Beta Type, 9 (LMP2); glycoprotein 100 (gplOO); oncogene fusion protein consisting of breakpoint cluster region (BCR) and Abelson murine leukemia viral oncogene homolog 1 (Abl) (bcr-abl); tyrosinase; ephrin type-A receptor 2 (EphA2); sialyl Lewis adhesion molecule (sLe); ganglioside GM3 (aNeu5Ac(2-3)bDClalp(l- 4)bDGlcp(l-l)Cer); transglutaminase 5 (TGS5); high molecular weight-melanoma associated antigen (HMWMAA); o-acetyl-GD2 ganglioside (OAcGD2); tumor endothelial marker 1 (TEM1/CD248); tumor endothelial marker 7-related (TEM7R); claudin 6 (CLDN6); thyroid
• anaplastic lymphoma kinase ALK
• Polysialic acid placenta-specific 1 (PLAC1); hexasaccharide portion of globoH glycoceramide (GloboH); mammary gland differentiation antigen (NY-BR-1); uroplakin 2 (UPK2); Hepatitis A virus cellular receptor 1 (HAVCR1); adrenoceptor beta 3 (ADRB3); pannexin 3 (PANX3); G protein-coupled receptor 20
• GPR20 lymphocyte antigen 6 complex, locus K 9 (LY6K); Olfactory receptor 51E2 (OR51E2); TCR Gamma Alternate Reading Frame Protein (TARP); Wilms tumor protein (WT1); Cancer/testis antigen 1 (NY-ESO-1); Cancer/testis antigen 2 (LAGE-la); Melanoma- associated antigen 1 (MAGE-A1); ETS translocation-variant gene 6, located on chromosome 12p (ETV6-AML); sperm protein 17 (SPA17); X Antigen Family, Member 1A (XAGE1); angiopoietin-binding cell surface receptor 2 (Tie 2); melanoma cancer testis antigen- 1 (MAD-CT-1); melanoma cancer testis antigen-2 (MAD-CT-2); Fos-related antigen 1; tumor protein p53 (p53); p53 mutant; prostein; survivin; telomerase; prostate carcinoma tumor antigen- 1 (PCT A-l)
• TMPRSS2 transmembrane protease, serine 2 (TMPRSS2) ETS fusion gene); N-Acetyl glucosaminyl- transferase V (NA17); paired box protein Pax-3 (PAX3); Androgen receptor; Cyclin Bl; v- myc avian myelocytomatosis viral oncogene neuroblastoma derived homolog (MYCN); Ras Homolog Family Member C (RhoC); Tyrosinase-related protein 2 (TRP-2); Cytochrome P450 IB 1 (CYP1B 1); CCCTC-Binding Factor (Zinc Finger Protein)-Like (BORIS or Brother of the Regulator of Imprinted Sites), Squamous Cell Carcinoma Antigen Recognized By T Cells 3 (SART3); Paired box protein Pax-5 (PAX5); proacrosin binding protein sp32 (OY- TES1); lymphocyte-specific protein t
• affinity is meant to describe a measure of binding strength. Affinity, in some instances, depends on the closeness of stereochemical fit between a binding agent and its target (e.g., between an antibody and antigen including epitopes specific for the binding domain), on the size of the area of contact between them, and on the distribution of charged and hydrophobic groups. Affinity generally refers to the“ability” of the binding agent to bind its target. There are numerous ways used in the art to measure“affinity”. For example, methods for calculating the affinity of an antibody for an antigen are known in the art, including use of binding experiments to calculate affinity.
• Binding affinity may be determined using various techniques known in the art, for example, surface plasmon resonance, bio-layer interferometry, dual polarization interferometry, static light scattering, dynamic light scattering, isothermal titration calorimetry, ELISA, analytical
• An exemplary method for determining binding affinity employs surface plasmon resonance.
• Surface plasmon resonance is an optical phenomenon that allows for the analysis of real-time biospecific interactions by detection of alterations in protein concentrations within a biosensor matrix, for example using the BIAcore system (Pharmacia Biosensor AB, Uppsala, Sweden and Piscataway, N.J.).
• An“antigen binding domain” refers to a polypeptide or peptide that due to its primary, secondary or tertiary sequence and or post-translational modifications and/or charge binds to an antigen with a high degree of specificity.
• the antigen binding domain may be derived from different sources, for example, an antibody, a non-immunoglobulin binding protein such as an affibody, affimer, DARPin or Pronectin (Skrlec et ctl, Trends Biotechnol, 33:408-418, 2015), a ligand or a receptor.
• “Avidity” refers to the strength of the interaction between a binding agent and its target (e.g., the strength of the interaction between an antibody and its antigen target, a receptor and its cognate and the like).
• the avidity can be weak or strong.
• Methods for calculating the affinity of an antibody for an antigen are known in the art, including use of binding experiments to calculate affinity.
• Antibody activity in functional assays e.g., flow cytometry assay
• Antibodies and affinities can be phenotypically characterized and compared using functional assays (e.g., flow cytometry assay).
• the term“Association constant (A ' a) is defined as the equilibrium constant of the association of a receptor and ligand.
• autoantigen refers to an endogenous antigen that stimulates production of an autoimmune response, such as production of autoantibodies.
• Autoantigen also includes a self-antigen or antigen from a normal tissue that is the target of a cell mediated or an antibody-mediated immune response that may result in the development of an autoimmune disease.
• autoantigens include, but are not limited to, desmoglein 1, desmoglein 3, and fragments thereof.
• beneficial results may include, but are in no way limited to, lessening or alleviating the severity of the disease condition, preventing the disease condition from worsening, curing the disease condition, preventing the disease condition from developing, lowering the chances of a patient developing the disease condition and prolonging a patient’s life or life expectancy.
• binding domain or "antibody molecule” refers to a protein, e.g., an immunoglobulin chain or fragment thereof, comprising at least one domain, e.g, immunoglobulin variable domain sequence that can bind to a target with affinity higher than a non-specific domain.
• the term encompasses antibodies and antibody fragments and also other non-immunoglobulin protein binding domains (Skrlec et al, supra).
• an antibody molecule is a multi-specific antibody molecule, e.g, it comprises a plurality of immunoglobulin variable domain sequences, wherein a first immunoglobulin variable domain sequence of the plurality has binding specificity for a first epitope and a second immunoglobulin variable domain sequence of the plurality has binding specificity for a second epitope.
• a multi-specific antibody molecule is a bispecific antibody molecule.
• a bispecific antibody has specificity for two antigens.
• a bispecific antibody molecule is characterized by a first immunoglobulin variable domain sequence which has binding specificity for a first epitope and a second immunoglobulin variable domain sequence that has binding specificity for a second epitope.
• cancer and“cancerous” refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth.
• Examples of cancer include, but are not limited to B-cell lymphomas (Hodgkin’s lymphomas and/or non- Hodgkins lymphomas), T cell lymphomas, myeloma, myelodysplastic syndrome, skin cancer, brain tumor, breast cancer, colon cancer, rectal cancer, esophageal cancer, anal cancer, cancer of unknown primary site, endocrine cancer, testicular cancer, lung cancer, hepatocellular cancer, gastric cancer, pancreatic cancer, cervical cancer, ovarian cancer, liver cancer, bladder cancer, cancer of the urinary tract, cancer of reproductive organs thyroid cancer, renal cancer, carcinoma, melanoma, head and neck cancer, brain cancer (e.g., glioblastoma multiforme), prostate cancer, including but not limited to androgen-dependent prostate cancer and androgen-independent prostate cancer, and leukemia.
• tumor and cancer are used interchangeably herein, e.g., both terms encompass solid and liquid, e.g., diffuse or circulating, tumors.
• cancer or “tumor” includes premalignant, as well as malignant cancers and tumors.
• chemotherapeutic agents are compounds that are known to be of use in chemotherapy for cancer.
• Non-limiting examples of chemotherapeutic agents can include alkylating agents such as thiotepa and CYTOXAN® cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizele
• spongistatin nitrogen mustards such as chlorambucil, chlomaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard;
• nitrogen mustards such as chlorambucil, chlomaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard;
• nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammall and calicheamicin omegall (see, e.g., Agnew, Chem. Inti. Ed. Engl., 33: 183-186 (1994)); dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as neocarzinostatin chromophore and related
• chromoprotein enediyne antiobiotic chromophores aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5-oxo-L-norleucine, ADRIAMYCIN® doxorubicin (including morpholino-doxorubicin, cyanomorpholino- doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin,
• TAXOL® paclitaxel Bristol-Myers Squibb Oncology, Princeton, N.J.
• ABRAXANE® Cremophor-free albumin-engineered nanoparticle formulation of paclitaxel
• TAXOTERE® doxetaxel Rhone-Poulenc Rorer, Antony, France
• chloranbucil e.g., TAXOL® paclitaxel (Bristol-Myers Squibb Oncology, Princeton, N.J.), ABRAXANE® Cremophor-free, albumin-engineered nanoparticle formulation of paclitaxel (American Pharmaceutical Partners, Schaumberg, Ill.), and TAXOTERE® doxetaxel (Rhone-Poulenc Rorer, Antony, France); chloranbucil;
• GEMZAR® gemcitabine 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as /.vplatin. oxaliplatin and carboplatin; vinblastine; platinum; etoposide (VP- 16); ifosfamide; mitoxantrone; vincristine; NAVELBINE; vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (Camptosar, CPT-11) (including the treatment regimen of irinotecan with 5-FU and leucovorin); topoisomerase inhibitor RFS 2000; difluoromethylomithine (DMFO); retinoids such as retinoic acid;
• DMFO difluoromethylomithine
• capecitabine combretastatin; leucovorin (LV); oxaliplatin, including the oxaliplatin treatment regimen (FOLFOX); lapatinib (Tykerb); inhibitors of PKC-alpha, Raf, H-Ras, EGFR (e.g., erlotinib (Tarceva®)) and VEGF-A that reduce cell proliferation and pharmaceutically acceptable salts, acids or derivatives of any of the above or combinations thereof.
• FOLFOX oxaliplatin treatment regimen
• lapatinib Tykerb
• inhibitors of PKC-alpha, Raf, H-Ras, EGFR e.g., erlotinib (Tarceva®)
• VEGF-A that reduce cell proliferation and pharmaceutically acceptable salts, acids or derivatives of any of the above or combinations thereof.
• CARs Chimeric antigen receptors
• CARs Chimeric antigen receptors
• CARs are artificial T cell receptors contemplated for use as a targeted therapy for cancer, using a technique called adoptive cell transfer.
• the essential antigen-binding, signaling, and stimulatory functions of the receptor polypeptide have been reduced by genetic recombination methods to a single polypeptide chain, generally referred to as a Chimeric Antigen Receptor (CAR) (See, e.g., Eshhar, U.S. Pat. No. 7,741,465; Eshhar, U.S. Patent Application Publication No. 2012/0093842).
• CARs are constructed specifically to stimulate T cell activation and proliferation in response to a specific antigen to which the CAR binds.
• a CAR refers to a set of polypeptides, typically two in the simplest embodiments, which when expressed in an immune effector cell, provides the cell with specificity for a target cell, typically a cancer cell, and with intracellular signal generation.
• a CAR comprises at least an extracellular antigen binding domain, a transmembrane domain (see, e.g., SEQ ID NO: l) and a cytoplasmic signaling domain (also referred to herein as "an intracellular signaling domain”) comprising a functional signaling domain derived from a stimulatory molecule and/or costimulatory molecule (see, e.g., SEQ ID NO:5).
• the set of polypeptides are contiguous with each other.
• the stimulatory molecule is the zeta chain associated with the T cell receptor complex.
• the cytoplasmic signaling domain further comprises one or more functional signaling domains derived from at least one costimulatory molecule as defined below.
• the costimulatory molecule is chosen from the costimulatory molecules described herein, e.g., 4-1BB (i.e., CD137; SEQ ID NO:5), CD27 and/or CD28.
• the CAR comprises an optional leader sequence at the amino-terminus (N-terminus) of a CAR fusion polypeptide (see, e.g., SEQ ID NO:6).
• the CAR further comprises a leader sequence at the N-terminus of the extracellular antigen binding domain, wherein the leader sequence is optionally cleaved from the antigen binding domain (e.g., a scFv) during cellular processing and localization of the CAR to the cellular membrane.
• the leader sequence is optionally cleaved from the antigen binding domain (e.g., a scFv) during cellular processing and localization of the CAR to the cellular membrane.
• a leader sequence e.g., a scFv
• CAR-T cells T lymphocytes bearing such CARs are generally referred to as CAR-T lymphocytes.
• Codon optimization or“controlling for species codon bias” refers to the preferred codon usage of a particular host cell. As will be understood by those of skill in the art, it can be advantageous to modify a coding sequence to enhance its expression in a particular host. The genetic code is redundant with 64 possible codons, but most organisms typically use a subset of these codons. The codons that are utilized most often in a species are called optimal codons, and those not utilized very often are classified as rare or low-usage codons.
• Optimized coding sequences containing codons preferred by a particular prokaryotic or eukaryotic host can be prepared, for example, to increase the rate of translation or to produce recombinant RNA transcripts having desirable properties, such as a longer half-life, as compared with transcripts produced from a non-optimized sequence.
• Translation stop codons can also be modified to reflect host preference.
• A“conservative substitution” or “conservative sequence modifications” refers to amino acid modifications that do not significantly affect or alter the binding characteristics or function of the encoded protein.
• “conservative sequence modifications” refers to amino acid modifications that do not significantly affect or alter the binding characteristics or function of the TCR constant chain, antibody, antibody fragment, or non immunoglobulin binding domains. Such conservative modifications include amino acid substitutions, additions and deletions. Modifications can be introduced into a TCR constant chain, antibody or antibody fragment, the non-immunoglobulin binding domain or other proteins or polypeptides of the disclosure by standard techniques known in the art, such as site-directed mutagenesis and PCR-mediated mutagenesis.
• Conservative amino acid substitutions are ones in which the amino acid residue is replaced with an amino acid residue having a similar side chain.
• Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine, tryptophan), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
• the antigen binding domain retains sufficient antibody structure such that is has the required function, namely, the ability to bind to an antigen it does not connotate or include a limitation to a particular process of producing the antibody, e.g., it does not mean that, to provide the antigen binding domain, one must start with an antibody sequence and delete unwanted sequence, or impose mutations, to arrive at the antigen binding domain.
• intracellular signaling domain refers to an intracellular signaling portion of a molecule.
• the intracellular signaling domain generates a signal that promotes an immune effector function of an immune cells.
• immune effector function include cytolytic activity and helper activity, including the secretion of cytokines.
• the intracellular signaling domain can comprise a primary intracellular signaling domain.
• Exemplary primary intracellular signaling domains include those derived from the molecules responsible for primary stimulation, or antigen dependent simulation.
• the intracellular signaling domain can comprise a costimulatory intracellular domain.
• Exemplary costimulatory intracellular signaling domains include those derived from molecules responsible for costimulatory signals, or antigen independent stimulation.
• a primary intracellular signaling domain can comprise a cytoplasmic sequence of CD3z
• a costimulatory intracellular signaling domain can comprise cytoplasmic sequence from co-receptor or costimulatory molecule, such as CD28 or 41BB.
• a primary intracellular signaling domain can comprise a signaling motif which is known as an immunoreceptor tyrosine-based activation motif or ITAM.
• ITAM containing primary cytoplasmic signaling sequences include, but are not limited to, those derived from CD3 zeta, common FeR gamma (FCER1G), Fe gamma Rlla, FeR beta (Fe Epsilon Rib), CD3 gamma, CD3 delta, CD3 epsilon, CD79a, CD79b, DAPIO, and DAP 12.
• the term "flexible polypeptide linker” as used in refers to a peptide linker that consists of amino acids such as glycine and/or serine residues used alone or in combination, to link polypeptide chains together (e.g., variable heavy and variable light chain regions together).
• the flexible polypeptide linkers include, but are not limited to, (Gly4Ser)4 or (Gly4Ser)3.
• the linkers include multiple repeats of (Gly2Ser),
• “Mammal” as used herein refers to any member of the class Mammalia, including, without limitation, humans and nonhuman primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, sheep, pigs, goats and horses;
• operably linked refers to functional linkage or association between a first component and a second component such that each component can be functional.
• operably linked includes the association between a regulatory sequence and a heterologous nucleic acid sequence resulting in expression of the latter.
• a first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence.
• a first polypeptide functions in the manner it would independent of any linkage and the second polypeptide functions as it would absent a linkage between the two.
• Percent identity in the context of two or more nucleic acids or polypeptide sequences, refers to two or more sequences that are the same. Two sequences are
• substantially identical if two sequences have a specified percentage of amino acid residues or nucleotides that are the same (e.g., 60% identity, optionally 70%, 71%. 72%. 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% identity over a specified region, or, when not specified, over the entire sequence), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection.
• the identity exists over a region that is at least about 50 nucleotides (or 10 amino acids) in length, or more preferably over a region that is 100 to 500 or 1000 or more nucleotides (or 20, 50, 200 or more amino acids) in length.
• sequence comparison For sequence comparison, generally one sequence acts as a reference sequence, to which test sequences are compared.
• test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated.
• sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.
• Methods of alignment of sequences for comparison are well known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith and Waterman, (1970) Adv. Appl. Math.
• polynucleotide refers to polymers of nucleotides such as deoxyribonucleic acid (DNA), and, where appropriate, ribonucleic acid (RNA).
• DNA deoxyribonucleic acid
• RNA ribonucleic acid
• a “protein” or “polypeptide”, which terms are used interchangeably herein, comprises one or more chains of chemical building blocks called amino acids that are linked together by chemical bonds called peptide bonds.
• RNV refers to a non-replicating viral vector, and may be a retroviral vector comprising long terminal repeats, packaging signals and a cloning site (see, SEQ ID NO: 12, which comprises the RNA backbone sequence of a construct of the disclosure).
• An RNV of the disclosure is produced from a plasmid comprising SEQ ID NO:3 transformed into a producer/packaging cell line such as an HT1080 derived packaging cell line HA-LB (Sheridan et al, Mol. Ther., 2:262-275,2000) or the similarly constructed HA-L2 packaging cell line, or by transfection with the appropriate helper genomes encoding viral protein into 293T of other efficient producer cell line.
• a producer/packaging cell line such as an HT1080 derived packaging cell line HA-LB (Sheridan et al, Mol. Ther., 2:262-275,2000) or the similarly constructed HA-L2 packaging cell line, or by transfection with the appropriate helper genomes
• an RNV can be produced by transfecting a packaging cell line comprising a gag, pol and env coding sequence with the plasmid of SEQ ID NO:3 comprising packaging signals.
• the method produces RNVs in which the retroviral genome is packaged in a capsid and envelope, through the use of a packaging cell.
• the packaging cells are provided with viral protein-coding sequences, typically in the form of two plasmids integrated into the genome of the cell, which produce all proteins necessary for production of viable retroviral particles, a DNA viral construct which codes for an RNA which will carry the desired gene, along with a packaging signal which will direct packaging of the RNA into the retroviral particles.
• RNVCAR refers to a non-replicating viral vector comprising long terminal repeats, packaging signals and containing a coding sequence for a chimeric antigen receptor (CAR).
• CAR comprises a binding domain that targets and selectively binds to any number of antigens (e.g., cancer antigens etc.).
• X is the name or acronym of a specific antigen (e.g., CD19- RNVCAR).
• the antigen can be targeted by any number of different binding domains as described herein (e.g., scFvs).
• RRV refers to a replicating viral vector, and may be a retroviral vector comprising long terminal repeats, gag, pol, env, packaging signals and a cloning site. An RRV of the disclosure does not require a help cell in order to produce infectious virons.
• the RRV comprises a gammaretroviral GAG protein
• gammaretroviral POL protein a gammaretroviral envelope
• a gammaretroviral RNA polynucleotide comprising 3' untranslated region (U3) and repeat region (R) sequences from murine leukemia virus (MLV), Moloney murine leukemia virus (MoMLV), Feline leukemia virus (FeLV), Baboon endogenous retrovirus (BEV), porcine endogenous virus (PERV), the cat derived retrovirus RD114, squirrel monkey retrovirus, Xenotropic murine leukemia virus- related virus (XMRV), avian reticuloendotheliosis virus (REV), or Gibbon ape leukemia virus (GALV) at the 3' end of the gammaretroviral polynucleotide sequence, an R and 5' untranslated region (U5) sequence from MLV, MoMLV, FeLV, BEV, PERV, RD114, squirrel monkey retrovirus, XMRV, REV or GALV
• RRV CAR refers to a replicating viral vector comprising, for example, a gammaretroviral GAG protein; a gammaretroviral POL protein; a
• gammaretroviral envelope a gammaretroviral RNA polynucleotide comprising 3' untranslated region (U3) and repeat region (R) sequences from murine leukemia virus (MLV), Moloney murine leukemia virus (MoMLV), Feline leukemia virus (FeLV), Baboon endogenous retrovirus (BEV), porcine endogenous virus (PERV), the cat derived retrovirus RD114, squirrel monkey retrovirus, Xenotropic murine leukemia virus-related virus
• XMRV avian reticuloendotheliosis virus
• GALV Gibbon ape leukemia virus
• the CAR comprises a binding domain that targets and selectively binds to any number of antigens (e.g., cancer antigens etc.).
• antigens e.g., cancer antigens etc.
• the disclosure uses“X”-RRVCAR, wherein X is the name or acronym of a specific antigen (e.g., CD19-RRVCAR).
• the antigen can be targeted by any number of different binding domains as described herein (e.g., scFvs).
• the sequences for various binding domains useful in the preparations of CAR constructs are known (see, e.g., International Application Publication WO 2018/102795 at Table 5; the sequences and disclosure of which is incorporated herein by reference).
• scFv refers to a fusion protein comprising at least one antibody fragment comprising a variable region of a light chain and at least one antibody fragment comprising a variable region of a heavy chain, wherein the light and heavy chain variable regions are contiguously linked, e.g., via a synthetic linker, e.g., a short flexible polypeptide linker, and capable of being expressed as a single chain polypeptide, and wherein the scFv retains the specificity of the intact antibody from which it is derived.
• a synthetic linker e.g., a short flexible polypeptide linker
• an scFv may have the vL and vH variable regions in either order, e.g., with respect to the N-terminal and C-terminal ends of the polypeptide, the scFv may comprise vL-(linker)- vH or may comprise vH-(linker)-vL.
• a scFv is also described as vL-(Gly- Ser-Linker)-vH.
• signaling domain refers to the functional region of a protein which transmits information within the cell to regulate cellular activity via defined signaling pathways by generating second messengers or functioning as effectors by responding to such messengers.
• subject is intended to include living organisms in which an immune response can be elicited (e.g., any domesticated mammal or a human).
• T-cell and“T-lymphocyte” are interchangeable and used synonymously herein. Examples include but are not limited to naive T cells (“lymphocyte progenitors”), central memory T cells, effector memory T cells, stem memory T cells (T SCm ), iPSC-derived T cells, synthetic T cells or combinations thereof.
• naive T cells (“lymphocyte progenitors”)
• central memory T cells central memory T cells
• effector memory T cells effector memory T cells
• T SCm stem memory T cells
• iPSC-derived T cells synthetic T cells or combinations thereof.
• Treatment and“treating,” as used herein refer to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted pathologic condition, prevent the pathologic condition, pursue or obtain beneficial results, or lower the chances of the individual developing the condition even if the treatment is ultimately unsuccessful.
• Those in need of treatment include those already with the condition as well as those prone to have the condition or those in whom the condition is to be prevented.
• Tumor refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues.
• the disclosure provides methods and compositions for producing CAR-T cells in vivo vs. ex vivo.
• the compositions include recombinant vectors (e.g. , viral vectors) that contain chimeric antigen receptor (CAR) coding sequences that can be integrated into T-Cells or immune cells in vivo.
• the methods of the disclosure include the introduction of recombinant vectors carrying CAR coding sequences in vivo (e.g., by intravenous administration).
• CAR T cells T cells expressing chimeric antigen receptors (CARs) are termed CAR T cells- this encompasses both synthetic non-HLA restricted hybrid molecules, for example, an external target antigen binding site from a monoclonal antibody, and also modified or unmodified HLA restricted conventional T cell receptor subunits that recognize intracellular HLA restricted epitope presentation.
• RNVs containing chimeric antigen receptor coding sequences are termed RNVCAR.
• T-cells transfected with an RNVCAR that express the CAR are referred to as gamma CAR-T cells RNV.
• the disclosure is based upon the identification of number of factors including: (a) the production of large amounts of high titer crude RNVCAR from retroviral vector producer lines, optionally in serum free and/or suspension culture; (b) purification and concentration of the vector to eliminate antigenic protein contaminants so that vector can be safely administered IV to patients as pharmaceutical preparations; (c) the observation that a small proportion of the vector gets taken up by patient T cells and this slowly decays over time; (d) the realization that specific CAR T cells that recognize a target will then amplify in vivo to achieve therapeutic benefit; (e) that because the gamma retrovirus will only effectively infect replicating cells, IV administration leads to transduction of activated T cells, because these will be a large percentage of accessible replicating cells in the blood.
• T cell stimulatory strategies including, but not limited to:
• RNVCAR may also be engineered to be“safety- modified” to reduce the possibility of insertional gene activation in some target cell populations (Schambach et al. , Methods in Molecular Biology, Methods and Protocols, 506: 191-205, 2009) for example with a self-inactivating (SIN) configuration.
• SIN self-inactivating
• Various“SIN” configurations are known in the art.
• Self-inactivating" (SIN) vectors refers to replication-defective vectors, e.g., retroviral or lentiviral vectors, in which the 3' LTR enhancer-promoter region, known as the U3 region, has been modified (e.g., by deletion or substitution) to prevent viral transcription beyond the first round of viral replication.
• the 3' LTR enhancer-promoter region known as the U3 region
• the 3' LTR is modified such that the U5 region is replaced, for example, with an ideal poly(A) sequence. It should be noted that modifications to the LTRs such as modifications to the 3' LTR, the 5' LTR, or both 3' and 5' LTRs, are also included in the disclosure.
• An additional safety enhancement can be provided by replacing the U3 region of the 5' LTR with a heterologous promoter to drive transcription of the viral genome during production of viral particles.
• heterologous promoters which can be used include, for example, viral simian virus 40 (SV40) (e.g., early or late), cytomegalovirus (CMV) (e.g., immediate early), Moloney murine leukemia virus (MoMLV), Rous sarcoma virus (RSV), and herpes simplex virus (HSV) (thymidine kinase) promoters.
• SV40 viral simian virus 40
• CMV cytomegalovirus
• MoMLV Moloney murine leukemia virus
• RSV Rous sarcoma virus
• HSV herpes simplex virus
• Typical promoters are able to drive high levels of transcription in a Tat-independent manner.
• the heterologous promoter has additional advantages in controlling the manner in which the viral genome is transcribed.
• the heterologous promoter can be inducible, such that transcription of all or part of the viral genome will occur only when the induction factors are present.
• Induction factors include, but are not limited to, one or more chemical compounds or the physiological conditions such as temperature or pH, in which the host cells are cultured.
• Engineered RNVCARs may also contain“control” genes such as prodrug activating genes including, but not limited to, herpes thymidine kinase, purine nucleoside phosphorylase, cytosine deaminase or nitroreductase, or dimerizable death or apoptosis inducing proteins such as Cas9 hybrids with mutated FK506 dimerizable tails, to delete CAR T cells after therapeutic endpoints have been met or when clinically important side effects occur (such as autoantigen or off-target-related adverse events or inadvertent transduction of tumor cells potentially rendering the tumor unrecognizable by the CAR T-cells).
• prodrug activating genes including, but not limited to, herpes thymidine kinase, purine nucleoside phosphorylase, cytosine deaminase or nitroreductase, or dimerizable death or apoptosis inducing proteins such as Ca
• Engineered RNV CAR may also contain“activation-enhancement” RNA- expression modifiers such as non-coding RNAs or proteins such as single-chain antibodies, affimers, that specifically down-regulate expression of T cell check point inhibitors such as PD-1, CTLA-4 or agonists for other appropriate immune accessory molecules.
• the RNV would transduce patient T cells so that a CAR T cell expresses the chimeric antigen receptor, a“control” gene such as cytosine deaminase, and a shRNA that degrades PD-1 transcripts and subsequently lowers PD-1 protein levels.
• the disclosure allows multiple chimeric receptors against multiple tumor associated antigens and tumor neoantigens or other disease-associated antigens to be simultaneously delivered intravenously by using a mixture of RNVCARs carrying chimeric receptors against multiple antigens and epitopes.
• RNVCAR delivery of chimeric antigen receptors to T cells is not an indication specific therapeutic and may be combined with personalized cancer-, or disease-profiling to select the chimeric receptors most likely to bind to antigens and neoantigens expressed by the patient regardless of indication.
• the ability of separate RNVCARs to intravenously delivery chimeric receptors with varying antigen binding capabilities allows temporal treatment regimens that can allow new CARs to be delivered following selective pressure and tumor or disease adaptation that deletes the original CAR epitopes.
• RNVCARs may be used in combination with immunotherapeutic enhancers such as checkpoint inhibitors (e.g. anti- CTLA4 and anti-PD-1), anti -tumor escape targeted drugs (e.g. IDO-1 inhibitors and anti- TGF ), and/or chemotherapeutics with known immune-modulating effects (e.g.,
• temozolomide temozolomide, cyclophosphamide and 5-FU.
• RNV delivery of chimeric receptors to patient T cells may be enhanced through the use of T-cell activating adjuvants at time of RNVCAR intravenous injection (e.g., 3-0-desacyl-4'-monophosphoryl lipid A (MPL) and interferon gamma).
• RNV may be delivered lymphatically and when appropriate, to the draining lymph node of solid tumor indications where tumor-associated and neoantigens are expected to be presented.
• RNV may also be pseudotyped to increase transduction efficiency of T cells (e.g. GALV, amphotropic env or measles virus glycoproteins H and F) or to direct specificity of T cell sub types (e.g., memory CD4 T cells using chimeric C-HIV envelope pseudotype or CD8 T cells with MLV-10A1 envelope).
• T cells e.g. GALV, amphotropic env or measles virus glycoproteins H and F
• direct specificity of T cell sub types e.g., memory CD4 T cells using chimeric C-HIV envelope pseudotype or CD8 T cells with MLV-10A1 envelope.
• an RNV CAR comprising a coding domain for targeting an antigen/cognate of interested (e.g., CD 19) is delivered in vivo as a pharmaceutically acceptable preparation to human patient T cells.
• a CD19-RNVCAR is injected intravenously into the blood stream for delivery to human T cells. This intravenous delivery can be done as a bolus injection or through slow infusion over minutes to hours. Injections may be repeated over several days to increase the frequency and likelihood of obtaining transduced T cells.
• the population of T cells can be further primed for RNVCAR vector uptake in vivo by administration of various T cell stimulatory strategies: vaccination with live viral vaccines such as measles, vaccinia or some flu vaccines; addition of adjuvant excipients currently approved in human vaccines, T cell stimulating bacterial proteins (direct and indirect), cytokine stimulation (IL2 and others), administration of allergy panel tests, various super antigens in clinically acceptable human doses, monoclonal antibodies such as OKT3 (Muromonab-CD3), and myeloid depletion using drugs such as cyclophosphamide.
• live viral vaccines such as measles, vaccinia or some flu vaccines
• adjuvant excipients currently approved in human vaccines
• T cell stimulating bacterial proteins direct and indirect
• IL2 and others cytokine stimulation
• allergy panel tests various super antigens in clinically acceptable human doses
• monoclonal antibodies such as OKT3 (Muromonab-CD3), and
• RNVCAR delivery to patient T cells may be enhanced through the use of T-cell activating adjuvants at time of RNVCAR intravenous injection (e.g. 3-0-desacyl-4'-monophosphoryl lipid A (MPL) and interferon gamma).
• T-cell activating adjuvants e.g. 3-0-desacyl-4'-monophosphoryl lipid A (MPL) and interferon gamma
• MPL monophosphoryl lipid A
• interferon gamma interferon gamma
• RNVCARs may be used in combination with immunotherapeutic enhancers such as checkpoint inhibitors (e.g. anti-CTLA4 and anti-PD-1), anti-tumor escape targeted drugs (e.g. IDO-1 inhibitors and anti-TGF ), chemotherapeutics with known immune-modulating effects (e.g. temozolimide and 5-FU), or personalized neoantigen vaccines.
• checkpoint inhibitors e.g
• An RNV may also be pseudotyped to increase transduction efficiency of T cells (e.g., GALV, amphotropic env or measles virus glycoproteins H and F) or to direct specificity of T cell sub types (e.g., memory CD4 T cells using chimeric C-HIV envelope pseudotype or CD8 T cells with MLV-10A1 envelope).
• Delivery of an RNVCAR e.g., a CD19-RNVCAR
• these intravenous methods produce patient T cells that target and destroy cells, microorganisms etc. that express the antigen that is specifically recognized by the binding domain of the RNVCAR (e.g., in the case of CD19-RNVCAR transduced T-cells would target and destroy CD19 + cells).
• an RNVCAR is delivered lymphatically and when appropriate, to the draining lymph node of solid tumor indications where tumor-associated and neoantigens are expected to be presented.
• Direct injection of lymph nodes are similarly enhanced through the use of adjuvants and combinations as mentioned above.
• the method includes addition of herpes simplex virus-thymidine kinase (HSV- TK), yeast cytosine deaminase (CD) or other suicide gene or pro-drug activator systems, to the RNVCAR as a method to deplete transduced cells in the case of adverse events or at end of treatment.
• HSV- TK herpes simplex virus-thymidine kinase
• CD yeast cytosine deaminase
• suicide gene or pro-drug activator systems to the RNVCAR as a method to deplete transduced cells in the case of adverse events or at end of treatment.
• the RNVCAR vector encoding a CD 19-CAR is engineered with TK, CD or other“control” genes (e.g., Tocagen’s modified yeast cytosine deaminase; see, U.S. Pat. No.
• RNVCAR e.g., CD19-RNVCAR
• a RNVCAR can be tracked to the tumor using radiolabeled pyrimidine (thymidine) and purine (acycloguanosine) derivatives as reporter probes for imaging of HSV- TK enzyme activity with PET.
• An additional advantage of including a prodrug activating enzyme such as HSV-TK or CD is that if some low percentage of tumor cells are also transduced with the CAR vector and this event renders the transduced tumor cells non - responsive to the CAR in T cells (M. Ruella et a/. Nat. Med., 24: 1499-1503, 2018), such tumor cells will automatically be eliminated by a course of prodrugs such valacyclovir or 5- fluorocytosine, respectively.
• the disclosure provides a recombinant nucleic acid construct comprising a nucleic acid molecule encoding a CAR targeting any of the antigens identified herein.
• the nucleic acid sequence comprises a DNA plasmid construct comprising SEQ ID NO:3 having cloned into it a CAR construct.
• SEQ ID NO: 18 to 22 provide plasmid sequences derived from SEQ ID NO:3 and containing various CAR constructs targeting CD 19.
• the disclosure provides an RNVCAR comprising an RNA sequence packaged into a viral capsid.
• the RNVCAR is obtained by transfecting a nucleic acid construct containing a CAR and comprising SEQ ID NO:3 into a packaging cell line and culturing the cell line to produce the RNVCAR.
• the RNVCAR will comprise SEQ ID NO: 12 and comprising an RNA sequence encoding a desired CAR construct (e.g., a CAR construct targeted to a desired antigen).
• the disclosure also provides a vector or vectors comprising a nucleic acid sequence or sequences encoding an RNV, RNVCAR or RNV comprising a suicide/prodrug activator sequence described herein.
• the disclosure provides one RNVCAR construct encoded by a single vector.
• the disclosure provides more than one vector, e.g., one vector encoding a CAR and a second vector encoding a suicide/prodrug activator gene.
• the vector or the vectors are chosen from DNA vector(s), RNA vector(s), plasmid(s), gamma-retrovirus vector(s).
• the vector is a gutted-gamma retroviral vector comprising LTRs and packaging sequences.
• DNA and/or RNA can be introduced into target cells using any of a number of different methods, for instance, commercially available methods which include, but are not limited to, electroporation (Amaxa Nucleofector-II (Amaxa Biosystems, Cologne,
• a method of treating a subj ect e.g. , reducing or ameliorating a hyperproliferative disorder or condition (e.g., a cancer, including, but not limited to, solid tumor, a soft tissue tumor, a blood cancer, or a metastatic lesion) in a subject is provided.
• a hyperproliferative disorder or condition e.g., a cancer, including, but not limited to, solid tumor, a soft tissue tumor, a blood cancer, or a metastatic lesion
• cancer is meant to include all types of cancerous growths or oncogenic processes, metastatic tissues or malignantly transformed cells, tissues, or organs, irrespective of histopathologic type or stage of invasiveness.
• Exemplary solid tumors include malignancies, e.g., adenocarcinomas, sarcomas, and carcinomas, of the various organ systems, such as those affecting breast, liver, lung, brain, lymphoid, gastrointestinal (e.g., colon), genitourinary tract (e.g., renal, urothelial cells), prostate and pharynx.
• Adenocarcinomas include cancers such as most colon cancers, rectal cancer, renal cell carcinoma, liver cancer, non-small cell carcinoma of the lung, cancer of the small intestine and cancer of the esophagus.
• the cancer is a melanoma, e.g., an advanced stage melanoma.
• Metastatic lesions of the aforementioned cancers can also be treated or prevented using the methods and compositions of the disclosure.
• other cancers that can be treated or prevented include pancreatic cancer, bone cancer, skin cancer, cutaneous or intraocular malignant melanoma, uterine cancer, ovarian cancer, rectal cancer, cancer of the head or neck, cancer of the anal region, stomach cancer, testicular cancer, uterine cancer, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the cervix, carcinoma of the vagina, carcinoma of the vulva, Hodgkin Disease, non-Hodgkin lymphoma, cancer of the esophagus, cancer of the small intestine, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, sarcoma of soft tissue, cancer of the urethra, cancer of the penis, chronic or acute leukemias including acute myeloid leukemia, chronic myeloid leukemia,
• Exemplary cancers whose growth can be inhibited include cancers typically responsive to immunotherapy.
• Non-limiting examples of cancers for treatment include renal cancer (e.g . clear cell carcinoma), melanoma (e.g., metastatic malignant melanoma), breast cancer, prostate cancer (e.g. hormone refractory prostate adenocarcinoma), colon cancer and lung cancer (e.g. non-small cell lung cancer).
• a non-replicating vector is constructed to contain a chimeric antigen receptor (CAR).
• CAR chimeric antigen receptor
• an RNVCAR is developed and targeted against murine CD 19.
• the murine CD 19 targeting is achieved using a single chain variable fragment (scFv) constructed from the rat hybridoma clone 1D3.
• the scFv contains the 1D3 variable heavy chain (VH) followed by a GS linker to the 1D3 variable light chain (VL).
• the amino acid sequence for the murine-targeted scFv are set out in Table 4.
• Nucleotides encoding the murine CD 19 scFv can be any codons deemed most appropriate for viral vector expression and stability.
• the nucleotide sequence encoding the 1D3 scFv (VH- GS-VL) can be expressed from one of: the retroviral vector promoter (e.g., LTR), an internal promoter, an internal ribosome entry site (IRES) (see, e.g., WO2010036986, incorporated herein by reference), or a protein fusion strategy (e.g., using a furin peptidase site, or 2 A cassette; see, e.g., U.S. Pat. Publ. No.
• the scFv is followed in-frame by the nucleotide sequence encoding either human CD8 hinge domain, the murine CD8 hinge domain, or the murine CD28 hinge domain as set forth in Table 5.
• the hinge domain is followed in-frame by the nucleotide sequence encoding either the human CD8
• transmembrane domain TMD
• the transmembrane domain is followed in-frame by the nucleotide sequence encoding either the human 4- IBB intracellular signaling domain (ICD), the murine 4- IBB ICD, or the murine CD28 ICD as set forth in Table 5.
• the intracellular domain is followed in-frame by the nucleotide sequence encoding either the human O ⁇ 3z intracellular signaling domain (ICD) or the murine CD3z ICD as set forth in Table 5.
• the complete murine CD19- targeted CAR construct in an RNV vector can then be delivered intravenously (IV) or intra- splenically for optimal CAR delivery, transduction and expression in T-cells.
• RNV-GFP red fluorescent protein
• cyclophosphamide pretreatment to dose 3E7 TU generally resulted in a doubling of GFP + cells in each population, about 1% GFP + .
• total dose of 3E3 TU about 10% of each of the evaluated PBMC populations was GFP + .
• the addition of cyclophosphamide pretreatment to dose 3E8 TU had no apparent impact on the percent of GFP + , RNV-infected cells in each evaluated PBMC population.
• A20 lymphoma cells 6 to 8-week old BALB/c mice were administered 100 mg/kg cyclophosphamide intraperitoneal (IP). Cyclophosphamide pretreatment allows A20 tumor engraftment into lymphnodes without significant lymphodepletion.
• A20 B-cell lymphoma cells were injected IV (5E5 cells in 100 pL) on day 0.
• the vector For tumor control to occur after IV administration of RNV-1D3CAR, the vector must enter the circulating T cells, the mCD 19-CAR must get expressed on the surface of those T cells, those T cells must then home to the tumor (primarily lymph nodes), and finally, the mCD 19-CAR on the surface of the T cells must engage CD 19 on the A20 tumor cells and activate killing of the A20 tumor cell.
• pBA9b-hCD19CAR vectors [ 00104 ] Construction of pBA9b-hCD19CAR vectors.
• pBA9b (SEQ ID NO:3) provides an MLV-based retroviral non-replicating vector (RNV) containing an extended packaging region.
• RSV retroviral non-replicating vector
• nucleic acid sequence of various single chain variable fragment (scFv) targeting human CD 19, leader sequence, hinge domain derived from human CD8, the transmembrane domain derived from human CD8, the intracellular domain derived from human 4-1BB, and the signaling domain derived from human CD3zeta are codon optimized and synthesized (Genewiz Inc.).
• hCD19CARl SEQ ID NO: 13
• hCD19CAR2 SEQ ID NO: 14
• hCD19CAR3 SEQ ID NO: 15
• hCD19CAR4 SEQ ID NOT6
• hCD19CAR5 SEQ ID NO: 17
• hCD19CARl SEQ ID NO: 13
• hCD19CAR2 SEQ ID NO: 14
• hCD19CAR3 SEQ ID NO: 15
• hCD19CAR4 SEQ ID NOT6
• hCD19CAR5 SEQ ID NO: 17
• MCS restriction enzyme sites
• the resulting plasmid DNA are designated pBA9b- hCD19CARl, pBA9b-hCD19CAR2, pBA9b-hCD19CAR3, pBA9b-hCD19CAR4, and pBA9b-hCD19CAR5 (SEQ ID NOs: 18, 19, 20, 21 and 22, respectively).
• the CD 19-CAR expression is mediated by the viral LTR promoter (FIG. 5A-B).
• Non-clonal HAL2-hCD19CAR vector producer cell line produces high hCD19-RNVCAR viral titer.
• Non-clonal HAL2-hCD19CAR producer cells are generated to confirm viral production, hCD19CAR expression.
• the pBA9b-hCD19CAR vectors pseudotyped with VSV-G are first produced by transient transfection in 293GP producer cells.
• HAL2 producer cells which stably express MLV-based gag-pol and 4070A amphotropic envelop protein are transduced with multiplicity of infection (MOI) of 100.
• 293GP cells are derived from HEK293 cells stably producing MLV-based gag-pol.
• HAL2 is a human packaging cell line constructed in the same way as the VPCL HA-LB (Sheridan et cil, Mol. Ther. 2000). All pBA9b-hCD19CAR vectors generated from stably transduced cells are titrated on human prostate PC-3 cells using qPCR method (5-MLV-U3- B: 5’-AGCCCACAACCCCTCACTC-3’ (SEQ ID NO: 120), 3-MLV-Psi: 5’- TCTCCCGATCCCGGACGA-3’ (SEQ ID NO: 121), probe: FAM-5’- CCCCAAATGAAAGACCCCCGCTGACG-3’-BHQl (SEQ ID NO: 122)).
• titer values of pBA9b-hCD19CAR vectors produced by HAL2 cells range from 5E5 to 1E7 TU/mL.
• 2*10 5 hCD19CAR VPCL cells are stained with FITC-conjugated recombinant human CD19 protein (ACROBiosystems, CD9- HF2H2). Cells are analyzed on a flow cytometer (Canto, BD Biosciences) to confirm CD 19 binding to hCD19CAR on the cell surface as surrogate readout for hCD19CAR expression on VPCL cell surface.
• hCD19CAR expression is also confirmed by anti-CD3zeta antibody (abeam, ab20059 i ) by immunoblotting.
• Clonal HAL2-hCD19CAR vector producer cell line produces high hCD19-RNVCAR viral titer for manufacturing.
• Cells from non-clonal VPCL are seeded to five 96-well plates targeting 1-cell-per-well based on cell count and limiting dilution.
• Wells confirmed to contain a single cell are grown to 75% confluency for screening for high titer producer clones by qRT-PCR using MLV specific primer and probe.
• Selected high titer producer clones are then transferred to 6-well plates followed by T75 flasks for cell expansion and further characterizations including growth characteristics, stability of retroviral components, titer, vector copy number, and transgene expression.
• top 25 high titer producer clones selected and cultured in T75 flasks they produce viral titer range from E6 to 2E8 TU/mL in a 5-day profiling titer assay. Subsequently, a working cell banks are generated from the highest titer clone selected and tested for a panel of safety assessment including sterility and mycoplasma, bacterial contamination, absence of RCR and other adventitious agents including bovine viruses.
• vials from both working cell bank and master cell bank are tested to confirm cell morphology, viability, integrity of vector sequence, average vector copy number, cell doubling times and vector production by transduction titer.
• hCD 19-RNV CAR clinical material is produced by large scale cellular fermentation as described in Sheridan et al op.cit. and US Pat. No. 10,316,333 (incorporated herein by reference), and subsequently purified (J.S. Powell et al, Blood, 102:2038-2045, 2003) by a ion exchange column then size exclusion chromatography in formulation buffer (sucrose and phosphate or Tris buffered saline), followed by filtration through 0.2 micron filters into 2 to 5ml vials. Typically this leads to purified formulated vector preparations of 5E7 to lE9/ml TU/ml. For GMP material this is performed at a sponsor approved GMP contract manufacturing facility.
• the vector is tested for efficacy in vitro using cultured human PBMC by methods such as those described by M.C.Milone et al, Molecular Therapy, 17: 1453-1464, 2009 and C. Sommer et al, Mol Ther., 27: 1126-1138, 2019 and further tested in a xenograft mouse model, e.g., Milone et ctl, supra) using infused human PBMC followed by IV administration of the vector.
• a xenograft mouse model e.g., Milone et ctl, supra
• the overall remission rate within 3 months is approximately 75%, with all patients who have a response to treatment found to be negative for minimal residual disease, as assessed by means of flow cytometry.
• the rates of event-free survival and overall survival are mostly over 60% and 90% respectively, at 6 months and mostly over 35% and 60% at 12 months. The exact numbers depend on the status of the patients initially, but are comparable to young adults in the ex vivo trial, described by Maude et al. , N.Eng.J. Med., 378:439-449, 2018.
• the overall criteria for utility is a 3 month remission rate of >20%.

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