US20230233609A1 - Therapeutic protein compositions and methods of making and using the same - Google Patents

Therapeutic protein compositions and methods of making and using the same Download PDF

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US20230233609A1
US20230233609A1 US18/053,203 US202218053203A US2023233609A1 US 20230233609 A1 US20230233609 A1 US 20230233609A1 US 202218053203 A US202218053203 A US 202218053203A US 2023233609 A1 US2023233609 A1 US 2023233609A1
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cells
protein
alkyl
cell
hydroxyl
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Thomas L. Andresen
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Torque Therapeutics Inc
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Torque Therapeutics Inc
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61K47/50—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates
    • A61K47/51—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent
    • A61K47/54—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic compound
    • A61K47/545—Heterocyclic compounds
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    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/14—Blood; Artificial blood
    • A61K35/17—Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes
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    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/177—Receptors; Cell surface antigens; Cell surface determinants
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    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
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    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
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    • A61K47/59—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being an organic macromolecular compound, e.g. an oligomeric, polymeric or dendrimeric molecule obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
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    • A61K47/62—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the non-active ingredient being a modifying agent the modifying agent being a protein, peptide or polyamino acid
    • A61K47/64—Drug-peptide, drug-protein or drug-polyamino acid conjugates, i.e. the modifying agent being a peptide, protein or polyamino acid which is covalently bonded or complexed to a therapeutically active agent
    • A61K47/645—Polycationic or polyanionic oligopeptides, polypeptides or polyamino acids, e.g. polylysine, polyarginine, polyglutamic acid or peptide TAT
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    • A61K47/6903—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being semi-solid, e.g. an ointment, a gel, a hydrogel or a solidifying gel
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    • A61K47/6921—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a particulate, a powder, an adsorbate, a bead or a sphere
    • A61K47/6927—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a particulate, a powder, an adsorbate, a bead or a sphere the form being a solid microparticle having no hollow or gas-filled cores
    • A61K47/6929—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a particulate, a powder, an adsorbate, a bead or a sphere the form being a solid microparticle having no hollow or gas-filled cores the form being a nanoparticle, e.g. an immuno-nanoparticle
    • A61K47/6931—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a particulate, a powder, an adsorbate, a bead or a sphere the form being a solid microparticle having no hollow or gas-filled cores the form being a nanoparticle, e.g. an immuno-nanoparticle the material constituting the nanoparticle being a polymer
    • A61K47/6935—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient the non-active ingredient being chemically bound to the active ingredient, e.g. polymer-drug conjugates the conjugate being characterised by physical or galenical forms, e.g. emulsion, particle, inclusion complex, stent or kit the form being a particulate, a powder, an adsorbate, a bead or a sphere the form being a solid microparticle having no hollow or gas-filled cores the form being a nanoparticle, e.g. an immuno-nanoparticle the material constituting the nanoparticle being a polymer the polymer being obtained otherwise than by reactions involving carbon to carbon unsaturated bonds, e.g. polyesters, polyamides or polyglycerol
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D207/00—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom
    • C07D207/46—Heterocyclic compounds containing five-membered rings not condensed with other rings, with one nitrogen atom as the only ring hetero atom with hetero atoms directly attached to the ring nitrogen atom
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D403/00—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00
    • C07D403/02—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings
    • C07D403/12—Heterocyclic compounds containing two or more hetero rings, having nitrogen atoms as the only ring hetero atoms, not provided for by group C07D401/00 containing two hetero rings linked by a chain containing hetero atoms as chain links
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
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    • C07K14/52—Cytokines; Lymphokines; Interferons
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    • C07K14/5443—IL-15
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    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
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    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/715—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons
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    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N11/00—Carrier-bound or immobilised enzymes; Carrier-bound or immobilised microbial cells; Preparation thereof
    • C12N11/02—Enzymes or microbial cells immobilised on or in an organic carrier
    • C12N11/08—Enzymes or microbial cells immobilised on or in an organic carrier the carrier being a synthetic polymer
    • C12N11/089—Enzymes or microbial cells immobilised on or in an organic carrier the carrier being a synthetic polymer obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds
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    • C07K1/107—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length by chemical modification of precursor peptides
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    • C07—ORGANIC CHEMISTRY
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Definitions

  • the present disclosure generally relates to compositions and methods for preparation and delivery of protein therapeutics, and more particularly protein clusters or backpacks having a plurality of therapeutic protein monomers reversibly crossed-linked by biodegradable linkers.
  • Protein therapeutics such as antibodies, cytokines, growth factors and vaccines, are important therapeutics for the treatment of a variety of diseases including, for example, cancer, diabetes and cardiovascular diseases. This class of protein therapeutics has been developed rapidly in the global pharmaceutical industry over the last few years. Protein therapeutics have the advantages of high specificity and potency relative to small molecule drugs. Nonetheless, the use of protein therapeutics is limited as a result of their intrinsic instability, immunogenicity and short half-life.
  • a therapeutic composition comprising:
  • a protein cluster comprising a plurality of therapeutic protein monomers reversibly crossed-linked to one another, wherein the protein cluster has a size between 30 nm and 1000 nm in diameter measured by dynamic light scattering;
  • biodegradable cross-linkers each having two, three or four functional groups capable of reacting with nucleophilic groups on the therapeutic protein monomers, thereby cross-linking the therapeutic protein monomers into the protein cluster, wherein the cross-linker degrades, after administration into a subject in need thereof, under physiological conditions so as to release the therapeutic protein monomers from the protein cluster;
  • a surface modification on the protein cluster wherein preferably the surface modification is poly cation.
  • the cross-linker has the formula of A-B-C wherein B is optional, wherein A represents a structural template, B represents a polymer spacer, C represents a hydrolysable linkage and a functional group that can react with nucleophilic groups.
  • A is selected from di-ols, tri-ols, tetra-ols, poly-ols, di-thiols, tri-thiols, tetra-thiols, poly-thiols, di-amines, tri-amines, tetra-amines, or poly-amines.
  • B can be selected from polyethylene glycol, saccharides, poly-ols, poly-ethers, poly-thioethers, poly-amines, poly-esters, alkanes, phenyls, or amino-acids.
  • C can have C has formula (Ia):
  • LG 2 is a leaving group selected from triflate, tosyl, Cl, N-hydroxysuccinimide and itnidazolide;
  • Y 2 is selected from O and S;
  • X at each occurrence, is independently selected from O, S, and N;
  • L is optional and is a linker such that
  • n is an integer selected from 1-6, preferably 2.
  • the cross-linker has formula (I):
  • LG 1 and LG 2 are each a leaving group, independently selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • Y 1 and Y 2 are each independently selected from O and S;
  • X at each occurrence, is independently selected from O, S, and N;
  • L is a linker such that
  • n is an integer selected from 1-6.
  • the cross-linker of formula (I) is symmetrical.
  • LG 1 and LG 2 are capable of reacting with a protein, a drug and/or a particle.
  • LG 1 and LG 2 are both imidazolide.
  • LG 1 and LG 2 are both N-hydroxysuccinimide.
  • L is selected from:
  • n is an integer selected from 0-5;
  • n is an integer selected from 0-5;
  • X at each occurrence, is independently selected from O, S, and N.
  • n is 2.
  • the cross-linker has formula (II):
  • X 1 and X 2 are each independently selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • a 1 and A 3 are each independently —(CR 1 R 2 ) n —;
  • a 2 is —(CR 1 R 2 ) m —;
  • Y 1 and Y 2 are each independently selected from NR 3 , O and S;
  • R 1 and R 2 at each occurrence are independently selected from hydrogen, halogen, hydroxyl, C 1-12 alkyl, C 2-12 alkenyl, C 3-12 cycloalkyl, C 2-12 heterocyclyl; C 6-12 aryl optionally substituted with 1 or more halo, hydroxyl, C 1-6 alkyl and/or C 1-6 alkoxyl; and C 4-12 heteroaryl optionally substituted with 1 or more halo, hydroxyl, C 1-6 alkyl and/or C 1-6 alkoxyl
  • R 3 is selected from hydrogen, C 1-12 alkyl, C 2-12 alkenyl, C 3-12 cycloalkyl, C 2-12 heterocyclyl; C 6-12 aryl optionally substituted with 1 or more halo, hydroxyl, C 1-6 alkyl and/or C 1-6 alkoxyl; and C 4-12 heteroaryl optionally substituted with 1 or more halo, hydroxyl, C 1-6 alkyl and/or C 1-6 alkoxyl;
  • n at each occurrence, is an integer independently selected from 1-12;
  • n is an integer selected from 0-12.
  • the cross-linker of formula (TT) is symmetrical.
  • X 1 and X 2 can each be a leaving group capable of reacting with a protein, a drug and/or a particle.
  • X 1 and X 2 are both imidazolide.
  • X 1 and X 2 are both N-hydroxysuccinimide.
  • R 1 and R 2 are both hydrogen.
  • a 1 and A 3 are both —(CH 2 ) 2 —.
  • a 2 is —(CH 2 ) 2 —.
  • Y 1 and Y 2 are both O.
  • the cross-linker is:
  • a 2 is a bond (e.g., when m is 0).
  • Y 1 and Y 2 are both NH.
  • the cross-linker in some embodiments, is:
  • the cross-linker can be used as a degradable or hydrolysable linker.
  • the degradable linker is a redox responsive linker.
  • the composition further comprises an agent that optimizes formation of the protein cluster.
  • the agent can increase yield of the protein cluster formation by reducing non-reacted proteins in comparison to a composition without the agent.
  • the agent increases yield of the protein cluster formation by reducing formation of clusters that are larger than 1000 nm in size compared to a composition without the agent.
  • the therapeutic protein monomers comprise one or more cytokine molecules and/or one or more costimulatory molecules, wherein:
  • Another aspect relates to a method for preparing any one of the composition disclosed herein, the method comprising reacting the plurality of therapeutic protein monomers with the plurality of cross-linkers to form the protein cluster.
  • the reacting step is performed at a temperature between about 5° C. and about 40° C. In some embodiments, the reacting step is performed for about 1 minute to about 8 hours.
  • the method can further include providing the surface modification to the protein cluster and/or purifying the protein cluster.
  • Also provided herein is a method for preparing a cell therapy composition, comprising: providing any one of the composition disclosed herein; and incubating the protein cluster with a nucleated cell such as T and NK cells, preferably for about 30-60 minutes.
  • a nucleated cell such as T and NK cells
  • a further aspect relates to a cell therapy composition, comprising any one of the composition disclosed herein, associated with a nucleated cell such as T and NK cells.
  • Still a further aspect relates to a method of providing cell therapy, comprising administering the cell therapy composition disclosed herein into a subject in need thereof.
  • FIGS. 1 A- 1 C illustrates exemplary backpacks and their making and using.
  • FIG. 2 Titratable loading of IL-15 backpack on human T cells.
  • FIG. 3 Consistent and precise loading of IL-15 backpack across multiple donors.
  • FIG. 4 IL-15 backpack release from labeled cells drives expansion.
  • FIG. 5 Cell-associated IL-15 backpack drives cell expansion at Day 14 following intermittent wash.
  • FIGS. 6 A- 6 C IL-15 backpack drives expansion of anti-EGFR CAR-expressing human CD3 T cells.
  • FIGS. 7 A- 7 C Contrasting effects of systemic IL15-Fc and IL-15 backpack in C 57 B6 mouse model with intact immune system.
  • FIGS. 8 A- 8 E CTLs from process completion were harvested and characterized
  • FIG. 9 Clinical chemistry parameters in na ⁇ ve mice at D1 and D4 post-dose.
  • HBSS vehicle control
  • DP-15 PMEL Deep IL-15 Primed PMEL cells
  • D Day.
  • FIG. 10 Clinical chemistry parameters in tumor—bearing mice at D1 and D4 post-dose.
  • HBSS vehicle control
  • DP-15 PMEL Deep IL-15 Primed PMEL cells
  • D Day.
  • FIG. 11 Serum levels of IFN- ⁇ in tumor—bearing compared to na ⁇ ve mice 24 hr after ACT. he serum levels of IFN- ⁇ in the PMEL+IL15-Fc group were significantly increased (2-way ANOVA with Tukey's multiple comparison, p ⁇ 0.001) compared to both the PMEL and DP-15 PMEL groups in both na ⁇ ve and tumor—bearing mice.
  • ACT adoptive cell transfer;
  • DP-15 PMEL Deep IL-15 Primed PMEL cells.
  • FIG. 12 IL15-Fc systemic exposure in mice treated with PMEL+IL15-Fc and Deep IL-15 Primed PMEL cells, in na ⁇ ve and tumor—bearing mice.
  • HBSS vehicle control;
  • DP-15 PMEL Deep IL-15 Primed PMEL cells.
  • Cancer immunotherapy including adoptive T cell therapy, is a promising strategy to treat cancer because it harnesses a subject's own immune system to attack cancer cells. Nonetheless, a major limitation of this approach is the rapid decline in viability and function of the transplanted T lymphocytes.
  • co-administration of immunostimulatory agents with transferred cells is necessary. When given systemically at high doses, these agents could enhance the in vivo viability of transferred (i.e., donor) cells, improve the therapeutic function of transferred cells, and thus lead to overall improved efficacy against cancer; however, high doses of such agents could also result in life-threatening side effects.
  • interleukin-2 IL-2
  • Tregs regulatory T cells
  • One approach to focus adjuvant activity on the transferred cells is to genetically engineer the transferred cells to secrete their own supporting factors.
  • the technical difficulty and challenges as well as the high cost for large-scale production of genetically engineered T lymphocytes have significantly limited the potential of this method in clinical applications, to date.
  • a technology platform that permits simple, safe and efficient delivery of biologically-active agents, such as a drug, protein (e.g., adjuvants such as IL-2) or particle to cells through chemical conjugation of protein, drug, or particle-loaded, carrier-free linkers directly onto the plasma membrane of cells.
  • biologically-active agents such as a drug, protein (e.g., adjuvants such as IL-2) or particle to cells through chemical conjugation of protein, drug, or particle-loaded, carrier-free linkers directly onto the plasma membrane of cells.
  • such composition is referred to as “nanogel,” “nanoparticle,” or “backpack,” which terms are used interchangeably herein.
  • the composition can be loaded or backpacked onto cells, e.g., nucleated cells.
  • the loading or backpacking process is also referred to as “priming.” Backpacked or primed cells can have many therapeutic applications.
  • backpacked T cells can be used in T cell therapies including ACT (adoptive cell therapy).
  • Other important immune cell types can also be backpacked, including for example, B cells, tumor infiltrating lymphocytes, NK cells, antigen-specific CD8+ T cells, T cells genetically engineered to express chimeric antigen receptors (CARs) or CAR-T cells, T cells genetically engineered to express T-cell receptors specific to an tumor antigen, tumor infiltrating lymphocytes (TTLs), and/or antigen-trained T cells (e.g., T cells that have been “trained” by antigen presenting cells (APCs) displaying antigens of interest, e.g. tumor associated antigens (TAA)).
  • APCs antigen presenting cells
  • TAA tumor associated antigens
  • the present disclosure further contemplates other nanostructures that comprise other protein therapeutics for purposes other than adjuvant effect on adoptively-transferred cells.
  • the disclosure has broader applications, as provided herein.
  • the articles “a” and “an” refer to one or more than one, e.g., to at least one, of the grammatical object of the article.
  • the use of the words “a” or “an” when used in conjunction with the term “comprising” herein may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.”
  • “about” and “approximately” generally mean an acceptable degree of error for the quantity measured given the nature or precision of the measurements. Exemplary degrees of error are within 20 percent (%), typically, within 10%, and more typically, within 5% of a given range of values.
  • the term “substantially” means more than 50%, preferably more than 80%, and most preferably more than 90% or 95%.
  • compositions, methods, and respective component(s) thereof are used in reference to compositions, methods, and respective component(s) thereof, that are present in a given embodiment, yet open to the inclusion of unspecified elements.
  • the term “consisting essentially of” refers to those elements required for a given embodiment. The term permits the presence of additional elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment of the disclosure.
  • compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.
  • a plurality of means more than 1, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more, e.g., 25, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, or more, or any integer therebetween.
  • therapeutic means any active pharmaceutical ingredient (“API”), including its pharmaceutically acceptable salts (e.g. the hydrochloride salts, the hydrobromide salts, the hydroiodide salts, and the saccharinate salts), as well as in the anhydrous, hydrated, and solvated forms, in the form of prodrugs, and in the individually optically active enantiomers of the API as well as polymorphs of the API.
  • Therapeutic agents include pharmaceutical, chemical or biological agents. Additionally, pharmaceutical, chemical or biological agents can include any agent that has a desired property or affect whether it is a therapeutic agent. For example, agents also include diagnostic agents, biocides and the like.
  • protein protein
  • peptide and “polypeptide” are used interchangeably herein to refer to polymers of amino acids of any length.
  • the polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids.
  • the terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component.
  • the polypeptide can be isolated from natural sources, can be a produced by recombinant techniques from a eukaryotic or prokaryotic host, or can be a product of synthetic procedures. It should bt understood that the term “protein” includes fusion or chimeric proteins, as well as cytokines, antibodies and antigen-binding fragments thereof.
  • Antibody or “antibody molecule” as used herein refers to a protein, e.g., an immunoglobulin chain or fragment thereof, comprising at least one immunoglobulin variable domain sequence.
  • An antibody molecule encompasses antibodies (e.g., full-length antibodies) and antibody fragments.
  • an antibody molecule comprises an antigen binding or functional fragment of a full length antibody, or a full length immunoglobulin chain.
  • a full-length antibody is an immunoglobulin (Ig) molecule (e.g., IgG) that is naturally occurring or formed by normal immunoglobulin gene fragment recombinatorial processes).
  • an antibody molecule refers to an immunologically active, antigen-binding portion of an immunoglobulin molecule, such as an antibody fragment.
  • An antibody fragment e.g., functional fragment, is a portion of an antibody, e.g., Fab, Fab′, F(ab′) 2 , F(ab) 2 , variable fragment (Fv), domain antibody (dAb), or single chain variable fragment (scFv).
  • a functional antibody fragment binds to the same antigen as that recognized by the intact (e.g., full-length) antibody.
  • antibody fragment or “functional fragment” also include isolated fragments consisting of the variable regions, such as the “Fv” fragments consisting of the variable regions of the heavy and light chains or recombinant single chain polypeptide molecules in which light and heavy variable regions are connected by a peptide linker (“scFv proteins”).
  • an antibody fragment does not include portions of antibodies without antigen binding activity, such as Fc fragments or single amino acid residues.
  • Exemplary antibody molecules include full length antibodies and antibody fragments, e.g., dAb (domain antibody), single chain, Fab, Fab′, and F(ab′) 2 fragments, and single chain variable fragments (scFvs).
  • Fab and “Fab fragment” are used interchangeably and refer to a region that includes one constant and one variable domain from each heavy and light chain of the antibody, i.e., V L , C L , V H and C H 1.
  • an antibody molecule is monospecific, e.g., it comprises binding specificity for a single epitope.
  • an antibody molecule is multispecific, e.g., it comprises a plurality of immunoglobulin variable domain sequences, where a first immunoglobulin variable domain sequence has binding specificity for a first epitope and a second immunoglobulin variable domain sequence has binding specificity for a second epitope.
  • an antibody molecule is a bispecific antibody molecule. “Bispecific antibody molecule” as used herein refers to an antibody molecule that has specificity for more than one (e.g., two, three, four, or more) epitope and/or antigen.
  • Antigen refers to a macromolecule, including all proteins or peptides.
  • an antigen is a molecule that can provoke an immune response, e.g., involving activation of certain immune cells and/or antibody generation. Antigens are not only involved in antibody generation. T cell receptors also recognized antigens (albeit antigens whose peptides or peptide fragments are complexed with an MHC molecule). Any macromolecule, including almost all proteins or peptides, can be an antigen. Antigens can also be derived from genomic recombinant or DNA.
  • any DNA comprising a nucleotide sequence or a partial nucleotide sequence that encodes a protein capable of eliciting an immune response encodes an “antigen.”
  • an antigen does not need to be encoded solely by a full length nucleotide sequence of a gene, nor does an antigen need to be encoded by a gene at all.
  • an antigen can be synthesized or can be derived from a biological sample, e.g., a tissue sample, a tumor sample, a cell, or a fluid with other biological components.
  • a “tumor antigen” or interchangeably, a “cancer antigen” includes any molecule present on, or associated with, a cancer, e.g., a cancer cell or a tumor microenvironment that can provoke an immune response.
  • an “immune cell antigen” includes any molecule present on, or associated with, an immune cell that can provoke an immune response.
  • the “antigen-binding site” or “antigen-binding fragment” or “antigen-binding portion” (used interchangeably herein) of an antibody molecule refers to the part of an antibody molecule, e.g., an immunoglobulin (Ig) molecule such as IgG, that participates in antigen binding.
  • the antigen-binding site is formed by amino acid residues of the variable (V) regions of the heavy (H) and light (L) chains.
  • hypervariable regions Three highly divergent stretches within the variable regions of the heavy and light chains, referred to as hypervariable regions, are disposed between more conserved flanking stretches called “framework regions” (FRs).
  • FRs are amino acid sequences that are naturally found between, and adjacent to, hypervariable regions in immunoglobulins.
  • the three hypervariable regions of a light chain and the three hypervariable regions of a heavy chain are disposed relative to each other in three dimensional space to form an antigen-binding surface, which is complementary to the three-dimensional surface of a bound antigen.
  • the three hypervariable regions of each of the heavy and light chains are referred to as “complementarity-determining regions,” or “CDRs.”
  • CDRs complementarity-determining regions
  • variable chain e.g., variable heavy chain and variable light chain
  • Each variable chain is typically made up of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the amino acid order: FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4.
  • VL CDRs are generally defined to include residues at positions 27-32 (CDR1), 50-56 (CDR2), and 91-97 (CDR3).
  • VH CDRs are generally defined to include residues at positions 27-33 (CDR1), 52-56 (CDR2), and 95-102 (CDR3).
  • CDR1 residues at positions 27-33
  • CDR2 52-56
  • CDR3 95-102
  • the loops can be of different length across antibodies and the numbering systems such as the Kabat or Chotia control so that the frameworks have consistent numbering across antibodies.
  • the antigen-binding fragment of an antibody can lack or be free of a full Fc domain.
  • an antibody-binding fragment does not include a full IgG or a full Fc but may include one or more constant regions (or fragments thereof) from the light and/or heavy chains.
  • the antigen-binding fragment can be completely free of any Fc domain.
  • the antigen-binding fragment can be substantially free of a full Fc domain.
  • the antigen-binding fragment can include a portion of a full Fc domain (e.g., CH 2 or CH 3 domain or a portion thereof).
  • the antigen-binding fragment can include a full Fc domain.
  • the Fc domain is an IgG domain, e.g., an IgG1, IgG2, IgG3, or IgG4 Fc domain.
  • the Fc domain comprises a CH 2 domain and a CH 3 domain.
  • cytokine refers to full length, a fragment or a variant of a naturally-occurring, wild type cytokine (including fragments and functional variants thereof having at least 10% of the activity of the naturally-occurring cytokine molecule).
  • the cytokine molecule has at least 30, 50, or 80% of the activity, e.g., the immunomodulatory activity, of the naturally-occurring molecule.
  • the cytokine molecule further comprises a receptor domain, e.g., a cytokine receptor domain, optionally, coupled to an immunoglobulin Fc region.
  • the cytokine molecule is coupled to an immunoglobulin Fc region.
  • the cytokine molecule is coupled to an antibody molecule (e.g., an immunoglobulin Fab or scFv fragment, a Fab fragment, a FAB 2 fragment, or an affibody fragment or derivative, e.g., a sdAb (nanobody) fragment, a heavy chain antibody fragment, single-domain antibody, a bi-specific or multispecific antibody), or non-antibody scaffolds and antibody mimetics (e.g., lipocalins (e.g., anticalins), affibodies, fibronectin (e.g., monobodies or Adnectins), knottins, ankyrin repeats (e.g., DARPins), and A domains (e.g., avimers)).
  • an antibody molecule e.g., an immunoglobulin Fab or scFv fragment, a Fab fragment, a F
  • administering means delivering the composition to an individual being treated.
  • the compositions of the present disclosure are administered by, e.g., parenteral, including subcutaneous, intramuscular, or preferably interventions routes.
  • 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, melanoma, carcinoma, lymphoma, blastoma, sarcoma, and leukemia or lymphoid malignancies.
  • cancers include squamous cell cancer (e.g., epithelial squamous cell cancer), lung cancer including small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung and squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial cancer or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, as well as head and neck cancer.
  • lung cancer including small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung and squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer
  • Nucleated cells are cells which contain nucleus.
  • the nucleated cells can be immune cells.
  • an “immune cell” refers to any of various cells that function in the immune system, e.g., to protect against agents of infection and foreign matter.
  • this term includes leukocytes, e.g., neutrophils, eosinophils, basophils, lymphocytes, and monocytes.
  • the term “immune cell” includes immune effector cells described herein.
  • Immunune cell also refers to modified versions of cells involved in an immune response, e.g. modified NK cells, including NK cell line NK-92 (ATCC cat. No.
  • haNK an NK-92 variant that expresses the high-affinity Fc receptor Fc ⁇ RIIIa (158V)
  • taNK targeted NK-92 cells transfected with a gene that expresses a CAR for a given tumor antigen
  • Immuno effector cell refers to a cell that is involved in an immune response, e.g., in the promotion of an immune effector response.
  • immune effector cells include, but are not limited to, T cells, e.g., CD4+ T cells, CD8+ T cells, alpha T cells, beta T cells, gamma T cells, and delta T cells; B cells; natural killer (NK) cells; natural killer T (NKT) cells; dendritic cells; and mast cells.
  • the immune cell is an immune cell (e.g., T cell or NK cell) that comprises, e.g., expresses, a Chimeric Antigen Receptor (CAR), e.g., a CAR that binds to a cancer antigen.
  • CAR Chimeric Antigen Receptor
  • the immune cell expresses an exogenous high affinity Fc receptor.
  • the immune cell comprises, e.g., expresses, an engineered T-cell receptor.
  • the immune cell is a tumor infiltrating lymphocyte.
  • the immune cells comprise a population of immune cells and comprise T cells that have been enriched for specificity for a tumor-associated antigen (TAA), e.g.
  • TAA tumor-associated antigen
  • immune cells comprise a population of immune cells and comprise T cells that have been “trained” to possess specificity against a TAA by an antigen presenting cell (APC), e.g. a dendritic cell, displaying TAA peptides of interest.
  • APC antigen presenting cell
  • the T cells are trained against a TAA chosen from one or more of MART-1, MAGE-A4, NY-ESO-1, SSX2, Survivin, or others.
  • the immune cells comprise a population of T cells that have been “trained” to possess specificity against a multiple TAAs by an APC, e.g.
  • the immune cell is a cytotoxic T cell (e.g., a CD8+ T cell).
  • the immune cell is a helper T cell, e.g., a CD4+ T cell.
  • CTLs Cytotoxic T lymphocytes
  • CTL activation can occur when two steps occur: 1) an interaction between an antigen-bound MHC molecule on the target cell and a T cell receptor on the CTL is made; and 2) a costimulatory signal is made by engagement of costimulatory molecules on the T cell and the target cell.
  • CTLs then recognize specific antigens on target cells and induce the destruction of these target cells, e.g., by cell lysis.
  • the CTL expresses a CAR.
  • the CTL expresses an engineered T-cell receptor.
  • an “effective amount” means the amount of bioactive agent or diagnostic agent that is sufficient to provide the desired local or systemic effect at a reasonable risk/benefit ratio as would attend any medical treatment or diagnostic test. This will vary depending on the patient, the disease, the treatment being effected, and the nature of the agent.
  • pharmaceutically acceptable shall refer to that which is useful in preparing a pharmaceutical composition that is generally safe, non-toxic, and neither biologically nor otherwise undesirable and includes that which is acceptable for veterinary use as well as human pharmaceutical use.
  • pharmaceutically acceptable liquid carriers include water and organic solvents.
  • Preferred pharmaceutically acceptable aqueous liquids include PBS, saline, and dextrose solutions etc.
  • treatment means administration of a drug for purposes including: (i) preventing the disease or condition, that is, causing the clinical symptoms of the disease or condition not to develop; (ii) inhibiting the disease or condition, that is, arresting the development of clinical symptoms; and/or (iii) relieving the disease or condition, that is, causing the regression of clinical symptoms.
  • alkyl refers to a saturated hydrocarbon chain that may be a straight chain or branched chain, containing the indicated number of carbon atoms.
  • C 1-6 alkyl indicates that the group may have 1 to 6 (inclusive) carbon atoms in it. Any atom can be optionally substituted, e.g., by one or more substituents.
  • alkyl groups include without limitation methyl, ethyl, n-propyl, isopropyl, and tert-butyl.
  • alkoxy refers to a group of formula-O(alkyl).
  • Alkoxy can be, for example, methoxy (—OCH 3 ), ethoxy, propoxy, isopropoxy, butoxy, iso-butoxy, sec-butoxy, pentoxy, 2-pentoxy, 3-pentoxy, or hexyloxy.
  • hydroxyl employed alone or in combination with other terms, refers to a group of formula —OH.
  • alkenyl refers to a straight or branched hydrocarbon chain containing the indicated number of carbon atoms and having one or more carbon-carbon double bonds. Any atom can be optionally substituted, e.g., by one or more substituents. Alkenyl groups can include, e.g., vinyl, allyl, 1-butenyl, and 2-hexenyl. One of the double bond carbons can optionally be the point of attachment of the alkenyl substituent.
  • alkynyl refers to a straight or branched hydrocarbon chain containing the indicated number of carbon atoms and having one or more carbon-carbon triple bonds.
  • Alkynyl groups can be optionally substituted, e.g., by one or more substituents.
  • Alkynyl groups can include, e.g., ethynyl, propargyl, and 3-hexynyl.
  • One of the triple bond carbons can optionally be the point of attachment of the alkynyl substituent,
  • heterocyclyl refers to a fully saturated monocyclic, bicyclic, tricyclic or other polycyclic ring system having one or more constituent heteroatom ring atoms independently selected from O, N (it is understood that one or two additional groups may be present to complete the nitrogen valence and/or form a salt), or S.
  • the heteroatom or ring carbon can be the point of attachment of the heterocyclyl substituent to another moiety. Any atom can be optionally substituted, e.g., by one or more substituents.
  • Heterocyclyl groups can include, e.g., tetrahydrofuryl, tetrahydropyranyl, piperidyl (piperidino), piperazinyl, morpholinyl (morpholino), pyrrolinyl, and pyrrolidinyl.
  • cycloalkyl refers to a fully saturated monocyclic, bicyclic, tricyclic, or other polycyclic hydrocarbon groups, Any atom can be optionally substituted, e.g., by one or more substituents.
  • a ring carbon serves as the point of attachment of a cycloalkyl group to another moiety.
  • Cycloalkyl moieties can include, e.g., cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, and norbornyl (bicycle[2.2.1]heptyl).
  • aryl refers to an aromatic monocyclic., bicyclic (2 fused rings), or tricyclic (3 fused rings), or polycyclic (>3 fused rings) hydrocarbon ring system.
  • One or more ring atoms can be optionally substituted, e.g., by one or more substituents.
  • Aryl moieties include, e.g., phenyl and naphthyl.
  • heteroaryl refers to an aromatic monocyclic, bicyclic (2 fused rings), tricyclic (3 fused rings), or polycyclic (>3 fused rings) hydrocarbon groups having one or more heteroatom ring atoms independently selected from O, N (it is understood that one or two additional groups may be present to complete the nitrogen valence and/or form a salt), or S.
  • One or more ring atoms can be optionally substituted, e.g., by one or more substituents.
  • heteroaryl groups include, but are not limited to, 2H-pyrrolyl, 3H-indolyl, 4H-quinolizinyl, acridinyl, benzo[b]thienyl, benzothiazolyl, P-carbolinyl, carbazolyl, coumarinyl, chromenyl, cinnolinyl, dibenzo[b,d]furanyl, furazanyl, furyl, imidazolyl, imidizolyl, indazolyl, indolyl, isobenzofuranyl, isoindolyl, isoquinolyl, isothiazolyl, isoxazolyl, naphthyridinyl, oxazolyl, perimidinyl, phenanthridinyl, phenanthrolinyl, phenarsazinyl, phenazinyl, phenothiazinyl, phenoxathiinyl, pheno
  • substituted refers to a group “substituted” on, e.g., an alkyl, haloalkyl, cycloalkyl, heterocyclyl, heterocycloalkenyl, cycloalkenyl, aryl, or heteroaryl group at any atom of that group.
  • the substituent(s) on a group are independently any one single, or any combination of two or more of the permissible atoms or groups of atoms delineated for that substituent.
  • a substituent may itself be substituted with any one of the above substituents.
  • the phrase “optionally substituted” means unsubstituted (e.g., substituted with an H) or substituted.
  • substituted means that a hydrogen atom is removed and replaced by a substituent. It is understood that substitution at a given atom is limited by valency.
  • At least one drug, protein, polymer and/or particle (collectively, “agents”) of the present disclosure are reversibly linked to one another through a degradable linker such that under physiological conditions, the linker degrades and releases the intact, biologically-active agent.
  • protein monomers can be cross-linked together to form a cluster that contains a plurality of the protein monomers.
  • various agents are linked to functional groups through a degradable linker.
  • the agents are reversibly modified or linked, as described below.
  • agent that is “reversibly linked to another” agent refers to a drug, protein, polymer or particle that is attached (e.g., covalently attached) to another drug, protein, polymer or particle through a degradable linker.
  • agent that is “reversibly linked to a functional group,” or an agent that is “reversibly modified,” herein refers to an agent that is attached (e.g., covalently attached) to a functional group through a degradable linker.
  • agent conjugate or a “reversibly modified agent conjugate”—the terms may be used interchangeably herein.
  • proteins and polymers e.g., polyethylene glycol
  • agent conjugates and reversibly modified proteins include without limitation, an agent reversibly linked (e.g., via a degradable linker) to another agent, an agent reversibly linked to a polymer, and a protein reversibly linked to another functional group.
  • agent conjugates and reversibly modified proteins include without limitation, an agent reversibly linked (e.g., via a degradable linker) to another agent, an agent reversibly linked to a polymer, and a protein reversibly linked to another functional group.
  • protein includes fusion proteins.
  • the cross-linker has the formula of A-B-C wherein B is optional, wherein A represents a structural template, B represents a polymer spacer, C represents a hydrolysable linkage and a functional group that can react with nucleophilic groups.
  • A is selected from di-ols, tri-ols, tetra-ols, poly-ols, di-thiols, tri-thiols, tetra-thiols, poly-thiols, di-amines, tri-amines, tetra-amines, or poly-amines.
  • B can be selected from polyethylene glycol, saccharides, poly-ols, poly-ethers, poly-thioethers, poly-amines, poly-esters, alkanes, phenyls, or amino-acids.
  • C can have C has formula (Ia):
  • LG 2 is a leaving group selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • Y 2 is selected from O and S;
  • X at each occurrence, is independently selected from O, S, and N;
  • L is optional and is a linker such that
  • n is an integer selected from 1-6, preferably 2.
  • LG 1 and LG 2 are each a leaving group, preferably independently selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • Y 1 and Y 2 are each independently selected from O and S;
  • X at each occurrence, is independently selected from O, S, and N;
  • L is a linkage such that
  • n is an integer selected from 1-6.
  • the cross-linker represented by formula (I) is symmetrical at L.
  • LG 1 and LG 2 can be the same.
  • Y 1 and Y 2 can be the same.
  • LG 1 and LG 2 may be capable of reacting with a protein, a drug and/or a particle.
  • LG 1 and LG 2 can both be imidazolide.
  • LG 1 and LG 2 are both N-hydroxysuccinimide.
  • L is hydrolysable. L can be selected from:
  • n is an integer selected from 0-5;
  • X at each occurrence, is independently selected from O, S, and N.
  • X 1 and X 2 are each independently selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • a 1 and A 3 are each independently —(CR 1 R 2 ) n —;
  • a 2 is —(CR 1 R 2 ) m —;
  • Y 1 and Y 2 are each independently selected from NR 3 , O and S;
  • R 1 and R 2 at each occurrence are independently selected from hydrogen, halogen, hydroxyl, C 1-12 alkyl, C 2-12 alkenyl, C 3-12 cycloalkyl, C 2-12 heterocyclyl; C 6-12 aryl optionally substituted with 1 or more halo, hydroxyl, C 1-6 alkyl and/or C 1-6 alkoxyl; and C 4-12 heteroaryl optionally substituted with 1 or more halo, hydroxyl, C 1-6 alkyl and/or C 1-6 alkoxyl
  • R 3 is selected from hydrogen, C 1-12 alkyl, C 2-12 alkenyl, C 3-12 cycloalkyl, C 2-12 heterocyclyl; C 6-12 aryl optionally substituted with 1 or more halo, hydroxyl, C 1-6 alkyl and/or C 1-6 alkoxyl; and C 4-12 heteroaryl optionally substituted with 1 or more halo, hydroxyl, C 1-6 alkyl and/or C 1-6 alkoxyl;
  • n at each occurrence, is an integer independently selected from 1-12;
  • n is an integer selected from 0-12.
  • the cross-linker represented by formula (II) is symmetrical.
  • X 1 and X 2 are each a leaving group capable of reacting with a protein, a drug and/or a particle. In certain embodiments, X 1 and X 2 are both imidazolide or N-hydroxysuccinimide.
  • R 1 and R 2 are both hydrogen.
  • a 1 and A 3 are both —(CH 2 ) 2 —.
  • a 2 is —(CH 2 ) 2 —.
  • Y 1 and Y 2 are both O.
  • the cross-linker is:
  • a 2 is a bond. In certain embodiments, Y 1 and Y 2 are both NH.
  • the cross-linker is:
  • antibodies e.g., IgG, Fab, mixed Fc and Fab
  • therapeutic protein monomers can be cross-linked using one or more cross-linkers disclosed herein.
  • the therapeutic protein monomers can comprise one or more cytokine molecules and/or one or more costimulatory molecules.
  • Cytokine molecules can be selected from IL-15, IL-2, IL-7, IL-10, IL-12, IL-18, IL-21, IL-23, IL-4, IL1alpha, IL1beta, IL-5, IFNgamma, TNFa, IFNalpha, IFNbeta, GM-CSF, or GCSF.
  • Costimulatory molecules are selected from CD137, OX40, CD28, GITR, VISTA, anti-CD40, or CD3.
  • protein monomers of the disclosure are immunostimulatory proteins.
  • an immunostimulatory protein is a protein that stimulates an immune response (including enhancing a pre-existing immune response) in a subject to whom it is administered, whether alone or in combination with another protein or agent.
  • immunostimulatory proteins examples include, without limitation, antigens, adjuvants (e.g., flagellin, muramyl dipeptide), cytokines including interleukins (e.g., IL-2, IL-7, IL-15, IL-10, IL-18, IL-21, IL-23 (or superagonist/mutant forms of these cytokines, such as, IL-15SA), IL-12, IFNgamma, IFN-alpha, GM-CSF, FLT3-ligand), and immunostimulatory antibodies (e.g., anti-CTLA-4, anti-CD28, anti-CD3, or single chain/antibody fragments of these molecules).
  • adjuvants e.g., flagellin, muramyl dipeptide
  • cytokines including interleukins e.g., IL-2, IL-7, IL-15, IL-10, IL-18, IL-21, IL-23 (or superagonist/mutant forms of these cytokines,
  • the immunostimulatory proteins can be an antibody or antigen-binding fragment thereof that binds an inhibitor of an immunosuppressor, e.g., an inhibitor of a checkpoint inhibitor, such as PD-1, PD-L 1, LAG-3, TIM-3, CTLA-4, inhibitory KIR, CD276, VTCN1, BTLA/HVEM, HAVCR2 and ADORA2A, e.g., as described in US 2016/0184399 incorporated herein by reference.
  • an immunosuppressor e.g., an inhibitor of a checkpoint inhibitor, such as PD-1, PD-L 1, LAG-3, TIM-3, CTLA-4, inhibitory KIR, CD276, VTCN1, BTLA/HVEM, HAVCR2 and ADORA2A, e.g., as described in US 2016/0184399 incorporated herein by reference.
  • protein monomers of the disclosure are antigens.
  • antigens that may be used in accordance with the disclosure include, without limitation, cancer antigens, self-antigens, microbial antigens, allergens and environmental antigens.
  • Other protein antigens are contemplated and may be used in accordance with the disclosure.
  • proteins of the disclosure are cancer antigens.
  • a cancer antigen is an antigen that is expressed preferentially by cancer cells (i.e., it is expressed at higher levels in cancer cells than on non-cancer cells) and, in some instances, it is expressed solely by cancer cells. Cancer antigens may be expressed within a cancer cell or on the surface of the cancer cell.
  • Cancer antigens that may be used in accordance with the disclosure include, without limitation, MART-1/Melan-A, gp100, adenosine deaminase-binding protein (ADAbp), FAP, cyclophilin b, colorectal associated antigen (CRC)-0017-1A/GA733, carcinoembryonic antigen (CEA), CAP-1, CAP-2, etv6, AML1, prostate specific antigen (PSA), PSA-1, PSA-2, PSA-3, prostate-specific membrane antigen (PSMA), T cell receptor/CD3-zeta chain and CD20.
  • MART-1/Melan-A gp100
  • ADAbp adenosine deaminase-binding protein
  • FAP cyclophilin b
  • CRC colorectal associated antigen
  • CEA carcinoembryonic antigen
  • CAP-1 CAP-2
  • etv6 etv6, AML1
  • the cancer antigen may be selected from the group consisting of MAGE-A1, MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A5, MAGE-A6, MAGE-A7, MAGE-A8, MAGE-A9, MAGE-A10, MAGE-A11, MAGE-A12, MAGE-Xp2 (MAGE-B2), MAGE-Xp3 (MAGE-B3), MAGE-Xp4 (MAGE-B4), MAGE-C1, MAGE-C2, MAGE-C3, MAGE-C4 and MAGE-C5.
  • the cancer antigen may be selected from the group consisting of GAGE-1, GAGE-2, GAGE-3, GAGE-4, GAGE-5, GAGE-6, GAGE-7, GAGE-8 and GAGE-9.
  • the cancer antigen may be selected from the group consisting of BAGE, RAGE, LAGE-1, NAG, GnT-V, MUM-1, CDK4, tyrosinase, p53, MUC family, HER2/neu, p2iras, RCAS1, ⁇ -fetoprotein, E-cadherin, ⁇ -catenin, ⁇ -catenin, ⁇ -catenin, p120ctn, gp100Pme1117, PRAME, NY-ESO-1, cdc27, adenomatous polyposis coli protein (APC), fodrin, Connexin 37, Ig-idiotype, p15, gp75, GM2 ganglioside, GD2 ganglioside, human papilloma virus proteins, Smad family of tumor antigens, Imp-1, PlA, EBV-encoded nuclear antigen (EBNA)-1, brain glycogen phosphorylase, SSX-1, SSX-2 (
  • proteins of the disclosure are antibodies or antibody fragments including, without limitation, bevacizumab (AVASTIN@), trastuzumab (HERCEPTIN®), alemtuzumab (CAMPATH®, indicated for B cell chronic lymphocytic leukemia,), gemtuzumab (MYLOTARG®, hP67.6, anti-CD33, indicated for leukemia such as acute myeloid leukemia), rituximab (RITUXAN@), tositumomab (BEXXARR, anti-CD20, indicated for B cell malignancy), MDX-210 (bispecific antibody that binds simultaneously to HER-2/neu oncogene protein product and type I Fc receptors for immunoglobulin G (IgG) (Fc gamma RI)), oregovomab (OVAREX®, indicated for ovarian cancer), edrecolomab (PANOREX®), daclizumab (ZENAPAX®),
  • Proteins may be linked (e.g., covalently linked) to a degradable linker through any terminal or internal nucleophilic groups such as a —NH 2 functional group (e.g., side chain of a lysine).
  • proteins can be contacted with a degradable linker under conditions that permit reversible covalent crosslinking of proteins to each other through the degradable linker.
  • the proteins can be cross-linked to form a plurality of protein nanogels
  • the conditions include contacting the protein with the degradable linker in an aqueous buffer at a temperature of 4° C. to 25° C. in some embodiments, the contacting step can be performed in an aqueous buffer tor 30 minutes to one hour.
  • the aqueous buffer comprises phosphate buffered saline (PBS).
  • PBS phosphate buffered saline
  • the concentration of the protein in the aqueous buffer is 10 ng/mL to 50 mg/mL (e.g., 10, 15, 20, 25, 30, 35, 40, 45 or 50 mg/mL).
  • cytokine molecules can be used to cross-link one or more cytokine molecules.
  • the cytokine molecule is full length, a fragment or a variant of a cytokine, e.g., a cytokine comprising one or more mutations.
  • the cytokine molecule comprises a cytokine chosen from interleukin-1 alpha (IL-1 alpha), interleukin-1 beta (IL-1 beta), interleukin-2 (IL-2), interleukin-4 (IL-4), interleukin-5 (IL-5), interleukin-6 (IL-6), interleukin-7 (IL-7), interleukin-10 (IL-10), interleukin-12 (IL-12), interleukin-15 (IL-15), interleukin-17 (IL-17), interleukin-18 (IL-18), interleukin-21 (IL-21), interleukin-23 (IL-23), interferon (IFN) alpha, IFN beta, IFN gamma, tumor necrosis alpha, GM-CSF, GCSF, or a fragment or variant thereof, or a combination of any of the aforesaid cytokines.
  • IL-1 alpha interleukin-1 alpha
  • IL-1 beta interleukin-1 beta
  • IL-2 interleukin-2
  • the cytokine molecule is chosen from interleukin-2 (IL-2), interleukin-7 (IL-7), interleukin-12 (IL-12), interleukin-15 (IL-15), interleukin-18 (IL-18), interleukin-21 (IL-21), interleukin-23 (IL-23) or interferon gamma, or a fragment or variant thereof, or a combination of any of the aforesaid cytokines.
  • the cytokine molecule can be a monomer or a dimer.
  • the cytokine molecule further comprises a receptor domain, e.g., a cytokine receptor domain.
  • the cytokine molecule comprises an IL-15 receptor, or a fragment thereof (e.g., an extracellular IL-15 binding domain of an IL-15 receptor alpha) as described herein.
  • the cytokine molecule is an IL-15 molecule, e.g., IL-15 or an IL-15 superagonist as described herein.
  • a “superagonist” form of a cytokine molecule shows increased activity, e.g., by at least 10%, 20%, 30%, compared to the naturally-occurring cytokine.
  • An exemplary superagonist is an IL-15 SA.
  • the IL-15 SA comprises a complex of IL-15 and an IL-15 binding fragment of an IL-15 receptor, e.g., IL-15 receptor alpha or an IL-15 binding fragment thereof, e.g., as described herein.
  • the cytokine molecule further comprises an antibody molecule, e.g., an immunoglobulin Fab or scFv fragment, a Fab fragment, a FAB 2 fragment, or an affibody fragment or derivative, e.g. a sdAb (nanobody) fragment, a heavy chain antibody fragment, e.g., an Fc region, single-domain antibody, a bi-specific or multispecific antibody).
  • the cytokine molecule further comprises an immunoglobulin Fc or a Fab.
  • the cytokine molecule is an IL-2 molecule, e.g., IL-2 or IL-2-Fc.
  • a cytokine agonist can be used in the methods and compositions disclosed herein.
  • the cytokine agonist is an agonist of a cytokine receptor, e.g., an antibody molecule (e.g., an agonistic antibody) to a cytokine receptor, that elicits at least one activity of a naturally-occurring cytokine.
  • the cytokine agonist is an agonist of a cytokine receptor, e.g., an antibody molecule (e.g., an agonistic antibody) to a cytokine receptor chosen from an IL-15Ra or IL-21R.
  • a cytokine receptor e.g., an antibody molecule (e.g., an agonistic antibody) to a cytokine receptor chosen from an IL-15Ra or IL-21R.
  • the cytokine molecule is an IL-15 molecule, e.g., a full length, a fragment or a variant of IL-15, e.g., human IL-15.
  • the IL-15 molecule is a wild-type, human IL-15.
  • the IL-15 molecule is a variant of human IL-5, e.g., having one or more amino acid modifications.
  • the IL-15 molecule comprises a mutation, e.g., an N72D point mutation.
  • the cytokine molecule further comprises a receptor domain, e.g., an extracellular domain of an IL-15R alpha, optionally, coupled to an immunoglobulin Fc or an antibody molecule.
  • the cytokine molecule is an IL-15 superagonist (IL-15SA) as described in WO 2010/059253.
  • the cytokine molecule comprises IL-15 and a soluble IL-15 receptor alpha domain fused to an Fc (e.g., a sIL-15Ra-Fc fusion protein), e.g., as described in Rubinstein et al PNAS 103:24 p. 9166-9171 (2006).
  • the IL-15 molecule can further comprise a polypeptide, e.g., a cytokine receptor, e.g., a cytokine receptor domain, and a second, heterologous domain.
  • the heterologous domain is an immunoglobulin Fc region.
  • the heterologous domain is an antibody molecule, e.g., a Fab fragment, a Fab 2 fragment, a scFv fragment, or an affibody fragment or derivative, e.g. a sdAb (nanobody) fragment, a heavy chain antibody fragment.
  • the polypeptide also comprises a third heterologous domain.
  • the cytokine receptor domain is N-terminal of the second domain, and in other embodiments, the cytokine receptor domain is C-terminal of the second domain.
  • cytokines and antibodies are disclosed in e.g., U.S. Publication No. 2017/0080104, U.S. Pat. No. 9,603,944, U.S. Publication No. 2014/0081012, and PCT Application No. PCT/US2017/037249 (each incorporated herein by reference in its entirety).
  • the cytokines or other immunemodulators can target receptors (e.g., on an immune cell) by way of a fusion protein, such as those disclosed in PCT Application Nos. PCT/US2018/040777, PCT/US18/40783 and PCT/US18/40786 (each incorporated herein by reference in its entirety).
  • Backpacks or nanoparticles can be prepared by cross-linking various therapeutic protein monomers using one or more cross-linkers disclosed herein, as shown in FIG. TA. While the figure shows disulfide-containing linker, other biodegradable linkers disclosed herein can also be used.
  • the backpacks can be prepared by reacting the plurality of therapeutic protein monomers with the plurality of cross-linkers to form protein clusters having a size of, e.g., about 30 nm to 1000 nm in diameter.
  • the reaction can be performed at a temperature between about 5° C. and about 40° C. The reaction can be performed for about 1 minute to about 8 hours.
  • the protein clusters can be provided with a surface modification such as polycation.
  • a surface modification such as polycation.
  • Certain surface modification is disclosed in U.S. Publication No. 2017/0080104 and U.S. Pat. No. 9,603,944, both incorporated herein by reference in their entirety. Examples include poly-Lysine (polyK), PEG-polyK, and polyArginine.
  • the cross-linking reaction can proceed in the presence of one or more crowding agents such as polyethylene glycol (PEGs) and triglycerides.
  • PEGs polyethylene glycol
  • triglycerides include PEG400, PEG1000, PEG1500, PEG2000, PEG3000 and PEG4000.
  • Certain protein solubility aids such as glycerol, ethylene glycol and propylene glycol, Sorbitol and Mannitol can also improve the yield of backpack formation.
  • certain crosslinkers of the invention due to the reaction of cationic lysine residues in the backpack, will result in a backpack having a net negative charge which will inhibit cell attachment.
  • the backpacks can be coated or surface modified with a polycation such as polylysine (poly-L-lysine), polyethyleneimine, polyarginine, polyhistidine, polybrene and/or DEAE-dextran. Polycation can help the backpacks non-specifically bind or adsorb on cell membranes which are negatively charged.
  • polycation to be contained in a mixed solution may be a polymeric compound having a cationic group or a group that may become a cationic group, and an aqueous solution of a free polycation shows basic.
  • group that may become a cationic group include an amino group, an imino group, and the like.
  • polycation examples include: polyamino acid such as polylysine, polyomithine, polyhistidine, polyarginine, polytryptophan, poly-2,4-diaminobutyric acid, poly-2,3-diaminopropionic acid, protamine, and polypeptide having at least one or more kinds of amino acid residues in a polypeptide chain selected from the group consisting of lysine, histidine, arginine, tryptophan, ornithine, 2,4-diaminobutyric acid and 2,3-diaminopropionic acid; polyamine such as polyallylamine, polyvinylamine, a copolymer of allylamine and diallylamine, and polydiallylamine; and polyimine such as polyethyleneimine.
  • polyamino acid such as polylysine, polyomithine, polyhistidine, polyarginine, polytryptophan, poly-2,4-diaminobutyric
  • the polycation coating or surface modifying agent used to promote backpack adhesion to the cell is a cationic block copolymer of PEG-polylysine such as [methoxy-poly(ethylene glycol)n-block-poly(L-lysine hydrochloride), PEG-polylysine](PK30).
  • PEG-polylysine such as [methoxy-poly(ethylene glycol)n-block-poly(L-lysine hydrochloride), PEG-polylysine](PK30).
  • This block copolymer may contain approximately 114 PEG units (MW approximately 5000 Da) and 30 lysine units (MW approximately 4900 Da).
  • the linear PEG polymer has a methoxy end group, the poly-lysines are in the hydrochloride salt form.
  • PK30 is a linear amphiphilic block copolymer which has a poly(L-lysine hydrochloride) block and a non-reactive PEG block.
  • the poly-L-lysine block provides a net cationic charge at physiological pH and renders the backpack with a net positive charge after association.
  • PK30 Structure [Methoxy-poly(ethylene gly col)n-block-poly(L-lysine hydrochloride)] is as follows.
  • the backpacks can be coated with an antibody or antigen-binding fragment thereof that bind to a receptor on the surface of an immune cell, so as to specifically target the backpacks to the immune cell.
  • exemplary antibodies include those disclosed herein, or fusion proteins containing the same.
  • IL15-Fc (IL15Ra-sushi-domain-Fc fusion homodimer protein with two associated IL-15 Proteins) monomers can be crossed linked and surface modified with polycation, to form IL-15 backpacks.
  • the IL-15 backpacks can then be loaded onto immune cells such as T cells to form primed T cells.
  • the backpacks can be optionally frozen until use in cell therapy, as illustrated in FIG. 1 C .
  • the cell therapy can be selected from, e.g., an adoptive cell therapy, CAR-T cell therapy, engineered TCR T cell therapy, a tumor infiltrating lymphocyte therapy, an antigen-trained T cell therapy, or an enriched antigen-specific T cell therapy.
  • a cell therapy composition can be prepared by providing the protein cluster or backpack composition disclosed herein, and incubating the protein cluster or backpack composition with nucleated cells such as immune cells, preferably for about 30-60 minutes.
  • the cells can be cryopreserved with backpacks until administration to a patient via, e.g., infusion.
  • a cell therapy composition comprising the protein cluster or backpack composition disclosed herein, associated with a nucleated cell such as T and NK cells.
  • a cell therapy composition may be administered into a subject in need thereof.
  • the cross-linkers can degrade under physiological conditions so as to release the therapeutic protein monomers from the protein cluster.
  • compositions including pharmaceutical compositions, comprising the backpacks are provided herein.
  • a composition can be formulated in pharmaceutically-acceptable amounts and in pharmaceutically-acceptable compositions.
  • pharmaceutically acceptable means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients (e.g., biologically-active proteins of the nanoparticles).
  • Such compositions may, in some embodiments, contain salts, buffering agents, preservatives, and optionally other therapeutic agents.
  • Pharmaceutical compositions also may contain, in some embodiments, suitable preservatives.
  • Pharmaceutical compositions may, in some embodiments, be presented in unit dosage form and may be prepared by any of the methods well-known in the art of pharmacy.
  • compositions suitable for parenteral administration comprise a sterile aqueous or non-aqueous preparation of the nanoparticles, which is, in some embodiments, isotonic with the blood of the recipient subject.
  • This preparation may be formulated according to known methods.
  • a sterile injectable preparation also may be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent.
  • the backpacks and compositions containing such have numerous therapeutic utilities, including, e.g., the treatment of cancers, autoimmune diseases and infectious diseases.
  • Methods described herein include treating a cancer in a subject by using backpacks or backpacked cells as described herein. Also provided are methods for reducing or ameliorating a symptom of a cancer in a subject, as well as methods for inhibiting the growth of a cancer and/or killing one or more cancer cells. In embodiments, the methods described herein decrease the size of a tumor and/or decrease the number of cancer cells in a subject administered with a described herein or a pharmaceutical composition described herein.
  • the cancer is a hematological cancer.
  • the hematological cancer is leukemia or lymphoma.
  • a “hematologic cancer” refers to a tumor of the hematopoietic or lymphoid tissues, e.g., a tumor that affects blood, bone marrow, or lymph nodes.
  • Exemplary hematologic malignancies include, but are not limited to, leukemia (e.g., acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), hairy cell leukemia, acute monocytic leukemia (AMoL), chronic myelomonocytic leukemia (CMML), juvenile myelomonocytic leukemia (JMML), or large granular lymphocytic leukemia), lymphoma (e.g., AIDS-related lymphoma, cutaneous T-cell lymphoma, Hodgkin lymphoma (e.g., classical Hodgkin lymphoma or nodular lymphocyte-predominant Hodgkin lymphoma), mycosis fungoides, non-Hodgkin lymphoma (e.g., B-cell non-Hodgkin lymphoma (e
  • the cancer is a solid cancer.
  • Exemplary solid cancers include, but are not limited to, ovarian cancer, rectal cancer, stomach cancer, testicular cancer, cancer of the anal region, uterine cancer, colon cancer, rectal cancer, renal-cell carcinoma, liver cancer, non-small cell carcinoma of the lung, cancer of the small intestine, cancer of the esophagus, melanoma, Kaposi's sarcoma, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, cutaneous or intraocular malignant melanoma, uterine cancer, brain stem glioma, pituitary adenoma, epidermoid cancer, carcinoma of the cervix squamous cell cancer, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the vagina, sarcoma of soft tissue, cancer of the urethr
  • the backpacks or backpacked cells are administered in a manner appropriate to the disease to be treated or prevented.
  • the quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient's disease. Appropriate dosages may be determined by clinical trials. For example, when “an effective amount” or “a therapeutic amount” is indicated, the precise amount of the pharmaceutical composition (or backpacks) to be administered can be determined by a physician with consideration of individual differences in tumor size, extent of infection or metastasis, age, weight, and condition of the subject.
  • the pharmaceutical composition described herein can be administered at a dosage of 104 to 10 9 cells/kg body weight, e.g., 10 to 10 6 cells/kg body weight, including all integer values within those ranges. In embodiments, the pharmaceutical composition described herein can be administered multiple times at these dosages. In embodiments, the pharmaceutical composition described herein can be administered using infusion techniques described in immunotherapy (see, e.g., Rosenberg et al., New Eng. J. of Med. 319:1676, 1988).
  • the backpacks or backpacked cells are administered to the subject parenterally.
  • the cells are administered to the subject intravenously, subcutaneously, intratumorally, intranodally, intramuscularly, intradermally, or intraperitoneally.
  • the cells are administered, e.g., injected, directly into a tumor or lymph node.
  • the cells are administered as an infusion (e.g., as described in Rosenberg et al., New Eng. J. of Med. 319:1676, 1988) or an intravenous push.
  • the cells are administered as an injectable depot formulation.
  • the subject is a mammal.
  • the subject is a human, monkey, pig, dog, cat, cow, sheep, goat, rabbit, rat, or mouse.
  • the subject is a human.
  • the subject is a pediatric subject, e.g., less than 18 years of age, e.g., less than 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1 or less years of age.
  • the subject is an adult, e.g., at least 18 years of age, e.g., at least 19, 20, 21, 22, 23, 24, 25, 25-30, 30-35, 35-40, 40-50, 50-60, 60-70, 70-80, or 80-90 years of age.
  • A 2,2′-disulfanediyldi(etha n-1-ol)(2.0 g, 1 equiv.)
  • B DSC (N,N′-Disuccinimidyl carbonate) (33.2 g, 10.0 equiv.) Pyridine (11.3 mL, 10.0 equiv.)
  • Step:2 Carbonate formation
  • C Bis(2-hydroxyethyl) butanedioate (1.5 g, 1 equiv.)
  • D DSC (18.66 g, 10 equiv.) pyridine (5.76 g, 10 equiv.)
  • Human cells e.g., Tcells, CAR-T, NK cells, other immune cells
  • IL15 backpack in HBSS at a cell concentration of 50M/mL. After labeling the cells can be tested for:
  • Backpacks should be stored at ⁇ 80C before use. Thawed backpacks can be re-frozen and re-used up to 3 or more freeze/thaw cycles.
  • the buffers, PBS, and media used in the steps below should be pre-warmed to 37° C.
  • the cells should be at ⁇ 5 ⁇ 10 6 cells/mL density and need to be further diluted by 1:10 during plating.
  • step 13 three additional times in three separate 96-well flat bottom plates (4 plates total: Day0, Day1, Day3, DayX for splitting for future time points)
  • CountBright Bead Solution contains (volumes for labeling 1 well is listed below):
  • Bovine Serum Albumin (BSA): AmericanBio, Inc. cat #AB01243-00050
  • Example 4 IL-15 Backpack Provides Autocrine Stimulation and Expansion of T Cells after Adoptive Transfer Driven by Controlled Concentrated Release of IL-15
  • Interleukin 15 a powerful stimulator of CD8 and NK cell expansion is capable of driving anti-tumor activity of adoptively transferred T cells.
  • systemic delivery does not safely provide sufficient doses to drive T cell expansion engraftment and anti-tumor activity.
  • the IL-15 backpack primed T-cells disclosed herein are autologous T cells that carry tightly controlled doses of IL-15, which is slowly released over a 7-14 day period for directed autocrine activation of infused T cells without affecting endogenous T cells.
  • IL-15 backpack primed cytotoxic T cells that are tumor antigen primed using a novel dendritic cell priming sequence.
  • CTLs cytotoxic T cells
  • fluorophore-containing IL-15 backpacks were titrated in a cell labeling reaction using healthy human CD8 T cells.
  • Fluorescent histograms (LHS) and MFI quantification (RHS) show that the extent of IL-15 backpack loading increases with increased IL-15 backpack loading concentration.
  • FIG. 3 shows dynabead-activated human CD3 T cells from four healthy donors were labeled with IL-15 backpack at three different concentrations.
  • Cell-associated IL-15 backpack loading was assessed by quantifying the remaining IL-15 backpack from the labeling reaction and subtracting that number from the total amount of IL-15 backpack added in the reaction.
  • FIG. 4 shows dynabead-activated human CD3 cells were treated with or without IL-15 backpack before culturing for 7 days.
  • IL-15 levels in the culture supernatants were assessed by ELISA. Expansion was assessed by flow cytometry.
  • FIG. 5 shows IL-15 backpack labeled human CD3 T cells were cultured for 14 days. Media exchange was carried out on Day 1, or Day 2, or Day3, or Day4 to remove secreted IL-15.
  • FIG. 6 A shows in vitro cell expansion measured by flow cytometry for ⁇ IL-15 backpack loaded CAR-T cells.
  • FIG. 6 B shows flow cytometry measured serum levels of CAR-T cells following injection into NSG mice bearing NSCLC tumor.
  • FIG. 6 C shows PET imaging of tumor size.
  • FIGS. 7 A- 7 B shows PMEL T cells, activated ex vivo with anti-CD3/anti-CD28 coated plates and either injected, primed with IL-15 backpack (“IL-15 BP”), or co-administered with IL15-Fc monomers into B16-F10 tumor-bearing C57B6 mice.
  • Mice were sacrificed on days 1, 4, 10 and 16 for blood and tissue collection. Blood was drawn at 2, 24, 48, and 96 hrs for quantification of IL15-Fc (ELISA) and IFN- ⁇ (Luminex) ( FIG. 7 A ), and for enumeration of CD8, NK, and PMEL cells ( FIG. 7 B , Flow Cytometry).
  • FIG. 7 A shows PMEL T cells, activated ex vivo with anti-CD3/anti-CD28 coated plates and either injected, primed with IL-15 backpack (“IL-15 BP”), or co-administered with IL15-Fc monomers into B16-F10 tumor-bearing C
  • FIG. 7 C shows IL15-Fc or IL-15 backpacks were injected into non-tumor bearing C56BL6 mice in the absence of PMEL T cell injection. Blood was drawn for quantification of IFN- ⁇ , and for enumeration of activated (CD25+) CD4, CD8, and NK cells.
  • Novel, closed, semi-automated cell manufacturing process with a yield of up to several billion of cytotoxic T lymphocytes (CTLs) that are targeted against a customizable set of tumor-associated antigens (TAAs).
  • CTLs cytotoxic T lymphocytes
  • TAAs tumor-associated antigens
  • the antigen-directed CTLs are loaded with IL-15 backpack to generate the TRQ15-01 cell product.
  • FIGS. 8 A- 8 E show that CTLs from process completion were harvested and characterized for: (A) Product TAA-specific cell count and reactivity (intracellular cytokine staining after peptide stimulation); (B) TCR sequencing comparing TRQ15-01 CTL products to their incoming apheresis, and (C) flow-based immune cell composition. (D) TAA-trained CTLs were labeled with an MHC tetramer bearing one of the antigen peptides; (E) CTLs ⁇ IL-15 backpack were injected into NSG mice and blood was drawn on days 1, 4, 8, 10. Cell expansion was measured by flow cytometry.
  • IL-15 backpack cell loading is robust and tunable giving a controlled IL-15 dose per cell.
  • the design of our IL-15 backpack technology provides slow and controllable release of IL-15 resulting in autocrine stimulation and sustained cell expansion in adoptive T cell therapy.
  • IL-15 backpack Priming induces orders of magnitude lower systemic IFNg levels, endogenous CD8 and NK cell expansion, due to lack of systemic exposure.
  • a fully closed, semi-automated cell process reproducibly generates several billion antigen-directed human CTLs with ⁇ 20% reactivity and 95% T cell purity from healthy donors despite ultra low frequency ( ⁇ 1%) precursors. Human CTLs are highly dependent on IL-15 backpack priming technology for cell survival and expansion in vivo.
  • Deep IL-15 refers to a multimer of human IL-15 receptor ⁇ -sushi-domain-Fc fusion homodimers with two associated IL-15 molecules (IL15-Fc), connected by a cleavable crosslinker (Linker-2), and non-covalently coated with a polyethylene glycol (PEG)-polylysine 30 block copolymer (PK30).
  • IL15-Fc IL-15 receptor ⁇ -sushi-domain-Fc fusion homodimers with two associated IL-15 molecules
  • Linker-2 cleavable crosslinker
  • PK30 polyethylene glycol-polylysine 30 block copolymer
  • Deep IL-15 is a multimer of human IL15-Fc monomers, connected by a hydrolysable crosslinker (CL17) and non-covalently coated with a polyethylene glycol (PEG)-polylysine 30 block copolymer (PK30).
  • IL15-Fc monomers consist of two subunits, each consisting of an effector attenuated IgG2 Fc variant fused with an IL-15 receptor ⁇ -sushi-domain noncovalently bound to a molecule of IL-15.
  • Deep IL-15 Primed T cells are generated via a loading process in which target cells are co-incubated with Deep IL-15 at high concentrations. Through this process, Deep IL-15 becomes associated with the cell via electrostatic interactions and is internalized to create intracellular reservoirs of Deep IL-15. From these reservoirs, Deep IL-15 slowly releases bioactive IL15-Fc by hydrolysis of the crosslinker. This extended release of IL15-Fc promotes proliferation and survival of Deep IL-15 Primed T cells, providing a targeted, controllable and time-dependent immune stimulus.
  • the objective of this study was to test the pharmacological activity of Deep IL-15 primed PMEL T cells in C57BL/6J mice with and without orthotopically placed B16-F10 melanoma tumors.
  • Control groups included vehicle control, PMEL cells alone and PMEL cells+IL15-Fc, administered in a separate injection (10 ⁇ g, maximum tolerated dose, MTD).
  • B16-F10 melanoma tumor cells (0.2 ⁇ 10 6 ) were injected intra-dermally into the shaved right flank of female C 57 BL/6 mice (Jackson Labs) on study day -12.
  • the body weights were recorded and tumor dimensions (length [L] and width [W], defined in the list of abbreviations) were measured with calipers 2 to 3 times per week. Tumor volumes were calculated using the formula: W 2 ⁇ L ⁇ /6.
  • PMEL cells were isolated from the spleens and lymph nodes (inguinal, axillary and cervical) of 14 female transgenic PMEL mice (Jackson Laboratories, Bar Harbor, Me.). The spleens and lymph nodes were processed with a GentleMACS Octo Dissociator (Miltenyi Biotech, Auburn, Calif.) and passed through a 40 ⁇ m strainer. The cells were washed by centrifugation and the CD8a+cells were purified using an IMACS na ⁇ ve CD8a+isolation kit (Miltenyi Biotech,) and a MultiMACS cell 24 block (Miltenyi Biotech) and separator (Miltenyi Biotech) with 18 columns following the manufacturer's protocol. The non-CD8a 1 cells were removed by an affinity column and the CD8a+T-cells were collected in the column eluate. The purity of CD8a+cells was confirmed by flow cytometry.
  • CD8a+cells from PMEL mice were plated into ten, 6-well tissue culture plates coated with anti-CD3 and anti-CD28 at a density of 5 ⁇ 10 6 cells/well and incubated for 24 hr at 37° C. and 5% CO2.
  • Murine IL-2 (20 ng/mL) and murine IL-7 (0.5 ng/mL) were added 24 hr post plating (D1).
  • D1 and D3 the cells were counted and diluted to a concentration of 0.2 ⁇ 10 6 cells/mL with fresh media containing murine IL-21 (10 ng/mL). The cells were collected on D4 to obtain a total of 100 ⁇ 10 6 PMEL cells/mL in 28 mL of vehicle control.
  • Deep IL-15 Primed PMEL cells Five mL of PMEL cells (100 ⁇ 10 6 cells/mL) were mixed with 5.5 mL of Deep IL-15 (1.36 mg/ml) and incubated with rotation for 1 hr at 37° C. to create Deep IL-15 Primed PMEL cells. Deep IL-15 Primed PMEL cells were washed (3X, first with medium and then twice with HBSS) by centrifugation (500g) and counted. Deep IL-15 Primed PMEL cells were resuspended at a concentration of 50 ⁇ 10 6 cells/mL. The mice in Groups 5A and 5B were injected with 200 ⁇ L of this preparation for a total of 10 ⁇ 10 6 Deep IL-15 Primed PMEL cells per mouse.
  • PMEL cells (15 mL at 100 ⁇ 10 6 cells/mL) were mixed with 15 mL of HBSS, incubated with rotation for 1 hr at 37° C., washed (3X, first with medium and then twice with HBSS) by centrifugation (500g) and counted. PMEL cells were resuspended at a concentration of 50 ⁇ 10 6 cells/mL. The mice in Groups 2A and 2B were injected IV with 200 ⁇ L of this preparation for a total of 10 ⁇ 10 6 PMEL cells per mouse.
  • mice in Groups 3A and 3B were injected IV with 200 ⁇ L of this preparation for a total of 10 ⁇ 10 6 PMEL cells per mouse, and received a retro-orbital injection of IL15-Fc (10 ⁇ g/mouse in 50 p1 HBSS; lot #TSO). Based on an average loading efficiency of 39%, the total amount of IL15-Fc associated with 10 ⁇ 10 6 PMEL cells is 58.5 jig, which is 5.85-fold higher than the amount delivered systemically by injection of IL15-Fc (10 ⁇ g) in Groups 3A and 3B.
  • ELISA Fc-IL15 Enzyme-Linked Immunosorbent Assay
  • the assay was run twice.
  • samples were evaluated at the following dilutions: 1: 20000 for the 2 hr time point, 1:5000 for the D1 time point, and 1:250 for the D2, D4 and D10 time points.
  • samples from groups 3A and 3B were diluted 1:5000 for the D1 time point, 1:250 for the D2 time point and 1:25 for the D4 and D10 time points.
  • Samples from groups 1A and 1B, 2A and 2B and 5A and 5B were diluted 1:25 for all the time points analyzed. The data is reported for the second run.
  • the lower limit of quantitation (LLOQ) in blood was 310 ng/ml for the 1:20000 dilution, 77.5 ng/ml for the 1:5000 dilution, 3.875 ng/ml for the 1:250 dilution and 0.3875 ng/ml for the 1:25 dilution.
  • ThermoFisher ProcartaPlex mouse high sensitivity panel 5plex Cat.#EPXSOSO-22199-901 kits were used according to manufacturer's protocol and samples were analyzed on a Bio-Plex 200 system. Serum was thawed on ice, and 20 L of serum were tested for IFN- ⁇ , TNF- ⁇ , IL-2, IL-4 and IL-6 levels. In a few samples, 20 ⁇ L of serum were not available, so a smaller volume was utilized. Dilution factors were adjusted, to calculate concentrations according to the standard curves. Statistical analysis was carried out in GraphPad Prism.
  • FIG. 9 shows clinical chemistry parameters where statistically significant changes were observed for the na ⁇ ve mice at D1 and D4 post-dose. At D1 post-dose, a significant reduction (p ⁇ 0.05) in Albumin levels was observed in the PMEL+IL15-Fc group relative to the Deep IL-15 Primed PMEL group as well as in the Blood Urea Nitrogen (BUN) levels compared to both vehicle control and Deep IL-15 Primed PMEL (p ⁇ 0.05 for both).
  • BUN Blood Urea Nitrogen
  • the PMEL+IL15-Fc group showed significantly reduced Albumin (p ⁇ 0.05 compared to all the other treatment groups), total protein (p ⁇ 0.05 compared to vehicle control), Glucose (p ⁇ 0.05 compared to the Deep IL-15 Primed PMEL), Albumin/Globulin (ALB/GLOB) ratio (p ⁇ 0.05 compared to vehicle control, and p ⁇ 0.01 compared to PMEL and Deep IL-15 Primed PMEL). Additionally, the PMEL+IL15-Fc group showed a significant increase (p ⁇ 0.05 compared to vehicle control and Deep IL-15 Primed PMEL) in Cholesterol levels.
  • FIG. 10 shows clinical chemistry parameters where statistically significant changes were observed for the tumor—bearing mice at D1 and D4 post-dose.
  • D1 post-dose the only statistically significant change in clinical chemistry was a reduction in Bilirubin—conjugated, observed with both the PMEL+IL15-Fc and with the Deep IL-15 Primed PMEL group (p ⁇ 0.05 compared to vehicle control for both).
  • D4 post-dose statistically significant increases in Albumin (p ⁇ 0.05 compared to vehicle control), Total Protein (p ⁇ 0.01 compared to vehicle control) and Bicarbonate TCO2 (p ⁇ 0.05 compared to vehicle control) were seen with the PMEL group.
  • a sandwich ELISA (anti-Fc capture antibody followed by anti-IL15 detection antibody) was used to measure IL15-Fc in the blood of mice injected with PMEL+IL15-Fc (10 ⁇ g) and Deep IL-15 Primed PMEL (carrying 58.5 ug of IL15-Fc).
  • PK pharmacokinetics
  • a single dose administration of Deep IL-15 Primed PMEL and PMEL+IL15-Fc were determined for a composite animal in na ⁇ ve and tumor—bearing mouse.
  • maximum concentration (Cmax) was attained at 2 hr post dose administration in both na ⁇ ve and tumor—bearing mice.
  • the first concentration measured was at 24 hr (the 2 hr samples were initially measured at a non-optimal dilution and no IL15-Fc was detected, and there was not sufficient sample available to repeat the measurement with ideal dilution).
  • Tumor—bearing mice attained slightly lower concentrations than the na ⁇ ve mice.
  • the calculated mean t1/2 for IL15-Fc in the PMEL+IL15-Fc group was 28.9 hr and 7.12 hr in tumor bearing mice and non-tumor bearing mice, respectively.
  • the IL15-Fc concentrations at the 24 hr timepoint were compared between the PMEL+IL15-Fc and Deep IL-15 Primed PMEL groups.
  • the total IL15-Fc concentration was higher in the PMEL+IL15-Fc (10 jig) group than in the Deep IL-15 Primed PMEL group (58.5 ug of IL15-Fc), approximately 3488-fold higher in the na ⁇ ve mice and 3299-fold higher in the tumor bearing mice.
  • Composite IL15-Fc PK parameters are summarized in Table 1 and the mean (SD) IL15-Fc PK profiles are depicted in FIG. 12 .
  • the serum levels of IL15-Fc in the Deep IL-15 Primed PMEL group were over 3000-fold lower compared to the levels detected in the PMEL+IL15-Fc group, corresponding to no weight loss, no significant changes in CBCs and in endogenous immune cells (CD8 + , NK1.1 + and CD4 + cells), reduced IFN- ⁇ serum levels and associated pharmacological changes compared to the PMEL+IL15-Fc group.

Abstract

Disclosed herein are compositions and methods for preparation and use of protein therapeutics, and more particularly protein clusters or backpacks having a plurality of therapeutic protein monomers reversibly crossed-linked by biodegradable linkers.

Description

    CROSS REFERENCE TO RELATED APPLICATIONS
  • This application claims priority to and the benefit of U.S. Provisional Application Nos. 62/554,058 filed Sep. 5, 2017 and 62/657,218 filed Apr. 13, 2018, the disclosures of both of which applications are hereby incorporated herein by reference in its entirety.
    • FIELD
  • The present disclosure generally relates to compositions and methods for preparation and delivery of protein therapeutics, and more particularly protein clusters or backpacks having a plurality of therapeutic protein monomers reversibly crossed-linked by biodegradable linkers.
    • BACKGROUND
  • Protein therapeutics, such as antibodies, cytokines, growth factors and vaccines, are important therapeutics for the treatment of a variety of diseases including, for example, cancer, diabetes and cardiovascular diseases. This class of protein therapeutics has been developed rapidly in the global pharmaceutical industry over the last few years. Protein therapeutics have the advantages of high specificity and potency relative to small molecule drugs. Nonetheless, the use of protein therapeutics is limited as a result of their intrinsic instability, immunogenicity and short half-life.
  • To address these limitations, there are generally two approaches: one is genetic fusion of the therapeutic protein, and the other is use of engineered carriers to deliver protein therapeutics. With engineered carriers, proteins are loaded by either encapsulation/adsorption or conjugation. Encapsulation or adsorption of proteins in/onto liposomes or nanoparticles is typically inefficient. Conjugation of proteins typically reduces their bioactivity. Therefore, both approaches are problematic.
  • Thus, a significant need exists for new compositions and methods that incorporate therapeutics into a delivery system with high efficiency.
    • SUMMARY
  • Disclosed herein are improved methods and compositions for protein therapeutics. More particularly, disclosed herein are protein clusters or backpacks having a plurality of therapeutic protein monomers reversibly crossed-linked by biodegradable linkers, and methods for preparing and using the same.
  • In one aspect, disclosed herein is a therapeutic composition comprising:
  • a protein cluster comprising a plurality of therapeutic protein monomers reversibly crossed-linked to one another, wherein the protein cluster has a size between 30 nm and 1000 nm in diameter measured by dynamic light scattering;
  • a plurality of biodegradable cross-linkers each having two, three or four functional groups capable of reacting with nucleophilic groups on the therapeutic protein monomers, thereby cross-linking the therapeutic protein monomers into the protein cluster, wherein the cross-linker degrades, after administration into a subject in need thereof, under physiological conditions so as to release the therapeutic protein monomers from the protein cluster;
  • a pharmaceutically acceptable carrier or excipient; and
  • optionally, a surface modification on the protein cluster, wherein preferably the surface modification is poly cation.
  • In some embodiments, the cross-linker has the formula of A-B-C wherein B is optional, wherein A represents a structural template, B represents a polymer spacer, C represents a hydrolysable linkage and a functional group that can react with nucleophilic groups.
  • In some examples, A is selected from di-ols, tri-ols, tetra-ols, poly-ols, di-thiols, tri-thiols, tetra-thiols, poly-thiols, di-amines, tri-amines, tetra-amines, or poly-amines. In some embodiments, B can be selected from polyethylene glycol, saccharides, poly-ols, poly-ethers, poly-thioethers, poly-amines, poly-esters, alkanes, phenyls, or amino-acids. In some embodiments, C can have C has formula (Ia):
  • Figure US20230233609A1-20230727-C00001
  • wherein:
  • LG2 is a leaving group selected from triflate, tosyl, Cl, N-hydroxysuccinimide and itnidazolide;
  • Y2 is selected from O and S;
  • X, at each occurrence, is independently selected from O, S, and N;
  • L is optional and is a linker such that
  • Figure US20230233609A1-20230727-C00002
  • is biodegradable; and
  • m is an integer selected from 1-6, preferably 2.
  • In certain embodiments, the cross-linker has formula (I):
  • Figure US20230233609A1-20230727-C00003
  • wherein:
  • LG1 and LG2 are each a leaving group, independently selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • Y1 and Y2 are each independently selected from O and S;
  • X, at each occurrence, is independently selected from O, S, and N;
  • L is a linker such that
  • Figure US20230233609A1-20230727-C00004
  • is biodegradable; and
  • m, at each occurrence, is an integer selected from 1-6.
  • In some embodiments, the cross-linker of formula (I) is symmetrical.
  • In some embodiments, LG1 and LG2 are capable of reacting with a protein, a drug and/or a particle. In one example, LG1 and LG2 are both imidazolide. In another example, LG1 and LG2 are both N-hydroxysuccinimide.
  • In some embodiments,
  • Figure US20230233609A1-20230727-C00005
  • is hydrolysable.
  • In some embodiments, e.g., when one or more X is N, L is selected from:
  • (a) —(CH2)n— wherein n is an integer selected from 0-5;
  • Figure US20230233609A1-20230727-C00006
  • wherein n is an integer selected from 0-5; or
  • Figure US20230233609A1-20230727-C00007
  • wherein X, at each occurrence, is independently selected from O, S, and N.
  • In some embodiments, m is 2.
  • In certain embodiments, the cross-linker has formula (II):
  • Figure US20230233609A1-20230727-C00008
  • wherein:
  • X1 and X2 are each independently selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • A1 and A3 are each independently —(CR1R2)n—;
  • A2 is —(CR1R2)m—;
  • Y1 and Y2 are each independently selected from NR3, O and S;
  • wherein R1 and R2 at each occurrence are independently selected from hydrogen, halogen, hydroxyl, C1-12 alkyl, C2-12 alkenyl, C3-12 cycloalkyl, C2-12 heterocyclyl; C6-12 aryl optionally substituted with 1 or more halo, hydroxyl, C1-6 alkyl and/or C1-6 alkoxyl; and C4-12 heteroaryl optionally substituted with 1 or more halo, hydroxyl, C1-6 alkyl and/or C1-6 alkoxyl
  • wherein R3 is selected from hydrogen, C1-12 alkyl, C2-12 alkenyl, C3-12 cycloalkyl, C2-12 heterocyclyl; C6-12 aryl optionally substituted with 1 or more halo, hydroxyl, C1-6 alkyl and/or C1-6 alkoxyl; and C4-12 heteroaryl optionally substituted with 1 or more halo, hydroxyl, C1-6 alkyl and/or C1-6 alkoxyl;
  • n, at each occurrence, is an integer independently selected from 1-12; and
  • m is an integer selected from 0-12.
  • In some embodiments, the cross-linker of formula (TT) is symmetrical. In some embodiments, X1 and X2 can each be a leaving group capable of reacting with a protein, a drug and/or a particle. In one example, X1 and X2 are both imidazolide. In another example, X1 and X2 are both N-hydroxysuccinimide. In some embodiments, R1 and R2 are both hydrogen. In one example, A1 and A3 are both —(CH2)2—. In one embodiment, A2 is —(CH2)2—. In some embodiments, Y1 and Y2 are both O.
  • In one embodiment, the cross-linker is:
  • Figure US20230233609A1-20230727-C00009
  • In some embodiments, in the cross-linker of formula (II), A2 is a bond (e.g., when m is 0). In one embodiment, Y1 and Y2 are both NH.
  • The cross-linker, in some embodiments, is:
  • Figure US20230233609A1-20230727-C00010
  • In some embodiments, the cross-linker can be used as a degradable or hydrolysable linker. In some embodiments, the degradable linker is a redox responsive linker. Methods of making and using various linkers (e.g., to make nanogels or backpacks) are disclosed in U.S. Publication No. 2017/0080104, U.S. Pat. No. 9,603,944, and U.S. Publication No. 2014/0081012, each of which is incorporated herein by reference in its entirety.
  • In some embodiments, the composition further comprises an agent that optimizes formation of the protein cluster. For example, the agent can increase yield of the protein cluster formation by reducing non-reacted proteins in comparison to a composition without the agent. In some embodiments, the agent increases yield of the protein cluster formation by reducing formation of clusters that are larger than 1000 nm in size compared to a composition without the agent.
  • In some embodiments, in the composition disclosed herein, the therapeutic protein monomers comprise one or more cytokine molecules and/or one or more costimulatory molecules, wherein:
      • (i) the one or more cytokine molecules are selected from IL15, IL2, IL7, IL10, IL12, IL18, IL21, IL-23, IL-4, IL1alpha, IL1beta, IL-5, IFNgamma, TNFa, IFNalpha, IFNbeta, GM-CSF, or GCSF; and
      • (ii) the one or more costimulatory molecules are selected from CD137, OX40, CD28, GITR, VISTA, anti-CD40, or CD3.
  • Another aspect relates to a method for preparing any one of the composition disclosed herein, the method comprising reacting the plurality of therapeutic protein monomers with the plurality of cross-linkers to form the protein cluster. In some embodiments, the reacting step is performed at a temperature between about 5° C. and about 40° C. In some embodiments, the reacting step is performed for about 1 minute to about 8 hours. The method can further include providing the surface modification to the protein cluster and/or purifying the protein cluster.
  • Also provided herein is a method for preparing a cell therapy composition, comprising: providing any one of the composition disclosed herein; and incubating the protein cluster with a nucleated cell such as T and NK cells, preferably for about 30-60 minutes.
  • A further aspect relates to a cell therapy composition, comprising any one of the composition disclosed herein, associated with a nucleated cell such as T and NK cells.
  • Still a further aspect relates to a method of providing cell therapy, comprising administering the cell therapy composition disclosed herein into a subject in need thereof.
    • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIGS. 1A-1C illustrates exemplary backpacks and their making and using.
  • FIG. 2 : Titratable loading of IL-15 backpack on human T cells.
  • FIG. 3 : Consistent and precise loading of IL-15 backpack across multiple donors.
  • FIG. 4 : IL-15 backpack release from labeled cells drives expansion.
  • FIG. 5 : Cell-associated IL-15 backpack drives cell expansion at Day 14 following intermittent wash.
  • FIGS. 6A-6C: IL-15 backpack drives expansion of anti-EGFR CAR-expressing human CD3 T cells.
  • FIGS. 7A-7C: Contrasting effects of systemic IL15-Fc and IL-15 backpack in C57B6 mouse model with intact immune system.
  • FIGS. 8A-8E: CTLs from process completion were harvested and characterized
  • FIG. 9 : Clinical chemistry parameters in naïve mice at D1 and D4 post-dose. HBSS=vehicle control; DP-15 PMEL=Deep IL-15 Primed PMEL cells; D=Day. Statistical comparisons were made using ANOVA followed by Tukey's multiple comparison test. *=p<0.05; **=p<0.01; ***=p<0.001; ****=p<0.0001.
  • FIG. 10 : Clinical chemistry parameters in tumor—bearing mice at D1 and D4 post-dose. HBSS=vehicle control; DP-15 PMEL=Deep IL-15 Primed PMEL cells; D=Day. Statistical comparisons were made using ANOVA followed by Tukey's multiple comparison test. *=p<0.05; **=p<0.01; ****=p<0.001.
  • FIG. 11 : Serum levels of IFN-γ in tumor—bearing compared to naïve mice 24 hr after ACT. he serum levels of IFN-γ in the PMEL+IL15-Fc group were significantly increased (2-way ANOVA with Tukey's multiple comparison, p<0.001) compared to both the PMEL and DP-15 PMEL groups in both naïve and tumor—bearing mice. ACT=adoptive cell transfer; DP-15 PMEL=Deep IL-15 Primed PMEL cells.
  • FIG. 12 : IL15-Fc systemic exposure in mice treated with PMEL+IL15-Fc and Deep IL-15 Primed PMEL cells, in naïve and tumor—bearing mice.
  • FIG. 13 : Mean tumor volume over time and on Day 16. Tumor volumes were measured on D -5, Day -3, DO, D1, D2, D4, D6, D9, D10, D11, D14 and D16. Data are mean±SEM (left panel). Tumor volumes for individual animals on D16 are shown in the right panel. Statistical comparisons were made using ANOVA followed by Tukey's multiple comparison test. *=p<0.05; **=p<0.01; ***=p<0.001; ****=p<0.0001. The color of the asterisk represents which groups are statistically different. For example, a green asterisk over the grey (HBSS) line indicates that there is a significant difference between HBSS and PMEL cells. HBSS=vehicle control; ACT=adoptive cell transfer. DP-15 PMEL=Deep IL-15 Primed PMEL cells.
  • FIG. 14 : Mean tumor weight at sacrifice (n=2-5/group/time point). Tumor weights were at sacrifice on Day 1, 4, 10 and 16 (n=2-5/group each time point). Statistical comparisons were made using ANOVA followed by Tukey's multiple comparison test. *=p<0.05; **=p<0.01; ****=p<0.0001. HBSS=vehicle control; DP-15 PMEL=Deep IL-15 Primed PMEL cells.
    •  DETAILED DESCRIPTION
  • Cancer immunotherapy, including adoptive T cell therapy, is a promising strategy to treat cancer because it harnesses a subject's own immune system to attack cancer cells. Nonetheless, a major limitation of this approach is the rapid decline in viability and function of the transplanted T lymphocytes. In order to maintain high numbers of viable tumor-specific cytotoxic T lymphocytes in tumors, co-administration of immunostimulatory agents with transferred cells is necessary. When given systemically at high doses, these agents could enhance the in vivo viability of transferred (i.e., donor) cells, improve the therapeutic function of transferred cells, and thus lead to overall improved efficacy against cancer; however, high doses of such agents could also result in life-threatening side effects. For example, the use of interleukin-2 (IL-2) as an adjuvant greatly supports adoptive T cell therapy of melanoma, where IL-2 provides key adjuvant signals to transferred T cells but also elicits severe dose-limiting inflammatory toxicity and expands regulatory T cells (Tregs). One approach to focus adjuvant activity on the transferred cells is to genetically engineer the transferred cells to secrete their own supporting factors. The technical difficulty and challenges as well as the high cost for large-scale production of genetically engineered T lymphocytes have significantly limited the potential of this method in clinical applications, to date.
  • Disclosed herein, in some aspects, is a technology platform that permits simple, safe and efficient delivery of biologically-active agents, such as a drug, protein (e.g., adjuvants such as IL-2) or particle to cells through chemical conjugation of protein, drug, or particle-loaded, carrier-free linkers directly onto the plasma membrane of cells. In certain embodiments, such composition is referred to as “nanogel,” “nanoparticle,” or “backpack,” which terms are used interchangeably herein. The composition can be loaded or backpacked onto cells, e.g., nucleated cells. The loading or backpacking process is also referred to as “priming.” Backpacked or primed cells can have many therapeutic applications. For example, backpacked T cells can be used in T cell therapies including ACT (adoptive cell therapy). Other important immune cell types can also be backpacked, including for example, B cells, tumor infiltrating lymphocytes, NK cells, antigen-specific CD8+ T cells, T cells genetically engineered to express chimeric antigen receptors (CARs) or CAR-T cells, T cells genetically engineered to express T-cell receptors specific to an tumor antigen, tumor infiltrating lymphocytes (TTLs), and/or antigen-trained T cells (e.g., T cells that have been “trained” by antigen presenting cells (APCs) displaying antigens of interest, e.g. tumor associated antigens (TAA)).
  • In addition to the foregoing, the present disclosure further contemplates other nanostructures that comprise other protein therapeutics for purposes other than adjuvant effect on adoptively-transferred cells. Those of skill in the art will readily recognize that the disclosure has broader applications, as provided herein.
  • Various aspects of the present disclosure may be used alone, in combination, or in a variety of arrangements not specifically discussed in the embodiments described in the foregoing and is therefore not limited in its application to the details and arrangement of components set forth in the foregoing description or illustrated in the drawings. For example, aspects described in one embodiment may be combined in any manner with aspects described in other embodiments.
    • Definitions
  • For convenience, certain terms employed in the specification, examples, and appended claims are collected here. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs.
  • As used herein, the articles “a” and “an” refer to one or more than one, e.g., to at least one, of the grammatical object of the article. The use of the words “a” or “an” when used in conjunction with the term “comprising” herein may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.”
  • As used herein, “about” and “approximately” generally mean an acceptable degree of error for the quantity measured given the nature or precision of the measurements. Exemplary degrees of error are within 20 percent (%), typically, within 10%, and more typically, within 5% of a given range of values. The term “substantially” means more than 50%, preferably more than 80%, and most preferably more than 90% or 95%.
  • As used herein the term “comprising” or “comprises” is used in reference to compositions, methods, and respective component(s) thereof, that are present in a given embodiment, yet open to the inclusion of unspecified elements.
  • As used herein the term “consisting essentially of” refers to those elements required for a given embodiment. The term permits the presence of additional elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment of the disclosure.
  • The term “consisting of” refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.
  • As used herein, “a plurality of” means more than 1, e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more, e.g., 25, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, or more, or any integer therebetween.
  • The term “therapeutic,” “therapeutic agent,” “active,” “active agent,” “active pharmaceutical agent,” “active drug” or “drug” as used herein means any active pharmaceutical ingredient (“API”), including its pharmaceutically acceptable salts (e.g. the hydrochloride salts, the hydrobromide salts, the hydroiodide salts, and the saccharinate salts), as well as in the anhydrous, hydrated, and solvated forms, in the form of prodrugs, and in the individually optically active enantiomers of the API as well as polymorphs of the API. Therapeutic agents include pharmaceutical, chemical or biological agents. Additionally, pharmaceutical, chemical or biological agents can include any agent that has a desired property or affect whether it is a therapeutic agent. For example, agents also include diagnostic agents, biocides and the like.
  • The terms “protein”, “peptide” and “polypeptide” are used interchangeably herein to refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation, such as conjugation with a labeling component. The polypeptide can be isolated from natural sources, can be a produced by recombinant techniques from a eukaryotic or prokaryotic host, or can be a product of synthetic procedures. It should bt understood that the term “protein” includes fusion or chimeric proteins, as well as cytokines, antibodies and antigen-binding fragments thereof.
  • “Antibody” or “antibody molecule” as used herein refers to a protein, e.g., an immunoglobulin chain or fragment thereof, comprising at least one immunoglobulin variable domain sequence. An antibody molecule encompasses antibodies (e.g., full-length antibodies) and antibody fragments. In an embodiment, an antibody molecule comprises an antigen binding or functional fragment of a full length antibody, or a full length immunoglobulin chain. For example, a full-length antibody is an immunoglobulin (Ig) molecule (e.g., IgG) that is naturally occurring or formed by normal immunoglobulin gene fragment recombinatorial processes). In embodiments, an antibody molecule refers to an immunologically active, antigen-binding portion of an immunoglobulin molecule, such as an antibody fragment. An antibody fragment, e.g., functional fragment, is a portion of an antibody, e.g., Fab, Fab′, F(ab′)2, F(ab)2, variable fragment (Fv), domain antibody (dAb), or single chain variable fragment (scFv). A functional antibody fragment binds to the same antigen as that recognized by the intact (e.g., full-length) antibody. The terms “antibody fragment” or “functional fragment” also include isolated fragments consisting of the variable regions, such as the “Fv” fragments consisting of the variable regions of the heavy and light chains or recombinant single chain polypeptide molecules in which light and heavy variable regions are connected by a peptide linker (“scFv proteins”). In some embodiments, an antibody fragment does not include portions of antibodies without antigen binding activity, such as Fc fragments or single amino acid residues. Exemplary antibody molecules include full length antibodies and antibody fragments, e.g., dAb (domain antibody), single chain, Fab, Fab′, and F(ab′)2 fragments, and single chain variable fragments (scFvs). The terms “Fab” and “Fab fragment” are used interchangeably and refer to a region that includes one constant and one variable domain from each heavy and light chain of the antibody, i.e., VL, CL, VH and C H1.
  • In embodiments, an antibody molecule is monospecific, e.g., it comprises binding specificity for a single epitope. In some embodiments, an antibody molecule is multispecific, e.g., it comprises a plurality of immunoglobulin variable domain sequences, where a first immunoglobulin variable domain sequence has binding specificity for a first epitope and a second immunoglobulin variable domain sequence has binding specificity for a second epitope. In some embodiments, an antibody molecule is a bispecific antibody molecule. “Bispecific antibody molecule” as used herein refers to an antibody molecule that has specificity for more than one (e.g., two, three, four, or more) epitope and/or antigen.
  • “Antigen” (Ag) as used herein refers to a macromolecule, including all proteins or peptides. In some embodiments, an antigen is a molecule that can provoke an immune response, e.g., involving activation of certain immune cells and/or antibody generation. Antigens are not only involved in antibody generation. T cell receptors also recognized antigens (albeit antigens whose peptides or peptide fragments are complexed with an MHC molecule). Any macromolecule, including almost all proteins or peptides, can be an antigen. Antigens can also be derived from genomic recombinant or DNA. For example, any DNA comprising a nucleotide sequence or a partial nucleotide sequence that encodes a protein capable of eliciting an immune response encodes an “antigen.” In embodiments, an antigen does not need to be encoded solely by a full length nucleotide sequence of a gene, nor does an antigen need to be encoded by a gene at all. In embodiments, an antigen can be synthesized or can be derived from a biological sample, e.g., a tissue sample, a tumor sample, a cell, or a fluid with other biological components. As used, herein a “tumor antigen” or interchangeably, a “cancer antigen” includes any molecule present on, or associated with, a cancer, e.g., a cancer cell or a tumor microenvironment that can provoke an immune response. As used, herein an “immune cell antigen” includes any molecule present on, or associated with, an immune cell that can provoke an immune response.
  • The “antigen-binding site” or “antigen-binding fragment” or “antigen-binding portion” (used interchangeably herein) of an antibody molecule refers to the part of an antibody molecule, e.g., an immunoglobulin (Ig) molecule such as IgG, that participates in antigen binding. In some embodiments, the antigen-binding site is formed by amino acid residues of the variable (V) regions of the heavy (H) and light (L) chains. Three highly divergent stretches within the variable regions of the heavy and light chains, referred to as hypervariable regions, are disposed between more conserved flanking stretches called “framework regions” (FRs). FRs are amino acid sequences that are naturally found between, and adjacent to, hypervariable regions in immunoglobulins. In embodiments, in an antibody molecule, the three hypervariable regions of a light chain and the three hypervariable regions of a heavy chain are disposed relative to each other in three dimensional space to form an antigen-binding surface, which is complementary to the three-dimensional surface of a bound antigen. The three hypervariable regions of each of the heavy and light chains are referred to as “complementarity-determining regions,” or “CDRs.” The framework region and CDRs have been defined and described, e.g., in Kabat, E. A., et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242, and Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917. Each variable chain (e.g., variable heavy chain and variable light chain) is typically made up of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the amino acid order: FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4. Variable light chain (VL) CDRs are generally defined to include residues at positions 27-32 (CDR1), 50-56 (CDR2), and 91-97 (CDR3). Variable heavy chain (VH) CDRs are generally defined to include residues at positions 27-33 (CDR1), 52-56 (CDR2), and 95-102 (CDR3). One of ordinary skill in the art would understand that the loops can be of different length across antibodies and the numbering systems such as the Kabat or Chotia control so that the frameworks have consistent numbering across antibodies.
  • In some embodiments, the antigen-binding fragment of an antibody (e.g., when included as part of a fusion molecule) can lack or be free of a full Fc domain. In certain embodiments, an antibody-binding fragment does not include a full IgG or a full Fc but may include one or more constant regions (or fragments thereof) from the light and/or heavy chains. In some embodiments, the antigen-binding fragment can be completely free of any Fc domain. In some embodiments, the antigen-binding fragment can be substantially free of a full Fc domain. In some embodiments, the antigen-binding fragment can include a portion of a full Fc domain (e.g., CH2 or CH3 domain or a portion thereof). In some embodiments, the antigen-binding fragment can include a full Fc domain. In some embodiments, the Fc domain is an IgG domain, e.g., an IgG1, IgG2, IgG3, or IgG4 Fc domain. In some embodiments, the Fc domain comprises a CH2 domain and a CH3 domain.
  • As used herein, a “cytokine” or “cytokine molecule” refers to full length, a fragment or a variant of a naturally-occurring, wild type cytokine (including fragments and functional variants thereof having at least 10% of the activity of the naturally-occurring cytokine molecule). In embodiments, the cytokine molecule has at least 30, 50, or 80% of the activity, e.g., the immunomodulatory activity, of the naturally-occurring molecule. In embodiments, the cytokine molecule further comprises a receptor domain, e.g., a cytokine receptor domain, optionally, coupled to an immunoglobulin Fc region. In other embodiments, the cytokine molecule is coupled to an immunoglobulin Fc region. In other embodiments, the cytokine molecule is coupled to an antibody molecule (e.g., an immunoglobulin Fab or scFv fragment, a Fab fragment, a FAB2 fragment, or an affibody fragment or derivative, e.g., a sdAb (nanobody) fragment, a heavy chain antibody fragment, single-domain antibody, a bi-specific or multispecific antibody), or non-antibody scaffolds and antibody mimetics (e.g., lipocalins (e.g., anticalins), affibodies, fibronectin (e.g., monobodies or Adnectins), knottins, ankyrin repeats (e.g., DARPins), and A domains (e.g., avimers)).
  • As used herein, “administering” and similar terms mean delivering the composition to an individual being treated. Preferably, the compositions of the present disclosure are administered by, e.g., parenteral, including subcutaneous, intramuscular, or preferably interventions routes.
  • As used herein, the terms “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, melanoma, carcinoma, lymphoma, blastoma, sarcoma, and leukemia or lymphoid malignancies. More particular examples of cancers include squamous cell cancer (e.g., epithelial squamous cell cancer), lung cancer including small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung and squamous carcinoma of the lung, cancer of the peritoneum, hepatocellular cancer, gastric or stomach cancer including gastrointestinal cancer, pancreatic cancer, glioblastoma, cervical cancer, ovarian cancer, liver cancer, bladder cancer, hepatoma, breast cancer, colon cancer, rectal cancer, colorectal cancer, endometrial cancer or uterine carcinoma, salivary gland carcinoma, kidney or renal cancer, prostate cancer, vulval cancer, thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma, as well as head and neck cancer.
  • “Nucleated cells” are cells which contain nucleus. In some embodiments, the nucleated cells can be immune cells.
  • As used herein, an “immune cell” refers to any of various cells that function in the immune system, e.g., to protect against agents of infection and foreign matter. In embodiments, this term includes leukocytes, e.g., neutrophils, eosinophils, basophils, lymphocytes, and monocytes. The term “immune cell” includes immune effector cells described herein. “Immune cell” also refers to modified versions of cells involved in an immune response, e.g. modified NK cells, including NK cell line NK-92 (ATCC cat. No. CRL-2407), haNK (an NK-92 variant that expresses the high-affinity Fc receptor FcγRIIIa (158V)) and taNK (targeted NK-92 cells transfected with a gene that expresses a CAR for a given tumor antigen), e.g., as described in Klingemann et al. supra.
  • “Immune effector cell,” as that term is used herein, refers to a cell that is involved in an immune response, e.g., in the promotion of an immune effector response. Examples of immune effector cells include, but are not limited to, T cells, e.g., CD4+ T cells, CD8+ T cells, alpha T cells, beta T cells, gamma T cells, and delta T cells; B cells; natural killer (NK) cells; natural killer T (NKT) cells; dendritic cells; and mast cells. In some embodiments, the immune cell is an immune cell (e.g., T cell or NK cell) that comprises, e.g., expresses, a Chimeric Antigen Receptor (CAR), e.g., a CAR that binds to a cancer antigen. In other embodiments, the immune cell expresses an exogenous high affinity Fc receptor. In some embodiments, the immune cell comprises, e.g., expresses, an engineered T-cell receptor. In some embodiments, the immune cell is a tumor infiltrating lymphocyte. In some embodiments the immune cells comprise a population of immune cells and comprise T cells that have been enriched for specificity for a tumor-associated antigen (TAA), e.g. enriched by sorting for T cells with specificity towards MHCs displaying a TAA of interest, e.g. MART-1. In some embodiments immune cells comprise a population of immune cells and comprise T cells that have been “trained” to possess specificity against a TAA by an antigen presenting cell (APC), e.g. a dendritic cell, displaying TAA peptides of interest. In some embodiments, the T cells are trained against a TAA chosen from one or more of MART-1, MAGE-A4, NY-ESO-1, SSX2, Survivin, or others. In some embodiments the immune cells comprise a population of T cells that have been “trained” to possess specificity against a multiple TAAs by an APC, e.g. a dendritic cell, displaying multiple TAA peptides of interest. In some embodiments, the immune cell is a cytotoxic T cell (e.g., a CD8+ T cell). In some embodiments, the immune cell is a helper T cell, e.g., a CD4+ T cell.
  • “Cytotoxic T lymphocytes” (CTLs) as used herein refer to T cells that have the ability to kill a target cell. CTL activation can occur when two steps occur: 1) an interaction between an antigen-bound MHC molecule on the target cell and a T cell receptor on the CTL is made; and 2) a costimulatory signal is made by engagement of costimulatory molecules on the T cell and the target cell. CTLs then recognize specific antigens on target cells and induce the destruction of these target cells, e.g., by cell lysis. In some embodiments, the CTL expresses a CAR. In some embodiments, the CTL expresses an engineered T-cell receptor.
  • As used herein, an “effective amount” means the amount of bioactive agent or diagnostic agent that is sufficient to provide the desired local or systemic effect at a reasonable risk/benefit ratio as would attend any medical treatment or diagnostic test. This will vary depending on the patient, the disease, the treatment being effected, and the nature of the agent.
  • As used herein, “pharmaceutically acceptable” shall refer to that which is useful in preparing a pharmaceutical composition that is generally safe, non-toxic, and neither biologically nor otherwise undesirable and includes that which is acceptable for veterinary use as well as human pharmaceutical use. Examples of “pharmaceutically acceptable liquid carriers” include water and organic solvents. Preferred pharmaceutically acceptable aqueous liquids include PBS, saline, and dextrose solutions etc.
  • The term “treatment” or “treating” means administration of a drug for purposes including: (i) preventing the disease or condition, that is, causing the clinical symptoms of the disease or condition not to develop; (ii) inhibiting the disease or condition, that is, arresting the development of clinical symptoms; and/or (iii) relieving the disease or condition, that is, causing the regression of clinical symptoms.
  • The following definitions for certain chemical groups are used, unless otherwise described. Specific and general values listed below for radicals, substituents, and ranges, are for illustration only; they do not exclude other defined values or other values within defined ranges for the radicals and substituents. Unless otherwise indicated, alkyl, alkoxy, alkenyl, and the like denote both straight and branched groups.
  • The term “alkyl” refers to a saturated hydrocarbon chain that may be a straight chain or branched chain, containing the indicated number of carbon atoms. For example, C1-6 alkyl indicates that the group may have 1 to 6 (inclusive) carbon atoms in it. Any atom can be optionally substituted, e.g., by one or more substituents. Examples of alkyl groups include without limitation methyl, ethyl, n-propyl, isopropyl, and tert-butyl.
  • As referred to herein, the term “alkoxy” refers to a group of formula-O(alkyl). Alkoxy can be, for example, methoxy (—OCH3), ethoxy, propoxy, isopropoxy, butoxy, iso-butoxy, sec-butoxy, pentoxy, 2-pentoxy, 3-pentoxy, or hexyloxy. As used herein, the term “hydroxyl,” employed alone or in combination with other terms, refers to a group of formula —OH.
  • The term “alkenyl” refers to a straight or branched hydrocarbon chain containing the indicated number of carbon atoms and having one or more carbon-carbon double bonds. Any atom can be optionally substituted, e.g., by one or more substituents. Alkenyl groups can include, e.g., vinyl, allyl, 1-butenyl, and 2-hexenyl. One of the double bond carbons can optionally be the point of attachment of the alkenyl substituent.
  • The term “alkynyl” refers to a straight or branched hydrocarbon chain containing the indicated number of carbon atoms and having one or more carbon-carbon triple bonds. Alkynyl groups can be optionally substituted, e.g., by one or more substituents. Alkynyl groups can include, e.g., ethynyl, propargyl, and 3-hexynyl. One of the triple bond carbons can optionally be the point of attachment of the alkynyl substituent,
  • The term “heterocyclyl” refers to a fully saturated monocyclic, bicyclic, tricyclic or other polycyclic ring system having one or more constituent heteroatom ring atoms independently selected from O, N (it is understood that one or two additional groups may be present to complete the nitrogen valence and/or form a salt), or S. The heteroatom or ring carbon can be the point of attachment of the heterocyclyl substituent to another moiety. Any atom can be optionally substituted, e.g., by one or more substituents. Heterocyclyl groups can include, e.g., tetrahydrofuryl, tetrahydropyranyl, piperidyl (piperidino), piperazinyl, morpholinyl (morpholino), pyrrolinyl, and pyrrolidinyl. By way of example, the phrase “heterocyclic ring containing from 5-6 ring atoms, wherein 1-2 of the ring atoms is independently selected from N, NH, N(C:—C(alkyl), NC(O)(C1-C6 alkyl), O, and S; and wherein said heterocyclic ring is optionally substituted with 1-3 independently selected Ra″ would include (but not be limited to) tetrahydrofuryl, tetrahydropyranyl, piperidyl (piperidino), piperazinyl, morpholinyl (morpholino), pyrrolinyl, and pyrrolidinyl.
  • The term “cycloalkyl” refers to a fully saturated monocyclic, bicyclic, tricyclic, or other polycyclic hydrocarbon groups, Any atom can be optionally substituted, e.g., by one or more substituents. A ring carbon serves as the point of attachment of a cycloalkyl group to another moiety. Cycloalkyl moieties can include, e.g., cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, adamantyl, and norbornyl (bicycle[2.2.1]heptyl).
  • The term “aryl” refers to an aromatic monocyclic., bicyclic (2 fused rings), or tricyclic (3 fused rings), or polycyclic (>3 fused rings) hydrocarbon ring system. One or more ring atoms can be optionally substituted, e.g., by one or more substituents. Aryl moieties include, e.g., phenyl and naphthyl.
  • The term “heteroaryl” refers to an aromatic monocyclic, bicyclic (2 fused rings), tricyclic (3 fused rings), or polycyclic (>3 fused rings) hydrocarbon groups having one or more heteroatom ring atoms independently selected from O, N (it is understood that one or two additional groups may be present to complete the nitrogen valence and/or form a salt), or S. One or more ring atoms can be optionally substituted, e.g., by one or more substituents. Examples of heteroaryl groups include, but are not limited to, 2H-pyrrolyl, 3H-indolyl, 4H-quinolizinyl, acridinyl, benzo[b]thienyl, benzothiazolyl, P-carbolinyl, carbazolyl, coumarinyl, chromenyl, cinnolinyl, dibenzo[b,d]furanyl, furazanyl, furyl, imidazolyl, imidizolyl, indazolyl, indolyl, isobenzofuranyl, isoindolyl, isoquinolyl, isothiazolyl, isoxazolyl, naphthyridinyl, oxazolyl, perimidinyl, phenanthridinyl, phenanthrolinyl, phenarsazinyl, phenazinyl, phenothiazinyl, phenoxathiinyl, phenoxazinyl, phthalazinyl, pteridinyl, purinyl, pyranyl, pyrazinyl, pyrazolyl, pyridazinyl, pyridyl, pyrimidinyl, pyrrolyl, quinazolinyl, quinolyl, quinoxalinyl, thiadiazolyl, thianthrenyl, thiazolyl, thienyl, triazolyl, and xanthenyl.
  • The term “substituent” refers to a group “substituted” on, e.g., an alkyl, haloalkyl, cycloalkyl, heterocyclyl, heterocycloalkenyl, cycloalkenyl, aryl, or heteroaryl group at any atom of that group. In one aspect, the substituent(s) on a group are independently any one single, or any combination of two or more of the permissible atoms or groups of atoms delineated for that substituent. In another aspect, a substituent may itself be substituted with any one of the above substituents. Further, as used herein, the phrase “optionally substituted” means unsubstituted (e.g., substituted with an H) or substituted. As used herein, the term “substituted” means that a hydrogen atom is removed and replaced by a substituent. It is understood that substitution at a given atom is limited by valency.
  • Various aspects of the disclosure are described in further detail below. Additional definitions are set out throughout the specification.
    • Linkers
  • In some embodiments, at least one drug, protein, polymer and/or particle (collectively, “agents”) of the present disclosure are reversibly linked to one another through a degradable linker such that under physiological conditions, the linker degrades and releases the intact, biologically-active agent. In an embodiment, protein monomers can be cross-linked together to form a cluster that contains a plurality of the protein monomers. In other embodiments, various agents are linked to functional groups through a degradable linker. In various embodiments, the agents are reversibly modified or linked, as described below.
  • An agent that is “reversibly linked to another” agent, as used herein, refers to a drug, protein, polymer or particle that is attached (e.g., covalently attached) to another drug, protein, polymer or particle through a degradable linker.
  • An agent that is “reversibly linked to a functional group,” or an agent that is “reversibly modified,” herein refers to an agent that is attached (e.g., covalently attached) to a functional group through a degradable linker. Such an agent may be referred to herein as an “agent conjugate” or a “reversibly modified agent conjugate”—the terms may be used interchangeably herein. It should be understood that proteins and polymers (e.g., polyethylene glycol) each contain functional groups to which an agent can be linked via a reversible linker, such as amine, silane, hydroxyl, poly(ethylene oxide), polylactic acid, poly(lactic-co-glycolic acid), etc. Examples of agent conjugates and reversibly modified proteins, as provided herein, include without limitation, an agent reversibly linked (e.g., via a degradable linker) to another agent, an agent reversibly linked to a polymer, and a protein reversibly linked to another functional group. It should be understood that the term “protein” includes fusion proteins.
  • In some embodiments, the cross-linker has the formula of A-B-C wherein B is optional, wherein A represents a structural template, B represents a polymer spacer, C represents a hydrolysable linkage and a functional group that can react with nucleophilic groups.
  • In some examples, A is selected from di-ols, tri-ols, tetra-ols, poly-ols, di-thiols, tri-thiols, tetra-thiols, poly-thiols, di-amines, tri-amines, tetra-amines, or poly-amines. In some embodiments, B can be selected from polyethylene glycol, saccharides, poly-ols, poly-ethers, poly-thioethers, poly-amines, poly-esters, alkanes, phenyls, or amino-acids. In some embodiments, C can have C has formula (Ia):
  • Figure US20230233609A1-20230727-C00011
  • wherein:
  • LG2 is a leaving group selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • Y2 is selected from O and S;
  • X, at each occurrence, is independently selected from O, S, and N;
  • L is optional and is a linker such that
  • Figure US20230233609A1-20230727-C00012
  • is biodegradable; and
  • m is an integer selected from 1-6, preferably 2.
  • An example of a degradable linker for use in accordance with the present disclosure is represented by formula (I):
  • Figure US20230233609A1-20230727-C00013
  • wherein:
  • LG1 and LG2 are each a leaving group, preferably independently selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • Y1 and Y2 are each independently selected from O and S;
  • X, at each occurrence, is independently selected from O, S, and N;
  • L is a linkage such that
  • Figure US20230233609A1-20230727-C00014
  • is biodegradable; and
  • m, at each occurrence, is an integer selected from 1-6.
  • In some embodiments, the cross-linker represented by formula (I) is symmetrical at L. For example, LG1 and LG2 can be the same. Y1 and Y2 can be the same.
  • In various embodiments, LG1 and LG2 may be capable of reacting with a protein, a drug and/or a particle. LG1 and LG2 can both be imidazolide. In another example, LG1 and LG2 are both N-hydroxysuccinimide.
  • In certain embodiments,
  • Figure US20230233609A1-20230727-C00015
  • is hydrolysable. L can be selected from:
  • (a) —(CH2)n—wherein n is an integer selected from 0-5;
  • Figure US20230233609A1-20230727-C00016
  • wherein n is an integer selected from 0-5; or
  • Figure US20230233609A1-20230727-C00017
  • wherein X, at each occurrence, is independently selected from O, S, and N.
  • Another example of a degradable linker for use in accordance with the present disclosure is represented by formula (II):
  • Figure US20230233609A1-20230727-C00018
  • wherein:
  • X1 and X2 are each independently selected from triflate, tosyl, Cl, N-hydroxysuccinimide and imidazolide;
  • A1 and A3 are each independently —(CR1R2)n—;
  • A2 is —(CR1R2)m—;
  • Y1 and Y2 are each independently selected from NR3, O and S;
  • wherein R1 and R2 at each occurrence are independently selected from hydrogen, halogen, hydroxyl, C1-12 alkyl, C2-12 alkenyl, C3-12 cycloalkyl, C2-12 heterocyclyl; C6-12 aryl optionally substituted with 1 or more halo, hydroxyl, C1-6 alkyl and/or C1-6 alkoxyl; and C4-12 heteroaryl optionally substituted with 1 or more halo, hydroxyl, C1-6 alkyl and/or C1-6 alkoxyl
  • wherein R3 is selected from hydrogen, C1-12 alkyl, C2-12 alkenyl, C3-12 cycloalkyl, C2-12 heterocyclyl; C6-12 aryl optionally substituted with 1 or more halo, hydroxyl, C1-6 alkyl and/or C1-6 alkoxyl; and C4-12 heteroaryl optionally substituted with 1 or more halo, hydroxyl, C1-6 alkyl and/or C1-6 alkoxyl;
  • n, at each occurrence, is an integer independently selected from 1-12; and
  • m is an integer selected from 0-12.
  • In some embodiments, the cross-linker represented by formula (II) is symmetrical.
  • In some embodiments, X1 and X2 are each a leaving group capable of reacting with a protein, a drug and/or a particle. In certain embodiments, X1 and X2 are both imidazolide or N-hydroxysuccinimide.
  • In some embodiments, R1 and R2 are both hydrogen.
  • In some embodiments, A1 and A3 are both —(CH2)2—.
  • In certain embodiments, A2 is —(CH2)2—.
  • In some embodiments, Y1 and Y2 are both O.
  • In some embodiments, the cross-linker is:
  • Figure US20230233609A1-20230727-C00019
  • In some embodiments, A2 is a bond. In certain embodiments, Y1 and Y2 are both NH.
  • In some embodiments, the cross-linker is:
  • Figure US20230233609A1-20230727-C00020
    • Monomers
  • Examples of protein monomers for use in accordance with the present disclosure include, without limitation, antibodies (e.g., IgG, Fab, mixed Fc and Fab), single chain antibodies, antibody fragments, engineered proteins such as Fc fusions, enzymes, co-factors, receptors, ligands, transcription factors and other regulatory factors, cytokines, chemokines, human serum albumin, and the like. These proteins may or may not be naturally occurring. Other proteins are contemplated and may be used in accordance with the disclosure. Any of the proteins can be reversibly modified through cross-linking to form a cluster or nanogel structure as disclosed in, e.g., U.S. Publication No. 2017/0080104, U.S. Pat. No. 9,603,944, U.S. Publication No. 2014/0081012, and PCT Application No, PCT/US17/37249 filed Jun. 13, 2017, all incorporated herein by reference.
  • In various embodiments, therapeutic protein monomers can be cross-linked using one or more cross-linkers disclosed herein. The therapeutic protein monomers can comprise one or more cytokine molecules and/or one or more costimulatory molecules. Cytokine molecules can be selected from IL-15, IL-2, IL-7, IL-10, IL-12, IL-18, IL-21, IL-23, IL-4, IL1alpha, IL1beta, IL-5, IFNgamma, TNFa, IFNalpha, IFNbeta, GM-CSF, or GCSF. Costimulatory molecules are selected from CD137, OX40, CD28, GITR, VISTA, anti-CD40, or CD3.
  • In some embodiments, protein monomers of the disclosure are immunostimulatory proteins. As used herein, an immunostimulatory protein is a protein that stimulates an immune response (including enhancing a pre-existing immune response) in a subject to whom it is administered, whether alone or in combination with another protein or agent. Examples of immunostimulatory proteins that may be used in accordance with the disclosure include, without limitation, antigens, adjuvants (e.g., flagellin, muramyl dipeptide), cytokines including interleukins (e.g., IL-2, IL-7, IL-15, IL-10, IL-18, IL-21, IL-23 (or superagonist/mutant forms of these cytokines, such as, IL-15SA), IL-12, IFNgamma, IFN-alpha, GM-CSF, FLT3-ligand), and immunostimulatory antibodies (e.g., anti-CTLA-4, anti-CD28, anti-CD3, or single chain/antibody fragments of these molecules). Other immunostimulatory proteins are contemplated and may be used in accordance with the disclosure. In some embodiments, the immunostimulatory proteins can be an antibody or antigen-binding fragment thereof that binds an inhibitor of an immunosuppressor, e.g., an inhibitor of a checkpoint inhibitor, such as PD-1, PD-L 1, LAG-3, TIM-3, CTLA-4, inhibitory KIR, CD276, VTCN1, BTLA/HVEM, HAVCR2 and ADORA2A, e.g., as described in US 2016/0184399 incorporated herein by reference.
  • In some embodiments, protein monomers of the disclosure are antigens. Examples of antigens that may be used in accordance with the disclosure include, without limitation, cancer antigens, self-antigens, microbial antigens, allergens and environmental antigens. Other protein antigens are contemplated and may be used in accordance with the disclosure.
  • In some embodiments, proteins of the disclosure are cancer antigens. A cancer antigen is an antigen that is expressed preferentially by cancer cells (i.e., it is expressed at higher levels in cancer cells than on non-cancer cells) and, in some instances, it is expressed solely by cancer cells. Cancer antigens may be expressed within a cancer cell or on the surface of the cancer cell. Cancer antigens that may be used in accordance with the disclosure include, without limitation, MART-1/Melan-A, gp100, adenosine deaminase-binding protein (ADAbp), FAP, cyclophilin b, colorectal associated antigen (CRC)-0017-1A/GA733, carcinoembryonic antigen (CEA), CAP-1, CAP-2, etv6, AML1, prostate specific antigen (PSA), PSA-1, PSA-2, PSA-3, prostate-specific membrane antigen (PSMA), T cell receptor/CD3-zeta chain and CD20. The cancer antigen may be selected from the group consisting of MAGE-A1, MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A5, MAGE-A6, MAGE-A7, MAGE-A8, MAGE-A9, MAGE-A10, MAGE-A11, MAGE-A12, MAGE-Xp2 (MAGE-B2), MAGE-Xp3 (MAGE-B3), MAGE-Xp4 (MAGE-B4), MAGE-C1, MAGE-C2, MAGE-C3, MAGE-C4 and MAGE-C5. The cancer antigen may be selected from the group consisting of GAGE-1, GAGE-2, GAGE-3, GAGE-4, GAGE-5, GAGE-6, GAGE-7, GAGE-8 and GAGE-9. The cancer antigen may be selected from the group consisting of BAGE, RAGE, LAGE-1, NAG, GnT-V, MUM-1, CDK4, tyrosinase, p53, MUC family, HER2/neu, p2iras, RCAS1, α-fetoprotein, E-cadherin, α-catenin, β-catenin, γ-catenin, p120ctn, gp100Pme1117, PRAME, NY-ESO-1, cdc27, adenomatous polyposis coli protein (APC), fodrin, Connexin 37, Ig-idiotype, p15, gp75, GM2 ganglioside, GD2 ganglioside, human papilloma virus proteins, Smad family of tumor antigens, Imp-1, PlA, EBV-encoded nuclear antigen (EBNA)-1, brain glycogen phosphorylase, SSX-1, SSX-2 (HOM-MEL-40), SSX-1, SSX-4, SSX-5, SCP-1 and CT-7, CD20 and c-erbB-2. Other cancer antigens are contemplated and may be used in accordance with the disclosure.
  • In some embodiments, proteins of the disclosure are antibodies or antibody fragments including, without limitation, bevacizumab (AVASTIN@), trastuzumab (HERCEPTIN®), alemtuzumab (CAMPATH®, indicated for B cell chronic lymphocytic leukemia,), gemtuzumab (MYLOTARG®, hP67.6, anti-CD33, indicated for leukemia such as acute myeloid leukemia), rituximab (RITUXAN@), tositumomab (BEXXARR, anti-CD20, indicated for B cell malignancy), MDX-210 (bispecific antibody that binds simultaneously to HER-2/neu oncogene protein product and type I Fc receptors for immunoglobulin G (IgG) (Fc gamma RI)), oregovomab (OVAREX®, indicated for ovarian cancer), edrecolomab (PANOREX®), daclizumab (ZENAPAX®), palivizumab (SYNAGIS®, indicated for respiratory conditions such as RSV infection), ibritumomab tiuxetan (ZEVALIN®, indicated for Non-Hodgkin's lymphoma), cetuximab (ERBITUX®), MDX-447, MDX-22, MDX-220 (anti-TAG-72), IOR-05, IOR-T6 (anti-CDi), IOR EGF/R3, celogovab (ONCOSCINT@ OV103), epratuzumab (LYMPHOCIDE®), pemtumomab (THERAGYN®) and Gliomab-H (indicated for brain cancer, melanoma). Other antibodies and antibody fragments are contemplated and may be used in accordance with the disclosure.
  • Proteins may be linked (e.g., covalently linked) to a degradable linker through any terminal or internal nucleophilic groups such as a —NH2 functional group (e.g., side chain of a lysine). For example, proteins can be contacted with a degradable linker under conditions that permit reversible covalent crosslinking of proteins to each other through the degradable linker. In some embodiments, the proteins can be cross-linked to form a plurality of protein nanogels In some embodiments, the conditions include contacting the protein with the degradable linker in an aqueous buffer at a temperature of 4° C. to 25° C. in some embodiments, the contacting step can be performed in an aqueous buffer tor 30 minutes to one hour. In some embodiments, the aqueous buffer comprises phosphate buffered saline (PBS). In some embodiments, the concentration of the protein in the aqueous buffer is 10 ng/mL to 50 mg/mL (e.g., 10, 15, 20, 25, 30, 35, 40, 45 or 50 mg/mL).
    • Cytokines
  • The methods and compositions, e.g., linker compounds, described herein can be used to cross-link one or more cytokine molecules. In embodiments, the cytokine molecule is full length, a fragment or a variant of a cytokine, e.g., a cytokine comprising one or more mutations. In some embodiments the cytokine molecule comprises a cytokine chosen from interleukin-1 alpha (IL-1 alpha), interleukin-1 beta (IL-1 beta), interleukin-2 (IL-2), interleukin-4 (IL-4), interleukin-5 (IL-5), interleukin-6 (IL-6), interleukin-7 (IL-7), interleukin-10 (IL-10), interleukin-12 (IL-12), interleukin-15 (IL-15), interleukin-17 (IL-17), interleukin-18 (IL-18), interleukin-21 (IL-21), interleukin-23 (IL-23), interferon (IFN) alpha, IFN beta, IFN gamma, tumor necrosis alpha, GM-CSF, GCSF, or a fragment or variant thereof, or a combination of any of the aforesaid cytokines. In other embodiments, the cytokine molecule is chosen from interleukin-2 (IL-2), interleukin-7 (IL-7), interleukin-12 (IL-12), interleukin-15 (IL-15), interleukin-18 (IL-18), interleukin-21 (IL-21), interleukin-23 (IL-23) or interferon gamma, or a fragment or variant thereof, or a combination of any of the aforesaid cytokines. The cytokine molecule can be a monomer or a dimer.
  • In embodiments, the cytokine molecule further comprises a receptor domain, e.g., a cytokine receptor domain. In one embodiment, the cytokine molecule comprises an IL-15 receptor, or a fragment thereof (e.g., an extracellular IL-15 binding domain of an IL-15 receptor alpha) as described herein. In some embodiments, the cytokine molecule is an IL-15 molecule, e.g., IL-15 or an IL-15 superagonist as described herein. As used herein, a “superagonist” form of a cytokine molecule shows increased activity, e.g., by at least 10%, 20%, 30%, compared to the naturally-occurring cytokine. An exemplary superagonist is an IL-15 SA. In some embodiments, the IL-15 SA comprises a complex of IL-15 and an IL-15 binding fragment of an IL-15 receptor, e.g., IL-15 receptor alpha or an IL-15 binding fragment thereof, e.g., as described herein.
  • In other embodiments, the cytokine molecule further comprises an antibody molecule, e.g., an immunoglobulin Fab or scFv fragment, a Fab fragment, a FAB2 fragment, or an affibody fragment or derivative, e.g. a sdAb (nanobody) fragment, a heavy chain antibody fragment, e.g., an Fc region, single-domain antibody, a bi-specific or multispecific antibody). In one embodiment, the cytokine molecule further comprises an immunoglobulin Fc or a Fab.
  • In some embodiments, the cytokine molecule is an IL-2 molecule, e.g., IL-2 or IL-2-Fc. In other embodiments, a cytokine agonist can be used in the methods and compositions disclosed herein. In embodiments, the cytokine agonist is an agonist of a cytokine receptor, e.g., an antibody molecule (e.g., an agonistic antibody) to a cytokine receptor, that elicits at least one activity of a naturally-occurring cytokine. In embodiments, the cytokine agonist is an agonist of a cytokine receptor, e.g., an antibody molecule (e.g., an agonistic antibody) to a cytokine receptor chosen from an IL-15Ra or IL-21R.
  • In some embodiments, the cytokine molecule is an IL-15 molecule, e.g., a full length, a fragment or a variant of IL-15, e.g., human IL-15. In embodiments, the IL-15 molecule is a wild-type, human IL-15. In other embodiments, the IL-15 molecule is a variant of human IL-5, e.g., having one or more amino acid modifications. In some embodiments, the IL-15 molecule comprises a mutation, e.g., an N72D point mutation.
  • In other embodiments, the cytokine molecule further comprises a receptor domain, e.g., an extracellular domain of an IL-15R alpha, optionally, coupled to an immunoglobulin Fc or an antibody molecule. In embodiments, the cytokine molecule is an IL-15 superagonist (IL-15SA) as described in WO 2010/059253. In some embodiments, the cytokine molecule comprises IL-15 and a soluble IL-15 receptor alpha domain fused to an Fc (e.g., a sIL-15Ra-Fc fusion protein), e.g., as described in Rubinstein et al PNAS 103:24 p. 9166-9171 (2006).
  • The IL-15 molecule can further comprise a polypeptide, e.g., a cytokine receptor, e.g., a cytokine receptor domain, and a second, heterologous domain. In one embodiment, the heterologous domain is an immunoglobulin Fc region. In other embodiments, the heterologous domain is an antibody molecule, e.g., a Fab fragment, a Fab2 fragment, a scFv fragment, or an affibody fragment or derivative, e.g. a sdAb (nanobody) fragment, a heavy chain antibody fragment. In some embodiments, the polypeptide also comprises a third heterologous domain. In some embodiments, the cytokine receptor domain is N-terminal of the second domain, and in other embodiments, the cytokine receptor domain is C-terminal of the second domain.
  • Certain cytokines and antibodies are disclosed in e.g., U.S. Publication No. 2017/0080104, U.S. Pat. No. 9,603,944, U.S. Publication No. 2014/0081012, and PCT Application No. PCT/US2017/037249 (each incorporated herein by reference in its entirety).
  • In some embodiments, the cytokines or other immunemodulators can target receptors (e.g., on an immune cell) by way of a fusion protein, such as those disclosed in PCT Application Nos. PCT/US2018/040777, PCT/US18/40783 and PCT/US18/40786 (each incorporated herein by reference in its entirety).
    • Backpacks and Cell Therapy
  • Backpacks or nanoparticles can be prepared by cross-linking various therapeutic protein monomers using one or more cross-linkers disclosed herein, as shown in FIG. TA. While the figure shows disulfide-containing linker, other biodegradable linkers disclosed herein can also be used.
  • In certain embodiments, the backpacks can be prepared by reacting the plurality of therapeutic protein monomers with the plurality of cross-linkers to form protein clusters having a size of, e.g., about 30 nm to 1000 nm in diameter. In some embodiments, the reaction can be performed at a temperature between about 5° C. and about 40° C. The reaction can be performed for about 1 minute to about 8 hours.
  • The protein clusters can be provided with a surface modification such as polycation. Certain surface modification is disclosed in U.S. Publication No. 2017/0080104 and U.S. Pat. No. 9,603,944, both incorporated herein by reference in their entirety. Examples include poly-Lysine (polyK), PEG-polyK, and polyArginine.
  • In some embodiments, the cross-linking reaction can proceed in the presence of one or more crowding agents such as polyethylene glycol (PEGs) and triglycerides. Exemplary PEGs include PEG400, PEG1000, PEG1500, PEG2000, PEG3000 and PEG4000.
  • Certain protein solubility aids such as glycerol, ethylene glycol and propylene glycol, Sorbitol and Mannitol can also improve the yield of backpack formation.
  • In certain embodiments, certain crosslinkers of the invention, due to the reaction of cationic lysine residues in the backpack, will result in a backpack having a net negative charge which will inhibit cell attachment. As such, it may be useful to first complex backpacks with a polycation via electrostatic interactions to drive cell attachment. For example, the backpacks can be coated or surface modified with a polycation such as polylysine (poly-L-lysine), polyethyleneimine, polyarginine, polyhistidine, polybrene and/or DEAE-dextran. Polycation can help the backpacks non-specifically bind or adsorb on cell membranes which are negatively charged. In some embodiments, polycation to be contained in a mixed solution may be a polymeric compound having a cationic group or a group that may become a cationic group, and an aqueous solution of a free polycation shows basic. Examples of the group that may become a cationic group include an amino group, an imino group, and the like. Examples of polycation include: polyamino acid such as polylysine, polyomithine, polyhistidine, polyarginine, polytryptophan, poly-2,4-diaminobutyric acid, poly-2,3-diaminopropionic acid, protamine, and polypeptide having at least one or more kinds of amino acid residues in a polypeptide chain selected from the group consisting of lysine, histidine, arginine, tryptophan, ornithine, 2,4-diaminobutyric acid and 2,3-diaminopropionic acid; polyamine such as polyallylamine, polyvinylamine, a copolymer of allylamine and diallylamine, and polydiallylamine; and polyimine such as polyethyleneimine.
  • In some embodiments, the polycation coating or surface modifying agent used to promote backpack adhesion to the cell is a cationic block copolymer of PEG-polylysine such as [methoxy-poly(ethylene glycol)n-block-poly(L-lysine hydrochloride), PEG-polylysine](PK30). This block copolymer may contain approximately 114 PEG units (MW approximately 5000 Da) and 30 lysine units (MW approximately 4900 Da). The linear PEG polymer has a methoxy end group, the poly-lysines are in the hydrochloride salt form. PK30 is a linear amphiphilic block copolymer which has a poly(L-lysine hydrochloride) block and a non-reactive PEG block. The poly-L-lysine block provides a net cationic charge at physiological pH and renders the backpack with a net positive charge after association. PK30 Structure [Methoxy-poly(ethylene gly col)n-block-poly(L-lysine hydrochloride)] is as follows.
  • Figure US20230233609A1-20230727-C00021
  • In some embodiments, the backpacks can be coated with an antibody or antigen-binding fragment thereof that bind to a receptor on the surface of an immune cell, so as to specifically target the backpacks to the immune cell. Exemplary antibodies include those disclosed herein, or fusion proteins containing the same.
  • In one example, as illustrated in FIG. 1B, “IL15-Fc” (IL15Ra-sushi-domain-Fc fusion homodimer protein with two associated IL-15 Proteins) monomers can be crossed linked and surface modified with polycation, to form IL-15 backpacks. The IL-15 backpacks can then be loaded onto immune cells such as T cells to form primed T cells.
  • In some embodiments, once prepared and purified, the backpacks can be optionally frozen until use in cell therapy, as illustrated in FIG. 1C. The cell therapy can be selected from, e.g., an adoptive cell therapy, CAR-T cell therapy, engineered TCR T cell therapy, a tumor infiltrating lymphocyte therapy, an antigen-trained T cell therapy, or an enriched antigen-specific T cell therapy.
  • In various embodiments, a cell therapy composition can be prepared by providing the protein cluster or backpack composition disclosed herein, and incubating the protein cluster or backpack composition with nucleated cells such as immune cells, preferably for about 30-60 minutes. The cells can be cryopreserved with backpacks until administration to a patient via, e.g., infusion.
  • Also disclosed herein is a cell therapy composition, comprising the protein cluster or backpack composition disclosed herein, associated with a nucleated cell such as T and NK cells. Such cell therapy composition may be administered into a subject in need thereof. Upon administration, the cross-linkers can degrade under physiological conditions so as to release the therapeutic protein monomers from the protein cluster.
  • Compositions, including pharmaceutical compositions, comprising the backpacks are provided herein. A composition can be formulated in pharmaceutically-acceptable amounts and in pharmaceutically-acceptable compositions. The term “pharmaceutically acceptable” means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients (e.g., biologically-active proteins of the nanoparticles). Such compositions may, in some embodiments, contain salts, buffering agents, preservatives, and optionally other therapeutic agents. Pharmaceutical compositions also may contain, in some embodiments, suitable preservatives. Pharmaceutical compositions may, in some embodiments, be presented in unit dosage form and may be prepared by any of the methods well-known in the art of pharmacy. Pharmaceutical compositions suitable for parenteral administration, in some embodiments, comprise a sterile aqueous or non-aqueous preparation of the nanoparticles, which is, in some embodiments, isotonic with the blood of the recipient subject. This preparation may be formulated according to known methods. A sterile injectable preparation also may be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent.
  • The backpacks and compositions containing such have numerous therapeutic utilities, including, e.g., the treatment of cancers, autoimmune diseases and infectious diseases. Methods described herein include treating a cancer in a subject by using backpacks or backpacked cells as described herein. Also provided are methods for reducing or ameliorating a symptom of a cancer in a subject, as well as methods for inhibiting the growth of a cancer and/or killing one or more cancer cells. In embodiments, the methods described herein decrease the size of a tumor and/or decrease the number of cancer cells in a subject administered with a described herein or a pharmaceutical composition described herein.
  • In embodiments, the cancer is a hematological cancer. In embodiments, the hematological cancer is leukemia or lymphoma. As used herein, a “hematologic cancer” refers to a tumor of the hematopoietic or lymphoid tissues, e.g., a tumor that affects blood, bone marrow, or lymph nodes. Exemplary hematologic malignancies include, but are not limited to, leukemia (e.g., acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), chronic myelogenous leukemia (CML), hairy cell leukemia, acute monocytic leukemia (AMoL), chronic myelomonocytic leukemia (CMML), juvenile myelomonocytic leukemia (JMML), or large granular lymphocytic leukemia), lymphoma (e.g., AIDS-related lymphoma, cutaneous T-cell lymphoma, Hodgkin lymphoma (e.g., classical Hodgkin lymphoma or nodular lymphocyte-predominant Hodgkin lymphoma), mycosis fungoides, non-Hodgkin lymphoma (e.g., B-cell non-Hodgkin lymphoma (e.g., Burkitt lymphoma, small lymphocytic lymphoma (CLL/SLL), diffuse large B-cell lymphoma, follicular lymphoma, immunoblastic large cell lymphoma, precursor B-lymphoblastic lymphoma, or mantle cell lymphoma) or T-cell non-Hodgkin lymphoma (mycosis fungoides, anaplastic large cell lymphoma, or precursor T-lymphoblastic lymphoma)), primary central nervous system lymphoma, Sezary syndrome, Waldenstrom macroglobulinemia), chronic myeloproliferative neoplasm, Langerhans cell histiocytosis, multiple myeloma/plasma cell neoplasm, myelodysplastic syndrome, or myelodysplastic/myeloproliferative neoplasm.
  • In embodiments, the cancer is a solid cancer. Exemplary solid cancers include, but are not limited to, ovarian cancer, rectal cancer, stomach cancer, testicular cancer, cancer of the anal region, uterine cancer, colon cancer, rectal cancer, renal-cell carcinoma, liver cancer, non-small cell carcinoma of the lung, cancer of the small intestine, cancer of the esophagus, melanoma, Kaposi's sarcoma, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, cutaneous or intraocular malignant melanoma, uterine cancer, brain stem glioma, pituitary adenoma, epidermoid cancer, carcinoma of the cervix squamous cell cancer, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the vagina, sarcoma of soft tissue, cancer of the urethra, carcinoma of the vulva, cancer of the penis, cancer of the bladder, cancer of the kidney or ureter, carcinoma of the renal pelvis, spinal axis tumor, neoplasm of the central nervous system (CNS), primary CNS lymphoma, tumor angiogenesis, metastatic lesions of said cancers, or combinations thereof.
  • In embodiments, the backpacks or backpacked cells are administered in a manner appropriate to the disease to be treated or prevented. The quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient's disease. Appropriate dosages may be determined by clinical trials. For example, when “an effective amount” or “a therapeutic amount” is indicated, the precise amount of the pharmaceutical composition (or backpacks) to be administered can be determined by a physician with consideration of individual differences in tumor size, extent of infection or metastasis, age, weight, and condition of the subject. In embodiments, the pharmaceutical composition described herein can be administered at a dosage of 104 to 109 cells/kg body weight, e.g., 10 to 106 cells/kg body weight, including all integer values within those ranges. In embodiments, the pharmaceutical composition described herein can be administered multiple times at these dosages. In embodiments, the pharmaceutical composition described herein can be administered using infusion techniques described in immunotherapy (see, e.g., Rosenberg et al., New Eng. J. of Med. 319:1676, 1988).
  • In embodiments, the backpacks or backpacked cells are administered to the subject parenterally. In embodiments, the cells are administered to the subject intravenously, subcutaneously, intratumorally, intranodally, intramuscularly, intradermally, or intraperitoneally. In embodiments, the cells are administered, e.g., injected, directly into a tumor or lymph node. In embodiments, the cells are administered as an infusion (e.g., as described in Rosenberg et al., New Eng. J. of Med. 319:1676, 1988) or an intravenous push. In embodiments, the cells are administered as an injectable depot formulation.
  • In embodiments, the subject is a mammal. In embodiments, the subject is a human, monkey, pig, dog, cat, cow, sheep, goat, rabbit, rat, or mouse. In embodiments, the subject is a human. In embodiments, the subject is a pediatric subject, e.g., less than 18 years of age, e.g., less than 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1 or less years of age. In embodiments, the subject is an adult, e.g., at least 18 years of age, e.g., at least 19, 20, 21, 22, 23, 24, 25, 25-30, 30-35, 35-40, 40-50, 50-60, 60-70, 70-80, or 80-90 years of age.
    • Examples Example 1: Synthesis of Linker-1
  • Figure US20230233609A1-20230727-C00022
    • Carbonate Formation
  • A: 2,2′-disulfanediyldi(etha n-1-ol)(2.0 g, 1 equiv.)
    B: DSC (N,N′-Disuccinimidyl carbonate) (33.2 g, 10.0 equiv.)
    Pyridine (11.3 mL, 10.0 equiv.)
    • CHCl3, r.t., 24 h
  • (1) Stir a solution of 2,2′-disulfanediyldi (etha n-1-ol) (2.0g, 12.98 mmol, 1 equiv.), in chloroform (333 mL, 165 V)
    (2) Add DSC (33.2 g, 12.98 mmol, 10.0 equiv.)
    (3) Add Pyridine (11.3 mL, 12.98 mmol, 10.0 equiv.)
    (4) Stir reaction mixture at room temperature for 24 h (TLC control)
    (5) Concentrate reaction mixture under reduced pressure to produce a semi solid
    (6) Dilute semi solid with ethyl acetate (200 mL) and wash with water (2×200 mL)
    (7) Concentrate the organic layer under reduced pressure to produce a white solid (2.4 g, impure)
    (8) Purify white solid by DCM to yield product (60% yield) HPLC purity-96.75%. 1HNMR contains 1.63% DCM
    • Example 2: Synthesis of Linker-2
  • Figure US20230233609A1-20230727-C00023
    • Step:1 (Ester Formation)
  • A: Succinic acid (5.0 g, 1 equiv.)
    • B: Mono Ethylene Glycol (10 V)
  • H2SO4 (35 drops)
    • 80° C., 18 h
  • (1) To succinic acid (A) (5.0 g, 42.34 mmol, 1 equiv.) at room temperature
  • (2) Add Mono Ethylene Glycol (B) (50 mL)
  • (3) Add H2SO4 (35 drops)
  • (4) Heat resulting reaction mixture to 80° C. for 18 h (TLC control)
  • (5) Cool to room temperature
  • (6) Neutralize with sodium bicarbonate (pH-7-8)
  • (7) Purify crude material by column chromatography; Elute desired compound with ethyl acetate
  • (8) Result is a colorless liquid C: (bis(2-hydroxyethyl) butanedioate) (3.96 g, 45.36% yield)
  • Step:2 (Carbonate formation)
    C: Bis(2-hydroxyethyl) butanedioate (1.5 g, 1 equiv.)
    D: DSC (18.66 g, 10 equiv.)
    pyridine (5.76 g, 10 equiv.)
    • CHCl3, r.t., 20 h
  • (1) Stir solution of bis(2-hydroxyethyl) butanedioate (C) (1.5g, 1 equiv., 7.2 mmol) in CHCl3 (150 mL, 100 V)
  • (2) Add DSC (D) (18.66 g, 72.74 mmol, 10 equiv.)
  • (3) Add pyridine (5.76 g, 72.74 mmol, 10 equiv.)
  • (4) Stir reaction mixture at room temperature for 20 h (TLC control)
  • (5) Concentrate reaction mixture under reduced pressure
  • (6) Dilute with DCM and wash with water (2×300 mL)
  • (7) Separate organic layer and dry over anhydrous sodium sulfate
  • (8) Concentrate under reduced pressure to produce 1.9 g off white semi solid,
  • (9) Lyophilize
  • (10) 1.9g (impure) compound was triturated with DCM: Methanol to afford 1.06 g of off white solid
    • Example 3: Backpacking of Immune Cells
  • Purpose: Human cells (e.g., Tcells, CAR-T, NK cells, other immune cells) can be labeled with 5 concentrations of IL15 backpack in HBSS at a cell concentration of 50M/mL. After labeling the cells can be tested for:
  • a. Viability via 7-AAD staining measured by FACS
  • b. Expansion in culture via counting beads measured by FACS
  • c. Backpack surface labeling via antibodies against IL15 and human anti-IgG
    • Thawing of IL15 Backpacks:
  • Backpacks should be stored at −80C before use. Thawed backpacks can be re-frozen and re-used up to 3 or more freeze/thaw cycles.
  • Take backpack aliquots out of the freezer, and thaw them on ice.
  • 1. After BP solution is thawed, let it warm up to room temperature 15 min prior to cell labeling experiments
  • 2. Adjust the BP stock solution to a final working solution of 3 mg/mL with HBSS
  • BP
    [BP] [BP] stock HBBS Total vol of
    stock working conc. needed needed BP working
    (mg/mL) (mg/mL) (uL) (uL) sol (uL)
    CYT15 4.2 3 100 40 140
    • Backpack Dilution and Cell Labeling:
  • 7 reactions total: one PBS only control, one soluble IL15 constant control added to cells after plating), and five backpack samples to be done in triplicate (21 samples total). The backpack samples are:
  • a. BP-Dose1: 3 mg/mL
  • b. BP-Dose2: 1.5 mg/mL
  • c. BP-Dose3: 0.75 mg/mL
  • d. BP-Dose 4: 0.375 mg/mL
  • e. BP-Dose 5: 0.1875 mg/mL
  • 1. Make serial dilutions of backpacks in round-bottom 96-well plate:
  • Backpack Volume Volume of Previous
    Dose Concentration HBSS (>3x) Dose (>3x)
    Dose 1    3 mg/mL NA 60 ul stock
    Dose
    2   1.5 mg/mL 60 ul 60 ul of stock
    Dose
    3  0.75 mg/mL 60 ul 60 ul of Dose 2
    Dose 4  0.375 mg/mL 60 ul 60 ul of Dose 3
    Dose 5 0.1875 mg/mL 60 ul 60 ul Dose 4
    PBS control 0 60 ul NA
    Soluble IL15 0 60 ul NA
    control
  • 2. Distribute 10ul of diluted backpack from each well above into three wells in a round-bottom 96-wel plate (backpacking in triplicate)-21 wells total. NOTE. Round-bottom plates are preferable to V-bottom as they limit backpack toxicity
    • Cell Washing and Backpacking:
  • The buffers, PBS, and media used in the steps below should be pre-warmed to 37° C.
  • 1. Collect 30×106 cells from culture and pellet them at 500 g for 5 minutes
  • 2. Remove cell supernatant by aspiration.
  • 3. Wash cells by resuspending the pellet in 10 mL pre-warmed (37° C.) HBSS buffer and count by Cellometer (with AOPI dye) or Trypan Blue.
  • 4. Centrifuge at 500 g for 5 min
  • 5. Aspirate supernatant and suspend cell pellet in pre-warmed (37° C.) HBSS to a concentration of 100×106/mL cells (approximately 300ul of buffer)
  • 6. Pipet 10ul of cells into each well with backpacks or HBSS and gently mix them by pipetting.
  • Cell BP Final BP Final
    Vol Vol Conc. HBSS vol.
    Samples Cell # (ul) (ul) (mg/mL) (uL) (uL)
    Dose 1 1 × 106 10 10 1.5 0 20
    Dose 2 1 × 106 10 10 0.75 0 20
    Dose 3 1 × 106 10 10 0.375 0 20
    Dose 4 1 × 106 10 10 0.188 0 20
    Dose 5 1 × 106 10 10 0.094 0 20
    PBS 1 × 106 10 0 0 10 20
    Soluble 1 × 106 10 0 0 10 20
    IL15
  • 7. Cover plate with a microfilm to prevent evaporation, and incubate in the cell culture incubator (typically 37° C. with 5% CO2 or what is best for culture).
  • 8. Incubate cells for one hour at 37° C.
  • 9. Add 180 uL pre-warmed complete cell media (with serum) to each well.
  • 10. Pellet cells at 500 g for 5 min, and aspirate media with a multiwell manifold
  • 11. Wash cells two more times with 200 uL full media, pellet cells, and aspirate supernatant as in steps 9 and 10.
  • 12. After the third wash, resuspend cells from each sample in 200 uL full media. The cells should be at ˜ 5×106 cells/mL density and need to be further diluted by 1:10 during plating.
  • 13. Dilute cells 1:10 by transferring 20ul of cell suspension from the 96-well U bottom to 96-well flat-bottom tissue culture plate and then adding 180ul cell media (without added cytokines) to achieve a final plating density of 5×105 cells/mL.
  • 14. Repeat step 13 three additional times in three separate 96-well flat bottom plates (4 plates total: Day0, Day1, Day3, DayX for splitting for future time points)
    • Note:
  • a. It is typical to plate several “splits” of cells into multiple 96-well pates which allows individual splits to be analyzed at different time points while allowing for continued propagation in other plates, hence the 4 plates of Day0, Day 1, Day3, DayX.
  • b. When cells grow too confluent, on DayX, they need to be passaged. We recommend passaging the cells by direct media dilution. For example, on DayX, take the 96-well plate out of the incubator. Resuspend the cells in media by pipetting up and down. Transfer 40 uL of cell solution to a new 96-well flat bottom plate, add 160 uL of fresh, warm media to each well to make a 1:5 splitting.
  • 15. Add soluble IL15 monomers to soluble IL15 constant control wells of each plate.
    • Cell Count and Viability Test:
  • Cells are counted using 7-AAD and CountBright counting beads on flow cy tometer.
  • 1. At each time point, take a 96-well flat bottom plate out of the incubator, resuspend cells in media by pipetting up and down
  • 2. Transfer 20 uL of cell solution to a 96-well V-bottom plate
  • 3. To each well, add 20 uL of “CountBright Bead solution”.
  • CountBright Bead Solution contains (volumes for labeling 1 well is listed below):
      • a. 19.6ul CountBright bead stock
      • b. 0.4ul of 100×7AAD (7-AAD, LifeTech, A1310, 10ug/mL is 100×)
  • 4. Repeat these steps on days 1, 3 and X after culturing to assess viability and expansion.
  • BP loading efficiency test by surface staining:
  • Analyze surface levels of IL-15 backpacks by flow cytometry on Days 0 and Day 1 using anti-IL15 and anti-human IgG antibodies.
  • 1. Take a 96-well flat bottom plate out of the incubator, resuspend cells in media by pipetting up and down
  • 2. Transfer 100 uL of cell solution to a new V-bottom 96-well plate (this should contain 50,000 cells)
  • 3. Pellet cells (500 g for 5 min) and aspirate supernatant
  • 4. Resuspend cells in 40 uL “Antibody Cell Surface Staining Solution” Antibody Staining Solution (volumes for labeling 1 well is listed below):
      • a. 0.4 uL of Mouse anti-human IgG BV421 —Biolegend cat. no. 409318, 1:100 dilution
      • b. 0.4 uL of Anti-IL15 PE: R&D Systems cat. no. IC2471IP, 1:100 dilution
      • c. 0.4 uL of 100×7AAD (7-AAD, LifeTech, A1310, 10ug/mL is 100×)
      • d. 38.8 uL of MACS buffer
  • 5. Incubate cells for 10 min at room temperature
  • 6. Add 160 uL of cold MACS buffer to each well, pellet cells at 500 g for 5 min, aspirate.
  • 7. Wash cells one additional time with 200 uL cold MACS buffer
  • 8. Resuspend in 30 uL per well of MACS buffer and analyze on flow cytometer (HTS mode)
    • Reagents Used:
  • Hank's Balanced Salt Solution (l-HBSS, Gibco, with calcium and magnesium, cat #14025-092)
    Phosphate-Buffered Saline (PBS, Glibco, no calcium, no magnesium. cat #10010-023)
    Round-bottom 96-well plate (Granier-Bio, clear, sterile, polypropylene plates, cat #650261)
    v-bottom 96-well plate (optional but recommended): Costar 3894
    Flat-bottom 96-well plate (FisherSci, cat #353072)
    • Counting Beads (LifeTech, COuntBright Absolute Counting Beads, cat #C36950)
  • 7-aminoactinomYcin-D (7-AAD, LifeTech, cat #A1310)
    • Human IL-15 PE-Conjugated Antibody (R&D Systems, cat #TC247IP)
  • Mouse anti-Human IgG, BV421 (Biolegend, cat #409318)
    Alternative Ab: Mouse anti-Human IgG, APC (Biolegend, cat #409306)
    Alternative Ab: Donkey anti-Human IgG (H+L), DyLight 650 (ThermoFisher, cat #SAS-10129)
    MACS Buffer (optional):
  • EDTA: LifeTechnologies, 15575-038
  • Phosphate-Buffered Saline, pH 7.4 (same as above)
  • Bovine Serum Albumin (BSA): AmericanBio, Inc. cat #AB01243-00050
    • Example 4: IL-15 Backpack Provides Autocrine Stimulation and Expansion of T Cells after Adoptive Transfer Driven by Controlled Concentrated Release of IL-15
  • Interleukin 15, a powerful stimulator of CD8 and NK cell expansion is capable of driving anti-tumor activity of adoptively transferred T cells. However, systemic delivery does not safely provide sufficient doses to drive T cell expansion engraftment and anti-tumor activity.
  • Our interleukin 15 backpack (IL-15 backpack) program was initiated with the aim of providing safe and effective doses of Interleukin 15 (IL-15)) by loading transferred T cells with an autocrine source of the cytokine (Stephan et al., Therapeutic cell engineering with surface-conjugated synthetic nanoparticles. Nat. Med. (2010) 16(9):1035-1041). High levels of IL-15 in the blood of cancer patients is associated with successful clinical responses (Kochenderfer et al., Lymphoma remissions caused by anti-CD19 chimeric antigen receptor T cells are associated with high serum interleukin-15 levels. J. Clinical Oncology (2017) 35(16):1803-1813).
  • The IL-15 backpack primed T-cells disclosed herein are autologous T cells that carry tightly controlled doses of IL-15, which is slowly released over a 7-14 day period for directed autocrine activation of infused T cells without affecting endogenous T cells.
  • One example is IL-15 backpack primed cytotoxic T cells (CTLs) that are tumor antigen primed using a novel dendritic cell priming sequence. We have developed a fully closed manufacturing process to produce autologous T cells, with tightly controlled loading of IL-15 backpack on these cells, at high yields of reactive cells, and with cell numbers exceeding one billion per apheresis.
  • As shown in FIG. 2 , fluorophore-containing IL-15 backpacks were titrated in a cell labeling reaction using healthy human CD8 T cells. Fluorescent histograms (LHS) and MFI quantification (RHS) show that the extent of IL-15 backpack loading increases with increased IL-15 backpack loading concentration.
  • FIG. 3 shows dynabead-activated human CD3 T cells from four healthy donors were labeled with IL-15 backpack at three different concentrations. Cell-associated IL-15 backpack loading was assessed by quantifying the remaining IL-15 backpack from the labeling reaction and subtracting that number from the total amount of IL-15 backpack added in the reaction.
  • FIG. 4 shows dynabead-activated human CD3 cells were treated with or without IL-15 backpack before culturing for 7 days. IL-15 levels in the culture supernatants were assessed by ELISA. Expansion was assessed by flow cytometry.
  • FIG. 5 shows IL-15 backpack labeled human CD3 T cells were cultured for 14 days. Media exchange was carried out on Day 1, or Day 2, or Day3, or Day4 to remove secreted IL-15.
  • FIG. 6A shows in vitro cell expansion measured by flow cytometry for ±IL-15 backpack loaded CAR-T cells. FIG. 6B shows flow cytometry measured serum levels of CAR-T cells following injection into NSG mice bearing NSCLC tumor. FIG. 6C shows PET imaging of tumor size.
  • FIGS. 7A-7B shows PMEL T cells, activated ex vivo with anti-CD3/anti-CD28 coated plates and either injected, primed with IL-15 backpack (“IL-15 BP”), or co-administered with IL15-Fc monomers into B16-F10 tumor-bearing C57B6 mice. Mice were sacrificed on days 1, 4, 10 and 16 for blood and tissue collection. Blood was drawn at 2, 24, 48, and 96 hrs for quantification of IL15-Fc (ELISA) and IFN-γ (Luminex) (FIG. 7A), and for enumeration of CD8, NK, and PMEL cells (FIG. 7B, Flow Cytometry). FIG. 7C shows IL15-Fc or IL-15 backpacks were injected into non-tumor bearing C56BL6 mice in the absence of PMEL T cell injection. Blood was drawn for quantification of IFN-γ, and for enumeration of activated (CD25+) CD4, CD8, and NK cells.
  • Novel, closed, semi-automated cell manufacturing process with a yield of up to several billion of cytotoxic T lymphocytes (CTLs) that are targeted against a customizable set of tumor-associated antigens (TAAs). In a final step the antigen-directed CTLs are loaded with IL-15 backpack to generate the TRQ15-01 cell product.
  • FIGS. 8A-8E show that CTLs from process completion were harvested and characterized for: (A) Product TAA-specific cell count and reactivity (intracellular cytokine staining after peptide stimulation); (B) TCR sequencing comparing TRQ15-01 CTL products to their incoming apheresis, and (C) flow-based immune cell composition. (D) TAA-trained CTLs were labeled with an MHC tetramer bearing one of the antigen peptides; (E) CTLs±IL-15 backpack were injected into NSG mice and blood was drawn on days 1, 4, 8, 10. Cell expansion was measured by flow cytometry.
  • In conclusion, IL-15 backpack cell loading is robust and tunable giving a controlled IL-15 dose per cell. The design of our IL-15 backpack technology provides slow and controllable release of IL-15 resulting in autocrine stimulation and sustained cell expansion in adoptive T cell therapy. In contrast to systemically delivered IL-15, IL-15 backpack Priming induces orders of magnitude lower systemic IFNg levels, endogenous CD8 and NK cell expansion, due to lack of systemic exposure. A fully closed, semi-automated cell process reproducibly generates several billion antigen-directed human CTLs with ˜20% reactivity and 95% T cell purity from healthy donors despite ultra low frequency (<1%) precursors. Human CTLs are highly dependent on IL-15 backpack priming technology for cell survival and expansion in vivo.
    • Example 5: Pharmacological Activity of Deep IL-15 Primed PMEL T Cells
  • Deep IL-15 refers to a multimer of human IL-15 receptor α-sushi-domain-Fc fusion homodimers with two associated IL-15 molecules (IL15-Fc), connected by a cleavable crosslinker (Linker-2), and non-covalently coated with a polyethylene glycol (PEG)-polylysine30 block copolymer (PK30). Specifically, Deep IL-15 is a multimer of human IL15-Fc monomers, connected by a hydrolysable crosslinker (CL17) and non-covalently coated with a polyethylene glycol (PEG)-polylysine30 block copolymer (PK30). IL15-Fc monomers consist of two subunits, each consisting of an effector attenuated IgG2 Fc variant fused with an IL-15 receptor α-sushi-domain noncovalently bound to a molecule of IL-15. Deep IL-15 Primed T cells are generated via a loading process in which target cells are co-incubated with Deep IL-15 at high concentrations. Through this process, Deep IL-15 becomes associated with the cell via electrostatic interactions and is internalized to create intracellular reservoirs of Deep IL-15. From these reservoirs, Deep IL-15 slowly releases bioactive IL15-Fc by hydrolysis of the crosslinker. This extended release of IL15-Fc promotes proliferation and survival of Deep IL-15 Primed T cells, providing a targeted, controllable and time-dependent immune stimulus.
  • The objective of this study was to test the pharmacological activity of Deep IL-15 primed PMEL T cells in C57BL/6J mice with and without orthotopically placed B16-F10 melanoma tumors. Control groups included vehicle control, PMEL cells alone and PMEL cells+IL15-Fc, administered in a separate injection (10 μg, maximum tolerated dose, MTD).
    • Materials and Methods
  • BI6-10 tumor establishment and tumor measurements
  • B16-F10 melanoma tumor cells (0.2×106) were injected intra-dermally into the shaved right flank of female C57BL/6 mice (Jackson Labs) on study day -12. The body weights were recorded and tumor dimensions (length [L] and width [W], defined in the list of abbreviations) were measured with calipers 2 to 3 times per week. Tumor volumes were calculated using the formula: W2×L×π/6.
  • Isolation and expansion of PMEL cells
  • PMEL cells were isolated from the spleens and lymph nodes (inguinal, axillary and cervical) of 14 female transgenic PMEL mice (Jackson Laboratories, Bar Harbor, Me.). The spleens and lymph nodes were processed with a GentleMACS Octo Dissociator (Miltenyi Biotech, Auburn, Calif.) and passed through a 40 μm strainer. The cells were washed by centrifugation and the CD8a+cells were purified using an IMACS naïve CD8a+isolation kit (Miltenyi Biotech,) and a MultiMACS cell 24 block (Miltenyi Biotech) and separator (Miltenyi Biotech) with 18 columns following the manufacturer's protocol. The non-CD8a1 cells were removed by an affinity column and the CD8a+T-cells were collected in the column eluate. The purity of CD8a+cells was confirmed by flow cytometry.
  • Upon isolation (DO) purified CD8a+cells from PMEL mice were plated into ten, 6-well tissue culture plates coated with anti-CD3 and anti-CD28 at a density of 5×106 cells/well and incubated for 24 hr at 37° C. and 5% CO2. Murine IL-2 (20 ng/mL) and murine IL-7 (0.5 ng/mL) were added 24 hr post plating (D1). On D2 and D3, the cells were counted and diluted to a concentration of 0.2×106 cells/mL with fresh media containing murine IL-21 (10 ng/mL). The cells were collected on D4 to obtain a total of 100×106 PMEL cells/mL in 28 mL of vehicle control.
    • Preparation of Deep IL-15 Primed PMEL T Cells
  • Five mL of PMEL cells (100×106 cells/mL) were mixed with 5.5 mL of Deep IL-15 (1.36 mg/ml) and incubated with rotation for 1 hr at 37° C. to create Deep IL-15 Primed PMEL cells. Deep IL-15 Primed PMEL cells were washed (3X, first with medium and then twice with HBSS) by centrifugation (500g) and counted. Deep IL-15 Primed PMEL cells were resuspended at a concentration of 50×106 cells/mL. The mice in Groups 5A and 5B were injected with 200 μL of this preparation for a total of 10×106 Deep IL-15 Primed PMEL cells per mouse. PMEL cells (15 mL at 100×106 cells/mL) were mixed with 15 mL of HBSS, incubated with rotation for 1 hr at 37° C., washed (3X, first with medium and then twice with HBSS) by centrifugation (500g) and counted. PMEL cells were resuspended at a concentration of 50×106 cells/mL. The mice in Groups 2A and 2B were injected IV with 200 μL of this preparation for a total of 10×106 PMEL cells per mouse. The mice in Groups 3A and 3B were injected IV with 200 μL of this preparation for a total of 10×106 PMEL cells per mouse, and received a retro-orbital injection of IL15-Fc (10 μg/mouse in 50 p1 HBSS; lot #TSO). Based on an average loading efficiency of 39%, the total amount of IL15-Fc associated with 10×106 PMEL cells is 58.5 jig, which is 5.85-fold higher than the amount delivered systemically by injection of IL15-Fc (10 μg) in Groups 3A and 3B.
    • Fe-IL-15 ELISA
  • An Fc-IL15 Enzyme-Linked Immunosorbent Assay (ELISA) was used to determine the IL15 Fc concentration in the samples collected at 2 hr, D1, 2, 4 and 10 post-dose. ELISA plates (were coated overnight at 4° C. with Goat Anti-human IgG Fc Capture Antibody. Plates were washed and blocked with reagent diluent for at least 2 hours at 30° C. Plates were washed, samples (diluted in reagent diluent) and IL15-Fc standards (in duplicate, 31 to 2000 pg/mL, in reagent diluent) were added to the wells, and plates were incubated for 1 hour at 37° C. Plates were washed followed by addition of biotin-anti-IL15 detection Antibody was added and incubated for 1 hour at 37° C. Plates were washed and incubated with Streptavidin-HRP for 20 min at 37° C. Plates were washed followed by addition of 3,3′,5,5′-Tetramethylbenzidine (TMB) Substrate Solution and incubated for 20 min at room temperature in the dark until the reaction was stopped. Plates were read on a microplate reader (450 nm).
  • The assay was run twice. For the first run, samples were evaluated at the following dilutions: 1: 20000 for the 2 hr time point, 1:5000 for the D1 time point, and 1:250 for the D2, D4 and D10 time points. For the second run, samples from groups 3A and 3B, were diluted 1:5000 for the D1 time point, 1:250 for the D2 time point and 1:25 for the D4 and D10 time points. Samples from groups 1A and 1B, 2A and 2B and 5A and 5B were diluted 1:25 for all the time points analyzed. The data is reported for the second run. However, because the samples for the 2 hr time point were exhausted for the second run, and given that IL15-Fc concentrations at 24 hr were similar in groups 3A and 3B across the two runs, the 2 hr values from the first run were included with the other data points from the second run for the purpose of calculating pharmacokinetic (PK) parameters.
  • The lower limit of quantitation (LLOQ) in blood was 310 ng/ml for the 1:20000 dilution, 77.5 ng/ml for the 1:5000 dilution, 3.875 ng/ml for the 1:250 dilution and 0.3875 ng/ml for the 1:25 dilution.
  • Serum Cytokine Levels in Serum from Mice
  • ThermoFisher ProcartaPlex mouse high sensitivity panel 5plex Cat.#EPXSOSO-22199-901 kits were used according to manufacturer's protocol and samples were analyzed on a Bio-Plex 200 system. Serum was thawed on ice, and 20 L of serum were tested for IFN-γ, TNF-α, IL-2, IL-4 and IL-6 levels. In a few samples, 20 μL of serum were not available, so a smaller volume was utilized. Dilution factors were adjusted, to calculate concentrations according to the standard curves. Statistical analysis was carried out in GraphPad Prism.
    • Results Clinical Chemistry
  • Clinical chemistry parameters were measured on serum samples. FIG. 9 shows clinical chemistry parameters where statistically significant changes were observed for the naïve mice at D1 and D4 post-dose. At D1 post-dose, a significant reduction (p<0.05) in Albumin levels was observed in the PMEL+IL15-Fc group relative to the Deep IL-15 Primed PMEL group as well as in the Blood Urea Nitrogen (BUN) levels compared to both vehicle control and Deep IL-15 Primed PMEL (p<0.05 for both). At D4 post-dose, the PMEL+IL15-Fc group showed significantly reduced Albumin (p<0.05 compared to all the other treatment groups), total protein (p<0.05 compared to vehicle control), Glucose (p<0.05 compared to the Deep IL-15 Primed PMEL), Albumin/Globulin (ALB/GLOB) ratio (p<0.05 compared to vehicle control, and p<0.01 compared to PMEL and Deep IL-15 Primed PMEL). Additionally, the PMEL+IL15-Fc group showed a significant increase (p<0.05 compared to vehicle control and Deep IL-15 Primed PMEL) in Cholesterol levels. All treatment groups showed a trend toward a reduction in Calcium levels compared to vehicle control, which was statistically significant with the PMEL group (p<0.05). The Deep IL-15 Primed PMEL group showed statistically significant changes in Total Bilirubin (p<0.05 compared to vehicle control and PMEL) and Phosphorus (p<0.05 compared to PMEL).
  • FIG. 10 shows clinical chemistry parameters where statistically significant changes were observed for the tumor—bearing mice at D1 and D4 post-dose. At D1 post-dose, the only statistically significant change in clinical chemistry was a reduction in Bilirubin—conjugated, observed with both the PMEL+IL15-Fc and with the Deep IL-15 Primed PMEL group (p<0.05 compared to vehicle control for both). At D4 post-dose, statistically significant increases in Albumin (p<0.05 compared to vehicle control), Total Protein (p<0.01 compared to vehicle control) and Bicarbonate TCO2 (p<0.05 compared to vehicle control) were seen with the PMEL group. Additionally, a statistically significant increase in Globulin was observed with the PMEL group (p<0.001 compared to vehicle control; and p<0.05 compared to DP-15 PMEL) and with the PMEL+IL15-Fc group (p<0.05 compared to vehicle control).
    • Systemic Cytokine Release
  • Using a Luminex 5-plex kit, serum cytokines (IFN-γ, IL-2, IL-4, IL-6, and TNFa) were measured at 2 hr, 24 hr and 96 hr post-dose. In the naïve non-tumor bearing mice, the levels of IFN-γ in the PMEL+IL15-Fc group were 12.8+3.7 pg/mL, while IFN-γ was below the lower limit of quantitation (LLOQ=0.06 pg/mL) in the Deep IL-15 Primed PMEL group (FIG. 11 ). In the tumor—bearing mice, there was on average a 41-fold higher IFN-γ concentration in the PMEL+IL15-Fc group (20.5±0.5 pg/mL) compared to the Deep IL-15 Primed PMEL group (0.5±0.1 pg/mL). Higher levels of IL-2, IL-6, and TNFa were also seen in the PMEL+IL15-Fc group compared to the other groups.
  • Pharmacokinetics of IL15-Fc in the blood
  • A sandwich ELISA (anti-Fc capture antibody followed by anti-IL15 detection antibody) was used to measure IL15-Fc in the blood of mice injected with PMEL+IL15-Fc (10 μg) and Deep IL-15 Primed PMEL (carrying 58.5 ug of IL15-Fc).
  • The pharmacokinetics (PK) of a single dose administration of Deep IL-15 Primed PMEL and PMEL+IL15-Fc were determined for a composite animal in naïve and tumor—bearing mouse. For the PMEL+IL15-Fc group, maximum concentration (Cmax) was attained at 2 hr post dose administration in both naïve and tumor—bearing mice. In the Deep IL-15 Primed PMEL group, the first concentration measured was at 24 hr (the 2 hr samples were initially measured at a non-optimal dilution and no IL15-Fc was detected, and there was not sufficient sample available to repeat the measurement with ideal dilution). Tumor—bearing mice attained slightly lower concentrations than the naïve mice. The calculated mean t1/2 for IL15-Fc in the PMEL+IL15-Fc group was 28.9 hr and 7.12 hr in tumor bearing mice and non-tumor bearing mice, respectively.
  • The IL15-Fc concentrations at the 24 hr timepoint were compared between the PMEL+IL15-Fc and Deep IL-15 Primed PMEL groups. The total IL15-Fc concentration was higher in the PMEL+IL15-Fc (10 jig) group than in the Deep IL-15 Primed PMEL group (58.5 ug of IL15-Fc), approximately 3488-fold higher in the naïve mice and 3299-fold higher in the tumor bearing mice. Composite IL15-Fc PK parameters are summarized in Table 1 and the mean (SD) IL15-Fc PK profiles are depicted in FIG. 12 .
  • TABLE 1
    Composite IL15-Fc PK parameters for the PMEL + IL15-Fc group,
    in naïve and tumor-bearing mice (10 ug dose of IL15-Fc)
    T½ Cmax Tmax Clast Tlast AUClast AUCINF
    Animal Compound Group (hr) (ng/mL) (hr) (ng/mL) (hr) (hr*ng/mL) (hr*ng/mL)
    Composite IL15-Fc Non-tumor 7.12 6931 2 3.64 96 202387 202424
    bearing
    Tumor 28.9 7300 2 0.448 240 156335 156353
    Bearing
    • Inhibition of Tumor Growth
  • On DO (the day of dosing) tumors had reached an average volume of approximately 140 mm3. A statistically significant inhibition of tumor growth was observed at D4 post-dose in all treatment groups compared to vehicle control (p<0.0001), and this difference became more pronounced over time (FIG. 13 , left panel). On study D16 there were only 2/5 animals remaining in the vehicle control group (the others were sacrificed due to extensive tumor burden) but 4/5 animals remaining in each of the treatment groups. Tumor volumes in the vehicle control group were significantly (p<0.0001) different from all other groups. Tumor volumes in the PMEL group were significantly (p<0.05) larger than those in the Deep IL-15 Primed PMEL and PMEL+TL15-Fc groups. The inhibition of tumor growth in the PMEL+IL15-Fc and Deep IL-15 Primed PMEL groups were not different from each other on D16 (FIG. 13 , left and right panels). Tumors were weighed post-sacrifice (n=2-5, each group, each time point) on D1, 4, 10 and 16 post-dose. Tumor weights are shown in FIG. 14 .
  • Some animals were found moribund or dead prior to the study-specified endpoints. These included mice in the vehicle control (4 total: 1 on D9, 1 on D10 and 2 on D14), in the PMEL group (2 total: 1 on D2, and 1 on D6), in the PMEL+IL15-Fc group (2 total: 1 on D9 and 1 on D11) and in the Deep IL-15 Primed PMEL group (2 total: 1 on D9 and 1 on D16). These were not considered related to treatment since they were distributed across groups with the highest numbers (n=4) in the vehicle control. Finally, there was no difference in animals found moribund or dead associated with the Deep IL-15 Primed PMEL group compared to PMEL.
    • CONCLUSIONS
  • Major findings of the study are summarized below.
  • 1. Deep IL-15 Primed PMEL cells were well tolerated at the administered dose of 10×106 cells.
  • 2. Both PMEL, PMEL+IL15-Fc and Deep IL-15 Primed PMEL cells resulted in tumor growth inhibition compared to vehicle control. Inhibition was higher with PMEL+IL15-Fc and Deep IL-15 Primed PMEL cells compared to PMEL.
  • 3. No toxicologically relevant clinical chemistry parameter changes were observed with either PMEL or Deep IL-15 Primed PMEL cells. Some changes were observed with PMEL+IL-15 Fc.
  • 4. No changes in serum IFN-γ, TNF-α or IL-6 were detected with PMEL or Deep IL-15 Primed PMEL cells at any time point. Significant changes in serum IFN-γ and TNF-α were observed with PMEL+IL15-Fc at 24 hr. IL-6 was increased with PMEL+IL15-Fc at 2 hr (Non-tumor—bearing (naïve) mice only) and 24 hr.
  • 5. The serum levels of IL15-Fc in the Deep IL-15 Primed PMEL group were over 3000-fold lower compared to the levels detected in the PMEL+IL15-Fc group, corresponding to no weight loss, no significant changes in CBCs and in endogenous immune cells (CD8+, NK1.1+ and CD4+ cells), reduced IFN-γ serum levels and associated pharmacological changes compared to the PMEL+IL15-Fc group.
  • Modifications and variations of the described methods and compositions of the present disclosure will be apparent to those skilled in the art without departing from the scope and spirit of the disclosure. Although the disclosure has been described in connection with specific embodiments, it should be understood that the disclosure as claimed should not be unduly limited to such specific embodiments. Indeed, various modifications of the described modes for carrying out the disclosure are intended and understood by those skilled in the relevant field in which this disclosure resides to be within the scope of the disclosure as represented by the following claims.
    • INCORPORATION BY REFERENCE
  • All patents and publications mentioned in this specification are herein incorporated by reference to the same extent as if each independent patent and publication was specifically and individually indicated to be incorporated by reference.

Claims (18)

1-25. (canceled)
26. A method for preparing a therapeutic composition the method comprising reacting a plurality of therapeutic protein monomers with A plurality of biodegradable cross-linkers, thereby cross-linking the therapeutic protein monomers into a protein cluster,
wherein the protein cluster has a size between 30 nm and 1000 nm in diameter measured by dynamic light scattering,
wherein the cross-linker has a formula of formula (II):
Figure US20230233609A1-20230727-C00024
wherein:
X1 and X2 are each independently selected from the group consisting of triflyl, tosyl, and N-succinimidyl:
A1 and A3 are both —(CH2)2—;
A2 is —(CR1R2)m—;
Y1 and Y2 are both O;
wherein R1 and R2 at each occurrence are independently selected from the group consisting of hydrogen, halogen, hydroxyl, C1-12 alkyl, C2-12 alkenyl, C3-12 cycloalkyl, C2-12 heterocyclyl, C6-12 aryl optionally substituted with 1 or more halo: hydroxyl: C1-6 alkyl and/or C1-6 alkoxyl, and C4-12 heteroaryl optionally substituted with 1 or more halo: hydroxyl: C1-6 alkyl and/or C1-6 alkoxyl: and
m is an integer selected from 0-12, and
wherein the cross-linker portion of the protein cluster degrades, after administration into a subject in need thereof, under physiological conditions so as to release the therapeutic protein monomers from the protein cluster.
27. The method of claim 26, wherein the reacting step is performed at a temperature between about 5° C. and about 40° C.
28. The method of claim 26, wherein the reacting step is performed for about 1 minute to about 8 hours.
29. The method of claim 26, further comprising providing the surface modification to the protein cluster.
30. The method of claim 26, further comprising purifying the protein cluster.
31. A method for preparing a cell therapy composition, comprising:
providing a therapeutic composition comprising (i) a protein cluster comprising a plurality of therapeutic protein monomers reversibly cross-linked to one another and (ii) a pharmaceutically acceptable carrier or excipient; and
incubating the protein cluster with a nucleated cell preferably for about 30-60 minutes,
wherein the protein cluster has a size between 30 nm and 1000 nm in diameter measured by dynamic light scattering and is produced by reacting the plurality of therapeutic protein monomers with a plurality of biodegradable cross-linkers of formula (II):
Figure US20230233609A1-20230727-C00025
wherein:
X1 and X2 are each independently selected from the group consisting of triflyl, tosyl, and N-succinimidyl;
A1 and A3 are each independently —(CR1R2)n —:
A2 is —(CR1R2)m;
Y1 and Y2 are each independently selected from NR3, O and S:
R1 and R2 at each occurrence are independently selected from the group consisting of hydrogen, halogen, hydroxyl, C1-12 alkyl, C2-12 alkenyl, C3-12 cycloalkyl, C2-12 heterocyclyl, C6-12 aryl optionally substituted with 1 or more halo: hydroxyl: C1-6 alkyl and/or C1-6 alkoxyl, and C4-12 heteroaryl optionally substituted with 1 or more halo: hydroxyl: C1-6 alkyl and/or C1-6 alkoxyl:
wherein R3 is selected from the group consisting of hydrogen, C1-12 alkyl, C2-12 alkenyl, C3-12 cycloalkyl, C2-12 heterocyclyl, C6-12 aryl optionally substituted with 1 or more halo: hydroxyl: C1-6 alkyl and/or C1-6 alkoxyl, and C4-12heteroaryl optionally substituted with 1 or more halo: hydroxyl:
C1-6 alkyl and/or C1-6 alkoxyl:
n, at each occurrence, is an integer independently selected from 1-12: and
m is an integer selected from 0-12,
thereby cross-linking the therapeutic protein monomers into the protein cluster, wherein the cross-linker portion of the protein cluster degrades, after administration into a subject in need thereof, under physiological conditions so as to release the therapeutic protein monomers from the protein cluster.
32. A cell therapy composition, comprising a therapeutic composition comprising a protein cluster comprising (i) a plurality of therapeutic protein monomers reversibly cross-linked to one another and (ii) a pharmaceutically acceptable carrier or excipient, associated with a nucleated cell,
wherein the protein cluster has a size between 30 nm and 1000 nm in diameter measured by dynamic light scattering and is produced by reacting the plurality of therapeutic protein monomers with a plurality of biodegradable cross-linkers of formula (II):
Figure US20230233609A1-20230727-C00026
wherein:
X1 and X2 are each independently selected from the group consisting of triflyl, tosyl, and N-succinimidyl:
A1 and A3 are each independently —(CR1R2)n—:
A2 is —(CR1R2)m—;
Y1 and Y2 are each independently selected from NR3, O and S:
R1 and R2 at each occurrence are independently selected from the group consisting of hydrogen, halogen, hydroxyl, C1-12 alkyl, C2-12 alkenyl, C3-12 cycloalkyl, C2-12 heterocyclyl, C6-12 aryl optionally substituted with 1 or more halo: hydroxyl: C1-6 alkyl and/or C1-6 alkoxyl, and C4-12 heteroaryl optionally substituted with 1 or more halo: hydroxyl: C1-6 alkyl and/or C1-6 alkoxyl: and
wherein R3 is selected from the group consisting of hydrogen, C1-12 alkyl, C2-12 alkenyl, C3-12 cycloalkyl, C2-12 heterocyclyl, C6-12 aryl optionally substituted with 1 or more halo: hydroxyl: C1-6 alkyl and/or C1-6 alkoxyl, and C4-12heteroaryl optionally substituted with 1 or more halo: hydroxyl:
C1-6 alkyl and/or C1-6 alkoxyl:
n, at each occurrence, is an integer independently selected from 1-12: and
m is an integer selected from 0-12,
thereby cross-linking the therapeutic protein monomers into the protein cluster,
wherein the cross-linker portion of the protein cluster degrades, after administration into a subject in need thereof, under physiological conditions so as to release the therapeutic protein monomers from the protein cluster.
33. A method of providing cell therapy, comprising administering the cell therapy composition of claim 32 into a subject in need thereof.
34. The method of claim 26, wherein the cross-linker is symmetrical.
35. The method of claim 26, wherein X1 and X2 are both N-succinimidyl.
36. The method of claim 26, wherein R1 and R2 are both hydrogen.
37. The method of claim 26, wherein A2 is —(CH2)2—.
38. The method of claim 26, wherein the cross-linker is:
Figure US20230233609A1-20230727-C00027
39. The method of claim 26, wherein A2 is a bond.
40. The method of claim 26, wherein the therapeutic protein monomers comprise one or more cytokine molecules selected from the group consisting of IL-15, IL-2, IL-7, IL-10, IL-12, IL-18, IL-21, IL-23, IL-4, IL-lα, IL-lβ, IL-5, IFNγ, TNFα, IFNα, IFNβ, GM-CSF, and GCSF.
41. The method of claim 26, wherein the therapeutic protein monomers comprise IL-15.
42. The method of claim 26, wherein the protein cluster further comprises a polycation on its surface.
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