Classifications

• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/2878—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K40/00—Cellular immunotherapy
  • A61K40/10—Cellular immunotherapy characterised by the cell type used
  • A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K40/00—Cellular immunotherapy
  • A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
  • A61K40/32—T-cell receptors [TCR]
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K40/00—Cellular immunotherapy
  • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
  • A61K40/41—Vertebrate antigens
  • A61K40/42—Cancer antigens
  • A61K40/428—Undefined tumor antigens, e.g. tumor lysate or antigens targeted by cells isolated from tumor
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P35/00—Antineoplastic agents
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P37/00—Drugs for immunological or allergic disorders
  • A61P37/02—Immunomodulators
  • A61P37/04—Immunostimulants
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
  • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
  • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
  • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
• • G—PHYSICS
  • G01—MEASURING; TESTING
  • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
  • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
  • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
  • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
  • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
  • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
  • G01N33/56966—Animal cells
  • G01N33/56972—White blood cells
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K39/00—Medicinal preparations containing antigens or antibodies
  • A61K2039/505—Medicinal preparations containing antigens or antibodies comprising antibodies
  • A61K2039/507—Comprising a combination of two or more separate antibodies
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
  • A61K2239/31—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterized by the route of administration
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
  • A61K2239/38—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterised by the dose, timing or administration schedule
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/75—Agonist effect on antigen
• • C—CHEMISTRY; METALLURGY
  • C07—ORGANIC CHEMISTRY
  • C07K—PEPTIDES
  • C07K2317/00—Immunoglobulins specific features
  • C07K2317/70—Immunoglobulins specific features characterized by effect upon binding to a cell or to an antigen
  • C07K2317/76—Antagonist effect on antigen, e.g. neutralization or inhibition of binding

Definitions

• compositions and methods for detecting and/or targeting dysfunctional tumor antigen-specific CD8 + T cells in the tumor microenvironment for diagnostic, therapeutic and/or research applications.
• dysfunctional tumor antigen-specific CD8 + T cells are detected and/or targeted via their expression of cell surface receptors described herein, such as 4- IBB, LAG-3, or additional markers that correlate with 4-1BB and LAG-3 expression, such as markers differentially expressed on the surface of the T cells.
• the immune system plays a critical role in protecting the host from cancer (Vesely et al., 2011 ; incorporated by reference in its entirety). Innate sensing of tumors leads to an adaptive T cell response through the presentation of tumor-associated antigens (TAAs) derived from mutations and epigenetic changes that contribute to carcinogenesis (Gajewski et al., 2013; incorporated by reference in its entirety). Spontaneously -primed CD8+ T cells home to tumor sites in mouse tumor models (Harlin et al, 2009; Fuertes et al., 2011 ;
• TIL tumor-infiltrating lymphocytes
• CD8+ T cells specific for tumor antigens are isolated from tumors, away from these extrinsic immune inhibitory factors, they still show altered functional properties ex vivo (Harlin et al, 2006; Baitsch et al, 2011 ; incorporated by reference in their entireties).
• T cells expressing PD-1 in the context of chronic infection can still retain effector function (Wherry and Kurachi, 2015; incorporated by reference in its entirety), and PD-1 is not required for the induction of T cell exhaustion (Odorizzi et al, 2015; incorporated by reference in its entirety).
• co-inhibitory receptors including CD223 (LAG-3), CD244 (2B4), T-cell immunoreceptor with Ig and ITIM domains (TIGIT), hepatitis A virus cellular receptor 2 (TIM-3), and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), are also be expressed on dysfunctional T cells and expression of a greater number of inhibitory receptors has been correlated with diminished cytokine secretion (in particular IFN-g and TNF-a) as well as proliferative capacity (Blackburn et al, 2009; incorporated by reference in its entirety). Expression of these receptors has been observed in both viral and cancer models, however, a complete analysis of both co-inhibitory and co-stimulatory receptors on the same population is lacking in the tumor setting.
• compositions and methods for detecting and/or targeting dysfunctional tumor antigen-specific CD8 + T cells in the tumor microenvironment for diagnostic, therapeutic and/or research applications.
• dysfunctional tumor antigen-specific CD8 + T cells are detected and/or targeted via their expression of cell surface receptors described herein, such as 4- IBB, LAG-3, or additional markers that correlate with 4-1BB and LAG-3 expression, such as markers differentially expressed on the surface of the T cells (e.g., PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nml, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, and TMEM126A, CRTAM and Sema7a).
• cell surface receptors described herein such as 4- IBB, LAG-3, or additional markers that correlate with 4-1BB and LAG-3 expression, such as markers differentially expressed on the surface of the T cells (e.g., PD-1, TIM-3, OX-40ICOS
• provided herein are methods of treating a subject with cancer comprising administering an agent that specifically targets dysfunctional tumor antigen-specific CD8 + T cells.
• the subject suffers from a solid tumor cancer.
• the tumor allows T cell infiltration, but is resistant to
• the tumor environment comprises dysfunctional tumor antigen-specific CD8 + T cells.
• the anti-4-lBB and/or anti-LAG3 agent is an antibody, antibody fragment, or antibody mimetic molecule.
• methods further comprise coadministration of an additional therapeutic agent.
• the additional therapeutic agent is a chemotherapeutic or an immunotherapeutic agent.
• the additional therapeutic agent is an immunotherapeutic agent selected from the list consisting of cell-based therapies, monoclonal antibody (mAb) therapy, cytokine therapy, and adjuvant treatment.
• the immunotherapeutic agent is a mAb therapy selected from the list consisting of anti-CTLA-4 monoclonal antibodies and/or anti-PD-Ll monoclonal antibodies.
• the immunotherapeutic agent is a cell-based therapy selected from the list consisting of dendritic-cell therapy and T-cell therapy.
• the additional therapeutic agent targets one of the markers/receptors listed in Table 2.
• the additional therapeutic targets a marker/receptor expressed on the surface of the T cells.
• the additional therapeutic targets PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nml, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, and TMEM126A, CRTAM or Sema7a.
• the additional therapeutic agent targets Nrnl, Sema7a, or CRTAM.
• provided herein are methods of treating a subject with cancer comprising administering a therapeutic agent that specifically targets dysfunctional tumor antigen-specific CD8 + T cells, wherein the agent targets one of the receptors listed in Table 2.
• the therapeutic targets a marker/receptor expressed on the surface of the T cells.
• the therapeutic targets PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nrnl, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, and TMEM126A, CRTAM or Sema7a.
• the therapeutic agent targets Nrnl, Sema7a, or CRTAM.
• the therapeutic agent is an antibody, antibody fragment, or antibody mimetic molecule that binds the target marker/receptor. In some embodiments, the therapeutic agent is an anti-Nrn antibody, antibody fragment, or antibody mimetic molecule. In some embodiments, the therapeutic agent is an anti-Sema7a antibody, antibody fragment, or antibody mimetic molecule. In some embodiments, the therapeutic agent is an anti-CRTAM antibody, antibody fragment, or antibody mimetic molecule.
• compositions comprising: (a) one or more of an anti-4-lBB agent, an anti-LAG-3 agent, an anti-Nrnl agent, an anti-Sema7a agent, and an anti-CRTAM agent; and (b) an immunotherapeutic agent, said composition formulated for therapeutic delivery to a subject.
• the anti-4-lBB agent, anti-LAG-3 agent, anti-Nrnl agent, anti-Sema7a agent, and/or anti-CRTAM agent is an antibody, antibody fragment, or antibody mimetic molecule.
• compositions comprising: (a) an agent that targets and/or binds one of PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nrnl, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, and TMEM126A; and (b) an immunotherapeutic agent, said composition formulated for therapeutic delivery to a subject.
• kits comprising: (a) testing CD8 + T cells from a cell population to determine whether the CD8+ T Cells co-express LAG-3 and 4- 1BB; and (b) administering one or more agents that target and/or bind one of PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nrnl, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, and TMEM126A.
• the agent is an anti-Nrnl agent, an anti-Sema7a agent, and an anti-CRTAM agent.
• the anti-Nrnl agent, anti-Sema7a agent, and/or anti-CRTAM agent is an antibody, antibody fragment, or antibody mimetic molecule. In some embodiments, testing is performed in vitro.
• provided herein are methods of identifying dysfunctional T cells by testing said cells for co-expression of 4-1BB and LAG-3.
• methods of identifying dysfunctional T cells by testing said cells for expression of one or more of the markers/receptors of Table 2 (e.g., a T-cell surface marker/receptor (e.g., PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nrnl, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, TMEM126A).
• a T-cell surface marker/receptor e.g., PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nrnl, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, TMEM126A.
• FIG. 1 A-J Co-expression of 4- IBB and LAG-3 identifies a significant fraction of the CD8 + TIL compartment found in progressing tumors.
• A Representative analysis of 4- IBB and LAG-3 expression on CD8 + T cells from B16.SIY tumors and the spleen and TdLN from tumor bearing mice on day 7, 14 and 21 after s.c. tumor inoculation.
• B-D Representative analysis of 4- IBB and LAG-3 expression on CD8 + T cells from B16.SIY tumors and the spleen and TdLN from tumor bearing mice on day 7, 14 and 21 after s.c. tumor inoculation.
• FIG. 2A-G Egr2 and a component of the Egr2 -transcriptional network are enriched in 4-lBB + LAG-3 + CD8 + TILs.
• B Expression of Egr2 target genes (Zheng et al, 2013).
• D Expression of Egr2 targets in the 4- IBB LAG-3 and 4- IBB LAG-3 subpopulations. The subpopulations were sorted and analyzed directly for the expression of targets by qRT-PCR.
• Egr3 and Hifl in Egr2GFP hi and Egr2GFP l0 from day 7 CD8 + TILs isolated from Egr2GFP mice. n 5; two-independent experiments. Error bars indicate ⁇ SEM. *:P ⁇ 0.05, **:P ⁇ 0.01, ***:P ⁇ 0.001.
• a two-way ANOVA with Bonferroni post-hoc test was used for longitudinal studies (A and C) and a Mann- Whitney test was used to compute significance in (B, D, E, F and G).
• FIG. 3A-H Co-expression of 4-lBB and LAG-3 identifies tumor antigen-specific
• TILs in progressing tumors are representative CDR3 distributions from the different 4- 1BB/LAG-3 subpopulations and CD8 + T cells isolated from the spleen. Boxed regions represent dominant peaks in the 4-lBB + LAG-3 + CD8 + TIL subpopulation.
• E Summary of the composition of H-2K b /SIY + and H-2K b /SIY CD8 + TILs co-expressing 4-lBB and LAG-3 comparing B16.SIY, MC38.SIY, MC57.SIY and 1969. SIY tumors on day 14 after tumor inoculation.
• n 5; three to four independent experiments.
• FIG. 4A-G Co-expression of 4-1BB and LAG-3 but not PD-1 define dysfunctional CD8 + TILs with diminished IL-2.
• C Egr2GFP hi and
• FIG. 5A-E Dysfunctional CD8 + TILs retain IFN- ⁇ production, cytolytic capacity and produce Treg-recruiting chemokines.
• C Ifn-y Tnf-a and Gzmb transcript levels in the 4-1BB/LAG-3 subpopulations analyzed directly ex vivo. Two
• FIG. 6A-D Dysfunctional CD8 + TILs express a wide range of co-inhibitory and co-stimulatory receptors.
• B Gene expression profile of cell surface receptors in the 4- 1BB/LAG-3 CD8 + TIL subsets. Probe sets that revealed a 1.5-fold increase in the 4- lBB + LAG-3 + population relative to the 4-1BB AG-3TD-1 population are displayed. Columns show the log 2 -transformed signal intensity.
• FIG. 7A-G Anti-4-lBB and anti-LAG-3 acts synergistically to control tumor outgrowth and restore TIL function.
• C-F Representative flow plot and summary of NRP1/2B4 (C and E) and KLRG-l/IL-7Ra (D and F) expression in H-2K b /SIY + CD8 + TILs without FTY720 (C and D) and with FTY720 (E and F) on day 14 after tumor inoculation.
• G IL-2 production after treatment. Sorted cells from treated or untreated day 14 B16.SIY tumor bearing mice were stimulated in vitro for 12 hours and analyzed for 11-2 transcript by qRT-PCR. Protein concentration was determined by the bead-based
• Figure 10A-B Statistical analysis of the cross-study comparison of gene expression profiles.
• A Rank-Rank Hypergeometric plots of each pair-wise comparison.
• B Pair-wise correlation of expression values between each data set. Rho (p) is the spearman rank correlation coefficient.
• Nrnl, CRT AM and Sema7a are regulators of anti-tumor immunity.
• A Tumor growth measured in mm2. Nrnl _/ ⁇ or Sema7a and littermate control mice were engrafted with 2 x 106 B16.SIY cells subcutaneously.
• B Gene expression analysis of Nrnl in T cell subsets of the spleen, TdLN and Tumor.
• C Representative flow plot and summary of IFN-g production of WT, Nrnl "7" or (D) CRTAM 7 2C T cells on day 7. Briefly, on the same day as tumor inoculation, lxlO 6 Cell Trace Violet-labeled 2C T cells were transferred into mice by tail vein injection.
• the term "comprise” and linguistic variations thereof denote the presence of recited feature(s), element(s), method step(s), etc. without the exclusion of the presence of additional feature(s), element(s), method step(s), etc.
• the term “consisting of and linguistic variations thereof denotes the presence of recited feature(s), element(s), method step(s), etc. and excludes any unrecited feature(s), element(s), method step(s), etc., except for ordinarily-associated impurities.
• the phrase “consisting essentially of denotes the recited feature(s), element(s), method step(s), etc. and any additional feature(s), element(s), method step(s), etc.
• compositions, system, or method that do not materially affect the basic nature of the composition, system, or method.
• Many embodiments herein are described using open “comprising” language. Such embodiments encompass multiple closed “consisting of and/or “consisting essentially of embodiments, which may alternatively be claimed or described using such language.
• the term “subject” broadly refers to any animal, including but not limited to, human and non-human animals (e.g., dogs, cats, cows, horses, sheep, poultry, fish, crustaceans, etc.).
• the term “patient” typically refers to a subject that is being treated for a disease or condition (e.g., cancer, solid tumor cancer, etc.).
• an "immune response” refers to the action of a cell of the immune system (e.g., T lymphocytes, B lymphocytes, natural killer (NK) cells, macrophages, eosinophils, mast cells, dendritic cells, neutrophils, etc.) and soluble macromolecules produced by any of these cells or the liver (including antibodies, cytokines, and complement) that results in selective targeting, binding to, damage to, destruction of, and/or elimination from a subj ect of invading pathogens, cells or tissues infected with pathogens, or cancerous or other abnormal cells.
• a cell of the immune system e.g., T lymphocytes, B lymphocytes, natural killer (NK) cells, macrophages, eosinophils, mast cells, dendritic cells, neutrophils, etc.
• soluble macromolecules produced by any of these cells or the liver (including antibodies, cytokines, and complement) that results in selective targeting, binding to, damage to
• the term “immunoregulator” refers to a substance, an agent, a signaling pathway or a component thereof that regulates an immune response.
• "Regulating,” “modifying” or “modulating” an immune response refers to any alteration in a cell of the immune system or in the activity of such cell. Such regulation includes stimulation or suppression of the immune system which may be manifested by an increase or decrease in the number of various cell types, an increase or decrease in the activity of these cells, or any other changes which can occur within the immune system.
• Both inhibitory and stimulatory immunoregulators have been identified, some of which may have enhanced function in the cancer microenvironment.
• immunotherapy refers to the treatment or prevention of a disease or condition by a method comprising inducing, enhancing, suppressing or otherwise modifying an immune response.
• potentiating an endogenous immune response means increasing the effectiveness or potency of an existing immune response in a subject. This increase in effectiveness and potency may be achieved, for example, by overcoming mechanisms that suppress the endogenous host immune response or by stimulating mechanisms that enhance the endogenous host immune response.
• an antibody refers to a whole antibody molecule or a fragment thereof (e.g., fragments such as Fab, Fab', and F(ab')2), unless otherwise specified (e.g., "whole antibody,” “antibody fragment”).
• An antibody may be a polyclonal or monoclonal antibody, a chimeric antibody, a humanized antibody, a human antibody, etc.
• a native antibody typically has a tetrameric structure.
• a tetramer typically comprises two identical pairs of polypeptide chains, each pair having one light chain (in certain embodiments, about 25 kDa) and one heavy chain (in certain embodiments, about 50-70 kDa).
• a heavy chain comprises a variable region, VH, and three constant regions, CHI, CH2, and CH3-
• the VH domain is at the amino-terminus of the heavy chain
• the CH3 domain is at the carboxy -terminus.
• a light chain comprises a variable region, VL, and a constant region, CL.
• the variable region of the light chain is at the amino-terminus of the light chain.
• the variable regions of each light/heavy chain pair typically form the antigen binding site.
• the constant regions are typically responsible for effector function.
• variable regions typically exhibit the same general structure in which relatively conserved framework regions (FRs) are joined by three hypervariable regions, also called complementarity determining regions (CDRs).
• the CDRs from the two chains of each pair typically are aligned by the framework regions, which may enable binding to a specific epitope.
• both light and heavy chain variable regions typically comprise the domains FR1 , CDR1 , FR2, CDR2, FR3, CDR3 and FR4.
• the CDRs on the heavy chain are referred to as HI , H2, and H3, while the CDRs on the light chain are referred to as LI , L2, and L3.
• CDR3 is the greatest source of molecular diversity within the antigen-binding site.
• H3 for example, in certain instances, can be as short as two amino acid residues or greater than 26.
• the assignment of amino acids to each domain is typically in accordance with the definitions of Kabat et al. (1991) Sequences of Proteins of Immunological Interest (National Institutes of Health, Publication No. 91-3242, vols. 1 -3, Bethesda, Md.); Chothia, C, and Lesk, A. M. (1987) J. Mol. Biol. 196:901-917; or Chothia, C. et al. Nature 342: 878-883 (1989).
• the term "CDR" refers to a CDR from either the light or heavy chain, unless otherwise specified.
• heavy chain refers to a polypeptide comprising sufficient heavy chain variable region sequence to confer antigen specificity either alone or in combination with a light chain.
• light chain refers to a polypeptide comprising sufficient light chain variable region sequence to confer antigen specificity either alone or in combination with a heavy chain.
• affinity which is substantially higher means affinity that is high enough to enable detection of an antigen or epitope which is distinguished from entities using a desired assay or measurement apparatus.
• binding affinity having a binding constant (K a ) of at least 10 7 M “1 (e.g., >10 7 M “1 , >10 8 M “1 , >10 9 M “1 , >10 10 M “1 , >10 n M “1 , >10 12 M “1 , >10 13 M “1 , etc.).
• K a binding constant
• an antibody is capable of binding different antigens so long as the different antigens comprise that particular epitope.
• homologous proteins from different species may comprise the same epitope.
• anti-4-lBB antibody or "4-1BB antibody” refers to an antibody which specifically recognizes an antigen and/or epitope presented by 4-1BB.
• anti-LAG-3 antibody and “LAG-3 antibody” refer to an antibody which specifically recognizes an antigen and/or epitope presented by LAG-3
• anti- Nrnl antibody and “Nrnl antibody” refer to an antibody which specifically recognizes an antigen and/or epitope presented by Nrnl
• anti-CRTAM antibody and “CRTAM antibody” refer to an antibody which specifically recognizes an antigen and/or epitope presented by CRTAM
• anti-Sema7a antibody and “Sema7a antibody” refer to an antibody which specifically recognizes an antigen and/or epitope presented by Sema7a.
• Antibodies that recognize epitopes on other molecular entities may be referred to according to a similar scheme (e.g., anti-CTLA-4, anti-PD-Ll, etc.).
• a monoclonal antibody refers to an antibody which is a member of a substantially homogeneous population of antibodies that specifically bind to the same epitope.
• a monoclonal antibody is secreted by a hybridoma.
• a hybridoma is produced according to certain methods known to those skilled in the art. See, e.g., Kohler and Milstein (1975) Nature 256: 495-499; herein incorporated by reference in its entirety.
• a monoclonal antibody is produced using recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567).
• a monoclonal antibody refers to an antibody fragment isolated from a phage display library. See, e.g., Clackson et al. (1991) Nature 352: 624-628; and Marks et al.
• antibody fragment refers to a portion of a full-length antibody, including at least a portion antigen binding region or a variable region.
• Antibody fragments include, but are not limited to, Fab, Fab', F(ab')2, Fv, scFv, Fd, diabodies, and other antibody fragments that retain at least a portion of the variable region of an intact antibody. See, e.g., Hudson et al. (2003) Nat. Med. 9: 129-134; herein incorporated by reference in its entirety.
• antibody fragments are produced by enzymatic or chemical cleavage of intact antibodies (e.g., papain digestion and pepsin digestion of antibody) produced by recombinant DNA techniques, or chemical polypeptide synthesis.
• a "Fab” fragment comprises one light chain and the CHI and variable region of one heavy chain.
• the heavy chain of a Fab molecule cannot form a disulfide bond with another heavy chain molecule.
• a "Fab”' fragment comprises one light chain and one heavy chain that comprises additional constant region, extending between the CHI and Cm domains.
• An interchain disulfide bond can be formed between two heavy chains of a Fab' fragment to form a "F(ab')2" molecule.
• an “Fv” fragment comprises the variable regions from both the heavy and light chains, but lacks the constant regions.
• a single-chain Fv (scFv) fragment comprises heavy and light chain variable regions connected by a flexible linker to form a single polypeptide chain with an antigen-binding region.
• Exemplary single chain antibodies are discussed in detail in WO 88/01649 and U.S. Pat. Nos. 4,946,778 and 5,260,203; herein incorporated by reference in their entireties.
• a single variable region e.g., a heavy chain variable region or a light chain variable region
• a chimeric antibody refers to an antibody made up of components from at least two different sources.
• a chimeric antibody comprises a portion of an antibody derived from a first species fused to another molecule, e.g., a portion of an antibody derived from a second species.
• a chimeric antibody comprises a portion of an antibody derived from a non-human animal fused to a portion of an antibody derived from a human.
• a chimeric antibody comprises all or a portion of a variable region of an antibody derived from a non-human animal fused to a constant region of an antibody derived from a human.
• a “humanized” antibody refers to a non-human antibody that has been modified so that it more closely matches (in amino acid sequence) a human antibody.
• a humanized antibody is thus a type of chimeric antibody.
• amino acid residues outside of the antigen binding residues of the variable region of the non-human antibody are modified.
• a humanized antibody is constructed by replacing all or a portion of a complementarity determining region (CDR) of a human antibody with all or a portion of a CDR from another antibody, such as a non-human antibody, having the desired antigen binding specificity.
• CDR complementarity determining region
• a humanized antibody comprises variable regions in which all or substantially all of the CDRs correspond to CDRs of a non- human antibody and all or substantially all of the framework regions (FRs) correspond to FRs of a human antibody.
• a humanized antibody further comprises a constant region (Fc) of a human antibody.
• human antibody refers to a monoclonal antibody that contains human antibody sequences and does not contain antibody sequences from a non-human animal.
• a human antibody may contain synthetic sequences not found in native antibodies. The term is not limited by the manner in which the antibodies are made.
• a human antibody may be made in a transgenic mouse, by phage display, by human B-lymphocytes, or by recombinant methods.
• natural antibody refers to an antibody in which the heavy and light chains of the antibody have been made and paired by the immune system of a multicellular organism.
• the antibodies produced by the antibody -producing cells isolated from a first animal immunized with an antigen are natural antibodies.
• Natural antibodies contain naturally -paired heavy and light chains.
• natural human antibody refers to an antibody in which the heavy and light chains of the antibody have been made and paired by the immune system of a human subject.
• Native human light chains are typically classified as kappa and lambda light chains.
• Native human heavy chains are typically classified as mu, delta, gamma, alpha, or epsilon, and define the antibody's isotype as IgM, IgD, IgG, IgA, and IgE, respectively.
• IgG has subclasses, including, but not limited to, IgGl, IgG2, IgG3, and IgG4.
• IgM has subclasses including, but not limited to, IgMl and IgM2.
• IgA has subclasses including, but not limited to, IgAl and IgA2.
• variable and constant regions are typically joined by a "J" region of about 12 or more amino acids, with the heavy chain also including a "D” region of about 10 more amino acids.
• J Fundamental Immunology (1989) Ch. 7 (Paul, W., ed., 2nd ed. Raven Press, N.Y.); herein incorporated by reference in its entirety.
• neutralizing antibody or “antibody that neutralizes” refers to an antibody that reduces at least one activity of a polypeptide comprising the epitope to which the antibody specifically binds. In certain embodiments, a neutralizing antibody reduces an activity in vitro and/or In vivo. In some embodiments, by neutralizing the polypeptide comprising the epitope, the neutralizing antibody inhibits the capacity of the cell displaying the epitope.
• glycoengineered includes any manipulation of the glycosylation pattern of a naturally occurring or recombinant protein, polypeptide or a fragment thereof.
• an antigen-binding site refers to a portion of an antibody capable of specifically binding an antigen.
• an antigen-binding site is provided by one or more antibody variable regions.
• epitope refers to any polypeptide determinant capable of specifically binding to an immunoglobulin or a T-cell or B-cell receptor.
• an epitope is a region of an antigen that is specifically bound by an antibody.
• an epitope may include chemically active surface groupings of molecules such as amino acids, sugar side chains, phosphoryl, or sulfonyl groups.
• an epitope may have specific three dimensional structural characteristics (e.g., a
• epitope is defined as "the same” as another epitope if a particular antibody specifically binds to both epitopes.
• polypeptides having different primary amino acid sequences may comprise epitopes that are the same.
• epitopes that are the same may have different primary amino acid sequences. Different antibodies are said to bind to the same epitope if they compete for specific binding to that epitope.
• a “conservative" amino acid substitution refers to the substitution of an amino acid in a polypeptide with another amino acid having similar properties, such as size or charge.
• a polypeptide comprising a conservative amino acid substitution maintains at least one activity of the unsubstituted polypeptide.
• a conservative amino acid substitution may encompass non-naturally occurring amino acid residues, which are typically incorporated by chemical peptide synthesis rather than by synthesis in biological systems. These include, but are not limited to, peptidomimetics and other reversed or inverted forms of amino acid moieties.
• Naturally occurring residues may be divided into classes based on common side chain properties, for example: hydrophobic: norleucine, Met, Ala, Val, Leu, and He; neutral hydrophilic: Cys, Ser, Thr, Asn, and Gin; acidic: Asp and Glu; basic: His, Lys, and Arg; residues that influence chain orientation: Gly and Pro; and aromatic: Trp, Tyr, and Phe.
• Non-conservative substitutions may involve the exchange of a member of one of these classes for a member from another class; whereas conservative substitutions may involve the exchange of a member of one of these classes for another member of that same class.
• sequence identity refers to the degree to which two polymer sequences (e.g., peptide, polypeptide, nucleic acid, etc.) have the same sequential composition of monomer subunits.
• sequence similarity refers to the degree with which two polymer sequences (e.g., peptide, polypeptide, nucleic acid, etc.) have similar polymer sequences. For example, similar amino acids are those that share the same biophysical characteristics and can be grouped into the families (see above).
• the "percent sequence identity” is calculated by: (1) comparing two optimally aligned sequences over a window of comparison (e.g., the length of the longer sequence, the length of the shorter sequence, a specified window, etc.), (2) determining the number of positions containing identical (or similar) monomers (e.g., same amino acids occurs in both sequences, similar amino acid occurs in both sequences) to yield the number of matched positions, (3) dividing the number of matched positions by the total number of positions in the comparison window (e.g., the length of the longer sequence, the length of the shorter sequence, a specified window), and (4) multiplying the result by 100 to yield the percent sequence identity or percent sequence similarity.
• a window of comparison e.g., the length of the longer sequence, the length of the shorter sequence, a specified window, etc.
• peptides A and B are both 20 amino acids in length and have identical amino acids at all but 1 position, then peptide A and peptide B have 95% sequence identity. If the amino acids at the non-identical position shared the same biophysical characteristics (e.g., both were acidic), then peptide A and peptide B would have 100% sequence similarity.
• peptide C is 20 amino acids in length and peptide D is 15 amino acids in length, and 14 out of 15 amino acids in peptide D are identical to those of a portion of peptide C, then peptides C and D have 70% sequence identity, but peptide D has 93.3% sequence identity to an optimal comparison window of peptide C.
• percent sequence identity or “percent sequence similarity” herein, any gaps in aligned sequences are treated as mismatches at that position.
• an effective dose or effective amount refers to an amount of an agent, e.g., an antibody, that results in the reduction of symptoms in a patient or results in a desired biological outcome. In certain embodiments, an effective dose or effective amount is sufficient to treat or reduce symptoms of a disease or condition.
• administering refers to the act of giving a drug, prodrug, or other agent, or therapeutic to a subject or in vivo, in vitro, or ex vivo cells, tissues, and organs.
• routes of administration to the human body can be through space under the arachnoid membrane of the brain or spinal cord (intrathecal), the eyes (ophthalmic), mouth (oral), skin (topical or transdermal), nose (nasal), lungs (inhalant), oral mucosa (buccal), ear, rectal, vaginal, by injection (e.g., intravenously, subcutaneously, intratumorally, intraperitoneally, etc.) and the like.
• treatment encompasses both therapeutic and prophylactic/preventative measures unless otherwise indicated.
• Those in need of treatment include, but are not limited to, individuals already having a particular condition as well as individuals who are at risk of acquiring a particular condition or disorder (e.g., those having a genetic or epigenetic predisposition; based on age, gender, lifestyle, etc.).
• treating refers to
• a “therapeutic agent” refers to an agent that may be administered In vivo to bring about a therapeutic and/or prophylactic/preventative effect.
• a “therapeutic antibody” refers to an antibody that may be administered In vivo to bring about a therapeutic and/or prophylactic/preventative effect.
• co-administration refers to the administration of at least two agent(s) or therapies to a subject. In some embodiments, the coadministration of two or more agents or therapies is concurrent. In other embodiments, a first agent/therapy is administered prior to a second agent/therapy.
• a first agent/therapy is administered prior to a second agent/therapy.
• the appropriate dosage for co-administration can be readily determined by one skilled in the art. In some embodiments, when agents or therapies are coadministered, the respective agents or therapies are administered at lower dosages than appropriate for their administration alone.
• co-administration is especially desirable in embodiments where the co-administration of the agents or therapies lowers the requisite dosage of a potentially harmful (e.g., toxic) agent(s), and/or when co-administration of two or more agents results in sensitization of a subject to beneficial effects of one of the agents via co-administration of the other agent.
• a potentially harmful agent e.g., toxic
• composition refers to the combination of an active agent (e.g., binding agent) with a carrier, inert or active, making the composition especially suitable for diagnostic or therapeutic use in vitro, in vivo or ex vivo.
• an active agent e.g., binding agent
• compositions that do not substantially produce adverse reactions, e.g., toxic, allergic, or immunological reactions, when administered to a subj ect.
• the term "pharmaceutically acceptable carrier” refers to any of the standard pharmaceutical carriers including, but not limited to, phosphate buffered saline solution, water, emulsions (e.g., such as an oil/water or water/oil emulsions), and various types of wetting agents, any and all solvents, dispersion media, coatings, sodium lauryl sulfate, isotonic and absorption delaying agents, disintigrants (e.g., potato starch or sodium starch glycolate), and the like.
• the compositions also can include stabilizers and
• preservatives examples include carriers, stabilizers and adjuvants, see, e.g., Martin,
• a "diagnostic” or “diagnostic test” includes the detection,
• a disease or condition may be characterized to determine the likelihood that a subject with a disease or condition will respond to a particular therapy, determine the prognosis of a subject with a disease or condition (or its likely progression or regression), determine the effect of a treatment on a subject with a disease or condition, or determine a future treatment course of action.
• compositions and methods for detecting and/or targeting dysfunctional tumor antigen-specific CD8 + T cells in the tumor microenvironment for diagnostic, therapeutic and/or research applications.
• dysfunctional tumor antigen-specific CD8 + T cells are detected and/or targeted via their expression of cell surface receptors described herein, such as 4-lBB,LAG-3, or additional markers that correlate with 4-1BB and LAG-3 expression, such as markers differentially expressed on the surface of the T cells (e.g., PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nml, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, and TMEM126A, CRTAM and Sema7a).
• cell surface receptors described herein such as 4-lBB,LAG-3, or additional markers that correlate with 4-1BB and LAG-3 expression, such as markers differentially expressed on the surface of the T cells (e.g., PD-1, TIM-3, OX-40ICOS
• markers/receptors that correlate and/or are responsible for tumor antigen-specific CD8 + T cell dysfunction.
• the markers/receptors are overexpressed in dysfunctional tumor antigen-specific CD8 + T cells.
• detecting the level (e.g., above a threshold) of such markers provides a diagnostic for detecting tumor antigen-specific CD8 + T cell dysfunction.
• targeting e.g., inhibiting (e.g., expression and/or activity of)
• such markers/receptors are underexpressed in dysfunctional tumor antigen-specific CD8 + T cells.
• detecting the level (e.g., below a threshold) of such markers provides a diagnostic for detecting tumor antigen-specific CD8 + T cell dysfunction.
• targeting e.g., enhancing (e.g., expression and/or activity of)
• Transcription factor Egr2 is a critical regulator of the anergic state in CD4 + T cell clones manipulated in vitro (Zheng et al, 2013; 2012; incorporated by reference in their entireties). Egr2 has also been shown to be involved in negative regulation of T cell activation in several in vivo model systems (Sumitomo et al, 2013; incorporated by reference in its entirety).
• Egr2 contributes to upregulation of DGKa and -z which act to blunt TCR- mediated Ras pathway activation (Zha et al, 2006; incorporated by reference in its entirety).
• Egr2 ChlP-Seq analysis multiple additional Egr2-driven gene targets were identified (Zheng et al, 2013; incorporated by reference in its entirety).
• gene targets include 4-1BB (Tnfrsf9 or CD137), Lag3, Nml, Sema7a, Crtam, and Rankl, which encode cell surface proteins.
• 4-1BB is a co-stimulatory molecule transiently expressed after TCR engagement.
• Lag3 lymphocyte-activation gene 3 or CD223
• CD223 is a CD4 homologue and functions as an inhibitory receptor.
• Expression of 4- IBB and Lag3 is regulated following TCR engagement and continues throughout differentiation.
• 4-1BB and LAG-3 are expressed on CD8+ TILs from human melanoma tumors (Gros et al, 2014; Baitsch et al, 2012;
• Additional gene expression profiling provided a complete phenotyping of this T cell subset, which revealed expression of a broad panel of both inhibitory receptors and co-stimulatory receptors (e.g., receptors of Table 2 (e.g. Nrnl , Sema7a, CRTAM, etc.)).
• Inhibitory receptors and co-stimulatory receptors idientified in this profiling that are displayed on the surface of T cells include PD-1 , TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF 18, Nrnl, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, and TMEM126A.
• this population is a target for immunotherapeutic approaches to restore desired functionality and promote tumor regression.
• the receptors/markers identified herein e.g., 4-1BB, LAG-3, receptors/markers of Table 2 (e.g., surface markers/receptors (e.g. Nrnl, Sema7a, CRTAM, etc.), etc.) etc.
• cancer treatment methods described herein comprise administration (or co-administration with one or more additional therapies/therapeutics) of one or more anti-4-lBB and/or anti-LAG-3 agents (e.g., antibodies, antibody fragments, antibody mimetic molecules (e.g., DARPins, affibodies, aptamers, nanobodies, etc.), etc.).
• an anti-4-lBB and/or anti-LAG-3 agents is administered to render cancer cells, tumor(s), and/or the tumor microenvironment accessible or susceptible to treatment with additional therapies/therapeutics (e.g., immunotherapeutics).
• Anti-4-lBB and/or anti- LAG-3 agents that find use in embodiments described herein are not limited by their mechanism of action. Agents may be small molecules, peptide, polypeptides, proteins, nucleic acids (e.g., antisense, RNAi, etc.), antibodies, antibody fragments, etc.
• cancer treatment methods described herein comprise enhancing the activity or expression of a marker/receptor identified herein that negatively correlates with tumor antigen-specific CD8 + T cell dysfunction.
• cancer treatment methods described herein comprise administration (or co-administration with one or more additional therapies/therapeutics) of agents (e.g., antibodies, antibody fragments, antibody mimetic molecules (e.g., DARPins, affibodies, aptamers, nanobodies, etc.), etc.) that target one or more receptors/markers of Table 2 (e.g.
• agents e.g., antibodies, antibody fragments, antibody mimetic molecules (e.g., DARPins, affibodies, aptamers, nanobodies, etc.
• an agent is administered to render cancer cells, tumor(s), and/or the tumor microenvironment accessible or susceptible to treatment with additional
• therapies/therapeutics e.g., immunotherapeutics.
• Agents targeting one or more of therapies/therapeutics e.g., immunotherapeutics.
• receptors/markers of Table 2 e.g. PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nml, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, and TMEM126A, Nml, CRTAM, Sema7a, etc.
• Agents may be small molecules, peptide, polypeptides, proteins, nucleic acids (e.g., antisense, RNAi, etc.), antibodies, antibody fragments, etc.
• an antagonist of Nml is administered.
• an antagonist of CRTAM is administered.
• an agonist of Sema7a is administered.
• antibodies, antibody fragments, antibody mimetic molecules e.g., DARPins, affibodies, aptamers, nanobodies, etc.
• Such agents may be naked, deriving their effect by target binding (e.g., neutralizing the target), or may be conjugated to a functional moiety (e.g., drug, toxin, effector moiety, etc.).
• receptors/markers of Table 2 e.g. PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nml, Nrpl, KLRG1, GM156, GPNMB, GPR65, TMEM205, and TMEM126A, CRTAM, Sema7a, etc.
• additional cancer therapies include chemotherapy, immunotherapy, radiation, surgery, etc.
• agents targeting the receptors/markers described herein are co-administered with one or more additional agents for the treatment of cancer.
• exemplary anticancer agents suitable for use in compositions and methods described herein include, but are not limited to: 1) alkaloids, including microtubule inhibitors (e.g., vincristine, vinblastine, and vindesine, etc.), microtubule stabilizers (e.g., paclitaxel (Taxol), and docetaxel, etc.), and chromatin function inhibitors, including topoisomerase inhibitors, such as epipodophyllotoxins (e.g., etoposide (VP-16), and teniposide (VM-26), etc.), and agents that target topoisomerase I (e.g., camptothecin and isirinotecan (CPT-1 1), etc.); 2) covalent DNA-binding agents (alkylating agents), including nitrogen mustards (e.g., mechlorethamine, chlorambucil, cyclophosphamide, ifosphamide, and busulfan (MYLERAN
• antimetabolites including antifolates (e.g., methotrexate, FOLEX, and MEXATE, etc.), purine antimetabolites (e.g., 6-mercaptopurine (6-MP, PURINETHOL), 6-thioguanine (6- TG), azathioprine, acyclovir, ganciclovir, chlorodeoxyadenosine, 2-chlorodeoxyadenosine (CdA), and 2'-deoxycoformycin (pentostatin), etc.), pyrimidine antagonists (e.g.,
• fluoropyrimi dines e.g., 5-fluorouracil (ADRUCIL), 5 -fluorodeoxy uridine (FdUrd)
• ADRUCIL 5-fluorouracil
• FdUrd 5 -fluorodeoxy uridine
• cytosine arabinosides e.g., CYTOSAR (ara-C) and fludarabine, etc.
• enzymes including L-asparaginase, and hydroxyurea, etc.
• hormones including glucocorticoids, antiestrogens (e.g., tamoxifen, etc.), nonsteroidal antiandrogens (e.g., flutamide, etc.), and aromatase inhibitors (e.g., anastrozole (ARIMIDEX), etc.); 7) platinum compounds (e.g., cisplatin and carboplatin, etc.); 8) monoclonal antibodies (e.g., conjugated with anticancer drugs, toxins, and/or radionuclides, etc. ; neutralizing antibodies; etc.); 9) biological response modifiers (e.g., interferons (e.g., IFN-.
• interferons e.g., IFN-.
• alpha., etc. and interleukins e.g., IL-2, etc.), etc.
• 10) adoptive immunotherapy 11) hematopoietic growth factors; 12) agents that induce tumor cell differentiation (e.g., all-trans-retinoic acid, etc.); 13) gene therapy techniques; 14) antisense therapy techniques; 15) tumor vaccines; 16) therapies directed against tumor metastases (e.g., batimastat, etc.); 17) angiogenesis inhibitors; 18) proteosome inhibitors (e.g., VELCADE); 19) inhibitors of acetylation and/or methylation (e.g., HDAC inhibitors); 20) modulators of NF kappa B; 21) inhibitors of cell cycle regulation (e.g., CDK inhibitors); and 22) modulators of p53 protein function.
• hematopoietic growth factors 12
• agents that induce tumor cell differentiation e.g., all-trans-retinoic acid, etc.
• agents targeting 4-1BB, LAG-3 and/or one or more receptors/markers of Table 2 are administered to overcome immune invasion of the cancer cells, tumor, tumor microenvironment, etc.
• one or more additional cancer immunotherapies are employed (e.g., concurrently or serially) to make use of the immune-responsiveness of the treated
• Suitable immunotherapies may include, but are not limited to: cell-based therapies (e.g., dendritic cell or T cell therapy, etc.), monoclonal antibody (mAb) therapy (e.g., naked mAbs, conjugated mAbs), cytokine therapy (e.g., interferons, interleukins, etc.), adjuvant treatment (e.g., polysaccharide-K), etc.
• cell-based therapies e.g., dendritic cell or T cell therapy, etc.
• mAb monoclonal antibody
• cytokine therapy e.g., interferons, interleukins, etc.
• adjuvant treatment e.g., polysaccharide-K
• agents targeting 4-1BB, LAG-3 and/or one or more receptors/markers of Table 2 are co-administered with agents (e.g., small molecules, peptides, antibodies, antibody fragments, etc.) that target one or more cancer cell or tumor) markers or
• such co-administration renders the cancer cells, tumor, and/or tumor microenvironment susceptible and/or accessible to the treatment with the additional agent.
• agents for use in the methods and compositions described herein target and/or binds a cancer or tumor cell marker or component, selected from the group including but not limited to, epidermal growth factor receptor (EGFR, EGFRl , ErbB-1 , HERl).
• EGFR epidermal growth factor receptor
• EGFRl epidermal growth factor receptor
• ErbB-1 ErbB-1
• HERl epidermal growth factor receptor
• ErbB-2 (HER2/neu), ErbB-3/HER3, ErbB-4/HER4, EGFR ligand family; insulin-like growth factor receptor (IGFR) family, IGF-binding proteins (IGFBPs), IGFR ligand family (IGF-1R); platelet derived growth factor receptor (PDGFR) family, PDGFR ligand family; fibroblast growth factor receptor (FGFR) family, FGFR ligand family, vascular endothelial growth factor receptor (VEGFR) family, VEGF family; HGF receptor family: TRK receptor family; ephrin (EPH) receptor family: AXL receptor family; leukocyte tyrosine kinase (LTK) receptor family; TIE receptor family, angiopoietin 1 , 2; receptor tyrosine kinase-like orphan receptor (ROR) receptor family; discoidin domain receptor (DDR) family; RET receptor family; KLG receptor family; RYK receptor family; MuSK receptor family
• beta-Dgalactose 2-alpha-Lfucosyltraosferase (LDLR/FUT) fusion protein, HLA-A2, MLA-A11, heat shock protein 70-2 mutated (HSP70-2M), KIAA0205, MART2, melanoma ubiquitous mutated 1, 2, 3 (MUM-1, 2, 3), prostatic acid phosphatase (PAP), neo-PAP, Myosin class 1, NFYC, OGT, OS-9, pml-RARalpha fusion protein, PRDX5, PTPRK, K-ras (KRAS2), N-ras (NRAS), HRAS, RBAF600, SIRT12, SNRPD1, SYT-SSXl or -SSX2 fusion protein, Triosephosphate Isomerase, BAGE, BAGE-1, BAGE-2, 3, 4, 5, GAGE-1, 2, 3, 4, 5, 6, 7, 8, GnT-V (aberrant N
• TRP2-1NT2 carcino-embryonic antigen
• CEA carcino-embryonic antigen
• PSA mammaglobin-A
• OA1 prostate specific antigen
• PSA prostate specific membrane antigen
• TRP-2 adipophilin, interferon inducible protein absent in melanoma 2 (AIM-2).
• BING-4 CPSF, cyclin Dl, epithelial cell adhesion molecule (Ep-CAM), EpbA3, fibroblast growth factor-5 (FGF-5), glycoprotein 250 (gp250intestinal carboxyl esterase (iCE), alpha-feto protein (AFP), M-CSF, mdm-2, MUCI, p53 (TP53), PBF, PRAME, PSMA, RAGE-1, RNF43, RU2AS, SOX10, STEAP1, survivin (BIRCS), human telomerase reverse transcriptase (hTERT), telomerase, Wilms' tumor gene (WT1), SYCP1, BRDT, SPANX, XAGE, ADAM2, PAGE-5, LIP1, CTAGE-1, CSAGE, MMA1, CAGE, BORIS, HOM-TES-85, AF15ql4, HCA66I, LDHC, MORC, SGY-1, SPOl l, TPX1, NY-SAR-35, F
• GM2 sargramostim
• CTLA-4 707 alanine proline (707-AP)
• 707-AP 707 alanine proline
• ART-4 adenocarcinoma antigen recognized by T cells 4
• CAP-1 carcinoembryogenic antigen peptide-1
• CLCA2 calcium- activated chloride channel-2
• Cyp-B cyclophilin B
• HCT-2 human signet ring tumor-2
• antibodies which can be incorporated into compositions and methods disclosed herein include, but are not limited, to antibodies such as trastuzumab (anti- HER2/neu antibody); Pertuzumab (anti-HER2 mAb); cetuximab (chimeric monoclonal antibody to epidermal growth factor receptor EGFR); panitumumab (anti-EGFR antibody); nimotuzumab (anti-EGFR antibody); Zalutumumab (anti-EGFR mAb); Necitumumab (anti- EGFR mAb); MDX-210 (humanized anti-HER-2 bispecific antibody); MDX-210 (humanized anti-HER-2 bispecific antibody); MDX-447 (humanized anti-EGF receptor bispecific antibody); Rituximab (chimeric murine/human anti-CD20 mAb); Obinutuzumab (anti-CD20 mAb); Ofatumumab (anti-CD20 mAb); Tositumumab-1131 (anti-CD20 m
• Catumaxomab (bispecific mAb that targets epithelial cell adhesion molecule and CD3); Naptumomab (anti-5T4 mAb); Girentuximab (anti-Carbonic anhydrase ix); or Farletuzumab (anti-folate receptor).
• Other examples include antibodies such as PanorexTM (17-1A) (murine monoclonal antibody); Panorex (@(17-1A)) (chimeric murine monoclonal antibody); BEC2 (ami-idiotypic mAb, mimics the GD epitope) (with BCG); Oncolym (Lym-1 monoclonal antibody); SMART M195 Ab, humanized 13' 1 LYM-1 (Oncolym).
• Ovarex (B43.13, anti- idiotypic mouse mAb); 3622W94 mAb that binds to EGP40 (17-1 A) pancarcinoma antigen on adenocarcinomas; Zenapax (SMART Anti-Tac (IL-2 receptor); SMART M195 Ab, humanized Ab, humanized); NovoMAb-G2 (pancarcinoma specific Ab); TNT (chimeric mAb to histone antigens); TNT (chimeric mAb to histone antigens); Gliomab-H
• an agent that finds use in embodiments herein specifically binds a component of a regulatory T cell, myeloid suppressor cell, or dendritic cell.
• the targeting moiety specifically binds one of the following molecules: CD4; CD25 (IL-2a receptor; IL-2aR); cytotoxic T-lymphocyte antigen-4 (CTLA-4; CD152); Interleukin-10 (IL-10); Transforming growth factor-beta receptor (TGF- R); Transforming growth factor-beta (TGF- ⁇ ); Programmed Death-1 (PD-1); Programmed death-1 ligand (PD- Ll or PD-L2); Receptor activator of nuclear factor- ⁇ (RANK); Receptor activator of nuclear factor- ⁇ (RANK) ligand (RANKL); LAG-3; glucocorticoid-induced tumor necrosis factor receptor family -related gene (GITR; TNFRSF18); or Interleukin-4 receptor (IL-4R).
• the agent is an IL-2a receptor; IL-2a
• an agent that finds use in embodiments herein binds a specific cytokine, cytokine receptor, co-stimulatory molecule, co-inhibitory molecule, or
• the targeting moiety specifically binds one of the following molecules: tumor necrosis factor (TNF) superfamily; tumor necrosis factor-a (TNF-a); tumor necrosis factor receptor (TNFR) superfamily; Interleukin-12 (IL-12); IL-12 receptor; 4-1BB (CD137); 4-1BB ligand (4- 1BBL; CD137L); OX40 (CD134; TNR4); OX40 ligand (OX40L; CD40; CD40 ligand (CD40L); CTLA-4; Programmed death-1 (PD-1); PD-1 ligand I (PD-L1 : B7-H1); or PD-1 ligand 2 (PD-L2; B7-DC); B7 family; B7-1 (CD80); B7-2 (CD86); B7-H3; B7-H4;
• TNF tumor necrosis factor
• TNFR tumor necrosis factor receptor
• IL-12 Interleukin-12
• 4-1BB CD137
• 4-1BB ligand (4- 1
• GITR/AITR GITRL/AITRL; BTLA; CD70; CD27; LIGHT; HVEM: Toll-like receptor (TLR) (TLR 1, 2, 3, 4, 5, 6, 7, 8, 9, 10).
• the agent is an agonist that increases the function of the targeted molecule. In other embodiments, the agent is an antagonist that inhibits the function of the targeted molecule.
• agents e.g., immunotherapeutics targeting 4-1BB, LAG-3 and/or one or more receptors/markers of Table 2 (e.g. PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nrnl , Nrpl , KLRG1 , GM156, GPNMB, GPR65, TMEM205, and TMEM126A, CRTAM, Sema7a, etc.) are co-administered (e.g., serially or sequentially) with one or more adjuvants.
• PD-1 e.g., PD-1, TIM-3, OX-40ICOS, TIGIT, CD244, TNFRSF18, Nrnl , Nrpl , KLRG1 , GM156, GPNMB, GPR65, TMEM205, and TMEM126A, CRTAM, Sema7a, etc.
• Suitable adjuvants include, but are not limited to, one or more of: oil emulsions (e.g., Freund's adjuvant); saponin formulations; virosomes and viral-like particles; bacterial and microbial derivatives; immunostimulatory oligonucleotides; ADP-ribosylating toxins and detoxified derivatives; alum; BCG; mineral-containing compositions (e.g., mineral salts, such as aluminium salts and calcium salts, hydroxides, phosphates, sulfates, etc.); bioadhesives and/or mucoadhesives; microparticles; liposomes; polyoxyethylene ether and poly oxy ethylene ester formulations; polyphosphazene; muramyl peptides; imidazoquinolone compounds; and surface active substances (e.g.
• oil emulsions e.g., Freund's adjuvant
• saponin formulations e.g.,
• Adjuvants may also include immunomodulators such as cytokines, interleukins (e.g., IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc.), interferons (e.g., interferon-. gamma.), macrophage colony stimulating factor, and tumor necrosis factor.
• immunomodulators such as cytokines, interleukins (e.g., IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12, etc.), interferons (e.g., interferon-. gamma.), macrophage colony stimulating factor, and tumor necrosis factor.
• co-stimulatory molecules including other polypeptides of the B7 family, may be administered.
• Proteinaceous adjuvants may be provided as the full-length polypeptide or an active fragment thereof, or in the form of DNA, such as plasmid DNA.
• compositions described herein may be delivered by any suitable route of administration (e.g., oral delivery, parenteral delivery, mucous membrane delivery, pulmonary delivery, intravenous delivery, etc.). Appropriate formulations for such delivery routes are understood in the field.
• Non-limiting examples of cancers that may be treated with the compositions and methods described herein include, but are not limited to: melanoma (e.g., metastatic malignant melanoma), renal cancer (e.g. clear cell carcinoma), prostate cancer (e.g. hormone refractory prostate adenocarcinoma), pancreatic cancer (e.g., adenocarcinoma), breast cancer, colon cancer, lung cancer (e.g. non-small cell lung cancer), esophageal cancer, squamous cell carcinoma of the head and neck, liver cancer, ovarian cancer, cervical cancer, thyroid cancer, glioblastoma, glioma, leukemia, lymphoma, and other neoplastic malignancies.
• the cancer is a solid tumor cancer.
• Some embodiments described herein are particularly useful for the treatment of tumors that do not otherwise respond to immunotherapeutic approaches.
• provided herein is the treatment of cancers that are non-responsive (or have a reduced response) to T cells or antigen presenting cells (e.g., dendritic cells (e.g.,
• compositions and methods described herein find use in the treatment of cancers that are non-responsive to treatments, despite T cell infiltration.
• compositions and methods described herein find use in the treatment of cancers in which T cells are not appropriately primed against tumor-associated antigens.
• compositions and methods described herein find use in the treatment of cancers comprising tumors or cells that are defective in recruitment of dendritic cells (e.g., CD 103 + DCs, etc.).
• dendritic cells e.g., CD 103 + DCs, etc.
• compositions and methods described herein find use in the treatment of cancers comprising tumors or cells that are defective in production of the chemokine CCL4.
• compositions and methods herein find use with those described in, for example WO 2016/141312; incorporated by reference in its entirety.
• methods are provided for testing sample (e.g., cell, tissue, population of cells, tumor, blood, urine, saliva, etc.) from a subject for one or more biomarkers (e.g., biomarkers of dysfunctional tumor antigen-specific CD8 T cells).
• biomarkers may comprise nucleic acids, small molecules, proteins, peptides, etc., and may be detected using any suitable assay of technique.
• DNA-, RNA-, small molecule, and/or protein-based diagnostic methods that either directly or indirectly detect the biomarkers of the evasion of immune response or immunotherapy by cancer cells or tumors.
• the present invention also provides compositions, reagents, and kits for such diagnostic purposes.
• biomarkers are detected at the nucleic acid (e.g., RNA) level.
• the presence or amount of biomarker nucleic acid (e.g.,mRNA) in a sample is determined (e.g., to determine the presence or level of biomarker expression).
• Biomarker nucleic acid e.g., RNA, amplified cDNA, etc.
• Biomarker nucleic acid may be detected/quantified using a variety of nucleic acid techniques known to those of ordinary skill in the art, including but not limited to nucleic acid sequencing, nucleic acid hybridization, nucleic acid amplification (e.g., by PCR, RT-PCR, qPCR, etc.), micorarray, Southern and Northern blotting, sequencing, etc.
• Non-amplified or amplified nucleic acids can be detected by any conventional means.
• nucleic acids are detected by hybridization with a detectably labeled probe and measurement of the resulting hybrids.
• Nucleic acid detection reagents may be labeled (e.g., fluorescently) or unlabeled, and may by free in solution or immobilized (e.g., on a bead, well, surface, chip, etc.).
• biomarkers are detected at the protein level. For example, the presence or amount of biomarker protein in a sample is determined (e.g., to determine the presence or level of biomarker expression or localization).
• reagents are provided for the detection and/or quantification of biomarker proteins. Suitable reagents include primary antibodies (e.g., that bind to the biomarkers), secondary antibodies (e.g., that bind primary antibodies), antibody fragments, aptamers, etc. Protein detection reagents may be labeled (e.g., fluorescently) or unlabeled, and may by free in solution or immobilized (e.g., on a bead, well, surface, chip, etc.).
• biomarker capture reagents are provided to localize, concentrate, aggregate, etc. a biomarker.
• a biomarker capture reagent that interacts with the biomarker is linked to a solid support (e.g., a bead, surface, resin, column, and the like) that allows manipulation by the user on a macroscopic scale.
• the solid support allows the use of a mechanical means to isolate and purify the biomarker from a heterogeneous solution.
• separation is achieved by removing the bead from the heterogeneous solution, e.g., by physical movement.
• the bead is magnetic or paramagnetic
• a magnetic field is used to achieve physical separation of the capture reagent (and thus the target) from the
• Magnetic beads used to isolate targets are described in the art, e.g., as described in European Patent Application No. 87309308, incorporated herein in its entirety for all purposes.
• compositions for use in the diagnostic methods or testing steps described herein include, but are not limited to, probes, amplification oligonucleotides, and antibodies.
• Any of the detection and/or diagnostic reagents used in embodiments described herein may be provided alone or in combination with other compositions in the form of a kit.
• Kits may include any and all components necessary or sufficient for assays including, but not limited to, the detection reagents, buffers, control reagents (e.g., tissue samples, positive and negative control sample, etc.), solid supports, labels, written and/or pictorial instructions and product information, inhibitors, labeling and/or detection reagents, package environmental controls (e.g., ice, desiccants, etc.), and the like.
• the kits provide a sub-set of the required components, wherein it is expected that the user will supply the remaining components.
• the kits comprise two or more separate containers wherein each container houses a subset of the components to be delivered.
• a computer-based analysis program is used to translate the raw data generated by the detection assay (e.g. , the presence, absence, or amount of expression a biomarker) into data of predictive value for a clinician.
• computer analysis combines various data into a single score or value that is predictive and/or diagnostic.
• the clinician can access the predictive data using any suitable means.
• the present invention provides the further benefit that the clinician, who is not likely to be trained in genetics or molecular biology, need not understand the raw data.
• the data is presented directly to the clinician in its most useful form. The clinician is then able to immediately utilize the information in order to optimize the care of the subject.
• a sample e.g. , a biopsy, cell, or blood sample
• a profiling service e.g. , clinical lab at a medical facility, third-party testing service, genomic profiling business, etc.
• the subject may visit a medical center to have the sample obtained and sent to the profiling center, or subjects may collect the sample themselves and directly send it to a profiling center.
• a report is generated (e.g., by a clinician, by a testing center, by a computer or other automated analysis system, etc.).
• a report may contain test results, diagnoses, and/or treatment recommendations.
• mice Female C57BL/6 mice ranging from 6 to 8 weeks were purchased from Taconic Farms. CD45.1 and Rag2 ⁇ mice on the C57BL/6 background were obtained from Taconic Farms and bred at the University of Chicago. 2C/Rag2 ⁇ and P14/Rag2 ⁇ mice have been previously described (Brown et al, 2006; incorporated by reference in its entirety). pLCK- CreERT2 x ROSA-YFP mice were generated and have been described (Evaristo et al, 2016; incorporated by reference in its entirety).
• B16.SIY.dsRed (Kline et al, 2012; incorporated by reference in its entirety), C1498.SIY.GFP (Zhang et al, 2009; incorporated by reference in its entirety), and MC57.SIY.GFP (Spiotto et al, 2002; incorporated by reference in its entirety) tumor cells were engineered to express either dsRed or GFP in frame with the H2-K b - restricted model antigen SIYRYYGL.
• the 1969.SIY.GFP cell line was engineered by retroviral transduction of the 1969 cell line (Diamond et al, 2011; incorporated by reference in its entirety) using the pLEGFP plasmid expressing cDNA for SIYRYYGL (Spiotto et al, 2002; incorporated by reference in its entirety).
• a 12.6kb mouse genomic DNA fragment including the egr2 gene was excised with SacII and cloned into a pEasy-Flox vector adjacent to the thymidine kinase (TK) selection marker.
• TK thymidine kinase
• a cassette containing IRES2-eGFP and a LoxP-flanked neomycin selection marker was inserted into an Nhel site between the translation stop codon (TGA) and the polyadenylation signal of the egr2 gene.
• ES cell clones from 129 mice were electroporated and selected for Neomycin resistance.
• ES cell clones were verified for homologous insertion in the endogenous locus by PCR and southern blot with 5' and 3' probes. Mice were backcrossed to C57BL/6 for over 8 generations. TIL isolation
• Tumors were harvested from mice at the indicated time points. Tumors were dissociated through a 50 ⁇ filter and washed with PBS. TILs were further enriched by layering Ficoll-Hypaque beneath the cell suspension followed by centrifugation without breaks for 30 min at 400 x g. The buffy-layer was isolated and washed twice with PBS before staining. For isolating specific cell populations by FACS, tumors were pooled when indicated and the cell layer was re-purified by Ficoll-Hypaque centrifugation twice. For day 28 tumors, after Ficoll-Hypaque separation, T cells were further purified by negative bead selection according to manufacturer's instructions (MAGNISORT, eBiosciences). Cells were then washed with PBS, stained at 4°C for 15 minutes before resuspending in complete
• DMEM fetal calf serum
• cDMEM 10% FBS, lOOU/mL Penicillin-Streptomycin, 1% MEM Non-Essential Amino Acids, 50 ⁇ ⁇ - ⁇ , 0.01M MOPS
• RLT lysis buffer QIAGEN
• cDMEM 10% FBS, lOOU/mL Penicillin-Streptomycin, 1% MEM Non-Essential Amino Acids, 50 ⁇ ⁇ - ⁇ , 0.01M MOPS
• CD3 (17A2, AX700), 2B4 (2B4, FITC), CD127 (A7R34, PE), OX-40 (OX-86, PE), 4-lBB (17B5, Biotin, APC), CD160 (7H1, PE-Cy7), LAG- 3 (C9B7W, PerCPeFluor710), PD-1 (RMP1 -30, PE-Cy7), NRP1 (3E12, BV421), GITR (DTA-1 , FITC), ICOS (7E.17G9, BV421), KLRG-1 (2F1, eF450, BV605), TIGIT (1G9, APC), TIM-3 (RMT3-23, PE), CD4 (RM4-5, BV
• Fixable Viability Dye 506 was used for live/dead discrimination. Staining of SIY-specific T cells was performed utilizing the SIYRYYGL-Pentamer (PE) (Proimmune); a SIINFEKL-pentamer (PE) was used as a non-specific control. All flow cytometric analysis was conducted on an LSRFortessa (BD) and analyzed using Flow Jo software (Tree Star).
• Gzmb 39 gctgctcactgtgaaggaagt tggggaatgeattttaccat 58 2
• In vivo proliferation was measured by a BrdU pulse 24 hours prior to flow cytometric analysis.
• Each mouse received 0.8 mg BrdU injected i.p. (intraperitoneal) on day 12 after tumor inoculation.
• TILs were isolated and surface stain was performed as described above. Following surface staining, cells were fixed and permeabilized using the Foxp3 staining kit (BD), according to manufacturer's protocol, and incubated with 100 ⁇ PBS/DNase solution (300 ⁇ g/ml) for 30 minutes at 37 °C. Cells were washed and incubated for 30 minutes at room temperature with anti-BrdU (FITC, Bu20a) and then washed with and resuspended in PBS.
• BD Foxp3 staining kit
• Tissue culture-treated 96-well round bottom plates were coated with anti-CD3s (1 ⁇ ; 2C1 1) in DPBS overnight at 4°C or for 2 hours at 37°C. Cells were sorted into cold cDMEM media and put on ice as soon as the sort was finished. Cells were then pelleted, resuspended in 50 ⁇ cDMEM and incubated with soluble anti-CD28 (2 ⁇ ; PV-1) for 10- 12 hours for a final volume of 100 ⁇ .
• RNAlater Stabilization Solution QIAGEN
• mice were injected with 2x10 6 B16.SIY.dsRed tumor cells. 14 days later, tumors were harvested and specific CD8 + TIL subpopulations were sorted into RLT buffer
• cDNA was synthesized from sorted cell populations and CDR3 regions were amplified by PCR with 21 different ⁇ -5' primers paired with a FAM- ⁇ .1 primer (Table 1). Three ⁇ PCR reactions did not reach significant amplification for analysis and were removed from the analysis.
• ⁇ - ⁇ PCR products were purified using the QIAquick PCR purification kit (QIAGEN) and sequenced at the University of Chicago Genomics Core Facility.
• C ⁇ -V ⁇ PCR products were analyzed by capillary electrophoresis at the University of Chicago Genomics core and CDR3 peaks were aligned using the Liz500 ladder.
• Spectratype graphs were displayed using the GeneiousR9 software (Kearse et al, 2012). To generate the frequency profile for each ⁇ spectratype, the area under each peak was measured using peak studio (fodorlab.uncc.edu/software/peakstudio). The Hamming Distance (Currier and Robinson, 2001; incorporated by reference in its entirety) was calculated between each ⁇ spectratype from each CD8 + spleen and TIL population within a given mouse. To determine significance between the HD from each comparison the HDs for each ⁇ from mice were averaged and a One-Way ANOVA with Dunn's correction for multiple comparisons was performed.
• TCR Transgenic (Tg) T cells were washed with PBS, resuspended at a concentration of 10x10 /ml and 1x10 TCR Tg cells were adoptively transferred into CD45.1 tumor bearing mice by tail vein transfer in a volume of 0.1 mL. After indicated times, 2C T cells and corresponding host CD8 + T cells were sorted and stimulated as described above.
• mice were injected s.c. (subcutaneous) with 2 x 10 6 B16.SIY cells on both left and right flanks.
• all 20 tumors were pooled and dissociated using the Tumor Dissociation Kit (Miltenyi Biotec) following the manufacturer's protocol.
• Tumor cell suspensions were washed 3-5 times with PBS and TILs were enriched for by Ficoll-Hypaque gradient centrifugation. TILs were stained, sorted and put directly on ice. TILs were titrated and added directly to a 96-well plate containing 50,000 P815 mastocytoma cells and 1 ⁇ g/mL anti-CD3.
• OT-I cells were isolated from OT-I/Rag2 ⁇ mice and stimulated with plate-bound anti-CD3 (0.25 ⁇ g/mL), anti-CD28 (2 ⁇ g/mL) and 100 U/mL IL-2 for 2-3 days.
• P815 cells were cultured alone or cultured with naive CD8 + T cells isolated from lymph nodes. After 12 hours of incubation, cells were stained for Thyl, CD45, CD8a, Fixable Viability Dye 450
• log2-fold change values were extracted using the GE02R online software from the hypofunctional CD8 + TIL data set, GSE79858 ((GSM2107353, GSM2107353 and GSM2107355) versus (GSM2107350, GSM2107351, GSM210732)) and the CD8 + T cell exhausted data set, GSE41870 ((GSM 1026819, GSM1026820, GSM1026821) versus (GSM1026786, GSM1026787, GSM1026788, GSM1026789)). Upregulated genes showing a 2-fold difference were used for analysis. Multiple genes names with from the GE02R extracted data were identified and matched to gene names from the Illumina data set.
• RRHO rank-rank hypergeometric overlap
• mice were treated i.p. with 100 ⁇ g/mouse of anti-4-lBB (Bio-X-Cell; LOB12.3) antibody and/or 100 ⁇ g/mouse anti-LAG-3 (Bio-X-Cell; C9B7W).
• mice were treated on day 7, 10, 13 and 16 after tumor inoculation.
• mice were treated on day 7, 10 and 13 and cells were sorted on day 14.
• 25 ⁇ g of FTY720 was given by gavage one day prior to first antibody treatment (day 6) and continued every day until endpoint on day 14.
• the expression partem of LAG-3 and 4- IBB was examined using the well-characterized B16.SIY model of melanoma.
• the 4-lBB + LAG-3 + population comprised 15.8% of all CD8 + TILs.
• the frequency of this population significantly increased to 44% by day 21.
• the frequency of 4-lBB AG-3 + (4 + ) population also increased 1.9- fold from day 7 to day 14 to comprise 25% of the CD8 + TIL compartment.
• the frequency of the 4- IBB LAG-3 (4 ) population decreased by 2.7-fold by day 21.
• CD8 + TILs were stained for Ki67 at day 14 after tumor inoculation and analyzed by flow cytometry. 81% of 4-1BB LAG-3 + cells and 85% of 4-lBB + LAG-3 + cells were Ki67 + compared to only 32% of the 4- IBB LAG-3 TILs ( Figure IE). Mice were pulsed with BrdU on day 12, and 24 hours later the CD8 + TIL subpopulations were analyzed for BrdU incorporation.
• SIY tumor model or if it is a more general feature of CD8 + T cells within tumors, T cells from three additional progressively growing tumor models, C1498. SIY, MC38. SIY, EL4.SIY and B16F 10 parental were analyzed. TILs were analyzed for expression of 4-1BB and LAG- 3 at day 14. A partem of expression was found that is similar to that seen in CD8 + TILs isolated from B16. SIY tumors ( Figure 1G and I). The results from the B 16F10 parental tumor confirm that presence of SIY is not required to see co-expression of 4- IBB and LAG- 3.
• CD8 4-1BB LAG-3 TILs express Egr2 and multiple Egr2 gene targets
• Egr2 GFP Egr2 GFP
• CD8 + TILs expressing high and low levels of EGFP were sorted and screened for Egr2 and several Egr2 targets by qRT-PCR.
• the Egr2-GFP hl population expressed greater levels of Egr2 and many Egr2-target genes previously defined using in vitro anergy models. These include Tnfrsf9, Lag3, Ngn, Sema7a, Crtam, Cell and Nrnl ( Figure 2B). Expression of 4-1BB and LAG-3 in the Egr2-GFP hi CD8 + TILs was confirmed by flow cytometry.
• Egr2-GFP hl cells expressed LAG-3 and/or 4- 1BB.
• the Egr2GFP l0 cells also showed expression of 4- IBB and LAG-3 on a subpopulation at day 14 ( Figure 2C). This result indicates either that CD8 + TILs expressing Egr2 encompass only a subset of the TILs expressing LAG-3 and/or 4-1BB, or that Egr2 is transiently expressed and is subsequently downregulated after the induction of LAG-3 and 4-1BB.
• Egr2 target genes from in vitro anergic CD4 + T cell clones (Zheng et al., 2013; incorporated by reference in its entirety)
• the Egr2-driven transcriptional program was examined in sorted 4- IBB LAG-3 and 4-lBB + LAG-3 + cells by qRT-PCR.
• 43 Egr2 target genes examined 10 showed detectably increased expression in 4-lBB + LAG-3 + population, while expression of a similar subset of genes was increased in the 4-1BB LAG-3 + population ( Figure 2D).
• Egr2 flox/flox X pLCK-CreERT2 x ROSA- YFP mice were utilized, in which oral tamoxifen administration results in a fraction of the CD8 + T cells deleting Egr2 and expressing YFP ( Figure 2E). This allowed comparison of both Egr2- sufficient (YFP ) and Egr2-deficient (YFP + ) CD8 + within the same tumor.
• both YFP + and YFP CD8 + TILs were sorted and Egr2 transcripts were measured directly ex vivo and upon ex vivo stimulation.
• the YFP + CD8 + TILs expressed substantially less Egr2 transcripts compared to the YFP counterparts ( Figure 2E).
• CD8 + TILs were analyzed at day 7 and 14 after tumor inoculation and compared the YFP + and YFP populations to mice not treated with tamoxifen.
• Egr3 has been shown to have overlapping function with Egr2 (Safford et al, 2005; incorporated by reference in its entirety) and HIFla can contribute to 4- IBB expression (Palazon et al., 2012).
• HIFla 4- IBB expression
• Egr3 and HIFla were indeed expressed in both the Egr2GFP hl and Egr2GFP l0 populations. It was confirmed differential expression of Egr2 and CCL1 to between the Egr2GFP hl and
• Egr2GFP l0 populations to assure sort purity (Figure 2G). Together, these data indicate that Egr2 contributes to upregulation of 4-lBB and LAG-3 expression at early time points, but that other transcriptional regulators compensate and drive expression of LAG-3 and 4-lBB as the T cell-tumor interaction progresses.
• CD8 + 4-lBB + LAG-3 + TILs are oligoclonal and enriched for tumor antigen specificity
• T cells in the tumor microenvironment are specific for tumor-associated antigens, as memory T cells specific for irrelevant antigens are often found among TIL, and non-specific T cell trafficking has been documented in vivo (Harlin et al, 2006; incorporated by reference in its entirety).
• LAG-3, 4- IBB and Egr2 are upregulated after TCR stimulation and experiments indicate that this population expands within the tumor microenvironment in situ.
• Three complementary techniques were employed. First, the CD8 + TILs were isolated based on LAG-3 and 4- IBB expression by cell sorting and performed TCR spectratype analysis.
• the 4-lBB + LAG-3 + TILs had a non-Gaussian distribution and shared one or two dominant peaks (Figure 3A).
• Analysis of several ⁇ displaying one dominant peak revealed that ⁇ 7 contained a single CDR3 sequence shared between the 4-lBB LAG-3 + and 4-lBB + LAG-3 + populations, indicating a clonal relationship ( Figure 3A).
• the Hamming Distance (HD) was calculated for each ⁇ between the CD8 + TIL subpopulations and the splenic CD8 + population within three separate mice ( Figure 8).
• the Hamming Distance computes the changes in frequency and reports a value of comparison between 0 and 1, with 0 indicating a completely identical frequency profile and 1 signifying a completely discordant profile.
• the HD of the splenic CD8 + populations between different mice was calculated ( Figure 3B, black bar). Since the splenic CD8 + spectratypes are largely Gaussian this value represents the HD between two similar distributions.
• SIYRYYGL SIYRYYGL/K b pentamer + (H-2K b /SIY) cells were found in expanded numbers within B16.SIY and MC38.SIY tumors at day 14 after tumor inoculation ( Figure 3C). Nearly 47% of the H-2K b /SIY + cells expressed both 4-1BB and LAG-3, in contrast to 32% of the H-2K b /SIY population ( Figure 3C and E). This enrichment of antigen-specific CD8 + TILs in the 4-lBB + LAG-3 + populations indicates that these markers identify tumor antigen-specific TILs.
• H-2K b /SIY cells also contained significant numbers of 4-lBB + LAG-3 + cells, which is consistent with the notion that tumor antigens other than SIY are also recognized by subsets of CD8 + TILs in vivo (Figure 3C).
• H-2K b /SIY + cells in the spleen or TdLN did not co-express 4- IBB and LAG-3, indicating that this phenotype is acquired within the tumor microenvironment.
• H-2K b /SIY-specific CD8 + TILs cells were evaluated from MC57.SIY and 1969.SIY tumors. At day 14 after tumor inoculation, approximately 5% of the H-2K b /SIY-specific CD8 + TILs were found in the 4- lBB + LAG-3 + fraction. As with the B16.SIY tumors, no H-2K b /SIY-specific CD8 T cells co- expressed 4- IBB and LAG-3 in the TdLN or spleen (not shown) (Figure 3D).
• 2C and P14 transgenic (Tg) T cells isolated from 2C/Rag2 ⁇ ⁇ and P14/Rag2 ⁇ ⁇ mice, were transferred into tumor-bearing hosts.
• the 2C TCR is specific for the SIY model antigen expressed by B16.SIY tumor cells, while P14 is an irrelevant TCR specific for the LCMV-derived gp33-4i epitope; both TCRs are H-2K b - restricted.
• 2C and P14 Tg CD8 + T cells were transferred via tail vein 7 days after tumor inoculation. Seven days after transfer, tumors and TdLNs were extracted and the phenotypic profile of the transferred populations was analyzed. This system allowed for the analysis of two T cell populations with defined antigen specificities within the same tumor
• CD8 + TILs expressing LAG-3 and 4-1 BB exhibit defective IL-2 production yet produce IFN-y and Treg-recruiting chemokines
• 2C T cells were adoptively transferred intravenously into tumor-bearing hosts and recovered the 2C T cells 7 days later from the tumor and TdLN.
• 2C T cells isolated from tumors exhibited a reduced capacity to produce 11-2 transcripts, at a level equivalent to 4-lBB + LAG-3 + TILs, compared to 2C CD44 + T cells isolated from the TdLN ( Figure 4D).
• expression of PD-1 has been suggested to identify intrinsically dysfunctional or "exhausted" CD8 + T cells.
• CD8 + TILs that lacked expression of LAG-3 and 4- IBB were isolated and tested for the ability of the PD-1 + fraction to produce IL-2. Approximately -10% of CD8 + TILs were 4-1BB LAG-3 PD-1 + on day 14 and 21
• IL-2, IFN- ⁇ and TNF-a were tested after TCR stimulation.
• loss of the ability of CD8 + TILs to produce cytokines is suggested to be a temporal process reported initiated following entry into the tumor microenvironment (Waugh et al, 2016; Schietinger et al, 2016;
• the 4-lBB + LAG-3 + population produced significantly greater amounts of IFN- ⁇ protein (Figure 5C).
• the 4-1BB LAG-3 TIL are not completely devoid of functionality, as they continue to produce IFN- ⁇ despite defective production of IL-2. This phenotype is consistent with in vitro T cell anergy models (Jenkins et al, 1987; incorporated by reference in its entirety).
• 4-lBB + LAG-3 + population still retains cytotoxic capacity
• redirected lysis was performed by co-culturing anti-CD3 bound P815 mastocytoma target cells with the different CD8 + TIL subpopulations directly after sorting.
• 4-lBB + LAG-3 + CD8 + TILs isolated from day 14 tumors were able to lyse target cells at a comparable efficacy to in vitro primed OT-I cells.
• 4-lBB + LAG-3 + TILs isolated from day 21 tumors were still able to lyse target cells, albeit to a lesser extent compared to primed OT-I cells (Figure 5D).
• CD8 + T cells in the tumor can be the source of the chemokine CCL22 that recruits FoxP3 + regulatory T cells (Tregs) to the tumor microenvironment (Spranger et al, 2013; incorporated by reference in its entirety).
• the chemokine Cell was an Egr2 target in anergic T cells (Zheng et al, 2013; incorporated by reference in its entirety), and it has been suggested that CCL1 also contribute to Treg recruitment in the tumor context in vivo (Hoelzinger et al, 2010; incorporated by reference in its entirety).
• CD8 + T cells in the tumor produce these chemokines or if they are only produced by subpopulations of T cells had not been determined.
• CD8 + TIL phenotypic subpopulations were analyzed for Cell and Ccl22 mRNA expression directly ex vivo by qRT- PCR.
• the 4-lBB + LAG-3 + TIL population produced substantially greater Cell and Ccl22 compared to their negative counterparts or to splenic CD8 + CD44 + T cells ( Figure 4K).
• expression of a distinct chemokine Ccl5 was found not to be differentially expressed.
• RRHO rank-rank hypergeometric overlap
• RPL6 ribosomal protein L6 7.14210 HAAO 3-hydroxyanthranilate 3,4- 7057 dioxygenase 1.55055
• IGF2BP3 insulin like growth factor 6.18685 KLHL22 kelch like family member
• HIST1H3C histone cluster 1 H3c 5.39746 PIGYL phosphatidylinositol
• homolog 1 (Drosophila) 6965 nuclear division 5 1.58396 homolog B 0816
• APLF aprataxin and PNKP like 4.95186 NEIL3 nei like DNA glycosylase
• DOK4 docking protein 4 4.52042 OLFR366 olfactory receptor
• nucleation factor 3431 (Drosophila) 1.60880
• IL4I1 interleukin 4 induced 1 3.80219 BLOC1S3 biogenesis of lysosomal
• CKAP2L cytoskeleton associated 3.79701 GTF3C4 general transcription factor
• ADAM3 a disintegrin and 3.78135 CYP2A12 cytochrome P450, family
• RNA binding protein 2 6592 2 (interferon gamma 1.65105 transducer 1) 0175
• glycoprotein beta- 1 ,4-N- 6625 domain family member 1A 1.65535 acetylglucosaminyltransf 1829 erase
• V0 subunit al 9145 member 1 1.65763
• HIST1H4B histone cluster 1 H4b 3.49185 NHP2L1 NHP2 non-histone
• LAD1 ladinin 1 3.49085 STOML2 stomatin like 2
• RAD51AP1 RAD51 associated 3.45943 SCOC short coiled-coil protein
• MO API modulator of apoptosis 3.39231 METTLl mefhyltransferase like 1
• SLC37A4 solute carrier family 37 3.11270 ZBTB1 zinc finger and BTB
• HPS5 HPS5 biogenesis of 2.97269 ZDHHC14 zinc finger DHHC-type
• SH3BGRL SH3 domain binding 2.93545 OLFR690 olfactory receptor
• TTYH2 tweety family member 2 2.89239 ATXN7L1 ataxin 7 like 1
• subfamily B member 8 8991 peptidase 11 1.72246
• IDI1 isopentenyl-diphosphate 2.81178 TRIP6 thyroid hormone receptor
• glycohydrolase 8208 (ankyrin G) 1.72792
• mismatch repair system 4341 metallopeptidase 2 1.73350 component 053
• HAVCR2 hepatitis A virus cellular 2.72976 ROGDI rogdi homolog
• TBC1D 14 TBC1 domain family 2.72246 OLFR1331 olfactory receptor
• APH1A aph-1 homolog A, 2.70597 CXCR4 C-X-C motif chemokine
• PDCD 1LG2 programmed cell death 1 2.58496 PLEKHG3 pleckstrin homology
• ORM1 orosomucoid 1 2.58496 LEF1 lymphoid enhancer
• linker protein 4954 1.76510 2 9548
• PLA2G15 phospholipase A2 group 2.48194 CAR11 carbonic anhydrase
• ZFP532 zinc finger protein 2.39313 KLHL7 kelch like family member
• RNA binding motif and 7423 intermediate chain 1 1.81343 serine/arginine rich 1 4179

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