WO2024102874A1 - Fenofibrate improves t-cell therapies - Google Patents
Fenofibrate improves t-cell therapies Download PDFInfo
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- WO2024102874A1 WO2024102874A1 PCT/US2023/079177 US2023079177W WO2024102874A1 WO 2024102874 A1 WO2024102874 A1 WO 2024102874A1 US 2023079177 W US2023079177 W US 2023079177W WO 2024102874 A1 WO2024102874 A1 WO 2024102874A1
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Definitions
- T cell therapies include transfer of ex vivo expanded TILs, which as polyclonal populations recognize multiple tumor-associated antigens. Response rates to TIL transfer are below 50% and even lower if given after treatments with anti- programmed death (PD)-1 antibodies or MAPK inhibitors. Alternatively, treatments with chimeric antigen receptor (CAR)-T cells with specificity against different melanoma associated antigens are being explored. Response rates to CAR-T cell transfer varies from 20-51% depending on concomitant treatment with interleukins (IL) or non-myeloablative lymphodepleting agents and the CAR-T cell receptors’ specificity.
- IL interleukins
- IL interleukins
- TILs and CAR-T cells achieve a delay in tumor progression and in some cases full remission by causing tumor cell death through release of lytic enzyme or interactions between Fas on T cells and Fas ligand on melanoma cells.
- Lack of efficacy of transferred T cells could reflect that melanoma cells down-regulate expression of the T cells’ target antigens, that some melanoma cells are relatively resistant to T cell-mediated lysis, that T cells fail to migrate and infiltrate the melanoma lesions, and that they are suppressed within the TME by regulatory T cells, myeloid suppressor cells and cancer associated fibroblasts.
- the method includes administering to a subject having a cancer a fenofibrate (FF), fenofibric acid (FFA), an FFA prodrug, or a derivative thereof that has PPAR- ⁇ agonist activity; and a T cell or T cell population.
- FF fenofibrate
- FFA fenofibric acid
- FFA prodrug or a derivative thereof that has PPAR- ⁇ agonist activity
- the T cell is an autologous or heterologous, naturally occurring T cell or a recombinantly or synthetically modified T cell construct, or a human T cell or natural killer (NK) T cell or T infiltrating lymphocyte (TIL) obtained from the subject or from a bone marrow transplant match for the subject, or a T cell obtained from human peripheral blood or from the tumor microenvironment of the subject, or a T cell modified to express a heterologous antigen receptor, or a chimeric antigen receptor or a chimeric endocrine receptor, or an endogenous or heterologous human T cell or human T cell line, or a CD8+ T cell.
- NK natural killer
- TIL T infiltrating lymphocyte
- the method further includes administering to a subject having a cancer an immunotherapeutic composition targeting an antigen or ligand on a tumor cell in the subject.
- the immunotherapeutic composition is a recombinant virus or virus-like particle that expresses a cancer antigen, a DNA construct that expresses a cancer antigen, a composition comprising a cancer antigen or fragment thereof, or a monoclonal antibody or antigen-binding fragment that specifically binds a cancer antigen.
- FIG.1 shows tumor diameter over time as of the day of onset in drug treatment.
- FIG.2A shows tumor volumes in individual mice that received T cells at the indicated days after initiation of drug treatment.
- FIG.2B shows tumor volumes in fenofibrate and DMSO treated mice that did not receive T cells.
- FIG.3A – FIG.3F show the effect of FF on human melanoma growth in a PDX model.
- FIG.3A Experimental design.
- FIG.3B Patient samples.
- FIG.3C Progression of tumor fragments from Patients D, E, and I in NSG mice treated with FF or DMSO.
- FIG.3D Same data as in FIG.1C but shown as linear regression curves of tumor diameter in cm over time for samples from individual patients. Data were normalized to a diameter of 1 on day 0 of drug treatment. Nubers show average slope of the linear regression curves.
- FIG.3E Numbers of human T cells in various tissues after 1-4 passages.0 passage reflects control mice that did not receive tumor fragments. Numbers were normalized to 10 5 live lymphoid cells.
- FIG.4A – FIG.4E show the effect of FF on TILs transferred into tissue fragment- derived tumor-bearing NSG mice.
- FIG.4A Experimental design.
- FIG.4B Progression of tumors from melanoma fragments of the indicated patients.
- FIG.4C Same data shown as linear regression curves. Boxes to the right show result of statistical analyses by 2-way Anova comparing the slope of the regression curve of individual animals fromn given groups.
- FIG.4D Recovery of live lymphocytes from tumors, human CD44 + CD8 + cells from spleens or tumors. The two latter counts were normalized to 10 5 live lymphoid cells. Data for the different patients are stacked. Data were compared by 2-way Anova. Differences were calculated by 2-way Anova with Tukey correction.
- FIG.4E Differences in Ct values between TILs from individual sample of groups A and averaged samples from group B are shown in a heatmap for individual mice receiving samples from the indicated patients.
- FIG.5A – FIG.5E show the effect of FF on the ability of transferred CD8+ TILs to slow tumor progression.
- FIG.5A Experimental design.
- FIG.5B Progression of tumors from the indicated patients in the 4 different treatment groups.
- FIG.5C Results of comparing the slope of the curves of individual mice by Fisher’s LSD test.
- FIG.5D Tumor progression shown as linear regression lines for tumor volume over time.
- FIG.5E Kaplan Meier survival graphs for the different groups receiving tumor cells from the indicated patients. Data were compared by Mantel-Cox test.
- FIG.6A – FIG.6H show the effect of FF on TILs transferred into cell line-derived tumor-bearing NSG mice.
- FIG.6A Recovery of lymphoid cells, human CD44 + CD8 + T cells and IFN-g producing human CD44 + CD8 + T cells from spleens and tumors. Counts (lymphoid cells) or counts normalized to 10 5 live lymphoid cells are stacked for samples from different patients.
- FIG.6B Lymphocyte and human CD8+ T cell counts by immunohistochemistry. Counts are normalized to a total area of 2 mm 2 .
- FIG.6C- TILs and mice treated with FA or FF Sections of tumors from NSG mice receiving Patient M tumor cells: FIG.6C- TILs and mice treated with FA or FF, FIG.6D- TILs and mice treated with DMSO.
- FIG.6E Percentages of human CD8 + T cells expressing the indicated markers.
- FIG.6F Percentages of cell expressing combinations of markers determine by Boolean gating. For FIG.6A, FIG.6B, FIG.6E, and FIG.6F, differences were calculated by 2-way Anova with Tukey correction.
- FIG.6G Differences in Ct values between TILs from individual sample of groups A and averaged samples from group B are shown in a heatmap for individual mice receiving samples from the indicated patients.
- FIG.6H Differences in Ct values between tumor cells isolated tumor samples of groups C and averaged tumor samples from group D are shown in a heatmap for individual mice receiving samples from the indicated patients.
- FIG.7 shows correlations in tumor growth.
- Graph shows as heatmaps r values by Spearman correlation correlations on top with matching p-values below.
- the methods and compositions described herein involve co-treatment of a subject having cancer with a T cell or T cell population and fenofibrate (FF), fenofibric acid (FFA), an FFA prodrug, or a derivative thereof that has PPAR- ⁇ agonist activity.
- FF fenofibrate
- FFA fenofibric acid
- FFA prodrug or a derivative thereof that has PPAR- ⁇ agonist activity.
- the described co-treatment promotes reduced tumor volume as compared to T cell therapy or fenofibrate alone.
- the methods and compositions provided herein offer additional therapeutic interventions in methods and compositions involving the use of FF, FFA, an FFA prodrug, or a derivative thereof that has PPAR- ⁇ agonist activity in combination with T cells. Further methods involve administering a tumor-specific vaccine composition with the FF, FFA prodrug, or a derivative thereof in combination with T cells. Certain components and definitions used in the description of these methods and compositions are defined below. “Patient” or “subject” as used herein means a mammalian animal, including a human, a veterinary or farm animal, a domestic animal or pet, and animals normally used for clinical research. More specifically, the subject of these methods and compositions is a human.
- the term “T cell(s)” or “T cell population” mean any human or mammalian T cell(s).
- the T cell or populated is activated.
- the T cell is an autologous or heterologous, naturally occurring T cell.
- the T cell is a recombinantly or synthetically modified T cell construct.
- the T cell is a primary T cell, a CD8 (cytotoxic) T cell, a CD8 (cytotoxic) T cell, a T infiltrating lymphocyte (TIL), an NK T cell, or another T cell.
- the T cell is obtained from the peripheral blood, TME or other fluid of the same mammalian subject into whom the T cell is to be administered.
- the T cell is a primary T cell, a CD8 (cytotoxic) T cell, an NK T cell, or other T cell obtained from a bone marrow transplant match for the subject.
- Other suitable T cells include T cells obtained from resected tumors, a polyclonal or monoclonal tumor- reactive T cell.
- the T cells are obtained by apheresis.
- the T cell is modified recombinantly or synthetically to express a heterologous antigen receptor.
- the T cell is expresses a chimeric antigen receptor (CAR) or a chimeric endocrine receptor (CER).
- CAR chimeric antigen receptor
- CER chimeric endocrine receptor
- CARs or CERs are described in e.g., Sadelain, M et al, “The basic principles of chimeric antigen receptor (CAR) design” 2013 April, Cancer Discov.3(4): 388–398; International Patent Application Publications WO2013/044255 and WO2016/054153, US patent application publication No. US 2013/0287748, and other publications directed to the use of such chimeric constructs. These publications are incorporated by reference to provide information concerning various components useful in the design of some of the constructs described herein.
- Such CAR or CER T cells are genetically modified lymphocytes expressing a ligand that allows them to recognize an antigen of choice.
- the modified T cells Upon antigen recognition, these modified T cells are activated via signaling domains converting these T cells into potent cell killers.
- An advantage over endogenous T cells is that they are not MHC restricted, which allows these T cells to overcome an immune surveillance evasion tactic used in many tumor cells by reducing MHC expression.
- the T cell is an endogenous or heterologous human T cell or human T cell line.
- cancer refers to or describes the physiological condition in mammals that is typically characterized by unregulated cell growth. More specifically, as used herein, the term “cancer” means any cancer characterized by the presence of a solid tumor.
- Suitable cancers for treatment by the methods described herein include, without limitation, melanoma, breast cancer, brain cancer, colon/rectal cancer, lung cancer, ovarian cancer, adrenal cancer, anal cancer, bile duct cancer, bladder cancer, bone cancer, endometrial cancer, esophagus cancer, eye cancer, kidney cancer, laryngeal cancer, liver cancer, head and neck cancer, nasopharyngeal cancer, osteosarcoma, oral cancer, ovarian cancer, pancreatic cancer, prostate cancer, rhabdomyosarcoma, salivary gland cancer, stomach cancer, testicular cancer, thyroid cancer, vaginal cancer, lung cancer, and neuroendocrine cancer.
- the tumor is melanoma.
- tumor refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues.
- the tumor targeted by the methods is characterized by hypoxia, significant infiltration with T lymphocytes, and/or low glucose in the tumor microenvironment.
- the compound or reagent useful in the methods and compositions described herein is fenofibrate (FF), fenofibric acid (FFA), an FFA prodrug, or a derivative thereof that has PPAR- ⁇ agonist activity.
- Fenofibrate a pro-drug
- FF pharmacologically inactive and undergoes rapid hydrolysis at the ester bond to form the active metabolite, fenofibric acid.
- the FF, FFA, FFA prodrug, and/or derivatives have a combination of these characteristics.
- FF, FFA, FFA prodrug, and derivatives that mimic FF, promote the use of fatty acid catabolism rather than glucose for energy. FF also promotes biomass production by the T cells.
- FF fluorescence-activated Fenor
- FFA FFA prodrug
- Various formulations of FF include, without limitation, nonmicronized, micronized, nanoparticle, and lipid melt formulations. See, Ling H, Luoma JT, Hilleman D. A Review of Currently Available Fenofibrate and Fenofibric Acid Formulations. Cardiol Res.2013 Apr;4(2):47-55. doi: 10.4021/cr270w. Epub 2013 May 9, which is incorporated herein by reference.
- the compound useful in these methods is the FFA prodrug or derivative, (S)-2-((S)-2-(2-(4-(4-chlorobenzoyl)phenoxy)-2-methylpropanamido) propanamido) pentanedioic acid (also known as FFP).
- FFA prodrug or derivative also known as FFP
- S FFA prodrug or derivative
- S 2-((S)-2-(2-(4-(4-chlorobenzoyl)phenoxy)-2-methylpropanamido) propanamido) pentanedioic acid
- FFP pentanedioic acid
- a compound useful in the methods described herein is GW7647 (2-(4-(2-(1-Cyclohexanebutyl)-3-cyclohexylureido)-ethyl)-phenyl-thio)-2- methyl-propionic acid), which also has PPAR- ⁇ agonist activity and does not affect cellular respiration.
- the compound useful in these methods is (S)-2-((S)-2-(2- (2-(4-(4-chlorobenzoyl)phenoxy)-2-methyl propanoyloxy) acetamido) propanamido) pentanedioic acid. This compound and its synthetic production scheme are illustrated in WO 2019/028096.
- the compound or reagent used for pre-treatment has PPAR- ⁇ agonist activity and does not inhibit complex I of the electron transport chain.
- the FF, prodrug, or derivative has limited toxicity for activated T cells in vitro.
- the FFP or a derivative enhances recovery of, or has limited toxicity for, activated T cells in vitro.
- prodrugs or derivatives of other known PPAR- ⁇ agonists may be used in these methods if they demonstrate no targeting of electron transport complex I and have limited toxicity for activated T cells in vitro.
- checkpoint inhibitor refers to a composition or composition in the form of an antibody or a small molecule that binds or inhibits various checkpoint proteins.
- checkpoint proteins including, without limitation, PD-1, PD- L1, CTLA-4, BTLA and CD160.
- known checkpoint inhibitors include the antibodies ipilimumab (Yervoy®), pembrolizumab (Keytruda®), and nivolumab (Opdivo®), among others.
- Other checkpoint inhibitors developed as small molecules or other checkpoint binding antibodies or antibody fragments are included in this definition.
- antibody refers to all types of immunoglobulins, including IgG, IgM, IgA, IgD, and IgE, including antibody fragments.
- the antibody can be monoclonal or polyclonal and can be of any species of origin, including (for example) mouse, rat, rabbit, horse, goat, sheep, camel, or human, or can be a chimeric antibody. See, e.g., Walker et al., Molec. Immunol.26:403 (1989).
- the antibodies can be recombinant monoclonal antibodies produced according to known methods, see, e.g., U.S. Patent Nos. 4,474,893 or 4,816,567, which are incorporated herein by reference.
- the antibodies can also be chemically constructed according to known methods, e.g., US Patent No. 4,676,980 which is incorporated herein by reference.
- Antibody fragments are antigen binding fragments which include, for example, Fab, Fab', F(ab')2, and Fv fragments; domain antibodies, bifunctional, diabodies; vaccibodies, linear antibodies; single-chain antibody molecules (scFV); heavy chain or light chain complementarity determining regions, and multispecific antibodies formed from antibody fragments.
- Such antigen-binding fragments can be produced by known techniques.
- therapeutic reagent or “regimen” is meant any type of treatment employed in the treatment of cancers with or without solid tumors, including, without limitation, chemotherapeutic pharmaceuticals, biological response modifiers, radiation, diet, vitamin therapy, hormone therapies, gene therapy, surgical resection, etc.
- an immunotherapeutic composition targeting an antigen or ligand on the tumor cell is meant any composition including cancer vaccines that target a cancer antigen in order to stimulate the subject’s immune system.
- immunotherapeutic compositions are designed to elicit a humoral (e.g., antibody) or cellular (e.g., a cytotoxic T cell or T helper) response, or, in one embodiment, an innate immune response, is mounted to a target gene product delivered by the immunogenic composition following delivery to a mammal or animal subject.
- immunotherapeutic compositions useful in these methods involve presentation of the antigen to the subject’s immune system via virus vectors, e.g., adenovirus, adeno-associated virus, lentivirus, retrovirus, poxvirus or others, or via virus-like particles (VLP).
- virus vectors e.g., adenovirus, adeno-associated virus, lentivirus, retrovirus, poxvirus or others, or via virus-like particles (VLP).
- the immunotherapeutic composition used in the methods described herein is a DNA or RNA construct that expresses a cancer antigen.
- the immunotherapeutic composition used in the methods described herein is a composition comprising cancer antigens or fragments thereof as peptides or proteins.
- the immunotherapeutic composition used in the methods described herein is a monoclonal antibody or antigen- binding fragment(s) that specifically bind cancer antigens.
- the compositions are those that are created using known recombinant and synthetic techniques. See, e.g., reference in the examples to an exemplary melanoma immunotherapeutic composition, AdC68- gDMelapoly described in detail in US Patent No.9,402,888 and in Fig.7 thereof.
- tumor-specific antigens are those epitopes and proteins found on a selected specific cancer or tumor cell, and not on all cancer cells.
- Cancer-associated antigens are antigens that may be associated with more than one cancer or tumor cell type.
- Exemplary cancer-specific antigens can include, without limitation, 707-AP, alpha (a)–fetoprotein, ART-4, BAGE; b- catenin/m, b-catenin/mutated Bacabal, CAMEL, CAP-1, mCASP-8, CDC27m, CDK4/m, CEA, CT, Cuyp-B, MAGE-B2, MAGE-B1, ELF2M, ETV6-AML1, G250, GAGE, GnT- V, Gp100, HAGE, HER-2/neu , HPV-E7, HSP70-2M HST-2, hTERT, iCE , KIAA0205, LAGE, LDLR/FUT, MAGE , MART-1, MC1R, MUC1, MUM-1, -2, -3, P15, p190 minor bcr-abl.
- tumor or cancer genes encode VEGFR1, VEGFR2, MAGE-A1, MUC-1, Thymosin ⁇ 1, EGFR, Her-2/neu, MAGE-3, Survivin, Heparinase 1, Heparinase 2, and CEA, among others.
- Still other suitable antigens are those listed in the references, and incorporated by reference herein. See, also, texts identifying suitable antigens, such as Scott and Renner, in Encyclopedia of life Sciences 2001 Eds., John Wiley & Sons, Ltd.
- vector is meant an entity that delivers a heterologous molecule to cells, either for therapeutic or vaccine purposes.
- a vector may include any genetic element including, without limitation, naked DNA, a phage, transposon, cosmid, episome, plasmid, or a virus or bacterium.
- Vectors are generated using the techniques and sequences provided herein, described in the examples, and in conjunction with techniques known to those of skill in the art. Such techniques include conventional cloning techniques of cDNA such as those described in texts such as Green and Sambrook, Molecular Cloning: A Laboratory Manual.4 th Edit, Cold Spring Harbor Laboratory Press, 2012, use of overlapping oligonucleotide sequences of the Salmonella genomes, polymerase chain reaction, and any suitable method which provides the desired nucleotide sequence.
- administering or “route of administration” is meant delivery of the T cells, FF or derivative thereof, immunotherapeutic composition, or the checkpoint inhibitor used in the methods herein, to the subject. As discussed in detail below, these methods can be independent for each components of the method. Each administration method can occur with or without a pharmaceutical carrier or excipient, or with or without another chemotherapeutic agent into the TME of the subject.
- Conventional and pharmaceutically acceptable routes of administration include, but are not limited to, systemic routes, such as intraperitoneal, intravenous, intranasal, intravenous, intramuscular, intratracheal, subcutaneous, and other parenteral routes of administration or intratumoral or intranodal administration. In one embodiment, the route of administration is oral.
- the route of administration is intraperitoneal. In another embodiment, the route of administration is intravascular. Routes of administration may be combined, if desired. In some embodiments, the administration is repeated periodically, as discussed in detail below.
- reference to “one or more,” “at least five,” etc. of the compositions, compounds or reagents listed means any one or all combinations of the compositions, reagents or compounds listed.
- the words “comprise”, “comprises”, and “comprising” are to be interpreted inclusively rather than exclusively, i.e., to include other unspecified components or process steps.
- a method for treating cancer includes administering to a subject having a cancer a composition comprising a T cell as described herein in combination with a fenofibrate (FF), fenofibric acid (FFA), FFA prodrug, or a derivative thereof that has PPAR- ⁇ agonist activity.
- FF fenofibrate
- FFA fenofibric acid
- the T cells for such pre-treatment are selected from the list of T cells identified above.
- the T cells may employ as the T cells an autologous or heterologous, naturally occurring T cell or a recombinantly or synthetically modified T cell construct.
- the T cell or population may be a human T cell or natural killer (NK) T cell or T infiltrating lymphocyte (TIL) obtained from the subject or from a bone marrow transplant match for the subject.
- NK natural killer
- TIL T infiltrating lymphocyte
- the T cell or population is obtained from human peripheral blood or from the tumor microenvironment of the subject.
- the T cell is modified to express a heterologous antigen receptor, or a chimeric antigen receptor (CAR-T) or a chimeric endocrine receptor (CER-T) prior to administration to the subject.
- CAR-T chimeric antigen receptor
- CER-T chimeric endocrine receptor
- the T cell or population is an endogenous or heterologous human T cell or human T cell line.
- the T cell is a TIL or a CD8+ T cell.
- the T cell is a CAR-T cell.
- the T cell is a tumor infiltration lymphocyte (TIL).
- the methods employ fenofibrate, fenofibric acid (FFA), FFA prodrug, or derivative thereof.
- the compound is fenofibrate.
- the compound is fenofibric acid.
- the compound is (S)-2-((S)-2-(2-(4-(4-chlorobenzoyl)phenoxy)-2-methylpropanamido) propanamido) pentanedioic acid (also known as FFP).
- a compound useful in the methods described herein is GW7647 (2-(4-(2-(1-Cyclohexanebutyl)-3-cyclohexylureido)- ethyl)-phenyl-thio)-2-methyl-propionic acid).
- a compound useful in these methods is (S)-2-((S)-2-(2-(2-(4-(4-chlorobenzoyl)phenoxy)-2-methyl propanoyloxy) acetamido) propanamido) pentanedioic acid.
- Other compounds that have PPAR- ⁇ agonist activity include gemfibrozil, bezafibrate, LY518674, BMS-711939, Pirinixic acid (Wy-14643) and GW 590735.
- Still other compounds that have PPAR- ⁇ agonist activity include MHY553, CAY10767, KRP297, CP775146, clofibrate, clofibric acid, pioglitazone, elafibranor, BMS687453, ciprofibrate, darglitazone, and GW 9578.
- a suitable concentration of the FF, FFA, FFA prodrug or derivative is at least 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, to at least about 500 ⁇ M.
- intervening concentration between any two numbers listed is encompassed in the term “suitable concentration”.
- this method involves further administration with an immunotherapeutic composition.
- the method can also include administering a checkpoint inhibitor in the form of an antibody or a small molecule either simultaneously with or sequentially with the T cells, combination with a fenofibrate (FF), FFA, FFA prodrug, or a derivative thereof that has PPAR- ⁇ agonist activity and/or the immunotherapeutic composition.
- FF fenofibrate
- FFA FFA prodrug
- the immunotherapeutic composition and the T cells are administered substantially simultaneously.
- the FF, FFA, FFA prodrug or derivative, or the immunotherapeutic composition is administered after the T cells.
- the FF, FFA, FFA prodrug or derivative, or the immunotherapeutic composition is administered prior to the T cells.
- the FF, FFA, FFA prodrug or derivative compound and the T cells are administered by the same or different routes of administration.
- the routes of administration selected depend upon the nature of the compositions. For example, for FF, FFA, FFA prodrug or another small chemical molecule derivative, such molecules may be administered orally in doses known and accepted for other pharmaceutical uses of these drugs.
- the immunotherapeutic composition and FF, FFA, FFA prodrug or derivative are independently administered systemically by intramuscular, intraperitoneal, intravenous, intratumoral or intranodal administration.
- the FF, FFA, FFA prodrug or derivative compound or the T cells are administered once or repeatedly from at least one to 14 days. In some protocols, the administration of the FF, FFA, FFA prodrug or derivative compound occurs one to 14 days after administration of the T cell composition. In certain embodiments, the T cells or FF, FFA, FFA prodrug or derivative compound is/are administered in a single dose. In other embodiments, the T cells or FF, FFA, FFA prodrug or derivative compound is/are administered as a booster dose. In another embodiment, an immunotherapeutic composition targeting an antigen or ligand on the tumor cell is also administered. In another embodiment, this method also involves administering a checkpoint inhibitor in the form of an antibody or a small molecule.
- the subject may be treated with other anti- cancer therapies before, during or after treatment with the T cells and/or FF, FFA, FFA prodrug or derivative thereof.
- Such treatment may be concurrent or simultaneous or overlap treatment with the T cell and/or the FF, prodrug or derivative compound.
- the methods involve treating the subject with chemotherapy before administering the T cells.
- the method further comprises depleting the subject of lymphocytes and optionally surgically resecting the tumor prior to treatment with the T cells and treatment with FF, an FFA prodrug or a derivative.
- the T cells are administered in a single dose, followed by administration of the FF, prodrug or derivative compound. These doses may be repeated.
- compositions and components of the methods may be administered to a patient, preferably suspended in a biologically compatible solution or pharmaceutically acceptable delivery vehicle.
- the various components of the methods are prepared for administration by being suspended or dissolved in a pharmaceutically or physiologically acceptable carrier such as isotonic saline; isotonic salts solution or other formulations that will be apparent to those skilled in such administration.
- a pharmaceutically or physiologically acceptable carrier such as isotonic saline; isotonic salts solution or other formulations that will be apparent to those skilled in such administration.
- the appropriate carrier will be evident to those skilled in the art and will depend in large part upon the route of administration.
- Other aqueous and non-aqueous isotonic sterile injection solutions and aqueous and non-aqueous sterile suspensions known to be pharmaceutically acceptable carriers and well known to those of skill in the art may be employed for this purpose.
- a useful dosage of a T cell is a single-infusion maximum tolerated dose (MTD), which may be determined by dose escalation studies in animal models.
- MTD maximum tolerated dose
- a typical efficacious and non-toxic dose of T cells is between about 2 x 10 4 to 5 x 10 9 cells per kg/subject body weight.
- Other doses, such as 10 5 or 10 6 or 10 7 or 10 8 can be useful. See, the methods for dose determination as described in e.g., WO2016/054153 and in other CAR publications in the art.
- a “standard” efficacious and non-toxic dose of T cells for adoptive transfer is about 10 7 cells.
- the number of adoptively transferred T cells can be optimized by one of skill in the art. In one embodiment, such a dosage can range from about 10 5 to about 10 11 cells per kilogram of body weight of the subject.
- a typical dosage of an immunotherapeutic composition depends upon the nature of the composition.
- a therapeutically effective adult human or veterinary dosage of a viral vector is generally in the range of from about 100 ⁇ L to about 100 mL of a carrier containing concentrations of from about 1 x 10 6 to about 1 x 10 15 particles, about 1 x 10 11 to 1 x 10 13 particles, or about 1 x 10 9 to 1x 10 12 particles virus.
- a composition e.g., the immunotherapeutic composition or checkpoint inhibitor
- the dosages may range between a unit dosage of between 0.01 mg to 100 mg of protein (which is equivalent to about 12.5 ⁇ g/kg body weight).
- the dosage of the checkpoint inhibitor may be adjusted based on known toxicities of the particular antibody or small molecule used. If any of the immunotherapeutic composition or the other components of the method is administered as naked DNA, the dosages may range from about 50 ⁇ g to about 1 mg of DNA per mL of a sterile solution. Similarly, the doses of the FF, FFA, FFA prodrug, or derivative compound may be similar to those administered for other uses, e.g., for cholesterol control or hyperlipidemia, of the similar compound. For example, FF may be administered at dosages of from 40 mg/day to 120 mg/day for adults.
- a therapeutic regimen for the treatment of cancer comprising administering to a subject having a cancer characterized by a solid tumor T cells in combination with FF, FFA, an FFA prodrug, or a derivative compound.
- the FF, FFA, FFA prodrug or derivative compound can occur on day 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or day 14 or even later than day 14, after administration of the T cells.
- Example 1 Materials and Methods Tumor specimen from patient Tumors were obtained directly after surgery from patients of Hospital of the University of Pennsylvania upon their informed consent. To protect patients’ confidentiality data on their gender, age, ethnicity were not provided to the investigators of this study. Mice and surgical procedure All animal procedures were approved by the Institutional Animal Care and Use Committee of the Wistar Institute (Philadelphia, PA, 19104). Male NSG mice (6-8 weeks) were obtained from Wistar Institute Animal Facility and kept under barriers conditions suited for severely immunocompromised mice.
- mice were under post-operative care for 2 weeks. Clips were removed 14 days post-surgery and tumors were measured using caliper 5 times/week. Treatment started when tumors reached ⁇ 0.5 cm in volume. Isolation of melanoma cells Tumor fragments were suspended in in HBSS with Ca + and Mg + (Corning, cat# 21- 023-CV) containing 50U/ml DNase I (Sigma-Aldrich, REF# 04716728001), 2mg/ml collagenase IV (Sigma-Aldrich, cat# C4-28), and 1mg/ml hyaluronidase V (Sigma- Aldrich, cat# H6254) diluted in HBSS with Ca + and Mg + (Corning, cat# 21-023-CV) at 37 o C for 1 hour followed by under agitation for 30 min.
- Ca + and Mg + Corning, cat# 21- 023-CV
- 50U/ml DNase I Sigma-
- tumor fragments were digested as described above and TILs were purified by Ficoll density gradient centrifugation at 2000 RPM for 20 min at room temperature. Enrichment of CD8 + T cells CD8+ TILs were selected for by using magnetic beads of the Human CD8 + T cell enrichment kit (Stemcell, cat# 19053) and EasySep RoboSep buffer (Stemcell, cat# 20104).
- CD8 + were cultured in AIMV media (Gibco, cat#12-055-091) supplemented with 30 IU/ml of human IL-2 (Sigma-Aldrich, cat# 11147528001), 10ng/ml of recombinant human IL-15 (Peprotech, Cat# 200-15), 5% human serum (Sigma-Aldrich, cat# H3667), 100U/ml penicillin, 100ug/ml streptomycin (Gibco, cat# 15140-122), and 25mmol/L Hepes (Gibco, cat# 15630) and 5.5 ⁇ 10 ⁇ 5 mol/L ⁇ -mercaptoethanol. T cell of patient I grew poorly under those conditions.
- RNAs were resuspended in 20ul of diethylpyrocarbonate-treated water (Ambion, AM9915G), treated with DNAse I (Sigma-aldrich, cat# 04716728001) and RNasin Plus (Promega, cat# N261B). Samples were incubated at 37 ° C for 20 min and then run on thermal cycler (Eppendorf Mastercycler) at 75 o C for 10 min. The purity of RNA samples was assessed by measuring UV absorbance at A 260 (260 nm) Complimentary (c)DNA was synthetized using the high-capacity cDNA reverse transcription kit (Applied biosystems cat# 4368814) according to the manufacturer protocol.
- Minus-RT control without reverse transcriptase was generated along with RNA samples to ensure lack of DNA contamination.
- the qRT-PCR was conducted in duplicates with Powerup SYBR Green Master Mix (Applied biosystems, cat# A25742) using 7500 standard mode Real-Time PCR system (Applied Biosystems, Foster City, CA). Isolation of lymphocytes from spleens Lymphocytes were isolated from spleen of mice as described before (43).
- Lymphocytes from tumors and spleens were stained with APC-labeled anti-human CD8 (Invitrogen eBioscience, cat# 17-0088-42), BV605-labeled anti-human CD4 (BD Horizon, cat# 565998), Alexa Fluor 700 anti-human CD44 (BioLegend, cat# 338813), PE anti-human PD1 (Biolegend, cat# 329906), Alexa Fluor 647 anti-human LAG3 (Biolegend, cat# 369304) and PerCP/Cyanine5.5-labeled anti-human CTLA-4 (BioLegend, cat# 349928) at 1 in 100ul of cell staining buffer (BioLegend, cat# 420201).
- APC-labeled anti-human CD8 Invitrogen eBioscience, cat# 17-0088-42
- BV605-labeled anti-human CD4 BD Horizon, cat# 565998
- Alexa Fluor 700 anti-human CD44 BioLegen
- Live/dead fixable violet dead cell stain (Invitrogen, cat#L34955) was diluted at 1 in 400ul of cell staining buffer. Cells were incubated with antibodies at 4C for 30 min. Next, cells were washed with cell staining buffer, fixed and permeabilized with BD cytofix/cytoperm (BD Biosciences, cat# 51-2090KZ) at 4C for 20 min. Then cells were washed with BD perm/wash (BD Biosciences, cat#51-2091KZ) and stained with FITC-labeled anti-human IFN- ⁇ (BioLegend, cat# 506504) at 4C for 30 min.
- BD cytofix/cytoperm BD Biosciences, cat# 51-2090KZ
- Sections were analyzed with Nikon Eclipse Ti Inverted Microscope, Light Engine SOLA SE II 365, PSF (Perfect Focus System), Motorized FL Filter Turret, Prior Stage, Piezo Stage, using a Nikon 20X Plan Apo, N.A..95 objective and the Nikon NIS Elements AR Version 5.30.02 (Build 1545) software.
- Statistical analysis All statistical analyses were conducted using GraphPad Prism 6 (GraphPad). Differences between 2 populations were calculated by Student’s t-test. Multiple comparisons between two groups were performed by multiple t-test with type I error correction. Differences among multiple populations were calculated by one- or two-way ANOVA. Differences in survival were calculated by Log-rank Mantel-Cox test. Differences between tumor growth curves were determined by repeated measures two-way ANOVA.
- Type I errors were corrected by Holm- ⁇ dák method. Significance was set at p values of or below 0.05. For all figures, ⁇ p ⁇ 0.05 – 0.01, ⁇ p ⁇ 0.01-0.001, ⁇ p ⁇ 0.001- 0.0001, ⁇ p ⁇ 0.0001. Unless noted in the figure legend, all data are shown as mean +/- SEM.
- Example 2 NSG mice that carried human tumor transplants had readily detectable human T cells in their blood which presumably originated from the tumor fragments. Treatment of mice with fenofibrate once tumor reached a certain size delayed tumor progression.
- Example 3 Lymphocytes were isolated from the tumor of a patient with metastatic melanoma. T cells were isolated from part of the tumor and expanded in vitro in IL-2. Tumor fragments were transplanted under the skin of NSG mice. Once tumors reached a certain size fragments were again transplanted into fresh NSG mice. For the experiment tumor fragments of passage 4 (3 previous passaged in NSG mice) were transplanted under the skin of 20 NSG mice. Tumors became visible 18 days later.
- FIG. 5A shows tumor volumes in individual mice that had received T cells at the indicated days after initiation of drug treatment. Fenofibrate treated mice are shown on the left, DMSO treated mice are shown on the right.
- FIG.5B shows tumor volumes in fenofibrate (left) and DMSO (right) treated mice that had not received T cells.
- TME tumor microenvironment
- TILs treated with a PPAR ⁇ agonist switch from glycolysis to fatty acid oxidation and this increases their ability to slow the progression of autologous melanomas as is shown with both freshly transplanted human tumor fragments and mice injected with tumor cell lines established from the patients’ melanomas and ex vivo expanded TILs from the same patients.
- the effect of a PPAR ⁇ agonist on melanoma growth in a PDX model To assess the effect of fenofibrate, a PPAR ⁇ agonist, on human melanomas and melanoma infiltrating lymphocytes we used a PDX model in which human melanoma fragments were transplanted into immunodeficient NOD SCID (NSG) mice.
- NSG immunodeficient NOD SCID
- Fresh primary or recurrent melanoma or melanoma metastasis samples (n 12, A-Q) obtained within hours after surgery were cut into small pieces, which were transplanted each under the skin of 4-5 NSG mice (FIG.3A). Tumor growth was observed after transplantation of 9 (D, E, G, I, M, N, O, P, Q) of 12 melanoma samples and tumors typically became visible within 3-8 weeks (FIG.3B). Once tumor reached a size of ⁇ 0.5-1 cm in diameter, mice, which had received fragments from Patients D, E and I, were treated for 3 weeks orally with fenofibrate (FF) or its dimethylsulfoxide (DMSO) containing diluent. Tumor growth was monitored.
- FF fenofibrate
- DMSO dimethylsulfoxide
- Oral FF treatment delayed progression of the primary melanoma of patient D, the recurrent melanoma of Patient E and the metastatic melanoma of Patient I (FIG.3C, FIG.3D).
- Mice that received tumors of patients D and E were tested for presence of human T cells that had infiltrated the human tumors and were transplanted as part of the tumor fragments.
- Peripheral blood mononuclear cells (PBMCs) were tested at 6 (E) and 8 (D) weeks after transplantation and spleens and tumors were tested at euthanasia.
- PBMCs Peripheral blood mononuclear cells
- human CD4 + and CD8 + T cells could be detected in blood and at lower and more variable numbers in spleens and tumors.
- mice melanomas of patients I, K, M, and N, once they exceeded a volume of 2-2.5 cm in NSG mice were excised and fragments were transplanted into new NSG mice. This process was repeated once or twice more. Mice that received the 3 rd (K,I) or 4 th (I) passage fragments were tested for human T cells in blood (K,I), spleens and tumors (I,M,N). Although there was a trend for reduced T cell recovery from blood upon serial passages, numbers remained unchanged in spleens and tumors.
- T cells once they had been enriched for CD8 + cells were expanded in vitro in medium containing IL-2.
- Mice that carried homologous tumor fragments were divided into 4 groups of 5 mice each.
- Group A received autologous CD8 + T cells that had been treated for 2 weeks with fenofibric acid (FA), a FF derivative that is suited for use in cell culture. Recipient mice were treated with FF after T cell transfer.
- Group B received DMSO treated T cells and was then treated with DMSO, Groups C and D were not injected with human T cells, they were only treated with FF or DMSO (FIG.4A).
- FFA fenofibric acid
- mice that received fragments from patients I, N and O showed reduced tumor growth if there were given T cells with FF compared to mice that only received the drug or its diluent.
- Mice with fragments from patients M benefited from FF regardless of CD8 + T cell transfer (FIG.4B, FIG.4C).
- TILs Most striking were results obtained with TILs; recovery of CD8 + T cells from tumors was significantly higher in group A than groups B and C and there were no significant differences between groups B and C indicating that without FF the transferred T cells had either not migrated to the tumors or more likely that they had not survived within the TME (FIG.4C). It is also noteworthy that small numbers of CD8 + TILs could be recovered from group C; these mice had not received ex vivo expanded T cells indicating that the cells originated from the serially transplanted tumor samples as already shown in FIG.3A – FIG.3E. TILs of groups A and B were tested by quantitative reverse transcription polymerase chain reaction (qRT-PCR) for transcripts encoding enzymes that play a role in different metabolic pathways.
- qRT-PCR quantitative reverse transcription polymerase chain reaction
- TILs from group 1 in comparison to group 2 showed modest increases in transcripts involved in fatty acid metabolism, i.e., Carnitine palmitoyltransferase I (CPT-1), which is instrumental to transport fatty acids into mitochondria, PPAR-a, the master regulator of fatty acid metabolism and D-beta- hydroxybutyrate dehydrogenase (BDH) an enzyme that is involved in catabolism of ketone bodies.
- CPT-1 Carnitine palmitoyltransferase I
- PPAR-a the master regulator of fatty acid metabolism
- BDH D-beta- hydroxybutyrate dehydrogenase
- TILs from patient I in addition showed a reduction in transcripts for some of the glycolytic enzymes (FIG.4D).
- T cells were treated for 2 weeks with FA or DMSO and then transferred into 2 groups of mice (A and B) that carried visible tumors ( ⁇ 0.2 cm in diameter).
- Mice of group A were treated with FF
- mice of group B received DMSO.
- Groups C and D were treated with FF or DMSO, respectively, but did not receive T cells (FIG.5A). Samples from the different patients showed comparable patters so we combined their data for most of the statistical analysis. Tumor growth was significantly delayed in group A compared to the other 3 groups indicating that the delay in tumor progression was caused by the combination of the PPAR-a agonist and the transferred CD8 + T cells.
- Group A had significantly higher CD8 + TIL counts compared to the other groups. Although some CD8 + T cells could be recovered from group B this failed to reach significance compared to the low numbers of recovered cells that exhibited non-specific staining in groups C and D. T cells were tested for production of IFN-g; 80-90% of CD8 + T cells from group A produced this cytokine. IFN-g production was less frequent in CD8 + T cells from group B suggesting that FF preserved T cell functions (FIG.6A).
- Immunohistology from tumors confirmed the data obtained by flow cytometry (FIG.6B); those of group A were heavily infiltrated by human CD8 + T cells that accumulated at the border between healthy and necrotic tumor tissue (FIG.6C) while CD8 + T cells were rare in group B. Those that could be detected in group B tumors commonly showed membrane blebbing that is typically associated with apoptosis (FIG. 6D). CD8 + T cells from the mice with recovery, were tested for exhaustion/differentiation markers (FIG.6E). Percentages of PD-1 + CD8 + cells were higher in group A than B tumors or group A spleens.
- lymphocyte activating protein LAG-3
- CTL-4 cytotoxic T-Lymphocyte associated protein
- TILs from groups A and B as well as tumor cells from groups C and D were tested for transcripts encoding metabolic enzymes. Samples from the 4 different patients showed comparable patterns.
- Group A T cells compared to group B T cells showed highly significant increases in transcripts for enzymes of fatty acid metabolism and decreases in those of glycolysis and histone methyltransferase (HMT), an enzyme of one-carbon metabolism (FIG.6G).
- HMT histone methyltransferase
- Lymphocyte and T cell counts in tumors showed strong inverse correlation with the Ct values for enzymes of fatty acid metabolism and direct correlations with those for glycolysis indicating that preservation of the transferred T cells was linked to their switch from glycolysis to fatty acid metabolism.
- enzymes of a given metabolic pathway showed strong positive correlations with each other and inverse correlation with those of the other pathway.
- percentages of human CD8 + cells that were only positive for PD-1 inversely correlated with the slope of tumor growth and Ct values for transcripts for enzymes of FAO but showed positive correlations for enzymes of glycolysis and CD8 + T cell recovery.
- CD8 + T cells that were only positive for LAG-3 showed the opposite pattern.
- T cell transfer has achieved remarkable successes in liquid tumors; their effectiveness in solid tumors remains limited. This is at least in part caused by rapid T cell impairment within the immunosuppressive TME. Resting T cells use the mitochondrial tricarboxylic acid (TCA) cycle to fuel their metabolism by glucose, amino acids and fatty acids.
- TCA mitochondrial tricarboxylic acid
- CD8 + T cells Upon engagement of the T cell receptor with its cognate antigen displayed by major histocompatibility antigens and co-stimulation through ligation of CD28, CD8 + T cells through activation of the phosphoinositide 3-kinase (PI3K)/ Protein kinase B (Akt) pathways increase expression of the glucose receptor (Glut)1and switch their metabolism to glycolysis; this in turn allows them to rapidly generate energy and building blocks for effect functions and cell divisions. As first described by Warburg tumor cell growth is also fueled by aerobic glycolysis, which depletes this nutrient from the TME.
- PI3K phosphoinositide 3-kinase
- Akt Protein kinase B
- Tumor cells can outcompete T cells for glucose, and lack of this nutrient leads to reduced activity of the mammalian target of rapamycin (mTOR), which impairs cytokine production. Lack of the glucose metabolite phosphoenolpyruvate, which is crucial for T cell receptor mediation activation of nuclear factor of activated T cells (Ca ++ NFAT) further impairs T cell functions. Regulatory T cells in contrast are relatively unaffected by hypoglycemia as they fuel their metabolism primarily through lactate and fatty acids. The tumor cells’ increased secretion of lactic acid, the final metabolite of glycolysis, decreases the TME’s pH, which impairs the T cells’ ability to migrate, produce cytokines or release lytic enzymes.
- mTOR mammalian target of rapamycin
- T cells in a hypoglycemic environment can switch from glycolysis to FAO, which is promoted by increased expression of PD-1.
- a switch to FAO in absence of glucose not necessarily terminates T cell activation and it was shown in vitro that T cells can be stimulated and acquire effector functions albeit less efficiently in absence of glucose.
- increased CD36 mediated uptake of fatty acids can blunt TIL functions.
- the PPARa agonist delayed tumor progression and, as was shown using the TIL transfer model, this was caused by a metabolic switch of TILs from glycolysis to FAO, as evidence by declines in transcripts encoding glycolytic enzymes accompanied by increases in those involved in metabolism of fatty acid and ketone body.
- the latter may have been provided by tumors cells as previous studies showed that FF in a PPARa independent way increases production and secretion of ketone bodies by melanoma cells, FF-driven metabolic changes in TILs in turn correlated with increased TIL recovery from human melanoma bearing mice and better preservation of their ability to produce IFN-g.
- PD-1 signaling is known to inhibit glycolysis by reducing expression of Glut1 and the activity of hexokinase (HK)2 the 1 st enzyme of the glycolysis pathway. Inhibition of the PI3K/Akt pathway further augments fatty acid metabolism as supported by our correlation studies.
- CTLA-4 has similar effects on glycolysis but fails to affect FAO and in our study did not show strong correlations with levels of transcripts of metabolic enzymes, while increased frequencies of human CD8+ T cells expressing LAG-3, which is regulated by HIF-1a and increases under hypoxia correlated with tumor progression, decreases in enzymes of FAO and increases in those involved in glycolysis. Others have attempted to reduce tumor progression by addressing the TILs metabolic defects. Endolase 1, a key glycolytic enzyme needed for production of pyruvate was found to be defective in melanoma infiltrating CD8 + T cells, whose functions improved at least in vitro if they were cultured in medium containing pyruvate.
- Metformin is another metabolic drug that has been shown to slow tumor progression both through mTORC1-dependant and independent mechanisms and in addition to improve fitness of CD8 + TILs in different types of solid cancer.
- Gemta LF et al. Impaired enolase 1 glycolytic activity restrains effector functions of tumor-infiltrating CD8 + T cells. Sci Immunol.2019 Jan 25;4(31):eaap9520. Hersey P, et al. Metabolic approaches to treatment of melanoma. Clin Cancer Res.2009 Nov 1;15(21):6490-4. Jaune E, Rocchi S. Metformin: Focus on Melanoma. Front Endocrinol (Lausanne).2018 Aug 21;9:472. Finisguerra V, et al. Metformin improves cancer immunotherapy by directly rescuing tumor-infiltrating CD8 T lymphocytes from hypoxia-induced immunosuppression.
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Abstract
Provided herein is a method for treating cancer comprising administering to a subject having a cancer a fenofibrate (FF), fenofibric acid (FFA), an FFA prodrug, or a derivative thereof that has PPAR-a agonist activity and a T cell or T cell population.
Description
FENOFIBRATE IMPROVES T-CELL THERAPIES STATEMENT OF GOVERNMENT INTEREST This invention was made with government support under W81XWH-19-1-0485, awarded by the United States Department of Defense ARMY. The government has certain rights in the invention. BACKGROUND OF THE INVENTION Melanoma is the most lethal type of skin cancer with a mere 22.5% 5-year survival rate for stage IV metastatic disease. Irradiation therapy and chemotherapy are not very effective and have largely been replaced by targeted therapies such as B-RAF and mitogen-activated protein kinase (MAPK) inhibitors or immunotherapies including checkpoint blockers or adoptively transferred T cells directed against antigens expressed by the melanoma cells. T cell therapies include transfer of ex vivo expanded TILs, which as polyclonal populations recognize multiple tumor-associated antigens. Response rates to TIL transfer are below 50% and even lower if given after treatments with anti- programmed death (PD)-1 antibodies or MAPK inhibitors. Alternatively, treatments with chimeric antigen receptor (CAR)-T cells with specificity against different melanoma associated antigens are being explored. Response rates to CAR-T cell transfer varies from 20-51% depending on concomitant treatment with interleukins (IL) or non-myeloablative lymphodepleting agents and the CAR-T cell receptors’ specificity. TILs and CAR-T cells achieve a delay in tumor progression and in some cases full remission by causing tumor cell death through release of lytic enzyme or interactions between Fas on T cells and Fas ligand on melanoma cells. Lack of efficacy of transferred T cells could reflect that melanoma cells down-regulate expression of the T cells’ target antigens, that some melanoma cells are relatively resistant to T cell-mediated lysis, that T cells fail to migrate and infiltrate the melanoma lesions, and that they are suppressed within the TME by regulatory T cells, myeloid suppressor cells and cancer associated fibroblasts. In addition, once T cells penetrate the TME they are faced with areas of hypoxia due to incomplete vessel formation and hypoglycemia due to ferocious glucose consumption by rapidly growing tumor cells. These metabolic challenges further drive T cell exhaustion and loss of functions (19). What is needed are improved cancer therapies.
SUMMARY OF THE INVENTION Provided herein is a method for treating cancer. The method includes administering to a subject having a cancer a fenofibrate (FF), fenofibric acid (FFA), an FFA prodrug, or a derivative thereof that has PPAR-α agonist activity; and a T cell or T cell population. In certain embodiments, the T cell is an autologous or heterologous, naturally occurring T cell or a recombinantly or synthetically modified T cell construct, or a human T cell or natural killer (NK) T cell or T infiltrating lymphocyte (TIL) obtained from the subject or from a bone marrow transplant match for the subject, or a T cell obtained from human peripheral blood or from the tumor microenvironment of the subject, or a T cell modified to express a heterologous antigen receptor, or a chimeric antigen receptor or a chimeric endocrine receptor, or an endogenous or heterologous human T cell or human T cell line, or a CD8+ T cell. In certain embodiments, the method further includes administering to a subject having a cancer an immunotherapeutic composition targeting an antigen or ligand on a tumor cell in the subject. In certain embodiments, the immunotherapeutic composition is a recombinant virus or virus-like particle that expresses a cancer antigen, a DNA construct that expresses a cancer antigen, a composition comprising a cancer antigen or fragment thereof, or a monoclonal antibody or antigen-binding fragment that specifically binds a cancer antigen. Other aspects and advantages of these compositions and methods are described further in the following detailed description of the preferred embodiments thereof. BRIEF DESCRIPTION OF THE DRAWINGS FIG.1 shows tumor diameter over time as of the day of onset in drug treatment. Data were normalized to the overall average tumor size at the 1st day of treatment. Significant differences by repeated corrected student t-test are highlighted by stars (** - p value below 0.01, *** p value below 0.001). FIG.2A shows tumor volumes in individual mice that received T cells at the indicated days after initiation of drug treatment. FIG.2B shows tumor volumes in fenofibrate and DMSO treated mice that did not receive T cells.
FIG.3A – FIG.3F show the effect of FF on human melanoma growth in a PDX model. (FIG.3A) Experimental design. (FIG.3B) Patient samples. (FIG.3C) Progression of tumor fragments from Patients D, E, and I in NSG mice treated with FF or DMSO. (FIG.3D) Same data as in FIG.1C but shown as linear regression curves of tumor diameter in cm over time for samples from individual patients. Data were normalized to a diameter of 1 on day 0 of drug treatment. Nubers show average slope of the linear regression curves. (FIG.3E) Numbers of human T cells in various tissues after 1-4 passages.0 passage reflects control mice that did not receive tumor fragments. Numbers were normalized to 105 live lymphoid cells. FIG.4A – FIG.4E show the effect of FF on TILs transferred into tissue fragment- derived tumor-bearing NSG mice. (FIG.4A) Experimental design. (FIG.4B) Progression of tumors from melanoma fragments of the indicated patients. (FIG.4C) Same data shown as linear regression curves. Boxes to the right show result of statistical analyses by 2-way Anova comparing the slope of the regression curve of individual animals fromn given groups. (FIG.4D) Recovery of live lymphocytes from tumors, human CD44+CD8+ cells from spleens or tumors. The two latter counts were normalized to 105 live lymphoid cells. Data for the different patients are stacked. Data were compared by 2-way Anova. Differences were calculated by 2-way Anova with Tukey correction. (FIG.4E) Differences in Ct values between TILs from individual sample of groups A and averaged samples from group B are shown in a heatmap for individual mice receiving samples from the indicated patients. P-Values comparing the original Ct values for Groups A and B. FIG.5A – FIG.5E show the effect of FF on the ability of transferred CD8+ TILs to slow tumor progression. (FIG.5A) Experimental design. (FIG.5B) Progression of tumors from the indicated patients in the 4 different treatment groups. (FIG.5C) Results of comparing the slope of the curves of individual mice by Fisher’s LSD test. (FIG.5D) Tumor progression shown as linear regression lines for tumor volume over time. (FIG.5E) Kaplan Meier survival graphs for the different groups receiving tumor cells from the indicated patients. Data were compared by Mantel-Cox test. FIG.6A – FIG.6H show the effect of FF on TILs transferred into cell line-derived tumor-bearing NSG mice. (FIG.6A) Recovery of lymphoid cells, human CD44+CD8+ T cells and IFN-g producing human CD44+CD8+ T cells from spleens and tumors. Counts (lymphoid cells) or counts normalized to 105 live lymphoid cells are stacked for samples
from different patients. (FIG.6B) Lymphocyte and human CD8+ T cell counts by immunohistochemistry. Counts are normalized to a total area of 2 mm2. (FIG.6C and FIG. 6D) Sections of tumors from NSG mice receiving Patient M tumor cells: FIG.6C- TILs and mice treated with FA or FF, FIG.6D- TILs and mice treated with DMSO. (FIG.6E) Percentages of human CD8+ T cells expressing the indicated markers. (FIG.6F) Percentages of cell expressing combinations of markers determine by Boolean gating. For FIG.6A, FIG.6B, FIG.6E, and FIG.6F, differences were calculated by 2-way Anova with Tukey correction. (FIG.6G) Differences in Ct values between TILs from individual sample of groups A and averaged samples from group B are shown in a heatmap for individual mice receiving samples from the indicated patients. P-Values comparing the original Ct values for Groups A and B. Differences were calculated by multiple unpaired t- test with two stage step-up method by Benjamini, Krieger and Yekutieli. (FIG.6H) Differences in Ct values between tumor cells isolated tumor samples of groups C and averaged tumor samples from group D are shown in a heatmap for individual mice receiving samples from the indicated patients. P-Values comparing the original Ct values for Groups C and D. Differences were calculated by multiple unpaired t-test with two stage step-up method by Benjamini, Krieger and Yekutieli. FIG.7 shows correlations in tumor growth. Graph shows as heatmaps r values by Spearman correlation correlations on top with matching p-values below. DETAILED DESCRIPTION The methods and compositions described herein involve co-treatment of a subject having cancer with a T cell or T cell population and fenofibrate (FF), fenofibric acid (FFA), an FFA prodrug, or a derivative thereof that has PPAR-α agonist activity. As disclosed herein, the described co-treatment promotes reduced tumor volume as compared to T cell therapy or fenofibrate alone. The methods and compositions provided herein offer additional therapeutic interventions in methods and compositions involving the use of FF, FFA, an FFA prodrug, or a derivative thereof that has PPAR-α agonist activity in combination with T cells. Further methods involve administering a tumor-specific vaccine composition with the FF, FFA prodrug, or a derivative thereof in combination with T cells.
Certain components and definitions used in the description of these methods and compositions are defined below. “Patient” or “subject” as used herein means a mammalian animal, including a human, a veterinary or farm animal, a domestic animal or pet, and animals normally used for clinical research. More specifically, the subject of these methods and compositions is a human. As used herein, the term “T cell(s)” or “T cell population” mean any human or mammalian T cell(s). In one embodiment, the T cell or populated is activated. In one embodiment, the T cell is an autologous or heterologous, naturally occurring T cell. In another embodiment, the T cell is a recombinantly or synthetically modified T cell construct. In some embodiments, the T cell is a primary T cell, a CD8 (cytotoxic) T cell, a CD8 (cytotoxic) T cell, a T infiltrating lymphocyte (TIL), an NK T cell, or another T cell. In one embodiment, the T cell is obtained from the peripheral blood, TME or other fluid of the same mammalian subject into whom the T cell is to be administered. In another embodiment, the T cell is a primary T cell, a CD8 (cytotoxic) T cell, an NK T cell, or other T cell obtained from a bone marrow transplant match for the subject. Other suitable T cells include T cells obtained from resected tumors, a polyclonal or monoclonal tumor- reactive T cell. In one embodiment, the T cells are obtained by apheresis. In still other embodiments, the T cell is modified recombinantly or synthetically to express a heterologous antigen receptor. In one embodiment, the T cell is expresses a chimeric antigen receptor (CAR) or a chimeric endocrine receptor (CER). Such CARs or CERs are described in e.g., Sadelain, M et al, “The basic principles of chimeric antigen receptor (CAR) design” 2013 April, Cancer Discov.3(4): 388–398; International Patent Application Publications WO2013/044255 and WO2016/054153, US patent application publication No. US 2013/0287748, and other publications directed to the use of such chimeric constructs. These publications are incorporated by reference to provide information concerning various components useful in the design of some of the constructs described herein. Such CAR or CER T cells are genetically modified lymphocytes expressing a ligand that allows them to recognize an antigen of choice. Upon antigen recognition, these modified T cells are activated via signaling domains converting these T cells into potent cell killers. An advantage over endogenous T cells is that they are not MHC restricted, which allows these T cells to overcome an immune surveillance evasion
tactic used in many tumor cells by reducing MHC expression. In still other embodiments, the T cell is an endogenous or heterologous human T cell or human T cell line. As used herein the term “cancer” refers to or describes the physiological condition in mammals that is typically characterized by unregulated cell growth. More specifically, as used herein, the term “cancer” means any cancer characterized by the presence of a solid tumor. Suitable cancers for treatment by the methods described herein, include, without limitation, melanoma, breast cancer, brain cancer, colon/rectal cancer, lung cancer, ovarian cancer, adrenal cancer, anal cancer, bile duct cancer, bladder cancer, bone cancer, endometrial cancer, esophagus cancer, eye cancer, kidney cancer, laryngeal cancer, liver cancer, head and neck cancer, nasopharyngeal cancer, osteosarcoma, oral cancer, ovarian cancer, pancreatic cancer, prostate cancer, rhabdomyosarcoma, salivary gland cancer, stomach cancer, testicular cancer, thyroid cancer, vaginal cancer, lung cancer, and neuroendocrine cancer. In certain embodiments, the tumor is melanoma. The term “tumor,” as used herein, refers to all neoplastic cell growth and proliferation, whether malignant or benign, and all pre-cancerous and cancerous cells and tissues. In one embodiment, the tumor targeted by the methods is characterized by hypoxia, significant infiltration with T lymphocytes, and/or low glucose in the tumor microenvironment. As used herein, the compound or reagent useful in the methods and compositions described herein is fenofibrate (FF), fenofibric acid (FFA), an FFA prodrug, or a derivative thereof that has PPAR-α agonist activity. Fenofibrate, a pro-drug, is pharmacologically inactive and undergoes rapid hydrolysis at the ester bond to form the active metabolite, fenofibric acid. In various other embodiments, the FF, FFA, FFA prodrug, and/or derivatives have a combination of these characteristics. FF, FFA, FFA prodrug, and derivatives that mimic FF, promote the use of fatty acid catabolism rather than glucose for energy. FF also promotes biomass production by the T cells. As used herein in reference to the methods, when FF, FFA, or FFA prodrug is referred to, it should be understood that other embodiments are comtemplated utilizing each of FF, FFA or an FFA prodrug individually, or combiantions thereof. Various formulations of FF are known in the art, and include, without limitation, nonmicronized, micronized, nanoparticle, and lipid melt formulations. See, Ling H, Luoma JT, Hilleman D. A Review of Currently Available Fenofibrate and Fenofibric Acid
Formulations. Cardiol Res.2013 Apr;4(2):47-55. doi: 10.4021/cr270w. Epub 2013 May 9, which is incorporated herein by reference. In another embodiment, the compound useful in these methods is the FFA prodrug or derivative, (S)-2-((S)-2-(2-(4-(4-chlorobenzoyl)phenoxy)-2-methylpropanamido) propanamido) pentanedioic acid (also known as FFP). This compound and its synthetic production scheme are illustrated in WO 2019/028096, which is incorporated herein by reference. In another embodiment, a compound useful in the methods described herein is GW7647 (2-(4-(2-(1-Cyclohexanebutyl)-3-cyclohexylureido)-ethyl)-phenyl-thio)-2- methyl-propionic acid), which also has PPAR-α agonist activity and does not affect cellular respiration. In another embodiment, the compound useful in these methods is (S)-2-((S)-2-(2- (2-(4-(4-chlorobenzoyl)phenoxy)-2-methyl propanoyloxy) acetamido) propanamido) pentanedioic acid. This compound and its synthetic production scheme are illustrated in WO 2019/028096. In one embodiment, the compound or reagent used for pre-treatment has PPAR-α agonist activity and does not inhibit complex I of the electron transport chain. In another embodiment, the FF, prodrug, or derivative has limited toxicity for activated T cells in vitro. In another embodiment, the FFP or a derivative enhances recovery of, or has limited toxicity for, activated T cells in vitro. In another embodiment, prodrugs or derivatives of other known PPAR-α agonists may be used in these methods if they demonstrate no targeting of electron transport complex I and have limited toxicity for activated T cells in vitro. Other compounds that have PPAR-α agonist activity include gemfibrozil, bezafibrate, LY518674, BMS-711939, Pirinixic acid (Wy-14643) and GW 590735. Still other compounds that have PPAR-α agonist activity include MHY553, CAY10767, KRP297, CP775146, clofibrate, clofibric acid, pioglitazone, elafibranor, BMS687453, ciprofibrate, darglitazone, and GW 9578. As used herein, the term “checkpoint inhibitor” refers to a composition or composition in the form of an antibody or a small molecule that binds or inhibits various checkpoint proteins. Such checkpoint proteins, including, without limitation, PD-1, PD- L1, CTLA-4, BTLA and CD160. As examples, known checkpoint inhibitors include the antibodies ipilimumab (Yervoy®), pembrolizumab (Keytruda®), and nivolumab
(Opdivo®), among others. Other checkpoint inhibitors developed as small molecules or other checkpoint binding antibodies or antibody fragments are included in this definition. As used herein, the term “antibody” refers to all types of immunoglobulins, including IgG, IgM, IgA, IgD, and IgE, including antibody fragments. The antibody can be monoclonal or polyclonal and can be of any species of origin, including (for example) mouse, rat, rabbit, horse, goat, sheep, camel, or human, or can be a chimeric antibody. See, e.g., Walker et al., Molec. Immunol.26:403 (1989). The antibodies can be recombinant monoclonal antibodies produced according to known methods, see, e.g., U.S. Patent Nos. 4,474,893 or 4,816,567, which are incorporated herein by reference. The antibodies can also be chemically constructed according to known methods, e.g., US Patent No. 4,676,980 which is incorporated herein by reference. See also, US Patent No.8,613,922, which is incorporated herein by reference. Antibody fragments are antigen binding fragments which include, for example, Fab, Fab', F(ab')2, and Fv fragments; domain antibodies, bifunctional, diabodies; vaccibodies, linear antibodies; single-chain antibody molecules (scFV); heavy chain or light chain complementarity determining regions, and multispecific antibodies formed from antibody fragments. Such antigen-binding fragments can be produced by known techniques. By “therapeutic reagent” or “regimen” is meant any type of treatment employed in the treatment of cancers with or without solid tumors, including, without limitation, chemotherapeutic pharmaceuticals, biological response modifiers, radiation, diet, vitamin therapy, hormone therapies, gene therapy, surgical resection, etc. By “an immunotherapeutic composition targeting an antigen or ligand on the tumor cell” is meant any composition including cancer vaccines that target a cancer antigen in order to stimulate the subject’s immune system. Such immunotherapeutic compositions are designed to elicit a humoral (e.g., antibody) or cellular (e.g., a cytotoxic T cell or T helper) response, or, in one embodiment, an innate immune response, is mounted to a target gene product delivered by the immunogenic composition following delivery to a mammal or animal subject. In one embodiment, immunotherapeutic compositions useful in these methods involve presentation of the antigen to the subject’s immune system via virus vectors, e.g., adenovirus, adeno-associated virus, lentivirus, retrovirus, poxvirus or others, or via virus-like particles (VLP). In another embodiment, the immunotherapeutic composition used in the methods described herein is a DNA or RNA construct that
expresses a cancer antigen. In another embodiment, the immunotherapeutic composition used in the methods described herein is a composition comprising cancer antigens or fragments thereof as peptides or proteins. In another embodiment, the immunotherapeutic composition used in the methods described herein is a monoclonal antibody or antigen- binding fragment(s) that specifically bind cancer antigens. The compositions are those that are created using known recombinant and synthetic techniques. See, e.g., reference in the examples to an exemplary melanoma immunotherapeutic composition, AdC68- gDMelapoly described in detail in US Patent No.9,402,888 and in Fig.7 thereof. Many immunotherapeutic cancer “vaccines” are known and described in the art that can be used in the methods described herein. By “antigen or ligand on the tumor cell” is meant a full-length, wild-type tumor- specific antigen or mutated tumor-specific antigens or tumor-associated antigens. Tumor- specific antigens are those epitopes and proteins found on a selected specific cancer or tumor cell, and not on all cancer cells. Cancer-associated antigens are antigens that may be associated with more than one cancer or tumor cell type. Exemplary cancer-specific antigens can include, without limitation, 707-AP, alpha (a)–fetoprotein, ART-4, BAGE; b- catenin/m, b-catenin/mutated Bacabal, CAMEL, CAP-1, mCASP-8, CDC27m, CDK4/m, CEA, CT, Cuyp-B, MAGE-B2, MAGE-B1, ELF2M, ETV6-AML1, G250, GAGE, GnT- V, Gp100, HAGE, HER-2/neu , HPV-E7, HSP70-2M HST-2, hTERT, iCE , KIAA0205, LAGE, LDLR/FUT, MAGE , MART-1, MC1R, MUC1, MUM-1, -2, -3, P15, p190 minor bcr-abl. Still other suitable tumor or cancer genes encode VEGFR1, VEGFR2, MAGE-A1, MUC-1, Thymosin β1, EGFR, Her-2/neu, MAGE-3, Survivin, Heparinase 1, Heparinase 2, and CEA, among others. Still other suitable antigens are those listed in the references, and incorporated by reference herein. See, also, texts identifying suitable antigens, such as Scott and Renner, in Encyclopedia of life Sciences 2001 Eds., John Wiley & Sons, Ltd. By “vector” is meant an entity that delivers a heterologous molecule to cells, either for therapeutic or vaccine purposes. As used herein, a vector may include any genetic element including, without limitation, naked DNA, a phage, transposon, cosmid, episome, plasmid, or a virus or bacterium. Vectors are generated using the techniques and sequences provided herein, described in the examples, and in conjunction with techniques known to those of skill in the art. Such techniques include conventional cloning techniques of cDNA such as those described in texts such as Green and Sambrook, Molecular Cloning: A
Laboratory Manual.4th Edit, Cold Spring Harbor Laboratory Press, 2012, use of overlapping oligonucleotide sequences of the Salmonella genomes, polymerase chain reaction, and any suitable method which provides the desired nucleotide sequence. By “administering” or “route of administration” is meant delivery of the T cells, FF or derivative thereof, immunotherapeutic composition, or the checkpoint inhibitor used in the methods herein, to the subject. As discussed in detail below, these methods can be independent for each components of the method. Each administration method can occur with or without a pharmaceutical carrier or excipient, or with or without another chemotherapeutic agent into the TME of the subject. Conventional and pharmaceutically acceptable routes of administration include, but are not limited to, systemic routes, such as intraperitoneal, intravenous, intranasal, intravenous, intramuscular, intratracheal, subcutaneous, and other parenteral routes of administration or intratumoral or intranodal administration. In one embodiment, the route of administration is oral. In another embodiment, the route of administration is intraperitoneal. In another embodiment, the route of administration is intravascular. Routes of administration may be combined, if desired. In some embodiments, the administration is repeated periodically, as discussed in detail below. In the context of the compositions and methods described herein, reference to “one or more,” “at least five,” etc. of the compositions, compounds or reagents listed means any one or all combinations of the compositions, reagents or compounds listed. The words “comprise”, “comprises”, and “comprising” are to be interpreted inclusively rather than exclusively, i.e., to include other unspecified components or process steps. The words “consist”, “consisting”, and its variants, are to be interpreted exclusively, rather than inclusively, i.e., to exclude components or steps not specifically recited. As used herein, the term “about” means a variability of 10 % from the reference given, unless otherwise specified. It is to be noted that the term “a” or “an”, refers to one or more, for example, “an antibody,” is understood to represent one or more antibodies. As such, the terms “a” (or “an”), “one or more,” and “at least one” are used interchangeably herein. Unless defined otherwise in this specification, technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art
to which this invention belongs and by reference to published texts, which provide one skilled in the art with a general guide to many of the terms used in the present application. Methods of Treatment Provided herein are methods of treating cancer. In one embodiment of the methods described herein, a method for treating cancer includes administering to a subject having a cancer a composition comprising a T cell as described herein in combination with a fenofibrate (FF), fenofibric acid (FFA), FFA prodrug, or a derivative thereof that has PPAR-α agonist activity. The T cells for such pre-treatment are selected from the list of T cells identified above. These methods may employ as the T cells an autologous or heterologous, naturally occurring T cell or a recombinantly or synthetically modified T cell construct. The T cell or population may be a human T cell or natural killer (NK) T cell or T infiltrating lymphocyte (TIL) obtained from the subject or from a bone marrow transplant match for the subject. In still other embodiments the T cell or population is obtained from human peripheral blood or from the tumor microenvironment of the subject. In still other embodiments, the T cell is modified to express a heterologous antigen receptor, or a chimeric antigen receptor (CAR-T) or a chimeric endocrine receptor (CER-T) prior to administration to the subject. In still other embodiments, the T cell or population is an endogenous or heterologous human T cell or human T cell line. In yet other embodiments, the T cell is a TIL or a CD8+ T cell. In certain embodiments, the T cell is a CAR-T cell. In other embodiments, the T cell is a tumor infiltration lymphocyte (TIL). The methods employ fenofibrate, fenofibric acid (FFA), FFA prodrug, or derivative thereof. in one embodiment, the compound is fenofibrate. In another embodiment, the compound is fenofibric acid. In another embodiment, the compound is (S)-2-((S)-2-(2-(4-(4-chlorobenzoyl)phenoxy)-2-methylpropanamido) propanamido) pentanedioic acid (also known as FFP). In another embodiment, a compound useful in the methods described herein is GW7647 (2-(4-(2-(1-Cyclohexanebutyl)-3-cyclohexylureido)- ethyl)-phenyl-thio)-2-methyl-propionic acid). In yet another embodiment, a compound useful in these methods is (S)-2-((S)-2-(2-(2-(4-(4-chlorobenzoyl)phenoxy)-2-methyl propanoyloxy) acetamido) propanamido) pentanedioic acid.
Other compounds that have PPAR-α agonist activity include gemfibrozil, bezafibrate, LY518674, BMS-711939, Pirinixic acid (Wy-14643) and GW 590735. Still other compounds that have PPAR-α agonist activity include MHY553, CAY10767, KRP297, CP775146, clofibrate, clofibric acid, pioglitazone, elafibranor, BMS687453, ciprofibrate, darglitazone, and GW 9578. In one embodiment a suitable concentration of the FF, FFA, FFA prodrug or derivative (or similar compound as described herein) is at least 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, to at least about 500 µM. Similarly, intervening concentration between any two numbers listed is encompassed in the term “suitable concentration”. In another embodiment, this method involves further administration with an immunotherapeutic composition. In still other embodiments, the method can also include administering a checkpoint inhibitor in the form of an antibody or a small molecule either simultaneously with or sequentially with the T cells, combination with a fenofibrate (FF), FFA, FFA prodrug, or a derivative thereof that has PPAR-α agonist activity and/or the immunotherapeutic composition. In any of the methods described herein, the FF, FFA, FFA prodrug or derivative, or the immunotherapeutic composition and the T cells are administered substantially simultaneously. In other embodiments, the FF, FFA, FFA prodrug or derivative, or the immunotherapeutic composition is administered after the T cells. In other embodiments, the FF, FFA, FFA prodrug or derivative, or the immunotherapeutic composition is administered prior to the T cells. In another embodiment, the FF, FFA, FFA prodrug or derivative compound and the T cells are administered by the same or different routes of administration. The routes of administration selected depend upon the nature of the compositions. For example, for FF, FFA, FFA prodrug or another small chemical molecule derivative, such molecules may be administered orally in doses known and accepted for other pharmaceutical uses of these drugs. In one embodiment, the immunotherapeutic composition and FF, FFA, FFA prodrug or derivative are independently administered systemically by intramuscular, intraperitoneal, intravenous, intratumoral or intranodal administration. In other
administration protocols, the FF, FFA, FFA prodrug or derivative compound or the T cells are administered once or repeatedly from at least one to 14 days. In some protocols, the administration of the FF, FFA, FFA prodrug or derivative compound occurs one to 14 days after administration of the T cell composition. In certain embodiments, the T cells or FF, FFA, FFA prodrug or derivative compound is/are administered in a single dose. In other embodiments, the T cells or FF, FFA, FFA prodrug or derivative compound is/are administered as a booster dose. In another embodiment, an immunotherapeutic composition targeting an antigen or ligand on the tumor cell is also administered. In another embodiment, this method also involves administering a checkpoint inhibitor in the form of an antibody or a small molecule. In still further aspects of these methods, the subject may be treated with other anti- cancer therapies before, during or after treatment with the T cells and/or FF, FFA, FFA prodrug or derivative thereof. Such treatment may be concurrent or simultaneous or overlap treatment with the T cell and/or the FF, prodrug or derivative compound. In one embodiment, the methods involve treating the subject with chemotherapy before administering the T cells. In still another embodiment, the method further comprises depleting the subject of lymphocytes and optionally surgically resecting the tumor prior to treatment with the T cells and treatment with FF, an FFA prodrug or a derivative. In some embodiments, the T cells are administered in a single dose, followed by administration of the FF, prodrug or derivative compound. These doses may be repeated. Any of these therapeutic compositions and components of the methods may be administered to a patient, preferably suspended in a biologically compatible solution or pharmaceutically acceptable delivery vehicle. The various components of the methods are prepared for administration by being suspended or dissolved in a pharmaceutically or physiologically acceptable carrier such as isotonic saline; isotonic salts solution or other formulations that will be apparent to those skilled in such administration. The appropriate carrier will be evident to those skilled in the art and will depend in large part upon the route of administration. Other aqueous and non-aqueous isotonic sterile injection solutions and aqueous and non-aqueous sterile suspensions known to be pharmaceutically acceptable carriers and well known to those of skill in the art may be employed for this purpose.
Dosages of these therapeutic compositions will depend primarily on factors such as type of composition (i.e., T cells, FF, FFA, FFA prodrug or derivative compound, nucleic acid constructs or proteins) the condition being treated, the age, weight, and health of the patient, and may thus vary among patients. The dosages for administration of the components of the methods are the conventional dosages known to be useful for administering that component. An attending physician may select appropriate dosages using the following as guidelines. In one embodiment, a useful dosage of a T cell is a single-infusion maximum tolerated dose (MTD), which may be determined by dose escalation studies in animal models. In one embodiment, a typical efficacious and non-toxic dose of T cells is between about 2 x 104 to 5 x 109 cells per kg/subject body weight. Other doses, such as 105 or 106 or 107 or 108 can be useful. See, the methods for dose determination as described in e.g., WO2016/054153 and in other CAR publications in the art. In yet another embodiment, a “standard” efficacious and non-toxic dose of T cells for adoptive transfer is about 107 cells. As another example, the number of adoptively transferred T cells can be optimized by one of skill in the art. In one embodiment, such a dosage can range from about 105 to about 1011 cells per kilogram of body weight of the subject. In one embodiment, a typical dosage of an immunotherapeutic composition depends upon the nature of the composition. For example, if the composition is delivered in a viral vector, a therapeutically effective adult human or veterinary dosage of a viral vector is generally in the range of from about 100 µL to about 100 mL of a carrier containing concentrations of from about 1 x 106 to about 1 x 1015 particles, about 1 x 1011 to 1 x 1013 particles, or about 1 x 109 to 1x 1012 particles virus. If a composition (e.g., the immunotherapeutic composition or checkpoint inhibitor) is administered as an antibody or other protein, the dosages may range between a unit dosage of between 0.01 mg to 100 mg of protein (which is equivalent to about 12.5 µg/kg body weight). The dosage of the checkpoint inhibitor may be adjusted based on known toxicities of the particular antibody or small molecule used. If any of the immunotherapeutic composition or the other components of the method is administered as naked DNA, the dosages may range from about 50 μg to about 1 mg of DNA per mL of a sterile solution.
Similarly, the doses of the FF, FFA, FFA prodrug, or derivative compound may be similar to those administered for other uses, e.g., for cholesterol control or hyperlipidemia, of the similar compound. For example, FF may be administered at dosages of from 40 mg/day to 120 mg/day for adults. Other dosages are taught in the references recited herein and can be readily adjusted by one of skill in the art depending upon the treatment regimen, physical condition of the patient, type and stage and location of the tumor being treated, and taking into consideration other ancillary chemotherapies being used to treat the patient. In yet another aspect, a therapeutic regimen is provided for the treatment of cancer comprising administering to a subject having a cancer characterized by a solid tumor T cells in combination with FF, FFA, an FFA prodrug, or a derivative compound. The FF, FFA, FFA prodrug or derivative compound can occur on day 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or day 14 or even later than day 14, after administration of the T cells. The following examples are provided for illustration only and the invention should in no way be construed as being limited to these examples but rather should be construed to encompass any and all variations that become evident as a result of the teaching provided herein. EXAMPLES Example 1 : Materials and Methods Tumor specimen from patient Tumors were obtained directly after surgery from patients of Hospital of the University of Pennsylvania upon their informed consent. To protect patients’ confidentiality data on their gender, age, ethnicity were not provided to the investigators of this study. Mice and surgical procedure All animal procedures were approved by the Institutional Animal Care and Use Committee of the Wistar Institute (Philadelphia, PA, 19104). Male NSG mice (6-8 weeks) were obtained from Wistar Institute Animal Facility and kept under barriers conditions suited for severely immunocompromised mice. Transfer of fresh human tumor fragments
Tumors were cut into small pieces. NSG mice received the analgesic drug Buprenorphine (1 mg/kg SQ) 20-30 min before surgery. Isoflurane was administrated to anaesthetize the mice. An ~5 mm incision was made in shaved skin of the lateral body wall posterior to the axillary area. A subcutaneous pouch was created by blunt dissection. Fresh human tumor fragments (n=4-5) were inserted, and incision was closed with sterile clips. Amoxicillin (Sandoz, NDC# 0781-6041-55) was given at 1.9 ml/22.7 mg in 250 ml of water orally for 14 days post-surgery. Mice were under post-operative care for 2 weeks. Clips were removed 14 days post-surgery and tumors were measured using caliper 5 times/week. Treatment started when tumors reached ~ 0.5 cm in volume. Isolation of melanoma cells Tumor fragments were suspended in in HBSS with Ca+ and Mg+ (Corning, cat# 21- 023-CV) containing 50U/ml DNase I (Sigma-Aldrich, REF# 04716728001), 2mg/ml collagenase IV (Sigma-Aldrich, cat# C4-28), and 1mg/ml hyaluronidase V (Sigma- Aldrich, cat# H6254) diluted in HBSS with Ca+ and Mg+ (Corning, cat# 21-023-CV) at 37oC for 1 hour followed by under agitation for 30 min. They were then filtered through 70 uM cell strainers, washed twice in HBSS and cultured in RPMI media containing 10% FBS. Prior to injection into mice cells were collected, washed and 5 x 105 cells in 100 µl of serum-free medium mixed with 100ul Matrigel matrix (Corning, cat# 356234) were injected subcutaneously into the left flanks of mice. Isolation of TILs For some experiments ~ 3 mm3 tumor fragments were cultured in 24 well-plates with AIMV media (Gibco, cat#12-055-091) supplemented with 300 IU/ml of human IL-2 (Sigma-Aldrich, cat# 11147528001), 10ng/ml of recombinant human IL-15 (Peprotech, cat# 200-15), 5% human serum (Sigma-Aldrich, cat# H3667), 100U/ml penicillin, 100ug/ml streptomycin (Gibco, cat# 15140-122), and 25mmol/L Hepes (Gibco, cat# 15630) and 5.5 × 10−5 mol/L β-mercaptoethanol in a 37°C incubator with 5% CO2. Half of the medium was replaced twice a week. After 10-14 days of culture residual tumor fragments were removed and lymphocytes were transferred to fresh wells and culture in medium containing 30 IU/ml of IL-2. Alternatively, tumor fragments were digested as described above and TILs were purified by Ficoll density gradient centrifugation at 2000 RPM for 20 min at room temperature. Enrichment of CD8+ T cells
CD8+ TILs were selected for by using magnetic beads of the Human CD8+ T cell enrichment kit (Stemcell, cat# 19053) and EasySep RoboSep buffer (Stemcell, cat# 20104). CD8+ were cultured in AIMV media (Gibco, cat#12-055-091) supplemented with 30 IU/ml of human IL-2 (Sigma-Aldrich, cat# 11147528001), 10ng/ml of recombinant human IL-15 (Peprotech, Cat# 200-15), 5% human serum (Sigma-Aldrich, cat# H3667), 100U/ml penicillin, 100ug/ml streptomycin (Gibco, cat# 15140-122), and 25mmol/L Hepes (Gibco, cat# 15630) and 5.5 × 10−5 mol/L β-mercaptoethanol. T cell of patient I grew poorly under those conditions. They were initially cultured in plates coated with 1ug/ml of anti-human CD3 (Invitrogen, REF# 16-0038-81; clone# OKT3; RRID: AB- 468854) and 1ug/ml anti-human CD28 (Invitrogen, eBioscience, Cat# 16-0289-81, clone# CD28.2; RRID: AA-468927) in a pre-coated 96 well-plate for 72 hrs. They were then maintained like the T cells from the other patients. In vitro FA treatment of CD8+ T cells Humans CD8+ TILs were expanded as described above. Once they reached to confluency, they were split into two groups and suspended in AIMV medium. One was treated with 100uM of FA in 2% DMSO (Sigma-Aldrich, cat# D2650), the other was treated with 2 % DMSO for 14 days. AIMV medium with the additives was changed 2-3 times a week. Adoptive transfer of autologous CD8+ T cells Human CD8+ cells were washed and 1x105 cells in 100 µl of serum-free medium with 30 IU/ml IL-2 were injected s.c. close to the growing tumors. Control group received 100ul of serum-free medium instead. FF treatment of mice FF (Sigma-Aldrich, cat# F6020) at 100mg/kg/day in PBS containing 2% DMSO was given orally to mice daily for 3-4 weeks and 1x PBS. Control mice received PBS with 2% DMSO. Treatment began when tumors reached 0.5 cm in diameter and was stopped when tumor reached to about 1.5-2 cm. Tumor volume was measured 5 times a week and calculated according to the formula: ½ (length x (width^2)). Tumors were once they exceeded a volume of 2.5-3.5 cm3. RNA extraction, cDNA synthesis and qPCR Tumors were collected from euthanized mice, digested as described above, TILs were purified and RNA was isolated using TRIzol reagent (Invitrogen, cat# 15596026).
RNAs were resuspended in 20ul of diethylpyrocarbonate-treated water (Ambion, AM9915G), treated with DNAse I (Sigma-aldrich, cat# 04716728001) and RNasin Plus (Promega, cat# N261B). Samples were incubated at 37°C for 20 min and then run on thermal cycler (Eppendorf Mastercycler) at 75oC for 10 min. The purity of RNA samples was assessed by measuring UV absorbance at A260 (260 nm) Complimentary (c)DNA was synthetized using the high-capacity cDNA reverse transcription kit (Applied biosystems cat# 4368814) according to the manufacturer protocol. Minus-RT control without reverse transcriptase was generated along with RNA samples to ensure lack of DNA contamination. The qRT-PCR was conducted in duplicates with Powerup SYBR Green Master Mix (Applied biosystems, cat# A25742) using 7500 standard mode Real-Time PCR system (Applied Biosystems, Foster City, CA). Isolation of lymphocytes from spleens Lymphocytes were isolated from spleen of mice as described before (43). Surface marker and intracellular cytokine staining Lymphocytes from tumors and spleens were stained with APC-labeled anti-human CD8 (Invitrogen eBioscience, cat# 17-0088-42), BV605-labeled anti-human CD4 (BD Horizon, cat# 565998), Alexa Fluor 700 anti-human CD44 (BioLegend, cat# 338813), PE anti-human PD1 (Biolegend, cat# 329906), Alexa Fluor 647 anti-human LAG3 (Biolegend, cat# 369304) and PerCP/Cyanine5.5-labeled anti-human CTLA-4 (BioLegend, cat# 349928) at 1 in 100ul of cell staining buffer (BioLegend, cat# 420201). Live/dead fixable violet dead cell stain (Invitrogen, cat#L34955) was diluted at 1 in 400ul of cell staining buffer. Cells were incubated with antibodies at 4C for 30 min. Next, cells were washed with cell staining buffer, fixed and permeabilized with BD cytofix/cytoperm (BD Biosciences, cat# 51-2090KZ) at 4C for 20 min. Then cells were washed with BD perm/wash (BD Biosciences, cat#51-2091KZ) and stained with FITC-labeled anti-human IFN-γ (BioLegend, cat# 506504) at 4C for 30 min. Followed by washing the cells once and analyzed by BD FACSCelesta Cell Analyzer (BD Biosciences). Data was calculated by FlowJo (TreeStar). Immunohistochemistry 4-μm sections of paraffin-embedded tumors were mounted on charged slides and baked at 60°C for 1 hour. Sections were deparaffinized and rehydrated in two consecutive changes of Xylene substitute, 100% EtOH, 95% EtOH, and deionized water. Hydrophobic
barriers were drawn around the tissue sections with Vector ImmEdge Pen. Antigen retrieval was achieved with DAKO EDT (pH 9) under pressure at 110°C for 10 minutes. Slides were cooled on the counter for 20 minutes and rinsed with water. They were immersed in a 3% hydrogen peroxide solution for 10 minutes, then rinsed in water. First primary antibody (anti-CD8 from Cell Signaling Technology) diluted with Cell Signaling Technology Signal Stain Ab diluent was applied to tissue sections and incubated overnight at 4°C. After rinsing, secondary antibody (Vector HRP anti-rabbit polymer) was applied to all sections and incubated for 30 minutes at room temperature. AEC (red) Vector peroxidase was applied for 30 minutes. Control sections were only treated with the 2nd antibody and the substrate. Sections were analyzed with Nikon Eclipse Ti Inverted Microscope, Light Engine SOLA SE II 365, PSF (Perfect Focus System), Motorized FL Filter Turret, Prior Stage, Piezo Stage, using a Nikon 20X Plan Apo, N.A..95 objective and the Nikon NIS Elements AR Version 5.30.02 (Build 1545) software. Statistical analysis All statistical analyses were conducted using GraphPad Prism 6 (GraphPad). Differences between 2 populations were calculated by Student’s t-test. Multiple comparisons between two groups were performed by multiple t-test with type I error correction. Differences among multiple populations were calculated by one- or two-way ANOVA. Differences in survival were calculated by Log-rank Mantel-Cox test. Differences between tumor growth curves were determined by repeated measures two-way ANOVA. Type I errors were corrected by Holm-Šídák method. Significance was set at p values of or below 0.05. For all figures, ∗p ≤0.05 – 0.01, ∗∗ p≤0.01-0.001, ∗∗∗ p ≤0.001- 0.0001, ∗∗∗∗ p≤0.0001. Unless noted in the figure legend, all data are shown as mean +/- SEM. Example 2 NSG mice that carried human tumor transplants had readily detectable human T cells in their blood which presumably originated from the tumor fragments. Treatment of mice with fenofibrate once tumor reached a certain size delayed tumor progression. It is possible that the delay of tumor progression was caused by the human T cells which upon fenofibrate treatment showed increased expression of PD-1 and fatty acid uptake by flow cytometry which is an indication that T cells were switching from glycolysis to fatty acid
metabolism. This was confirmed by an analysis of the T cells transcriptome. Alternatively it could reflect that the drugs affected tumor cells directly. This was tested by transferring tumor cells that that we had cultured from one of the melanoma patients (Patient K) into NSG mice. Once tumors became visible, we treated mice with DMSO or fenofibrate and measured tumor progression (FIG.1). Treatment initially delayed tumor progression and differences between the two groups were significant between days 11-18 of treatment but then differences declined, suggesting that fenofibrate delayed tumor progression although the effect might be transient. At euthanasia we isolated RNA from the tumors and upon reverse transcription analyzed samples for expression of transcripts for metabolic markers by qPCR. Due to the small number of samples the data did not reach significance. Nevertheless, there were some trends. Increases were seen upon fenofibrate treatment in transcripts for CPT-1, a fatty acid transporter, SHMT, which plays a role in one carbon metabolism and GDLC involved in amino acid metabolism and GPI, an enzyme of the glycolytic pathway, which is also considered a tumor cell cytokine and has angiogenic functions while LDH, which converts pyruvate to lactate, decreased. To further assess how fenofibrate affects metabolism of human melanoma cells we cultured tumor cells of patient K in medium containing glucose or galactose. Twenty-four hours of changing medium fenofibrate (a metabolite of fenofibrate that is more suitable than fenofibrate for in vitro studies) or DMSO were added to the cells. Cells were harvested 7 days later, and transcripts were analyzed. In cell cultured in presence of glucose changes in presence of fenofibrate were marginal presumably reflecting that availability of this nutrient overcame the effects of the PPARα agonist on fatty acid metabolism. In contrast in cells cultured in galactose without glucose increased enzymes of fatty acid metabolism. We repeated the galactose part of this experiment with larger numbers of replicates. In this experiment we shortened the time of drug-treatment to 3 days. The results were unexpected – they showed that fenofibrate decreased transcripts for all tested markers. The likely explanation for the discrepancy in results was that we shortened the duration of drug treatment ad that cells need a period of adjustment before they show metabolic changes.
Example 3 Lymphocytes were isolated from the tumor of a patient with metastatic melanoma. T cells were isolated from part of the tumor and expanded in vitro in IL-2. Tumor fragments were transplanted under the skin of NSG mice. Once tumors reached a certain size fragments were again transplanted into fresh NSG mice. For the experiment tumor fragments of passage 4 (3 previous passaged in NSG mice) were transplanted under the skin of 20 NSG mice. Tumors became visible 18 days later. Three days later ten mice received 1 x 10e5 of the autologous T cells, which had prior to transfer been depleted of CD4+ T cells. Three days later 5 of the mice that had received T cells as well as 5 additional tumor-bearing NSG mice were given fenofibrate at 200 mg/kg/day till the end of the experiment. The other mice received DMSO. Tumor volumes were measured. FIG. 5A shows tumor volumes in individual mice that had received T cells at the indicated days after initiation of drug treatment. Fenofibrate treated mice are shown on the left, DMSO treated mice are shown on the right. FIG.5B shows tumor volumes in fenofibrate (left) and DMSO (right) treated mice that had not received T cells. Significance of differences were calculated within groups by multiple student t-test. ** p value between 0.001-0.01, *** p-value between 0.001-0.0001. Example 4 Adoptive transfer of tumor antigen specific CD8+ T cells can limit tumor progression but is hampered by the T cells’ rapid functional impairment within the tumor microenvironment (TME). This is in part caused by metabolic stress due to lack of oxygen and glucose. Here we show that metabolic reprogramming of human ex vivo expanded tumor infiltrating lymphocytes (TILs) improves their ability to limit melanoma progression in a patient-derived xenograft (PDX) mouse model. TILs treated with a PPARα agonist switch from glycolysis to fatty acid oxidation and this increases their ability to slow the progression of autologous melanomas as is shown with both freshly transplanted human tumor fragments and mice injected with tumor cell lines established from the patients’ melanomas and ex vivo expanded TILs from the same patients.
The effect of a PPARα agonist on melanoma growth in a PDX model To assess the effect of fenofibrate, a PPARα agonist, on human melanomas and melanoma infiltrating lymphocytes we used a PDX model in which human melanoma fragments were transplanted into immunodeficient NOD SCID (NSG) mice. Fresh primary or recurrent melanoma or melanoma metastasis samples (n=12, A-Q) obtained within hours after surgery were cut into small pieces, which were transplanted each under the skin of 4-5 NSG mice (FIG.3A). Tumor growth was observed after transplantation of 9 (D, E, G, I, M, N, O, P, Q) of 12 melanoma samples and tumors typically became visible within 3-8 weeks (FIG.3B). Once tumor reached a size of ~0.5-1 cm in diameter, mice, which had received fragments from Patients D, E and I, were treated for 3 weeks orally with fenofibrate (FF) or its dimethylsulfoxide (DMSO) containing diluent. Tumor growth was monitored. Oral FF treatment delayed progression of the primary melanoma of patient D, the recurrent melanoma of Patient E and the metastatic melanoma of Patient I (FIG.3C, FIG.3D). Mice that received tumors of patients D and E were tested for presence of human T cells that had infiltrated the human tumors and were transplanted as part of the tumor fragments. Peripheral blood mononuclear cells (PBMCs) were tested at 6 (E) and 8 (D) weeks after transplantation and spleens and tumors were tested at euthanasia. As shown in FIG.3E, human CD4+ and CD8+ T cells could be detected in blood and at lower and more variable numbers in spleens and tumors. To assess if T cells remain present upon serial passages of tumors, melanomas of patients I, K, M, and N, once they exceeded a volume of 2-2.5 cm in NSG mice were excised and fragments were transplanted into new NSG mice. This process was repeated once or twice more. Mice that received the 3rd (K,I) or 4th (I) passage fragments were tested for human T cells in blood (K,I), spleens and tumors (I,M,N). Although there was a trend for reduced T cell recovery from blood upon serial passages, numbers remained unchanged in spleens and tumors. Blood of control mice that did nor receive melanoma fragments had no detectable human CD8+ T cells in blood and less than 10 cells/105 live lymphoid cells that stained non-specifically with an antibody to human CD4 (FIG.3E). These data show that a PPARα agonist delays tumor progression in a PDX melanoma model and that human TILs survive sequential passages of melanoma fragments. The effect of a PPARα agonist in a human melanoma PDX model with autologous T cell transfer
Next, we isolated T cells from the initial tumor samples. Tumors from the same patients were maintained by sequential passages in NSG mice. T cells once they had been enriched for CD8+ cells were expanded in vitro in medium containing IL-2. Mice that carried homologous tumor fragments were divided into 4 groups of 5 mice each. Group A received autologous CD8+ T cells that had been treated for 2 weeks with fenofibric acid (FA), a FF derivative that is suited for use in cell culture. Recipient mice were treated with FF after T cell transfer. Group B received DMSO treated T cells and was then treated with DMSO, Groups C and D were not injected with human T cells, they were only treated with FF or DMSO (FIG.4A). Mice that received fragments from patients I, N and O showed reduced tumor growth if there were given T cells with FF compared to mice that only received the drug or its diluent. Mice with fragments from patients M benefited from FF regardless of CD8+ T cell transfer (FIG.4B, FIG.4C). We isolated TILs at euthanasia from spleens and tumors from mice of groups A-C. Flow cytometric analyses that overall recovery of live lymphoid cells was highest from tumors of mice that received CD8+ T cells and FF and there was also a significant difference between mice of groups B and C. Mice showed low recovery of human CD8+ T cells from spleens and there was no difference between mice of the 3 groups (A-C). Most striking were results obtained with TILs; recovery of CD8+ T cells from tumors was significantly higher in group A than groups B and C and there were no significant differences between groups B and C indicating that without FF the transferred T cells had either not migrated to the tumors or more likely that they had not survived within the TME (FIG.4C). It is also noteworthy that small numbers of CD8+ TILs could be recovered from group C; these mice had not received ex vivo expanded T cells indicating that the cells originated from the serially transplanted tumor samples as already shown in FIG.3A – FIG.3E. TILs of groups A and B were tested by quantitative reverse transcription polymerase chain reaction (qRT-PCR) for transcripts encoding enzymes that play a role in different metabolic pathways. TILs from group 1 in comparison to group 2 showed modest increases in transcripts involved in fatty acid metabolism, i.e., Carnitine palmitoyltransferase I (CPT-1), which is instrumental to transport fatty acids into mitochondria, PPAR-a, the master regulator of fatty acid metabolism and D-beta- hydroxybutyrate dehydrogenase (BDH) an enzyme that is involved in catabolism of ketone bodies. TILs from patient I in addition showed a reduction in transcripts for some
of the glycolytic enzymes (FIG.4D). Overall, these results confirm the 1st set of studies that fenofibrate slows tumor progression. Nevertheless, the results do not allow us to conclude that reduced tumor progression was caused by metabolic changes within CD8+ T cells or alternatively by a direct effect of the drug on tumor growth as even after several passages T cells were transferred alongside the melanoma fragments. To measure the effects of FF on the ability of ex vivo expanded TILs to delay tumor progression without potential interference by TILs that had been passaged with the melanoma fragments, we established tumor cell lines from the melanomas of patients I, M, N and Q. After expansion 1.5 x 105 of each set of tumor cells were injected into 4 groups of NSG mice. TILs from the same patients were expanded in vitro using in this experiment medium containing both IL-2 and IL-15. T cells were treated for 2 weeks with FA or DMSO and then transferred into 2 groups of mice (A and B) that carried visible tumors (~ 0.2 cm in diameter). Mice of group A were treated with FF, mice of group B received DMSO. Groups C and D were treated with FF or DMSO, respectively, but did not receive T cells (FIG.5A). Samples from the different patients showed comparable patters so we combined their data for most of the statistical analysis. Tumor growth was significantly delayed in group A compared to the other 3 groups indicating that the delay in tumor progression was caused by the combination of the PPAR-a agonist and the transferred CD8+ T cells. Small differences were also seen between Groups C and D suggesting that FF by itself has a modest effect on tumor progression and groups B and D indicating an effect of transferred CD8+ T cells even when they were left untreated (FIG. 5B – FIG.5D). Mice were euthanized once tumors exceeded a volume of ~ 2.5 cm and survival time was recorded. Regardless of the tumors’ origin only group A showed an increase in survival time (FIG.5E). An analysis of splenocytes and TILs showed again higher recovery of live lymphoid cells from tumors of group A compared to the other 3 groups (FIG.5A). There was a trend in groups A and B towards higher recovery of CD8+ T cells from tumors than spleens. Group A had significantly higher CD8+ TIL counts compared to the other groups. Although some CD8+ T cells could be recovered from group B this failed to reach significance compared to the low numbers of recovered cells that exhibited non-specific staining in groups C and D. T cells were tested for production of IFN-g; 80-90% of CD8+ T cells from group A produced this cytokine. IFN-g production
was less frequent in CD8+ T cells from group B suggesting that FF preserved T cell functions (FIG.6A). Immunohistology from tumors confirmed the data obtained by flow cytometry (FIG.6B); those of group A were heavily infiltrated by human CD8+ T cells that accumulated at the border between healthy and necrotic tumor tissue (FIG.6C) while CD8+ T cells were rare in group B. Those that could be detected in group B tumors commonly showed membrane blebbing that is typically associated with apoptosis (FIG. 6D). CD8+ T cells from the mice with recovery, were tested for exhaustion/differentiation markers (FIG.6E). Percentages of PD-1+CD8+ cells were higher in group A than B tumors or group A spleens. Expression of lymphocyte activating protein (LAG-3) was not increased while percentages of cytotoxic T-Lymphocyte associated protein (CTLA-4) were increased in group A tumors compared to spleens. In tumors especially those from group A triple positive CD8+ T cells were most common (FIG.6F). TILs from groups A and B as well as tumor cells from groups C and D were tested for transcripts encoding metabolic enzymes. Samples from the 4 different patients showed comparable patterns. Group A T cells compared to group B T cells showed highly significant increases in transcripts for enzymes of fatty acid metabolism and decreases in those of glycolysis and histone methyltransferase (HMT), an enzyme of one-carbon metabolism (FIG.6G). No metabolic differences were observed between tumor cells from mice of groups C and D (FIG.6H). The combined data of groups A and B were analyzed for correlations by Spearman. As shown in FIG.7, there were strong inverse correlations between tumor growth, represented by the slope of the linear regression curves in FIG.5 and lymphocyte, CD8+ and IFN-g+CD8+ T cell counts in tumors. For the cycle threshold (Ct) values there were strong positive correlations between tumor growth and transcripts for enzymes of fatty acid metabolism and inverse correlations between tumor growth and enzymes of glycolysis. As Ct values are inversely related to levels of transcripts, high levels of fatty acid metabolism combined with reduced glycolysis correlated with delayed tumor growth. Lymphocyte and T cell counts in tumors showed strong inverse correlation with the Ct values for enzymes of fatty acid metabolism and direct correlations with those for glycolysis indicating that preservation of the transferred T cells was linked to their switch from glycolysis to fatty acid metabolism. As expected, enzymes of a given metabolic
pathway showed strong positive correlations with each other and inverse correlation with those of the other pathway. Regarding exhaustion markers percentages of human CD8+ cells that were only positive for PD-1 inversely correlated with the slope of tumor growth and Ct values for transcripts for enzymes of FAO but showed positive correlations for enzymes of glycolysis and CD8+ T cell recovery. CD8+ T cells that were only positive for LAG-3 showed the opposite pattern. These data indicated that PD-1 unlike LAG-3 expression on CD8+ T cells facilitated delay of tumor progression while enhancing FAO and blocking glycolysis. Immunotherapy by T cell transfer has achieved remarkable successes in liquid tumors; their effectiveness in solid tumors remains limited. This is at least in part caused by rapid T cell impairment within the immunosuppressive TME. Resting T cells use the mitochondrial tricarboxylic acid (TCA) cycle to fuel their metabolism by glucose, amino acids and fatty acids. Upon engagement of the T cell receptor with its cognate antigen displayed by major histocompatibility antigens and co-stimulation through ligation of CD28, CD8+ T cells through activation of the phosphoinositide 3-kinase (PI3K)/ Protein kinase B (Akt) pathways increase expression of the glucose receptor (Glut)1and switch their metabolism to glycolysis; this in turn allows them to rapidly generate energy and building blocks for effect functions and cell divisions. As first described by Warburg tumor cell growth is also fueled by aerobic glycolysis, which depletes this nutrient from the TME. Tumor cells can outcompete T cells for glucose, and lack of this nutrient leads to reduced activity of the mammalian target of rapamycin (mTOR), which impairs cytokine production. Lack of the glucose metabolite phosphoenolpyruvate, which is crucial for T cell receptor mediation activation of nuclear factor of activated T cells (Ca++NFAT) further impairs T cell functions. Regulatory T cells in contrast are relatively unaffected by hypoglycemia as they fuel their metabolism primarily through lactate and fatty acids. The tumor cells’ increased secretion of lactic acid, the final metabolite of glycolysis, decreases the TME’s pH, which impairs the T cells’ ability to migrate, produce cytokines or release lytic enzymes. In turn in animal models increasing the TME’s pH was shown to improve the efficacy of T cell-mediated immunotherapy. T cells in a hypoglycemic environment can switch from glycolysis to FAO, which is promoted by increased expression of PD-1. A switch to FAO in absence of glucose not
necessarily terminates T cell activation and it was shown in vitro that T cells can be stimulated and acquire effector functions albeit less efficiently in absence of glucose. We have shown previously in a mouse melanoma model that training T cells to switch to FAO by drug-mediated activation of the PPARa pathway, through FF or its derivative FA preserves their effector functions within the TME and provides them with a survival advantage. In contrast others have shown that increased CD36 mediated uptake of fatty acids can blunt TIL functions. Our initial studies on the effect of FF on melanoma penetrating T cells were conducted in immunocompetent mice that had been injected with mouse tumor cells. Here we extend the validity of these original finding to a human melanoma PDX model in which mice initially received transplants of tumor fragments from patients with metastatic or recurrent melanoma. This model has the advantage that all components of melanoma including tumor and stromal cells as well as TIL subsets are present and thereby mirror the human TME. In order to distinguish if the PPARa agonist delayed tumor progression by negatively affecting the metabolism of tumor cells or improving TIL functions we had to switch to the use of tumor cell lines and adoptively transferred CD8+ TILs. In both models the PPARa agonist delayed tumor progression and, as was shown using the TIL transfer model, this was caused by a metabolic switch of TILs from glycolysis to FAO, as evidence by declines in transcripts encoding glycolytic enzymes accompanied by increases in those involved in metabolism of fatty acid and ketone body. The latter may have been provided by tumors cells as previous studies showed that FF in a PPARa independent way increases production and secretion of ketone bodies by melanoma cells, FF-driven metabolic changes in TILs in turn correlated with increased TIL recovery from human melanoma bearing mice and better preservation of their ability to produce IFN-g. Although FF had previously been shown to slow progression of transplanted mouse melanoma cell line, the drug had no significant effect on growth or metabolism of human melanoma cells. Without treatment with the PPARa agonist only very few human CD8+ TILs could be recovered from the tumors while in contrast sections from mice of group A showed robust infiltration with the human TILs that were commonly clustered around large areas of dead tumor tissue suggesting the T cells had been able to kill the tumor cells. Human CD8+ T cells from spleens and tumors expressed exhaustion markers and ~ 15-20% were triple positive for PD-1, LAG-3 and CTLA-4. The only population that was
significantly increased in group A tumors compared to spleens or group B tumors were human CD8+ T cells that only expressed PD-1. This population correlated with a delay in tumor progression and with the cells’ metabolic switch from glycolysis to FAO. PD-1 signaling is known to inhibit glycolysis by reducing expression of Glut1 and the activity of hexokinase (HK)2 the 1st enzyme of the glycolysis pathway. Inhibition of the PI3K/Akt pathway further augments fatty acid metabolism as supported by our correlation studies. CTLA-4 has similar effects on glycolysis but fails to affect FAO and in our study did not show strong correlations with levels of transcripts of metabolic enzymes, while increased frequencies of human CD8+ T cells expressing LAG-3, which is regulated by HIF-1a and increases under hypoxia correlated with tumor progression, decreases in enzymes of FAO and increases in those involved in glycolysis. Others have attempted to reduce tumor progression by addressing the TILs metabolic defects. Endolase 1, a key glycolytic enzyme needed for production of pyruvate was found to be defective in melanoma infiltrating CD8+ T cells, whose functions improved at least in vitro if they were cultured in medium containing pyruvate. Other metabolic manipulations targeting melanoma cells such as proton pump inhibitors, blockade of glycolysis or inhibition of FAO may block tumor progression but will most likely also impair TIL functions. Metformin is another metabolic drug that has been shown to slow tumor progression both through mTORC1-dependant and independent mechanisms and in addition to improve fitness of CD8+ TILs in different types of solid cancer. Pham JP, et al. Chemotherapy in Cutaneous Melanoma: Is There Still a Role? Curr Oncol Rep.2023 Jun;25(6):609-621. Larkin, J., et al. (2014). Combined vemurafenib and cobimetinib in BRAF-mutated melanoma. New England Journal of Medicine, 371, 1867–1876. Long, G. V., et al. (2017). Dabrafenib plus trametinib versus dabrafenib monotherapy in patients with metastatic BRAF V600E/K-mutant melanoma: Long-term survival and safety analysis of a phase 3 study. Annals of Oncology, 28, 1631–1639. Wahid, M., et al. (2018). Recent developments and obstacles in the treatment of melanoma with BRAF and MEK inhibitors. Critical Reviews in Oncology Hematology, 125, 84– 88.
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Bedogni B, Powell MB. Hypoxia, melanocytes and melanoma - survival and tumor development in the permissive microenvironment of the skin. Pigment Cell Melanoma Res.2009 Apr;22(2):166-74. Einarsdottir BO, et al. Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions. Oncotarget.2014 Oct 30;5(20):9609-18. Garman B, et al. Genetic and Genomic Characterization of 462 Melanoma Patient-Derived Xenografts, Tumor Biopsies, and Cell Lines. Cell Rep.2017 Nov 14;21(7):1936-1952. Pearce EL. Metabolism in T cell activation and differentiation. Curr Opin Immunol.2010 Jun;22(3):314-20. Vander Heiden MG, et al. Understanding the Warburg effect: the metabolic requirements of cell proliferation. Science.2009 May 22;324(5930):1029-33. Kouidhi S, et al. Impact of Metabolism on T-Cell Differentiation and Function and Cross Talk with Tumor Microenvironment. Front Immunol.2017 Mar 13;8:270. Ho PC, et al. Phosphoenolpyruvate is a metabolic checkpoint of anti-tumor T cell responses. Cell (2015) 162(6):1217–28. Kempkes RWM, et al. Metabolic Pathways Involved in Regulatory T Cell Functionality. Front Immunol.2019 Dec 3;10:2839. Fischer K, et al. Inhibitory effect of tumor cell-derived lactic acid on human T cells. Blood.2007;109(9):3812–3819. Pilon-Thomas S, et al. Neutralization of Tumor Acidity Improves Antitumor Responses to Immunotherapy. Cancer Res.2016 Mar 15;76(6):1381-90. Parry RV, et al. CTLA-4 and PD-1 Receptors Inhibit T-Cell Activation by Distinct Mechanisms. Mol Cell Biol.2005;25:9543–9553. Patsoukis N, et al. PD-1 alters T-cell metabolic reprogramming by inhibiting glycolysis and promoting lipolysis and fatty acid oxidation. Nature Communications.2015;6:6692. Cao Y, et al. Metabolic reprogramming towards aerobic glycolysis correlates with greater proliferative ability and resistance to metabolic inhibition in CD8 versus CD4 T cells. PLoS One.2014 Aug 4;9(8):e104104. Doedens AL, et al. Hypoxia-inducible factors enhance the effector responses of CD8(+) T cells to persistent antigen. Nat Immunol 14: 1173–1182, 2013.
Grabacka MM, et al. Fenofibrate Induces Ketone Body Production in Melanoma and Glioblastoma Cells. Front Endocrinol (Lausanne).2016 Feb 2;7:5. Panigrahy D, et al. PPARalpha agonist fenofibrate suppresses tumor growth through direct and indirect angiogenesis inhibition. Proc Natl Acad Sci U S A.2008 Jan 22;105(3):985-90. Gemta LF, et al. Impaired enolase 1 glycolytic activity restrains effector functions of tumor-infiltrating CD8+ T cells. Sci Immunol.2019 Jan 25;4(31):eaap9520. Hersey P, et al. Metabolic approaches to treatment of melanoma. Clin Cancer Res.2009 Nov 1;15(21):6490-4. Jaune E, Rocchi S. Metformin: Focus on Melanoma. Front Endocrinol (Lausanne).2018 Aug 21;9:472. Finisguerra V, et al. Metformin improves cancer immunotherapy by directly rescuing tumor-infiltrating CD8 T lymphocytes from hypoxia-induced immunosuppression. J Immunother Cancer.2023 May;11(5):e005719. Wang R, et al. Metformin Inducing the Change of Functional and Exhausted Phenotypic Tumor-Infiltrated Lymphocytes and the Correlation with JNK Signal Pathway in Triple-Negative Breast Cancer. Breast Cancer (Dove Med Press).2022 Dec 2;14:391- 403. Tsogas FK, et al. Possible Role of Metformin as an Immune Modulator in the Tumor Microenvironment of Ovarian Cancer. Int J Mol Sci.2021 Jan 16;22(2):867. Chekaoui A, Ertl HCJ. PPARα Agonist Fenofibrate Enhances Cancer Vaccine Efficacy. Cancer Res.2021 Sep 1;81(17):4431-4440. Long, G. V., et al. (2017). Dabrafenib plus trametinib versus dabrafenib monotherapy in patients with metastatic BRAF V600E/K-mutant melanoma: Long-term survival and safety analysis of a phase 3 study. Annals of Oncology, 28, 1631–1639. Each and every patent, patent application, and publication cited throughout the disclosure and listed herein is expressly incorporated herein by reference in its entirety. US Provisional Patent Application No.63/383,201, filed Novemeber 10, 2022, is incorporated herein by reference in its entirety. While this invention has been disclosed with reference to specific embodiments, it is apparent that other embodiments and variations of this invention may be devised by others skilled in the art without departing
from the true spirit and scope of the invention. The appended claims include such embodiments and equivalent variations.
Claims
CLAIMS: 1. A method for treating cancer comprising administering to a subject having a cancer a fenofibrate (FF), fenofibric acid (FFA), an FFA prodrug, or a derivative thereof that has PPAR-α agonist activity; and a T cell or T cell population.
2. The method according to claim 1, wherein the FFA prodrug is (S)-2-((S)-2-(2-(4- (4-chlorobenzoyl)phenoxy)-2-methyl propanamido) propanamido) pentanedioic acid (FFP).
3. The method according claim 1, wherein the FFA prodrug is (S)-2-((S)-2-(2-(2-(4- (4-chlorobenzoyl)phenoxy)-2-methylpropanoyloxy) acetamido) propanamido) pentanedioic acid.
4. The method according to any one of claims 1 to 3, wherein the T cell is an autologous or heterologous, naturally occurring T cell or a recombinantly or synthetically modified T cell construct, or a human T cell or natural killer (NK) T cell or T infiltrating lymphocyte (TIL) obtained from the subject or from a bone marrow transplant match for the subject, or a T cell obtained from human peripheral blood or from the tumor microenvironment of the subject, or a T cell modified to express a heterologous antigen receptor, or a chimeric antigen receptor or a chimeric endocrine receptor, or an endogenous or heterologous human T cell or human T cell line, or a CD8+ T cell.
5. The method according to any one of claims 1 to 4, wherein the T cells are autologous tumor infiltrating lymphocytes (TIL).
6. The method according to any one of claims 1 to 3, wherein the T cells are modified to express a heterologous antigen receptor, a chimeric antigen receptor, or a chimeric endocrine receptor.
7. The method according to any one of claims 1 to 6, wherein the T cells have been depleted of CD4+ T cells.
8. The method according to any one of claims 1 to 7, further comprising co- administering to a subject having a cancer an immunotherapeutic composition targeting an antigen or ligand on a tumor cell in the subject.
9. The method according to claim 8, wherein said immunotherapeutic composition is a recombinant virus or virus-like particle that expresses a cancer antigen, a DNA construct that expresses a cancer antigen, a composition comprising a cancer antigen or fragment thereof, or a monoclonal antibody or antigen-binding fragment that specifically binds a cancer antigen.
10. The method according to any one of claims 1 to 9, further comprising administering a checkpoint inhibitor in the form of an antibody or a small molecule.
11. The method according to claim 10, wherein the checkpoint inhibitor is an anti-PD- 1 antibody or small molecule ligand.
12. The method according to any one of claims 1 to 11, wherein the fenofibrate (FF), FFA, FFA prodrug, or derivative thereof that has PPAR-α agonist activity is administered after administering the T cells.
13. The method according to claim 12, wherein the fenofibrate (FF), FFA, FFA prodrug, or derivative thereof that has PPAR-α agonist activity is administered 1, 2, 3, 4, 5, 6, 7 or more days after administering the T cells.
14. The method according to any one of claims 1 to 13, wherein the FF, FFA, FFA prodrug, or derivative thereof that has PPAR-α agonist activity and the T cells are independently administered systemically by oral, intramuscular, intraperitoneal, intravenous, intratumoral, or intranodal administration.
15. The method according to any one of claims 1 to 13, wherein the FF, FFA, FFA prodrug, or derivative thereof that has PPAR-α agonist activity and/or the T cells are administered intratumorally or to the site of the tumor.
16. The method according to any one of claims 1 to 15, wherein the T cells are administered once or repeatedly.
17. The method according to any one of claims 1 to 16, further comprising (a) treating the subject with another anti-cancer therapy; and/or (b) treating the subject with chemotherapy before administering the T cells.
18. The method according to claim 17, wherein the anti-cancer therapy comprises depleting the subject of lymphocytes and/or surgically resecting the tumor prior to administration of the T cells.
19. The method according to any one of claims 1 to 18, wherein the cancer or tumor targeted by the method is characterized by hypoxia, significant infiltration with T lymphocytes, and/or low glucose in the tumor microenvironment.
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US20060009506A1 (en) * | 2004-07-09 | 2006-01-12 | Odyssey Thera, Inc. | Drugs for the treatment of neoplastic disorders |
WO2016065353A1 (en) * | 2014-10-24 | 2016-04-28 | University Of Miami | Combination therapy with fenofibrate and 2-deoxyglucose or 2-deoxymannose |
US20210113613A1 (en) * | 2017-08-02 | 2021-04-22 | The Wistar Institute Of Anatomy And Biology | Methods and compositions for treating cancer |
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US20060009506A1 (en) * | 2004-07-09 | 2006-01-12 | Odyssey Thera, Inc. | Drugs for the treatment of neoplastic disorders |
WO2016065353A1 (en) * | 2014-10-24 | 2016-04-28 | University Of Miami | Combination therapy with fenofibrate and 2-deoxyglucose or 2-deoxymannose |
US20210113613A1 (en) * | 2017-08-02 | 2021-04-22 | The Wistar Institute Of Anatomy And Biology | Methods and compositions for treating cancer |
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