Complex biomarkers for cancer therapy

Abstract

The present disclosure provides a method for treating a subject with cancer, comprising administering to the subject with cancer a therapeutically effective amount of an anti-PD-1 antagonist, e.g., an anti-PD-1 or anti-PD-L1 antibody, in combination with an indoleamine 2,3-deoxygenase inhibitor, wherein the subject is identified as exhibiting a combination biomarker comprising (a) a high IFNγ inflammation signature score and (b) a low tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score. The high IFNγ inflammation signature score is determined by measuring the expression of a panel of IFNγ-related inflammation genes in a cancer sample obtained from the subject, wherein the gene panel comprises, e.g., IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, and STAT1. In some aspects, the gene panel further comprises CCR5, CXCL11, GZMA, and PRF1. In some aspects, the gene panel includes CXCR6, TIGIT, PD-L1, PD-L2, LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, and TDO2.

Description

Technology Field

[0001] The present disclosure provides a method for treating a subject suffering from cancer using immunotherapy. Background Technology

[0002] Human cancers possess numerous genetic and epigenetic alterations that generate neoantigens potentially recognizable by the immune system (Sjoblom et al., Science (2006) 314(5797):268-274). The adaptive immune system, composed of T and B lymphocytes, possesses potent anticancer potential due to its broad ability to respond to various tumor antigens and its sophisticated specificity. Additionally, the immune system exhibits significant plasticity and memory components. The successful utilization of all these properties of the adaptive immune system will make immunotherapy unique among all modes of cancer treatment.

[0003] Until recently, cancer immunotherapy has focused significant efforts on approaches that enhance anti-tumor immune responses through the adoptive delivery of activated effector cells, immunization against relevant antigens, or the provision of non-specific immunostimulators such as cytokines. However, over the past decade, intensive efforts to develop specific immune checkpoint pathway inhibitors have begun to provide new immunotherapeutic approaches for treating cancer, including the development of antibodies that specifically bind to programmed death-1 (PD-1) receptors and block the inhibitory PD-1 / PD-1 ligand pathway, such as nivolumab and pembrolizumab (formerly lambrolizumab; [USAN Council Statement, 2013]) (Topalian et al., 2012a, b; Topalian et al., 2014; Hamid et al., 2013; Hamid and Carvajal, 2013; McDermott and Atkins, 2013).

[0004] PD-1 is a major immune checkpoint receptor expressed by activated T and B cells and mediates immunosuppression. PD-1 is a member of the CD28 family of receptors, which includes CD28, CTLA-4, ICOS, PD-1, and BTLA. Two cell surface glycoprotein ligands for PD-1, programmed death ligand-1 (PD-L1) and programmed death ligand-2 (PD-L2), have been identified; these are expressed in antigen-presenting cells as well as many human cancers and have been suggested to downregulate T cell activation and cytokine secretion upon binding to PD-1. Inhibition of the PD-1 / PD-L1 interaction mediates potent antitumor activity in preclinical models (U.S. Patent Nos. 8,008,449 and 7,943,743), and the use of antibody inhibitors of the PD-1 / PD-L1 interaction for treating cancer has entered clinical trials (Brahmer et al., 2010; Topalian et al., 2012a; Topalian et al., 2014; Hamid et al., 2013; Brahmer et al., 2012; Flies et al., 2011; Pardoll, 2012; Hamid and Carvajal, 2013).

[0005] Nivolumab (previously designated as 5C4, BMS-936558, MDX-1106, or ONO-4538) is a fully human IgG4 (S228P) PD-1 immune checkpoint inhibitor antibody that blocks the down-regulation of anti-tumor T-cell function by selectively blocking interactions with PD-1 ligands (PD-L1 and PD-L2) (U.S. Patent No. 8,008,449; Wang et al., 2014). Nivolumab has demonstrated activity in various advanced solid tumors, including renal cell carcinoma (renal adenocarcinoma or adrenal tumor), melanoma, and non-small cell lung cancer (NSCLC) (Topalian et al., 2012a; Topalian et al., 2014; Drake et al., 2013; WO 2013 / 173223). A combination therapy including nivolumab and the indoleamine 2,3-deoxygenase 1 (IDO1) inhibitor lindodostat (BMS-986205) is currently in clinical trials (ClinicalTrials.gov identifier NCT02658890).

[0006] Indoleamine 2,3-deoxygenase (IDO1) is a heme-containing enzyme that catalyzes the O2-dependent oxidation of L-tryptophan to N-formylkynurenine. This reaction is the first and rate-limiting step in the kynurenine pathway, which leads to the production of nicotinamide adenine dinucleotide from the degradation of tryptophan. IDO1 is upregulated by IFNγ in patients and further upregulated by anti-PD-1 therapy (e.g., nivolumab) (Moon YW, et al. J Immunother Cancer 2015;3:51; Liu M et al. J Hematol Oncol 2018;11(1):100). IDO1 and TDO2 catalyze the rate-limiting step in the tryptophan pathway to produce kynurenine (KYN) (Moon YW, et al. J Immunother Cancer 2015;3:51; Liu M, et al. J Hematol Oncol 2018;11(1):100). Lindodostat reduces kynurenine levels and potentially increases effector T-cell function by inhibiting the metabolism of tryptophan to kynurenine (Hunt JT, et al. Clin Cancer Res 2017;77(suppl.). Abstract 4964). For example, see U.S. Patent No. 9,643,972, the full text of which is incorporated herein by reference.

[0007] The immune system and responses to immunotherapy are complex. Additionally, the efficacy of anticancer drugs can vary based on unique patient characteristics. Therefore, there is a need for targeted treatment strategies that identify patients more likely to respond to specific anticancer drugs and, accordingly, improve clinical outcomes for patients diagnosed with cancer.

[0008] The present disclosure provides a method for treating a human subject with cancer, comprising the step of administering an anti-PD-1 antagonist and an indoleamine 2,3-deoxygenase 1 (IDO1) inhibitor to a human subject with cancer, wherein the subject is identified to exhibit a combination biomarker including (a) a high IFNγ inflammation signature score and (b) a low tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score prior to administration; wherein the IFNγ inflammation signature score is determined by measuring the expression of a panel of inflammation genes ("IFNγ inflammation gene panel") including interferon gamma (IFNγ) related genes in a sample obtained from the subject and calculating a score from the expression values.

[0009] Additionally, a method for treating a human subject with cancer is provided, comprising the steps of: (i) identifying a subject exhibiting a combination of biomarkers including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score; and (ii) administering an anti-PD-1 antagonist and an IDO1 inhibitor to the subject; wherein the IFNγ inflammation signature score is determined by measuring the expression of an IFNγ inflammation gene panel in a sample obtained from the subject and calculating a score from the expression values.

[0010] Additionally, a method is provided for identifying a human subject with cancer suitable for treatment with an anti-PD-1 antagonist and an IDO1 inhibitor, comprising the step of measuring an IFNγ inflammation signature score and TDO2 gene expression in a sample obtained from a human subject with cancer; wherein the IFNγ inflammation signature score is determined by measuring the expression of an IFNγ inflammation gene panel in a sample obtained from the subject and calculating a score from the expression values. In some aspects, the subject exhibits a combination biomarker comprising (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score. In some aspects, the method further comprises the step of administering an anti-PD-1 antagonist and an IDO1 inhibitor to the subject.

[0011] The present application also provides an IDO1 inhibitor for treating cancer in combination with an anti-PD-1 antagonist in a human subject requiring treatment for cancer, wherein the subject is identified to exhibit combination biomarkers including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score prior to administration; wherein the IFNγ inflammation signature score is determined by measuring the expression of an IFNγ inflammation gene panel in a sample obtained from the subject and calculating a score from the expression values.

[0012] Additionally, a combination biomarker is provided for identifying human subjects with cancer suitable for treatment with an IDO1 inhibitor in combination with treatment with an anti-PD-1 antagonist, wherein the combination biomarker comprises (i) an IFNγ inflammation signature score and (ii) TDO2 gene expression measured in a sample obtained from the subject; wherein the IFNγ inflammation signature score is determined by measuring the expression of an IFNγ inflammation gene panel in a sample obtained from the subject and calculating a score from the expression values. In some aspects, the subject exhibits a combination biomarker comprising (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score.

[0013] In some aspects, the IFNγ inflammation gene panel essentially consists of 1 inflammation gene, 2 inflammation genes, 3 inflammation genes, 4 inflammation genes, 5 inflammation genes, 6 inflammation genes, 7 inflammation genes, 8 inflammation genes, 9 inflammation genes, 10 inflammation genes, 11 inflammation genes, 12 inflammation genes, 13 inflammation genes, 14 inflammation genes, 15 inflammation genes, 16 inflammation genes, 17 inflammation genes, 18 inflammation genes, 19 inflammation genes, or 20 inflammation genes. In some aspects, inflammatory genes are selected from the group consisting of IFNγ, CXCL10, HLA-DRA, CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, CCR5, CXCL11, GZMA, PRF1, IR2RG, CD3D, CD2, ITGAL, TAGAP, CIITA, PTPRC, CD3E, GZMK, GZMB, PDCD1, SLAMF6, CXCL13 and any combination thereof.

[0014] In some respects, the IFNγ inflammation gene panel consists of or is essentially composed of:

[0015] (i) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1 and STAT1;

[0016] (ii) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1, CCR5, CXCL11, GZMA and PRF1;

[0017] (iii) CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1 and HLA.E; or

[0018] (vi) any combination of the or any combination of genes in (i) to (iii).

[0019] In some aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score greater than the average IFNγ inflammation signature score, where the average IFNγ inflammation signature score is determined by averaging the expression of genes from the IFNγ inflammation gene panel in cancer samples obtained from a population of subjects with cancer. In some aspects, the average IFNγ inflammation signature score is determined by averaging the expression of genes from the IFNγ inflammation gene panel in cancer samples obtained from a population of subjects. In some aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score higher than the average IFNγ inflammation signature score of a reference sample.

[0020] In some aspects, the reference sample includes non-tumor tissue of the subject, the corresponding non-tumor tissue of the subject, or the corresponding tissue of the subject without a tumor. In some aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score that is at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, or at least about 300% higher than the average IFNγ inflammation signature score.

[0021] In some aspects, high IFNγ inflammation signature scores are characterized by IFNγ inflammation signature scores that are at least about 50% higher than the average IFNγ inflammation signature score. In some aspects, high IFNγ inflammation signature scores are characterized by IFNγ inflammation signature scores that are at least about 75% higher than the average IFNγ inflammation signature score.

[0022] In some aspects, a low TDO2 gene expression score is characterized by TDO2 gene expression lower than the average TDO2 gene expression score, where the average TDO2 gene expression score is determined by averaging the expression of the TDO2 gene in cancer samples obtained from a population of subjects with cancer. In some aspects, the average TDO2 gene expression score is determined by averaging the expression of the TDO2 gene in cancer samples obtained from a population of subjects. In some aspects, a low TDO2 gene expression score is characterized by TDO2 gene expression lower than the average TDO2 gene expression score of a reference sample. In some aspects, the reference sample includes non-tumor tissue of a subject, corresponding non-tumor tissue of a subject, or corresponding tissue of a subject without a tumor. In some aspects, the low TDO2 gene expression score is characterized by a TDO2 gene expression score that is at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, or at least about 300% lower than the average TDO2 gene expression score.

[0023] In some aspects, a low TDO2 gene expression score is characterized by a TDO2 gene expression score that is at least about 50% lower than the average TDO2 gene expression score. In some aspects, a low TDO2 gene expression score is characterized by a TDO2 gene expression score that is at least about 75% lower than the average TDO2 gene expression score.

[0024] In some respects, cancer is a tumor. In some respects, a tumor is a carcinoma. In some respects, a tumor is selected from bladder cancer, cervical cancer, lung cancer, pancreatic cancer, kidney cancer, head and neck cancer, melanoma, endometrial cancer, hepatocellular carcinoma (HCC), or glioblastoma. In some respects, lung cancer is non-small cell lung cancer (NSCLC). In some respects, kidney cancer is renal cell carcinoma (RCC). In some respects, head and neck cancer is squamous cell carcinoma of the head and neck (SCCHN). In some respects, glioblastoma is glioblastoma pleomorpha (GBM). In some respects, a tumor is not melanoma. In some respects, cancer is blood cancer. In some respects, blood cancer is lymphoma. In some respects, lymphoma is diffuse large B-cell lymphoma (DLBCL).

[0025] In some aspects, the sample is a tumor tissue biopsy. In some aspects, the sample is obtained from the stroma of the tumor. In some aspects, the sample is formalin-fixed paraffin-embedded tissue, fresh-frozen tissue, or blood sample.

[0026] In some aspects, the expression of genes within the IFNγ inflammation gene panel and / or the TDO2 gene is determined by detecting the presence of gene mRNA, the presence of the protein encoded by the gene, or both. In some aspects, the presence of mRNA encoding the gene and / or the TDO2 gene within the IFNγ inflammation gene panel is determined using reverse transcription PCR. In some aspects, the presence of the protein encoded by the gene and / or the TDO2 gene within the IFNγ inflammation gene panel is determined using an immunohistochemistry (IHC) assay. In some aspects, the IHC assay is an automated IHC assay. In some aspects, the assay is a protein IHC assay involving phases correlated with the IFNγ inflammation gene panel.

[0027] In some aspects, the anti-PD-1 antagonist is an anti-PD-1 antibody or its antigen-binding portion. In some aspects, the anti-PD-1 antibody or its antigen-binding portion cross-competes with nivolumab for binding to human PD-1. In some aspects, the anti-PD-1 antibody or its antigen-binding portion binds to the same epitope as nivolumab. In some aspects, the anti-PD-1 antibody is a chimeric, humanized, or human monoclonal antibody or its portion. In some aspects, the anti-PD-1 antibody contains a heavy chain constant region of a human IgG1 or IgG4 isoform. In some aspects, the anti-PD-1 antibody contains nivolumab, pembrolizumab, or its antigen-binding portion. In some aspects, the anti-PD-1 antibody is nivolumab, pembrolizumab, or semiplimab.

[0028] In some aspects, anti-PD-1 antagonists are anti-PD-L1 antibodies or their antigen-binding portions. In some aspects, anti-PD-L1 antibodies include avelumab, atezolizumab, durvalumab, or their antigen-binding portions. In some aspects, anti-PD-L1 antibodies are avelumab, atezolizumab, or durvalumab.

[0029] In some aspects, the anti-PD-1 or anti-PD-L1 antibody is administered once every approximately 1 week, once every approximately 2 weeks, or once every approximately 3 weeks at a dose ranging from at least about 0.1 mg / kg to at least about 10.0 mg / kg body weight. In some aspects, the anti-PD-1 or anti-PD-L1 antibody is administered once every approximately 2 weeks at a dose of at least about 3 mg / kg body weight. In some aspects, the anti-PD-1 or anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose. In some aspects, an anti-PD-1 or anti-PD-L1 antibody or its antigen-binding portion is administered in a uniform dose of at least about 200 mg / dose, at least about 220 mg / dose, at least about 240 mg / dose, at least about 260 mg / dose, at least about 280 mg / dose, at least about 300 mg / dose, at least about 320 mg / dose, at least about 340 mg / dose, at least about 360 mg / dose, at least about 380 mg / dose, at least about 400 mg / dose, at least about 420 mg / dose, at least about 440 mg / dose, at least about 460 mg / dose, at least about 480 mg / dose, at least about 500 mg / dose, at least about 520 mg / dose, at least about 540 mg / dose, or at least about 550 mg / dose.

[0030] In some aspects, the anti-PD-1 or anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose of about 240 mg / dose. In some aspects, the anti-PD-1 or anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose of about 480 mg / dose. In some aspects, the anti-PD-1 or anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose approximately once every 1 week, once every 2 weeks, once every 3 weeks, or once every 4 weeks. In some aspects, the anti-PD-1 or anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose of about 240 mg / dose once every 2 weeks. In some aspects, the anti-PD-1 or anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose of about 480 mg / dose once every 4 weeks. In some aspects, anti-PD-1 or anti-PD-L1 antibodies are administered as long as clinical benefit is observed or until unmanageable toxicity or disease progression occurs. In some aspects, anti-PD-1 or anti-PD-L1 antibodies are formulated for intravenous administration. In some aspects, anti-PD-1 or anti-PD-L1 antibodies are administered at sub-therapeutic doses.

[0031] In some aspects, IDO1 inhibitors selectively inhibit IDO1. In some aspects, IDO1 inhibitors do not inhibit TDO2 enzymatic activity. In some aspects, IDO1 inhibitors are lindostat ((2R)-N-(4-chlorophenyl)-2-(cis-4-(6-fluoroquinoline-4-yl)cyclohexyl)propanamide). In some aspects, IDO1 inhibitors are lindostat salts. In some aspects, lindostat salts are lindostat mesylate. In some aspects, IDO1 inhibitors are selected from the group consisting of lindostat, 1-methyl-DL-tryptophan, p-(3-benzofuranyl)-DL-alanine, p-[3-benzo(b)thienyl]-DL-alanine; 6-nitro-L-tryptophan and any combination thereof. In some aspects, IDO1 inhibitors are formulated for oral administration. In some aspects, IDO1 inhibitors are administered at a uniform dose of about 25 mg / dose, 50 mg / dose, or 100 mg / dose. In some aspects, IDO1 inhibitors are administered at a uniform dose of about 200 mg / dose.

[0032] In some aspects, IDO1 inhibitors are administered at a uniform dose of at least about 50 mg / dose, at least about 60 mg / dose, at least about 70 mg / dose, at least about 80 mg / dose, at least about 90 mg / dose, at least about 100 mg / dose, at least about 120 mg / dose, at least about 140 mg / dose, at least about 160 mg / dose, at least about 180 mg / dose, at least about 200 mg / dose, at least about 220 mg / dose, at least about 240 mg / dose, at least about 260 mg / dose, at least about 280 mg / dose, at least about 300 mg / dose, at least about 330 mg / dose, at least about 340 mg / dose, at least about 360 mg / dose, at least about 380 mg / dose, or at least about 400 mg / dose.

[0033] In some aspects, IDO1 inhibitors are administered daily at a uniform dose of about 100 mg / dose. In some aspects, IDO1 inhibitors are administered daily at a uniform dose of about 200 mg / dose.

[0034] In some aspects, the anti-PD-1 antagonist is an anti-PD-1 antibody administered intravenously at a dose of 240 mg every 2 weeks or at a dose of 480 mg every 4 weeks, and the IDO1 inhibitor is administered orally daily at a dose of 100 mg or 200 mg. In some aspects, the anti-PD-1 antagonist is an anti-PD-1 antibody administered intravenously at a dose of 240 mg every 2 weeks, and the IDO1 inhibitor is administered orally daily at a dose of 100 mg. In some aspects, the anti-PD-1 antagonist is an anti-PD-1 antibody administered intravenously at a dose of 480 mg every 4 weeks, and the IDO1 inhibitor is administered orally daily at a dose of 100 mg. In some aspects, the anti-PD-1 antagonist is an anti-PD-1 antibody administered intravenously at a dose of 240 mg every 2 weeks, and the IDO1 inhibitor is administered orally daily at a dose of 200 mg. In some aspects, the anti-PD-1 antagonist is an anti-PD-1 antibody administered intravenously every 4 weeks at a dose of 480 mg, and the IDO1 inhibitor is administered orally every day at a dose of 200 mg.

[0035] In some aspects, the anti-PD-1 antibody is nivolumab, and the IDO1 inhibitor is lindostat mesylate. In some aspects, the cancer is relapsed. In some aspects, the cancer is refractory. In some aspects, the PD-1 antagonist is administered before or after the IDO1 inhibitor. In some aspects, the PD-1 antagonist is administered co-administered with the IDO1 inhibitor. In some aspects, the cancer is refractory after at least one prior therapy including the administration of at least one anticancer agent. In some aspects, at least one anticancer agent includes standard management therapy. In some aspects, at least one anticancer agent includes immunotherapy. In some aspects, the cancer is locally advanced. In some aspects, the cancer is metastatic.

[0036] In some aspects of the methods and / or compositions disclosed herein, administration of an anti-PD-1 antagonist and an indoleamine 2,3-deoxygenase 1 (IDO1) inhibitor to a subject treats cancer. In some aspects, administration reduces the cancer burden. In some aspects, the cancer burden is reduced by at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% compared to the cancer burden before administration.

[0037] In some aspects, the subject exhibits progression-free survival for at least about 1 month, at least about 2 months, at least about 3 months, at least about 4 months, at least about 5 months, at least about 6 months, at least about 7 months, at least about 8 months, at least about 9 months, at least about 10 months, at least about 11 months, at least about 1 year, at least about 18 months, at least about 2 years, at least about 3 years, at least about 4 years, or at least about 5 years after initial administration.

[0038] In some aspects, the subject exhibits stable disease after administration. In some aspects, the subject exhibits a partial response after administration. In some aspects, the subject exhibits a complete response after administration. In some aspects, administration resulted in a progression-free survival probability of at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 105%, at least about 110%, at least about 115%, at least about 120%, at least about 125%, at least about 130%, at least about 135%, at least about 140%, at least Improves progression-free survival probability by about 145% or at least about 150%.

[0039] In some aspects, administration is at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, at least about 300%, at least about 325%, at least about 350%, or at least about 375% compared to the overall survival probability of subjects not exhibiting combination biomarkers including (a) high IFNγ inflammation signature score and (b) low TDO2 gene expression score Improves overall survival probability.

[0040] The present disclosure also provides a kit or manufactured product for treating a subject with cancer, comprising (a) a dose of an anti-PD-1 antagonist; (b) a dose of an IDO1 inhibitor; and (c) instructions for using an anti-PD-1 or anti-PD-L1 antibody and an IDO1 inhibitor according to any method disclosed herein.

[0041] The present disclosure also provides (i) identifying subjects suitable for therapy using a combination of an anti-PD-1 antagonist and an IDO1 inhibitor; (ii) determining the prognosis of subjects receiving therapy using a combination of an anti-PD-1 antagonist and an IDO1 inhibitor; (iii) initiating, discontinuing, or modifying the administration of a combination of an anti-PD-1 antagonist and an IDO1 inhibitor; or (iv) a gene panel comprising at least IFNγ and TDO2 genes for use in the combination.

[0042] In some aspects, the gene panel comprises TDO2, and at least one of IFNγ, CXCL10, HLA-DRA, CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, CCR5, CXCL11, GZMA, PRF1, IR2RG, CD3D, CD2, ITGAL, TAGAP, CIITA, PTPRC, CD3E, GZMK, GZMB, PDCD1, SLAMF6, CXCL13, or a combination thereof.

[0043] In some respects, gene panels are performed or are essentially performed.

[0044] (i) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1 and TDO2;

[0045] (ii) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1, CCR5, CXCL11, GZMA, PRF1 and TDO2;

[0046] (iii) CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1 and HLA.E; or

[0047] (iv) any combination of his or any combination of genes in (i) to (iii). Brief explanation of the drawing

[0048] Figures 1a and 1b show the percentage of samples of each tumor type obtained from patients, pooled together, and used in subsequent experiments / analyses. These figures illustrate the biomarker samples used and the evaluations performed with each sample set. Gene expression results were analyzed in relation to response, progression-free survival, and overall survival. Figure 1a shows the percentage of each tumor type used to collect, freeze, and perform liquid chromatography-mass spectrometry experiments to detect kynurenin (KYN) tumor and serum samples. Serum and tumor samples were collected at the start of treatment (Cycle 1, Day 1; C1D1) and during treatment (Cycle 1, Day 15; C1D15). Figure 1b shows the percentage of each tumor type formalin-fixed and paraffin-embedded samples prior to treatment (baseline). These samples were used in RNA sequencing experiments to determine the IFNγ signature, expression of IDO1, and expression of TDO2. C1D1 = Cycle 1, Day 1; C1D15 = Cycle 1 Day 15; DLBCL = Diffuse large B-cell lymphoma; IDO1 = Indoleamine 2,3-deoxygenase-1; IFNγ = Interferon gamma; KYN = Kynurenin; LC-MS / MS = Liquid chromatography-mass spectroscopy; NSCLC = Non-small cell lung cancer; OS = Overall survival; PFS = Progression-free survival; RCC = Renal cell carcinoma; seq = Sequencing; SCCHN = Squamous cell carcinoma of the head and neck; TDO2 = Tryptophan 2,3-deoxygenase 2. Figures 2a and 2b illustrate the association between the clinical response of immuno-oncology naive patients to treatment with nivolumab and the IDO1 inhibitor lindostat and the IFNγ signature. The best overall response (Figure 2a) and objective response (Figure 2b) of pooled tumor samples are presented. CR = Complete response; IFNγ = Interferon gamma; NE = Not evaluable; PD = Progressive disease; PR = Partial response; SD = Stable disease. Figures 3a and 3b are survival probability curves for immuno-oncology naive patients with low, intermediate, or high IFNγ signatures after treatment with nivolumab and lindostat. Progression-free survival curve (Figure 3a) and overall survival curve (Figure 3b) show the survival probability (%) corresponding to pooled tumor samples with low, intermediate, or high IFNγ signature scores. Pooled tumor types were evaluated, and P-values ​​are stated based on IFNγ as a continuous variable. Survival curves are visually displayed as territories. IFNγ = Interferon gamma; OS = Overall survival; PFS = Progression-free survival. Figures 4a and 4b are box plots showing the association between KYN levels and TDO2 tumor levels in immuno-oncology naive patients during treatment with nivolumab and lindostat. Figure 4a shows tumor KYN levels from tumors, and Figure 4b shows KYN levels from serum. Non-tumor tissue levels of tumor KYN and levels of serum KYN from healthy volunteers are indicated by gray bars. Pooled tumor types were evaluated. n indicates the overlap of KYN and TDO2 expression. TDO2 high and low were defined by the median TDO2 level. C1D1 = Cycle 1, Day 1; C1D15 = Cycle 1, Day 15; KYN = Kynurenin; TDO2 = Tryptophan 2,3-deoxygenase 2. Figures 5a and 5b are box plots showing the association between TDO2 expression and response to nivolumab monotherapy (Figure 5b) or nivolumab and lindostat combination therapy (Figure 5a) in patients with immuno-oncology naivety. TDO2 expression was determined by the median. All tumors are responders from the biomarker cohort (clinical trial number NCT02658890). Nivolumab monotherapy data are from the CheckMate trial. NE = Not evaluable; PD = Advanced disease; PR = Partial response; SCCHN = Squamous cell carcinoma of the head and neck; SD = Stable disease; TDO2 = Tryptophan 2,3-deoxygenase 2. Figures 6a and 6b show the relationship between objective response rates and IFNγ expression and TDO2 expression in all tumor types (Figure 6a) or non-melanoma tumors (Figure 6b) in immuno-oncology naive patients treated with nivolumab and lindostat. Lines represent the median values ​​of markers in each cohort. CR = Complete response; IFNγ = Interferon gamma; NE = Not evaluable; ORR = Objective response rate; PD = Progressive disease; PR = Partial response; SD = Stable disease; TDO2 = Tryptophan 2,3-deoxygenase 2. Figures 7a and 7b are receiver operation feature curves of the objective response rate and sensitivity and specificity for the IFNγ signature (Figure 7a) or the objective response rate, IFNγ signature, and TDO2 expression (Figure 7b) in non-melanoma tumors from immuno-oncology naive patients treated with nivolumab and lindostat. The analysis was based on the total sample size and was not limited to the biomarker cohort. AUC = Area under the curve; CI = Confidence interval; IFNγ = Interferon gamma; ORR = Objective response rate; TDO2 = Tryptophan 2,3-deoxygenase 2. Specific details for implementing the invention

[0049] The present disclosure provides a method for treating cancer, a method for making treatment decisions (e.g., a method for deciding whether to initiate, stop, or modify treatment using a specific therapeutic composition or combination thereof), a method for selecting or excluding a patient from treatment, or a method for determining the prognosis of a patient based on the presence or absence of a complex or combination biomarker comprising (i) an IFNγ inflammatory signature score and (ii) a tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score.

[0050] The composite biomarker disclosed herein was determined to predict a positive outcome (disease stabilization, partial response, or complete response) when a combination therapy comprising an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, e.g., nivolumab) and an IDO1 inhibitor (e.g., lindostat mesylate) is administered to subjects suffering from cancer, e.g., tumors, when the IFNγ inflammation signature score is high and the TDO2 gene expression score is low prior to administration.

[0051] Accordingly, the present disclosure provides a method for treating a human subject suffering from cancer, e.g., a tumor, comprising the step of administering an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, an anti-PD-L1 antibody or its antigen-binding portion) and an IDO1 inhibitor (e.g., lindostat mesylate) to a human subject suffering from cancer, e.g., a tumor, wherein the subject is identified to exhibit a combination biomarker including (a) a high IFNγ inflammation signature score and (b) a low tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score prior to administration; wherein the IFNγ inflammation signature score is determined by measuring the expression of a panel of inflammatory genes ("IFNγ inflammation gene panel") including interferon gamma (IFNγ) related genes in a sample obtained from the subject and subsequently calculating a score based on the expression values.

[0052] Additionally, a method for treating a human subject with cancer is provided, comprising the steps of: (i) identifying a subject exhibiting a combination of biomarkers including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score; and (ii) administering to the subject an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, an anti-PD-L1 antibody or its antigen-binding portion) and an IDO1 inhibitor (e.g., lindostat mesylate); wherein the IFNγ inflammation signature score is determined by measuring the expression of an IFNγ inflammation gene panel in a sample obtained from the subject and subsequently calculating a score based on the expression values.

[0053] Additionally, a method is provided for identifying a human subject with cancer suitable for treatment with an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, an anti-PD-L1 antibody, or its antigen-binding portion) and an IDO1 inhibitor (e.g., lindostat mesylate), comprising the step of measuring an IFNγ inflammation signature score and TDO2 gene expression in a sample obtained from a human subject with cancer; wherein the IFNγ inflammation signature score is determined by measuring the expression of an IFNγ inflammation gene panel in a sample obtained from the subject and subsequently calculating a score based on the expression values. In some specific aspects, the anti-PD-1 antibody is nivolumab.

[0054] I. Terminology

[0055] To facilitate a better understanding of the present disclosure, specific terms are defined first. Unless otherwise explicitly provided herein, each of the following terms used in this application will have the meaning set forth below. Additional definitions are provided throughout the application.

[0056] "Administering" refers to the physical introduction of a composition containing a therapeutic agent to a subject using any of the various methods and delivery systems known to a person skilled in the art. Preferred routes of administration for immunotherapy, e.g., anti-PD-1 antibody (e.g., nivolumab) or anti-PD-L1 antibody, include intravenous, intramuscular, subcutaneous, intraperitoneal, spinal, or other parenteral administration routes, e.g., by injection or infusion. As used herein, the term "parenteral administration" means a mode of administration, typically by injection, other than enteral and local administration, and includes, without limitation, intravenous, intramuscular, intra-arterial, intrathecal, intralymphatic, intralesional, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transcanal, subcutaneous, interarticular, subcapsular, subarachnoid, intraspinal, epidural, and intrasternal injections and infusions, as well as in vivo electroporation. Other parenteral routes include oral, topical, epidermal, or mucosal administration routes, e.g., intranasally, vaginally, rectally, sublingually, or topically. Additionally, administration may be performed, e.g., once, multiple times, and / or over one or more extended periods. In some aspects, anti-PD-1 antibodies (e.g., nivolumab) are administered intravenously. In some aspects, IDO1 inhibitors (e.g., lindostat) are administered orally.

[0057] As used herein, “Adverse Event” (AE) is any undesirable, generally unintended, or unwanted sign (including abnormal laboratory findings), symptom, or disease associated with the use of a medical treatment. For example, an adverse event may be associated with the activation of the immune system or the expansion of immune system cells (e.g., T cells) occurring in response to treatment. A medical treatment may have one or more associated AEs, and each AE may have the same or different levels of severity. Reference to a method that may “change an adverse event” means a treatment regimen that reduces the incidence and / or severity of one or more AEs associated with the use of a different treatment regimen.

[0058] The "antibody" (Ab) will, without limitation, comprise a glycoprotein immunoglobulin or its antigen-binding portion comprising at least two heavy chains (H) and two light chains (L) interconnected by disulfide bonds, which specifically bind to an antigen. Each H chain is a heavy chain variable region (V in this application). H It includes the heavy chain invariant region (abbreviated as ). The heavy chain invariant region consists of three invariant domains C H1 , C H2 and C H3 Each light chain includes a light chain variable region (V in this application). L It includes (abbreviated as ) and a light chain invariant region. The light chain invariant region consists of one invariant domain C L Includes. V H and V L The region can be further subdivided into a hypermutability region referred to as the Complementarity Decision Region (CDR), which is interspersed with more conserved regions referred to as the Framework Region (FR). Each V H and V LIt comprises three CDRs and four FRs arranged in the following order from amino-terminus to carboxy-terminus: FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4. The variable regions of the heavy and light chains contain binding domains that interact with the antigen. The constant region of the antibody can mediate the binding of immunoglobulins to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (C1q) of the typical complement system. Thus, the term "anti-PD-1 antibody" comprises a full-length antibody having two heavy chains and two light chains that specifically bind to PD-1, and the antigen-binding portion of the full-length antibody. Non-limiting examples of the antigen-binding portion are presented elsewhere in this invention. In some aspects of this disclosure, the anti-PD-1 antibody is nivolumab or its antigen-binding portion.

[0059] Immunoglobulins may be derived from any commonly known isoforms, including but not limited to IgA, secreted IgA, IgG, and IgM. IgG subclasses are also widely known to those skilled in the art and include, but are not limited to, human IgG1, IgG2, IgG3, and IgG4. “Isoform” refers to a class or subclass of antibodies (e.g., IgM or IgG1) encoded by a heavy chain constant region gene. The term “antibody” includes, for example, both naturally occurring and non-naturally occurring antibodies; monoclonal and polyclonal antibodies; chimeric and humanized antibodies; human or non-human antibodies; fully synthetic antibodies; and single-chain antibodies. Non-human antibodies may be humanized by recombinant methods so as to reduce their immunogenicity in humans. Unless explicitly stated and otherwise indicated by the context, the term “antibody” also includes antigen-binding fragments or antigen-binding portions of any of the aforementioned immunoglobulins, and includes monovalent and divalent fragments or portions and single-chain antibodies.

[0060] "Isolated antibody" refers to an antibody that is substantially free of other antibodies having different antigen specificities (for example, an isolated antibody that specifically binds to PD-1 is substantially free of antibodies that specifically bind to antigens other than PD-1). However, an isolated antibody that specifically binds to PD-1 may have cross-reactivity with other antigens, such as PD-1 molecules from different species. Furthermore, the isolated antibody may be substantially free of other cellular materials and / or chemicals.

[0061] The term "monoclonal antibody" (mAb) refers to a non-naturally occurring preparation of an antibody molecule of single molecular composition, that is, an antibody molecule in which the primary sequence is essentially identical and exhibits single-binding specificity and affinity for a specific epitope. Monoclonal antibodies are examples of isolated antibodies. Monoclonal antibodies may be produced by hybridoma, recombinant, transgenic, or other techniques known to those skilled in the art.

[0062] "Human antibody" (HuMAb) refers to an antibody having a variable region in which both the framework and the CDR region are derived from a human wiring immunoglobulin sequence. Additionally, if the antibody contains a constant region, the constant region is also derived from a human wiring immunoglobulin sequence. The human antibodies of this disclosure may contain amino acid residues not encoded by the human wiring immunoglobulin sequence (e.g., mutations introduced by in vitro random or site-specific mutagenesis or by in vivo somatic mutation). However, the term "human antibody" as used herein is not intended to include antibodies in which a CDR sequence derived from the wiring of another mammalian species, e.g., mouse, is grafted onto a human framework sequence. The terms "human antibody" and "fully human antibody" are used synonyms.

[0063] "Humanized antibody" refers to an antibody in which some, most, or all of the amino acids outside the CDR of a non-human antibody have been replaced with corresponding amino acids derived from human immunoglobulin. In one aspect of the humanized form of the antibody, some, most, or all of the amino acids outside the CDR have been replaced with amino acids from human immunoglobulin, while one or more of the amino acids within the CDR have not been changed. Minor additions, deletions, insertions, substitutions, or modifications of amino acids are acceptable, provided that they do not eliminate the antibody's ability to bind to a specific antigen. "Humanized antibody" retains antigen specificity similar to that of the original antibody.

[0064] "Chimeric antibody" refers to an antibody in which the variable region is derived from one species and the constant region is derived from another species, for example, an antibody in which the variable region is derived from a mouse antibody and the constant region is derived from a human antibody.

[0065] "Anti-antigen antibody" refers to an antibody that specifically binds to an antigen. For example, an anti-PD-1 antibody specifically binds to PD-1, and an anti-PD-L1 antibody specifically binds to PD-L1.

[0066] The “antigen-binding portion” (also referred to as “antigen-binding fragment”) of an antibody refers to one or more fragments of an antibody that retain the ability to specifically bind to an antigen bound by the whole antibody. It has been suggested that the antigen-binding function of an antibody can be performed by a fragment of a full-length antibody. Examples of binding fragments encompassed within the term “antigen-binding portion” of antibodies, for example, the anti-PD-1 antibody or anti-PD-L1 antibody described herein, are (i) V L , V H(ii) a Fab fragment (fragment from papain cleavage) or a similar monovalent fragment consisting of , LC and CH1 domains; (ii) an F(ab')2 fragment (fragment from pepsin cleavage) or a similar divalent fragment comprising two Fab fragments connected by a disulfide crosslink at the hinge region; (iii) V H and an Fd fragment consisting of a CH1 domain; (iv) V of a single arm of the antibody L and V H Fv fragments consisting of domains, (v) V H A dAb fragment composed of domains (Ward et al., (1989) Nature 341:544-546); comprising (vi) an isolated complementarity determining region (CDR) and (vii) a combination of two or more isolated CDRs that can be arbitrarily linked by a synthetic linker. Additionally, V, which is two domains of the Fv fragment. L and V H Although they are encoded by separate genes, they can be linked by a synthetic linker that enables them to be manufactured into a single protein chain using a recombination method, where V L and V H The regions pair to form a monovalent molecule (known as single-stranded Fv (scFv); see, for example, the literature [Bird et al. (1988) Science 242:423-426; and Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85:5879-5883]). These single-stranded antibodies are also intended to be encompassed within the term "antigen-binding portion" of antibodies. These antibody fragments are obtained using conventional techniques known to those skilled in the art, and the fragments are screened for utility in the same manner as intact antibodies. The antigen-binding portion may be produced by recombinant DNA technology or by enzymatic or chemical cleavage of intact immunoglobulin.

[0067] "Cancer" refers to a broad group of various diseases characterized by the uncontrolled growth of abnormal cells within the body. Uncontrolled cell division and growth lead to the formation of malignant tumors that divide and grow, invading neighboring tissues and potentially metastasizing to distal parts of the body via the lymphatic system or bloodstream. The term "tumor" refers to solid cancer. The term "carcinoma" refers to cancer of epithelial origin.

[0068] As used herein, the term "IDO1" refers to indoleamine 2,3-deoxygenase 1. Indoleamine-pyrrole 2,3-deoxygenase (IDO or INDO EC 1.13.11.52) is a heme-containing enzyme encoded by the IDO1 gene in humans. It is one of three enzymes that catalyze the O2-dependent oxidation of L-tryptophan to N-formylkynurenine, which is the first and rate-limiting step of the kynurenine pathway; the others are IDO2 and tryptophan 2,3-deoxygenase (TDO). IDO has been implicated in immune modulation through its ability to limit T-cell function and participate in the mechanisms of immune tolerance. IDO is activated during oncogenesis, helping malignant cells evade eradication by the immune system. Interferon gamma has an antiproliferative effect on many tumor cells, at least partially due to the induction of indoleamine 2,3-deoxygenase.

[0069] As used herein, the term "IDO1 inhibitor" refers to an indoleamine 2,3-deoxygenase 1 inhibitor. IDO1 inhibitors inhibit indoleamine 2,3-deoxygenase, thereby inducing a decrease in kynurenine levels as well as reducing the activity of pro-inflammatory cytokines. 1-methyltryptophan is a racemic compound that weakly inhibits indoleamine deoxygenase, but it is also a very slow substrate. The specific racemic mixture 1-methyl-D-tryptophan (known as indoxymod) is currently undergoing clinical trials for various cancers. Epacadostat (INCB24360) and naboximod (GDC-0919) are potent inhibitors of the indoleamine 2,3-deoxygenase enzyme and are currently undergoing clinical trials for various cancers. In some respects, an IDO1 inhibitor is lindostat (BMS-986205). In some aspects, the IDO1 inhibitor is a lindostat salt, e.g., lindostat mesylate. See WO2015031295, WO2016073770 and WO201809049, all of which are incorporated herein by reference in their entirety.

[0070] The term “immunotherapy” refers to treating a subject who has a disease, is at risk of developing the disease, or is experiencing a recurrence of the disease by means of methods including inducing, enhancing, suppressing, or otherwise modifying an immune response. “Treatment” or “therapy” of a subject refers to any type of intervention or process performed on a subject, or the administration of an activator to a subject, for the purpose of reversing, alleviating, improving, suppressing, slowing, or preventing the onset, progression, development, severity, or recurrence of symptoms, complications, or conditions or biochemical indications associated with the disease.

[0071] "Programmed Death-1" (PD-1) refers to an immunosuppressive receptor belonging to the CD28 family. PD-1 is predominantly expressed on previously activated T cells in vivo and binds to two ligands, PD-L1 and PD-L2. As used herein, the term "PD-1" includes human PD-1 (hPD-1), variants, isoforms, and species homologs of hPD-1, and analogs having at least one common epitope with hPD-1. The complete hPD-1 sequence can be found under GenBank accession number U64863.

[0072] "Programmed death ligand-1" (PD-L1) is one of two cell surface glycoprotein ligands for PD-1 that downregulate T cell activation and cytokine secretion upon binding to PD-1 (the other is PD-L2). As used herein, the term "PD-L1" includes human PD-L1 (hPD-L1), variants, isoforms, and species homologs of hPD-L1, and analogs having at least one common epitope with hPD-L1. The complete hPD-L1 sequence is available under GeneBank accession number Q9NZQ7. The human PD-L1 protein is encoded by the human CD274 gene (NCBI Gene ID: 29126).

[0073] As used herein, the term “subject” includes any human or non-human animal. The term “non-human animal” includes, but is not limited to, vertebrates, e.g., non-human primates, sheep, dogs, and rodents, e.g., mice, rats, and guinea pigs. In a specific sense, the subject is a human. The terms “subject” and “patient” are used interchangeably herein.

[0074] In relation to the methods and dosages of the present disclosure, the use of the term “uniform dose” means a dose administered to a patient regardless of the patient’s body weight or body surface area (BSA). Accordingly, the uniform dose is not provided as a mg / kg dose, but rather as an absolute amount of the agent (e.g., anti-PD-1 antibody). For example, a 60 kg person and a 100 kg person will receive the same dose of antibody (e.g., 240 mg of anti-PD-1 antibody).

[0075] In connection with the methods of the present disclosure, the use of the term “fixed dose” means that a therapeutic agent, e.g., an anti-PD-1 antagonist (e.g., nivolumab) or an IDO1 inhibitor (e.g., lindostat), is present in a composition or pharmaceutical composition in a specific (fixed) amount. In some aspects, the fixed dose is based on the weight of the therapeutic agent (e.g., mg). In certain aspects, the fixed dose is based on the concentration of the therapeutic agent (e.g., mg / ml). The term “weight-based dose” as used herein means that the dose administered to a patient is calculated based on the patient’s weight. For example, if a patient weighing 60 kg requires 3 mg / kg of anti-PD-1 antibody, an appropriate amount of anti-PD-1 antibody (i.e., 180 mg) can be calculated and used for administration.

[0076] "Immune response" is understood in the relevant technical field and generally refers to a biological response within a vertebrate against foreign agents or abnormal cells, e.g., cancerous cells, which protects the organism against these agents or the disease induced by them. The immune response is mediated by the action of one or more types of cells of the immune system (e.g., T lymphocytes, B lymphocytes, natural killer (NK) cells, macrophages, eosinophils, mast cells, dendritic cells, or neutrophils) and soluble macromolecules (including antibodies, cytokines, and complement) produced by any of these cells or the liver, which cause the selective targeting, binding to, damage to, and / or removal from the vertebrate body of invading pathogens, cells or tissues infected with pathogens, cancerous or other abnormal cells, or, in the case of autoimmune or pathological inflammation, normal human cells or tissues. The immune response, e.g., T cells, e.g., effector T cells, Th cells, CD4 + Cell, CD8 + It includes the activation or inhibition of T cells or Treg cells, or the activation or inhibition of any other cells of the immune system, such as NK cells.

[0077] "Immune-related response patterns" refer to clinical response patterns often observed in cancer patients treated with immunotherapies that generate anticancer effects by inducing cancer-specific immune responses or by modifying natural immune processes. These response patterns are characterized by beneficial therapeutic effects followed by an early increase in cancer burden or the appearance of new lesions, which are classified as disease progression and synonymous with drug failure in the evaluation of traditional chemotherapy. Therefore, the proper evaluation of immunotherapies may require long-term monitoring of the effects of these agents on the target disease.

[0078] As used herein, the terms “treat,” “treating,” and “treatment” refer to any type of intervention or process performed on a subject, or the administration of an activator to a subject, for the purpose of reversing, alleviating, improving, suppressing, slowing, or preventing the progression, development, severity, or relapse of symptoms, complications, conditions, or biochemical indications associated with the disease, or for the purpose of promoting overall survival. Treatment may be the treatment of a subject having the disease or the treatment of a subject not having the disease (e.g., for prevention).

[0079] The term "effective dose" or "effective dosage" is defined as an amount sufficient to achieve the desired effect, or at least partially achieve it.

[0080] The “therapeutic effective dose” or “therapeutic effective dosage” of a drug or therapeutic agent is any amount of drug that, when used alone or in combination with another therapeutic agent, protects the subject from the onset of the disease or promotes disease regression, as evidenced by a reduction in the severity of disease symptoms, an increase in the frequency and duration of disease-free periods, or the prevention of damage or disability caused by disease suffering. The therapeutic effective dose or effective dosage of a drug includes the “preventive effective dose” or “preventive effective dosage,” which is any amount of drug that, when administered alone or in combination with another therapeutic agent to a subject at risk of developing the disease or experiencing a recurrence of the disease, suppresses the onset or recurrence of the disease.

[0081] The ability of a therapeutic agent to promote disease regression, for example, cancer regression, can be evaluated using various methods known to skilled physicians, such as in human subjects during clinical trials, in animal model systems that predict efficacy in humans, or by testing the activity of the agent in in vitro assays.

[0082] For example, an “anticancer agent” or a combination thereof promotes cancer regression in a subject. In some aspects, a therapeutically effective dose of the agent promotes cancer regression to the point of eliminating the cancer. In some aspects of the disclosure, the anticancer agent is administered as a combination of therapy: an intravenous therapy including the administration of an anti-PD-1 antibody (e.g., nivolumab) and an oral therapy including the administration of an IDO1 inhibitor (e.g., lindostat mesylate). “Promoting cancer regression” means that the administration of an effective dose of the drug or a combination thereof (as discussed above, administered together as a single therapeutic composition or as individual compositions in individual therapy) causes a reduction in the burden of cancer, e.g., a reduction in tumor growth or size, necrosis of the tumor, a reduction in the severity of at least one disease symptom, an increase in the frequency and duration of disease-free periods, or a prevention of damage or disability due to disease suffering.

[0083] Additionally, the terms “effective” and “effectiveness” relating to the treatments disclosed herein include both pharmacological efficacy and physiological safety. Pharmacological efficacy refers to the ability of a drug to promote cancer regression in a patient. Physiological safety refers to the level of toxicity or other harmful physiological effects (adverse effects) at the cellular, organ, and / or organism level resulting from the administration of the drug.

[0084] As an example of the treatment of a tumor, a therapeutically effective dose of anticancer agent inhibits cancer cell growth or tumor growth by preferably at least about 20%, more preferably at least about 40%, even more preferably at least about 60%, and even more preferably at least about 80% compared to a non-treated subject. Similarly, in blood cancer, a therapeutically effective dose of anticancer agent inhibits cell growth or reduces the number of circulating cancer cells by preferably at least about 20%, more preferably at least about 40%, even more preferably at least about 60%, and even more preferably at least about 80% compared to a non-treated subject.

[0085] In some aspects, the therapeutically effective dose or dosage of the drug inhibits cancer cell growth or tumor growth by at least about 20% to about 40%, at least about 30% to about 50%, at least about 40% to about 60%, at least about 50% to about 70%, at least about 60% to about 80%, at least about 70% to about 90%, at least about 30% to about 60%, at least about 40% to about 70%, at least about 50% to about 80%, and at least about 60% to about 90% compared to untreated subjects. In some aspects, the therapeutically effective dose or dosage of the drug completely inhibits cell growth or tumor growth, that is, inhibits cell growth or tumor growth by 100%.

[0086] In some aspects of the present disclosure, cancer regression (e.g., tumor regression) may be observed and continued for a period of at least about 1 month, at least about 2 months, at least about 3 months, at least about 4 months, at least about 5 months, at least about 6 months, at least about 7 months, at least about 8 months, at least about 9 months, at least about 10 months, at least about 11 months, at least about 12 months, at least about 13 months, at least about 14 months, at least about 15 months, at least about 16 months, at least about 17 months, at least about 18 months, at least about 19 months, at least about 20 months, at least about 21 months, at least about 22 months, at least about 23 months, at least about 24 months, at least about 3 years, at least about 4 years, or at least about 5 years. Despite these ultimate measures of therapeutic efficacy, the evaluation of immunotherapy drugs must also take into account immune-related response patterns. The ability of a therapeutic agent to inhibit cancer growth, e.g., tumor growth, may be evaluated using the assays described herein and other assays known in the relevant art. Alternatively, this property of the composition may be evaluated by investigating the ability of the compound to inhibit cell growth, and such inhibition may be measured in vitro by assays known to those skilled in the art.

[0087] In another aspect, for example, in the treatment of blood cancer, a therapeutically effective dose or dosage of a drug inhibits cancer cell growth or reduces the cancer burden by at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% compared to untreated subjects. In some aspects, a therapeutically effective dose or dosage of a drug completely inhibits cell growth or eliminates the cancer burden, that is, inhibits cell growth or the total population of detectable cancer cells by 100%. The ability of a compound to reduce the cancer burden may be evaluated using the assays described herein and other assays known in the relevant art.

[0088] In some aspects, cancer, e.g., tumor, stabilization or regression (partial response or complete response) may be observed and continued for a period of at least about 20 days, at least about 30 days, at least about 40 days, at least about 50 days, at least about 60 days, at least about 70 days, at least about 80 days, at least about 90 days, at least about 100 days, at least about 120 days, at least about 140 days, at least about 160 days, at least about 180 days, at least about 200 days, at least about 225 days, at least about 250 days, at least about 275 days, at least about 300 days, at least about 350 days, at least about 400 days, at least about 450 days, at least about 500 days, at least about 550 days, or at least about 600 days.

[0089] As used herein, the term "biological sample" refers to biological material isolated from a subject. A biological sample may contain any biological material suitable for determining target gene expression by sequencing nucleic acids in, for example, cancer, for example, tumor cells or circulating cancer cells, and identifying genomic alterations in the sequenced nucleic acids. In some respects, genomic alterations are mutations. In other respects, genomic alterations are changes in the expression levels of specific genes in cancer cells relative to a reference.

[0090] The biological sample may be any suitable biological tissue or fluid, e.g., cancer tissue, blood, plasma, and serum. In one aspect, the sample is a tumor tissue biopsy, e.g., formalin-fixed paraffin-embedded (FFPE) tumor tissue or fresh-frozen tumor tissue. In another aspect, the biological sample is, in some aspects, a liquid biopsy containing one or more of blood, serum, plasma, circulating tumor cells, exoRNA, ctDNA, and cfDNA.

[0091] As used herein, the terms “about once a week,” “about once every two weeks,” or any other similar dosing interval term refer to an approximate number of times. “About once a week” may include every 7 ± 1 day, i.e., every 6 to 8 days. “About once every two weeks” may include every 14 ± 3 days, i.e. every 11 to 17 days. Similar approximations apply, for example, once every three weeks, once every four weeks, once every five weeks, once every six weeks, and once every twelve weeks.

[0092] In some aspects, an administration interval of about 6 weeks or about 12 weeks means that the first dose may be administered on any day of the first week, and then the next dose may be administered on any day of the sixth or twelfth week, respectively. In other aspects, an administration interval of about 6 weeks or about 12 weeks means that the first dose is administered on a specific day of the first week (e.g., Monday), and then the next dose is administered on the same day of the sixth or twelfth week, respectively (i.e., Monday).

[0093] The singular form includes plural referents unless the context clearly indicates otherwise. The singular term, as well as the terms "one or more" and "at least one," may be used interchangeably herein. In a specific aspect, the singular term means "single." In another aspect, the singular term includes "two or more" or "multiple."

[0094] Additionally, as used herein, "and / or" should be construed as specifically disclosing each of the two specified features or components, either together with or without the other. Accordingly, the term "and / or" as used herein in phrases such as "A and / or B" is intended to include "A and B," "A or B," "A" (alone), and "B" (alone). Likewise, the term "and / or" as used in phrases such as "A, B and / or C" is intended to encompass each of the following aspects: A, B and C; A, B or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone).

[0095] The terms “about” or “essentially containing” refer to a value or composition within a tolerance range for a specific value or composition as determined by a person skilled in the art, which will be partly dependent on the method by which the value or composition is measured or determined, i.e., the limitations of the measurement system. For example, “about” or “essentially containing” may mean being within 1 or greater than 1 standard deviation according to practice in the art. Alternatively, “about” or “essentially containing” may mean a range of up to 10%. Additionally, particularly in relation to biological systems or processes, the term may mean up to 10 times or up to 5 times the value. Where a specific value or composition is provided in the application and claims, unless otherwise noted, the meaning of “about” or “essentially containing” should be assumed to be within a tolerance range for such specific value or composition.

[0096] As used herein, the term “approximately” refers to a value similar to the mentioned reference value, as applied to one or more values ​​of interest. In certain aspects, the term “approximately” refers to a range of values ​​falling within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in any direction (greater than or less than) the mentioned reference value, unless otherwise stated or otherwise evident from the context (excluding cases where such a number exceeds 100% of possible values).

[0097] Any concentration range, percentage range, ratio range, or integer range described herein shall be understood to include any integer value within the mentioned range, and, where appropriate, fractions thereof (e.g., 1 / 10 and 1 / 100 of an integer), unless otherwise indicated.

[0098] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by a person skilled in the art to which this disclosure relates. For example, the literature [the Concise Dictionary of Biomedicine and Molecular Biology, Juo, Pei-Show, 2nd ed., 2002, CRC Press; The Dictionary of Cell and Molecular Biology, 3rd ed., 1999, Academic Press; and the Oxford Dictionary of Biochemistry and Molecular Biology, Revised, 2000, Oxford University Press] provides a general dictionary of many terms used in this disclosure to a person skilled in the art.

[0099] In all cases where aspects are described herein with the term "comprising," it is understood that other similar aspects described in terms of "consisting of" and / or "essentially composed of" are also provided.

[0100] Units, prefixes, and symbols are indicated in the Systeme International de Unites (SI) accepted forms. The headings provided herein are not a limitation on various aspects of the disclosure and refer to the specification in its entirety. Accordingly, defined terms are more fully defined by referring to the specification in its entirety.

[0101] Abbreviations used herein are defined throughout this disclosure. Various aspects of this disclosure are further described in detail in the following subsections.

[0102] II. Method of Use and Composition

[0103] The present disclosure relates to a method for treating a human subject suffering from cancer, e.g., a tumor, comprising the step of administering an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, e.g., nivolumab, an anti-PD-L1 antibody, or its antigen-binding portion) and an indoleamine 2,3-deoxygenase 1 (IDO1) inhibitor (e.g., lindostat mesylate) to a human subject suffering from cancer, e.g., a tumor, wherein the subject is identified prior to administration to exhibit a combination biomarker comprising (a) a high IFNγ inflammation signature score and (b) a low tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score; wherein the IFNγ inflammation signature score is determined by measuring the expression of a panel of inflammatory genes ("IFNγ inflammation gene panel") including interferon gamma (IFNγ)-related genes in a sample obtained from the subject. The IFNγ inflammation signature score is calculated from the expression levels measured for all genes within the IFNγ inflammation gene panel.

[0104] As used herein, the term “IFNγ-related gene” refers to a gene associated with IFNγ-mediated cell signaling. In one aspect of the disclosure, IFNγ-related genes include, for example, IFNγ, CXCL10, HLA-DRA, CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, CCR5, CXCL11, GZMA, PRF1, IR2RG, CD3D, CD2, ITGAL, TAGAP, CIITA, PTPRC, CD3E, GZMK, GZMB, PDCD1, SLAMF6, and CXCL13. Accordingly, the "IFNγ inflammation gene panel" may include any subset of these genes. In one aspect, the IFNγ inflammation gene panel includes, is composed of, or is essentially composed of IFNγ, CXCL10, HLA-DRA, CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, CCR5, CXCL11, GZMA, PRF1, IR2RG, CD3D, CD2, ITGAL, TAGAP, CIITA, PTPRC, CD3E, GZMK, GZMB, PDCD1, SLAMF6, and CXCL13.In another aspect, the IFNγ inflammation gene panel includes, is composed of, or is essentially composed of IR2RG, CXCR6, CD3D, CD2, ITGAL, TAGAP, CIITA, HLA-DRA, PTPRC, CXCL9, CCL5, NKG7, GZMA, PRF1, CCR5, CD3E, GZMK, IFNγ, HLA-E, GZMB, PDCD1, SLAMF6, CXCL13, CXCL10, IDO1, LAG3, STAT1, and CXCL11. In another aspect, the IFNγ inflammation gene panel includes, consists of, or is essentially composed of CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, and HLA.E. In another aspect, the IFNγ inflammation gene panel includes, consists of, or is essentially composed of IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1, CCR5, CXCL11, GZMA, and PRF1. In another aspect, the IFNγ inflammation gene panel includes, consists of, or is essentially composed of IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, and STAT1. Refer to Table 1, which provides the gene names, descriptions, and RefSeq sequence identifiers for the IFNγ-related genes and TDO2 disclosed herein.

[0105] The Reference Sequence (RefSeq) database is an open-access, annotated, curated collection of publicly available nucleotide sequences (DNA, RNA) and their protein products. Built by the National Center for Biotechnology Information (NCBI), this database, unlike GenBank, provides only a single record of each natural biological molecule (i.e., DNA, RNA, or protein) for major organisms ranging from viruses through bacteria to eukaryotes. The RefSeq database can be accessed at www.ncbi.nlm.nih.gov / refseq.

[0106] Table 1

[0107]

[0108]

[0109] The present disclosure also provides a method for treating a human subject suffering from cancer, e.g., a tumor, comprising: (i) identifying a subject exhibiting a combination biomarker including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score; and (ii) administering to the subject an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, e.g., nivolumab, an anti-PD-L1 antibody, or its antigen-binding portion) and an IDO1 inhibitor (e.g., lindostat mesylate); wherein the IFNγ inflammation signature score is determined by measuring the expression of an IFNγ inflammation gene panel in a sample obtained from the subject and subsequently calculating a score from the measured expression levels.

[0110] Additionally, a method is provided for identifying a human subject with cancer, e.g., a tumor, suitable for treatment with an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, e.g., nivolumab, an anti-PD-L1 antibody, or its antigen-binding portion) and an IDO1 inhibitor (e.g., lindostat mesylate), comprising the step of measuring an IFNγ inflammatory signature score and TDO2 gene expression in a sample obtained from a human subject with cancer, e.g., a tumor; wherein the IFNγ inflammatory signature score is determined by measuring the expression of an IFNγ inflammatory gene panel in a sample obtained from the subject and subsequently calculating a score from the measured expression levels.

[0111] In some aspects, the subject exhibits a combination of biomarkers including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score. In some aspects, the method further comprises the step of administering an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, e.g., nivolumab, an anti-PD-L1 antibody, or its antigen-binding portion) and an IDO1 inhibitor (e.g., lindostat mesylate) to the subject.

[0112] The present disclosure also provides an IDO1 inhibitor (e.g., lindostat mesylate) for treating cancer, e.g., a tumor in combination with an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, e.g., nivolumab, an anti-PD-L1 antibody, or its antigen-binding portion) in a human subject requiring treatment of cancer, e.g., a tumor, wherein the subject is identified to exhibit a combination biomarker comprising (a) a high IFNγ inflammatory signature score and (b) a low TDO2 gene expression score prior to administration; wherein the IFNγ inflammatory signature score is determined by measuring the expression of a panel of inflammatory genes including interferon gamma (IFNγ) in a sample obtained from the subject and subsequently calculating a score from the measured expression levels.

[0113] Additionally, an IDO1 inhibitor (e.g., lindostat mesylate) is provided for identifying human subjects with cancer suitable for treatment with the IDO1 inhibitor (e.g., lindostat mesylate) in combination with an anti-PD-1 antagonist (e.g., anti-PD-1 antibody, e.g., nivolumab, anti-PD-L1 antibody, or its antigen-binding portion), wherein the IFNγ inflammation signature score and TDO2 gene expression are measured in samples obtained from the subjects; wherein the IFNγ inflammation signature score is determined by measuring the expression of an IFNγ inflammation gene panel in samples obtained from the subjects and subsequently calculating a score from the measured expression levels. In some aspects, the subjects exhibit combined biomarkers comprising (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score.

[0114] As used herein, the term “biomarker” refers to a factor that is a unique indicator of a biological process, biological event, and / or pathological condition, e.g., a predictor of clinical response to the treatment of cancer, e.g., the treatment of cancer using an IDO1 inhibitor (e.g., lindostat) in combination with an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, e.g., nivolumab, an anti-PD-L1 antibody, or its antigen-binding portion). As used herein, the term “biomarker” encompasses both molecular biomarkers and measurements and / or scores derived from the measurement of such molecular biomarkers. Accordingly, in the context of this disclosure, the term “biomarker” encompasses, for example, biological biomarkers (e.g., specific genes or genes or expression products, e.g., mRNA or proteins) and numerical or other quantitative or qualitative descriptors, e.g., “scores” integrating one or more measurements.

[0115] In a specific aspect, the term biomarker refers to a gene product (e.g., nucleic acid or protein) or a combination thereof that is determined as a result of, for example, the treatment of cancer and may be associated with it.

[0116] In some aspects, the biomarker is a “combination biomarker” or “complex biomarker,” that is, a biomarker comprising several distinct biomarkers. In one aspect of the disclosure, the biomarker is a “combination biomarker” comprising two scores: a score associated with a polygenetic interferon gamma inflammatory signature and a second score corresponding to the expression level of the TDO2 gene. The components of the combination biomarker of the disclosure may be elevated (i.e., “may be higher”) or decreased (i.e., “may be lower”) with respect to a reference level. As used herein, the term “reference level” refers to a level of one or more biomarkers disclosed herein or a score derived from the measurement of one or more biomarkers disclosed herein, wherein the level is higher or lower than the reference level or reference score corresponding to a reference group (e.g., naive individuals, a specific group, e.g., a prognostic group, e.g., individuals associated with cancer recurrence or non-response of cancer to a specific therapeutic agent, or a combination thereof).

[0117] In some aspects, the IFNγ inflammation signature score is determined by measuring the expression of a panel of IFNγ-related inflammation genes ("IFNγ inflammation gene panel") in cancer samples obtained from subjects, e.g., tumor samples, wherein the IFNγ inflammation gene panel comprises 1 inflammation gene, 2 inflammation genes, 3 inflammation genes, 4 inflammation genes, 5 inflammation genes, 6 inflammation genes, 7 inflammation genes, 8 inflammation genes, 9 inflammation genes, 10 inflammation genes, 11 inflammation genes, 12 inflammation genes, 13 inflammation genes, 14 inflammation genes, 15 inflammation genes, 16 inflammation genes, 17 inflammation genes, 18 inflammation genes, 19 inflammation genes, or 20 inflammation genes, wherein the inflammation genes are IFNγ, CXCL10, HLA-DRA, CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), It is an IFNγ-related inflammatory gene selected from the group consisting of LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, CCR5, CXCL11, GZMA, PRF1, IR2RG, CD3D, CD2, ITGAL, TAGAP, CIITA, PTPRC, CD3E, GZMK, GZMB, PDCD1, SLAMF6, and CXCL13.

[0118] In some respects, the IFNγ inflammation signature score is determined by measuring the expression of a panel of IFNγ inflammation genes ("IFNγ inflammation gene panel") in cancer samples obtained from a subject, e.g., tumor samples, wherein the IFNγ inflammation gene panel consists of or is essentially composed of 1 inflammation gene, 2 inflammation genes, 3 inflammation genes, 4 inflammation genes, 5 inflammation genes, 6 inflammation genes, 7 inflammation genes, 8 inflammation genes, 9 inflammation genes, 10 inflammation genes, 11 inflammation genes, 12 inflammation genes, 13 inflammation genes, 14 inflammation genes, 15 inflammation genes, 16 inflammation genes, 17 inflammation genes, 18 inflammation genes, 19 inflammation genes, or 20 inflammation genes, wherein the inflammation genes are IFNγ, CXCL10, HLA-DRA, CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 It is an IFNγ-related inflammatory gene selected from the group consisting of (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, CCR5, CXCL11, GZMA, PRF1, IR2RG, CD3D, CD2, ITGAL, TAGAP, CIITA, PTPRC, CD3E, GZMK, GZMB, PDCD1, SLAMF6, and CXCL13.

[0119] In some aspects, the IFNγ inflammatory gene panel consists of fewer than about 25, fewer than about 24, fewer than about 23, fewer than about 22, fewer than about 21, fewer than about 20, fewer than about 19, fewer than about 18, fewer than about 17, fewer than about 16, fewer than about 15, fewer than about 14, fewer than about 13, fewer than about 12, fewer than about 11, fewer than about 10, fewer than about 9, fewer than about 8, fewer than about 7, fewer than about 6, or fewer than about 5 IFNγ-related inflammatory genes.

[0120] In some aspects, the IFNγ inflammation gene panel consists of fewer than 25 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 24 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 23 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 22 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 21 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 20 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 19 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 18 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 17 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 16 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 15 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 14 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 13 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 12 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 11 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 10 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 9 IFNγ-related inflammation genes.In some aspects, the IFNγ inflammation gene panel consists of fewer than 8 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 7 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 6 IFNγ-related inflammation genes. In some aspects, the IFNγ inflammation gene panel consists of fewer than 5 IFNγ-related inflammation genes. In certain aspects, the IFNγ inflammation gene panel consists of 4 IFNγ-related inflammation genes. In certain aspects, the IFNγ inflammation gene panel consists of 3 IFNγ-related inflammation genes.

[0121] In some aspects, the IFNγ inflammation gene panel comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 selected from the group consisting of IFNγ, CXCL10, HLA-DRA, CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, CCR5, CXCL11, GZMA, PRF1, IR2RG, CD3D, CD2, ITGAL, TAGAP, CIITA, PTPRC, CD3E, GZMK, GZMB, PDCD1, SLAMF6, and CXCL13. It includes 15, 16, 17, 18, 19, or 20 types of genes.

[0122] Accordingly, in some aspects, the IFNγ inflammation gene panel may include genes associated with cytolytic activity (e.g., granzyme A / B / K and / or PRF1), cytokines / chemokines for the initiation of inflammation (e.g., CXCR6, CXCL9, CCL5 and / or CCR5), T cell markers (e.g., CD3D, Cd3E, CD2 and / or IL2RG [coding for IL-2Rγ]), NK cell activity (e.g., NKG7 and / or HLA-E), antigen presentation (e.g., CIITA and / or HLA-DRA) and / or additional immunomodulatory factors (e.g., LAG3, IDO1 and / or SLAMF6). For example, see literature [Ayers et al. (2017) J. Clin. Invest. 127:2930-40]; and U.S. Application Publication No. US2016-0304969, the full text of which is incorporated herein by reference.

[0123] In some respects, the IFNγ inflammation gene panel consists of or is essentially composed of:

[0124] (i) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1 and STAT1;

[0125] (ii) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1, CCR5, CXCL11, GZMA and PRF1;

[0126] (iii) IFNγ, CXCR6, CD3D, CD2, ITGAL, TAGAP, CIITA, HLA-DRA, PTPRC, CXCL9, CCL5, NKG7, GZMA, PRF1, CCR5, CD3E, HLA-E, GZMK, GZMB, PDCD, SLAMF6, CXCL13, CXCL10, IDO1, LAG3, STAT1 and CXCL11;

[0127] (iv) IR2RG, CXCR6, CD3D, CD2, ITGAL, TAGAP, CIITA, HLA-DRA, PTPRC, CXCL9, CCL5, NKG7, GZMA, PRF1, CCR5, CD3E, GZMK, IFNG, HLA-E, GZMB, PDCD1, SLAMF6, CXCL13, CXCL10, IDO1, LAG3, STAT1 and CXCL11; or

[0128] (v) any combination of his or (i)-(iv) any combination of genes within.

[0129] In one aspect, the IFNγ inflammation gene panel consists of IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, and STAT1.

[0130] In one aspect, the IFNγ inflammation gene panel consists of IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1, CCR5, CXCL11, GZMA, and PRF1.

[0131] In one aspect, the IFNγ inflammation gene panel consists of CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, and HLA.E.

[0132] In one aspect, the IFNγ inflammation gene panel consists of IR2RG, CXCR6, CD3D, CD2, ITGAL, TAGAP, CIITA, HLA-DRA, PTPRC, CXCL9, CCL5, NKG7, GZMA, PRF1, CCR5, CD3E, GZMK, IFNG, HLA-E, GZMB, PDCD1, SLAMF6, CXCL13, CXCL10, IDO1, LAG3, STAT1, and CXCL11.

[0133] In some aspects, the IFNγ inflammation gene panel includes IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, and STAT1, and 1 additional IFNγ-related inflammation gene, 2 additional IFNγ-related inflammation genes, 3 additional IFNγ-related inflammation genes, 4 additional IFNγ-related inflammation genes, 5 additional IFNγ-related inflammation genes, 6 additional IFNγ-related inflammation genes, 7 additional IFNγ-related inflammation genes, 8 additional IFNγ-related inflammation genes, 9 additional IFNγ-related inflammation genes, 10 additional IFNγ-related inflammation genes, 11 additional IFNγ-related inflammation genes, 12 additional IFNγ-related inflammation genes, 13 additional IFNγ-related inflammation genes, 14 additional IFNγ-related inflammation genes, 15 additional IFNγ-related inflammation genes, 16 additional IFNγ-related inflammation genes, and 17 additional It consists of IFNγ-related inflammatory genes, 18 additional IFNγ-related inflammatory genes, 19 additional IFNγ-related inflammatory genes, or 20 additional IFNγ-related inflammatory genes.

[0134] In another aspect, the IFNγ inflammation gene panel includes IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1, CCR5, CXCL11, GZMA, and PRF1, and 1 additional IFNγ-related inflammation gene, 2 additional IFNγ-related inflammation genes, 3 additional IFNγ-related inflammation genes, 4 additional IFNγ-related inflammation genes, 5 additional IFNγ-related inflammation genes, 6 additional IFNγ-related inflammation genes, 7 additional IFNγ-related inflammation genes, 8 additional IFNγ-related inflammation genes, 9 additional IFNγ-related inflammation genes, 10 additional IFNγ-related inflammation genes, 11 additional IFNγ-related inflammation genes, 12 additional IFNγ-related inflammation genes, 13 additional IFNγ-related inflammation genes, 14 additional IFNγ-related inflammation genes, 15 additional IFNγ-related inflammation genes, It consists of 16 additional IFNγ-related inflammatory genes, 17 additional IFNγ-related inflammatory genes, 18 additional IFNγ-related inflammatory genes, 19 additional IFNγ-related inflammatory genes, or 20 additional IFNγ-related inflammatory genes.

[0135] In another aspect, the IFNγ inflammation gene panel includes CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, and HLA.E, and 1 additional IFNγ-related inflammation gene, 2 additional IFNγ-related inflammation genes, 3 additional IFNγ-related inflammation genes, 4 additional IFNγ-related inflammation genes, 5 additional IFNγ-related inflammation genes, 6 additional IFNγ-related inflammation genes, 7 additional IFNγ-related inflammation genes, 8 additional IFNγ-related inflammation genes, 9 additional IFNγ-related inflammation genes, 10 additional IFNγ-related inflammation genes, 11 additional IFNγ-related inflammation genes, and 12 types It consists of additional IFNγ-related inflammatory genes, 13 additional IFNγ-related inflammatory genes, 14 additional IFNγ-related inflammatory genes, 15 additional IFNγ-related inflammatory genes, 16 additional IFNγ-related inflammatory genes, 17 additional IFNγ-related inflammatory genes, 18 additional IFNγ-related inflammatory genes, 19 additional IFNγ-related inflammatory genes, or 20 additional IFNγ-related inflammatory genes.

[0136] In another aspect, the IFNγ inflammation gene panel includes IFNγ IR2RG, CXCR6, CD3D, CD2, ITGAL, TAGAP, CIITA, HLA-DRA, PTPRC, CXCL9, CCL5, NKG7, GZMA, PRF1, CCR5, CD3E, GZMK, HLA-E, GZMB, PDCD1, SLAMF6, CXCL13, CXCL10, IDO1, LAG3, STAT1, CXCL11, and one additional IFNγ-related inflammation gene, two additional IFNγ-related inflammation genes, three additional IFNγ-related inflammation genes, four additional IFNγ-related inflammation genes, five additional IFNγ-related inflammation genes, six additional IFNγ-related inflammation genes, seven additional IFNγ-related inflammation genes, eight additional IFNγ-related inflammation genes, nine additional IFNγ-related inflammation genes, and ten types It consists of additional IFNγ-related inflammatory genes, 11 additional IFNγ-related inflammatory genes, 12 additional IFNγ-related inflammatory genes, 13 additional IFNγ-related inflammatory genes, 14 additional IFNγ-related inflammatory genes, 15 additional IFNγ-related inflammatory genes, 16 additional IFNγ-related inflammatory genes, 17 additional IFNγ-related inflammatory genes, 18 additional IFNγ-related inflammatory genes, 19 additional IFNγ-related inflammatory genes, or 20 additional IFNγ-related inflammatory genes.

[0137] The molecular biomarkers IFNγ, CXCL10, HLA-DRA, CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, CCR5, CXCL11, GZMA, PRF1, IR2RG, CD3D, CD2, ITGAL, TAGAP, CIITA, PTPRC, CD3E, GZMK, GZMB, PDCD1, SLAMF6, and CXCL13 disclosed herein also include the following:

[0138] (i) a protein or fragment thereof having at least about 70%, at least about 71%, at least about 72%, at least about 73%, at least about 74%, at least about 75%, at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98% or at least about 99% sequence identity with respect to the corresponding wild-type sequence; and

[0139] (ii) Nucleic acid (e.g., mRNA) having at least about 70%, at least about 71%, at least about 72%, at least about 73%, at least about 74%, at least about 75%, at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity with respect to each wild-type nucleic acid sequence encoding the corresponding molecular biomarker.

[0140] The molecular biomarker disclosed herein also includes its isoforms and / or variants. As used herein, the “variant” biomarker contains at least one amino acid sequence alteration compared to the amino acid sequence of the corresponding wild-type polypeptide. The amino acid sequence alteration may be, for example, a substitution, deletion, or insertion of one or more amino acids, preferably a conservative substitution. The variant biomarker may have any combination of amino acid substitutions, deletions, or insertions. In one aspect, the biomarker variant polypeptide may have an integer number of amino acid alterations such that its amino acid sequence shares at least about 60, at least about 70, at least about 80, at least about 85, at least about 90, at least about 95, at least about 97, at least about 98, at least about 99, at least about 99.5, or 100% identity with the amino acid sequence of the corresponding wild-type polypeptide.

[0141] In another aspect, the variant biomarker contains at least one nucleic acid sequence alteration compared to the nucleic acid sequence of the corresponding DNA or RNA (e.g., mRNA). The nucleic acid sequence alteration may be, for example, a substitution, deletion, or insertion of one or more nucleotides, preferably a conservative substitution. The variant biomarker may have any combination of nucleic acid substitutions, deletions, or insertions. In one aspect, the biomarker variant gene or gene product (e.g., mRNA) may have an integer number of nucleotide alterations such that its nucleotide sequence shares at least about 60%, at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or 100% identity with the nucleic acid sequence of the corresponding wild-type gene or gene product (e.g., mRNA).

[0142] In some aspects, the methods disclosed herein may include determining the expression level or activity of the molecular biomarkers or combinations thereof disclosed herein, submitting samples taken from a subject for determination, or directing a clinical laboratory to make a determination.

[0143] The present disclosure relates to a method for treating a human subject with cancer, comprising the step of administering to the human subject with cancer a combination therapy comprising (i) a therapy using an anti-PD-1 antagonist, e.g., an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody or its antigen-binding portion, which is generally administered intravenously, and (ii) a therapy using an IDO1 inhibitor, e.g., lindostat mesylate, which is generally administered orally.

[0144] In certain aspects, the anti-PD-1 antibody or its antigen-binding portion cross-competes with nivolumab for binding to human PD-1. In some aspects, the anti-PD-1 antibody or its antigen-binding portion binds to the same epitope as nivolumab. In some aspects, the anti-PD-1 antibody is a chimeric, humanized, or human monoclonal antibody or its antigen-binding portion. In some aspects, the anti-PD-1 antibody contains a heavy chain constant region of a human IgG1 or IgG4 isoform.

[0145] In some aspects, anti-PD-1 antibodies include nivolumab, pembrolizumab, semiplimab, or their antigen-binding portions. In some aspects, anti-PD-1 antibodies are nivolumab, pembrolizumab, or semiplimab.

[0146] In some aspects, anti-PD-L1 antibodies include avelumab, atezolizumab, durvalumab, or their antigen-binding portions. In some aspects, anti-PD-L1 antibodies are avelumab, atezolizumab, or durvalumab.

[0147] In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody is administered once a week, once every two weeks, once every three weeks, once every four weeks, once every five weeks, or once every six weeks. In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody is administered at a dose ranging from about 0.1 mg / kg to about 20.0 mg / kg body weight. In some aspects, anti-PD-1 antibodies (e.g., nivolumab) or anti-PD-L1 antibodies are administered at doses of about 0.1 mg / kg, about 0.5 mg / kg, about 1 mg / kg, about 2 mg / kg, about 3 mg / kg, about 4 mg / kg, about 5 mg / kg, about 6 mg / kg, about 7 mg / kg, about 8 mg / kg, about 9 mg / kg, about 10 mg / kg, about 11 mg / kg, about 12 mg / kg, about 13 mg / kg, about 14 mg / kg, about 15 mg / kg, about 16 mg / kg, about 17 mg / kg, about 18 mg / kg, about 19 mg / kg, or about 20 mg / kg.

[0148] In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody is administered once every approximately 1, 2, 3, 4, 5, or 6 weeks at doses ranging from at least about 0.1 mg / kg to at least about 10.0 mg / kg body weight, e.g., about 0.1 mg / kg, about 0.5 mg / kg, about 1 mg / kg, about 2 mg / kg, about 3 mg / kg, about 4 mg / kg, about 5 mg / kg, about 6 mg / kg, about 7 mg / kg, about 8 mg / kg, about 9 mg / kg, about 10 mg / kg, about 11 mg / kg, about 12 mg / kg, about 13 mg / kg, about 14 mg / kg, about 15 mg / kg, about 16 mg / kg, about 17 mg / kg, about 18 mg / kg, about 19 mg / kg, or about 20 mg / kg. It is administered. In one aspect, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody is administered once every 1, 2, or 3 weeks at a dose ranging from at least about 0.1 mg / kg to at least about 10.0 mg / kg body weight. In another aspect, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody is administered once every 2 weeks at a dose of at least about 3 mg / kg body weight.

[0149] In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose. In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody or its antigen-binding portion is at least about 25 mg / dose, at least about 50 mg / dose, at least about 75 mg / dose, at least about 100 mg / dose, at least about 125 mg / dose, at least about 150 mg / dose, at least about 175 mg / dose, at least about 200 mg / dose, at least about 220 mg / dose, at least about 240 mg / dose, at least about 260 mg / dose, at least about 280 mg / dose, at least about 300 mg / dose, at least about 320 mg / dose, at least about 340 mg / dose, at least about 360 mg / dose, at least about 380 mg / dose, at least about 400 mg / dose, at least about 420 mg / dose, at least about 440 mg / dose, at least about 460 mg / dose, at least about 480 It is administered in uniform doses of mg / dose, at least about 500 mg / dose, or at least about 550 mg / dose.

[0150] In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose of about 240 mg / dose. In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose of about 480 mg / dose. In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose approximately once every 1, 2, 3, or 4 weeks. In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody or its antigen-binding portion is administered at a uniform dose of about 240 mg / dose once every 2 weeks. In some aspects, an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody or its antigen-binding portion is administered once every four weeks at a uniform dose of about 480 mg / dose.

[0151] In some aspects, anti-PD-1 antibodies (e.g., nivolumab) or anti-PD-L1 antibodies are administered as long as clinical benefit is observed or until unmanageable toxicity or disease progression occurs. In some aspects, anti-PD-1 antibodies (e.g., nivolumab) or anti-PD-L1 antibodies are formulated for intravenous administration. In some aspects, anti-PD-1 antibodies (e.g., nivolumab) or anti-PD-L1 antibodies are administered via a bolus intravenous infusion. In some aspects, the bolus is a rapid bolus. In other aspects, the bolus is a slow bolus. In some aspects, anti-PD-1 antibodies (e.g., nivolumab) or anti-PD-L1 antibodies are administered via intravenous infusion. In some aspects, anti-PD-1 antibodies (e.g., nivolumab) or anti-PD-L1 antibodies are administered at a sub-therapeutic dose.

[0152] In some aspects, immunotherapy using an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody is accompanied by a second therapy comprising the step of administering an IDO1 inhibitor (e.g., lindostat mesylate) to the subject. In some aspects, the IDO1 inhibitor is a compound that selectively inhibits IDO1. In some aspects, the IDO1 inhibitor does not inhibit TDO2 enzymatic activity. In some specific aspects of the present disclosure, the IDO1 inhibitor is lindostat ((2R)-N-(4-chlorophenyl)-2-(cis-4-(6-fluoroquinoline-4-yl)cyclohexyl)propanamide) or its salt. In some aspects, the lindostat salt is lindostat mesylate. In some aspects, IDO1 inhibitors are lindostat, 1-methyl-DL-tryptophan, p-(3-benzofuranyl)-DL-alanine, p-[3-benzo(b)thienyl]-DL-alanine; 6-Nitro-L-Tryptophan, Epacadostat, PF-06840003 (3-(5-fluoro-1H-indole-3-yl)pyrrolidine-2,5-dione), Naboxymod, IOM2983, RG-70099, TPST-8844, SRX-3217, PDX-26116, NLG-802, MK-7162, LY-3381916, LY-01013, KHK-2455, IO-102, IO-101, Indoxymod, HTI-1090, EOS-200271, DN-1406131, DN-016, BLH-1131, BGB-5777, BEBT-303, AN-0015, It is selected from the group consisting of AI-001 and any combination thereof. See the literature [Prendergast et al. (2017) Cancer Res. 77 (24); 6795-811], the full text of which is incorporated herein by reference.

[0153] In some aspects, IDO1 inhibitors (e.g., lindostat mesylate) are formulated for oral administration. In some aspects, IDO1 inhibitors (e.g., lindostat mesylate) are administered at a uniform dose of about 100 mg. In some aspects, IDO1 inhibitors (e.g., lindostat mesylate) are administered at a uniform dose of about 200 mg. In some aspects, IDO1 inhibitors (e.g., lindostat mesylate) are administered daily at a uniform dose of about 100 mg. In some aspects, IDO1 inhibitors (e.g., lindostat mesylate) are administered daily at a uniform dose of about 200 mg. In some aspects, IDO1 inhibitors are administered at uniform doses of about 25 mg / day, about 50 mg / day, about 75 mg / day, about 100 mg / day, about 125 mg / day, about 150 mg / day, about 175 mg / day, about 200 mg / day, about 225 mg / day, about 250 mg / day, about 275 mg / day, or about 300 mg / day.

[0154] In some aspects, an IDO1 inhibitor (e.g., lindostat mesylate) is administered daily at a uniform dose of about 100 mg during a course of treatment with an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody. In some aspects, an IDO1 inhibitor (e.g., lindostat mesylate) is administered daily at a uniform dose of about 200 mg during a course of treatment with an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody. In some aspects, IDO1 inhibitors are administered at uniform doses of about 25 mg / day, about 50 mg / day, about 75 mg / day, about 100 mg / day, about 125 mg / day, about 150 mg / day, about 175 mg / day, about 200 mg / day, about 225 mg / day, about 250 mg / day, about 275 mg / day, or about 300 mg / day during a course of treatment with anti-PD-1 antibodies (e.g., nivolumab) or anti-PD-L1 antibodies.

[0155] In specific details, the anti-PD-1 antibody is nivolumab, and the IDO1 inhibitor is lindostat mesylate. In some aspects, nivolumab is administered once every two weeks at a uniform dose of about 240 mg / dose to subjects who require it during a course of treatment with nivolumab (e.g., subjects with cancer), and lindostat mesylate is administered daily at a uniform dose of about 100 mg / dose. In some aspects, nivolumab is administered once every four weeks at a uniform dose of about 480 mg / dose to subjects who require it during a course of treatment with nivolumab (e.g., subjects with cancer), and lindostat mesylate is administered daily at a uniform dose of about 100 mg / dose. In some aspects, nivolumab is administered once every two weeks at a uniform dose of about 240 mg / dose to subjects requiring it during a course of treatment with nivolumab (e.g., subjects with cancer), and lindostat mesylate is administered daily at a uniform dose of about 200 mg / dose. In some aspects, nivolumab is administered once every four weeks at a uniform dose of about 480 mg / dose to subjects requiring it during a course of treatment with nivolumab (e.g., subjects with cancer), and lindostat mesylate is administered daily at a uniform dose of about 200 mg / dose. In some aspects, these treatments are administered to subjects who exhibit combination biomarkers including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score. In some aspects, the treatment described herein may be administered to subjects with refractory cancer, for example, after anticancer therapy including at least one neoadjuvant anticancer therapy, for example, administration of at least one anticancer agent. In some aspects, at least one anticancer agent comprises immunotherapy.

[0156] In some aspects, an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, e.g., nivolumab) is administered on the same day as the administration of an IDO1 inhibitor (e.g., lindostat mesylate), before or after, e.g., immediately before or immediately after the administration of the IDO1 inhibitor. In some aspects, an anti-PD-1 antagonist (e.g., an anti-PD-1 antibody, e.g., nivolumab) is administered co-administered with an IDO1 inhibitor (e.g., lindostat mesylate).

[0157] In some aspects, administration of the combination therapy disclosed herein (e.g., an anticancer therapy including administration of nivolumab and an IDO1 inhibitor, such as lindostat mesylate, to subjects requiring administration) treats cancer. In some aspects, administration of the combination therapy reduces the cancer burden. In some aspects, the cancer burden is reduced by at least about 10%, at least 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% compared to the cancer burden before administration.

[0158] In some aspects, the administration of combination therapy reduces tumor volume. In some aspects, the tumor volume is reduced by at least about 10%, at least 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% compared to the tumor volume before administration.

[0159] In some aspects, the administration of combination therapy reduces cancer cell proliferation. In some aspects, cancer proliferation is reduced by at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% compared to cancer cell proliferation before administration.

[0160] In some aspects, the administration of combination therapy reduces tumor growth. In some aspects, tumor growth is reduced by at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or about 100% compared to tumor growth before administration.

[0161] In some aspects, the subject exhibits progression-free survival of at least about 1 month, at least about 2 months, at least about 3 months, at least about 4 months, at least about 5 months, at least about 6 months, at least about 7 months, at least about 8 months, at least about 9 months, at least about 10 months, at least about 11 months, at least about 1 year, at least about 18 months, at least about 2 years, at least about 3 years, at least about 4 years, or at least about 5 years after the initial administration of the combination therapy disclosed herein (e.g., an anticancer therapy including the administration of nivolumab and an IDO1 inhibitor, such as lindostat mesylate, administered to a subject in cases where the subject exhibits combination biomarkers including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score).

[0162] In some aspects, the subject exhibits stable disease after administration of the combination therapy disclosed herein (e.g., an anticancer therapy comprising the administration of nivolumab and an IDO1 inhibitor, such as lindostat mesylate, to a subject requiring administration, administered to a subject when the subject exhibits combination biomarkers including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score).

[0163] In some aspects, the subject exhibits a partial response after administration of the combination therapy disclosed herein (e.g., an anticancer therapy comprising the administration of nivolumab and an IDO1 inhibitor, such as lindostat mesylate, to a subject requiring administration to a subject in cases where the subject exhibits combination biomarkers including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score).

[0164] In some aspects, the subject exhibits a complete response after administration of the combination therapy disclosed herein (e.g., an anticancer therapy comprising the administration of nivolumab and an IDO1 inhibitor, such as lindostat mesylate, to a subject requiring administration to a subject in cases where the subject exhibits combination biomarkers including (a) a high IFNγ inflammation signature score and (b) a low TDO2 gene expression score).

[0165] In some aspects, the administration of the combination therapy disclosed herein to a subject requiring the combination therapy (e.g., an anticancer therapy comprising the administration of nivolumab and an IDO1 inhibitor, such as lindostat mesylate, to a subject requiring the administration of the combination therapy, administered to a subject in a case where the subject exhibits a combination biomarker comprising (a) a high IFNγ inflammatory signature score and (b) a low TDO2 gene expression score) results in a progression-free survival probability of at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 100%, at least about 110%, at least about 120%, at least about 130%, at least about 140%, or at least Improves progression-free survival probability by approximately 150%.

[0166] In some aspects, the administration of the combination therapy disclosed herein to a subject requiring the combination therapy (e.g., an anticancer therapy comprising the administration of nivolumab and an IDO1 inhibitor, such as lindostat mesylate, to a subject requiring the administration of the combination therapy to a subject in a case where the subject exhibits a combination biomarker comprising (a) a high IFNγ inflammatory signature score and (b) a low TDO2 gene expression score) results in at least about 25%, at least about 50%, at least about 75%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, at least about 300%, at least about 325%, at least about Improves overall survival probability by 350% or at least about 375%.

[0167] III. Combination Biomarkers and Gene Panels

[0168] The method of the present disclosure relates to the predictive use of a combination biomarker having two components: an IFNγ inflammation signature score obtained from an IFNγ inflammation gene panel and a second score, which is a TDO2 gene expression score derived from the expression level of the TDO2 gene.

[0169] The IFNγ inflammation signature score used herein is a measure of the combined expression level of genes present in an IFNγ inflammation gene panel, for example, comprising, consisting of, or essentially comprising the following, in a sample obtained from a subject:

[0170] (i) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1 and STAT1;

[0171] (ii) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1, CCR5, CXCL11, GZMA 및 PRF1; 또는

[0172] (iii) CXCR6, CD3D, CD2, ITGAL, TAGAP, CIITA, HLA-DRA, PTPRC, CXCL9, CCL5, NKG7, GZMA, PRF1, CCR5, CD3E, HLA-E, GZMK, GZMB, PDCD, SLAMF6, CXCL13, CXCL10, IDO, LDO, STAT13, STAT13 및 CXCL11; 또는

[0173] (iv) IFNγ, IR2RG, CXCR6, CD3D, CD2, ITGAL, TAGAP, CIITA, HLA-DRA, PTPRC, CXCL9, CCL5, NKG7, GZMA, PRF1, CCR5, CD3E, GZMK, HLA-E, GZMB, PDCD1, CXCLMF, CXCL1 IDO1, LAG3, STAT1 및 CXCL11.

[0174] In principle, any biological sample containing one or more cancer cells may be used in the method disclosed herein. In some aspects, the sample is selected from a cancer (e.g., tumor) biopsy, a blood sample, a serum sample, or any combination thereof. In some aspects, the sample is obtained from the stroma of a tumor. In certain aspects, the sample is a tumor biopsy collected from a subject prior to administration of an anti-PD-1 antagonist (e.g., anti-PD-1 or anti-PD-L1 antibody) and / or prior to administration of an IDO1 inhibitor (e.g., lindostat mesylate). In some aspects, the sample obtained from the subject is a formalin-fixed tumor biopsy. In some aspects, the sample obtained from the subject is a paraffin-embedded tumor biopsy. In some aspects, the sample obtained from the subject is formalin-fixed paraffin-embedded tissue. In some aspects, the sample obtained from the subject is a fresh-frozen tumor biopsy. In some aspects, the sample obtained from the subject is a blood sample or is obtained by processing a blood sample (for example, the sample is a specific subset of cells extracted from a blood sample).

[0175] Any method known in the art for measuring the expression of a specific gene (e.g., TDO2) or a panel of genes (e.g., genes within an IFNγ inflammatory gene panel) may be used in the method of the present disclosure. In some aspects, the expression of one or more inflammatory genes within an IFNγ inflammatory gene panel is determined by detecting the presence of mRNA transcribed from an IFNγ-related inflammatory gene or a TDO2 gene, the presence of a protein encoded by an IFNγ-related inflammatory gene or a TDO2 gene, or both.

[0176] In some aspects, the expression of one or more genes within the IFNγ inflammation gene panel and / or the TDO2 gene is determined by measuring the levels of inflammation gene mRNA in at least one sample obtained from a subject, for example, by measuring the levels of one or more of IFNγ mRNA, CXCL10 mRNA, CXCL9 mRNA, HLA-DRA mRNA, IDO1 mRNA, STAT1 mRNA, CCR5 mRNA, CXCL11 mRNA, GZMA mRNA, PRF1 mRNA or TDO2 mRNA.

[0177] In a specific aspect, the IFNγ inflammation signature score is determined by measuring the levels of IFNγ mRNA, CXCL10 mRNA, CXCL9 mRNA, HLA-DRA mRNA, IDO1 mRNA, and STAT1 mRNA in at least one sample obtained from a subject.

[0178] In a specific aspect, the IFNγ inflammation signature score is determined by measuring the levels of IFNγ mRNA, CXCL10 mRNA, CXCL9 mRNA, HLA-DRA mRNA, IDO1 mRNA, STAT1 mRNA, CCR5 mRNA, CXCL11 mRNA, GZMA mRNA, and PRF1 mRNA in at least one sample obtained from a subject.

[0179] In a specific aspect, the IFNγ inflammatory signature score is determined by measuring the levels of CXCR6 mRNA, TIGIT mRNA, CD274 (PD-L1) mRNA, PDCD1LG2 (PD-L2) mRNA, LAG3 mRNA, NKG7 mRNA, PSMB10 mRNA, CMKLR1 mRNA, CD8A mRNA, IDO1 mRNA, CCL5 mRNA, CXCL9 mRNA, HLA.DQA1 mRNA, CD276 mRNA, HLA.DRB1 mRNA, STAT1 mRNA, and HLA.E mRNA in at least one sample obtained from a subject.

[0180] In a specific aspect, the IFNγ inflammation signature score is determined by measuring the levels of IFNγ mRNA, IR2RG mRNA, CXCR6 mRNA, CD3D mRNA, CD2 mRNA, ITGAL mRNA, TAGAP mRNA, CIITA mRNA, HLA-DRA mRNA, PTPRC mRNA, CXCL9 mRNA, CCL5 mRNA, NKG7 mRNA, GZMA mRNA, PRF1 mRNA, CCR5 mRNA, CD3E mRNA, GZMK mRNA, HLA-E mRNA, GZMB mRNA, PDCD1 mRNA, SLAMF6 mRNA, CXCL13 mRNA, CXCL10 mRNA, IDO1 mRNA, LAG3 mRNA, STAT1 mRNA, and CXCL11 mRNA in at least one sample obtained from a subject.

[0181] In some aspects, the TDO2 expression score is determined by measuring the level of TDO2 mRNA in at least one sample obtained from the subject. In some aspects, all mRNA level measurements are performed using a single sample. In other aspects, all mRNA level measurements are performed using more than one sample.

[0182] The levels of mRNA from genes and / or the TDO2 gene within the IFNγ inflammation gene panel can be measured using any method known in the relevant art. In some aspects, the presence of mRNA encoding genes and / or the TDO2 gene within the IFNγ inflammation gene panel is determined using reverse transcription PCR. In some aspects, mRNA from genes and / or the TDO2 gene within the IFNγ inflammation gene panel is measured using reverse transcription PCR. In some aspects, mRNA from genes and / or the TDO2 gene within the IFNγ inflammation gene panel is measured using RNA in-system hybridization.

[0183] In some aspects, the expression of one or more genes within the IFNγ inflammation gene panel and / or the TDO2 gene is determined by measuring the levels of proteins expressed in at least one sample obtained from a subject, for example, by measuring the levels of one or more proteins among IFNγ, CXCL10, HLA-DRA, CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E, CCR5, CXCL11, GZMA, PRF1, IR2RG, CD3D, CD2, ITGAL, TAGAP, CIITA, PTPRC, CD3E, GZMK, GZMB, PDCD1, SLAMF6, CXCL13, and TDO2. It is decided.

[0184] In certain aspects, the IFNγ inflammation signature score is determined by measuring the levels of IFNγ protein, CXCL10 protein, CXCL9 protein, HLA-DRA protein, IDO1 protein, and STAT1 protein in at least one sample obtained from a subject.

[0185] In certain aspects, the IFNγ inflammation signature score is determined by measuring the levels of IFNγ protein, CXCL10 protein, CXCL9 protein, HLA-DRA protein, IDO1 protein, STAT1 protein, CCR5 protein, CXCL11 protein, GZMA protein, and PRF1 protein in at least one sample obtained from a subject.

[0186] In a specific aspect, the IFNγ inflammation signature score is determined by measuring the levels of CXCR6 protein, TIGIT protein, CD274 (PD-L1) protein, PDCD1LG2 (PD-L2) protein, LAG3 protein, NKG7 protein, PSMB10 protein, CMKLR1 protein, CD8A protein, IDO1 protein, CCL5 protein, CXCL9 protein, HLA.DQA1 protein, CD276 protein, HLA.DRB1 protein, STAT1 protein and HLA.E protein in at least one sample obtained from a subject.

[0187] In a specific aspect, the IFNγ inflammation signature score is determined by measuring the levels of IFNγ protein, IR2RG protein, CXCR6 protein, CD3D protein, CD2 protein, ITGAL protein, TAGAP protein, CIITA protein, HLA-DRA protein, PTPRC protein, CXCL9 protein, CCL5 protein, NKG7 protein, GZMA protein, PRF1 protein, CCR5 protein, CD3E protein, GZMK protein, HLA-E protein, GZMB protein, PDCD1 protein, SLAMF6 protein, CXCL13 protein, CXCL10 protein, IDO1 protein, LAG3 protein, STAT1 protein and CXCL11 protein in at least one sample obtained from a subject.

[0188] In a specific aspect, the TDO2 gene expression score is determined by measuring the level of TDO2 protein in at least one sample obtained from the subject.

[0189] The levels of expressed proteins corresponding to one or more genes within the IFNγ inflammation gene panel and / or the TDO2 gene can be measured using any method known in the relevant art. In some aspects, the presence of proteins encoded by genes within the IFNγ inflammation gene panel and / or the TDO2 gene is determined using an IHC assay. In some aspects, the levels of expressed proteins are measured using an immunohistochemistry (IHC) assay. In certain aspects, the IHC is an automated IHC. In some aspects, the assay is a protein IHC assay including phases correlated with the IFNγ inflammation gene panel.

[0190] In some aspects, the expression of one or more genes within the IFNγ inflammation gene panel and / or the TDO2 gene is normalized to the expression of one or more housekeeping genes. In some aspects, one or more housekeeping genes consist of genes that have relatively consistent expression across various cancer types (e.g., tumor types) in various subjects.

[0191] In some aspects, raw gene expression values ​​are normalized according to standard gene expression profiling (GEP) protocols. In these aspects, the IFNγ inflammation signature score and / or TDO2 gene expression score can be calculated as the median or mean of log2-transformed, normalized, and scaled expression values ​​across all target genes and / or TDO2 genes within the IFNγ inflammation gene panel, and can be presented on a linear scale. In certain aspects, the score has a positive or negative value depending on whether gene expression is upregulated or downregulated under specific conditions.

[0192] In certain aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score greater than the reference IFNγ inflammation signature score.

[0193] In some aspects, the reference IFNγ inflammation signature score is the average inflammation signature score. In some aspects, the average IFNγ inflammation signature score is determined by measuring the expression of genes present in the IFNγ inflammation gene panel in cancer (e.g., tumor) samples obtained from a subject population and calculating the average for the subject population. In some aspects, the average IFNγ inflammation signature score is determined by averaging the expression of IFNγ inflammation gene panel genes in cancer samples obtained from a subject population.

[0194] In some aspects, the reference IFNγ inflammation signature score is the median inflammation signature score. In some aspects, the median IFNγ inflammation signature score is determined by measuring the expression of genes present in the IFNγ inflammation gene panel in cancer (e.g., tumor) samples obtained from a subject population and calculating the median of the distribution in the subject population. In some aspects, the median IFNγ inflammation signature score is determined by measuring the expression of genes present in the IFNγ inflammation gene panel in cancer (e.g., tumor) samples obtained from a subject population and calculating the median of the distribution in the subject population. In some aspects, the median IFNγ inflammation signature score is determined from the distribution of expression of IFNγ inflammation gene panel genes in cancer samples obtained from a subject population.

[0195] In some respects, the reference IFNγ inflammation signature score is a predetermined cut-off or threshold value.

[0196] In some aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score higher than the mean IFNγ inflammation signature score of a reference sample (e.g., a sample or set of samples obtained from a subject or group of subjects). In some aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score higher than the median IFNγ inflammation signature score of a reference sample (e.g., a sample or set of samples obtained from a subject or group of subjects). In some aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score higher than a predetermined cut-off or threshold value.

[0197] In some aspects, the reference sample comprises non-tumor tissue of the subject, corresponding non-tumor tissue of the subject, or corresponding tissue of a tumor-free subject. In some aspects, the reference sample comprises non-tumor tissue from a subject population, corresponding non-tumor tissue of a subject population, or corresponding tissue of a tumor-free subject population.

[0198] In some aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score that is at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, or at least about 300% higher than the average IFNγ inflammation signature score.

[0199] In some aspects, high IFNγ inflammation signature scores are characterized by IFNγ inflammation signature scores that are at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, or at least about 300% higher than the median IFNγ inflammation signature score.

[0200] In some aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score that is at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, or at least about 300% higher than a predetermined cut-off or threshold IFNγ inflammation signature score.

[0201] In some aspects, high IFNγ inflammatory signature scores are at least about 1.25 times, at least about 1.30 times, at least about 1.35 times, at least about 1.40 times, at least about 1.45 times, at least about 1.50 times, at least about 1.55 times, at least about 1.60 times, at least about 1.65 times, at least about 1.70 times, at least about 1.75 times, at least about 1.80 times, at least about 1.85 times, at least about 1.90 times, at least about 1.95 times, at least about 2 times, at least about 2.25 times, at least about 2.50 times, at least about 2.75 times, at least about 3 times, at least about 3.25 times, and at least about It features an IFNγ inflammation signature score that is 3.50 times, at least about 3.75 times, or at least about 400 times higher.

[0202] In certain aspects, a high IFNγ inflammation signature score is characterized by an IFNγ inflammation signature score of at least about -0.20, at least about -0.15, at least about -0.10, at least about -0.05, at least about 0.00, at least about 0.05, at least about 0.10, at least about 0.15, at least about 0.20, at least about 0.25, at least about 0.30, at least about 0.35, at least about 0.40, at least about 0.45, at least about 0.50, at least about 0.55, at least about 0.60, at least about 0.65, at least about 0.70, at least about 0.75, at least about 0.80, at least about 0.85, at least about 0.90, at least about 0.95, or at least about 1.00, wherein the IFNγ inflammation signature score is determined according to the method disclosed herein.

[0203] In certain aspects, the average IFNγ inflammation signature score is about -0.2, about -0.15, about -0.1, about -0.05, about 0, about 0.05, about 0.1, about 0.15, about 0.2, about 0.25, about 0.3, about 0.35, about 0.4, about 0.45, about 0.5, about 0.55, about 0.6, about 0.65, about 0.7, about 0.75, about 0.8, about 0.85, about 0.9, about 0.95, or about 1, where the average IFNγ inflammation signature score is determined according to the method disclosed herein.

[0204] In certain aspects, the average IFNγ inflammation signature score is -0.2, -0.15, -0.1, -0.05, 0, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, or 1, wherein the average IFNγ inflammation signature score is determined according to the method disclosed herein.

[0205] In certain aspects, the median IFNγ inflammation signature score is about -0.2, about -0.15, about -0.1, about -0.05, about 0, about 0.05, about 0.1, about 0.15, about 0.2, about 0.25, about 0.3, about 0.35, about 0.4, about 0.45, about 0.5, about 0.55, about 0.6, about 0.65, about 0.7, about 0.75, about 0.8, about 0.85, about 0.9, about 0.95, or about 1, where the median IFNγ inflammation signature score is determined according to the method disclosed herein.

[0206] In certain aspects, the median IFNγ inflammatory signature score is -0.2, -0.15, -0.1, -0.05, 0, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, or 1, wherein the median IFNγ inflammatory signature score is determined according to the method disclosed herein.

[0207] In certain aspects, the threshold IFNγ inflammation signature score is about -0.2, about -0.15, about -0.1, about -0.05, about 0, about 0.05, about 0.1, about 0.15, about 0.2, about 0.25, about 0.3, about 0.35, about 0.4, about 0.45, about 0.5, about 0.55, about 0.6, about 0.65, about 0.7, about 0.75, about 0.8, about 0.85, about 0.9, about 0.95, or about 1, where the threshold IFNγ inflammation signature score is determined according to the method disclosed herein.

[0208] In certain aspects, the threshold IFNγ inflammation signature score is -0.2, -0.15, -0.1, -0.05, 0, 0.05, 0.1, 0.15, 0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.55, 0.6, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, or 1, wherein the threshold IFNγ inflammation signature score is determined according to the method disclosed herein.

[0209] In certain aspects, a low TDO2 gene expression score is characterized by a smaller (lower) TDO2 gene expression score than the reference TDO2 gene expression score.

[0210] In some aspects, the reference TDO2 gene expression score is the average TDO2 gene expression score. In some aspects, the average TDO2 gene expression score is determined by measuring the expression of the TDO2 gene in cancer (e.g., tumor) samples obtained from a subject population and calculating the average for the subject population. In some aspects, the average TDO2 gene expression score is determined by averaging the expression of the TDO2 gene in cancer samples obtained from a subject population.

[0211] In some aspects, the reference TDO2 gene expression score is the median TDO2 gene expression score. In some aspects, the median TDO2 gene expression score is determined by measuring the expression of the TDO2 gene in cancer (e.g., tumor) samples obtained from a subject population and calculating the median of the distribution within the subject population. In some aspects, the median TDO2 gene expression score is determined by measuring the expression of the TDO2 gene present in cancer (e.g., tumor) samples obtained from a subject population and calculating the median of the distribution within the subject population. In some aspects, the median TDO2 gene expression score is determined from the distribution of TDO2 gene expression in cancer samples obtained from a subject population.

[0212] In some respects, the reference TDO2 gene expression score is a predetermined cut-off or threshold value.

[0213] In some aspects, a low TDO2 gene expression score is characterized by a TDO2 gene expression score lower than the average TDO2 gene expression score of a reference sample (e.g., a sample or set of samples obtained from a subject or group of subjects). In some aspects, a low TDO2 gene expression score is characterized by a TDO2 gene expression score lower than the median TDO2 gene expression score of a reference sample (e.g., a sample or set of samples obtained from a subject or group of subjects). In some aspects, a low TDO2 gene expression score is characterized by a TDO2 gene expression score lower than a predetermined cut-off or threshold value.

[0214] In some aspects, the TDO2 reference sample comprises non-tumor tissue of a subject, corresponding non-tumor tissue of a subject, or corresponding tissue of a tumor-free subject. In some aspects, the TDO2 reference sample comprises non-tumor tissue from a subject population, corresponding non-tumor tissue of a subject population, or corresponding tissue of a tumor-free subject population.

[0215] In some aspects, the low TDO2 gene expression score is characterized by a TDO2 gene expression score that is at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, or at least about 300% lower than the average TDO2 gene expression score.

[0216] In some aspects, the low TDO2 gene expression score is characterized by a TDO2 gene expression score that is at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, or at least about 300% lower than the median TDO2 gene expression score.

[0217] In some aspects, the low TDO2 gene expression score is characterized by a TDO2 gene expression score that is at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 100%, at least about 125%, at least about 150%, at least about 175%, at least about 200%, at least about 225%, at least about 250%, at least about 275%, or at least about 300% lower than a predetermined cut-off or threshold IFNγ inflammation signature score.

[0218] In some respects, a low TDO2 gene expression score is at least about 1.25 times, at least about 1.30 times, at least about 1.35 times, at least about 1.40 times, at least about 1.45 times, at least about 1.50 times, at least about 1.55 times, at least about 1.60 times, at least about 1.65 times, at least about 1.70 times, at least about 1.75 times, at least about 1.80 times, at least about 1.85 times, at least about 1.90 times, at least about 1.95 times, at least about 2 times, at least about 2.25 times, at least about 2.50 times, at least about 2.75 times, at least about 3 times, at least about 3.25 times, at least about 3.50 times, at least about 3.75 times, or at least It features a TDO2 gene expression score that is about 400 times lower.

[0219] In specific aspects, low TDO2 gene expression scores are approximately <5, <4.9, <4.8, <4.7, <4.6, <4.5, <4.4, <4.3, <4.2, <4.1, <4, <4, <3.9, <3.8, <3.7, <3.6, <3.5, <3.4, ​​<3.3, <3.2, <3.1, <3, <3, <2.9, <2.8, <2.7, <2.6, <2.5, <2.4, <2.3, <2.2, <2.1, <2, <1.9, <1.8, <1.7, <1.6 It is characterized by a TDO2 gene expression score of less than, about less than 1.5, about less than 1.4, about less than 1.3, about less than 1.2, about less than 1.1, about less than 1, about less than 0.9, about less than 0.8, about less than 0.7, about less than 0.6, about less than 0.5, about less than 0.4, about less than 0.3, about less than 0.2, about less than 0.1, or about less than 0, wherein the TDO2 gene expression score is determined according to the method disclosed herein.

[0220] In certain aspects, the average TDO2 gene expression scores were approximately 5, approximately 4.9, approximately 4.8, approximately 4.7, approximately 4.6, approximately 4.5, approximately 4.4, approximately 4.3, approximately 4.2, approximately 4.1, approximately 4, approximately 3.9, approximately 3.8, approximately 3.7, approximately 3.6, approximately 3.5, approximately 3.4, approximately 3.3, approximately 3.2, approximately 3.1, approximately 3, approximately 2.9, approximately 2.8, approximately 2.7, approximately 2.6, approximately 2.5, approximately 2.4, approximately 2.3, approximately 2.2, approximately 2.1, approximately 2, approximately 1.9, approximately 1.8, approximately 1.7, approximately 1.6, approximately 1.5, approximately 1.4, approximately 1.3, approximately 1.2, approximately 1.1, approximately 1, approximately 0.9, approximately 0.8, approximately 0.7, approximately 0.6, approximately 0.5, approximately 0.4, approximately 0.3, approximately 0.2, approximately 0.1, or approximately 0, wherein the average TDO2 gene expression score is determined according to the method disclosed herein.

[0221] In certain aspects, the average TDO2 gene expression scores were 5, 4.9, 4.8, 4.7, 4.6, 4.5, 4.4, 4.3, 4.2, 4.1, 4, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3, 2.9, 2.8, 2.7, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 2, 1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3, 1.2, 1.1, 1, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1 or 0, where the average TDO2 gene expression score is determined according to the method disclosed herein.

[0222] In certain aspects, the median TDO2 gene expression scores are approximately 5, approximately 4.9, approximately 4.8, approximately 4.7, approximately 4.6, approximately 4.5, approximately 4.4, approximately 4.3, approximately 4.2, approximately 4.1, approximately 4, approximately 3.9, approximately 3.8, approximately 3.7, approximately 3.6, approximately 3.5, approximately 3.4, approximately 3.3, approximately 3.2, approximately 3.1, approximately 3, approximately 2.9, approximately 2.8, approximately 2.7, approximately 2.6, approximately 2.5, approximately 2.4, approximately 2.3, approximately 2.2, approximately 2.1, approximately 2, approximately 1.9, approximately 1.8, approximately 1.7, approximately 1.6, approximately 1.5, approximately 1.4, approximately 1.3, approximately 1.2, approximately 1.1, approximately 1, approximately 0.9, approximately 0.8, approximately 0.7, approximately 0.6, approximately 0.5, approximately 0.4, approximately 0.3, approximately 0.2, approximately 0.1, or approximately 0, where the median TDO2 gene expression score is determined according to the method disclosed herein.

[0223] In certain aspects, the median TDO2 gene expression scores were 5, 4.9, 4.8, 4.7, 4.6, 4.5, 4.4, 4.3, 4.2, 4.1, 4, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3, 2.9, 2.8, 2.7, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 2, 1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3, 1.2, 1.1, 1, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, or 0, where the median TDO2 gene expression score is determined according to the method disclosed herein.

[0224] In certain aspects, the threshold TDO2 gene expression scores are approximately 5, approximately 4.9, approximately 4.8, approximately 4.7, approximately 4.6, approximately 4.5, approximately 4.4, approximately 4.3, approximately 4.2, approximately 4.1, approximately 4, approximately 3.9, approximately 3.8, approximately 3.7, approximately 3.6, approximately 3.5, approximately 3.4, approximately 3.3, approximately 3.2, approximately 3.1, approximately 3, approximately 2.9, approximately 2.8, approximately 2.7, approximately 2.6, approximately 2.5, approximately 2.4, approximately 2.3, approximately 2.2, approximately 2.1, approximately 2, approximately 1.9, approximately 1.8, approximately 1.7, approximately 1.6, approximately 1.5, approximately 1.4, approximately 1.3, approximately 1.2, approximately 1.1, approximately 1, approximately 0.9, approximately 0.8, approximately 0.7, approximately 0.6, approximately 0.5, approximately 0.4, approximately 0.3, approximately 0.2, approximately 0.1, or approximately 0, wherein the threshold value TDO2 gene expression score is determined according to the method disclosed herein.

[0225] In a specific aspect, the threshold TDO2 gene expression scores are 5, 4.9, 4.8, 4.7, 4.6, 4.5, 4.4, 4.3, 4.2, 4.1, 4, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3, 2.9, 2.8, 2.7, 2.6, 2.5, 2.4, 2.3, 2.2, 2.1, 2, 1.9, 1.8, 1.7, 1.6, 1.5, 1.4, 1.3, 1.2, 1.1, 1, 0.9, 0.8, 0.7, 0.6, 0.5, 0.4, 0.3, 0.2, 0.1, or 0, where the threshold TDO2 gene expression score is determined according to the method disclosed herein.

[0226] IV. Anti-PD-1 antibodies useful for the present disclosure

[0227] In some aspects of the present disclosure, an anti-PD-1 antagonist is an anti-PD-1 antibody or its antigen-binding portion. Anti-PD-1 antibodies known in the art may be used in the compositions and methods described herein. Various human monoclonal antibodies that bind specifically to PD-1 with high affinity are disclosed in U.S. Patent No. 8,008,449. The human anti-PD-1 antibody disclosed in U.S. Patent No. 8,008,449 has been demonstrated to exhibit one or more of the following features: (a) 1 x 10⁶ when determined by surface plasmon resonance using a Biacore biosensor system -7 K less than or equal to M D (a) binds to human PD-1; (b) does not substantially bind to human CD28, CTLA-4, or ICOS; (c) increases T-cell proliferation in a mixed lymphocyte response (MLR) assay; (d) increases interferon-γ production in an MLR assay; (e) increases IL-2 secretion in an MLR assay; (f) binds to human PD-1 and cynomolgus monkey PD-1; (g) inhibits the binding of PD-L1 and / or PD-L2 to PD-1; (h) stimulates an antigen-specific memory response; (i) stimulates an antibody response; and / or (j) inhibits tumor cell growth in vivo. Anti-PD-1 antibodies available in the present disclosure comprise monoclonal antibodies that specifically bind to human PD-1 and exhibit at least one, in some aspects at least five, of the above features.

[0228] Other anti-PD-1 monoclonal antibodies are, for example, U.S. Patent Nos. 6,808,710, 7,488,802, 8,168,757, and 8,354,509, U.S. Publication No. 2016 / 0272708, and PCT Publications WO 2012 / 145493, WO 2008 / 156712, WO 2015 / 112900, WO 2012 / 145493, WO 2015 / 112800, WO 2014 / 206107, WO 2015 / 35606, WO 2015 / 085847, WO 2014 / 179664, WO 2017 / 020291, WO 2017 / 020858, WO WO 2016 / 197367, WO 2017 / 024515, WO 2017 / 025051, WO 2017 / 123557, WO 2016 / 106159, WO 2014 / 194302, WO 2017 / 040790, WO 2017 / 133540, WO 2017 / 132827, WO 2017 / 024465, WO 2017 / 025016, WO 2017 / 106061, WO 2017 / 19846, WO 2017 / 024465, WO 2017 / 025016, WO 2017 / 132825, and WO 2017 / 133540, the full text of each of these being submitted to this document It is included as a reference.

[0229] In some aspects, anti-PD-1 antibodies include nivolumab (also known as Opdivo®, 5C4, BMS-936558, MDX-1106, and ONO-4538), pembrolizumab (Merck; also known as Keytruda®, lambrolizumab, and MK-3475; see WO2008 / 156712), PDR001 (Novartis; see WO 2015 / 112900), MEDI-0680 (AstraZeneca; also known as AMP-514; see WO 2012 / 145493), cemiplimab (Regeneron; also known as REGN-2810; see WO 2015 / 112800), and JS001 (Taizhou Junxi Pharma (TAIZHOU JUNSHI PHARMA); also known as toripalimab; see reference [Si-Yang Liu et al., J. Hematol. Oncol. 10:136 (2017)]), BGB-A317 (Beigene; also known as tislellizumab; see WO 2015 / 35606 and US 2015 / 0079109), INCSHR1210 (Jiangsu Hengrui Medicine; also known as SHR-1210; WO 2015 / 085847; see reference [Si-Yang Liu et al., J. Hematol. Oncol. 10:136 (2017)]), TSR-042 (Tesaro Biopharmaceutical; also known as ANB011; See WO2014 / 179664), GLS-010 (Wuxi / Harbin Gloria Pharmaceuticals; also known as WBP3055; literature [Si-Yang Liu et al., J. Hematol. Oncol.[Reference 10:136 (2017)]), AM-0001 (Armo), STI-1110 (Sorrento Therapeutics; reference WO 2014 / 194302), AGEN2034 (Agenus; reference WO 2017 / 040790), MGA012 (Macrogenics, reference WO 2017 / 19846), BCD-100 (Biocad; reference [Kaplon et al., mAbs 10(2):183-203 (2018)]), and IBI308 (Innovent; WO 2017 / 024465, WO 2017 / 025016, WO 2017 / 132825 and WO It is selected from a group consisting of (see 2017 / 133540).

[0230] In one aspect, an anti-PD-1 antibody is nivolumab. Nivolumab is a fully human IgG4 (S228P) PD-1 immune checkpoint inhibitor antibody that blocks the down-regulation of anti-tumor T-cell function by selectively blocking interactions with PD-1 ligands (PD-L1 and PD-L2) (U.S. Patent No. 8,008,449; reference [Wang et al., 2014 Cancer Immunol Res. 2(9):846-56]).

[0231] In another aspect, an anti-PD-1 antibody is pembrolizumab. Pembrolizumab is a humanized monoclonal IgG4 (S228P) antibody directed against the human cell surface receptor PD-1 (programmed cell death-1 or programmed apoptosis-1). Pembrolizumab is described, for example, in U.S. Patent Nos. 8,354,509 and 8,900,587.

[0232] The anti-PD-1 antibodies available for use in the disclosed compositions and methods also comprise isolated antibodies that specifically bind to human PD-1 and cross-compete with any anti-PD-1 antibody disclosed herein, e.g., nivolumab, for binding to human PD-1 (e.g., see U.S. Patent Nos. 8,008,449 and 8,779,105; WO 2013 / 173223). In some aspects, the anti-PD-1 antibodies bind to the same epitope as any anti-PD-1 antibody described herein, e.g., nivolumab. The ability of the antibodies to cross-compete for binding to an antigen indicates that these monoclonal antibodies bind to the same epitope region of the antigen and stereochemically interfere with the binding of other cross-competing antibodies to such a specific epitope region. These cross-competing antibodies are expected to have functional characteristics very similar to the reference antibody, e.g., nivolumab, in their binding to the same epitope region of PD-1. Cross-competing antibodies can be easily identified based on their ability to cross-compete with nivolumab in standard PD-1 binding assays, such as Viacor assays, ELISA assays, or flow cytometry (see, for example, WO 2013 / 173223).

[0233] In certain aspects, antibodies that cross-compete with the human PD-1 antibody nivolumab for binding to human PD-1 or bind to the same epitope region are monoclonal antibodies. For administration to human subjects, these cross-competing antibodies are chimeric antibodies, engineered antibodies, or humanized or human antibodies. Such chimeric, engineered, humanized, or human monoclonal antibodies can be prepared and isolated by methods widely known in the art.

[0234] The anti-PD-1 antibody usable in the compositions and methods of the disclosed present disclosure also comprises the antigen-binding portion of said antibody. It has been sufficiently demonstrated that the antigen-binding function of an antibody can be performed by a fragment of a full-length antibody.

[0235] An anti-PD-1 antibody suitable for use in the disclosed compositions and methods is an antibody that binds to PD-1 with high specificity and affinity, blocks the binding of PD-L1 and / or PD-L2, and inhibits the immunosuppressive effects of the PD-1 signaling pathway. In any of the compositions or methods disclosed herein, the anti-PD-1 "antibody" comprises an antigen-binding portion or fragment that binds to the PD-1 receptor, inhibits ligand binding, and exhibits functional characteristics similar to those of a whole antibody in upregulating the immune system. In certain aspects, the anti-PD-1 antibody or its antigen-binding portion cross-competes with nivolumab for binding to human PD-1.

[0236] In some aspects, the anti-PD-1 antibody is administered once every 2, 3, 4, 5, 6, 7, or 8 weeks at a dose ranging from 0.1 mg / kg to 20.0 mg / kg body weight, for example, once every 2, 3, or 4 weeks at a dose ranging from 0.1 mg / kg to 10.0 mg / kg body weight. In other aspects, the anti-PD-1 antibody is administered once every 2 weeks at a dose of about 2 mg / kg, about 3 mg / kg, about 4 mg / kg, about 5 mg / kg, about 6 mg / kg, about 7 mg / kg, about 8 mg / kg, about 9 mg / kg, or 10 mg / kg body weight. In another aspect, the anti-PD-1 antibody is administered once every 3 weeks at a dose of about 2 mg / kg, about 3 mg / kg, about 4 mg / kg, about 5 mg / kg, about 6 mg / kg, about 7 mg / kg, about 8 mg / kg, about 9 mg / kg, or 10 mg / kg body weight. In one aspect, the anti-PD-1 antibody is administered about once every 3 weeks at a dose of about 5 mg / kg body weight. In yet another aspect, the anti-PD-1 antibody, e.g., nivolumab, is administered about once every 2 weeks at a dose of about 3 mg / kg body weight. In another aspect, the anti-PD-1 antibody, e.g., pembrolizumab, is administered about once every 3 weeks at a dose of about 2 mg / kg body weight.

[0237] The anti-PD-1 antibody useful for the present disclosure may be administered in uniform doses. In some aspects, the anti-PD-1 antibody is administered in uniform doses of about 100 to about 1000 mg, about 100 mg to about 900 mg, about 100 mg to about 800 mg, about 100 mg to about 700 mg, about 100 mg to about 600 mg, about 100 mg to about 500 mg, about 200 mg to about 1000 mg, about 200 mg to about 900 mg, about 200 mg to about 800 mg, about 200 mg to about 700 mg, about 200 mg to about 600 mg, about 200 mg to about 500 mg, about 200 mg to about 480 mg, or about 240 mg to about 480 mg. In one aspect, the anti-PD-1 antibody is administered in homogeneous doses of at least about 200 mg, at least about 220 mg, at least about 240 mg, at least about 260 mg, at least about 280 mg, at least about 300 mg, at least about 320 mg, at least about 340 mg, at least about 360 mg, at least about 380 mg, at least about 400 mg, at least about 420 mg, at least about 440 mg, at least about 460 mg, at least about 480 mg, at least about 500 mg, at least about 520 mg, at least about 540 mg, at least about 550 mg, at least about 560 mg, at least about 580 mg, at least about 600 mg, at least about 620 mg, at least about 640 mg, at least about 660 mg, at least about 680 mg, at least about 700 mg, or at least about 720 mg, about 1, 2, It is administered at intervals of 3, 4, 5, 6, 7, 8, 9, or 10 weeks.In another aspect, anti-PD-1 antibodies are administered at equal doses of about 200 mg to about 800 mg, about 200 mg to about 700 mg, about 200 mg to about 600 mg, and about 200 mg to about 500 mg at intervals of about 1, 2, 3, or 4 weeks.

[0238] In some aspects, the anti-PD-1 antibody is administered approximately once every 3 weeks at a uniform dose of about 200 mg. In other aspects, the anti-PD-1 antibody is administered approximately once every 2 weeks at a uniform dose of about 200 mg. In other aspects, the anti-PD-1 antibody is administered approximately once every 2 weeks at a uniform dose of about 240 mg. In certain aspects, the anti-PD-1 antibody is administered approximately once every 4 weeks at a uniform dose of about 480 mg.

[0239] In some aspects, nivolumab is administered once every two weeks at a uniform dose of about 240 mg. In some aspects, nivolumab is administered once every three weeks at a uniform dose of about 240 mg. In some aspects, nivolumab is administered once every three weeks at a uniform dose of about 360 mg. In some aspects, nivolumab is administered once every four weeks at a uniform dose of about 480 mg.

[0240] In some aspects, pembrolizumab is administered once every two weeks at a uniform dose of about 200 mg. In some aspects, pembrolizumab is administered once every three weeks at a uniform dose of about 200 mg. In some aspects, pembrolizumab is administered once every four weeks at a uniform dose of about 400 mg.

[0241] V. Anti-PD-L1 antibodies useful for the present disclosure

[0242] In certain aspects of the present disclosure, the anti-PD-1 antagonist is an anti-PD-L1 antibody or its antigen-binding portion. Anti-PD-L1 antibodies known in the art may be used in the compositions and methods of the present disclosure. Examples of anti-PD-L1 antibodies useful in the compositions and methods of the present disclosure include the antibody disclosed in U.S. Patent No. 9,580,507. The anti-PD-L1 human monoclonal antibody disclosed in U.S. Patent No. 9,580,507 has been demonstrated to exhibit one or more of the following features: (a) 1 x 10⁶ when determined by surface plasmon resonance using a ViaCore biosensor system -7 K less than or equal to M D (a) binds to human PD-L1; (b) increases T-cell proliferation in a mixed lymphocyte response (MLR) assay; (c) increases interferon-γ production in an MLR assay; (d) increases IL-2 secretion in an MLR assay; (e) stimulates an antibody response; and (f) reverses the effects of T regulatory cells on T cell effector cells and / or dendritic cells. Anti-PD-L1 antibodies available in the present disclosure comprise monoclonal antibodies that specifically bind to human PD-L1 and exhibit at least one, and in some aspects at least five, of the above features.

[0243] In certain aspects, anti-PD-L1 antibodies are BMS-936559 (also known as 12A4, MDX-1105; see, e.g., U.S. Patent No. 7,943,743 and WO 2013 / 173223), atezolizumab (Roche; also known as TECENTRIQ®; MPDL3280A, RG7446; see US 8,217,149; see also [Herbst et al. (2013) J Clin Oncol 31(suppl):3000]), durvalumab (AstraZeneca; also known as IMFINZI™, MEDI-4736; see WO 2011 / 066389), avelumab (Pfizer; also known as BAVENCIO®, MSB-0010718C) Noticed; see WO 2013 / 079174), STI-1014 (Sorrento; see WO2013 / 181634), CX-072 (Cytomx; see WO2016 / 149201), KN035 (3D Med / Alphamab; see reference [Zhang et al., Cell Discov. 7:3 (March 2017)]), LY3300054 (Eli Lilly Co.; see WO 2017 / 034916), BGB-A333 (BeiGene; see reference [Desai et al., JCO 36 (15suppl):TPS3113 (2018)]), and CK-301 (Checkpoint Therapeutics; It is selected from a group consisting of literature [refer to Gorelik et al., AACR: Abstract 4606 (Apr 2016)].

[0244] In a specific aspect, the PD-L1 antibody is atezolizumab (Tecentriq®). Atezolizumab is a fully humanized IgG1 monoclonal anti-PD-L1 antibody. In a specific aspect, the PD-L1 antibody is durvalumab (Imfinzi™). Durvalumab is a human IgG1 kappa monoclonal anti-PD-L1 antibody. In a specific aspect, the PD-L1 antibody is avelumab (Bavencio®). Avelumab is a human IgG1 lambda monoclonal anti-PD-L1 antibody.

[0245] The anti-PD-L1 antibodies available for use in the disclosed compositions and methods also comprise isolated antibodies that specifically bind to human PD-L1 and cross-compete with any anti-PD-L1 antibodies disclosed herein, e.g., atezolizumab, durvalumab, and / or avelumab, for binding to human PD-L1. In some aspects, the anti-PD-L1 antibodies bind to the same epitope as any anti-PD-L1 antibodies described herein, e.g., atezolizumab, durvalumab, and / or avelumab. The ability of the antibodies to cross-compete for binding to an antigen indicates that these antibodies bind to the same epitope region of the antigen and stereochemically interfere with the binding of other cross-competing antibodies to such a specific epitope region. These cross-competing antibodies are expected to have functional characteristics very similar to the reference antibodies, e.g., atezolizumab and / or avelumab, in their binding to the same epitope region of PD-L1. Cross-competing antibodies can be easily identified based on their ability to cross-compete with atezolizumab and / or avelumab in standard PD-L1 binding assays, such as the Viacor assay, ELISA assay, or flow cytometry (see, e.g., WO 2013 / 173223).

[0246] In certain aspects, antibodies that cross-compete with human PD-L1 antibodies, atezolizumab, durvalumab, and / or avelumab for binding to human PD-L1, or that bind to the same epitope region, are monoclonal antibodies. For administration to human subjects, these cross-competing antibodies are chimeric antibodies, engineered antibodies, or humanized or human antibodies. Such chimeric, engineered, humanized, or human monoclonal antibodies can be prepared and isolated by methods widely known in the art.

[0247] The anti-PD-L1 antibody usable in the compositions and methods of the disclosed present disclosure also comprises the antigen-binding portion of said antibody. It has been sufficiently demonstrated that the antigen-binding function of an antibody can be performed by a fragment of a full-length antibody.

[0248] An anti-PD-L1 antibody suitable for use in the disclosed compositions and methods is an antibody that binds to PD-L1 with high specificity and affinity, blocks the binding of PD-1, and inhibits the immunosuppressive effects of the PD-1 signaling pathway. In any of the compositions or methods disclosed herein, the anti-PD-L1 "antibody" comprises an antigen-binding portion or fragment that binds to PD-L1 and exhibits functional characteristics similar to those of a whole antibody in inhibiting receptor binding and upregulating the immune system. In certain aspects, the anti-PD-L1 antibody or its antigen-binding portion cross-competes with atezolizumab, durvalumab, and / or avelumab for binding to human PD-L1.

[0249] An anti-PD-L1 antibody useful for the present disclosure may be any PD-L1 antibody that specifically binds to PD-L1, for example, an antibody that cross-competes with durvalumab, avelumab, or atezolizumab for binding to human PD-1, for example, an antibody that binds to the same epitope as durvalumab, avelumab, or atezolizumab. In a specific aspect, the anti-PD-L1 antibody is durvalumab. In another aspect, the anti-PD-L1 antibody is avelumab. In some aspect, the anti-PD-L1 antibody is atezolizumab.

[0250] In some aspects, anti-PD-L1 antibodies are administered about once every 2, 3, 4, 5, 6, 7, or 8 weeks at doses ranging from about 0.1 mg / kg to about 20.0 mg / kg body weight, about 2 mg / kg, about 3 mg / kg, about 4 mg / kg, about 5 mg / kg, about 6 mg / kg, about 7 mg / kg, about 8 mg / kg, about 9 mg / kg, about 10 mg / kg, about 11 mg / kg, about 12 mg / kg, about 13 mg / kg, about 14 mg / kg, about 15 mg / kg, about 16 mg / kg, about 17 mg / kg, about 18 mg / kg, about 19 mg / kg, or about 20 mg / kg.

[0251] In some aspects, the anti-PD-L1 antibody is administered about once every 3 weeks at a dose of about 15 mg / kg body weight. In other aspects, the anti-PD-L1 antibody is administered about once every 2 weeks at a dose of about 10 mg / kg body weight.

[0252] In another aspect, the anti-PD-L1 antibody useful for the present disclosure is a uniform dose. In some aspects, the anti-PD-L1 antibody is administered in uniform doses of about 200 mg to about 1600 mg, about 200 mg to about 1500 mg, about 200 mg to about 1400 mg, about 200 mg to about 1300 mg, about 200 mg to about 1200 mg, about 200 mg to about 1100 mg, about 200 mg to about 1000 mg, about 200 mg to about 900 mg, about 200 mg to about 800 mg, about 200 mg to about 700 mg, about 200 mg to about 600 mg, about 700 mg to about 1300 mg, about 800 mg to about 1200 mg, about 700 mg to about 900 mg, or about 1100 mg to about 1300 mg. In some aspects, anti-PD-L1 antibodies are administered at intervals of about 1, 2, 3, or 4 weeks in uniform doses of at least about 240 mg, at least about 300 mg, at least about 320 mg, at least about 400 mg, at least about 480 mg, at least about 500 mg, at least about 560 mg, at least about 600 mg, at least about 640 mg, at least about 700 mg, at least 720 mg, at least about 800 mg, at least about 840 mg, at least about 880 mg, at least about 900 mg, at least 960 mg, at least about 1000 mg, at least about 1040 mg, at least about 1100 mg, at least about 1120 mg, at least about 1200 mg, at least about 1280 mg, at least about 1300 mg, at least about 1360 mg, or at least about 1400 mg. In some aspects, the anti-PD-L1 antibody is administered about once every three weeks at a uniform dose of about 1200 mg. In other aspects, the anti-PD-L1 antibody is administered about once every two weeks at a uniform dose of about 800 mg.In another aspect, the anti-PD-L1 antibody is administered about once every two weeks at a uniform dose of about 840 mg.

[0253] In some aspects, atezolizumab is administered once every 3 weeks at a uniform dose of about 1200 mg. In some aspects, atezolizumab is administered once every 2 weeks at a uniform dose of about 800 mg. In some aspects, atezolizumab is administered once every 2 weeks at a uniform dose of about 840 mg.

[0254] In some aspects, avelumab is administered once every two weeks at a uniform dose of about 800 mg.

[0255] In some aspects, durvalumab is administered once every two weeks at a dose of about 10 mg / kg. In some aspects, durvalumab is administered once every two weeks at a uniform dose of about 800 mg / kg. In some aspects, durvalumab is administered once every three weeks at a uniform dose of about 1200 mg / kg.

[0256] VI. Cancer

[0257] In some respects, cancer is a tumor, that is, a solid cancer. In other respects, cancer is a tumor of epithelial origin, that is, a carcinoma. In some respects, a tumor originates from a cancer selected from the group consisting of bladder cancer, cervical cancer, lung cancer, pancreatic cancer, kidney cancer, head and neck cancer, hepatocellular carcinoma, glioblastoma, melanoma, or endometrial cancer. In some respects, a tumor is not melanoma.

[0258] In certain aspects, the tumor originates from cancer having a high IFNγ inflammatory signature score. In certain aspects, the tumor originates from the bladder, where the tumor has a high IFNγ inflammatory signature score. In certain aspects, the tumor originates from cervical cancer, where the tumor has a high IFNγ inflammatory signature score. In certain aspects, the tumor originates from lung cancer, where the tumor has a high IFNγ inflammatory signature score. In certain aspects, the tumor originates from pancreatic cancer, where the tumor has a high IFNγ inflammatory signature score. In some aspects, the tumor originates from kidney cancer, where the tumor has a high IFNγ inflammatory signature score. In some aspects, the tumor originates from head and neck cancer, where the tumor has a high IFNγ inflammatory signature score. In some aspects, the tumor originates from hepatocellular carcinoma, where the tumor has a high IFNγ inflammatory signature score. In some aspects, the tumor originates from glioblastoma, where the tumor has a high IFNγ inflammatory signature score. In some aspects, the tumor originates from melanoma, where the tumor has a high IFNγ inflammatory signature score. In some aspects, the tumor originates from endometrial cancer, where the tumor has a high IFNγ inflammatory signature score.

[0259] In certain aspects, the tumor originates from cancer having a low TDO2 gene expression score. In certain aspects, the tumor originates from the bladder, where the tumor has a low TDO2 gene expression score. In certain aspects, the tumor originates from cervical cancer, where the tumor has a low TDO2 gene expression score. In certain aspects, the tumor originates from lung cancer, where the tumor has a low TDO2 gene expression score. In certain aspects, the tumor originates from pancreatic cancer, where the tumor has a low TDO2 gene expression score. In some aspects, the tumor originates from kidney cancer, where the tumor has a low TDO2 gene expression score. In some aspects, the tumor originates from head and neck cancer, where the tumor has a low TDO2 gene expression score. In some aspects, the tumor originates from hepatocellular carcinoma, where the tumor has a low TDO2 gene expression score. In some aspects, the tumor originates from glioblastoma, where the tumor has a low TDO2 gene expression score. In some aspects, the tumor originates from melanoma, where the tumor has a low TDO2 gene expression score. In some aspects, the tumor originates from endometrial cancer, where the tumor has a low TDO2 gene expression score.

[0260] In certain aspects, the tumor originates from cancer having a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In certain aspects, the tumor originates from the bladder, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In certain aspects, the tumor originates from cervical cancer, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In certain aspects, the tumor originates from lung cancer, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In certain aspects, the tumor originates from pancreatic cancer, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In some aspects, the tumor originates from kidney cancer, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In some aspects, the tumor originates from head and neck cancer, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In some aspects, the tumor originates from hepatocellular carcinoma, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In some aspects, the tumor originates from glioblastoma, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In some aspects, the tumor originates from melanoma, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score. In some aspects, the tumor originates from endometrial cancer, where the tumor has a high IFNγ inflammatory signature score and a low TDO2 gene expression score.

[0261] In some respects, lung cancer is non-small cell lung cancer (NSCLC). In some respects, kidney cancer is renal cell carcinoma (RCC). In some respects, head and neck cancer is squamous cell carcinoma of the head and neck (SCCHN). In some respects, glioblastoma is glioblastoma pleomorphic (GBM).

[0262] In some aspects, cancer is blood cancer. In some aspects, blood cancer is lymphoma. In some aspects, lymphoma is diffuse large B-cell lymphoma (DLBCL). In some aspects, blood cancer (e.g., lymphoma) has a high IFNγ inflammatory signature score. In some aspects, blood cancer (e.g., lymphoma) has a low TDO2 gene expression score. In some aspects, blood cancer (e.g., lymphoma) has a high IFNγ inflammatory signature score and a low TDO2 gene expression score.

[0263] In certain aspects, the subject received Type 1, 2, 3, 4, 5, or more of prior cancer treatment. In other aspects, the subject is treatment-naive. In some aspects, the subject progressed during other cancer treatment. In certain aspects, prior cancer treatment included immunotherapy. In other aspects, prior cancer treatment included chemotherapy. In some aspects, the tumor recurred. In some aspects, the tumor is metastatic. In other aspects, the tumor is not metastatic. In some aspects, the tumor is locally advanced.

[0264] In some aspects, the subject received prior therapy to treat the tumor, and the tumor is relapsed or refractory. In certain aspects, at least one prior therapy includes standard management therapy. In some aspects, at least one prior therapy includes surgery, radiation therapy, chemotherapy, immunotherapy, or any combination thereof. In some aspects, at least one prior therapy includes chemotherapy. In some aspects, the subject received prior immuno-oncology (IO) therapy to treat the tumor, and the tumor is relapsed or refractory. In some aspects, the subject received more than one prior therapy to treat the tumor, and the subject is relapsed or refractory. In other aspects, the subject received anti-PD-1 or anti-PD-L1 antibody therapy.

[0265] In some aspects, the previous regimen includes chemotherapy. In some aspects, the previous regimen includes the administration of anticancer agents selected from the group consisting of platinum agonists (e.g., cisplatin, carboplatin), taxane agonists (e.g., paclitaxel, albumin-conjugated paclitaxel, docetaxel), vinorelbine, vinblastine, etoposide, pemetrexed, gemcitabine, bevacizumab (Avastin®), erlotinib (Tarceva®), crizotinib (Xalkori®), cetuximab (Erbitux®), and any combination thereof.

[0266] In some aspects, the subject experienced disease progression after at least one prior therapy. In certain aspects, the subject received at least two prior therapies, at least three prior therapies, at least four prior therapies, or at least five prior therapies. In certain aspects, the subject received at least two prior therapies. In one aspect, the subject experienced disease progression after at least two prior therapies. In certain aspects, at least two prior therapies include a first prior therapy and a second prior therapy, wherein the subject experienced disease progression after the first prior therapy and / or the second prior therapy, wherein the first prior therapy includes surgery, radiation therapy, chemotherapy, immunotherapy, or any combination thereof; and wherein the second prior therapy includes surgery, radiation therapy, chemotherapy, immunotherapy, or any combination thereof. In some aspects, the first prior therapy includes platinum-based dual chemotherapy, and the second prior therapy includes single-acting chemotherapy. In certain aspects, the single-acting chemotherapy includes docetaxel.

[0267] VII. Pharmaceutical Composition and Dosage

[0268] The therapeutic agents of the present disclosure, e.g., anti-PD-1 antagonists (e.g., nivolumab) and IDO1 inhibitors (e.g., lindostat mesylate), may be composed of a pharmaceutical composition containing, e.g., an anti-PD-1 antagonist (e.g., nivolumab) and / or an IDO1 inhibitor (e.g., lindostat mesylate) and a pharmaceutically acceptable carrier. As used herein, "pharmaceutically acceptable carrier" includes any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic agents and absorption retardants, etc. that are physiologically compatible. In some aspects, a carrier for a composition containing an antibody, e.g., an anti-PD-1 antibody, e.g., nivolumab, is suitable for intravenous, intramuscular, subcutaneous, parenteral, spinal, or epidermal administration (e.g., by injection or infusion), whereas a carrier for a composition containing an IDO1 inhibitor, e.g., lindostat mesylate, is suitable for parenteral, e.g., oral administration.

[0269] In some respects, subcutaneous injection is based on Halozyme Therapeutics’ ENHANZE® drug delivery technology (see U.S. Patent No. 7,767,429, the full text of which is incorporated herein by reference). ENHANZE® uses a co-preparation of an antibody and a recombinant human hyaluronidase enzyme (rHuPH20), which overcomes traditional limitations on the volume of bioagents and drugs that can be delivered subcutaneously due to the extracellular matrix (see U.S. Patent No. 7,767,429).

[0270] The pharmaceutical composition of the present disclosure may comprise one or more pharmaceutically acceptable salts, antioxidants, aqueous and non-aqueous carriers, and / or ajuvants, such as preservatives, wetting agents, emulsifiers, and dispersants. Accordingly, in some aspects, the pharmaceutical composition of the present disclosure may further comprise a recombinant human hyaluronidase enzyme, for example, rHuPH20.

[0271] Although higher nivolumab monotherapy with up to 10 mg / kg administered every two weeks has been achieved without reaching the maximum allowable dose (MTD), significant toxicity reported in other trials of checkpoint inhibitor plus anti-angiogenic therapy (e.g., see literature [Johnson et al., 2013; Rini et al., 2011]) supports selecting a nivolumab dose of less than 10 mg / kg.

[0272] Treatment is continued as long as clinical benefit is observed or until unacceptable toxicity or disease progression occurs. Nevertheless, in certain aspects, the dosage of the anti-PD-1 antagonist (e.g., anti-PD-1 antibody or anti-PD-L1 antibody) and / or IDO1 inhibitor (e.g., lindostat mesylate) administered is significantly lower than the approved dosage of the agent, i.e., less than the therapeutic dosage.

[0273] Anti-PD-1 antagonists (e.g., anti-PD-1 antibodies or anti-PD-L1 antibodies) may be administered at doses suggested to produce maximum efficacy as monotherapy in clinical trials, for example, about 3 mg / kg of nivolumab administered once every 3 weeks (Topalian et al., 2012a; Topalian et al., 2012) or at significantly lower doses, i.e., below the therapeutic dose. In some aspects, IDO1 inhibitors (e.g., lindostat) are administered at doses below the therapeutic dose.

[0274] The dosage and frequency depend on the half-lives of the antibody (e.g., nivolumab) and IDO1 inhibitor (e.g., lindostat mesylate) in the subject. Generally, human antibodies present the longest half-lives, followed by humanized antibodies, chimeric antibodies, and non-human antibodies. The dosage and frequency may vary depending on whether the treatment is prophylactic or therapeutic. For prophylactic use, relatively low doses are typically administered over a long period at relatively infrequent intervals. Some patients continue treatment for the rest of their lives. For therapeutic use, relatively high doses at relatively short intervals are sometimes required until disease progression is reduced or terminated, preferably until the patient shows partial or complete improvement in disease symptoms. After that, prophylactic therapy may be administered to the patient.

[0275] The actual dosage level of the active ingredient in the pharmaceutical composition of the present disclosure may vary to obtain an amount of the active ingredient effective in achieving a desired therapeutic response for a specific patient, composition, and mode of administration, without being excessively toxic to the patient.

[0276] The selected dosage level will depend on various pharmacokinetic factors, including the activity of the specific composition of the present disclosure used, the route of administration, the time of administration, the elimination rate of the specific compound used, the duration of treatment, other drugs, compounds and / or substances used in combination with the specific composition used, the age, sex, weight, condition, overall health and medical history of the patient to be treated, and other factors widely known in the medical field.

[0277] The compositions of the present disclosure may be administered through one or more routes of administration using one or more of the various methods widely known in the relevant art. As will be recognized by a person skilled in the art, the route and / or method of administration will vary depending on the desired result.

[0278] VIII. Kits, Manufactured Products, and Gene Panels

[0279] Additionally, kits and manufactured products comprising (a) a dose of an anti-PD-1 antagonist, e.g., an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody, and (b) a dose of an IDO1 inhibitor (e.g., lindostat) for therapeutic use, e.g., the treatment of cancer, are within the scope of the present disclosure. The kit typically includes a label indicating the intended use of the contents of the kit and instructions for use, e.g., instructions for use in administering an anti-PD-1 antagonist, e.g., an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody and an IDO1 inhibitor (e.g., lindostat) to a subject with cancer, e.g., a tumor, when the subject is identified as having (a) a high IFNγ inflammatory signature score and (b) a low tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score. The term "label" includes any written or recorded material supplied on or with the kit or manufactured product, or otherwise accompanied by the kit or manufactured product. The term "label" also encompasses instructions that are, for example, distributed electronically via a web server and / or are electronically accessible.

[0280] In one aspect, the present disclosure provides a kit or manufactured article for treating a subject with cancer, comprising (a) a dosage of an anti-PD-1 antagonist (e.g., nivolumab), (b) a dosage of an IDO1 inhibitor (e.g., lindostat), and (c) instructions for using an anti-PD-1 or anti-PD-L1 antibody and an IDO1 inhibitor according to the method disclosed herein. In one aspect, the present disclosure provides a kit or manufactured article for treating a subject with cancer, comprising (a) a dosage of an anti-PD-1 antagonist (e.g., nivolumab), and (b) instructions for using an anti-PD-1 or anti-PD-L1 antibody according to the method disclosed herein. In one aspect, the present disclosure provides a kit or manufactured article for treating a subject with cancer, comprising (a) a dosage of an IDO1 inhibitor (e.g., lindostat), and (b) instructions for using an IDO1 inhibitor according to the method disclosed herein.

[0281] A person skilled in the art will readily recognize that the kit of the present disclosure may contain, for example, the following:

[0282] (a) accompanied by additional vial(s) comprising an anti-PD-1 antagonist, e.g., an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody in one or more vials and one or more solvents in some aspects;

[0283] (b) additional vial(s) comprising an IDO1 inhibitor (e.g., lindostat) in one or more vials and one or more solvents in some aspects;

[0284] (c) Test to determine IFNγ inflammation signature score;

[0285] (d) Test to determine tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score;

[0286] (e) Guidelines for performing and quantifying the IFNγ inflammation signature score test and / or the TDO2 gene expression score test;

[0287] (f) Guidelines for administering anti-PD-1 antagonists and / or IDO1 inhibitors;

[0288] (g) Guidelines for determining whether to administer an anti-PD-1 antagonist and / or an IDO1 inhibitor to a subject in accordance with the methods disclosed herein (e.g., when a subject is identified to have (i) a high IFNγ inflammatory signature score and (ii) a low tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score);

[0289] (h) His arbitrary combination.

[0290] A person skilled in the art will also readily recognize that the kit or manufactured product may include any of the components disclosed above or combinations thereof, and that these may be easily incorporated into one of the established kit formats widely known in the art or as part of a companion diagnostic.

[0291] Accordingly, the present disclosure provides a kit or manufactured product for treating a subject suffering from cancer, e.g., a tumor, comprising: (a) an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody in a dosage in the range of 0.1 to 10 mg / kg body weight; and (b) instructions for using the anti-PD-1 antibody (e.g., nivolumab) or the anti-PD-L1 antibody according to the method disclosed herein.

[0292] The present disclosure further provides a kit or manufactured product for treating a subject suffering from cancer, e.g., a tumor, comprising: (a) an anti-PD-1 antibody (e.g., nivolumab) in a dosage ranging from about 4 mg to about 500 mg or an anti-PD-L1 antibody in a dosage ranging from about 4 mg to about 2000 mg; and (b) instructions for using the anti-PD-1 antibody (e.g., nivolumab) or the anti-PD-L1 antibody according to the method disclosed herein.

[0293] In some aspects, the present disclosure provides a kit or manufactured product for treating a subject suffering from cancer, e.g., a tumor, comprising: (a) an anti-PD-1 antibody (e.g., nivolumab) in a dosage range of 200 mg to 800 mg or an anti-PD-L1 antibody in a dosage range of 200 mg to 1800 mg; and (b) instructions for using the anti-PD-1 antibody (e.g., nivolumab) or the anti-PD-L1 antibody according to the method disclosed herein.

[0294] In a specific aspect for treating a human patient with cancer, e.g., a tumor, the kit or manufactured product comprises an anti-human PD-1 antibody disclosed herein, e.g., nivolumab or pembrolizumab or its antigen-binding portion. In a specific aspect for treating a human patient with cancer, e.g., a tumor, the kit or manufactured product comprises an anti-human PD-L1 antibody disclosed herein, e.g., atezolizumab, durvalumab or avelumab or its antigen-binding portion.

[0295] In some aspects, the kit or manufactured product further comprises an IDO1 inhibitor (e.g., lindostat) and instructions for administering the IDO1 inhibitor (e.g., lindostat) to a subject identified as having (a) a high IFNγ inflammatory signature score and (b) a low tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score according to the method disclosed herein.

[0296] In some aspects, the kit further comprises an inflammation gene panel assay disclosed herein, e.g., a gene panel assay quantifying an IFNγ inflammation signature score and / or a gene assay quantifying a tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score. In some aspects, the kit or manufactured product further comprises instructions for administering (a) an anti-PD-1 antibody (e.g., nivolumab) or an anti-PD-L1 antibody and (b) an IDO1 inhibitor (e.g., lindostat) to subjects identified as having (a) a high IFNγ inflammation signature score and (b) a low tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score according to the methods disclosed herein.

[0297] In some aspects, the present disclosure provides a gene panel comprising at least IFNγ and TDO2 genes for use below:

[0298] (i) to identify subjects suitable for therapy using a combination of anti-PD-1 antagonists and IDO1 inhibitors;

[0299] (ii) to determine the prognosis of subjects receiving therapy using a combination of anti-PD-1 antagonists and IDO1 inhibitors;

[0300] (iii) initiating, stopping, or modifying the administration of a combination comprising an anti-PD-1 antagonist and an IDO1 inhibitor; or

[0301] (iv) His combination.

[0302] In some aspects, gene panels include the following:

[0303] (i) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1 and TDO2;

[0304] (ii) IFNγ, CXCL10, CXCL9, HLA-DRA, IDO1, STAT1, CCR5, CXCL11, GZMA, PRF1 and TDO2;

[0305] (iii) CXCR6, TIGIT, CD274 (PD-L1), PDCD1LG2 (PD-L2), LAG3, NKG7, PSMB10, CMKLR1, CD8A, IDO1, CCL5, CXCL9, HLA.DQA1, CD276, HLA.DRB1, STAT1, HLA.E and TDO2; or

[0306] (iv) IFNγ, IR2RG, CXCR6, CD3D, CD2, ITGAL, TAGAP, CIITA, HLA-DRA, PTPRC, CXCL9, CCL5, NKG7, GZMA, PRF1, CCR5, CD3E, GZMK, HLA-E, GZMB, PDCD1, SLAMF6, CXCL13, CXCL10, IDO1, LAG3, STAT1, CXCL11 and TDO2.

[0307] In some aspects, the present disclosure provides a set of reagents (e.g., antibodies) or arrays (e.g., oligonucleotide arrays) for the detection and / or quantification of genes and / or their expression products (e.g., mRNA or proteins) within a gene panel, and guidance on using the reagents or arrays as predictive biomarkers according to the methods of the present disclosure.

[0308] ***

[0309] All references cited above, as well as all references cited herein, are incorporated herein by reference in their entirety.

[0310] The following examples are provided as examples without limitation.

[0311] Examples

[0312] Example 1

[0313] Biomarker Samples and Evaluation

[0314] A clinical trial was developed to investigate the efficacy of a combination therapy using nivolumab and the IDO1 inhibitor lindostat in patients with advanced tumors (clinical trial identifier NCT02658890).

[0315] Part 1 of the clinical trial included a dose escalation study in selected previously treated advanced tumors. Prior treatment with immune checkpoint inhibitors and T-cell co-stimulatory targeted therapy was permitted. Patients were treated with 240 mg of nivolumab (intravenously, once every 2 weeks) and lindostat was administered orally daily at various dosages (25 mg, 50 mg, 100 mg, 200 mg, 400 mg, 600 mg, or 800 mg). Part 2 of the clinical trial included a dose expansion study. These patients were treated with nivolumab monotherapy (240 mg, intravenously, once every 2 weeks) or combination therapy of nivolumab and lindostat (480 mg nivolumab, intravenously, once every 4 weeks and 100 mg or 200 mg lindostat, orally, daily).

[0316] Serum and tumor samples were taken from patients participating in the dose expansion phase (Part 2) of the study. Tumor and serum samples were obtained from patients with solid tumors (bladder, cervical, melanoma, lung, pancreatic, renal cell, head and neck) or lymphomas at baseline (cycle 1, day 1; C1D1) and during treatment (cycle 1, day 15; C1D15). These samples were subsequently used for the quantification of KYN and tryptophan levels by liquid chromatography-mass spectrometry. Solid tumor samples were also obtained at baseline and formalin-fixed paraffin-embedded. Using these samples, the expression levels of the IFN-γ signature gene, IDO1, and TDO2 were quantified by RNA sequencing. Figures 1a and 1b show the percentage of each tumor type obtained from the total patient population.

[0317] Example 2

[0318] Association between IFNγ signature and clinical response

[0319] IFNγ gene signatures predicting the response to PD-1 checkpoint blockade in melanoma have been previously established (Ayers et al. J Clin Invest. 2017;127(8):2930-2940). In this example, the association between the expression of IFNγ signature genes and clinical response to combination therapy with nivolumab and lindostat was investigated. The expression of IFNγ signature genes was quantified by RNA sequencing from formalin-fixed, paraffin-embedded solid tumor samples. Tumors were classified into five groups to determine clinical response: unevaluated (NE), progressive disease (PD), stable disease (SD), partial response (PR), and complete response (CR). The expression of IFNγ signature genes was associated with improved clinical response in patients treated with nivolumab and lindostat (Figs. 2a and 2b).

[0320] Example 3

[0321] Association between IFN-γ signature and progression-free survival and overall survival

[0322] We evaluated the association between IFNγ signature gene expression and survival in patients treated with nivolumab and lindostat. Patients were divided into three groups based on IFNγ signature gene expression: low, medium, or high expression. Patient survival was monitored in 200-day increments up to 600 days. High IFNγ signature was associated with improved progression-free survival (Figure 3a and Table 2) and overall survival (Figure 3b and Table 3) in immuno-oncology naive patients treated with nivolumab and lindostat.

[0323] Table 2. Number of surviving patients based on progression-free survival

[0324]

[0325] Table 3. Number of surviving patients based on overall survival

[0326]

[0327] Example 4

[0328] Effect of Tumor TDO2 Expression on KYN Reduction

[0329] Levels of KYN expression were investigated in TDO2 high and TDO2 low tumors from patients treated with nivolumab and lindostat.

[0330] Tumor and serum samples were obtained from patients at baseline (cycle 1, day 1; C1D1) and during treatment (cycle 1, day 15; C1D15). Low tumor TDO2 expression was associated with a greater reduction in KYN in tumors (Fig. 4a) and serum (Fig. 4b) and a decrease in KYN to normal levels. High tumor TDO2 expression was associated with less inhibition of KYN, particularly in tumors.

[0331] Example 5

[0332] Association between TDO2 expression and response

[0333] Since lindostat selectively inhibits IDO1 but not TDO2 enzymatic activity, high TDO2 expression may induce resistance to nivolumab and lindostat combination therapy. Therefore, the association between TDO2 expression and clinical response was evaluated. High or low TDO2 expression levels were determined by the median. Based on objective response rates, 26% of patients with low TDO2 expression responded to treatment, whereas only 13% of patients with high TDO2 expression responded (Table 4). Low TDO2 expression was observed among responders in non-melanoma samples treated with nivolumab and lindostat (Figure 5a). No association between TDO2 expression and response was observed with nivolumab monotherapy (Figure 5b).

[0334] Table 4. Association between TDO2 expression and objective response rate

[0335]

[0336] Example 6

[0337] Association between IFNγ signature and TDO2 expression and objective response rate

[0338] The association between IFN-γ and TDO2 and objective response rates was evaluated for all tumors. High IFNγ signature and low TDO2 expression were associated with peak response rates to nivolumab and lindostat treatment in patients with immuno-oncology naive disease (Fig. 6a). Low IFNγ signature and high TDO2 expression were associated with non-response to nivolumab and lindostat treatment in patients with immuno-oncology naive disease. Additionally, in the non-melanoma subset (n=49), the combined biomarker of IFNγ signature and TDO2 gene expression was more significantly associated with response (P = 0.021) than IFNγ signature alone (P = 0.063) (Fig. 6b).

[0339] Example 7

[0340] IFN-γ signature and TDO2 expression as combined biomarkers are improved compared to IFNγ alone in a non-melanoma cohort.

[0341] The sensitivity and specificity of IFNγ signature gene and TDO2 expression as combined biomarkers were compared with the expression of the IFNγ signature gene alone. In the non-melanoma subset (n=49), the combined biomarkers IFNγ and TDO2 expression performed numerically better as predictors of response than IFNγ signature alone (Fig. 7b) in immuno-oncology naive patients (n=79) (Fig. 7a). In the melanoma subset (n=30), IFNγ signature and TDO2 expression [AUC 79% (95% CI, 62-95)] showed no difference in response prediction compared to IFNγ signature alone [AUC 77% (95% CI, 59-95)]. Therefore, IFNγ signature and TDO2 gene expression can function as composite biomarkers to identify patients with specific tumor types who are more likely to respond to treatment with lindostat mesylate and nivolumab.

Claims

Claim 1 A pharmaceutical composition comprising an anti-PD-1 antagonist for use in a method of treating a human subject with cancer, wherein the anti-PD-1 antagonist is to be administered in combination with an indoleamine 2,3-deoxygenase 1 (IDO1) inhibitor, wherein the subject is identified prior to administration to exhibit combination biomarkers including (a) a high IFNγ inflammation signature score and (b) a low tryptophan 2,3-deoxygenase 2 (TDO2) gene expression score; wherein the IFNγ inflammation signature score is determined by measuring the expression of a panel of inflammatory genes ("IFNγ inflammation gene panel") including interferon gamma (IFNγ)-related genes in a sample obtained from the subject; wherein the cancer is bladder cancer or squamous cell carcinoma of the head and neck (SCCHN); wherein the inflammatory genes are IFNγ, CXCL10, HLA-DRA, IDO1, CXCL9, STAT1, CCR5, CXCL11, A pharmaceutical composition comprising GZMA and PRF1; wherein a high inflammation signature score is characterized by an inflammation signature score greater than the average IFNγ inflammation signature score, where the average IFNγ inflammation signature score is determined by averaging the expression of genes from an IFNγ inflammation gene panel in tumor samples obtained from a population of subjects with cancer; where a low TDO2 gene expression score is characterized by TDO2 gene expression smaller than the average TDO2 gene expression score, where the average TDO2 gene expression score is determined by averaging the expression of TDO2 genes in tumor samples obtained from a population of subjects with cancer. Claim 2 A pharmaceutical composition according to claim 1, characterized in that the high IFNγ inflammation signature score is at least 50% higher than the average IFNγ inflammation signature score. Claim 3 A pharmaceutical composition according to claim 1, characterized in that the low TDO2 gene expression score is at least 50% lower than the average TDO2 gene expression score. Claim 4 A pharmaceutical composition according to any one of claims 1 to 3, wherein the sample is a tumor tissue biopsy, formalin-fixed paraffin-embedded tissue, fresh-frozen tissue, or blood sample. Claim 5 A pharmaceutical composition according to any one of claims 1 to 3, wherein the expression of a gene and / or TDO2 gene expression within an IFNγ inflammation gene panel is determined by detecting the presence of gene mRNA, the presence of a protein encoded by the gene, or both. Claim 6 A pharmaceutical composition according to claim 5, wherein (i) the presence of mRNA encoding a gene and / or the TDO2 gene within an IFNγ inflammation gene panel is determined using reverse transcription PCR; or (ii) the presence of a protein encoding a gene and / or the TDO2 gene within an IFNγ inflammation gene panel is determined using an IHC assay. Claim 7 A pharmaceutical composition according to any one of claims 1 to 3, wherein the anti-PD-1 antagonist comprises an anti-PD-1 antibody or an anti-PD-L1 antibody. Claim 8 A pharmaceutical composition according to claim 7, wherein the anti-PD-1 antibody comprises nivolumab or its antigen-binding portion. Claim 9 A pharmaceutical composition according to claim 7, wherein the anti-PD-1 antibody comprises pembrolizumab or its antigen-binding portion. Claim 10 A pharmaceutical composition according to claim 7, wherein the anti-PD-L1 antibody comprises avelumab, atezolizumab, durvalumab, or its antigen-binding portion. Claim 11 A pharmaceutical composition according to claim 1, wherein the IDO1 inhibitor is selected from lindostat mesylate ((2R)-N-(4-chlorophenyl)-2-(cis-4-(6-fluoroquinoline-4-yl)cyclohexyl)propanamide), lindostat, indoxymod, p-(3-benzofuranyl)-DL-alanine, p-[3-benzo(b)thienyl]-DL-alanine; 6-nitro-L-tryptophan and any combination thereof. Claim 12 A pharmaceutical composition according to any one of claims 1 to 3, wherein the anti-PD-1 antagonist is nivolumab and the IDO1 inhibitor is lindostat mesylate ((2R)-N-(4-chlorophenyl)-2-(cis-4-(6-fluoroquinoline-4-yl)cyclohexyl)propanamide). Claim 13 A pharmaceutical composition according to any one of claims 1 to 3, wherein (i) the anti-PD-1 antagonist is administered once every 2 weeks at a dose of at least 3 mg / kg body weight; or (ii) the anti-PD-1 antagonist is administered once every 2 weeks at a uniform dose of 240 mg or once every 4 weeks at a uniform dose of 480 mg. Claim 14 A pharmaceutical composition according to any one of claims 1 to 3, wherein the anti-PD-1 antagonist is an anti-PD-1 antibody intended to be administered intravenously at a dose of 240 mg every 2 weeks or at a dose of 480 mg every 4 weeks, and the IDO1 inhibitor is intended to be administered orally daily at a dose of 100 mg or 200 mg. Claim 15 A pharmaceutical composition according to any one of claims 1 to 3, wherein the cancer is recurrent, refractory, locally progressive, metastatic, or any combination thereof. 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