Dynamic biomarker signature profile

Abstract

This disclosure provides methods for identifying subjects with cancer who are unresponsive to treatment (e.g., monotherapy with an immune checkpoint inhibitor), wherein the expression levels of a set of biomarkers of the cancer are altered (e.g., increased or decreased), and methods for administering combination therapy (e.g., a therapeutic agent targeting a bone marrow immunosuppressive checkpoint (e.g., LILRB4) and an immune checkpoint inhibitor) to the subjects with cancer using the methods described.

Description

[0001] Related applications

[0002] This application claims the benefit of U.S. Provisional Application No. 63 / 536,223, filed September 1, 2023, the entire contents of which are incorporated herein by reference. Background Technology

[0003] Despite advances in the types and amounts of cancer treatments available, many patients do not respond to them. Clinical readouts determining whether a patient is responding to treatment can take at least six months. During this time, if a patient does not respond, they may suffer unnecessary financial, social, emotional, and physical distress. Furthermore, waiting to determine a response to cancer treatment delays the administration of combination therapies that the patient could potentially benefit from. Summary of the Invention

[0004] In some aspects, this disclosure provides a method for delivering a therapeutic agent targeting LILRB4 to treat a subject's cancer, comprising: (i) Identifying the subject as unlikely to respond to single therapy with an immune checkpoint inhibitor administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers includes one or more of the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B; and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapy alone or in combination with the immune checkpoint inhibitor monotherapy; and (iii) The subject’s cancer is treated by administering the LILRB4-targeting therapeutic agent alone or in combination with the immune checkpoint inhibitor.

[0005] In some aspects, this disclosure provides a method for delivering a therapeutic agent targeting LILRB4 to treat a subject's cancer, comprising: (i) Identifying the subject as unlikely to respond to single therapy with an immune checkpoint inhibitor administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers includes one or more of the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B; and (b) Comparing the amount or level of the first set of biomarkers at two or more different time points to determine a non-response score, wherein the non-response score indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapy alone or in combination with the immune checkpoint inhibitor monotherapy; and (iii) The subject’s cancer is treated by administering the LILRB4-targeting therapeutic agent alone or in combination with the immune checkpoint inhibitor.

[0006] In some aspects, this disclosure provides a method for identifying subjects unresponsive to monotherapy with an immune checkpoint inhibitor for administering a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as unlikely to respond to single therapy with an immune checkpoint inhibitor administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers includes one or more of the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B; and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapy alone or in combination with the immune checkpoint inhibitor monotherapy; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the immune checkpoint inhibitor to the subject who has been determined to have a response score.

[0007] In some aspects, this disclosure provides a method for identifying subjects unresponsive to monotherapy with an immune checkpoint inhibitor for administering a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as unlikely to respond to single therapy with an immune checkpoint inhibitor administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers includes one or more of the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B; and (b) Comparing the amount or level of the first set of biomarkers at two or more different time points to determine a non-response score, wherein the non-response score indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapy alone or in combination with the immune checkpoint inhibitor monotherapy; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the immune checkpoint inhibitor to the subject who has been determined to have a response score.

[0008] In some implementations, the immune checkpoint inhibitor monotherapy targets PD-1, PD-L1, CTLA4, LAG3, or any combination thereof. In some implementations, the immune checkpoint inhibitor monotherapy is an antibody. In some implementations, the antibody is ipilimumab, nivolumab, relatlimab, pembrolizumab, atezolizumab, durvalumab, durvalumab, cemiplimab, and dostarlimab.

[0009] In some implementations, the first set of biomarkers includes CA6, CDNF, MIA, MYOC, NEFL, and TCL1B. In some implementations, the first set of biomarkers includes one or more of the following: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, H... GF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS. In some implementations, the first set of biomarkers includes at least six of the following: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HG F, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.In some implementations, the first set of biomarkers includes one or more of the following: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN. In some implementations, the first set of biomarkers includes at least six of the following: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN. In some implementations, the first set of biomarkers includes one or more of the following: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS. In some implementations, the first set of biomarkers includes at least six of the following: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.In some implementations, the first set of biomarkers includes one or more of the following: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS. In some implementations, the first set of biomarkers includes at least six of the following: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

[0010] In some embodiments, the second set of biomarkers includes at least four of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4. In some embodiments, the second set of biomarkers includes two to thirteen of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4. In some embodiments, the second set of biomarkers includes AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4. In some embodiments, the second set of biomarkers also includes LAIR1 and VSIG4.

[0011] In some embodiments, the first set of biomarkers includes proteins. In some embodiments, (i)(a) includes a first set of biomarkers for detection in a biological sample by enzyme-linked immunosorbent assay (ELISA) or proximity extension assay (PEA).

[0012] In some embodiments, the second set of biomarkers includes proteins. In some embodiments, (ii)(a) includes a second set of biomarkers for detection in biological samples by enzyme-linked immunosorbent assay (ELISA) or proximity extension assay (PEA).

[0013] In some implementations, the first suite of biomarkers includes nucleic acid molecules. In some implementations, (i)(a) includes a first suite of biomarkers for detection in biological samples by nucleic acid hybridization assay, nucleic acid amplification assay, or sequencing.

[0014] In some implementations, the second suite of biomarkers includes nucleic acid molecules. In some implementations, (ii)(a) includes a second suite for detecting biomarkers in biological samples by nucleic acid hybridization assays, nucleic acid amplification assays, or sequencing.

[0015] In some implementations, therapeutic agents targeting LILRB4 are antibodies, nucleic acid molecules, protein therapeutic agents, cell therapies, or small molecules. In some implementations, therapeutic agents targeting LILRB4 are antibodies.

[0016] In some embodiments, the biological sample is a blood sample, serum sample, or plasma sample. In some embodiments, the biological sample is a plasma sample.

[0017] In some embodiments, at least one subsequent time point is prior to clinical readout. In some embodiments, a first set of biomarkers and a second set of biomarkers are determined at at least two subsequent time points. In some embodiments, the amount or level of the first set of biomarkers increases between the first time point and at least one subsequent time point. In some embodiments, the increase in the amount or level of the first set of biomarkers between the first time point and at least one subsequent time point is statistically significant. In some embodiments, the amount or level of the second set of biomarkers increases between the first time point and at least one subsequent time point. In some embodiments, the increase in the amount or level of the first set of biomarkers between the first time point and at least one subsequent time point is statistically significant. In some embodiments, the amount or level of the set of biomarkers increases to at least 1.5-fold, 2-fold, 5-fold, 10-fold, 15-fold, or 20-fold. In some embodiments, the amount or level of the set of biomarkers increases to at least 1.5-fold.

[0018] In some implementations, the diagnostic accuracy is at least 0.8.

[0019] In some implementations, the non-response score indicates that a subject will not respond to immune checkpoint inhibitor therapy.

[0020] In some implementations, therapeutic agents targeting LILRB4 improve the response of subjects to immune checkpoint inhibitor monotherapy.

[0021] In some aspects, this disclosure provides a kit suitable for carrying out methods in some or any of the foregoing or related embodiments, comprising (i) one or more reagents for detecting the amount or level of a first set of said biomarkers, and (ii) instructions for detecting the amount or level of said biomarkers in biological samples obtained from a subject at two or more different time points. In some embodiments, the kit comprises (iii) one or more reagents for detecting the amount or level of a second set of said biomarkers, and (iv) instructions for detecting the amount or level of said biomarkers in biological samples obtained from a subject at two or more different time points.

[0022] In some aspects, this disclosure provides a kit suitable for carrying out methods in some or any of the foregoing or related embodiments, comprising (i) one or more reagents for detecting the amount or level of a second set of the biomarker, and (ii) instructions for detecting the amount or level of the second set of the biomarker in biological samples obtained from a subject at two or more different time points. In some embodiments, the kit comprises (iii) one or more reagents for detecting the amount or level of a first set of the biomarker, and (iv) instructions for detecting the amount or level of the first set of the biomarker in biological samples obtained from a subject at two or more different time points.

[0023] In some embodiments, the kit includes instructions for identifying that the subject is unlikely to respond to immune checkpoint inhibitor monotherapy. In some embodiments, the kit includes instructions for identifying that the subject may respond to combination therapy with a LILRB4-targeting therapeutic agent.

[0024] In some implementations, the biological sample is a blood sample, serum sample, or plasma sample.

[0025] In some aspects, this disclosure provides a method for identifying subjects who are unresponsive to or predicted to be unresponsive to immune checkpoint inhibitor monotherapy for administering a therapeutic agent targeting LILRB4, comprising: (i) Provide the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of the immune checkpoint inhibitor monotherapy and at least one subsequent time point is from about 3 weeks to about 6 months after administration of the immune checkpoint inhibitor monotherapy, wherein the suite of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8 and LILRB4; (ii) Comparing the amounts or levels of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapy alone or in combination with the immune checkpoint inhibitor monotherapy; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the immune checkpoint inhibitor to the subject who has been determined to have a response score.

[0026] In some implementations, therapeutic agents targeting LILRB4 are antibodies, nucleic acid molecules, protein therapeutic agents, cell therapies, or small molecules. In some implementations, therapeutic agents targeting LILRB4 are antibodies.

[0027] In some embodiments, the biomarker suite includes at least four of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4. In some embodiments, the biomarker suite includes two to thirteen of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4. In some embodiments, the biomarker suite includes AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4. In some embodiments, the biomarker suite also includes LAIR1 and VSIG4.

[0028] In some aspects, this disclosure provides a method for identifying a subject for administering a therapeutic agent targeting a bone marrow immunosuppressive checkpoint, comprising: (i) Provide subjects who are identified as non-responders to immune checkpoint inhibitor monotherapy or who are predicted to be non-responders to immune checkpoint inhibitor monotherapy; (ii) Determine the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the suite of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (iii) Comparing the amount or level of one or more proteins at two or more different time points to determine a response score, wherein the response score is correlated with the subject's potential response to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the immune checkpoint inhibitor; and (iv) Administer the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the immune checkpoint inhibitor, to the subject who has been determined to have the response score.

[0029] In some embodiments, the biomarker suite includes at least four of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the biomarker suite includes two to twelve of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the biomarker suite includes AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the biomarker suite further includes at least one of the following: LAIR1, LILRB4, and VSIG4. In some embodiments, the biomarker suite further includes LAIR1, LILRB4, and VSIG4.

[0030] In some implementations, therapeutic agents that target bone marrow immunosuppressive checkpoints are antibodies, nucleic acid molecules, protein therapeutic agents, cell therapies, or small molecules.

[0031] In some embodiments, the immune checkpoint inhibitor targets PD-1, PD-L1, CTLA4, LAG3, or any combination thereof. In some embodiments, the immune checkpoint inhibitor is an antibody. In some embodiments, the antibody is ipilimumab, nivolumab, relatlimab, pembrolizumab, atezolizumab, durvalumab, durvalumab, cemiplimab, and dostarlimab.

[0032] In some embodiments, the biomarker set includes proteins. In some embodiments, determining the amount or level of the biomarker set includes detecting the biomarker set in a biological sample by enzyme-linked immunosorbent assay (ELISA) or proximity extension assay (PEA).

[0033] In some implementations, the biomarker suite includes nucleic acid molecules. In some implementations, determining the amount or level of the biomarker suite includes detecting the biomarker suite in a biological sample by nucleic acid hybridization assays, nucleic acid amplification assays, or sequencing.

[0034] In some embodiments, the biological sample is a blood sample, serum sample, or plasma sample. In some embodiments, the biological sample is a plasma sample.

[0035] In some embodiments, at least one subsequent time point is prior to clinical readout. In some embodiments, the biomarker set is determined at at least two subsequent time points. In some embodiments, the amount or level of the biomarker set increases between the first time point and at least one subsequent time point. In some embodiments, the increase in the amount or level of the biomarker set between the first time point and at least one subsequent time point is statistically significant.

[0036] In some implementations, the response score indicates whether a subject will respond to a therapeutic agent that targets the bone marrow immunosuppressive checkpoint, either alone or in combination with an immune checkpoint inhibitor.

[0037] In some aspects, this disclosure provides a kit suitable for carrying out methods in some or any of the foregoing or related embodiments, comprising (i) one or more reagents for detecting the amount or level of the set of said biomarkers, and (ii) instructions for detecting the amount or level of the set of said biomarkers in biological samples obtained from a subject at two or more different time points. In some embodiments, the instructions include steps for identifying a subject as potentially responsive to a therapeutic agent targeting LILRB4 or a combination therapy of a therapeutic agent targeting a bone marrow immunosuppressive checkpoint and an immune checkpoint inhibitor. In some embodiments, the biological sample is a blood sample, serum sample, or plasma sample. Attached Figure Description

[0038] Figures 1A to 1B The protein signature profiles of non-reactants (NRs) at baseline (pretreated with one or more immune checkpoint inhibitors, either anti-PD-1 or a combination of anti-PD-1 and anti-CTLA-4) are shown. Figure 1A A graph showing the ROC curve is provided, which plots the sensitivity versus specificity used to predict NR. AUC=0.59. Figure 1B A graph showing the plasma proteins that constitute the predictive models, identified using Olink proteomics analysis, are provided, ranked based on their selection frequency in the cross-validation of the predictive models. ROC = Receiver Operating Characteristic; AUC = Area Under the ROC Curve.

[0039] Figures 2A to 2B Dynamic protein signatures of non-responders (NRs) are shown at baseline and 6 weeks after initiation of treatment with one or more immune checkpoint inhibitors (anti-PD-1 or a combination of anti-PD-1 and anti-CTLA-4). Figure 2A A graph showing the ROC curve is provided, which plots the sensitivity versus specificity used to predict NR. AUC=0.71. Figure 2B A graph showing the plasma proteins that constitute the predictive models, identified using Olink proteomics analysis, are provided, ranked based on their selection frequency in the cross-validation of the predictive models. ROC = Receiver Operating Characteristic; AUC = Area Under the ROC Curve.

[0040] Figures 3A to 3B Dynamic protein signatures of non-responders (NRs) are shown at baseline and 6 months after initiation of treatment with one or more immune checkpoint inhibitors (anti-PD-1 or a combination of anti-PD-1 and anti-CTLA-4). Figure 3A A graph showing the ROC curve is provided, which plots the sensitivity versus specificity used to predict NR. AUC=0.76. Figure 3BA graph showing the plasma proteins that constitute the predictive models, identified using Olink proteomics analysis, are provided, ranked based on their selection frequency in the cross-validation of the predictive models. ROC = Receiver Operating Characteristic; AUC = Area Under the ROC Curve.

[0041] Figures 4A to 4B Dynamic proteomic profiles of non-responders (NRs) at baseline, 6 weeks and 6 months after initiation of treatment with one or more immune checkpoint inhibitors (anti-PD-1 or a combination of anti-PD-1 and anti-CTLA-4). Figure 4A A graph showing the ROC curve is provided, which plots the sensitivity versus specificity used to predict NR. AUC = 0.80. Figure 4B A graph showing the plasma proteins that constitute the predictive models, identified using Olink proteomics analysis, are provided, ranked based on their selection frequency in the cross-validation of the predictive models. ROC = Receiver Operating Characteristic; AUC = Area Under the ROC Curve.

[0042] Figures 5A to 5B Dynamic protein signature profiles of non-responders (NRs) were shown at 6 weeks and 6 months after initiation of treatment with one or more immune checkpoint inhibitors (anti-PD-1 or a combination of anti-PD-1 and anti-CTLA-4). Figure 5A A graph showing the ROC curve is provided, which plots the sensitivity versus specificity used to predict NR. AUC=0.74. Figure 5B A graph showing the plasma proteins that constitute the predictive models, identified using Olink proteomics analysis, are provided, ranked based on their selection frequency in the cross-validation of the predictive models. ROC = Receiver Operating Characteristic; AUC = Area Under the ROC Curve.

[0043] Figures 6A to 6B Gene set enrichment analysis (GSEA) of plasma protein samples from patients identified as responders and non-responders to immune checkpoint inhibitor therapy is shown, where the values ​​at baseline are displayed. Figure 6A ), or at baseline, 6 weeks after treatment, and 6 months after treatment ( Figure 6B Statistically significant differences between patient groups. Gene set enrichment is expressed as adjusted p-value (p. adjusted) and count. NES = normalized enrichment score.

[0044] Figure 7 The changes in relative LILRB4 expression over 6 months are shown in patients identified as responders or non-responders to one or more immune checkpoint inhibitors. Detailed Implementation

[0045] Overview

[0046] In some respects, this disclosure is based, at least in part, on the discovery of a dynamic profile that predicts with at least 0.7 the likelihood of a subject with cancer responding to immune checkpoint inhibitor (ICI) monotherapy. As demonstrated herein, biological samples from a population of subjects with cancer treated with ICI monotherapy were analyzed at different time points before and after ICI monotherapy. Subjects identified as non-responders by clinical readout expressed a set of biomarkers that changed over time. As shown herein, when evaluated at multiple time points, the set of biomarkers provided a higher predictive value for non-respondership to ICI monotherapy compared to evaluation at a single time point. Specifically, when the set of biomarkers was evaluated at baseline (i.e., before treatment), 6 weeks post-treatment, and 6 months post-treatment, an AUC of 0.80 was identified. In contrast, the set of biomarkers evaluated only at baseline provided an AUC of 0.59. Therefore, it is not intended to be theoretically construed as predicting whether a subject will respond to ICI monotherapy based on the quantity or level of a time-determined set of biomarkers. It is believed that the dynamic characterization profile described in this article can predict whether a subject is unlikely to respond to ICI monotherapy prior to clinical readout, thereby providing improved patient care.

[0047] In another aspect, this disclosure is at least partly based on the findings of a dynamic myelogenous signature profile used to predict whether subjects with cancer identified or predicted to be unresponsive to ICI monotherapy are likely to respond to therapeutic agents targeting myelogenous immunosuppressive checkpoints, alone or in combination with ICIs. As demonstrated herein, differentially regulated proteins between non-responders and responders were identified and assessed using Gene Set Enrichment Analysis (GSEA) and a Gene Ontology (GO) database, and these proteins were annotated with biological processes relevant to bone marrow biology. Specifically, the analysis annotated the regulation of macrophage activation, positive regulation of macrophage activation, macrophage activation, and myeloid leukocyte activation. Based on this analysis, a suite of biomarkers was identified as changing over time in non-responders by comparison with responders. This paper further demonstrates that the myelogenous immunosuppressive checkpoint LILRB4 was identified as increasing over time in patients unresponsive to ICI monotherapy.

[0048] Therefore, it is undesirable to be bound by theoretical, time-determined sets of biomarkers used to identify subjects unresponsive to or predicted to be unresponsive to ICI monotherapy for administration of therapeutic agents targeting bone marrow immunosuppressive checkpoints (e.g., LILRB4), alone or in combination with ICIs. It is believed that the dynamic bone marrow profiling described herein predicts whether subjects identified as or predicted to be unresponsive to ICI monotherapy are likely to respond to therapeutic agents targeting bone marrow immunosuppressive checkpoints (e.g., LILRB4), alone or in combination with ICIs.

[0049] In some aspects, this disclosure provides methods for identifying subjects with cancer who may not respond to immune checkpoint inhibitor (ICI) monotherapy. In some aspects, this disclosure provides methods for administering a LILRB4-targeting therapeutic agent to a subject with cancer to treat the subject's cancer. In some embodiments, the biomarker suite includes one or more of the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B. In some embodiments, the methods described herein include comparing the amount or level of the biomarker suite from two or more time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 for the non-response score indicates that the subject is unlikely to respond to immune checkpoint inhibitor monotherapy. In some embodiments, the methods described herein include administering a LILRB4-targeting therapeutic agent to a subject with cancer identified as having a non-response score, thereby treating the subject's cancer.

[0050] In some aspects, this disclosure provides methods for identifying subjects with cancer who may respond to a therapeutic agent targeting a bone marrow immunosuppressive checkpoint (e.g., LILRB4) but are unresponsive to monotherapy with an immune checkpoint inhibitor (ICI). In some aspects, this disclosure provides methods for administering a therapeutic agent targeting a bone marrow immunosuppressive checkpoint (e.g., LILRB4) to a subject with cancer to treat the subject's cancer.

[0051] In some aspects, this disclosure provides methods for identifying subjects with cancer who may respond to combination therapy of a therapeutic agent targeting a bone marrow immunosuppressive checkpoint (e.g., LILRB4) with an ICI, but are unresponsive to monotherapy with an immune checkpoint inhibitor (ICI). In some aspects, this disclosure provides methods for administering combination therapy of a therapeutic agent targeting a bone marrow immunosuppressive checkpoint (e.g., LILRB4) with an ICI to a subject with cancer to treat the subject's cancer.

[0052] In some embodiments, the methods described herein include providing the amount or level of a suite of biomarkers in biological samples obtained from a subject at two or more different time points. In some embodiments, the biomarkers are blood-based biomarkers. In some embodiments, the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and one or more subsequent time points are approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor. In some embodiments, the suite of biomarkers includes one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the methods described herein include comparing the amount or level of a suite of biomarkers obtained from two or more time points to determine a response score, wherein the response score indicates whether the subject is likely to respond to a therapeutic agent targeting a bone marrow immunosuppressive checkpoint (e.g., LILRB4), alone or in combination with an immune checkpoint inhibitor. In some embodiments, the bone marrow suppressive therapeutic agent targets LILRB4.

[0053] Dynamic biomarker profile

[0054] In some respects, this disclosure provides a dynamic biomarker profile. As used herein, a "dynamic profile" refers to a suite of one or more biomarkers used in therapeutic agents ( For example The level or amount of immune checkpoint inhibitor monotherapy changes over time from before to after treatment. Dynamic characteristics can be used, for example, to predict the response of non-responders to other treatments in patients with standard of care (SOC), or to predict the biological mechanisms (e.g., bone marrow biology) and specific targets (e.g., LILRB4) that lead to a lack of response to SOC.

[0055] As used herein, the term “reactivity” refers to the degree to which diseased tissue (e.g., tumor) in a subject experiences the desired therapeutic change when exposed to a therapeutic intervention (e.g., ICI monotherapy).

[0056] In some implementations, the dynamic characterization profile is based on the amount or level of a set of biomarkers determined at two additional time points. In some implementations, these two or more time points include a pre-treatment time point and at least one subsequent time point after treatment.

[0057] In some embodiments, the dynamic characterization profile is based on the quantity or level of a suite of biomarkers determined from two or more time points. In some embodiments, this disclosure provides a suite of biomarkers that have altered (e.g., increased or decreased) expression levels and / or activities in one or more subjects with cancer treated with ICI monotherapy.

[0058] As used herein, a "biomarker" refers to a gene or its transcribed or translated product, the expression level and / or activity of which can be detected in a biological sample obtained from a subject with a disease or condition (e.g., cancer), wherein altered (e.g., increased or decreased) expression levels and / or activities of the biomarker serve as indicators (e.g., diagnostic, predictive, and / or prognostic indicators). In some embodiments, a biomarker is a predictive indicator, wherein altered expression levels and / or activities of the biomarker indicate the responsiveness of the disease to a particular therapeutic intervention. In some embodiments, a biomarker is a prognostic indicator, wherein altered expression levels and / or activities of the biomarker indicate the outcome of the disease or disease progression, regardless of the therapeutic intervention. In some embodiments, a biomarker is a predictive or prognostic indicator when its expression levels and / or activities are determined at two or more time points.

[0059] In some embodiments, the amount or level of the biomarker is compared to a reference sample. As used herein, “reference sample,” “reference cell,” “reference tissue,” “control sample,” “control cell,” or “control tissue” each refers to a sample, cell, tissue, standard, or level used for comparison to determine whether the amount or level of the biomarker in a subject has changed. In some embodiments, the reference is the amount or level of the biomarker in a subject prior to the administration of a therapeutic intervention (e.g., ICI monotherapy). In some embodiments, the reference is a predetermined amount or level of the biomarker.

[0060] Dynamic non-responder characteristic spectrum

[0061] In some aspects, this disclosure provides a dynamic characterization profile for identifying subjects with cancer who are unlikely to respond to immune checkpoint inhibitor monotherapy. In some embodiments, the dynamic characterization profile includes a suite of biomarkers analyzed at more than one time point.

[0062] Biomarker kit

[0063] In some implementations, the biomarker suite includes one or more biomarkers selected from the following: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37 , HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA , PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.

[0064] In some implementations, the biomarker set includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 3 9, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, or 68 biomarkers: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP 4. BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK 4. ECE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT 5. LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFT PD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.

[0065] In some implementations, the biomarker suite includes 2 to 30, 5 to 25, 10 to 20, 15 to 30, 20 to 40, 30 to 60, 30 to 50, or 40 to 68 biomarkers selected from the following: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1. FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, N RP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.

[0066] In some implementations, the biomarker suite includes ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, and HMB. S, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRT G, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS.

[0067] In some embodiments, the biomarker suite includes ADAM22. In some embodiments, the biomarker suite includes ADAMTS8. In some embodiments, the biomarker suite includes AMTS8. In some embodiments, the biomarker suite includes ANGPT2. In some embodiments, the biomarker suite includes AOC1. In some embodiments, the biomarker suite includes BCL2L11. In some embodiments, the biomarker suite includes BMP4. In some embodiments, the biomarker suite includes BRK1. In some embodiments, the biomarker suite includes CA6. In some embodiments, the biomarker of this disclosure is CCL13. In some embodiments, the biomarker suite includes CCL25. In some embodiments, the biomarker suite includes CD14. In some embodiments, the biomarker suite includes CD34. In some embodiments, the biomarker suite includes CDH17. In some embodiments, the biomarker suite includes CDNF. In some embodiments, the biomarker suite includes CERT. In some embodiments, the biomarker suite includes CES3. In some embodiments, the biomarker suite includes CLEC4A. In some embodiments, the biomarker of this disclosure is CPVL. In some embodiments, the biomarker suite includes CSF3. In some embodiments, the biomarker suite includes CTSF. In some embodiments, the biomarker suite includes CTSL. In some embodiments, the biomarker suite includes DKK4. In some embodiments, the biomarker suite includes ECE1. In some embodiments, the biomarker suite includes ENG. In some embodiments, the biomarker suite includes FBP1. In some embodiments, the biomarker suite includes FRZB. In some embodiments, the biomarker suite includes GBP2. In some embodiments, the biomarker suite includes GFBP2. In some embodiments, the biomarker suite includes GLT8D2. In some embodiments, the biomarker suite includes GPR37. In some embodiments, the biomarker suite includes HGF. In some embodiments, the biomarker suite includes HMBS. In some embodiments, the biomarker suite includes IGFBP2. In some embodiments, the biomarker suite includes IL5. In some embodiments, the biomarker of this disclosure is IL6. In some embodiments, the biomarker suite includes ITGB6. In some embodiments, the biomarker suite includes ITM2A. In some embodiments, the biomarker suite includes KRT5. In some embodiments, the biomarker suite includes LILRB4.In some embodiments, the biomarker suite includes MIA. In some embodiments, the biomarker suite includes MMP13. In some embodiments, the biomarker suite includes MMP3. In some embodiments, the biomarker suite includes MMP8. In some embodiments, the biomarker suite includes MYOC. In some embodiments, the biomarker suite includes NEFL. In some embodiments, the biomarker suite includes NID1. In some embodiments, the biomarker suite includes NOS3. In some embodiments, the biomarker suite includes NRP1. In some embodiments, the biomarker suite includes PAEP. In some embodiments, the biomarker suite includes PAPPA. In some embodiments, the biomarker suite includes PRTG. In some embodiments, the biomarker suite includes PSPN. In some embodiments, the biomarker suite includes PTGDS. In some embodiments, the biomarker suite includes SFTPD. In some embodiments, the biomarker suite includes SMOC1. In some embodiments, the biomarker suite includes TCL1A. In some embodiments, the biomarker suite includes TCL1B. In some embodiments, the biomarker suite includes TCN2. In some embodiments, the biomarker suite includes TDGF1. In some embodiments, the biomarker suite includes TFPI. In some embodiments, the biomarker suite includes TGREM2. In some embodiments, the biomarker suite includes TINAGL1. In some embodiments, the biomarker suite includes TNC. In some embodiments, the biomarker suite includes TNFRSF10B. In some embodiments, the biomarker suite includes TNFSF14. In some embodiments, the biomarker suite includes VASN. In some embodiments, the biomarker suite includes WARS.

[0068] In some implementations, the biomarker suite includes one or more biomarkers selected from the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B.

[0069] In some implementations, the biomarker suite includes one, two, three, four, five, or six biomarkers selected from the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B.

[0070] In some implementations, the biomarker suite includes two to five, two to six, or three to six biomarkers selected from the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B.

[0071] In some implementations, the biomarker suite includes CA6, CDNF, MIA, MYOC, NEFL, and TCL1B.

[0072] In some implementations, the biomarker suite includes one or more biomarkers selected from the following: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN.

[0073] In some implementations, the biomarker suite includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or 31 biomarkers selected from the following: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14 and VASN.

[0074] In some implementations, the biomarker suite includes 2 to 30, 5 to 25, 10 to 20, 15 to 30, 20 to 31, or 10 to 31 biomarkers selected from the following: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN.

[0075] In some implementations, the biomarker suite includes ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN.

[0076] In some implementations, the biomarker suite includes one or more biomarkers selected from the following: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.

[0077] In some implementations, the biomarker suite includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, or 38 biomarkers selected from the following: AMTS8, ANGPT2, BCL2L. 11. BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D 2. ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1 and WARS.

[0078] In some implementations, the biomarker suite includes 2 to 30, 5 to 25, 10 to 20, 15 to 30, 20 to 38, 30 to 38, or 10 to 30 biomarkers selected from the following: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.

[0079] In some implementations, the biomarker suite includes AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.

[0080] In some implementations, the biomarker suite includes one or more biomarkers selected from the following: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

[0081] In some implementations, the biomarker suite includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, or 34 biomarkers selected from the following: ADAMTS8, ANGPT2, AOC 1. BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, L ILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN and WARS.

[0082] In some implementations, the biomarker suite includes 2 to 30, 5 to 25, 10 to 20, 15 to 30, 20 to 30, and 25 to 34 biomarkers selected from the following: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

[0083] In some implementations, the biomarker suite includes ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

[0084] Dynamic bone marrow characteristic spectrum

[0085] In some aspects, this disclosure provides a dynamic profile for identifying subjects with cancer who are unresponsive to monotherapy with an immune checkpoint inhibitor but will benefit from additional immunosuppressive therapy. In some embodiments, the dynamic profile includes a suite of biomarkers analyzed at more than one time point.

[0086] Biomarker kit

[0087] In some embodiments, the biomarker suite includes one or more biomarkers selected from the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the biomarker suite includes one or more biomarkers selected from the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the biomarker suite includes one or more biomarkers selected from the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0088] In some embodiments, the biomarker suite includes one, two, three, four, five, six, seven, eight, nine, ten, eleven, or twelve biomarkers selected from the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the biomarker suite includes one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, or thirteen biomarkers selected from the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some implementations, the biomarker suite includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 biomarkers selected from the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0089] In some embodiments, the biomarker suite includes 2 to 12, 5 to 12, 10 to 12, or 2 to 10 biomarkers selected from the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the biomarker suite includes 2 to 13, 5 to 13, 10 to 13, or 2 to 10 biomarkers selected from the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some implementations, the biomarker suite includes 2 to 15, 5 to 15, 10 to 15, or 2 to 10 biomarkers selected from the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0090] In some embodiments, the biomarker suite includes AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the biomarker suite includes LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the biomarker suite includes LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0091] In some embodiments, the biomarker suite includes LILRB4. In some embodiments, the biomarker suite includes LAIR1. In some embodiments, the biomarker suite includes VSIG4. In some embodiments, the biomarker suite includes AZU1. In some embodiments, the biomarker suite includes CCL3. In some embodiments, the biomarker suite includes CST7. In some embodiments, the biomarker suite includes HAVCR2. In some embodiments, the biomarker suite includes IFNG. In some embodiments, the biomarker suite includes IL10. In some embodiments, the biomarker suite includes IL1RL1. In some embodiments, the biomarker suite includes IL4R. In some embodiments, the biomarker suite includes IL6. In some embodiments, the biomarker suite includes LBP. In some embodiments, the biomarker suite includes MIF. In some embodiments, the biomarker suite includes MMP8.

[0092] Detection of biomarkers

[0093] In some aspects, this disclosure provides methods for detecting one or more biomarkers in a biological sample obtained from a subject. In some embodiments, the biomarker is a protein. In some embodiments, the biomarker is a nucleic acid molecule (e.g., DNA or RNA) encoding a protein. In some embodiments, a suite of biomarkers includes one or more proteins. In some embodiments, a suite of biomarkers includes one or more nucleic acid molecules. In some embodiments, a suite of biomarkers includes a combination of protein and nucleic acid molecules. Methods for detecting proteins and nucleic acid molecules encoding proteins are known to those skilled in the art and are described herein.

[0094] Protein detection

[0095] In some embodiments, this disclosure provides methods for detecting proteins in biological samples. Methods for detecting proteins and their fragments are known to those skilled in the art. Exemplary methods include enzyme-linked immunosorbent assay (ELISA), Western blotting, proximity extension assay (PEA), mass spectrometry, and bead-based methods.

[0096] In some embodiments, more than one protein biomarker is detected using the same protein detection method. In some embodiments, more than one protein biomarker is detected using different protein detection methods. For example, in some embodiments, a first protein biomarker is detected by a first ELISA, and a second protein biomarker is detected by a second ELISA. In some embodiments, more than one protein biomarker is detected simultaneously with the protein. In some embodiments, more than one protein biomarker is detected in multiplex form. For example, in some embodiments, a first protein biomarker and a second protein biomarker are detected in the same assay.

[0097] In some embodiments, antibodies are used to detect one or more protein biomarkers. Antibodies include any type of antibody, including antibodies that specifically bind to unmodified proteins, glycosylated protein variants, or other post-translational modified proteins. In some embodiments, these antibodies are used in protein detection methods. Methods for generating antibodies suitable for binding to proteins of interest are known to those skilled in the art and are described herein. In some embodiments, the antibodies used to detect one or more protein biomarkers are commercially available.

[0098] Exemplary immunoassay methods include radioimmunoassay (RIA), ELISA, fluorescence immunoassay, immunoradioassay, bead-based immunoassay, chemiluminescence assay, and bioluminescence assay.

[0099] In some embodiments, a suitable method for detecting the presence or amount of one or more protein biomarkers is proximity extension assay (PEA). In this assay, a pair of antibodies linked to a unique oligonucleotide (proximity probe) binds to a protein target. Based on this binding, the probes become very close to each other and hybridize. The method also includes adding DNA polymerase to extend the hybridized oligonucleotide and generate DNA amplicon, which can then be detected and quantified by quantitative real-time PCR or next-generation sequencing (NGS).

[0100] In some implementations, a suitable method for detecting the presence or amount of one or more protein biomarkers is ELISA. In this method, one or more antibodies specific to one or more protein biomarkers are immobilized on a selected surface exhibiting protein affinity, such as wells in a polystyrene microtiter plate. A test composition suspected of containing one or more protein biomarkers (such as a diluted clinical sample) is then added to the wells. After binding and / or washing to remove non-specifically bound immune complexes, the bound protein biomarker can be detected. Detection can be achieved by contacting the sample with a reagent such as a second antibody linked to a detectable marker. This type of ELISA is a “sandwich ELISA.”

[0101] Regardless of the form used, ELISA shares certain common characteristics, such as coating, incubation and binding, washing to remove non-specifically bound substances, and detection of bound immune complexes. These will be described below.

[0102] In some embodiments, the method for detecting one or more protein biomarkers is based on an immunobead assay (e.g., Luminex). In some embodiments, the method for detecting one or more protein biomarkers is based on a multiplex immunobead assay. In some embodiments, an antibody targeting one or more protein biomarkers is conjugated to beads. In some embodiments, after the antibody has bound to one or more protein biomarkers, the beads are detected using methods known to those skilled in the art or described herein.

[0103] Nucleic acid testing

[0104] In some embodiments, this disclosure provides methods for detecting nucleic acid molecules in biological samples. Methods for detecting nucleic acid molecules are known to those skilled in the art, and these methods include, but are not limited to: nucleic acid sequencing; nucleic acid hybridization; and nucleic acid amplification.

[0105] In some implementations, nucleic acid sequencing methods are utilized (e.g., for detecting amplified nucleic acids). In some implementations, the technologies provided herein can be used for second-generation (also known as next-generation or Next-Gen), third-generation (also known as Next-Next-Gen), or fourth-generation (also known as N3-Gen) sequencing technologies, including but not limited to pyrosequencing, ligation sequencing, single-molecule sequencing, sequencing by synthesis (SBS), semiconductor sequencing, massively parallel cloning, massively parallel single-molecule SBS, massively parallel single-molecule real-time sequencing, massively parallel single-molecule real-time nanopore technology, etc. Morozova and Marra in GenomicsA review of some such techniques is provided in , 92:255 (2008), the full text of which is incorporated herein by reference. Those skilled in the art will recognize that, because RNA is less stable in cells and more susceptible to nuclease attack, it is possible to reverse transcribe RNA into DNA prior to sequencing.

[0106] Many DNA sequencing technologies are suitable, including fluorescence-based sequencing methodologies (see, for example, Birren et al., Genome Analysis: Analyzing DNA, 1, Cold Spring Harbor, NY; this literature is incorporated herein by reference in its entirety). In some implementations, automated sequencing technologies as understood in the art are utilized.

[0107] Illustrative and non-limiting examples of nucleic acid hybridization techniques include, but are not limited to, In situ Hybridization (ISH), microarrays, and Southern or Northern imprints.

[0108] In situ Hybridization (ISH) is a type of hybridization that uses labeled complementary DNA or RNA strands as probes to locate specific DNA or RNA sequences in a portion or slice of tissue. In situ Alternatively, if the tissue is small enough, the entire tissue can be localized (intact specimen ISH). DNA ISH can be used to determine chromosome structure. RNA ISH can be used to measure and localize mRNA and other transcripts (e.g., cancer markers) within tissue sections or intact slides. Sample cells and tissues can be processed to immobilize target transcripts in place and increase probe accessibility. Probes hybridize to the target sequence at elevated temperatures, followed by washing away excess probes. Probes labeled with radioactive, fluorescent, or antigen-labeled bases are localized and quantified in tissues using autoradiography, fluorescence microscopy, or immunohistochemistry, respectively. ISH can also use two or more probes labeled with radioactive or other non-radioactive markers to simultaneously detect two or more transcripts.

[0109] In some embodiments, one or more biomarkers are detected by performing one or more hybridization reactions. In some embodiments, the one or more hybridization reactions include one or more hybridization arrays, hybridization reactions, hybridization chain reactions, isothermal hybridization reactions, nucleic acid hybridization reactions, or combinations thereof. In some embodiments, the one or more hybridization arrays include hybridization array genotyping, hybridization array ratio sensing, DNA hybridization arrays, macroarrays, microarrays, high-density oligonucleotide arrays, genomic hybridization arrays, comparative hybridization arrays, or combinations thereof.

[0110] In some implementations, microarrays are used to determine the amount or level of one or more biomarkers described herein. Microarrays include, but are not limited to: DNA microarrays (e.g., cDNA microarrays and oligonucleotide microarrays); protein microarrays; tissue microarrays; transfection or cell microarrays; compound microarrays; and antibody microarrays. DNA microarrays, commonly referred to as gene chips, DNA chips, or biochips, are attached to a solid surface (…). For example A DNA microarray is an array of microscopic DNA dots on a glass, plastic, or silicon chip, forming an array for simultaneously profiling or monitoring the expression levels of thousands of genes. The attached DNA segments are called probes, and thousands of probes can be used in a single DNA microarray. Microarrays can be fabricated using a variety of techniques, including but not limited to: printing on a glass slide using fine needles; photolithography using pre-fabricated masks; photolithography using dynamic micromirror devices; inkjet printing; or electrochemistry on microelectrode arrays.

[0111] biological samples

[0112] The methods described herein can be used to detect a suite of biomarkers in biological samples obtained from a subject at one or more time points. Exemplary biological samples include, but are not limited to, plasma, urine, saliva, whole blood, dried blood spots, serum, dried serum spots, feces, and / or hair. In some embodiments, the biological sample is derived from blood. In some embodiments, the biological sample is serum. In some embodiments, the biological sample is plasma. In some embodiments, the biological sample is whole blood, serum, or plasma. In some embodiments, the processed biological sample ( For example Plasma or serum is frozen for transport and / or long-term storage.

[0113] In some embodiments, the same type of biological sample is obtained at two or more different time points. In some embodiments, different biological samples are obtained at two or more different time points. For example, a blood sample is obtained at a first time point and a urine sample is obtained at a second time point. In contrast, a first blood sample is obtained from the first time point and a second blood sample is obtained from the second time point.

[0114] In some implementations, two or more biological samples obtained from the same subject are processed simultaneously. In some implementations, two or more biological samples obtained from the same subject are processed at different time points. In some implementations, a set of biomarkers is detected simultaneously in two or more biological samples. In some implementations, a set of biomarkers is detected at different time points in two or more biological samples.

[0115] In some implementation schemes, biological samples obtained from subjects ( For exampleThe method involves detecting one or more biomarkers in plasma, urine, saliva, whole blood, dried blood spots, serum, dried serum spots, feces, and / or hair. In some embodiments, one or more biomarkers are detected in plasma. In some embodiments, one or more biomarkers are detected in urine. In some embodiments, one or more biomarkers are detected in saliva. In some embodiments, one or more biomarkers are detected in whole blood. In some embodiments, one or more biomarkers are detected in dried blood spots. In some embodiments, one or more biomarkers are detected in serum. In some embodiments, one or more biomarkers are detected in dried serum spots. In some embodiments, one or more biomarkers are detected in feces. In some embodiments, one or more biomarkers are detected in hair.

[0116] In some embodiments, biological samples are processed to allow for the detection of biomarkers. In some embodiments, biological samples are processed in a manner consistent with methods used for the detection of proteins or nucleic acids. In some embodiments, samples are processed to isolate proteins for detection. Methods for isolating proteins are known to those skilled in the art. In some embodiments, samples are processed to isolate nucleic acid molecules for detection. Methods for isolating nucleic acid molecules are known to those skilled in the art.

[0117] Determine the set and dynamic characterization of biomarkers

[0118] In some embodiments, this disclosure provides a method for determining a dynamic characterization spectrum suitable for use in the methods disclosed herein. In some embodiments, the dynamic characterization spectrum is based on a set of biomarkers described herein.

[0119] In some embodiments, a suite of biomarkers for a dynamic profile is identified by determining the amount or level of one or more biomarkers from one or more biological samples from a subject. In some embodiments, the amount or level of one or more biomarkers is determined at two or more time points. In some embodiments, the amount or level of one or more biomarkers is determined before the subject receives treatment (e.g., ICI monotherapy). In some embodiments, the amount or level of one or more biomarkers is determined after the subject receives treatment (e.g., ICI monotherapy). In some embodiments, the amount or level of one or more biomarkers is determined both before and after the subject receives treatment.

[0120] In some embodiments, biomarkers are ranked according to their identification frequency. For example, in some embodiments, biomarkers are ranked according to their identification frequency in repeated cross-validation. In some embodiments, biomarkers have identification frequencies ranging from 0% to 100%. In some embodiments, biomarkers have identification frequencies of approximately 0%, 2%, 4%, 6%, 8%, 10%, 12%, 14%, 16%, 18%, 20%, 22%, 24%, 26%, 28%, 30%, 32%, 34%, 36%, 38%, 40%, 42%, 44%, 46%, 48%, 50%, 52%, 54%, 56%, 58%, 60%, 62%, 64%, 66%, 68%, 70%, 72%, 74%, 76%, 78%, 80%, 82%, 84%, 86%, 88%, 90%, 92%, 94%, 96%, 98%, up to a maximum of 100%. In some embodiments, the biomarker has an identification frequency of about 1% to about 10%, about 5% to about 20%, about 10% to about 30%, about 20% to about 40%, about 30% to about 50%, about 40% to about 100%, about 50% to about 90%, about 15% to about 40%, about 20% to about 50%, about 10% to about 45%, or about 25% to about 50%. In some embodiments, the biomarker has an identification frequency of about 25%.

[0121] In some embodiments, computational methods are used to identify the suites and dynamic profiles of biomarkers. In some embodiments, predictive algorithms are applied from a compiled dataset to identify the suites and dynamic profiles of biomarkers of this disclosure. Predictive algorithms are applied to large datasets to identify the association between the quantity or level of one or more biomarkers detected over time and responsiveness to a therapeutic intervention (e.g., ICI monotherapy). In some embodiments, the predictive algorithm includes performing statistical tests to determine the association between the quantity or level of one or more biomarkers detected over time and responsiveness to a therapeutic intervention (e.g., ICI monotherapy). In some embodiments, the predictive algorithm is a linear mixed-effects model (LMM). In some embodiments, the quantity or level of one or more biomarkers is the dependent variable, and the time point, response state, and interaction between the two are independent variables. In some embodiments, the significance of the variables is determined using an F-test with Satterthwaite degrees of freedom and type III sum of squares.

[0122] In some implementations, statistical modeling is used to analyze biomarkers. Exemplary methods of statistical modeling include, but are not limited to, linear mixture modeling (LMM), analysis of variance (ANOVA), and hierarchical linear modeling (HLM). In some implementations, LMM is used to analyze biomarkers with altered expression levels (e.g., increases or decreases). In some implementations, ANOVA is used to analyze biomarkers with altered expression levels (e.g., increases or decreases). In some implementations, HLM is used to analyze biomarkers with altered expression levels (e.g., increases or decreases).

[0123] In some implementations, statistical modeling methods are independently fitted to each biomarker using at least two distinct time points and corresponding biomarkers showing changes in expression levels (e.g., increases or decreases) as input. In some implementations, models are generated using biomarkers showing changes in expression levels (e.g., increases or decreases) at one or more time points as analyzed through statistical modeling.

[0124] In some implementations, the predictive performance of the model is evaluated. Exemplary measures of predictive performance include, but are not limited to, cross-validation methods such as k-fold cross-validation (e.g., 5-fold, 10-fold, etc.), leave-one-out cross-validation (LOOCV), and Monte Carlo methods, etc. In some implementations, k-fold cross-validation (e.g., 5-fold cross-validation) is used to evaluate the predictive performance of the model. In some implementations, LOOCV is used to evaluate the model. In some implementations, Monte Carlo methods are used to evaluate the model. In some implementations, the cross-validation method can be repeated any number of times. In some implementations, the cross-validation method may be repeated approximately 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or approximately 1000 times. In some implementations, the cross-validation method may be repeated approximately 1 to approximately 10 times, approximately 5 to approximately 20 times, approximately 10 to approximately 30 times, approximately 20 to approximately 40 times, approximately 30 to approximately 50 times, approximately 40 to approximately 100 times, approximately 50 to approximately 200 times, approximately 100 to approximately 300 times, approximately 200 to approximately 400 times, approximately 300 to approximately 500 times, approximately 400 to approximately 600 times, approximately 500 to approximately 700 times, approximately 600 to approximately 800 times, approximately 700 to approximately 900 times, approximately 800 to approximately 1000 times, or approximately 900 to approximately 1000 times. In some implementations, the cross-validation method may be repeated approximately 100 times.

[0125] In some embodiments, a dynamic characterization profile is determined by comparing biomarker expression levels (e.g., increases or decreases) from two or more different time points. In some embodiments, the expression levels of two or more biomarkers are obtained from a sample. In some embodiments, samples are obtained from the subject before treatment (e.g., day -1 post-treatment). In some embodiments, samples are obtained from the subject after treatment. In some embodiments, samples are obtained from the subject concurrently with treatment. In some embodiments, "post-treatment" means after the start of treatment, i.e., after the first administration of the therapeutic agent to the subject. In some embodiments, samples are obtained from the subject at time points of day -1, day 0, day 1, day 2, day 3, day 4, day 5, day 6, or day 7 post-treatment. In some embodiments, samples are obtained from subjects at week 0, week 1, week 2, week 3, week 4, week 5, week 6, week 7, week 8, week 9, week 10, week 11, week 12, week 13, week 14, week 15, week 16, week 17, week 18, week 19, week 20, week 21, week 22, week 23, or week 24 after treatment. In some embodiments, samples are obtained from subjects at month 0, month 1, month 2, month 3, month 4, month 5, or month 6 after treatment. In some embodiments, samples are obtained from subjects on day -1 after treatment. In some embodiments, samples are obtained from subjects at week 3 after treatment. In some embodiments, samples are obtained from subjects at week 6 after treatment. In some embodiments, samples are obtained from subjects at month 6 after treatment.

[0126] In some embodiments, a dynamic characterization profile is obtained by comparing the expression levels (e.g., increase or decrease) of two or more biomarkers from two or more different time points. In some embodiments, the two or more time points are selected from: day -1, day 0, day 1, day 2, day 3, day 4, day 5, day 6, or day 7 after treatment; week 0, week 1, week 2, week 3, week 4, week 5, week 6, week 7, week 8, week 9, week 10, week 11, week 12, week 13, week 14, week 15, week 16, week 17, week 18, week 19, week 20, week 21, week 22, week 23, or week 24 after treatment; and month 0, month 1, month 2, month 3, month 4, month 5, or month after treatment. In some embodiments, a dynamic characterization profile is obtained by comparing the expression levels (e.g., increases or decreases) of two or more biomarkers from two or more different time points, wherein the time points are selected from day 1, day 0, day 1, day 2, day 3, day 4, day 5, day 6, or day 7 after treatment. In some embodiments, a dynamic characterization profile is obtained by comparing the expression levels (e.g., increases or decreases) of two or more biomarkers from two or more different time points, wherein the time points are selected from week 0, week 1, week 2, week 3, week 4, week 5, week 6, week 7, week 8, week 9, week 10, week 11, week 12, week 13, week 14, week 15, week 16, week 17, week 18, week 19, week 20, week 21, week 22, week 23, or week 24 after treatment. In some embodiments, a dynamic profile is obtained by comparing the expression levels (e.g., increases or decreases) of two or more biomarkers from two or more different time points, wherein the time points are selected from 0 months, 1 month, 2 months, 3 months, 4 months, 5 months, or 6 months post-treatment. In some embodiments, a dynamic profile is obtained by comparing the expression levels (e.g., increases or decreases) of two or more biomarkers from two or more different time points, wherein the time points are at least baseline and 3 weeks post-treatment. In some embodiments, a dynamic profile is obtained by comparing the expression levels (e.g., increases or decreases) of two or more biomarkers from two or more different time points, wherein the time points are at least baseline and 6 weeks post-treatment. In some embodiments, a dynamic profile is obtained by comparing the expression levels (e.g., increases or decreases) of two or more biomarkers from two or more different time points, wherein the time points are at least baseline and 6 months post-treatment. In some implementations, a dynamic profile is obtained by comparing the expression levels (e.g., increase or decrease) of two or more biomarkers from two or more different time points, where the time points are at least baseline, 3 weeks after treatment, and 6 months after treatment.In some embodiments, a dynamic profile is obtained by comparing the expression levels (e.g., increases or decreases) of two or more biomarkers from two or more different time points, where the time points are at least baseline, 6 weeks post-treatment, and 6 months post-treatment.

[0127] In some implementations, computational methods are used to identify dynamic characteristic profiles. Unbound by theory, computational methods can determine whether a defined set of biomarkers shows statistically significant and consistent differences between two biological groups. For example The expression of changes in one or more biomarkers between two or more time points. Exemplary computational methods include, but are not limited to, Gene Set Enrichment Analysis (GSEA), Gene Ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. In some embodiments, GSEA is used to assess dynamic characterization. In some embodiments, GO analysis is used to assess dynamic characterization. In some embodiments, KEGG analysis is used to assess dynamic characterization. In some embodiments, two or more computational methods are used to assess dynamic characterization. In some embodiments, GSEA, GO analysis, and KEGG analysis are used to assess dynamic characterization.

[0128] In some embodiments, biomarkers of the dynamic signature profile are evaluated using the GO database via GSEA and annotated with GO. Without being bound by theory, GO annotation identifies one or more common biological domains among the biomarkers of the dynamic signature profile in the GO database (http: / / www.geneontology.org). Exemplary annotations include, but are not limited to, molecular functions (active biomarkers of the dynamic signature profile, e.g., catalysis, transport, receptors), cellular components (where the biomarkers of the dynamic signature profile are active, e.g., compartments, complexes, organelles), and biological processes (the pathways and larger processes in which the biomarkers of the dynamic signature profile participate through their respective activities, e.g., signal transduction, DNA repair, bone marrow biology). In some embodiments, the dynamic signature profile is evaluated using the GO database via GSEA and identifies one or more common molecular functions. In some embodiments, the dynamic signature profile is evaluated using the GO database via GSEA and identifies one or more common cellular components. In some embodiments, the dynamic signature profile is evaluated using the GO database via GSEA and identifies one or more common biological processes. In some implementations, dynamic characterization profiles are evaluated using the GO database via GSEA to identify one or more common molecular functions, cellular components, and biological processes, as well as combinations thereof.

[0129] In some embodiments, GSEA uses the GO database to annotate a biological process, such as Gene Ontology Bioprocesses (GOBP). In some embodiments, GSEA uses the GO database to annotate two or more biological processes. In some embodiments, GSEA uses the GO database to annotate dynamic signature profiles and identify bone marrow biology. In some embodiments, the biological process includes bone marrow biology. Exemplary biological process components include, but are not limited to, regulation of macrophage activation, positive regulation of macrophage activation, macrophage activation, and myeloid leukocyte activation. In some embodiments, the biological process component is the regulation of macrophage activation. In some embodiments, the biological process component is the positive regulation of macrophage activation. In some embodiments, the biological process component is macrophage activation. In some embodiments, the biological process component is myeloid leukocyte activation.

[0130] In some implementations, GSEA uses the GO database to annotate dynamic characterization profiles and identify bone marrow biology, i.e., dynamic bone marrow characterization profiles.

[0131] Diagnostic accuracy of dynamic feature spectrum

[0132] The diagnostic accuracy of a method or kit used to predict the responsiveness of a subject with cancer to a therapeutic intervention (e.g., ICI monotherapy) can be determined by analyzing the area under the curve (AUC) derived from a receiver operating characteristic (ROC) curve. An ROC curve is a graph illustrating the ability of a binary classifier system to discriminate changes in its threshold. An ROC curve is plotted against the false positive rate, with the true positive rate on the y-axis and the false positive rate on the x-axis. The true positive rate, also known as sensitivity, is calculated by dividing the number of true positives by the sum of true positives and false negatives. The false positive rate is calculated by (1) dividing the number of false positives by the sum of true negatives and false positives, or (2) subtracting specificity from one, where specificity is calculated by dividing the number of true negatives by the sum of true negatives and false positives. In some embodiments, the ROC curve is generated based on the individual expression level of each biomarker. In some embodiments, the ROC curve is generated based on a combination of the expression levels of each biomarker.

[0133] In some embodiments, the AUC value of the method or kit described herein is greater than 0.50. In some embodiments, the AUC value of the method or kit described herein is at least 0.60. In some embodiments, the AUC value of the method or kit described herein is at least 0.70. In some embodiments, the AUC value of the method or kit described herein is at least 0.71. In some embodiments, the AUC value of the method or kit described herein is at least 0.72. In some embodiments, the AUC value of the method or kit described herein is at least 0.73. In some embodiments, the AUC value of the method or kit described herein is at least 0.74. In some embodiments, the AUC value of the method or kit described herein is at least 0.75. In some embodiments, the AUC value of the method or kit described herein is at least 0.76. In some embodiments, the AUC value of the method or kit described herein is at least 0.77. In some embodiments, the AUC value of the method or kit described herein is at least 0.78. In some embodiments, the AUC value of the method or kit described herein is at least 0.79. In some embodiments, the AUC value of the methods or kits described herein is at least 0.80. In some embodiments, the AUC value of the methods or kits described herein is at least 0.81. In some embodiments, the AUC value of the methods or kits described herein is at least 0.82. In some embodiments, the AUC value of the methods or kits described herein is at least 0.83. In some embodiments, the AUC value of the methods or kits described herein is at least 0.84. In some embodiments, the AUC value of the methods or kits described herein is at least 0.85. In some embodiments, the AUC value of the methods or kits described herein is at least 0.86. In some embodiments, the AUC value of the methods or kits described herein is at least 0.87. In some embodiments, the AUC value of the methods or kits described herein is at least 0.88. In some embodiments, the AUC value of the methods or kits described herein is at least 0.89. In some embodiments, the AUC value of the methods or kits described herein is at least 0.90.

[0134] The diagnostic accuracy of expression levels of a single biomarker or a combination of specific biomarkers can be maximized by performing cutoff analyses that take into account clinical utility, considering sensitivity, specificity, negative predictive value (NPV), positive predictive value (PPV), positive likelihood ratio (PLR), and negative likelihood ratio (NLR). Expression levels can be analyzed using any of a variety of methods. In some implementations, univariate or univariate (SV) analyses are used. In some implementations, multivariate (MV) analyses are used.

[0135] The generation of ROC curves and analysis of the sample population can be used to establish cutoff values ​​for distinguishing different subject subgroups. For example, cutoff values ​​can be used to distinguish between a high probability of response to a treatment intervention (e.g., ICI monotherapy) and a low probability of response to a treatment intervention (e.g., ICI monotherapy). In some implementations, cutoff values ​​can differentiate between these subjects.

[0136] In some embodiments, the methods or kits described herein provide a score indicating the likelihood that a subject with cancer will be unresponsive to ICI monotherapy with a diagnostic accuracy of at least 0.70. In some embodiments, the methods or kits described herein provide a score indicating the likelihood that a subject with cancer will be unresponsive to ICI monotherapy with a diagnostic accuracy of at least 0.75. In some embodiments, the methods or kits described herein provide a score indicating the likelihood that a subject with cancer will be unresponsive to ICI monotherapy with a diagnostic accuracy of at least 0.80. In some embodiments, the methods or kits described herein provide a score indicating the likelihood that a subject with cancer will be unresponsive to ICI monotherapy with a diagnostic accuracy of at least 0.85. In some embodiments, the methods or kits described herein provide a score indicating the likelihood that a subject with cancer will be unresponsive to ICI monotherapy with a diagnostic accuracy of at least 0.90.

[0137] In some embodiments, the methods or kits described herein provide a score indicating, with a diagnostic accuracy of at least 0.70, that a subject with cancer will be unresponsive to ICI monotherapy. In some embodiments, the methods or kits described herein provide a score indicating, with a diagnostic accuracy of at least 0.75, that a subject with cancer will be unresponsive to ICI monotherapy. In some embodiments, the methods or kits described herein provide a score indicating, with a diagnostic accuracy of at least 0.80, that a subject with cancer will be unresponsive to ICI monotherapy. In some embodiments, the methods or kits described herein provide a score indicating, with a diagnostic accuracy of at least 0.85, that a subject with cancer will be unresponsive to ICI monotherapy. In some embodiments, the methods or kits described herein provide a score indicating, with a diagnostic accuracy of at least 0.90, that a subject with cancer will be unresponsive to ICI monotherapy.

[0138] Exemplary dynamic characterization spectrum of non-responders

[0139] In some embodiments, the dynamic characterization profile of this disclosure includes detecting a suite of biomarkers disclosed herein at two or more time points in subjects with cancer who have received ICI monotherapy. In some embodiments, the dynamic characterization profile of this disclosure includes detecting a suite of biomarkers disclosed herein at one or more time points, approximately 3 weeks to approximately 6 months after administration of ICI monotherapy, in subjects with cancer.

[0140] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from one or more of the following at two or more time points in subjects with cancer who have received ICI monotherapy: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, GBP 2. GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.

[0141] In some implementations, the dynamic profiling includes detecting a suite of at least six biomarkers selected from the following at two or more time points in subjects with cancer who have received ICI monotherapy: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, GBP 2. GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.

[0142] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from one or more of the following at one or more time points: before a subject with cancer receives ICI monotherapy and from approximately 3 weeks to approximately 6 months after ICI monotherapy: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FB. P1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3 , NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.

[0143] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from at least six of the following at one or more time points: before a subject with cancer receives ICI monotherapy and from approximately 3 weeks to approximately 6 months after ICI monotherapy: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, and FBP. 1. FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.

[0144] In some implementations, the dynamic profiling includes detecting a suite of biomarkers, including one or more of the following, at two or more time points in subjects with cancer who have received ICI monotherapy: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B.

[0145] In some implementations, the dynamic profiling includes a suite of biomarkers, including CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, detected at two or more time points in subjects with cancer who have received ICI monotherapy.

[0146] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from one or more of the following at one or more time points, before a subject with cancer receives ICI monotherapy and from approximately 3 weeks to approximately 6 months after ICI monotherapy: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B.

[0147] In some implementations, the dynamic profiling includes detecting a suite of biomarkers, including CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, at one or more time points, from approximately 3 weeks to approximately 6 months after administration of ICI monotherapy to subjects with cancer.

[0148] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from one or more of the following at two or more time points in subjects with cancer who have received ICI monotherapy: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN.

[0149] In some implementations, the dynamic profiling includes detecting a suite of at least six biomarkers selected from the following at two or more time points in subjects with cancer who have received ICI monotherapy: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN.

[0150] In some implementations, the dynamic profiling includes detecting a suite of biomarkers, including ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, at two or more time points in subjects with cancer who have received ICI monotherapy.

[0151] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from one or more of the following at one or more time points, before a subject with cancer receives ICI monotherapy and from approximately 3 weeks to approximately 6 months after ICI monotherapy: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN.

[0152] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from at least six of the following at one or more time points, before a subject with cancer receives ICI monotherapy and from approximately 3 weeks to approximately 6 months after ICI monotherapy: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN.

[0153] In some implementations, the dynamic profiling includes detecting a suite of biomarkers, including ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, at one or more time points, from approximately 3 weeks to approximately 6 months after administration of ICI monotherapy to subjects with cancer.

[0154] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from one or more of the following at two or more time points in subjects with cancer who have received ICI monotherapy: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.

[0155] In some implementations, the dynamic profiling includes detecting a suite of at least six biomarkers selected from the following at two or more time points in subjects with cancer who have received ICI monotherapy: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.

[0156] In some implementations, the dynamic profiling includes detecting a suite of biomarkers, including AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, at two or more time points in subjects with cancer who have received ICI monotherapy.

[0157] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from one or more of the following at one or more time points, before a subject with cancer receives ICI monotherapy and from approximately 3 weeks to approximately 6 months after ICI monotherapy: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.

[0158] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from at least six of the following at one or more time points, before a subject with cancer receives ICI monotherapy and from approximately 3 weeks to approximately 6 months after ICI monotherapy: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.

[0159] In some implementations, the dynamic profiling includes detecting a suite of biomarkers, including AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, at one or more time points, from approximately 3 weeks to approximately 6 months after administration of ICI monotherapy, before subjects with cancer receive ICI monotherapy.

[0160] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from one or more of the following at two or more time points in subjects with cancer who have received ICI monotherapy: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

[0161] In some implementations, the dynamic profiling includes detecting a suite of at least six biomarkers selected from the following at two or more time points in subjects with cancer who have received ICI monotherapy: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

[0162] In some implementations, the dynamic profiling includes detecting a suite of biomarkers, including ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, at two or more time points in subjects with cancer who have received ICI monotherapy.

[0163] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from one or more of the following at one or more time points, before a subject with cancer receives ICI monotherapy and from approximately 3 weeks to approximately 6 months after ICI monotherapy: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

[0164] In some implementations, the dynamic profiling includes detecting a suite of biomarkers selected from at least six of the following at one or more time points, before a subject with cancer receives ICI monotherapy and from approximately 3 weeks to approximately 6 months after ICI monotherapy: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

[0165] In some implementations, the dynamic profiling includes detecting a suite of biomarkers, including ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, at one or more time points, approximately 3 weeks to 6 months after administration of ICI monotherapy, before subjects with cancer receive ICI monotherapy.

[0166] Exemplary dynamic bone marrow feature spectrum

[0167] In some embodiments, the dynamic bone marrow profiling of this disclosure includes detecting a suite of biomarkers disclosed herein at two or more time points in subjects with cancer who are unresponsive to ICI monotherapy. In some embodiments, the dynamic bone marrow profiling of this disclosure includes detecting a suite of biomarkers disclosed herein at two or more time points in subjects with cancer who are predicted to be unlikely to respond to ICI monotherapy. In some embodiments, the dynamic bone marrow profiling of this disclosure includes detecting a suite of biomarkers disclosed herein before administration of ICI monotherapy to the subject, and at one or more time points from approximately 3 weeks to approximately 6 months after administration of ICI monotherapy.

[0168] In some embodiments, dynamic myelogenous profiling includes detecting a suite of biomarkers selected from one or more of the following at two or more time points in subjects with cancer who are unresponsive to ICI monotherapy: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, dynamic myelogenous profiling includes detecting a suite of biomarkers selected from one or more of the following at two or more time points in subjects with cancer who are predicted to be likely unresponsive to ICI monotherapy: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0169] In some implementations, dynamic bone marrow profiling includes detecting a suite of biomarkers selected from one or more of the following at one or more time points, approximately 3 weeks to 6 months after administration of ICI monotherapy: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0170] In some implementations, dynamic myelogenous profiling includes detecting a suite of biomarkers selected from one or more of the following at two or more time points in subjects with cancer who are unresponsive to ICI monotherapy: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some implementations, dynamic myelogenous profiling includes detecting a suite of biomarkers selected from one or more of the following at two or more time points in subjects with cancer who are predicted to be likely unresponsive to ICI monotherapy: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0171] In some implementations, dynamic bone marrow profiling includes detecting a suite of biomarkers selected from one or more of the following at one or more time points, before administering ICI monotherapy to the subject and at approximately 3 weeks to approximately 6 months after administering ICI monotherapy: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0172] In some implementations, dynamic bone marrow profiling includes detecting a suite of biomarkers selected from one or more of the following at one or more time points, before administering ICI monotherapy to the subject and from approximately 3 weeks to approximately 6 months after administering ICI monotherapy: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0173] In some implementations, dynamic bone marrow profiling includes detecting a suite of biomarkers selected from one or more of the following at one or more time points, before administering ICI monotherapy to the subject and from approximately 3 weeks to approximately 6 months after administering ICI monotherapy: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

[0174] How to use

[0175] In some aspects, this disclosure provides methods for identifying a set and / or dynamic profile of biomarkers in subjects with cancer who have received ICI monotherapy. In some embodiments, the set and / or dynamic profile of biomarkers described herein predicts whether a subject will respond to ICI monotherapy. In some embodiments, the set and / or dynamic profile of biomarkers described herein predicts that a patient is unlikely to respond to ICI monotherapy.

[0176] In some aspects, this disclosure provides a set of biomarkers and / or dynamic myeloprofilometry profiles for identifying subjects with cancer who are identified or predicted to be unresponsive to ICI monotherapy. In some embodiments, the set of biomarkers and / or dynamic myeloprofilometry profiles described herein predict whether a subject will respond to a combination therapy of a therapeutic agent targeting myeloimmunosuppressive checkpoints and an ICI. In some embodiments, the set of biomarkers and / or dynamic myeloprofilometry profiles described herein predict whether a patient is likely to respond to a combination therapy of a therapeutic agent targeting myeloimmunosuppressive checkpoints and an ICI.

[0177] In some embodiments, this disclosure provides a method for administering an additional cancer therapeutic agent to a subject identified or predicted to be unresponsive to ICI monotherapy. In some embodiments, the additional cancer therapeutic agent is a therapeutic agent targeting a bone marrow immunosuppressive checkpoint. In some embodiments, the additional cancer therapeutic agent is a combination therapy of a therapeutic agent targeting a bone marrow immunosuppressive checkpoint and an ICI. In some embodiments, the additional cancer therapeutic agent is administered as a monotherapy, i.e., without ICI therapy.

[0178] In some embodiments, the ICI monotherapy is an antibody. In some embodiments, the antibody is specific to PD1 (e.g., anti-PD1), PDL1 (e.g., anti-PDL1), LAG3 (e.g., anti-LAG3), or CTLA4 (e.g., anti-CTLA4). In some embodiments, an anti-PD1 antibody is administered to a subject with cancer. In some embodiments, an anti-PDL1 antibody is administered to a subject with cancer. In some embodiments, an anti-LAG3 antibody is administered to a subject with cancer. In some embodiments, an anti-CTLA4 antibody is administered to a subject with cancer. In some embodiments, one or more of the following are administered to a subject with cancer: an anti-PD1 antibody, an anti-PDL1 antibody, an anti-LAG3 antibody, and an anti-CTLA4 antibody. Exemplary antibodies include, but are not limited to, ipilimumab, nivolumab, renalalimumab, pembrolizumab, atezolizumab, durvalumab, avelumab, cimiprimab, or dotalimumab.

[0179] In some embodiments, the therapeutic agent targeting the bone marrow immunosuppressive checkpoint is an anticancer therapeutic agent, such as an immunotherapy agent or a chemotherapy agent. In some embodiments, the therapeutic agent targeting the bone marrow immunosuppressive checkpoint is an immunotherapy agent (e.g., an antibody). In some embodiments, the therapeutic agent targeting the bone marrow immunosuppressive checkpoint is a chemotherapy agent (e.g., a small molecule). In some embodiments, the therapeutic agent targeting the bone marrow immunosuppressive checkpoint targets bone marrow cells. Exemplary bone marrow cells include, but are not limited to, bone marrow progenitor cells, basophils, neutrophils, eosinophils, monocytes, macrophages, erythrocytes, and platelets. In some embodiments, an antibody targeting bone marrow cells is administered to a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy. In some embodiments, a small molecule targeting bone marrow cells is administered to a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy. Exemplary therapeutic agents targeting bone marrow immunosuppressive checkpoints include, but are not limited to, acalabrutinib, alemtuzumab, arsenic trioxide, asciminib hydrochloride, asparaginase erwinia chrysanthemi, recombinant erwinia chrysanthemi asparaginase-rywn, azacitidine, bendamustine hydrochloride, blinatumomab, bortezomib, bosutinib, busulfan, and long-acting pegylated asparaginase-MKNL (calaspargase). pegol-mknl, carfilzomib, carmustine, chlorambucil, ciltacabtagene autoleucel, cladribine, clofarabine, cyclophosphamide, cytarabine, daratumumab, daratumumab and hyaluronidase-fihj, dasatinib, daunorubicin hydrochloride, dexamethasone, doxorubicin hydrochloridehydrochloride, doxorubicin hydrochloride liposome, duvelisib, elotuzumab, enasidenib mesylate, fludarabine phosphate, gemtuzumab ozogamicin, gilteritinib fumarate, glasdegib maleate, hydroxyurea, ibrutinib, idarubicin hydrochloride, idecabtagene vicleucel, idelalisib, imatinib mesylate, inotuzumab ozogamicin ozogamicin, isatuximab-irfc, ivosidenib, ixazomib citrate, lenalidomide, melphalan, melphalan hydrochloride, mercaptopurine, methotrexate sodium, midostaurin, mitoxantrone hydrochloride, moxetumomab pasudotox-tdfk, nelarabine, nilotinib, obinutuzumab, ofatumumab, olutasidenib, omacetaxine mepesuccinate, pamidronate disodium disodium, pegaspargase, pemigatinib, plerixafor, pomalidomide, ponatinib hydrochlorideHydrochloride, prednisone, recombinant interferon alpha-2b, rituximab, selinexor, tagraxofusp-erzs, teclistamab-cqyv, thalidomide, thioguanine, tisagenlecleucel, venetoclax, vincristine sulfate, zanubrutinib, and zoledronicacid, as well as combinations thereof.

[0180] In some embodiments, the therapeutic agent targeting the myeloid immunosuppression checkpoint is gene-specific, for example, targeting a specific nucleic acid or protein. In some embodiments, the therapeutic agent targeting the myeloid immunosuppression checkpoint targets a specific nucleic acid. In some embodiments, the therapeutic agent targeting the myeloid immunosuppression checkpoint targets a specific protein. In some embodiments, the therapeutic agent targeting the myeloid immunosuppression checkpoint targets a biomarker disclosed herein. In some embodiments, the therapeutic agent targeting the myeloid immunosuppression checkpoint targets one or more biomarkers selected from the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8. In some embodiments, the therapeutic agent targets LILRB4. In some embodiments, the therapeutic agent targets AZU1. In some embodiments, the therapeutic agent targets CCL3. In some embodiments, the therapeutic agent targets CST7. In some embodiments, the therapeutic agent targets HAVCR2. In some embodiments, the therapeutic agent targets IFNG. In some embodiments, the therapeutic agent targets IL10. In some embodiments, the therapeutic agent targets IL1RL1. In some embodiments, the therapeutic agent targets IL4R. In some embodiments, the therapeutic agent targets IL6. In some embodiments, the therapeutic agent targets LBP. In some embodiments, the therapeutic agent targets MIF. In some embodiments, the therapeutic agent targets MMP8.

[0181] In some embodiments, the therapeutic agent targeting bone marrow immunosuppressive checkpoints is an antibody. In some embodiments, the antibody targets LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, or MMP8. In some embodiments, the antibody targets LILRB4 (e.g., anti-LILRB4). In some embodiments, the antibody targets AZU1 (e.g., anti-AZU1). In some embodiments, the antibody targets CCL3 (e.g., anti-CCL3). In some embodiments, the antibody targets CST7 (e.g., anti-CST7). In some embodiments, the antibody targets HAVCR2 (e.g., anti-HAVCR2). In some embodiments, the antibody targets IFNG (e.g., anti-IFNG). In some embodiments, the antibody targets IL10 (e.g., anti-IL10). In some embodiments, the antibody targets IL1RL1 (e.g., anti-IL1RL1). In some embodiments, the antibody targets IL4R (e.g., anti-IL4R). In some embodiments, the antibody targets IL6 (e.g., anti-IL6). In some embodiments, the antibody targets LBP (e.g., anti-LBP). In some embodiments, the antibody targets MIF (e.g., anti-MIF). In some embodiments, the antibody targets MMP8 (e.g., anti-MMP8). Methods for generating the antibody are known to those skilled in the art.

[0182] In some embodiments, the therapeutic agent targeting bone marrow immunosuppressive checkpoints is a protein or a fragment thereof. In some embodiments, the protein or fragment thereof comprises a wild-type or non-mutated amino acid sequence. In some embodiments, the protein or fragment thereof comprises a recombinant or mutant amino acid sequence. Exemplary proteins or fragments thereof include, but are not limited to, anticoagulants, blood factors, bone morphogenetic proteins, engineered protein scaffolds, enzymes, growth factors, hormones, interferons, interleukins, thrombolytics, and cytokines. In some embodiments, the protein or fragment thereof is an anticoagulant. In some embodiments, the protein or fragment thereof is a blood factor. In some embodiments, the protein or fragment thereof is a bone morphogenetic protein. In some embodiments, the protein or fragment thereof is an engineered protein scaffold. In some embodiments, the protein or fragment thereof is an enzyme. In some embodiments, the protein or fragment thereof is a growth factor. In some embodiments, the protein or fragment thereof is a hormone. In some embodiments, the protein or fragment thereof is an interferon. In some embodiments, the protein or fragment thereof is an interleukin. In some embodiments, the protein or fragment thereof is a thrombolytic. In some embodiments, the protein or fragment thereof is a cytokine.

[0183] In some embodiments, the protein or a fragment thereof is LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, or MMP8. In some embodiments, the protein or a fragment thereof is LILRB4. In some embodiments, the protein or a fragment thereof is AZU1. In some embodiments, the protein or a fragment thereof is CCL3. In some embodiments, the protein or a fragment thereof is CST7. In some embodiments, the protein or a fragment thereof is HAVCR2. In some embodiments, the protein or a fragment thereof is IFNG. In some embodiments, the protein or a fragment thereof is IL10. In some embodiments, the protein or a fragment thereof is IL1RL1. In some embodiments, the protein or a fragment thereof is IL4R. In some embodiments, the protein or a fragment thereof is IL6. In some embodiments, the protein or a fragment thereof is LBP. In some embodiments, the protein or a fragment thereof is MIF. In some embodiments, the protein or a fragment thereof is MMP8. Methods for generating the protein or its fragment thereof are known to those skilled in the art.

[0184] As used herein, the terms “subject” and “patient” are used interchangeably. As used herein, a subject can be a mammal, such as a non-primate (e.g., cattle, pigs, horses, cats, dogs, rats, etc.) or a primate (e.g., monkeys and humans). In some embodiments, the subject is a human. In some embodiments, the patient to be treated or tested for responsiveness to treatment according to the methods described herein is a patient diagnosed with cancer (such as any cancer described herein). The diagnosis can be made by any method or technique known in the art, such as x-ray, MRI, or biopsy, and can also be confirmed by a physician. To minimize patient exposure to potentially non-therapeutic drug treatments, it can be determined, according to the methods described herein, whether the patient is responsive or unresponsive to cancer treatments (such as myelosuppressive agents described herein) prior to treatment.

[0185] As used herein, the terms “treat,” “treating,” and “treatment” refer to an action that occurs when a subject has the disease, condition, or symptom described herein. “Treat,” “treatment,” and “treating” also refer to a reduction or improvement in the progression, severity, and / or duration of the disease, condition, or symptom described herein due to the administration of one or more therapeutic agents described herein.

[0186] As used herein, the terms “cancer” and “cancerous” refer to or describe a physiological condition in mammals typically characterized by unregulated cell growth. In some embodiments, the subject has a hematologic malignancy. As used herein, a hematologic malignancy refers to a blood-derived tumor (e.g., multiple myeloma, lymphoma, and leukemia). In some embodiments, the subject has a solid tumor. As used herein, “tumor” and “solid tumor” refer to all lesions and neoplastic cell growth and proliferation, whether malignant or benign, as well as all precancerous and cancerous cells and tissues. As used herein, “necroplastic” refers to any form of disordered or unregulated cell growth that leads to abnormal tissue growth, whether malignant or benign. Therefore, “necroplastic cells” include both malignant and benign cells with disordered or unregulated cell growth.

[0187] In some implementations, the subject has a solid tumor. In some implementations, the solid tumor is a sarcoma (e.g., a solid tumor containing a densely packed mass of cells embedded in fibrous or homogeneous material). Exemplary sarcomas treated, prevented, and / or managed using the compositions and methods described herein include chondrosarcoma, fibrosarcoma, lymphosarcoma, melanosarcoma, myxosarcoma, osteosarcoma, Abemethyst's sarcoma, liposarcoma, liposarcoma, alveolar soft tissue sarcoma, ameloblastic sarcoma, botryoid sarcoma, chlorosarcoma, choriocarcinoma, embryonal sarcoma, Wilms' tumor sarcoma, endometrial sarcoma, stromal sarcoma, Ewing's sarcoma, fascial sarcoma, fibroblastic sarcoma, giant cell sarcoma, granulocytic sarcoma, Hodgkin's sarcoma, idiopathic multiple pigmented hemorrhage sarcoma, B-cell immunoblastic sarcoma, lymphoma, T-cell immunoblastic sarcoma, Jensen's sarcoma, and Kaposi's sarcoma. Sarcoma, Kupffer cell sarcoma, angiosarcoma, leukemic sarcoma, malignant stromal tumor sarcoma, osteosarcoma, reticulum cell sarcoma, Rous sarcoma, serous cystic sarcoma, synovial sarcoma, and telangiectaltic sarcoma.

[0188] In some implementations, a solid tumor is a carcinoma (e.g., a malignant growth comprising epithelial cells that have infiltrated surrounding tissue). Exemplary carcinomas treated, prevented, and / or managed using the compositions and methods described herein include adenocarcinoma, colorectal cancer, colorectal adenocarcinoma, acinar carcinoma, lung cancer, alveolar cell carcinoma, basal cell carcinoma, bronchoalveolar carcinoma, bronchial carcinoma, bronchogenic carcinoma, brain-like carcinoma, choriocarcinoma, colloid carcinoma, uterine corpus carcinoma, cribriform carcinoma, columnar carcinoma, columnar cell carcinoma, ductal carcinoma, colloid carcinoma, colloid carcinoma, giant cell carcinoma, giant cell carcinoma gigantocellulare, adenocarcinoma, hemangiocarcinoma, hepatocellular carcinoma, Hurthle cell carcinoma, Krompecher's carcinoma, and Kulchitzky-cell carcinoma. Carcinoma, large cell carcinoma, lymphoepithelial carcinoma, nasopharyngeal carcinoma, papillary carcinoma, renal cell carcinoma of the kidney, scleroderma, small cell carcinoma, spherical cell carcinoma, squamous cell carcinoma, squamous cell carcinoma, telangiectatic carcinoma, and verrucous carcinoma.

[0189] In some implementations, solid tumors are solid tumors of the oral cavity, lungs, gastrointestinal tract, genitourinary tract, liver, bones, nervous system, gynecology, skin, thyroid, or adrenal glands. In some implementations, solid tumors are solid tumors of the oral cavity (buccal mucosa cancer, lip cancer, tongue cancer, oral cancer, pharyngeal cancer); solid tumors of the heart (sarcomas (angiosarcoma, fibrosarcoma, rhabdomyosarcoma, liposarcoma), myxoma, rhabdomyosarcoma, fibroma, lipoma, and teratoma); solid tumors of the lungs (bronchial carcinomas (squamous cell or epidermoid carcinoma, undifferentiated small cell carcinoma, undifferentiated large cell carcinoma, adenocarcinoma), alveolar (bronchial) carcinoma, bronchial adenoma, sarcoma, lymphoma, chondroid hamartoma, mesothelioma); solid tumors of the gastrointestinal tract (esophageal cancer (squamous cell carcinoma, laryngeal carcinoma, adenocarcinoma, leiomyosarcoma, lymphoma)). Tumors of the stomach (gastric cancer, lymphoma, leiomyosarcoma), pancreatic cancer (ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma, carcinoid tumor, vasoactive intestinal peptide tumor), small intestinal cancer (adenocarcinoma, lymphoma, carcinoid tumor, Kaposi's sarcoma, leiomyoma, hemangioma, lipoma, neurofibroma, fibroma), colorectal cancer (adenocarcinoma, tubular adenoma, villous adenoma, hamartoma, leiomyoma), colon cancer, colon-rectal cancer, colorectal cancer, rectal cancer; solid tumors of the genitourinary tract (renal cancer (adenocarcinoma, Wilms' tumor [nephroblastoma], lymphoma, leukemia), bladder and urethral cancer (squamous cell carcinoma)). Solid tumors of the liver include: hepatocellular carcinoma (hepatocellular carcinoma, transitional cell carcinoma, adenocarcinoma), prostate cancer (adenocarcinoma, sarcoma), testicular cancer (seminomatous seminoma), teratoma, embryonal carcinoma, choriocarcinoma, sarcoma, stromal cell carcinoma, fibroma, fibroadenoma, adenoid tumor, lipoma; solid tumors of the bone include: osteosarcoma, fibrosarcoma, malignant fibrous histiocytoma, chondrosarcoma, Ewing's sarcoma, malignant lymphoma (reticular cell sarcoma), multiple myeloma, malignant giant cell tumor, chordoma. Osteochondroma (osteochondral exostosis), benign chondroma, chondroblastoma, chondromyxoid fibroma, osteoid osteoma, and giant cell tumor; solid tumors of the nervous system (skull tumors (osteoma, hemangioma, granuloma, xanthoma, osteitis deformans), meningeal tumors (meningioma, meningeal sarcoma, gliomatosis), brain tumors (astrocytoma, medulloblastoma, glioma, ependymoma, germ cell tumor [pineal tumor], glioblastoma multiforme, oligodendroglioma, schwannoma, retinoblastoma, congenital tumors), spinal neurofibroma, meningioma, glioma, sarcoma);Gynecological solid tumors (uterine tumors (endometrial cancer), cervical tumors (cervical cancer, precancerous cervical intraepithelial neoplasia), ovarian tumors (ovarian cancer [serous cystadenocarcinoma, mucinous cystadenocarcinoma, unclassified carcinoma], granulosa cell carcinoma, Sertoli-Leydig cell tumor, dysgerminoma, malignant teratoma), vulvar tumors (squamous cell carcinoma, intraepithelial carcinoma, adenocarcinoma, fibrosarcoma, melanoma), vaginal tumors (clear cell carcinoma, squamous cell carcinoma, botryoid sarcoma (embryonic rhabdomyosarcoma), fallopian tube (cancer)), breast cancer); hematologic solid tumors (hematologic malignancies (myeloid leukemia [acute and chronic], acute lymphoblastic leukemia, chronic lymphocytic leukemia, myeloproliferative disorders, multiple myeloma, myelodysplastic syndromes), Hodgkin's disease, non-Hodgkin's lymphoma [malignant lymphoma]). [Leukemia] Hairy cell leukemia, lymphoma; solid tumors of the skin (malignant melanoma, basal cell carcinoma, squamous cell carcinoma, Kaposi's sarcoma, keratoacanthoma, nevus, dysplastic nevus, lipoma, hemangioma, dermatofibroma, keloid, psoriasis), thyroid tumors (papillary thyroid carcinoma, follicular thyroid carcinoma, undifferentiated thyroid carcinoma, medullary thyroid carcinoma, type 2A multiple endocrine neoplasia, type 2B multiple endocrine neoplasia, familial medullary thyroid carcinoma, pheochromocytoma, paraganglioma); and solid tumors of the adrenal glands (neuroblastoma).

[0190] In some implementations, the subject has a myeloproliferative disorder (e.g., blood cancer). The term "myeloproliferative disorder" includes diseases such as polycythemia vera, thrombocythemia, metaplasia of the bone marrow with myelofibrosis, eosinophilic syndrome, juvenile myelomonocytic leukemia, systemic mast cell disease, and hematopoietic disorders, particularly acute myeloid leukemia (AML), chronic myeloid leukemia (CML), acute promyelocytic leukemia (APL), and acute lymphoblastic leukemia (ALL).

[0191] Methods for identifying dynamic characteristic spectra and predicting no-response

[0192] In some embodiments, this disclosure provides methods for identifying dynamic characterization profiles in subjects with cancer who are receiving ICI monotherapy. In some embodiments, this disclosure provides methods for identifying subjects with cancer as unlikely to respond to ICI monotherapy. In some embodiments, the subject has received ICI monotherapy, and the dynamic characterization profile predicts that the subject is unlikely to respond to ICI monotherapy prior to clinical readout.

[0193] In some embodiments, this disclosure provides a method for predicting whether a subject with cancer receiving ICI monotherapy will respond to ICI monotherapy, comprising determining the amount or level of a set of biomarkers disclosed herein at two or more time points. In some embodiments, the amount or level of the biomarker set changes (e.g., increases or decreases) between two or more time points (e.g., between baseline and at least one time point after administration of ICI monotherapy). In some embodiments, the amount or level of the biomarker set increases between two or more time points (e.g., between baseline and at least one time point after administration of ICI monotherapy). In some embodiments, the increase in the amount or level of the biomarker set between two or more time points is statistically significant. In some embodiments, the amount or level of the biomarker set decreases between two or more time points (e.g., between baseline and at least one time point after administration of ICI monotherapy). In some embodiments, the decrease in the amount or level of the biomarker set between two or more time points is statistically significant.

[0194] In some embodiments, the amount or level of the biomarker set is altered relative to a reference sample. In some embodiments, the amount or level of the biomarker set increases relative to a reference sample. In some embodiments, the amount or level of the biomarker set decreases relative to a reference sample. In some embodiments, an increase or decrease in the amount or level of the biomarker set indicates that the subject is unlikely to respond to a therapeutic intervention (e.g., ICI monotherapy).

[0195] In some embodiments, this disclosure provides a method for identifying a subject with cancer who may not respond to one or more cancer treatments, comprising: (i) providing the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of one or more cancer treatments, and the second time point is from about 3 weeks to about 6 months after administration of one or more cancer treatments, wherein the suite of biomarkers comprises one or more biomarkers selected from: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, GBP2, GFBP 2. GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 for the non-response score indicates that the subject is unlikely to respond to one or more cancer treatments.

[0196] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is unlikely to respond to one or more cancer treatments, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of one or more cancer treatments and the second time point is from about 3 weeks to about 6 months after administration of one or more cancer treatments, wherein the set of biomarkers includes one or more of CA6, CDNF, MIA, MYOC, NEFL, and TCL1B; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 for the non-response score indicates that the subject is unlikely to respond to one or more cancer treatments.

[0197] In some embodiments, this disclosure provides a method for identifying a subject with cancer who may not respond to one or more cancer treatments, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of one or more cancer treatments, and the second time point is from about 3 weeks to about 6 months after administration of one or more cancer treatments, wherein the set of biomarkers includes ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5 (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 for the non-response score indicates that the subject is unlikely to respond to one or more cancer treatments.

[0198] In some embodiments, this disclosure provides a method for identifying a subject with cancer who may not respond to one or more cancer treatments, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of one or more cancer treatments, and the second time point is from about 3 weeks to about 6 months after administration of one or more cancer treatments, wherein the set of biomarkers includes AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CT (i) one or more of the following biomarkers: SF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 for the non-response score indicates that the subject is unlikely to respond to one or more cancer treatments.

[0199] In some embodiments, this disclosure provides a method for identifying a subject with cancer who may not respond to one or more cancer treatments, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of one or more cancer treatments, and the second time point is from about 3 weeks to about 6 months after administration of one or more cancer treatments, wherein the set of biomarkers includes ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CP One or more of VL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 for the non-response score indicates that the subject is unlikely to respond to one or more cancer treatments.

[0200] In some embodiments, this disclosure provides a method for identifying a subject with cancer who may not respond to monotherapy with one or more immune checkpoint inhibitors, comprising: (i) providing the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of monotherapy with one or more immune checkpoint inhibitors, and the second time point is approximately 3 weeks to approximately 6 months after administration of monotherapy with one or more immune checkpoint inhibitors, wherein the suite of biomarkers comprises one or more biomarkers selected from: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, G BP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine the non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to one or more immune checkpoint inhibitor monotherapy.

[0201] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is unlikely to respond to one or more immune checkpoint inhibitor monotherapy, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of one or more immune checkpoint inhibitor monotherapy and the second time point is from about 3 weeks to about 6 months after administration of one or more immune checkpoint inhibitor monotherapy, wherein the set of biomarkers includes one or more of CA6, CDNF, MIA, MYOC, NEFL, and TCL1B; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 for the non-response score indicates that the subject is unlikely to respond to one or more immune checkpoint inhibitor monotherapy.

[0202] In some embodiments, this disclosure provides a method for identifying a subject with cancer who may not respond to monotherapy with one or more immune checkpoint inhibitors, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of monotherapy with one or more immune checkpoint inhibitors, and the second time point is approximately 3 weeks to approximately 6 months after administration of monotherapy with one or more immune checkpoint inhibitors, wherein the set of biomarkers includes ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, (i) one or more of HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 for the non-response score indicates that the subject is unlikely to respond to monotherapy with one or more immune checkpoint inhibitors.

[0203] In some embodiments, this disclosure provides a method for identifying a subject with cancer who may not respond to monotherapy with one or more immune checkpoint inhibitors, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of monotherapy with one or more immune checkpoint inhibitors, and the second time point is from about 3 weeks to about 6 months after administration of monotherapy with one or more immune checkpoint inhibitors, wherein the set of biomarkers includes AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to monotherapy with one or more immune checkpoint inhibitors.

[0204] In some embodiments, this disclosure provides a method for identifying a subject with cancer who may not respond to monotherapy with one or more immune checkpoint inhibitors, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of monotherapy with one or more immune checkpoint inhibitors, and the second time point is approximately 3 weeks to approximately 6 months after administration of monotherapy with one or more immune checkpoint inhibitors, wherein the set of biomarkers includes ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, C One or more of LEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 for the non-response score indicates that the subject is unlikely to respond to monotherapy with one or more immune checkpoint inhibitors.

[0205] In some or any of the foregoing embodiments, one or more immune checkpoint inhibitor monotherapy is selected from anti-PD1, anti-PDL1, anti-LAG3, and anti-CTLA4 antibodies.

[0206] Methods for identifying subjects eligible for myelosuppression therapy

[0207] In some embodiments, this disclosure provides methods for identifying dynamic myeloprofiling profiles in subjects with cancer who are identified as or predicted to be unresponsive to ICI monotherapy. In some embodiments, the subject is unresponsive to ICI monotherapy, and the dynamic myeloprofiling profile identifies the subject as potentially responsive to a therapeutic agent targeting myeloimmunosuppressive checkpoints. In some embodiments, the subject is unresponsive to ICI monotherapy, and the dynamic myeloprofiling profile identifies the subject as potentially responsive to a combination therapy of a therapeutic agent targeting myeloimmunosuppressive checkpoints and an ICI.

[0208] In some embodiments, this disclosure provides a method for predicting whether a subject with cancer identified or predicted to be unresponsive to ICI monotherapy will respond to a therapeutic agent targeting myeloid immunosuppression checkpoints, comprising determining the amount or level of a set of biomarkers disclosed herein at two or more time points. In some embodiments, this disclosure provides a method for predicting whether a subject with cancer identified or predicted to be unresponsive to ICI monotherapy will respond to a combination therapy of a therapeutic agent targeting myeloid immunosuppression checkpoints and an ICI, comprising determining the amount or level of a set of biomarkers disclosed herein at two or more time points. In some embodiments, the amount or level of the biomarker set changes (e.g., increases or decreases) between two or more time points (e.g., between baseline and at least one time point after administration of ICI monotherapy).

[0209] In some embodiments, increases in the amount or level of a biomarker set are compared between two or more time points. In some embodiments, the amount or level of a biomarker set increases between two or more time points (e.g., between baseline and at least one time point following ICI monotherapy). In some embodiments, the amount or level of a biomarker set decreases between two or more time points (e.g., between baseline and at least one time point following ICI monotherapy). In some embodiments, increases in the amount or level of a biomarker set are compared between two or more time points to generate a response score. In some embodiments, the response score is associated with the likelihood of a subject responding to a therapeutic agent targeting myeloid immunosuppression checkpoints. In some embodiments, the response score is associated with the likelihood of a subject responding to a combination therapy of a therapeutic agent targeting myeloid immunosuppression checkpoints and an ICI.

[0210] In some embodiments, the amount or level of the biomarker set is altered relative to a reference sample. In some embodiments, the amount or level of the biomarker set increases relative to a reference sample. In some embodiments, the amount or level of the biomarker set decreases relative to a reference sample. In some embodiments, an increase or decrease in the amount or level of the biomarker set indicates that the subject may be responding to a therapeutic intervention (e.g., a therapeutic agent targeting bone marrow immunosuppressive checkpoints, alone or in combination with an ICI).

[0211] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0212] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0213] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0214] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0215] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0216] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0217] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0218] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0219] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0220] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0221] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0222] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0223] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0224] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0225] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy to administer a therapeutic agent targeting myeloid immunosuppressive checkpoints, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI.

[0226] In some implementations, the aforementioned method includes administering the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI, to the subject determined to have a response score.

[0227] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0228] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0229] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0230] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0231] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0232] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0233] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0234] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0235] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0236] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0237] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0238] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0239] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0240] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0241] In some embodiments, this disclosure provides a method for identifying subjects with cancer who are unresponsive to ICI monotherapy for administration of a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Comparing the amount or level of the first set of the biomarkers at two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Compare the amount or level of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0242] In some implementations, the aforementioned method includes administering the LILRB4-targeting therapeutic agent, alone or in combination with the ICI, to the subject determined to have a response score.

[0243] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy but will respond to an additional cancer treatment agent, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the additional cancer treatment agent, alone or in combination with the ICI.

[0244] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is unresponsive to ICI monotherapy but will respond to an additional cancer treatment agent, comprising: (i) providing a subject identified or predicted to be unresponsive to ICI monotherapy; (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (iii) comparing the amount or level of one or more proteins at the two or more different time points to determine a response score, wherein the response score is correlated with the likelihood that the subject will respond to a combination therapy of the additional cancer treatment agent and the ICI.

[0245] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy but will respond to a therapeutic agent targeting myeloimmunosuppressive checkpoints, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting myeloimmunosuppressive checkpoints, alone or in combination with the ICI.

[0246] In some embodiments, this disclosure provides a method for identifying a cancer-stricken subject who is identified or predicted to be unresponsive to ICI monotherapy but will respond to a therapeutic agent targeting myeloimmunosuppressive checkpoints, comprising: (i) providing the subject who is identified or predicted to be unresponsive to ICI monotherapy; (ii) determining the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the suite of biomarkers comprises one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (iii) comparing the amount or level of one or more proteins at the two or more different time points to determine a response score, wherein the response score is correlated with the subject’s potential response to the therapeutic agent targeting myeloimmunosuppressive checkpoints, alone or in combination with the ICI.

[0247] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy but will respond to an additional cancer treatment agent, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the additional cancer treatment agent, alone or in combination with the ICI.

[0248] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is unresponsive to ICI monotherapy but will respond to an additional cancer treatment agent, comprising: (i) providing a subject identified or predicted to be unresponsive to ICI monotherapy; (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (iii) comparing the amount or level of one or more biomarkers at the two or more different time points to determine a response score, wherein the response score is correlated with the likelihood that the subject will respond to the additional cancer treatment agent, alone or in combination with the ICI.

[0249] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy but will respond to a therapeutic agent targeting myeloimmunosuppressive checkpoints, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting myeloimmunosuppressive checkpoints, alone or in combination with the ICI.

[0250] In some embodiments, this disclosure provides a method for identifying a cancer-stricken subject who is identified or predicted to be unresponsive to ICI monotherapy but will respond to a therapeutic agent targeting myelosuppressive checkpoints, comprising: (i) providing the subject who is identified or predicted to be unresponsive to ICI monotherapy; (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of the ICI monotherapy and the second time point is from about 3 weeks to about 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (iii) comparing the amount or level of one or more biomarkers at the two or more different time points to determine a response score, wherein the response score is associated with the subject’s likely response to the therapeutic agent targeting myelosuppressive checkpoints, alone or in combination with the ICI.

[0251] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy but will respond to an additional cancer treatment agent, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the additional cancer treatment agent, alone or in combination with the ICI.

[0252] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is unresponsive to ICI monotherapy but will respond to an additional cancer treatment agent, comprising: (i) providing a subject identified or predicted to be unresponsive to ICI monotherapy; (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (iii) comparing the amount or level of one or more biomarkers at the two or more different time points to determine a response score, wherein the response score is correlated with the likelihood that the subject will respond to the additional cancer treatment agent, alone or in combination with the ICI.

[0253] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy but will respond to a therapeutic agent targeting myeloimmunosuppressive checkpoints, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting myeloimmunosuppressive checkpoints, alone or in combination with the ICI.

[0254] In some embodiments, this disclosure provides a method for identifying a cancer-stricken subject who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting a bone marrow immunosuppressive checkpoint, comprising: (i) providing the subject who is identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 to approximately 6 weeks after administration of the immune checkpoint inhibitor. The period is one month, wherein the set of said biomarkers includes one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (iii) comparing the amount or level of one or more biomarkers at two or more different time points to determine a response score, wherein said response score is related to the subject’s potential response to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with said ICI.

[0255] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting LILRB4, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4, alone or in combination with the ICI.

[0256] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy but will respond to a therapeutic agent targeting LILRB4, comprising: (i) providing the subject who is identified or predicted to be unresponsive to ICI monotherapy; (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (iii) comparing the amount or level of one or more biomarkers at the two or more different time points to determine a response score, wherein the response score is related to the likelihood that the subject will respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0257] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting LILRB4, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting LILRB4, alone or in combination with the ICI.

[0258] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting LILRB4, comprising: (i) providing the subject who is identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 to 6 weeks after administration of the immune checkpoint inhibitor. The biomarker suite comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; and (iii) comparing the amount or level of one or more proteins at two or more different time points to determine a response score, wherein the response score is related to the likelihood that the subject will respond to the therapeutic agent targeting LILRB4 alone or in combination with the ICI.

[0259] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy but will respond to an additional cancer treatment agent, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (ii) comparing the amount or level of the set of biomarkers at the two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the additional cancer treatment agent alone or in combination with the ICI; and (iii) administering the additional cancer treatment agent alone or in combination with the ICI to the subject identified as having a response score.

[0260] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is unresponsive to ICI monotherapy but will respond to another cancer treatment agent, comprising: (i) providing a subject identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises the following One or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (iii) comparing the amount or level of one or more proteins at two or more different time points to determine a response score, wherein the response score is related to the likelihood that the subject will respond to the additional cancer treatment agent alone or in combination with the ICI; and (iv) administering the additional cancer treatment agent alone or in combination with the ICI to the subject determined to have the response score.

[0261] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting a bone marrow immune checkpoint, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following: AZU1, (ii) comparing the amount or level of the set of biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppression checkpoint alone or in combination with the ICI; and (iii) administering the therapeutic agent targeting the bone marrow immunosuppression checkpoint alone or in combination with the ICI to the subject who has been determined to have a response score.

[0262] In some embodiments, this disclosure provides a method for identifying a cancer-stricken subject who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting a bone marrow immunosuppressive checkpoint, comprising: (i) providing the subject who is identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the suite of biomarkers comprises... Including one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (iii) comparing the amount or level of one or more proteins at two or more different time points to determine a response score, wherein the response score is related to the subject’s possible response to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint alone or in combination with the ICI; and (iv) administering the therapeutic agent targeting the bone marrow immunosuppressive checkpoint alone or in combination with the ICI to the subject who has been determined to have the response score.

[0263] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to additional cancer treatment agents, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following: LILRB 4. AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (ii) comparing the amount or level of the set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the additional cancer treatment agent alone or in combination with the ICI; and (iii) administering the additional cancer treatment agent alone in combination with the ICI to the subject determined to have a response score.

[0264] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is unresponsive to ICI monotherapy but will respond to an additional cancer treatment agent, comprising: (i) providing a subject identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one of the following: One or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (iii) comparing the amount or level of one or more proteins at two or more different time points to determine a response score, wherein the response score is related to the likelihood that the subject will respond to the additional cancer treatment agent alone or in combination with the ICI; and (iv) administering the additional cancer treatment agent alone or in combination with the ICI to the subject determined to have the response score.

[0265] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting a bone marrow immune checkpoint, comprising: (i) providing the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the suite of biomarkers includes one or more of the following: LILRB4, A ZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (ii) comparing the amount or level of the set of biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppression checkpoint alone or in combination with the ICI; and (iii) administering the therapeutic agent targeting the bone marrow immunosuppression checkpoint alone or in combination with the ICI to the subject who has been determined to have a response score.

[0266] In some embodiments, this disclosure provides a method for identifying a cancer-stricken subject identified or predicted to be unresponsive to ICI monotherapy and to respond to a therapeutic agent targeting a bone marrow immune checkpoint, comprising: (i) providing the subject identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises the following One or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (iii) comparing the amount or level of one or more biomarkers at two or more different time points to determine a response score, wherein the response score is related to the subject’s possible response to the therapeutic agent targeting the bone marrow immunosuppression checkpoint, alone or in combination with the ICI; and (iv) administering the therapeutic agent targeting the bone marrow immunosuppression checkpoint, alone or in combination with the ICI, to the subject who has been determined to have the response score.

[0267] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to additional cancer treatment agents, comprising: (i) providing the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of the ICI monotherapy, and at least one subsequent time point is from about 3 weeks to about 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following: LILRB4, LAIR 1. VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (ii) comparing the amount or level of the set of biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the additional cancer treatment agent alone or in combination with the ICI; and (iii) administering the additional cancer treatment agent alone or in combination with the ICI to the subject determined to have a response score.

[0268] In some embodiments, this disclosure provides a method for identifying a cancer-stricken subject who is unresponsive to ICI monotherapy but will respond to another cancer treatment agent, comprising: (i) providing a subject identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises the following One or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (iii) comparing the amount or level of one or more proteins at the two or more different time points to determine a response score, wherein the response score is related to the likelihood that the subject will respond to the additional cancer treatment agent alone or in combination with the ICI; and (iv) administering the additional cancer treatment agent alone or in combination with the ICI to the subject determined to have the response score.

[0269] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting a bone marrow immune checkpoint, comprising: (i) providing the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the suite of biomarkers includes one or more of the following: LILRB4, LAIR1, V (ii) comparing the amount or level of the set of biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppression checkpoint alone or in combination with the ICI; and (iii) administering the therapeutic agent targeting the bone marrow immunosuppression checkpoint alone or in combination with the ICI to the subject who has been determined to have a response score.

[0270] In some embodiments, this disclosure provides a method for identifying a cancer-stricken subject identified or predicted to be unresponsive to ICI monotherapy and to respond to a therapeutic agent targeting a bone marrow immunosuppressive checkpoint, comprising: (i) providing the subject identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers comprises one or more of the following (iii) Comparing the amount or level of one or more proteins at two or more different time points to determine a response score, wherein the response score is related to the subject’s potential response to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint alone or in combination with the ICI; and (iv) administering the therapeutic agent targeting the bone marrow immunosuppressive checkpoint alone or in combination with the ICI to the subject who has been determined to have the response score.

[0271] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting LILRB4, comprising: (i) providing amounts or levels of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein a first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the suite of biomarkers includes one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (ii) comparing the amount or level of the set of biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iii) administering the LILRB4-targeting therapeutic agent alone or in combination with the ICI to the subject determined to have a response score.

[0272] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting LILRB4, comprising: (i) providing the subject who is identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of the ICI monotherapy, and at least one subsequent time point is from about 3 weeks to about 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes the following One or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (iii) comparing the amount or level of one or more proteins at the two or more different time points to determine a response score, wherein the response score is related to the likelihood that the subject will respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iv) administering the LILRB4-targeting therapeutic agent alone or in combination with the ICI to the subject determined to have the response score.

[0273] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting LILRB4, comprising: (i) providing the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the ICI monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the suite of biomarkers includes one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (ii) comparing the amount or level of the set of biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iii) administering the LILRB4-targeting therapeutic agent alone or in combination with the ICI to the subject determined to have a response score.

[0274] In some embodiments, this disclosure provides a method for identifying a subject with cancer who is identified or predicted to be unresponsive to ICI monotherapy and will respond to a therapeutic agent targeting LILRB4, comprising: (i) providing the subject who is identified or predicted to be unresponsive to ICI monotherapy; and (ii) determining the amount or level of a set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of the ICI monotherapy, and at least one subsequent time point is from about 3 weeks to about 6 months after administration of the immune checkpoint inhibitor, wherein the set of biomarkers includes one or more of the following (iii) Comparing the amount or level of one or more proteins at two or more different time points to determine a response score, wherein the response score is related to the likelihood that the subject will respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iv) Administering the LILRB4-targeting therapeutic agent alone or in combination with the ICI to the subject determined to have the response score.

[0275] Methods of treating cancer

[0276] In some embodiments, this disclosure provides a method for treating a subject's cancer, comprising identifying the subject as unlikely to respond to ICI monotherapy based on the dynamic characterization profile disclosed herein, and administering at least one additional cancer treatment agent to the subject.

[0277] In some embodiments, this disclosure provides a method for treating cancer in a subject identified or predicted to be unresponsive to ICI monotherapy, comprising identifying the subject as potentially responsive to additional cancer treatment agents (e.g., treatment agents targeting myelosuppressive checkpoints) alone or in combination with ICI based on the dynamic myeloprofiling profile disclosed herein, and administering the additional cancer treatment agent (e.g., treatment agents targeting myelosuppressive checkpoints) alone or in combination with ICI monotherapy to the subject.

[0278] In some embodiments, additional cancer treatments include, but are not limited to, surgery, radiation therapy (e.g., gamma radiation, neutron beam radiation therapy, electron beam radiation therapy, proton therapy, brachytherapy, and / or whole-body radioisotopes), chemotherapy, immunotherapy, endocrine therapy, hyperthermia, cryotherapy, grafts (e.g., stem cells or bone marrow), agents to reduce adverse reactions, corticosteroids (e.g., triamcinolone, methylprednisolone, budesonide, dexamethasone, triamcinolone, prednisone, hydrocortisone, dexamethasone, betamethasone, prednisolone, defcodone, aldosterone, and combinations thereof) or combinations thereof. In some embodiments, cancer treatment is radiation therapy (e.g., gamma radiation, neutron beam radiation therapy, electron beam radiation therapy, proton therapy, brachytherapy, and / or whole-body radioisotopes). In some embodiments, the cancer treatment agent is chemotherapy. In some embodiments, the cancer treatment agent is immunotherapy. In some embodiments, the cancer treatment agent is endocrine therapy. In some embodiments, the cancer treatment agent is hyperthermia. In some embodiments, the cancer treatment agent is cryotherapy. In some embodiments, the cancer treatment agent is a graft (e.g., stem cells or bone marrow). In some embodiments, the cancer treatment agent is a drug that reduces adverse reactions.

[0279] Exemplary immunotherapies include, but are not limited to, immune checkpoint inhibitors (ICIs; e.g., antibodies), T-cell transfer therapies (e.g., CAR T-cell therapy and TIL therapy), monoclonal antibodies (also known as therapeutic antibodies), cancer therapeutic vaccines (e.g., tumor cell-derived or dendritic cell-derived oncolytic virus therapy), immune system modulators (e.g., cytokines, BCG), and immunomodulatory drugs (also known as biological response modulators). Exemplary cytokines include, but are not limited to, interferon (INF) and interleukin (IL). Exemplary immunomodulatory drugs include, but are not limited to, thalidomide, lenalidomide, pomalidomide, and imiquimod. In some embodiments, one or more ICI therapies (e.g., antibodies) are administered to a subject with cancer. In some embodiments, T-cell transfer therapies (e.g., CAR T-cell therapy) are administered to a subject with cancer. T-cell therapy and TIL therapy. In some embodiments, a monoclonal antibody (also known as a therapeutic antibody) is administered to a subject with cancer. In some embodiments, a cancer treatment vaccine (e.g., tumor cell-derived, dendritic cell-derived, or oncolytic virus therapy) is administered to a subject with cancer. In some embodiments, an immune system modulator (e.g., cytokines, BCG, and immunomodulatory drugs (also known as biological response modulators)) is administered to a subject with cancer. In some embodiments, an ICI monotherapy (e.g., antibody), T-cell transfer therapy (e.g., CAR T-cell therapy and TIL therapy), a monoclonal antibody (also known as a therapeutic antibody), a cancer treatment vaccine (e.g., tumor cell-derived or dendritic cell-derived oncolytic virus therapy), an immune system modulator (e.g., one or more of cytokines, BCG, and immunomodulatory drugs (also known as biological response modulators)) is administered to a subject with cancer.

[0280] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0281] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0282] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0283] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0284] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0285] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0286] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0287] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0288] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0289] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0290] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0291] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0292] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0293] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0294] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting the bone marrow immunosuppressive checkpoint, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, LAIR1, VSIG4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the ICI; and (iii) The therapeutic agent targeting the bone marrow immunosuppressive checkpoint is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0295] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0296] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0297] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0298] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0299] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0300] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, E CE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PAPPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN, and WARS, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0301] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more biomarkers selected from: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent alone or in combination with the ICI; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the ICI to the subject who has been determined to have a response score.

[0302] In some embodiments, this disclosure provides a method for treating a subject suffering from cancer, comprising: (i) Identifying the subject as potentially unresponsive to ICI monotherapy administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of an immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers comprises one or more of the following biomarkers: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN, and (b) Compare the amount or level of the first set of the biomarkers at the two or more different time points to determine a non-response score, wherein a diagnostic accuracy (AUC) of at least 0.7 indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: LILRB4, AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8, and (b) Comparing the amounts or levels of a second set...

Claims

1. A method of providing a therapeutic agent targeting LILRB4 to treat a subject's cancer, comprising: (i) Identifying the subject as unlikely to respond to single therapy with an immune checkpoint inhibitor administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers includes one or more of the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B; and (b) Comparing the amount or level of the first set of biomarkers at two or more different time points to determine a non-response score, wherein the non-response score indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent, alone or in combination with the immune checkpoint inhibitor; and (iii) The subject’s cancer is treated by administering the LILRB4-targeting therapeutic agent alone or in combination with the immune checkpoint inhibitor.

2. A method for identifying subjects unresponsive to monotherapy with an immune checkpoint inhibitor for administering a therapeutic agent targeting LILRB4, comprising: (i) Identifying the subject as unlikely to respond to single therapy with an immune checkpoint inhibitor administered to the subject, including: (a) Providing the amount or level of a first set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the first set of biomarkers includes one or more of the following: CA6, CDNF, MIA, MYOC, NEFL, and TCL1B; and (b) Comparing the amount or level of the first set of biomarkers at two or more different time points to determine a non-response score, wherein the non-response score indicates that the subject is unlikely to respond to the immune checkpoint inhibitor monotherapy; and (ii) Identifying the subject as potentially responsive to a therapeutic agent targeting LILRB4, including: (a) Providing the amount or level of a second set of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the second set of biomarkers comprises one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4, and (b) Comparing the amounts or levels of a second set of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent, alone or in combination with the immune checkpoint inhibitor; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the immune checkpoint inhibitor to the subject who has been determined to have a response score.

3. The method of any one of claims 1 to 2, wherein the immune checkpoint inhibitor monotherapy targets PD-1, PD-L1, CTLA4, LAG3, or any combination thereof.

4. The method of any one of claims 1 to 3, wherein the immune checkpoint inhibitor monotherapy is an antibody.

5. The method of claim 4, wherein the antibody is ipilimumab, nivolumab, renalalimab, pembrolizumab, atezolizumab, durvalumab, avelumab, simipremab, or dotalimab.

6. The method of any one of claims 1 to 5, wherein the first set of biomarkers comprises CA6, CDNF, MIA, MYOC, NEFL, and TCL1B.

7. The method of any one of claims 1 to 5, wherein the first set of biomarkers comprises one or more of the following: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PA PPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.

8. The method of any one of claims 1 to 5, wherein the first set of biomarkers comprises at least six of the following: ADAM22, ADAMTS8, AMTS8, ANGPT2, AOC1, BCL2L11, BMP4, BRK1, CA6, CCL13, CCL25, CD14, CD34, CDH17, CDNF, CERT, CES3, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FBP1, FRZB, GBP2, GFBP2, GLT8D2, GPR37, HGF, HMBS, IGFBP2, IL5, IL6, ITGB6, ITM2A, KRT5, LILRB4, MIA, MMP13, MMP3, MMP8, MYOC, NEFL, NID1, NOS3, NRP1, PAEP, PA PPA, PRTG, PSPN, PTGDS, SFTPD, SMOC1, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TGREM2, TINAGL1, TNC, TNFRSF10B, TNFSF14, VASN and WARS.

9. The method of any one of claims 1 to 5, wherein the first set of biomarkers comprises one or more of the following: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN.

10. The method of any one of claims 1 to 5, wherein the first set of biomarkers comprises at least six of the following: ADAM22, BMP4, CA6, CCL25, CDH17, CDNF, CES3, GBP2, HGF, HMBS, IL5, IL6, ITGB6, KRT5, MIA, MMP13, MMP3, MYOC, NEFL, NID1, NRP1, PAEP, PTGDS, SFTPD, SMOC1, TCL1B, TGREM2, TNC, TNFRSF10B, TNFSF14, and VASN.

11. The method of any one of claims 1 to 5, wherein the first set of biomarkers comprises one or more of the following: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.

12. The method of any one of claims 1 to 5, wherein the first set of biomarkers comprises at least six of the following: AMTS8, ANGPT2, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CERT, CLEC4A, CPVL, CSF3, CTSF, CTSL, DKK4, ECE1, ENG, FRZB, GFBP2, GLT8D2, ITGB6, LILRB4, MIA, MMP8, MYOC, NEFL, PAEP, PAPPA, PRTG, PSPN, TCL1A, TCL1B, TCN2, TDGF1, TFPI, TINAGL1, and WARS.

13. The method of any one of claims 1 to 5, wherein the first set of biomarkers comprises one or more of the following: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

14. The method of any one of claims 1 to 5, wherein the first set of biomarkers comprises at least six of the following: ADAMTS8, ANGPT2, AOC1, BCL2L11, BRK1, CA6, CCL13, CD14, CD34, CDNF, CLEC4A, CPVL, DKK4, ECE1, FBP1, GPR37, IGFBP2, ITM2A, LILRB4, MIA, MMP13, MMP8, MYOC, NEFL, NOS3, PAPPA, PSPN, TCL1A, TCL1B, TCN2, TFPI, TINAGL1, VASN, and WARS.

15. The method of any one of claims 1 to 14, wherein the second set of said biomarkers comprises at least four of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4.

16. The method of any one of claims 1 to 14, wherein the second set of biomarkers comprises 2 to 13 of the following biomarkers: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4.

17. The method of any one of claims 1 to 14, wherein the second set of biomarkers comprises AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4.

18. The method of any one of claims 1 to 17, wherein the second set of said biomarkers further comprises LAIR1 and VSIG4.

19. The method of any one of claims 1 to 18, wherein the first set of said biomarkers comprises proteins.

20. The method of claim 19, wherein (i) (a) comprises a first kit for detecting the biomarker in the biological sample by enzyme-linked immunosorbent assay (ELISA) or proximity extension assay (PEA).

21. The method of any one of claims 1 to 21, wherein the second set of said biomarkers comprises proteins.

22. The method of claim 21, wherein (ii) (a) comprises a second kit for detecting the biomarker in the biological sample by enzyme-linked immunosorbent assay (ELISA) or proximity extension assay (PEA).

23. The method of any one of claims 1 to 22, wherein the first set of said biomarkers comprises nucleic acid molecules.

24. The method of claim 23, wherein (i) (a) comprises a first kit for detecting the biomarker in the biological sample by means of nucleic acid hybridization assay, nucleic acid amplification assay or sequencing.

25. The method of any one of claims 1 to 24, wherein the second set of said biomarkers comprises nucleic acid molecules.

26. The method of claim 25, wherein (ii) (a) comprises a second kit for detecting the biomarker in the biological sample by means of nucleic acid hybridization assay, nucleic acid amplification assay or sequencing.

27. The method of any one of claims 1 to 26, wherein the therapeutic agent targeting LILRB4 is an antibody, nucleic acid molecule, protein therapeutic agent, cell therapy, or small molecule.

28. The method of claim 27, wherein the therapeutic agent targeting LILRB4 is an antibody.

29. The method of any one of claims 1 to 28, wherein the biological sample is a blood sample, serum sample, or plasma sample.

30. The method of claim 29, wherein the biological sample is a plasma sample.

31. The method of any one of claims 1 to 30, wherein the at least one subsequent time point is prior to clinical readout.

32. The method of any one of claims 1 to 31, wherein the first set of biomarkers and the second set of biomarkers are determined at at least two subsequent time points.

33. The method of any one of claims 1 to 32, wherein the amount or level of the first set of biomarkers increases between the first time point and the at least one subsequent time point.

34. The method of claim 33, wherein the increase in the amount or level of the first set of biomarkers between the first time point and the at least one subsequent time point is statistically significant.

35. The method of any one of claims 1 to 34, wherein the amount or level of the second set of biomarkers increases between the first time point and the at least one subsequent time point.

36. The method of claim 35, wherein the increase in the amount or level of the first set of biomarkers between the first time point and the at least one subsequent time point is statistically significant.

37. The method of any one of claims 1 to 36, wherein the non-reaction score has a diagnostic accuracy (AUC) of at least 0.7, optionally wherein the diagnostic accuracy is at least 0.

8.

38. The method of any one of claims 1 to 37, wherein the non-response score indicates that the subject will not respond to the immune checkpoint inhibition therapy.

39. The method of any one of claims 1 to 38, wherein the therapeutic agent targeting LILRB4 improves the response of the subject to the immune checkpoint inhibitor monotherapy.

40. A kit suitable for performing the method of any one of claims 1 to 39, comprising (i) one or more reagents for detecting the amount or level of a first set of the biomarkers, and (ii) instructions for detecting the amount or level of the first set of the biomarkers in biological samples obtained from a subject at two or more different time points.

41. The kit of claim 40, comprising (iii) one or more reagents for detecting the amount or level of a second set of the biomarkers, and (iv) instructions for detecting the amount or level of the second set of the biomarkers in biological samples obtained from the subject at two or more different time points.

42. A kit suitable for performing the method of any one of claims 1 to 39, comprising (i) one or more reagents for detecting the amount or level of a second set of the biomarker, and (ii) instructions for detecting the amount or level of the second set of the biomarker in biological samples obtained from a subject at two or more different time points.

43. The kit of claim 42, comprising (iii) one or more reagents for detecting the amount or level of a first set of the biomarkers, and (iv) instructions for detecting the amount or level of the first set of the biomarkers in biological samples obtained from the subject at two or more different time points.

44. The kit according to any one of claims 40 to 43, comprising instructions for identifying that the subject is unlikely to respond to immune checkpoint inhibitor monotherapy.

45. The kit of any one of claims 40 to 44, comprising instructions for identifying the potential response of the subject to combination therapy with a therapeutic agent targeting LILRB4.

46. ​​The kit according to any one of claims 40 to 45, wherein the biological sample is a blood sample, serum sample, or plasma sample.

47. A method for identifying subjects who are unresponsive to or predicted to be unresponsive to immune checkpoint inhibitor monotherapy for administering a therapeutic agent targeting LILRB4, comprising: (i) Provide the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is before administration of the immune checkpoint inhibitor monotherapy and at least one subsequent time point is from about 3 weeks to about 6 months after administration of the immune checkpoint inhibitor monotherapy, wherein the suite of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8 and LILRB4; (ii) Comparing the amounts or levels of the biomarkers at two or more different time points to determine a response score, wherein the response score indicates that the subject may respond to the LILRB4-targeting therapeutic agent, alone or in combination with the immune checkpoint inhibitor; and (iii) The LILRB4-targeting therapeutic agent is administered alone or in combination with the immune checkpoint inhibitor to the subject who has been determined to have a response score.

48. The method of claim 47, wherein the therapeutic agent targeting LILRB4 is an antibody, nucleic acid molecule, protein therapeutic agent, cell therapy, or small molecule.

49. The method of claim 48, wherein the therapeutic agent targeting LILRB4 is an antibody.

50. The method of any one of claims 47 to 49, wherein the set of biomarkers comprises at least four of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4.

51. The method of any one of claims 47 to 49, wherein the set of biomarkers comprises 2 to 13 of the following biomarkers: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4.

52. The method of any one of claims 47 to 49, wherein the set of biomarkers comprises AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, MMP8, and LILRB4.

53. The method of any one of claims 47 to 52, wherein the kit of biomarkers further comprises LAIR1 and VSIG4.

54. A method for identifying a subject for administration of a therapeutic agent targeting a bone marrow immunosuppressive checkpoint, comprising: (i) Provide subjects who are identified as non-responders to immune checkpoint inhibitor monotherapy or who are predicted to be non-responders to immune checkpoint inhibitor monotherapy; (ii) Determine the amount or level of a suite of biomarkers in biological samples obtained from the subject at two or more different time points, wherein the first time point is prior to administration of the immune checkpoint inhibitor monotherapy, and at least one subsequent time point is approximately 3 weeks to approximately 6 months after administration of the immune checkpoint inhibitor, wherein the suite of biomarkers includes one or more of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8; (iii) Comparing the amount or level of one or more proteins at two or more different time points to determine a response score, wherein the response score is correlated with the subject's potential response to the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the immune checkpoint inhibitor; and (iv) Administer the therapeutic agent targeting the bone marrow immunosuppressive checkpoint, alone or in combination with the immune checkpoint inhibitor, to the subject who has been determined to have the response score.

55. The method of claim 54, wherein the set of biomarkers comprises at least four of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

56. The method of claim 54, wherein the set of biomarkers comprises 2 to 12 of the following: AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

57. The method of claim 54, wherein the set of biomarkers comprises AZU1, CCL3, CST7, HAVCR2, IFNG, IL10, IL1RL1, IL4R, IL6, LBP, MIF, and MMP8.

58. The method of any one of claims 54 to 57, wherein the set of biomarkers further comprises at least one of the following: LAIR1, LILRB4, and VSIG4.

59. The method of claim 58, wherein the set of biomarkers further comprises LAIR1, LILRB4 and VSIG4.

60. The method of any one of claims 54 to 59, wherein the therapeutic agent targeting the bone marrow immunosuppressive checkpoint is an antibody, nucleic acid molecule, protein therapeutic agent, cell therapy, or small molecule.

61. The method of any one of claims 47 to 60, wherein the immune checkpoint inhibitor targets PD-1, PD-L1, CTLA4, LAG3, or any combination thereof.

62. The method of claim 61, wherein the immune checkpoint inhibitor is an antibody.

63. The method of claim 62, wherein the antibody is ipilimumab, nivolumab, renalalimumab, pembrolizumab, atezolizumab, durvalumab, avelumab, simipremab, or dotalimab.

64. The method of any one of claims 47 to 63, wherein the set of biomarkers comprises proteins.

65. The method of claim 64, wherein determining the amount or level of the biomarker set comprises detecting the biomarker set in the biological sample by enzyme-linked immunosorbent assay (ELISA) or proximity extension assay (PEA).

66. The method of any one of claims 47 to 65, wherein the kit of biomarkers comprises nucleic acid molecules.

67. The method of claim 66, wherein determining the amount or level of the biomarker set comprises detecting the biomarker set in the biological sample by means of nucleic acid hybridization assay, nucleic acid amplification assay, or sequencing.

68. The method of any one of claims 47 to 67, wherein the biological sample is a blood sample, serum sample, or plasma sample.

69. The method of claim 68, wherein the biological sample is a plasma sample.

70. The method of any one of claims 47 to 69, wherein the at least one subsequent time point is prior to clinical readout.

71. The method of any one of claims 47 to 70, wherein the set of biomarkers is determined at at least two subsequent time points.

72. The method of any one of claims 47 to 71, wherein the amount or level of the set of biomarkers increases between the first time point and the at least one subsequent time point.

73. The method of claim 72, wherein the increase in the amount or level of the set of biomarkers between the first time point and the at least one subsequent time point is statistically significant.

74. The method of any one of claims 47 to 73, wherein the response score indicates that the subject will respond to the combination therapy.

75. A kit suitable for performing the method of any one of claims 47 to 74, comprising (i) one or more reagents for detecting the amount or level of the kit of said biomarkers, and (ii) instructions for detecting the amount or level of the kit of said biomarkers in biological samples obtained from a subject at two or more different time points.

76. The kit of claim 75, wherein the description includes a step of identifying the subject as potentially responsive to a combination therapy of a therapeutic agent targeting LILRB4 or a therapeutic agent targeting the bone marrow immunosuppressive checkpoint and an immune checkpoint inhibitor.

77. The kit of claim 75 or claim 76, wherein the biological sample is a blood sample, serum sample or plasma sample.

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