Methods of predicting and treating immunotherapy toxicity based on immune cell populations

Abstract

The present disclosure relates generally to compositions and methods for predicting or diagnosing an immune-related adverse event (irAE) before, during, or after immune checkpoint inhibitor (ICI) treatment in a cancer subject. The methods include assessing transcripts, autoantibody levels, cytokine levels, and immune cells. The irAE may be ICI-associated myositis, ICI-associated myocarditis, or ICI-associated myositis and myocarditis.

Description

[0001] CROSS-REFERENCE TO RELATED APPLICATIONS

[0002] This application claims the benefit of U.S. Provisional Patent Application No. 63 / 382,972, entitled “Methods for Predicting and Treating Immunotherapy Toxicity Based on Biomarkers Including RNA,” filed on November 9, 2022, and U.S. Provisional Patent Application No. 63 / 503,946, entitled “Methods for Predicting and Treating Immunotherapy Toxicity Based on Biomarkers Including RNA,” filed on May 23, 2023, the contents of which are incorporated herein by reference in their entireties.

[0003] Government Funding Statement

[0004] This invention was made with support from the National Institutes of Health (NIH) under Grant Nos. AI156189 and CA201543. The government may have certain rights in this invention.

[0005] background

[0006] 1. Field

[0007] The present disclosure relates to the identification of biomarkers for predicting, diagnosing, or monitoring immune-related adverse events associated with immune checkpoint inhibitor therapy.

[0008] 2. Background

[0009] Immune-related adverse events (irAEs) can affect virtually any organ system during and after treatment with immune checkpoint inhibitors (ICIs). Although rare, ICI-associated myositis and myocarditis can be potentially fatal toxicities. Understanding the etiology of these cases and their pathophysiology, which differ from non-ICI-associated inflammatory myopathies and myocarditis, is crucial for optimal monitoring and treatment of patients receiving ICIs. Summary of the Invention

[0010] In some aspects, the present disclosure provides a method for predicting the risk of an immune-related adverse event (irAE) associated with immune checkpoint inhibitor (ICI) treatment in a subject and / or a method for diagnosing an immune-related adverse event (irAE) associated with immune checkpoint inhibitor (ICI) treatment in a subject, comprising: providing a sample from the subject, assessing the level of one or more transcripts in the sample, and predicting the risk of irAE in the subject / diagnosing irAE in the subject, wherein,

[0011] If before ICI treatment (baseline), leukocyte immunoglobulin like receptor B4 (LILRB4), cytokine inducible SH2 containing protein (CISH), poly (ADP-ribose) polymerase family member 9 (PARP9), ring finger protein 145 (RNF145), asialoglycoprotein receptor 2 (ASGR2), solute carrier family 16 member 13 (SLC16A13), lysophosphatidic acid receptor 6 (LPAR6), GTPase, IMAP family member 7 (GIMAP7), CXC motif chemokine receptor 6 (CXC motif chemokine receptor 6) Elevated transcript levels of one or more of CXCR6 (CXCR6), dehydrogenase / reductase 9 (DHRS9), Fc gamma receptor Ic, pseudogene (FCGR1CP), and / or ankyrin repeat domain 34B (ANKRD34B) compared to a control sample; and / or

[0012] Amphiregulin (AREG), epiregulin (EREG), oncostatin M (OSM), cysteine and serine rich nuclear protein 1 (CSRNP1), DNA damage inducible transcript 4 (DDIT4), IL-10 (interleukin 10), prostaglandin-endoperoxide synthase (PTGS2), dual specificity phosphatase 1 (DUSP1), CXC chemokine receptor type 4 (CXCR4), nuclear factor, interleukin 3 regulated (NFIL3), Fos proto-oncogene, AP-1 transcription factor subunit (FOS), NFKB inhibitory factor α (NFKB inhibitor alpha) (NFKBIA), PPP1R15A (protein phosphatase 1 regulatory subunit 15A), CD79A, JUNB proto-oncogene, AP-1 transcription factor subunit (JUNB) (JUNB), CXC motif chemokine ligand 8 (CXCL8), early growth response 1 (EGR1), G0 / G1 switch 2 (G0S2), paired box 8 (PAX8), activating transcription factor 6beta (ATF6B), PAX8 antisense RNA1 (PAX8-AS1), RNA, variant U1 smallnuclear 19 (RNA, variant U1 smallnuclear19)(RNVU1-19), vitelline membrane outer layer 1 homolog (VMO1), heparin binding EGF like growth factor (HBEGF), coiled-coil domain containing 144A (CCDC144A), shisa family member 8 (SHISA8), nuclear receptor subfamily 4 group A member 2 (NR4A2), prostaglandin E synthase (PTGES), synapsin I (SYN1), CXC motif chemokine ligand 2 (CXCL2), peripheral myelin protein 22 (PMP22), CD83, early growth response 3 (EAR3 ... 3)(EGR3), NUAK family kinase 1 (NUAK1), nocturnin (NOCT), atonal bHLH transcription factor 8 (ATOH8), polo like kinase 2 (PLK2), inhibitor of DNA binding 1 (ID1), adrenoceptor beta1 (ADRB1), snail family transcriptional repressor 1 (SNAI1), notch receptor 3 (NOTCH3), activating transcription factor 3 (ATF3), dual specificity phosphatase 2 (DUSP2), period circadian regulator 1 (PER1), TNF superfamily member 9 (TNF superfamilymember 9) (TNFSF9), MAF bzip transcription factor F (MAFF), microRNA4420 (MIR4420), glutathione peroxidase (GPX3), TNF alpha induced protein 3 (TNFAIP3), potassium voltage-gated channel modifier subfamily G member 1 (KCNG1), prostaglandin-endoperoxidase synthase 2 (PTGS2), A-kinase anchoring protein 5 (AKAP5), dual specificity phosphatase 1 (DUSP1), diacylglycerol kinase kappa (DMG-1) kappa) (DGKK), beta-1,4,-N-acetylgalactosaminyltransferase 3 (B4GALNT3), tribbles pseudokinase 1 (TRIB1), phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1), CXC motifchemokine receptor 4 (CXCR4), tumor protein p53inducible nuclear protein 2 (TP53INP2), nuclear factor, interleukin 3regulated (NFIL3), dual specificity phosphatase 4 (DUSP4), NFKB inhibitor α (NFKB inhibitor alpha)(NFKBIA), arginine vasopressin induced protein 11)(AVPI1), CD79a, ADP ribosylation factor like GTPase 4D(ARL4D), joining chain of multimeric IgAand IgM(JCHAIN), BTG anti-proliferation factor 2(BTG2), TLE family member 1, transcriptional corepressor(TLE1), nuclear transport factor 2like export factor1(NXT1), transducer of ERBB2,1(TOB1), phosphodiesterase 4D(PDE4D), DNAJ heat shock protein family member B1(DNAJB1), AT-rich interaction domain 5B(AT-rich interaction domain 5B) (ARID5B), G protein-coupled receptor 153 (GPR153), KLF transcription factor 9 (KLF9), SBDS ribosome maturation factor (SBDS), immediate early response 2 (IER2), TSC22 domain family member 3 (TSC22D3), GABAA type Areceptor associated protein like 1 (GABARAPL1), JunD proto-oncogene, AP-1 transcription factor subunit (JUND), RUNX family transcription factor 3 (RUNX3), BABAM2 antisense RNA1 (BABAM2 antisense RNA1)The transcript level of one or more of creatine phosphate-binding protein (CRP) 1 (BRE-AS1), putative salt inducible kinas 1B (LOC102724428), FAM46C (FAM46C), and / or general receptor for phosphoinositides 1-associated scaffold protein (GRASP) is lower than the transcript level of the control sample,

[0013] The subject is then predicted to have a high risk of developing an irAE or is diagnosed with an irAE.

[0014] Further provided is a method for monitoring the risk of irAEs associated with ICI treatment in a subject, the method comprising: providing a sample from the subject, assessing the level of one or more transcripts in the sample, and monitoring the risk of the subject developing an irAE, wherein:

[0015] If before ICI treatment (baseline), the level of one or more transcripts of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, ANKRD34B, and / or FCGR1CP is elevated compared to the level of the transcript in a control sample; and / or

[0016] AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3 in the samples of the subjects. , TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is lower than the transcript level of the control sample, then the subject is predicted to have a high risk of developing irAE.

[0017] In some aspects, irAEs include ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

[0018] In some aspects of the method, assessment of transcript levels is performed prior to ICI treatment.

[0019] In some aspects, a subject is predicted to be at high risk for developing an irAE if, before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated compared to the transcript level in a control sample.

[0020] In some aspects, a subject is predicted to be at high risk for developing an irAE if, before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, GIMAP7, CXCR6, DHRS9, ANKRD34B, and / or FCGR1CP is elevated compared to the transcript level in a control sample.

[0021] In some aspects, if before ICI treatment, AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGE If the transcript level of one or more of S, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing irAE.

[0022] In some aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

[0023] In some aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

[0024] In some aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

[0025] In some aspects, if before ICI treatment (baseline), the transcript level of PARP9 is elevated compared to the transcript level in the control sample; and / or before ICI treatment (baseline), the transcript level of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

[0026] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2 is elevated compared to the transcript level in a control sample; and / or before ICI treatment (baseline), KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGK If the transcript level of one or more of K, PTGES, CSRNP1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1 is lower than the transcript level in the control sample, the subject is predicted to be at high risk for irAE.

[0027] In some aspects, the sample is whole blood, serum, plasma, cerebrospinal fluid, pleural effusion, pericardial effusion, peritoneal effusion, bone marrow or tissue, urine, cerebrospinal fluid (CSF), or other body fluid.

[0028] In some aspects, the ICI therapy is administered as part of a cancer treatment.

[0029] In some aspects, the ICI treatment comprises administering an inhibitor of PD-1, PD-L1, TIM-3, LAG-3, CTLA-4, CSF-1R, or any combination thereof.

[0030] In some aspects, assessing transcript levels (step b) comprises RNA sequencing, nanopore sequencing, Nanostring, multiplex RT-PCR, single-plex RT-PCR, NASBA, fluorescence measurement, or spectrophotometry.

[0031] In some aspects, the method further comprises assessing the expression of one or more of Mi-2, GAD65, myosin, thyroglobulin, and / or TPO in the sample from the subject.

[0032] In some aspects, evaluating comprises identifying whether expression of one or more autoantibodies is elevated in a sample from the subject compared to their abundance in a control sample.

[0033] In some aspects, the method further comprises assessing the expression of one or more of CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, and / or CXCL10 in a sample from the subject.

[0034] In some aspects, evaluating comprises identifying whether expression of one or more cytokines is elevated in a sample from the subject compared to expression in a control sample.

[0035] In some aspects, the method further comprises assessing the abundance of one or more of PD-L+ naive B cells, switched memory B cells, and / or CTLA-4+ monocytes in the sample from the subject.

[0036] In some aspects, the assessment includes identifying whether the abundance of one or more of PD-L+ naive B cells and / or switched memory B cells is reduced in the subject sample compared to the abundance in the control sample, and / or CTLA-4 + Whether the abundance of monocytes is elevated compared to that in control samples.

[0037] In some aspects, the method further comprises repeating steps (a)-(c) at a second time point, thereby enabling determination of a change in the risk of the subject developing an irAE compared to a control sample and / or a diagnosis of an irAE in the subject's sample.

[0038] In some aspects, the method further comprises predicting that the subject has a low risk if,

[0039] Before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, ANKRD34B, and / or FCGR1CP is lower than or equivalent to the transcript level in a control sample; and / or

[0040] In ICI treatment, AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, and MIR44 20, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP transcript levels are increased or comparable to transcript levels in a control sample.

[0041] In some aspects, the method further comprises treating the subject with ICI therapy when the subject is predicted to have a low risk of developing an irAE.

[0042] In some aspects, the method further comprises treating a subject predicted to be at high risk for developing an irAE with a non-ICI therapy or with an ICI therapy and an irAE-mitigating therapy, wherein the irAE-mitigating therapy is selected from a corticosteroid (e.g., prednisone, methylprednisolone, dexamethasone, budesonide), a TNF inhibitor (e.g., infliximab), or a hormone replacement (e.g., hydrocortisone, levothyroxine), a CXCL8 inhibitor (e.g., repertaxin), or any combination thereof.

[0043] In some aspects, the present disclosure also includes a method for treating a cancer subject, the method comprising: (a) providing a sample from the subject; (b) assessing the level of one or more transcripts in the sample; (c) predicting the risk of the subject developing an irAE, wherein the subject is diagnosed as low risk when the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, ANKRD34B, and / or FCGR1CP is lower than or equal to the transcript level in the control sample; and the subject is diagnosed as high risk when the transcript level of one or more of AREG, EREG, OSM, CSRN1 is lower than or equal to the transcript level in the control sample. P1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3 , DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GA When the transcript level of one or more of BARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is elevated or comparable to the transcript level in the control sample, the subject is diagnosed as low risk; when the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, ANKRD34B, and / or FCGR1CP is higher than the transcript level in a control subject without irAEs or a healthy subject, the subject is diagnosed as high risk;and / or when AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES , SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1 , TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXC R4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP transcript levels in the sample are lower than the transcript levels in the control sample, and the subject is diagnosed with high risk; (d) treating the subject with the following methods: (i) if the subject is diagnosed with a low risk of developing an irAE, using ICI therapy; (ii) if the subject is diagnosed with a high risk of developing an irAE, using non-ICI therapy; or (iii) if the subject is diagnosed with a high risk of developing an irAE, using ICI therapy and irAE mitigation therapy.;

[0044] In some aspects, irAEs include ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

[0045] In some aspects, a subject is predicted to be at high risk for developing an irAE if, before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated compared to the transcript level in a control sample.

[0046] In some aspects, a subject is predicted to be at high risk for developing an irAE if, before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, GIMAP7, CXCR6, DHRS9, ANKRD34B, and / or FCGR1CP is elevated compared to the transcript level in a control sample.

[0047] In some aspects, if before ICI treatment, AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTG If the transcript level of one or more of ES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing irAE.

[0048] In some aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

[0049] In some aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

[0050] In some aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

[0051] In some aspects, if the transcript level of PARP9 is elevated before ICI treatment (baseline) compared to the transcript level of a control sample, the subject is predicted to be at high risk for an irAE; and / or if the transcript level of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3 is lower than the transcript level of a control sample before ICI treatment (baseline), the subject is predicted to be at high risk for an irAE.

[0052] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2 is elevated compared to the transcript level in a control sample; and / or if before ICI treatment (baseline), KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DG If the transcript level of one or more of KK, PTGES, CSRNP1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1 is lower than the transcript level in the control sample, the subject is predicted to be at high risk for irAE.

[0053] In some aspects, the evaluating further comprises detecting the expression of one or more of CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, and / or CXCL10 in the sample from the subject.

[0054] In some aspects, evaluating comprises identifying whether expression of one or more cytokines is elevated in a sample from the subject compared to expression in a control sample.

[0055] In some aspects, the assessing further comprises detecting the expression of one or more of Mi-2, GAD65, myosin, thyroglobulin, and / or TPO in the sample from the subject.

[0056] In some aspects, evaluating comprises identifying whether expression of one or more autoantibodies is elevated in a sample from the subject compared to expression in a control sample.

[0057] In some aspects, the method further comprises assessing the abundance of one or more of PD-L+ naive B cells, switched memory B cells, and / or CTLA-4+ monocytes in the sample from the subject.

[0058] In some aspects, the assessment includes identifying whether the abundance of one or more of PD-L+ naive B cells and / or switched memory B cells is reduced in the subject sample as compared to their abundance in a control sample, and / or whether the abundance of CTLA-4+ monocytes is increased as compared to their abundance in a control sample.

[0059] In some aspects, ICI therapy comprises administering an inhibitor of PD-1, PD-L1, TIM-3, LAG-3, CTLA-4, CSF-1R, or any combination thereof.

[0060] Also provided herein is a method for identifying the presence of at least one differentially expressed transcript associated with irAE in a biological sample of a cancer subject, the method comprising: providing a sample from the subject, assessing the transcript level in the sample, wherein the assessment comprises detecting whether the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, ANKRD34B, and / or FCGR1CP is higher than that in a control sample. and / or transcript levels of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXC L2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MI R4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP 4. Whether the transcript level of one or more of NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is lower than the transcript level in the control sample.

[0061] In some aspects, the subject is planned to receive treatment with an immune checkpoint inhibitor (ICI).

[0062] In some aspects, irAEs include ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

[0063] In some aspects, the method further comprises detecting the expression of one or more of CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL, 9 and / or CXCL10 in a sample from the subject.

[0064] In some aspects, evaluating comprises identifying whether expression of one or more cytokines is elevated in a sample from the subject compared to expression in a control sample.

[0065] In some aspects, the method further comprises detecting the expression of one or more of Mi-2, GAD65, myosin, thyroglobulin, and / or TPO in a sample from the subject.

[0066] In some aspects, evaluating comprises identifying whether expression of one or more autoantibodies is elevated in a sample from the subject compared to expression in a control sample.

[0067] In some aspects, the method further comprises assessing the abundance of one or more of PD-L+ naive B cells, switched memory B cells, and / or CTLA-4+ monocytes in the sample from the subject.

[0068] In some aspects, the assessment includes identifying whether the abundance of one or more of PD-L+ naive B cells and / or switched memory B cells is reduced in the subject sample compared to expression in a control sample, and / or whether the abundance of CTLA-4+ monocytes is increased compared to abundance in a control sample.

[0069] In some aspects, the assessment includes determining a baseline or pre-treatment profile that is associated with future toxicities.

[0070] In some aspects, the baseline or pre-treatment profile includes elevated transcript levels of one or more of LILRB4, CISH, and / or PARP9 compared to transcript levels in a control sample.

[0071] In some aspects, the baseline or pre-treatment profile includes elevated transcript levels of one or more of LILRB4, CISH, GIMAP7, CXCR6, DHRS9, ANKRD34B, and / or FCGR1CP compared to transcript levels in a control sample.

[0072] In some aspects, the baseline or pre-treatment profile includes, compared to transcript levels in a control sample, AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC Decreased transcript levels of one or more of 144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP.

[0073] In some aspects, the baseline or pre-treatment profile includes decreased transcript levels of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB, compared to the transcript levels in a control sample.

[0074] In some aspects, the baseline or pre-treatment profile includes decreased transcript levels of one or more of AREG, EREG, CXCL8, EGR1, GOS2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144, and / or SHISA8, as compared to the transcript levels in a control sample.

[0075] In some aspects, the baseline or pre-treatment profile includes decreased transcript levels of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9, as compared to the transcript levels in a control sample.

[0076] In some aspects, the baseline or pre-treatment profile includes elevated transcript levels of PARP9, compared to the transcript levels in a control sample; and / or decreased transcript levels of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3, compared to the transcript levels in a control sample.

[0077] In some aspects, the baseline or pre-treatment profile includes: elevated transcript levels of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2, compared to transcript levels in a control sample; and / or elevated transcript levels of KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, compared to transcript levels in a control sample. , EREG, AREG, DGKK, PTGES, CSRNP1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1.

[0078] In some aspects, the control sample is obtained from a subject at low risk for developing an irAE.

[0079] In some aspects, the transcript levels of the disclosed methods are relative transcript levels. BRIEF DESCRIPTION OF THE DRAWINGS

[0080] Figure 1 Depicted are contour plots for CyTOF analysis showing surface markers defined within clusters (immune cell subsets).

[0081] Figures 2A-2K Cytokine profiles of myositis / myocarditis cases and nontoxic controls are shown. Figure 2A Baseline cytokines are described. Figures 2B-2H Baseline cytokines that differed significantly according to the presence and grade of myositis / myocarditis were described. Figure 2IThe changes in cytokines after ICI initiation were shown, with significant differences depending on the occurrence of myositis / myocarditis. Figures 2J-2K Figure 3. Cytokine changes after ICI initiation, with significant differences according to the occurrence and grade of myositis / myocarditis. ICI: immune checkpoint inhibitor; irAE: immune-related adverse event; NT: nontoxicity.

[0082] Figures 3A-3F Figures 3A-3F The autoantibody profiles of myositis / myocarditis cases and nontoxic controls were described. Figure 3A Baseline autoantibodies are shown. Figures 3B-3F Significant differences in baseline autoantibodies were shown according to the occurrence and grade of myositis / myocarditis.

[0083] Figures 4A-4C Immune cell profiles of myositis / myocarditis cases and nontoxic controls were described. Figure 4A The figure shows 28 clusters (immune cell subsets) identified using CyTOF. Four immune cell subsets were shown to be significantly different between irAE cases and non-toxic controls. Figure 4B Results showed that compared with the non-toxic control group, in the pre-treatment baseline samples, irAE cases had decreased PD-L1+ naive B cells (P = 0.004), decreased converted memory B cells (P = 0.03), and increased CTLA4+ monocytes (P = 0.03) (Mann-Whitney test). Figure 4C We demonstrated that after initiation of ICI, irAE cases had greater increases in PD-L1+ naive B cells (P = 0.03), switched memory B cells (P = 0.02), and CXCR3+ CD8 T cells (P = 0.01) (two-way ANOVA).

[0084] Figures 5A-5D Using bulk RNA sequencing analysis, the transcriptional profiles of myositis / myocarditis cases (N=4) and non-toxic controls (N=3) were characterized. Figure 5A Shown is a principal component analysis (PCA) demonstrating differences in pre-treatment baseline transcriptional profiles according to the occurrence of irAEs. Figure 5B A volcano plot is depicted showing differentially expressed genes (DEGs) between irAE cases and non-toxic controls in baseline samples. Of the 14,174 genes, 94 showed statistically significant differences, including 12 upregulated genes and 82 downregulated genes (false discovery rate (FDR) < 0.05). Among them, 7 upregulated genes (red) and 75 downregulated genes (blue) met the condition of |Log2 fold change (FC)|>1. Figure 5CA heat map of the transcriptional profiles of irAE cases and non-toxic controls in baseline samples is depicted, with eight clusters showing differences. The right side shows the most enriched terms and their FDRs for each cluster obtained from the GO_Biological_Process_2021 gene library by gene ontology (GO) analysis. Figure 5D The relative differences in expression between irAE cases and nontoxic controls are shown for 18 genes (out of 94) associated with gene sets in eight functional biological processes.

[0085] Figure 6 PCA plots of RNA-seq data before treatment baseline and after ICI initiation for irAE cases and non-toxicity cases are shown.

[0086] The accompanying drawings do not limit the present disclosure to the specific embodiments disclosed and described herein. The accompanying drawings are not necessarily drawn to scale, emphasis instead being placed upon clearly illustrating the principles of some embodiments of the present disclosure. DETAILED DESCRIPTION

[0087] The following detailed description refers to the accompanying drawings that illustrate various aspects of the present disclosure. The drawings and description are intended to describe various aspects of the present disclosure in sufficient detail to enable those skilled in the art to practice the present disclosure. Other components may be used and changes may be made without departing from the scope of the present disclosure. Therefore, the following description is not intended to be limiting.

[0088] Provided herein are methods for predicting, diagnosing, and / or monitoring immune-related adverse events (irAEs) in subjects receiving or planning to receive immune checkpoint inhibitors (ICI) therapy. The present disclosure is based on a surprising discovery that in cancer patients, at baseline or before treatment, subjects will have unique transcripts, autoantibodies, cytokines, and / or immune cell profiles related to irAEs during ICI treatment. These transcripts, autoantibodies, cytokines, and / or immune cell profiles can be used as biomarkers for predicting, diagnosing, and / or monitoring irAEs during ICI treatment, and help guide more effective cancer treatment strategies, reduce toxic side effects, especially toxic side effects associated with ICI treatment.

[0089] I. Terminology

[0090] To facilitate an understanding of the principles of the present disclosure, reference will now be made to preferred aspects and specific language will be used to describe these aspects, but it will be understood that this is not intended to limit the scope of the present disclosure and that changes and further modifications of the present disclosure, as shown herein, are as would normally occur to one skilled in the art to which the present disclosure relates.

[0091] As used herein, the articles "a" and "an" refer to one or more than one (ie, at least one) of the grammatical object of the article. For example, "an element" refers to at least one element and may include multiple elements.

[0092] "About" is used to provide flexibility for numerical range endpoints, providing that a given value can be "a little above" or "a little below" the endpoint without affecting the expected result. The term "about" in relation to a numerical value means that the value can vary by 5% or less.

[0093] In this specification, unless the context requires otherwise, the words "comprise" and "comprising" will be understood to mean the inclusion of stated components, features, elements, or steps, or groups of components, features, elements, or steps, but not the exclusion of any other integers or steps or groups of integers or steps.

[0094] As used herein, "and / or" is intended to include any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted as an alternative ("or").

[0095] As used herein, the transitional phrase "consisting essentially of" (and grammatical variations) should be construed to include the recited materials or steps, as well as those that do not materially affect the basic and novel characteristics of the claimed invention. Therefore, the term "consisting essentially of" as used herein should not be construed as equivalent to "comprising."

[0096] Furthermore, the present disclosure contemplates that, in some aspects, any feature or combination of features described herein may be excluded or omitted. For example, if the specification states that a complex includes components A, B, and C, it is specifically intended that any one of A, B, or C, or any combination thereof, may be omitted or disclaimed, individually or in any combination.

[0097] Unless otherwise indicated herein, recitation of numerical ranges in this specification is merely a shorthand method of referring individually to each separate value falling within the range, and each separate value is incorporated into this specification as if it were individually recited herein. For example, if a concentration range is recited as 1% to 50%, it is intended that values such as 2% to 40%, 10% to 30%, or 1% to 3% are specifically enumerated herein. These are only examples of what is specifically intended, and all possible combinations of values between and including the lowest and highest values enumerated are to be considered to be expressly stated in this disclosure.

[0098] As used herein, "treatment," "therapy," and / or "therapeutic regimen" refers to clinical interventions taken in response to a disease, disorder, or physiological condition that a patient exhibits or to which the patient may be susceptible. The goals of treatment include alleviating or preventing symptoms, slowing or arresting the development or worsening of a disease, disorder, or condition, and / or ameliorating the disease, disorder, or condition.

[0099] As used herein, "prevent" or "prevent" refers to eliminating or delaying the onset of, or lessening the severity of, a particular disease, disorder, or physiological condition relative to the timing and / or extent or severity of the disease, disorder, or physiological condition in the absence of intervention.

[0100] The term "effective amount" or "therapeutically effective amount" refers to an amount sufficient to produce beneficial or desired biological and / or clinical effects.

[0101] As used herein, "individual," "subject," "host," and "patient" are used interchangeably herein to refer to any mammalian subject, such as a human, pet, livestock, horse, or other animal, in need of diagnosis, treatment, prevention, or therapy. As used herein, the terms "subject" and "patient" are used interchangeably herein to refer to a human and a non-human animal. The term "non-human animal" of the present disclosure includes all vertebrates, such as mammals and non-mammals, such as non-human primates, sheep, dogs, cats, horses, cows, chickens, amphibians, reptiles, and the like. In some aspects, the subject can be a human. In other aspects, the subject can be a human in need of treatment for cancer.

[0102] As used herein, "immune-related adverse events" or "irAEs" refer to various toxicities, side effects, or problems associated with cancer immunotherapy. Immunotherapy includes the use of immunotoxins, T cell transfer, chimeric antigen receptors, antibodies, immune system modulators and immune checkpoint inhibitors, and / or other immunotherapies known to those skilled in the art.

[0103] As used herein, "immune checkpoint inhibitors" are drugs that block immune checkpoints. These checkpoints are a normal part of the immune system that prevent the immune response from being too strong. By blocking them, these drugs allow immune cells to respond more strongly to cancer, etc. The working principle of immune checkpoint inhibitors is to prevent cancer cells from shutting down T cells (white blood cells that detect infection and abnormalities). Non-limiting examples of immune checkpoint inhibitors include inhibitors of PD-1, PD-L1, TIM-3, LAG-3, CTLA-4, and CSF-1R and any combination thereof. Immune checkpoint receptors may be present on tumor cells or immune cells, such as T cells, monocytes, microglia and macrophages, without limitation. The agents advocating immune checkpoint blockade can be small chemical entities or polymers, antibodies, antibody fragments, single-chain antibodies or other antibody constructs, including but not limited to bispecific antibodies and diantibodies. Immune checkpoint inhibitors that can be used according to the present disclosure include any inhibitors that can destroy the inhibitory interaction between cytotoxic T cells and tumor cells. These inhibitors include, but are not limited to, anti-PD-1 antibodies, anti-PD-L1 antibodies, anti-CTLA4 antibodies, anti-LAG-3 antibodies, and anti-TIM-3 antibodies. Inhibitors are not necessarily antibodies and may also be small molecules or other polymers. If the inhibitor is an antibody, it may be a polyclonal, monoclonal, fragment, single chain, or other antibody variant construct. Inhibitors can target any immune checkpoint known in the art, including but not limited to CTLA-4, PDL1, PDL2, PD1, B7-H3, B7-H4, BTLA, HVEM, TIM3, GAL9, LAG3, CSF-1R, VISTA, KIR, 2B4, CD160, CGEN-15049, CHK1, CHK2, A2aR, CD28, CD86, CD69, CD48, CD113, CEACAM-1, Galectin-1, TIGIT, GPR56, CD48, GARP, PD1H, LAIR1, TIM1, TIM4 and B-7 family ligands. Combinations of inhibitors targeting a single target immune checkpoint or different inhibitors targeting different immune checkpoints can be used.Examples of immune checkpoint inhibitors include CTLA-4 blocking antibodies (ipilimumab (Yervoy), tremelimumab (Imjuno)), PD-1 inhibitors (pembrolizumab (Keytruda), nivolumab (Opdivo), cemiplimab (Libtayo), CT-011 (Pidilizumab), AMP224), L1 inhibitors (Atezolizumab (tecentriq), Avelumab (Bavencio), Durvalumab (Imfinzi), BMS-936559), Lag3 inhibitors (Relatlimab), Lag3 and PD1 inhibitor combinations (PD-1 inhibitor Nivolumab (Opdualag), OX40 inhibitor (MEDI6469), CD160 inhibitor (BY55)). Non-limiting examples of CSF-1R inhibitors include PLX3397, PLX486, RG7155, AMG820, ARRY-382, FPA008, IMC-CS4, JNJ-40346527, and MCS110. The terms "ICI treatment," "ICI therapy," "ICI compound," and the like refer to one or more ICIs (or uses thereof) disclosed herein or known to those skilled in the art.

[0104] As used herein, "transcript" or "RNA transcript" or "RNA" can be a messenger RNA (mRNA) molecule. In some aspects, the RNA can be total RNA, mRNA, pre-mRNA, or any combination thereof.

[0105] As used herein, "self-antigens" refer to normal proteins or protein complexes (sometimes also DNA or RNA) that are recognized by the immune system of patients with specific autoimmune diseases. Under normal circumstances, these antigens should not be the target of the immune system, but the T cells associated with them are not eliminated and instead initiate an attack.

[0106] "Cytokine" as used herein refers to a small protein of a wide range that plays an important role in the cell signaling process. The release of cytokines can have an impact on the behavior of surrounding cells. Cytokines participate in the conduction of autocrine signals, paracrine signals and endocrine signals as immunomodulatory molecules. Non-limiting examples of cytokines include chemokines, interferons, interleukins, lymphokines and tumor necrosis factors. Cytokines are produced by various types of cells, including immune cells such as macrophages, monocytes, dendritic cells, B lymphocytes, T lymphocytes and mast cells, as well as endothelial cells, fibroblasts and various stromal cells. A given cytokine can be produced by more than one type of cell.

[0107] As used herein, "immune cells" refer to cells that develop from stem cells in the bone marrow and become different types of white blood cells. Immune cells include neutrophils, eosinophils, basophils, mast cells, monocytes, macrophages, dendritic cells, natural killer cells, and lymphocytes (B cells and T cells).

[0108] As used herein, "abundance" refers to the amount of a particular analyte (e.g., an immune cell subset) present in a sample. This amount can be a numerical value, ratio, proportion, or percentage of the analyte compared to a control sample, or can be determined using a standard curve. The amount can be absolute or relative (e.g., relative to an internal control, etc.).

[0109] As used herein, "expression" or "expression level" or "level of expression" refers to the amount of a particular analyte (e.g., an antibody or cytokine) present in a sample. The amount can be the concentration, number, ratio, proportion, or percentage of the analyte compared to a control sample, or can be determined using a standard curve. The amount can be absolute or relative.

[0110] As used herein, "myositis" refers to inflammation of the muscles that help the body move.

[0111] As used herein, "myocarditis" refers to inflammation of the myocardium.

[0112] As used herein, "cancer" can be one or more tumors or cancers. Tumors can be malignant or benign; cancers can be primary or metastatic; and tumors or cancers can be early or late. Non-limiting examples of tumors or cancers include acute lymphoblastic leukemia, acute myeloid leukemia, adrenocortical carcinoma, AIDS-related cancers, AIDS-related lymphomas, anal cancer, appendiceal cancer, astrocytoma (cerebellum or cerebrum in children), basal cell carcinoma, bile duct cancer, bladder cancer, bone cancer, brain stem glioma, brain tumors (cerebellar astrocytoma, brain astrocytoma / malignant glioma, ependymoma, medulloblastoma, supratentorial primitive neuroectodermal tumor, visual pathway and hypothalamic glioma), breast cancer, bronchial adenoma / carcinoid, Burkitt's lymphoma, carcinoid (children, gastrointestinal tract), cancer of unknown primary, central nervous system lymphoma (primary), cerebellar astrocytoma, brain astrocytoma / Malignant glioma, cervical cancer, childhood cancer, chronic lymphocytic leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, chronic myeloid leukemia, chronic myeloproliferative disorders, colon cancer, cutaneous T-cell lymphoma, small round cell tumor of desmoplasia, endometrial cancer, ependymoma, esophageal cancer, Ewing's sarcoma in the Ewing family of tumors, extracranial germ cell tumor (children), extragonadal germ cell tumor, extrahepatic bile duct cancer, eye cancer (intraocular melanoma, retinoblastoma), gallbladder cancer, gastric cancer, gastrointestinal carcinoid, gastrointestinal stromal tumor, germ cell tumor (extracranial, extragonadal, ovarian in children), gestational trophoblastic tumor, glioma (adult, brainstem, cerebrospinal fluid in children), leukemia (acute lymphoblastic, acute myeloid, chronic lymphocytic, chronic myeloid, hairy cell), lip and oral cavity cancer, liver cancer (primary), lung cancer (non-small cell, small cell), lymphoma (AIDS-related, Burkitt's, cutaneous T-cell, Hodgkin's, non-Hodgkin's, primary central nervous system), macroglobulinemia (Waldenstrom's disease), malignant fibrous histiocytoma of bone / bone Sarcoma, medulloblastoma (children), melanoma, intraocular melanoma, Merkel cell carcinoma, mesothelioma (malignant in adults, in children), metastatic squamous neck cancer with occult primary, oral cancer, multiple endocrine neoplasia syndrome (children), multiple myeloma / plasmacytoma, mycosis fungoides, myelodysplastic syndrome, myelodysplastic / myeloproliferative disorders, myeloid leukemia (chronic), myeloid leukemia (acute in adults, acute in children), multiple myeloma, myeloproliferative disorders (chronic), nasal cavity and paranasal sinus cancer, nasopharyngeal cancer, neuroblastoma, non-Hodgkin lymphoma, non-small cell lung cancer, oral cancer, oropharyngeal cancer, osteosarcoma / malignant fibrous histiocytoma of bone, ovarian cancer,Ovarian epithelial cancer (surface epithelial-stromal tumor), ovarian germ cell tumor, ovarian low malignant potential tumor, pancreatic cancer, pancreatic cancer (islet cell), sinus and nasal cavity cancer, parathyroid cancer, penile cancer, pharyngeal cancer, pheochromocytoma, pineal astrocytoma, pineal germ cell tumor, pineoblastoma and supratentorial primitive neuroectodermal tumor (children), pituitary adenoma, plasmacytoma, pleuropulmonary blastoma, primary central nervous system lymphoma, prostate cancer, rectal cancer, renal cell carcinoma (kidney cancer), transitional cell carcinoma of the renal pelvis and ureter, retinoblastoma, rhabdomyosarcoma (children), salivary gland cancer, sarcomas (Ewing's family of tumors, Kaposi's, soft tissue, uterine), Sézary syndrome, skin cancer (non Melanoma, melanoma), skin cancer (Merkel cell carcinoma), small cell lung cancer, small bowel cancer, soft tissue sarcoma, squamous cell carcinoma, squamous cell carcinoma of the neck with occult primary (metastatic), gastric cancer, supratentorial primitive neuroectodermal tumor (children), T-cell lymphoma (skin), testicular cancer, pharyngeal cancer, thymoma (children), thymoma and thymic carcinoma, thyroid cancer, thyroid cancer (children), transitional cell carcinoma of the renal pelvis and ureter, trophoblastic tumor (pregnancy), cancer of unknown primary site (adults, children), transitional cell carcinoma of the ureter and renal pelvis, urethral cancer, uterine cancer (endometrium), uterine sarcoma, vaginal cancer, visual pathway and hypothalamic glioma (children), vulvar cancer and Wilms' tumor (children).

[0113] As used herein, cancer treatment can include increasing the inhibition of cancer progression and / or metastasis, inhibiting the increase in tumor volume, reducing tumor volume and / or growth, reducing tumor growth rate, eradicating tumors and / or cancer cells, or any combination thereof. In some aspects, treatment can also prolong the survival of the subject, improve prognosis and / or improve the quality of life of the subject.

[0114] As used herein, a biological sample can be any biological tissue, liquid or cell from a subject. The sample can be a solid or liquid. The sample can be a heterogeneous cell population. Non-limiting examples of suitable biological samples include sputum, serum, blood, blood cells (such as white blood cells), biopsy, urine, peritoneal fluid, pleural fluid or cells extracted therefrom. The biopsy can be a fine needle aspiration biopsy, a core needle biopsy, a vacuum-assisted biopsy, an open surgical biopsy, a scraping biopsy, a punch biopsy, an incisional biopsy, a curettage biopsy or a deep scraping biopsy. The biological sample can also include tissue sections, such as frozen sections or formalin-fixed sections for histological purposes. The sample can be tumor tissue, peritumoral tissue or non-tumor tissue. Methods for collecting biological samples from a subject are well known in the art. In some aspects, the biological sample is a peripheral blood sample. In some aspects, the biological sample is a peripheral blood mononuclear cell (PBMC). In some aspects, the biological sample is plasma.

[0115] Samples from the subject may be collected one or more times before, during, and / or after diagnosis. In some aspects, samples may be obtained from the subject before, during, and / or after cancer treatment, wherein the cancer treatment includes ICI treatment. In some aspects, samples may be collected from the subject before the start of ICI treatment. In some aspects, samples may be obtained from a subject receiving ICI treatment before an irAE occurs. In other aspects, samples may be collected after the subject develops an irAE. In some aspects, samples may be collected before, during, and / or after non-ICI cancer treatment or ICI treatment combined with steroid treatment to monitor the treatment of irAEs. In addition, after the initial sample collection, samples may be repeatedly collected at multiple stages to determine and / or monitor the subject's irAEs.

[0116] In some aspects, the control sample can be taken from a healthy subject and / or a subject who is receiving ICI treatment but has a low risk of irAE or ICI toxicity. In some aspects, the control sample can include non-cancerous cells. In some aspects, non-cancerous cells can be from the same tissue type as the cancer cells. For example, if the cancer cells are from breast cancer, then the non-cancerous cells can be from healthy breast tissue. In some aspects, the control can include the average level of biomarker spectrum in the subject sample before the onset of cancer. In some aspects, the control sample can be a sample of the subject before diagnosis or treatment. In some aspects, the biomarker spectrum can be measured in one or several people other than the cancer patient. In some aspects, the control is a person or several people with similar characteristics to the cancer patient. In some aspects, the control can be the average value of the biomarker level combination disclosed from different health sources (for example, more than one healthy control subject and / or more than one subject with a low risk of irAE). In some aspects, the control sample can be a collection sample. In some aspects, the control sample is from a subject with a low risk of irAE. As used herein, a subject with a low risk of irAE can be a subject or population that does not have irAE after receiving ICI treatment. In one aspect, a subject at low risk of developing an irAE can be a subject or population that does not develop an irAE after ICI treatment, as determined by retrospective analysis.

[0117] II. Biomarkers

[0118] This disclosure provides immunological characteristics of ICI-associated irAEs of myositis and / or myocarditis, as well as insights into the biological characteristics of ICI-associated myositis and / or myocarditis. These characteristics can be used as biomarkers to provide a basis for potential cancer treatment options.

[0119] Transcript profiling

[0120] In some aspects, the present disclosure provides a method for predicting the risk of immune-related adverse events (irAEs) associated with immune checkpoint inhibitors (ICI) treatment in a subject and / or a method for diagnosing immune-related adverse events (irAEs) associated with immune checkpoint inhibitors (ICI) treatment in a subject. The method includes providing a sample of a subject, assessing the transcript level of one or more transcripts in the sample; predicting the risk of irAEs occurring in a subject / diagnosing irAEs in a subject. In some aspects, the assessment of transcripts includes comparing the transcript levels of one or more transcripts in the subject sample with the same transcript levels in the control sample. In some aspects, transcript levels are relative transcript levels. In some aspects, the transcript profiles relevant to ICI-related irAEs include transcript profiles in which the transcript levels of one or more transcripts in the subject are elevated compared to the transcript levels in the control sample. In some aspects, the transcript profiles relevant to ICI-related irAEs include transcript profiles in which the transcript levels of one or more transcripts in the subject are lower than the transcript levels in the control sample.

[0121] In some aspects, the transcript is one or more transcripts disclosed in Table 5. In some aspects, the transcript is one or more transcripts disclosed in Table 6. In some aspects, the transcript is one or more transcripts disclosed in Table 8. In some aspects, the transcript is one or more transcripts disclosed in Table 9. In some aspects, the transcript is one or more transcripts disclosed in Table 10. In some aspects, the transcript is one or more transcripts disclosed in Table 11. In some aspects, the transcript profile associated with ICI-related irAEs includes transcript levels of one or more transcripts that are increased in the subject compared to the transcript levels in the control sample, and transcript levels of one or more transcripts that are reduced in the subject compared to the transcript levels in the control sample. In some aspects, the transcript profile includes one or more transcripts disclosed in Table 5, Table 6, Table 8, Table 9, Table 10, Table 11, or any combination thereof.

[0122] In some aspects, when the transcript level of one or more transcripts in the subject is increased compared to the transcript level of the same transcript in the control sample, the subject is predicted or diagnosed as having a high risk of ICI-related irAE. In some aspects, when the transcript level of one or more transcripts in the subject is reduced compared to the transcript level of the same transcript in the control sample, the subject is predicted or diagnosed as having a high risk of ICI-related irAE. In other aspects, when the transcript level of one or more transcripts in the subject is increased compared to the transcript level of the same transcript in the control sample, the subject is predicted or diagnosed as having a low risk of ICI-related irAE. On the other hand, when the transcript level of one or more transcripts in the subject is reduced compared to the transcript level of the same transcript in the control sample, the subject is predicted or diagnosed as having a low risk of ICI-related irAE.

[0123] In some aspects, the transcript profile includes a baseline or pre-treatment transcript profile associated with future toxicity. These transcripts are used as biomarkers to assess the risk of a subject developing an irAE during ICI treatment. In some aspects, the subject is planned to receive or is currently receiving ICI treatment as part of cancer treatment.

[0124] In some aspects, a transcript with elevated expression levels has an elevated expression level that is at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, about 99%, or at least about 100% greater than the expression level of the same transcript in a control sample.

[0125] In some aspects, the transcript has an elevated expression level having a log 2 fold change value of from about 0.1 to about 5. For example, the log 2 fold change value can be about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, or 5.

[0126] In some aspects, a transcript with reduced expression has an expression level that is at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least 100% lower than the expression level of the same transcript in a control sample.

[0127] In some aspects, the transcript has a decreased expression level. The decreased expression level has a log 2 fold change value of from about -0.1 to about -5. For example, the log 2 fold change value can be about -0.1, -0.2, -0.3, -0.4, -0.5, -0.6, -0.7, -0.8, -0.9, -1, -1.1, -1.2, -1.3, -1.4, -1.5, -1.6, -1.7, -1.8, -1.9, -2, -2.1, -2.2, -2.3, -2.4 , -2.5, -2.6, -2.7, -2.8, -2.9, -3, -3.1, -3.2, -3.3, -3.4, -3.5, -3.6, -3.7, -3.8, -3.9, -4, -4.1, -4.2, -4.3, -4.4, -4.5, -4.6, -4.7, -4.8, -4.9, or -5.

[0128] In some aspects, a subject is predicted to be at high risk for developing an irAE or is diagnosed with an irAE if, before ICI treatment (baseline), the transcript level of one or more of leukocyte immunoglobulin-like receptor B4 (LILRB4), cytokine-inducible SH2-containing protein (CISH), poly (ADP-ribose) polymerase family member 9 (PARP9), RING finger protein 145 (RNF145), asialoglycoprotein receptor 2 (ASGR2), solute carrier family 16 member 13 (SLC16A13), lysophosphatidic acid receptor 6 (LPAR6), GTPase, IMAP family member 7 (GIMAP7), CXC motif chemokine receptor 6 (CXCR6), dehydrogenase / reductase 9 (DHRS9), Fcγ receptor Ic, pseudogene (FCGR1CP), and / or ankyrin repeat domain 34B (ANKRD34B) is elevated compared to the transcript level in a control sample.

[0129] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated compared to the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE or is diagnosed with an irAE. In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, GIMAP7, CXCR6, DHRS9, ANKRD34B, and / or FCGR1CP is elevated compared to the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE or is diagnosed with an irAE.

[0130] In some aspects, if the transcript level of LILRB4 is increased compared to the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of CISH is increased compared to the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of PARP9 is increased compared to the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of RNF145 is increased compared to the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of ASGR2 is increased compared to the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of SLC16A13 before ICI treatment is increased compared with the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of LPAR6 before ICI treatment is increased compared with the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of GIMAP7 before ICI treatment is increased compared with the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of CXCR6 before ICI treatment is increased compared with the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of DHRS9 before ICI treatment is increased compared with the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of FCGR1CP is elevated before ICI treatment compared to the transcript level in a control sample, the subject is predicted to be at high risk for developing an irAE or is diagnosed with an irAE. In some aspects, if the transcript level of ANKRD34B is elevated before ICI treatment compared to the transcript level in a control sample, the subject is predicted to be at high risk for developing an irAE or is diagnosed with an irAE.

[0131] In some aspects, if the transcript level of at least LILRB4 in the subject before ICI treatment is increased compared to the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of at least CISH in the subject before ICI treatment is increased compared to the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of at least PARP9 in the subject before ICI treatment is increased compared to the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of at least GIMAP7 in the subject before ICI treatment is increased compared to the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of at least CXCR6 in the subject before ICI treatment is increased compared to the transcript level in the control sample, the subject is predicted to have a high risk of irAE or is diagnosed with irAE. In some aspects, if the transcript level of at least DHRS9 in the subject is elevated compared to the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE or is diagnosed with an irAE. In some aspects, if the transcript level of at least FCGR1CP is elevated compared to the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE or is diagnosed with an irAE. In some aspects, if the transcript level of at least ANKRD34B is elevated compared to the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE or is diagnosed with an irAE.

[0132] In some aspects, if the subject is amphiregulin (AREG), epiregulin (EREG), oncostatin M (OSM), cysteine and serine rich nuclear protein 1 (CSRNP1), DNA damage-induced transcript 4 (DDIT4), IL-10 (interleukin 10), prostaglandin endoperoxide synthase (PTGS2), dual specificity phosphatase 1 (DUSP1), CXC chemokine receptor type 4 (CXCR4), nuclear factor, interleukin 3 regulatory factor (NFIL3), Fos proto-oncogene, AP-1 transcription factor subunit (FOS), NFKB inhibitory factor alpha (NFKBIA), PPP1R15A (protein phosphatase 1 regulatory subunit 15A), CD79A, JUNB proto-oncogene, AP-1 transcription factor subunit (JUNB), CXC motif chemokine ligand 8 (CXCL8), early growth response 1 (EGR1), G0 / G1 switch 2 (G0S2), paired box 8 (PAX8), activating transcription factor 6 beta (ATF6B), PAX8 antisense RNA 1 (PAX8-AS1), variant U1 small nuclear 19 (RNVU1-19), vitelline membrane outer 1 homolog (VMO1), heparin-binding EGF-like growth factor (HBEGF), coiled-coil domain containing 144A (CCDC144A), shisa family member 8 (SHISA8), nuclear receptor subfamily 4A group 2 (NR4A2), prostaglandin E synthase (PTGES), synaptophysin I (SYN1), CXC motif chemokine ligand 2 (CXCL2), peripheral myelin protein 22 (PMP22), CD83, early growth response 3 (EGR3), NUAK family kinase 1 (NUAK1), nocturnin (NOCT), atonal bHLH transcription factor 8 (ATOH8), polo-like kinase 2 (PLK2), DNA binding inhibitor 1 (ID1), adrenergic receptor β1 (ADRB1), snail family transcription repressor 1 (SNAI1), notch receptor 3 (NOTCH3), activating transcription factor 3 (ATF3), dual specificity phosphatase 2 (DUSP2), period circadian regulator 1 (PER1), TNF superfamily member 9 (TNFSF9), MAF bZIP transcription factor F (MAFF), microRNA 4420 (MIR4420), glutathione peroxidase (GPX3), TNFα-induced protein 3 (TNFAIP3), potassium voltage-gated channel regulatory subfamily G member 1 (KCNG1), prostaglandin endoperoxidase synthase 2 (PTGS2), A kinase anchoring protein 5 (AKAP5), dual specificity phosphatase 1 (DUSP1), diacylglycerol kinase kappa (DGKK), β-1,4,-N-acetylgalactosaminyltransferase 3 (B4GALNT3), tribbles pseudokinase 1 (TRIB1), phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1), CXC motif chemokine receptor 4 (CXCR4), tumor protein p53-induced nuclear protein 2 (TP53INP2), nuclear factor, interleukin 3 regulatory factor (NFIL3), dual-specificity phosphatase 4 (DUSP4), NFKB inhibitor α (NFKBIA), arginine vasopressin-induced protein 1 (AVPI1), CD79a, ADP-ribosylation factor-like GTPase 4D (ARL4D), poly IgA and IgM linking chain (JCHAIN), BTG antiproliferative factor 2 (BTG2), TLE family member 1, core repressor of transcription (TLE1), nuclear transport factor 2 export factor 1 (NXT1), transduction factor of ERBB2 1 (TOB1), phosphodiesterase 4D (PDE4D), DNAJ If the transcript level of one or more of heat shock protein family member B1 (DNAJB1), AT-rich interaction domain 5B (ARID5B), G protein-coupled receptor 153 (GPR153), KLF transcription factor 9 (KLF9), SBDS ribosome maturation factor (SBDS), immediate early response 2 (IER2), TSC22 domain family member 3 (TSC22D3), GABAA type receptor associated protein-like 1 (GABARAPL1), JunD proto-oncogene, AP-1 transcription factor subunit (JUND), RUNX family transcription factor 3 (RUNX3), BABAM2 antisense RNA1 (BRE-AS1), putative salt-induced kinase 1B (LOC102724428), FAM46C (FAM46C), and / or creatine phosphate receptor 1-associated scaffold protein (GRASP) is lower than the transcript level of the control sample, the subject is predicted to have a high risk of developing an irAE or is diagnosed with an irAE.

[0133] In some aspects, if the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, If the transcript level of one or more of CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP is lower than the transcript level of the control sample, the subject is predicted to be at high risk of developing irAE, or is diagnosed with irAE.

[0134] In some aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In various aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some other aspects, a subject is predicted to be at high risk for developing an irAE, or is diagnosed with an irAE, if before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 is lower than the transcript level in a control sample.

[0135] In some aspects, if the transcript level of at least AREG in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least EREG in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least OSM in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least CSRNP1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least DDIT4 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least IL-10 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least PTGS2 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least DUSP1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least CXCR4 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least NFIL3 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least FOS in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least NFKBIA in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least PPP1R15A in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least CD79A in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE.In some respects, if in subject, at least JUNB transcript level is lower than the transcript level in control sample, subject is predicted to have the high risk of irAE occurring, or is diagnosed with irAE. In some respects, if in subject, at least CXCL8 transcript level is lower than the transcript level in control sample, subject is predicted to have the high risk of irAE occurring, or is diagnosed with irAE. In some respects, if in subject, at least EGR1 transcript level is lower than the transcript level in control sample, subject is predicted to have the high risk of irAE occurring, or is diagnosed with irAE. In some respects, if in subject, at least GOS2 transcript level is lower than the transcript level in control sample, subject is predicted to have the high risk of irAE occurring, or is diagnosed with irAE. In some respects, if in subject, at least PAX8 transcript level is lower than the transcript level in control sample, subject is predicted to have the high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least ATF6B in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least PAX8-AS1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least RNVU1-19 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least VMO1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least HBEGF in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least CCDC144A in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least SHISA8 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least NR4A2 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least PTGES in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE.In some aspects, if the transcript level of at least SYN1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least CXCL2 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least PMP22 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least CD83 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least EGR3 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least NUAK1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least NOCT in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least ATOH8 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least PLK2 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least ID1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least ADRB1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least SNAI1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least NOTCH3 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least ATF3 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE.In some aspects, if the transcript level of DUSP2 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least PER1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least TNFSF9 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least MAFF in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least MIR4420 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the transcript level of at least BRE-AS1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least LOC102724428 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least GRASP in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least TNFAIP3 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the transcript level of at least TRIB1 in the subject is lower than the transcript level in the control sample, the subject is predicted to have a high risk of irAE occurring, or is diagnosed with irAE. In some aspects, if the level of at least PMAIP1 transcript in the subject is lower than the level of transcript in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the level of at least FAM46C transcript in the subject is lower than the level of transcript in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the level of at least NXT1 transcript in the subject is lower than the level of transcript in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE. In some aspects, if the level of at least KLF9 transcript in the subject is lower than the level of transcript in the control sample, the subject is predicted to have a high risk of irAE, or is diagnosed with irAE.

[0136] In some aspects, if the transcript level of AREG is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of EREG is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of OSM is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of CSRNP1 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of DDIT4 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of IL-10 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of PTGS2 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of DUSP1 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of CXCR4 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of NIFL3 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of FOS is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of NFKBIA is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of PPP1R15A is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE.In some aspects, if the transcript level of CD79A is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to be at high risk for developing an irAE, or is diagnosed with an irAE. In some aspects, if the transcript level of JUNB is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to be at high risk for developing an irAE, or is diagnosed with an irAE.

[0137] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the subject is elevated in the presence of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP3, IL-13, IL-14, IL-16, IL-17, IL-18, IL-20, IL-31, IL-40, IL-50, IL-60, IL-70, IL-80, IL-90, IL-19, IL-20, IL-21, IL-32, IL-40, IL-50, IL-60, IL-70, IL-80, IL-90, IL-19 ... 1. CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, V MO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1 , DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2 , TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is lower than the transcript level in the control sample, then the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE.

[0138] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the subject has elevated levels of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, GOS2, PAX8, ATF If the transcript level of one or more of 6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, and / or LOC102724428 is lower than the transcript level in the control sample, the subject is predicted to be at high risk of developing irAE, or is diagnosed with irAE.

[0139] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB in the subject is lower than the transcript level in the control sample, then the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE.

[0140] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 in the subject is lower than the transcript level in the control sample, then the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE.

[0141] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the transcript level of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 in the subject is lower than the transcript level in the control sample, then the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE.

[0142] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB in the subject is lower than the transcript level in the control sample, then the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE.

[0143] In some aspects, if the transcript levels of LILRB4, CISH, and PARP9 are elevated before ICI treatment (baseline) compared to the transcript levels in the control sample; and the transcript levels of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and JUNB in the subject are lower than the transcript levels in the control sample, the subject is predicted to be at high risk for developing an irAE, or is diagnosed with an irAE.

[0144] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1 in the subject. If the transcript level of one or more of -19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, and / or LOC102724428 is lower than the transcript level in the control sample, the subject is predicted to be at high risk of developing an irAE, or is diagnosed with an irAE.

[0145] In some aspects, if the transcript level of CISH is elevated before ICI treatment compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 in the subject is lower than the transcript level in the control sample, then the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE.

[0146] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, GIMAP7, CISH, and / or CXCR6 is elevated compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 in the subject is lower than the transcript level in the control sample, then the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE.

[0147] In some aspects, if the transcript level of PARP9 is elevated before ICI treatment (baseline) compared to the transcript level in a control sample; and the transcript level of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3 in the subject is lower than the transcript level in the control sample, then the subject is predicted to be at high risk for developing an irAE, or is diagnosed with an irAE.

[0148] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2 is elevated compared to the transcript level in a control sample; and KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSRNP in the subject. 1. If the transcript level of one or more of DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing irAE or is diagnosed with irAE.

[0149] In some aspects, a subject is predicted to have a low risk of developing an irAE if the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in a control sample before ICI treatment (baseline).

[0150] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated compared to the transcript level in the control sample, the subject is predicted to have a low risk of developing an irAE. In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE, or is diagnosed with an irAE.

[0151] In some aspects, if the transcript level of LILRB4 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of CISH is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of PARP9 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of RNF145 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of ASGR2 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of SLC16A13 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some respects, if the transcript level of LPAR6 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some respects, if the transcript level of GIMAP7 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some respects, if the transcript level of CXCR6 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some respects, if the transcript level of DHRS9 is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some respects, if the transcript level of FCGR1CP is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some respects, if the transcript level of ANKRD34B is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE.

[0152] In some aspects, if the transcript level of at least LILRB4 of the subject is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of at least CISH of the subject is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of at least PARP9 of the subject is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of at least GIMAP7 of the subject is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of at least CXCR6 of the subject is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of at least DHRS9 of the subject is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of irAE. In some aspects, if the transcript level of at least FCGR1CP is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of developing an irAE. In some aspects, if the transcript level of at least ANKRD34B is lower than the transcript level in the control sample before ICI treatment, the subject is predicted to have a low risk of developing an irAE.

[0153] In some aspects, if the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, T If the transcript level of one or more of NFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0154] In some aspects, if the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN 1. If the transcript level of one or more of CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing irAE.

[0155] In some aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE. In various aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE. In some other aspects, a subject is predicted or diagnosed as having a low risk of developing an irAE if the transcript level of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 is elevated before ICI treatment compared to the transcript level in a control sample.

[0156] In some respects, if the transcript level of at least AREG in the subject is compared with the transcript level in the control sample and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least EREG in the subject is compared with the transcript level in the control sample and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least OSM in the subject is compared with the transcript level in the control sample and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least CSRNP1 in the subject is compared with the transcript level in the control sample and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least DDIT4 in the subject is compared with the transcript level in the control sample and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least IL-10 in the subject is compared with the transcript level in the control sample and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least PTGS2 in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least DUSP1 in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least CXCR4 in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least NFIL3 in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least FOS in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least NFKBIA in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some aspects, if the transcript level of at least PPP1R15A in the subject is elevated compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE. In some aspects, if the transcript level of at least CD79A in the subject is elevated compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE.In some respects, if in subject body at least JUNB transcript level is compared with the transcript level in control sample and raises, subject is predicted or diagnosed as having the low risk of irAE occurring. In some respects, if in subject body at least CXCL8 transcript level is compared with the transcript level in control sample and raises, subject is predicted or diagnosed as having the low risk of irAE occurring. In some respects, if in subject body at least EGR1 transcript level is compared with the transcript level in control sample and raises, subject is predicted or diagnosed as having the low risk of irAE occurring. In some respects, if in subject body at least GOS2 transcript level is compared with the transcript level in control sample and raises, subject is predicted or diagnosed as having the low risk of irAE occurring. In some respects, if in subject body at least PAX8 transcript level is compared with the transcript level in control sample and raises, subject is predicted or diagnosed as having the low risk of irAE occurring. In some respects, if in subject body at least ATF6B transcript level is compared with the transcript level in control sample and raises, subject is predicted or diagnosed as having the low risk of irAE occurring. In some aspects, if the transcript level of at least PAX8-AS1 in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least RNVU1-19 in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least VMO1 in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least HBEGF in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least CCDC144A in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least SHISA8 in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least NR4A2 in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least PTGES in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE.In some respects, if the transcript level of at least SYN1 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least CXCL2 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least PMP22 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least CD83 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least EGR3 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least NUAK1 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some aspects, if the transcript level of at least NOCT in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least ATOH8 in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least PLK2 in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least ID1 in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least ADRB1 in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least SNAI1 in the subject is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least NOTCH3 in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least ATF3 in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of at least DUSP2 in the subject is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE.In some respects, if the transcript level of at least PER1 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least TNFSF9 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least MAFF in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least MIR4420 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least BRE-AS1 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of at least LOC102724428 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having the low risk of irAE occurring. In some respects, if the transcript level of at least GRASP in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having the low risk of irAE occurring. In some respects, if the transcript level of at least TNFAIP3 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having the low risk of irAE occurring. In some respects, if the transcript level of at least TRIB1 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having the low risk of irAE occurring. In some respects, if the transcript level of at least PMAIP1 in the subject is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having the low risk of irAE occurring. In some aspects, if the transcript level of at least FAM46C in the subject is elevated compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE. In some aspects, if the transcript level of at least NXT1 in the subject is elevated compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE. In some aspects, if the transcript level of at least KLF9 in the subject is elevated compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0157] In some respects, if the transcript level of AREG is compared with the transcript level in the control sample before ICI treatment and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of EREG is compared with the transcript level in the control sample before ICI treatment and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of OSM is compared with the transcript level in the control sample before ICI treatment and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of CSRNP1 is compared with the transcript level in the control sample before ICI treatment and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of DDIT4 is compared with the transcript level in the control sample before ICI treatment and increases, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of IL-10 before ICI treatment is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of PTGS2 before ICI treatment is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of DUSP1 before ICI treatment is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of CXCR4 before ICI treatment is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some respects, if the transcript level of NIFL3 before ICI treatment is compared with the transcript level in the control sample and raises, the subject is predicted or diagnosed as having a low risk of irAE occurring. In some aspects, if the transcript level of FOS before ICI treatment is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of NFKBIA before ICI treatment is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of PPP1R15A before ICI treatment is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE. In some aspects, if the transcript level of CD79A before ICI treatment is increased compared with the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of irAE.In some aspects, if the transcript level of JUNB is elevated before ICI treatment compared to the transcript level in a control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0158] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1 in the subject is lower than the transcript level in the control sample; , CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, V MO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1 , ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUS P1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, B If the transcript level of one or more of TG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing irAE.

[0159] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, AT If the transcript level of one or more of F6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, and / or LOC102724428 is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0160] In some aspects, if before ICI treatment, the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1C, P and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB in the subject is increased compared to the transcript level in the control sample, then the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0161] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, and / or CXCR6 is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 in the subject is increased compared to the transcript level in the control sample, then the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0162] In some aspects, a subject is predicted or diagnosed as having a low risk of developing an irAE if before ICI treatment (baseline) the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 is elevated in the subject compared to the transcript level in the control sample.

[0163] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH and / or PARP9 is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB in the subject is increased compared to the transcript level in the control sample, then the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0164] In some aspects, if the transcript levels of LILRB4, CISH, and PARP9 are lower than the transcript levels in the control sample before ICI treatment (baseline); and the transcript levels of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and JUNB in the subject are increased compared to the transcript levels in the control sample, then the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0165] In some aspects, if the transcript level of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample before ICI treatment; and the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1- 19. If the transcript level of one or more of VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, and / or LOC102724428 is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing irAE.

[0166] In some aspects, if the transcript level of CISH is lower than the transcript level in the control sample before ICI treatment; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1 and / or KLF9 is increased in the subject compared to the transcript level in the control sample, then the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0167] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 in the subject is increased compared to the transcript level in the control sample, then the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0168] In some aspects, if the transcript level of PARP9 is lower than the transcript level in the control sample before ICI treatment (baseline); and the level of one or more transcripts of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3 in the subject is increased compared to the transcript level in the control sample, then the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0169] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2 is lower than the transcript level in the control sample; and KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSRN in the subject. If the transcript level of one or more of P1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1 is increased compared to the transcript level in the control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0170] In some aspects, the present disclosure provides a method for monitoring the risk of immune-related adverse events (irAEs) associated with immune checkpoint inhibitors (ICI) treatment in a subject. The method includes providing a sample of the subject, assessing the transcript level in the sample; and predicting the risk of irAE occurrence in the monitored subject / diagnosing irAE in the subject. In some aspects, transcript assessment includes comparing the level of one or more transcripts in the subject sample with the level of the same transcript in the control sample. In some aspects, the transcript profile related to ICI-related irAEs includes transcript profiles in which the level of one or more transcripts in the subject is increased compared to the level of the same transcript in the control sample. In some aspects, the transcript profile related to ICI-related irAEs includes transcript profiles in which the level of one or more transcripts in the subject is lower than the level of the same transcript in the control sample.

[0171] In some aspects, the transcript is one or more transcripts disclosed in Table 5. In some aspects, the transcript is one or more transcripts disclosed in Table 6. In some aspects, the transcript is one or more transcripts disclosed in Table 8. In some aspects, the transcript is one or more transcripts disclosed in Table 9. In some aspects, the transcript is one or more transcripts disclosed in Table 10. In some aspects, the transcript is one or more transcripts disclosed in Table 11. In some aspects, the transcript profile associated with ICI-related irAEs includes transcripts of one or more transcripts that are elevated in the subject compared to the transcript level in the control sample, and transcripts of one or more transcripts that are reduced in the subject compared to the transcript level in the control sample. In some aspects, the transcript profile includes one or more transcripts disclosed in Table 5, Table 6, Table 8, Table 9, Table 10, Table 11, or any combination thereof.

[0172] In some aspects, when the transcript level of one or more transcripts in the subject is increased compared to the transcript level of the same transcript in the control sample, the monitored subject may have a high risk of ICI-related irAEs. In some aspects, when the transcript level of one or more transcripts in the subject is reduced compared to the transcript level of the same transcript in the control sample, the monitored subject may have a high risk of ICI-related irAEs. In other aspects, when the transcript level of one or more transcripts in the subject is increased compared to the transcript level of the same transcript in the control sample, the monitored subject may have a low risk of ICI-related irAEs. On the other hand, when the transcript level of one or more transcripts in the subject is reduced compared to the transcript level of the same transcript in the control sample, the monitored subject may have a low risk of ICI-related irAEs.

[0173] In some aspects, the transcript profile includes a baseline or pre-treatment transcript profile that is associated with future toxicity. These transcripts can be used as biomarkers to assess the risk of a subject developing an irAE during ICI treatment. In some aspects, the subject is planned to receive or is currently receiving ICI treatment as part of cancer treatment.

[0174] In some aspects, transcripts having elevated levels have elevated expression levels that are at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least about 100% greater than a control sample during monitoring.

[0175] In some aspects, during monitoring, a transcript has an increased level with a log 2 fold change value of the increased expression level from about 0.1 to about 5. For example, the log 2 fold change value can be about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 2.8, 2.9, 3, 3.1, 3.2, 3.3, 3.4, 3.5, 3.6, 3.7, 3.8, 3.9, 4, 4.1, 4.2, 4.3, 4.4, 4.5, 4.6, 4.7, 4.8, 4.9, or 5.

[0176] In some aspects, the transcript having a decreased level has a decreased expression level of at least about 0.01%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least 100% lower than that of a control sample during monitoring.

[0177] In some aspects, during monitoring, a transcript has a decreased level with a log 2 fold change value of the decreased expression level ranging from about -0.1 to about -5. For example, the log 2 fold change value can be about -0.1, -0.2, -0.3, -0.4, -0.5, -0.6, -0.7, -0.8, -0.9, -1, -1.1, -1.2, -1.3, -1.4, -1.5, -1.6, -1.7, -1.8, -1.9, -2, -2.1, -2.2, -2.3, -2.4 , -2.5, -2.6, -2.7, -2.8, -2.9, -3, -3.1, -3.2, -3.3, -3.4, -3.5, -3.6, -3.7, -3.8, -3.9, -4, -4.1, -4.2, -4.3, -4.4, -4.5, -4.6, -4.7, -4.8, -4.9, or -5.

[0178] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample, the monitored subject can be at high risk for developing an irAE or be diagnosed with an irAE.

[0179] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated compared to the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE or be diagnosed with an irAE. In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE or be diagnosed with an irAE.

[0180] In some aspects, if the transcript level of LILRB4 is elevated compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of CISH is elevated compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of PARP9 is elevated compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of RNF145 is elevated compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of ASGR2 is elevated compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of SLC16A13 is elevated compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some respects, if the transcript level of LPAR6 is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some respects, if the transcript level of GIMAP7 is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some respects, if the transcript level of CXCR6 is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some respects, if the transcript level of DHRS9 is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some respects, if the transcript level of FCGR1CP is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some respects, if the transcript level of ANKRD34B is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE.

[0181] In some aspects, if the transcript level of at least LILRB4 in the subject is increased compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least CISH in the subject is increased compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least PARP9 in the subject is increased compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least GIMAP7 in the subject is increased compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least CXCR6 in the subject is increased compared to the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least DHRS9 in the subject is elevated compared to the transcript level in the control sample before ICI treatment, the monitored subject may be at high risk for developing an irAE. In some aspects, if the transcript level of at least FCGR1CP is elevated compared to the transcript level in the control sample before ICI treatment, the monitored subject may be at high risk for developing an irAE. In some aspects, if the transcript level of at least ANKRD34B is elevated compared to the transcript level in the control sample before ICI treatment, the monitored subject may be at high risk for developing an irAE.

[0182] In some aspects, if the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3 , TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, GABARAPL1, JUND, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE.

[0183] In some aspects, if the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, S If the level of one or more transcripts of YN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE.

[0184] In some aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE. In various aspects, if before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE. In some other aspects, if the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 is lower than the transcript level in the control sample, the monitored subject can be at high risk for developing an irAE.

[0185] In some aspects, if the transcript level of at least AREG in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least EREG in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least OSM in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least CSRNP1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least DDIT4 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least IL-10 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least PTGS2 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least DUSP1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least CXCR4 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least NFIL3 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least FOS in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least NFKBIA in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least PPP1R15A in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE. In some aspects, if the transcript level of at least CD79A in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE. In some aspects, if the transcript level of at least JUNB in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE.In some respects, if the transcript level of at least CXCL8 in the subject is lower than the transcript level in the control sample, the subject being monitored can have the high risk of irAE occurring. In some respects, if the transcript level of at least EGR1 in the subject is lower than the transcript level in the control sample, the subject being monitored can have the high risk of irAE occurring. In some respects, if the transcript level of at least GOS2 in the subject is lower than the transcript level in the control sample, the subject being monitored can have the high risk of irAE occurring. In some respects, if the transcript level of at least PAX8 in the subject is lower than the transcript level in the control sample, the subject being monitored can have the high risk of irAE occurring. In some respects, if the transcript level of at least ATF6B in the subject is lower than the transcript level in the control sample, the subject being monitored can have the high risk of irAE occurring. In some respects, if the transcript level of at least PAX8-AS1 in the subject is lower than the transcript level in the control sample, the subject being monitored can have the high risk of irAE occurring. In some aspects, if the transcript level of at least RNVU1-19 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least VMO1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least HBEGF in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least CCDC144A in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least SHISA8 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least NR4A2 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least PTGES in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE. In some aspects, if the transcript level of at least SYN1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE. In some aspects, if the transcript level of at least CXCL2 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE.In some respects, if the transcript level of at least PMP22 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE occurring. In some respects, if the transcript level of at least CD83 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE occurring. In some respects, if the transcript level of at least EGR3 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE occurring. In some respects, if the transcript level of at least NUAK1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE occurring. In some respects, if the transcript level of at least NOCT in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE occurring. In some respects, if the transcript level of at least ATOH8 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE occurring. In some aspects, if the transcript level of at least PLK2 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least ID1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least ADRB1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least SNAI1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least NOTCH3 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least ATF3 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least DUSP2 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least PER1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least TNFSF9 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least MAFF in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE.In some aspects, if the transcript level of at least MIR4420 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least BRE-AS1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least LOC102724428 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least GRASP in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least TNFAIP3 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least TRIB1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least PMAIP1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least FAM46C in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least NXT1 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of at least KLF9 in the subject is lower than the transcript level in the control sample, the monitored subject may have a high risk of irAE.

[0186] In some aspects, if the transcript level of AREG is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of EREG is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of OSM is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of CSRNP1 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of DDIT4 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of IL-10 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of PTGS2 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of DUSP1 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of CXCR4 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of NIFL3 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of FOS is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of NFKBIA is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of irAE. In some aspects, if the transcript level of PPP1R15A is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of developing an irAE. In some aspects, if the transcript level of CD79A is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of developing an irAE. In some aspects, if the transcript level of JUNB is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a high risk of developing an irAE.

[0187] In some aspects, if the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated before ICI treatment (baseline) compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DU is elevated in the subject. SP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1- 19. VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2 , ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP 5. DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCH If the transcript level of one or more of AIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C and / or GRASP is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE.

[0188] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX 8. If the transcript level of one or more of ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, and / or LOC102724428 is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing irAE.

[0189] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB in the subject is lower than the transcript level in the control sample, then the monitored subject may have a high risk of developing an irAE.

[0190] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 in the subject is lower than the transcript level in the control sample, then the monitored subject may have a high risk of developing an irAE.

[0191] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 in the subject is lower than the transcript level in the control sample, then the monitored subject may have a high risk of developing an irAE.

[0192] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB in the subject is lower than the transcript level in the control sample, then the monitored subject may have a high risk of developing an irAE.

[0193] In some aspects, if the transcript levels of LILRB4, CISH, and PARP9 are elevated before ICI treatment (baseline) compared to the transcript levels in the control sample; and the transcript levels of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and JUNB in the subject are lower than the transcript levels in the control sample, then the monitored subject may have a high risk of developing an irAE.

[0194] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the subject is expressed in a protein encoding an enzyme, e.g., AEG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, R If the transcript level of one or more of NVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, and / or LOC102724428 is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE.

[0195] In some aspects, if the transcript level of CISH is elevated before ICI treatment compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 in the subject is lower than the transcript level in the control sample, then the monitored subject may have a high risk of developing an irAE.

[0196] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is elevated compared to the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 in the subject is lower than the transcript level in the control sample, then the monitored subject may have a high risk of developing an irAE.

[0197] In some aspects, if the transcript level of PARP9 is elevated before ICI treatment (baseline) compared to the transcript level in a control sample; and the transcript level of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3 in the subject is lower than the transcript level in the control sample, then the monitored subject may have a high risk of developing an irAE.

[0198] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2 is elevated compared to the transcript level in a control sample; and KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, C If the transcript level of one or more of SRNP1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1 is lower than the transcript level in the control sample, the monitored subject may have a high risk of developing an irAE.

[0199] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE.

[0200] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated compared to the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE. In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE.

[0201] In some aspects, if the transcript level of LILRB4 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of CISH is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of PARP9 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of RNF145 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of ASGR2 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of SLC16A13 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of LPAR6 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of GIMAP7 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of CXCR6 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of DHRS9 is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of FCGR1CP is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of ANKRD34B is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE.

[0202] In some aspects, if the transcript level of at least LILRB4 in the subject is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least CISH in the subject is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least PARP9 in the subject is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least GIMAP7 in the subject is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least CXCR6 in the subject is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least DHRS9 in the subject is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of developing an irAE. In some aspects, if the transcript level of at least FCGR1CP is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of developing an irAE. In some aspects, if the transcript level of at least ANKRD34B is lower than the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of developing an irAE.

[0203] In some aspects, if the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, If the transcript level of one or more of TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is elevated compared to the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE.

[0204] In some aspects, if the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN 1. If the transcript level of one or more of CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of developing irAE.

[0205] In some aspects, if the transcript levels of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB are elevated compared to the transcript levels in the control samples before ICI treatment, the monitored subject may have a low risk of developing an irAE. In various aspects, if the transcript levels of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 are elevated compared to the transcript levels in the control samples before ICI treatment, the monitored subject may have a low risk of developing an irAE. In some other aspects, if the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 is elevated before ICI treatment compared to the transcript level in the control sample, the monitored subject can have a low risk of developing an irAE.

[0206] In some aspects, if the transcript level of at least AREG in the subject is raised compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the transcript level of at least EREG in the subject is raised compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the transcript level of at least OSM in the subject is raised compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the transcript level of at least CSRNP1 in the subject is raised compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the transcript level of at least DDIT4 in the subject is raised compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the transcript level of at least IL-10 in the subject is raised compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE occurring. In some respects, if the transcript level of at least PTGS2 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least DUSP1 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least CXCR4 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least NFIL3 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least FOS in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least NFKBIA in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least PPP1R15A in the subject is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least CD79A in the subject is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least JUNB in the subject is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of irAE.In some respects, if the transcript level of at least CXCL8 in the subject body is compared with the transcript level in the control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least EGR1 in the subject body is compared with the transcript level in the control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least GOS2 in the subject body is compared with the transcript level in the control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least PAX8 in the subject body is compared with the transcript level in the control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least ATF6B in the subject body is compared with the transcript level in the control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least PAX8-AS1 in the subject body is compared with the transcript level in the control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least RNVU1-19 in the subject is raised compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least VMO1 in the subject is raised compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least HBEGF in the subject is raised compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least CCDC144A in the subject is lower than the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least SHISA8 in the subject is lower than the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least NR4A2 in the subject is lower than the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least PTGES in the subject is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least SYN1 in the subject is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least CXCL2 in the subject is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of irAE.In some respects, if the transcript level of at least PMP22 in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk that irAE occurs. In some respects, if the transcript level of at least CD83 in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk that irAE occurs. In some respects, if the transcript level of at least EGR3 in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk that irAE occurs. In some respects, if the transcript level of at least NUAK1 in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk that irAE occurs. In some respects, if the transcript level of at least NOCT in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk that irAE occurs. In some respects, if the transcript level of at least ATOH8 in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk that irAE occurs. In some respects, if the transcript level of at least PLK2 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least ID1 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least ADRB1 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least SNAI1 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least NOTCH3 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of at least ATF3 in the subject is increased compared with the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least DUSP2 in the subject is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least PER1 in the subject is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of at least TNFSF9 in the subject is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of irAE.In some respects, if the transcript level of at least MAFF in the subject is raised compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of at least MIR4420 in the subject is raised compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of at least BRE-AS1 in the subject is raised compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of at least LOC102724428 in the subject is raised compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of at least GRASP in the subject is raised compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of at least TNFAIP3 in the subject is raised compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of at least TRIB1 in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least PMAIP1 in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least FAM46C in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least NXT1 in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk of irAE occurring. In some respects, if the transcript level of at least KLF9 in subject body is compared with the transcript level in control sample and raises, the subject being monitored can have the low risk of irAE occurring.

[0207] In some aspects, if the transcript level of EREG is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of EREG is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of OSM is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of CSRNP1 is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of DDIT4 is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some aspects, if the transcript level of IL-10 is increased compared with the transcript level in the control sample before ICI treatment, the monitored subject may have a low risk of irAE. In some respects, if the transcript level of PTGS2 before ICI treatment is compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of DUSP1 before ICI treatment is compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of CXCR4 before ICI treatment is compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of NIFL3 before ICI treatment is compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of FOS before ICI treatment is compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the transcript level of NFKBIA before ICI treatment is compared with the transcript level in the control sample, the monitored subject can have a low risk of irAE occurring. In some aspects, if the transcript level of PPP1R15A is elevated before ICI treatment compared to the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE. In some aspects, if the transcript level of CD79A is elevated before ICI treatment compared to the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE. In some aspects, if the transcript level of JUNB is elevated before ICI treatment compared to the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE.

[0208] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1 in the subject is lower than the transcript level in the control sample; , CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID 1. ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, D USP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN , BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C and / or GRASP transcript levels are elevated compared to the transcript levels in the control sample, the monitored subject may have a low risk of developing irAEs.

[0209] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, A If the transcript level of one or more of TF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, and / or LOC102724428 is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE.

[0210] In some aspects, if before ICI treatment, the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB is elevated in the subject compared to the transcript level in the control sample, then the monitored subject may have a low risk of developing an irAE.

[0211] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 in the subject is increased compared to the transcript level in the control sample, then the monitored subject may have a low risk of developing an irAE.

[0212] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 in the subject is elevated compared to the transcript level in the control sample, then the monitored subject may have a low risk of developing an irAE.

[0213] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, and / or PARP9 is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB in the subject is increased compared to the transcript level in the control sample, then the monitored subject may have a low risk of developing an irAE.

[0214] In some aspects, if before ICI treatment (baseline), the transcript levels of LILRB4, CISH, and PARP9 are lower than the transcript levels in the control sample; and the transcript levels of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and JUNB in the subject are elevated compared to the transcript levels in the control sample, then the monitored subject may have a low risk of developing an irAE.

[0215] In some aspects, if before ICI treatment, the transcript level of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the subject has AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNV If the level of one or more transcripts of U1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, and / or LOC10272442 is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE.

[0216] In some aspects, if the transcript level of transcript CISH is lower than the transcript level in the control sample before ICI treatment; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 in the subject is increased compared to the transcript level in the control sample, then the monitored subject can have a low risk of developing an irAE.

[0217] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, and / or ANKRD34B is lower than the transcript level in the control sample; and the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 in the subject is increased compared to the transcript level in the control sample, then the monitored subject may have a low risk of developing an irAE.

[0218] In some aspects, if the transcript level of PARP9 before ICI treatment (baseline) is lower than the transcript level in the control sample; and the transcript level of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3 in the subject is increased compared to the transcript level in the control sample, then the monitored subject may have a low risk of developing an irAE.

[0219] In some aspects, if before ICI treatment (baseline), the transcript level of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2 is lower than the transcript level in the control sample; and KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSR If the transcript level of one or more of NP1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1 is increased compared to the transcript level in the control sample, the monitored subject may have a low risk of developing an irAE.

[0220] Any known method in the art can be used to measure and / or monitor the level of transcripts. As a non-limiting example, RNA sequencing, nanopore sequencing, Nanostring, multiplex RT-PCR, single RT-PCR, NASBA, fluorescence measurement or spectrophotometry can be used to measure the level of transcripts. The sample to be tested may include whole blood, serum, plasma, urine, CSF or other suitable body fluids. Samples can be obtained from the subject before, during and / or after ICI treatment, and transcript levels are quantified to assess the risk of irAEs. In some aspects, the transcriptional profile is an RNA peripheral blood transcriptional profile. Risk assessment includes predicting, diagnosing, or monitoring ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

[0221] Autoantibody profile

[0222] In some aspects, the present disclosure provides autoantibody profiles associated with ICI-related irAEs. In some aspects, the autoantibody profile includes autoantibodies that express elevated levels in irAE subjects compared to control samples before or at baseline. In some aspects, the autoantibody profile includes autoantibodies that express lower levels in irAE subjects than in control samples before or at baseline. In some aspects, the autoantibody profile is one or more of autoantibodies Mi-2, GAD65, myosin, thyroglobulin, and / or TPO, or any combination thereof.

[0223] In some aspects, the autoantibody profile includes a baseline or pre-treatment transcript profile that is associated with future toxicities. These autoantibodies can be used as biomarkers to assess a subject's risk of developing an irAE during ICI treatment. In some aspects, the subject is planned to receive or is currently receiving ICI treatment as part of their cancer treatment.

[0224] In some aspects, the autoantibodies may include one or more autoantibodies disclosed in U.S. Patent Application No. 16 / 487,335 (U.S. Patent Application Publication No. US2020 / 0284803), the disclosure of which is incorporated herein by reference in its entirety.

[0225] In some aspects, the present disclosure provides a method comprising predicting or diagnosing a subject as having a high risk of developing an irAE if the expression of one or more autoantibodies is elevated compared to the expression of the same autoantibodies in a control sample. The method comprises providing a sample of the subject before treatment or at baseline, assessing one or more autoantibodies in the sample, and predicting the risk of the subject developing an irAE or diagnosing the subject as having an irAE.

[0226] In some aspects, the method further includes predicting or diagnosing that the subject is at high risk for developing an irAE if the expression of one or more autoantibodies in the subject is different from that in the control sample (as described in U.S. patent application Ser. No. 16 / 487,335 (U.S. Patent Application Publication No. US2020 / 0284803), the disclosure of which is incorporated herein by reference in its entirety).

[0227] In some aspects, the method for predicting or diagnosing that a subject has a high risk of irAE occurring related to ICI treatment includes assessing the expression of one or more of autoantibody Mi-2, GAD65, myosin, thyroglobulin, and / or TPO or any combination thereof. In some aspects, if the expression of one or more of autoantibody Mi-2, GAD65, myosin, thyroglobulin, and / or TPO or any combination thereof is increased compared with the expression in the control sample, then predicting or diagnosing that the subject has a high risk of irAE occurring. In some aspects, if the expression of autoantibody Mi-2 is increased compared with the expression in the control sample, then predicting or diagnosing that the subject has a high risk of irAE occurring. In some aspects, if the expression of autoantibody GAD65 is increased compared with the expression in the control sample, then predicting or diagnosing that the subject has a high risk of irAE occurring. In some aspects, if the expression of autoantibody myosin is increased compared with the expression in the control sample, then predicting or diagnosing that the subject has a high risk of irAE occurring. In some aspects, if the expression of autoantibody thyroglobulin is increased compared with the expression in the control sample, then predicting or diagnosing that the subject has a high risk of irAE occurring. In some aspects, if expression of the autoantibody TPO is elevated compared to expression in a control sample, the subject is predicted or diagnosed as having a high risk of developing an irAE.

[0228] In some aspects, the present disclosure provides a method comprising predicting or diagnosing a subject as having a low risk of developing an irAE if the expression of one or more autoantibodies is lower than that in a control sample. The method comprises providing a sample of the subject before treatment or at baseline, assessing one or more autoantibodies in the sample, and predicting the risk of developing an irAE or diagnosing the subject as having an irAE.

[0229] In some aspects, the method further includes predicting or diagnosing that the subject is at high risk for developing an irAE if the expression of one or more autoantibodies in the subject is different from that in the control sample (as described in U.S. patent application Ser. No. 16 / 487,335 (U.S. Patent Application Publication No. US2020 / 0284803), the disclosure of which is incorporated herein by reference in its entirety).

[0230] In some aspects, if the expression of one or more of autoantibody Mi-2, GAD65, myosin, thyroglobulin and / or TPO or any combination thereof is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE occurring. In some aspects, if the expression of autoantibody Mi-2 is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE occurring. In some aspects, if the expression of autoantibody GAD65 is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE occurring. In some aspects, if the expression of autoantibody myosin is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE occurring. In some aspects, if the expression of autoantibody thyroglobulin is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE occurring. In some aspects, if the expression of autoantibody TPO is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE occurring.

[0231] In some aspects, during prediction or diagnosis of irAE risk, one or more of the disclosed autoantibodies have an expression greater than at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least about 100% of the elevated expression compared to the control sample. In some aspects, the disclosed autoantibodies can have an elevated expression greater than 100% of the expression in the control sample.

[0232] In some aspects, during prediction or diagnosis of irAE risk, expression of one or more autoantibodies can be lower than that of a control sample by at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 0.6%, at least about 0.7%, at least about 0.8%, at least about 0.9%, at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 11%, at least about 12%, at least about 13%, at least about 14%, at least about 15%, at least about 16%, at least about 17%, at least about 18%, at least about 19%, at least about 20%, at least about 21%, at least about 22%, at least about 23%, at least about 24%, at least about 25%, at least about 26%, at least about 27%, at least about 28%, at least about 29%, at least about 30%, at least about 31%, at least about 32%, at least about 33%, at least about 34%, at least about 35%, at least about 36%, at least about 37%, at least about 38%, at least about 39%, at least about 40%, at least about 41%, at least about 42%, at least about 43%, at least about 44%, at least about 45%, at least about 46%, at least about 47%, at least about 48%, at least about 49%, at least about 50%, at least about 51%, at least about 52%, at least about 53%, at least about 54%, at least about 55%, at least about 56%, at least about 57%, at least about 58%, at least about 59%, at least At least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least about 100%. In some aspects, one or more autoantibodies may be underexpressed compared to a control sample by at least about 25%, at least 50%, or 100%.

[0233] In some aspects, the present disclosure provides a kind of autoantibody spectrum, for monitoring the risk of irAE associated with ICI treatment in subjects. In some aspects, the autoantibody spectrum includes autoantibodies that express increased levels in irAE subjects compared with the expression in control samples before treatment or at baseline. In some aspects, the autoantibody spectrum includes autoantibodies that express decreased levels in irAE subjects compared with the expression in control samples before treatment or at baseline. In some aspects, the autoantibody is one or more of autoantibodies Mi-2, GAD65, myosin, thyroglobulin and / or TPO or any combination thereof.

[0234] In some aspects, if the expression of one or more autoantibodies in the subject is different from that in the control sample (as described in U.S. Patent Application No. 16 / 487,335 (U.S. Patent Application Publication No. US2020 / 0284803), the entire disclosure of which is incorporated herein by reference), the monitored subject may be at high risk for developing an irAE.

[0235] In some aspects, if the expression of one or more autoantibodies Mi-2, GAD65, myosin, thyroglobulin and / or TPO or any combination thereof is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of autoantibody Mi-2 is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of autoantibody GAD65 is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of autoantibody myosin is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of autoantibody thyroglobulin is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of autoantibody TPO is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE.

[0236] In some aspects, if the expression of one or more autoantibodies in the subject is different from that in the control sample (as described in U.S. Patent Application No. 16 / 487,335 (U.S. Patent Application Publication No. US2020 / 0284803), the disclosure of which is incorporated by reference in its entirety herein), the monitored subject can have a low risk of developing an irAE.

[0237] In some aspects, if the expression of one or more autoantibodies Mi-2, GAD65, myosin, thyroglobulin and / or TPO or any combination thereof is lower than the expression in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the expression of autoantibody Mi-2 is lower than the expression in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the expression of autoantibody GAD65 is lower than the expression in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the expression of autoantibody myosin is lower than the expression in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the expression of autoantibody thyroglobulin is lower than the expression in the control sample, the monitored subject may have a low risk of irAE occurring. In some aspects, if the expression of autoantibody TPO is lower than the expression in the control sample, the monitored subject may have a low risk of irAE occurring.

[0238] In some aspects, during monitoring irAE risk, one or more of the disclosed autoantibodies have at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99% or at least about 100% of the elevated expression greater than the expression in the control sample. In some aspects, the disclosed autoantibodies can have an elevated expression greater than 100% of the expression in the control sample.

[0239] In some aspects, during monitoring of the risk of an irAE, the expression of one or more autoantibodies can be lower than that of a control sample by at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 0.6%, at least about 0.7%, at least about 0.8%, at least about 0.9%, at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, at least about 10%, at least about 11%, at least about 12%, at least about 13%, at least about 14%, at least about 15%, at least about 16%, at least about 17%, at least about 18%, at least about 19%, at least about 20%, at least about 21%, at least about 22%, at least about 23%, at least about 24%, at least about 25%, at least about 26%, at least about 27%, at least about 28%, at least about 29%, at least about 30%, at least about 31%, at least about 32%, at least about 33%, at least about 34%, at least about 35%, at least about 36%, at least about 37%, at least about 38%, at least about 39%, at least about 40%, at least about 41%, at least about 42%, at least about 43%, at least about 44%, at least about 45%, at least about 46%, at least about 47%, at least about 48%, at least about 49%, at least about 50%, at least about 51%, at least about 52%, at least about 53%, at least about 54%, at least about 55%, at least about 56%, at least about 57%, at least about 58%, at least about 59%, In some aspects, the expression of one or more autoantibodies is at least about 25%, at least 50%, or 100% less than that in a control sample.

[0240] The expression of autoantibodies can be separated, purified, measured and / or monitored using any method known in the art. As a non-limiting example, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), immunoradiometric assay, fluorescent immunoassay, chemiluminescence assay, bioluminescence assay and Western blot can be used to detect autoantibodies. In some aspects, a protein array combination (panel) comprising various antigens can be used to perform autoantibody analysis. As a non-limiting example, the protein array combination can be a customized protein array combination of autoantigens, which include nuclear antigens, cytoplasmic / matrix antigens, and tissue / organ specific antigens. The sample to be tested may include whole blood, serum, plasma, urine, CSF or other suitable body fluids. Samples can be obtained from the subject before, during and / or after ICI treatment, and the expression of autoantibodies can be quantified to assess the risk of irAEs. In some aspects, the autoantibody spectrum is a plasma autoantibody spectrum. Risk assessment includes predicting, diagnosing, or monitoring ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

[0241] Cytokine profile

[0242] In some aspects, present disclosure provides cytokine profiles associated with ICI-related irAEs. In some aspects, cytokine profiles include one or more cytokines with elevated levels compared to control samples in irAE subjects. In some aspects, cytokine profiles include one or more cytokines with reduced levels compared to control samples in irAE subjects.

[0243] In some aspects, the cytokine is one or more of CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, or any combination thereof. In some aspects, the disclosed cytokines may include one or more cytokines disclosed in U.S. Patent Application No. 14 / 045,482 (U.S. Patent Application Publication No. US2021 / 0263045), the disclosures of which are incorporated herein by reference in their entirety.

[0244] In some aspects, the cytokine profile includes baseline or pre-treatment cytokines that are associated with future toxicities. In some aspects, the cytokine profile includes cytokines that are continuously expressed during treatment. In some aspects, these cytokines can be used as biomarkers to assess a subject's risk of developing an irAE before, during, or after ICI treatment.

[0245] In some aspects, the method for predicting or diagnosing that a subject has a high risk of irAE associated with ICI treatment includes assessing the expression of one or more of cytokines CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, or any combination thereof. In some aspects, if the expression of one or more of cytokines CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, or any combination thereof is increased compared to the expression in the control sample, then predicting or diagnosing that the subject has a high risk of irAE. In some aspects, if the expression of cytokine CXCL2 is increased compared to the expression in the control sample, then predicting or diagnosing that the subject has a high risk of irAE. In some aspects, if the expression of cytokine CXCL5 is increased compared to the expression in the control sample, then predicting or diagnosing that the subject has a high risk of irAE. In some aspects, if the expression of cytokine CXCL6 is increased compared to the expression in the control sample, then predicting or diagnosing that the subject has a high risk of irAE. In some respects, if the expression of cytokine CCL7 is increased compared with the expression in control samples, the prediction or diagnosis subject has a high risk of irAE. In some respects, if the expression of cytokine CCL19 is increased compared with the expression in control samples, the prediction or diagnosis subject has a high risk of irAE. In some respects, if the expression of cytokine IFNγ is increased compared with the expression in control samples, the prediction or diagnosis subject has a high risk of irAE. In some respects, if the expression of cytokine IL-6 is increased compared with the expression in control samples, the prediction or diagnosis subject has a high risk of irAE. In some respects, if the expression of cytokine CXCL9 is increased compared with the expression in control samples, the prediction or diagnosis subject has a high risk of irAE. In some respects, if the expression of cytokine CXCL10 is increased compared with the expression in control samples, the prediction or diagnosis subject has a high risk of irAE.

[0246] In some aspects, the cytokine profile includes cytokines that have continued to increase expression after starting ICI treatment. In some aspects, the cytokines that continue to increase expression after starting ICI treatment are one or more of CXCL5, IL-6, IFN-γ, CXCL9, CXCL10, or any combination thereof. In some aspects, the cytokine that continues to increase expression is CXCL5. In some aspects, the cytokine that continues to increase expression is IL-6. In some aspects, the cytokine that continues to increase expression is IFN-γ. In some aspects, the cytokine that continues to increase expression is CXCL9. In some aspects, the cytokine that continues to increase expression is CXCL10.

[0247] In some aspects, the method for predicting or diagnosing a subject to have a low risk of irAE associated with ICI treatment includes assessing the expression of one or more of cytokines CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, or any combination thereof. In some aspects, if the expression of one or more of cytokines CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, or any combination thereof is lower than the expression in the control sample, then predicting or diagnosing the subject to have a low risk of irAE. In some aspects, if the expression of cytokine CXCL2 is lower than the expression in the control sample, then predicting or diagnosing the subject to have a low risk of irAE. In some aspects, if the expression of cytokine CXCL5 is lower than the expression in the control sample, then predicting or diagnosing the subject to have a low risk of irAE. In some aspects, if the expression of cytokine CXCL6 is lower than the expression in the control sample, then predicting or diagnosing the subject to have a low risk of irAE. In some respects, if the expression of cytokine CCL7 is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE. In some respects, if the expression of cytokine CCL19 is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE. In some respects, if the expression of cytokine IFNγ is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE. In some respects, if the expression of cytokine IL-6 is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE. In some respects, if the expression of cytokine CXCL9 is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE. In some respects, if the expression of cytokine CXCL10 is lower than the expression in the control sample, the prediction or diagnosis subject has a low risk of irAE.

[0248] In some aspects, in a prognostic or diagnostic process, one or more of the disclosed cytokines having elevated expression has an elevated expression level that is at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, about 99%, or at least about 100% greater than the expression in a control sample.

[0249] In some aspects, in a prognostic or diagnostic process, one or more of the disclosed cytokines having decreased expression has an expression level that is at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least about 100% lower than the expression in a control sample.

[0250] In some aspects, during prognosis or diagnosis, the concentration of one or more of the disclosed cytokines is about 10 pg / ml, about 20 pg / ml, about 30 pg / ml, about 40 pg / ml, about 50 pg / ml, about 60 pg / ml, about 70 pg / ml, about 80 pg / ml, about 90 pg / ml, about 100 pg / ml, about 120 pg / ml, about 140 pg / ml, about 150 pg / ml, about 160 pg / ml, about 180 pg / ml, about 200 pg / ml, about 300 pg / ml, about 400 pg / ml, about 500 pg / ml, about 600 pg / ml, about 700 pg / ml, or about 800 pg / ml.

[0251] In some aspects, during prognosis or diagnosis, one or more of the disclosed cytokines has an elevated expression level, wherein the expression has a fold change of at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, or at least about 20 as compared to the expression level in a control sample.

[0252] In some aspects, the present disclosure provides a cytokine profile for monitoring the risk of irAEs associated with ICI therapy in a subject. In some aspects, the cytokine profile includes one or more cytokines with elevated levels compared to a control sample in an irAE subject. In some aspects, the cytokine profile includes one or more cytokines with reduced levels compared to a control sample in an irAE subject.

[0253] In some aspects, the cytokines used to monitor the risk of irAEs associated with ICI therapy are one or more of CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, or any combination thereof. In some aspects, the disclosed cytokines may include one or more cytokines disclosed in U.S. Patent Application No. 14 / 045,482 (U.S. Patent Application Publication No. US2021 / 0263045), the disclosures of which are incorporated herein by reference in their entirety.

[0254] In some aspects, the cytokine profile used to monitor the risk of irAEs associated with ICI treatment includes baseline or pre-treatment cytokines associated with future toxicity. In some aspects, the cytokine profile used to monitor the risk of irAEs associated with ICI treatment includes cytokines that are continuously expressed during treatment. In some aspects, these cytokines are used as biomarkers to assess the risk of irAEs in subjects before, during, or after ICI treatment.

[0255] In some aspects, if the expression of one or more of cytokines CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10 or any combination thereof is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of cytokine CXCL2 is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of cytokine CXCL5 is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of cytokine CXCL6 is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of cytokine CCL7 is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of cytokine CCL19 is increased compared to the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of the cytokine IFNγ is increased compared with the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of the cytokine IL-6 is increased compared with the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of the cytokine CXCL9 is increased compared with the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of the cytokine CXCL10 is increased compared with the expression in the control sample, the monitored subject may have a high risk of irAE.

[0256] In some aspects, the cytokine profile for monitoring the risk of irAEs associated with ICI treatment includes cytokines that have continued to increase expression after starting ICI treatment. In some aspects, the cytokines that have continued to increase expression after starting ICI treatment are one or more of CXCL5, IL-6, IFN-γ, CXCL9, CXCL10, or any combination thereof. In some aspects, the cytokine that has continued to increase expression is CXCL5. In some aspects, the cytokine that has continued to increase expression is IL-6. In some aspects, the cytokine that has continued to increase expression is IFN-γ. In some aspects, the cytokine that has continued to increase expression is CXCL9. In some aspects, the cytokine that has continued to increase expression is CXCL10.

[0257] In some respects, if the expression of one or more of cytokines CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10 or any combination thereof is lower than the expression in the control sample, the monitored subject can have a low risk of irAE occurring. In some respects, if the expression of cytokine CXCL2 is lower than the expression in the control sample, the monitored subject can have a high risk of irAE occurring. In some respects, if the expression of cytokine CXCL5 is lower than the expression in the control sample, the monitored subject can have a high risk of irAE occurring. In some respects, if the expression of cytokine CXCL6 is lower than the expression in the control sample, the monitored subject can have a high risk of irAE occurring. In some respects, if the expression of cytokine CCL7 is lower than the expression in the control sample, the monitored subject can have a high risk of irAE occurring. In some respects, if the expression of cytokine CCL19 is lower than the expression in the control sample, the monitored subject can have a high risk of irAE occurring. In some aspects, if the expression of the cytokine IFNγ is lower than the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of the cytokine IL-6 is lower than the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of the cytokine CXCL9 is lower than the expression in the control sample, the monitored subject may have a high risk of irAE. In some aspects, if the expression of the cytokine CXCL10 is lower than the expression in the control sample, the monitored subject may have a high risk of irAE.

[0258] In some aspects, during monitoring, one or more of the disclosed cytokines having elevated expression has an elevated expression level that is at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least about 100% greater than the expression in a control sample.

[0259] In some aspects, during monitoring, one or more of the disclosed cytokines having decreased expression has an expression level that is at least about 0.01%, at least about 0.05%, at least about 0.1%, at least about 0.2%, at least about 0.3%, at least about 0.4%, at least about 0.5%, at least about 1%, at least about 5%, at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least about 100% lower than the expression in a control sample.

[0260] In some aspects, during the monitoring process, the concentration of one or more of the disclosed cytokines is about 10 pg / ml, about 20 pg / ml, about 30 pg / ml, about 40 pg / ml, about 50 pg / ml, about 60 pg / ml, about 70 pg / ml, about 80 pg / ml, about 90 pg / ml, about 100 pg / ml, about 120 pg / ml, about 140 pg / ml, about 150 pg / ml, about 160 pg / ml, about 180 pg / ml, about 200 pg / ml, about 300 pg / ml, about 400 pg / ml, about 500 pg / ml, about 600 pg / ml, about 700 pg / ml, or about 800 pg / ml.

[0261] In some aspects, during monitoring, one or more of the disclosed cytokines has elevated expression, wherein the expression has a fold change of at least about 1, at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, or at least about 20 compared to the expression in the control sample.

[0262] The detection, quantification and / or monitoring of cytokines can adopt methods well known in the art, including enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), immunoradiometric assay, fluorescence immunoassay, chemiluminescence assay, bioluminescence assay and Western blotting. In some aspects, cytokine levels are monitored using a ready-made cytokine panel (such as Bio-Plex Pro Human Chemokine 40-plex Panel, Bio-Rad Laboratories, Hercules City, California). The concentration of cytokines can be determined based on the fitting of the provided mean fluorescence intensity standard curve. The sample to be tested may include whole blood, serum, plasma, urine, CSF or other suitable body fluids. Samples can be obtained from the subject before, during and / or after ICI treatment, and cytokine concentrations are quantified to assess the risk of irAEs. In some aspects, the sample is obtained from the subject before starting ICI treatment. Risk assessment includes prediction, diagnosis, or monitoring of ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

[0263] Immune cell profile

[0264] In some aspects, the present disclosure provides immune cell profiles associated with ICI-related irAEs. In some aspects, the immune cell profiles include the presence of immune cell subpopulations in irAE subjects that are different from the immune cell subpopulations in control samples. In some aspects, the immune cell profiles include Figure 4A One or more of the indicated immune cells or any combination thereof.

[0265] In some aspects, the immune cell profile includes baseline or pre-treatment immune cell subsets associated with future toxicity. In some aspects, immune cell subsets can be used as biomarkers to assess the risk of irAEs in subjects before or during ICI treatment. In some aspects, the immune cell profile includes one or more immune cell subsets whose abundance is increased in the subject's pre-treatment or baseline sample compared to the abundance of the same immune cell subset in the control sample. In some aspects, the immune cell profile includes one or more immune cell subsets whose abundance is lower in the subject's pre-treatment or baseline sample than in the control sample. In some aspects, the immune cell profile includes immune cell subsets whose abundance increases after starting ICI treatment in the subject's sample compared to the abundance of the same immune cell subset in the control sample. In some aspects, immune cell subsets include PD-L1+ initial B cells, converted memory B cells, CTLA4+ monocytes, and CXCR3+CD8T cells.

[0266] In some aspects, present disclosure provides a method for predicting or diagnosing that a subject has a high risk of irAE associated with ICI treatment, the method including assessing the abundance of one or more of immune cell subpopulation PD-L1+ initial B cells, conversion memory B cells, and / or CTLA4+ monocytes. In some aspects, if the abundance of one or more of immune cell subpopulation PD-L1+ initial B cells, conversion memory B cells, or any combination thereof is lower than the abundance in the control sample, and / or the abundance of CTLA4+ monocytes is increased compared to the abundance in the control sample, then the subject is predicted or diagnosed to have a high risk of irAE. In some aspects, if the abundance of immune cell subpopulation PD-L1+ initial B cells is lower than the abundance in the control sample, the subject is predicted or diagnosed to have a high risk of irAE. In some aspects, if the abundance of immune cell subpopulation PD-L1+ initial B cells is lower than the abundance in the control sample, the subject is predicted or diagnosed to have a high risk of irAE. In some aspects, if the abundance of immune cell subpopulation conversion memory B cells is lower than the abundance in the control sample, the subject is predicted or diagnosed to have a high risk of irAE. In some aspects, a subject is predicted or diagnosed as having a high risk of developing an irAE if the abundance of the immune cell subset CTLA4+ monocytes is elevated compared to the abundance in a control sample.

[0267] In some aspects, present disclosure provides a method for predicting or diagnosing that a subject has a low risk of irAE associated with ICI treatment, the method including assessing the abundance of one or more of immune cell subpopulations PD-L1+ initial B cells, conversion memory B cells, and / or CTLA4+ monocytes. In some aspects, if the abundance of immune cell subpopulations PD-L1+ initial B cells, conversion memory B cells, or any combination thereof is increased compared with the abundance in a control sample, and / or the abundance of CTLA4+ monocytes is lower than the abundance in a control sample, then the prediction or diagnosis subject has a low risk of irAE occurring. In some aspects, if the abundance of immune cell subpopulations PD-L1+ initial B cells is increased compared with the abundance in a control sample, then the prediction or diagnosis subject has a low risk of irAE occurring. In some aspects, if the abundance of immune cell subpopulations PD-L1+ initial B cells is increased compared with the abundance in a control sample, then the prediction or diagnosis subject has a low risk of irAE occurring. In some aspects, if the abundance of immune cell subpopulations conversion memory B cells is increased compared with the abundance in a control sample, then the prediction or diagnosis subject has a low risk of irAE occurring. In some aspects, if the abundance of the immune cell subset CTLA4+ monocytes is lower than that in a control sample, the subject is predicted or diagnosed as having a low risk of developing an irAE.

[0268] In some aspects, if the abundance of one or more of the immune cell subsets PD-L1+ initial B cells, converted memory B cells, and / or CXCR3+CD8T cells in the subject sample changes after ICI treatment starts, compared to the abundance in the control sample, it is predicted or diagnosed that the subject has a high risk of irAE. In some aspects, if the change in the abundance of the immune cell subset PD-L1+ initial B cells strengthens after ICI treatment starts, compared to the abundance in the control sample, it is predicted or diagnosed that the subject has a high risk of irAE. In some aspects, if the change in the abundance of the immune cell subset PD-L1+ initial B cells strengthens after ICI treatment starts, compared to the abundance in the control sample, it is predicted or diagnosed that the subject has a high risk of irAE. In some aspects, if the change in the abundance of the immune cell subset CXCR3+CD8T cells strengthens after ICI treatment starts, compared to the abundance in the control sample, it is predicted or diagnosed that the subject has a high risk of irAE.

[0269] In some aspects, in a prognostic or diagnostic process, the abundance of immune cells in an immune cell subpopulation can be determined from a sample by determining the percentage of immune cells in the sample that fall into that subpopulation (e.g., X% of the immune cells in the sample are subpopulation 1). The percentage of immune cells in a given subpopulation can then be compared to the percentage of immune cells in that subpopulation in a control sample. In some aspects, the abundance of immune cells in one or more immune cell subpopulations (e.g., percentage) can be lower than the abundance of immune cells in one or more immune cell subpopulations in a control sample by at least about 0.1 percentage points (e.g., 1.0% compared to 1.1%), at least about 0.2 percentage points, at least about 0.3 percentage points, at least about 0.4 percentage points, at least about 0.5 percentage points, at least about 0.6 percentage points, at least about 0.7 percentage points, at least about 0.8 percentage points, at least about 0.9 percentage points, at least about 1 percentage point, at least about 2 percentage points, at least about 3 percentage points, at least about 4 percentage points, at least about 5 percentage points, at least about 6 percentage points. , at least about 7 percentage points, at least about 8 percentage points, at least about 9 percentage points, about 10 percentage points, at least about 15 percentage points, at least about 20 percentage points, at least about 25 percentage points, at least about 30 percentage points, at least about 35 percentage points, at least about 40 percentage points, at least about 45 percentage points, at least about 50 percentage points, at least about 55 percentage points, at least about 60 percentage points, at least about 65 percentage points, at least about 70 percentage points, at least about 75 percentage points, at least about 80 percentage points, at least about 85 percentage points, at least about 90 percentage points, at least about 95 percentage points, at least about 99 percentage points, or at least about 100 percentage points.

[0270] In some aspects, during a prediction or diagnosis, the abundance of immune cells in an immune cell subpopulation can be determined from a sample by determining the percentage of immune cells in the sample that fall into that subpopulation (e.g., X% of the immune cells in the sample are subpopulation 1). The percentage of immune cells in a given subpopulation can then be compared to the percentage of immune cells in that subpopulation in a control sample. In some aspects, the abundance (e.g., percentage) of immune cells in one or more immune cell subpopulations can be higher than the abundance of immune cells in one or more immune cell subpopulations in a control sample by at least about 0.1 percentage points (e.g., 1.0% compared to 1.1%), at least about 0.2 percentage points, at least about 0.3 percentage points, at least about 0.4 percentage points, at least about 0.5 percentage points, at least about 0.6 percentage points, at least about 0.7 percentage points, at least about 0.8 percentage points, at least about 0.9 percentage points, at least about 1 percentage point, at least about 2 percentage points, at least about 3 percentage points, at least about 4 percentage points, at least about 5 percentage points, at least about 6 percentage points, or more. at least about 7 percentage points, at least about 8 percentage points, at least about 9 percentage points, about 10 percentage points, at least about 15 percentage points, at least about 20 percentage points, at least about 25 percentage points, at least about 30 percentage points, at least about 35 percentage points, at least about 40 percentage points, at least about 45 percentage points, at least about 50 percentage points, at least about 55 percentage points, at least about 60 percentage points, at least about 65 percentage points, at least about 70 percentage points, at least about 75 percentage points, at least about 80 percentage points, at least about 85 percentage points, at least about 90 percentage points, at least about 95 percentage points, at least about 99 percentage points, or at least about 100 percentage points.

[0271] In some aspects, the methods of the present disclosure provide an immune cell profile for monitoring the risk of irAEs associated with ICI therapy in a subject. In some aspects, the immune cell profile includes the presence of different immune cell subpopulations in the irAE subject compared to a control sample. In some aspects, the immune cell profile includes Figure 4A One or more of the immune cells shown or any combination thereof.

[0272] In some aspects, the monitoring method includes providing a sample of the subject before ICI treatment, assessing the subject's immune cell profile, and comparing the immune cell profile with a control sample. In some aspects, the immune cell profile includes a baseline or pre-treatment immune cell subset associated with future toxicity. In some aspects, immune cell subsets can be used as biomarkers to assess the risk of irAEs in subjects before or during ICI treatment. In some aspects, the immune cell profile includes one or more immune cell subsets whose abundance is increased in the subject's pre-treatment or baseline sample compared with the abundance in the control sample. In some aspects, the immune cell profile includes one or more immune cell subsets whose abundance is reduced in the subject's pre-treatment or baseline sample compared with the abundance in the control sample. In some aspects, the immune cell profile includes immune cell subsets whose abundance increases after the start of ICI treatment in the subject's sample compared with the control sample. In some aspects, immune cell subsets include PD-L1+ initial B cells, converted memory B cells, CTLA4+ monocytes, and CXCR3+CD8T cells.

[0273] In some aspects, if the abundance of one or more of the immune cell subset PD-L1+ initial B cells, converted memory B cells, or any combination thereof is lower than the abundance in the control sample, and / or if the abundance of CTLA4+ monocytes is increased compared to the abundance in the control sample, the monitored subject has a high risk of irAE associated with ICI treatment. In some aspects, if the abundance of the immune cell subset PD-L1+ initial B cells is lower than the abundance in the control sample, the monitored subject has a high risk of irAE. In some aspects, if the abundance of the immune cell subset PD-L1+ memory B cells is lower than the abundance in the control sample, the monitored subject has a high risk of irAE. In some aspects, if the abundance of the immune cell subset CTLA4+ monocytes is increased compared to the abundance in the control sample, the monitored subject has a high risk of irAE.

[0274] In some aspects, if the abundance of one or more of the immune cell subset PD-L1+ initial B cells, conversion memory B cells, or any combination thereof is increased compared to the abundance in the control sample, and / or if the abundance of CTLA4+ monocytes is lower than the abundance in the control sample, the monitored subject has a low risk of irAE occurring. In some aspects, if the abundance of the immune cell subset PD-L1+ initial B cells is increased compared to the abundance in the control sample, the monitored subject has a low risk of irAE occurring. In some aspects, if the abundance of the immune cell subset PD-L1+ initial B cells is increased compared to the abundance in the control sample, the monitored subject has a low risk of irAE occurring. In some aspects, if the abundance of the immune cell subset CTLA4+ monocytes is lower than the abundance in the control sample, the monitored subject has a low risk of irAE occurring.

[0275] In some aspects, if the abundance of one or more of the immune cell subsets PD-L1+ initial B cells, converted memory B cells, and / or CXCR3+CD8T in the subject sample is enhanced after ICI treatment starts, compared to the abundance in the control sample, the monitored subject has a high risk of irAE. In some aspects, if the change in the abundance of the immune cell subset PD-L1+ initial B cells is enhanced after ICI treatment starts, compared to the abundance in the control sample, the monitored subject has a high risk of irAE. In some aspects, if the change in the abundance of the immune cell subset PD-L1+ initial B cells is enhanced after ICI treatment starts, compared to the abundance in the control sample, the monitored subject has a high risk of irAE. In some aspects, if the change in the abundance of the immune cell subset CXCR3+CD8T cells is enhanced after ICI treatment starts, compared to the abundance in the control sample, the monitored subject has a high risk of irAE.

[0276] In some aspects, during monitoring, the abundance of immune cells in an immune cell subpopulation can be determined from a sample by determining the percentage of immune cells in the sample that fall into that subpopulation (e.g., X% of the immune cells in the sample are subpopulation 1). The percentage of immune cells in a given subpopulation can then be compared with the percentage of immune cells in that subpopulation in a control sample. In some aspects, the abundance (e.g., percentage) of immune cells in one or more immune cell subpopulations can be lower than the abundance of immune cells in one or more immune cell subpopulations in a control sample by at least about 0.1 percentage points (e.g., 1.0% compared to 1.1%), at least about 0.2 percentage points, at least about 0.3 percentage points, at least about 0.4 percentage points, at least about 0.5 percentage points, at least about 0.6 percentage points, at least about 0.7 percentage points, at least about 0.8 percentage points, at least about 0.9 percentage points, at least about 1 percentage point, at least about 2 percentage points, at least about 3 percentage points, at least about 4 percentage points, at least about 5 percentage points, at least about 6 percentage points, or less. at least about 7 percentage points, at least about 8 percentage points, at least about 9 percentage points, about 10 percentage points, at least about 15 percentage points, at least about 20 percentage points, at least about 25 percentage points, at least about 30 percentage points, at least about 35 percentage points, at least about 40 percentage points, at least about 45 percentage points, at least about 50 percentage points, at least about 55 percentage points, at least about 60 percentage points, at least about 65 percentage points, at least about 70 percentage points, at least about 75 percentage points, at least about 80 percentage points, at least about 85 percentage points, at least about 90 percentage points, at least about 95 percentage points, at least about 99 percentage points, or at least about 100 percentage points.

[0277] In some aspects, during monitoring, the abundance of immune cells in an immune cell subpopulation can be determined from a sample by determining the percentage of immune cells in the sample that fall into that subpopulation (e.g., X% of the immune cells in the sample are subpopulation 1). The percentage of immune cells in a given subpopulation can then be compared with the percentage of immune cells in that subpopulation in a control sample. In some aspects, the abundance (e.g., percentage) of immune cells in one or more immune cell subpopulations can be higher than the abundance of immune cells in one or more immune cell subpopulations in a control sample by at least about 0.1 percentage points (e.g., 1.0% compared to 1.1%), at least about 0.2 percentage points, at least about 0.3 percentage points, at least about 0.4 percentage points, at least about 0.5 percentage points, at least about 0.6 percentage points, at least about 0.7 percentage points, at least about 0.8 percentage points, at least about 0.9 percentage points, at least about 1 percentage point, at least about 2 percentage points, at least about 3 percentage points, at least about 4 percentage points, at least about 5 percentage points, at least about 6 percentage points, or more. at least about 7 percentage points, at least about 8 percentage points, at least about 9 percentage points, about 10 percentage points, at least about 15 percentage points, at least about 20 percentage points, at least about 25 percentage points, at least about 30 percentage points, at least about 35 percentage points, at least about 40 percentage points, at least about 45 percentage points, at least about 50 percentage points, at least about 55 percentage points, at least about 60 percentage points, at least about 65 percentage points, at least about 70 percentage points, at least about 75 percentage points, at least about 80 percentage points, at least about 85 percentage points, at least about 90 percentage points, at least about 95 percentage points, at least about 99 percentage points, or at least about 100 percentage points.

[0278] Immune cell signatures can be detected, quantified and / or monitored using methods well known in the art, including immune spectrum analysis assays, mass cytometry (time-of-flight flow cytometry CyTOF), flow cytometry, and cell sorting (including FACS and immunomagnetic separation). In some aspects, immune cell signatures are detected by high-dimensional mass cytometry (time-of-flight flow cytometry (CyTOF)). Samples to be tested may include whole blood, serum, plasma, urine, CSF, or other suitable body fluids. Samples can be obtained from subjects before, during, and / or after ICI treatment, and immune cell signatures can be identified to assess the risk of irAEs. Risk assessment includes predicting, diagnosing, or monitoring ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

[0279] In some aspects, the method for evaluating the occurrence of irAE risk in a subject disclosed is to evaluate ICI-related myositis, ICI-related myocarditis or the risk of ICI-related combined myositis and myocarditis.Myositis and myocarditis may occur as separate toxicities, or may occur simultaneously with one or more other ICI-related irAEs, and the other ICI-related irAEs include ocular toxicity, rash, dermatitis, pruritus, colitis, hepatitis, nephritis, arthritis, myositis, myocarditis, pneumonia, thyroiditis, hypophysitis, adrenalitis, gastritis, pancreatitis, vasculitis, diabetes, myasthenia gravis, encephalitis, peripheral neuropathy, meningitis, hemolytic anemia, thrombocytopenia, hemophagocytic lymphohistiocytosis / macrophage activation syndrome (HLH / MAS), aplastic anemia, pure red cell aplasia, and / or neutropenia. Autoimmune inflammatory myopathy (such as myositis or myocarditis) can occur spontaneously or as a paraneoplastic phenomenon.

[0280] Combination Spectrum

[0281] In some aspects, the present disclosure further provides a profile comprising one or more of a transcript profile, a cytokine profile, an autoantibody profile, an immune cell profile, or any combination thereof. The profile comprises the following: Figure 2B -K, Figure 3B -F, Figure 4A In some aspects, the spectrum includes transcripts, autoantibodies, cytokines, and / or immune cells provided in the present invention, or a combination thereof. In some aspects, the spectrum includes transcripts, cytokines, autoantibodies, immune cells, or any combination thereof before the baseline or treatment related to future toxicity. In some aspects, one or more of transcripts, autoantibodies, cytokines, immune cell subsets, or any combination thereof are used as biomarkers to assess the risk of irAEs occurring before, during, or after treatment of an ICI treatment subject. In some aspects, irAEs are ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

[0282] In some aspects, the method includes providing a sample of a subject, evaluating one or more transcripts, autoantibody expression, cytokine expression, immune cell subset abundance, or any combination thereof in the sample, and predicting the risk of occurrence / diagnosis of irAE in the subject. In some aspects, when the spectrum includes one or more transcripts, autoantibodies, cytokines, immune cells, or any combination thereof, and its level, expression, or abundance is higher than that of the control sample, the subject can be predicted to have a high risk of irAE associated with ICI treatment or be diagnosed with irAE. In some aspects, when the spectrum includes one or more transcripts, autoantibodies, cytokines, immune cells, or any combination thereof, and its level, expression, or abundance is lower than that of the control sample, the subject can be predicted to have a low risk of irAE associated with ICI treatment.

[0283] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with increased levels, expression, or abundance of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, I compared to the transcript levels, expression, or abundance in control samples at baseline or before the start of ICI treatment. Higher transcript levels, expression, or abundance of one or more of FNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC14 4A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, N Lower level, expression, or abundance of one or more of FIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, GRASP, PD-L1+ naive B cells, and / or switched memory B cells.

[0284] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with: higher transcript levels, expression, or abundance of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTG, compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment. In some embodiments, the present invention relates to a method for inhibiting the expression of at least one of the following proteins: S2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, PD-L1+ naive B cells, and / or switched memory B cells.

[0285] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with increased transcript levels, expression, or abundance of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFN-γ, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IL-20, IL-21, IL-22, IL-23, IL-24, IL-25, IL-26, IL-27, IL-28, IL-30, IL-31, IL-32, IL-33, IL-34, IL-35, IL-36, IL-37, IL-38, IL-40, IL-50, IL-60, IL-7 In some embodiments, the present invention provides a method for detecting the expression of a higher transcript level, expression, or abundance of one or more of IL-17, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or a lower transcript level, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells.

[0286] In some aspects, prediction or diagnosis of a subject at higher risk for developing an irAE is associated with increased expression, or abundance, of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, C-terminal domains, compared to the transcript level, expression, or abundance in a control sample at baseline or before initiation of ICI treatment. In some embodiments, the present invention provides a method for detecting the expression of amplified phosphatase inhibitory factor (PAGE) in monocytes, wherein the PAGE is amplified by amplifying the phosphatase inhibitory factor (PAGE) inhibitor, wherein the PAGE is amplified by amplifying the phosphatase inhibitory factor (PAGE) inhibitor, wherein the PAGE is amplified by amplifying the phosphatase inhibitory factor (PAGE) inhibitor, wherein the PAGE is amplified by amplifying the phosphatase inhibitory factor (PAGE) inhibitor, and / or the PAGE is amplified by amplifying the phosphatase inhibitory factor (PAGE) inhibitor, wherein the PAGE is amplified by amplifying the phosphatase inhibitory factor (PAGE) inhibitor, wherein the PAGE is amplified by amplifying the phosphatase inhibitor, PAGE is amplified by amplifying the phosphatase inhibitor, PAGE is amplified by amplifying the phosphatase inhibitor,

[0287] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with elevated levels, expression, or abundance of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment. 4+ monocytes, and / or lower levels, expression, or abundance of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, KLF9, PD-L1+ naive B cells, and / or switched memory B cells.

[0288] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with: higher transcript levels, expression, or abundance of one or more of LILRB4, CISH, PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or lower levels, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells, compared to the transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment.

[0289] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with: higher transcript levels, expression, or abundance of one or more of LILRB4, CISH, PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and lower levels, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells, compared to the transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment.

[0290] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with: higher transcript levels, expression, or abundance of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NF Lower level, expression, or abundance of one or more of IL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, PD-L1+ naive B cells, and / or switched memory B cells.

[0291] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with: higher transcript levels, expression, or abundance of one or more of CISH, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or AREG, EGF, IL-6, IL-1β, IL-1β, IL-2β, IL-3β, IL-4β, IL-6β, IL-7β, IL-8β, IL-9β, IL-10β, IL-11β, IL-12β, IL-13β, IL-14β, IL-15β, IL-16β, IL-17β, IL-18β, IL-19β, IL-20β, IL-21β, IL-22β, IL-23β, IL-24β, IL-25β, IL-27β, IL-28β, IL-29β, IL-30β, IL-31β, IL-32β, IL-33β, IL-34β, IL-35β, IL-36β, IL-37β, IL-38β, IL-39β, IL-40β, IL-41β, IL-42β, IL-43β, IL-50β, IL-51β, IL-52β, IL-6β, IL-18β, IL-29β, IL-31β, IL-43β, IL-51β, IL- Lower level, expression, or abundance of one or more of REG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, KLF9, PD-L1+ naive B cells, and / or switched memory B cells.

[0292] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with increased levels, expression, or abundance of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, I, compared to the transcript levels, expression, or abundance in control samples at baseline or before the start of ICI treatment. In some embodiments, the present invention provides a method for detecting the expression of amplified phosphatase inhibitory factor (PAGE) in monocytes, wherein the phosphatase inhibitory factor (PAGE) is expressed in an amount greater than or equal to 100kDa. ...

[0293] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with: higher transcript levels, expression, or abundance of one or more of PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or lower levels, expression, or abundance of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, TSC22D3, PD-L1+ naive B cells, and / or switched memory B cells, compared to the transcript levels, expression, or abundance in a control sample at baseline or before initiation of ICI treatment.

[0294] In some aspects, subjects predicted or diagnosed as having a higher risk of developing an irAE are associated with: higher transcript levels, expression, or abundance of one or more of PARP9, CISH, CXCR6, LPAR6, ASGR2, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTG2, compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment. In some embodiments, the present invention relates to a method for inhibiting the expression of at least one of the following proteins: S2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSRNP1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, EGR1PD-L1+ naive B cells, and / or switched memory B cells.

[0295] In some aspects, a higher risk of developing an irAE is associated with lower expression of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4 in monocytes. Decreased transcript level, expression, or abundance of one or more of, or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1 , CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4 420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBI Elevated transcript levels, expression, or abundance of one or more of: A, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, GRASP and / or PD-L1+ naive B cells, and / or switched memory B cells.

[0296] In some aspects, subjects predicted or diagnosed as having a lower risk of developing an irAE are associated with lower transcript levels, expression, or abundance of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR6, compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment. 4, higher transcript levels, expression, or abundance of one or more of NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, PD-L1+ naive B cells, and / or switched memory B cells.

[0297] In some aspects, subjects predicted or diagnosed as having a lower risk of developing an irAE are associated with increased levels, expression, or abundance of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment. Lower transcript levels, expression, or abundance of one or more of CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or higher transcript levels, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells.

[0298] In some aspects, subjects predicted or diagnosed as having a lower risk of developing an irAE are associated with increased levels, expression, or abundance of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment. Transcript levels, expression, or abundance of one or more of CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or higher transcript levels, expression, or abundance of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, PD-L1+ naive B cells, and / or switched memory B cells.

[0299] In some aspects, subjects predicted or diagnosed as having a lower risk of developing an irAE are associated with increased expression, or abundance, of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ compared to the transcript level, expression, or abundance in a control sample at baseline or before initiation of ICI treatment. In some embodiments, the present invention provides a method for detecting the expression of a novel phosphatase inhibitory protein α (API) in monocytes, lower transcript levels, expression, or abundance of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, KLF9, PD-L1+ naive B cells, and / or switched memory B cells.

[0300] In some aspects, a subject predicted or diagnosed as having a lower risk of developing an irAE is associated with: higher transcript levels, expression, or abundance of one or more of LILRB4, CISH, PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or higher transcript levels, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells, compared to transcript levels, expression, or abundance in a control sample at baseline or before initiation of ICI treatment.

[0301] In some aspects, subjects predicted or diagnosed as having a lower risk of developing an irAE are associated with lower transcript levels, expression, or abundance of one or more of LILRB4, CISH, PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and higher transcript levels, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells, compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment.

[0302] In some aspects, subjects predicted or diagnosed as having a lower risk of developing an irAE are associated with lower transcript levels, expression, or abundance of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL, compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment. 3, higher transcript levels, expression, or abundance of one or more of FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, PD-L1+ naive B cells, and / or switched memory B cells.

[0303] In some aspects, subjects predicted or diagnosed as having a lower risk of developing an irAE are associated with lower transcript levels, expression, or abundance of one or more of CISH, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or AREG, ERE, compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment. G, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, KLF9, PD-L1+ naive B cells, and / or switched memory B cells.

[0304] In some aspects, subjects predicted or diagnosed as having a lower risk of developing an irAE are associated with increased levels, expression, or abundance of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL- 6, lower transcript levels, expression, or abundance of one or more of CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or higher transcript levels, expression, or abundance of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, PD-L1+ naive B cells, and / or switched memory B cells.

[0305] In some aspects, a subject predicted or diagnosed as having a lower risk of developing an irAE is associated with lower transcript levels, expression, or abundance of one or more of PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or higher transcript levels, expression, or abundance of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, TSC22D3, PD-L1+ naive B cells, and / or switched memory B cells, compared to the transcript levels, expression, or abundance in a control sample at baseline or before initiation of ICI treatment.

[0306] In some aspects, subjects predicted or diagnosed as having a lower risk of developing an irAE are associated with lower transcript levels, expression, or abundance of one or more of PARP9, CISH, CXCR6, LPAR6, ASGR2, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes, and / or KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, compared to transcript levels, expression, or abundance in control samples at baseline or before initiation of ICI treatment. , NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSRNP1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, EGR1, PD-L1+ naive B cells, and / or switched memory B cells.

[0307] In some aspects, the present disclosure also provides a spectrum for monitoring the risk of irAE, which includes one or more of a transcript spectrum, a cytokine spectrum, an autoantibody spectrum, an immune cell spectrum, or any combination thereof. The spectrum includes Table 5, Table 6, Table 8, Table 9, Table 10, Table 11, Figure 2B -K, Figure 3B -F, Figure 4A In some aspects, irAE is the risk of ICI-related myositis, ICI-related myocarditis or ICI-related myositis and myocarditis.

[0308] In some aspects, the method for monitoring irAE risk includes providing a sample of a subject, evaluating one or more transcripts, autoantibody expression, cytokine expression, immune cell subset abundance, or any combination thereof in the sample, and predicting the risk of irAE in the subject / diagnosing that the subject has irAE. In some aspects, when the spectrum includes one or more transcripts, autoantibodies, cytokines, immune cells, or any combination thereof, and its level, expression, or abundance is higher than that of the control sample, the monitored subject may have a higher risk of irAE associated with ICI treatment. In some aspects, when the spectrum includes one or more transcripts, autoantibodies, cytokines, immune cells, or any combination thereof, and its level, expression, or abundance is lower than that of the control sample, the monitored subject may have a lower risk of irAE associated with ICI treatment.

[0309] In some aspects, when LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTL is expressed as compared to the transcript level, expression, or abundance in a control sample at baseline or before initiation of ICI treatment. The transcript levels, expression, or abundance of one or more of the following genes are higher in A4+ monocytes, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, C XCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GP X3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD7 When the transcript level, expression, or abundance of one or more of 9a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, GRASP, PD-L1+ naive B cells, and / or switched memory B cells is lower, the monitored subject may have a higher risk of developing irAEs.

[0310] In some aspects, when the transcript level, expression, or abundance of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is higher, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFK When the transcript level, expression, or abundance of one or more of BIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, PD-L1+ naive B cells, and / or switched memory B cells is lower, the monitored subject may have a higher risk of developing an irAE.

[0311] In some aspects, when LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXC When the transcript level, expression, or abundance of one or more of L10, and / or CTLA4+ monocytes is higher, and / or the transcript level, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or converted memory B cells is lower, the monitored subject may have a higher risk of developing an irAE.

[0312] In some aspects, when LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, When the transcript level, expression, or abundance of one or more of CXCL10, and / or CTLA4+ monocytes is higher, and / or the transcript level, expression, or abundance of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, PD-L1+ naive B cells, and / or switched memory B cells is lower, the monitored subject may have a higher risk of developing an irAE.

[0313] In some aspects, when the transcript level, expression, or abundance of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is higher compared to the transcript level, expression, or abundance in a control sample at baseline or before initiation of ICI treatment , and / or lower transcript levels, expression, abundance of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, KLF9, PD-L1+ naive B cells, and / or switched memory B cells, the monitored subject may have a higher risk of developing an irAE.

[0314] In some aspects, the monitored subject may have a higher risk of developing an irAE when the transcript level, expression, or abundance of one or more of LILRB4, CISH, PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is higher, and / or the transcript level, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells is lower, compared to the transcript level, expression, or abundance in a control sample at baseline or before the start of ICI treatment.

[0315] In some aspects, the monitored subject may have a higher risk of developing an irAE when the transcript level, expression, or abundance of one or more of LILRB4, CISH, PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is higher, and the transcript level, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells is lower, compared to the transcript level, expression, or abundance in a control sample at baseline or before the start of ICI treatment.

[0316] In some aspects, when the transcript level, expression, or abundance of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is higher, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD7 is higher, compared to the transcript level, expression, or abundance in a control sample at baseline or before the start of ICI treatment. 9A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, PD-L1+ naive B cells, and / or switched memory B cells have lower transcript levels, expression, or abundance, then the monitored subject may have a higher risk of developing an irAE.

[0317] In some aspects, when the transcript level, expression, or abundance of one or more of CISH, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is higher, and / or AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VM When the transcript level, expression, or abundance of one or more of O1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, KLF9, PD-L1+ naive B cells, and / or converted memory B cells is lower, the monitored subject may have a higher risk of developing an irAE.

[0318] In some aspects, when LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monoclonal antibody is expressed compared to the transcript level, expression, or abundance in a control sample at baseline or before initiation of ICI treatment. When the transcript level, expression, or abundance of one or more of the above-mentioned genes is higher in the nuclear cells, and / or the transcript level, expression, or abundance of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, PD-L1+ naive B cells, and / or converted memory B cells is lower, the monitored subject may have a higher risk of developing an irAE.

[0319] In some aspects, the monitored subject may have a higher risk of developing an irAE when the transcript level, expression, or abundance of one or more of PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is higher, and / or the transcript level, expression, or abundance of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, TSC22D3, PD-L1+ naive B cells, and / or switched memory B cells is lower, compared to the transcript level, expression, or abundance in a control sample at baseline or before the start of ICI treatment.

[0320] In some aspects, when the transcript level, expression, or abundance of one or more of PARP9, CISH, CXCR6, LPAR6, ASGR2, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is higher, and / or KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, T When the transcript level, expression, or abundance of one or more of RIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSRNP1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, EGR1, PD-L1+ naive B cells, and / or converted memory B cells is lower, the monitored subject may have a higher risk of developing an irAE.

[0321] In some aspects, when LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTL is expressed as compared to the transcript level, expression, or abundance in a control sample at baseline or before initiation of ICI treatment. The transcript levels, expression, or abundance of one or more of the following genes are lower in A4+ monocytes, or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, C XCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GP X3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD7 When the transcript level, expression, or abundance of one or more of 9a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, GRASP, PD-L1+ naive B cells, and / or converted memory B cells is higher, the monitored subject can have a lower risk of developing irAEs.

[0322] In some aspects, when the transcript level, expression, or abundance of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is lower, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFK When the transcript level, expression, or abundance of one or more of BIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, PD-L1+ naive B cells, and / or switched memory B cells is higher, the monitored subject may have a lower risk of developing an irAE.

[0323] In some aspects, LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXC When the transcript level, expression, or abundance of one or more of L10, and / or CTLA4+ monocytes is lower, and / or the transcript level, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or converted memory B cells is higher, the monitored subject may have a lower risk of developing irAEs.

[0324] In some aspects, LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, C When the transcript level, expression, or abundance of one or more of XCL10, and / or CTLA4+ monocytes is lower, and / or the transcript level, expression, or abundance of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, PD-L1+ naive B cells, and / or switched memory B cells is higher, the monitored subject may have a lower risk of developing an irAE.

[0325] In some aspects, when the transcript level, expression, or abundance of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, CXCR6, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is lower, and / or AREG, ERK10 is lower, compared to the transcript level, expression, or abundance in a control sample at baseline or before initiation of ICI treatment. When the transcript level, expression, or abundance of one or more of EG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, KLF9, PD-L1+ naive B cells, and / or converted memory B cells is higher, the monitored subject can have a lower risk of developing irAEs.

[0326] In some aspects, the monitored subject may have a lower risk of developing an irAE when the transcript level, expression, or abundance of one or more of LILRB4, CISH, PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is lower, and / or the transcript level, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells is higher, compared to the transcript level, expression, or abundance in a control sample at baseline or before the start of ICI treatment.

[0327] In some aspects, the monitored subject may have a lower risk of developing an irAE when the transcript level, expression, or abundance of one or more of LILRB4, CISH, PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is lower and the transcript level, expression, or abundance of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, PD-L1+ naive B cells, and / or switched memory B cells is higher compared to the transcript level, expression, or abundance in a control sample at baseline or before the start of ICI treatment.

[0328] In some aspects, when the transcript level, expression, or abundance of one or more of LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is lower, and / or AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79 is lower, compared to the transcript level, expression, or abundance in a control sample at baseline or before initiation of ICI treatment. A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, PD-L1+ naive B cells, and / or converted memory B cells. When the transcript level, expression, or abundance of one or more of the following is higher, the monitored subject can have a lower risk of developing an irAE.

[0329] In some aspects, when the transcript level, expression, or abundance of one or more of CISH, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is lower, and / or AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VM When the transcript level, expression, or abundance of one or more of O1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, KLF9, PD-L1+ naive B cells, and / or converted memory B cells is higher, the monitored subject may have a lower risk of developing irAEs.

[0330] In some aspects, when LILRB4, GIMAP7, CISH, CXCR6, DHRS9, FCGR1CP, ANKRD34B, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monoclonal antibody is expressed compared to the transcript level, expression, or abundance in a control sample at baseline or before initiation of ICI treatment. When the transcript level, expression, or abundance of one or more of the following proteins are lower in the nucleated B cells, and / or the transcript level, expression, or abundance of one or more of the following proteins are higher in the nucleated B cells, the monitored subject may have a lower risk of developing an irAE.

[0331] In some aspects, the monitored subject may have a lower risk of developing an irAE when the transcript level, expression, or abundance of one or more of PARP9, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is lower, and / or the transcript level, expression, or abundance of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, TSC22D3, PD-L1+ naive B cells, and / or switched memory B cells is higher, compared to the transcript level, expression, or abundance in a control sample at baseline or before the start of ICI treatment.

[0332] In some aspects, when the transcript level, expression, or abundance of one or more of PARP9, CISH, CXCR6, LPAR6, ASGR2, Mi-2, GAD65, myosin, thyroglobulin, TPO, CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, CXCL10, and / or CTLA4+ monocytes is lower, and / or KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TR When the transcript level, expression, or abundance of one or more of IB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSRNP1, DNAJB1, CXCL8, OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, EGR1, PD-L1+ naive B cells, and / or converted memory B cells is higher, the monitored subject may have a lower risk of developing an irAE.

[0333] Treatment

[0334] The present disclosure further provides a method for treating cancer patients. The method includes assessing one or more of transcripts, autoantibodies, cytokines, immune cell spectrum or any combination thereof, and determining the risk level of irAE. In some aspects, risk assessment is carried out before or during ICI treatment. In some aspects, risk assessment includes prediction, diagnosis or monitoring ICI-related myositis, ICI-related myocarditis or ICI-related myositis and myocarditis. If the spectrum is related to the future occurrence of irAE or irAE, the subject will be determined to have a high risk of irAE. If the spectrum is not related to irAE, the subject is determined to have a low risk of irAE.

[0335] In some aspects, ICI therapy includes one or more ICI therapies disclosed herein. The progression of cancer treatment with ICI is guided by profile assessment and the determination of risk level. Based on the profile assessment and the determined risk level, ICI therapy can be continued, withdrawn, or modified accordingly.

[0336] In some aspects, the method for treating cancer includes providing a sample from a subject, evaluating one or more of transcripts, autoantibodies, cytokines, immune cell subsets, or any combination thereof, and treating the subject with an ICI treatment method if the subject is predicted, diagnosed, or monitored as having a low risk of irAE. In some aspects, if the subject is predicted, diagnosed, or monitored as having a high risk, the subject receives a non-ICI treatment. In some aspects, if the subject is diagnosed as having a high risk, the subject receives ICI treatment and irAE relief treatment.

[0337] In some respects, ICI includes the inhibitor of using PD-1, PD-L1, TIM-3, LAG-3, CTLA-4, CSF-1R or its any combination.In some respects, irAE is ICI correlation myositis, ICI correlation myocarditis or ICI correlation myositis and myocarditis.In some respects, irAE relief therapy is selected from corticosteroids (such as prednisone, methylprednisolone, dexamethasone, budesonide), TNF inhibitors (such as infliximab) or hormone substitutes (such as hydrocortisone, levothyroxine), CXCL8 inhibitors (such as rapatacin).

[0338] In some aspects, depending on the severity of the irAE, ICI treatment can be suspended and consideration can be given to resuming treatment after the irAE symptoms subside. In some aspects, the dose of ICI treatment can be reduced or skipped. In addition, irAE relief therapy (e.g., administration of corticosteroids) can be administered. High-dose corticosteroids (such as prednisone 1 to 2 mg / kg / day or methylprednisolone 1 to 2 mg / kg / day) can be administered to subjects and the dose can be gradually reduced over a period of at least 4 to 6 weeks. In some aspects, infliximab or other immunosuppressive therapies can be used alone or in combination with other irAE relief therapies. In some aspects, irAE relief therapy can be administered sequentially or simultaneously with ICI treatment. In some aspects, permanent discontinuation of ICI may be recommended. In some aspects, non-ICI treatment may be recommended.

[0339] In some aspects, corticosteroids include, for example, betamethasone sodium phosphate, desonide sodium phosphate, dexamethasone sodium phosphate, hydrocortisone sodium phosphate, hydrocortisone sodium succinate, methylprednisolone disodium phosphate, methylprednisolone sodium succinate, prednisolone sodium phosphate, prednisolone sodium succinate, prednisolone hydrochloride, prednisone disodium phosphate, prednisone sodium succinate, triamcinolone acetonide disodium phosphate, alclometasone dipropionate, amcinonide, beclomethasone monopropionate, betamethasone 17-valerate, clobetasol propionate, clobetasone butyrate, Deprodone propionate, desonide, desoximetasone, dexamethasone acetate, diflucortolone valerate, diflorasone diacetate, diflucortolone, difluprednate, flumethasone pivalate, flunisolide, fluocinolone acetonide, fluocinolone acetonide, flucortolone pivalate, fluorometholone acetate, fluorometholone acetate, fluprednidene acetate, halcinonide, halometasone, hydrocortisone acetate, medrysone, methylprednisolone acetate, mometasone furoate, paramethasone acetate, prednicarbate, prednisone acetate, prednididine, rimexolone, tixocortolone pivalate, and triamcinolone hexane acetonide.

[0340] In some aspects, non-ICI therapies include chemotherapy, hormone therapy, small molecule therapy, toxin therapy, prodrug-activated enzyme therapy, biological therapy, surgical therapy, anti-angiogenic therapy, targeted therapy, epigenetic therapy, demethylation therapy, histone deacetylase inhibitor therapy, differentiation therapy, radiation therapy, stem cell transplantation, and / or any combination thereof.

[0341] Cancer therapeutic or chemotherapeutic agents include alkylating agents such as thiotepa and cyclophosphamide (CYTOXAN); alkyl sulfonates such as busulfan, improsulfan, and piposulfan; aziridines such as benzodopa, carboquinone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethylenethiophosphaoramide, and trimethylolomelamine; nitrogen mustards such as chlorambucil, naphthyl mustard, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine hydrochloride, and chlorambucil. oxide hydrochloride), melphalan, nembixin, phenylephrine, prednimustine, trofosamide, uracil mustard; nitrosoureas, such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, ranimustine; antibiotics, such as aclarubicin, actinomycin, authramycin, azaserine, bleomycin, actinomycin C, calicheamicin, carabicin, caminomycin, carzinophilin, chromomycin, actinomycin D, daunomycin, detoxibacin, 6-diazo-5-oxo-L-norleucine (6-diaz o-5-oxo-L-norleucine), doxorubicin, epirubicin, esorubicin, idarubicin, marcellomycin, mitomycin, mycophenolic acid, norgamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rhodorubicin, streptomycin, streptozotocin, tuberculin, ubenimex, zoloft, daunorubicin; antimetabolites, such as methotrexate and 5-fluorouracil (5-FU); folic acid analogs, such as denopterin, methotrexate, pteropterin, and trimetrexate; purine analogs, such as fludarabine, 6-mercaptopurine, thiopurine, and thioguanine;Pyrimidine analogs, such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine, and 5-FU; androgens, such as captestosterone, dromostanolone propionate, cyclothiosteroid, melastane, and testolactone; antiadrenal agents, such as aminoglutethimide, mitotane, and trilostane; folic acid supplements, such as folinic acid; aceglucuronolide; and aldophosphamide glucoside. glycoside; aminolevulinic acid; amsacrine; bestrabucil; bisantrene; edatraxate; defofamine; demecolcine; diacronitrile; elfornithine; elliptonium acetate; etogluconol; gallium nitrate; hydroxyurea; lentinan; lonidamine; mitoguanidine; mitoxantrone; mopidarol; diamine nitrazepam; pentostatin; phenamide; pirarubicin; podophyllinic acid acid); 2-ethylhydrazide; benzylhydrazine; PSK.RTM.; razoxane; sizolan; spirogermanamine; tricholonylalanine; triimidoquinone; 2,2',2"-trichlorotriethylamine; urethan; vindesine; dacarbazine; mannomustine; dibromomannitol; dibromodulcitol; pipobroman; gacytosine; arabinoside ("Ara-C"); cyclophosphamide; thiotepa; taxanes, such as paclitaxel (TAXOL; TM , Bristol-Myers Squibb Oncology, Princeton, NJ) and docetaxel (TAXOTEPvE TM Rhone-Poulenc Lean (Antony, France); chlorambucil; gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin and carboplatin; vinblastine; trastuzumab, docetaxel, platinum; etoposide (VP-16); ifosfamide; mitomycin C; mitoxantrone; vincristine; vinorelbine; navelbine; novantrone; teniposide; daunorubicin; aminopterin; xeloda; ibandronate; CPT-11; the topoisomerase inhibitor RFS2000; difluoromethylomithine (DMFO); retinoic acid derivatives such as targretin TM (bexarotene), Panretin TM(alitretinoin); ONTAKT TM (denileukin-2); esperamicins; capecitabine; and pharmaceutically acceptable salts, acids, or derivatives of any of the foregoing. This definition also includes antihormonal agents that modulate or inhibit the effects of hormones on tumors, such as antiestrogens, including, for example, tamoxifen, raloxifene, aromatase-inhibiting 4(5)-imidazoles, 4-hydroxytamoxifen, troxifene, keoxifene, LY 1 17018, onapristone, and toremifene (Fareston); and antiandrogens, such as flutamide, nilutamide, bicalutamide, leuprolide, and goserelin; and pharmaceutically acceptable salts, acids, or derivatives of any of the foregoing. Further cancer therapeutics include sorafenib and other protein kinase inhibitors, such as afatinib, axitinib, bevacizumab, cetuximab, crizotinib, dasatinib, erlotinib, fostamatinib, gefitinib, imatinib, lapatinib, lenvatinib, mulitinib, nilotinib, panitumumab, pazopanib, pegaptanib, ranibizumab, ruxolitinib, trastuzumab, vandetanib, vemurafenib, and sunitinib; sirolimus (rapamycin), everolimus and other mTOR inhibitors. Examples of other chemotherapeutic agents include topoisomerase I inhibitors (e.g., irinotecan, topotecan, camptothecin and its analogs or metabolites, and doxorubicin); topoisomerase II inhibitors (e.g., etopo...

Claims

1. A method for predicting the risk of an immune-related adverse event (irAE) associated with immune checkpoint inhibitor (ICI) treatment in a subject and / or a method for diagnosing an immune-related adverse event (irAE) associated with immune checkpoint inhibitor (ICI) treatment in a subject, the method comprising: a. providing a sample of the subject; b. assessing the level of one or more transcripts in the sample; as well as c. predicting the risk of occurrence of an irAE in the subject / diagnosing an irAE in the subject, wherein: i. Before ICI treatment (baseline), leukocyte immunoglobulin-like receptor B4 (LILRB4), The transcript level of one or more of cytokine-inducible SH2-containing protein (CISH), poly (ADP-ribose) polymerase family member 9 (PARP9), RING finger protein 145 (RNF145), asialoglycoprotein receptor 2 (ASGR2), solute carrier family 16, member 13 (SLC16A13), lysophosphatidic acid receptor 6 (LPAR6), GTPase, IMAP family member 7 (GIMAP7), and / or CXC motif chemokine receptor 6 (CXCR6) is increased compared to the transcript level in a control sample; and / or ii. If the subject has amphiregulin (AREG), epiregulin (EREG), oncostatin M (OSM), cysteine and serine rich nuclear protein 1 (CSRNP1), DNA damage-induced transcript 4 (DDIT4), IL-10 (interleukin 10), prostaglandin endoperoxide synthase (PTGS2), dual specificity phosphatase 1 (DUSP1), CXC chemokine receptor type 4 (CXCR4), nuclear factor regulated by interleukin 3 (NFIL3), Fos proto-oncogene, AP-1 transcription factor subunit (FOS), NFKB inhibitory factor alpha (NFKBIA), PPP1R15A (protein phosphatase 1 regulatory subunit 15A), CD79A, JUNB proto-oncogene, AP-1 transcription factor subunit (JUNB), CXC motif chemokine ligand 8 (CXCL8), Early growth response 1 (EGR1), G0 / G1 switch 2 (G0S2), paired box 8 (PAX8), activating transcription factor 6 beta (ATF6B), PAX8 antisense RNA1 (PAX8-AS1), RNA, variant U1 small nuclear 19 (RNVU1-19), vitelline membrane outer 1 homolog (VMO1), heparin-binding EGF-like growth factor (HBEGF), coiled-coil domain containing 144A (CCDC144A), shisa family member 8 (SHISA8), nuclear receptor subfamily 4A group 2 (NR4A2), prostaglandin E synthase (PTGES), synaptophysin I (SYN1), CXC motif chemokine ligand 2 (CX CL2), peripheral myelin protein 22 (PMP22), CD83, early growth response 3 (EGR3), NUAK family kinase 1 (NUAK1), nocturnin (NOCT), atonal bHLH transcription factor 8 (ATOH8), polo-like kinase 2 (PLK2), DNA binding inhibitor 1 (ID1), adrenergic receptor β1 (ADRB1), snail family transcription repressor 1 (SNAI1), notch receptor 3 (NOTCH3), activating transcription factor 3 (ATF3), dual specificity phosphatase 2 (DUSP2), period circadian regulator 1 (PER1), TNF superfamily member 9 (TNFSF9), MAF bZIP transcription factor F (MAFF), microRNA 4420 (MIR4420), glutathione peroxidase (GPX3), TNFα-induced protein 3 (TNFAIP3), potassium voltage-gated channel regulatory subfamily G member 1 (KCNG1), prostaglandin endoperoxidase synthase 2 (PTGS2), A kinase anchoring protein 5 (AKAP5), Dual specificity phosphatase 1 (DUSP1), diacylglycerol kinase kappa (DGKK), beta-1,4-N-acetylgalactosaminyltransferase 3 (B4GALNT3), tribbles pseudokinase 1 (TRIB1), phorbol-12-myristate-13-acetate-induced protein 1 (PMAIP1), CXC motif chemokine receptor 4 (CXCR4), tumor protein p53-induced nuclear protein 2 (TP53INP2), nuclear factor regulated by interleukin 3 (NFIL3), dual specificity phosphatase 4 (DUSP4), NFKB inhibitor alpha (NFKBIA), arginine vasopressin-induced protein 1 (AVPI1), CD79a, ADP-ribosylation factor-like GTPase 4D (AR L4D), poly IgA and IgM connecting chain (JCHAIN), BTG antiproliferative factor 2 (BTG2), TLE family member 1, transcriptional core repressor (TLE1), nuclear transporter type 2 export factor 1 (NXT1), transduction factor of ERBB2 1 (TOB1), phosphodiesterase 4D (PDE4D), DNAJ heat shock protein family member B1 (DNAJB1), AT-rich interaction domain 5B (ARID5B), G protein-coupled receptor 153 (GPR153), KLF transcription factor 9 (KLF9), SBDS ribosome maturation factor (SBDS), immediate early response 2 (IER2), TSC22 domain family member 3 (TSC22D3), GABA The transcript level of one or more of type A receptor-associated protein-like 1 (GABARAPL1), JunD proto-oncogene, AP-1 transcription factor subunit (JUND), RUNX family transcription factor 3 (RUNX3), BABAM2 antisense RNA 1 (BRE-AS1), putative salt-induced kinase 1B (LOC102724428), FAM46C (FAM46C), and / or creatine phosphate receptor 1-associated scaffold protein (GRASP) is lower than the transcript level of the control sample, The subject is then predicted to have a high risk of developing an irAE or is diagnosed with an irAE.

2. A method for monitoring the risk of ICI-related irAEs in a subject, comprising: a. providing a sample of the subject; b. assessing the level of one or more transcripts in the sample; as well as c. Monitoring the risk of irAEs in the subject, where: i. before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, DHRS9, FCGR1CP, ANKRD34B and / or CXCR6 is increased compared to the transcript level in the control sample; and / or ii. AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MI the transcript level of one or more of R4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is lower than the transcript level in the control sample, The subject is then predicted to have a high risk of developing irAE.

3. The method according to claim 1 or 2, wherein the irAE comprises ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

4. The method of claim 1 or 2, wherein the assessment of transcript levels is performed before ICI treatment.

5. The method according to claim 1 or 2, wherein: If the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated before ICI treatment (baseline) compared to the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

6. The method according to claim 1 or 2, wherein: If before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, GIMAP7 and / or CXCR6, DHRS9, FCGR1CP and / or ANKRD34B is elevated compared to the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

7. The method according to claim 1 or 2, wherein: If before ICI treatment (baseline), AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, If the transcript level of one or more of SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing irAE.

8. The method according to claim 1 or 2, wherein: If before ICI treatment (baseline), the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

9. The method according to claim 1 or 2, wherein: If before ICI treatment (baseline), the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

10. The method according to claim 1 or 2, wherein: If before ICI treatment (baseline), the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

11. The method according to claim 1 or 2, wherein: The subject is predicted to be at high risk of developing an irAE if: i. Before ICI treatment (baseline), PARP9 transcript levels are elevated compared to transcript levels in control samples; and / or ii. Before ICI treatment (baseline), the transcript level of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3 is lower than the transcript level in the control sample.

12. The method according to claim 1 or 2, wherein the subject is predicted to have a high risk of developing an irAE if: i. Prior to ICI treatment (baseline), the transcript level of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2 is elevated compared to the transcript level in a control sample; and / or ii. Before ICI treatment (baseline), KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSRNP1, DNAJB1, CXCL8, OSM, The transcript level of one or more of ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1 is lower than the transcript level in the control sample.

13. The method of claim 1 or 2, wherein the sample is whole blood, serum, plasma, cerebrospinal fluid, pleural effusion, pericardial effusion, peritoneal effusion, bone marrow, tissue, urine, cerebrospinal fluid (CSF), or other body fluids.

14. The method of claim 1 or 2, wherein the ICI therapy is administered as part of a cancer treatment.

15. The method of claim 10, wherein the ICI treatment comprises administering an inhibitor of PD-1, PD-L1, TIM-3, LAG-3, CTLA-4, CSF-1R, or any combination thereof.

16. The method of claim 1 or 2, wherein assessing transcript levels (step b) comprises RNA sequencing, nanopore sequencing, Nanostring, multiplex RT-PCR, singleplex RT-PCR, NASBA, fluorescence measurement, or spectrophotometry.

17. The method of claim 1 or 2, wherein the method further comprises assessing the expression of one or more of Mi-2, GAD65, myosin, thyroglobulin, and / or TPO in a sample from the subject.

18. The method of claim 17, wherein the evaluating comprises identifying whether expression of one or more autoantibodies is elevated in the subject's sample compared to expression in a control sample.

19. The method of any one of claims 1, 2, or 17, wherein the method further comprises assessing the expression of one or more of CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, and / or CXCL10 in the subject sample.

20. The method of claim 19, wherein the evaluating comprises identifying whether expression of one or more cytokines is elevated in the subject sample compared to expression in a control sample.

21. The method of any one of claims 1, 2, 17, or 19, wherein the method further comprises assessing the abundance of one or more of PD-L+ naive B cells, switched memory B cells, and / or CTLA-4+ monocytes in the subject sample.

22. The method of claim 21, wherein the assessing comprises identifying whether the abundance of one or more of PD-L+ naive B cells, and / or switched memory B cells is reduced in the subject sample compared to that in a control sample, and / or whether the abundance of CTLA-4+ monocytes is increased compared to that in a control sample.

23. The method according to claim 1 or 2 further comprises repeating steps (a)-(c) at a second time point, thereby enabling determination of a change in the risk of the subject developing an irAE compared to a control sample and / or a diagnosis of an irAE in the subject's sample.

24. The method of claim 1 or 2, further comprising predicting that the subject has a low risk if: i. Before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, GIMAP7, and / or CXCR6 is lower than or equivalent to the transcript level in the control sample; and / or ii. During ICI treatment, AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, and MIR The transcript level of one or more of 4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C and / or GRASP is increased or comparable to the transcript level in the control sample.

25. The method of claim 24, further comprising treating the subject with ICI therapy when the subject is predicted to have a low risk of developing an irAE.

26. The method of claim 1 or 2, further comprising treating a subject predicted to be at high risk of developing an irAE with a non-ICI therapy, or treating the subject at high risk of developing an irAE with an ICI therapy and an irAE-relief therapy, wherein the irAE-relief therapy is selected from a corticosteroid (e.g., prednisone, methylprednisolone, dexamethasone, budesonide), a TNF inhibitor (e.g., infliximab), a hormone replacement (e.g., hydrocortisone, levothyroxine), a CXCL8 inhibitor (e.g., rapatacin), or any combination thereof.

27. A method of treating a subject suffering from cancer, comprising: (a) provide samples from subjects; (b) assessing the level of one or more transcripts in the sample; (c) predicting the risk of the subject developing an irAE, wherein: i. When LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, The subject is diagnosed as low risk when the transcript level of one or more of LPAR6, GIMAP7, and / or CXCR6 is lower than or equal to the transcript level in the control sample; ii. Before ICI treatment (baseline), AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, The subject is diagnosed as low risk when the transcript level of one or more of KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is elevated or equal to the transcript level in the control sample; iii. When LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, When the transcript level of one or more of LPAR6, GIMAP7, and / or CXCR6 is elevated compared to the transcript level in a control sample, the subject is diagnosed as being at high risk; and / or iv. When AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, The transcript level of one or more of TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or GRASP is lower than the transcript level of the control sample; and (d) treating the subject by: (i) if the subject is diagnosed as having a low risk of developing an irAE, ICI therapy is used; (ii) if the subject is diagnosed as being at high risk for developing an irAE, non-ICI therapy is used; or (iii) If the subject is diagnosed as being at high risk of developing an irAE, ICI therapy and irAE mitigation therapy are administered.

28. The method of claim 27, wherein the irAE comprises ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

29. The method according to claim 27, wherein If the transcript level of one or more of LILRB4, CISH, and / or PARP9 is elevated before ICI treatment (baseline) compared to the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

30. The method of claim 27, wherein: If before ICI treatment (baseline), the transcript level of one or more of LILRB4, CISH, GIMAP7, and / or CXCR6 is elevated compared to the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

31. The method of claim 27, wherein: If before ICI treatment, AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SY If the transcript level of one or more of N1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing irAE.

32. The method of claim 27, wherein: If before ICI treatment, the transcript level of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

33. The method of claim 27, wherein: If before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

34. The method of claim 27, wherein: If before ICI treatment, the transcript level of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9 is lower than the transcript level in the control sample, the subject is predicted to have a high risk of developing an irAE.

35. The method of claim 27, wherein: The subject is predicted to be at high risk for irAEs in the following circumstances: i. Before ICI treatment (baseline), PARP9 transcript levels are elevated compared to transcript levels in control samples; and / or ii. Before ICI treatment (baseline), the transcript level of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3 is lower than the transcript level in the control sample.

36. The method of claim 27, wherein: The subject is predicted to be at high risk for irAEs in the following circumstances: i. Prior to ICI treatment (baseline), the transcript level of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2 is elevated compared to the transcript level in a control sample; and / or ii. Before ICI treatment (baseline), KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSRNP1, DNAJB1, CXCL8, OSM, The transcript level of one or more of ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, G0S2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1 is lower than the transcript level in the control sample.

37. The method of claim 27, wherein the evaluating further comprises detecting the expression of one or more of CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, and / or CXCL10 in a sample from the subject.

38. The method of claim 37, wherein the assessing comprises identifying whether expression of one or more cytokines is elevated in the subject's sample compared to expression in a control sample.

39. The method of claim 27 or 37, wherein the evaluating further comprises detecting the expression of one or more of Mi-2, GAD65, myosin, thyroglobulin, and / or TPO in a sample from the subject.

40. The method of claim 39, wherein the assessing comprises identifying whether expression of one or more autoantibodies is elevated in a sample from the subject compared to expression in a control sample.

41. The method of any one of claims 27, 37, or 39, wherein the method further comprises assessing the abundance of one or more immune cells in the subject sample, wherein the one or more immune cells are PD-L+ naive B cells, switched memory B cells, and / or CTLA-4+ monocytes.

42. The method of claim 41, wherein the assessment comprises identifying whether the abundance of one or more of PD-L+ naive B cells, and / or switched memory B cells is reduced in the subject's sample compared to a control sample, and / or whether the abundance of CTLA-4+ monocytes is increased compared to a control sample.

43. The method of claim 27, wherein the ICI treatment comprises administering an inhibitor of PD-1, PD-L1, TIM-3, LAG-3, CTLA-4, CSF-1R, or any combination thereof.

44. A method for identifying the presence of at least one differentially expressed transcript associated with an irAE in a biological sample of a cancer subject, the method comprising: a. Provide samples from subjects; as well as b. assessing the level of one or more transcripts in the sample, wherein the assessing comprises detecting: i.LILRB4, CISH, PARP9, RNF145, ASGR2, SLC16A13, LPAR6, whether the transcript level of one or more of GIMAP7, and / or CXCR6 is higher than the transcript level in a control sample; and / or ii.AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, GPX3, TNFAIP3, KCNG1, PTGS2, AKAP5, DUSP1, DGKK, B4GALNT3, TRIB1, PMAIP1, CXCR4, TP53INP2, NFIL3, DUSP4, NFKBIA, AVPI1, CD79a, ARL4D, JCHAIN, BTG2, TLE1, NXT1, TOB1, PDE4D, DNAJB1, ARID5B, GPR153, KLF9, SBDS, IER2, TSC22D3, JUND, GABARAPL1, RUNX3, BRE-AS1, LOC102724428, FAM46C, and / or whether the transcript level of one or more of GRASP is lower than the transcript level in the control sample.

45. The method of claim 44, wherein the subject is planned to receive treatment with an immune checkpoint inhibitor (ICI).

46. The method of claim 44, wherein the irAE comprises ICI-related myositis, ICI-related myocarditis, or ICI-related myositis and myocarditis.

47. The method of claim 44, wherein the method further comprises detecting the expression of one or more of CXCL2, CXCL5, CXCL6, CCL7, CCL19, IFNγ, IL-6, CXCL9, and / or CXCL10 in the subject sample.

48. The method of claim 47, wherein the assessing comprises identifying whether expression of one or more cytokines is elevated in the subject's sample compared to expression in a control sample.

49. The method of claim 44 or 47, wherein the method further comprises detecting the expression of one or more of Mi-2, GAD65, myosin, thyroglobulin, and / or TPO in the subject sample.

50. The method of claim 49, wherein the assessing comprises identifying whether expression of one or more autoantibodies is elevated in the subject's sample compared to expression in a control sample.

51. The method of any one of claims 44, 47, or 49, wherein the method further comprises assessing the abundance of one or more of PD-L+ naive B cells, switched memory B cells, and / or CTLA-4+ monocytes in the subject sample.

52. The method of claim 51, wherein the assessing comprises identifying whether the abundance of one or more of PD-L+ naive B cells, and / or switched memory B cells is reduced in the subject sample compared to a control sample, and / or whether the abundance of CTLA-4+ monocytes is increased compared to a control sample.

53. The method of claim 45, wherein the assessing comprises determining a baseline or pre-treatment profile associated with future toxicity.

54. The method of claim 53, wherein the baseline or pre-treatment profile comprises: Elevated transcript levels of one or more of LILRB4, CISH, and / or PARP9 compared to transcript levels in a control sample.

55. The method of claim 53, wherein the baseline or pre-treatment profile comprises: Elevated transcript levels of one or more of LILRB4, CISH, GIMAP7, and / or CXCR6 compared to transcript levels in a control sample.

56. The method of claim 53, wherein the baseline or pre-treatment profile comprises: Decreased transcript levels of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, JUNB, CXCL8, EGR1, G0S2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, SHISA8, NR4A2, PTGES, SYN1, CXCL2, PMP22, CD83, EGR3, NUAK1, NOCT, ATOH8, PLK2, ID1, ADRB1, SNAI1, NOTCH3, ATF3, DUSP2, PER1, TNFSF9, MAFF, MIR4420, BRE-AS1, LOC102724428, and / or GRASP, compared to the transcript levels in a control sample.

57. The method of claim 53, wherein the baseline or pre-treatment profile comprises: Decreased transcript levels of one or more of AREG, EREG, OSM, CSRNP1, DDIT4, IL-10, PTGS2, DUSP1, CXCR4, NFIL3, FOS, NFKBIA, PPP1R15A, CD79A, and / or JUNB, compared to transcript levels in a control sample.

58. The method of claim 53, wherein the baseline or pre-treatment profile comprises: Decreased transcript levels of one or more of AREG, EREG, CXCL8, EGR1, GOS2, PAX8, ATF6B, PAX8-AS1, RNVU1-19, VMO1, HBEGF, CCDC144A, and / or SHISA8, compared to transcript levels in a control sample.

59. The method of claim 53, wherein the baseline or pre-treatment profile comprises: Decreased transcript levels of one or more of AREG, EREG, CXCL8, EGR1, PAX8, ATF6B, VMO1, HBEGF, BRE-AS1, NR4A2, OSM, NOCT, PLK2, LOC102724428, DUSP2, GRASP, PER1, TNFSF9, CSRNP1, MAFF, TNFAIP3, DUSP1, TRIB1, PMAIP1, FAM46C, NXT1, and / or KLF9, as compared to transcript levels in a control sample.

60. The method of claim 53, wherein the baseline or pre-treatment profile comprises: i. Elevated transcript levels of PARP9 compared to transcript levels in control samples; and / or ii. Decreased transcript levels of one or more of CD79A, CD83, PLK2, PDE4D, TR1B1, EREG, CXCL8, EGR3, JUNB, DUSP1, NFKBIA, TNFSF9, TNFAIP3, IL-10, JUND, FOS, RUNX3, and / or TSC22D3, as compared to the transcript levels in a control sample.

61. The method of claim 53, wherein the baseline or pre-treatment profile comprises: i. elevated transcript levels of one or more of PARP9, CISH, CXCR6, LPAR6, and / or ASGR2 compared to transcript levels in a control sample; and / or ii. Compared with the transcript levels in control samples, KLF9, CXCR4, ATF6B, CD79A, CD83, PLK2, GRASP, PPP1R15A, GPX3, PARP9, BTG2, PTGS2, NOTCH3, AKAP5, PDE4D, SBDS, TRIB1, SNAI1, PAX8, NFIL3, EREG, AREG, DGKK, PTGES, CSRNP1, DNAJB1, CXCL 8, decreased transcript levels of one or more of OSM, ARID5B, ID1, NR4A2, EGR3, JUNB, TLE1, CXCL2, DUSP1, GPR153, GOS2, ATF3, NFKBIA, TNFS9, NUAK1, ATOH8, TNFAIP3, ADRB1, HBEGF, IL-10, JUND, FOS, GABARAPL1, PMAIP1, DDIT4, and / or EGR1.

62. The method of any one of the preceding claims, wherein the control sample is taken from a subject at low risk of developing an irAE.

63. The method of any one of the preceding claims, wherein the transcript levels are relative transcript levels.

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