Role of ATRX, a chromatin remodeler, in immunotherapy response

ATRX（染色质重塑剂）在免疫治疗反应中的作用

• 批准号: 10367734
• 负责人: Daniel SANGHOON Shin
• 金额: --
• 依托单位: VA GREATER LOS ANGELES HEALTHCARE SYSTEM
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-04-01 至 2026-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10367734
• 关键词: ATAC-seq; ATRX gene; Advanced Malignant Neoplasm; Atlases; Binding; Biological Assay; C57BL/6 Mouse; CRISPR/Cas technology; Cancer Model; Cancer cell line; Cell Line; Cells; ChIP-seq; Chromatin; Chromatin Structure; Clinical; Coculture Techniques; Colorectal Cancer; Complex; Coupled; Data; Development; Diagnosis; EZH2 gene; Elements; Embryo; Epigenetic Process; Exhibits; Feedback; Fibroblasts; Genes; Genetic Transcription; Genetically Engineered Mouse; Genome; Genomics; Granzyme; Health; Histone Deacetylase Inhibitor; Human; IRF1 gene; Immune; Immune Evasion; Immune system; Immunocompetent; Immunooncology; Immunotherapy; Institutes; Interferon Receptor; Interferon Type II; Interferons; JAK1 gene; JAK2 gene; Janus kinase; Kidney; Knock-out; Lead; Lentivirus Vector; MC38; Malignant Neoplasms; Malignant neoplasm of lung; Mediating; Melanoma Cell; Military Personnel; Modeling; Morbidity - disease rate; Mus; Mutation; Outcome; PD-1 blockade; Parents; Pathway interactions; Patients; Phenotype; Play; Polycomb; Process; Proteins; RNA Sequences; Reporting; Research; Research Design; Research Proposals; Resistance; Rest; Role; Signal Pathway; Signal Transduction; Signaling Molecule; Sleeping Beauty; Small Interfering RNA; Specificity; System; T-Lymphocyte; Testing; The Cancer Genome Atlas; Therapeutic; Transcript; Transposase; Treatment Efficacy; Untranslated RNA; Veterans; XCL1 gene; anti-PD1 antibodies; anti-PD1 therapy; antitumor effect; base; cBioPortal; cancer cell; cancer immunotherapy; chromatin remodeling; design; experimental study; immune checkpoint blockade; improved; in vivo; inhibitor; loss of function; loss of function mutation; lung cancer cell; melanoma; mouse model; mutant; patient subsets; perforin; polybromo; programmed cell death ligand 1; promoter; receptor; resistance mechanism; response; screening; side effect; tool; transcriptome; transcriptome sequencing; treatment response; trend; tumor; tumor growth; vector

Background: Cancer immunotherapy is a major breakthrough for many patients with advanced cancer. However, benefits are still limited to a subset of patients, and we need to better understand the mechanisms of response and resistance to improve therapeutic efficacy. We have identified loss of function (LoF) mutations in JAK1 or JAK2 (immediate downstream signaling molecule of interferon receptor) that are associated with resistance to PD-1 blockade. We also found these mutations in human melanoma cell lines by screening PD- L1 expression with IFN-g treatment (48 cell lines). Tumors harbor LoF in JAK1/2, completely lost PD-L1 expression. Interestingly, one of them harbors no mutation with an active signaling pathway, yet lost PD-L1 expression. We explored why some human cancer cells lost adaptive PD-L1 expression even with intact interferon signaling and hypothesized that the epigenetic perturbation is mediating this phenotype. With this approach, we observed reduced PD-L1 expression with ATRX siRNA which was further tested with in vivo mouse models. In vivo mouse experiments with ATRX KO MC38 cells, anti-PD-1 antibody therapy produced either accelerated tumor growth or no effect. The current study is designed to understand the mechanism of resistance mediated by loss of ATRX in cancer immunotherapy. Objective/hypothesis: ATRX, a SWI/SNF-like chromatin remodeler is modulating the accessibility of interferon responsive genes that are associated with immunotherapy response. Specific aims: I have two aims for this study. The first aim is to interrogate the mechanisms of immune evasion with loss of ATRX using various tools to probe epigenetic state. The second aim is to establish in vivo tumor growth with ATRX KO using various murine cancer models. Study design: Aim 1. Subaim1) Generate ATRX KO B16 cells followed by Assess epigenetics state with IFN-g stimulation (both MC38 and B16 ATRX KO clones) using ChIP/ATAC-seq. Subaim 2) Correlate genomic studies (ChIP/ATAC) with Chromatin-Associated RNA-sequence (ChAR). Subaim 3) Assess the impact of epigenetic modifiers in IFN-g response in ATRX KO clones (using various epigenetic modifiers, such as HDAC inhibitor, demethylating agents and EZH2 inhibitor). Subaim 4) Coculture assay with murine T cells with ATRX wild-type parent cells and KO clones. Aim 2. Subaim 1) In vivo experiments with MC38 and B16 models with ATRX KO. Subaim2) Kras mutant murine lung cancer cell line models with ATRX KO. Subaim 3) ATRX KO in lung cancer and melanoma genetically engineered mouse models using sleeping beauty transposase vector system. Relevant to Military health: Improving treatment of many types of advanced cancers is critically important to the health of Veterans. Many Veterans suffer from significant morbidity when they are diagnosed with cancer that limits their therapeutic options. Immunotherapy is generally well tolerated and has a significant potential for durable response, however, the benefit is limited to a subset of patients (and Veterans). Therefore, it is imperative to improve therapeutic efficacy of immunotherapy by understanding the mechanisms of response and resistance. The proposed research is designed to understand the mechanisms of how cancer cells evade the immune system by modulating the chromatin state, focusing on the role of ATRX.

背景：癌症免疫治疗是许多晚期癌症患者的重大突破。