Project 1: Remodeling Chromatin and the Tumor Microenvironment: Direct Oncogenesis and Therapeutic Targeting

项目 1：重塑染色质和肿瘤微环境：直接肿瘤发生和治疗靶向

基本信息

批准号：
10443720
负责人：
DAVID E FISHER
金额：
$ 33.26万
依托单位：
MASSACHUSETTS GENERAL HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-03-12 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10443720
关键词：
ATAC-seq Alleles BRAF gene Behavior Bioinformatics Biological Markers Biopsy Biopsy Specimen Cancer cell line Catalytic Domain Cell Line Cell Survival Cells ChIP-seq Chromatin Chromatin Remodeling Factor Clinical Collaborations Cytotoxic T-Lymphocytes DNA Packaging Data Set Dependence Development Dimerization EZH2 gene Engineering Enzymes Epigenetic Process Exhibits Gene Expression Regulation Genes Genetic Genetic Transcription Genomics Goals Growth Histones Human Immune Immune Evasion Immunologics Immunosuppression Immunotherapy In Vitro Lysine MEK inhibition MEKs Malignant Neoplasms Measurement Measures Mediator of activation protein Melanoma Cell Messenger RNA Methylation Methyltransferase Modeling Mus Mutation Oncogenes Oncogenic Pathway interactions Patients Pharmacology Point Mutation Pre-Clinical Model Recurrence Resistance Role SET Domain Shapes Signal Transduction Specimen T-Lymphocyte Testing The Cancer Genome Atlas Therapeutic Titrations Translations Treatment Efficacy WNT Signaling Pathway Xenograft procedure Zebrafish antagonist anti-PD-1 beta catenin cell motility checkpoint therapy chromatin remodeling combinatorial draining lymph node drug candidate genome-wide improved in vivo inhibitor interest knock-down loss of function loss of function mutation melanoma mouse model mutant neoantigens neoplastic cell novel novel marker overexpression refractory cancer response screening small hairpin RNA small molecule inhibitor synergism targeted treatment therapeutic target transcriptome sequencing treatment response tumor tumor microenvironment tumor-immune system interactions tumorigenesis tumorigenic

ATAC-seq Alleles BRAF gene Behavior Bioinformatics Biological Markers Biopsy Biopsy Specimen Cancer cell line Catalytic Domain Cell Line Cell Survival Cells ChIP-seq Chromatin Chromatin Remodeling Factor Clinical Collaborations Cytotoxic T-Lymphocytes DNA Packaging Data Set Dependence Development Dimerization EZH2 gene Engineering Enzymes Epigenetic Process Exhibits Gene Expression Regulation Genes Genetic Genetic Transcription Genomics Goals Growth Histones Human Immune Immune Evasion Immunologics Immunosuppression Immunotherapy In Vitro Lysine MEK inhibition MEKs Malignant Neoplasms Measurement Measures Mediator of activation protein Melanoma Cell Messenger RNA Methylation Methyltransferase Modeling Mus Mutation Oncogenes Oncogenic Pathway interactions Patients Pharmacology Point Mutation Pre-Clinical Model Recurrence Resistance Role SET Domain Shapes Signal Transduction Specimen T-Lymphocyte Testing The Cancer Genome Atlas Therapeutic Titrations Translations Treatment Efficacy WNT Signaling Pathway Xenograft procedure Zebrafish antagonist anti-PD-1 beta catenin cell motility checkpoint therapy chromatin remodeling combinatorial draining lymph node drug candidate genome-wide improved in vivo inhibitor interest knock-down loss of function loss of function mutation melanoma mouse model mutant neoantigens neoplastic cell novel novel marker overexpression refractory cancer response screening small hairpin RNA small molecule inhibitor synergism targeted treatment therapeutic target transcriptome sequencing treatment response tumor tumor microenvironment tumor-immune system interactions tumorigenesis tumorigenic

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项目摘要

PROJECT SUMMARY A synthetic lethality screen was performed to identify hyper-dependencies in melanomas harboring deficiencies in ARID genes—components of the SWI/SNF chromatin remodelers—which occur in 20-30% of human cancers. ARID mutant melanomas exhibited extreme dependency on the H3K9-dimethylase G9a, a druggable enzyme. This led to discovery of 6 melanoma cases harboring recurrent point mutation at an identical residue in G9a’s catalytic domain. The mutation hyper-activates G9a and aligns to oncogenic mutations in EZH2, a previously known oncogenic methyltransferase that targets a different histone-3 lysine (K27). Beyond these rare activating G9a mutations we identified more common genomic G9a copy gains in 27.8% of melanomas in TCGA and found G9a dependency (via genetic or pharmacologic means) in human melanoma lines with as little as one extra G9a copy. Corroborating our results, the Achilles Project (genome- scale loss-of-function viability screening in many deeply annotated cancer cell lines) confirmed G9a dependency among melanoma lines harboring either G9a amplification or ARID deficiency. The same dependencies were also seen in multiple cancers beyond melanoma in Achilles. Furthermore, G9a copy gain was accompanied by global elevations in H3K9 dimethylation, which correlated as a biomarker of G9a dependency in G9a gained/amplified melanoma cells. Mechanistic studies revealed activation of the canonical Wnt pathway as a vital dependency target, which is induced by G9a’s suppression of Wnt antagonist DKK1. Tumor intrinsic Wnt activation is common in melanomas, though usually without pathway-intrinsic mutations—a phenomenon now largely explained by G9a activation. Importantly, Wnt activity has been strongly implicated by others as a trigger of tumor-induced immune evasion—of keen interest for efficacy of immunotherapy. Here, Aim 1 will validate dependencies of G9a copy-gained and ARID loss-of-function human melanoma lines on G9a, GLP, MITF, DKK1, and Wnt signaling. Global ATAC-seq, RNA-seq, and H3K9me2-ChIP-seq will be used to identify additional G9a targets and mediators of viability in these melanomas. Aim 2 will test pharmacologic G9a inhibition in multiple mouse and zebrafish models containing copy gains of G9a or GLP, or ARID2 deficiency, combined with either BRAF-targeted therapy or anti-PD1 immunotherapy. The latter study will utilize novel isogenic engineered syngeneic murine melanomas containing or lacking UV-neoantigens, permitting measurements of G9a targeting as a strategy to blunt the Wnt pathway’s immunosuppressive activity, together with direct targeting of G9a’s cell-intrinsic oncogenic function. Human melanoma biopsies will also be interrogated to corroborate preclinical models. These studies identify a novel oncogene (G9a) and, through vital collaborations with Dr. Zon (zebrafish melanoma model), Drs. Liu and Zon (epigenetic mechanisms), and Drs. Wucherpfennig and Rodig (immunological profiling), will reveal mechanisms, novel biomarkers, and therapeutic opportunities in melanoma, with relevance to other treatment-resistant cancers.

项目摘要进行了合成的致死性屏幕，以鉴定黑色素瘤中的超依赖性干旱基因的缺陷 - SWI/SNF染色质重塑剂的组成部分 - 发生在20-30％人类癌。干旱突变黑色素瘤暴露了对H3K9-二甲基酶G9A的极端依赖性，A 可吸毒酶。这导致发现了6例黑色素瘤病例，该病例含有复发点突变 G9A催化域中的相同住宅。突变超激活G9a并与致癌 EZH2中的突变，一种以前已知的致癌甲基转移酶，靶向不同的组蛋白-3歌词（K27）。除了这些罕见的激活G9A突变，我们确定了更常见的基因组G9A复制收益 TCGA中的黑色素瘤的27.8％，并在人类中发现了G9A的依赖性（通过遗传或药理手段）黑色素瘤线几乎只有一份G9A副本。佐证我们的结果，阿喀琉斯项目（基因组 - 在许多深层注释的癌细胞系中，量表丧失了功能的生存能力筛选）证实了G9A 具有G9A扩增或干旱缺乏的黑色素瘤系之间的依赖性。相同在阿喀琉斯黑色素瘤以外的多种癌症中也可以看到依赖性。此外，G9A复制增益伴随着H3K9二甲基化的全球升高，该二甲基化与G9A的生物标志物相关获得/扩增的黑色素瘤细胞的依赖性。机械研究揭示了规范的激活 Wnt途径是至关重要的依赖性目标，这是由G9A抑制Wnt拮抗剂DKK1引起的。肿瘤固有的Wnt激活在黑色素瘤中很常见，尽管通常没有途径 - intrinsic突变 - A 现象现在主要用G9A激活来解释。重要的是，Wnt活动已被强烈暗示其他人则是肿瘤诱导的免疫避难所的触发，这是对免疫疗法效率的敏锐感兴趣。这里， AIM 1将验证G9A复制的依赖性，并在功能丧失的人黑色素瘤线上验证 G9A，GLP，MITF，DKK1和WNT信号传导。将使用全局ATAC-SEQ，RNA-SEQ和H3K9ME2-CHIP-SEQ 确定这些黑色素瘤中的其他G9A靶标和可行性介质。 AIM 2将测试药理学多种小鼠和斑马鱼模型中的G9A抑制缺乏症，结合BRAF靶向治疗或抗PD1免疫疗法。以后的研究将利用含有或缺乏UV-NeoAntigens的新型同源性工程性鼠黑色素瘤，允许将G9A靶向的测量作为钝化WNT途径的免疫抑制的策略活性，以及直接靶向G9A的细胞中性致癌功能。人类黑色素瘤活检将也需要审问以证实临床前模型。这些研究确定了一种新颖的癌基因（G9A），并确定通过与Zon博士（斑马鱼黑色素瘤模型）的重要合作，Drs。刘和Zon（表观遗传学机制）和博士。 Wucherpfennig和Rodig（免疫学分析）将揭示机制，新颖黑色素瘤的生物标志物和治疗机会，与其他耐药癌症有关。