Defining and targeting epigenetic plasticity-driven drug resistance and immune escape in melanoma

定义和针对黑色素瘤中表观遗传可塑性驱动的耐药性和免疫逃逸

• 批准号: 10666665
• 负责人: Jonathan D. Licht
• 金额: $ 47.85万
• 依托单位: H. LEE MOFFITT CANCER CTR & RES INST
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-15 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10666665
• 关键词: 3-Dimensional; ATAC-seq; Acetylation; Address; Affect; Antigen Presentation; Antigens; BRAF gene; CD8-Positive T-Lymphocytes; CRISPR screen; Cell Line; Cell Lineage; Cells; Chromatin; Chromatin Loop; Clinical; Clinical Trials; Complex; Data; Deacetylation; Development; Drug resistance; EP300 gene; Environment; Enzymes; Epidermal Growth Factor Receptor; Epigenetic Process; Excision; Exclusion; Future; Gene Expression; Genes; Genetic Transcription; Grant; HDAC8 gene; Hi-C; Histocompatibility Antigens Class I; Histone Deacetylase; Histone Deacetylase Inhibitor; Immune; Immune Evasion; Immune checkpoint inhibitor; Immune system; Immunosuppression; Immunotherapy; In Vitro; Interferons; Interleukin-11; MEKs; Mediating; Melanoma Cell; Mesenchymal; Modeling; Mus; Mutation; Myelogenous; PTEN gene; Pathway interactions; Pharmaceutical Preparations; Phenotype; Prevention; Proteins; Proteomics; Resistance; Role; Signal Transduction; Signaling Protein; Specimen; T cell infiltration; T-Lymphocyte; Testing; Transcription Factor AP-1; Work; cancer type; checkpoint therapy; cofactor; cohesin; drug maintenance; drug withdrawal; immune checkpoint; immunoregulation; improved; in vivo; inhibitor; inhibitor therapy; insight; jun Oncogene; loss of function; melanoma; mouse model; multiple omics; novel; novel therapeutic intervention; novel therapeutics; overexpression; prevent; programs; recruit; response; sample fixation; single-cell RNA sequencing; small molecule inhibitor; targeted treatment; therapy resistant; transcription factor; treatment response; tumor; tumor eradication; tumor-immune system interactions

Project summary Melanoma is a heterogeneous tumor, with a high degree of phenotypic plasticity that allows for rapid adaptation to BRAF-MEK inhibitor therapy. Initial therapeutic responses are typically followed by a period of quiescence in which signaling is rewired to evade therapy, followed by the emergence of a bona fide resistant state. Little is known about how the initial persister cell state transitions to an irreversibly resistant state, the role of the immune system in the emergence of these lineages, and whether this resistant state can be targeted. In preliminary studies we identified the type I histone deacetylase HDAC8 as a master regulator of a lineage switch to a resistance-associated melanoma cell state. Activation of HDAC8 alters the phenotype of melanoma cells with loss of function of lineage identity genes such as MITF, increased activity of AP-1/TEAD transcription factors and resistance to therapy. The resistant cell state persisted even after removal of targeted therapy, and was associated with increased mutational load. HDAC8 overexpression also led to the reduced expression of melanoma antigens, increased levels of the immune checkpoint proteins and reduced T cell infiltration. We believe the stability of this state may be at least in part be epigenetic due to altered acetylation and function of transcription factors, cofactors as well as altered function of the cohesin complex involved in chromatin looping, and gene expression. We hypothesize that HDAC8 is a master regulator of a resistance-associated melanoma cell state and represents a target for the prevention of lineage switching. In this proposal, we will use multi-omics approaches (ATAC-Seq, scRNA-Seq, Hi-C, proteomics) to define the mechanisms by which HDAC8 reprograms melanoma cells, and will determine if HDAC8 affects the cohesin complex, leading to fixed resistance-conferring genetic or epigenetic changes. We will utilize a mouse model of BRAF/PTEN-HDAC8-driven melanoma and single cell RNA-Seq to investigate how the HDAC8 modulates the immune microenvironment leading to the emergence of drug resistant melanoma lineages. We will specifically determine whether HDAC8 drives a transcriptional program associated with decreased MHC class I and antigen expression leading to decreased tumor-T cell recognition. Further studies will define whether JUN-mediated transcription of IL-11 reprograms the myeloid compartment leading to a suppressive melanoma immune environment that eradicates tumor-reactive CD8 T cells. CRISPR screens will be performed to identify targets to prevent the emergence of drug resistant lineages in mouse models. We will then evaluate these targets and HDAC8 inhibitors as strategies to improve therapeutic responses to BRAF-MEK inhibitor and immune checkpoint inhibitor therapy in syngeneic mouse melanoma models. We expect that new insights into the mechanisms underpinning the emergence and maintenance of drug resistant lineages in melanoma will lead to the development of new therapeutic strategies to improve the depth and duration of responses to immunotherapy and targeted therapy in melanoma. Our findings will have important implications across multiple cancer types and many different therapies.

项目摘要 黑色素瘤是一种异质性肿瘤，具有高度的表型可塑性，可以快速适应 BRAF-MEK抑制剂治疗。最初的治疗反应之后通常是一段时间的静止期， 该信号被重新连接以逃避治疗，随后出现真正的抵抗状态。之甚少 已知最初的持续细胞状态如何转变为不可逆的抵抗状态，免疫系统的作用 系统在这些血统的出现，以及这种抵抗状态是否可以被针对。初步 研究中，我们确定了I型组蛋白脱乙酰酶HDAC 8作为谱系转换的主要调节因子， 耐药相关黑色素瘤细胞状态。HDAC 8的激活改变了黑色素瘤细胞的表型， MITF等谱系识别基因功能丧失，AP-1/TEAD转录因子活性增加 和对治疗的抵抗即使在去除靶向治疗后，耐药细胞状态仍持续存在， 与突变负荷增加有关。HDAC 8过表达也导致了 黑色素瘤抗原，免疫检查点蛋白水平增加和T细胞浸润减少。我们 我相信这种状态的稳定性可能至少部分是由于乙酰化和功能的改变而引起的表观遗传。 转录因子、辅因子以及参与染色质成环的粘附素复合物的改变的功能， 和基因表达。我们假设HDAC 8是耐药相关黑色素瘤的主要调节因子， 细胞状态，并表示用于防止谱系切换的目标。在本提案中，我们将使用多组学 方法（ATAC-Seq，scRNA-Seq，Hi-C，蛋白质组学）来定义HDAC 8重编程的机制 黑色素瘤细胞，并将确定HDAC 8是否影响粘附素复合物，导致固定的耐药性赋予。 遗传或表观遗传变化。我们将利用BRAF/PTEN-HDAC 8驱动的黑素瘤的小鼠模型， 单细胞RNA-Seq来研究HDAC 8如何调节免疫微环境，从而导致 抗药性黑素瘤谱系的出现。我们将具体确定HDAC 8是否驱动 与MHC I类和抗原表达降低相关的转录程序导致 肿瘤-T细胞识别。进一步的研究将确定JUN介导的IL-11转录是否会重新编程IL-11。 骨髓腔室导致抑制性黑色素瘤免疫环境，根除肿瘤反应性 CD 8 T细胞。将进行CRISPR筛选，以确定目标，以防止耐药性的出现。 小鼠模型中的谱系。然后，我们将评估这些目标和HDAC 8抑制剂作为改善 在同基因小鼠中对BRAF-MEK抑制剂和免疫检查点抑制剂疗法的治疗应答 黑素瘤模型。我们期待着新的见解的机制基础的出现， 在黑色素瘤中维持耐药谱系将导致新的治疗策略的发展 改善对黑色素瘤免疫疗法和靶向疗法的反应的深度和持续时间。我们 这些发现将对多种癌症类型和许多不同的治疗方法产生重要影响。