Elucidating transcriptional and epigenetic regulators of aggressive cutaneous T cell lymphoma

阐明侵袭性皮肤 T 细胞淋巴瘤的转录和表观遗传调节因子

• 批准号: 10582529
• 负责人: Calvin Yuen Yee Law
• 金额: $ 4.29万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-02-15 至 2024-02-14
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10582529
• 关键词: ATAC-seq; Address; Aggressive behavior; Algorithms; Bioinformatics; Biological Assay; Biological Models; Blood; CD4 Positive T Lymphocytes; CD8-Positive T-Lymphocytes; Cell Proliferation; Cells; Cellular Immunology; Characteristics; Chromatin; Chronic; Clinical; Collection; Communication; Cutaneous Lymphoma; Cutaneous T-cell lymphoma; Data; Development; Disease; Disease Outcome; Down-Regulation; Enhancers; Epigenetic Process; Exhibits; Fellowship; Foundations; Functional disorder; Future; Genes; Genetic; Genetic Transcription; Goals; Homing; Human; Immunologics; Indolent; Institution; Joints; Knock-out; Knowledge; Ligands; Lymphoma; Malignant Neoplasms; Mediating; Mentors; Methods; Modeling; Molecular; Non-Hodgkin' s Lymphoma; Organ; Outcome; Pathogenesis; Patients; Phenotype; Physicians; Production; Proliferating; Receptor Signaling; Research; Role; Sampling; Scientist; Signal Pathway; Signal Transduction; Skin; System; T-Cell Activation; T-Cell Receptor; T-Lymphocyte; Techniques; Training; Transcriptional Regulation; Tumor Suppressor Proteins; Up-Regulation; Visceral; advanced disease; career; cohort; computerized tools; cytokine; differential expression; digital; disease heterogeneity; disease phenotype; epigenetic regulation; epigenome; exhaust; exhaustion; genetic signature; genome sequencing; genome-wide; high throughput screening; in vivo; lead candidate; lymph nodes; melanoma; multimodality; mutant; next generation; novel therapeutic intervention; programmed cell death ligand 1; programmed cell death protein 1; programs; promoter; rational design; receptor; skills; standard of care; therapeutic target; transcription factor; transcriptome sequencing; transcriptomics; tumor; whole genome

Project Summary/Abstract Cutaneous T-cell lymphoma (CTCL) is an incurable non-Hodgkin lymphoma of skin homing T cells. Clinical outcomes of CTCL are highly heterogenous with some patients surviving <6 months and others >10 years in stage matched patients with advanced disease. The molecular mechanisms that drive heterogeneity of disease outcomes remain poorly understood. We have employed whole genome sequencing, RNA sequencing, and functional assays in a large cohort of primary patient samples to understand the genetic basis of CTCLs. We have identified deletion of PDCD1, a gene encoding the co-inhibitory receptor PD1, as a monogenic driver of CTCL disease aggression and phenotypes. Analysis of CTCLs in a multi-institutional cohort showed that PD1 deletion predicts a significantly worse overall survival in patients. This is recapitulated in our functional assays with primary patient samples where CTCLs with PD1 deletion displayed increased proliferation ex vivo. Notably, PD1 expressing CTCLs had increased expression of co-inhibitory receptors and gene signatures of T cell exhaustion, a dysfunctional state in T cells that limits effector functions. Interestingly, PD1 appears to drive a durable exhaustion phenotype that is retained by cells ex vivo even in the absence of ligand, suggesting that exhausted CTCLs have an epigenetic tumor suppressor program that is lost in PD1 deleted CTCLs. In addition, our preliminary RNA-seq data identified 60 transcription factors differentially expressed between PD1 expressing and deleted cohorts of CTCL, many but not all have been implicated in T cell exhaustion from studies with tumor models. Therefore, in this proposal, we aim to mechanistically dissect the epigenetic and transcriptional regulation of aggressive phenotypes in PD1-deleted CTCL samples. In Aim 1, we will identify whether transcription factors upregulated in PD1 expressing CTCLs are necessary or sufficient for in promoting CTCL exhaustion. In addition, we will also utilize primary patient samples to determine if the reversal of downregulation/upregulation of transcription factors in each CTCL cohort can reverse or increase exhaustion phenotypes. In Aim 2, we will elucidate the PD1 dependent epigenetic regulators in primary CTCLs We will combine epigenetic and transcriptomic data to identify differentially expressed transcription factors in each CTCL cohort in an unbiased way. My overall career goal is to become a successful, independent research scientist. The rigorous training plan proposed in this fellowship will allow me to achieve that goal by gaining research skills and knowledge in cellular immunology, cancer signaling pathways, and epigenetics. I will be mentored by Dr. Jaehyuk Choi, an expert physician-scientist in CTCL, and Dr. Deyu Fang, a world-renowned T cell biologist, who have devised a joint training plan to develop all necessary research skills, communication skills and promote my professional development. This fellowship will broaden our understanding of CTCL pathogenesis and T cell exhaustion, identify potential novel therapeutic strategies, and provide the necessary foundation for my future career as a research scientist.

项目总结/摘要 皮肤T细胞淋巴瘤（CTCL）是一种无法治愈的皮肤归巢T细胞非霍奇金淋巴瘤。临床 CTCL的结局具有高度异质性，一些患者存活<6 months and others >10年， 与晚期疾病分期匹配的患者。驱动疾病异质性的分子机制 对结果仍然知之甚少。我们使用了全基因组测序，RNA测序， 在一个大的原始患者样本队列中进行功能测定，以了解CTCL的遗传基础。我们 已经鉴定了PDCD 1的缺失，PDCD 1是编码共抑制受体PD 1的基因，作为 CTCL疾病侵袭和表型。多机构队列中CTCL的分析显示，PD 1 缺失预测患者的总体存活率显著更差。这在我们的功能测定中得到了概括 其中PD 1缺失的CTCL显示出离体增殖增加的原代患者样品。值得注意的是， 表达PD 1的CTCL增加了共抑制受体的表达和T细胞的基因特征， 衰竭，T细胞中限制效应子功能的功能障碍状态。有趣的是，PD 1似乎驱动一个 持久耗竭表型，即使在配体不存在的情况下也被离体细胞保留，这表明 耗尽的CTCL具有在PD 1缺失的CTCL中丢失的表观遗传肿瘤抑制程序。此外，本发明还提供了一种方法， 我们初步的RNA-seq数据鉴定了60个转录因子在PD 1表达和PD 2表达之间的差异表达。 和CTCL的删除队列，许多但不是所有的都与肿瘤研究中的T细胞耗竭有关。 模型因此，在这项建议中，我们的目标是机械地剖析表观遗传和转录 PD 1缺失的CTCL样品中侵袭性表型的调节。在目标1中，我们将确定 在表达CTCL的PD 1中上调的转录因子对于促进CTCL是必要的或足够的 疲惫不堪此外，我们还将利用原始患者样本来确定逆转 每个CTCL队列中转录因子的下调/上调可以逆转或增加耗竭 表型在目标2中，我们将阐明原发性CTCL中的PD 1依赖性表观遗传调节因子。 结合联合收割机表观遗传学和转录组学数据，以鉴定每个CTCL中差异表达的转录因子 以一种不带偏见的方式我的总体职业目标是成为一名成功的、独立的研究科学家。 在这个奖学金中提出的严格的培训计划将使我通过获得研究技能来实现这一目标 以及细胞免疫学、癌症信号通路和表观遗传学方面的知识。我将由博士指导。 CTCL的专家医生兼科学家Jaehyuk Choi和世界知名的T细胞生物学家Deyu Fang博士， 我们制定了一项联合培训计划，以发展所有必要的研究技能、沟通技能，并促进我的 专业发展。该研究将拓宽我们对CTCL发病机制和T细胞 疲劳，确定潜在的新的治疗策略，并为我的未来提供必要的基础 作为研究科学家的职业生涯。