Elucidating transcriptional and epigenetic regulators of aggressive cutaneous T cell lymphoma

项目摘要/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的预后是高度不同的，一些患者存活6个月，另一些患者存活10年。 分期匹配的晚期疾病患者。驱动疾病异质性的分子机制 人们对结果仍然知之甚少。我们采用了全基因组测序、RNA测序和 对大量原始患者样本进行功能分析，以了解CTCL的遗传基础。我们 已经发现编码共抑制受体PD1的基因PDCD1的缺失是导致 CTCL病的攻击性和表型。对多机构队列中CTCL的分析表明，PD1 缺失预示着患者的总体存活率显著下降。这在我们的功能分析中得到了概括。 在原始患者样本中，带有PD1缺失的CTCL在体外显示出更多的增殖。值得注意的是， 表达PD1的CTCL增加共抑制受体的表达和T细胞的基因标志 衰竭，T细胞的一种功能失调状态，限制了效应器的功能。有趣的是，PD1似乎驱动着一辆 即使在没有配体的情况下，细胞在体外也能保持持久的耗竭表型，这表明 衰竭的CTCL有一个表观遗传的肿瘤抑制程序，该程序在PD1缺失的CTCL中丢失。此外, 我们的初步rna-seq数据鉴定出60个转录因子在pd1表达的 并删除了CTCL的队列，许多但不是所有的都与肿瘤研究中的T细胞衰竭有关 模特们。因此，在这个提议中，我们的目标是机械地剖析表观遗传和转录 PD1缺失的CTCL样本中攻击性表型的调节。在目标1中，我们将确定是否 在表达CTCL的PD1中上调的转录因子是促进CTCL的必要条件或充分条件 疲惫不堪。此外，我们还将利用初级患者样本来确定是否逆转了 每个CTCL队列中转录因子的下调/上调可以逆转或增加力竭 表型。在目标2中，我们将阐明初级CTCL中依赖PD1的表观遗传调节因子 结合表观遗传学和转录学数据确定在每个CTCL中差异表达的转录因子 以不偏不倚的方式进行分组。我的整个职业目标是成为一名成功的、独立的研究科学家。 在此奖学金中提出的严格的培训计划将使我能够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Dr. CTCL内科专家兼科学家Jaehyuk Choi和世界知名T细胞生物学家方德裕博士 我制定了一项联合培训计划，以发展所有必要的研究技能、沟通技能和推广我的 职业发展。这项研究将扩大我们对CTCL发病机制和T细胞的了解 精疲力竭，确定潜在的新治疗策略，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。

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.