Transcriptome and epigenome analysis of helper T cell specification and plasticit

辅助 T 细胞规格和可塑性的转录组和表观基因组分析

• 批准号: 7849398
• 负责人: CHEN DONG
• 金额: $ 144.41万
• 依托单位: UNIVERSITY OF TX MD ANDERSON CAN CTR
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-29 至 2011-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7849398
• 关键词: Address; Arthritis; Autoimmune Diseases; Bioinformatics; CD4 Positive T Lymphocytes; Cell Differentiation process; Cell Lineage; Cells; Data; Development; Effector Cell; Employment; Epigenetic Process; Faculty; Fostering; Gene Expression; Gene Expression Profile; Generations; Goals; Grant; Hand; Helper-Inducer T-Lymphocyte; Human Resources; Inflammation; Inflammatory; Interleukin-6; Lupus; Mediating; Mediator of activation protein; Methods; Mission; Molecular; National Institute of Arthritis and Musculoskeletal and Skin Diseases; Pathogenesis; Psoriasis; Reagent; Recovery; Regulation; Reporting; STAT3 gene; Sequence Analysis; Signal Pathway; Signal Transduction; Skin; T-Lymphocyte; Th2 Cells; Time; Tissues; Up-Regulation; Work; base; career development; cell type; chromatin immunoprecipitation; genome-wide; insight; member; novel; programs; research study; transcription factor

DESCRIPTION (provided by applicant): CD4+ helper T (Th) cells are critical mediators in autoimmune diseases, such as arthritis, psoriasis and lupus. Upon activation, naove Th cells differentiate into effector cell subsets that are characterized by their distinct gene expression and immunoregulatory function. In the past several years, a number of novel Th subsets have been identified, including Foxp3+ regulatory T cells, pro-inflammatory Th17 cells and T follicular helper (Tfh) cells. These cells not only have been shown to be important positive or negative regulators in autoimmune diseases, but also share reciprocal developmental regulation. TGF2 signaling in activated T cells induces Foxp3 expression, while the combination of TGF2 and IL-6 or IL-21 drives Th17 cell differentiation. On the other hand, we recently reported that IL-6 or IL-21, in the absence of TGF2 signaling, drives Tfh cell differentiation. How STAT3, a common transcription factor downstream of IL-6 and IL-21, and TGF2-activated SMAD transcription factors interplay in T cell fate decision has not been understood. Our data suggest that they may mediate the upregulation of lineage-specific transcription factors, such as Foxp3 in Treg cells, ROR1/3 in Th17 cells and Bcl6 in Tfh cells. Although these cell-specific transcription factors have been shown by others and us to be essential in Th cell lineage specification, the exact mechanisms of their action have not been understood either, nor their cross-inhibitory functions. The proposed work is based on our well-established, multi-disciplinary collaborative team that has made important contributions in the past five years. The central goal of this project is to perform large-scale, genome-wide transcriptome and epigenome analysis of Treg, Th17 and Tfh cells to determine the direct functions of key transcription factors and their likely agonistic and antagonistic interactions. Our central hypothesis is that transcriptional and epigenetic mechanisms induced by key transcription factors underscore the specification and plasticity of novel Th lineage cells. To address this hypothesis, we will perform transcriptome analysis of T cells deficient in TGF2 and STAT3 signaling pathways or Foxp3, ROR1/3 and Bcl6 transcription factors. Moreover, we will perform genome-wide epigenome analysis of T cells deficient in TGF2 and STAT3 signaling pathways or Foxp3, ROR1/3 and Bcl6 transcription factors. Thirdly, we will perform genome-wide chromatin immunoprecipitation-sequencing analysis on the targets of SMAD, STAT3, ROR3/1 and Bcl6. The results of these experiments will be subject to bioinformatic analysis to understand Th lineage specification and plasticity. The project is highly feasible and can be accomplished within the two-year time frame as all the necessary reagents are in hand and methods are well established. The proposed project will provide systemic insights into Th cell lineage commitment and cellular plasticity. The study suits the mission of NIAMS by analyzing the critical cell types that positively or negatively regulate the pathogenesis of skin and rheumatic autoimmune diseases.

描述（由申请人提供）：CD4+ 辅助 T (Th) 细胞是自身免疫性疾病（例如关节炎、牛皮癣和狼疮）中的关键介质。激活后，幼稚 Th 细胞分化为效应细胞亚群，其特征在于其独特的基因表达和免疫调节功能。在过去几年中，许多新的 Th 亚群已被识别，包括 Foxp3+ 调节性 T 细胞、促炎性 Th17 细胞和滤泡辅助性 T (Tfh) 细胞。这些细胞不仅被证明是自身免疫性疾病中重要的正向或负向调节因子，而且还具有相互的发育调节作用。活化 T 细胞中的 TGF2 信号传导诱导 Foxp3 表达，而 TGF2 与 IL-6 或 IL-21 的组合则驱动 Th17 细胞分化。另一方面，我们最近报道，在缺乏 TGF2 信号传导的情况下，IL-6 或 IL-21 可驱动 Tfh 细胞分化。 STAT3（IL-6 和 IL-21 下游的常见转录因子）和 TGF2 激活的 SMAD 转录因子如何在 T 细胞命运决定中相互作用尚不清楚。我们的数据表明它们可能介导谱系特异性转录因子的上调，例如Treg细胞中的Foxp3、Th17细胞中的ROR1/3和Tfh细胞中的Bcl6。尽管这些细胞特异性转录因子已被其他人和我们证明在 Th 细胞谱系规范中至关重要，但它们作用的确切机制以及它们的交叉抑制功能尚不清楚。拟议的工作基于我们完善的多学科协作团队，该团队在过去五年中做出了重要贡献。该项目的中心目标是对 Treg、Th17 和 Tfh 细胞进行大规模、全基因组转录组和表观基因组分析，以确定关键转录因子的直接功能及其可能的激动和拮抗相互作用。我们的中心假设是，关键转录因子诱导的转录和表观遗传机制强调了新型 Th 谱系细胞的规范和可塑性。为了解决这一假设，我们将对缺乏 TGF2 和 STAT3 信号通路或 Foxp3、ROR1/3 和 Bcl6 转录因子的 T 细胞进行转录组分析。此外，我们将对缺乏 TGF2 和 STAT3 信号通路或 Foxp3、ROR1/3 和 Bcl6 转录因子的 T 细胞进行全基因组表观基因组分析。第三，我们将对SMAD、STAT3、ROR3/1和Bcl6的靶标进行全基因组染色质免疫沉淀测序分析。这些实验的结果将接受生物信息学分析，以了解 Th 谱系规范和可塑性。该项目可行性很高，所需试剂齐备，方法也已成熟，可在两年内完成。拟议的项目将为 Th 细胞谱系定向和细胞可塑性提供系统的见解。该研究通过分析对皮肤和风湿性自身免疫性疾病发病机制产生正向或负向调节的关键细胞类型，符合 NIAMS 的使命。