NIAMS: Center for Research Translation (CORT)

NIAMS：研究翻译中心 (CORT)

• 批准号: 10317277
• 负责人: ROBERT A. LAFYATIS
• 金额: $ 1.42万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10317277
• 关键词: Algorithms; Binding Sites; Biological; Biological Markers; CRISPR interference; Cells; ChIP-seq; Chromatin Structure; Chromosomes; Collagen; Complication; Cutaneous sclerosis; DNA; Data; Deposition; Dimensions; Doctor of Philosophy; Fibroblasts; Genetic; Goals; Health; Human Genetics; Individual; Interstitial Lung Diseases; Lung; Lung Transplantation; Lung diseases; Mediator of activation protein; Mentorship; Myofibroblast; National Institute of Arthritis and Musculoskeletal and Skin Diseases; Normal Cell; Pathogenesis; Pathogenicity; Patients; Population; Proteins; Pulmonary Fibrosis; Regulation; Regulatory Element; Reporting; Research; Resources; Scleroderma; Specific qualifier value; Structure of parenchyma of lung; Students; Systemic Scleroderma; Therapeutic; Transcriptional Regulation; Translational Research; Universities; Validation; Work; XCL1 gene; cell type; disadvantaged background; epigenome; epigenomics; graduate student; insight; novel; programs; single cell analysis; single-cell RNA sequencing; skin fibrosis; stem cells; transcription factor; transcriptome; transcriptomics

The goal of this supplement is to support a graduate student to promote diversity under PA-21-071: Research Supplements to Promote Diversity in Health-Related Research. Ms. Bulik is a PhD candidate in the Human Genetics Program at the University of Pittsburgh, working under the mentorship of Dr. Lafyatis, Director of the P50, Scleroderma Center of Research Translation and PI on Project 1: Systemic Sclerosis Skin Biomarkers & Therapeutics. Ms. Bulik will work on an extension of the aims of Project 1, taking advantage of explant lungs from patients with systemic sclerosis associated interstitial lung disease (SSc-ILD) undergoing lung transplant (Obtained through the P50 Lung Tissue Core). Increased myofibroblasts drive excessive deposition of collagen and other matrix proteins and thus act as the final mediator of skin and lung fibrosis in systemic sclerosis. However, little is known regarding the origin of myofibroblasts or their differentiation from progenitor cell type(s). Understanding transcriptomic features and genetic regulation that occurs in the transition from normal cell populations to pathogenic myofibroblasts can provide insight into the transcription factors (TFs) involved in myofibroblast differentiation. We have recently reported expression profiles of individual cells by analyzing single cell RNA sequencing (scRNA-seq) data and clustering cell types through dimensional reduction algorithms. We have shown that control and SSc-ILD lung tissue contain multiple fibroblast populations. Ongoing single cell ATAC sequencing (scATAC-seq) studies in our group reveal changes in chromosome availability between control and SSc-ILD fibroblasts, indicating that myofibroblast differentiation is associated with parallel changes in both chromatin structure and transcriptome features. Compiling data between epigenomes and transcriptomes for fibroblast and myofibroblasts allows for robust identification of putative transcription factors regulating myofibroblast differentiation. These computational predictions provide hypotheses for underlying mechanisms but require biological validation. In the first aim Ms. Bulik will Identify putative transcription factors regulating myofibroblast differentiation in SSc-ILD lungs, integrating transcriptomic analyses (SCENIC) and epigenomic analyses (Signac), and publicly available ChIP-seq data to define TFs most likely to regulate myofibroblast differentiation in SSC-ILD. She will repress TFs implicated in regulating myofibroblast transcriptome in primary SSc-ILD fibroblasts using Perturb-seq using CRISPRi. In the second aim she will study cis-regulatory elements in DNA that act as TF binding sites for key TF involved in myofibroblast regulation. She will align scATAC-seq data with publicly available resources to better understand the transcriptional regulation of the myofibroblasts.

本补充材料的目标是支持研究生根据 PA-21-071：研究促进多样性 促进健康相关研究多样性的补充剂。 Bulik 女士是人类学博士生 匹兹堡大学遗传学项目，在项目主任 Lafyatis 博士的指导下工作 P50，硬皮病研究翻译中心和项目 1 的 PI：系统性硬化症皮肤生物标志物 & 疗法。 Bulik 女士将致力于利用外植肺来扩展项目 1 的目标 来自接受肺移植的系统性硬化症相关间质性肺疾病 (SSc-ILD) 患者 （通过 P50 肺组织核心获得）。肌成纤维细胞增加导致胶原蛋白过度沉积 和其他基质蛋白，因此充当系统性硬化症中皮肤和肺纤维化的最终介质。 然而，关于肌成纤维细胞的起源或其从祖细胞的分化知之甚少 类型。了解从正常转变过程中发生的转录组特征和基因调控 致病性肌成纤维细胞的细胞群可以提供对参与的转录因子（TF）的深入了解 肌成纤维细胞分化。我们最近通过分析报告了单个细胞的表达谱 单细胞 RNA 测序 (scRNA-seq) 数据并通过降维算法对细胞类型进行聚类。 我们已经证明对照和 SSc-ILD 肺组织含有多个成纤维细胞群体。正在进行的单细胞 我们小组的 ATAC 测序 (scATAC-seq) 研究揭示了对照之间染色体可用性的变化 和 SSc-ILD 成纤维细胞，表明肌成纤维细胞分化与两者的平行变化相关 染色质结构和转录组特征。编译表观基因组和转录组之间的数据 成纤维细胞和肌成纤维细胞可以可靠地识别假定的转录因子调节 肌成纤维细胞分化。这些计算预测为潜在机制提供了假设 但需要生物学验证。在第一个目标中，Bulik 女士将识别假定的转录因子调节 SSc-ILD 肺中肌成纤维细胞分化，整合转录组分析 (SCENIC) 和表观基因组 分析 (Signac) 和公开的 ChIP-seq 数据来定义最有可能调节肌成纤维细胞的 TF SSC-ILD 的分化。她将抑制与调节原发性肌成纤维细胞转录组有关的 TF 使用 CRISPRi 使用 Perturb-seq 生成 SSc-ILD 成纤维细胞。在第二个目标中，她将研究顺式监管要素 作为参与肌成纤维细胞调节的关键 TF 的 TF 结合位点的 DNA。她将对齐 scATAC-seq 数据 利用公开资源更好地了解肌成纤维细胞的转录调控。