NIAMS: Center for Research Translation (CORT)

NIAMS：研究翻译中心 (CORT)

基本信息

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
项目类别：
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

项目摘要

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) 研究揭示了对照组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。