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.

该补充的目的是支持研究生在PA-21-071下促进多样性：研究 补充剂以促进与健康相关的研究的多样性。布里克女士​​是人类的博士学位候选人 匹兹堡大学的遗传学计划，在Lafyatis博士的指导下工作 P50，硬皮病研究翻译中心和项目1：系统性硬化症皮肤生物标志物和 疗法。 Bulik女士将利用Epplant肺部延伸项目1的目标 来自接受肺移植的全身性硬化症患者（SSC-ILD） （通过P50肺组织核心获得）。增加肌纤维细胞驱动胶原蛋白的过度沉积 和其他基质蛋白，因此充当全身性硬化症中皮肤和肺纤维化的最终介体。 但是，关于肌纤维细胞的起源或它们与祖细胞的分化知之甚少 类型。了解转录组特征和遗传调节在从正常的过渡中发生 致病性肌纤维细胞的细胞群体可以洞悉涉及的转录因子（TF） 肌纤维细胞的分化。我们最近通过分析了单个细胞的表达谱。 单细胞RNA测序（SCRNA-SEQ）数据和通过尺寸还原算法聚类细胞类型。 我们已经表明，对照和SSC-dILD肺组织包含多个成纤维细胞群体。正在进行的单细胞 我们组中的ATAC测序（SCATAC-SEQ）研究揭示了控制之间染色体可用性的变化 和SSC-ild成纤维细胞，表明肌纤维细胞的分化与两者的平行变化有关 染色质结构和转录组特征。在表观基因组和转录组之间编译数据 成纤维细胞和成肌纤维细胞可牢固地识别定义的转录因子 肌纤维细胞的分化。这些计算预测为基本机制提供了假设 但是需要生物学验证。在第一个目标中，布里克女士​​将确定规范的推定转录因子 SSC-ILD肺中的肌纤维细胞分化，整合转录组分析（风景）和表观基因组学 分析（signac）和公开可用的芯片播种数据来定义最有可能调节肌纤维细胞的TF SSC-ILD的分化。她将压制与调节肌成纤维细胞转录组有关的TF SSC-ILD成纤维细胞使用intturb-seq使用CRISPRI。在第二个目标中，她将研究顺式调节元素 作为肌纤维细胞调节的键TF充当TF结合位点的DNA。她将使scatac-seq数据对齐 借助公共资源，可以更好地了解成肌纤维细胞的转录调节。