NIAMS: Center for Research Translation (CORT)

该补充的目标是支持研究生在PA-21-071下促进多样性：研究 促进健康相关研究多样性的补充材料。Bulik女士是人类学博士候选人， 匹兹堡大学遗传学项目，在Lafyatis博士的指导下工作，Lafyatis博士是 P50，硬皮病研究翻译中心和PI项目1：系统性硬化症皮肤生物标志物和 治疗学Bulik女士将致力于项目1目标的扩展，利用移植肺 来自接受肺移植的系统性硬化症相关间质性肺病（SSc-ILD）患者 （通过P50肺组织芯获得）。肌成纤维细胞增加导致胶原过度沉积 和其它基质蛋白，因此在系统性硬化症中作为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分化的知之甚少 类型。理解转录组学特征和发生在从正常 细胞群与致病性肌成纤维细胞的相互作用可以提供对转录因子（TF）的深入了解， 肌成纤维细胞分化我们最近报道了通过分析单个细胞的表达谱， 单细胞RNA测序（scRNA-seq）数据和通过降维算法聚类细胞类型。 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 我们组的ATAC测序（scATAC-seq）研究揭示了对照组和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这两种细胞的平行变化有关。 染色质结构和转录组特征。编辑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允许稳健地鉴定推定的转录因子调节 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女士将确定调节 SSc-ILD肺中的肌成纤维细胞分化，整合转录组学分析（SCENIC）和表观基因组学 分析（Signac）和公开可用的ChIP-seq数据，以确定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成肌纤维细胞转录组有关的转录因子， 使用Perturb-seq使用CRISPRi的SSc-ILD成纤维细胞。在第二个目标，她将研究顺式调节元件， 作为肌成纤维细胞调节中关键TF结合位点的DNA。她会将scATAC-seq数据 利用公开可用的资源，以更好地理解肌成纤维细胞的转录调控。

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.