NIAMS: Center for Research Translation (CORT)

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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.