Melissa Bulik - Final Dissertation Defense - HUGEN PhD Candidate

Department of Human Genetics Doctoral Candidate, Melissa Bulik, defends her dissertation on “Transcriptional Dysregulation Associated with Pathologic Development and Maintenance of Myofibroblasts in Systemic Sclerosis” 

COMMITTEE CHAIR: Robert A. Lafyatis, MD

Committee Members:

• Beth L. Roman, PhD
• Johnathan K. Alder, PhD
• Hyun Jung Park, PhD

ABSTRACT:

Systemic sclerosis (SSc) is rare disease that is both complex and heterogenous. It can affect multiple organ systems and varies greatly in severity. The leading cause of SSc-related mortality is lung fibrosis, i.e., interstitial lung disease (ILD). Patients with SSc-ILD have an expanded population of myofibroblasts in their lungs. Myofibroblasts contribute to pathogenicity through their ability to increase extracellular matrix and the formation of fibrotic foci. In end-stage lung disease, there is a major distortion of the pulmonary architecture and diminished gas exchange. The transcriptional drivers of myofibroblasts are incompletely understood, particularly in the direct context of the human disease. My research has focused on two areas of dysregulation.

In the first, I used single cell data collected from control and SSc-ILD lungs, to identify upregulated expression of transcription factor 12 (TCF12), along with downstream target genes, within the myofibroblast population using pySCENIC. Perturbation of TCF12 in vitro identified altered gene expression implicating pathways associated with actin regulation, TGFb signaling, and cell cycle interruption. Overexpression of TCF12 led to upregulation of other genes often associated with SSc. TCF12 overexpression was also associated with differentially accessible regions in chromatin compared to baseline TCF12 expression associate with myofibroblast populations. This data supports the role of aberrant TCF12 activity in SSc-ILD myofibroblasts.

My second focus was to associate skewing of chromatin accessibility and transcription factor binding site access with variants that have been associated with GWAS associate single nucleotide variants (SNVs). I found that nearly 20% of the investigated SNVs were enriched for SMAD2 binding motifs, noteworthy because of the role TGFb is thought to play in SSc. Though none of the SMAD2 sites are altered by the index SNV, these data suggest that these SNV loci are important in pathogenesis. Finally, whole genome sequencing was carried out to compare genotype to the snATAC-seq alignment to identify accessibility differences at GWAS associated SNVs. Determining dysregulation in gene expression of the myofibroblast can provide insight into the disease progression and potentially allow for the development of new therapeutics. These projects have helped define the roles of TGFb and TCF12 in myofibroblast differentiation.