Author ORCID Identifier

Date of Award


Document Type

Thesis (Ph.D.)

Department or Program

Molecular and Systems Biology

First Advisor

Dr. Michael L. Whitfield


Systemic sclerosis (SSc) is a rare fibrotic autoimmune disease with high mortality and limited FDA approved therapies. Clinical concordance among twins is low; however, a modest familial heritability implicates complex interactions between polygenic risk alleles and the environment as causal – interactions that are mediated by epigenetics. Although mechanisms of tissue fibrosis have been successfully identified and targeted in established in vitro models for SSc, these molecules have ultimately failed in clinical trials. This likely reflects the lack of a reliable in vitro model that faithfully recapitulates the disease.

I utilized a 3D skin-like tissue model to study SSc skin fibrosis. I paired this model with epigenomic analysis of Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq). The goal was two-fold: 1) to epigenetically characterize and validate this 3D model and 2) to elucidate epigenetic mechanisms of skin fibrosis at a single-cell level using our 3D tissue model.

In Chapter 2, I showed that SSc 3D tissues have patterns of chromatin accessibility that are distinct from monolayer fibroblasts. I also identified a novel region of SSc dysregulation predicted to regulate expression of the gene FER1L6. In Chapter 3, I used a similar experimental strategy to determine if select variants implicated in disease susceptibility impact chromatin accessibility. I identified a region of potential chromatin dysregulation in fibroblasts from an SSc individual with African-Ancestry specific variants of interest. This study demonstrates the potential to determine causality of SSc-associated non-coding variants. In Chapter 4, I applied single-cell ATAC-seq to a 3D tissue model containing increased cellular complexity. I identified several fibroblast subpopulations that correlated with those identified in human skin. Finally, I proposed a model for epigenetic dysregulation in SSc skin fibrosis.

These findings establish that 3D tissues are epigenetically distinct from monolayer cultures and closely approximate human skin fibroblast populations. Using this model, I validated previous findings in addition to generating novel insights. Collectively, I believe this body of work contributes to a more accurate understanding of SSc skin fibrosis and establishes a reliable in vitro model for identification of targeted epigenetic therapies that can more effectively translate to clinical improvement.