# Cell epigenetics & communication in systemic sclerosis and localized scleroderma skin disease

> **NIH NIH P50** · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · 2022 · $302,100

## Abstract

Skin fibrosis in systemic sclerosis (SSc) leads to significant morbidity resulting from disfiguring, painful and itchy
skin, and joint contractures. We have recently shown by single cell RNA-sequencing (scRNA-seq) that SSc
dermal fibroblasts (expressing increased THBS1, PRSS23) and dermal myofibroblasts (also expressing
increased SFRP4, ADAM12, TNFSF18 and CTGF) arise from SFRP2-expressing progenitors found in healthy
control skin. These studies provide a framework for understanding the profibrotic drivers of these cell states.
Transcription factors (TFs) are pivotal in regulating gene expression and provide a powerful landmark for these
cell states. Using SCENIC, a computational method developed for detecting TF-associated regulatory networks
(regulons) in single cell datasets, we identified putative TFs driving myofibroblast differentiation: FOXP1, HIF1A,
IRF7, STAT1 and FOSL2. Additionally, in preliminary results we employed Assay for Transposase Accessible
Chromatin by Sequencing (scATAC-seq) data supporting the importance of these TFs in SSc myofibroblast
differentiation. In our first aim, we will assess the importance of these TFs in further multiome studies, and confirm
their roles in myofibroblast differentiation by measuring the effects of TF knock-down on fibroblast transcriptome
and epigenome. Markers of macrophage activation correlate strongly with the main clinical measure of skin
disease severity, the modified Rodnan skin score (MRSS), suggesting that macrophages deliver profibrotic
signals to drive myofibroblast differentiation. Recent studies in SSc-ILD have confirmed IL-6 in pathogenesis of
lung disease and we see its downstream target CCL18 also upregulated in skin macrophages. In our second
aim, we will use a novel system biology methodology, CausER, to analyze latent factors regulating the
macrophage-fibroblast interaction and generate snRNA-seq data before and after tocilizumab to better
understand the role of IL-6 in activating profibrotic macrophages in SSc skin. We expect that this will inform the
similar process occurring in SSc-interstitial lung disease. Localized scleroderma (LS) continues to cause
disfiguring and functional disabilities in children as well as adults. Our preliminary results implicate IFNg as
activating macrophages and fibroblasts in LS skin. In aim 3, using similar approaches to study of SSc, we will
compare the immune and non-immune cell populations in LS to SSc skin. First, we will combine our existing LS
(n=14), SSc (n=27) and healthy control (n=14) scRNA-seq datasets, and examine differences in fibroblast and
myeloid cell transcriptome-phenotypes and differentially expressed genes. Then as in aim 2, we will employ
CausER to identify latent factors regulating the interaction between these cells. We will then identify TFs
regulating myeloid and fibroblast phenotypes using SCENIC and multiome. We expect these studies of LS to
provide new insights into the cytokines and intracellular pathways activatin...

## Key facts

- **NIH application ID:** 10404143
- **Project number:** 1P50AR080612-01
- **Recipient organization:** UNIVERSITY OF PITTSBURGH AT PITTSBURGH
- **Principal Investigator:** ROBERT A. LAFYATIS
- **Activity code:** P50 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $302,100
- **Award type:** 1
- **Project period:** 2022-09-20 → 2027-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10404143

## Citation

> US National Institutes of Health, RePORTER application 10404143, Cell epigenetics & communication in systemic sclerosis and localized scleroderma skin disease (1P50AR080612-01). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10404143. Licensed CC0.

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