Background/Purpose: Systemic sclerosis (SSc) is characterized by fibrosis, microangiopathy and immune dysregulation. Despite many years of research, the pathogenesis of SSc is poorly understood; there is no approved therapy and biomarkers for early diagnosis, assessment of disease activity, prediction of complications and prognosis. Current technologies that investigate bulk populations of cells lack the depth and resolution needed to define the small skin stromal and immune subsets that drive SSc progression. Advances in the field of single-cell RNA has opened the way for unbiased dissection of complex niches into single cells, and identification of unique cell subtypes, pathways, markers and target genes. Our aims are to understand SSc pathogenesis by comprehensive characterization of stromal and immune cells in the skin and blood of SSc patients and detection of specific intra-skin cell states, pathways, and cell-cell interactions in SSc patients compared to healthy controls.

Methods: We applied the massively parallel single cell RNA-seq (MARS-seq) technique developed in our lab to conduct a comprehensive single-cell analysis of skin stromal and immune cells obtained from punch biopsy together with blood immune cells from 79 SSc patients (44 dSSc, 35 lSSc) at different stages of disease progression, and 35 healthy controls. The perturbed signaling pathways, pathogenic stromal or immune cell subsets are characterized using CyTOF, Immunohistochemistry, Physical Interacting Cell sequencing (PIC-seq), and in vitro functional assays.

Results: We collected data from a total of 49,831 high-quality skin stromal cells, and 61,365 high-quality blood and skin immune cells. Our MetaCell analytical method resulting in a detailed map of 389 meta cells in the immune cell compartment organized into 14 broad lineages (e.g skin T, B and NK cells, Dendritic cells, Monocyte). In the stromal cell compartment, we found 294 meta cells organized into 17 broad lineages including: Fibroblasts, Pericytes, Vascular cells, and other cells.  To our surprise, analysis of the immune cell compartment revealed only minor changes in the cell composition and gene expression in patients compared with controls. In the dermal fibroblast lineage we found a small cluster of cells that were significantly diminished in the SSc patients compared with control. This subset expressed genes associated with fibrosis, vascular remodeling, and most importantly, display stem cell-like phenotypic markers that are different from other known skin stem cells located in the hair follicle and subcutaneous fat. We further found significant increased number of subsets of pericytes and vascular cells in SSc patients compared with controls. Finally, we found known and novel pathways that play crucial roles in SSc pathogenesis.

Conclusion: Our study provides the most comprehensive dataset in single cell resolution in SSc, and suggests a paradigm shift in the understanding of SSc. The MARS-seq can serve as a vehicle for discovering immune-stromal cell crosstalk, for finding new biomarkers for early SSc diagnosis and for tailoring and identification of new therapeutic targets.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/single-cell-analysis-of-skin-and-blood-of-scleroderma-patients-towards-identification-of-new-disease-mechanisms-prognostic-biomarkers-and-potential-therapeutic-targets/