Background/Purpose: Systemic sclerosis (SSc) is a complex and highly heterogeneous disease with multi-organ involvement. Accurate tools for disease sub-classification are lacking. In most patients, skin and subcutaneous tissue are affected, and circulating immune cells are activated. We performed what is to our knowledge the first RNA-Seq on simultaneously obtained skin, intradermal white adipose tissue, and peripheral blood mononuclear cells (PBMCs) from patients with well-characterized SSc.

Methods: We obtained PBMCs and skin biopsies from healthy controls and individuals with limited cutaneous systemic sclerosis (lcSSc), diffuse cutaneous systemic sclerosis (dcSSc), and scleroderma sine scleroderma (SSS). Intradermal adipose tissue was separated from skin. Patients were followed longitudinally, and PBMCs and skin were obtained serially with repeat clinical phenotyping. We then performed stranded, total RNA-Seq for transcriptome profiling.

Results: We found increased expression of COMP, THY1, and IGFBP4 in SSc skin biopsies with resolution to the specific differentially expressed (DE) gene isoform. In contrast, we detected a marked decreased expression of SPAG17, part of the ciliary axoneme central pair complex, in SSc skin. A limited set of DE genes can perfectly separate SSc from control skin. Genes with lower expression in SSc skin were enriched for the selenocysteine synthesis pathway. On the other hand, genes with increased expression in SSc skin were substantially enriched for both extracellular matrix and immune response pathways, and in particular interferon signaling. Microbial species on the skin can also be detected using de novo assembly. Remarkably, we found that number of DE genes and magnitude of their changes in PBMCs from SSc vs. controls was modest compared to differences detected in the skin. This dataset allows us to correlate skin scores with the transcriptome profiles of different tissues simultaneously obtained from the same individual.

Conclusion: In this initial RNA-Seq of simultaneously obtained skin, intradermal adipose tissue, and PBMCs, novel patterns of gene expression differences can be revealed that could not be recognized by earlier microarray-based transcriptome approaches. It is unclear at this time whether the matrix & immune activation signatures in the skin samples represent different SSc types, or different stages of SSc evolution. Ideally this technique could be applied to further serial biopsies to observe SSc evolution over time. Broad transcriptome profiling has excellent potential for unsupervised classification of different SSc types for further study and correlation with clinical phenotypes.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/biomarker-identification-molecular-sub-classification-in-systemic-sclerosis-for-precision-medicine-using-rna-seq/