Comparative transcriptomic analysis validates iPSC derived in-vitro progressive fibrosis model as a screening tool for drug discovery and development in systemic sclerosis

• Published in: Scientific reports Vol. 14; no. 1; pp. 24428 - 14
• Main Authors: Nathan, Shyam, Wang, Yifei, D’ambrosio, Matthew, Paul, Reeba, Lyu, Huimin, Delic, Denis, Bretschneider, Tom, Falana, Kimberly, Li, Li, Vijayaraj, Preethi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.10.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114; 631/154; Autoimmune diseases; Cell culture; Cell Differentiation - drug effects; Cell plasticity; Cells, Cultured; Drug development; Drug Discovery - methods; Drug Evaluation, Preclinical - methods; Drug screening; Fibrosis; Gene expression analysis; Gene Expression Profiling; Glycolysis; Heterogeneity; Humanities and Social Sciences; Humans; Hypoxia; Immunosuppressive agents; In vitro models; Induced Pluripotent Stem Cells - drug effects; Induced Pluripotent Stem Cells - metabolism; Mesenchymal Stem Cells - drug effects; Mesenchymal Stem Cells - metabolism; Mesenchyme; multidisciplinary; Phenotypes; Pluripotency; Progressive fibrosis; Ribonucleic acid; RNA; Scars; Science; Science (multidisciplinary); Scleroderma; Scleroderma, Systemic - genetics; Scleroderma, Systemic - metabolism; Scleroderma, Systemic - pathology; Senescence; Stem cells; Systemic sclerosis; Transcriptome; Transcriptomes; Transcriptomics; Vascular diseases; Wound healing; Gene expression analysis; In vitro models; Systemic sclerosis; Progressive fibrosis; Cell plasticity
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-024-74610-2

Systemic sclerosis (SSc) is an autoimmune disease characterized by vasculopathy, immune dysregulation, and systemic fibrosis. Research on SSc has been hindered largely by lack of relevant models to study the progressive nature of the disease and to recapitulate the cell plasticity that is observed in this disease context. Generation of models for fibrotic disease using pluripotent stem cells is important for recapitulating the heterogeneity of the fibrotic tissue and are a potential platform for screening anti-fibrotic drugs. We previously reported a novel in-vitro model for fibrosis using induced pluripotent stem cell-derived mesenchymal cells (iSCAR). Here we report the generation of a “scar-like phenotype” when iPSC derived mesenchymal cells are cultured on hydrogel that mimicks a wound healing/scarring response (iSCAR). First, we performed RNA sequencing (RNA-seq) based transcriptome profiling of iSCAR culture at 48 h and 13 days to characterize early and latestage scarring phenotypes. The next generation RNA-seq of these iSCAR culture at different timepoints detected expression 92% of early “scar associated” genes and 85% late “scar associated” genes, respectively. Comparative transcriptomic analysis of a gene level SSc compendium matrix to the iSCAR wound associated model revealed genes common in both data sets. Early scar formation genes showed biological processes of hypoxia (27.5%), vascular development (13.7%) and glycolysis (27.5), while late scar formation showed genes associated with senescence (22.6%). Next we show the effects of two different antifibrotic compounds to validate the utility of the model as a screening tool to study early and late-stagelate-stage fibrosis. An autotaxin inhibitor was used to validate the iSCAR late stage fibrotic model (iSCAR-T) and an antifibrotic tool screening compound of unknown mechanism (EX00015097) was used to study and validate both early (iSCAR-P) and late-stage (iSCAR-T) fibrosis in the iSCAR model.