Re-Analysis of GSE293186 Human Dermal Fibroblast Gene Signature Induced by ECEVs

Abstract

Skin wound healing requires coordinated activation of endothelial cells and fibroblasts to rebuild tissue, yet how endothelialderived extracellular vesicles influence fibroblast behavior remains unclear. We revisited the GSE293186 dataset to clarify this question and to identify molecular signatures that could inform therapeutic modulation of fibrosis. Our reanalysis leveraged the ARCHS4 portal to download raw counts and metadata, constructed an AnnData object, applied limmavoom for differential expression, and then submitted the result- ing up and downregulated gene lists to Enrichr and PerturbSeqr for enrichment against GO, KEGG, ChEA, and KOMP2 libraries, as well as for perturbation mimicry and reversal. The analysis revealed a transcriptional shift toward cellcycle progression and DNArepair processes, highlighted by enrichment of E2F7, E2F4, and FOXM1 and supported by GO and KEGG pathways for DNA replication and cell cycle and KOMP2 phenotypes related to cardiac stroke volume and bone morphology. A pronounced suppression of extracellularmatrix remodeling pathways such as heparansulfate catabolism and ECMreceptor interaction was also observed, consistent with GO and KEGG enrichment for ECM interaction and heparan sulfate catabolic process. PerturbSeqr highlighted KDM2B and cry2 as key nodes in the mimic signature, sourced from Perturb Atlas and RummaGEO databases and identified nicotinamide and palbociclib as potent reversers, supported by RummaGEO, LINCS, and Ginkgo chemical libraries. The overlap of the onecarbon pool by folate pathway in both up and downregulated signatures points to a broader metabolic reprogramming that may affect fibroblast differentiation. These insights highlight extracellular vesiclemediated modulation of fibroblast phenotype as a potential target for controlling scar formation and fibrosis.