Genome-wide profiling reveals pervasive transcriptional alterations in fibroblasts derived from lesional skin in vitiligo including a reduced potential to proliferate

Fibroblasts interact with keratinocytes and melanocytes to maintain skin homeostasis. However, the impact of selective melanocyte loss on the transcriptome of fibroblasts is not fully understood. Thus, we sought to understand the genome-wide transcriptome of fibroblasts derived from non-lesional (NL) and lesional (L) dermis in patients with non-segmental vitiligo. Transcriptional profiling of NL and L fibroblasts was performed on three individuals with vitiligo using next-generation-sequencing. Functional protein-protein interaction (PPI) networks were constructed for the significantly upregulated and downregulated genes, as well as for a common set of genes that were downregulated in both fibroblasts and epidermis in L skin (identified previously). Proliferation potential of NL and L fibroblasts was assessed experimentally. Genome-wide transcriptome analysis revealed a total of 414 (282, downregulated; 132, upregulated) differentially expressed (DE)-transcripts in L as compared to NL fibroblasts. Unsupervised hierarchical clustering of DE-transcripts segregated L and NL fibroblasts into two distinct clades, despite the apparent heterogeneity in lesions of different vitiligo patients. Gene Ontology analysis of downregulated genes revealed enrichment of keratinocyte-specific biological processes such as cornification and keratinization. PPI networks constructed for the downregulated and upregulated genes revealed deregulation of several hub genes associated with cell cycle regulation and cAMP metabolism respectively. Similarly, the PPI networks constructed for 67 genes downregulated in both fibroblasts as well as epidermis of L skin revealed downregulation of hub genes including stratifin, PIK3CG and CDH1. Analysis of the in vitro proliferation potential of L fibroblasts revealed a decrease in the expression of proliferation markers Ki67, MCM6, pERK and pCDK2, a decreased S phase population and an increase in alpha-SMA and collagen expression, corroborating the downregulation of hub genes associated with proliferation identified by PPI network analysis. Our study revealed pervasive transcriptional alterations in L compared to NL fibroblasts in vitiligo. The PPI analysis suggested a reduced potential to proliferate in melanocyte-deprived lesional fibroblasts, which was validated experimentally as well.

Automated summary

There are pervasive transcriptional alterations in the fibroblasts of patients with non-segmental vitiligo. Downregulated genes are involved in keratinocyte-specific processes, while upregulated genes are associated with cell cycle regulation and cAMP metabolism. Experimental validation shows that melanocyte-deprived lesional fibroblasts have reduced proliferation potential.