Long-term cytokine exposure remodels the methylome and transcriptome of recessive dystrophic epidermolysis bullosa keratinocytes – a bioinformatic analysis

Background Recessive dystrophic epidermolysis bullosa (RDEB) is a monogenic skin disorder characterized by severe skin fragility and pronounced clinical variability, even among individuals sharing identical genotypes. Transforming growth factor beta 1 (TGF-β1) and Interleukin-6 (IL-6) signaling have previously been linked to disease severity, but the molecular changes of long-term exposure of patient keratinocytes (KCs) - especially at the level of DNA methylation and gene expression - remain relatively unexplored. Methods Data on differential DNA-methylation and gene expression were generated from RDEB-KCs following a 4-week exposure to TGF-β1 or IL-6, as well as after an additional 4-week period without treatment, using the EPIC array and RNA-sequencing, respectively. Cytokine induced epigenetic and transcriptional alterations upon treatment and such that remained stable upon treatment withdrawal were identified using bioinformatic tools based on R/Bioconductor packages for data integration and analysis. Results Bioinformatic analysis demonstrated that prolonged cytokine exposure, reflecting chronic inflammation, induced predominantly reversible but also a subset of long-lasting transcriptomic changes in RDEB-KCs. Notably, pathways associated with the RDEB disease phenotype were enriched, with focal adhesion and p53 signaling among the stably altered pathways. Integration of transcriptomic and methylome data identified three genes - GPR68 and FBLIM1 modulated by TGF-β1, and ODF2 responsive to IL-6, as persistently deregulated and demethylated even 4 weeks after treatment termination, a finding that was further confirmed in vitro . Moreover, their significant deregulation in RDEB-tumor tissue compared to RDEB-skin controls suggests that cytokine exposure may induce a stable, pro-tumorigenic shift in RDEB-KCs. Conclusion Overall, our bioinformatic results highlight stable cytokine-driven molecular alterations in RDEB-KCs that may contribute to disease pathogenesis and potentially revealed candidate pathways and genes for future mechanistic and therapeutic investigation.