Enhanced IFNy response in dedifferentiated melanoma cells is due to chromatin remodeling as revealed by ATAC-seq

Background Differentiation status influences immunomodulatory gene expression in melanoma. Loss of Microphthalmia-Associated Transcription Factor (MITF) drives dedifferentiation and enhances the transcriptional responses to Interferon-γ (IFNγ), leading to non-additive increase in inflammatory cytokine and Programmed Death-Ligand 1 (PD-L1) expression. Whilst these transcriptional responses are well characterized, it remains unclear how shifts in differentiation status affect the epigenetic response to inflammatory stimulus. Methods We used Assay for Transposase Accessible Chromatin with sequencing (ATAC-seq) to assess how differentiation status and IFNγ affect chromatin organization in 624Mel melanoma cells. Dedifferentiation was induced by MITF knockdown using siRNA, followed by IFNγ stimulation prior to ATAC-seq. Data were processed with the nfcore/atacseq pipeline and analyzed with DESeq2, Analysis of Motif Enrichment, Gene Ontology and KEGG Pathway analysis. Results Both MITF loss and IFNγ stimulation produced significant but distinct changes in chromatin accessibility. MITF knockdown favored chromatin opening, whereas IFNγ induced milder increases in accessibility. Integration with previously published RNA-seq data revealed concordant regulation of chromatin accessibility and gene expression following MITF loss and IFNγ treatment. Regions of altered accessibility following MITF knockdown were enriched for migration related genes, while IFNγ primarily increased access near inflammatory genes, an effect amplified under MITFlow conditions. MITF loss also enhanced IFNγ-driven transcription factor motif enrichment. Conclusions These findings exemplify the epigenetic consequences of MITF loss in melanoma and demonstrate that the established link between differentiation status and immunomodulatory gene expression extends to chromatin organization. This extends the implication of modulating differentiation to shape inflammatory responsiveness in melanoma cells.