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

Differentiation status affects immunomodulatory gene expression in melanoma. Dedifferentiation, driven by the loss of Microphthalmia-Associated Transcription Factor (MITF), enhances the transcriptional responses to Interferon-γ (IFNγ), leading to a non-additive increase in inflammatory cytokines 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 IFNγ. 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 siRNA-mediated MITF knockdown, followed by IFNγ stimulation prior to ATAC-seq. Data were analyzed with the nfcore/atacseq pipeline and DESeq2, Analysis of Motif Enrichment, Gene Ontology and KEGG Pathway analysis. Both MITF loss and IFNγ stimulation produced substantial but distinct changes in chromatin accessibility. MITF knockdown and IFNγ stimulation favored chromatin opening. Integration with previously published RNA-seq data from our lab revealed concordant regulation of chromatin accessibility and gene expression following MITF loss and IFNγ stimulation. Regions of altered accessibility following MITF knockdown were enriched for migration related genes (e.g., HDAC5, ITB1, NRP1), while IFNγ stimulation affected regions enriched in inflammatory response genes (e.g., DUSP10, HLA-E, TNC), an effect amplified four-fold under MITFlow conditions in terms of the number of affected genes. Similarly, IFNγ-driven transcription factor motif enrichment was enhanced under MITFlow conditions. 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 further elucidates the molecular mechanism linking differentiation status to IFNγ response in melanoma cells.