MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells

Abstract

Background: The MAPK/ERK signaling pathway is an essential regulator of numerous cell processes that are crucial for normal development as well as cancer progression. While much is known regarding MAPK/ERK signal conveyance from the cell membrane to the nucleus, the transcriptional and epigenetic mechanisms that govern gene expression downstream of MAPK signaling are not fully elucidated. Results: This study employed an integrated epigenome analysis approach to interrogate the effects of MAPK/ERK pathway inhibition on the global transcriptome, the active chromatin landscape, and protein-DNA interactions in 501mel melanoma cells. Treatment of these cells with the small-molecule MEK inhibitor AZD6244 induces hyperpigmentation, widespread gene expression changes including alteration of genes linked to pigmentation, and extensive epigenomic reprogramming of transcriptionally distinct regulatory regions associated with the active chromatin mark H3K27ac. Regulatory regions with differentially acetylated H3K27ac regions following AZD6244 treatment are enriched in transcription factor binding motifs of ETV/ETS and ATF family members as well as the lineage-determining factors MITF and SOX10. H3K27ac-dense enhancer clusters known as super-enhancers show similar transcription factor motif enrichment, and furthermore, these super-enhancers are associated with genes encoding MITF, SOX10, and ETV/ETS proteins. Along with genome-wide resetting of the active enhancer landscape, MEK inhibition also results in widespread SOX10 recruitment throughout the genome, including increased SOX10 binding density at H3K27acmarked enhancers. Importantly, these MEK inhibitor-responsive enhancers marked by H3K27ac and occupied by SOX10 are located near melanocyte lineage-specific and pigmentation genes and overlap numerous human SNPs associated with pigmentation and melanoma phenotypes, highlighting the variants located within these regions for prioritization in future studies. Conclusions: These results reveal the epigenetic reprogramming underlying the re-activation of melanocyte pigmentation and developmental transcriptional programs in 501mel cells in response to MEK inhibition and suggest extensive involvement of a MEK-SOX10 axis in the regulation of these processes. The dynamic chromatin changes identified here provide a rich genomic resource for further analyses of the molecular mechanisms governing the MAPK pathway in pigmentation-and melanocyte-associated diseases.

Quantitative landscapes reveal trajectories of cell-state transitions associated with drug resistance in melanoma

“…The state transitions for hyperpigmentation (M to H), not only reveal an increase in expression levels of MITF, a well characterized regulator of pigmentation in melanocytes, but also an increase in expression of ETV5 and TFAP2A. Previous studies have reported regulation of MITF, ETV5 and TFAP2A by super-enhancer motifs during hyper-pigmentation 43 . While MITF and TFAP2A have been reported to display clear upregulation during hyperpigmentation.…”

Non-canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function

“…One possibility could be that impairing ERK2 phosphorylation leads to transcriptional disinhibition at Sox10 and other key development genes, as has been shown in cancer and mouse embryonic stem cells (Tee et al, 2014;Yohe et al, 2018). MEK inhibitors have also been shown to directly upregulate SOX10 translocation to the nucleus, which would then drive downstream oligodendrocyte gene programs (Fufa et al, 2019). Continued dissection of the roles of MEK/ERK signaling during the process of differentiation would provide critical insight to how this pathway plays a bidirectional role regulating oligodendrocyte formation from OPCs.…”

Targeted chromatin conformation analysis identifies novel distal neural enhancers of ZEB2 in pluripotent stem cell differentiation

“…Altogether, and also considering its listing as a super-enhancer top-gene ( 35 , 36 ), the gene desert upstream of the human ZEB2 becomes a priority for identifying candidate and/or pathologic ZEB2 REs. Given the critical role of Zeb2 during exit from primed pluripotency, its dynamic regulation during neural and general differentiation of mouse embryonic stem cells, and applied rescues in knockout stem cells with inserted Zeb2 expressible cDNA ( 14 ), we decided to study chromatin conformation dynamics of the human ZEB2 locus during neural differentiation of induced PSCs (iPSCs).…”