Shuyun Xu

Background: The induction of peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α; encoded by PPARGC1A) expression and activation of oxidative phosphorylation (OXPHOS) is associated with disease progression and treatment resistance in patients with cutaneous melanoma. Loss of the TET2 (ten-eleven translocation 2)/5-hydroxymethylcytosine (5-hmC) epigenetic pathway is linked to melanoma aggressiveness, although the underlying mechanisms remain unclear. Objectives: To explore a relationship between TET2-mediated DNA hydroxymethylation and the induction of PPARGC1A/PGC-1α expression and activation of OXPHOS in melanoma. Methods: RNA sequencing data from 368 melanoma metastases and 102 primary melanoma tumours were analysed, with tumours categorized as ‘TET2-low’ or ‘TET2-high’, based on TET2 gene expression. Differential gene expression and gene set enrichment analyses were done, with further validation using a tissue microarray comprised of 33 clinical specimens and a publicly available gene expression dataset from 209 primary tumours. Confirmatory in vitro and in vivo studies were performed using melanoma cell lines with altered TET2 and PGC-1α expression. 5-hmC and 5-methylcytosine levels at PPARGC1A were assessed using hydroxymethylated (hMeDIPseq) and methylated DNA immunoprecipitation sequencing. Results: PGC-1α expression and activation of OXPHOS were significantly upregulated in TET2-low metastases and primary tumours. Tissue microarray analysis and gene expression studies showed an inverse relationship between TET2/5-hmC and PPARGC1A/PGC-1α expression and OXPHOS. In vitro and in vivo, PPARGC1A/PGC-1α expression and activation of OXPHOS was higher in TET2-low cells. hMeDIPseq identified significantly lower 5-hmC levels at an upstream PPARGC1A active enhancer in melanoma compared with naevi, in TET2-low compared with TET2-high cells and in cells expressing catalytically inactive TET2 compared with cells expressing wildtype TET2. Inhibition of PGC-1α expression and activation of OXPHOS mitigated migration and invasion in vitro and metastasis in vivo; TET2 loss was associated with resistance to mitogen-activated protein kinase (MAPK) pathway inhibition and enhanced sensitivity to OXPHOS inhibition. Conclusions: Loss of TET2 promotes activation of PGC-1α/OXPHOS in melanoma, driving metabolic reprogramming that supports tumour progression and resistance to MAPK inhibition in a subset of tumours. Importantly, this phenotype renders TET2-deficient melanomas selectively vulnerable to OXPHOS inhibition, identifying an actionable therapeutic opportunity. These findings establish an epigenetic–metabolic axis as a critical determinant of melanoma aggressiveness and highlight TET2/5-hmC as a potential biomarker and a targetable pathway.

Summary: Squamous Cell Carcinoma (SCC) develops in stratified epithelial tissues and demonstrates frequent alterations in transcriptional regulators. We sought to discover SCC-specific transcriptional programs and identified the transcription factor Basonuclin 1 (BNC1) as highly expressed in SCC compared to other tumor types. RNA-seq and ChIP-seq analysis identified pro-proliferative genes activated by BNC1 in SCC cells and keratinocytes. Inhibition of BNC1 in SCC cells suppressed proliferation and increased migration via FRA1. In contrast, BNC1 reduction in keratinocytes caused differentiation, which was abrogated by IRF6 knockdown, leading to increased migration. Protein interactome analysis identified PRMT1 as a co-activator of BNC1-dependent proliferative genes. Inhibition of PRMT1 resulted in a dose-dependent reduction in SCC cell proliferation without increasing migration. Importantly, therapeutic inhibition of PRMT1 in SCC xenografts significantly reduced tumor size, resembling functional effects of BNC1 knockdown. Together, we identify BNC1-PRMT1 as an SCC-lineage specific transcriptional axis that promotes cancer growth, which can be therapeutically targeted to inhibit SCC tumorigenesis. Abstract Figure: