Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers

Abstract

Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesized that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer cohorts. We performed emQTL (expression-methylation quantitative trait loci) analyses in each cohort and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding site in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF-binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumour-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer.

Pan-cancer predictions of transcription factors mediating aberrant DNA methylation

“…Based on our computational predictions, we chose to validate experimentally if binding of two candidate TFs FOXA1 and GATA3, were indeed upstream of DNA methylation changes. Previous studies also observed a local DNA hypo-methylation at FOXA1 binding sites [40,41], which was recently confirmed by Lemma et al [39]. Both TFs have been described as pioneer TFs as they can bind and open closed chromatin [42].…”

“…Although Rhie et al did not integrate TF motif or binding sites, FOXA1 and GATA3 in BRCA were identified in their study [15]. The method from Fleischer et al had also associated FOXA1 and GATA3 with changes in DNA methylation patterns in BRCA [16], which they confirmed in a recent study across 19 cancer types [39].…”

MethMotif.org 2023: The transcription factor binding motifs database that integrates cell-specific functions, co-factors and DNA methylation profiles.

“…Furthermore, the group of TFs known as pioneer transcription factors can bind densely closed inactive chromatin, leading to the recruitment of remodeling complexes, changing chromatin con guration, and epigenetic modi cations, ultimately facilitating the binding of other transcription factors (Mayran and Drouin, 2018;Zaret and Carroll, 2011). Noteworthy, aberrant methylation patterns are found in numerous disease conditions, including cancer (Detilleux et al, 2022;Lemma et al, 2022). It is now established that DNA methylation is an epigenetic modi cation crucial for the recruitment and/or selection of transcription factors (TF) within the chromatin, ultimately resulting to profound alteration of transcriptomic pro les.…”