Identification of activated enhancers and linked transcription factors in breast, prostate, and kidney tumors by tracing enhancer networks using epigenetic traits

Abstract

BackgroundAlthough technological advances now allow increased tumor profiling, a detailed understanding of the mechanisms leading to the development of different cancers remains elusive. Our approach toward understanding the molecular events that lead to cancer is to characterize changes in transcriptional regulatory networks between normal and tumor tissue. Because enhancer activity is thought to be critical in regulating cell fate decisions, we have focused our studies on distal regulatory elements and transcription factors that bind to these elements.ResultsUsing DNA methylation data, we identified more than 25,000 enhancers that are differentially activated in breast, prostate, and kidney tumor tissues, as compared to normal tissues. We then developed an analytical approach called Tracing Enhancer Networks using Epigenetic Traits that correlates DNA methylation levels at enhancers with gene expression to identify more than 800,000 genome-wide links from enhancers to genes and from genes to enhancers. We found more than 1200 transcription factors to be involved in these tumor-specific enhancer networks. We further characterized several transcription factors linked to a large number of enhancers in each tumor type, including GATA3 in non-basal breast tumors, HOXC6 and DLX1 in prostate tumors, and ZNF395 in kidney tumors. We showed that HOXC6 and DLX1 are associated with different clusters of prostate tumor-specific enhancers and confer distinct transcriptomic changes upon knockdown in C42B prostate cancer cells. We also discovered de novo motifs enriched in enhancers linked to ZNF395 in kidney tumors.ConclusionsOur studies characterized tumor-specific enhancers and revealed key transcription factors involved in enhancer networks for specific tumor types and subgroups. Our findings, which include a large set of identified enhancers and transcription factors linked to those enhancers in breast, prostate, and kidney cancers, will facilitate understanding of enhancer networks and mechanisms leading to the development of these cancers.Electronic supplementary materialThe online version of this article (doi:10.1186/s13072-016-0102-4) contains supplementary material, which is available to authorized users.

ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters

“…The ZFX binding pattern at promoter regions is very similar in different cancer types Many oncogenic TFs bind to distinct celltype-specific distal regulatory elements in different types of tumors (Rhie et al 2016). However, the majority of ZFX peaks are in promoter regions, suggesting that ZFX may bind to regulatory elements that are common to all cell types, rather than to cell-type-specific regulatory elements.…”

“…Unlike enhancers, which are located far from a TSS, are cell-type specific, and are closely linked to cellular identity (Rhie et al 2014(Rhie et al , 2016, promoter elements are crucial for basal transcription of genes. The majority of human promoters are classified as CpG island promoters; these promoters are generally active in most cell types (Deaton and Bird 2011).…”

“…In many cases, the transcriptional dysregulation is driven by altered expression levels or activity of transcription factors (TFs) (Yao et al 2015;Rhie et al 2016). There are about 2000 DNA-binding TFs in the human genome, but little is known about most of these regulators (Vaquerizas et al 2009;Wingender et al 2015).…”

“…There are about 2000 DNA-binding TFs in the human genome, but little is known about most of these regulators (Vaquerizas et al 2009;Wingender et al 2015). We previously identified distinct sets of TFs having increased expression associated with different cancers (Yao et al 2015;Rhie et al 2016). In contrast, ZFX, a zinc finger protein (ZNF) that contains a DNA binding domain, has been implicated in the initiation or progression of many different types of human cancers, including prostate cancer, breast cancer, colorectal cancer, renal cell carcinoma, glioma, gastric cancer, gallbladder adenocarcinoma, non-small cell lung carcinoma, and laryngeal squamous cell carcinoma (Zhou et al 2011;Fang et al 2012;Jiang et al 2012b,c;Nikpour et al 2012;Li et al 2013;Fang et al 2014a,b;Yang et al 2014;Weng et al 2015).…”

VHL Deficiency Drives Enhancer Activation of Oncogenes in Clear Cell Renal Cell Carcinoma

“…Moreover, previous studies profiling histone modifications in ccRCCs have also been limited by small sample sizes (2 cases; ref. 42), reliance on in vitro systems, and the lack of long-range interactome data and functional enhancer testing to accurately assign cognate enhancer targets.…”