Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer

Abstract

Background: Epigenetic information can be used to identify clinically relevant genomic variants single nucleotide polymorphisms (SNPs) of functional importance in cancer development. Super-enhancers are cell-specific DNA elements, acting to determine tissue or cell identity and driving tumor progression. Although previous approaches have been tried to explain risk associated with SNPs in regulatory DNA elements, so far epigenetic readers such as bromodomain containing protein 4 (BRD4) and super-enhancers have not been used to annotate SNPs. In prostate cancer (PC), androgen receptor (AR) binding sites to chromatin have been used to inform functional annotations of SNPs.

Results: Here we establish criteria for enhancer mapping which are applicable to other diseases and traits to achieve the optimal tissue-specific enrichment of PC risk SNPs. We used stratified Q-Q plots and Fisher test to assess the differential enrichment of SNPs mapping to specific categories of enhancers. We find that BRD4 is the key discriminant of tissue-specific enhancers, showing that it is more powerful than AR binding information to capture PC specific risk loci, and can be used with similar effect in breast cancer (BC) and applied to other diseases such as schizophrenia.

Conclusions: This is the first study to evaluate the enrichment of epigenetic readers in genome-wide associations studies for SNPs within enhancers, and provides a powerful tool for enriching and prioritizing PC and BC genetic risk loci. Our study represents a proof of principle applicable to other diseases and traits that can be used to redefine molecular mechanisms of human phenotypic variation.

Keywords: BRD4; Chromatin; Functional annotation; Genome-wide association studies; Prostate cancer risk; Risk loci; SNPs; breast cancer risk; schizophrenia; super-enhancer.

Fig. 1

Definition of enhancers using chromatin marks and generic epigenetic readers. UCSC genome browser snapshot of the kallikreins locus showing enhancers identified in LNCaP based on MED12 binding information retrieved from Wang et al., (2012), and H3K27Ac profile retrieved from Hnisz et al., (2014) [12]; Enhancers identified in VCaP based on BRD4 binding and H3K27Ac retrieved from Asangani et al., (2014) [14]; and common enhancers in prostate cancer (PC) identified selecting enhancers in LNCaP which also had BRD4 and acetylation signature according to the compendium of enhancers in VCaP cells. In the locus shown here the long stretch of H3K27Ac includes also MED12 according to Wang et al., (2011) [23] and BRD4 binding sites. At the bottom of the figure SNPs within these particular enhancers are indicated with the red line for SNPs found in the enhancers in LNCaP cells and PC common enhancers, and with the blue line for SNPs found in the enhancer in VCaP cells. Independent tracks for the androgen receptor (AR) binding sites in common in LNCaP and VCaP cells according to Massie et al., (2011) [22] re-analyzed for this study are also shown

Fig. 2

Enrichment of SNPs lying within enhancers. Q-Q plots visualizing the p-value enrichment of sets of SNPs mapping within genomic intervals identified as regions of putative enhancers or key transcription factor binding sites. The p-values describe the association of a specific SNP with prostate (iCOGs in panel a & b; PRACTICAL in panel c) and breast cancer (BCAC in panel d & e). The genomic intervals represent regions bound by MED12, BRD4 with a H3K27Ac modification in prostate cancer cell lines (LNCaP and VCaP), or in overlapping regions profiled for a combination of the features in the prostate cancer (PC) cell-lines as indicated (a, c, d), intersected with AR binding sites (b), or regions found in MCF7 (e), as indicated in the legends. (f) Q-Q plots visualizing the p-value enrichment of schizophrenia associated SNPs (PGC) lying within enhancers identified in Schwann cells

Fig. 3

Circular plots of GWAS significant SNPs overlapping with putative super-enhancers. The outmost circles depict chromosome-wise histograms showing p-values of SNP loci (LD r^2 < 0.2 within 1Mbase) representatives for SNPs in iCOGS (a), for SNPs in BCAC (b), and for SNPs associated with schizophrenia according to PGC (c). GWAS-significant SNPs are labeled and the nearby genes are also indicated. The inmost circle represents super-enhancers regions identified in prostate cancer cells (SE_PC_BRD4_MED12_H3K27Ac) (a), breast cancer cells (SE_MCF7_BRD4) (b), and in Schwann cells (SE_Schwann_BRD4) (c) that were most enriched of low p-value SNPs

Fig. 4

Tissue-specific super-enhancers usage and identification of clinically relevant genetic variations associated with diseases and traits. The method for prioritization of clinically relevant SNPs is based on the identification of risk SNPs with GWAS significance that are associated with BRD4 binding to chromatin, within tissue-specific super-enhancers rather transcription factors binding