Allele-specific miRNA-binding analysis identifies candidate target genes for breast cancer risk

Ana Jacinta-Fernandes,Joel G Lage,Joana M Xavier,Ana-Teresa Maia,Ramiro Magno

doi:10.1038/s41525-019-0112-9

Ana Jacinta-Fernandes, Joel G Lage + Show 3 more

Open Access

https://doi.org/10.1038/s41525-019-0112-9

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Abstract

Most breast cancer (BC) risk-associated single-nucleotide polymorphisms (raSNPs) identified in genome-wide association studies (GWAS) are believed to cis-regulate the expression of genes. We hypothesise that cis-regulatory variants contributing to disease risk may be affecting microRNA (miRNA) genes and/or miRNA binding. To test this, we adapted two miRNA-binding prediction algorithms—TargetScan and miRanda—to perform allele-specific queries, and integrated differential allelic expression (DAE) and expression quantitative trait loci (eQTL) data, to query 150 genome-wide significant (Ple 5times {10}^{-8}) raSNPs, plus proxies. We found that no raSNP mapped to a miRNA gene, suggesting that altered miRNA targeting is an unlikely mechanism involved in BC risk. Also, 11.5% (6 out of 52) raSNPs located in 3′-untranslated regions of putative miRNA target genes were predicted to alter miRNA::mRNA (messenger RNA) pair binding stability in five candidate target genes. Of these, we propose RNF115, at locus 1q21.1, as a strong novel target gene associated with BC risk, and reinforce the role of miRNA-mediated cis-regulation at locus 19p13.11. We believe that integrating allele-specific querying in miRNA-binding prediction, and data supporting cis-regulation of expression, improves the identification of candidate target genes in BC risk, as well as in other common cancers and complex diseases.

Highlights

In the past 10 years, genome-wide association studies (GWAS) identified hundreds of common low-penetrance variants to be associated with breast cancer (BC) risk.[1]
To evaluate the contribution to BC risk of genetic variation modelling miRNA::messenger RNA (mRNA) binding, we first assessed how many GWAS SNPs and their proxies were located in either miRNA genes or 3′-untranslated region (UTR) of protein-coding genes (PCGs)
None of the riskassociated single-nucleotide polymorphisms (raSNPs) mapped to miRNA genes, even after the linkage disequilibrium (LD) threshold was lowered to r2 ! 0:2 when defining proxy SNPs

Summary

INTRODUCTION

In the past 10 years, genome-wide association studies (GWAS) identified hundreds of common low-penetrance variants to be associated with breast cancer (BC) risk.[1]. Our initial list of raSNPs was established by selecting the 150 most significant (P 5 ́ 10À8) BC raSNPs from published GWAS (retrieved on 13 February 2017), along with their proxies in high LD We filtered these by genomic location, keeping those in or near miRNA genes and/or in protein-coding genes (PCGs; potential miRNA target sequences). We modified existing prediction tools to perform allele-specific miRNA target prediction analysis We used both miRNAs and putative mRNA target genes, expressed in normal breast tissue, and cisregulated genes as supported by DAE and eQTL data in normal breast tissue. We present a systematic miRNA pathway-based study from published BC GWAS, using allele-differential prediction analysis, further improved by integration of DAE and eQTL data from normal breast tissue

RESULTS

DISCUSSION

Jacinta-Fernandes et al 5

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