Abstract 54: An miRNA transcriptome-wide association study of prostate cancer risk
Authors: Larson Nicholas B. , McDonnell Shannon K. , Fogarty Zachary , Thibodeau Stephen N. 
Published: September 2020

Abstract
Background: Large genome-wide association studies (GWAS) have identified hundreds of single-nucleotide polymorphisms (SNPs) associated with increased risk of prostate cancer (PRCA). The majority of these risk loci are intergenic and the underlying causal variants are presumed to confer regulatory effects on gene expression. While follow-up eQTL studies have begun to explore putative regulatory targets of PRCA risk SNPs, these have largely focused on protein-coding genes. Recent evidence demonstrates that pri-miRNA transcripts are susceptible to the same cis-acting regulatory effects as other long RNAs, and PRCA risk SNPs may confer systemic impacts on the prostate transcriptome through miRNA expression dysregulation. However, no miRNA transcriptome-wide association studies (TWAS) of PRCA risk have been conducted to date, and the role of miRNA dysregulation in PRCA risk is poorly understood.
Methods: We performed a comprehensive miRNA TWAS of PRCA risk using small RNA sequencing and genome-wide genotyping data from N = 441 normal prostate tissue samples from Mayo Clinic along with N = 411 prostate adenocarcinoma (PRAD) tumor samples from the Cancer Genome Atlas (TCGA). Both miRNA expression datasets were uniformly processed separately using the CAP-miRSeq miRNA workflow and trimmed mean of M (TMM) normalization. Expressed mature miRNAs were identified as ≥ 5 reads in &gt;25% of samples. PEER was used to remove known and latent factors on miRNA expression levels, and subsequent analyses were performed on residual values. Genetically regulated expression (GReX) prediction models were trained for all expressed miRNAs with evidence of cis-heritability (P&lt;0.01) in the respective normal and tumor datasets using the FUSION TWAS software. TWAS for PRCA risk was performed with both sets of GReX models using single-SNP summary statistics from the recent PRACTICAL consortium PRCA case-control OncoArray GWAS meta-analysis. Significant TWAS associations were declared at a false discovery rate of 0.05.
Results: A total of 615 and 571 distinct expressed miRNAs were identified in the normal and tumor tissue datasets, respectively (overlap: 480). Among these, 98 (16%) normal tissue miRNAs demonstrated significant cis-heritability (median cis-h2 = 0.09, range: 0.04-0.79) for GReX model training. Similar results were obtained from TCGA tumor samples, with 63 (11%) miRNA GReX models successfully trained (median cis-h2 = 0.11, range: 0.05-0.60). Using normal tissue GReX models, we identified three significant TWAS miRNA associations with PRCA risk: over-expression of mir-941 family miRNAs (PTWAS = 3.1E-04) and reduced expression of miR-3617-5p (PTWAS = 1.7E-04) and hsa-miR-16-2-3p (PTWAS = 9.1E-04). The TCGA tumor TWAS also identified a significant association with miR-941 overexpression (PTWAS = 9.7E-04). All associated miRNAs have previously reported oncogenic or tumor-suppressive associations in other cancer types.
Conclusions: We identified significant associations with PRCA genetic risk and miRNA expression dysregulation using tumor and normal prostate tissue data. Future work will examine downstream regulatory effects of miRNA dysregulation as well as miRNA-mediated risk mechanisms via competing endogenous RNA relationships.
Citation Format: Nicholas B. Larson, Shannon K. McDonnell, Zachary Fogarty, Stephen N. Thibodeau. An miRNA transcriptome-wide association study of prostate cancer risk [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 54.