Abstract 491: Understanding the roles of miRNAs in melanoma susceptibility through miQTL study using miRNA transcriptomes from 106 individuals
Authors: Jiyeon Choi, Tongwu Zhang, Michael Kovacs, Mai Xu, Andrew Vu, Stacie Loftus, William Pavan, Kevin Brown
Journal: Cancer Research (2018)

Abstract microRNAs (miRNA) are important mediators of post-transcriptional gene regulation and play critical roles in tumorigenesis. In melanoma, miRNAs are involved in proliferation, migration, invasion and drug resistance modulating RAS/MAPK and MITF pathways and others. Melanoma arises in melanocytes, and understanding heritable regulation of miRNAs in primary melanocytes could enhance our knowledge of genes and pathways contributing to melanoma risk. While a handful of studies in limited tissue types have identified miRNA transcripts with expression levels that are correlated with common genotypes using an expression quantitative loci approach (miQTL), expression levels of miRNAs are highly tissue-specific, further correlating with tissue-specific mRNA expression. Given the lack of cell-type specific miQTL data, we established a miQTL dataset using primary cultures of human melanocytes from 106 newborn males mainly of European decent. To assess comprehensive miRNA transcript levels from these samples, we performed RNA sequencing of the small RNA population (single-end, stranded, 51bp). An average of 63M reads per sample were obtained, and subsequently processed following miRMaster pipeline (ccb-compute.cs.uni-saarland.de/mirmaster) to detect known and novel miRNAs. A total of 961 known and 1262 novel miRNA transcripts were expressed above the background noise (&amp;gt; 0.05 Read Per Million and &amp;gt;5 reads per transcript in &amp;gt;=10 samples). Genotypes of 106 individuals were also assessed by direct genotyping using Illumina OmniExpress arrays followed by imputation using Michigan Imputation Server to produce a total of 10,687,550 genotypes. Subsequent QTL analyses using FastQTL (fastqtl.sourceforge.net) and QTLtools (qtltools.github.io/qtltools) identified 33 known and 34 novel miRNA transcripts as cis-miQTLs (q-value &amp;lt; 0.05) and 2 known and 6 novel miRNAs as trans-miQTLs (FDR &amp;lt; 0.1), respectively. We also observed a subset of significant cis-miQTLs overlapping with marginally significant mRNA trans-eQTLs from the same RNA samples, suggesting miRNA-mediated trans regulation. Further identification of melanocyte-specific miQTLs and their target genes will provide better understanding of melanocyte-specific miRNA regulation network. To identify candidate melanoma susceptibility genes functioning through heritable miRNA expression, melanocyte miQTLs will also be overlaid with melanoma genome-wide association data. In addition to the results from these analyses, further analyses of differentially expressed miRNAs and target genes between our primary melanocytes and melanoma tumors (available through The Cancer Genome Atlas) will shed light on the altered gene networks in melanomagenesis that might have therapeutic relevance through miRNA-mediated intervention. Citation Format: Jiyeon Choi, Tongwu Zhang, Michael Kovacs, Mai Xu, Andrew Vu, NISC Comparative Sequencing Program, Stacie Loftus, William Pavan, Kevin Brown. Understanding the roles of miRNAs in melanoma susceptibility through miQTL study using miRNA transcriptomes from 106 individuals [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 491.