Mapping the miRNA‐mRNA Interactome in Human Hepatocytes and Identification of Functional mirSNPs in Pharmacogenes
Year: 2021
Type: article
Abstract: MiRNAs regulate the expression of hepatic genes involved in pharmacokinetics and pharmacodynamics. Genetic variants affecting miRNA binding (mirSNPs) have been associated with altered drug response, but previously used methods to identify miRNA binding sites and functional mirSNPs in pharmacogenes are indirect and limited by low throughput. We utilized the high-throughput chimeric-eCLIP assay to directly map thousands of miRNA-mRNA interactions and define the miRNA binding sites in primary hepatocytes. We then used the high-throughput PASSPORT-seq assay to functionally test 262 potential mirSNPs with coordinates overlapping the identified miRNA binding sites. Using chimeric-eCLIP, we identified a network of 448 miRNAs that collectively target 11,263 unique genes in primary hepatocytes pooled from 100 donors. Our data provide an extensive map of miRNA binding of each gene, including pharmacogenes, expressed in primary hepatocytes. For example, we identified the hsa-mir-27b-DPYD interaction at a previously validated binding site. A second example is our identification of 19 unique miRNAs that bind to CYP2B6 across 20 putative binding sites on the transcript. Using PASSPORT-seq, we then identified 24 mirSNPs that functionally impacted reporter mRNA levels. To our knowledge, this is the most comprehensive identification of miRNA binding sites in pharmacogenes. Combining chimeric-eCLIP with PASSPORT-seq successfully identified functional mirSNPs in pharmacogenes that may affect transcript levels through altered miRNA binding. These results provide additional insights into potential mechanisms contributing to interindividual variability in drug response.
DOI: 10.1002/cpt.2379
Authors: Nicholas R. Powell, Harrison Zhao, Joseph Ipe, Yunlong Liu, Todd C. Skaar
Language: English
Subfield: Pharmacology
Domain: Life Sciences
Open Access status: bronze
Funders: Van Andel Research Institute, University of Miami, University of Pennsylvania, Indiana Clinical and Translational Sciences Institute, Harvard University, University of Chicago, North Carolina State University, Broad Institute, Leidos, Université de Genève, National Institutes of Health, School of Medicine, Indiana University, National Heart, Lung, and Blood Institute, National Institute of Mental Health, National Institute on Drug Abuse, National Human Genome Research Institute, NIH Office of the Director, National Cancer Institute, National Institute of General Medical Sciences, National Institute of Neurological Disorders and Stroke, National Center for Research Resources, National Center for Advancing Translational Sciences, Common Fund
Awards: Methods for high-resolution analysis of genetic effects on gene expression, G1206703408, G1217436835, G1534570039, G1561323845, G1650773652, Identification and validation of cell specific eQTLs by Bayesian modeling, G1883398070, Using the Transcriptome for SNP and Gene Annotation, G2158443041, MODELING THE EFFECTS OF STRUCTURAL VARIATION IN GTEX DATA AND MENDELIAN DISEASE, G2651523388, G2835668146, G2877753951, G3221727586, G32319252, G3387558946, G3443372292, G347407575, G3503792436, G3510491964, G3547560438, G3747755827, G3754633476, G3793778294, G386607036, G3952396931, Genetic Regulation of Gene Expression and its Impact on Phenotypes, G4110903388, G4124418613, G4382062407, Systems approaches to link tissue-specific expression to disease, Harnessing GTEx to Create Transcriptome Knowledge and Inform Disease Biology, G4478373029, EXTRAMURAL RESEARCH FACILITIES IMPROVEMENT, G4606556408, G4715193760, G4729234894, Epistatic and Cross Tissue Analysis for Human Gene Expression Traits, G4954646042, G563538711, G5737582129, G5888954722, Statistical analysis of gene expression quantitative trait loci (eQTL), Methods for high-resolution analysis of genetic effects on gene expression, G6223059496, G6317516893, G634178657, G652183828, G6875631655, G7075004892, G724942601, G7274654584, G7353525908, FACILITATING GTEx, DISEASE, AND GxE ANALYSES VIA FAST EXPRESSION (e)QTL MAPPING, Statistical analysis of gene expression quantitative trait loci (eQTL), CNS Mechanisms in Cocaine-Related Sudden Death, G7665525972, G7761642487, Indiana Clinical and Translational Sciences Institute, MIRA-Regulation of drug metabolizing enzymes, G7953026188, G8719970897, G8788848806, G8906494432, Indiana University Comprehensive Training in Clinical Pharmacology
OpenAlex ID: W3183937320