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Title: | Genetic Effects on Transcriptome Profiles in Colon Epithelium Provide Functional Insights for Genetic Risk Loci |
Author: | Diez Obrero, Virginia Dampier, Christopher H. Moratalla Navarro, Ferran Devall, Matthew Plummer, Sarah J. Díez Villanueva, Anna Peters, Ulrike Bien, Stephanie Huyghe, Jeroen R. Kundaje, Anshul Ibáñez Sanz, Gemma Guinó, Elisabet Obón Santacana, Mireia Carreras Torres, Robert Casey, Graham Moreno Aguado, Víctor |
Keywords: | Biòpsia Expressió gènica Còlon Biopsy Gene expression Colon (Anatomy) |
Issue Date: | 1-Jan-2021 |
Publisher: | Elsevier BV |
Abstract: | Background & aims: The association of genetic variation with tissue-specific gene expression and alternative splicing guides functional characterization of complex trait-associated loci and may suggest novel genes implicated in disease. Here, our aims were as follows: (1) to generate reference profiles of colon mucosa gene expression and alternative splicing and compare them across colon subsites (ascending, transverse, and descending), (2) to identify expression and splicing quantitative trait loci (QTLs), (3) to find traits for which identified QTLs contribute to single-nucleotide polymorphism (SNP)-based heritability, (4) to propose candidate effector genes, and (5) to provide a web-based visualization resource. Methods: We collected colonic mucosal biopsy specimens from 485 healthy adults and performed bulk RNA sequencing. We performed genome-wide SNP genotyping from blood leukocytes. Statistical approaches and bioinformatics software were used for QTL identification and downstream analyses. Results: We provided a complete quantification of gene expression and alternative splicing across colon subsites and described their differences. We identified thousands of expression and splicing QTLs and defined their enrichment at genome-wide regulatory regions. We found that part of the SNP-based heritability of diseases affecting colon tissue, such as colorectal cancer and inflammatory bowel disease, but also of diseases affecting other tissues, such as psychiatric conditions, can be explained by the identified QTLs. We provided candidate effector genes for multiple phenotypes. Finally, we provided the Colon Transcriptome Explorer web application. Conclusions: We provide a large characterization of gene expression and splicing across colon subsites. Our findings provide greater etiologic insight into complex traits and diseases influenced by transcriptomic changes in colon tissue. |
Note: | Reproducció del document publicat a: https://doi.org/10.1016/j.jcmgh.2021.02.003 |
It is part of: | Cellular and Molecular Gastroenterology and Hepatology, 2021, vol. 12, num. 1, p. 181-197 |
URI: | http://hdl.handle.net/2445/179935 |
Related resource: | https://doi.org/10.1016/j.jcmgh.2021.02.003 |
ISSN: | 2352-345X |
Appears in Collections: | Articles publicats en revistes (Institut d'lnvestigació Biomèdica de Bellvitge (IDIBELL)) |
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PIIS2352345X21000369.pdf | 3.56 MB | Adobe PDF | View/Open |
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