BarcUVa-seq: University of Barcelona and University of Virginia Genotyping and RNA Sequencing Project

`Characterization of transcription in healthy colon mucosa`

Joint Project of the Catalan Institute of Oncology-IDIBELL (Barcelona, Spain) and the University of Virginia (Virginia, USA).

Aims

BarcUVa-Seq is a public-health genomics study of gene expression in the human colon. The principle aim is to characterize regulation of transcription in superficial epithelial cells across different colon subsites. We measure effects of variables such as genotype, sex, colon subsite, lifestyle, and diet on the composition of healthy colon transcriptomes.

Methods

BarcUVa-Seq is a population-based, cross-sectional study of 485 adult volunteers found to have endoscopically healthy (i.e normal, without polyps or other lesions) colon. Transcriptomic profiles were measured with bulk RNA sequencing of total RNA from superficial mucosal biopsies collected at different subsites across the colon during colonoscopy. Genotypes were measured with the OncoArray 500K BeadChip using DNA from peripheral blood samples.

Results

We find transcriptional differences between anatomic subsites in the colon. We also find genotype-transcription level associations at thousands of variants across the genome. Many of the transcription-associated variants co-localize with disease risk loci identified in genome-wide association studies of various diseases. The BarcUVa-Seq dataset is a valuable resource for researchers interested in colon-related phenotypes and other traits.

Papers

Dampier CH, Devall M, Jennelle LT, Díez-Obrero V, Plummer SJ, Moreno V, Casey G. Oncogenic Features in Histologically Normal Mucosa: Novel Insights Into Field Effect From a Mega-Analysis of Colorectal Transcriptomes.
Clin. Transl. Gastroenterol. 2020 Jul;11(7):e00210. doi: 10.14309/ctg.0000000000000210 . PMID: 32764205 ; PMCID: PMC7386360 .

Díez-Obrero V, Dampier CH, Moratalla-Navarro F, Devall M, Plummer SJ, Díez-Villanueva A, Peters U, Bien S, Huyghe JR, Kundaje A, Ibáñez-Sanz G, Guinó E, Obón-Santacana M, Carreras-Torres R, Casey G, Moreno V. Genetic Effects on Transcriptome Profiles in Colon Epithelium Provide Functional Insights for Genetic Risk Loci.
Cell Mol Gastroenterol Hepatol. 2021;12(1):181-197. doi: 10.1016/j.jcmgh.2021.02.003 . Epub 2021 Feb 16. Erratum in: Cell Mol Gastroenterol Hepatol. 2024;17(2):320. doi: 10.1016/j.jcmgh.2023.11.003 . PMID: 33601062 ; PMCID: PMC8102177 . Genetic effects on transcriptome profiles in colon epithelium provide functional insights for genetic risk loci. Cell Mol Gastroenterol Hepatol (2021) doi:10.1016/j.jcmgh.2021.02.003.