Cis-expression QTL analysis of established colorectal cancer risk variants in colon tumors and adjacent normal tissue

Lenora W.M. Loo, Iona Cheng, Maarit Tiirikainen, Annette Lum-Jones, Ann Seifried, Lucas M. Dunklee, James M. Church, Robert Gryfe, Daniel J. Weisenberger, Robert W. Haile, Steven Gallinger, David J. Duggan, Stephen N. Thibodeau, Graham Casey, Loïc Le Marchand

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Abstract

Genome-wide association studies (GWAS) have identified 19 risk variants associated with colorectal cancer. As most of these risk variants reside outside the coding regions of genes, we conducted cis-expression quantitative trait loci (cis-eQTL) analyses to investigate possible regulatory functions on the expression of neighboring genes. Forty microsatellite stable and CpG island methylator phenotype-negative colorectal tumors and paired adjacent normal colon tissues were used for genome-wide SNP and gene expression profiling. We found that three risk variants (rs10795668, rs4444235 and rs9929218, using near perfect proxies rs706771, rs11623717 and rs2059252, respectively) were significantly associated (FDR q-value ≤0.05) with expression levels of nearby genes (<2 Mb up- or down-stream). We observed an association between the low colorectal cancer risk allele (A) for rs10795668 at 10p14 and increased expression of ATP5C1 (q = 0.024) and between the colorectal cancer high risk allele (C) for rs4444235 at 14q22.2 and increased expression of DLGAP5 (q = 0.041), both in tumor samples. The colorectal cancer low risk allele (A) for rs9929218 at 16q22.1 was associated with a significant decrease in expression of both NOL3 (q = 0.017) and DDX28 (q = 0.046) in the adjacent normal colon tissue samples. Of the four genes, DLGAP5 and NOL3 have been previously reported to play a role in colon carcinogenesis and ATP5C1 and DDX28 are mitochondrial proteins involved in cellular metabolism and division, respectively. The combination of GWAS findings, prior functional studies, and the cis-eQTL analyses described here suggest putative functional activities for three of the colorectal cancer GWAS identified risk loci as regulating the expression of neighboring genes.

Original languageEnglish (US)
Article numbere30477
JournalPloS one
Volume7
Issue number2
DOIs
StatePublished - Feb 17 2012

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ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Loo, L. W. M., Cheng, I., Tiirikainen, M., Lum-Jones, A., Seifried, A., Dunklee, L. M., Church, J. M., Gryfe, R., Weisenberger, D. J., Haile, R. W., Gallinger, S., Duggan, D. J., Thibodeau, S. N., Casey, G., & Marchand, L. L. (2012). Cis-expression QTL analysis of established colorectal cancer risk variants in colon tumors and adjacent normal tissue. PloS one, 7(2), [e30477]. https://doi.org/10.1371/journal.pone.0030477