TY - JOUR
T1 - Multi-omics analysis to identify susceptibility genes for colorectal cancer
AU - Yuan, Yuan
AU - Bao, Jiandong
AU - Chen, Zhishan
AU - Villanueva, Anna Diéz
AU - Wen, Wanqing
AU - Wang, Fangqin
AU - Zhao, Dejian
AU - Fu, Xianghui
AU - Cai, Qiuyin
AU - Long, Jirong
AU - Shu, Xiao Ou
AU - Zheng, Deyou
AU - Moreno, Victor
AU - Zheng, Wei
AU - Lin, Weiqiang
AU - Guo, Xingyi
N1 - Publisher Copyright:
© 2021 The Author(s) 2021. Published by Oxford University Press. All rights reserved. For Permissions, please email: Journals.permissions@oup.com.
PY - 2021/3/1
Y1 - 2021/3/1
N2 - Most genetic variants for colorectal cancer (CRC) identified in genome-wide association studies (GWAS) are located in intergenic regions, implying pathogenic dysregulations of gene expression. However, comprehensive assessments of target genes in CRC remain to be explored. We conducted a multi-omics analysis using transcriptome and/or DNA methylation data from the Genotype-Tissue Expression, The Cancer Genome Atlas and the Colonomics projects. We identified 116 putative target genes for 45 GWAS-identified variants. Using summary-data-based Mendelian randomization approach (SMR), we demonstrated that the CRC susceptibility for 29 out of the 45 CRC variants may be mediated by cis-effects on gene regulation. At a cutoff of the Bonferroni-corrected PSMR < 0.05, we determined 66 putative susceptibility genes, including 39 genes that have not been previously reported. We further performed in vitro assays for two selected genes, DIP2B and SFMBT1, and provide functional evidence that they play a vital role in colorectal carcinogenesis via disrupting cell behavior, including migration, invasion and epithelial-mesenchymal transition. Our study reveals a large number of putative novel susceptibility genes and provides additional insight into the underlying mechanisms for CRC genetic risk loci.
AB - Most genetic variants for colorectal cancer (CRC) identified in genome-wide association studies (GWAS) are located in intergenic regions, implying pathogenic dysregulations of gene expression. However, comprehensive assessments of target genes in CRC remain to be explored. We conducted a multi-omics analysis using transcriptome and/or DNA methylation data from the Genotype-Tissue Expression, The Cancer Genome Atlas and the Colonomics projects. We identified 116 putative target genes for 45 GWAS-identified variants. Using summary-data-based Mendelian randomization approach (SMR), we demonstrated that the CRC susceptibility for 29 out of the 45 CRC variants may be mediated by cis-effects on gene regulation. At a cutoff of the Bonferroni-corrected PSMR < 0.05, we determined 66 putative susceptibility genes, including 39 genes that have not been previously reported. We further performed in vitro assays for two selected genes, DIP2B and SFMBT1, and provide functional evidence that they play a vital role in colorectal carcinogenesis via disrupting cell behavior, including migration, invasion and epithelial-mesenchymal transition. Our study reveals a large number of putative novel susceptibility genes and provides additional insight into the underlying mechanisms for CRC genetic risk loci.
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U2 - 10.1093/hmg/ddab021
DO - 10.1093/hmg/ddab021
M3 - Article
C2 - 33481017
AN - SCOPUS:85106143806
SN - 0964-6906
VL - 30
SP - 321
EP - 330
JO - Human molecular genetics
JF - Human molecular genetics
IS - 5
ER -