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| Status |
Public on Oct 23, 2018 |
| Title |
Integrative genomic analyses revealed colorectal cancer susceptibility genes in risk loci identified in genome-wide association studies |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Genome-wide association studies (GWAS) have identified approximately 50 loci associated with colorectal cancer (CRC) risk. However, the target genes and underlying mechanisms are largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using data from the Genotype-Tissue Expression (GTEx), The Cancer Genome Atlas (TCGA), and the Colonomics projects. We identified 24 putative target genes for 17 index SNPs at Benjamini-Hochberg adjusted P < 0.05 in at least one of the datasets. By analyzing functional genomic data, our result further indicated that 18 genes (75%) showed evidence of cis-regulation by putative functional SNPs via promoter or enhancer-promoter interactions. We next performed in vitro functional assays for three genes, TMBIM1, AAMP, and CABLES2, and confirmed that they play a vital role in colorectal carcinogenesis via disruption of cell behavior. Furthermore, our results indicate that silencing CABLES2 can promote the PI3K/AKT pathway. Our study reveals new candidate susceptibility genes and provides novel insight into the biological mechanisms for CRC development.
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| Overall design |
We conducted RNA-sequencing in the CABLES2 shRNA-1 and control vehicle cells with two technical replicates
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| Contributor(s) |
Lin W, Guo X |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Oct 22, 2018 |
| Last update date |
Jan 07, 2019 |
| Contact name |
Weiqiang Lin |
| E-mail(s) |
wlin@zju.edu.cn
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| Phone |
+86-86971990
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| Organization name |
Zhejiang University
|
| Street address |
866 Yuhangtang Rd
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platforms (1) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA497782 |
| SRA |
SRP166266 |
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