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Cited 2 time in webofscience Cited 2 time in scopus
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RNA-sequencing identification and validation of genes differentially expressed in high-risk adenoma, advanced colorectal cancer, and normal controls

Authors
Kim, NamjooGim, Jeong-AnLee, Beom JaeChoi, Byung ilPark, Seung BinYoon, Hee SookKang, Sang HeeKim, Seung HanJoo, Moon KyungPark, Jong-JaeKim, ChungyeulKim, Han-Kyeom
Issue Date
Jul-2021
Publisher
SPRINGER HEIDELBERG
Keywords
High risk adenoma; Advanced colorectal cancer; RNA sequencing; Precision medicine; ANAX3; CD44
Citation
FUNCTIONAL & INTEGRATIVE GENOMICS, v.21, no.3-4, pp.513 - 521
Indexed
SCIE
SCOPUS
Journal Title
FUNCTIONAL & INTEGRATIVE GENOMICS
Volume
21
Number
3-4
Start Page
513
End Page
521
URI
https://scholarworks.korea.ac.kr/kumedicine/handle/2020.sw.kumedicine/53989
DOI
10.1007/s10142-021-00795-8
ISSN
1438-793X
Abstract
Distinct gene expression patterns that occur during the adenoma-carcinoma sequence need to be determined to analyze the underlying mechanism in each step of colorectal cancer progression. Elucidation of biomarkers for colorectal polyps that harbor malignancy potential is important for prevention of colorectal cancer. Here, we use RNA sequencing to determine gene expression profile in patients with high-risk adenoma treated with endoscopic submucosal dissection by comparing with gene expression in patients with advanced colorectal cancer and normal controls. We collected 70 samples, which consisted of 27 colorectal polyps, 24 cancer tissues, and 19 normal colorectal mucosa. RNA sequencing was performed on an Illumina platform to select differentially expressed genes (DEGs) between colorectal polyps and cancer, polyps and controls, and cancer and normal controls. The Kyoto Gene and Genome Encyclopedia (KEGG) and gene ontology (GO) analysis, gene-concept network, GSEA, and a decision tree were used to evaluate the DEGs. We selected the most highly expressed genes in high-risk polyps and validated their expression using real-time PCR and immunohistochemistry. Compared to patients with colorectal cancer, 82 upregulated and 24 downregulated genes were detected in high-risk adenoma. In comparison with normal controls, 33 upregulated and 79 downregulated genes were found in high-risk adenoma. In total, six genes were retrieved as the highest and second highest expressed in advanced polyps and cancers among the three groups. Among the six genes, ANAX3 and CD44 expression in real-time PCR for validation was in good accordance with RNA sequencing. We identified differential expression of mRNAs among high-risk adenoma, advanced colorectal cancer, and normal controls, including that of CD44 and ANXA3, suggesting that this cluster of genes as a marker of high-risk colorectal adenoma.
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2. Clinical Science > Department of Pathology > 1. Journal Articles
2. Clinical Science > Department of Colon and Rectal Surgery > 1. Journal Articles
2. Clinical Science > Department of Gastroenterology and Hepatology > 1. Journal Articles
5. Others > Medical Science Research Management Center > 1. Journal Articles

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Kim, Seung Han
Guro Hospital (Department of Gastroenterology and Hepatology, Guro Hospital)
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