Analysis of potential genes and pathways associated with the colorectal normal mucosa–adenoma–carcinoma sequence

Abstract

This study aimed to identify differentially expressed genes (DEGs) related to the colorectal normal mucosa–adenoma–carcinoma sequence using bioinformatics analysis. Raw data files were downloaded from Gene Expression Omnibus (GEO) and underwent quality assessment and preprocessing. DEGs were analyzed by the limma package in R software (R version 3.3.2). Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed with the DAVID online tool. In a comparison of colorectal adenoma (n = 20) and colorectal cancer (CRC) stage I (n = 31), II (n = 38), III (n = 45), and IV (n = 62) with normal colorectal mucosa (n = 19), we identified 336 common DEGs. Among them, seven DEGs were associated with patient prognosis. Five (HEPACAM2, ITLN1, LGALS2, MUC12, and NXPE1) of the seven genes presented a sequentially descending trend in expression with tumor progression. In contrast, TIMP1 showed a sequentially ascending trend. GCG was constantly downregulated compared with the gene expression level in normal mucosa. The significantly enriched GO terms included extracellular region, extracellular space, protein binding, and carbohydrate binding. The KEGG categories included HIF‐1 signaling pathway, insulin secretion, and glucagon signaling pathway. We discovered seven DEGs in the normal colorectal mucosa–adenoma–carcinoma sequence that was associated with CRC patient prognosis. Monitoring changes in these gene expression levels may be a strategy to assess disease progression, evaluate treatment efficacy, and predict prognosis.

Mutational Landscape of Esophageal Squamous Cell Carcinoma in an Indian Cohort

“…HEPACAM2 is involved in centrosome maturation during the mitotic cell division. Its expression is significantly downregulated in progressive manner from normal mucosa to adenoma to carcinoma in colorectal cancer and its higher expression is significantly associated with better survival ( 44 ).…”

Comparison of rheumatoid arthritis (RA) and osteoarthritis (OA) based on microarray profiles of human joint fibroblast‐like synoviocytes

“…21 R language (version 3.4.3) (http://www.r-project.org/) and Bioconductor (http://bioconductor.org/) were used to perform data analysis.…”

Identification of MicroRNA-Target Gene-Transcription Factor Regulatory Networks in Colorectal Adenoma Using Microarray Expression Data

“…Of these DEGs, certain genes have previously been reported to be related to the genesis and development in CRA. A previous study demonstrated that GCG was constantly down-regulated in adenomas in comparison with the gene expression level in normal colorectal mucosa (Wu et al, 2018). Hashimoto et al (2017) reported that MYC overexpression and nuclear β-catenin accumulation, which indicated that the WNT signal pathway was activated, were identified in the majority of sessile serrated adenoma/polyps with dysplasia.…”

“…GCG, one of genes with high degrees in PPI network, was downregulated when comparing the CRA samples with normal ones in our study. Past study has shown that GCG was constantly downregulated in the colorectal normal mucosa-adenomacarcinoma sequence (Wu et al, 2018). The expression of GCG could be upregulated by metformin in the gastrointestinal tract, subsequently elevating the plasma concentrations of GLP-1 that could provide hypoglycemic effect of exogenously for patients with type 2 diabetes (Migoya et al, 2010).…”