结肠癌核心基因和独立预后因子筛选的生物信息学分析

doi:10.13481/j.1671-587X.20220325

Abstract

Abstract: Objective

To mine the gene expression data of colon cancer in Gene Expression Omnibus （GEO） database and The Cancer Genome Atlas （TCGA） database，and to explore the potential core genes and the independent prognostic factors of colon cancer.

Methods

TCGA database was used to retrieve the gene expression levels and clinical feature data in colon cancer， and the GEO database was used to retrieve the core gene expression levels in colon cancer and adjacent tissues. Weighted correlation network analysis（WGCNA）， Wenn analysis， protein-protein interaction（PPI） network construction and Hub gene screening， Gene Ontology（GO）enrichment analysis and Kyoto Encylopaedia of Genes and Genomes （KEGG） enrichment analysis， immune cell subtype analysis on pan oncogene，pan cancer heat map and correlation analysis of core gene， correlation analysis on core gene and tumor microenvironment and risk regression model analysis on core gene were performed. The expression levels of NKD1 and AXIN2 in the colon cancer tissue and adjacent tissue were detected by real-time fluorescence quantitative PCR （RT-qPCR），Western blotting and immunohistochemistry to further confirm the screening results.

Results

The TCGA data analysis results showed that 1 208 genes were highly expressed， 252 genes were highly expressed in the GSE37182 chip. The intersection of 4 groups of differential analysis data was taken， 13 common genes were obtained by Venn analysis. The PPI network was constructed， and 7 genes （ARID3A，SALL4，NKD1，KND2，AXIN2，CA9，and TACSTD2） were found to be the potential core genes of colon cancer. The GO analysis results showed that these 7 genes were mainly involved in positive/negative regulation of Wnt signaling pathway， basolateral plasma membrane or bound to ubiquitin protein ligases. The KEGG enrichment analysis results showed that these 7 genes were mainly involved in the Hippo signaling pathway and Wnt signaling pathway.The pan-cancer gene analysis results showed that these 7 core genes were significantly highly expressed in the colon cancer tissue， and the expression levels of NKD1 and AXIN2 genes in the colon cancer tissue had a high positive correlation （r=0.69）. High expression of TACSTD2 gene was shown in the C1，C2，C3， and C6 immune cell subtypes.The correlation analysis results between the expression of core genes and the tumor microenvironment showed that the expression levels of NKD2，AXIN2，ARID3A，and NKD1 genes in the colon cancer tissue were negatively correlated with the comprehensive score（P<0.01）. The survival prognostic analysis results of colon cancer patients showed that only AXIN2 was a significant independent prognostic factor （P<0.05）， and it was a low-risk independent prognostic factor in the colon cancer patients. The RT-qPCR，Western blotting，and immunohistochemistry detection results showed that NKD1 was highly expressed in both the colon cancer tissue and colon cancer cells， and the expression levels of NKD1 and AXIN2 were significantly positively correlated（P<0.01）.

Conclusion

Seven core genes are screened by the bioinformatics screening of colon cancer database， among which AXIN2 is an independent prognostic factor for the colon cancer patients， and the expression level of NKD1 in the colon cancer tissue is positively correlated with the expression level of AXIN2.

Key words: Colon neoplasms, Core genes, Prognostic factors, Weighted correlation network analysis, Bioinformatics

CLC Number:

R735.35

Qian LIU,Guoping QI,Huayi YU,Yuyang DAI,Wenbin LU,Jianhua JIN. Bioinformatics analysis on screening of colon cancer core genes and independent prognostic factors[J].Journal of Jilin University(Medicine Edition), 2022, 48(3): 755-765.

Figures/Tables 16

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References 33

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Clinical parameter	Univariate risk analysis			Multivariate risk analysis
Clinical parameter	HR	95%CI	P	HR	95%CI	P
Age	1.03	1.01－1.05	0.008	1.04	1.01－1.06	0.001
Gender	1.11	0.70－1.77	0.653	10.5	0.65－1.69	0.836
Stage	2.26	1.73－2.93	1.59E－09	1.21	0.57－2.60	0.622
T	2.85	1.80－4.52	7.77E－06	1.76	1.01－3.07	0.045
M	4.45	2.74－7.21	1.40E－09	2.28	0.81－6.41	0.118
N	2.02	1.54－2.65	3.47E－07	1.42	0.88－2.28	0.150
AXIN2	0.99	0.98－1.00	0.023	0.82	0.69－0.98	0.026

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Bioinformatics analysis on screening of colon cancer core genes and independent prognostic factors

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