Evidence map›Paper›PMID 37400791›Full record

ArticleBMC cancer2023

Optimized screening of DNA methylation sites combined with gene expression analysis to identify diagnostic markers of colorectal cancer.

Zhen Ye, Guangle Song, Jianwei Liang, Shuying Yi, Yuqi Gao, Hanming Jiang

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In one paragraph

Article in BMC cancer, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

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5citing papers in PubMed
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1 · What the graph read from it

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3 · Its place in the literature

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5 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

6 authors.

Zhen YeDepartment of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China.
Guangle SongDepartment of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China.
Jianwei LiangDepartment of General Surgery, Tai'an City Center Hospital, Taian, 271000, Shandong, China.
Shuying YiDepartment of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China.
Yuqi GaoDepartment of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China. gaoyuqi@sdfmu.edu.cn.
Hanming JiangDepartment of Health Management, The First Affiliated Hospital, Shandong Provincial Qianfoshan Hospital, Shandong First Medical University, Jinan, 250013, Shandong, China. hmjiang1976@126.com.

Funding

Shandong Provincial Medical Science and Technology Development Project 202002021270
6 · The paper itself

Abstract

backgroundThe prognosis of patients with colorectal cancer is related to early detection. However, commonly used screening markers lack sensitivity and specificity. In this study, we identified diagnostic methylation sites for colorectal cancer.

methodsAfter screening the colorectal cancer methylation dataset, diagnostic sites were identified via survival analysis, difference analysis, and ridge regression dimensionality reduction. The correlation between the selected methylation sites and the estimation of immune cell infiltration was analyzed. The accuracy of the diagnosis was verified using different datasets and the 10-fold crossover method.

resultsAccording to Gene Ontology, the main enrichment pathways of genes with hypermethylation sites are axon development, axonogenesis, and pattern specification processes. However, the Kyoto Encyclopedia of Genes and Genomes (KEGG) suggests the following main enrichment pathways: neuroactive ligand-receptor interaction, calcium signaling, and cAMP signaling. In The Cancer Genome Atlas (TCGA) and GSE131013 datasets, the area under the curve of cg07628404 was > 0.95. For the NaiveBayes machine model of cg02604524, cg07628404, and cg27364741, the accuracies of 10-fold cross-validation in the GSE131013 and TCGA datasets were 95% and 99.4%, respectively. The survival prognosis of the hypomethylated group (cg02604524, cg07628404, and cg27364741) was better than that of the hypermethylated group. The mutation risk did not differ between the hypermethylated and hypomethylated groups. The correlation coefficient between the three loci and CD4 central memory T cells, hematological stem cells, and other immune cells was not high (p < 0.05).

conclusionIn cases of colorectal cancer, the main enrichment pathway of genes with hypermethylated sites was axon and nerve development. In the biopsy tissues, the hypermethylation sites were diagnostic for colorectal cancer, and the NaiveBayes machine model of the three loci showed good diagnostic performance. Site (cg02604524, cg07628404, and cg27364741) hypermethylation predicts poor survival for colorectal cancer. Three methylation sites were weakly correlated with individual immune cell infiltration. Hypermethylation sites may be a useful repository for diagnosing colorectal cancer.

Indexed as

Colorectal NeoplasmsDNA MethylationBiomarkers, TumorCpG IslandsEarly Detection of CancerGene Expression ProfilingHumansBiomarkers, Tumor10-fold cross-validationColorectal cancerHypermethylationImmune estimationsNaiveBayes

Identifiers

PMID37400791
PMCPMC10318760

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