Identification and Validation of Key miRNAs for Colon Cancer Based on miRNA-Gene Integration Analysis

Yi Ji,1,* Jialin Gu,1,2,* Hongqun Zhang,1,2 Houxi Xu3 1Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, People’s Republic of China; 2The Third Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, 210046, People’s Republic of China; 3Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210046, People’s Republic of China*These authors contributed equally to this workCorrespondence: Houxi Xu, Key Laboratory of Acupuncture and Medicine Research of Ministry of Education, Nanjing University of Chinese Medicine, Nanjing, 210046, People’s Republic of China, Email xuhouxi@njucm.edu.cnBackground: MicroRNAs (miRNAs) plays an essential role in the pathogenesis of colon cancer. This study aims to identify and verify key miRNAs that may serve as potential biomarkers for early diagnosis and treatment of colon cancer.Methods: Two miRNA microarray datasets (GSE53339 and GSE126093) were downloaded from the Gene Expression Omnibus (GEO) database, and the common differentially expressed miRNAs (DEMis) of both were identified by the “limma” package and the intersect function in R. Then, the miRwalk online tool was used to predict the target genes of the common DEMis and perform Gene Ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis on those DEMis. The miRNA-gene network was constructed using Cytoscape software to identify key miRNAs and validated using quantitative real-time PCR (qRT-PCR) and The Cancer Genome Atlas (TCGA) dataset information for experimental and external database validation, respectively. In addition, we explored the correlation between key miRNAs and infiltrating immune cells and immunotherapy biomarkers.Results: Fourteen common DEMis were identified from the GEO database, and five targeted genes were predicted. A microRNA-gene network was subsequently constructed to identify three key miRNAs (miR-363-3p, miR-520e, and miR-330-5p). Both qRT-PCR and external database validation confirmed our findings. In addition, we found that miR-520e was significantly associated with infiltrating immune cells and established immune checkpoints.Conclusion: Our study identified three key miRNAs that influence the development of colon cancer. In addition, further studies suggest that infiltrating immune cells may play an essential role in the pathogenesis of colon cancer. These findings assist in early diagnosis and precision-targeted therapies.Keywords: colon cancer, GEO, miRNA, qRT-PCR, immune cell infiltration