Effects of N6-methyladenosine methylation regulators on prognosis and cell biological behaviors of colorectal cancer

Abstract

Objective To investigate the effects of N6-methyladenosine (M6A) related genes on the prognosis and cell biological behaviors of colorectal cancer. Methods The long non-coding RNA (lncRNA) for colorectal cancer and the expression profile data of 21 M6A-related genes were downloaded from The Cancer Genome Atlas (TCGA), and the differential genes were analyzed with R software. Cluster analysis and principal component analysis (PCA) were further conducted, and prognostic related M6A genes were screened by univariate Cox regression analysis. The risk prediction model was then established with LASSO algorithm. In addition, differentially expressed lncRNA associated with colorectal cancer (DElncRNA) were screened out, and a co-expression network with M6A-related genes was subsequently established. Moreover, RT-qPCR was performed to determine the gene expression of fragile X mental retardation 1 (FMR1) in colorectal cancer tissues. After FMR1 gene was knocked out in colorectal cancer cells, the cell proliferation, migration, invasion and apoptosis were detected by CCK8 assay, cell scratch test, Transwell assay and flow cytometry, respectively. Results Fifteen of the 21 M6A-related genes were differentially expressed in colorectal cancer, and cluster analysis indicated 2 subtypes of colorectal cancer tumors. According to the risk model, ALKBH5 (a-ketoglutarate-dependent dioxygenase alk B homolog 5), YTHDC2 (YTH domain-containing protein 2) and FMR1 may be the independent prognostic factors. With a total of 1 784 DElncRNAs screened out, a co-expression network was successfully constructed containing the 3 prognostic factors and 18 DElncRNAs. FMR1 was found to be the hub gene in the network diagram. RT-qPCR showed that FMR1 was up-regulated in colorectal cancer tissues. Knockout of FMR1 gene inhibited the proliferation, migration and invasion, and promoted cell apoptosis in colorectal cancer HT-29 cells. Conclusion M6A methylation regulators ALKBH5, YTHDC2 and FMR1 may be the independent prognostic factors in colorectal cancer. FMR1 knockout can inhibit the proliferation, migration and invasion, and promote the apoptosis of colorectal cancer cells.

Keywords

• m6a methylation
• prognosis
• lasso risk model
• fragile x mental retardation 1