Identification and Functional Characterization of m1A-Related Genes in Colorectal Cancer: Implications for Prognosis, Immune Infiltration, and Therapeutic Strategies

Lan Sun ¹ Liwei Huangpu ¹ Fang Li ² Yuhui Yan ¹ Ruiping Kong ¹ Kun Ji ¹ Jiachun Li ^3*

• ¹ Jiangsu Food & Pharmaceutical Science College, Huai'an, China
• ² Key Laboratory of New-tech for Chinese Medicine Pharmaceutical Process, Jiangsu Kanion Pharmaceutical Co. Ltd., Jiangsu, China
• ³ Jiangsu Vocational College of Finance and Economics, Huaian, China

Colorectal cancer (CRC), which is characterized by its complex genetic heterogeneity and varied responses to treatment, is a leading cause of cancer-related mortality worldwide. This study aimed to investigate the prognostic value of N1-methyladenosine (m1A)-related genes in CRC, characterize these genes’ role in tumor molecular subtyping, and explore their influence on the tumor microenvironment (TME) and immune infiltration. To this end, a total of 43 m1A-related genes were identified as prognostic markers through univariate Cox analysis using multiple datasets, including TCGA and GEO. Using non-negative matrix factorization (NMF), four distinct molecular subtypes of CRC were defined based on the expression of these m1A-related genes, which exhibited significant differences in survival outcomes and clinical characteristics. Specifically, stromal cells demonstrated higher m1A scores, and regions with elevated m1A scores were predominantly stromal, suggesting a regulatory role in the TME. The results of immune infiltration analysis revealed a positive correlation between m1A-related gene expression and immune checkpoint genes, and the TIDE algorithm predicted better response to immune checkpoint inhibitors (ICIs) in the low-risk group as compared to the high-risk group. Furthermore, a prognostic model, which was constructed based on m1A-related genes and then validated across multiple datasets, demonstrated robust predictive performance and outperformed other recently published models. Single-cell RNA sequencing (scRNA-seq) revealed heterogeneity in m1A-related gene expression across different cell types within the TME, highlighting distinct functional roles of these modifications. We selected human cell lines and tissues to evaluate the function of the “SLC12A2” in colorectal cancer cells through multiple experimental approaches (namely, CCK-8 assays, RT-qPCR, flow cytometry for apoptosis, Western blot and transwell assay analysis). The results demonstrated that the SLC12A2 enhances invasion, proliferation, and migration of colorectal cancer cells while also inhibiting apoptosis. Taken together, the results of the present study suggest that, along with being are valuable biomarkers for CRC prognosis, m1A-related genes have significant implications for the immune landscape and could serve as potential targets for therapeutic intervention, particularly in the context of immunotherapy.