Diagnostic and prognostic value of m5C regulatory genes in hepatocellular carcinoma

Xiawei Yang; Feng Yang; Liugen Lan; Ning Wen; Haibin Li; Xuyong Sun

doi:10.3389/fgene.2022.972043

Diagnostic and prognostic value of m5C regulatory genes in hepatocellular carcinoma

Front Genet. 2022 Aug 29:13:972043. doi: 10.3389/fgene.2022.972043. eCollection 2022.

Authors

Xiawei Yang¹, Feng Yang², Liugen Lan^{3

4

5

6}, Ning Wen^{3

4

5

6}, Haibin Li^{3

4

5

6}, Xuyong Sun^{1

3

4

5

6}

Affiliations

¹ Graduate School, Guangxi Medical University, Nanning, China.
² Department of Gynocology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China.
³ Transplant Medical Center, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China.
⁴ Guangxi Key Laboratory of Organ Donation and Transplantation, Nanning, China.
⁵ Guangxi Key Laboratory for Transplantation Medicine, Nanning, China.
⁶ Guangxi Transplantation Medicine Research Center of Engineering Technology, Nanning, China.

Abstract

Background: A high mortality rate makes hepatocellular carcinoma (HCC) one of the most common types of cancer globally. 5-methylcytosine (m5C) is an epigenetic modification that contributes to the prognosis of several cancers, but its relevance to HCC remains unknown. We sought to determine if the m5C-related regulators had any diagnostic or prognostic value in HCC. Methods: M5C regulatory genes were screened and compared between HCC and normal tissue from The Cancer Genome Atlas (TCGA)and Gene Expression Omnibus (GEO) databases. Least absolute shrinkage and selection operator method (LASSO) and univariate Cox regression analysis of differentially expressed genes were then performed to identify diagnostic markers. A LASSO prognostic model was constructed using M5C regulatory genes with prognostic values screened by TCGA expression data. HCC patients were stratified based on risk score, then clinical characteristics analysis and immune correlation analysis were performed for each subgroup, and the molecular functions of different subgroups were analyzed using both Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA). The prognostic model was evaluated using univariate and multivariate Cox analyses as well as a nomogram. Molecular typing was performed according to m5C regulatory genes and immune checkpoint genes expression respectively, and clinical characterization and immune correlation analysis were performed for each subgroup. Results: M5C regulatory genes are expressed differently in HCC patients with different clinical and pathological characteristics, and mutations in these genes are frequent. Based on five m5C regulators (NOP2, NSUN2, TET1, YBX1, and DNMT3B), we constructed a prognostic model with high predictive ability. The risk score was found to be an independent prognostic indicator. Additionally, risk scores can also be applied in subgroups with different clinical characteristics as prognostic indicators. Conclusion: The study combined data from TCGA and GEO for the first time to reveal the genetic and prognostic significance of m5C-related regulators in HCC, which provides new directions for identifying predictive biomarkers and developing molecularly targeted therapies for HCC.

Keywords: 5-methylcytosine; HCC; biomarkers; hepatocellular carcinoma; m5C; prognosis.