Stratification of Hepatocellular Carcinoma Using N6-Methyladenosine

Cancers, vol. 17, pp. 2220

Abstract

Background: The N6-methyladenosine (m6A) modification of eukaryotic mRNA is the most prevalent of such epigenetic modifications and has recently been identified as a potential player in the pathogenesis and progression of hepatocellular carcinoma (HCC). With the increasing emergence of immunotherapy in the treatment of HCC, we have evaluated the potential of m6A-related genes in predicting overall survival and the therapeutic efficacy of immunotherapy in HCC patients. Methods: We employed transcriptomic data from TCGA-LIHC and GSE76427, comprising a total of 485 HCC patients, as the training set. Based on 23 recognized m6A regulators, we performed clustering analysis on HCC patients. The intersecting differentially expressed genes (DEGs) among subtypes were used in least absolute shrinkage and selection operator (LASSO) Cox and multivariate Cox regression analyses to construct the risk model. For the quantification of a risk model of HCC patients, a risk score was developed and correlated with clinical and immunological parameters. Furthermore, a single-cell transcriptomic atlas was used to analyze the relationship between model genes and immune cell subpopulations. Mechanistic studies included in vitro assays to validate the association between the m6A-related gene ANLN and the progression of HCC. Results: Internal (TCGA and GEO) and external validation (ICGC) suggested that an 8-gene risk score provides an accurate and stable prognostic assessment for HCC. Furthermore, the high-risk score, characterized by elevated TP53 mutation frequency, tumor mutation burden (TMB), and tumor stem cell characteristics indicated a poor prognosis. The prognostic signature was associated with immune cell infiltration in HCC. Those patients with a high-risk score had lower immune tolerance with a better prediction of the efficacy of immunotherapy. The risk model helps to assess and predict the response and prognosis of HCC patients to immune checkpoint inhibitors (ICIs). Additionally, single-cell RNA sequencing data revealed that the high-risk group had a higher proportion of T cells and fewer immunosuppressive T cells, potentially correlating with a better response to immunotherapy. Finally, in vitro experiments showed that ANLN, an m6A-related gene, promoted the proliferation and migration of HCC cells. Conclusions: In this study, we identified and validated an m6A gene signature consisting of eight genes that can be used to predict prognosis and immunotherapy efficacy in HCC patients.

Authors 5

1. Nan Wang Aachen Department of Internal Medicine III

   RWTH Aachen University · Universitätsklinikum Aachen · Shanghai Jiao Tong University · Ruijin Hospital

   Affiliation as printed

   Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China

   Department of Internal Medicine III, University Hospital RWTH Aachen, 52074 Aachen, Germany

2. Jiaxin Shi Aachen Institute of Pathology, Medical Faculty

   RWTH Aachen University

   Affiliation as printed

   Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), 52074 Aachen, Germany

   Institute of Pathology, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany

3. Matthias Bartneck Aachen Department of Internal Medicine III

   RWTH Aachen University · Universitätsklinikum Aachen

   Affiliation as printed

   Department of Internal Medicine III, University Hospital RWTH Aachen, 52074 Aachen, Germany

4. Edgar Dahl corresponding Aachen Institute of Pathology, Medical Faculty

   RWTH Aachen University

   Affiliation as printed

   Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), 52074 Aachen, Germany

   Institute of Pathology, Medical Faculty, RWTH Aachen University, 52074 Aachen, Germany

5. Junqing Wang corresponding

   Shanghai Jiao Tong University · Ruijin Hospital

   Affiliation as printed

   Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China