Identification of METTL3 as a myeloid-related prognosis biomarker in hepatocellular carcinoma using bioinformatics analysis and engineered mice model

Abstract

Background Hepatocellular carcinoma (HCC) is a significant contributor to cancer-related mortality, ranking third in this regard. The epigenetic regulation of RNA N6-methyladenosine (m6A) modification in HCC has garnered considerable attention. This study utilized bioinformatics analysis and biologically engineered mice models to explore the immune and prognostic role of m6A modification in HCC. Methods We systematically analyzed genetic alterations, expression patterns, signaling pathways, prognostic features, and immunotherapy efficacy of the 21 m6A regulators in HCC as obtained from the Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO, GSE14520, GSE76427), and International Cancer Genome Consortium (IGCG) database; Unsupervised clustering, gene set variation analysis (GSVA), LASSO-COX regression, multivariate Cox regression, Nomogram, receiver operating characteristic (ROC) analysis, TIMER 2.0 and ImmuCellAI were used to perform the above analysis. Our analysis was verified with Mettl3F/FAlbumin-cre (liver-specific knockout, LKO) mice to establish a chemo-induced HCC model. The tumor immune microenvironment was analyzed with immunohistochemistry, immunofluorescence staining, and flow cytometry. Results The genetic alteration of the m6A modification gene set exhibited a correlation with reduced progression-free survival, diminished abundance of macrophage cells, and a lower score for immune cell infiltration. The cluster characterized by lower expression of the m6A gene set was linked to a more favorable overall survival (OS) and immune signaling, including IL2-STAT5, IL6-STAT3, IFN-gamma, and IFN-alpha signaling. Notably, the cluster with higher expression of m6A was associated with a higher homologous recombination deficiency (HRD) score and tumor mutational burden (TMB) score. Results of LASSO COX and the nomogram model underscored the significant contribution of METTL3 in the prognosis and ICB therapy of HCC. The results of Mettl3 LKO mice confirmed that Mettl3 LKO acted as a "rheostat" in the progression of HCC by regulating the mouse liver's myeloid-related innate and adaptive immune landscape. Conclusions In this study, we characterized the genetic, immune, and clinic landscape of the m6A gene set in HCC development and unveiled METTL3 as a molecular biomarker in epigenetic-related progress and ICB therapy of HCC from both informatics database analysis and engineered mice model.