METTL1-Driven Nucleotide Metabolism Reprograms the Immune Microenvironment in Hepatocellular Carcinoma: A Multi-Omics Approach for Prognostic Biomarker Discovery

Dayong Zheng^1*Xie Weng²Yangyue Huang³Zhuoya Fu³Xingli Liu²Fuli Xie²Jiale Wang²Qiaohua Zhu²

• ¹Southern Medical University, Guangzhou, China
• ²Department of Oncology, Shunde Hospital, Southern Medical University(The First People’s Hospital of Shunde, Foshan), Foshan, Guangdong Province, China
• ³Hepatic Department, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China

Background: Hepatocellular carcinoma (HCC) remains one of the leading causes of cancer-related mortality worldwide, partly due to an incomplete understanding of the metabolic and immune dysregulation driving its progression. Here, we uncover a novel role of METTL1 in driving nucleotide metabolism reprogramming, which significantly modulates the tumor immune microenvironment.Methods: Utilizing an integrated multi-omics approach, we analyzed nucleotide metabolism-related genes derived from TCGA, GEO, and ICGC datasets. Non-negative matrix factorization (NMF) clustering stratified HCC patients into distinct subgroups with varied clinical features. Weighted Gene Co-expression Network Analysis (WGCNA) identified hub genes that were subsequently used to construct robust prognostic models via multiple machine learning algorithms. These computational findings were validated through in vitro experiments, immune infiltration assessments, and singlecell RNA sequencing analysis.Our analyses demonstrate that METTL1 is markedly upregulated in HCC, driving a reprogramming of nucleotide metabolism that modulates the expression of key immune checkpoints, including PD-L1 and CTLA-4. This regulation is associated with an immunosuppressive tumor microenvironment, reduced infiltration of activated T cells, and poorer clinical outcomes. Moreover, the prognostic model integrating METTL1 expression and immune checkpoint profiles shows strong predictive performance across independent cohorts, highlighting its potential clinical utility.This study highlights the innovative role of METTL1-driven nucleotide metabolism reprogramming in reshaping the immune microenvironment of HCC. The findings provide novel insights into HCC pathogenesis and pave the way for developing personalized therapeutic strategies based on targeting METTL1 and its associated metabolic pathways.