Single-cell and spatial transcriptomics reveal correlation between RNA methylation-related miRNA risk model and immune infiltration in hepatocellular carcinoma.

INTRODUCTION

Increasing evidence highlights the pivotal role of RNA methylation and miRNAs in hepatocellular carcinoma (HCC). However, the risk associated with RNA methylation-related miRNAs (RMRMs) in the HCC immune microenvironment remains largely unknown. Here, we predicted the correlation between RMRM risk and immune cell infiltration in HCC using machine learning.

METHODS

MiRNA sequencing data was used to identify RMRMs. A risk score model of HCC was developed utilizing four RMRMs, including miR-551a, miR-4739, miR-326, and miR-210-3p.

RESULTS

Patients with high-risk scores exhibited poorer prognoses. Single-cell RNA sequencing (scRNA-seq) analysis revealed the high-risk group exhibited increased infiltration levels of several immune cell subtypes, including myeloid-derived suppressor cell (MDSC), macrophage, and T cells. The data integration of scRNA-seq and bulk RNA-seq showed the decreased TIDE score in the high-risk patients and the elevated levels of Macro-secreted phosphoprotein 1 (SPP1), MDSC-meiotic nuclear divisions 1 (MND1), γδ T cells, and Macro-complement C1q C chain (C1QC) predicted adverse prognosis. ScRNA-seq and spatial transcriptomics data integration unveiled the spatial distribution of RMRMs risk scores and their correlation with immune cell subtype localization. Risk model-based clustering of HCC samples revealed that cluster 2, characterized by a higher risk score, correlated with a poorer prognosis and reduced immune and stromal scores. In vitro, the overexpression of miR-4739 in Huh-7 cells significantly induced SPP1 macrophages, and the culture medium derived from SPP1 macrophages further promoted the proliferation and migration of Huh-7 cells. Furthermore, miR-4739 reduced m1A methylation by inhibiting tRNA methyltransferase 61A (TRMT61A) expression.

DISCUSSION

Our study reveals that the RMRM risk model could effectively predict the prognosis of HCC, and SPP1 macrophages regulated by miR-4739-RNA methylation promote the proliferation and migration of HCC cells. These results highlight the potential of RMRMs in predicting the prognosis of HCC.