# Deep learning model and omics screening highlight angiotensinogen as a 5-methylcytosine (m5C) regulated mediator of tumor-microenvironment communication in liver cancer

## TL;DR

This study identifies angiotensinogen as a key RNA modification-regulated protein that influences communication between liver cancer cells and their environment, potentially improving cancer treatment.

## Contribution

The study introduces a new deep learning model (GAT-MeRIP) and identifies angiotensinogen as a novel m5C-regulated mediator in liver cancer TME communication.

## Key findings

- Angiotensinogen (AGT) is a key m5C-regulated secretory factor in liver cancer TME communication.
- NSUN2 knock-down increases AGT expression and enhances NK cell cytotoxicity.
- Low NSUN2 and high AGT levels correlate with better survival and immune infiltration in liver cancer patients.

## Abstract

The tumor microenvironment (TME) is critical for liver cancer progression and therapy response. As a key RNA modification, 5-methylcytosine (m5C) methylation is implicated in this process, yet the molecular mechanisms by which m5C modification mediates intercellular crosstalk within the TME remain less understood.

The m5C methylomes in wildtype and m5C-catalyzing enzyme NSUN2-perturbed liver cancer cells were profiled via MeRIP-seq. GAT-MeRIP, a graph attention neural network-based algorithm, was developed to identify functional m5C-modified target genes from MeRIP-seq data. TME-related functional m5C targets were screened through cell-cell communication analysis of single-cell transcriptomic data. In vitro functional validation of the key target gene was performed via a combination of cell co-culture, qRT-PCR, MeRIP-qPCR, ELISA, and flow cytometry assays. Additionally, public liver cancer cohort data were used for clinical correlation and prognostic analysis.

Angiotensinogen (AGT) was identified as a key m5C-regulated secretory factor contributing to tumor-microenvironment communication in liver cancer. NSUN2 knock-down increased AGT’s expression and enhanced cytotoxicity of co-cultured NK cells, which can be canceled by AGT-neutralizing antibody. Exogenous AGT treatment significantly enhanced NK cell cytotoxicity by upregulating IFN-γ, TNF-α, and perforin, as well as the proportion of CD107a⁺ NK cells. Liver cancer patients with low NSUN2 and high AGT exhibited significantly improved overall survival rates and higher immune infiltration.

This study unveils novel regulatory function of m5C-modified AGT in modulating the liver TME that could be helpful for improving liver cancer prognosis and immunotherapy.