Uncovering the Association Between m5C Regulator-Mediated Methylation Modification Patterns and Tumour Microenvironment Infiltration Characteristics in Hepatocellular Carcinoma.

Xinyu Gu,Haibo Zhou,Jing Wang,Qingfei Chu,Qiuxian Zheng,Haihong Zhu

doi:10.3389/fcell.2021.727935

Xinyu Gu, Haibo Zhou + Show 4 more

Open Access

https://doi.org/10.3389/fcell.2021.727935

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Abstract

Background: 5-Methylcytosine (m5C) plays essential roles in hepatocellular carcinoma (HCC), but the association between m5C regulation and immune cell infiltration in HCC has not yet been clarified.Methods: In this study, we analysed 371 patients with HCC from The Cancer Genome Atlas (TCGA) database, and the expression of 13 m5C regulators was investigated. Additionally, gene set variation analysis (GSVA), unsupervised clustering analysis, single-sample gene set enrichment analysis (ssGSEA), correlation analysis, and immunohistochemical (IHC) staining were performed.Results: Among the 371 patients, 41 had mutations in m5C regulators, the frequency of which was 11.26%. Compared with normal hepatic tissues, the expression of m5C regulators with copy number variations (CNVs) expansion was significantly higher than that in HCC tissues. Then, we identified three m5C modification patterns that had obvious tumour microenvironment (TME) cell infiltration characteristics. The prognostic analysis of the three major m5C modification subtypes showed that Cluster-2 had a clear survival advantage over the others. In addition, we found that DNMT1 was highly expressed in tumour tissues compared with normal tissues in a tissue microarray (TMA) and that it was positively correlated with many TME-infiltrating immune cells. High expression of the m5C regulator DNMT1 was related to a poor prognosis in patients with HCC. Furthermore, we developed three distinct Immu-clusters. Importantly, mRNAs related to the transcription of growth factor β (TGF-β)/EMT pathway were significantly up-regulated in Immu-cluster 2, indicating that this cluster is considered to be the immune rejection phenotype. Immu-cluster 3 showed elevated expression of mRNAs related to immune checkpoint genes.Conclusion: Our work revealed the association between m5C modification and immune regulators in the TME. These findings also suggest that DNMT1 has great potential as a prognostic biomarker and therapeutic target for HCC.

Highlights

Hepatocellular carcinoma (HCC) is the sixth most common cancer and the fourth leading cause of cancer-related death worldwide (Llovet et al, 2021)
Our analysis showed that activated CT4 T cells, immature B cells, regulatory T cells, natural killer (NK) cells, macrophages, mast cells, myeloid-derived suppressor cells (MDSCs), monocytes, neutrophils, and plasmacytoid dendritic cells (DCs) were significantly different among the Immu-clusters
Kaplan–Meier curve analysis and univariable and multivariable Cox regression analysis further demonstrated that the expression of DNMT1 is an independent risk factor for HCC

Summary

Introduction

Hepatocellular carcinoma (HCC) is the sixth most common cancer and the fourth leading cause of cancer-related death worldwide (Llovet et al, 2021). Risk factors for HCC include hepatitis B virus (HBV), hepatitis C virus (HCV), non-alcoholic fatty liver disease, obesity with diabetes, etc. Most HCC patients are diagnosed at advanced stages, and limited effective therapeutic strategies are available (Hernandez-Gea et al, 2013). Tumour cells are the driving cause of tumour development and progression. The TME includes the surrounding blood vessels, fibroblasts, immune cells, extracellular matrix, and signalling molecules. These elements contribute to the processes of carcinogenesis and progression, while it is still a major challenge to fully evaluate the complex TME (Hanahan and Coussens, 2012)

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