PRMT1 Integrates Immune Microenvironment and Fatty Acid Metabolism Response in Progression of Hepatocellular Carcinoma

Abstract

Background: Protein arginine methyltransferase (PRMT) family members have important roles in cancer processes. However, its functions in the regulation of cancer immunotherapy of hepatocellular carcinoma (HCC) are incompletely understood. This study aimed to investigate the roles of PRMT1 in HCC.

Methods: Single-cell RNA sequencing (scRNA-seq) and clinicopathological data were obtained and used to explore the diagnostic and prognostic value, cellular functions and roles in immune microenvironment regulation of PRMT1 in HCC. The functions of PRMT1 were explored using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO), as well as gene set enrichment analysis (GSEA). TIMER and CIBERSORT were used to analyze the relationships between PRMT1 expression and immune cell infiltration. The STRING database was used to construct a protein-protein interaction (PPI) network.

Results: PRMT1 was aberrantly expressed in HCC, which high expression was associated with tumor progression, worse overall survival (OS) and disease-free survival (DFS) of patients with HCC. PRMT1 was also associated with immune cell infiltration. Moreover, it was specifically expressed in immune cells, including exhausted CD8 T cells, B cells, and mono/macro cells in patients with immunotherapy. The expression of immune checkpoints was significantly increased in the high-PRMT1 expression groups of HCC patients. Regarding biological mechanisms, cell viability, migration and invasion, and the expression of genes related to fatty acid metabolism were suppressed in PRMT1 knockdown HCC cells. Moreover, genes co-expressed with PRMT1 were involved in the fatty acid metabolic process and enriched in fatty and drug-induced liver disease.

Conclusion: Taken together, these results indicate that PRMT1 might exert its oncogenic effects via immune microenvironment regulation and fatty acid metabolism in HCC. Our finding will provide a foundation for further studies and indicate a potential clinical therapeutic target for liver cancer.

Keywords: PRMT1; fatty acid metabolism; prognosis; protein arginine methyltransferase; tumor-infiltrating.

Figure 1

Expression patterns and prognostic potential of PRMT1 in HCC. (A) The expression of PRMT1 in pan cancers. (B) The expression of PRMT1 liver cancers. (C) The expression of PRMT1 was significantly associated with TNM stage based on TCGA results using UALCAN analysis. (D) The expression of PRMT1 was associated with the tumor grade of HCC in TCGA samples using UALCAN database analysis. Grade 1, well differentiated (low grade); Grade 2, moderately differentiated (intermediate grade); Grade 3, poorly differentiated (high grade); Grade 4, undifferentiated (high grade). Statistical significance determined by t-test. **P<0.01; ***P<0.001. (E) Kaplan–Meier survival analysis of PRMT1 expression and OS to compare the five-year survival of HCC patients. (F) Kaplan–Meier survival analysis of PRMT1 expression and disease-free survival in GEPIA.

Figure 2

Association of PRMT1 with tumor immune cell infiltration in HCC. (A–D) UMAP dimensionality reduction of scRNA-seq data from non-tumor and HCC patients, (A and B) GSE140226_10×, (C and D) GSE140228_smartseq2. (E) Correlations of PRMT1 with immune infiltrates in HCC. (F) Correlations of PRMT1 expression with abundance of immune cell subtypes. (G) Overall Kaplan–Meier survival curves for patients with HCC and high or low levels of macrophages. Statistical significance determined by t-test. *P<0.05; **P<0.01; ***P<0.001; ****P<0.0001.

Figure 3

PRMT1 expression in HCC patients treated with immunotherapy. (A) The expression of PRMT1 in the HCC patient’s liver cells of HCC patients treated with immunotherapy. (B and C) UMAP dimensionality reduction of scRNA-seq data from HCC patients treated with immunotherapy. (D) Diagrams of PRMT1 genes expression between different immune cells.

Figure 4

Correlations of differentially expressed PRMT1 and immune infiltration-associated marker genes in HCC. (A) Correlations of PRMT1 expression with immunomodulators, MHC molecules, chemokines, and receptors. (B) Correlations between the PRMT1 expression and immune checkpoints. (C) Correlations between PRMT1 expression and PDCD1, CD274, CLAT4, TGFB1 and IL10 in HCC. *P<0.05; ****P<0.0001.

Figure 5

The function of PRMT1 in HCC cells. (A) Cell growth rate was decreased after downregulation of PRMT1 in HCC cells. (B and C) HCC cells with downregulated PRMT1 showed lower motility in a wound healing assay. (D and E) Cell migration ability in PRMT1 knockdown HCC cells analyzed by transwell migration assay. *P<0.05; **P<0.01.

Figure 6

Enrichment analysis of PRMT1 associated genes in LIHC. (A and B) Functional pathways associated with PRMT1 expression from KEGG and GO enrichment analyses. (C) Functional pathways of PRMT1-associated genes. (D) Summary of enrichment analysis of PRMT1-related genes in DisGeNET.

Figure 7

PRMT1 is involved in fatty acid metabolism. (A) Network of PRMT1-related genes and metabolic pathways. (B) Protein interaction network for PRMT1 and proteins related to fatty metabolism. (C) The expression of genes related to fatty acid metabolism in PRMT1-knockdown HCC cells. (D) Correlations of PRMT1-related genes that were also involved in metabolic pathways, with immune infiltrates in HCC. FDR-adjusted P-values are shown *P value ≤ 0.05; ^#FDR ≤ 0.05.