Vital roles of m5C RNA modification in cancer and immune cell biology

Abstract

RNA modification plays an important role in epigenetics at the posttranscriptional level, and 5-methylcytosine (m⁵C) has attracted increasing attention in recent years due to the improvement in RNA m⁵C site detection methods. By influencing transcription, transportation and translation, m⁵C modification of mRNA, tRNA, rRNA, lncRNA and other RNAs has been proven to affect gene expression and metabolism and is associated with a wide range of diseases, including malignant cancers. RNA m⁵C modifications also substantially impact the tumor microenvironment (TME) by targeting different groups of immune cells, including B cells, T cells, macrophages, granulocytes, NK cells, dendritic cells and mast cells. Alterations in immune cell expression, infiltration and activation are highly linked to tumor malignancy and patient prognosis. This review provides a novel and holistic examination of m⁵C-mediated cancer development by examining the exact mechanisms underlying the oncogenicity of m⁵C RNA modification and summarizing the biological effects of m⁵C RNA modification on tumor cells as well as immune cells. Understanding methylation-related tumorigenesis can provide useful insights for the diagnosis as well as the treatment of cancer.

Keywords: RNA modification; cancer; cancer immunity; immune cells; m5C.

Figure 1

m⁵C modifications of mRNA. (A) mRNA is methylated at m⁵C sites by DNMT2, NSUN2, NSUN4 and NSUN6. ALYREF and YBX1 bind and stabilize m⁵C-modulated mRNAs. TET1, TET2 and ALKBH1 remove m⁵C sites by turning them into hm⁵C. (B) Target mRNAs of NSUN2 include GRB2, CD44, PIK3R1, PCYTIA, FOXC2, p57Kip2, TEAD1, AR, KRT13, IL-17A, and p21. Most target mRNAs are stabilized due to m⁵C modification, with the exception of p57Kip2, and are associated with enhanced cell proliferation and migration. (C) NSUN4-mediated m⁵C at the 3’-UTR of Sox9 mRNA promotes chondrogenic differentiation. (D) NSUN6-mediated m⁵C modification suppresses pancreatic cancer by promoting tumor-suppressive CDK10. (E) ALYREF binds with MYC, YAP, PKM2 and NEAT1 lncRNA, promoting tumor development and drug resistance. ALYREF facilitates nuclear export of YBX2, CDKN1A and SMO mRNAs, inhibiting adipogenesis and enhancing myogenesis. (F) YBX1 binds to m⁵C sites on the FOXC2, HDGF, PEBRQ, AR and KRT13 mRNAs, leading to enhanced mRNA translation and promoting tumorigenesis. YBX1 recognizes and stabilizes m⁵C-modified mRNAs by recruiting Pabpc1a, facilitating maternal-to-zygotic transition.

Figure 2

m⁵C modifications of tRNA. SAM induces tRNA m⁵C modification. DNMT2, NSUN2-4, and NSUN6 catalyze m⁵C modification of various tRNAs at different sites, causing distinct biological effects. ALKBH1 removes m5C sites from tRNA^Leu-CAA and converts them into f⁵C (5-formylcytidine) sites, promoting the decoding of Leu codons under stress.

Figure 3

m⁵C modifications of rRNA, lncRNA and eRNA. (A) rRNA m⁵C modification is mediated by NSUN1, NSUN4 and NSUN5, facilitating ribosome biogenesis, healthspan modulation, mitoribosomal assembly, protein synthesis and cell proliferation. (B) NSUN2 catalyzes m⁵C modification of H19 lncRNA, which stimulates MYC expression and HCC development. YBX1 recognizes and stabilizes m⁵C-modified NKILA, promoting cholangiocarcinoma development. (C) NSUN7 m⁵C-methylates eRNA associated with PGC-1α, promoting its transcriptional coactivator function.

Figure 4

Expression of m⁵C-related genes and immune cell infiltration in different cancer types. (A) HCC. NSUN2-mediated m⁵C modulation of H19 lncRNA increases its stability, leading to enhanced recruitment of G3BP1 and MYC. NSUN2 also promotes HCC progression by modulating the Ras signaling pathway, the cell cycle and drug resistance. NSUN5 facilitates ribosomal functions and protein translation. ALYREF upregulates eIF4A3 expression, which leads to uncontrolled mitosis. The abundance of CD4+ T cells (including Tregs), M0, M1 and M2 macrophages and resting mast cells is higher in HCC tissues from patients with poor prognoses. (B) GC. NSUN2 methylates PIK3R1 and PCYT1A mRNA, stabilizing them and activating downstream cancerous signaling pathways. NSUN2 methylates FOXC2 mRNA, enhancing its interaction with the m⁵C reader YBX1. NSUN2 destabilizes tumor-suppressive p57Kip2 mRNA by m⁵C-methylation in its 3’-UTR. (C) Bladder cancer. ALYREF binds to the 3’-UTR of PKM2 mRNA, stabilizing it and enhancing PKM2-mediated glycolysis. NSUN2 mediates m⁵C modification in the 3’-UTR of oncogenic HDGF mRNA; YBX1 recruits ELAVL1 to form a m⁵C-binding complex to stabilize HDGF mRNA. Lower Treg, CD8+ T-cell and plasma cell infiltration rates indicate poor prognosis. (D) Prostate cancer. NSUN2 catalyzes and YBX1 recognizes m⁵C modification sites on androgen receptor (AR) mRNA, and AR positively regulates NSUN2 transcription in return. NSUN2 expression also leads to drug resistance and immune cell infiltration. (E) Leukemia. NSUN1 forms an active drug-resistant chromatin structure with BRD4 and RNA polymerase-II, while SUN3 and DNMT2 form a drug-sensitive structure with hnRNPK, GATA1, SPI1/PU.1, and CDK9/P-TEFb to recruit RNA polymerase-II. (F) HNSCC. NSUN2 promotes HNSCC by suppressing immune infiltration and methylates and stabilizes TEAD1 mRNA. ALYREF increases mitochondrial activity to ensure tumor cells are supplied with energy. Lower Treg, naïve B-cell and NK cell infiltration indicates poor prognosis, while higher M2 macrophage infiltration indicates poor prognosis. (G) Breast cancer. ALYREF promotes breast cancer by enhancing the transcription of NEAT1 lncRNA. DNMT3B targets VEGFA and EZH2 as tumor promoters. NSUN5, TET2 and DNMT2 exert inhibitory effects on breast cancer by modifying three lncRNAs. (H) Pancreatic cancer. NSUN2 promotes pancreatic cancer and epithelial differentiation. (I) ccRCC. YBX1 negatively modulates ccRCC by binding and stabilizing PEBR1 mRNA. The abundance of CD4+ T cells and CD8+ T cells was higher in ccRCC tissues. (J) Cholangiocarcinoma. YBX1 promotes tumor development by stabilizing m⁵C-methylated NKILA. (K) Glioma. ALYREF activates the Wnt/β-catenin signaling pathway and stabilizes MYC mRNA, promoting the development of glioblastoma, a malignant type of glioma. The infiltration of CD4+ T cells, monocytes and NK cells decreases in glioma tissues, while macrophage and Treg infiltration increases. (L) Neuroblastoma. ALYREF forms a nuclear coactivator complex with MYCN to stimulate USP3 transcription, which promotes tumorigenesis. (M) Lung adenocarcinoma. SUN2 and ALYREF increase YAP mRNA stability, thus enhancing exosome secretion, tumor malignancy and drug resistance. Lower plasma cell, eosinophil, NK cell and DC infiltration rates and higher neutrophil infiltration rates indicate poor prognosis. (N) ESCC. NSUN2 methylates GRB2 in a LIN28B-dependent manner, thus activating the PI3K/AKT and ERK/MAPK signaling pathways. NSUN2 also promotes TIGAR to enhance tumor growth. (O) Cervical cancer. NSUN2 and YBX1 promote cervical cancer by increasing the expression levels of KRT13 mRNA. (P) Ovarian cancer. YBX1 modulates CD44 expression to enhance chemoresistance.