Overview of distinct 5-methylcytosine profiles of messenger RNA in normal and knock-down NSUN2 colorectal cancer cells

Yu Lin; Zhifang Zhao; Wenqiang Nie; Manting Huang; Jiazhong Cai; Yadong Wang; Hesong Wang; Yongmei Huang; Yang Bai

doi:10.3389/fgene.2023.1121063

Overview of distinct 5-methylcytosine profiles of messenger RNA in normal and knock-down NSUN2 colorectal cancer cells

Front Genet. 2023 Apr 24:14:1121063. doi: 10.3389/fgene.2023.1121063. eCollection 2023.

Authors

Yu Lin^{1

2

3}, Zhifang Zhao¹, Wenqiang Nie⁴, Manting Huang⁵, Jiazhong Cai³, Yadong Wang¹, Hesong Wang², Yongmei Huang², Yang Bai^{1

2}

Affiliations

¹ Department Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Institute of Gastroenterology of Guangdong Province, Nan Fang Hospital, Southern Medical University, Guangzhou, China.
² Department of Gastroenterology, Baiyun Branch, Nan Fang Hospital, Southern Medical University, Guangzhou, China.
³ Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China.
⁴ Department of Traditional Chinese Medicine, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China.
⁵ Department of Vascular Intervention, Zhongshan Hospital of Traditional Chinese Medicine, Affiliated to Guangzhou University of Chinese Medicine, Zhongshan, China.

Abstract

Background: Colorectal cancer (CRC) is a harmful cancer with high morbidity and poor prognosis. There is growing evidence that RNA methylation is closely related to the occurrence of cancer and its malignant biological behavior. N6-methyladenosine (m⁶A) methylation is the most common RNA modification in eukaryotes, and its multiple regulatory mechanisms in CRC have been elucidated from multiple perspectives. At the same time, the role of 5-methylcytosine (m5C), another important and widely distributed methylation modification, in CRC is far from being elucidated. Methods: In this study, we used RNA immunoprecipitation sequencing combined with bioinformatics methods to identify the m5C peaks on messenger RNA (mRNA) in HCT15 cells and sh-NSUN2 HCT15 cells, understand which transcripts are modified by m5C, and characterize the distribution of m5C modifications. In addition, we performed further bioinformatics analysis of the detected data to initially clarify the potential function of these m5C-modified transcripts. Results: We found significant differences in the distribution of m5C between HCT15 cells and sh-NSUN2 HCT15 cells, suggesting that m5C is likely to play a key role in the occurrence and development of CRC. Furthermore, Gene Ontology (GO) enrichment analysis showed that genes altered by m5C were mainly enriched in phylogeny, synaptic membrane, and transcription factor binding. The Kyoto Encyclopedia of Genes and Genomes (KEGG)pathway analysis showed that the genes altered by m5C are enriched in ECM receptor interaction pathway, the circadian pathway, and the cAMP signaling pathway. Conclusion: Here, our study preliminarily revealed the different distribution patterns of m5C between HCT15 cell and sh-NSUN2 HCT15 cell. Our results open a new window to understand the role of m5C RNA methylation of mRNA in the development of CRC.

Keywords: 5-methylcytosine; MeRIP-seq; NSun2; RNA methylation; colorectal cancer.

Grants and funding

This research was supported by the Guangdong Natural Science Funds (No. 2022A1515011625, No. 2022A1515011230). Guizhou Province Natural Science Funds (No [2020]1Y341). Guizhou Provincial People’s Hospital Youth Funds (GZSYQN [2022]12). Guangzhou Science and Technology Program (No: 202002030186). Guangdong Basic and Applied Basic Research Foundation (No: 2021A-1515220009).