Abstract
DNA methylation is a widespread epigenetic signal in human genome. With Nanopore technology, differential methylation modifications including 5-methylcytosine (5mC) and 6-methyladenine (6mA) can be identified. 5mC is the most important modification in mammals, although 6mA may also function in growth and development as well as in pathogenesis. While the role of 5mC at CpG islands in promoter regions associated with transcriptional regulation has been well studied, but the relationship between 6mA and transcription is still unclear. Thus, we collected two pairs of tumor tissues and adjacent normal tissues from hepatocellular carcinoma (HCC) surgical samples for Nanopore sequencing and transcriptome sequencing. It was found that 2,373 genes had both 5mC and 6mA, along with up- and down-regulated methylation sites. These genes were regarded as unstable methylation genes. Compared with 6mA, 5mC had more inclined distribution of unstable methylation sites. Chi-square test showed that the levels of 5mC were consistent with both up- and down-regulated genes, but 6mA was not significant. Moreover, the top three unstable methylation genes, TBC1D3H, CSMD1, and ROBO2, were all related to cancer. Transcriptome and survival analyses revealed four potential tumor suppressor genes including KCNIP4, CACNA1C, PACRG, and ST6GALNAC3. In this study, we firstly proposed to combine 5mC and 6mA methylation sites to explore functional genes, and further research found top of these unstable methylation genes might be functional and some of them could serve as potential tumor suppressor genes. Our study provided a new solution for epigenetic regulation research and therapy of HCC.
Highlights
Hepatocellular carcinoma (HCC) is a common malignant tumor and the fourth leading cause of cancer-related death worldwide (Kole et al, 2020; Sung et al, 2021)
In hepatocellular carcinoma (HCC), 2,373 genes had both 5mC and 6mA, with up- and down-regulated methylation sites. We considered these genes as unstable methylation genes
We found eleven genes in top 100 unstable methylation genes could affect the prognosis of patients and four of them could be potential tumor suppressor genes
Summary
Hepatocellular carcinoma (HCC) is a common malignant tumor and the fourth leading cause of cancer-related death worldwide (Kole et al, 2020; Sung et al, 2021). Cytosine DNA methylation (5methylcytosine, 5mC) is a widespread form of methylation and can function by directly regulating the occurrence and development of cancers (Mo et al, 2020; Lowe et al, 2021). The 5mC derived from cell-free DNA can be markers in HCC (Hlady et al, 2019), reveals potential advantages of methylation to the development of liquid biopsy. In c-kit gene, a single 5mC methylation site is enough to affect the binding of the transcription factor GATA-1 to the gene body and regulate the normal development of hematopoietic system (Yang et al, 2020). We found eleven genes in top 100 unstable methylation genes could affect the prognosis of patients and four of them could be potential tumor suppressor genes
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
