Background
With decades of epitranscriptomal studies, it is increasingly clear that the covalent modifications in RNAs are a crucial additional aspect of gene regulation. It is convinced that 163 post-transcriptional modifications of RNA contribute strongly to the diversity of functions fulfilled by RNA molecules, especially during the process of tumor progression [
1]. Methylations are among the most common RNA modifications, which include N6-methyladenosine (m6A) [
2], N1-methyladenosine (m1A) [
3], N5-methylcytidine (m5C) [
4], and N3-methylcytidine (m3C) [
5]. Various methylation modifications have a wide range of effects on the RNA secondary structure folding, stability, and function, which influence the physiological processes and are closely related to numerous human diseases [
1].
The m6A modification, one of the most well-known mRNA modifications, is extensively involved in all sorts of tumor development [
2]. In contrast, the relationship between m3C modification and tumorigenesis has very rarely been studied. The 3-methylcytidine modification at position 32 (m3C32) is discovered in fission yeast with two enzymes, Trm140 and Trm141, catalyze tRNA
Thr and tRNA
Ser m3C32 modification, respectively [
6]. The N6-threonylcarbamoyladenosine (t6A) or N6-isopentenyladenosine (i6A) modification at position 37 (t6A37 or i6A37) of yeast tRNA
Thr or tRNA
Ser function as a key determinant for the m3C process [
7]. While the m3C modification for tRNA
thr/tRNA
Arg and tRNA
ser are catalyzed by Mettl2 and Mettl6 in mice, respectively. In addition, the deletion of Mettl8 has little influence on the abundance of tRNAs which supports the hypothesis that Mettl8 is an mRNA m3C methyltransferase rather than a tRNA [
8]. In human cells, N3-methylcytidine of RNA can be catalyzed by methyltransferase-like proteins (METTLs) that contain 4 members of METTL2A, METTL2B, METTL6, and METTL8 [
8]. METTL2A and METTL2B are two homologs of Mettl2 with only six amino acids differ. With G35 and t6A at position 37 (t6A37) on the anticodon loop, METTL2A catalyzes the m3C32 in human tRNA
Thr, while there is little m3C32 modification activity presented by METTL2B. METTL6 interacts with seryl-tRNA synthetase (SerRS, encoded by SARS1) to mediate the biogenesis of m3C32 modification in human tRNA
Ser [
9]. In contrast to the preceding three cytoplasmic m3C32-modifying enzymes, it had been established that METTL8 functioned in mitochondria [
10,
11].
There were several studies figuring out the vital important relationship between METTL6 and the prognostic of malignant tumor patients. It was convinced that knockdown of METTL6 could significantly decrease sensitivity of lung cancer cells to cisplatin [
12]. A bioinformatics analysis revealed that METTL6 tended to amplify in luminal breast tumors with highly proliferative capacity [
13,
14]. Recently, it is demonstrated that the deletion of METTL6 showed a significant inhibition on the proliferation of liver cancer cell lines and the high expression of METTL6 in malignant patients tended to indicate a poor prognostic [
15,
16]. The m3C32 modification of mitochondria tRNA
Ser and tRNA
Thr were catalyzed by the mitochondrial protein METTL8 and the high expression of METTL8 contributed an enhanced respiratory chain activity in pancreatic cancer [
10]. The alternative mRNA splicing research reported that one of the isoforms of METTL8, METLL8-iso1, had been investigated to be transported to mitochondrial with the assistance of its N-terminal mitochondrial targeting sequence [
11]. Aside from the classical m3C32 modification of mitochondrial tRNAs, upregulated of METTL8 by Yin Yang 1 (YY1) transcription factor mediated the m3C modification on the mRNA of AT-rich interactive domain-containing protein 1A and attenuated its translation, which induced the migration of breast cancer cell lines [
17]. In addition, the SUMOylated METTL8 induces the R-loop formation and promotes tumorigenesis in colorectal cancer [
18,
19]. Nevertheless, the functions and mechanisms of m3C enzymes in cancer progression remain poorly understood.
Herein, we conducted the landscape analysis of four m3C enzymes' expressions and their relationship with prognosis across multiple cancer types. We also analyzed the DNA copy numbers and mutations of the four m3C associated genes using multi-omic data from The Cancer Genome Atlas (TCGA). Furthermore, we determined the correlation of METTL2A expression with clinical parameters of patients with breast cancer and analyzed related signaling pathways and potential therapeutic agents of METTL2A in BRCA patients. Finally, we detected METTL2A expression in tumor tissues of BRCA using immunohistochemistry. The data and analyses suggest that m3C associated genes, especially METTL2A, play a key function and are tightly linked to the development of various cancers.
Discussion
M3C modification was first found in Saccharomyces cerevisiae [
5]. In S. cerevisiae, Trm140 and Trm141 catalyze m3C formation in tRNA
Thr and tRNA
Ser, respectively [
7]. Four Trm140 and Trm141 homologs have been discovered in humans: METTL2A, METTL2B, METTL6, and METTL8. METTL2A and METTL2B were shown to modify m3C at position 32 of tRNA
Thr isoacceptors and tRNA
Arg(CCU) [
8]. Here, we found significant correlation between m3C associated genes and tumor malignancy in transcription and genetic alteration in a variety of tumor types. Consistent with the former researches [
12,
15], the negative relationship between the expression of METTL6 and the prognostic of LUAD and LIHC had been verified in the TCGA cohort. In addition, the four m3C associated genes shared the same expression pattern among several cancer types (containing BRCA, LIHC, LUAD, PAAD, and READ), which implied that they all function as oncogenes in these cancers. As described above, METTL8 had been proved to be an oncogene in BRCA with its direct m3C modification on the mRNA of ARID1A [
17], while METTL6 shown a tendency of amplification in malignant breast cancer patients [
13]. Interestingly, compared with METTL8 and METTL6, differential expression of METTL2A in BRCA tumor tissues and adjacent normal tissues was more significantly.
Expectedly, METTL2A high expression correlated with poorer survival outcomes of BRCA patients in the TCGA and multiple GEO cohorts. Based on the genetic alteration analysis of m3C associated genes in BRCA, it was convinced that there was a higher genetic alteration of METTL2A with the rate of amplification up to 7% which was about seven times higher than METTL6 [
13]. Therefore, it was further proved that METTL2A played a more important oncogene role in BRCA than the other m3C associated genes. Furthermore, we uncovered that the expression level of METTL2A was significantly positively related to T stage, grade, P53 mutation status, HER2, and ER positive status. Using IHC and CPTAC, we found that the protein level of METTL2A was up-regulated in BRCA tumor tissues. These results suggest that METTL2A might be an oncogene that plays an important role in BRCA progression. However, larger sample sizes and further research would be necessary for validation and expanding on our research.
The related Hallmark signaling pathway of METTL2A in BRCA was analyzed by the GSEA and GO database. The results showed that G2M_CHECKPOINT, E2F_TARGETS, DNA_REPAIR, and proliferation and DNA damage response pathways were correlated with the high expression of METTL2A. These results suggested that METTL2A may affect cell cycle and proliferation of cells to promote the progression of BRCA. In addition, Trifluridine, PD407824 and Taselisib were considered to be potential therapeutic agents for METTL2A high expression BRCA patients. Taselisib is currently in Phase III trials for postmenopausal women with estrogen receptor-positive (ER +) breast cancer [
41] and non-small cell lung cancer (NSCLC) [
42]. Taselisib is a potent PI3K inhibitor that inhibits the activity of PIK3CA, PIK3CB and PIK3CG [
43]. Taselisib may be a potential treatment strategy for METTL2A high expression ER-positive BRCA patients. Furthermore, we identified another compound, Trifluridine, which interferes with DNA synthesis and inhibits cell proliferation [
44,
45]. PD407824 is a CHK1 and WEE1 inhibitor which associated with METTL2A regulated gene network of DNA synthesis and cell proliferation in BRCA tumors. Taken together, METTL2A maybe a potential new therapeutic target for BRCA treatment. Nevertheless, future in-depth research and clinical studies are warranted to substantiate our findings.
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