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Li, Y.;  Niu, C.;  Wang, N.;  Huang, X.;  Cao, S.;  Cui, S.;  Chen, T.;  Huo, X.;  Zhou, R. m6A Modification and m6A Regulators in Esophageal Cancer. Encyclopedia. Available online: https://encyclopedia.pub/entry/31689 (accessed on 27 July 2024).
Li Y,  Niu C,  Wang N,  Huang X,  Cao S,  Cui S, et al. m6A Modification and m6A Regulators in Esophageal Cancer. Encyclopedia. Available at: https://encyclopedia.pub/entry/31689. Accessed July 27, 2024.
Li, Yuekao, Chaoxu Niu, Na Wang, Xi Huang, Shiru Cao, Saijin Cui, Tianyu Chen, Xiangran Huo, Rongmiao Zhou. "m6A Modification and m6A Regulators in Esophageal Cancer" Encyclopedia, https://encyclopedia.pub/entry/31689 (accessed July 27, 2024).
Li, Y.,  Niu, C.,  Wang, N.,  Huang, X.,  Cao, S.,  Cui, S.,  Chen, T.,  Huo, X., & Zhou, R. (2022, October 28). m6A Modification and m6A Regulators in Esophageal Cancer. In Encyclopedia. https://encyclopedia.pub/entry/31689
Li, Yuekao, et al. "m6A Modification and m6A Regulators in Esophageal Cancer." Encyclopedia. Web. 28 October, 2022.
m6A Modification and m6A Regulators in Esophageal Cancer
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This entry is adapted from the peer-reviewed paper 10.3390/cancers14205139

N6-methyladenosine (m6A) refers to the methylation at the N6 position of adenosine, which is considered to be the most prevalent RNA modification.

m6A modification m6A regulators occurrence progression treatment

1. Introduction

N6-methyladenosine (m6A) refers to the methylation at the N6 position of adenosine, which is considered to be the most prevalent RNA modification. Approximately one to two m6A residues are found in every 1000 nucleotides [1][2], and are mainly located in the RRACH sequence (R = A or G, H = A, C, or U) [3][4]. However, not all RRACH motifs are methylated, which suggests that methylation at the N6 position of adenosine is specific and selective [5][6]. N6-methyladenosine occurs in mRNA, rRNA, long non-coding RNA (lncRNA), microRNA (miRNA), circular RNA (circRNA), etc., and is involved in all aspects of RNA metabolism, including RNA processing, nuclear export, stability, translation and degradation. Therefore, m6A modification can participate in various physiological functions, such as tissue development, heat shock response, DNA damage response, circadian clock control and even in carcinogenesis through regulating the expression or structure of the gene [5][6][7][8][9][10][11][12][13][14][15][16][17][18][19].
Esophageal cancer (ESCA) is one of the most common malignant tumors, ranking tenth all over the world in 2020 [20]. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are the main pathological subtypes of ESCA. Genetic factors and environmental factors interplay to cause the occurrence of ESCA. Smoking, drinking, obesity, etc., are associated with a higher risk of ESCA. Genome-wide association studies and candidate gene association studies both found some susceptible genes of ESCA [21][22][23][24][25]. Furthermore, epigenetic modifications, such as DNA methylation, RNA methylation, histone modifications, et al., also play a critical role in the occurrence and development of ESCA [26][27]. The m6A modification is the most frequent RNA modification, and was firstly identified in 1974 [28]. It was considered as a static process until the fat mass and obesity-associated (FTO) gene was firstly found to be a demethylase in 2010 [29]. With the discovery of FTO and the application of m6A detection technology, m6A modification became a hotspot in the research field of cancer, including ESCA.

2. m6A Modification and m6A Regulators

N6-methyladenosine modification is a dynamic and reversible process. In this process, methyltransferases are responsible for the addition of methyl, while removals of m6A are performed by demethylases. The fate of m6A-modified RNA depends on the protein that recognizes and binds to it. All of the methyltransferases, demethylases and m6A-modified RNA bound proteins that take part in the m6A-modification-associated process belong to m6A regulators.

2.1. Methyltransferases

Methyltransferases are also called “writers”. They catalyze the installation of m6A in the form of a complex, the m6A methyltransferase complex (MTC), which consists of methyltransferase-like 3 (METTL3), methyltransferase-like 14 (METTL14), Wilms = tumor-1-associated protein (WTAP), RNA binding protein 15 (RBM15), RNA binding protein 15B (RBM15B), vir like m6Amethyltransferase associated (VIRMA) (also known as KIAA1429), zinc finger CCCH-type containing13 (ZC3H13) and HAKAI. METTL3, METTL14 and WTAP constitute the catalytic core of MTC. METTL3 is the main subunit of MTC, with catalytic activity, and can bind S-adenosylmethionine (SAM) and transfer methyl to the N6 position of adenosine [30]. In addition, cytoplasmic METTL3 can bind to the m6A-modified 3′-untranslated region (UTR) of target mRNA, recruit eukaryotic translation initiation factor 3 subunit H (EIF3H) and enhance the translation efficiency [31][32]. METTL14 forms a stable heterodimer with METTL3 at a 1:1 ratio, stabilizes METTL3 and recognizes and binds to target RNA through its C-terminal RGG repeats [30][33]. With the help of WTAP, the METTL3-METTL14 heterodimer can be located in the nuclear speckle [34]. In addition to the catalytic core of MTC, other components are associated with WTAP and are helpful for the recruitment and localization of the METTL3-METTL14 heterodimer [35][36][37][38][39]. In a WTAP-dependent manner, RBM15/RBM15B correlates with METTL3 and recruits MTC to U-rich regions immediately adjacent to RRACH motifs to catalyze the deposition of m6A [37][40][41]. VIRMA is also a WTAP-associated factor and recruits MTC to 3′-UTR and near the stop codon for m6A catalysis [39]. ZC3H13 connects RBM15/RBM15B with WTAP through its C-terminal structure domain [36][38]. The knockdown of ZC3H13 leads to translocation from the nucleus to cytoplasm for a large proportion of WTAP, VIRMA, HAKAI, METTL3 and METTL14, indicating the important role of ZC3H13 for the nuclear localization of MTC [38]. HAKAI is an E3 ubiquitin-protein ligase, while its role in m6A catalysis is unclear. It is worth noting that m6A deposition depends on transcription. METTL3 and METTL14 form a heterodimer in the cytoplasm and then the heterodimer enters the nucleus with the help of a nuclear localization signal in METTL3. METTL4 can recognize and bind to histone H3 trimethylation at Lys36 (H3k36me3), promote the binding of MTC with RNA polymerase II and transfer MTC to actively transcribing RNAs to install m6A cotranscriptionally [42].
In addition to MTC, there are other methyltransferases, such as methyltransferase-like protein 16 (METTL16), cap-specific adenosine methyltransferase (CAPAM), methyltransferase-like protein 5 (METTL5)/tRNA methyltransferase activator subunit 11-2 (TRMT112) complex and zinc finger CCHC-type containing 4 (ZCCHC4). METTL16 catalyzes m6A deposition in the A43 of U6 small nuclear RNA (snRNA), and is involved in the splicing of RNA [43][44]. The m6A 43 is considered to affect the interaction between snRNA and pre-mRNA and thus regulate the splicing of pre-mRNA [44]. Methionine adenosyl transferase 2A (MAT2A) encodes SAM synthetase. The 3′-UTR hairpins of MAT2A mRNA are substrates of METTL16. The m6A modification of 3′-UTR hairpins influences the splicing of MAT2A pre-mRNA and maintains SAM homeostasis [43][45]. If 2′-O-methyladenosine (Am) is the first transcribed nucleotide of eukaryotic capped mRNAs, CAPAM can recognize it and deposit m6A on it to form a m7GPPPm6Am motif [46][47]. The METTL5/TRMT112 complex and ZCCHC4 are responsible for the methylation of the A1832 of 18S and A4220 of 28S rRNA, respectively [48][49][50].

2.2. Demethylases

Demethylases are termed as “erasers”. The m6A demethylation occurs on nascent transcripts. FTO is the first identified demethylase, and alkB homolog 5 (ALKBH5) is the second one. Ferrous iron and α-ketoglutarate are cofactors of FTO and ALKBH5 [51]. Both FTO and ALKBH5 can remove m6A modification on single RNA and DNA [8][52]. In addition, FTO also can act as demethylase for N6,-2′-O-dimethyladenosine (m6Am) near the N7-methylguanosine (m7G) cap [53].

2.3. m6A RNA Binding Proteins

The fate of m6A-modified RNA depends on the protein that binds to it. This kind of RNA binding protein is referred to as a “reader”. Readers include YT521-B homology (YTH) family proteins, insulin like growth factor 2 mRNA binding proteins (IGF2BPs), heterogeneous nuclear ribonucleoproteins (HNRNPs) and eukaryotic translation initiation factor 3 (EIF3).

3. m6A Modification and Its Effect on Various RNAs in ESCA

A proper m6A level, mainly relying on the appropriate expression and function of m6A regulators, is necessary for sustaining normal bioprocesses. The disruption of the dynamic balance between the installation and removal of m6A modification will lead to the development of diseases, including cancer. An aberrant m6A level associated with the dysregulation of m6A regulators has been reported in a variety of cancers, such as gastric cancer, hepatocellular carcinoma, bladder cancer, etc. [54][55][56]. Nucleotide sequence changes could also result in the gain or loss of m6A sites and contribute to carcinogenesis [57][58]. For example, a base transition from the G to A of rs5746136 in SOD2 led to an increased m6A modification level of SOD2 and an increased binding of HNRNPC with SOD2 through an “m6A switch” mechanism followed by the upregulation of SOD2. The overexpression of SOD2 inhibited the proliferation, migration and invasion of bladder cancer cells, which suggested that SOD2 acted as a tumor suppressor gene for bladder cancer. Thus, the A allele of rs5746136 in SOD2 was associated with a reduced risk of bladder cancer [57]. m6A could deposit on various type of RNA, such as coding RNA and non-coding RNA, participate in all steps of RNA metabolism and post-transcriptionally regulate the expression of the gene (Table 1) [59][60][61][62][63][64][65][66][67][68][69][70][71][72][73][74][75][76][77][78][79][80][81][82][83].
Table 1. The m6A methylation modified various RNAs in ESCA.
m6A Regulator Target Type of Target RNA Function Molecular Mechanism Reference
METTL3 GLS2 mRNA Writer Increase m6A level of GLS2 mRNA, upregulate GLS2 expression [59]
METTL3 NOTCH1 mRNA Writer Increase m6A level of NOTCH1 mRNA, upregulate NOTCH1 expression [60]
METTL3 TNFR1 mRNA Writer Increase m6A level of TNFR1 mRNA, upregulate TNFR1 expression [61]
ALKBH5 CDKN1A mRNA Eraser Decrease m6A level of CDKN1A mRNA, decrease stability of CDKN1A mRNA, downregulate p21 expression [62]
FTO SIM2 mRNA Eraser Decrease m6A level of SIM2 mRNA, decrease stability of SIM2 mRNA, downregulate SIM2 expression [63]
IGF2BP2 CTNNB1 mRNA Reader Increase stability of CTNNB1 mRNA, upregulate CTNNB1 expression [64]
IGF2BP2 FOXP4 mRNA Reader Increase stability of FOXP4 mRNA, upregulate FOXP4 expression [65]
IGF2BP2 TK1 mRNA Reader Recognize m6A of TK1 mRNA, upregulate TK1 expression [66]
IGF2BP2 KIF18A mRNA Reader Increase stability of KIF18A mRNA, upregulate expression of KIF18A [67]
HNRNPC ZEB1 and ZEB2 mRNA Reader Increase stability of ZEB1 and ZEB2 mRNA, upregulate expression of ZEB1 and ZEB2 [68]
METTL3, METTL14, and YTHDF2 APC mRNA METTL3 and METTL14 as writer; YTHDF2 as reader METTL3 increases m6A level of APC mRNA in an METTL14-dependent way; YTHDF2 promotes degradation of APC mRNA [69]
IGF2BP2 and IGF2BP3 HTR3A mRNA Reader Increase stability of HTR3A mRNA, upregulate HTR3A expression [70]
METTL3 and YTHDF1 HK2 mRNA METTL3 as writer; YTHDF1 as reader Increase stability of HK2 mRNA, upregulate HK2 expression [71]
METTL3 and YTHDF3 EGR1 mRNA METTL3 as writer; YTHDF3 as reader Increase stability of EGR1 mRNA, upregulate EGR1 expression [72]
FTO and YTHDF1 ERBB2 mRNA FTO as eraser; YTHDF1 as reader Increase stability of ERBB2 mRNA, upregulate ERBB2 expression [73]
FTO and YTHDF1 HSD17B11 mRNA FTO as eraser; YTHDF1 as reader Decrease the translation efficiency of HSD17B11 mRNA, downregulate HSD17B11 expression [74]
METTL3 pri-miR-200-5p miRNA Writer Increase m6A level of pri-miR-200-5p, upregulate miR-200-5p expression [75]
METTL3 pri-miR-320b miRNA Writer Increase m6A level of pri-miR-320b, upregulate miR-320b expression [76]
METTL14 pri-miR-99a miRNA Writer Increase m6A level of pri-miR-99a, upregulate miR-99a-5p expression [77]
ALKBH5 pri-miR-194-2 miRNA Eraser Decrease m6A level of pri-miR-194-2, downregulate miR-194-2 expression [78]
HNRNPA2B1 miR-17-92 cluster miRNA Reader Bind to m6A of miR-17-92 cluster, upregulate expression of miR-17-92 cluster [79]
METTL3 and ALKBH5 pri-miR-193a-3p miRNA METTL3 as writer; ALKBH5 as eraser METTL3 increases m6A level of pri-miR-193a-3p, upregulates miR-193a-3p expression; ALKBH5 decreases m6A level of pri-miR-193a-3p, downregulates miR-193a-3p expression [80]
METTL3, METTL14, WTAP, ALKBH5, and YTHDF1 LINC00278 lncRNA METTL3, METTL14, and WTAP as writers; ALKBH5 as eraser; YTHDF1 as reader METTL3, METTL14, and WTAP increase m6A level of LINC00278; ALKBH5 decreases m6A level of LINC00278; YTHDF1 promotes translation of LINC00278 [81]
METTL3, RBM15, WTAP, and YTHDC2 MALAT1 lncRNA METTL3, RBM15, and WTAP as writer; YTHDC2 as reader RBM15 interacts with METTL3 in a WTAP-dependent way to deposit m6A onto MALAT1; YTHDC1 binds to m6A of MALAT1 and maintains composition of nuclear speckle [82]
FTO and YTHDF2 LINC00022 lncRNA FTO as eraser; YTHDF2 as reader FTO reduces the enrichment of m6A at site 2 of LINC00022 transcript; YTHDF2 promotes degradation of LINC00022 [83]

3.1. m6A Modification in ESCA

Most studies revealed that the m6A level was elevated in ESCC tissues and cell lines [73][84][85][86]. However, Cui et al. [83] found lower m6A levels in ESCC cell lines and tissues compared to their counterparts. Some studies indicated that the m6A level could act as a diagnostic and prognostic marker. In gastric cancer, the m6A level might be used to distinguish patients from healthy individuals and predict the prognosis of patients treated with immunotherapy [87][88]. In lung cancer, a higher m6A level in circulating tumor cells than in whole blood cells might be associated with tumor metastasis [89]. Inconsistent results of the m6A level in ESCC suggested that further large sample studies are needed to draw a reliable conclusion.

3.2. The Effect of m6A Modification on mRNA in ESCA

The fate of m6A-modified RNA relies on the m6A reader that binds to it. YTH family proteins, consisting of YTH m6A-binding protein 1 (YTHDF1), YTHDF2, YTHDF3, YTH domain-containing 1 (YTHDC1) and YTHDC2, contain a specific YTH domain, through which, they can recognize and bind to target RNA in an m6A-dependent way [90][91]. YTHDF1 promotes translation initiation and protein synthesis [10]. On the contrary, YTHDF2, the first discovered m6A reader, enhances the degradation of m6A-modified mRNA, either by delivering them to the mRNA decay site or recruiting the CCR4-NOT deadenylase complex to initiate mRNA degradation [9][92]. YTHDF3 interacts with YTHDF1 or YTHDF2, playing opposite roles by promoting mRNA translation or enhancing mRNA degradation [93][94]. YTHDC1 regulates the splicing of the exon and promotes the translocation of m6A-modified mRNA from the nucleus to the cytoplasm [95][96][97]. YTHDC2 elevates the translation efficiency of m6A-modified mRNA; accordingly, the abundance of target mRNA is reduced [98][99]. IGF2BPs, including IGF2BP1, IGF2BP2 and IGF2BP3, enhance mRNA stability [100]. HNRNPs contain HNRNPA2B1, HNRNPC and HNRNPG. HNRNPC and HNRNPG regulate the alternative splicing of mRNA in an m6A-dependent way [13][101]. EIF3 can act as reader of m6A in the 5′-UTR of mRNA [17]. EIF3 participates in almost all steps of translation initiation, which is a rate-limiting process. EIF3 promotes the formation of the 43S pre-initiation complex (PIC), bridges 43S PIC and mRNA bound to the EIF4F complex and takes part in the AUG start codon scanning process [102][103][104][105].
It is generally acknowledged that YTHDF1 plays a facilitating role in translation initiation and protein synthesis [10]. That was true in the study from Zhao et al. [73], which demonstrated that YTHDF1 upregulated the protein level of ERBB2 through recognizing m6A-modified ERBB2 mRNA. Conversely, the knockdown of YTHDF1 enhanced the protein level of HSD17B11, which suggested that YTHDF1 decreased the translation efficiency of m6A-modified HSD17B11 mRNA [74]. YTHDF2 promoted the degradation of APC mRNA and decreased APC expression via binding to m6A-modified APC mRNA [69]. IGF2BP2 enhanced the stability of m6A-modified TK1 and KIF18A mRNA and upregulated their expression [66]. In addition, m6A readers could regulate the stability and expression of their downstream mRNAs through interacting with lncRNA [63][64][65][68][70]. For example, LBX2-AS1 and HNRNPC synergized to increase the stability of ZEB1 and ZEB2 mRNA, upregulated their expression and consequently promoted the migration and epithelial mesenchymal transition (EMT) of ESCC cells [68].

3.3. The Effect of m6A Modification on Non-Coding RNAs in ESCA

Although without a coding ability, non-coding RNAs (ncRNAs), such as miRNA, lncRNA and circRNA, serve a critical role in regulating the expression of the gene.
The miRNAs bind to the 3′-UTR of the target mRNA, and then silence or inhibit the expression of corresponding genes. miRNA biogenesis includes the following steps: firstly, primary miRNA (pri-miRNA) is transcribed from DNA; secondly, pri-miRNA is cleaved into precursor miRNA (pre-miRNA), which requires a microprocessor complex composed of drosha ribonuclease III (DROSHA) and DiGeorge syndrome critical region 8 (DGCR8); thirdly, pre-miRNA is cleaved into mature miRNA. In ESCC, m6A writers and erasers deposit and remove m6A on pri-miRNA, respectively [75][77][78][79]. For instance, METTL3 elevates the m6A level of pri-miR-200-5p, whereas ALKBH5 reduces the m6A level of pri-miR-194-2 [75][78]. A previous study showed that HNRNPA2B1 played a crucial role in the maturation of miRNA through recognizing m6A on pri-miRNA and interacting with DROSHA and DDGCR8 [106]. In ESCC, HNRNPA2B1 promoted the proliferation of ESCC cells through binding to a m6A-modified miR-17-92 cluster and upregulating the expression of a miR-17-92 cluster [79].
m6A modification could also be found on lncRNAs, which might be involved in the regulation of gene expression via influencing the interaction of lncRNAs with RNA binding proteins through an “m6A switch” mechanism or impacting the interaction between lncRNAs and miRNAs [13][107]. In ESCC, the overexpression of FTO significantly reduced the enrichment of m6A at site 2 of the LINC00022 transcript and led to a decrease in the degradation of LINC00022 by YTHDF2 [83]. The study of Wu et al. [81] showed that lncRNA LINC00278 encoded a micropeptide named Yin Yang 1 (YY1)-binding micropeptide (YY1BM), and the binding of YTHDF1 to m6A-modified LINC00278 led to an increased translation of YY1BM. LncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is located at nuclear speckles (NSs). The MALAT1-m6A-enriched sequence and the binding of YTHDC1 to the m6A of MALAT1 were necessary for maintaining the composition of NSs and migratory capability of ESCC cells [82]. In addition, as mentioned above, lncRNA could interact with m6A readers to regulate the expression of target mRNAs [64][65][68][70].
circRNAs perform different biological functions based on their diverse distribution in cells. Nuclear circRNAs might affect transcription and splicing [108][109]. Cytoplasmic circRNAs might not only absorb miRNAs and alleviate their depression of the target mRNA [110][111] but also might interact with RNA binding proteins and enhance their functional impacts [112][113]. It is worth mentioning that the exon-derived circRNAs might have a protein-encoding ability [114][115]. m6A regulators regulated the expression, distribution and function of circRNAs through installing, removing and recognizing m6A on circRNAs in all sorts of cancers [112][113][116][117][118][119]. In gastric cancer and cervical cancer, METTL14 and ALKBH5 acted as a transmethylase of circORC5 and demethyltransferase of circCCDC134, respectively [116][117]. YTHDC1 facilitated m6A-modified circMET and circNSUN2 exportation from the nucleus to cytoplasm in NONO-TFE3 fusion renal cell carcinoma and colorectal carcinoma, respectively [112][113]. IGF2BP2 interacted with circNSUN2 to increase the stability of HMGA2 mRNA and promote the metastasis of colorectal carcinoma [113]. IGF2BP1 promoted the translation of m6A-modified circMAP3K4 into circMAP3K4-455aa via recognizing m6A modification on circMAP3K4 in hepatocellular carcinoma [118]. Interestingly, m6A modification on circALG1 enhanced its ability as competitive endogenous RNA (ceRNA) of miR-342-5p by increasing its binding to miR-342-5p in colorectal cancer [119]. It is a pity that no study has reported how m6A modification regulates the expression and function of circRNAs during the development and progression of ESCA until now, which provides a direction for future research in ESCA.

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Subjects: Oncology
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Yuekao Li
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Chaoxu Niu
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Na Wang
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Xi Huang
,
Shiru Cao
,
Saijin Cui
,
Tianyu Chen
,
Xiangran Huo
,
Rongmiao Zhou
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