Diverse molecular functions of m⁶A mRNA modification in cancer

Abstract

N⁶-methyladenosine (m⁶A), the most prevalent chemical modification found on eukaryotic mRNA, is associated with almost all stages of mRNA metabolism and influences various human diseases. Recent research has implicated the aberrant regulation of m⁶A mRNA modification in many human cancers. An increasing number of studies have revealed that dysregulation of m⁶A-containing gene expression via the abnormal expression of m⁶A methyltransferases, demethylases, or reader proteins is closely associated with tumorigenicity. Notably, the molecular functions and cellular consequences of m⁶A mRNA modification often show opposite results depending on the degree of m⁶A modification in specific mRNA. In this review, we highlight the current progress on the underlying mechanisms of m⁶A modification in mRNA metabolism, particularly the functions of m⁶A writers, erasers, and readers in the context of tumorigenesis.

Cancer: monitoring messenger RNA modifications

A thorough investigation into the role and function of RNA modifications in cancers could yield novel therapies. The chemical modification of messenger RNA (mRNA), the molecule that carries code from DNA to synthesize proteins, is thought to play a role in influencing genetically inherited traits and diseases. A common modification found in mRNA is N⁶-methyladenosine (m⁶A). Disruption to the regulation of m⁶A modification has been linked with human cancers. Junho Choe and Seung Hun Han at Hanyang University in Seoul, South Korea, reviewed current understanding of the molecular mechanisms behind m⁶A modification, with particular reference to tumor formation. The researchers point out that abnormal expression of proteins associated with m⁶A may lead to heightened expression of cancer-related genes. More extensive m⁶A modification levels are also linked to tumor formation.

Introduction

Since the discovery of the DNA double-helix structure in the 1950s, how genetic information is controlled and inherited has been a fundamental question. The discovery that alteration of the chromatin structure and DNA modifications affect heritable phenotypes in addition to the DNA sequence itself opened up a new field of epigenetics¹. Similarly, many recent studies have proposed various chemical modifications of RNA as another layer of post-transcriptional gene expression regulation termed “epitranscriptomics”^2–4. Post-transcriptional regulation is critical for the control of gene expression programs that dictate a variety of cellular functions and cell fate decisions. To date, at least 160 different chemical modifications have been identified in multiple RNA species, including messenger RNAs (mRNAs), transfer RNAs (tRNAs), ribosomal RNAs (rRNAs), noncoding RNAs (ncRNAs), and viral RNA genomes^4,5. Although the majority of these modifications map to noncoding RNAs, increasing evidence implicates multiple mRNA modifications as components of another layer of gene expression regulation^2,6.

Discovered in the 1970s, N6-methyladenosine (m⁶A) is the best-characterized RNA modification and particularly is involved in almost all stages of the mRNA life cycle, including splicing, export, translation, and stability^7–11. It is the most prevalent mRNA modification, with approximately one-fourth of the eukaryotic mRNAs harboring at least one m⁶A-modified base^3,12. The m⁶A modification is found in multiple organisms and associated with various cell functions, including meiosis in yeast^13,14, plant development¹⁵, mouse spermatogenesis¹⁶, mouse embryogenesis¹⁷, and various cancers^18–22.

In this review, we discuss the current understanding of m⁶A mRNA modification regulation at the molecular level and its various cellular effects. In particular, we highlight the emerging understanding of m⁶A mRNA modification in cancer.

Mechanism of dynamic m⁶A modification

The discovery of methyltransferases (also known as m⁶A writers) and demethylases (also known as m⁶A erasers) provided evidence that m⁶A modification is a dynamic and reversible event²³. In addition to the combined action of m⁶A writers and erasers on m⁶A modification regulation, m⁶A reader proteins contribute to the regulation of the fate of m⁶A-containing RNAs. The m⁶A modification is the methylation of the sixth position of nitrogen atom of adenosine, with the cellular methyltransferase substrate S‑adenosylmethionine serving as the methyl donor for m⁶A formation^24,25. Methyltransferase-like protein 3 (METTL3, also known as MT-A70) and METTL14 form a heterodimer at a ratio of 1:1, and they functions as a catalytic core complex recognizing the DRACH motif (D = A, G, or U; R = G or A; and H = A, C, or U) and inducing m⁶A modification of mRNA^12,24. Growing evidence has revealed that METTL3 plays a central role in introducing m⁶A onto nascent transcripts cotranscriptionally, while METTL14 supports binding of the METTL3 protein to the target mRNA (Fig. 1)^26,27. In addition, at least five other proteins are involved in the regulation of m⁶A mRNA modification, although it often shows a slightly different composition of the protein complex in each study. While they lack methyltransferase activity, they stabilize the METTL3/14 complex and facilitate its localization to the specific RNA sites for m⁶A modification^28,29. Wilms tumor 1-associated protein [WTAP, also known as female-lethal(2)d] recruits other proteins to the METTL3/14 complex, thereby affecting the overall levels of m⁶A modification³⁰. RNA-binding motif 15 (RBM15) protein and its paralog RBM15B have been shown to interact with METTL3 in a WTAP-dependent manner^28,31. It has been suggested that they preferentially bind to U-rich regions in RNA and recruit the METTL3/14-WTAP complex to sites proximal to the m⁶A consensus motifs³¹. Vir-like m⁶A methyltransferase associated protein (VIRMA, also known as Virilizer or KIAA1429) was recently found to mediate mRNA methylation near the stop codon in the 3′ untranslated region (UTR), where it plays a role in alternative polyadenylation³². In mouse embryonic stem cells (mESCs), Cbl proto-oncogene like 1 (CBLL1, also known as Hakai) protein and zinc finger CCCH-type containing 13 (ZC3H13) proteins have been shown to be required for the nuclear localization of ZC3H13-WTAP-VIRMA-CBLL1, which promotes m⁶A mRNA modification²⁹. In Drosophila, ZC3H13 has also been shown to act as an adapter protein between WTAP and RBM15 in the methyltransferase complex to support efficient methylation²⁸. On the other hand, methyltransferase-like protein 16 (METTL16) was recently found to be critical for m⁶A modification in several pre-mRNAs, U6 small nuclear RNAs (U6 snRNAs), and noncoding RNAs containing a specific stem-loop structure^33–35. Interestingly, METTL16 has been shown to control S-adenosylmethionine levels by regulating the expression of a S-adenosylmethionine synthetase methionine adenosyltransferase 2 A (MAT2A) by the enhanced splicing of a retained intron^33,34. When METTL16 is depleted, the level of m⁶A in a cell decreases by ~20%³³.

Fig. 1. An overview of cotranscriptional m⁶A mRNA modification.

Introduction of m⁶A modification is currently suggested to occur cotranscriptionally in the nucleus. Individually transcribing mRNAs illustrate the different modes of cotranscriptional m⁶A modification, including different compositions of associated DNA- and RNA-binding proteins with distinct methylation sites. The thick line represents the coding sequence, and the thin line represents the UTR. The dashed box indicates the heat shock condition.

To date, two mammalian m⁶A demethylating enzymes have been identified, namely, the fat mass and obesity-associated protein (FTO) and a-ketoglutarate-dependent dioxygenase alk B homolog 5 (ALKBH5) protein^36,37. FTO was the first identified m⁶A demethylase originally found to be associated with increased body mass and obesity in humans^36,38. Demethylation of m⁶A by FTO generates an intermediate product, N6-hydroxymethyladenosine (hm⁶A), which is then further oxidized to N6-formyladenosine (f⁶A)³⁹. However, the potential functions of these intermediate products remain unclear. While several studies have provided evidence that depletion of FTO increases the level of total m⁶A, another recent report suggested FTO preferentially demethylates 2′-O-dimethyladenosine (m⁶Am), which is found adjacent to the 7-methylguanosine (m⁷G) cap in mRNA, thereby influencing mRNA stability⁴⁰. Most recently, FTO was also shown to demethylate N1-methyladenosine (m¹A) in tRNAs⁴¹. ALKBH5, the second identified m⁶A demethylase, preferentially recognizes the m⁶A mark for demethylation in a consensus sequence-dependent manner; thus, it is considered as a better candidate for global m⁶A demethylation³⁷.

Molecular functions of m⁶A in mRNA metabolism

Gene expression is the result of orchestrated transcriptional and post-transcriptional regulation. Recently, an increasing number of studies have suggested m⁶A mRNA modification as a layer of gene expression regulation previously unrecognized. Various m⁶A reader proteins are involved in many processes of overall mRNA metabolism (Fig. 2).

Fig. 2. Molecular details for m⁶A-mediated mRNA metabolism.

Multiple m⁶A reader proteins dynamically regulate m⁶A-containing mRNA metabolism, including alternative splicing, mRNA export, structural switch, translation, and mRNA stability, depending on the specific m⁶A-bound reader protein. The thick line represents the coding sequence, and the thin line represents the UTR. The dashed box indicates the heat shock condition.

Cotranscriptional m⁶A modification

In general, m⁶A modifications of mRNAs are enriched near translation stop codons in the 3′ UTR^3,12,42. However, this characteristic varies among different mRNAs and depends on the tissue. There are several lines of evidence indicating that the m⁶A modification is a cotranscriptional event (Fig. 1)^18,26,27. One report showed that METTL3 binds to chromatin in a transcription-dependent manner and cotranscriptionally methylates nascent transcripts²⁶. In a case of acute myeloid leukemia (AML), METTL3 can be recruited to the promoter region independent of METTL14 by binding to CCAAT/enhancer-binding protein zeta (CEBPZ)¹⁸. METTL3 can induce m⁶A modification cotranscriptionally within the coding region of the associated transcripts, ultimately resulting in translation enhancement¹⁸. Moreover, it has been shown that cotranscriptional modification of m⁶A is dependent on the activity of RNA polymerase II (RNAP II)²⁷. A low rate of transcriptional activity induces increased levels of m⁶A modification throughout the gene body, resulting in reduced levels of translation²⁷. On the other hand, in the case of heat shock stress, METTL3 can be recruited with DGCR8 to the chromatin of heat shock responsive genes in the region of the transcription ending site, where it subsequently methylates nascent mRNAs, leading to the degradation of the target mRNAs as a consequence²⁶. Considering the accumulating evidence that the m⁶A modification is mainly found around the translation stop codon in mRNAs^3,12,42 and that VIRMA preferentially mediates mRNA methylation near the stop codon in the 3′ UTR³², further studies are required to clarify such discrepancies in the methylation mechanism. Moreover, despite consistent results showing that m⁶A modification is a cotranscriptional event, the molecular consequences of this modification vary among different studies. Therefore, further research is required to determine the regulating factors that lead to these discrepancies.

m⁶A promotes alternative splicing

Multiple model organism studies have shown that dynamic m⁶A modification alters mRNA splicing. In Drosophila, mutation of IME4 (a METTL3 homolog) influences sex determination by modulating female-specific splicing of the Sex-lethal (Sxl) gene^43,44. In addition, the Drosophila orthologs of VIRMA and/or ZC3H13 have been shown to regulate alternative splicing of pre-mRNAs involved in sex determination²⁸. m⁶A demethylases were also reported to be involved in splicing machinery^37,45,46. FTO regulates mouse pre-adipocyte differentiation by regulating the alternative splicing of the genes involved in adipogenesis⁴⁵. ALKBH5 regulates splicing by removing m⁶A from pre-mRNAs and allows the production of a subset of mRNAs containing relatively long 3′ UTRs in mouse germ cells^37,46. While m⁶A writers and erasers regulate alternative splicing by modulating the levels of m⁶A modification, m⁶A reader proteins directly regulate splicing^8,47. The m⁶A-bound YTHDC1 associating with splicing factor SRSF3 has been shown to block the binding of SRSF10 to m⁶A-modified RNA, promoting exon inclusion in the selected transcripts^8,48. Moreover, m⁶A modification influences mRNA structural changes, which allows heterogeneous nuclear ribonucleoprotein C (hnRNPC) and hnRNPG binding^9,47. While hnRNPC binds opposite strand U-rich sequences after the disruption of RNA base pairing by m⁶A modification⁹, hnRNPG preferentially binds to purine-rich motifs, including m⁶A sites⁴⁷. Binding of either hnRNPC or hnRNPG influences the alternative splicing of m⁶A-modified transcripts^9,47. Finally, METTL16 induces the m⁶A modification of U6 snRNA, which base pairs with 5′ splice sites of pre-mRNAs during splicing, suggesting that METTL16 plays an important role in mRNA splicing^34,35.

m⁶A facilitates mRNA export

mRNA export is also influenced by m⁶A modification. ALKBH5-deficient cells exhibit increased levels of cytoplasmic m⁶A-containing mRNA, suggesting that the m⁶A modification accelerates mRNA export³⁷. Another report showed that YTHDC1 facilitates the export of m⁶A-modified mRNAs via its interaction with nuclear RNA export factor 1 (NXF1)¹⁰.

m⁶A alters RNA structure

It has been well established that gene expression is largely affected by the secondary and tertiary structures of mRNA⁴⁹. Introduction of m⁶A modification promotes the destabilization of A/U pairings, resulting in alterations to the thermostability of RNA duplexes and changes in the RNA secondary structure⁵⁰. Another study demonstrated that RNA structural changes caused by the introduction of m⁶A also alter the interaction between RNAs and proteins^9,47.

m⁶A regulates translation efficiency

Many m⁶A reader proteins are reported to be crucial for the efficient translation of methylated mRNAs. Members of the YT521-B homology (YTH) domain-containing protein family have been identified as direct m⁶A readers, including YTHDF1, YTHDF2, YTHDF3, YTHDC1, and YTHDC2^7,11,51–56. Among these proteins, YTHDF1, YTHDF3, and YTHDC2 have been shown to promote target mRNA translation^11,51–53. YTHDF1 selectively binds to m⁶A sites near the stop codon and cooperates with translation initiation factors to promote the translation of the target mRNAs⁵¹. YTHDF3 cooperates with YTHDF1 in the regulation of translation by interacting with a common set of ribosomal proteins⁵². YTHDC2 has been suggested to play a role in enhanced translation levels while reducing target mRNA abundance⁵³. Furthermore, increased levels of YTHDF2 translocate to the nucleus under heat shock stress and bind m⁶A in the 5′ UTR of a subset of stress-induced mRNAs, protecting them from FTO-mediated demethylation and promoting their cap-independent translation⁵⁷. Eukaryotic translation initiation factor 3 (eIF3) is also considered an m⁶A-binding protein. mRNAs containing m⁶A modification in the 5′ UTR can be recognized by direct binding of eIF3 to the methylated region, which in turn recruits the 43 S complex to initiate translation in a cap-independent manner in the absence of the cap-binding protein eIF4E⁵⁸. However, the mechanism of eIF3 in the recognition of m⁶A is not yet clearly understood. Interestingly, most recent studies have suggested that the m⁶A writer protein METTL3 also functions as a reader protein in the cytoplasm, promoting the translation of a large subset of target mRNAs^21,22. These studies revealed that 3′ UTR m⁶A modification near the stop codon significantly increases translation through mRNA looping, governed by the interaction between METTL3 at the 3′ UTR and the translation initiation factor eIF3 subunit h (eIF3h) at the 5′ end^21,22.

m⁶A regulates mRNA stability

An increasing number of studies have demonstrated that m⁶A modification influences mRNA stability. Various structural and functional studies suggest that all three YTHDF reader proteins (YTHDF1, YTHDF2, and YTHDF3) may share the same subset of target mRNAs^51,52. However, accumulating evidence suggests that YTHDF2 is the major factor involved in the degradation of m⁶A-containing mRNA either through exoribonucleolytic decay or the endoribonucleolytic cleavage pathway^55,56. YTHDF2 has been shown to selectively recognize m⁶A sites and recruit the CCR4-NOT deadenylase complex directly, which in turn recruits exosomes (3′-to-5′ exoribonuclease) to initiate mRNA decay⁵⁶. Other recent studies revealed that YTHDF2 promotes the translocation of m⁶A-containing mRNA from the translation machinery to processing bodies (P bodies), where cellular proteins participating in mRNA degradation are enriched^7,59. In addition, a very recent study revealed the YTHDF2-mediated endoribonucleolytic cleavage of m⁶A-containing mRNAs⁵⁵. Mechanistically, heat-responsive protein 12 (HRSP12, also known as reactive intermediate imine deaminase A homolog, UK114 antigen homolog, and 14.5 kDa translational inhibitor protein) bridges m⁶A-bound YTHDF2 to an endoribonuclease, RNase P/MRP, triggering the endoribonucleolytic cleavage of an m⁶A-containing mRNA⁵⁵. Another study suggested that YTHDC2 recruits the 5′ to 3′ exoribonuclease XRN1 for subsequent m⁶A-containing mRNA degradation⁵⁴. In addition to the YTH proteins, a variety of other RNA-binding proteins are involved in the regulation of m⁶A-containing mRNA stability. Fragile X mental retardation protein (FMRP) can bind to the sequence motifs YGGA (Y = C or U) and GAC, which likely overlap with the DRACH motif involved in m⁶A modification, resulting in stabilization of the m⁶A-containing mRNA through the competition of FMRP with YTHDF2⁶⁰. In another case, stress granule protein (G3BP1) has binding affinity for m⁶A-methylated transcripts, promoting their demethylation and resulting in stabilization of the target mRNAs⁶¹. Insulin-like growth factor 2 mRNA-binding protein (IGF2BP) 1, 2, and 3 or human antigen R (HuR, also known as ELAVL1) have also been reported to stabilize m⁶A-containing mRNAs^62,63.

Molecular functions of m⁶A in various cancers

Interest in m⁶A modification has been extended to many human diseases as well as to its molecular function. In particular, an increasing number of studies are examining the role of m⁶A-mediated gene expression regulation in cancers. In general, many different signaling pathways converge onto translation machinery to satisfy the increased anabolic demands of cancers. Given the crucial function of m⁶A modification in regulating mRNA metabolism, it is reasonable to speculate that m⁶A modification plays an important role in human carcinogenesis. Nonetheless, the molecular details of how m⁶A modification affects the cellular phenotype of cancer are still being investigated. The physiological effects of m⁶A mRNA modification in cancer often lead to opposite results (Table 1); thus, further understanding of a balanced m⁶A modification is required for the treatment of cancer. Here, we highlight recent insights into the biological functions of m⁶A mRNA modification and the underlying molecular mechanisms of m⁶A regulatory proteins in various cancers (Fig. 3 and Table 1).

Table 1.

Cellular effects of m⁶A mRNA modification in cancer.

	Positive regulation of m6A in cancer			Negative regulation of m6A in cancer
	Molecular function	Target	Reference	Molecular function	Target	Reference
Lung cancer	Translation	A subset of mRNAs	21,22	mRNA level change	A subset of mRNAs	68
		EGFR, TAZ, MAPKAPK2, DNMT3A mRNA	67
	Protein level change	BAX, BCL-2	66	mRNA stabilization	MZF1 mRNA	69
Acute myeloid leukemia	Translation	A subset of mRNAs	18	mRNA stabilization	ASB2, RARA mRNA	19
		MYC, BCL2, PTEN mRNA	71
	Translation	MYB, MYC mRNA	73	mRNA decay	A subset of mRNAs	72
	mRNA stabilization		73
Hepatocellular carcinoma	mRNA level change	SOCS2 mRNA	75	NR	NR
	mRNA decay	EGFR mRNA	76
	mRNA level change	SON, SREBBP mRNA	77
Breast cancer	mRNA level change	HBXIP mRNA	79	mRNA level change	NANOG, KFL4 mRNA	80,81
Gastric cancer	mRNA stabilization	SEC62 mRNA	83	Unknown	Unknown	85,86
		HDGF mRNA	84
Bladder cancer	mRNA level change	AFF4, MYC mRNA	20	NR	NR
	Protein level change	AFF4, MYC, IKBKB, RELA	20
	Translation	ITGA6 mRNA	87
Glioblastoma	mRNA stabilization	SOX2 mRNA	92	mRNA level change	Nascent FOXM1 transcript	89
				mRNA level change	A subset of mRNAs	91
Colorectal cancer	mRNA stabilization	SOX2 mRNA	93	NR	NR
Renal cell carcinoma	NR	NR		Unknown	Unknown	95
Endometerial Cancer	NR	NR		Translation	PHLPP2 mRNA	96
				mRNA decay	PRR5, PRR5L, mTOR mRNA	96
Cervical cancer	NR	NR		Unknown	Unknown	97
Pancreatic cancer	NR	NR		Protein level change	YAP	98

Some studies did not identify molecular mechanisms or targets, but only measured m⁶A levels and their effects on cancer, which are marked as “unknown”. “Translation” indicates the m⁶A-mediated translation enhancement. “Protein level change” and “mRNA level change” indicate their steady-state levels without specifying the translation efficiency or mRNA stability.

NR not reported.

Fig. 3. m⁶A-mediated mRNA regulation in tumorigenesis.

A number of studies have identified the molecular mechanism of m⁶A-mediated mRNA regulation and their effects on tumorigenesis. To date, m⁶A-mediated regulation of translation or mRNA stability has been demonstrated, while the relevance of pre-mRNA splicing or mRNA export remains unclear for specific cancer types.

Lung cancer

Lung cancer causes the greatest number of cancer-related deaths worldwide. There are two main histological types of lung cancer: small-cell lung cancer and non-small-cell lung cancer (NSCLC). Approximately 85% are classified as NSCLC, which statistically shows just a 15.9% 5-year survival rate^64,65. Nevertheless, therapeutic efforts have improved only slightly over the last few decades. Therefore, it is urgent to explore new treatments and deepen our understanding of the underlying mechanisms of lung cancer occurrence and development. The relevance of m⁶A modification in lung cancer has been extensively studied, and several lines of evidence show that METTL3 is highly expressed in NSCLC cells and is associated with cell proliferation, invasion, and viability^{21,22,66–68}. Two recent studies from the same group revealed intriguing effects of METTL3 in lung cancer progression. These studies showed that cytoplasm-localized METTL3 functions as an m⁶A reader protein that enhances translation of a large subset of oncogenic mRNAs without affecting mRNA abundance^21,22. Mechanistically, the 3′ UTR near the stop codon-bound METTL3 directly interacts with eIF3h. This interaction mediates mRNA looping to facilitate the recycling of ribosomes at the termination codon in a similar way to canonical eukaryotic mRNA looping mediated by the interactions between eIF4E (a cap-binding protein), eIF4G (a translation initiation factor), and PABP (a poly(A)-binding protein)^21,22. Indeed, ectopic expression of METTL3, but not a mutant that fails to interact with eIF3h, promotes cell proliferation, invasion, and oncogenic transformation²¹. Other studies have shown that METTL3 mRNA can be targeted by microRNAs (miRNAs)^66,67. Exogenously expressed miR-600 targets the 3′ UTR of METTL3 mRNA, resulting in the inhibition of METTL3 expression⁶⁶. Depletion of METTL3 inhibits the survival and proliferation of A549 and H1299 cells and leads to increased levels of the pro-apoptotic regulator BAX and decreased levels of the anti-apoptotic regulator BCL-2, suggesting that the altered expression ratio of BAX/BCL-2 triggers the mitochondrial apoptotic pathway⁶⁶. In addition, knocking down METTL3 decreases the phosphorylation of AKT, thus affecting cell growth and apoptosis via the alteration of the PI3K/AKT/mTOR pathway⁶⁶. Another miRNA, miR-33a, has also been shown to reduce METTL3 expression and, as a result, inhibits NSCLC cell proliferation⁶⁷. On the other hand, METTL3 is SUMOylated by small ubiquitin-related modifier 1 (SUMO1), which modifies METTL3 at lysine residues and represses its methyltransferase activity without altering its stability, localization, or interaction with two other writer proteins, METTL14 and WTAP⁶⁸. The SUMOylation of METTL3 reduces m⁶A levels and subsequently changes the mRNA expression profiles, ultimately promoting the development of NSCLC⁶⁸. Besides, the m⁶A demethylase FTO has also been shown to play a critical role in lung squamous cell carcinoma (LUSC), one of the most common NSCLCs. FTO knockdown effectively inhibits cell proliferation and invasion while promoting apoptosis of L78 and NCI-H520 cells⁶⁹. In contrast, overexpression of FTO, but not its mutant form, facilitates the acquisition of malignant phenotypes⁶⁹. Mechanistically, FTO increases the stability of myeloid zinc finger 1 (MZF1) mRNA by reducing its m⁶A level, leading to high levels of protein expression, which has an oncogenic function⁶⁹. MZF1 is a member of the SCAN-zinc finger transcription factor family, which contributes to cell proliferation, migration, and metastasis through the regulation of diverse target genes.

Acute myeloid leukemia (AML)

AML is one of the most prevalent hematopoietic malignancies. It is often derived from genetic mutations and aberrant regulation of epigenetic modification, including DNA methylation and histone modification⁷⁰. Recently, many studies have pointed to m⁶A mRNA modification as a new role for a gene expression regulator associated with AML^18,19,71,72. As previously described, promoter-bound METTL3 induces m⁶A modification within coding regions of a subset of nascent transcripts independent of METTL14¹⁸. In this way, the genes necessary for AML growth enhance their translation efficiency by relieving ribosome stalling at the GAN (GAG, GAT, GAC, and GAA) codons during translation elongation¹⁸. Another study revealed that increased expression levels of METTL3 promote the translation of MYC proto-oncogene (c-MYC), B-cell lymphoma 2 (BCL2), and phosphatase and tensin homolog (PTEN) mRNAs by increasing the levels of m⁶A modification, thereby altering phosphoinositide 3-kinase (PI3K) and protein kinase B (PKB, also known as AKT) signaling, an intracellular signaling pathway important in regulating the cell cycle, to control cell differentiation and self-renewal⁷¹. METTL14 was also shown to function in a similar way by promoting translation of its target mRNAs, the proto-oncogenes MYB and MYC, through m⁶A modifications, which in turn leads to block the myeloid differentiation⁷³. Notably, in addition to m⁶A writers, differentially expressed eraser or reader proteins seem to contribute to various AML subtypes through the modulation of m⁶A modification in a target mRNA-specific manner. Elevated expression of FTO enhances cell transformation and leukemogenesis by downregulating both the mRNA and protein expression of targets, such as ASB2 and RARA mRNAs, by reducing the m⁶A levels in their UTRs¹⁹. On the other hand, YTHDF2 overexpression plays a crucial role in disease initiation and propagation in human and mouse AML by destabilizing a subset of mRNAs, including tumor necrosis factor receptor TNFRSF2 mRNA⁷².

Hepatocellular carcinoma (HCC)

HCC is a major type of primary liver cancer and is a highly progressive malignant tumor associated with a low survival rate⁷⁴. It was recently reported that METTL3 levels are increased in human HCC, leading to increased m⁶A modification of the tumor suppressor SOCS2 mRNA⁷⁵. Increased levels of m⁶A in SOCS2 mRNA can be targeted by YTHDF2, leading to its rapid degradation, which is associated with the efficient proliferation of HCC cells⁷⁵. Besides, overexpression of YTHDF2 has been shown to suppress cell proliferation and tumor growth in HCC cells⁷⁶. Mechanistically, the m⁶A-modified 3′ UTR of epidermal growth factor receptor (EGFR) mRNA is recognized by YTHDF2 and undergoes degradation, which in turn impairs mitogen-activated protein kinase kinase (MEK) and extracellular signal-regulated kinases (ERK)⁷⁶. Similarly, another report showed that YTHDF2 mRNA can be targeted by miR145, leading to an increase in overall m⁶A levels in HCC cells, which is associated with HCC malignancy⁷⁷.

Breast cancer (BrC)

Of all malignant tumors in women, BrC is highly metastatic and has the highest cancer-related mortality⁷⁸. One interesting report suggested a potential positive feedback loop between mammalian hepatitis B X-interacting protein (HBXIP) and METTL3⁷⁹. High expression levels of HBXIP elevate METTL3 expression through the suppression of let-7g, and increased METTL3 upregulates HBXIP expression through m⁶A modifications of mRNA. This positive feedback loop leads to the acceleration of cell proliferation in BrC. On the other hand, a decrease in m⁶A modification also promotes BrC tumorigenesis. In BrC stem cells, hypoxic stress induces overexpression of ALKBH5 and/or ZNF217, leading to inhibition of the methylation of pluripotency markers NANOG and KLF4 mRNAs^80,81. Increasing the expression of NANOG and KLF4 mRNA by inhibiting m⁶A modification promotes the specification of BrC stem cells^80,81. Another report also showed that m⁶A levels increased by METTL14 overexpression or ALKBH5 knockdown inhibited BrC growth and metastasis⁸².

Gastric cancer (GC)

GC is a prevalent tumor occurring in the digestive system. One clear mechanism showed that the preprotein translocation factor SEC62 mRNA can undergo m⁶A modification by METTL3⁸³. In turn, IGF2BP1 recognizes m⁶A and facilitates the stabilization of SEC62 mRNA. Moreover, miR4429 has been suggested to target METTL3 and prevent the m⁶A modification of SEC62 mRNA, thus destabilizing SEC62 mRNA⁸³. Downregulated SEC62 inhibits GC cell proliferation and promotes apoptosis⁸³. Another report showed that METTL3 transcription is elevated in GC by a histone acetyltransferase, P300, which mediates H3K27 acetylation at the METTL3 promoter region, which in turn induces the methylation of hepatoma-derived growth factor (HDGF) mRNA⁸⁴. The methylated HDGF mRNA is then recognized and stabilized by IGF2BP3. Overexpressed HDGF protein can be secreted and promotes tumor angiogenesis, while nuclear HDGF stimulates the expression of glucose transporter type 4 (GLUT-4) and enolase 2 (ENO2) mRNAs, resulting in increased levels of glycolysis and subsequently causing tumor growth and liver metastasis⁸⁴. On the other hand, it has been suggested that FTO and ALKBH1 play crucial roles in GC progression and metastasis, although the relevance of m⁶A in these processes is unclear⁸⁵. It has been shown statistically that lower ALKBH1 protein expression correlates with larger tumor size, while lower FTO protein expression is associated with shorter overall survival in patients with GC⁸⁵. Another report revealed that the downregulation of m⁶A modification by METTL14 knockdown leads to the acquisition of oncogenic phenotypes through the alteration of Wnt and PI3K-AKT signaling pathways, although the exact upstream regulatory mechanism is unclear⁸⁶.

Bladder cancer (BlC)

BlC is the most prevalent urogenital cancer. Recent studies suggest that increased levels of m⁶A modification are correlated with BlC^20,87. One study identified the mRNAs of AF4/FMR2 family member 4 (AFF4), two key regulators of the NF-κB pathway (IKBKB and RELA), and MYC as direct METTL3 targets for m⁶A modification²⁰. METTL3 depletion led to a reduction in AFF4 and MYC mRNA and protein expression, while only the protein expression was reduced for IKBKB and RELA. METTL3 downregulation in BlC drastically reduced cell proliferation, invasion, and survival in vitro and tumorigenicity in vivo²⁰. Considering the results indicating that (1) MYC is a well-known oncogene that triggers the expression of target genes to benefit cell proliferation, cell survival, and stemness maintenance and (2) AFF4 and NF-κB are known to regulate MYC expression, through which NF-κB signaling enhances the proliferation and survival of cancer cells during the development and recurrence of BlC, it can be speculated that m⁶A modification by METTL3 affects the AFF4/NF-κB/MYC signaling network to regulate BlC progression²⁰. In addition, upregulated METTL3 promotes the translation of integrin alpha-6 (ITGA6) mRNA via the recognition of m⁶A in the 3′ UTR by the m⁶A reader proteins YTHDF1 and YTHDF3⁸⁷. As a result, the upregulated ITGA6 protein promotes BlC cell adhesion, migration, and invasion, similar to multiple other types of cancer, in which ITGA6 overexpression promotes tumorigenesis and metastasis⁸⁷.

Glioblastoma (GBM)

GBM is a primary malignant brain tumor prevalent in adults⁸⁸. GBMs have heterogeneous characteristics and contain cells with stem-like properties⁸⁹. These self-renewing GBM stem-like cells (GSCs) contribute to tumor initiation and therapeutic resistance⁹⁰. Intriguingly, the expression levels of both METTL3 and ALKBH5 are elevated in GSCs, with opposite results on m⁶A-mediated tumor formation in a target-specific manner^89,91,92. High METTL3 expression levels exhibit oncogenic function through efficient m⁶A modification in the 3′ UTR of sex-determining region Y (SRY)-box 2 (SOX2) mRNA, which is stabilized by binding of HuR⁹². Silencing METTL3 expression reduces SOX2 expression and, as a result, inhibits GBM tumor growth and prolongs the survival of mice⁹². In contrast, ALKBH5 is highly expressed in GSCs and demethylates FOXM1 nascent transcripts, leading to FOXM1 overexpression, stem-like cell proliferation, and tumorigenesis⁸⁹. The elevated levels of the transcription factor FOXM1 play critical roles in regulating GSC proliferation, self-renewal, and tumorigenicity⁸⁹. Similarly, another study suggested a tumor-suppressive function for the m⁶A modification in GSCs⁹¹. Reduction of m⁶A modification by the depletion of METTL3 or METTL14 or the chemical inhibition of FTO upregulates the mRNA expression of critical oncogenes such as ADAM19, EPHA3, and KLF4 and downregulates the mRNA expression of many tumor suppressors, including CDKN2A, BRCA2, and TP53I11 mRNAs, resulting in overall enhanced GBM stem cell growth, self-renewal, and tumorigenesis⁹¹.

Colorectal cancer (CrC)

In CrC, METTL3 and YTHDF1 expression is significantly upregulated^93,94. High levels of METTL3 expression have been shown to significantly upregulate m⁶A methylation in the coding sequences of SOX2 mRNA, a well-known CrC marker that is involved in maintaining the properties of tumor-initiating cells⁹³. Methylated SOX2 mRNA is subsequently recognized by IGF2BP2, preventing mRNA degradation. Indeed, knocking down METTL3 reduces the SOX2 expression level, inhibiting CrC development and metastasis⁹³. On the other hand, c-MYC has been suggested to promote YTHDF1 transcription⁹⁴. A statistical analysis suggests that patients with high YTHDF1 expression have significantly poorer overall survival⁹⁴. Moreover, knocking down YTHDF1 results in the inhibition of cell proliferation and sensitization of cells to anticancer drugs such as fluorouracil and oxaliplatin⁹⁴.

Other cancers

Similar to the cancers discussed above, modulation of m⁶A modification plays a critical role in renal cell carcinoma, endometrial cancer, and cervical cancer^95–97. In renal cell carcinoma, depletion of METTL3 promotes cell proliferation, cell invasion, and migration, and induces G0/G1 arrest⁹⁵. Conversely, upregulation of METTL3 results in significant suppression of tumor growth⁹⁵. Moreover, knocking down METTL3 promotes the acquisition of an epithelial phenotype and represses the manifestation of a mesenchymal phenotype, while overexpression of METTL3 reverses epithelial–mesenchymal transition progression⁹⁵. Furthermore, the observation that increased phosphorylation levels of PI3K/AKT/mTOR due to METTL3 knockdown suggests that these METTL3-mediated pathways may also be involved in renal cell carcinoma progression⁹⁵. A report revealed that METTL14 is frequently mutated and METTL3 expression is significantly reduced in endometrial cancer⁹⁶. Mechanistically, m⁶A mRNA modification affects the YTHDF1-dependent translation enhancement of the negative AKT regulator PHLPP2 and YTHDF2-dependent destabilization of the mRNAs of positive AKT regulators PRR5, PRR5L, and mTOR. Thus, either METTL14 mutation or decreased METTL3 expression leads to m⁶A reduction in these target mRNAs and, as a result, promotes cell proliferation and tumorigenicity of endometrial cancer through AKT activation⁹⁶. In cervical cancer, downregulation of m⁶A modification enhances cell proliferation, while upregulation inhibits tumor development⁹⁷. However, the exact mechanism remains unknown. Last, YTHDF2 is upregulated in pancreatic cancer and has two roles in cancer development: 1) YTHDF2 promotes cell proliferation, since it was observed that knocking down YTHDF2 results in the activation of the AKT/GSK3β/Cyclin D1 pathway, leading to G1 arrest, and 2) the YTHDF2-mediated decay of yes-associated protein (YAP) may influence the epithelial–mesenchymal transition, since overexpression of YAP results in decreased expression of epithelial markers and increases in mesenchymal markers⁹⁸.

Concluding remarks and future perspectives

Considering the increasing number of studies revealing that m⁶A modification plays a critical role in almost all stages of mRNA metabolism^10,48,56,62, we can easily speculate that aberrant regulation of these modifications affects many cellular phenotypes. Nevertheless, the molecular mechanisms and cellular effects of m⁶A mRNA modifications are not yet fully understood, since they do not always function in the same way. For instance, although it is well known that the m⁶A modification sites in mRNAs are mainly enriched in the 3′ UTR near the stop codon^3,12,42, several recent findings showed that cotranscriptional methylation occurs in coding sequences (Fig. 1)^18,27. In addition, it is still unclear why some mRNAs are not methylated. Considering that the m⁶A modification is reversible, the demethylases FTO and/or ALKBH5 may play critical roles in balancing the methylation of specific mRNAs in a cell type-dependent manner.

In recent years, m⁶A modification studies in various cancers have been conducted. Remarkably, an increasing number of studies have revealed that altered expression levels of m⁶A methyltransferases, demethylases, and reader proteins aberrantly regulate m⁶A modification on target mRNAs, resulting in abnormal expression of cancer-associated genes. In particular, increased methyltransferase expression levels were detected in most cancers, suggesting that higher m⁶A modification levels are closely related to tumorigenesis. However, the molecular functions and cellular consequences of m⁶A modification differed in each study, depending on the degree of methylation in the specific target mRNAs (Table 1). For instance, increased levels of m⁶A modification by higher levels of METTL3 or METTL14 expression promoted the translation or stabilization of c-MYC, BCL2, PTEN, or MYB mRNAs in AML^71,73. In contrast, FTO also showed an elevated level of expression, which downregulated both the translation and abundance of ASB2 and RARA mRNAs through demethylation¹⁹. Taken together, the coordinated functions of methylation and demethylation of specific targets seem to be critical for tumorigenesis.

Interest in m⁶A modification resurged quite recently. To date, most of the m⁶A studies in cancer have been demonstrated based on the discovery of the m⁶A modification itself rather than the underlying mechanisms with reader proteins (Fig. 3 and Table 1) because efforts to define the molecular mechanism and the biological relevance have been carried out in parallel. To date, only a single m⁶A reader-dependent molecular mechanism has been demonstrated in most cancer types (Fig. 3). In addition, cancer-related studies on other outcomes of m⁶A-dependent mRNA regulation, such as pre-mRNA splicing or mRNA export, remain insufficient. Considering that multiple reader proteins recognize m⁶A, it might be possible to crosstalk between readers on a single or a multiple m⁶A modification in an mRNA for the tight gene expression regulation. Therefore, to develop novel tumor therapies based on the regulation of m⁶A modifications, more thorough mechanistic and functional studies are required for each cancer type.

Conflict of interest

The authors declare that they have no conflict of interest.