Switching from messenger RNAs to noncoding RNAs, METTL3 is a novel colorectal cancer diagnosis and treatment target

Abstract

N6-methyladenosine (m6A) modification, one of the most prevalent RNA epigenetic modifications in eukaryotes, constitutes over 60% of all RNA methylation modifications. This dynamic modification regulates RNA processing, maturation, nucleocytoplasmic transport, translation efficiency, phase separation, and stability, thereby linking its dysregulation to diverse physiological and pathological processes. METTL3, a core catalytic component of the methyltransferase complex responsible for m6A deposition, is frequently dysregulated in diseases, including colorectal cancer (CRC). Although METTL3’s involvement in CRC pathogenesis has been documented, its precise molecular mechanisms and functional roles remain incompletely understood. METTL3 mediates CRC progression-encompassing proliferation, invasion, drug resistance, and metabolic reprogramming-through m6A-dependent modulation of both coding RNAs and noncoding RNAs. Its regulatory effects are primarily attributed to interactions with key signaling pathways at multiple stages of CRC development. Emerging evidence highlights METTL3 as a promising biomarker for CRC diagnosis and prognosis, as well as a potential therapeutic target. By synthesizing recent advances in METTL3 research within CRC, this review provides critical insights into novel strategies for clinical diagnosis and targeted therapy.

Key Words: METTL3; N6-methyladenosine; Epigenetics; Biomarker; Targeted treatment; Colorectal cancer

Core Tip: METTL3 is a member of methyltransferase involved in N6-methyladenosine (m6A) generation, and its aberrant expression is usually associated with the occurrence and development of various diseases. Although METTL3 has been studied in the molecular pathological mechanisms of colorectal cancer (CRC), its function and regulatory mechanism in this disease are still unclear. Via m6A modification of both messenger RNAs and noncoding RNAs, METTL3 participates in CRC proliferation, invasion, drug resistance, and metabolism. Its molecular mechanisms are emphasized in regulating diverse signaling pathways during various CRC stages. As a potential biomarker or target in CRC, its clinical application in diagnosis, prognosis, and treatment is also highlighted. By reviewing the latest research progress of METTL3 in CRC, this article provides new insights into the theoretical investigation of clinical diagnosis and targeted treatment for this disease.

INTRODUCTION

Colorectal cancer (CRC) remains the leading cause of cancer-related deaths globally, posing a significant threat to public health. Data from the International Agency for Research on Cancer reveal that CRC ranked third in tumor incidence and second in mortality worldwide in 2020[1]. Its development is strongly associated with aging, poor dietary habits (e.g., high red meat consumption)[2], obesity[3], sedentary lifestyles, and predominantly affects individuals over 40 years of age[4]. Early-stage CRC often progresses asymptomatically, contributing to delayed diagnosis[5]. Current standard therapies include surgical resection combined with chemoradiotherapy[6]. The aggressive biological behavior of CRC, characterized by invasion and metastasis, drives poor prognosis, with the liver and lungs being common metastatic sites[7]. Advances in radiotherapy, chemotherapy, immunotherapy, and targeted therapies have improved patient survival rates[8,9]. Despite progress in understanding CRC pathogenesis, diagnostic techniques, and therapeutic strategies, mortality rates remain alarmingly high, underscoring the need for novel interventions[10].

The progression of CRC is driven by well-characterized genetic and epigenetic alterations, which accumulate throughout disease development[11]. Three primary molecular mechanisms underlie this process: (1) Chromosomal instability (CIN): Characterized by large-scale chromosomal abnormalities, including copy number variations and loss of heterozygosity, leading to tumor heterogeneity and aggressive phenotypes; (2) Microsatellite instability (MSI): Caused by defects in DNA mismatch repair genes (e.g., MLH1, MSH2), resulting in hypermutation and increased immunogenicity; and (3) Serrated tumor pathways: Associated with BRAF V600E mutations and CpG island methylator phenotypes, promoting tumorigenesis through mitogen-activated protein kinase (MAPK) pathway activation[11,12]. These mechanisms collectively shape CRC’s molecular heterogeneity, influencing prognosis and therapeutic strategies. The CIN pathway may involve both mutations in tumor suppressor genes (APC and TP53) and activating mutations in oncogenes such as KRAS and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA)[13]. The main gain-of-function mutation in PIK3CA activates protein kinase B (AKT) signaling through mammalian target of rapamycin (MTOR), thereby promoting cell proliferation[14,15]. Loss of APC activity leads to nuclear translocation of β-catenin and activation of the Wnt signaling pathway[16]. Activation of KRAS triggers the Rapidly accelerated fibrosarcoma (Raf)-mitogen-activated protein kinase (MEK)/extracellular regulated protein kinases (ERK) pathway, phosphatidylinositol 3-kinase (PI3K) signaling via MTOR, and activation of the transcription factor nuclear factor kappa-B[17,18]. MSI mutations include alterations in transforming growth factor-β receptor-2 (TGFBR2), a gene encoding a protein that inhibits colonic epithelial cell proliferation. TGFBR2 is mutated in over 90% of MSI colorectal tumors[19]. Other genes disrupted by MSI include those encoding proteins that regulate proliferation, cell cycle arrest, apoptosis, and DNA repair processes[20,21]. Serrated polyps are a diverse group characterized by stellate crypt folding patterns; they encompass benign hyperplastic polyps along with precancerous sessile serrated adenomas or polyps and traditional serrated adenomas[22].

Epigenetic modification refers to heritable genetic material that occurs without nucleic acid sequence alterations, leading to stable phenotypic alterations[23]. Over 170 types of epigenetic modifications have been identified across histones, DNA, and RNA, with N6-methyladenosine (m6A) being the most prevalent internal modification in eukaryotic messenger RNA (mRNA)[24,25]. Recent studies demonstrate that m6A also regulates noncoding RNAs (ncRNAs) endogenous RNA molecules that lack protein-coding potential[26]. These ncRNAs play critical roles in human diseases, including cancer, and are emerging as promising biomarkers and therapeutic targets[27]. Mechanistically, m6A modulates RNA metabolism by influencing ncRNA stability, transport, and degradation processes, particularly in microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs)[28]. Additionally, m6A-modified ncRNAs can reciprocally regulate the expression of m6A-associated genes, such as METTL3, a key methyltransferase implicated in cancer progression[29]. And targeting METTL3 has garnered significant interest as a therapeutic strategy for cancer[30]. Therefore, elucidating METTL3’s role in tumorigenesis and developing novel treatment paradigms are critical for advancing cancer therapeutics.

WHAT’S METTL3

The m6A modification system consists of three functional components: The “writers” that create m6A labels, the “erasers” that exhibit demethylation activity, and the “readers” that decode m6A modifications to control the fate of modified transcripts[31-33]. As a reverse and dynamic process, the fate of target RNAs is changed, including stability, translation, degradation, splicing, translocation, pri-mRNA processing, and structure switching (Figure 1). The biological process of m6A modification is mediated by the methyltransferase complex, wherein MT-A is a key subunit complex containing a methyl donor (SAM) with a molecular weight of 70 kDa, also known as METTL3[34,35]. METTL3, a core writer protein, forms a heterodimer with METTL14 and recruits WTAP to nuclear speckles, enhancing m6A deposition[36-38]. As a highly conserved protein, METTL3 is capable of recognizing the 5-nucleotide sequence 5’-DRACH-3’ [D (not cytosine) = A (adenine), G (guanine), or U (uracil); R (purine) = A, G; H (not G) = A, C (Cytosine), or U] in single-stranded RNA[39,40]. While METTL14 stabilizes RNA binding and complex integrity[31,41]. The structure of the METTL3 molecule includes an N-terminal extension with a leading helix and a nuclear localization signal region[42]. Following this region, two consecutive cysteine-cysteine-cysteine-histidine zinc finger motifs (ZF1 and ZF2), a zinc finger domain, a partially ordered linker, and a C-terminal MT enzyme domain are present[32,43]. Over 80% of METTL3 binding sites localize to the protein-coding transcripts [coding sequence (CDS) regions], with additional enrichment observed in the 5’ untranslated region (UTR) and 3’UTR regions, particularly near termination codons, which is consistent with the distribution of m6A[44,45].

Figure 1 Dynamic regulation of N6-methyladenosine modification. N6-methyladenosine (m6A) writers, erasers, and readers control the process of m6A modification. Writers (METTL3, METTL14, WTAP, METTL5, and METTL16) catalyze m6A deposition, erasers (FTO and ALKBH5) remove methyl groups, and readers (YTHDF1/YTHDF2/YTHDF3, YTHDC1/YTHDC2/YTHDC3, IGF2BP1/IGF2BP2/IGF2BP3) decode these marks to influence RNA stability, messenger RNA translation, RNA degradation, translocation, RNA splicing, structure switching, and primary microRNA processing. M6A: N6-methyladenosine.

METTL3 critically regulates cellular processes by modulating RNA m6A levels, with dysregulated expression implicated in tumorigenesis across diverse cancers, including glioblastoma, lung cancer, hepatocellular carcinoma, and acute myeloid leukemia[41,46-50]. Beyond oncology, METTL3 deficiency disrupts T cell homeostasis by altering mRNA decay rates and amplifying suppressor of cytokine signaling family activity, which suppresses interleukin-7/ signal transducer and activator of transcription 5 signaling and impairs T cell proliferation and differentiation-a mechanism linked to immune dysregulation in colitis[51]. METTL3 further governs post-transcriptional regulation by: (1) Enhancing miRNA maturation: Methylation of primary miRNAs (pri-miRNAs) improves DGCR8 recognition, facilitating miRNA processing[52]; (2) Modulating RNA dynamics: Influencing pre-mRNA splicing, mRNA stability, translation efficiency, and nuclear export[53-57]; and (3) Driving oncogenic pathways: Regulating cell cycle progression, apoptosis, metastasis, and inflammatory responses through m6A-dependent RNA modifications[58,59]. This integrated framework underscores METTL3’s dual role in disease pathogenesis and therapeutic vulnerability.

This article comprehensively reviews the role of METTL3 in the progression of CRC. METTL3 can influence the progression of CRC by upregulating oncogenes, downregulating tumor suppressor genes, or activating specific signaling pathways linked to CRC. Furthermore, METTL3 influences gene regulation and induces metabolic disorders in CRC by impacting metabolism, thereby regulating tumor progression. Meanwhile, METTL3 plays a crucial role in the occurrence and development of CRC by participating in the epithelial-mesenchymal transition (EMT). Although there is currently limited research on the treatment and drug resistance of METTL3 in CRC, further exploration of its mechanism is anticipated to offer novel insights into the diagnosis, prognosis, and targeted drug development of CRC.

M6A-MODIFIED MRNAS IN CRC

As one of the most abundant chemical modifications in mRNA, m6A-modified mRNAs play an important role in various cellular activities[60]. In CRC, different mRNAs with m6A modification mediated by METTL3 were summarized (Table 1)[45,61-71].

Table 1 Summary of N6-methyladenosine modification of messenger RNAs in colorectal cancer.

METTL3 expression	M6A modified mRNAs	Function of METTL3	Ref.
Upregulation	CCN1	Cell proliferation	Zhu et al[61]
Upregulation	YPEL5	Cell proliferation	Zhou et al[62]
Upregulation	PTTG3P	Cell proliferation	Zheng et al[63]
Upregulation	KIF26B	Cell invasion and migration	Chen et al[64]
Downregulation	P38/ERK	Cell invasion and migration	Deng et al[65]
Upregulation	HK2 and GLUT1	Metabolism	Shen et al[45]
Upregulation	GLUT1	Metabolism	Chen et al[66]
Upregulation	REG1α	Metabolism	Zhou et al[67]
Upregulation	P53R273H	Drug resistance	Uddin et al[68]
Upregulation	RAD51AP1	Drug resistance	Li et al[69]
Upregulation	TRAF5	Drug resistance	Lan et al[70]
Upregulation	LDHA	Drug resistance	Zhang et al[71]

ERK: Extracellular regulated protein kinases; HK2: Hexokinase 2; GLUT1: Glucose transporter type 1; mRNAs: Messenger RNAs; m6A: N6-methyladenosine.

METTL3, a key m6A methyltransferase, orchestrates multiple oncogenic processes in CRC through dynamic regulation of downstream mRNA modifications. Its functional roles span four critical domains: (1) Cell proliferation: METTL3 stabilizes CCNE1 mRNA by mediating m6A modification at the 3’UTR, enhancing CRC cell proliferation via cyclin E1 upregulation[61]. Conversely, METTL3-mediated m6A modification of YPEL5 mRNA facilitates its degradation through YTHDF2 binding, suppressing tumor suppressor activity and accelerating CRC pathogenesis[62]; (2) Invasion and migration: Reduced METTL3 expression in specific CRC models activates p38 and ERK phosphorylation, promoting metastatic potential and serving as a prognostic biomarker[65]; (3) Metabolic reprogramming: METTL3 drives glucose metabolism by enhancing glucose transporter type 1 (GLUT1) translation through m6A-dependent mechanisms, increasing glucose uptake and lactate production to fuel tumor growth; and (4) Chemoresistance: In 5-FU-resistant CRC cells, METTL3 overexpression upregulates RAD51AP1, enhancing DNA repair capacity and conferring drug resistance[69]. These findings underscore METTL3’s dual regulatory role: Stabilizing oncogenic transcripts (e.g., CCNE1) while destabilizing tumor suppressors (e.g., YPEL5). Such mechanisms position METTL3 as a central therapeutic target for CRC intervention. The following paragraphs will detail its mechanism in these cellular processes.

MECHANISM STUDIES OF METTL3-MODIFIED MRNAS IN CRC

CRC cells exhibit hallmark features including uncontrolled proliferation, enhanced invasiveness, metabolic dysregulation, and chemoresistance. These phenotypes are driven by dysregulated activation of multiple signaling pathways[13-18]. Wnt/β-catenin, Raf-MEK-ERK, mTOR/PI3K, mTOR/ATK, and nuclear factor kappa-B signaling cascades are frequently hyperactivated in CRC, contributing to tumor initiation and progression. Meanwhile, METTL3-dependent m6A modification further modulates additional pathways such as YAP1 and hypoxia-inducible factor-1 alpha (HIF-1α), expanding its role in CRC pathogenesis (Figure 2).

Figure 2 METTL3-mediated N6-methyladenosine modification of messenger RNAs in colorectal cancer. METTL3 participates in colorectal cancer (CRC) by regulating N6-methyladenosine modification of messenger RNAs (mRNAs) involved in proliferation, invasion and metastasis, metabolic disorder, and resistance of CRC cells. Every mRNA was detailed with a name. HK2: Hexokinase 2; GLUT1: Glucose transporter type 1; mRNAs: Messenger RNAs; m6A: N6-methyladenosine; CRC: Colorectal cancer.

METTL3-mediated m6A modification stabilizes hexokinase 2 (HK2) and GLUT1 transcripts, enhancing glycolysis and driving CRC cell proliferation[45]. m6A-dependent GLUT1 translation increases glucose uptake and lactate production, activating the mTORC1 signaling pathway to promote CRC progression[66]. Elevated REG1α expression in CRC correlates with lymph node metastasis, advanced tumor stages, and poor prognosis. Mechanistically, METTL3-mediated m6A modification regulates REG1α expression, which activates the Wnt/β-catenin pathway to drive metastasis and proliferation via the β-catenin/MYC axis[67]. Hence, METTL3 simultaneously enhances glycolytic flux (HK2/GLUT1) and activates oncogenic pathways (REG1α/β-catenin), creating metabolic and proliferative synergy in CRC. β-catenin signaling upregulates METTL3 expression, creating a feedforward loop. Sphingomyelin metabolites (e.g., ceramide glycosylation products) activate β-catenin, which enhances METTL3-dependent m6A methylation of TP53 R273H mutant transcripts, conferring chemoresistance in CRC cells[68]. Therefore, targeting METTL3 may disrupt both the β-catenin/MYC axis and TP53 mutant-driven drug resistance.

Recent studies highlight metabolic reprogramming as a central driver of drug resistance in CRC[72]. These cells exhibit elevated glucose consumption, adenosine triphosphate synthesis, lactate output, and maximal oxygen consumption rates, indicating enhanced glycolytic flux and mitochondrial activity in chemoresistance CRC cells[71]. METTL3 promotes LDHA expression through dual mechanisms: (1) Stabilizing HIF-1α mRNA to enhance transcription under hypoxic conditions; and (2) Facilitating LDHA translation via m6A methylation of its CDS and recruitment of the YTHDF1 reader protein[73]. Conversely, METTL3 knockdown disrupts HIF-1α protein synthesis and suppresses glycolytic enzymes (LDHA, HK2), restoring chemosensitivity in resistant CRC models[73]. Hence, METTL3 promotes drug resistance in CRC through metabolic reprogramming using following mechanisms: (1) METTL3 coordinates hypoxia adaptation (HIF-1α) and enzymatic activation (LDHA) to sustain glycolysis in chemoresistant cells at the transcriptional level; and (2) METTL3 mediated m6A modifications in the CDS region enable YTHDF1-mediated ribosomal recruitment, amplifying LDHA production at the translational level.

Researchers have further discovered that the tumor microenvironment is closely associated with chemotherapy resistance in CRC[74]. Programmed cell death 1 (PD-1) checkpoint-blocking immunotherapy has been used in various cancers; colorectal tumors with MSI or proficient base mismatch repair (PMMR-MSI-L) have a lower mutation burden[75]. METTL3 enhances oxaliplatin resistance in CRC by stabilizing TRAF5 mRNA through m6A modifications. METTL3 deficiency increases oxaliplatin-induced necrotic cell death and disrupts chemoresistance, as TRAF5 is critical for executing necrosis and evading apoptosis[70]. PD-1 immunotherapy efficacy is influenced by METTL3/m6A activity. In pMMR-MSI-L CRC, knockout of METTL3/METTL14 reduces m6A levels on immunosuppressive transcripts, sensitizing tumors to anti-PD-1 therapy[75]. Preclinical evidence suggests this approach may circumvent resistance mechanisms in CRC subtypes unresponsive to conventional chemotherapy or single-agent immunotherapy[75,76]. The therapeutic synergy arises from METTL3 inhibition-induced endogenous interferon responses combined with PD-1 blockade-mediated T-cell activation[75,76]. Therefore, an important clinical implication could be drawn: Dual inhibition of METTL3 and PD-1 may overcome resistance in both chemotherapy-refractory and immunologically “cold” CRC subtypes.

Crosstalk between METTL3-regulated signaling pathways are also found in CRC, coordinating multiple oncogenic pathways in CRC through m6A-dependent mRNA stabilization and translation. Bioinformatics analysis of CRC transcriptomes reveals that METTL3-regulated mRNAs (e.g., MYC, VEGFA) are enriched in pathways related to angiogenesis, apoptosis resistance, and immune evasion. These targets form interconnected networks with nodes overlapping across Wnt, MAPK, and PI3K-AKT pathways, suggesting METTL3 acts as a central hub for pathway integration[77]. METTL3 stabilizes CCND1 mRNA (encoding cyclin D1) via m6A modification, activating Wnt/β-catenin signaling to promote cell cycle progression. Simultaneously, METTL3 enhances KRAS translation, which activates the Raf-MEK-ERK cascade to drive proliferation and invasion[65,67,68]. Hence, Wnt/β-catenin and Raf-MEK-ERK synergy regulatory network promotes the occurrence and progression of CRC. Interestingly, the interplay between mTOR/PI3K and MAPK are also found. METTL3-mediated m6A modification of HK2 and GLUT1 activates mTORC1 signaling, while its regulation of miR-1246/sprouty-related EVH1 domain-containing protein 2 (SPRED2) further amplifies MAPK signaling, creating a feedforward loop that sustains metabolic reprogramming and EMT in CRC[45,78].

M6A-MODIFIED NCRNAS IN CRC

NcRNAs are huge quantities and, by definition, are not translated into proteins. Since their discovery, increasing ncRNAs have been important regulators across various cell types and tissues, and their abnormal expression has been implicated in disease[27]. Based on their length, ncRNAs can be divided into small RNAs (less than 200 nt) and lncRNAs, equal to or more than 200 nt[79]. As a kind of classic small ncRNAs, miRNAs are about 22-nt, which can dynamically regulate the process of gene expression via binding to the miRNA response elements on target RNAs[80]. Notably, a novel covalently closed RNA molecule named circRNAs is found, generating from back-splicing without 5’ end capped structures and 3’ end polyadenylate tails[81]. Current understanding of the roles of miRNAs, lncRNAs, and circRNAs in cancer and other major human diseases provides the potential use of ncRNAs as disease biomarkers and therapeutic targets[27,82,83]. Being important regulators, fates of ncRNAs can also be regulated by m6A modification. In CRC, different ncRNAs with m6A modification mediated by METTL3 were summarized (Table 2)[78,84-89].

Table 2 Summary of N6-methyladenosine modification of noncoding RNAs in colorectal cancer.

METTL3 expression	M6A modified ncRNAs	Function of METTL3	Ref.
Upregulation	SNHG1	Cell proliferation	Xu et al[84]
Upregulation	FAM83H-AS1	Cell proliferation	Luo et al[85]
Upregulation	pri-miRNA-1246	Cell invasion and migration	Peng et al[78]
Upregulation	circ1662	Cell invasion and migration	Chen et al[86]
Upregulation	POU6F2-AS1	Metabolism	Jiang et al[87]
Upregulation	miR-181b-5p	Drug resistance	Pan et al[88]
Upregulation	Circ0124554	Drug resistance	Zhong et al[89]

pri-miRNA: Primary miRNA; ncRNAs: Noncoding RNAs; m6A: N6-methyladenosine.

While m6A modification dictates distinct functional outcomes for mRNAs, its regulatory roles in ncRNAs remain nascent[90]. In miRNA biogenesis, m6A modification critically governs the initiation phase through following steps: M6A-modified pri-miRNAs recruit DGCR8 for nuclear processing. METTL3 depletion disrupts DGCR8-pri-miRNA binding and reduces mature miRNA production[52]. METTL3 overexpression leads to proliferation, invasion and migration, disorder metabolism, and drug resistance of CRC cells through m6A-mediated regulation of multiple ncRNA classes (Figure 3). Overexpressed METTL3 stabilizes lncRNAs SNHG1/FAM83H-AS1 through m6A epitranscriptional editing[84,85]. M6A-modified pri-miRNA-1246 and circRNA circ1662 enhance invasion/migration capacity of CRC cells[78,86]. During CRC metabolic reprogramming, METTL3 upregulates FASN via m6A-modified lncRNA POU6F2-AS1 to promote fatty acid metabolism[87]. In CRC chemoresistance, METTL3 elevates miR-181d-5p and circ0124554 expression through m6A modification[88,89]. These results collectively establish METTL3 as a master regulator of CRC progression through coordinated ncRNA modification networks.

Figure 3 METTL3-mediated N6-methyladenosine modification of noncoding RNAs in colorectal cancer. METTL3 participates in colorectal cancer (CRC) by regulating N6-methyladenosine modification of noncoding RNAs (ncRNAs) involved in proliferation, invasion and metastasis, metabolic disorder, and resistance of CRC cells. Each ncRNA was detailed with a name. ncRNAs: Noncoding RNAs; m6A: N6-methyladenosine; CRC: Colorectal cancer.

MECHANISM STUDIES OF METTL3-MODIFIED NCRNAS IN CRC

The oncogenic lncRNA SNHG1 drives CRC proliferation through m6A-mediated stabilization, where METTL3 enhances SNHG1 RNA stability via epitranscriptional modification, accelerating tumor growth and metastasis[84]. Similarly, the upregulated lncRNA FAM83H-AS1 in advanced-stage CRC promotes cancer progression by: (1) Stabilizing RNA via METTL3: M6A modifications by METTL3 prolong FAM83H-AS1 half-life, facilitating its oncogenic activity; (2) Splicing regulation: FAM83H-AS1 reduces phosphorylation of the splicing factor PTBP1, dysregulating RNA processing to enhance CRC aggressiveness; and (3) Therapeutic sensitivity: FAM83H-AS1 knockdown synergizes with oxaliplatin or cisplatin, significantly suppressing tumor growth in patient-derived xenograft models[85]. During invasion and metastasis of CRC cells, METTL3 upregulation enhances pri-miRNA-1246 maturation via m6A modification. This process suppresses the tumor suppressor SPRED2, a downstream target of miR-1246, thereby activating pro-metastatic pathways through the METTL3/miR-1246/SPRED2 axis[78]. The m6A-modified circRNA circ1662 demonstrates elevated expression in CRC tissues, where METTL3-dependent m6A methylation stabilizes its transcript. Circ1662 directly binds to YAP1 to promote its nuclear translocation, thereby activating EMT and CRC metastasis[86].

Lipogenic reprogramming revealed that METTL3-induced m6A modification upregulates lncRNA POU6F2-AS1, which recruits YBX1 to the FASN promoter, driving transcriptional activation of fatty acid synthesis. This metabolic reprogramming mechanism facilitates CRC cell proliferation and positions POU6F2-AS1 as a therapeutic target[87]. In CRC chemo-resistance, METTL3 enhances miR-181d-5p maturation through m6A modification, leading to suppression of the tumor suppressor gene neurocalcin δ (NCALD). This axis drives chemoresistance and CRC progression, highlighting NCALD as a critical downstream effector[88]. In addition to chemo-resistance, METTL3 has also been found to be involved in radiosensitivity. METTL3-mediated m6A methylation elevates circ0124554, which sponges miR-1184 to upregulate LASP1 expression. Circ0124554 depletion sensitizes CRC cells to radiotherapy, while LASP1 overexpression rescues radio resistance, establishing this circuit as a key therapeutic vulnerability[89].

This integrated framework underscores METTL3 as a central orchestrator of CRC malignancy through m6A-dependent ncRNA networks: (1) The stabilization of oncogenic circRNAs (e.g., circ1662, circ0124554) through m6A modification aligns with broader regulatory roles of epitranscriptomic editing in CRC progression; (2) METTL3’s dual role in chemoresistance (via miRNA maturation) and metabolic reprogramming (via lncRNA stabilization) reflects its pleiotropic impact on CRC pathogenesis; and (3) The circRNA-miRNA sponge mechanism (e.g., circ0124554/miR-1184/LASP1) exemplifies m6A-driven post-transcriptional regulation in therapy resistance. METTL3-mediated m6A modification of ncRNAs establishes a regulatory feedback loop, where ncRNAs such as circRNAs reciprocally modulate METTL3 expression through competitive miRNA sponging mechanisms[29]. The METTL3-associated circRNA hsacirc0000523 competitively binds miR-let-7b via shared miRNA response elements, thereby shielding METTL3 mRNA from miR-let-7b-mediated repression and driving CRC cell proliferation[91]. While distinct ncRNAs exhibit stage-dependent associations with CRC progression, their precise functional contributions and regulatory networks remain incompletely characterized.

POTENTIAL USE OF METTL3 IN THE CLINIC

According to UALCAN platform[92,93], Pan-cancer analysis revealed METTL3 upregulation in most cancers (Figure 4A), particularly in colon adenocarcinoma (COAD) from the Cancer Genome Atlas database (Figure 4B). This is consistent in many studies that METTL3 is highly expressed in CRC tissues and acts as an oncogene[45,63,64,78,86]. On the contrary, Deng et al[65] observed that METTL3 exhibits low expression in CRC tissues and acts as a tumor suppressor gene. Although the prognostic role of METTL3 in CRC is inconsistent, its abnormal expression provides a potential target for CRC treatment. METTL3 expression increased progressively across COAD stages (Figure 4C), and higher expression correlated with poor prognosis was found using the Kaplan Meier plotter[94] (Figure 4D). Integrating 150 top target genes of METTL3 identified important genes such as MYC, VEGFA, CASP3 and BCL2 that are participated in angiogenesis and apoptosis resistance via RM2Target[95] (Figure 4E). The enrichment analysis of METTL3 targets in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways highlighted METTL3-associated pathways, including ribosome biogenesis, cancer, and cell cycle regulation (Figure 4F). The KEGG result is consistent with functional analysis of METTL3 in CRC via transcriptome studies: This gene functions as a central hub, forming interconnected networks with Wnt, MAPK, and PI3K-AKT pathways[77].

Figure 4 Expression and function analysis of METTL3. A: Pan-cancer analysis of METTL3; B: Expression of METTL3 in colon adenocarcinoma (COAD); C: METTL3 expression across COAD stages; D: Prognosis of METTL3 in COAD; E: Integration of the top 150 METTL3 target genes; F: Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of METTL3 targets; G: Drug-protein interaction analysis of Patupilone, YM-155, KIN001-266, and METTL3 in prostate adenocarcinoma. TCGA: The Cancer Genome Atlas; TPM: Transcripts per million; BLCA: Bladder urothelial carcinoma; BRCA: Breast invasive carcinoma; CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma; CHOL: Cholangiocarcinoma; COAD: Colon adenocarcinoma; ESCA: Esophageal carcinoma; GBM: Glioblastoma multiforme; HNSC: Head and neck squamous cell carcinoma; KICH: Kidney chromophobe; KIRC: Kidney renal clear cell carcinoma; KIRP: Kidney renal papillary cell carcinoma; LIHC: Liver hepatocellular carcinoma; LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma; PAAD: Pancreatic adenocarcinoma; PRAD: Prostate adenocarcinoma; PCPG: Pheochromocytoma and paraganglioma; READ: Rectum adenocarcinoma; SARC: Sarcoma; SKCM: Skin cutaneous melanoma; STAD: Stomach adenocarcinoma; UCEC: Uterine corpus endometrial carcinoma; KEGG: Kyoto Encyclopedia of Genes and Genomes.

Drug-protein interaction analysis identified drugs such as Patupilone, YM-155, and KIN001-266 as potential inhibitors for METTL3-targeted therapy in PRAD via cancer proteome[96] (Figure 4G). Selberg et al[97] found that four molecules can enhance the activity of the METTL3-METTL14 complex. These molecules may enhance the binding affinity of SAM and reduce the energy barrier of substrate RNA methylation reactions. Bedi et al[98] employed cofactor simulation methods to screen libraries of adenosine analogs and their derivatives, and identified the activity of several compounds in vitro experiments. Compared with adenosine analogs, STM2457, a highly potent and selective first-in-class catalytic inhibitor of METTL3 was found. Moreover, this molecule has higher specificity to METTL3 and shows no inhibitory effect on other RNA methyltransferases[99]. Emerging METTL3 inhibitors (e.g., STM2457) show preclinical efficacy: Suppressing METTL3 reduces both Wnt/β-catenin and MAPK activity in patient-derived xenografts. And METTL3 knockdown sensitizes CRC organoids to 5-FU by downregulating thymidylate synthase[77]. Recently, inhibitors have been designed based on protein-protein interaction strategies. Proteolysis targeting chimeras can specifically degrade various proteins. They are bifunctional molecules composed of target protein ligands and E3 ubiquitin ligands covalently linked[100]. Collective evidences-abnormal expression, prognostic relevance, pathway enrichment, and druggability-supports the potential clinical utility of METTL3 as a therapeutic target in CRC.

CONCLUSION

METTL3 drives CRC progression by directly upregulating oncogenes (e.g., YAP1), suppressing tumor suppressors, and modulating signaling pathways linked to proliferation, invasion, and metastasis[101]. Beyond carcinogenesis, METTL3 influences metabolic reprogramming (e.g., fatty acid synthesis) and angiogenesis, highlighting its systemic impact on CRC biology[102]. These reveals multifunctional role of METTL3 in CRC pathogenesis, however, unresolved mechanistic complexities still remain. First, METTL3’s regulatory effects in CRC involve intricate crosstalk between m6A-modified RNAs (e.g., circRNAs, lncRNAs) and different signaling pathways, though their interactions remain unclear. Second, METTL3 activity is context-dependent and influenced by interactions with other m6A writers/erasers (e.g., FTO, ALKBH5), requiring advanced profiling to clarify their combinatorial roles in CRC. Additionally, inhibitor strategies (e.g., small molecules, RNA interference) show preclinical promise in reducing METTL3-driven chemoresistance and radio resistance, though clinical validation is pending. Furthermore, the mechanism research on drug resistance still faces limitations. Addressing these requires expanded cohort studies and single-cell sequencing to map METTL3’s stage-specific roles in CRC progression and prognosis. Investigating METTL3’s interplay with immune checkpoints and metabolic pathways to develop combinatorial therapies remains unresolved. This synthesis integrates METTL3’s dual roles as a molecular driver and therapeutic target, emphasizing the need for mechanistic and translational studies to address current gaps.