Ubiquitination and N⁶‑methyladenosine in cancer: Convergent regulation of oncogenic signaling pathways (Review)

Introduction

Among the diverse regulatory mechanisms in cell biology, post-translational modifications are vital in the process of tumorigenesis (1). Ubiquitination, a pivotal post-translational modification (PTM), involves the covalent attachment of the 76-amino-acid ubiquitin to substrate proteins and thus regulates their stability, activity and intracellular signaling (2). Such modification is catalyzed by a multi-step enzymatic cascade consisting of ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2) and ubiquitin ligases (E3) (3). Ubiquitination contributes to cell-cycle control and genome stability, as well as influencing cellular growth, proliferation and death. The dysregulation of ubiquitination in cancer frequently degrades tumor suppressors such as p53, thereby facilitating the proliferation and metastasis of tumor cells (4). Furthermore, counterbalancing ubiquitination, deubiquitinating enzymes (DUBs) remove ubiquitin moieties and disassemble ubiquitin chains, thereby playing a key role in maintaining ubiquitin system homeostasis and restraining signal transduction, thus preventing pathway overactivation in cancer (5).

N6-methyladenosine (m6A) is among the most prevalent RNA modifications, gaining increasing attention in recent years (6). m6A modulates the stability and translational efficiency of mRNA, and is also indispensable in RNA splicing and decay (7). Accumulating evidence indicates that m6A regulates gene expressions implicated in tumorigenesis, thereby directly influencing malignant phenotypes (8). For instance, m6A-modified circNEK11 has been reported to promote hepatocellular carcinoma (HCC) progression via the miR-1236-3p/glutathione peroxidase 2 axis (9). m6A is also engaged in tumor micro-environment remodeling by altering intercellular signaling networks (10).

Recent studies have uncovered extensive crosstalk between ubiquitin-dependent and m6A-dependent regulation, such that these pathways do not act in isolation but converge on shared molecular nodes and signaling circuits (11,12). Mechanisms of interplay include ubiquitin-mediated control of the abundance and activity of m6A writers/erasers/readers, m6A-dependent regulation of mRNAs encoding components of ubiquitin pathways, and coordinated actions at the chromatin-transcription interface where co-transcriptional m6A deposition and histone ubiquitination collectively influence RNAPII dynamics and nascent RNA processing (13). Through these interactions, ubiquitination and m6A cooperatively modulate core oncogenic signaling networks, for example, PI3K-AKT (14), Wnt/β-catenin (15) and NK-κB (16), thereby governing proliferation, metastasis, immune interactions and resistance to therapy. Hence, a systematic dissection of their reciprocal regulation and pathogenic mechanisms helps deepen the current understandings of tumor biology and may uncover new therapeutic avenues.

The present review synthesizes current knowledge on the molecular mechanisms by which ubiquitination and m6A intersect to regulate oncogenic signaling. The core enzymology and functional consequences of each modification were first summarized, and mechanistic examples of crosstalk at the levels of protein, RNA and chromatin were subsequently summarized. The ways through which these interactions impinge on major cancer signaling pathways were also addressed. Ultimately, the present review considers translational implications and outlines challenges and future directions, emphasizing the need for integrated multi-omics and refined functional models to disentangle context specificity and to exploit the ubiquitin-m6A axis for cancer therapy.

Ubiquitination in cancer

Ubiquitin is a 76-amino-acid protein widely expressed in eukaryotes (17). Ubiquitination, referring to the covalent attachment of ubiquitin to substrate proteins, is the second most common PTM after phosphorylation (2). This modification is facilitated by a highly specific ATP-dependent enzymatic cascade (18). This process involves a series of steps that utilize ubiquitin along with E1 enzymes for activation, E2 enzymes for conjugation, and E3 ligases for transfer. Ubiquitination serves as a dynamic post-translational protein modification conserved across eukaryotes (Fig. 1). The activation of ubiquitin starts with the formation of a thioester bond between the thiol group of E1 and the carboxyl group of the ubiquitin molecule, driven by ATP. Once activated, E1 transfers the ubiquitin to E2 through a transesterification reaction, binding it to a cysteine residue at the active site of E2. E2 then facilitates the transfer of ubiquitin to E3, which in turn catalyzes the ubiquitin to the substrate and releases E2, thereby generating a defined ubiquitinated product (19).

Figure 1. Schematic representation of the ubiquitin-proteasome-mediated protein degradation pathway. The process is initiated by the ATP-dependent activation of ubiquitin via an E1 activating enzyme, which catalyzes the formation of a thioester bond between its catalytic cysteine and the C-terminal glycine of ubiquitin. The activated ubiquitin is subsequently transferred to the E2 conjugating enzyme through a transesterification reaction. The E3 ubiquitin ligase then mediates the final conjugation step, facilitating the transfer of ubiquitin from the E2 to a lysine residue on the substrate protein via an isopeptide bond. The resulting ubiquitinated substrate is ultimately targeted to the 26S proteasome for proteolytic degradation. Figure generated using Adobe Illustrator (v29.8.1.2, Adobe Systems, Inc.). E1, Ubiquitin - activating enzyme; E2, Ubiquitin - conjugating enzyme; E3, Ubiquitin ligase; ATP, adenosine triphosphate; AMP, adenosine monophosphate; DUB, deubiquitinating enzyme.

Recent studies have suggested that ubiquitination, together with its reversal by DUBs, plays instrumental roles in regulating multiple hallmarks of cancer, including evasion of growth-suppressive signals, reprogramming of energy metabolism and modulation of tumor immune responses (20–22). For instance, E3 ubiquitin ligase Tripartite Motif Containing (TRIM)-21-mediated ubiquitination of Sohlh2 inhibits M2 macrophage polarization, thus suppressing the progression of triple-negative breast cancer and colorectal cancer (23,24). Additionally, research by Chen et al (25) shown that LHPP disrupts energy metabolism in glioblastoma by promoting the ubiquitin-dependent degradation of PKM2. Moreover, USP13 stabilizes NLRP3 and enhances inflammasome activation by preventing TRIM31-mediated ubiquitination and degradation of NLRP3 (26). A recent study found that UCHL3 deficiency promoted ENO1 ubiquitination, attenuated the AKT/CCND1 signaling axis, suppressed the progression of gastric cancer and enhanced the sensitivity to palbociclib (27).

Previous reports highlighted emerging approaches involving ubiquitination in cancer therapy, such as proteolysis-targeting chimeras (PROTACs) and molecular glues (28,29). The PROTAC technology serves as an effective platform for targeted protein degradation and is advancing the development of related drugs (30). ARV-110 (bavdegalutamide) and ARV-471 (vepdegestrant) represent the forefront of PROTAC drug development currently in clinical practice, and both have progressed to Phase II trials (31,32). Meanwhile, ARV-110 is designed to selectively target the androgen receptor and promote its degradation through the recruitment of E3 ligases (33,34). Previous data from the first-in-human Phase I study indicated that ARV-110 demonstrated satisfying safety and tolerability in patients with metastatic castration-resistant prostate cancer (35). Compared with PROTACs, molecular glues are smaller molecules, which simplifies their chemical optimization. To date, several molecular glue degraders have been identified (36). Notably, CC-90009 has been shown to facilitate the ubiquitin-mediated degradation of G1 to S phase transition protein 1 by recruiting the E3 complex CUL4-DB1-CRBN-RBX1 and it is also undergoing Phase II clinical trials for treating leukemia (37).

m6A modification in cancer

The m6A denotes methylation at the N6 position of adenosine within RNA and constitutes the most abundant internal modification of eukaryotic mRNA (38). It is broadly distributed across transcripts but preferentially occurs at the consensus RRACH motif (R=A/G; H=A/C/U), and is often enriched near the stop codons (39). Genome-wide analyses further indicate that m6A deposition is generally quicker and more efficient within coding sequences than in the 3′ untranslated regions (40). Functionally, m6A impacts nearly every step of mRNA metabolism: It regulates nuclear processing and export, modulates cytosolic translation efficiency and transcript turnover, and thereby enables precise spatiotemporal control of gene expression. Structurally, m6A alters local base stacking via enhancing π-π interactions in unpaired regions, which reduces conformational flexibility and stabilizes tertiary RNA structures (41). Mechanistically, m6A promotes translation by recruiting or modulating eukaryotic initiation factors, thereby enhancing the translation of capped mRNAs (42). It is known that m6A is implicated in physiological processes, including immune and inflammatory responses (43). The m6A mark is dynamic and reversible: It is installed by methyltransferase ‘writers’, removed by demethylase ‘erasers’ and interpreted by specific ‘reader’ proteins that mediate downstream effects on RNA fate (44). This epitranscriptomic circuitry permits combinatorial, context-dependent regulation of RNA metabolism, enabling m6A to act as a tunable molecular rheostat that integrates extracellular cues with intracellular regulatory networks. Unlike genetic mutations, m6A modifications present few alterations to the nucleotide sequence. Instead, a rapid and reversible mechanism to reprogram transcriptome function is provided, and gene expression outputs are dynamically adjusted in response to changing cellular or environmental cues (45).

Dysregulation of the m6A methylation apparatus, which is indispensable for normal cellular homeostasis, is capable of promoting carcinogenesis and fostering resistance to therapy, highlighting its pivotal role in cancer (46) (Fig. 2). The impact of this progress is highly context-specific: Methyltransferase-like 3 (METTL3)-driven hypermethylation is associated with increased proliferation, metastasis and apoptosis resistance in breast cancer and implicated in several lung cancer subtypes, whereas METTL14 over-expression has been reported to limit metastatic spread in HCC (47). Given the involvement of m6A in a broad spectrum of tumor-relevant processes, including cell-cycle progression, epithelial-mesenchymal transition (EMT), angiogenesis, dissemination, immune modulation and treatment response, its functions must be defined in a cancer-type-specific manner to inform precision interventions (48). In clinical practice, m6A landscapes and the expression of m6A regulators hold promise as prognostic biomarkers. For example, higher levels of YTH m6A RNA binding protein 1 (YTHDF1) and insulin-like growth factor 2 mRNA-binding protein 2 (both are m6A readers) associate with worse overall survival in HCC (49). However, therapeutic targeting of the m6A machinery faces substantial hurdles, including the omnipresence of RNA modifications, their pleiotropic and occasionally opposing functions, risks of off-target and toxic effects, as well as delivery constraints (50). Despite these challenges, targeted strategies such as small-molecule inhibitors and antisense oligonucleotides, are under active pre-clinical and early-phase clinical investigation.

Figure 2. Schematic representation of the m6A modification in cancer. This figure illustrates the reversible m6A enzymatic cycle and its role in governing the fate of mRNA transcripts within oncogenic signaling pathways. The modification is installed by ‘writer’ complexes, such as METTL3 and METTL14, which catalyze methylation at the RRACH consensus motif, and is removed by ‘eraser’ demethylases such as FTO and ALKBH5. These marks are subsequently interpreted by specific ‘reader’ proteins, including members of the YTH family and IGF2BPs, that mediate downstream effects on RNA metabolism, such as splicing, nuclear export, transcript stability and translational efficiency. Dysregulation of these regulators disrupts normal cellular homeostasis and promotes hallmarks of cancer, such as cell-cycle progression, epithelial-mesenchymal transition, metastatic dissemination and therapeutic resistance, in a highly context-specific manner. Figure generated using Adobe Illustrator (v29.8.1.2, Adobe Systems, Inc.). METTL3, methyltransferase-like 3; HNRNPA2/B1, heterogeneous nuclear ribonucleoprotein A2/B1; YTHDC1, YTH domain-containing 1; m6A, N6-methyladenosine; FTO, fat mass and obesity-associated protein; ALKBH5, ALKB homolog 5; WTAP, Wilms' tumor 1-associated protein; YTHDC2/F2/F3, YTH domain - containing 2/F2/F3; IGF2BP 2/3, insulin-like growth factor 2 mRNA-binding protein 2/3; METTL14, methyltransferase-like 14.

m6A modification and key cancer-related pathways

Recent research highlights the intricate regulatory roles of m6A modification in cellular signaling pathways, positioning this epitranscriptomic mark as a key target for unraveling pathogenic molecular mechanisms and advancing targeted therapeutic strategies (51). Of note, the major signaling pathway modulated by m6A modification include pathways such as NF-κB, PI3K-AKT, MAPK, Wnt and mechanistic target of mTOR (52). These signaling pathways are essential in cellular growth regulation, proliferative signaling, lineage commitment and programmed cell death (53), the dysregulation of which is mediated by m6A modification and is associated to the development of various diseases, especially in the context of oncogenic transformation.

The NF-κB pathway

Specifically, Steroid receptor coactivator-1 facilitates METTL3-mediated m6A modification by coactivating NF-κB and promotes the malignant progression of glioblastoma (54). STAT1 activation and m6A-mediated enhancement of IL15RA expression cooperatively promote metastatic progression in clear cell renal cell carcinoma by activating the ZEB1/NF-κB signaling axis (55). METTL3 promotes bladder cancer progression via the AF4/FMR2 family member 4/NF-κB signaling network (56). Fat mass and obesity-associated protein (FTO) enhances oral squamous cell carcinoma progression via m6A-dependent stabilization of PKM2 mRNA through YTHDF2 modulation (57). Two key regulators of the NF-κB pathway, namely IKBKB and RELA, have been identified as direct targets of METTL3-catalyzed m6A methylation (58). The cylindromatosis lysine 63 deubiquitinase (CYLD)/NF-κB pathway has been confirmed to be downstream of YTHDC2, and this axis is mediated by m6A modification in lung cancer (59). YTHDC2 exerts its anti-tumor effects via the CYLD/NF-κB signaling pathway, a process modulated by m6A modification.

The PI3K-AKT pathway

The PI3K-AKT pathway is a central intracellular signaling cascade involved in tumor growth, therapeutic resistance and metastasis, and is frequently dysregulated in human cancer (60). FTO promotes GnRH expression by demethylating m6A sites on brain-derived neurotrophic factor (BDNF) and activating the BDNF/PI3K-AKT axis (61). It is also known that METTL14 suppresses colorectal cancer progression by modulating the PI3K-AKT pathway and inhibiting SOX4-driven EMT (62). YTHDF1 enhances the translation of polo-like kinase 1 (PLK1) through m6A-modified PLK1 mRNA, leading to hyperactivation of PI3K-AKT signaling. This YTHDF1-PLK1-PI3K-AKT axis is key for prostate cancer progression and represents a potential therapeutic target (63). In addition, studies have shown that WTAP/YTHDF1-mediated m6A modification upregulates PXDN, which remodels the extracellular matrix and activates the PI3K-AKT pathway, thereby promoting nasopharyngeal carcinoma progression (64,65). Wang et al (66) found that METTL3-mediated m6A methylation of the long non-coding RNAs (ncRNA) DUXAP8 promoted esophageal squamous cell carcinoma progression by activating the PI3K-AKT signaling pathway. Moreover, according to previous research findings, m6A-modified circDCP2 accelerates carbon black nanoparticle-induced malignant transformation of human bronchial epithelial cells by activating the PI3K-AKT pathway and disrupting macrophage homeostasis (67,68) (Fig. S1).

Ubiquitination in oncogenic signaling pathways

Ubiquitination, a reversible PTM orchestrated by the sequential action of E1, E2 and E3, and antagonized by DUBs, serves as a pivotal molecular switch in regulating the spatiotemporal dynamics of oncogenic signaling pathways (69). Through dictating the stability, sub-cellular localization and protein-protein interactions of key signaling molecules, the balance between E3 ligase-mediated ubiquitination and DUB-mediated deubiquitination fine-tunes the amplitude and duration of signaling outputs, thereby governing key cellular processes such as proliferation, survival, migration and metabolism, all of which are dysregulated in cancer (70). In this section, how E3 ligases and DUBs modulate the NF-κB, and PI3K-AKT pathway is summarized, highlighting the symmetrical regulatory networks that underpin tumorigenesis and progression.

Modulation of NF-κB signaling pathway by E3 ligases and DUBs

The NF-κB family of transcription factors (including RelA/p65, RelB, c-Rel, p50 and p52) is necessary in mediating inflammatory responses, immune regulation and cell survival, and its aberrant activation is a hallmark of numerous types of cancer (71). Ubiquitination plays dual roles in regulating both the canonical and non-canonical NF-κB pathways, with E3 ligases and DUBs acting as reciprocal regulators to maintain signaling homeostasis or drive oncogenic dysregulation (72). Specifically, ubiquitin ligases regulate NF-κB activation through distinct ubiquitination modes: K48-associated polyubiquitination mediates proteasomal degradation of inhibitory molecules, whereas K63-associated or M1-associated linear polyubiquitination serves as a non-degradative scaffold to support signaling complex assembly (73,74). In the canonical pathway, tumor necrosis factor receptor-associated factors (TRAFs), particularly TRAF6, act as key ubiquitin ligases that catalyze K63-associated ubiquitination of themselves and downstream kinases including TAK1 and the IKK complex, thereby recruiting ubiquitin-binding adaptors and activating the kinase cascade (75).

Modulation of PI3K-AKT signaling pathway by E3 ligases and DUBs

The PI3K-AKT signaling pathway serves as a core oncogenic cascade governing cell growth, survival, metabolism and angiogenesis, and its hyperactivation represents one of the most frequent alterations in human cancer (76). E3 ligases and DUBs tightly control this pathway by targeting key components, including PI3K, AKT, PTEN (a major negative regulator) and mTOR, to modulate their stability and activity (77,78).

For example, MDM2, a well-characterized E3 ubiquitin ligase, negatively regulates AKT signaling by targeting AKT for K48-associated ubiquitination and proteasomal degradation. Notably, its oncogenic activity is more commonly attributed to promoting the degradation of p53 (79). On the contrary, tumor-suppressive E3 ligases, such as RNF43 and CHIP, inhibit PI3K-AKT signaling by targeting oncogenic components: RNF43 mediates the degradation of B-RAF (a downstream effector of PI3K-AKT), while CHIP promotes PTEN stability by ubiquitinating and degrading PTEN-targeting E3 ligases (80,81). Furthermore, TRAF6 functions as a positive regulator by catalyzing K63-associated ubiquitination of AKT, which promotes AKT recruitment to the plasma membrane and its subsequent phosphorylation by 3′-phosphoinositide-dependent kinase (PDK)-1 and mTORC2, thereby augmenting its kinase activity (82).

Molecular mechanisms and functional consequences of ubiquitin-m6A crosstalk

Ubiquitination, a PTM regulating protein fate, and m6A which is the most abundant internal post-transcriptional modification of eukaryotic RNAs, constitute two core epigenetic regulatory systems that orchestrate gene expression programs in both physiological and pathological processes, especially during tumorigenesis (83,84). The crosstalk between these two modifications constructs a complex, multi-layered regulatory network that functions at the protein, RNA and chromatin levels.

Ubiquitin-m6A crosstalk at the protein level

At the protein level, crosstalk is primarily defined by reciprocal regulation between the ubiquitination machinery (E3 ligases and DUBs) and m6A regulators (writers, readers and erasers) (85,86). This reciprocal interplay fine-tunes the abundance and activity of m6A modifiers, thereby indirectly shaping the global m6A landscape and governing the downstream RNA metabolism (87).

Ubiquitination directly modulates the stability of m6A writers, the core components responsible for m6A deposition (88). For instance, METTL14, a core subunit of the m6A methyltransferase and a key determinant of cellular m6A homeostasis, is precisely targeted by the E3 ubiquitin ligase STUB1. STUB1 catalyzes K48-associated polyubiquitination at lysine residues K148, K156 and K162 of METTL14, thereby promoting its proteasomal degradation (88,89). Notably, METTL3, another core writer subunit, competes with STUB1 for binding to METTL14, thus shielding METTL14 from ubiquitin-dependent degradation and preserving m6A homeostasis in cells (90). Dysregulation of the METTL3-STUB1-METTL14 axis disturbs m6A equilibrium and drives malignant progression, highlighting the therapeutic potential of targeting STUB1 to modulate METTL14 ubiquitination and cellular m6A levels. Furthermore, the m6A writer METTL3 is itself regulated by PTMs. SUMOylation, a modification associated with ubiquitination, occurs at its lysine residues and represses its m6A methyltransferase activity; additional ubiquitination events, which remain incompletely characterized, might further fine-tune its function (91).

Conversely, m6A modification indirectly governs the ubiquitination machinery by modulating the expression or activity of E3 ligases and DUBs. For example, the m6A reader YTHDF2, whose expression is upregulated by melatonin in ovarian cells, enhances the expression of E3 ligase Ubiquitin-conjugating enzyme (UBE)3C via m6A-dependent regulation (92). UBE3C subsequently catalyzes the polyubiquitination and degradation of the senescence-related protein p53, thereby attenuating ovarian aging and potentially influencing the survival of tumor cells (93). This YTHDF2/m6A/UBE3C/P53 axis illustrates how m6A readers associate RNA modification to protein ubiquitination, thereby directing cellular fate decisions.

Ubiquitin-m6A crosstalk at the RNA level

At the RNA level, ubiquitination and m6A modification converge to regulate RNA metabolism, including mRNA stability, translation, splicing and nuclear export (94). This crosstalk is mainly mediated either by m6A readers that recruit ubiquitination machinery to target RNAs, or by ubiquitination of RNA-binding proteins that modulate their interaction with m6A-modified RNAs.

A key mechanism involves m6A readers serving as adaptors that bridge m6A-modified RNAs to E3 ubiquitin ligases, thereby promoting the ubiquitination and degradation of target RNAs or their associated proteins. For example, in acute myeloid leukemia (AML), the m6A writer METTL3 mediates m6A modification of FOXO3 mRNA, enhancing its stability and expression (95). Subsequently, the expressed protein FOXO3 regulates autophagy, promoting AML cell proliferation and resistance to anthracycline chemotherapy. The stability of m6A-modified FOXO3 mRNA is tightly controlled by a balance between m6A-mediated stabilization and potential ubiquitination of RNA-bound proteins that regulate its turnover. Similarly, the m6A reader YTHDF2 binds to m6A-modified RNAs and recruits the CCR4-NOT deadenylase complex, which may be further regulated by ubiquitination to modulate mRNA degradation efficiency (96).

Ubiquitination of m6A readers and/or erasers also modulates their ability to interact with m6A-modified RNAs. For instance, ubiquitination of the m6A eraser ALKBH5 by E3 ligases (for example, RNF130) regulates its sub-cellular localization and RNA-binding activity, thereby altering the global m6A levels and impacting RNA splicing and translation. Moreover, in gastric cancer, METTL3-mediated m6A modification of RAB27A mRNA promotes its expression, thereby enhancing exosome biogenesis (97). These exosomes, enriched in miRNA-17-92 clusters, reshape the peritoneal immune microenvironment to facilitate tumor metastasis (97), highlighting the downstream oncogenic consequences of RNA-level ubiquitin-m6A crosstalk.

Ubiquitin-m6A crosstalk at the chromatin level

At the chromatin level, ubiquitin-m6A crosstalk regulates transcriptional dynamics and chromatin structure by coordinating histone ubiquitination, m6A modification of chromatin-associated RNAs (caRNAs), and the recruitment of epigenetic regulatory complexes (98). This layer of crosstalk directly influences gene transcription, particularly oncogenes and tumor suppressors, by shaping chromatin accessibility and transcriptional elongation.

A striking example is the co-transcriptional regulation of m6A modification governed by chromatin-associated ubiquitination cascades. The DEAD-box helicase DDX21 associates with the m6A writer complex (METTL3/METTL14/WTAP) and colocalizes with R-loops (DNA-RNA hybrid structures) at chromatin regions (99). DDX21, whose enzymatic activity can be modulated by ubiquitination, facilitates the recruitment of METTL3 to chromatin, thereby promoting co-transcriptional m6A modification on caRNAs (100). In turn, such m6A marks recruit the reader protein YTHDC1, which enhances XRN2-mediated transcription termination and preserves genome stability. Dysregulation of this R-loop-DDX21-METTL3-m6A regulatory axis disrupts transcriptional homeostasis and compromises genome integrity, ultimately driving tumorigenesis.

In addition, m6A modification of ncRNAs involved in chromatin regulation is capable of modulating histone ubiquitination. For example, in Arabidopsis, m6A modification of retrotransposon RNAs recruits m6A readers (CPSF30-L and ECT12), which in turn recruit histone methyltransferases to promote inhibitory histone modifications (H3K9me2 and H3K27me1), silencing retrotransposon transcription and maintaining chromatin stability (101). While this mechanism is well-characterized in plants, emerging evidence suggests the existence of similar crosstalk in mammalian cells, where m6A-modified ncRNAs regulate histone ubiquitination and chromatin state to regulate the expression of oncogenes.

Downstream effects on oncogenic signaling

Crosstalk between ubiquitination and m6A RNA modification is key in modulating oncogenic signaling pathways (102). Primarily, m6A marks regulate the stability, splicing, translation and localization of mRNAs encoding oncogenes or tumor suppressors, thereby modulating signaling activity at the post-transcriptional level (103). On the contrary, components of the ubiquitination machinery control the protein stability, abundance and sub-cellular distribution of m6A writers, erasers and readers, leading to dynamic changes in the global m6A landscape and influencing downstream pathway outputs (87). In addition, m6A modification is also able to affect the expression or activity of E3 ubiquitin ligases and deubiquitinases, creating reciprocal feedback loops that fine-tune signaling strength. Studies showed that the m6A eraser FTO impaired gemcitabine resistance in pancreatic cancer by influencing the stability of NEDD4 mRNA through regulation of the PTEN/PI3K-AKT pathway (104). TRIM17, a member of the TRIM family with E3 ligase activity, has recently been implicated in the progression of various tumors, particularly in promoting cancer cell clonogenicity, survival and drug resistance (105). TRIM17 promotes the ubiquitination and degradation of FTO, enhances PDK1 mRNA stability via m6A modification, and subsequently facilitates phosphorylation-dependent activation of the AKT/mTOR signaling pathway, thereby driving osteosarcoma progression (12). UBE2C is also involved in tumorigenesis, and studies have revealed that METTL3 upregulates UBE2C expression through m6A modification, activating the PI3K-AKT pathway and promoting the development of retinoblastoma (106,107). Ubiquitination and m6A modifications can regulate the mTORC1/p70S6K signaling pathway, thereby contributing to docetaxel resistance and liver metastasis (108). Furthermore, TP53TG1 contains abundant m6A modification sites, and the demethylase ALKBH5 reduces its stability and expression (109). TP53TG1 interacts with cancerous inhibitor of protein phosphatase 2A and triggers its ubiquitin-mediated degradation, leading to inhibition of the PI3K-AKT pathway in gastric cancer (109).

Conclusions and perspectives

Ubiquitination and m6A RNA methylation have emerged as two highly dynamic and interconnected regulatory systems shaping almost every aspect of cancer biology (110). Accumulating evidence demonstrates the interactions of the two pathways: They converge to modulate the stability, localization and activity of key oncogenic signaling proteins and RNAs (111). Through multilayered crosstalk, the two pathways jointly influence hallmark cancer processes, including proliferation, stemness, metabolic reprogramming, immune evasion and therapeutic resistance (112). Based on the existing evidence, the present review advances the field in several important ways. The multi-layered crosstalk between ubiquitination and m6A modification at the protein, RNA and chromatin levels is systematically summarized, and how these two regulatory systems converge on core oncogenic signaling pathways to cooperatively modulate tumor cell proliferation, metastasis, metabolic reprogramming and therapeutic resistance has also been discussed. In addition, the present review highlights the context-dependent nature of ubiquitin-m6A crosstalk and identifies key regulatory nodes with diagnostic and therapeutic potential. By providing a unified conceptual framework, the present review deepens mechanistic knowledge of cancer signaling networks and offers clear directions for the development of novel targeted strategies and combination therapies in precision oncology.

Unfortunately, current understanding remains fragmented. To date, the majority of studies have focused on individual molecules or pathways, leaving the broader regulatory network largely uncharacterized (113,114). The context-dependent roles of m6A and ubiquitination further complicate interpretations, as the same enzyme can act as either an oncogene or a tumor suppressor, depending on the tumor type or micro-environment. In addition, how these pathways integrate signals from stress, inflammation and metabolism to rewire oncogenic circuits remains largely defined.

The bidirectional interplay between ubiquitination and m6A modification provides a strong rationale for combination therapies, such as PROTACs combined with m6A inhibitors. PROTACs leverage E3 ligases to induce targeted degradation of oncogenic proteins, while m6A inhibitors (for example, METTL3 inhibitors and YTHDF2 inhibitors such as DC-Y13-27) disrupt m6A-dependent RNA metabolism. Combining these agents yields synergistic effects by simultaneously targeting the ubiquitin-m6A network at both the protein and RNA levels: For example, PROTACs directed against oncogenic E3 ligases (such as STUB1) can restore the stability of METTL14, while m6A inhibitors further normalize m6A modification profiles, collectively reversing the dysregulation of oncogenic signaling pathways. For instance, co-targeting the m6A writer METTL3 and the E3 ligase STUB1 represents a rational dual-modulation strategy: STUB1 inhibition blocks METTL14 ubiquitination and degradation to restore m6A homeostasis, while METTL3 inhibitors correct aberrant m6A landscapes, thereby synergistically reversing oncogenic signaling hyperactivation (88,89).

In addition, combining YTHDF2 inhibitors with radiotherapy or immunotherapy enhances anti-tumor efficacy by overcoming myeloid-derived suppressor cells-induced immune suppression, highlighting the translational potential of targeting ubiquitin-m6A crosstalk in combination regimens. Key translational challenges remain substantial: First, off-target effects are prevalent due to the pleiotropic and ubiquitous functions of ubiquitin and m6A regulators; second, strong context specificity means the same target may exert opposing oncogenic or tumor-suppressive effects across cancer types; third, several small-molecule inhibitors targeting E3 ligases, DUBs and m6A modifiers show poor solubility and bioavailability, which compromise in vivo delivery and therapeutic efficacy (3,50,115).

Other limitations also exist. Firstly, current understanding of ubiquitin-m6A crosstalk remains largely molecule- or pathway-specific rather than systematic and the strong context specificity of regulatory axes has not been fully categorized. Secondly, although to summarize the compiling key regulators, signaling pathways and cancer types, as well as a focused discussion on biomarkers and combination therapies would provide a clearer reference, the present review prioritizes mechanistic dissection over large-scale summary and clinical translation. Moreover, several areas warrant further in-depth investigation. Systematic mapping of ubiquitination-m6A crosstalk across diverse cancer types and single-cell contexts holds great potential to uncover novel regulatory nodes and clinically relevant biomarkers (116). Structural and biochemical analyses are imperative to elucidate how ubiquitination modulates the m6A regulatory machinery and how m6A modification, in turn, reciprocally affects ubiquitination processes. Expanding research efforts into the roles of such crosstalk in immune regulation and the tumor micro-environment may reveal previously unrecognized links that are key to immunotherapy response. From a therapeutic perspective, targeting the interplay between these two pathways represents a highly promising direction for anticancer drug development. Dual-modulation strategies, selective degraders and inhibitors targeting specific enzyme interfaces are expected to yield next-generation anticancer agents with enhanced precision and diminished off-target toxicity (117).

In summary, the convergence of ubiquitination and m6A modification constitutes a fundamental layer of post-transcriptional and post-translational regulation in cancer. Deciphering their integrated regulatory networks will not only deepen the current understanding of tumor biology but also pave new avenues for the innovation of diagnostic strategies and therapeutic interventions.

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Acknowledgements

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Funding

The study was supported by grants from the Wings Scientific and Technological Foundation of The First People's Hospital of Changde City (grant no. 2025ZC04) and the Changde City Science and Technology Innovation Guidance Plan Project (grant no. 2025ZD245).

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Authors' contributions

HL drafted the original manuscript. XL supervised the project and revised the manuscript critically. Data authentication is not applicable. Both authors have read and approved the final manuscript.

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Competing interests

The authors declare that they have no competing interests.

Glossary

Abbreviations

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References