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.

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).

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).

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.

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.

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.

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.

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.