METTL3, one of the methyltransferases responsible for m6A methylation, has been shown to potentially contribute to cancer radioresistance by improving DNA repair capacity in malignant cells, promoting CSCs generation, and inducing tumor cell autophagy.

The methyltransferase WTAP enhances stemness and EMT in tumor cells, which in turn increases radioresistance. NRP1, a transmembrane glycoprotein, is highly expressed across multiple cancer types. Studies have shown that radiotherapy alone significantly increases double-strand DNA (dsDNA) damage in breast cancer (BC) cells, whereas NRP1 overexpression combined with radiotherapy does not significantly affect dsDNA breaks, indicating that NRP1 plays a key role in BC radioresistance. Mechanistically, NRP1 downregulates Bcl-2 expression in BC through WTAP-mediated m6A modification, thus reducing radiation-induced apoptosis, promoting stemness in BC cells, and increasing their radioresistance (19). Similarly, Liu et al. reported that, after irradiation, WTAP overexpression in gastric cancer (GC) cells promotes EMT by accelerating TGF-β signaling, increasing radioresistance, whereas WTAP downregulation reduces radioresistance (20). Additionally, WTAP stabilizes SQLE mRNA expression through an m⁶A-dependent mechanism, enhancing CSC properties in high-grade serous ovarian carcinoma (HGSOC), which may indirectly contribute to radioresistance (61). These studies demonstrate that WTAP regulates downstream gene expression through m6A modification across multiple cancer types, affecting radioresistance.

METTL14 is a well-characterized m6A regulator. In ESCC cells, METTL14 promotes pri-miR-99a maturation and miR-99a-5p stability, enhancing stemness in cancer cells and increasing radioresistance (21). Additionally, METTL14 mediates the regulation of radioresistance through ferroptosis pathways. Studies demonstrate that METTL14 reverses radioresistance in ESCC by promoting ferroptosis via enhanced m⁶A modification of ACSL4 (62). In endometrial cancer (EC), protein arginine methyltransferase 3 (PRMT3)-mediated METTL14 promotes ferroptosis sensitivity by reducing the expression and stability of glutathione peroxidase 4 (GPX4). Further studies have revealed that PRMT3 inhibition increases radiosensitivity, whereas PRMT3 depletion suppresses radioresistance by promoting ferroptosis in EC (22). In acute myeloid leukemia (AML), AML-derived mesenchymal stem cells (AML-MSCs) deliver METTL14 to leukemia cells via exosomes, where it stabilizes ROCK1 expression through the m⁶A-IGF2BP3 axis, thereby mediating radioresistance. Specifically, exosome-transferred METTL14 enhances the m⁶A modification of ROCK1 mRNA, facilitating its binding to and stabilization by the reader protein IGF2BP3. Consequently, ROCK1 protein levels are upregulated, driving AML cell proliferation and contributing to radioresistance (63).

Research indicates that the m⁶A reader protein YTHDC2 plays a critical role in radioresistance across various malignancies, with IGF1R acting as the central hub mediating YTHDC2-driven therapeutic resistance. In NPC, previous studies demonstrate that IGF1R inhibition, such as through Linsitinib, blocks downstream Akt/ERK phosphorylation, suppresses proliferation, induces apoptosis, and significantly radiosensitizes tumors by reversing resistance. This highlights the therapeutic targeting potential of IGF1R and establishes a definitive association between IGF1R and NPC radioresistance (64). Further investigations reveal that YTHDC2 is highly expressed in radioresistant NPC cells and clinical specimens. It facilitates the translation of IGF1R, activating the PI3K-AKT/S6 signaling pathway to confer radioresistance, thereby emerging as a promising therapeutic target for NPC radiosensitization. Experimentally, the depletion of YTHDC2 downregulates IGF1R expression and suppresses PI3K-AKT/S6 signaling, consequently alleviating radioresistance in NPC cells (23). In neuroblastoma (NB), the activation of the STAT3/AKT axis stimulates CSC properties and EMT, both of which are intrinsically linked to radioresistance. Although the response to radiotherapy remains untested in NB, the identified IGF1R-kinase signaling (STAT3/AKT)-CSC/EMT mechanistic logic aligns with the NPC axis, demonstrating a shared dependence on IGF1R-driven downstream pathways to sustain resistance phenotypes (65). Therefore, targeting YTHDC2, IGF1R, or their downstream kinases (PI3K/AKT, STAT3) represents a viable strategy to overcome radioresistance and achieve radiosensitization by suppressing CSC traits and aberrant signaling cascades.

The m6A “reader” protein YTHDF3 contributes to radiotherapy resistance by modulating gene expression. A study by Du et al. found that the levels hepatocyte nuclear factor 1-alpha (HNF1-α) are markedly higher in radiotherapy-resistant cervical cancer (CC) tissues and cell lines. This upregulation increases the transcription of YTHDF3, leading to m6A modifications of RAD51D mRNA. Furthermore, YTHDF3 mediates HNF1-α-regulated radiotherapy resistance in CC by promoting m6A-dependent translation of RAD51D translationr. Depletion of HNF1-α reduces radiotherapy resistance, whereas its overexpression enhances it in CC cells and tissues. In summary, YTHDF3 affects radiotherapy resistance in CC cells (24).

FTO, a critical RNA m⁶A demethylase, plays a pivotal role in radioresistance across diverse malignancies. It drives therapeutic resistance through epitranscriptomic regulation of downstream effectors, including CSC properties, EMT, DNA repair, and oncogenic signaling pathways.Studies demonstrate that in colorectal cancer, cytoplasmic FTO suppresses CSC phenotypes via its m⁶A demethylase activity. Conversely, low FTO expression induces m⁶A hypermethylation, significantly enhancing the in vivo tumorigenicity and radioresistance of CSCs (66). In lung adenocarcinoma (LUAD), FTO stabilizes PHF1 mRNA through demethylation, forming a tumor-suppressive axis. The downregulation of the FTO/PHF1 axis promotes tumor cell self-renewal, progression, and poor prognosis by enhancing FOXM1 expression, thereby compromising therapeutic efficacy (67). Breast cancer research reveals that chemotherapy-induced senescent neutrophils upregulate intratumoral FTO via exosomal piR-17560 secretion. Elevated FTO subsequently reduces m⁶A modification on ZEB1 mRNA, stabilizing its transcript and promoting EMT and radioresistance (68). In glioblastoma (GBM), pharmacological inhibition of FTO (e.g., using FB23-2) increases m⁶A modification on the target gene VEGFA, downregulating its expression and impairing DNA damage repair (e.g., sustaining γH₂AX foci and reducing Rad51 recruitment). This significantly enhances the radiosensitivity of glioblastoma stem cells (GSCs), suppresses tumor growth, and prolongs survival, indicating that FTO upregulation promotes GBM radioresistance (69). Additionally, FTO in NPC promotes OTUB1 expression by erasing m⁶A marks on OTUB1 transcripts, suppressing radiation-induced ferroptosis (25), and induces CD44 splice variant switching (CD44v) via lncRNA-HOTAIRM1 interaction to inhibit ferroptosis, collectively driving radioresistance (26). In CSCC, FTO upregulates β-catenin expression by reducing the m⁶A levels of its mRNA, thereby enhancing chemoradioresistance both in vitro and in vivo (27). Collectively, FTO acts as a core determinant of pan-cancer radioresistance, positioning it as a promising therapeutic target for overcoming resistance and improving the efficacy of radiotherapy.

ALKBH5, an m6A “eraser”, increases radiotherapy resistance in hepatocellular carcinoma (HCC) and GBM by influencing CSCs. CSCs are closely linked to cancer therapy resistance through various pathways, including activating DNA damage repair processes, the EMT, and modulating the levels of genes associated with self-renewal (28, 29). Studies demonstrate that elevated expression of ALKBH5 enhances glioblastoma (GBM) radioresistance by modulating homologous recombination (HR) (70). Further investigations confirm that glioblastoma stem cells (GSCs) are the primary source of radioresistance in GBM, with the MST4-USP14-ALKBH5 signaling axis serving as its core mechanism. Specifically, ALKBH5 undergoes deubiquitination mediated by USP14 (a deubiquitinase), which confers protein stability that is further potentiated by phosphorylation from the upstream kinase MST4. This pathway sustains GSC stemness and tumorigenicity, while robustly promoting DNA damage repair and driving therapeutic radioresistance (71). Liver cancer stem cells (LCSCs) exhibit CSC-like properties and significantly affect HCC progression and therapeutic resistance (72). ALKBH5 is upregulated in LCSCs, where it promotes SOX4 expression through demethylation. The ALKBH5/SOX4 axis enhances LCSC properties by the activation of SHH signaling (73). In summary, ALKBH5 overexpression in HCC may contribute to radiotherapy resistance.

In NSCLC, m6A RNA methylation-mediated regulation of mitochondrial RNA-processing endoribonuclease (RNase MRP) enhances the properties of cancer stem cells and promotes the EMT through the TGFB/SMAD2/SMAD3 pathway, thus contributing to radiotherapy resistance (74). Meanwhile, m6A-modified enhancer RNAs (eRNAs) are closely linked to the progression of bone-metastatic prostate cancer (mPCa) and its resistance to radiotherapy. Zhao et al (75) employed RNA sequencing and other methods to identify the m6A-modified bone-specific eRNA, MLXIP, associated with radiotherapy resistance. This eRNA inhibits RNA degradation by facilitating the interaction between the RNA-binding protein KHSRP and mRNA, affecting PC progression and its sensitivity to radiotherapy.

FMRP is an m5C “reader” that recognizes and binds to m5C-modified RNA. Through its interaction with the m5C eraser ten-eleven translocation protein 1 (TET1), FMRP induces the demethylation of m5C RNA modifications, therefore promoting mRNA-dependent DNA damage repair processes (34). Furthermore, FMRP interacts with the m5C methyltransferase TRDMT1, which facilitates transcription-coupled homologous recombination at reactive oxygen species (ROS)-induced DSBs through the TRDMT1– m5C-RAD52-RAD51 axis (31). The absence of FMRP and TRDMT1 increases radiation sensitivity in BC cells (30, 31), and BC cells with low TRDMT1 expression exhibit greater sensitivity to radiotherapy (31).

The mechanistic and functional diversity of NSUN6-mediated tumor radioresistance operates through the m⁵C-NDRG1 axis. Yu et al. discovered that in cervical cancer, NDRG1, as a transcriptional regulatory target of NSUN6, participates in radioresistance mechanisms. Elevated NSUN6 expression initiates the NSUN6/ALYREF-m⁵C signaling cascade, enhancing NDRG1 stability by augmenting its m⁵C RNA methylation levels, ultimately conferring radioresistance (33). Given that NDRG1 significantly promotes tumor progression and brain metastasis in aggressive breast cancer (83), NSUN6 may potentially co-drive breast cancer radioresistance via NDRG1 regulation. However, the molecular interactome of this signaling axis in breast cancer remains to be elucidated further. Conversely, NDRG1 exhibits context-dependent functional reversal in HCC, where it significantly suppresses HCC tumorigenesis and metastasis by inducing tumor cell ferroptosis (84). This highlights the cancer type-dependent biological effects mediated by NDRG1.Whether the NSUN6-m⁵C-NDRG1 axis universally drives pan-cancer radioresistance requires.

NSUN2, an m5C “writer,” participates in radiotherapy resistance by regulating gene expression. Niu et al. found that cis-expression quantitative trait loci (cis-eQTLs) in NSUN2 promote radiotherapy resistance in ESCC through mRNA-m5C methylation. Mechanistically, the NSUN2 rs10076470 G-to-A mutation acts as a cis-eQTL for STAT1, a key transcription factor that is markedly upregulated in ESCC. This genetic variation increases NSUN2 activity, leading to enhanced m5C methylation and upregulation of multiple cancer-related genes, promoting ESCC progression and increasing resistance to radiotherapy (32).

RNA methylation can serve as a biomarker for identifying malignant tumors resistant to radiotherapy. In GBM, METTL3 expression is associated with radioresistance, and its downregulation reduces DNA damage repair and increases radiosensitivity (12). Similarly, in NSCLC, METTL3 is upregulated, and its knockout increases cellular sensitivity to radiotherapy (14). These findings suggest that RNA methylation levels can function as biomarkers to predict radiotherapy efficacy, facilitating the identification of radiotherapy-resistant patients and enabling individualized precision treatment.

Enzymes involved in RNA methylation modifications and their downstream regulatory targets hold significant therapeutic potential for overcoming radiotherapy resistance across various cancers. Studies have shown that METTL3 increases radiotherapy resistance in OSCC by targeting SALL4 (13), while METTL3 knockdown increases PDAC cell sensitivity to low-dose radiotherapy, suggesting its possible application as a target in treating the disease (15). In NPC, METTL3-mediated m6A methylation upregulates KIF15 expression, contributing to radiotherapy resistance. Inhibiting KIF15 expression has been found to mitigate this resistance (17). Collectively, these findings suggest that METTL3 is a promising therapeutic target for radiosensitization across various cancer types. Currently, small-molecule inhibitors targeting METTL3 are undergoing preclinical investigation (95), which may inform future combinatorial radiosensitization strategies. Similarly, in CSCC, FTO promotes β-catenin expression by reducing m6A modification levels, aggravating radiotherapy resistance. This suggests that targeting FTO or β-catenin may optimize therapeutic outcomes (27). However, FTO exhibits broad substrate specificity. Targeting FTO may influence the expression of metabolism-related genes, potentially resulting in metabolic dysregulation. This underscores the necessity for more precise strategies to target RNA methylation (69, 96). Furthermore, m5C modification-related proteins, including FMRP and members of the NSUN family, as well as the key m7G tRNA modification enzyme METTL1, have been reported to be involved in regulating the radiotherapy response in malignant tumors. Inhibiting the activity of these modification enzymes has been shown to improve radiotherapy efficacy in killing cancer cells (30–33). These findings not only highlight the key role of RNA methylation modifications in radiotherapy resistance but also provide diverse potential targets for developing precision radiotherapy sensitization strategies based on RNA modification regulation, offering significant clinical implications.

Combining methylation-modulating inhibitors with radiotherapy has been shown to suppress tumor growth and progression. Research indicates that STM2457, a novel inhibitor targeting METTL3, exhibits significant efficacy in preclinical models of AML (97). To evaluate its anti-leukemic effects in conjunction with radiotherapy, experiments were conducted using METTL3-knockout cells and murine models. The results demonstrate that the targeted inhibition of METTL3 by STM2457, when combined with in vivo radiotherapy, synergistically suppresses tumor growth (95). Furthermore, Zhang et al. found that inhibiting METTL3 enhances the radiosensitivity of HCC by activating the radiation-induced ferroptosis pathway (60). Additionally, studies have shown that the FTO inhibitor FB23-2, when combined with radiotherapy, significantly inhibits tumor spheroid formation and the self-renewal capacity of GSCs, suppresses cell proliferation, and induces apoptosis in GBM cells. Animal experiments further confirmed that FB23-2 combined with radiotherapy effectively inhibits intracranial tumor growth in mice (69). Collectively, these findings suggest that the targeted inhibition of METTL3 and FTO, in combination with radiotherapy, enhances the suppression of tumor growth and progression.

Moreover, studies have indicated that cyclooxygenase-2 (COX-2) is a potential target for radioprotection and radiosensitization. Inhibition of COX-2 (e.g., celecoxib) can reduce the resistance of malignant tumor cells to radiotherapy (98). In NPC, the resistance to radiotherapy is primarily mediated by EBV-encoded products (such as LMP1) and non-coding RNAs (miRNA/lncRNA/circRNA), which inhibit DNA damage repair, activate anti-apoptotic pathways (such as PI3K/AKT, NF-κB), and promote EMT. Combined chemoradiotherapy or targeting EBV/non-coding RNAs (e.g., olaparib inhibiting miR-519d, curcumin downregulating lncRNA AK294004) can reverse radiotherapy resistance (99).

In summary, targeting epigenetic regulation (such as METTL3, FTO, COX-2 inhibitors) or viral/non-coding RNA pathways (such as EBV-LMP1, miRNA/lncRNA), in conjunction with radiotherapy, can significantly enhance antitumor efficacy through synergistic mechanisms, providing new strategies to reverse radiotherapy resistance.