Mitochondria at the intersections of RNA modifications and metabolism reprogramming implications in cell death, tumor microenvironment, and immunotherapy.

Here, we summarize the potential role of RNA modifications in regulating mitochondria-related antitumor immunity based on recent findings, with the aim of providing new scientific research directions for tumor treatment at the posttranscriptional level (Fig.  6 ). Fig. 6 RNA modifications in the regulation of mitochondria-related tumor microenvironment. Mitochondria-related glucose metabolism, regulated cell death and mitochondrial dynamics are significantly correlated with the dynamic changes of the TME and tumor immune response. The role of RNA modifications in the regulation of the TME has not been discussed, yet it can be hypothesized and deduced. RNA modifiers that regulate the key molecules of mitochondria-related TME include writers (red), readers (blue) and erasers (yellow). TME tumor microenvironment RNA modifications in the regulation of mitochondria-related tumor microenvironment. Mitochondria-related glucose metabolism, regulated cell death and mitochondrial dynamics are significantly correlated with the dynamic changes of the TME and tumor immune response. The role of RNA modifications in the regulation of the TME has not been discussed, yet it can be hypothesized and deduced. RNA modifiers that regulate the key molecules of mitochondria-related TME include writers (red), readers (blue) and erasers (yellow). TME tumor microenvironment The intimate metabolic interplay between glucose metabolism in cancer cells and immune cells in the TME is crucial for cancer immunity. Pan-cancer single-cell RNA-seq data revealed that GLUT1 is highly expressed in cancer cells, while GLUT3 exhibits elevated expression in immune cells, indicating distinct regulatory mechanisms governing glucose transporter families in cancer and immune cells, with RNA modifications potentially serving as a regulatory factor [ 280 ]. A dual-targeting strategy combining GLUT1/NSUN2 axis inhibitor WZB117 with PD-L1 blockade, which synergistically suppressed tumor evolution and reversed immunosuppression in preclinical models, suggesting a novel synergistic therapeutic strategy for treatment-resistant HCC [ 41 ]. In addition to GLUTs, high glucose levels in glioblastoma and breast cancer cells, promote the dissociation of HK2 from mitochondria and positively mediate PD-L1 expression via the IκBα/NF-κB pathway [ 281 , 282 ]. Conversely, it has also been reported that PD-L1 enhances glycolysis in NSCLC by upregulating HK2 [ 283 ]. An in vivo study has confirmed that the cGAS-STING pathway can inhibit HK2 to restrict tumor aerobic glycolysis and promote antitumor immunity [ 284 ]. Considering that RNA modifications significantly regulate the expression of HK2, it is reasonable to hypothesize that m 6 A modifiers, including METTL3, METTL14, KIAA1429, YTHDC1, YTHDF1-3, IGF2BP2, FTO and ALKBH5, may mediate PD-L1 expression and tumor immune escape through the regulation of HK2 mRNA modifications. The role of another key enzyme in glycolysis, PFK, in antitumor immunity has been obscured by recent findings. PFKFB3 can upregulate PD-L1 expression via the EGFR/ERK/c-Jun pathway in renal cell carcinoma. Conversely, elevated PD-L1 expression can reciprocally enhance PFKFB3 levels [ 285 ]. However, a separate study indicated that the inhibition of PFKFB3 activated HIF-1α and transcriptionally upregulated PD-L1 expression with reduced levels of CD8 and GZMB and shorter survival times in ESCC patients, suggesting that PFKFB3 may act as a protumor-immunity factor [ 286 ]. RNA modifications mediated by METTL3, METTL14, IGF2BP2, YTHDF1-3 and FTO directly or indirectly regulate PFK expression, indicating that RNA modifications may modulate PD-L1 expression through PFK. Further investigation is needed to determine whether the distinct role of PFK in antitumor immunity is influenced by RNA modifications. Lactate has been shown to play a pivotal role in tumor immunosuppression, with potential involvement of RNA modifications. Tumor cell-derived lactate accumulates in the TME and is sensed by its receptor, G protein-coupled receptor 81 (GPR81). The activation of GPR81 leads to the activation of the TAZ/TEAD pathway which transcriptionally induces PD-L1 expression [ 287 ]. The production and secretion of lactate can be modulated by the tumor suppressor gene serine/threonine kinase STK11 encoding the LKB1 protein (STK11/LKB1). Notably, mutations in STK11 /LKB1 are associated with increased expression of MCT4 and enhanced lactate secretion, as well as the polarization of M2 macrophages and the suppression of cytotoxic T cells [ 288 ]. An in vivo study demonstrated that tumor-derived lactate activated macrophage G protein-coupled receptor 132 (GPR132), promoting the tumor associated macrophage (TAM) phenotype in breast cancer [ 289 ]. A similar molecular mechanism was identified in lung cancer, where OLFR78 collaborates with GPR132 to mediate the lactate-induced generation of TAMs [ 290 ]. Moreover, lactate facilitates M2 polarization through the mTORC2 and ERK signaling pathway [ 291 ]. Interestingly, lactate-induced M2 TAMs enhance tumor cell proliferation in pituitary adenoma via the CCL17/CCR4/LDH/lactate axis. A feed-forward loop exists between TAMs and tumor cells, as lactate upregulates HIF-1α-stabilizing long noncoding RNA (HISLA) in macrophages, subsequently inhibiting the hydroxylation and degradation of HIF-1α in breast cancer [ 292 ]. Lactate in the TME can impede the activation and functionality of cytotoxic CD8 + T cells. Numerous studies have demonstrated various lactate-induced metabolic alterations in CD8 + T cells [ 293 , 294 ]. In the absence of extracellular lactate, cytotoxic T cells depend on pyruvate carboxylase (PC) to replenish TCA cycle intermediates and shunt succinate out of the TCA cycle to facilitate autocrine signaling via the succinate receptor (SUCNR1), ultimately promoting the production and secretion of cytotoxic cytokines and GZMB. However, extracellular tumor-derived lactate reduces PC-mediated anaplerosis and redirects pyruvate flux from PC to PDH, reactivating succinate dehydrogenase (SDHA) and resulting in succinate oxidation rather than secretion. This sequence of events leads to increased production of fumarate but a decreased capacity to activate SUCNR1 due to reduced succinate secretion, which impairs CD8 + T cell effector function and inhibits antitumor immunity. Furthermore, recent studies have examined the positive role of lactate in enhancing the stemness of CD8 + T cells, which appears slightly contradictory to findings regarding its immunosuppressive role reported in other studies. Recent studies have confirmed that the administration of lactate inhibits the activity of histone deacetylase, leading to increased acetylation at H3K27 of the TCF7 super enhancer locus and increased TCF1/TCF7 gene expression, thereby upregulating CD8 + T cell stemness [ 295 ]. Conversely, Hermans D et al. reported that LDH inhibition rewired IL-2-induced effector-like metabolism, promoted pyruvate entry into the TCA cycle and subsequent OXPHOS, and suppressed the expression of IL-21-induced exhaustion markers, enhancing the formation of stem cell memory T cells (T SCM ) and augmenting antitumor immune responses [ 296 ]. Therefore, the role of lactate in contributing to CD8 + T cell stemness warrants further investigation. Furthermore, lactate in the TME plays a critical role in the functionality of regulatory T (Treg) cells [ 297 ]. Treg cells actively uptake lactate through MCT1, which facilitates the NFAT1 translocation into the nucleus, thereby promoting the expression of PD-1 and contributing to tumor immune inhibition [ 298 ]. The lactylation of lysine residues in MOESIN improves its interaction, subsequently activating the TGF-βRI/SMAD3/FOXP3 signaling cascade and augmenting Treg functions [ 299 ]. Research indicates that lactate derived from tumors has a negative effect on NK cells, diminishing NFAT levels and impairing NK cells activation, which results in reduced production of IFN-γ and inhibited tumor immunosurveillance [ 294 ]. In hepatocellular carcinoma, tumor-derived lactate induces the expression of PD-L1 on neutrophils via the MCT1/NF-κB/COX-2 signaling cascade, leading to decreased T cell cytotoxicity and compromised antitumor immunity [ 300 ]. Importantly, RNA modifications participate in the regulation of lactate production in tumor cells via the expression of LDH. m 6 A modifiers that regulate LDH expression, including METTL3, METTL14, YTHDF1 and YTHDF2, might play a pivotal role in the modulation of lactate production, secretion and accumulation in the TME. Fumarate, a metabolite generated in the TCA cycle, plays a significant role in tumor immunosurveillance. Depletion of Fumarate hydratase in tumor cells causes an accumulation of fumarate in the TME, which directly succinates ZAP70 at C96 and C102 and effectively blocks the phosphorylation of the ZAP70 substrate LAT as well as the downstream TCR signaling pathway, leading to suppressed CD8 + T cell activation and reduced IFN-γ, TNF-α and GZMB production [ 301 ]. Tumor cell metabolism also generates FFAs that promote fatty acid oxidation (FAO) in TAMs, which in conjunction with lactate produced by anaerobic glycolysis and the enhanced OXPHOS in macrophages, collectively induces the M2 polarization of these cells, leading to the formation of an immunosuppressive tumor microenvironment, further enabling tumor cells to evade immune surveillance and sustain proliferation [ 302 ]. The TCA cycle can be indirectly regulated by RNA modifications through NSUN2 and ALKBH5, while the ETC can be mediated by METTL3, METTL8, WTAP, NSUN2, NSUN3, IGF2BP1, IGF2BP3 and ALKBH3, suggesting that RNA modifications may regulate antitumor immunity via the TCA cycle and OXPHOS in tumor cells. The interaction between RNA modifications and glucose metabolism in the antitumor immune response has not been extensively reported, until recently, an interesting study produced by Chen T et al. revealed that the m 5 C writer NSUN2 is a glucose sensor that directly binds to glucose, which posttranscriptionally stabilizes three prime repair exonuclease 2 (TREX2) mRNA and sustains its expression. TREX2 degrades cytosolic DNA, repressing cGAS-STING activation, leading to less apoptosis of tumor cells and downregulated CD8 + T cell infiltration in the TME, ultimately enhancing resistance to immunoblockade therapy [ 17 ]. In macrophages, GLUT1 and glycolysis can be upregulated through the tumor-derived exosome (TDE)/TLR2/NF-κB/HIF-1α signaling pathway, leading to increased cellular lactate, which subsequently feeds back on NF-κB to further enhances PD-L1 expression [ 303 ]. In CD8 + T cells treated with metformin, GLUT1 can be upregulated by mitochondrial ROS, leading to an increase in glycolysis and IFN-γ production. Additionally, mtROS trigger NF-E2-related factor 2 (NRF2) activation and mTORC1, while mTORC1, in turn, activates NRF2 in a p62-dependent manner, which enhances autophagy, glutaminolysis and the production of α-KG, thereby supporting CD8 + T cells proliferation [ 304 ]. Regarding ENO, ENO1-specific Tregs accumulate in the tumor tissue of pancreatic cancer, accompanied by decreased levels of ENO1-specific Th17 cells, highlighting a possible role in promoting pancreatic cancer progression [ 305 ]. Treg differentiation is associated with glucose metabolism, as increased α-KG facilitates the TCA cycle and OXPHOS in Tregs, thereby enhancing PUFA generation and triacylglyceride synthesis, which alters the DNA modifications profile of naive CD4 T cells, significantly reducing FOXP3 + Treg differentiation and increasing inflammatory cytokine production [ 306 ]. Further investigations are warrented to determine the role of RNA modifications in the regulation of glucose metabolism in immune cells in the TME. Mitochondria-related ferroptosis is pivotal for the regulation of antitumor immunity. Inhibition of the anti-ferroptosis factor SLC7A11/SLC3A2 upregulates PD-L1 expression in tumor cells via IRF4/EGR1. PD-L1 in tumor cells can be secreted through exosomes into the TME, which leads to M2 macrophage polarization [ 307 ]. IFN-γ released from CD8 + T cells downregulates the expression of SLC7A11/SLC3A2 by activating the JAK/STAT pathway, which promotes tumor ferroptosis, contributing to the antitumor efficacy of immunotherapy [ 308 , 309 ]. Analysis of the human transcriptome before and during nivolumab therapy further revealed that clinical benefits correlate with reduced Xc − expression and increased IFN-γ [ 308 ]. In addition, IFN-γ secreted by CD8 + T cells stimulates ASCL4 expression in tumor cells through IRF1, which leads to the upregulation of ferroptosis in tumor cells, improving the immune checkpoint blockade (ICB)-induced antitumor immunity [ 310 ]. RNA modifiers, including METTL3, IGF2BP1, YTHDC2, which modulate the stability of SLC7A11 mRNA, and IGF2BP3, which mediates the expression of SLC3A2 and ACSL4, can be theoretically hypothesized to be correlated with the regulation of antitumor immunity, which deserves further investigation. Mitochondria-related ferroptosis in immune cells is also a vital regulator of immunosurveillance. Recently, Tang B et al. discovered that Xc − in macrophages can induce M2 macrophage phenotype shifting via the SOCS3-STAT6-PPAR-γ signaling pathway [ 311 ]. Moreover, the ferroptosis in TAMs significantly increases PD-L1 expression in macrophages and, interestingly improves the efficacy of anti-PD-L1 therapy [ 311 ]. Furthermore, Xc − in macrophages can activate the JAK/STAT1 signaling cascade and induce the expression and secretion of PD-L1 and CXCL10, while it can also activate the AKT/STAT6 signaling pathway and upregulate M2 polarization [ 312 ]. Although the RNA modifications of ferroptosis-related genes mRNA in immune cells have not been reported, it is predictable that they might participate in the regulation of antitumor immunity. Another type of regulated cell death, apoptosis, plays a significant role in the antitumor immune response. CD8 + T cells can induce apoptotic signals in tumor cells by activating caspase-3 and enhancing the T cell-dependent immune response [ 313 ]. BCL-2 + CD4 + T cells are enriched in Tregs with high expression of IL-10 and TGF-β, while BCL-2 + CD8 + T cells are associated with exhausted cells, reduced cytotoxicity and weak expression of GZMB and perforin [ 314 ]. In addition, genome-wide CRISPR screen analysis revealed that inhibition of BCL-2 enhanced dendritic cell (DC) antigen presentation as well as the capacity of DCs to control tumors and to synergize with PD-1 blockade [ 315 ]. RNA modifications modifiers that target BCL-2 mRNA, such as METTL3, WTAP, YTHDF1 and ALKBH5, may be correlated with the antitumor immune response via the regulation of apoptosis. Pyroptosis is commonly used as a strategy for cancer elimination. However, pyroptosis plays a different role in the antitumor immune response. The NLRP3 inflammasome in the tumor cells leads to markedly elevated IL-18 levels, which positively regulate PD-L1 expression and reduce the proportion of cytotoxic T cells [ 316 ]. In addition, it has been shown that NLRP3-mediated IL-18 receptor signaling acts as a stimulator of intratumoral T cell exhaustion, by activating the IL-2/STAT5 and AKT/mTORC1 signaling pathways [ 317 ]. Nevertheless, it seems that NLRP3/IL-18 are not always immunosuppressive factors, particularly in the context of colorectal cancer metastasis in the liver, where the NLRP3 inflammasome generated in Kuppfer cells induces immunosurveillance via NK cells but not CD8 + T cells, and IL-18 positively mediates NK cell maturation and tumoricidal activity independent of IFN-γ and suppresses metastasis [ 318 ]. IL-1β, another cytokine activated in pyroptosis, has also been shown to promote immune suppression through the establishment of an immunosuppressive milieu mediated by M2 macrophages and myeloid-derived suppressor cells (MDSCs) [ 319 ]. Inhibition of IL-1β significantly enhances the antitumor activity of anti-PD-1 therapy, accompanied by increased infiltration of CD8 + T cells [ 319 ]. The mechanism by which IL-1β induces M2 polarization was further investigated by Weichand B et al., who reported that IL-1β enhances TAMs formation via S1P receptor 1 (S1PR1) [ 320 ]. Remarkably, IL-1β plays a dual role. As mtDNA and mtROS induce IL-1β production in macrophages, IL-1β signals in DCs, leading to increased glycolysis, pro-inflammatory cytokines (IL-12, IFN-I) production as well as surface expression of T-cell stimulatory molecules (MHC, CD80,86) [ 321 ]. These advance the cross-priming activity of DCs by inducing mitochondrial Ca 2+ signaling, elevating ROS production and increased IL-12, promoting radiation-induced antitumor immunity and helping overcome the radioresistance of tumors [ 322 ]. RNA modifications modifiers, including METTL3, WTAP, IGF2BP1-2, YTHDF1-2, FTO and ALKBH5, might play pivotal roles in antitumor immunity via the regulation of the NLRP3 inflammasomes, integrating the epitransciptional regulation and mitochondrial programs including ROS production, mtDNA sensing and metabolic reprogramming. GSDMD has emerged as an effective target for tumor immunotherapy. GSDMD impairs cGAS-STING activation via K + efflux, reducing IFN-γ production, and promotes PD-L1 expression via the import of Ca 2+ followed by the activation of the STAT1 signaling pathway, alleviating the antitumor immune response [ 323 ]. Interestingly, GSDMD in cytotoxic T cells plays a distinct role, as the colocalization of GSDMD with GZMB has been reported to occur in the proximity of immune synapses, and GSDMD cleavage increases in activated CD8 + T cells, indicating that GSDMD is required for an optimal cytotoxic T cells response [ 324 ]. This duality underscores the nuanced role of RNA modifications in pyroptosis regulation in different TME components. While the impact of RNA modifications on GSDMD mRNA, which is modulated by METTL3, in the TME has not yet been uncovered, it is plausible to speculate that RNA modifications could potentially contribute to the antitumor immunity via regulating GSDMD. Mitophagy is closely correlated with tumor immunosurveillance. PINK1-Parkin-mediated mitophagy modulates the degradation of SLC25A37 and SLC25A28, which are crucial for mitochondrial iron transport. SLC25A37 and SLC25A28 increase mitochondrial iron accumulation, leading to the upregulation of PD-L1 through the HIF-1α/AIM2/high mobility group box 1 (HMGB1) axis, resulting in immune dysfunction [ 325 ]. PINK1-mediated mitophagy can also recruit PD-L1 to mitochondria for degradation [ 326 ]. Moreover, the deficiency of Parkin is linked with PTEN degradation and enhanced AKT signaling, which leads to the dysregulation of antigen presentation and promotes tumor immune evasion [ 327 ]. Furthermore, in T SCM PINK1-mediated mitophagy triggers cytosolic release of the mitochondrial phosphatase PGAM5 that dephosphorylates β-catenin, which drives Wnt signaling and compensatory mitochondrial biogenesis, inducing T SCM formation and an improved immune response [ 328 ]. In addition, MEK inhibition facilitates OPTN-mediated mitophagy in lung cancer cells, leading to increased mt-DNA accumulation in the cytosol and the TLR9 signaling cascade, enhancing CD8 + T cells recruitment [ 329 ]. RNA modifications that directly or indirectly mediate the level of PINK1-Parkin-mediated mitophagy, is potentially correlated with antitumor immunity via RNA modifications modifiers. In recent years, mitochondrial fission and fusion have been reported to be closely related to antitumor immunity. In cancer cells, DRP1-mediated mitochondrial fission induces cytosolic mtDNA stress to enhance the CCL2 secretion from cancer cells via the TLR9-mediated NF-κB signaling pathway, which promotes M2 polarization [ 330 ]. Interestingly, in effector T cells however, DRP1 promotes correct thymocyte maturation by promoting T cell metabolic reprogramming and expansion, which allows efficient T cell extravasation from the blood and infiltration into tumors [ 331 ]. RNA modifications modifiers that directly or indirectly modulate the expression of DRP1, are believed to have a strong connection with the antitumor immune response via the regulation of DRP1-mediated mitochondrial fission. Investigations into whether the distinct roles of DRP1 and DRP1-dependent mitochondrial fission in different cells mentioned above are related to the different levels of RNA modifications that regulate DRP1 expression, are still needed.

Mitochondria function as versatile centers that are crucial for energy production, redox balance, biosynthetic capacity, cellular metabolism, programmed cell death, signal transduction, and intercellular organelle communication [ 1 – 3 ]. Glucose uptake and catalysis represent the primary sources of cellular energy production, while mitochondria are responsible for the majority of ATP generation through the tricarboxylic acid cycle (TCA) and the oxidative phosphorylation (OXPHOS) chain [ 4 ]. Reactive oxygen species (ROS) are primarily generated during glucose catabolism and are involved in various forms of regulated cell death, including pyroptosis, ferroptosis and necroptosis. Conversely, apoptosis is modulated by Cytochrome C and SMAC located in the mitochondrial intermembrane space (IMS) [ 5 , 6 ]. In the realm of mitophagy and mitochondrial fusion and fission, mitochondrial dynamics dramatically regulate mitochondrial morphology, quantity and position within eukaryotic cells, which are essential for preserving the critical functions of mitochondria and cellular processes [ 7 , 8 ]. Recent research has advanced our understanding of the relationship between mitochondria and tumor microenvironment (TME), revealing that mitochondria-related cellular metabolism, cell death and mitochondrial dynamics are closely linked to tumor immunosurveillance and antitumor immunity. These findings provide valuable insights into the potential application of immunotherapy in tumor treatment [ 9 , 10 ]. Methionine metabolism is implicated in various cellular biological and molecular functions, including methylation reactions and redox maintenance, and plays a crucial role in tumor progression [ 11 ]. S-adenosylmethionine, a product of methionine metabolism, promotes RNA modifications and influences RNA splicing, nuclear export, stability and translation, thereby contributing to antitumor immunity [ 12 , 13 ]. The types of RNA modifications, along with advanced, quantitative and sensitive transcriptome-wide sequencing techniques have been comprehensively detailed (Table 1 and 2 ). Recent discoveries have unveiled the intriguing regulatory mechanisms through which RNA modifications modulate glucose metabolism by controlling the translational efficacy of OXPHOS proteins, thereby facilitating tumor metastasis [ 14 , 15 ]. Moreover, cuproptosis and antitumor immunity have been identified for the first time as being regulated by RNA modifications in malignancies, underscoring their clinical and research significance in tumor treatment [ 16 , 17 ]. A plethora of reviews have been published regarding the association between RNA modifications and diseases. However, only a limited number of these reviews focus on the subcellular level, particularly with mitochondria. RNA modifications exert both direct and indirect effects on the expression of genes involved in physiological and pathological processes associated with mitochondria, which holds significant value for elucidating specific mechanisms [ 1 , 18 ]. In this review, we provide an overview of recent research concerning RNA modifications in mitochondria-related glucose metabolism, cell death, mitochondrial dynamics and antitumor immunity (Fig. 1 ), and briefly summarize the hallmark findings related to mitochondrial function and RNA modifications (Fig. 2 ). Additionally, we summarize small molecule inhibitors of RNA modification modifiers related to mitochondria, suggesting potential strategies for disease treatment. Fig. 1 The role of mitochondria-related RNA modifications in cancer and non-cancer diseases. Disease-promoting (red) and disease-inhibiting (blue) roles of RNA modifications on downstream targets, including coding and non-coding RNAs, are listed for different cancer types (grey) and non-cancer diseases (blue). The associated genes are categorized on the basis of mitochondrial functions (glucose metabolism, regulated cell death and mitochondrial dynamics). RNA modifications modifiers are listed at the outer column, including writers (purple), readers (green) and erasers (yellow). GBMLGG: Low Grade Glioma and Glioblastoma, HNSC: Head and Neck cancer, THCA: Thyroid Cancer, LUAD: Lung Adenocarcinoma, LIHC: Liver Hepatocellular Carcinoma, AKI: Acute Kidney Injury, PAAD: Pancreatic Adenocarcinoma, PRAD: Prostate Adenocarcinoma, BLCA: Bladder Urothelial Carcinoma, ESCA: Esophageal Carcinoma, AML: Acute Myeloid Leukemia, BRCA: Breast Invasive Carcinoma, STAD: Stomach Adenocarcinoma, COADREAD: Colon Adenocarcinoma and Rectum Adenocarcinoma, CESC: Cervical Squamous Cell Carcinoma The role of mitochondria-related RNA modifications in cancer and non-cancer diseases. Disease-promoting (red) and disease-inhibiting (blue) roles of RNA modifications on downstream targets, including coding and non-coding RNAs, are listed for different cancer types (grey) and non-cancer diseases (blue). The associated genes are categorized on the basis of mitochondrial functions (glucose metabolism, regulated cell death and mitochondrial dynamics). RNA modifications modifiers are listed at the outer column, including writers (purple), readers (green) and erasers (yellow). GBMLGG: Low Grade Glioma and Glioblastoma, HNSC: Head and Neck cancer, THCA: Thyroid Cancer, LUAD: Lung Adenocarcinoma, LIHC: Liver Hepatocellular Carcinoma, AKI: Acute Kidney Injury, PAAD: Pancreatic Adenocarcinoma, PRAD: Prostate Adenocarcinoma, BLCA: Bladder Urothelial Carcinoma, ESCA: Esophageal Carcinoma, AML: Acute Myeloid Leukemia, BRCA: Breast Invasive Carcinoma, STAD: Stomach Adenocarcinoma, COADREAD: Colon Adenocarcinoma and Rectum Adenocarcinoma, CESC: Cervical Squamous Cell Carcinoma Fig. 2 Hallmark findings of mitochondria-related RNA modifications. The hallmark findings are categorized on the basis of mitochondrial functions (glucose metabolism—green area, regulated cell death—yellow area and mitochondrial dynamics—red area) and into 3 levels (mitochondrial biology—inner circle, cell biology—median circle and antitumor immunology—outer circle) Hallmark findings of mitochondria-related RNA modifications. The hallmark findings are categorized on the basis of mitochondrial functions (glucose metabolism—green area, regulated cell death—yellow area and mitochondrial dynamics—red area) and into 3 levels (mitochondrial biology—inner circle, cell biology—median circle and antitumor immunology—outer circle)

In the proceeding context, we provided a concise overview of the latest findings about the involvement of RNA modifications in mitochondrial functions. However, many problems remain to be solved in this area, and more research needs to be devoted. The connection between OXPHOS and RNA modifications was identified by hallmark findings that mitochondrial tRNA can be positively modulated via m 5 C modification, leading to the upregulated translation efficacy of OXPHOS complexes and increased tumor metastasis. It is reasonable to explore whether RNA modifications on mt-tRNAs regulate the regulated cell death in addition to glucose metabolism, for the ROS generated from OXPHOS are confirmed to induce various forms of cell death. In addition, whether RNA modifications can regulate mitochondrial mRNAs and other mitochondrial non-coding RNAs needs further investigation. While existing literature has primarily concentrated on the role of RNA modifications in the biosynthesis of mitochondrial complexes, it is also known that proteins such as COA1 and COX18 are crucial for the subsequent complex assembly and membrane insertion. Nevertheless, the regulatory role of these RNA modifications in these processes remains uncharacterized. The elucidation of this regulatory mechanism would be pivotal to advancing our understanding of mitochondrial respiratory function in disease pathogenesis and tumor immune evasion, thereby identifying novel targets for therapeutic intervention. Consequently, a comprehensive investigation into this regulatory axis is warranted. Emerging as a novel form of metal-ion-related cell death, the molecular mechanism of cuproptosis is currently being explored, and its correlation with RNA modifications was unknown; however, until recently, concrete evidence has shown that the lactylation of METTL16 upregulated cuproptosis through m 6 A modification of FDX1 mRNA. Further research should be conducted to evaluate whether other cuprotosis-related genes that are regulated by RNA modifications are correlated with antitumor immunity. The direct correlation between RNA modifications and mitochondria-related antitumor immunity was recently discovered for the first time, as the m 5 C writer NSUN2 directly binds to glucose and represses the cGAS-STING pathway, leading to decreased apoptosis of tumor cells and CD8 + T cells infiltration. Therefore, further studies on the mechanisms by which RNA modifications control antitumor immunity are warranted. Cancer cells always exhibit increased glycolysis and decreased OXPHOS, resulting in elevated lactate secretion and the induction of immunosuppressive TME. Whether the metabolic reprogramming in cancer cells is due to the switch of RNA modifications remains to be determined. The efficiency of OXPHOS is critically dependent on the proper assembly of mitochondrial complexes, significantly influence the immunometabolism and anti-tumor immune activity of immune cells. Thus, the regulatory role of RNA modifications in mitochondrial complex assembly, especially assembly insertases and chaperones, warrants further investigation. The TME is generally associated with reduced cell death of cancer cells and immunosuppressive cells, and increased cell death of cytotoxic cells. Unlike other types of cell death, pyroptosis in cancer cells has contradictory effects, as IL-18 and IL-1β are produced during the process of pyroptosis, inducing M2 polarization and cytotoxic T cells exhaustion. Hence, the role of RNA modifications in the regulation of pyroptosis process needs to be explored. Moreover, histone lactylation-regulated METTL3 promotes ferroptosis via m 6 A modification of ACSL4. Therefore, whether the high lactate levels in the TME may lead to the ferroptosis in tumor cells or immune cells, or whether this occurs through the histone lactylation of m 6 A modifiers needs further investigation. Novel small-molecule inhibitors of RNA modifications modifiers have emerged in recent years, but few clinical trials have explored their use in clinical practice. A phase I study ( NCT05584111 ) evaluated the safety and tolerability of STC-15, a METTL3 inhibitor, in advanced malignancies. The lately results indicates that treatment with STC-15 is well tolerated across pharmacologically active dose range with encouraging signs of clinical activity [ 332 ]. TEAEs were mainly mild to moderate, manageable and reversible. The DCR is 66% with 3 confirmed PR ongoing in angiosarcoma, IO-refractory NSCLC and thymoma in 29 patients evaluable for response [ 333 ]. A phase Ib/2 clinical trial ( NCT06975293 ) of STC-15 is in progress, assessing the clinical activity and antitumor activity of STC-15 in combination with toripalimab. Combined treatment of small-molecule inhibitors of RNA modifications oncogenic modifiers and existing therapies, such as chemotherapy, targeted therapy and immunotherapy, may possibly augment the therapeutic effect and improve patient outcomes. Furthermore, a phase I study ( NCT06762925 ) on the efficacy and mechanism of METTL3 peptide inhibitors in enhancing anti-tumor immune response in patients with urological tumors is conducting. Although RNA modifications hold great potential as therapeutic targets, challenges of RNA-modification-targeted therapeutics remain. Given the highly context- and temporal-dependent nature of RNA modification functions, therapeutic molecules targeting these proteins must be dosed within a strictly controlled time window. For example, Mettl3 knockout in mice is embryonically lethal, whereas METTL3 is oncogenic in various cancers [ 334 ]. An optimal strategy involves coupling these agents with targeted delivery and controlled release to ensure specific inhibition at disease sites. In addition, developing specific inhibitors for RNA-modifying and binding proteins is challenging due to their shared catalytic domains. The selectivity of proteins like FTO and ALKBH comes not from their conserved catalytic domain, but from their unique substrate-binding domain [ 335 ]. Consequently, inhibitors that simply compete with the α-KG co-factor risk inhibiting all α-KG-dependent enzymes. To ensure specificity, inhibitors must be designed to perturb the substrate-binding domain. Moreover, drug developers must recognize that many RNA modification effectors possess additional functions independent of RNA modifications. For instance, METTL3 and METTL14 play critical roles in transcription and translation regulation even without methylase activity. Studies confirming that METTL3 knockout affects a broader range of lineages than its catalytic inhibitor highlight the importance of the inhibition modality [ 336 ]. Therefore, using PROTACs to degrade the protein is beneficial as it simultaneously ablates both enzymatic and non-enzymatic functions [ 337 ]. Furthermore, the dual roles of RNA modification effectors like FTO and ALKBH5 (which can act as both oncogenes and tumor suppressors) must be considered. Although FTO and ALKBH5 have oncogenic roles in the majority of cancers studied, they can also be tumor suppressors [ 338 , 339 ]. In these complex scenarios, achieving site-specific m 6 A demethylation on discrete targets may provide a viable path to attenuate tumorigenesis with minimal side effects [ 334 ].

In this review, we present the characteristics and role of RNA modifications in mitochondria-related glucose metabolism, regulated cell death and mitochondrial dynamics (Fig.  7 ), describe the molecular mechanisms underlying the posttranscriptional regulation of the related signaling pathways in different diseases (Table  4 ), and discuss the predictive role of RNA modifications in the mitochondria-related tumor microenvironment and tumor immune response, suggesting new therapeutic strategies for cancer and other diseases. In conclusion, posttranscriptional regulation of mitochondria-related functions via RNA modifications is pivotal for disease development and treatment. With the advancement of research in this field, targeting mitochondrial functions through RNA modifications modifiers can be a strategy for various diseases. Fig. 7 Overview of mitochondrial functions and their links with RNA modifications. Mitochondria play a crucial role in glucose metabolism, apoptosis, ferroptosis, necroptosis, pyroptosis, cuproptosis, mitophagy, mitochondrial fission and fusion and the tumor immune response. The key molecules involved in mitochondrial functions, which are reported to be associated with RNA modifications are depicted in color, whereas other molecules are in gray Overview of mitochondrial functions and their links with RNA modifications. Mitochondria play a crucial role in glucose metabolism, apoptosis, ferroptosis, necroptosis, pyroptosis, cuproptosis, mitophagy, mitochondrial fission and fusion and the tumor immune response. The key molecules involved in mitochondrial functions, which are reported to be associated with RNA modifications are depicted in color, whereas other molecules are in gray Table 4 The relationship between mitochondria-related RNA modifications modifiers and diseases Modifier Type of RNA modification Type of enzyme Related mitochondrial functions Changes of mitochondrial functions Disease Main target Role Ref METTL3-METTL14, METTL16 m 6 A Writer Glycolysis Upregulated Liver cancer LINCAROD, HIF-1α, WWP2 Promote [ 174 , 340 , 341 ] Upregulated Prostate cancer CircRBM33 Promote [ 194 ] Downregulated Glioma MiR-27b-3p Suppress [ 342 ] Upregulated Esophageal squamous cell carcinoma GLS2, APC Promote [ 343 , 344 ] Upregulated Lung cancer ENO1, ABHD11-AS1, DLGAP1-AS2 Promote [ 29 , 187 , 345 ] Upregulated Gastric cancer NDUFA4, HDGF, LHPP Promote [ 173 , 198 , 346 ] Upregulated Breast cancer LATS1 Promote [ 161 ] Upregulated Cervical cancer HK2 Promote [ 177 ] Upregulated Colorectal cancer LDHA, circQSOX1, PNN, COAD, SOGA1 Promote [ 32 , 167 , 185 , 347 ] OXPHOS Upregulated Gastric cancer AVEN, DAZAP2, DNAJB1 Promote [ 348 ] Ferroptosis Downregulated Breast cancer GPX4 Promote [ 219 ] Downregulated Glioblastoma Hepatoblastoma SLC7A11 Promote [ 212 ] Downregulated Aortic Dissection GPX4, SLC7A11 Suppress [ 215 ] Pyroptosis Upregulated Liver fibrosis MALAT1 promote [ 238 ] Upregulated MI/R injury. MiR-143-3p promote [ 349 ] Upregulated Arsenic-induced hepatic insulin resistance Intervertebral disc degeneration Lung cancer NLRP3 promote [ 229 – 231 ] Upregulated Crohn’s colitis CircPRKAR1B promote [ 350 ] Apoptosis Downregulated Lung cancer Breast cancer BCL-2 Promote [ 244 ] Downregulated Temporomandibular joint osteoarthritis BCL-2 Suppress [ 242 ] Mitophagy Downregulated Glioblastoma OPTN Promote [ 264 ] Upregulated Small cell Lung cancer DCP2 Promote [ 79 ] Upregulated Colorectal cancer Pri-miR-17 Promote [ 34 ] Fission/fusion Upregulated Cd neurotoxicity FIS1 promote [ 279 ] Upregulated Cardiac fibrosis Gas5 promote [ 277 ] WTAP m 6 A Writer Glycolysis Upregulated Colorectal cancer PDK4 Promote [ 193 ] Upregulated Breast cancer ENO1 Promote [ 188 ] Upregulated Colorectal cancer FOXP3 Promote [ 195 ] Upregulated Ovarian cancer MiR-200 Promote [ 38 ] OXPHOS Upregulated Multiple myeloma NDUFS6 Promote [ 199 ] Pyroptosis Upregulated Diabetic nephropathy NLRP3 promote [ 232 ] Apoptosis Downregulated Breast cancer BCL-2 Promote [ 244 ] KIAA1429 m 6 A Writer Glycolysis Upregulated Oral squamous cell carcinoma PGK1 Promote [ 184 ] Upregulated Colorectal cancer HK2 Promote [ 179 ] Upregulated Ovarian cancer ENO1 Promote [ 189 ] YTHDF1 to YTHDF3 m 6 A Reader Glycolysis Upregulated Cervical cancer PDK4 Promote [ 27 ] Upregulated Liver cancer PDK4, PFKL Promote [ 27 , 30 ] Upregulated Lung cancer ENO1, HK2, LDHA, LDHB and SLC2A1 Promote [ 351 ] Upregulated Breast cancer LATS1, PKM2 Promote [ 161 , 352 ] Ferroptosis Upregulated Colorectal cancer ATF4 Promote [ 353 ] Cuproptosis Upregulated Glioma FDX1 Promote [ 260 ] YTHDC1 and YTHDC2 m 6 A Reader Glycolysis Upregulated Pancreatic cancer MiR-30d Promote [ 171 ] Ferroptosis Downregulated Lung cancer SLC7A11 Suppress [ 214 ] IGF2BP1 to IGF2BP3 m 6 A Reader Glycolysis Upregulated Liver cancer PDK4, LINCAROD Promote [ 27 , 341 ] Upregulated Cervical cancer PDK4, MYC Promote [ 27 , 165 ] Upregulated Gastric cancer HDGF Promote [ 173 ] Upregulated Colorectal cancer CircQSOX1 Promote [ 185 ] Upregulated Oral squamous cell carcinoma CircFOXK2 Promote [ 28 ] OXPHOS Upregulated Lung cancer COX6B2 Promote [ 37 ] Ferroptosis Upregulated Lung cancer GPX4 Promote [ 217 ] Upregulated Hepatoblastoma SLC7A11 Promote [ 213 ] Pyroptosis Upregulated Acute kidney injury E2F1 Promote [ 235 ] hnRNPCL2 m 6 A Reader OXPHOS Upregulated Colorectal Cancer miR-483, miR-877, miR-676 Promote [ 207 ] FTO m 6 A Eraser Glycolysis Upregulated Acute myeloid leukemia PFKP Promote [ 31 ] Downregulated Papillary thyroid cancer APOE Suppress [ 172 ] Downregulated Lung cancer MYC Suppress [ 338 ] Downregulated Colorectal cancer HK2 Suppress [ 178 ] Upregulated Endometriosis ATG5 Promote [ 190 ] Upregulated Gastric cancer PRKAA1 Promote [ 339 ] Downregulated Diabetic nephropathy NPAS2 Suppress [ 169 ] Pyroptosis Upregulated Cerebral Ischemic Stroke MEG3 Promote [ 240 ] Downregulated Diabetic kidney injury NLRP3 Suppress [ 234 ] Fission/fusion Upregulated Gastric cancer Caveolin-1 Promote [ 354 ] ALKBH5 m 6 A Eraser Glycolysis Downregulated Papillary thyroid cancer CircNRIP1 Suppress [ 186 ] Upregulated Lung cancer ENO1 Promote [ 187 ] Downregulated Colorectal cancer HK2 Suppress [ 178 ] Ferroptosis Upregulated Thyroid cancer TIAM1 Suppress [ 223 ] Pyroptosis Downregulated Rheumatoid arthritis NLRP3 Suppress [ 233 ] Apoptosis Downregulated Ovarian cancer BCL-2 Promote [ 245 ] Fission/fusion Downregulated Liver fibrosis DRP1 Promote (effector T cells)/Suppress (cancer cells and fibrosis) [ 278 ] NSUN1 to NSUN7 m 5 C Writer Glycolysis Upregulated Bladder cancer, Liver cancer PKM2 Promote [ 43 , 191 ] Upregulated Liver cancer GLUT1 Promote [ 41 ] Upregulated Liver cancer c-Myc Promote [ 208 ] TCA Upregulated Gastric cancer LncRNA NR_033928 Promote [ 197 ] Downregulated Viral infection OGDH Suppress [ 15 ] OXPHOS Upregulated Oral cancer 34 in mt-tRNA Met Promote [ 14 ] Upregulated Neurodevelopmental disorders 48, 49 and 50 in mt RNA Promote [ 201 ] Ferroptosis Upregulated - GPX4 - [ 221 ] YBX1 m 5 C Reader Glycolysis Upregulated Lung cancer PFKFB4 Promote [ 182 ] ALKBH3 m 1 A Eraser Glycolysis Downregulated Cervical cancer ATP5D Suppress [ 200 ] Glycolysis Upregulated Age-related macular degeneration HK2 Promote [ 40 ] Ferroptosis Upregulated Acute myeloid leukemia ATF4 Promote [ 216 ] TRMT61A m 1 A Writer Glycolysis Upregulated Head and neck squamous cell carcinoma tRNA Promote [ 166 ] TRMT10C m 1 A Writer mt tRNA Upregulated Alzheimer’s disease tRNA Suppress [ 39 ] METTL8 m 3 C Writer OXPHOS Upregulated Pancreatic cancer 32 in mt-tRNA Ser , mt-tRNA Thr Promote [ 44 ] mt tRNA Upregulated Pancreatic cancer C32 in tRNA Promote [ 44 ] METTL1 m 7 G Writer OXPHOS Upregulated Oral squamous cell carcinoma mt-tRNA Promote [ 209 ] The relationship between mitochondria-related RNA modifications modifiers and diseases Glioblastoma Hepatoblastoma Arsenic-induced hepatic insulin resistance Intervertebral disc degeneration Lung cancer Lung cancer Breast cancer