Conventional cancer therapies, including surgery, radiation therapy, and chemotherapy, have been the cornerstone of cancer treatment for decades. While effective, they often suffer from limitations such as systemic toxicity, lack of specificity, and potential resistance (Liu et al., 2024a). Recent research has focused on refining these approaches to improve their efficacy and reduce potential side effects. Conventional therapies include surgery, radiation, and chemotherapy.

Surgery remains the gold standard for treating localized cancers. Advances in minimally invasive techniques, such as robotic-assisted surgery, laparoscopic procedures, and fluorescence-guided surgery, have improved surgical precision and reduced complications (Nagaya et al., 2017). However, the risk of incomplete tumor excision and disease recurrence remains a challenge, particularly in cases with micrometastases (Liu et al., 2024b).

Radiation therapy employs high-energy ionizing radiation to induce DNA damage in cancer cells, leading to apoptosis (Liu et al., 2021). Technological innovations, such as proton beam therapy and stereotactic body radiation therapy, have significantly enhanced targeting accuracy while minimizing collateral damage to healthy tissues (Koka et al., 2022). Despite these advances, concerns about long-term complications, including radiation-induced fibrosis and secondary malignancies, persist (Fijardo et al., 2024).

Chemotherapy remains a key component of cancer treatment, particularly for metastatic diseases (Ganesh and Massagué, 2021). Recent efforts have focused on optimizing drug combinations to alleviate resistance and enhance efficacy (Hu et al., 2024). Emerging studies suggest that integrating microRNAs (miRNAs) with chemotherapy can modulate drug resistance in cancers such as breast and colorectal malignancies (Hu et al., 2024). Nonetheless, systemic toxicity, including oxidative damage, myelosuppression, and cardiotoxicity, remains a major drawback (Katanić Stanković et al., 2023).

Targeted therapies offer a more precise approach to cancer treatment by interfering with specific molecular pathways that drive tumor progression. These therapies typically involve monoclonal antibodies (mAbs), small-molecule inhibitors, and immune checkpoint inhibitors (Min and Lee, 2022). Targeted therapies function by inhibiting key signaling pathways responsible for cancer cell proliferation, angiogenesis, and immune evasion. These include tyrosine kinase inhibitors (TKIs), monoclonal antibodies, and immune checkpoint inhibitors (ICIs) (Nouri et al., 2020; Li et al., 2024).

Over the past two decades, cancer therapy has broadly evolved from cytotoxic agents toward target-specific and immune-modulatory approaches that reshape intracellular signaling and cell-death pathways. The principal classes of these therapies include mAbs that selectively block extracellular receptors or ligands; TKIs that interfere with oncogenic kinase signaling; and ICIs that restore antitumor immunity. Targeted therapies have led to significant improvements in cancer treatment. For example, trastuzumab has revolutionized the management of HER2-positive breast cancer by specifically inhibiting HER2 signaling (Swain et al., 2023). Similarly, pembrolizumab has emerged as a standard treatment for metastatic melanoma and lung cancer (Goldberg et al., 2016). In addition, two rapidly emerging modalities, including antibody-drug conjugates (ADCs) and chimeric antigen receptor T cell (CAR-T) therapies, represent hybrid or cell-based strategies that combine precise target recognition with potent effector mechanisms (Puppi et al., 2025). While ADCs directly deliver cytotoxic agents to tumor cells and often trigger mitochondria-mediated intrinsic apoptosis (Wang et al., 2025), CAR-T therapies utilize patient-derived or engineered T cells (Pourzia et al., 2023). The health of mitochondria and the metabolic reprogramming of these T cells are essential for their durability and their capacity to eradicate cancer cells (Rad et al., 2021). Together, these therapeutic categories illustrate the expanding therapeutic landscape that indirectly or directly intersects with mitochondrial signaling (Table 1).

Although conventional and targeted cancer therapies are not designed to directly modify epigenetic machinery, increasing evidence indicates that many of these treatments exert indirect epigenetic and mitoepigenetic effects (Sharma et al., 2010). Chemotherapy and radiotherapy can alter chromatin accessibility and DNA methylation patterns through oxidative stress, while targeted therapies and immune-based treatments reshape cellular metabolism and mitochondrial function, thereby influencing epigenetic states (Reid et al., 2017; Li et al., 2025). Integrating these therapies within an epigenetic framework provides a more comprehensive understanding of treatment response and resistance.

Beyond direct epigenetic targeting, such therapy-induced changes include alterations in DNA methylation patterns, chromatin accessibility, transcriptional reprogramming, and metabolic adaptation driven by mitochondrial stress and redox imbalance (Huang et al., 2012; Martínez-Reyes and Chandel, 2020; Hung et al., 2024). These epigenetically mediated adaptive responses have been implicated in both transient drug tolerance and the emergence of therapy resistance across multiple cancer types. A conceptual summary of these reported interactions between major classes of oncological therapies and epigenetic or mitoepigenetic regulation is provided in Table 2.

Epigenetic drugs are developed as inhibitors of proteins that add (writers), recognize (readers), and delete (erasers) chemical groups such as methyl and acetyl, to modulate epigenetic modifications. These inhibitors can reverse existing DNA and histone modifications (Table 3) (Suraweera et al., 2025; Kaplánek et al., 2023). Writers are DNA methyltransferase (DNMT), histone acetyltransferase (HAT), and histone methyltransferase (HMT) families. Erasers are histone deacetylases (HDACs), histone demethylases, and the Ten-Eleven Translocation (TET) family.

DNMT1 inhibitors include nucleoside analogs or non-nucleoside chemicals. 5′-azacytidine and 5′-deoxy-2′-azacytidine are nucleoside analogs, used as epigenetic drugs due to their similarity to cytosine nucleoside (Suraweera et al., 2025). When these nucleoside analogs are present, they replace methylated cytosines in newly synthesized DNA during DNA replication. Thus, the amount of methylation decreases as the number of methylated cytosines gradually decreases with each replication. Therefore, the epigenetic drug effect of nucleoside analogs is a replication-dependent process. Non-nucleoside analogs contain chemical groups with completely different structures that do not resemble the nucleoside structure (Mohan, 2025). Figure 1 shows some examples of these molecules. Some of these are natural, and some are synthetic compounds. Examples of natural ones are epigallocatechin-3-gallate (Epigallocatechin gallate, EGCG) found in tea and curcumin found in the turmeric plant (Pandey et al., 2025). The most well-known of the synthetic ones is the RG108 molecule. These drugs reduce DNA methylation levels by directly inhibiting the DNMT1 enzyme (Figure 1). Nucleoside analogs 5-azacitidine and 5-aza-2′-deoxy-azacitidine are FDA-approved and are routinely used in cancer treatment.

TET inhibitors are compounds that suppress the activity of TET enzymes—a family of Fe²⁺/α-ketoglutarate–dependent dioxygenases (TET1, TET2, and TET3) responsible for oxidizing 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), initiating DNA demethylation. By blocking this process, TET inhibitors lead to DNA hypermethylation, which can alter gene expression patterns, including those involved in differentiation, cell cycle control, and tumor suppression. Common TET inhibitors act by blocking the catalytic activity of TET enzymes, which normally convert 5mC to 5hmC during DNA demethylation. The oncometabolite 2-hydroxyglutarate (2-HG), produced by mutant IDH1/2 enzymes, is a potent competitive inhibitor that mimics α-ketoglutarate and leads to genome-wide DNA hypermethylation. Similarly, dimethyloxalylglycine (DMOG) is a broad-spectrum α-ketoglutarate analog that inhibits TETs and other dioxygenases by occupying their cofactor binding site. Bobcat339 represents a more selective synthetic small-molecule inhibitor that directly targets the TET catalytic domain, reducing 5hmC formation in a dose-dependent manner. Additionally, metabolic intermediates such as succinate and fumarate can accumulate under mitochondrial dysfunction and competitively inhibit α-ketoglutarate-dependent TET activity, linking altered cellular metabolism to epigenetic dysregulation (Kaplánek et al., 2023). Together, these inhibitors modulate DNA methylation landscapes, providing important tools for studying epigenetic regulation and potential therapeutic strategies in cancer and developmental disorders.

Histone acetyltransferase (HAT) inhibitors are divided into three main groups: bisubstrate, natural, and synthetic inhibitors. Lys-CoA p300, one of the bisubstrate inhibitors, binds to the binding site of the HAT enzyme with a specific affinity and inhibits it (Huang et al., 2019). Anacardic acid, curcumin, garcinol, and EGCG, which are natural compounds, have HAT inhibition activity. Studies have shown that synthetic compounds, especially thiazole, isothiazole, and similarly derived compounds with heterocyclic structures, are promising in terms of HAT inhibition (Gorsuch et al., 2009).

The common features of HDAC inhibitors (HDACi) are that they contain three pharmacophore groups, including 1) zinc-binding group (ZBG), 2) linker, and 3) capping group, abbreviated as CAP (Neganova et al., 2022). HDAC inhibitors are often used in combination with other drugs (Smalley et al., 2020). This approach is called the “polypharmacological approach” (Ryszkiewicz et al., 2025). Polypharmacology is defined as the design or use of pharmaceutical agents that act on more than one target. Pharmaceutical agents can be applied as combinations of multiple drugs that bind to different targets; this approach is called drug combination, or can be a single drug that binds to various targets, defined as multi-target ligands (Lembo and Bottegoni, 2024).

The bromodomain is a protein region of approximately 110 amino acids that recognizes acetylated lysines at the N-terminal ends of histones. Proteins containing this region are known as the BET (bromodomain and extra-terminal motif-containing) protein family. The mammalian BET protein family has four members: BRD2, BRD3, BRD4, and BRDT, and these proteins are associated with cancer and immunity (To et al., 2023). The most well-known BET inhibitor is the JQ1 molecule, which inhibits BRD4. BRD4 is a type of epigenetic reader protein and is involved in histone acetylation, gene transcription, and alternative splicing mechanisms (Zhang et al., 2021; Zhou et al., 2020). BRD4 protein binds to the acetylated lysine residues of histones and reads them. This reading directs the RNA polymerase II towards transcription. Thus, it contributes to gene expression in conjunction with histone acetylation. When the JQ1 molecule inhibits BRD4, active transcription cannot occur (Dey et al., 2003).

The most studied group of HMT inhibitors is EZH2 inhibitors. EZH2 is a type of HMT enzyme and is involved in maintaining the heterochromatin structure. Since it has been found that the EZH2 gene, which encodes the EZH2 enzyme, is generally overexpressed in cancer, inhibition of this enzyme is one of the targeted mechanisms for cancer treatment. The drug Valemetostat has the potential to inhibit both EZH1 and EZH2 activity. Since both enzymes show increased activity in some types of cancer, Valemetostat harbors promising potential against these cancers (Liu and Yang, 2023). Pinometostat is the first identified HMT inhibitor that has reached the Phase 1 clinical stage for use in the treatment of leukemia (Menghrajani et al., 2019).

Among the histone demethylases, most studies are on the lysine-specific histone demethylase 1A (LSD1) enzyme. LSD1 enzyme is an enzyme that specifically removes methyl groups from H3K4me1/2 and H3K9me1/2 modifications. In many cancer cells, histone demethylase enzymes such as LSD1 show more activity than in normal cells. LSD1 inhibitors are divided into two groups: covalent and non-covalent. Each group includes some hybrid compounds (dual or multi-target compounds) that can simultaneously inhibit LSD1 and other targets. To date, 9 LSD1 inhibitors for hematological and/or solid cancers have entered clinical trials (Noce et al., 2023).

Epigenetic modifications play crucial roles in cancer progression by regulating gene expression without altering the DNA sequence. Epigenetic drugs primarily target DNA methylation, histone modification, and chromatin remodeling enzymes. These include DNMTs, HDACs, and BRDs of BET proteins (Suraweera et al., 2025). Epigenetic therapies have revolutionized the treatment of hematologic malignancies and lymphomas by targeting aberrant epigenetic modifications, such as DNA hypermethylation and histone deacetylation (Olsen et al., 2007; Piekarz et al., 2011). These modifications often silence tumor suppressor genes, contributing to cancer progression. This review synthesizes the clinical development, mechanisms of action, and efficacy of five epigenetic drugs approved by the FDA before 2015: Azacitidine, Decitabine, Vorinostat, Romidepsin, and Belinostat. These agents target DNMTs or HDACs, offering novel therapeutic alternatives for myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), cutaneous T cell lymphoma (CTCL), peripheral T cell lymphoma (PTCL), and multiple myeloma.

Mitochondrial DNMT1 (mtDNMT1), a form of DNMT1 that localizes to mitochondria, methylates mtDNA, regulating genes like MT-ND6, which is vital for oxidative phosphorylation. Altered mtDNA methylation is observed in cancer cells (e.g., colorectal cancer) and may affect mitochondrial metabolism, with implications for cancer biology (Shock et al., 2011). Experiments in cancer cell lines (e.g., HCT116) using mtDNMT1 knockdown demonstrate reduced mtDNA methylation, increasing transcription of genes like MT-ND6, though the specificity relative to nuclear DNA methylation was not assessed in this study (Shock et al., 2011). No clinical trials explicitly target mtDNMT1 currently. Developing mtDNMT1-specific inhibitors could offer a novel cancer therapy by directly disrupting mitochondrial bioenergetics.

Mitochondrial TET enzyme modulation is a promising area in mitoepigenetics, potentially impacting cancer by altering mtDNA demethylation and mitochondrial function. TET enzymes (TET1, TET2, TET3) oxidize 5mC to 5hmC to promote DNA demethylation. These enzymes may function in mitochondria, where mtDNA 5hmC could regulate gene expression critical to cancer metabolism, such as oxidative phosphorylation and ROS production (Kaplánek et al., 2023). mtDNA epigenetic changes, including 5hmC dysregulation, are observed in cancers like leukemia and hepatocellular carcinoma, suggesting the crucial roles of mitochondrial TETs in tumor progression (Kaplánek et al., 2023). This concept is indirectly supported by Cramer-Morales et al. (2020), who demonstrated that succinate accumulation, caused by mitochondrial MnSOD depletion, inhibits TET activity, leading to nuclear DNA hypermethylation and altered cell fate in erythroleukemia models (e.g., HEL 92.1.7 cells). While their focus was nuclear, their finding suggested that succinate, a TET inhibitor, disrupts epigenetic regulation, suggesting a potential parallel effect on mitochondrial TET activity, which could influence mtDNA methylation and mitochondrial function in cancer cells under oxidative stress (Cramer-Morales et al., 2020), as (Kaplánek et al., 2023) suggests for broader mitoepigenetic dynamics. However, direct evidence of mitochondrial TET activity in cancer remains limited, requiring further research. Enhancing or inhibiting mitochondrial TET activity could offer a new epigenetic mechanism for mtDNA regulation in cancer.

The interplay between SIRT3, SIRT4, and SIRT5 in coordinating mitochondrial responses shows their collective impact on mitoepigenetic regulation. SIRT4, known for its role in repressing glutamine metabolism, may inhibit cancer cell proliferation by limiting nutrient availability, though specific studies on its modulation in cancer remain sparse. Jeong et al. (2013) demonstrated that SIRT4 inhibits mitochondrial glutamine metabolism by ADP-ribosylating and repressing glutamate dehydrogenase, reducing glutamine flux into the tricarboxylic acid cycle, and this tumor-suppressive activity was linked to decreased proliferation in cancer cells (Jeong et al., 2013). Similarly, SIRT5, which regulates lysine desuccinylation and demalonylation, fine-tunes mitochondrial enzyme activity. Du et al. (2011) established SIRT5 as an NAD + -dependent lysine demalonylase and desuccinylase, showing its ability to remove these modifications from mitochondrial proteins (Du et al., 2011), while Greene et al. (2019) found that SIRT5 stabilizes glutaminase via desuccinylation in breast cancer cells, enhancing glutamine metabolism and potentially supporting tumor growth or survival under stress conditions (Greene et al., 2019). Lei et al. (2024) emphasize that mitochondrial transcription, modulated by sirtuins, influences cancer cell survival and proliferation. Specifically, SIRT3 regulates mitochondrial biogenesis and metabolism, which are often dysregulated in cancer cells to support rapid growth and adaptation to stress (Lei et al., 2024). In colon cancer, Torrens-Mas et al. (2019) demonstrated that silencing SIRT3 impairs mitochondrial biogenesis and disrupts metabolic homeostasis, leading to reduced cell viability and increased oxidative stress in vitro (Torrens-Mas et al., 2019). These findings suggest that SIRT3 may function as a metabolic gatekeeper; however, its role appears context-dependent and dualistic, with studies indicating both tumor-promoting and tumor-suppressive activities depending on the cancer type and stage. Its tumor-suppressive role is also evident, as SIRT3 enhances mitochondrial integrity, which may counteract the Warburg effect. Beyond metabolism, SIRT3 modulates mtDNA repair, a critical mechanism for maintaining genomic stability in cancer cells. Kabziński et al. (2019) revealed that in colorectal cancer, SIRT3 deacetylates key mtDNA repair enzymes, including NEIL1, NEIL2, OGG1, MUTYH, APE1, and LIG3. This deacetylation enhances their activity, reducing mtDNA damage accumulation, which is a factor linked to cancer progression and chemotherapy resistance (Kabziński et al., 2019). The study suggests that the regulation of mtDNA repair by SIRT3 could serve as a therapeutic target, as its inhibition might sensitize cancer cells to oxidative damage and apoptosis. While SIRT3 has garnered significant attention, SIRT4 and SIRT5 also contribute to mitochondrial regulation in cancer, albeit with less characterized mechanisms. Lei et al. (2024) note that mitochondrial sirtuins influence transcription of mtDNA-encoded genes, which are essential for respiratory chain function (Lei et al., 2024). TTorrens-Mas et al. (2019) suggest that SIRT3 silencing in animal models of colon cancer could disrupt tumor progression by compromising mitochondrial function, aligning with in vitro observations (Torrens-Mas et al., 2019). Similarly, Kabziński et al. (2019) propose that targeting SIRT3-mediated mtDNA repair pathways in colorectal cancer could enhance therapeutic efficacy, offering a translational bridge from bench to bedside (Kabziński et al., 2019). The modulation of mitochondrial sirtuins (SIRT3/4/5) thus emerges as a pivotal factor in cancer biology. The dual role of SIRT3 in metabolism and mtDNA repair, alongside the emerging functions of SIRT4 and SIRT5, shows their potential as therapeutic targets. Future research should focus on elucidating the context-specific roles of SIRT4 and SIRT5 and exploring combinatorial strategies to manipulate mitochondrial sirtuin activity, offering new avenues for combating cancer through mitoepigenetic intervention.

Mitochondrial RNA (mtRNA) methylation, including m⁵C and m⁶A modifications, is a critical mitoepigenetic process in cancer, driven by writers and potentially erasers that regulate mitochondrial function and tumor progression. NSUN3, an m⁵C writer, methylates mitochondrial tRNA-Met at cytosine 34 (m⁵C34), enhancing translation of mtDNA-encoded proteins vital for oxidative phosphorylation (Van Haute et al., 2016). Van Haute et al. (2016) demonstrated that NSUN3 deficiency impairs this methylation, reducing mitochondrial protein synthesis in patient-derived cells. mtRNA methylation, particularly m5C modification, plays a critical role in regulating mitochondrial gene expression and function. NSUN family methyltransferases, including NSUN2, NSUN3, and NSUN4, act as key m5C writers within mitochondria (Li et al., 2022). NSUN3 primarily modifies mitochondrial tRNAs, while NSUN4 targets 12S rRNA, contributing to mitoribosome assembly and mitochondrial translation. Additionally, the demethylase ALKBH1 functions as an m5C eraser by oxidizing m5C to 5-formylcytosine (f5C) in mitochondrial tRNAs, influencing RNA stability. Dysregulation of these enzymes may alter mitochondrial metabolism and contribute to cancer progression by impacting cellular energy production and apoptosis pathways (Li et al., 2022).

mtRNA methylation, particularly N6-methyladenosine (m6A), plays a pivotal role in regulating mitochondrial function and cancer progression. METTL3, an m6A methyltransferase, has been shown to methylate mtRNAs, thereby enhancing mitochondrial respiration. In colorectal cancer cells, METTL3 installs m6A modifications on mitochondrial mRNAs and rRNAs, leading to increased proliferation in vitro and tumor growth in vivo (Pan et al., 2022).

Consequently, considering their fundamental and differentiated roles in mitochondrial processes, the three-dimensional (3D) structures of the studied mitoepigenetic proteins are exemplified here to further highlight their differences (Figure 5).

Regarding m6A demethylases, ALKBH5 is known to demethylate nuclear m6A RNAs. ALKBH5 suppresses gastric cancer progression by demethylating m6A on uncapped WRAP53 RNA isoforms, reducing their translation and impacting downstream pathways. ALKBH5 downregulation is associated with poor prognosis, supporting its tumor-suppressive role in gastric cancer (Zheng et al., 2025b). Zeng et al. (2024) suggest that FTO may demethylate mitochondrial m6A, though its specific role in cancer is still under exploration Zeng et al. (2024). Dysregulation of mtRNA methylation by enzymes such as NSUN3 and METTL3 can alter cellular metabolism and ROS production, thereby supporting tumorigenesis. Targeting these methylation pathways in vivo has been shown to reduce tumor burden, showing their therapeutic potential, despite limited evidence regarding m6A erasers in mitochondria.