DNA methylation refers to the biological process of transferring the methyl group of S-adenosylmethionine (SAM) to cytosine or adenine and is mediated by DNA methyltransferases (DNMTs) (Aran et al., 2013). The cytosine component in DNA cytosine phospho-guanine (CpG) dinucleotide (one 5′-cytosine and one 3′-guanine) is a key site of methylation. The CpG dinucleotide is overexpressed in the gene promoter, and its methylation can silence related genes (Papanicolau-Sengos and Aldape, 2022). Compared with non-tumor tissues, cancers have a complex methylation profile, including overall hypomethylation of the genome, but hypermethylation of CpG islands in gene promoter regions (Gama-Sosa et al., 1983). The c-Myc gene is generally considered to be a transcription factor of oncogenes (Prendergast and Ziff, 1991). In cancer cells, hypomethylation is often associated with c-Myc. In 1984, hypomethylation of c-Myc was first demonstrated in cancer cells cultured in vitro and was subsequently identified in a variety of malignant tumors, such as hepatocellular carcinoma, leukemia, gastric cancer, and colorectal cancer (Cheah et al., 1984; Guinney et al., 2015).

Histones are the main protein components in eukaryotic chromatin and are divided into five types: H1, H2A, H2B, H3, and H4 (Audia and Campbell, 2016). In eukaryotic cells, two copies of these histones form octamers and 147 bp of DNA is wound around them to form nucleosomes. Histones are prone to post-transcriptional modifications, including acetylation, methylation, phosphorylation, and ubiquitination. Covalent modification of histones plays an important role in chromatin dynamics and transcriptional regulation (Tsukada et al., 2006).

Mammalian chromatin remodeling complexes can be divided into four major families: SWI/SNF, ISWI, NuRD/Mi-2/CHD, and INO80 (Wang et al., 2007). As the first to be discovered, the SWI/SNF family comprised ATP-dependent chromatin remodeling complexes (CRCs), which regulate functions such as gene expression and DNA replication, and are related to the occurrence of various cancers. SWI/SNF chromatin remodeling factors are associated with increased chromatin accessibility, which can promote nucleosome repositioning in promoter and enhancer regions, transcription factor binding, recruitment of histone-modifying enzymes and regulation of chromatin loops, promoting the interactions between enhancers and promoters (Wu and Roberts, 2013; Vaicekauskaite et al., 2022). Monterde et al. described recurrent alterations of different SWI/SNF genes in nearly 20% of lung cancer patients, which were significantly associated with poorer prognosis, suggesting that SWI/SNF genes plays an important role in lung cancer (Monterde and Varela, 2022).

Non-coding RNAs (ncRNAs) are functional RNA molecules that are not translated into proteins. Based on their length, shape, and location, ncRNAs in cancer have been classified into four major types with distinct functions: microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and PIWI interacting RNA (piRNA). A large body of evidence indicates that ncRNAs can act as oncogenes or suppressors to regulate cancer initiation and progression. Many ncRNAs can be released from cancer cells into blood or urine and serve as diagnostic markers or prognostic indicators (Yan and Bu, 2021). Targeted ncRNA therapy has been evaluated in many clinical trials, and the combination with other therapeutic methods will help to achieve better therapeutic effects.

Clear cell renal cell carcinoma (ccRCC) is the most common type of human RCC. The SETD2 gene is a frequently mutated in renal cancer, especially ccRCC (Li L et al., 2019). In ccRCC, the PBRM1 gene is often co-mutated with SETD2 (Varela et al., 2011), and some studies have predicted that SETD2 mutations are associated with poor prognosis in primary ccRCC (Piva et al., 2015). In RCC, SETD2 participates not only in epigenetic dysfunction, but also in metabolic regulation (Chen et al., 2020). H3K36me3 protein downregulation in the absence of SEDT2 resulted in incomplete gene methylation modification in RCC (Ho et al., 2016). Liu et al. (Liu et al., 2019) found that the loss of SETD2 downregulated the metabolism of creatine, glycosaminoglycans and carbohydrates via a mechanism that may be related to the peroxisome proliferator-activated receptor γ co-activator 1α (PGC-1α)-mediated metabolic network. This suggests that dysfunction in the SETD2-PGC-1α metabolic pathway in ccRCC may act as a stimulating factor, which provides a new target for drug development and individualized treatment. Wang et al. (Wang J. et al., 2016) showed that low SETD2 expression was associated with poor prognosis in patients with metastatic RCC (mRCC) treated with tyrosine kinase inhibitors (TKIs), and the frequency of SETD2 mutation was positively correlated with mRCC progression. This suggested to us that SETD2 may serve as a potential prognostic biomarker in mRCC patients receiving targeted therapy. However, whether it is applicable to other RCC types requires prospective external validation studies.

Prostate cancer is a common malignant tumor in men. Zhang et al. (Zhang et al., 2019) performed Integrated Genome Analysis (IGA) on 51 HMT genes in prostate cancer samples collected from The Cancer Genome Atlas (TCGA) database. The results indicated that the SETD2 gene may be involved in the androgen receptor response pathway of prostate cancer, and that the SETD2 gene mutations have a potential role in the occurrence and development of castration-resistant prostate cancer (CRPC). In addition, analysis of mouse models and patient data showed that loss of SETD2 significantly promotes distant metastasis of prostate cancer. SETD2 promotes the degradation of EZH2 by methylating the EZH2 K735 site, preventing transformation of cells to a high H3K27me3 chromatin state, thereby inhibiting the molecular mechanism of prostate cancer metastasis. Interestingly, the study also showed that changes in extracellular energy are “sensed” by the AMPK-FOXO3 signaling pathway to regulate SETD2 expression levels. Furthermore, metformin inhibited the progression of EZH2-high expression prostate cancer by activating the AMPK-FOXO3-SETD2 signaling axis (Yuan et al., 2020). Nevertheless, the potential roles of SETD2 in the diagnosis, treatment and prognosis of prostate cancer remain to be explored.

Lung cancer is the leading cause of cancer-related deaths in humans, among which lung adenocarcinoma (LUAD) is the main histological subtype with a high mortality rate (Siegel et al., 2023). Hao et al. (Hao et al., 2015) collected surgical specimens from 88 lung cancer patients and established 23 patient-derived xenograft (PDX) models. SETD2 mutations were identified in both the primary LUAD tissues and the PDX models, with a mutation rate of 21.7%. Walter et al. (Walter et al., 2017) found that loss of SETD2 and downregulation of H3K36me3 promoted the rapid growth and progression of LUAD. Subsequent studies showed that SETD2 mutations were significantly associated with poor prognosis (Kadara et al., 2017). These studies suggest that SETD2 mutations are closely related to the occurrence, development and prognosis of LUAD. Li et al. (Li et al., 2022) retrospectively analyzed the clinical characteristics of 248 Chinese patients with LUAD and found that high tumor mutation burden was significantly associated with high expression of PD-L1. Compared with the PD-L1 low expression group, SETD2 gene mutations were significantly enriched in the PD-L1 high expression group and correlated with the overall survival of patients. In addition, pathway analysis showed that SETD2 mutations were involved in the DNA damage repair (DDR) pathway, TP53 pathway, cell cycle pathway and Drosophila double wing margin nickeled homologous gene (NOTCH) pathway. The proportions of IFN-γ, CD8⁺ T cells, and NK cells in the SETD2 mutant group were significantly higher than those in the wild-type group, suggesting that SETD2 may be a potential target for LUAD immunotherapy. The results of in vitro and in vivo experiments highlighted the ability of SETD2/H3K36me3 to inhibit cell proliferation, migration, invasion and epithelial-mesenchymal transition (EMT) in LUAD by regulating the STAT1-IL‐8 signaling pathway (Yang et al., 2022). Cisplatin is one of the most commonly used chemotherapeutic drugs in the treatment of non-small cell lung cancer (NSCLC), but the mechanism of cisplatin resistance is not fully understood. By high-throughput sequencing of cisplatin-resistant A549 cells selected in vivo, Kim et al. (Kim et al., 2019) identified a missense mutation in SETD2 and showed that SETD2-mediated trimethylation of H3K36 and CREB1 phosphorylation are key targets for cisplatin sensitivity. This study confirms that downregulation of the expression of SETD2 or CREB1 in LUAD cells inhibit the activation of H3K36me3 and ERK, resulting in cisplatin resistance. These studies provide evidence that SETD2 functions as a tumor suppressor in LUAD and may serve as a novel prognostic biomarker and potential therapeutic target, although in-depth studies are required to elucidate the mechanism.

After knocking out the SETD2 gene in nasopharyngeal carcinoma (NPC) cells, Zeng et al. detected numerous differentially expressed genes, suggesting that SETD2 plays an important role in the biological function of NPC. Preliminary classification of the upregulated proteins showed that some were involved in the processes of cell proliferation, adhesion, migration and EMT. Loss of SETD2 expression in NPC affects 20 classic signaling pathways closely related to tumors, suggesting the potential feasibility of SETD2-targeted therapy (Zeng et al., 2019).

Using a SETD2 gene-specific knockout mouse model, Li et al. (Huang et al., 2016) showed that the loss of SETD2 can lead to spontaneous liver cancer, and can significantly promote diethylnitrosamine (DEN)-induced liver cancer. In DEN-induced liver cancer mouse model, the loss of SETD2 can significantly increase the number and size of liver tumors. Mechanistic analysis showed that, in addition to regulating the DNA damage response, SETD2 also inhibited the occurrence of liver cancer by regulating the balance of hepatic lipid metabolism. Loss of SETD2 resulted in the downregulation of H3K36me3 in lipid efflux-related genes and repressed their expression, which in turn promoted lipid accumulation. Loss of SETD2 also promoted hepatocarcinogenesis in a high-fat diet-induced model. Chromatin immunoprecipitation sequencing (ChIP-seq) analysis revealed that SETD2 knockdown induced activation of the c-Jun/activating protein-1 (c-Jun/activating protein-1, c-Jun/AP-1) transcription factor in the liver by promoting lipid accumulation. As an oncogene, c-Jun can inhibit the expression of the p53 gene in SETD2-null mice to promote the occurrence of liver cancer. SETD2 loss promotes the occurrence and development of hepatocellular carcinoma (HCC), and therefore, further studies on the role of SETD2 and cholesterol homeostasis in tumorigenesis are warranted.

SETD2 functions as a tumor suppressor in different stages of pancreatic carcinogenesis, and SETD2/H3K36me3 simultaneously inhibits acinar-ductal reprogramming and EMT. Furthermore, loss of SETD2-H3K36me3 affects pancreatic size and acinar cell homeostasis, promoting Kras-induced pancreatic carcinogenesis and metastasis (Niu et al., 2020b). However, the role of SETD2 mutations in TME remodeling and immune evasion is poorly understood. In another study, in the process of pancreatic carcinogenesis, intratumoral SETD2 deficiency not only participated in the regulation of pancreatic tumor cell fate, but also regulated immune escape by remodeling neutrophils, which may provide potential therapeutic targets for pancreatic cancer patients with SETD2 mutation or loss (Niu et al., 2023).

Studies have shown that the migration, proliferation and invasion abilities of the gastric cancer (GC) cell lines HGC-27 and AGS decreased as the level of SETD2 expression increased. Low SETD2 expression was significantly correlated with clinicopathological parameters such as tumor size, TNM stage, and lymph node metastasis. In addition, patients with low SETD2 expression had a significantly lower 5-year survival rate compared with patients with high SETD2 expression (Chen et al., 2018). Further studies showed that H3K36me3 levels were reduced in SETD2 mutants in GI stromal tumors (GISTs), and SETD2 silencing promoted DNA damage in GIST-T1 cells. Univariate analysis showed that SETD2 mutation was associated with shorter recurrence-free survival (RFS) in patients with GISTs (Huang et al., 2016). These findings suggested that downregulation of the SETD2 gene may be significantly related to the development and poor prognosis of GC.

In colorectal cancer (CRC), SETD2 has been shown to regulate the Wnt signaling pathway in engineered mouse models (GEMs), and SETD2 loss promoted tumor progression (Yuan et al., 2017). Furthermore, SETD2 gene inactivation promoted self-renewal and tissue regeneration of intestinal stem or progenitor cells in mouse intestinal epithelium (Zhang et al., 2014). However, the description of SETD2 in CRC is limited to clinical case reports (Choi et al., 2014; Liu M. et al., 2021). A recent study of the largest cohort to date revealed that the clinical presentation of SETD2-mutant CRC was similar to CRC reported in the general population, although it may be more commonly present in the proximal colon. SETD2-mutant CRC may also be found in the presence of p53 mutations and abnormal expression of β-catenin, two proteins known to interact to regulate DNA repair. Furthermore, multiple mutations in the SETD2 gene may be required for the regulation of H3K36 trimethylation, but further studies are needed to confirm the clinical relevance of this observation. The emergence of next-generation sequencing (NGS) will help to clarify the significance of SETD2 mutations in CRC (Bushara et al., 2023).

The maintenance of hematopoietic homeostasis depends on the balance between hematopoietic stem cell self-renewal and differentiation, a process regulated by both genetic and epigenetic mechanisms (Rice et al., 2007; Cullen et al., 2014). Accumulating evidence suggests that this homeostasis may be perturbed by mutations in some key regulatory genes, ultimately leading to hematopoietic malignancy (Papaemmanuil et al., 2016). SETD2 mutations play an important role in the development and treatment of hematologic malignancies (Huether et al., 2014; Mar et al., 2014). Using the SETD2 gene conditional knockout mouse model, it was found that SETD2 plays an important role in maintaining the balance between self-renewal and differentiation of hematopoietic stem cells, and SETD2-deficient hematopoietic stem cells (HSPCs) can continue to evolve into systemic malignancies (Zhang et al., 2018). This study provided the first animal model that provides evidence of a causal role for SETD2 loss in tumorigenesis. SETD2-deficient HSPC can acquire the ability to overcome growth disadvantage during the latency period, eventually acquiring to the malignant hematopoietic features of myelodysplastic syndrome (MDS) (Zhang et al., 2018). Studies have shown that SETD2 plays a tumor suppressor role in chronic myeloid leukemia (CML), and SETD2 loss significantly promotes imatinib resistance and leukemia stem cell enrichment in CML cells. In addition, the demethylase inhibitor JIB‐04 was shown to restore H3K36me3 levels by blocking H3K36me3 demethylation, thus enhancing the effects of chemotherapy (Sheng et al., 2019). After conditional knockout the SETD2 gene in MLL-AF9 AML mouse model, homozygous SETD2 loss was found to delay leukemogenesis, whereas heterozygous SETD2 loss resulted in accelerated disease progression and chemotherapy resistance (Mar et al., 2017; Skucha et al., 2018). Taken together, these studies provide evidence that SETD2 functions as a tumor suppressor in hematologic malignancies and that targeting the H3K36me3 demethylase may reverse chemotherapy resistance.

High-grade gliomas (HGGs) are a type of poorly differentiated, highly aggressive and migratory brain tumors that occur frequently in both adults and children (Greenall et al., 2017). In whole exome sequencing (WES) analysis of 60 children with HGG, Fontebasso et al. (Fontebasso et al., 2013) found that 15% (11/73) of the children had SETD2 gene mutations that were mainly truncating mutations. SETD2 mutations were detected in 8% (5/65) of adult HGGs when analyzed in another independent validation cohort. In addition, the study revealed that SETD2 mutations are common in older children and young adults, and are distributed mainly in the brain hemispheres. Further Western blot analysis showed that the expression level of H3K36me3 in tumor tissues with SETD2 gene mutations was decreased. In subsequent studies, Huether et al. (Cheah et al., 1984) confirmed that SETD2 gene mutations could be detected in childhood HGG tissues and glioblastoma cell lines. SETD2 mutations are also present in low-grade gliomas, mainly in people aged over 55 years (Brennan et al., 2013). These studies suggest that SETD2 functions as a tumor suppressor in glioma.

Although there are many treatment methods for breast cancer (BC), including surgery, radiotherapy, chemotherapy, and immunotherapy, the morbidity and mortality remain high (Kashyap et al., 2022). Sarakbi et al. (Al Sarakbi et al., 2009) analyzed the expression of SETD2 mRNA in a long-term follow-up cohort of breast cancer patients and found that SETD2 expression levels were significantly reduced in samples from patients who developed metastasis, local recurrence, or died of BC. In addition, SETD2 expression levels were negatively correlated with tumor stage, grade, and lymph node metastasis. According to TCGA and METABRIC databases, SETD2 is mutated in 2.62% of all BC subtypes and 1.2% of triple-negative breast cancer cases. However, whether SETD2 is mutated in other BC subtypes is unknown. Further studies suggested that the expression level of SETD2 was significantly positively correlated with the prognosis of patients. However, SETD2 mutations have little effect on the outcome of chemotherapy in patients (Morcillo-Garcia et al., 2019). Thus, SETD2 may function as a tumor suppressor, and may be a potential prognostic marker in BC.

Osteosarcoma (OS) is the most common primary bone malignancy in children and adolescents, and occurs most frequently in the distal femur, tibia, and proximal humerus (Gill and Gorlick, 2021). In 2017, Behjati et al. detected SETD2 mutations in less than 2% of human osteosarcoma samples. Subsequent WES on osteosarcoma-susceptible dogs indicated that osteosarcoma may originate from SETD2 mutations, which function as oncogenic drivers (Behjati et al., 2017; Sakthikumar et al., 2018). SETD2 mutations have also been detected in osteosarcoma, myxoid liposarcoma (MLPS), and synovial sarcoma (SYN) (Sakthikumar et al., 2018), although the effect of SETD2 on the biological function of osteosarcoma has not yet been reported. Comprehensive genome analysis of 24 choriocarcinoma patients showed that chromatin regulatory genes, particularly SETD2, were frequently altered in chordoma (Wang L. et al., 2016). SETD2 mutations were also reported in 22% (11/50) of patients with malignant peritoneal mesothelioma (MPM) (Offin et al., 2022). These studies suggest that SETD2 may provide a new therapeutic target for various types of malignancies.