SETD2 in cancer: functions, molecular mechanisms, and therapeutic regimens

SETD2 catalyzes protein methylation

SETD2 primarily catalyzes trimethylation of histone H3 at lysine 36 (H3K36me3) from H3K36me2 within gene body regions to guarantee transcription elongation¹. Deficiency of SETD2-H3K36me3 restrains transcription of critical tumor suppressor genes and establishes a direct correlation between SETD2-H3K36me3 and carcinogenesis. SETD2 protein includes the SET domain responsible for methyltransferase activity, the post-SET domain that enhances catalytic activity, the WW domain involved in protein-protein interactions, and the SRI domain that interacts with RNA polymerase II. These domains collectively enable SETD2 to recognize and bind the histone H3 tail, which catalyzes H3K36me3¹.

In addition, the SETD2-H3K36me3 level is closely related to other types of epigenetic modifications to change chromatin accessibility^2,3. Our previous studies revealed that SETD2-H3K36me3 deficiency facilitates H3K27me3 and H3K27Ac ectopic gain, which contributes to immune escape and metabolic reprogramming in pancreatic ductal adenocarcinoma (PDAC)^2,3. SETD2-H3K36me3 also enhances recruitment of the DNA methyltransferase DNMT3B to gene bodies. The epigenetic interplay involving SETD2, H3K36me3, DNA methyltransferase 3 beta (DNMT3B), and DNA methylation ensures the fidelity of gene transcription initiation with implications for intragenic hypomethylation in cancer⁴. In addition, H3K36me3 is recognized and directly bound by the m6A methyltransferase, methyltransferase-like protein 14 (METTL14), guiding global m6A deposition co-transcriptionally⁵.

Non-histone proteins are also SETD2 substrates. SETD2 mediates methylation of lysine 525 on signal transducer and activator of transcription 1 (STAT1), enhancing IFNα-dependent antiviral immunity⁶. Additionally, SETD2 methylates lysine 735 on enhancer of zeste homolog 2 (EZH2), which suppresses prostate cancer metastasis⁷. SETD2 is also necessary for p53 tumor suppressor interactions⁸. Researchers are currently using novel techniques, such as the amino acid specificity profile, to delve deeper into the specific substrate sequences of SETD2. It is anticipated that these approaches will uncover and elucidate novel substrates and functions of SETD2 in the future.

SETD2 mutations and/or copy number variation (CNV) are widespread in various tumor types

SETD2 is frequently mutated or deleted to alter the epigenetic landscape by causing depletion of H3K36me3 in a variety of tumors, including hematologic malignancies⁹, clear cell renal cell carcinoma (ccRCC)¹⁰, colorectal cancer (CRC)^11,12, prostate cancer (PCa)⁷, and PDAC^2,3,13. Among the pan-cancer cohort comprised of 10,953 patients in the cancer genome atlas (TCGA), 521 (4.76%) were shown to harbor SETD2 mutations³. These mutations mainly include missense, inframe, and truncating mutations, structural variants, copy number deep deletions, and a small number of amplifications. Additionally, SETD2 gene inactivating mutations are directly associated with the survival and prognosis of certain tumors. For example, a high frequency of SETD2 gene inactivating mutations is more frequently found in late-stage ccRCC. These mutations are associated with a higher and earlier risk of recurrence as well as poorer survival outcomes¹⁴. Our previous studies showed that SETD2 is mutated in 3%–8% of PDAC patients with low expression in 33%–50% of PDAC patients^2,3,13. These studies have demonstrated that the loss of the SETD2-H3K36me3 axis leads to epigenetic changes that reshape tumor cell metabolism and the immune microenvironment, showing a unique influence on the development and progression of PDAC.

SETD2 deficiency promotes tumor progression through multiple pathways

SETD2 deficiency modulates CAF heterogeneity

As crucial components of the tumor microenvironment (TME), CAFs have pivotal roles in tumor initiation, metastasis, metabolic reprogramming, immune evasion, and drug resistance. Given the complex function of CAFs, scRNAseq has confirmed the presence of myofibroblast CAFs (myCAFs), inflammatory CAFs (iCAFs), and antigen-presenting CAFs (apCAFs) in mouse and human pancreatic tumors. By analyzing pancreatic tumors with different mutations and morphology, additional CAF types were identified. During early tumor initiation, reciprocal tumor-stroma signaling drives the reprogramming of progenitor cells to CAFs. In addition, CAF heterogeneity in fate and function is spatially regulated by signals derived from genetically diverse tumor cells and tumor microenvironment conditions. Our study demonstrated that the loss of SETD2 induces epigenetic reprogramming and unleashes BMP signaling, fostering the differentiation of a lipid-laden CAF subpopulation marked by ABCA8a. These ABCA8a⁺ lipid-laden CAFs metabolically sustain tumor cell OXPHOS and tumor growth by transporting lipids. These findings illuminate the role of SETD2 loss in reshaping CAFs to support tumor energy demands².

In summary, SETD2 has a pivotal role in regulating tumor progression through diverse mechanisms (Figure 1). Our recent systematic research analyzed SETD2 function and the mechanism by which SETD2 regulates pancreatic tumorigenesis from multiple perspectives, including tumor cell fate, immune microenvironment, CAF heterogeneity, and metabolic remodeling^2,3,13,17. These findings suggest that tumor cells possess remarkable abilities to choose different strategies to maintain survival and development, and adapt to adverse diverse environmental conditions. This exploration of the multiple effects of epigenetic mutations and disorders enhances our understanding of tumor characteristics and offers promising avenues for the development of novel patient-tailored precision therapies.

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Figure 1

Multiple molecular pathways, cellular functions, and biological processes regulated by SETD2. CAF, cancer-associated fibroblast; EMT, epithelial–mesenchymal transition; TIME, tumor immune microenvironment; OXPHOS, oxidative phosphorylation.

Current status of therapeutic regimens for SETD2-deficient tumors

As a tumor suppressor, SETD2 mutations and copy number variations are widespread in diverse tumor types, suggesting the significance of developing patient-tailored therapies based on SETD2-H3K36me3 deficiency. However, there are currently no small-molecule drugs that can compensate for the loss of SETD2 and/or H3K36me3, thus limiting therapeutic options. Therefore, by elucidating the molecular and mechanistic pathways using mouse, cell, and patient-derived xenograft (PDX) models, researchers have proposed a series of precise alternative treatment options for SETD2-deficient tumors (Figure 2 and Table 1).

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Figure 2

Potential alternative therapies for patients with SETD2 deficiency.

Chemotherapy remains a cornerstone in the treatment of various cancers, with ongoing research efforts aimed at enhancing effectiveness and identifying suitable patient cohorts. The loss of SETD2-H3K36me3 has emerged as a sensitive indicator of drug responsiveness. Given the role of SETD2 in DNA methylation and damage repair, a combination therapy strategy using DNA hypomethylating agents (HMAs) and PARP inhibitors (PARPis) may exhibit potent antitumor effects in SETD2-deficient renal cell carcinoma²². According to Dong et al.²⁰, combining S and G2/M checkpoint inhibition with chemotherapy offers a promising therapeutic strategy. This approach effectively resensitizes chemo-resistant acute leukemia (AL) cases with SETD2 mutations by targeting unique vulnerabilities²⁰. Our recent study elucidated the mechanistic underpinnings of how SETD2 deficiency induces reprogramming of glycolytic metabolism to compensate for inadequate nucleoside synthesis. This finding suggests that restricting glycolysis in combination with gemcitabine could be a promising therapeutic approach for PDAC patients with SETD2 deficiency¹⁷.

Synthetic lethality offers a strategy for targeting genetic defects in cancer. A previous study showed that WEE1 inhibition selectively kills H3K36me3-deficient cancer cells by targeting a ribonucleotide reductase subunit (RRM2) as the synthetic lethal interaction²¹. SETD2-H3K36me3 safeguards RRM2 transcription, while WEE1 inhibition degrades RRM2 through untimely CDK activation. WEE1 inhibition in H3K36me3-deficient cells results in RRM2 reduction, critical dNTP depletion, S-phase arrest, and cell death²¹.

Our study revealed that cultured SETD2-deficient pancreatic tumor cells increase glycolytic flux to compensate for insufficient nucleoside synthesis and support tumor growth. Consequently, glycolysis inhibition via STF-31 has potential as an effective tumor suppression strategy¹⁷. Notably, intratumoral SETD2-deficient cells manifest dramatically strengthened OXPHOS and remodeled H3K27Ac distribution due to the additional lipid provided by surrounding CAFs. Using a mouse model and PDX models from pancreatic cancer patients, our recent study demonstrated that pancreatic tumors with low levels of SETD2/H3K36me3 are associated with increased sensitivity to S-Gboxin and JQ1 compared to pancreatic tumors with high H3K36me3 levels².

Recent studies have highlighted the significance of TIME heterogeneity as an intrinsic trait of tumor cells. The loss of SETD2, known for its pivotal roles in DNA damage repair, genomic stability maintenance, and mRNA splicing, results in accumulation of tumor mutation-specific neoantigens on the cell surface. Bioinformatic analysis and research have suggested a potential link between SETD2 and the efficacy of immune checkpoint inhibitor (ICI) immunotherapy^3,19. Additionally, Zheng et al.¹⁸ concluded that cancer patients with SETD2 mutations undergoing ICI treatment are associated with improved durable clinical outcomes and survival rates. SETD2 inactivation reprograms intratumoral immune cells, leading to increased tumor inflammation characterized by increased T cell infiltration and enhanced antigen presentation¹⁸. This process activates CD8⁺ T cell-mediated killing¹⁸. Our previous investigation provided mechanistic insight into how tumor cell-intrinsic SETD2 deficiency promotes neutrophil recruitment and reprograms toward an immunosuppressive phenotype during pancreatic tumorigenesis. These findings offer potential therapeutic implications for pancreatic cancer patients with SETD2 deficiency³.

Conclusions

SETD2 is generally considered a tumor suppressor with mutations or CNV in many tumors. SETD2 deficiency accelerates tumor initiation, progression, metastasis, and escape from immune surveillance. Multiple investigations have revealed the multiple molecular functions of SETD2, including influencing tumor cell fate, regulating cellular metabolic balance, remodeling the TIME, and interacting with stromal cells. A deeper understanding of the SETD2 role in tumor progression is crucial for future advances in the diagnosis, precision therapies, alternative therapies, and prevention of cancer for PDAC patients with SETD2 deficiency.

Author contributions

Writing original draft: Yawen Weng and Ningning Niu.

Modify the manuscript: Ningning Niu.

Proofread the manuscript: Jing Xue and Ningning Niu.

All authors read and approved the final manuscript.