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Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity
Open accessAbstract
Epigenetic dysregulation is a defining feature of tumorigenesis that is implicated in immune escape 1,2. Here, to identify factors that modulate the immune sensitivity of cancer cells, we performed in vivo CRISPR-Cas9 screens targeting 936 chromatin regulators in mouse tumour models treated with immune checkpoint blockade. We identified the H3K9 methyltransferase SETDB1 and other members of the HUSH and KAP1 complexes as mediators of immune escape 3-5. We also found that amplification of SETDB1 (1q21.3) in human tumours is associated with immune exclusion and resistance to immune checkpoint blockade. SETDB1 represses broad domains, primarily within the open genome compartment. These domains are enriched for transposable elements (TEs) and immune clusters associated with segmental duplication events, a central mechanism of genome evolution 6. SETDB1 loss derepresses latent TE-derived regulatory elements, immunostimulatory genes, and TE-encoded retroviral antigens in these regions, and triggers TE-specific cytotoxic T cell responses in vivo. Our study establishes SETDB1 as an epigenetic checkpoint that suppresses tumour-intrinsic immunogenicity, and thus represents a candidate target for immunotherapy.
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“Targeting specific H3K9 methyltransferases, such as SUV39H1 and SETDB1, has been shown to enhance immunotherapy responses in various cancer models.”
From Multi-omics analysis identifies glioblastoma dependency on H3K9me3 methyltransferase activity (2025) · cites this paper as [24]
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“SETDB1 targeting can promote cytotoxic T cell-based immunotherapy in cancer mouse models24.”
From Multi-omics analysis identifies glioblastoma dependency on H3K9me3 methyltransferase activity (2025) · cites this paper as [24]
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“In contrast to other recently characterized immune evasion genes 4,8,45 , tumour-specific loss of TBK1 did not result in dramatic remodeling of the immune compartment.”
From Targeting TBK1 to overcome resistance to cancer immunotherapy (2023) · cites this paper as [45]
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Transposable elements in health and disease: Molecular basis and clinical implications
Hong, Y., & Liu, N. (2025) · Chinese Medical Journal · doi:10.1097/cm9.0000000000003775 · Cited by 15
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Increased Expression of SETDB1 Predicts Poor Prognosis in Multiple Myeloma
Xiang, J., Chen, X., Chen, M., & Hou, J. (2022) · BioMed Research International · doi:10.1155/2022/3307873 · Cited by 10
What can Ribo-seq and proteomics tell us about the non-canonical proteome?Preprint
Prensner, J. R., Abelin, J. G., Kok, L. W., Clauser, K. R., Mudge, J. M., Ruiz‐Orera, J., Bassani‐Sternberg, M., Deutsch, E. W., & van Heesch, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.05.16.541049 · Cited by 10
Molecular Susceptibility and Treatment Challenges in Melanoma
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Li, K., Yi, X., Yu, Z., Xue, K., Wu, Y., Zhao, Y., Zhang, E., He, P., & Zeng, Q. (2025) · European Journal of Pharmacology · doi:10.1016/j.ejphar.2025.178211 · Cited by 9
Cao, Y. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1092667 · Cited by 10
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Epigenetic checkpoint blockade: new booster for immunotherapy
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Zhong, Z., Wang, J., Han, Q., Lin, H., Luo, H., Guo, D., Jiang, Y., & Liu, A. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.969536 · Cited by 9
Multi-omics analysis identifies glioblastoma dependency on H3K9me3 methyltransferase activity
Xie, Q., Du, Y., Ghosh, S., Rajendran, S., Cohen-Gadol, A. A., Baizabal, J.-M., Nephew, K. P., Han, L., & Shen, J. (2025) · NPJ Precision Oncology · doi:10.1038/s41698-025-00829-5 · Cited by 10
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SETDB1 activity is globally directed by H3K14 acetylation via its Triple Tudor Domain
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Metadata
- Authors
- Griffin, G. K., Wu, J., Iracheta-Vellve, A., Patti, J. C., Hsu, J., Davis, T., Dele-Oni, D., Du, P. P., Halawi, A. G., Ishizuka, J. J., Kim, S. Y., Klaeger, S., Knudsen, N. H., Miller, B. C., Nguyen, T. H., Olander, K. E., Papanastasiou, M., Rachimi, S., Robitschek, E. J., Schneider, E. M., Yeary, M. D., Zimmer, M. D., Jaffe, J. D., Carr, S. A., Doench, J. G., Haining, W. N., Yates, K. B., Manguso, R. T., & Bernstein, B. E.
- Affiliations
- Broad Institute (US)
- Harvard University (US)
- Corresponding author
- Manguso, Robert T.
- Bernstein, Bradley E.
- ORCID
- Griffin, Gabriel K.
- Wu, Jingyi
- Iracheta-Vellve, Arvin
- Patti, James C.
- Hsu, Jeffrey
- Dele-Oni, Deborah
- Du, Peter P.
- Halawi, Aya G.
- Ishizuka, Jeffrey J.
- Kim, Sarah Y.
- Klaeger, Susan
- Knudsen, Nelson H.
- Miller, Brian C.
- Nguyen, Tung H.
- Olander, Kira E.
- Papanastasiou, Malvina
- Rachimi, Suzanna
- Robitschek, Emily J.
- Schneider, Emily M.
- Yeary, Mitchell D.
- Zimmer, Margaret D.
- Jaffe, Jacob D.
- Carr, Steven A.
- Doench, John G.
- Haining, W. Nicholas
- Yates, Kathleen B.
- Manguso, Robert T.
- Bernstein, Bradley E.
- Venue
- Nature
- Published
- 2021-05-05
- Volume
- 595
- Issue
- 7866
- Pages
- 309-314
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC9166167
- OpenAlex
- W3158155618
- Cited by
- 370
- References
- 61
- Citations by year
- 2026: 57 · 2025: 78 · 2024: 77 · 2023: 69 · 2022: 70 · 2021: 19
- FWCI
- 21.55
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- National Cancer Institute (DP1CA216873, K08CA245112, U24CA210986, U01CA214125)
- Topics
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- SETDB1, H3K9 methyltransferase, epigenetic silencing, tumor immunogenicity, immune evasion, immune checkpoint blockade, transposable elements, segmental duplication, retroviral antigens, cytotoxic T lymphocytes, HUSH complex, chromatin regulators, immunotherapy targets
- MeSH terms
- Animals, Antigens, Viral, Chromatin, Disease Models, Animal, DNA Transposable Elements, Female, Humans, Neoplasms, Histone-Lysine N-Methyltransferase, T-Lymphocytes, Cytotoxic, Histocompatibility Antigens Class I, Gene Silencing, Mice, Programmed Cell Death 1 Receptor, CRISPR-Cas Systems
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