DNA demethylating agents suppress preclinical models of synovial sarcoma
Nobuhiko Hasegawa, Nezha S. Benabdallah, Kyllie Smith-Fry, Li Li, Sarah McCollum, Jinxiu Li, Caelen A. Jones, Lena Wagner, Vineet Dalal, Viola Golde, Anastasija Pejkovska, Lara Carroll, Malay Haldar, Seth M. Pollack, Scott W. Lowe, Torsten O. Nielsen, Ana Banito, Kevin B. Jones
Nobuhiko Hasegawa, Nezha S. Benabdallah, Kyllie Smith-Fry, Li Li, Sarah McCollum, Jinxiu Li, Caelen A. Jones, Lena Wagner, Vineet Dalal, Viola Golde, Anastasija Pejkovska, Lara Carroll, Malay Haldar, Seth M. Pollack, Scott W. Lowe, Torsten O. Nielsen, Ana Banito, Kevin B. Jones
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Research Article Genetics Oncology

DNA demethylating agents suppress preclinical models of synovial sarcoma

Abstract

Synovial sarcoma is an aggressive soft-tissue cancer driven by the chimeric SS18::SSX fusion oncoprotein, which disrupts chromatin remodeling by combining two antagonistic transcriptional regulators. SS18 participates in BAF complexes that open chromatin, while the SSX genes are cancer-testis antigens that interface with chromatin decorated with monoubiquitinated histone H2A placed by polycomb repressive complex activity. Because KDM2B brings polycomb repressive complex to unmethylated CpG islands, it is plausible that methylation directly determines the distribution of SS18::SSX to target loci. Given that synovial sarcoma is also characterized by a peculiarly low DNA hypomethylation profile, we hypothesized that further disturbance of DNA methylation would have a negative impact on synovial sarcoma growth. DNMT1 disruption by CRISPR/Cas9 targeting or pharmacological inhibition with cytidine analogs 5-aza-2′-deoxycytidine (decitabine) and 5-azacytidine led to decreased genome-wide methylation, redistribution of SS18::SSX, and altered gene expression profiles, most prominently including upregulation of tumor suppressor genes, immune-related genes, and mesenchymal differentiation-related genes. These drugs suppressed growth of synovial sarcoma cell lines and drove cytoreduction in mouse genetic models. DNMT1 inhibitors, already approved for treating myelodysplastic syndromes, warrant further clinical investigation for synovial sarcoma as repurposed, targeted treatments exploiting a vulnerability in the intrinsic biology of this cancer.

Authors

Nobuhiko Hasegawa, Nezha S. Benabdallah, Kyllie Smith-Fry, Li Li, Sarah McCollum, Jinxiu Li, Caelen A. Jones, Lena Wagner, Vineet Dalal, Viola Golde, Anastasija Pejkovska, Lara Carroll, Malay Haldar, Seth M. Pollack, Scott W. Lowe, Torsten O. Nielsen, Ana Banito, Kevin B. Jones

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Figure 1

The synovial sarcoma genome is hypomethylated by increased TET and decreased DNMT1 expression.

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The synovial sarcoma genome is hypomethylated by increased TET and decre...
(A) DNMT1, DNMT3A, and DNMT3B mRNA expression and mutational profile from cBioPortal analysis. Expression levels for 20,532 genes in 264 soft-tissue cases (RNA Seq V2 RSEM). GISTIC 2.0; –2 = deep deletion; –1 = shallow deletion; 0 = diploid; 1 = gain; 2 = amplification. P values were determined by Mann-Whitney U test. *P < 0.05, **P < 0.005, ***P < 0.0005; ns, not significant. (B) TET1, TET2, and TET3 mRNA expression and mutational status. (C) Gene-specific dependence scores for each synovial sarcoma cell line in the Target Drive initiative accessed by DepMap. (D) Cell competition assay performed in the osteosarcoma cell line KHOS-240S-Cas9 (fusion negative control) or in the synovial sarcoma line HS-SY-II-Cas9 transduced with a safe sgRNA as control or with guides targeting DNMT1.