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 3

Synovial sarcoma is sensitive to decitabine and azacytidine.

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Synovial sarcoma is sensitive to decitabine and azacytidine. (A) Viabili...
(A) Viability of 6 synovial sarcoma cell lines and 2 untransformed mesenchymal cell lines treated with decitabine or 5-AZA. The blue dotted line indicates the points where the P value of the cell survival rate compared with the reference point in decitabine is significant. The red dotted line indicates the comparison to the reference for 5-AZA. (1273/99, YaFuSS, KCO2, and MSC are compared based on pooling of the initial 2 points.) The purple dotted line indicates the significantly different regions in each point of decitabine and 5-AZA in HS-SY-II, SYO-1, ASKA, and MoJo. In MoJo, outlier values of more than 5 times the decitabine at 100 μM were excluded. P values were determined by 2-tailed paired t tests. (P values of less than 0.0045 were considered significant in the upper row, less than 0.007 for the lower row, each Bonferroni corrected from 0.05). (B) Necrosis areas similarly framed for control (vehicle), decitabine-treated, and 5-AZA–treated groups. (C) Diagram of a xenograft mouse model and details of drug administration. (D) Comparison of tumor mass after 2 weeks of treatment. P value was determined by 2-tailed homoscedastic t test. (n = 8 control, n = 10 decitabine treatments).