The dCMP deaminase DCTD and the E3 ligase TOPORS are central mediators of decitabine cytotoxicity

Carnie, C. J.; Gotz, M. J.; Palma-Chaundler, C. S.; Weickert, P.; Wanders, A. R.; Serrano-Benitez, A.; Li, H.-Y.; Gupta, V.; Blum, C. J.; Sczaniecka-Clift, M.; Zagnoli-Vieira, G.; D'Alessandro, G.; Richards, S. L.; Gueorguieva, N.; Beli, P.; Stingele, J.; Jackson, S. P.

doi:10.1101/2023.12.21.572728

bioRxiv · 10.1101/2023.12.21.572728

The dCMP deaminase DCTD and the E3 ligase TOPORS are central mediators of decitabine cytotoxicity

Carnie, C. J.·Gotz, M. J.·Palma-Chaundler, C. S.·Weickert, P.·Wanders, A. R.·Serrano-Benitez, A.·Li, H.-Y.·Gupta, V.·Blum, C. J.·Sczaniecka-Clift, M.·Zagnoli-Vieira, G.·D'Alessandro, G.·Richards, S. L.·Gueorguieva, N.·Beli, P.·Stingele, J.·Jackson, S. P.

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Abstract

The nucleoside decitabine (5-aza-dC) is used to treat several hematological cancers. Upon triphosphorylation and incorporation into DNA, 5-aza-dC induces covalent DNMT1 DNA-protein crosslinks (DPCs) and DNA hypomethylation. However, 5-aza-dC treatment success varies, and relapse is common. Using genome-scale CRISPR/Cas9 screens, we map factors determining 5-aza-dC susceptibility. Unexpectedly, we find that loss of the dCMP deaminase DCTD causes 5-aza-dC resistance, suggesting that 5-aza-dUMP generation underlies most 5-aza-dC cytotoxicity in wild-type cells. Combining results from a subsequent genetic screen in DCTD-deficient cells with identification of the proximal proteome of DNMT1-DPCs, we uncover the ubiquitin/SUMO1 E3 ligase, TOPORS, as a new DPC repair factor. TOPORS is recruited to DNMT1-DPCs in a SUMO-dependent manner and promotes their degradation. Our study suggests that 5-aza-dC-induced DPCs cause cytotoxicity when DPC repair is compromised, while cytotoxicity in wild-type cells arises from perturbed nucleotide metabolism and lays the foundations for the development of predictive biomarkers for decitabine treatment.

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Carnie, C. J., Gotz, M. J., Palma-Chaundler, C. S., Weickert, P., Wanders, A. R., Serrano-Benitez, A., Li, H.-Y., Gupta, V., Blum, C. J., Sczaniecka-Clift, M., Zagnoli-Vieira, G., D'Alessandro, G., Richards, S. L., Gueorguieva, N., Beli, P., Stingele, J., Jackson, S. P.. 2023-12-21. The dCMP deaminase DCTD and the E3 ligase TOPORS are central mediators of decitabine cytotoxicity. https://doi.org/10.1101/2023.12.21.572728

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