Abstract
APOBEC family members play crucial roles in antiviral restriction. However, certain APOBEC3 (A3) proteins drive harmful hypermutation in humans, contributing to cancer. The cancer-associated A3 proteins are capable of transiting from the cytosol to the nucleus, where they can cause genome mutations. Here, we uncover a specific set of cellular pathways that protect genomic DNA from the major cancer-associated A3 proteins. Through genetic and proteomic screening, we identify UBR4, UBR5, and HUWE1 as key ubiquitin E3 ligases marking cancer-associated A3B and A3H-I for degradation, thereby limiting A3-driven hypermutation. Mechanistically, UBR5 and HUWE1 recognize A3s in the absence of their RNA binding partner, thus promoting proteasomal degradation of APOBEC3 protein that is not engaged in its antiviral cellular function. Depletion or mutation of the E3 ligases in cells and human cancer samples increases A3-driven genome mutagenesis. Our findings reveal that UBR4, UBR5, and HUWE1 are crucial factors in a ubiquitination cascade that maintains human genome stability.
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Data availability
Cancer genetic analysis data are available from the ICGC Data portal and through granted access of the TCGA Research Network (https://www.cancer.gov/ccg/research/genome-sequencing/tcga). The mass-spectrometry data generated in this study are available in Supplementary Data 2 and have been deposited to the ProteomeXchange consortium via the PRIDE partner repository with the accession code PXD051267
Public cancer whole-genome sequencing data from ICGC are available through the ICGC Data Portal (public) (https://dcc.icgc.org/releases/PCAWG). The NCBI dbGaP data are under restricted access as per NIH policy, access can be obtained through (https://dbgap.ncbi.nlm.nih.gov/home/).The genetic screen data generated in this study are provided as Supplementary Data 1 and in the Source Data file. Source data are provided with this paper.
Code availability
Data and code pertaining to cancer genome analysis and sequence context analysis can be found on GitHub (https://github.com/menchelab/apobex)154.
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Acknowledgements
Next Generation Sequencing analysis was performed by the Vienna Biocenter Core Facilities using the VBCF instrument pool. Proteomics analyses were performed by the Mass Spectrometry Facility at Max Perutz Labs using the VBCF instrument pool; we particularly thank Markus Hartl and WeiQiang Chen for their expert support. Flow cytometry analyses were performed at the BioOptics FACS Facility at the Max Perutz Labs using the Max Perutz Labs instrument pool; we particularly acknowledge Kitti Csalyi, Thomas Sauer, and Johanna Stranner for expert support. Microscopy was performed at the BioOptics Light Microscopy Facility at the Max Perutz Labs; we thank Thomas Peterbauer and Irmgard Fischer for their expert support and training. We thank Johannes Bock for establishing TurboID-related reagents and methodology, Robert Kurzbauer for purification of recombinant proteins, Anna Hakobyan for advice on cancer genome data analysis, Joanna Loizou for expert advice on DNA damage assays, Magdalini Nigritinou and Pablo Araguas-Rodriguez for experimental support, and Marcel Ooms for APOBEC expertise, discussions, and manuscript feedback. We are grateful to the ‘Signaling Mechanisms in Cellular Homeostasis’ doctoral program community, in particular Thomas Decker, Pavel Kovarik and their labs for their technical expertise and help. We thank Life Science Editors for editing services. The results shown here are in whole or part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga. This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grants 10.55776/P36572, 10.55776/P30415, 10.55776/P30231, 10.55776/P36945, 10.55776/F79, and 10.55776/W1261 to G.A.V.). For the purpose of open access, the author has applied a CC-BY public copyright license to any author accepted manuscript version arising from this submission. This work was funded by Austrian Science Fund Special Research Grant (FWF, SFB F79) and an ERC European Union’s Horizon 2020 research and innovation program grant (AdG 694978) to TC, and an Austrian Science Fund Special Research Grant (SFB grant F79) to GEK. VB and S.Sci are the recipients of a DOC fellowship of the Austrian Academy of Sciences. Research at the IMP is supported by Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
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Conceptualization, G.A.V., I.S., V.B., D.H., T.C., and E.K.; Methodology, G.A.V., I.S., V.B., M.M., H.H., Z.H., D.B.G., and J.F.E.; Software, M.M, I.S., and S.S.; Validation, I.S. and V.B.; Formal analysis, I.S., V.B., and M.M.; Investigation, I.S., V.B., and K.H.; Resources, Z.H., D.B.G., J.F.E., and S.Sci.; Data Curation, I.S., V.B., M.M and G.A.V.; Writing—original draft, I.S., V.B. and G.A.V.; Writing—review and editing, I.S., V.B., M.M., H.H., K.H., S.S., Z.H., D.B.G., J.F.E., S.Sci, D.H., J.M., T.C., E.K., and G.A.V.; Visualization, I.S., V.B., and M.M.; Supervision G.A.V.; Project administration, G.A.V.; Funding acquisition, G.A.V.
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Schwartz, I., Budroni, V., Meyenberg, M. et al. Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity. Nat Commun (2026). https://doi.org/10.1038/s41467-026-68420-5
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DOI: https://doi.org/10.1038/s41467-026-68420-5
