Defining APOBEC-induced mutation signatures and modifying activities in yeast
Tony M Mertz1, Zachary W Kockler2, Margo Coxon3
1Department of Microbiology and Molecular Genetics, University of Vermont Cancer Center, University of Vermont, Burlington, VT, United States.
Abstract:
APOBEC cytidine deaminases guard cells in a variety of organisms from invading viruses and foreign nucleic acids. Recently, several human APOBECs have been implicated in mutating evolving cancer genomes. Expression of APOBEC3A and APOBEC3B in yeast allowed experimental derivation of the substitution patterns they cause in dividing cells, which provided critical links to these enzymes in the etiology of the COSMIC single base substitution (SBS) signatures 2 and 13 in human tumors. Additionally, the ability to scale yeast experiments to high-throughput screens allows use of this system to also investigate cellular pathways impacting the frequency of APOBEC-induced mutation. Here, we present validated methods utilizing yeast to determine APOBEC mutation signatures, genetic interactors, and chromosomal substrate preferences. These methods can be employed to assess the potential of other human APOBECs and APOBEC orthologs in different species to contribute to cancer genome evolution as well as define the pathways that protect the nuclear genome from inadvertent APOBEC activity during viral restriction.
Insights
This study introduces yeast-based methods to analyze APOBEC cytidine deaminases, crucial enzymes linked to cancer genome mutations. These validated techniques identify APOBEC mutation signatures and pathways, aiding cancer research.
Area of Science:
- Molecular Biology
- Genetics
- Cancer Research
Background:
- APOBEC cytidine deaminases protect against viruses but are implicated in cancer genome mutations.
- Human APOBEC3A and APOBEC3B are linked to specific COSMIC single base substitution (SBS) signatures in tumors.
Purpose of the Study:
- To present validated yeast-based methods for studying APOBEC cytidine deaminases.
- To determine APOBEC mutation signatures, genetic interactors, and chromosomal preferences.
- To assess APOBECs' role in cancer genome evolution and host defense.
Main Methods:
- Expression of human APOBEC3A and APOBEC3B in yeast.
- Experimental derivation of APOBEC-induced substitution patterns in dividing cells.
- High-throughput screening in yeast to investigate mutation-influencing pathways.
Main Results:
- Established yeast as a model to derive APOBEC mutation signatures, linking them to COSMIC SBS 2 and 13.
- Demonstrated the utility of yeast for high-throughput screening of APOBEC activity.
- Validated methods to study APOBEC genetic interactors and substrate preferences.
Conclusions:
- Yeast-based methods provide a scalable system to study APOBEC functions in cancer and viral restriction.
- These methods can assess the oncogenic potential of various APOBECs and orthologs.
- Understanding protective pathways against APOBEC activity is crucial for genome integrity.
