Mesoscale DNA Features Impact APOBEC3A and APOBEC3B Deaminase Activity and Shape Tumor Mutational Landscapes

Abstract

Antiviral DNA cytosine deaminases APOBEC3A and APOBEC3B are major sources of mutations in cancer by catalyzing cytosine-to-uracil deamination. APOBEC3A preferentially targets singlestranded DNAs, with a noted affinity for DNA regions that adopt stem-loop secondary structures. However, the detailed substrate preferences of APOBEC3A and APOBEC3B have been fully established, and the specific influence of the DNA sequence on APOBEC3A APOBEC3B deaminase activity remains to be investigated. Here, we find that APOBEC3B selectively targets DNA stem-loop structures, and they are distinct from those subjected deamination by APOBEC3A. We develop Oligo-seq, a novel in vitro sequencing-based to identify specific sequence contexts promoting APOBEC3A and APOBEC3B activity. Through this approach, we demonstrate that APOBEC3A an APOBEC3B deaminase activity is strongly regulated by specific sequences surrounding the targeted cytosine. Moreover, we identify structural features of APOBEC3B and APOBEC3A responsible for their substrate preferences. Importantly, we determine that APOBEC3B-induced mutations in hairpin-forming sequences within tumor genomes differ from the DNA stem-loop sequences mutated by APOBEC3A. Together, our study provides evidence that APOBEC3A and APOBEC3B can generate mutation landscapes in cancer genomes, driven by their unique substrate selectivity.

Guardian ubiquitin E3 ligases target cancer-associated APOBEC3 deaminases for degradation to promote human genome integrity

“…We show that the loss of the central E3 ligases, UBR4, UBR5, and HUWE1 stabilizes A3B and A3H-I proteins, resulting in their accumulation and eventually increased APOBEC-related mutational burden. Our findings reveal a previously unconsidered layer of regulation of cellular A3 protein levels, which may broaden the mutational landscape in late-stage cancer, and affect development of therapy resistance 32,[61][62][63][64] .…”

“…A3mediated mutagenesis has been shown to drive some of the most prevalent mutational signatures in cancer, characterized by C-to-T transitions and clustered mutations (kataegis) at TCN trinucleotides 17,[22][23][24][25][26][27][28][29] . APOBEC-associated mutational signatures have been identified in more than 70% of cancer types and around 50% of all cancer genomes, with prominence in breast, lung, and bladder cancer, as well as other cancer types 17,18,[30][31][32] . A3A is overexpressed in a wide spectrum of human cancers and can induce kataegis and omikli, a form of extreme kataegis with more than 100 mutations per megabase [15][16][17]29,32 .…”

“…APOBEC-associated mutational signatures have been identified in more than 70% of cancer types and around 50% of all cancer genomes, with prominence in breast, lung, and bladder cancer, as well as other cancer types 17,18,[30][31][32] . A3A is overexpressed in a wide spectrum of human cancers and can induce kataegis and omikli, a form of extreme kataegis with more than 100 mutations per megabase [15][16][17]29,32 . A3B is overexpressed in many cancers and can generate APOBEC-specific SBS2 and SBS13 signatures 17,33,34 .…”