The APOBEC3A deaminase drives episodic mutagenesis in cancer cells

Abstract

The APOBEC3 family of cytidine deaminases is widely speculated to be a major source of somatic mutations in cancer1-3. However, causal links between APOBEC3 enzymes and mutations in human cancer cells have not been established. The identity of the APOBEC3 paralog(s) that may act as prime drivers of mutagenesis and the mechanisms underlying different APOBEC3-associated mutational signatures are unknown. To directly investigate the roles of APOBEC3 enzymes in cancer mutagenesis, candidate APOBEC3 genes were deleted from cancer cell lines recently found to naturally generate APOBEC3-associated mutations in episodic bursts4. Deletion of the APOBEC3A paralog severely diminished the acquisition of mutations of speculative APOBEC3 origins in breast cancer and lymphoma cell lines. APOBEC3 mutational burdens were undiminished in APOBEC3B knockout cell lines. APOBEC3A deletion reduced the appearance of the clustered mutation types kataegis and omikli, which are frequently found in cancer genomes. The uracil glycosylase UNG and the translesion polymerase REV1 were found to play critical roles in the generation of mutations induced by APOBEC3A. These data represent the first evidence for a long-postulated hypothesis that APOBEC3 deaminases generate prevalent clustered and non-clustered mutational signatures in human cancer cells, identify APOBEC3A as a driver of episodic mutational bursts, and dissect the roles of the relevant enzymes in generating the associated mutations in breast cancer and B cell lymphoma cell lines.

Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA

“…By contrast, MBSs have not been comprehensively investigated, presumably owing to their small numbers in cancer genomes. Moreover, only a handful of processes have been associated with omikli and kataegic events, with most processes attributed to the AID and APOBEC3 family Article of deaminases 3,[6][7][8]13,14,[20][21][22][23] . Specifically, the APOBEC3 enzymes, which are typically responsible for antiviral responses [24][25][26][27][28][29][30] , give rise to omikli and kataegis by requiring single-stranded DNA as a substrate 6,8,23,31 .…”

“…Moreover, only a handful of processes have been associated with omikli and kataegic events, with most processes attributed to the AID and APOBEC3 family Article of deaminases 3,[6][7][8]13,14,[20][21][22][23] . Specifically, the APOBEC3 enzymes, which are typically responsible for antiviral responses [24][25][26][27][28][29][30] , give rise to omikli and kataegis by requiring single-stranded DNA as a substrate 6,8,23,31 . Omikli were found to be enriched in early replicating regions and more prevalent in microsatellite stable tumours, indicating that mismatch repair has a role in exposing short single-stranded DNA regions 6 .…”

Comprehensive analysis of clustered mutations in cancer reveals recurrent APOBEC3 mutagenesis of ecDNA

“…In cancer genomes, omikli were previously attributed to APOBEC3 mutagenesis 15 with some indirect evidence from experimental models 24,[37][38][39] . Our analysis of sequencing data 40 from the clonally expanded breast cancer cell line BT474 with active APOBEC3 mutagenesis experimentally confirmed the existence of APOBEC3 omikli events (cosine similarity: 0.99; Extended Data Fig.…”

“…In contrast, multi-base substitutions have not been comprehensively explored presumably due to their small numbers in most cancer genomes. Moreover, only a handful of reported processes have been associated with omikli and kataegic events with majority of these processes attributed to AID/APOBEC3 family of deaminases 4,5,12,[14][15][16][21][22][23][24] . For example, in B-cell lymphomas clustered tracks of C>T and C>G mutations at WRCY motifs are the result of direct replication over AID lesions 21 .…”

“…In addition to AID, the APOBEC3 enzymes, which are typically responsible for anti-viral responses and for limiting the mobility of mobile elements [25][26][27][28][29][30][31] , are a substantial contributor of clustered mutational events 2,4,12,[14][15][16]24,32 . Specifically, the APOBEC3 enzymes give rise to omikli and kataegis by requiring single-stranded DNA as a substrate 14,15,24,32 . Omikli were found enriched in early replicating regions and more prevalent in microsatellite stable tumors indicating a role of mismatch repair in exposing short single-stranded DNA regions while processing mismatched bases during replication 15 .…”