Elevated APOBEC3B expression drives a kataegic-like mutation signature and replication stress-related therapeutic vulnerabilities in p53-defective cells

Abstract

Background:Elevated APOBEC3B expression in tumours correlates with a kataegic pattern of localised hypermutation. We assessed the cellular phenotypes associated with high-level APOBEC3B expression and the influence of p53 status on these phenotypes using an isogenic system.Methods:We used RNA interference of p53 in cells with inducible APOBEC3B and assessed DNA damage response (DDR) biomarkers. The mutational effects of APOBEC3B were assessed using whole-genome sequencing. In vitro small-molecule inhibitor sensitivity profiling was used to identify candidate therapeutic vulnerabilities.Results:Although APOBEC3B expression increased the incorporation of genomic uracil, invoked DDR biomarkers and caused cell cycle arrest, inactivation of p53 circumvented APOBEC3B-induced cell cycle arrest without reversing the increase in genomic uracil or DDR biomarkers. The continued expression of APOBEC3B in p53-defective cells not only caused a kataegic mutational signature but also caused hypersensitivity to small-molecule DDR inhibitors (ATR, CHEK1, CHEK2, PARP, WEE1 inhibitors) as well as cisplatin/ATR inhibitor and ATR/PARP inhibitor combinations.Conclusions:Although loss of p53 might allow tumour cells to tolerate elevated APOBEC3B expression, continued expression of this enzyme might impart a number of therapeutic vulnerabilities upon tumour cells.

Apolipoprotein B mRNA editing enzyme catalytic polypeptide‐like family genes activation and regulation during tumorigenesis

“…Targeting replication stress‐directed APOBEC3B activation has broad implications for many inhibitors including afatinib and lapatinib for ERBB2 amplification, LY294002 and rapamycin for PI3K/mTOR signaling, U0126 for MAPK, CHK1 inhibitor, and ATM/ATR inhibitor . P53 defective cells with high expression of APOBEC3B are more sensitive to DNA damage response inhibitors (eg, PARP inhibitor), which have been used in clinical trials . In addition, APOBEC3 highly expressed tumors are correlated with high mutation burden, and overexpression of APOBEC3 paralogs appear to play pivotal roles in the regulation of programmed death‐ligand 1 (PD‐L1) expression, which is the predictive biomarker for subset cancer immunotherapy.…”

“…54 P53 defective cells with high expression of APOBEC3B are more sensitive to DNA damage response inhibitors (eg, PARP inhibitor), which have been used in clinical trials. 64 In addition, APO-BEC3 highly expressed tumors are correlated with high mutation burden, and overexpression of APOBEC3 paralogs appear to play pivotal roles in the regulation of programmed death-ligand 1 (PD-L1) expression, 65,66 which is the predictive biomarker for subset cancer immunotherapy. It is reasoned that these subtypes of patients may respond to immune checkpoint blockage therapies such as programmed cell death protein 1 (PD-1)/PD-L1 and cytotoxic T-lympho- 53 DNA replication stress 54 and HPV E6/7 oncoproteins and mutant p53 52 are able to turn on APOBEC3B expression.…”

A rabbit monoclonal antibody against the antiviral and cancer genomic DNA mutating enzyme APOBEC3B

“…We subsequently used it in IB experiments to study SIV Vif-mediated degradation of endogenous A3B 64 , endogenous A3B upregulation by polyomavirus infection 11 , A3B lysine post-translational modification 65 , and endogenous A3B interaction with EBV BORF2 16 . The 5210-87-13 mAb has also been shared with colleagues, who have independently demonstrated utility in anti-A3B IB experiments 66,67 . In addition, another independent study used 5210-87-13 to monitor A3A and A3B induction in IB and IF experiments 68 .…”

Biochemical Basis of APOBEC3 Deoxycytidine Deaminase Activity on Diverse DNA Substrates

“…However, with the development of Next Generation Sequencing technology and the availability of large sequence datasets, it has become clear that mutations in many cancers have a C/G→T/A bias, and most cancer cells or tumors also overexpress of A3B or A3H hap I mRNA, suggesting that A3s are inducing somatic mutations [16,17,[171][172][173][174][175]. The uracils created by A3 mutations also can lead to C→G or C→A mutations depending on the repair pathway initiated by the abasic site after APE-mediated removal [176,177] (Figure 1.2A). Several lines of evidence demonstrate that A3…”

“…The generation of increased amounts of ssDNA promotes the activity of A3 and increases the mutational frequency Thus, it is notable that A3B is not problematic until a cellular alteration occurs that increases A3B expression and increases replication stress [177,192,203]. In contrast, the ssDNA generated on the nontranscribed strand during transcription is accessible at multiple times during the cell cycle of a normal or transformed cell, especially during RNA polymerase stalling [20,21].…”