Investigating the diverse cellular functions of APOBEC3A and APOBEC3B in urothelial carcinoma

Abstract

Urothelial carcinoma (UCC) is characterised by a high mutational burden, with many of the identified mutations resulting from the mutagenic activity of the APOBEC3 (A3) family of cytidine deaminases. A3B expression is frequently elevated in tumours and correlates with mutational load, suggesting that A3B is the primary driver of these A3 mutations. However, despite A3A expression being low and not elevated relative to normal tissue, several studies have shown that it is the more dominant mutagen. Experimental evidence suggests that mutations are not accumulated at a constant rate but are instead generated in bursts, and this may explain the disconnect between expression and the A3 signature. Anticancer agents with diverse mechanisms of action induce A3A/B expression in UCC cells, and this is likely driving episodic mutagenesis in patients. Investigation into the mechanism of induction revealed that A3A and A3B are differentially regulated in response to gemcitabine treatment in UCC cells; A3A induction is mediated by NF-kB and A3B induction occurs via ATR activation in response to replication stress. Expression of both A3A and A3B is attenuated with receptor tyrosine kinase inhibitors, highlighting that induction can be curbed with clinically available drugs. RNA sequencing revealed that acute expression of A3A and A3B has subtle effects on gene expression, but the identification of putative RNA editing events, provides initial evidence that A3B, like A3A, is an RNA editing enzyme, and suggests that A3A/B may be driving adaptability independently of genomic alteration. While A3B can cause DNA damage, a proliferation defect and increase sensitivity to DNA damage response inhibitors in several cell lines, acute A3B expression had no effect on growth or drug sensitivity in UCC cells, suggesting that they tolerate transient elevated expression. Finally, A3A's interacting partners were identified using the proximity-labelling technique, BioID, and this revealed interactions with R-loop-binding proteins, suggesting that A3A has novel role in R-loop homeostasis.