Whole-genome mapping of APOBEC mutagenesis in metastatic urothelial carcinoma identifies driver hotspot mutations and a novel mutational signature

Abstract

Background: In urothelial carcinoma (UC), apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) enzymes are major contributors to the mutational burden. The APOBEC family mutates specific DNA sequences and hairpin-loop structures, creating Hotspot Mutations (ApoHM). The vast majority of ApoHM are passengers and only a few appear more frequently than expected (drivers). In this study, we aimed to characterize 115 whole-genomes of metastatic UC (mUC) to identify APOBEC mutagenic hotspot drivers of mUC. Results: APOBEC-associated mutations (TpC context) were detected in 92% of mUC samples and were equally present across the genome. However, ApoHM were enriched in open chromatin and DNA hairpin-loop structures. The hairpin-loops were frequent targets of two hotspot mutations we called didymi (twins in Greek). Didymi were characterized by the APOBEC mutational signature SBS2, in conjunction with an uncharacterized mutational context (C>T mutations in ApC context), which was associated with DNA mismatch. Next, we developed a statistical framework that identified 0.40% of ApoHM as drivers of mUC, which affected the protein-coding regions of known driver genes FGFR3, PIK3CA, RXRA, and TP53, and non-coding regions near exons of potential novel driver genes. Our results and statistical framework were validated in independent cohorts of 23 non-metastatic UC and 442 metastatic breast cancers (mBC), showing that drivers are cancer-type-specific and only 0.07% of ApoHM were drivers of mBC. Conclusion: By whole-genome DNA-sequencing analysis of mUC, we identified a novel mutational signature associated with APOBEC-targeted hairpin-loops and found that 0.07%-0.40% of ApoHM were drivers. Our study highlights the consequences of APOBEC in cancer development and may serve to develop novel targeted therapy options for APOBEC-driven mUC.