FHIT loss-induced DNA damage creates optimal APOBEC substrates: Insights into APOBEC-mediated mutagenesis

Catherine E Waters,Joshua C Saldivar,Morgan S Schrock,Kay Huebner,Zaynab A Amin

doi:10.18632/oncotarget.2636

Catherine E Waters, Joshua C Saldivar + Show 3 more

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https://doi.org/10.18632/oncotarget.2636

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Abstract

APOBEC cytidine deaminase activity is a major source of hypermutation in cancer. But previous studies have shown that the TC context signature of these enzymes is not observed in sizable fractions of cancers with overexpression of APOBEC, suggesting that cooperating factors that contribute to this mutagenesis should be identified. The fragile histidine triad protein (Fhit) is a tumor suppressor and DNA caretaker that is deleted or silenced in >50% of cancers. Loss of Fhit protein activity causes replication stress through reduced Thymidine Kinase 1 expression, increased DNA breaks, and global genome instability in normal and cancer cells. Using data from The Cancer Genome Atlas (TCGA), we show that FHIT-low/APOBEC3B-high expressing lung adenocarcinomas display significantly increased numbers of APOBEC signature mutations. Tumor samples in this cohort with normal FHIT expression do not exhibit APOBEC hypermutation, despite having high APOBEC3B expression. In vitro, silencing Fhit expression elevates APOBEC3B-directed C > T mutations in the TP53 gene. Furthermore, inhibition of Fhit loss-induced DNA damage via thymidine supplementation decreases the TP53 mutation burden in FHIT-low/APOBEC3B-high cells. We conclude that APOBEC3B overexpression and Fhit-loss induced DNA damage are independent events that, when occurring together, result in a significantly increased frequency of APOBEC-induced mutations that drive cancer progression.

Highlights

Cancer genomes are riddled with single base substitutions (SBSs), the predominant genetic alteration found in cancer cells [1,2,3,4,5]
We have recently described a source of endogenous DNA replication stress and double-stranded DNA (dsDNA) breaks that neither activates cell cycle checkpoints nor induces apoptosis; in other words, this damage is checkpoint “blind.” Through ongoing research on functions of common chromosome fragile site (CFS)-associated genes, we found that loss of fragile histidine triad protein (Fhit) protein expression causes a nucleotide imbalance, a decrease in dTTP pools due to lack of sufficient thymidine kinase 1 (TK1) protein activity
Analysis of The Cancer Genome Atlas (TCGA) datasets for lung adenocarcinoma revealed that the APOBEC signature was prevalent in this type of cancer, for both C > T and C > G mutations

Summary

Introduction

Cancer genomes are riddled with single base substitutions (SBSs), the predominant genetic alteration found in cancer cells [1,2,3,4,5]. Mutations in cancer genomes are not always randomly scattered, but can occur in discreet patterns. Large-scale sequencing efforts have uncovered patterns of spatially close and strandcoordinated mutations that likely occur at the same time [6,7,8]. Knowledge of endogenous enzymatic sources of mutations has been elusive, but cancer genome and exome sequencing endeavors have exposed striking cancerspecific mutation signatures that suggested previously unconsidered candidates. The frequency of SBSs reportedly due to www.impactjournals.com/oncotarget

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