Mutation Processes in 293-Based Clones Overexpressing the DNA Cytosine Deaminase APOBEC3B

PLoS One. 2016 May 10;11(5):e0155391. doi: 10.1371/journal.pone.0155391. eCollection 2016.

Abstract

Molecular, cellular, and clinical studies have combined to demonstrate a contribution from the DNA cytosine deaminase APOBEC3B (A3B) to the overall mutation load in breast, head/neck, lung, bladder, cervical, ovarian, and other cancer types. However, the complete landscape of mutations attributable to this enzyme has yet to be determined in a controlled human cell system. We report a conditional and isogenic system for A3B induction, genomic DNA deamination, and mutagenesis. Human 293-derived cells were engineered to express doxycycline-inducible A3B-eGFP or eGFP constructs. Cells were subjected to 10 rounds of A3B-eGFP exposure that each caused 80-90% cell death. Control pools were subjected to parallel rounds of non-toxic eGFP exposure, and dilutions were done each round to mimic A3B-eGFP induced population fluctuations. Targeted sequencing of portions of TP53 and MYC demonstrated greater mutation accumulation in the A3B-eGFP exposed pools. Clones were generated and microarray analyses were used to identify those with the greatest number of SNP alterations for whole genome sequencing. A3B-eGFP exposed clones showed global increases in C-to-T transition mutations, enrichments for cytosine mutations within A3B-preferred trinucleotide motifs, and more copy number aberrations. Surprisingly, both control and A3B-eGFP clones also elicited strong mutator phenotypes characteristic of defective mismatch repair. Despite this additional mutational process, the 293-based system characterized here still yielded a genome-wide view of A3B-catalyzed mutagenesis in human cells and a system for additional studies on the compounded effects of simultaneous mutation mechanisms in cancer cells.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cell Death / genetics
  • Cell Engineering / methods*
  • Cell Line
  • Clone Cells
  • Cytidine Deaminase / genetics*
  • Cytidine Deaminase / metabolism
  • Cytosine / metabolism
  • DNA Mismatch Repair
  • Doxycycline / pharmacology
  • Gene Expression Regulation*
  • Genetic Vectors / chemistry
  • Genetic Vectors / metabolism
  • Green Fluorescent Proteins / genetics
  • Green Fluorescent Proteins / metabolism
  • HEK293 Cells
  • Humans
  • Minor Histocompatibility Antigens / genetics*
  • Minor Histocompatibility Antigens / metabolism
  • Mutation*
  • Polymorphism, Single Nucleotide*
  • Proto-Oncogene Proteins c-myc / genetics
  • Proto-Oncogene Proteins c-myc / metabolism
  • Recombinant Fusion Proteins / genetics*
  • Recombinant Fusion Proteins / metabolism
  • Thymine / metabolism
  • Tissue Array Analysis
  • Transfection
  • Tumor Suppressor Protein p53 / genetics
  • Tumor Suppressor Protein p53 / metabolism

Substances

  • MYC protein, human
  • Minor Histocompatibility Antigens
  • Proto-Oncogene Proteins c-myc
  • Recombinant Fusion Proteins
  • TP53 protein, human
  • Tumor Suppressor Protein p53
  • enhanced green fluorescent protein
  • Green Fluorescent Proteins
  • Cytosine
  • APOBEC3B protein, human
  • Cytidine Deaminase
  • Doxycycline
  • Thymine

Grant support

Work in the Grigoriadis and Tutt laboratories is supported by Breakthrough Breast Cancer (recently merged with Breast Cancer Campaign forming Breast Cancer Now). JQ is on a PhD studentship in Translational Medicine from the NIHR Biomedical Research Centre at Guy’s and St Thomas. Cancer studies in the Harris laboratory are supported by grants from the Department of Defense Breast Cancer Research Program (BC121347), the Jimmy V Foundation for Cancer Research, the Norwegian Centennial Chair Program, the Minnesota Partnership for Biotechnology and Medical Genomics, and the Randy Shaver Cancer Research and Community Fund. Salary support for GJS was provided by a National Science Foundation Graduate Research Fellowship (DGE 13488264). RSH is an Investigator of the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.