APOBEC3B is an enzymatic source of mutation in breast cancer

A Corrigendum to this article was published on 23 October 2013

Abstract

Several mutations are required for cancer development, and genome sequencing has revealed that many cancers, including breast cancer, have somatic mutation spectra dominated by C-to-T transitions1,2,3,4,5,6,7,8,9. Most of these mutations occur at hydrolytically disfavoured10 non-methylated cytosines throughout the genome, and are sometimes clustered8. Here we show that the DNA cytosine deaminase APOBEC3B is a probable source of these mutations. APOBEC3B messenger RNA is upregulated in most primary breast tumours and breast cancer cell lines. Tumours that express high levels of APOBEC3B have twice as many mutations as those that express low levels and are more likely to have mutations in TP53. Endogenous APOBEC3B protein is predominantly nuclear and the only detectable source of DNA C-to-U editing activity in breast cancer cell-line extracts. Knockdown experiments show that endogenous APOBEC3B correlates with increased levels of genomic uracil, increased mutation frequencies, and C-to-T transitions. Furthermore, induced APOBEC3B overexpression causes cell cycle deviations, cell death, DNA fragmentation, γ-H2AX accumulation and C-to-T mutations. Our data suggest a model in which APOBEC3B-catalysed deamination provides a chronic source of DNA damage in breast cancers that could select TP53 inactivation and explain how some tumours evolve rapidly and manifest heterogeneity.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: APOBEC3B upregulation and activity in breast cancer cell lines.
Figure 2: A3B-dependent uracil lesions and mutations in breast cancer genomic DNA.
Figure 3: Cancer phenotypes triggered by inducing A3B overexpression.
Figure 4: APOBEC3B upregulation and mutation in breast tumours.

References

  1. 1

    Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007)

    CAS  ADS  Article  Google Scholar 

  2. 2

    Jones, S. et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330, 228–231 (2010)

    CAS  ADS  Article  Google Scholar 

  3. 3

    Sjöblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268–274 (2006)

    ADS  Article  Google Scholar 

  4. 4

    Kumar, A. et al. Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers. Proc. Natl Acad. Sci. USA 108, 17087–17092 (2011)

    CAS  ADS  Article  Google Scholar 

  5. 5

    Parsons, D. W. et al. The genetic landscape of the childhood cancer medulloblastoma. Science 331, 435–439 (2011)

    CAS  ADS  Article  Google Scholar 

  6. 6

    Berger, M. F. et al. The genomic complexity of primary human prostate cancer. Nature 470, 214–220 (2011)

    CAS  ADS  Article  Google Scholar 

  7. 7

    Stransky, N. et al. The mutational landscape of head and neck squamous cell carcinoma. Science 333, 1157–1160 (2011)

    CAS  ADS  Article  Google Scholar 

  8. 8

    Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979–993 (2012)

    CAS  Article  Google Scholar 

  9. 9

    Stephens, P. J. et al. The landscape of cancer genes and mutational processes in breast cancer. Nature 486, 400–404 (2012)

    CAS  Article  Google Scholar 

  10. 10

    Ehrlich, M., Norris, K. F., Wang, R. Y., Kuo, K. C. & Gehrke, C. W. DNA cytosine methylation and heat-induced deamination. Biosci. Rep. 6, 387–393 (1986)

    CAS  Article  Google Scholar 

  11. 11

    Pavri, R. & Nussenzweig, M. C. AID targeting in antibody diversity. Adv. Immunol. 110, 1–26 (2011)

    CAS  Article  Google Scholar 

  12. 12

    Yamanaka, S. et al. Apolipoprotein B mRNA-editing protein induces hepatocellular carcinoma and dysplasia in transgenic animals. Proc. Natl Acad. Sci. USA 92, 8483–8487 (1995)

    CAS  ADS  Article  Google Scholar 

  13. 13

    Harris, R. S., Petersen-Mahrt, S. K. & Neuberger, M. S. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol. Cell 10, 1247–1253 (2002)

    CAS  Article  Google Scholar 

  14. 14

    Refsland, E. W. et al. Quantitative profiling of the full APOBEC3 mRNA repertoire in lymphocytes and tissues: implications for HIV-1 restriction. Nucleic Acids Res. 38, 4274–4284 (2010)

    CAS  Article  Google Scholar 

  15. 15

    Lackey, L. et al. APOBEC3B and AID have similar nuclear import mechanisms. J. Mol. Biol. 419, 301–314 (2012)

    CAS  Article  Google Scholar 

  16. 16

    Albin, J. S. & Harris, R. S. Interactions of host APOBEC3 restriction factors with HIV-1 in vivo: implications for therapeutics. Expert Rev. Mol. Med. 12, e4 (2010)

    Article  Google Scholar 

  17. 17

    Stenglein, M. D., Burns, M. B., Li, M., Lengyel, J. & Harris, R. S. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nature Struct. Mol. Biol. 17, 222–229 (2010)

    CAS  Article  Google Scholar 

  18. 18

    Suspène, R. et al. Somatic hypermutation of human mitochondrial and nuclear DNA by APOBEC3 cytidine deaminases, a pathway for DNA catabolism. Proc. Natl Acad. Sci. USA 108, 4858–4863 (2011)

    ADS  Article  Google Scholar 

  19. 19

    Hanahan, D. & Weinberg, R. A. Hallmarks of cancer: the next generation. Cell 144, 646–674 (2011)

    CAS  Article  Google Scholar 

  20. 20

    Landry, S., Narvaiza, I., Linfesty, D. C. & Weitzman, M. D. APOBEC3A can activate the DNA damage response and cause cell-cycle arrest. EMBO Rep. 12, 444–450 (2011)

    CAS  Article  Google Scholar 

  21. 21

    The Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012)

  22. 22

    Wei, X. et al. Exome sequencing identifies GRIN2A as frequently mutated in melanoma. Nature Genet. 43, 442–446 (2011)

    CAS  Article  Google Scholar 

  23. 23

    Zhang, J. et al. International Cancer Genome Consortium Data Portal—a one-stop shop for cancer genomics data. Database 2011, bar026 (2011)

    PubMed  PubMed Central  Google Scholar 

  24. 24

    Di Noia, J. M. & Neuberger, M. S. Molecular mechanisms of antibody somatic hypermutation. Annu. Rev. Biochem. 76, 1–22 (2007)

    CAS  Article  Google Scholar 

  25. 25

    Loeb, L. A., Springgate, C. F. & Battula, N. Errors in DNA replication as a basis of malignant changes. Cancer Res. 34, 2311–2321 (1974)

    CAS  PubMed  Google Scholar 

  26. 26

    Kidd, J. M., Newman, T. L., Tuzun, E., Kaul, R. & Eichler, E. E. Population stratification of a common APOBEC gene deletion polymorphism. PLoS Genet. 3, e63 (2007)

    Article  Google Scholar 

  27. 27

    Carpenter, M. A. et al. Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A. J. Biol. Chem. 287, 34801–34808 (2012)

    CAS  Article  Google Scholar 

  28. 28

    Shlyakhtenko, L. S. et al. Atomic force microscopy studies provide direct evidence for dimerization of the HIV restriction factor APOBEC3G. J. Biol. Chem. 286, 3387–3395 (2011)

    CAS  Article  Google Scholar 

  29. 29

    Lea, D. E. & Coulson, C. A. The distribution of the numbers of mutants in bacterial populations. J. Genet. 49, 264–285 (1949)

    CAS  Article  Google Scholar 

  30. 30

    Di Noia, J. & Neuberger, M. S. Altering the pathway of immunoglobulin hypermutation by inhibiting uracil-DNA glycosylase. Nature 419, 43–48 (2002)

    CAS  ADS  Article  Google Scholar 

  31. 31

    Huang, X. & Darzynkiewicz, Z. Cytometric assessment of histone H2AX phosphorylation: a reporter of DNA damage. Methods Mol. Biol. 314, 73–80 (2006)

    CAS  Article  Google Scholar 

  32. 32

    Fairbairn, D. W., Olive, P. L. & O’Neill, K. L. The comet assay: a comprehensive review. Mutat. Res. 339, 37–59 (1995)

    CAS  Article  Google Scholar 

Download references

Acknowledgements

We thank J. Hultquist and R. Vogel for statistics, T. Hwang for bioinformatic assistance, V. Polunovsky for hTERT-HMECs, V. Simon for shRNA, S. Kaufmann, C. Lange and D. Largaespada for consultation, and the Masonic Cancer Center Breast Cancer Research Fund for purchasing the ATCC breast cancer panel. Tissues were obtained from the Masonic Cancer Center Tissue Procurement Facility, which is part of BioNet, supported by the Academic Health Center and National Institutes of Health (NIH) grants P30 CA77598 (D.Y.), P50 CA101955 (D. Buchsbaum) and KL2 RR033182 (B. Blazar). M.B.B. was supported in part by a Cancer Biology Training Grant (NIH NCI T32 CA009138) and a Department of Defense Breast Cancer Research Program Predoctoral Fellowship (BC101124). L.L. was supported in part by a National Science Foundation Predoctoral Fellowship and by a position on the Institute for Molecular Virology Training Grant NIH T32 AI083196. M.A.C. was supported by an NIH postdoctoral fellowship (F32 GM095219). A.M.L. was supported by a CIHR postdoctoral fellowship. E.W.R. was supported by a position on the Institute for Molecular Virology Training Grant NIH T32 AI083196 and subsequently by an NIH predoctoral fellowship (F31 DA033186). Computational analyses (N.A.T. and D.E.D.) were supported by federal funds from the National Cancer Institute, NIH, CBIIT/caBIG ISRCE yellow task 09-260. The Harris laboratory was supported in part by NIH R01 AI064046, NIH P01 GM091743, the Children's Cancer Research Fund, and a seed grant from the University of Minnesota Clinical and Translational Science Institute (supported by NIH 1UL1RR033183).

Author information

Affiliations

Authors

Contributions

R.S.H. conceived and managed the overall project. M.B.B. assisted R.S.H. with experimental design, project management and manuscript preparation. M.B.B., E.W.R. and B.L. generated mRNA expression profiles; L.L. and E.K.L. performed microscopy; L.L. and A.R. performed biochemical fractionations and DNA deaminase assays; M.B.B. performed uracil quantifications; A.M.L. performed thymidine kinase fluctuations; A.R. generated 3D-PCR sequences; and L.L., A.M.L., A.R. and M.A.C. determined the effect of induced A3B overexpression. M.A.C. performed deaminase assays with recombinant protein; and M.A.C. and D.K. assisted with the HPLC-ESI-MS/MS set up. N.T. was involved in HPLC-ESI-MS/MS method development. J.B.N. conducted the search and performed the bioinformatic analysis of the microarray data and developed the normalization algorithm for this analysis. N.A.T., D.E.D. and M.B.B. contributed bioinformatic analyses. All authors contributed to manuscript revisions.

Corresponding author

Correspondence to Reuben S. Harris.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion, Supplementary Methods, Supplementary References, Supplementary Tables 1-11 and Supplementary Figures 1-16. (PDF 3228 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Burns, M., Lackey, L., Carpenter, M. et al. APOBEC3B is an enzymatic source of mutation in breast cancer. Nature 494, 366–370 (2013). https://doi.org/10.1038/nature11881

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing