Evidence for APOBEC3B mutagenesis in multiple human cancers

Nature Genetics

Volumn 45, Issue 9, 2013, Pages 977-983

  Burns, Michael B ^a,b,c,d   Temiz, Nuri A ^a,b   Harris, Reuben S ^a,b,c,d  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c UNIVERSITY OF MINNESOTA   (United States)

^d UNIVERSITY OF MINNESOTA MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APOBEC 3B PROTEIN; CYTIDINE DEAMINASE; UNCLASSIFIED DRUG; APOBEC3B PROTEIN, HUMAN;

ACUTE GRANULOCYTIC LEUKEMIA; ARTICLE; BLADDER CANCER; BREAST CARCINOMA; COLON ADENOCARCINOMA; CUTANEOUS MELANOMA; EXOME; GENE EXPRESSION; GENE MUTATION; GLIOBLASTOMA; GLIOMA; HEAD AND NECK SQUAMOUS CELL CARCINOMA; HUMAN; KIDNEY CARCINOMA; LUNG ADENOCARCINOMA; LUNG SQUAMOUS CELL CARCINOMA; MULTIPLE CANCER; MUTAGENESIS; PRIORITY JOURNAL; PROSTATE ADENOCARCINOMA; RECTUM CARCINOMA; SEQUENCE ANALYSIS; SOMATIC MUTATION; STOMACH ADENOCARCINOMA; UPREGULATION; UTERINE CERVIX CANCER; CLUSTER ANALYSIS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; HUMAN GENOME; MALE; MUTATION; NEOPLASM;

CLUSTER ANALYSIS; CYTIDINE DEAMINASE; EXOME; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; HUMANS; MALE; MUTAGENESIS; MUTATION; NEOPLASMS;

EID: 84883356320     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.2701     Document Type: Article

References (50)

1. Stephens, P. et al. A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer. Nat. Genet. 37, 590-592 (2005).
2. Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153-158 (2007).
3. Jones, S. et al. Frequent mutations of chromatin remodeling gene ARID1A in ovarian clear cell carcinoma. Science 330, 228-231 (2010).
4. Sjöblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268-274 (2006).
5. 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).
6. Parsons, D.W. et al. The genetic landscape of the childhood cancer medulloblastoma. Science 331, 435-439 (2011).
7. Berger, M.F. et al. The genomic complexity of primary human prostate cancer. Nature 470, 214-220 (2011).
8. Stransky, N. et al. The mutational landscape of head and neck squamous cell carcinoma. Science 333, 1157-1160 (2011).
9. Nik-Zainal, S. et al. Mutational processes molding the genomes of 21 breast cancers. Cell 149, 979-993 (2012).
10. Stephens, P.J. et al. The landscape of cancer genes and mutational processes in breast cancer. Nature 486, 400-404 (2012).
11. Makridakis, N.M. & Reichardt, J.K. Translesion DNA polymerases and cancer. Front. Genet. 3, 174 (2012).
12. Roberts, S.A. et al. Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. Mol. Cell 46, 424-435 (2012).
13. Drier, Y. et al. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res. 23, 228-235 (2013).
14. 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).
15. Di Noia, J.M. & Neuberger, M.S. Molecular mechanisms of antibody somatic hypermutation. Annu. Rev. Biochem. 76, 1-22 (2007).
16. Longerich, S., Basu, U., Alt, F. & Storb, U. AID in somatic hypermutation and class switch recombination. Curr. Opin. Immunol. 18, 164-174 (2006).
17. Conticello, S.G. The AID/APOBEC family of nucleic acid mutators. Genome Biol. 9, 229 (2008).
18. LaRue, R.S. et al. Guidelines for naming nonprimate APOBEC3 genes and proteins. J. Virol. 83, 494-497 (2009).
19. Malim, M.H. APOBEC proteins and intrinsic resistance to HIV-1 infection. Phil. Trans. R. Soc. Lond. B 364, 675-687 (2009).
20. Harris, R.S., Hultquist, J.F. & Evans, D.T. The restriction factors of human immunodeficiency virus. J. Biol. Chem. 287, 40875-40883 (2012).
21. Blanc, V. & Davidson, N.O. C-to-U RNA editing: mechanisms leading to genetic diversity. J. Biol. Chem. 278, 1395-1398 (2003).
22. Bishop, K.N., Holmes, R.K., Sheehy, A.M. & Malim, M.H. APOBEC-mediated editing of viral RNA. Science 305, 645 (2004).
23. Petit, V. et al. Murine APOBEC1 is a powerful mutator of retroviral and cellular RNA in vitro and in vivo. J. Mol. Biol. 385, 65-78 (2009).
24. Ikeda, T. et al. Intrinsic restriction activity by apolipoprotein B mRNA editing enzyme APOBEC1 against the mobility of autonomous retrotransposons. Nucleic Acids Res. 39, 5538-5554 (2011).
25. Petersen-Mahrt, S.K., Harris, R.S. & Neuberger, M.S. AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification. Nature 418, 99-103 (2002).
26. Petersen-Mahrt, S.K. & Neuberger, M.S. In vitro deamination of cytosine to uracil in single-stranded DNA by apolipoprotein B editing complex catalytic subunit 1 (APOBEC1). J. Biol. Chem. 278, 19583-19586 (2003).
27. Pham, P., Bransteitter, R., Petruska, J. & Goodman, M.F. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature 424, 103-107 (2003).
28. Chelico, L., Pham, P., Calabrese, P. & Goodman, M.F. APOBEC3G DNA deaminase acts processively 3′ → 5′ on single-stranded DNA. Nat. Struct. Mol. Biol. 13, 392-399 (2006).
29. Hultquist, J.F. et al. Human and rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H demonstrate a conserved capacity to restrict Vif-deficient HIV-1. J. Virol. 85, 11220-11234 (2011).
30. Robbiani, D.F. & Nussenzweig, M.C. Chromosome translocation, B cell lymphoma, and activation-induced cytidine deaminase. Annu. Rev. Pathol. 8, 79-103 (2013).
31. Okazaki, I.M. et al. Constitutive expression of AID leads to tumorigenesis. J. Exp. Med. 197, 1173-1181 (2003).
32. 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).
33. Burns, M.B. et al. APOBEC3B is an enzymatic source of mutation in breast cancer. Nature 494, 366-370 (2013).
34. Jarmuz, A. et al. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. Genomics 79, 285-296 (2002).
35. 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).
36. Koning, F.A. et al. Defining APOBEC3 expression patterns in human tissues and hematopoietic cell subsets. J. Virol. 83, 9474-9485 (2009).
37. Lackey, L. et al. APOBEC3B and AID have similar nuclear import mechanisms. J. Mol. Biol. 419, 301-314 (2012).
38. Kohli, R.M. et al. Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification. J. Biol. Chem. 285, 40956-40964 (2010).
39. Wang, M., Rada, C. & Neuberger, M.S. Altering the spectrum of immunoglobulin V gene somatic hypermutation by modifying the active site of AID. J. Exp. Med. 207, 141-153 (2010).
40. 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).
41. Palles, C. et al. Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat. Genet. 45, 136-144 (2013).
42. Vogelstein, B. et al. Cancer genome landscapes. Science 339, 1546-1558 (2013).
43. Berger, M.F. et al. Melanoma genome sequencing reveals frequent PREX2 mutations. Nature 485, 502-506 (2012).
44. Fujino, T., Navaratnam, N. & Scott, J. Human apolipoprotein B RNA editing deaminase gene (APOBEC1). Genomics 47, 266-275 (1998).
45. Muramatsu, M. et al. Specific expression of activation-induced cytidine deaminase (AID), a novel member of the RNA-editing deaminase family in germinal center B cells. J. Biol. Chem. 274, 18470-18476 (1999).
46. Stenglein, M.D., Burns, M.B., Li, M., Lengyel, J. & Harris, R.S. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat. Struct. Mol. Biol. 17, 222-229 (2010).
47. Sato, Y. et al. Deficiency in APOBEC2 leads to a shift in muscle fiber type, diminished body mass, and myopathy. J. Biol. Chem. 285, 7111-7118 (2010).
48. Rogozin, I.B., Basu, M.K., Jordan, I.K., Pavlov, Y.I. & Koonin, E.V. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. Cell Cycle 4, 1281-1285 (2005).
49. Rada, C., Jarvis, J.M. & Milstein, C. AID-GFP chimeric protein increases hypermutation of Ig genes with no evidence of nuclear localization. Proc. Natl. Acad. Sci. USA 99, 7003-7008 (2002).
50. Land, A.M. et al. Endogenous APOBEC3A DNA cytosine deaminase is cytoplasmic and non-genotoxic. J. Biol. Chem. 288, 17253-17260 (2013).