1932

Abstract

The initiation, progression, and relapse of cancers often result from mutations occurring within somatic cells. Consequently, processes that elevate mutation rates accelerate carcinogenesis and hinder the development of long-lasting therapeutics. Recent sequencing of human cancer genomes has identified patterns of mutations, termed mutation signatures, many of which correspond to specific environmentally induced and endogenous mutation processes. Some of the most frequently observed mutation signatures are caused by dysregulated activity of APOBECs, which deaminate cytidines in single-stranded DNA at specific sequence motifs causing C-to-T and C-to-G substitutions. In humans, APOBEC-generated genetic heterogeneity in tumor cells contributes to carcinogenesis, metastasis, and resistance to therapeutics. Here, we review the current understanding of APOBECs’ role in cancer mutagenesis and impact on disease and the biological processes that influence APOBEC mutagenic capacity.

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2022-11-30
2024-05-09
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Literature Cited

  1. 1.
    Adamsen BL, Kravik KL, Clausen OPF, De Angelis PM. 2007. Apoptosis, cell cycle progression and gene expression in TP53-depleted HCT116 colon cancer cells in response to short-term 5-fluorouracil treatment. Int. J. Oncol. 31:1491–500
    [Google Scholar]
  2. 2.
    Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Ng AWT et al. 2020. The repertoire of mutational signatures in human cancer. Nature 578:94–101
    [Google Scholar]
  3. 3.
    Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S et al. 2013. Signatures of mutational processes in human cancer. Nature 500:415–21
    [Google Scholar]
  4. 4.
    Almeida RR, Raposo RA, Coirada FC, da Silva JR, de Souza Ferreira LC et al. 2015. Modulating APOBEC expression enhances DNA vaccine immunogenicity. Immunol. Cell Biol. 93:868–76
    [Google Scholar]
  5. 5.
    Angus L, Smid M, Wilting SM, van Riet J, Van Hoeck A et al. 2019. The genomic landscape of metastatic breast cancer highlights changes in mutation and signature frequencies. Nat. Genet. 51:1450–58
    [Google Scholar]
  6. 6.
    Aynaud M-M, Suspéne R, Vidalain P-O, Mussil B, Guétard D et al. 2012. Human Tribbles 3 protects nuclear DNA from cytidine deamination by APOBEC3A. J. Biol. Chem. 287:39182–92
    [Google Scholar]
  7. 7.
    Barreto VM, Pan-Hammarstrom Q, Zhao Y, Hammarstrom L, Misulovin Z, Nussenzweig MC. 2005. AID from bony fish catalyzes class switch recombination. J. Exp. Med. 202:733–38
    [Google Scholar]
  8. 8.
    Barrett BS, Guo K, Harper MS, Li SX, Heilman KJ et al. 2014. Reassessment of murine APOBEC1 as a retrovirus restriction factor in vivo. Virology 468–470:601–8
    [Google Scholar]
  9. 9.
    Basu U, Chaudhuri J, Alpert C, Dutt S, Ranganath S et al. 2005. The AID antibody diversification enzyme is regulated by protein kinase A phosphorylation. Nature 438:508–11
    [Google Scholar]
  10. 10.
    Basu U, Meng FL, Keim C, Grinstein V, Pefanis E et al. 2011. The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates. Cell 144:353–63
    [Google Scholar]
  11. 11.
    Beale RC, Petersen-Mahrt SK, Watt IN, Harris RS, Rada C, Neuberger MS. 2004. Comparison of the differential context-dependence of DNA deamination by APOBEC enzymes: correlation with mutation spectra in vivo. J. Mol. Biol. 337:585–96
    [Google Scholar]
  12. 12.
    Bertucci F, Ng CKY, Patsouris A, Droin N, Piscuoglio S et al. 2019. Genomic characterization of metastatic breast cancers. Nature 569:560–64
    [Google Scholar]
  13. 13.
    Betts L, Xiang S, Short SA, Wolfenden R, Carter CW Jr. 1994. Cytidine deaminase. The 2·3 Å crystal structure of an enzyme: transition-state analog complex. J. Mol. Biol. 235:635–56
    [Google Scholar]
  14. 14.
    Biayna J, Garcia-Cao I, Alvarez MM, Salvadores M, Espinosa-Carrasco J et al. 2021. Loss of the abasic site sensor HMCES is synthetic lethal with the activity of the APOBEC3A cytosine deaminase in cancer cells. PLOS Biol 19:e3001176
    [Google Scholar]
  15. 15.
    Bogerd HP, Wiegand HL, Doehle BP, Lueders KK, Cullen BR. 2006. APOBEC3A and APOBEC3B are potent inhibitors of LTR-retrotransposon function in human cells. Nucleic Acids Res 34:89–95
    [Google Scholar]
  16. 16.
    Bogerd HP, Wiegand HL, Hulme AE, Garcia-Perez JL, O'Shea KS et al. 2006. Cellular inhibitors of long interspersed element 1 and Alu retrotransposition. PNAS 103:8780–85
    [Google Scholar]
  17. 17.
    Boichard A, Tsigelny IF, Kurzrock R. 2017. High expression of PD-1 ligands is associated with kataegis mutational signature and APOBEC3 alterations. OncoImmunology 6:e1284719
    [Google Scholar]
  18. 18.
    Bransteitter R, Pham P, Scharff MD, Goodman MF. 2003. Activation-induced cytidine deaminase deaminates deoxycytidine on single-stranded DNA but requires the action of RNase. PNAS 100:4102–7
    [Google Scholar]
  19. 19.
    Bransteitter R, Prochnow C, Chen XS. 2009. The current structural and functional understanding of APOBEC deaminases. Cell. Mol. Life Sci. 66:3137–47
    [Google Scholar]
  20. 20.
    Brown AL, Collins CD, Thompson S, Coxon M, Mertz TM, Roberts SA. 2021. Single-stranded DNA binding proteins influence APOBEC3A substrate preference. Sci. Rep. 11:21008
    [Google Scholar]
  21. 21.
    Buisson R, Langenbucher A, Bowen D, Kwan EE, Benes CH et al. 2019. Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features. Science 364:eaaw2872
    [Google Scholar]
  22. 22.
    Burns MB, Lackey L, Carpenter MA, Rathore A, Land AM et al. 2013. APOBEC3B is an enzymatic source of mutation in breast cancer. Nature 494:366–70
    [Google Scholar]
  23. 23.
    Burns MB, Temiz NA, Harris RS. 2013. Evidence for APOBEC3B mutagenesis in multiple human cancers. Nat. Genet. 45:977–83
    [Google Scholar]
  24. 24.
    Carpenter MA, Li M, Rathore A, Lackey L, Law EK et al. 2012. Methylcytosine and normal cytosine deamination by the foreign DNA restriction enzyme APOBEC3A. J. Biol. Chem. 287:34801–8
    [Google Scholar]
  25. 25.
    Carrió E, Magli A, Muñoz M, Peinado MA, Perlingeiro R, Suelves M. 2016. Muscle cell identity requires Pax7-mediated lineage-specific DNA demethylation. BMC Biol 14:30
    [Google Scholar]
  26. 26.
    Caval V, Suspene R, Shapira M, Vartanian JP, Wain-Hobson S. 2014. A prevalent cancer susceptibility APOBEC3A hybrid allele bearing APOBEC3B 3′UTR enhances chromosomal DNA damage. Nat. Commun. 5:5129
    [Google Scholar]
  27. 27.
    Caval V, Suspene R, Vartanian JP, Wain-Hobson S. 2014. Orthologous mammalian APOBEC3A cytidine deaminases hypermutate nuclear DNA. Mol. Biol. Evol. 31:330–40
    [Google Scholar]
  28. 28.
    Chan K, Resnick MA, Gordenin DA. 2013. The choice of nucleotide inserted opposite abasic sites formed within chromosomal DNA reveals the polymerase activities participating in translesion DNA synthesis. DNA Repair 12:878–89
    [Google Scholar]
  29. 29.
    Chan K, Roberts SA, Klimczak LJ, Sterling JF, Saini N et al. 2015. An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers. Nat. Genet. 47:1067–72
    [Google Scholar]
  30. 30.
    Chaudhuri J, Khuong C, Alt FW. 2004. Replication protein A interacts with AID to promote deamination of somatic hypermutation targets. Nature 430:992–98
    [Google Scholar]
  31. 31.
    Chelico L, Pham P, Goodman MF. 2009. Stochastic properties of processive cytidine DNA deaminases AID and APOBEC3G. Philos. Trans. R. Soc. B 364:583–93
    [Google Scholar]
  32. 32.
    Chen J, Miller BF, Furano AV 2014. Repair of naturally occurring mismatches can induce mutations in flanking DNA. eLife 3:e02001
    [Google Scholar]
  33. 33.
    Chen Y, Shen B, Zheng X, Long Q, Xia J et al. 2020. DHX9 interacts with APOBEC3B and attenuates the anti-HBV effect of APOBEC3B. Emerg. Microbes Infect. 9:366–77
    [Google Scholar]
  34. 34.
    Chervova A, Fatykhov B, Koblov A, Shvarov E, Preobrazhenskaya J et al. 2021. Analysis of gene expression and mutation data points on contribution of transcription to the mutagenesis by APOBEC enzymes. NAR Cancer 3:zcab025
    [Google Scholar]
  35. 35.
    Chesi M, Robbiani DF, Sebag M, Chng WJ, Affer M et al. 2008. AID-dependent activation of a MYC transgene induces multiple myeloma in a conditional mouse model of post-germinal center malignancies. Cancer Cell 13:167–80
    [Google Scholar]
  36. 36.
    Chiba T, Marusawa H. 2009. A novel mechanism for inflammation-associated carcinogenesis; an important role of activation-induced cytidine deaminase (AID) in mutation induction. J. Mol. Med. 87:1023–27
    [Google Scholar]
  37. 37.
    Chiba T, Marusawa H, Seno H, Watanabe N. 2008. Mechanism for gastric cancer development by Helicobacter pylori infection. J. Gastroenterol. Hepatol. 23:1175–81
    [Google Scholar]
  38. 38.
    Chou W-C, Chen W-T, Hsiung C-N, Hu L-Y, Yu J-C et al. 2017. B-Myb induces APOBEC3B expression leading to somatic mutation in multiple cancers. Sci. Rep. 7:44089
    [Google Scholar]
  39. 39.
    Conticello SG, Ganesh K, Xue K, Lu M, Rada C, Neuberger MS. 2008. Interaction between antibody-diversification enzyme AID and spliceosome-associated factor CTNNBL1. Mol. Cell 31:474–84
    [Google Scholar]
  40. 40.
    Conticello SG, Thomas CJ, Petersen-Mahrt SK, Neuberger MS 2005. Evolution of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases. Mol. Biol. Evol. 22:367–77
    [Google Scholar]
  41. 41.
    Cortez LM, Brown AL, Dennis MA, Collins CD, Brown AJ et al. 2019. APOBEC3A is a prominent cytidine deaminase in breast cancer. PLOS Genet 15:e1008545
    [Google Scholar]
  42. 42.
    Covino DA, Gauzzi MC, Fantuzzi L. 2018. Understanding the regulation of APOBEC3 expression: Current evidence and much to learn. J. Leukoc. Biol. 103:433–44
    [Google Scholar]
  43. 43.
    Davidson NO, Shelness GS. 2000. APOLIPOPROTEIN B: mRNA editing, lipoprotein assembly, and presecretory degradation. Annu. Rev. Nutr. 20:169–93
    [Google Scholar]
  44. 44.
    de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC et al. 2014. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 346:251–56
    [Google Scholar]
  45. 45.
    Delviks-Frankenberry KA, Desimmie BA, Pathak VK 2020. Structural insights into APOBEC3-mediated lentiviral restriction. Viruses 12:587
    [Google Scholar]
  46. 46.
    Demorest ZL, Li M, Harris RS. 2011. Phosphorylation directly regulates the intrinsic DNA cytidine deaminase activity of activation-induced deaminase and APOBEC3G protein. J. Biol. Chem. 286:26568–75
    [Google Scholar]
  47. 47.
    Diamond CP, Im J, Button EA, Huebert DNG, King JJ et al. 2019. AID, APOBEC3A and APOBEC3B efficiently deaminate deoxycytidines neighboring DNA damage induced by oxidation or alkylation. Biochim. Biophys. Acta Gen. Subj. 1863:129415
    [Google Scholar]
  48. 48.
    Dickerson SK, Market E, Besmer E, Papavasiliou FN. 2003. AID mediates hypermutation by deaminating single stranded DNA. J. Exp. Med. 197:1291–96
    [Google Scholar]
  49. 49.
    Du Y, Tao X, Wu J, Yu H, Yu Y, Zhao H. 2018. APOBEC3B up-regulation independently predicts ovarian cancer prognosis: a cohort study. Cancer Cell Int 18:78
    [Google Scholar]
  50. 50.
    Duquette ML, Pham P, Goodman MF, Maizels N. 2005. AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation. Oncogene 24:5791–98
    [Google Scholar]
  51. 51.
    Elango R, Osia B, Harcy V, Malc E, Mieczkowski PA et al. 2019. Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements. Nucleic Acids Res 47:9666–84
    [Google Scholar]
  52. 52.
    Endo Y, Marusawa H, Chiba T. 2011. Involvement of activation-induced cytidine deaminase in the development of colitis-associated colorectal cancers. J. Gastroenterol. 46:6–10
    [Google Scholar]
  53. 53.
    Endo Y, Marusawa H, Kinoshita K, Morisawa T, Sakurai T et al. 2007. Expression of activation-induced cytidine deaminase in human hepatocytes via NF-κB signaling. Oncogene 26:5587–95
    [Google Scholar]
  54. 54.
    Feng Y, Baig TT, Love RP, Chelico L. 2014. Suppression of APOBEC3-mediated restriction of HIV-1 by Vif. Front. Microbiol. 5:450
    [Google Scholar]
  55. 55.
    Florkowska A, Meszka I, Nowacka J, Granica M, Jablonska Z et al. 2021. PAX7 balances the cell cycle progression via regulating expression of Dnmt3b and Apobec2 in differentiating PSCs. Cells 10:2205
    [Google Scholar]
  56. 56.
    Gaillard H, Garcia-Muse T, Aguilera A. 2015. Replication stress and cancer. Nat. Rev. Cancer 15:276–89
    [Google Scholar]
  57. 57.
    Gazumyan A, Timachova K, Yuen G, Siden E, Di Virgilio M et al. 2011. Amino-terminal phosphorylation of activation-induced cytidine deaminase suppresses c-myc/IgH translocation. Mol. Cell. Biol. 31:442–49
    [Google Scholar]
  58. 58.
    Gerhauser C, Favero F, Risch T, Simon R, Feuerbach L et al. 2018. Molecular evolution of early-onset prostate cancer identifies molecular risk markers and clinical trajectories. Cancer Cell 34:996–1011.e8
    [Google Scholar]
  59. 59.
    Glaser AP, Fantini D, Wang Y, Yu Y, Rimar KJ et al. 2018. APOBEC-mediated mutagenesis in urothelial carcinoma is associated with improved survival, mutations in DNA damage response genes, and immune response. Oncotarget 9:4537–48
    [Google Scholar]
  60. 60.
    Green AM, DeWeerd RA, O'Leary DR, Hansen AR, Hayer KE et al. 2021. Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity. EMBO Rep 22:e52145
    [Google Scholar]
  61. 61.
    Greenwell-Wild T, Vazquez N, Jin W, Rangel Z, Munson PJ, Wahl SM 2009. Interleukin-27 inhibition of HIV-1 involves an intermediate induction of type I interferon. Blood 114:1864–74
    [Google Scholar]
  62. 62.
    Haradhvala NJ, Polak P, Stojanov P, Covington KR, Shinbrot E et al. 2016. Mutational strand asymmetries in cancer genomes reveal mechanisms of DNA damage and repair. Cell 164:538–49
    [Google Scholar]
  63. 63.
    Harris RS, Petersen-Mahrt SK, Neuberger MS 2002. RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol. Cell 10:1247–53
    [Google Scholar]
  64. 64.
    Henderson S, Chakravarthy A, Su X, Boshoff C, Fenton TR. 2014. APOBEC-mediated cytosine deamination links PIK3CA helical domain mutations to human papillomavirus-driven tumor development. Cell Rep 7:1833–41
    [Google Scholar]
  65. 65.
    Hix MA, Wong L, Flath B, Chelico L, Cisneros GA. 2020. Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer. NAR Cancer 2:zcaa023
    [Google Scholar]
  66. 66.
    Hoopes JI, Cortez LM, Mertz TM, Malc EP, Mieczkowski PA, Roberts SA. 2016. APOBEC3A and APOBEC3B preferentially deaminate the lagging strand template during DNA replication. Cell Rep 14:1273–82
    [Google Scholar]
  67. 67.
    Hoopes JI, Hughes AL, Hobson LA, Cortez LM, Brown AJ, Roberts SA. 2017. Avoidance of APOBEC3B-induced mutation by error-free lesion bypass. Nucleic Acids Res 45:5243–54
    [Google Scholar]
  68. 68.
    Hu Y, Ericsson I, Doseth B, Liabakk NB, Krokan HE, Kavli B. 2014. Activation-induced cytidine deaminase (AID) is localized to subnuclear domains enriched in splicing factors. Exp. Cell Res. 322:178–92
    [Google Scholar]
  69. 69.
    Hultquist JF, Lengyel JA, Refsland EW, LaRue RS, Lackey L et al. 2011. Human and rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H demonstrate a conserved capacity to restrict Vif-deficient HIV-1. J. Virol. 85:11220–34
    [Google Scholar]
  70. 70.
    Hüttenhain R, Xu J, Burton LA, Gordon DE, Hultquist JF et al. 2019. ARIH2 Is a Vif-dependent regulator of CUL5-mediated APOBEC3G degradation in HIV infection. Cell Host Microbe 26:86–99.e7
    [Google Scholar]
  71. 71.
    Ikeda T, Shimoda M, Ebrahimi D, VandeBerg JL, Harris RS et al. 2017. Opossum APOBEC1 is a DNA mutator with retrovirus and retroelement restriction activity. Sci. Rep. 7:46719
    [Google Scholar]
  72. 72.
    Isozaki H, Abbasi A, Nikpour N, Langenbucher A, Su W et al. 2021. APOBEC3A drives acquired resistance to targeted therapies in non-small cell lung cancer. bioRxiv 2021.01.20.426852. https://doi.org/10.1101/2021.01.20.426852
    [Crossref]
  73. 73.
    Ito F, Fu Y, Kao SA, Yang H, Chen XS. 2017. Family-wide comparative analysis of cytidine and methylcytidine deamination by eleven human APOBEC proteins. J. Mol. Biol. 429:1787–99
    [Google Scholar]
  74. 74.
    Jalili P, Bowen D, Langenbucher A, Park S, Aguirre K et al. 2020. Quantification of ongoing APOBEC3A activity in tumor cells by monitoring RNA editing at hotspots. Nat. Commun. 11:2971
    [Google Scholar]
  75. 75.
    Kanu N, Cerone MA, Goh G, Zalmas L-P, Bartkova J et al. 2016. DNA replication stress mediates APOBEC3 family mutagenesis in breast cancer. Genome Biol 17:185
    [Google Scholar]
  76. 76.
    Kazuma Y, Shirakawa K, Sarca AD, Horisawa Y, Fukuda H et al. 2019. Interactome analysis of APOBEC3B in multiple myeloma. Blood 134:Suppl. 11259
    [Google Scholar]
  77. 77.
    Kobayashi M, Takaori-Kondo A, Miyauchi Y, Iwai K, Uchiyama T. 2005. Ubiquitination of APOBEC3G by an HIV-1 Vif-Cullin5-Elongin B-Elongin C complex is essential for Vif function. J. Biol. Chem. 280:18573–78
    [Google Scholar]
  78. 78.
    Kohli RM, Maul RW, Guminski AF, McClure RL, Gajula KS et al. 2010. Local sequence targeting in the AID/APOBEC family differentially impacts retroviral restriction and antibody diversification. J. Biol. Chem. 285:40956–64
    [Google Scholar]
  79. 79.
    Komori J, Marusawa H, Machimoto T, Endo Y, Kinoshita K et al. 2008. Activation-induced cytidine deaminase links bile duct inflammation to human cholangiocarcinoma. Hepatology 47:888–96
    [Google Scholar]
  80. 80.
    Koning FA, Newman EN, Kim EY, Kunstman KJ, Wolinsky SM, Malim MH. 2009. Defining APOBEC3 expression patterns in human tissues and hematopoietic cell subsets. J. Virol. 83:9474–85
    [Google Scholar]
  81. 81.
    Kou T, Marusawa H, Kinoshita K, Endo Y, Okazaki IM et al. 2007. Expression of activation-induced cytidine deaminase in human hepatocytes during hepatocarcinogenesis. Int. J. Cancer 120:469–76
    [Google Scholar]
  82. 82.
    Kouno T, Silvas TV, Hilbert BJ, Shandilya SMD, Bohn MF et al. 2017. Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity. Nat. Commun. 8:15024
    [Google Scholar]
  83. 83.
    Lada AG, Waisertreiger IS, Grabow CE, Prakash A, Borgstahl GE et al. 2011. Replication protein A (RPA) hampers the processive action of APOBEC3G cytosine deaminase on single-stranded DNA. PLOS ONE 6:e24848
    [Google Scholar]
  84. 84.
    Land AM, Law EK, Carpenter MA, Lackey L, Brown WL, Harris RS. 2013. Endogenous APOBEC3A DNA cytosine deaminase is cytoplasmic and nongenotoxic. J. Biol. Chem. 288:17253–60
    [Google Scholar]
  85. 85.
    Landry S, Narvaiza I, Linfesty DC, Weitzman MD. 2011. APOBEC3A can activate the DNA damage response and cause cell-cycle arrest. EMBO Rep 12:444–50
    [Google Scholar]
  86. 86.
    LaRue RS, Andrésdottir V, Blanchard Y, Conticello SG, Derse D et al. 2009. Guidelines for naming nonprimate APOBEC3 genes and proteins. J. Virol. 83:494–97
    [Google Scholar]
  87. 87.
    Laude HC, Caval V, Bouzidi MS, Li X, Jamet F et al. 2018. The rabbit as an orthologous small animal model for APOBEC3A oncogenesis. Oncotarget 9:27809–22
    [Google Scholar]
  88. 88.
    Law EK, Levin-Klein R, Jarvis MC, Kim H, Argyris PP et al. 2020. APOBEC3A catalyzes mutation and drives carcinogenesis in vivo. J. Exp. Med. 217:e20200261
    [Google Scholar]
  89. 89.
    Law EK, Sieuwerts AM, LaPara K, Leonard B, Starrett GJ et al. 2016. The DNA cytosine deaminase APOBEC3B promotes tamoxifen resistance in ER-positive breast cancer. Sci. Adv. 2:e1601737
    [Google Scholar]
  90. 90.
    Le Q, Maizels N. 2015. Cell cycle regulates nuclear stability of AID and determines the cellular response to AID. PLOS Genet 11:e1005411
    [Google Scholar]
  91. 91.
    Leonard B, McCann JL, Starrett GJ, Kosyakovsky L, Luengas EM et al. 2015. The PKC/NF-κB signaling pathway induces APOBEC3B expression in multiple human cancers. Cancer Res 75:4538–47
    [Google Scholar]
  92. 92.
    Li MM, Emerman M. 2011. Polymorphism in human APOBEC3H affects a phenotype dominant for subcellular localization and antiviral activity. J. Virol. 85:8197–207
    [Google Scholar]
  93. 93.
    Li X, Caval V, Wain-Hobson S, Vartanian J-P. 2019. Elephant APOBEC3A cytidine deaminase induces massive double-stranded DNA breaks and apoptosis. Sci. Rep. 9:728
    [Google Scholar]
  94. 94.
    Lin L, Holmes B, Shen MW, Kammeron D, Geijsen N et al. 2020. Comprehensive mapping of key regulatory networks that drive oncogene expression. Cell Rep 33:108426
    [Google Scholar]
  95. 95.
    Long J, Delahanty RJ, Li G, Gao YT, Lu W et al. 2013. A common deletion in the APOBEC3 genes and breast cancer risk. J. Natl. Cancer Inst. 105:573–79
    [Google Scholar]
  96. 96.
    Marin M, Rose KM, Kozak SL, Kabat D. 2003. HIV-1 Vif protein binds the editing enzyme APOBEC3G and induces its degradation. Nat. Med. 9:1398–403
    [Google Scholar]
  97. 97.
    Maruyama W, Shirakawa K, Matsui H, Matsumoto T, Yamazaki H et al. 2016. Classical NF-κB pathway is responsible for APOBEC3B expression in cancer cells. Biochem. Biophys. Res. Commun. 478:1466–71
    [Google Scholar]
  98. 98.
    Matsumoto T, Shirakawa K, Yokoyama M, Fukuda H, Sarca AD et al. 2019. Protein kinase A inhibits tumor mutator APOBEC3B through phosphorylation. Sci. Rep. 9:8307
    [Google Scholar]
  99. 99.
    Matsumoto Y, Marusawa H, Kinoshita K, Endo Y, Kou T et al. 2007. Helicobacter pylori infection triggers aberrant expression of activation-induced cytidine deaminase in gastric epithelium. Nat. Med. 13:470–76
    [Google Scholar]
  100. 100.
    Maura F, Petljak M, Lionetti M, Cifola I, Liang W et al. 2018. Biological and prognostic impact of APOBEC-induced mutations in the spectrum of plasma cell dyscrasias and multiple myeloma cell lines. Leukemia 32:1044–48
    [Google Scholar]
  101. 101.
    McBride KM, Gazumyan A, Woo EM, Barreto VM, Robbiani DF et al. 2006. Regulation of hypermutation by activation-induced cytidine deaminase phosphorylation. PNAS 103:8798–803
    [Google Scholar]
  102. 102.
    McBride KM, Gazumyan A, Woo EM, Schwickert TA, Chait BT, Nussenzweig MC. 2008. Regulation of class switch recombination and somatic mutation by AID phosphorylation. J. Exp. Med. 205:2585–94
    [Google Scholar]
  103. 103.
    McCann JL, Klein MM, Leland EM, Law EK, Brown WL et al. 2019. The DNA deaminase APOBEC3B interacts with the cell-cycle protein CDK4 and disrupts CDK4-mediated nuclear import of Cyclin D1. J. Biol. Chem. 294:12099–111
    [Google Scholar]
  104. 104.
    McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C. 2015. Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Sci. Transl. Med. 7:283ra54
    [Google Scholar]
  105. 105.
    Menendez D, Nguyen TA, Snipe J, Resnick MA. 2017. The cytidine deaminase APOBEC3 family is subject to transcriptional regulation by p53. Mol. Cancer Res. 15:735–43
    [Google Scholar]
  106. 106.
    Middlebrooks CD, Banday AR, Matsuda K, Udquim KI, Onabajo OO et al. 2016. Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors. Nat. Genet. 48:1330–38
    [Google Scholar]
  107. 107.
    Mishra N, Reddy KS, Timilsina U, Gaur D, Gaur R. 2018. Human APOBEC3B interacts with the heterogenous nuclear ribonucleoprotein A3 in cancer cells. J. Cell Biochem. 119:6695–703
    [Google Scholar]
  108. 108.
    Mitra M, Hercík K, Byeon I-JL, Ahn J, Hill S et al. 2014. Structural determinants of human APOBEC3A enzymatic and nucleic acid binding properties. Nucleic Acids Res 42:1095–110
    [Google Scholar]
  109. 109.
    Mohni KN, Wessel SR, Zhao R, Wojciechowski AC, Luzwick JW et al. 2019. HMCES maintains genome integrity by shielding abasic sites in single-strand DNA. Cell 176:144–53.e13
    [Google Scholar]
  110. 110.
    Morganella S, Alexandrov LB, Glodzik D, Zou X, Davies H et al. 2016. The topography of mutational processes in breast cancer genomes. Nat. Commun. 7:11383
    [Google Scholar]
  111. 111.
    Mu Y, Zelazowska MA, McBride KM. 2017. Phosphorylation promotes activation-induced cytidine deaminase activity at the Myc oncogene. J. Exp. Med. 214:3543–52
    [Google Scholar]
  112. 112.
    Mussil B, Suspene R, Aynaud MM, Gauvrit A, Vartanian JP, Wain-Hobson S. 2013. Human APOBEC3A isoforms translocate to the nucleus and induce DNA double strand breaks leading to cell stress and death. PLOS ONE 8:e73641
    [Google Scholar]
  113. 113.
    Nabel CS, Jia H, Ye Y, Shen L, Goldschmidt HL et al. 2012. AID/APOBEC deaminases disfavor modified cytosines implicated in DNA demethylation. Nat. Chem. Biol. 8:751–58
    [Google Scholar]
  114. 114.
    Nik-Zainal S, Alexandrov LB, Wedge DC, Van Loo P, Greenman CD et al. 2012. Mutational processes molding the genomes of 21 breast cancers. Cell 149:979–93
    [Google Scholar]
  115. 115.
    Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD et al. 2012. The life history of 21 breast cancers. Cell 149:994–1007
    [Google Scholar]
  116. 116.
    Nik-Zainal S, Wedge DC, Alexandrov LB, Petljak M, Butler AP et al. 2014. Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer. Nat. Genet. 46:487–91
    [Google Scholar]
  117. 117.
    Oh S, Bournique E, Bowen D, Jalili P, Sanchez A et al. 2021. Genotoxic stress and viral infection induce transient expression of APOBEC3A and pro-inflammatory genes through two distinct pathways. Nat. Commun. 12:4917
    [Google Scholar]
  118. 118.
    OhAinle M, Kerns JA, Li MMH, Malik HS, Emerman M. 2008. Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. Cell Host Microbe 4:249–59
    [Google Scholar]
  119. 119.
    Ohtsubo H, Sato Y, Suzuki T, Mizunoya W, Nakamura M et al. 2017. APOBEC2 negatively regulates myoblast differentiation in muscle regeneration. Int. J. Biochem. Cell Biol. 85:91–101
    [Google Scholar]
  120. 120.
    Okuyama S, Marusawa H, Matsumoto T, Ueda Y, Matsumoto Y et al. 2012. Excessive activity of apolipoprotein B mRNA editing enzyme catalytic polypeptide 2 (APOBEC2) contributes to liver and lung tumorigenesis. Int. J. Cancer 130:1294–301
    [Google Scholar]
  121. 121.
    Pasqualucci L, Kitaura Y, Gu H, Dalla-Favera R. 2006. PKA-mediated phosphorylation regulates the function of activation-induced deaminase (AID) in B cells. PNAS 103:395–400
    [Google Scholar]
  122. 122.
    Pefanis E, Wang J, Rothschild G, Lim J, Chao J et al. 2014. Noncoding RNA transcription targets AID to divergently transcribed loci in B cells. Nature 514:389–93
    [Google Scholar]
  123. 123.
    Periyasamy M, Patel H, Lai CF, Nguyen VTM, Nevedomskaya E et al. 2015. APOBEC3B-mediated cytidine deamination is required for estrogen receptor action in breast cancer. Cell Rep 13:108–21
    [Google Scholar]
  124. 124.
    Periyasamy M, Singh AK, Gemma C, Kranjec C, Farzan R et al. 2017. p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells. Nucleic Acids Res 45:11056–69
    [Google Scholar]
  125. 125.
    Petljak M, Dananberg A, Chu K, Bergstrom EN, Striepen J et al. 2022. Mechanisms of APOBEC3 mutagenesis in human cancer cells. Nature 607799807
  126. 126.
    Pham P, Bransteitter R, Petruska J, Goodman MF. 2003. Processive AID-catalysed cytosine deamination on single-stranded DNA simulates somatic hypermutation. Nature 424:103–7
    [Google Scholar]
  127. 127.
    Pham P, Landolph A, Mendez C, Li N, Goodman MF. 2013. A biochemical analysis linking APOBEC3A to disparate HIV-1 restriction and skin cancer. J. Biol. Chem. 288:29294–304
    [Google Scholar]
  128. 128.
    Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H. 2017. AID recognizes structured DNA for class switch recombination. Mol. Cell 67:361–73.e4
    [Google Scholar]
  129. 129.
    Ramiro AR, Jankovic M, Eisenreich T, Difilippantonio S, Chen-Kiang S et al. 2004. AID is required for c-myc/IgH chromosome translocations in vivo. Cell 118:431–38
    [Google Scholar]
  130. 130.
    Refsland EW, Harris RS. 2013. The APOBEC3 family of retroelement restriction factors. Curr. Top. Microbiol. Immunol. 371:1–27
    [Google Scholar]
  131. 131.
    Refsland EW, Stenglein MD, Shindo K, Albin JS, Brown WL, Harris RS. 2010. Quantitative profiling of the full APOBEC3 mRNA repertoire in lymphocytes and tissues: implications for HIV-1 restriction. Nucleic Acids Res 38:4274–84
    [Google Scholar]
  132. 132.
    Renard M, Henry M, Guetard D, Vartanian JP, Wain-Hobson S. 2010. APOBEC1 and APOBEC3 cytidine deaminases as restriction factors for hepadnaviral genomes in non-humans in vivo. J. Mol. Biol. 400:323–34
    [Google Scholar]
  133. 133.
    Robbiani DF, Bothmer A, Callen E, Reina-San-Martin B, Dorsett Y et al. 2008. AID is required for the chromosomal breaks in c-myc that lead to c-myc/IgH translocations. Cell 135:1028–38
    [Google Scholar]
  134. 134.
    Roberts SA, Lawrence MS, Klimczak LJ, Grimm SA, Fargo D et al. 2013. An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. Nat. Genet. 45:970–76
    [Google Scholar]
  135. 135.
    Roberts SA, Sterling J, Thompson C, Harris S, Mav D et al. 2012. Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. Mol. Cell 46:424–35
    [Google Scholar]
  136. 136.
    Roelofs PA, Goh CY, Chua BH, Jarvis MC, Stewart TA et al. 2020. Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B. eLife 9:e61287
    [Google Scholar]
  137. 137.
    Rogozin IB, Basu MK, Jordan IK, Pavlov YI, Koonin EV. 2005. APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. Cell Cycle 4:1281–85
    [Google Scholar]
  138. 138.
    Rogozin IB, Lada AG, Goncearenco A, Green MR, De S et al. 2016. Activation induced deaminase mutational signature overlaps with CpG methylation sites in follicular lymphoma and other cancers. Sci. Rep. 6:38133
    [Google Scholar]
  139. 139.
    Roper N, Gao S, Maity TK, Banday AR, Zhang X et al. 2019. APOBEC mutagenesis and copy-number alterations are drivers of proteogenomic tumor evolution and heterogeneity in metastatic thoracic tumors. Cell Rep 26:2651–66.e6
    [Google Scholar]
  140. 140.
    Rosenbaum JC, Bonilla B, Hengel SR, Mertz TM, Herken BW et al. 2019. The Rad51 paralogs facilitate a novel DNA strand specific damage tolerance pathway. Nat. Commun. 10:3515
    [Google Scholar]
  141. 141.
    Saini N, Roberts SA, Sterling JF, Malc EP, Mieczkowski PA, Gordenin DA. 2017. APOBEC3B cytidine deaminase targets the non-transcribed strand of tRNA genes in yeast. DNA Repair 53:4–14
    [Google Scholar]
  142. 142.
    Sakhtemani R, Senevirathne V, Stewart J, Perera MLW, Pique-Regi R et al. 2019. Genome-wide mapping of regions preferentially targeted by the human DNA-cytosine deaminase APOBEC3A using uracil-DNA pulldown and sequencing. J. Biol. Chem. 294:15037–51
    [Google Scholar]
  143. 143.
    Sakofsky CJ, Saini N, Klimczak LJ, Chan K, Malc EP et al. 2019. Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation. PLOS Biol 17:e3000464
    [Google Scholar]
  144. 144.
    Salter JD, Bennett RP, Smith HC. 2016. The APOBEC protein family: united by structure, divergent in function. Trends Biochem. Sci. 41:578–94
    [Google Scholar]
  145. 145.
    Saraconi G, Severi F, Sala C, Mattiuz G, Conticello SG. 2014. The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas. Genome Biol 15:417
    [Google Scholar]
  146. 146.
    Sato Y, Ohtsubo H, Nihei N, Kaneko T, Sato Y et al. 2018. Apobec2 deficiency causes mitochondrial defects and mitophagy in skeletal muscle. FASEB J 32:1428–39
    [Google Scholar]
  147. 147.
    Scholtes GK, Sawyer AM, Vaca CC, Clerc I, Roh M et al. 2021. The von Hippel–Lindau Cullin-RING E3 ubiquitin ligase regulates APOBEC3 cytidine deaminases. Transl. Res. 237:1–15
    [Google Scholar]
  148. 148.
    Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI. 2016. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. Genome Res 26:174–82
    [Google Scholar]
  149. 149.
    Serebrenik AA, Argyris PP, Jarvis MC, Brown WL, Bazzaro M et al. 2020. The DNA cytosine deaminase APOBEC3B is a molecular determinant of platinum responsiveness in clear cell ovarian cancer. Clin. Cancer Res. 26:3397–407
    [Google Scholar]
  150. 150.
    Sheehy AM, Gaddis NC, Choi JD, Malim MH. 2002. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature 418:646–50
    [Google Scholar]
  151. 151.
    Shen B, Chapman JH, Custance MF, Tricola GM, Jones CE, Furano AV 2020. Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations. eLife 9:e51605
    [Google Scholar]
  152. 152.
    Shi K, Carpenter MA, Banerjee S, Shaban NM, Kurahashi K et al. 2017. Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B. Nat. Struct. Mol. Biol. 24:131–39
    [Google Scholar]
  153. 153.
    Shi K, Carpenter MA, Kurahashi K, Harris RS, Aihara H. 2015. Crystal structure of the DNA deaminase APOBEC3B catalytic domain. J. Biol. Chem. 290:28120–30
    [Google Scholar]
  154. 154.
    Shirakawa K, Takaori-Kondo A, Yokoyama M, Izumi T, Matsui M et al. 2008. Phosphorylation of APOBEC3G by protein kinase A regulates its interaction with HIV-1 Vif. Nat. Struct. Mol. Biol. 15:1184–91
    [Google Scholar]
  155. 155.
    Sieuwerts AM, Willis S, Burns MB, Look MP, Meijer-Van Gelder ME et al. 2014. Elevated APOBEC3B correlates with poor outcomes for estrogen-receptor-positive breast cancers. Horm. Cancer 5:405–13
    [Google Scholar]
  156. 156.
    Smith HC, Bennett RP, Kizilyer A, McDougall WM, Prohaska KM. 2012. Functions and regulation of the APOBEC family of proteins. Semin. Cell Dev. Biol. 23:258–68
    [Google Scholar]
  157. 157.
    Starrett GJ, Luengas EM, McCann JL, Ebrahimi D, Temiz NA et al. 2016. The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis. Nat. Commun. 7:12918
    [Google Scholar]
  158. 158.
    Stenglein MD, Burns MB, Li M, Lengyel J, Harris RS. 2010. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat. Struct. Mol. Biol. 17:222–29
    [Google Scholar]
  159. 159.
    Stenglein MD, Harris RS. 2006. APOBEC3B and APOBEC3F inhibit L1 retrotransposition by a DNA deamination-independent mechanism. J. Biol. Chem. 281:16837–41
    [Google Scholar]
  160. 160.
    Stephens P, Edkins S, Davies H, Greenman C, Cox C et al. 2005. A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer. Nat. Genet. 37:590–92
    [Google Scholar]
  161. 161.
    Stopak K, de Noronha C, Yonemoto W, Greene WC 2003. HIV-1 Vif blocks the antiviral activity of APOBEC3G by impairing both its translation and intracellular stability. Mol. Cell 12:591–601
    [Google Scholar]
  162. 162.
    Takai A, Toyoshima T, Uemura M, Kitawaki Y, Marusawa H et al. 2009. A novel mouse model of hepatocarcinogenesis triggered by AID causing deleterious p53 mutations. Oncogene 28:469–78
    [Google Scholar]
  163. 163.
    Taylor BJ, Nik-Zainal S, Wu YL, Stebbings LA, Raine K et al. 2013. DNA deaminases induce break-associated mutation showers with implication of APOBEC3B and 3A in breast cancer kataegis. eLife 2:e00534
    [Google Scholar]
  164. 164.
    Trapp S, Derby NR, Singer R, Shaw A, Williams VG et al. 2009. Double-stranded RNA analog poly(I:C) inhibits human immunodeficiency virus amplification in dendritic cells via type I interferon-mediated activation of APOBEC3G. J. Virol. 83:884–95
    [Google Scholar]
  165. 165.
    Udquim KI, Zettelmeyer C, Banday AR, Lin SH, Prokunina-Olsson L. 2020. APOBEC3B expression in breast cancer cell lines and tumors depends on the estrogen receptor status. Carcinogenesis 41:1030–37
    [Google Scholar]
  166. 166.
    Vuong BQ, Lee M, Kabir S, Irimia C, Macchiarulo S et al. 2009. Specific recruitment of protein kinase A to the immunoglobulin locus regulates class-switch recombination. Nat. Immunol. 10:420–26
    [Google Scholar]
  167. 167.
    Walker BA, Wardell CP, Murison A, Boyle EM, Begum DB et al. 2015. APOBEC family mutational signatures are associated with poor prognosis translocations in multiple myeloma. Nat. Commun. 6:6997
    [Google Scholar]
  168. 168.
    Wang S, Jia M, He Z, Liu XS. 2018. APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer. Oncogene 37:3924–36
    [Google Scholar]
  169. 169.
    Waters CE, Saldivar JC, Amin ZA, Schrock MS, Huebner K. 2015. FHIT loss-induced DNA damage creates optimal APOBEC substrates: Insights into APOBEC-mediated mutagenesis. Oncotarget 6:3409–19
    [Google Scholar]
  170. 170.
    Wen WX, Soo JS-S, Kwan PY, Hong E, Khang TF et al. 2016. Germline APOBEC3B deletion is associated with breast cancer risk in an Asian multi-ethnic cohort and with immune cell presentation. Breast Cancer Res 18:56
    [Google Scholar]
  171. 171.
    Wörmann SM, Zhang A, Thege FI, Cowan RW, Rupani DN et al. 2021. APOBEC3A drives deaminase domain-independent chromosomal instability to promote pancreatic cancer metastasis. Nat. Cancer 2:1338–56
    [Google Scholar]
  172. 172.
    Xuan D, Li G, Cai Q, Deming-Halverson S, Shrubsole MJ et al. 2013. APOBEC3 deletion polymorphism is associated with breast cancer risk among women of European ancestry. Carcinogenesis 34:2240–43
    [Google Scholar]
  173. 173.
    Yamanaka S, Balestra ME, Ferrell LD, Fan J, Arnold KS et al. 1995. Apolipoprotein B mRNA-editing protein induces hepatocellular carcinoma and dysplasia in transgenic animals. PNAS 92:8483–87
    [Google Scholar]
  174. 174.
    Yu K, Roy D, Bayramyan M, Haworth IS, Lieber MR. 2005. Fine-structure analysis of activation-induced deaminase accessibility to class switch region R-loops. Mol. Cell. Biol. 25:1730–36
    [Google Scholar]
  175. 175.
    Yu Q, Chen D, Konig R, Mariani R, Unutmaz D, Landau NR. 2004. APOBEC3B and APOBEC3C are potent inhibitors of simian immunodeficiency virus replication. J. Biol. Chem. 279:53379–86
    [Google Scholar]
  176. 176.
    Yu X, Yu Y, Liu B, Luo K, Kong W et al. 2003. Induction of APOBEC3G ubiquitination and degradation by an HIV-1 Vif-Cul5-SCF complex. Science 302:1056–60
    [Google Scholar]
  177. 177.
    Zan H, Casali P. 2013. Regulation of Aicda expression and AID activity. Autoimmunity 46:83–101
    [Google Scholar]
  178. 178.
    Zhou L, Ren JH, Cheng ST, Xu HM, Chen WX et al. 2019. A functional variant in ubiquitin conjugating enzyme E2 L3 contributes to hepatitis B virus infection and maintains covalently closed circular DNA stability by inducing degradation of apolipoprotein B mRNA editing enzyme catalytic subunit 3A. Hepatology 69:1885–902
    [Google Scholar]
  179. 179.
    Zhou L, Wang X, Wang YJ, Zhou Y, Hu S et al. 2009. Activation of Toll-like receptor-3 induces interferon-λ expression in human neuronal cells. Neuroscience 159:629–37
    [Google Scholar]
  180. 180.
    Zhu M, Wang Y, Wang C, Shen W, Liu J et al. 2015. The eQTL-missense polymorphisms of APOBEC3H are associated with lung cancer risk in a Han Chinese population. Sci. Rep. 5:14969
    [Google Scholar]
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