1887

Abstract

HIV-1 replication in CD4-positive T lymphocytes requires counteraction of multiple different innate antiviral mechanisms. Macrophage cells are also thought to provide a reservoir for HIV-1 replication but less is known in this cell type about virus restriction and counteraction mechanisms. Many studies have combined to demonstrate roles for APOBEC3D, APOBEC3F, APOBEC3G and APOBEC3H in HIV-1 restriction and mutation in CD4-positive T lymphocytes, whereas the APOBEC enzymes involved in HIV-1 restriction in macrophages have yet to be delineated fully. We show that multiple APOBEC3 genes including APOBEC3G are expressed in myeloid cell lines such as THP-1. Vif-deficient HIV-1 produced from THP-1 is less infectious than Vif-proficient virus, and proviral DNA resulting from such Vif-deficient infections shows strong G to A mutation biases in the dinucleotide motif preferred by APOBEC3G. Moreover, Vif mutant viruses with selective sensitivity to APOBEC3G show Vif null-like infectivity levels and similarly strong APOBEC3G-biased mutation spectra. Importantly, APOBEC3G-null THP-1 cells yield Vif-deficient particles with significantly improved infectivities and proviral DNA with background levels of G to A hypermutation. These studies combine to indicate that APOBEC3G is the main HIV-1 restricting APOBEC3 family member in THP-1 cells.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001276
2019-05-30
2024-04-19
Loading full text...

Full text loading...

/deliver/fulltext/jgv/100/7/1140.html?itemId=/content/journal/jgv/10.1099/jgv.0.001276&mimeType=html&fmt=ahah

References

  1. Malim MH, Bieniasz PD. HIV restriction factors and mechanisms of evasion. Cold Spring Harb Perspect Med 2012; 2:a006940 [View Article]
    [Google Scholar]
  2. Refsland EW, Harris RS. The APOBEC3 family of retroelement restriction factors. Curr Top Microbiol Immunol 2013; 371:1–27 [View Article]
    [Google Scholar]
  3. Moris A, Murray S, Cardinaud S. Aid and APOBECs span the gap between Innate and adaptive immunity. Front Microbiol 2014; 5:534 [View Article]
    [Google Scholar]
  4. Harris RS, Dudley JP. APOBECs and virus restriction. Virology 2015; 479-480:131–145 [View Article]
    [Google Scholar]
  5. Simon V, Bloch N, Landau NR. Intrinsic host restrictions to HIV-1 and mechanisms of viral escape. Nat Immunol 2015; 16:546–553 [View Article]
    [Google Scholar]
  6. Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS et al. Vif hijacks CBF-β to degrade APOBEC3G and promote HIV-1 infection. Nature 2012; 481:371–375 [View Article]
    [Google Scholar]
  7. Zhang W, Du J, Evans SL, Yu Y, Yu XF. T-cell differentiation factor CBF-β regulates HIV-1 Vif-mediated evasion of host restriction. Nature 2012; 481:376–379 [View Article]
    [Google Scholar]
  8. Anderson BD, Harris RS. Transcriptional regulation of APOBEC3 antiviral immunity through the CBF-β/RUNX axis. Sci Adv 2015; 1:e1500296 [View Article]
    [Google Scholar]
  9. Mulder LCF, Harari A, Simon V. Cytidine deamination induced HIV-1 drug resistance. Proc Natl Acad Sci U S A 2008; 105:5501–5506 [View Article]
    [Google Scholar]
  10. Jern P, Russell RA, Pathak VK, Coffin JM. Likely role of APOBEC3G-mediated G-to-A mutations in HIV-1 evolution and drug resistance. PLoS Pathog 2009; 5:e1000367 [View Article]
    [Google Scholar]
  11. Kim EY, Bhattacharya T, Kunstman K, Swantek P, Koning FA et al. Human APOBEC3G-mediated editing can promote HIV-1 sequence diversification and accelerate adaptation to selective pressure. J Virol 2010; 84:10402–10405 [View Article]
    [Google Scholar]
  12. Kim EY, Lorenzo-Redondo R, Little SJ, Chung Y-S, Phalora PK et al. Human APOBEC3 induced mutation of human immunodeficiency virus type-1 contributes to adaptation and evolution in natural infection. PLoS Pathog 2014; 10:e1004281 [View Article]
    [Google Scholar]
  13. Noguera-Julian M, Cozzi-Lepri A, Di Giallonardo F, Schuurman R, Däumer M et al. Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants. Clin Microbiol Infect 2016; 22:191–200 [View Article]
    [Google Scholar]
  14. Stevenson M. Role of myeloid cells in HIV-1-host interplay. J Neurovirol 2015; 21:242–248 [View Article]
    [Google Scholar]
  15. Sattentau QJ, Stevenson M. Macrophages and HIV-1: an unhealthy constellation. Cell Host Microbe 2016; 19:304–310 [View Article]
    [Google Scholar]
  16. Wacleche V, Tremblay C, Routy JP, Ancuta P. The biology of monocytes and dendritic cells: contribution to HIV pathogenesis. Viruses 2018; 10:65 [View Article]
    [Google Scholar]
  17. Herskovitz J, Gendelman HE. HIV and the macrophage: from cell reservoirs to drug delivery to viral eradication. J Neuroimmune Pharmacol 2019; 14:52–67 [View Article]
    [Google Scholar]
  18. Berger G, Durand S, Fargier G, Nguyen XN, Cordeil S et al. APOBEC3A is a specific inhibitor of the early phases of HIV-1 infection in myeloid cells. PLoS Pathog 2011; 7:e1002221 [View Article]
    [Google Scholar]
  19. Laguette N, Sobhian B, Casartelli N, Ringeard M, Chable-Bessia C et al. SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature 2011; 474:654–657 [View Article]
    [Google Scholar]
  20. Goujon C, Moncorgé O, Bauby H, Doyle T, Ward CC et al. Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection. Nature 2013; 502:559–562 [View Article]
    [Google Scholar]
  21. Kane M, Yadav SS, Bitzegeio J, Kutluay SB, Zang T et al. MX2 is an interferon-induced inhibitor of HIV-1 infection. Nature 2013; 502:563–566 [View Article]
    [Google Scholar]
  22. Koning FA, Newman ENC, Kim EY, Kunstman KJ, Wolinsky SM et al. Defining APOBEC3 expression patterns in human tissues and hematopoietic cell subsets. J Virol 2009; 83:9474–9485 [View Article]
    [Google Scholar]
  23. Refsland EW, Stenglein MD, Shindo K, Albin JS, Brown WL et al. Quantitative profiling of the full APOBEC3 mRNA repertoire in lymphocytes and tissues: implications for HIV-1 restriction. Nucleic Acids Res 2010; 38:4274–4284 [View Article]
    [Google Scholar]
  24. Stenglein MD, Burns MB, Li M, Lengyel J, Harris RS. APOBEC3 proteins mediate the clearance of foreign DNA from human cells. Nat Struct Mol Biol 2010; 17:222–229 [View Article]
    [Google Scholar]
  25. Thielen BK, McNevin JP, McElrath MJ, Hunt BVS, Klein KC et al. Innate immune signaling induces high levels of TC-specific deaminase activity in primary monocyte-derived cells through expression of APOBEC3A isoforms. J Biol Chem 2010; 285:27753–27766 [View Article]
    [Google Scholar]
  26. Burns MB, Lackey L, Carpenter MA, Rathore A, Land AM et al. APOBEC3B is an enzymatic source of mutation in breast cancer. Nature 2013; 494:366–370 [View Article]
    [Google Scholar]
  27. Hultquist JF, Lengyel JA, Refsland EW, LaRue RS, Lackey L et al. Human and rhesus APOBEC3D, APOBEC3F, APOBEC3G, and APOBEC3H demonstrate a conserved capacity to restrict Vif-deficient HIV-1. J Virol 2011; 85:11220–11234 [View Article]
    [Google Scholar]
  28. Refsland EW, Hultquist JF, Harris RS. Endogenous origins of HIV-1 G-to-A hypermutation and restriction in the nonpermissive T cell line CEM2n. PLoS Pathog 2012; 8:e1002800 [View Article]
    [Google Scholar]
  29. Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA et al. The cancer cell line encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012; 483:603–607 [View Article]
    [Google Scholar]
  30. Brockman MA, Tanzi GO, Walker BD, Allen TM. Use of a novel GFP reporter cell line to examine replication capacity of CXCR4- and CCR5-tropic HIV-1 by flow cytometry. J Virol Methods 2006; 131:134–142 [View Article]
    [Google Scholar]
  31. Refsland EW, Hultquist JF, Luengas EM, Ikeda T, Shaban NM et al. Natural polymorphisms in human APOBEC3H and HIV-1 Vif combine in primary T lymphocytes to affect viral G-to-A mutation levels and infectivity. PLoS Genet 2014; 10:e1004761 [View Article]
    [Google Scholar]
  32. Harris RS, Bishop KN, Sheehy AM, Craig HM, Petersen-Mahrt SK et al. DNA deamination mediates innate immunity to retroviral infection. Cell 2003; 113:803–809 [View Article]
    [Google Scholar]
  33. Mangeat B, Turelli P, Caron G, Friedli M, Perrin L et al. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature 2003; 424:99–103 [View Article]
    [Google Scholar]
  34. Zhang H, Yang B, Pomerantz RJ, Zhang C, Arunachalam SC et al. The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA. Nature 2003; 424:94–98 [View Article]
    [Google Scholar]
  35. Yu Q, König R, Pillai S, Chiles K, Kearney M et al. Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat Struct Mol Biol 2004; 11:435–442 [View Article]
    [Google Scholar]
  36. Russell RA, Smith J, Barr R, Bhattacharyya D, Pathak VK. Distinct domains within APOBEC3G and APOBEC3F interact with separate regions of human immunodeficiency virus type 1 Vif. J Virol 2009; 83:1992–2003 [View Article]
    [Google Scholar]
  37. Smith JL, Pathak VK. Identification of specific determinants of human APOBEC3F, APOBEC3C, and APOBEC3DE and African green monkey APOBEC3F that interact with HIV-1 Vif. J Virol 2010; 84:12599–12608 [View Article]
    [Google Scholar]
  38. Albin JS, Haché G, Hultquist JF, Brown WL, Harris RS. Long-term restriction by APOBEC3F selects human immunodeficiency virus type 1 variants with restored Vif function. J Virol 2010; 84:10209–10219 [View Article]
    [Google Scholar]
  39. Ooms M, Brayton B, Letko M, Maio SM, Pilcher CD et al. HIV-1 Vif adaptation to human APOBEC3H haplotypes. Cell Host Microbe 2013; 14:411–421 [View Article]
    [Google Scholar]
  40. Harris RS, Petersen-Mahrt SK, Neuberger MS. RNA editing enzyme Apobec1 and some of its homologs can act as DNA mutators. Mol Cell 2002; 10:1247–1253 [View Article]
    [Google Scholar]
  41. Jarmuz A, Chester A, Bayliss J, Gisbourne J, Dunham I et al. An anthropoid-specific locus of orphan C to U RNA-editing enzymes on chromosome 22. Genomics 2002; 79:285–296 [View Article]
    [Google Scholar]
  42. Sheehy AM, Gaddis NC, Choi JD, Malim MH. Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral vif protein. Nature 2002; 418:646–650 [View Article]
    [Google Scholar]
  43. Gabuzda DH, Li H, Lawrence K, Vasir BS, Crawford K et al. Essential role of Vif in establishing productive HIV-1 infection in peripheral blood T lymphocytes and monocyte/macrophages. J Acquir Immune Defic Syndr 1994; 7:908–915
    [Google Scholar]
  44. Kawamura M, Ishizaki T, Ishimoto A, Shioda T, Kitamura T et al. Growth ability of human immunodeficiency virus type 1 auxiliary gene mutants in primary blood macrophage cultures. J Gen Virol 1994; 75:2427–2431 [View Article]
    [Google Scholar]
  45. Michaels FH, Hattori N, Gallo RC, Franchini G. The human immunodeficiency virus type 1 (HIV-1) Vif protein is located in the cytoplasm of infected cells and its effect on viral replication is equivalent in HIV-2. AIDS Res Hum Retroviruses 1993; 9:1025–1030 [View Article]
    [Google Scholar]
  46. von Schwedler U, Song J, Aiken C, Trono D. Vif is crucial for human immunodeficiency virus type 1 proviral DNA synthesis in infected cells. J Virol 1993; 67:4945–4955
    [Google Scholar]
  47. Chowdhury IH, Chao W, Potash MJ, Sova P, Gendelman HE et al. vif-negative human immunodeficiency virus type 1 persistently replicates in primary macrophages, producing attenuated progeny virus. J Virol 1996; 70:5336–5345
    [Google Scholar]
  48. Fan L, Peden K. Cell-free transmission of Vif mutants of HIV-1. Virology 1992; 190:19–29 [View Article]
    [Google Scholar]
  49. Gargan S, Ahmed S, Mahony R, Bannan C, Napoletano S et al. HIV-1 promotes the degradation of components of the type 1 IFN JAK/STAT pathway and blocks anti-viral ISG induction. EBioMedicine 2018; 30:203–216 [View Article]
    [Google Scholar]
  50. Du J, Rui Y, Zheng W, Li P, Kang J et al. Vif-CBFβ interaction is essential for Vif-induced cell cycle arrest. Biochem Biophys Res Commun 2019; 511:910–915 [View Article]
    [Google Scholar]
  51. Koning FA, Goujon C, Bauby H, Malim MH. Target cell-mediated editing of HIV-1 cDNA by APOBEC3 proteins in human macrophages. J Virol 2011; 85:13448–13452 [View Article]
    [Google Scholar]
  52. Peng G, Greenwell-Wild T, Nares S, Jin W, Lei KJ et al. Myeloid differentiation and susceptibility to HIV-1 are linked to APOBEC3 expression. Blood 2007; 110:393–400 [View Article]
    [Google Scholar]
  53. Stopak KS, Chiu YL, Kropp J, Grant RM, Greene WC. Distinct patterns of cytokine regulation of APOBEC3G expression and activity in primary lymphocytes, macrophages, and dendritic cells. J Biol Chem 2007; 282:3539–3546 [View Article]
    [Google Scholar]
  54. Land AM, Law EK, Carpenter MA, Lackey L, Brown WL et al. Endogenous APOBEC3A DNA cytosine deaminase is cytoplasmic and nongenotoxic. J Biol Chem 2013; 288:17253–17260 [View Article]
    [Google Scholar]
  55. Mohanram V, Sköld AE, Bächle SM, Pathak SK, Spetz AL. IFN-α induces APOBEC3G, F, and A in immature dendritic cells and limits HIV-1 spread to CD4+ T cells. J Immunol 2013; 190:3346–3353 [View Article]
    [Google Scholar]
  56. Chaipan C, Smith JL, Hu WS, Pathak VK. APOBEC3G restricts HIV-1 to a greater extent than APOBEC3F and APOBEC3DE in human primary CD4+ T cells and macrophages. J Virol 2013; 87:444–453 [View Article]
    [Google Scholar]
  57. OhAinle M, Kerns JA, Malik HS, Emerman M. Adaptive evolution and antiviral activity of the conserved mammalian cytidine deaminase APOBEC3H. J Virol 2006; 80:3853–3862 [View Article]
    [Google Scholar]
  58. OhAinle M, Kerns JA, Li MMH, Malik HS, Emerman M. Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. Cell Host Microbe 2008; 4:249–259 [View Article]
    [Google Scholar]
  59. Pion M, Granelli-Piperno A, Mangeat B, Stalder R, Correa R et al. APOBEC3G/3F mediates intrinsic resistance of monocyte-derived dendritic cells to HIV-1 infection. J Exp Med 2006; 203:2887–2893 [View Article]
    [Google Scholar]
  60. Chen K, Huang J, Zhang C, Huang S, Nunnari G et al. Alpha interferon potently enhances the anti-human immunodeficiency virus type 1 activity of APOBEC3G in resting primary CD4 T cells. J Virol 2006; 80:7645–7657 [View Article]
    [Google Scholar]
  61. Kreisberg JF, Yonemoto W, Greene WC. Endogenous factors enhance HIV infection of tissue naive CD4 T cells by stimulating high molecular mass APOBEC3G complex formation. J Exp Med 2006; 203:865–870 [View Article]
    [Google Scholar]
  62. Pido-Lopez J, Whittall T, Wang Y, Bergmeier LA, Babaahmady K et al. Stimulation of cell surface CCR5 and CD40 molecules by their ligands or by HSP70 up-regulates APOBEC3G expression in CD4(+) T cells and dendritic cells. J Immunol 2007; 178:1671–1679 [View Article]
    [Google Scholar]
  63. Lafferty MK, Sun L, DeMasi L, Lu W, Garzino-Demo A. CCR6 ligands inhibit HIV by inducing APOBEC3G. Blood 2010; 115:1564–1571 [View Article]
    [Google Scholar]
  64. Kane M, Zang TM, Rihn SJ, Zhang F, Kueck T et al. Identification of interferon-stimulated genes with antiretroviral activity. Cell Host Microbe 2016; 20:392–405 [View Article]
    [Google Scholar]
  65. Schoggins JW, Rice CM. Interferon-stimulated genes and their antiviral effector functions. Curr Opin Virol 2011; 1:519–525 [View Article]
    [Google Scholar]
  66. Platt EJ, Bilska M, Kozak SL, Kabat D, Montefiori DC. Evidence that ecotropic murine leukemia virus contamination in TZM-bl cells does not affect the outcome of neutralizing antibody assays with human immunodeficiency virus type 1. J Virol 2009; 83:8289–8292 [View Article]
    [Google Scholar]
  67. Leibman RS, Richardson MW, Ellebrecht CT, Maldini CR, Glover JA et al. Supraphysiologic control over HIV-1 replication mediated by CD8 T cells expressing a re-engineered CD4-based chimeric antigen receptor. PLoS Pathog 2017; 13:e1006613 [View Article]
    [Google Scholar]
  68. Parry RV, Rumbley CA, Vandenberghe LH, June CH, Riley JL. CD28 and inducible costimulatory protein Src homology 2 binding domains show distinct regulation of phosphatidylinositol 3-kinase, Bcl-xL, and IL-2 expression in primary human CD4 T lymphocytes. J Immunol 2003; 171:166–174 [View Article]
    [Google Scholar]
  69. Haché G, Liddament MT, Harris RS. The retroviral hypermutation specificity of APOBEC3F and APOBEC3G is governed by the C-terminal DNA cytosine deaminase domain. J Biol Chem 2005; 280:10920–10924 [View Article]
    [Google Scholar]
  70. Carpenter MA, Law EK, Serebrenik A, Brown WL, Harris RS. A lentivirus-based system for Cas9/gRNA expression and subsequent removal by Cre-mediated recombination. Methods 2019; 156:79–84 [View Article]
    [Google Scholar]
  71. Ito K, Murphy D. Application of ggplot2 to pharmacometric graphics. CPT: pharmacomet syst pharmacol 2013; 2:e79 [View Article]
    [Google Scholar]
  72. RDC R: a Language and ENvironmenral for Statistical Computing Vienna, Austria: the R Foundation for Statistical Computing; 2011 http://www.r-project.org
    [Google Scholar]
  73. Haché G, Shindo K, Albin JS, Harris RS. Evolution of HIV-1 isolates that use a novel Vif-independent mechanism to resist restriction by human APOBEC3G. Curr Biol 2008; 18:819–824 [View Article]
    [Google Scholar]
  74. Sato K, Takeuchi JS, Misawa N, Izumi T, Kobayashi T et al. APOBEC3D and APOBEC3F potently promote HIV-1 diversification and evolution in humanized mouse model. PLoS Pathog 2014; 10:e1004453 [View Article]
    [Google Scholar]
  75. Ikeda T, Symeonides M, Albin JS, Li M, Thali M et al. HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G. PLoS Pathog 2018; 14:e1007010 [View Article]
    [Google Scholar]
  76. Leonard B, McCann JL, Starrett GJ, Kosyakovsky L, Luengas EM et al. The PKC/NF-κB signaling pathway induces APOBEC3B expression in multiple human cancers. Cancer Res 2015; 75:4538–4547 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001276
Loading
/content/journal/jgv/10.1099/jgv.0.001276
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error