Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Human genes that limit AIDS

Abstract

Discernable genetic variation among people and populations has an important role in infectious disease epidemics, including that of acquired immune deficiency syndrome (AIDS). Genetic association analysis of several large AIDS cohorts implicate 14 AIDS restriction genes, polymorphic variants in loci that regulate HIV-1 cell entry, acquired and innate immunity, and cytokine defenses to HIV-1. The influence and translational impact of these genes on individual and population sensitivity to AIDS is considerable.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Illustration of how HIV-1 enters cells, suggesting candidate ARGs for inspection.
Figure 2: Predicted survival pattern based on GPI of four composite ARG genotypes from Table 3.
Figure 3: Ability of imputed GPI-based median survival to predict actual AIDS survival.

Similar content being viewed by others

References

  1. Palella, F.J. Jr. et al. Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV outpatient Study Investigators. N. Engl. J. Med. 338, 853–860 (1998).

    PubMed  Google Scholar 

  2. Mocroft, A. et al. Changing patterns of mortality across Europe in patients infected with HIV-1. EuroSIDA Study Group. Lancet 352, 1725–1730 (1998).

    CAS  PubMed  Google Scholar 

  3. Finzi, D. et al. Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV-1, even in patients on effective combination therapy. Nat. Med. 5, 512–517 (1999).

    CAS  PubMed  Google Scholar 

  4. Cohen, J. Shots in the Dark. The wayward search for an AIDS vaccine. (W. Norton, New York, 2001).

  5. Fauci, A.S. HIV and AIDS: 20 years of science. Nat. Med. 9, 839–843 (2003).

    Article  CAS  PubMed  Google Scholar 

  6. Weiss, R.A. HIV and AIDS: looking ahead. Nat. Med. 9, 887–891 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. Annan, K. Forward. in AIDS in Africa (eds. Essex, M., Mboup, S., Kanki, P.J., Marlink, R. & Tlou, S.D.) 2nd edn. (Kluwer Academic, New York, 2002).

    Google Scholar 

  8. O'Brien, S.J. & Moore, J. The effect of genetic variation in chemokines and their receptors on HIV transmission and progression to AIDS. Immunol. Rev. 177, 99–111 (2000).

    CAS  PubMed  Google Scholar 

  9. Carrington, M. & O'Brien, S.J. The influence of HLA genotype on AIDS. Ann. Rev. Med. 54, 535–551 (2003).

    CAS  PubMed  Google Scholar 

  10. O'Brien, S.J. & Dean, M. In search of AIDS-resistance genes. Sci. Am. 277, 44–51 (1997).

    CAS  PubMed  Google Scholar 

  11. O'Brien, S.J. AIDS: A role for host genes. Hosp. Pract. 33, 53–79 (1998).

    CAS  Google Scholar 

  12. Cox, D.R. & Oakes, D. Analysis of Survival Data, London (Chapman and Hall, 1984).

    Google Scholar 

  13. Allison, P.D. Survival analyses using the SAS system: A practical guide. 155–197 (SAS Institute, Cary, North Carolina, 1995).

    Google Scholar 

  14. O'Brien, S.J., Nelson, G.W., Winkler, C.A. & Smith, M.W. Polygenic and multifactorial disease gene association in man: Lessons from AIDS. Annu. Rev. Genet. 34, 563–591 (2000).

    CAS  PubMed  Google Scholar 

  15. Gulick, R.M. New antiretroviral drugs. Clin. Microbiol. Infect. 9, 186–193 (2003).

    CAS  PubMed  Google Scholar 

  16. Carrington, M., Nelson, G. & O'Brien, S.J. Considering genetic profiles in functional studies of immune responsiveness to HIV-1. Immunol. Lett. 79, 131–140 (2001).

    CAS  PubMed  Google Scholar 

  17. Dean, M. et al. Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Science 273, 1856–1862 (1996).

    CAS  PubMed  Google Scholar 

  18. Liu, R. et al. Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86, 367–377 (1996).

    CAS  PubMed  Google Scholar 

  19. Samson, M. et al. Molecular cloning and functional expression of a new human CC chemokine receptor gene. Biochemistry 35, 3362–3367 (1996).

    CAS  PubMed  Google Scholar 

  20. Winkler, C.A. & O'Brien, S.J. AIDS restriction genes in human ethnic groups: An assessment. in AIDS in Africa (eds. Essex, M., Mboup, S., Kanki, P.J., Marlink, R. & Tlou, S.D.) 2nd edn. (Kluwer Academic, New York, 2002).

    Google Scholar 

  21. Winkler, C., Ping, A. & O'Brien, S.J. Patterns of ethnic diversity among the genes that influence AIDS. Hum. Mol. Genet. 13, R9–R19 (2004).

    CAS  PubMed  Google Scholar 

  22. D'Souza, M.P. & Harden, V.A. Chemokines and HIV-1 second receptors - confluence of two fields generates optimism in AIDS research. Nat. Med. 2, 1293–1300 (1996).

    CAS  PubMed  Google Scholar 

  23. Berger, E.A., Murphy, P.M. & Farber, J.M. Chemokine receptors as HIV-1 coreceptors: Roles in Viral Entry, Tropism, and Disease. Annu. Rev. Immunol. 17, 657–700 (1999).

    CAS  PubMed  Google Scholar 

  24. McNicholl, J.M., Smith, D.K., Qari, S.H. & Hodge, T. Host genes and HIV: The role of the chemokine receptor gene CCR5 and its allele (?32 CCR5) Emerging. Infect. Dis. 3, 261–271 (1997).

    CAS  Google Scholar 

  25. Schemper, M. Predictive accuracy and explained variation. Stat. Med. 22, 2299–2308 (2003).

    PubMed  Google Scholar 

  26. Risch, N. & Merikangas, K. The future of genetic studies of complex human diseases. Science 273, 1517–1517 (1996).

    Google Scholar 

  27. Pritchard, J.K., Stephens, M., Rosenberg, N.A. & Donnelly, P. Association mapping in structured populations. Am. J. Hum. Genet. 67, 170–181 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Glazier, A.M., Nadeau, J.H. & Aitman, T.J. Finding genes that underlie complex traits. Science 298, 2345–2349 (2003).

    Google Scholar 

  29. Anonymous. Freely associating. Nat. Genet. 22, 1–2 (1999).

  30. Pritchard, J.K. & Donnelly, P. Case-control studies of association in structured or admixed populations. Theor. Popul. Biol. 60, 227–237 (2001).

    CAS  PubMed  Google Scholar 

  31. Falush, D., Stephens, D. & Pritchard, J.K. Inferences of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567–1587 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Wu, L. et al. CCR5 levels and expression, pattern correlate with infectability by macrophage-tropic HIV-1, in vitro. J. Exp. Med. 185, 1681–1691 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. Benkirane, M., Jin, D.Y., Chun, R.F., Koup, R.A. & Jeang, K-T. Mechanism of transdominant inhibition of CCR5-mediated HIV-1 infection by CCR5 Delta 32. J. Biol. Chem. 272, 30603–30606 (1997).

    CAS  PubMed  Google Scholar 

  34. Martin, M.P. et al. Genetic acceleration of AIDS progression by a promoter variant of CCR5. Science 282, 1907–1911 (1998).

    CAS  PubMed  Google Scholar 

  35. Carrington, M., Dean, M., Martin, M.P. & O'Brien, S.J. Genetics of HIV-1 infection: Chemokine receptor CCR5 polymorphism and its consequences. Hum. Mol. Genet. 8, 1939–1945 (1999).

    CAS  PubMed  Google Scholar 

  36. Salkowitz, J.R. et al. CCR5 promoter polymorphism determines macrophage CCR5 density and magnitude of HIV-1 propagation in vitro. Clin. Immunol. 108, 234–240 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Bream, J.H. et al. CCR5 promoter alleles distinguished by specific DNA binding factors. Science 284, 223a (1999).

    Google Scholar 

  38. Smith, M.W. et al. Contrasting genetic influence of CCR2 and CCR5 receptor gene variants on HIV-1 infection and disease progression. Science 277, 959–965 (1997).

    CAS  PubMed  Google Scholar 

  39. Anzala, A.O. et al. CCR2-64I allele and genotype association with delayed AIDS progression in African women. Lancet 351, 1632–1633 (1998).

    CAS  PubMed  Google Scholar 

  40. Lee, B. et al. Influence of the CCR2-V64I polymorphism on human immunodeficiency virus type 1 coreceptor activity and on chemokine receptor function of CCR2b, CCR3, CCR5, and CXCR4. J. Virol. 72, 7450–7458 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  41. Mariani, R. et al. CCR2-64I polymorphism is not associated with altered CCR5 expression or coreceptor function. J. Virol. 73, 2450–2459 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Mellado, M., Rodriguez-Frade, J.M., Vila-Coro, A.J., de Ana, A.M. & Martinez, A.C. Chemokine control of HIV-1 infection. Nature 400, 723–724 (1999).

    CAS  PubMed  Google Scholar 

  43. Zagury, D. et al. C-C chemokines, pivotal in protection against HIV type 1 infection. Proc. Natl. Acad. Sci. USA 95, 3857–3861 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  44. Gallo, R.C., Garzino-Demo, A. & DeVico, A.L. HIV infection and pathogenesis: what about chemokines? J. Clin. Immunol. 19, 293–299 (1999).

    CAS  PubMed  Google Scholar 

  45. An, P. et al. Modulation of HIV infection and disease progression by interacting RANTES variants. Proc. Natl. Acad. Sci USA 99, 10002–10007 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. Winkler, C. et al. Genetic restriction of AIDS pathogenesis by an SDF-1 chemokine gene variant. Science 279, 389–393 (1998).

    CAS  PubMed  Google Scholar 

  47. Bleul, C.C. et al. The lymphocyte chemoattractant SDF-1 is a ligand for LESTR/fusin and blocks HIV-1 entry. Nature 382, 829–833 (1996).

    CAS  PubMed  Google Scholar 

  48. Duggal, P. et al. Genetic influence of CXCR6 chemokine receptor alleles on PCP-mediated AIDS progression among African-Americans. Genes Immun. 4, 245–250 (2003).

    CAS  PubMed  Google Scholar 

  49. Modi, W.S. et al. Directional selection in the MCP-1 MCP-3 Eotaxin gene cluster in influences HIV-1 transmission. AIDS 17, 2357–2365 (2003).

    CAS  PubMed  Google Scholar 

  50. Bagiolini, M. et al. IL-8 and related chemotactic cytokines-CXC and CC chemokines. Adv. Immunol. 55, 97–179 (1994).

    Google Scholar 

  51. He, J.L. et al. CCR3 and CCR5 are co-receptors for HIV-1 infection of microglia. Nature 385, 645–649 (1997).

    CAS  PubMed  Google Scholar 

  52. Sozzani, S. et al. Differential regulation of chemokine receptors during dendritic cell maturation: a model for their trafficking properties. J. Immunol. 161, 1083–1086 (1998).

    CAS  PubMed  Google Scholar 

  53. Shin, H.D. et al. Genetic restriction of HIV-1 infection and AIDS progression by promoter alleles of interleukin 10. Proc. Natl. Acad. Sci. USA. 97, 14467–14472 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. Bream, J.H., An, P., Zhang, X., Winkler, C.A. & Young, H.A. A single nucleotide polymorphism in the proximal IFN-gamma promoter alters control of gene transcription. Genes Immun. 3, 165–169 (2002).

    CAS  PubMed  Google Scholar 

  55. An, P. et al. A TNF-inducible promoter variant of interferon-gamma accelerates CD4 T cell depletion in HIV-1 infected individuals. J. Infect. Dis. 188, 228–231 (2003).

    CAS  PubMed  Google Scholar 

  56. Aguado, B. et al. Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium. Nature 401, 921–923 (1999).

    Google Scholar 

  57. Parham, P. & Ohta, T. Population biology of antigen presentation by MHC class I molecules. Science 272, 67–74 (1996).

    CAS  PubMed  Google Scholar 

  58. Hughes, A.L. & Yeager, M. Natural selection at major histocompatibility complex loci of vertebrates. Annu. Rev. Genet. 32, 415–435 (1998).

    CAS  PubMed  Google Scholar 

  59. Barber, L.D. et al. Overlap in the repertoires of peptides bound in-vivo by a group of related Class-I HLA-B allotypes. Curr. Biol. 5, 179–190 (1995).

    CAS  PubMed  Google Scholar 

  60. Gao, X. et al. Effect of a single amino acid change in MHC class I molecules on the rate of progression to AIDS. N. Engl. J. Med. 344, 1668–1675 (2001).

    CAS  PubMed  Google Scholar 

  61. Moore, C.B. et al. Evidence of HIV-1 adaptation to HLA-restricted immune response at a population level. Science 296, 1439–1443 (2003).

    Google Scholar 

  62. Carrington, M. et al. HLA and HIV-1: Heterozygote advantage and B*35-Cw*04 disadvantage. Science 283, 1748–1752 (1999).

    CAS  PubMed  Google Scholar 

  63. Steinle, A. et al. Motif of HLA-B*3503 peptide ligands. Immunogenetics 43, 105–107 (1996).

    CAS  PubMed  Google Scholar 

  64. Jin, X. et al. Human immunodeficiency virus Type 1 (HIV-1)-specific CD8+-T-Cell responses for groups of HIV-1-infected individuals with different HLA-B*35 genotypes. J. Virol. 76, 12603–12610 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. O'Brien, S.J., Gao, X. & Carrington, M. HLA and AIDS: A cautionary tale. Trends Mol. Med. 7, 379–381 (2002).

    Google Scholar 

  66. Tang, J.M. et al. HLA class I homozygosity accelerates disease progression in human immunodeficiency virus type I infection. AIDS Res. Hum. Retroviruses 15, 317–324 (1999).

    CAS  PubMed  Google Scholar 

  67. Flores-Villanueva, P.O. et al. Control of HIV-1 viremia and protection from AIDS are associated with HLA-Bw4 homozygosity. Proc. Natl. Acad. Sci. USA 98, 5140–5145 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Trachtenberg, E. et al. Advantage of rare HLA supertype in HIV disease progression. Nat. Med. 9, 928–935 (2003).

    CAS  PubMed  Google Scholar 

  69. Lanier, L.L. NK cell receptors. Annu. Rev. Immunol. 16, 359–393 (1998).

    CAS  PubMed  Google Scholar 

  70. Martin, M.P. et al. Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS. Nat. Genet. 31, 429–434 (2002).

    CAS  PubMed  Google Scholar 

  71. Cairns, J.S. & D'Souza, M.P. Chemokines and HIV-1 second receptors: The therapeutic connection. Nat. Med. 4, 563–568 (1998).

    CAS  PubMed  Google Scholar 

  72. O'Brien, S.J. A new approach to therapy. HIV Newsline 4, 3–6 (1998).

    Google Scholar 

  73. LaBranche, C.C. et al. HIV fusion and its inhibition. Antiviral Res. 50, 95–115 (2001).

    CAS  PubMed  Google Scholar 

  74. Stevenson, M. New targets for inhibitors of HIV-1 replication. Nat. Rev. Mol. Cell Biol. 1, 40–49 (2000).

    PubMed  Google Scholar 

  75. Hazuda, D.J. et al. Inhibitors of strand transfer that prevent integration and inhibit HIV-1 replication in cells. Science 287, 646–650 (2000).

    CAS  PubMed  Google Scholar 

  76. Best, S., Le Tissier, P., Towers, G. & Stoye, J.P. Positional cloning of the mouse retrovirus restriction gene Fv-1. Nature 382, 826–829 (1996).

    CAS  PubMed  Google Scholar 

  77. Levin, M.L. The occurrence of lung cancer in man. Acta Unio Int. Contra Cancrum 9, 531–541 (1953).

    CAS  PubMed  Google Scholar 

  78. Benichou, J. Attributable Risk. in Encyclopedia of Statistics. (eds. Armitage, P. & Colton, T.) (Wiley, New York, 1998).

    Google Scholar 

  79. Goedert, J.J. et al. A prospective study of human immunodeficiency virus type 1 infection and the development of AIDS in subjects with hemophilia. N. Engl. J. Med. 321, 1141–1148 (1989).

    CAS  PubMed  Google Scholar 

  80. Darby, S.C., Doll, R., Thakrar, B., Rizza, C.R. & Cox, D.R. Time from infection with HIV to onset of AIDS in patients with haemophilia in the UK. Stat. Med. 6, 681–689 (1990).

    Google Scholar 

  81. The International Hap Map Project. Nature 426, 789–796 (2003).

  82. Phair, J. et al. Acquired-Immune-Deficiency-Syndrome occurring within 5 years of infection with Human-Immunodeficiency-Virus Type-1 - the Multicenter AIDS Cohort Study. J. Acquir. Immune Defic. Syndr. 5, 490–496 (1992).

    CAS  PubMed  Google Scholar 

  83. Detels, R. et al. For the Multicenter AIDS Cohort Study: Resistance to HIV-1 infection. J. Acquir. Immune Defic. Syndr. 7, 1263–1269 (1994).

    CAS  PubMed  Google Scholar 

  84. Kaslow, R.A. et al. The Multicenter AIDS Cohort Study - Rationale, organization, and selected characteristics of the participants. Am. J. Epidemiol. 26, 310–318 (1987).

    Google Scholar 

  85. Buchbinder, S.P., Katz, M.H., Hessol, N.A., O'Malley, P.M. & Holmberg, S.D. Long-term HIV-1 infection without immunologic progression. AIDS 8, 1123–1128 (1994).

    CAS  PubMed  Google Scholar 

  86. Goedert, J.J. et al. Decreased helper lymphocytes-T in homosexual men. 1. Sexual contact in high-incidence areas for the Acquired Immunodeficiency Syndrome. Am. J. Epidemiol. 121, 629–636 (1985).

    CAS  PubMed  Google Scholar 

  87. Hilgartner, M.W. et al. Hemophilia growth and development study - design, methods, and entry data. Am. J. Ped. Hematol. Oncol. 15, 208–218 (1993).

    CAS  Google Scholar 

  88. Lederman, M.M. et al. Human immunodeficiency virus (HIV) type 1 infection status and in vitro susceptibility to HIV infection among high-risk HIV-1-seronegative hemophiliacs. J. Infect. Dis. 172, 228–231 (1995).

    CAS  PubMed  Google Scholar 

  89. Vlahov, D. et al. Association of drug injection patterns with antibody to human immunodeficiency virus type 1 among intravenous durg users in Baltimore, Maryland. Am. J. Epidemiol. 132, 847–856 (1990).

    CAS  PubMed  Google Scholar 

  90. Dean, M. et al. Reduced risk of AIDS lymphoma in individuals heterozygous for the CCR5-?32 mutation. Cancer Res. 59, 3561–3564 (1999).

    CAS  PubMed  Google Scholar 

  91. US Centers for Disease Control. Morb. Mortal. Wkly. Rep. 36 Suppl 1 (1987).

  92. Goldsmith, M.A. & Doms, R.W. HIV entry: are all receptors created equal? Nat. Immunol. 3, 709–710 (2002).

    CAS  PubMed  Google Scholar 

  93. Littman, D.R. Chemokine receptors: keys to AIDS pathogenesis? Cell 93, 677–680 (1998).

    CAS  PubMed  Google Scholar 

  94. Kullback, S. Information Theory and Statistics (Dover, Mineola, New York, 1968).

    Google Scholar 

  95. Nilsson, S., Carstensen, J.M. & Pershagen, G. Mortality among male and female smokers in Sweden: a 33 year follow up. J. Epidemiol. Community Health 55, 825–830 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stephen J O'Brien.

Rights and permissions

Reprints and permissions

About this article

Cite this article

O'Brien, S., Nelson, G. Human genes that limit AIDS. Nat Genet 36, 565–574 (2004). https://doi.org/10.1038/ng1369

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue date:

  • DOI: https://doi.org/10.1038/ng1369

This article is cited by

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