DQ haplotypes that were identified in two or fewer than two individuals were designated as rare DQ haplotypes. We compared the distribution of rare DQ haplotypes between HIV-1 resistant group and the HIV-1 positive group and did not observe significant differences in rare haplotype frequencies between the two groups (P = 0.398).
Women who have DQB1*0603 and DQB1*0609 were more likely to be resistant to HIV-1 infection [P = 0.037, odds ratio (OR) = 3.25, 95% confidence interval (CI) = 1.12–9.47] (Table 3). The presence of DQB1*050301 also appeared to offer protection from HIV-1 infection (P = 0.055, OR = 12.77, 95% CI = 1.44–112) (Table 3). DQB1*0602 (P = 0.048, OR = 0.68, 95% CI = 0.44–1.05) and DQA1*010201–DQB1*0602 haplotype (P = 0.039, OR = 0.64, 95% CI = 0.41–1.03) increased the susceptibility to HIV-1 infection, while DQA1*010201–DQB1*0603 conferred protection from HIV-1 (P = 0.044, OR = 17.33, 95% CI = 1.79–168).
Several DQ haplotypes were only found in the HIV-1 positive group (OR = 0.30–0.31, 95% CI = 0.03–3.70), including DQA1*010201-DQB1*0201, DQA1*0504-DQB1*0201, DQA1*0402-DQB1*0402 and DQA1*0402-DQB1*030101. Kaplan–Meier survival analysis showed that women with these haplotypes seroconverted faster when compared with women without them [Fig. 1. (a)–(d)]. We also noted that women with the DQA1*010201-DQB1*0602 haplotype, associated with increased susceptibility to HIV-1, seroconverted faster than women without this haplotype, and women who are homozygous for DQA1*010201-DQB1*0602 fared even worse [Fig. 1. (e)].
Sensitivity analysis, using weighted analyses analogous to those above yielded associations that were consistent with the results obtained using nonweighted analyses, showed that differences in time of enrollment did not impact on our findings.
To examine whether the DQ haplotype associations identified in this study were due to linkage with previously reported HLA alleles or supertypes, we conducted binary logistic regression analysis. As seen in Table 4, the associations of DQB1*0603, DQB1*0609 and DQA1*010201-DQB1*0603 haplotype with resistance were independent of HLA-DRB1*01 genotype and HLA A2/6802 supertype, which had previously been shown to associate with HIV-1 resistance in this cohort . Also, the association of DQA1*010201-DQB1*0602 haplotype with susceptibility to HIV-1 infection was independent of HLA-A*2301, which was previously shown to associate with increased susceptibility to HIV-1 infection in the Pumwani cohort  (Table 4).
The associations of DQB1*0603 and DQA1*010201-DQB1*0603 haplotype with HIV-1 resistance in the Pumwani cohort are consistent with the previous report that DQB1*0603 allele was associated with protection from HIV-1 infection in Caucasians . The observed associations of DQB1*0602 genotype and the DQB1*010201-0602 haplotype with susceptibility to HIV-1 infection in the Pumwani cohort also agree with observations that DQB1*0602 was associated with increased HIV-1 susceptibility in Caucasians [35,44] and was associated with accelerated seroconversion in a Zambian discordant couple cohort when present on a haplotype with DRB1*1503 [44,45]. This consistency among different ethnic populations, which experience infections from different subtypes of HIV-1, suggests that the influence of ethnicity and viral subtype diversity on the role of DQ in resistance/susceptibility to HIV-1 infection is not as great as previously thought. Thus, understanding the role of DQ in HIV-1 resistance/susceptibility could have broader applications. Furthermore, our observations in the Pumwani cohort would likely be applicable to other populations in sub-Saharan Africa because of the similarity in DQ allele/haplotype frequencies in the region [http://www.ncbi.nlm.nih.gov/projects/mhc/ihwg.cgi. (Accessed 2006)].
HLA alleles have been reported to be associated with over 40 autoimmune, allergic, neoplastic and infectious diseases, but linkage disequilibrium in the HLA region makes it difficult to attribute disease risk to individual genes/alleles. HLA class II alleles have been identified as the major genetic factors influencing many chronic inflammatory diseases , indicating that class II antigens play an important role in the immune response. The DQ alleles and haplotypes associated with HIV-1 resistance/susceptibility in the Pumwani cohort have also been associated with other diseases. DQA1*0102-DQB1*0602 haplotype was associated with increased susceptibility to narcolepsy  and multiple sclerosis , and decreased susceptibility to Type 1 diabetes [49,50]. DQB1*050301 was associated with increased risk of vitiligo  and pemphigus vulgaris in a Chinese population , but had a protective effect against Type 1 diabetes in Czechs . DQB1*0603 was found to be protective against Type 1 diabetes in Czechs  and British Caucasians . Both DQB1*0609 and DQB1*0602 were protective against Type 1 diabetes in Jewish and Israeli Arab populations . As autoimmune diseases are often associated with greater immune activation, these observations suggest a mechanism for DQ immune response similar to foreign pathogens and the lack of self-tolerance observed in autoimmunity. The incidence of autoimmune disorders in the Pumwani cohort is unknown. Future studies should determine whether alleles associated with autoimmunity in other populations have similar associations in the Pumwani cohort.
Variability in tolerating epitope mutations could influence the ability of DQ molecules in antigen presentation. The tolerance of epitope mutations of alleles associated with differential susceptibility to HIV-1 infection could be different, therefore further molecular modeling of HLA-DQ will allow for a better understanding of the effect of residue changes and the interactions between α and β chains, and a better understanding of the DQ molecule's role in HIV-1 resistance and susceptibility.
Although the exact mechanism for HLA-DQ disease associations is unclear, it is likely that its role involves the initiation of CD4+ T helper cell immune responses, creating a cytokine-rich environment and helping the CD8+ T cell response, which controls viral spread during acute and chronic infection [60,61]. Further studies should determine if the identified alleles vary in their ability to prime the anti-HIV-1-specific immune response, resulting in differential virus transmissibility.
The differential susceptibility to HIV-1 infection involves many factors. We showed that HLA-DQ genes play an important role in the natural resistance to HIV-1 infection in the Pumwani cohort. Although it is likely that this involves direct immune responses to HIV-1, alternative but equally important pathways cannot be ruled out. Identification of DQ alleles/haplotypes associated with resistance/susceptibility to HIV-1 infection will help in the design of HIV vaccines targeting specific HLA-DQ alleles/haplotypes. Ultimately, the full repertoire of HLA antigens possessed by an individual is the key in determining their immune response to infectious pathogens, so we expect that full class I and class II haplotype analysis will provide further insight into other potential associations and linkages between protective/susceptible alleles, as well as the effect of whole haplotypes on anti-HIV-1 immunity.
We thank Thomas Bielawny, Sue Ramdahin, John Rutherford, and Leslie Slaney for technical assistance; and Dr Gary Van Domselaar for the data converting program. We thank the dedicated nurses and staff who work with the Pumwani Sex Worker Cohort, Jane Njoki, Jane Kamene, Elizabeth Bwibo, Edith Amatiwa; and the women of the Pumwani cohort for their participation in this study. Dr Francis A. Plummer is a Tier I CIHR Canada Research Chair. Presented at Keystone Symposium: HIV Pathogenesis, Whistler, British Columbia, Canada, 25–30 March 2007, and XVI International AIDS Conference, Toronto, Ontario, Canada, 13–18 August 2006.
1. Carrington M, O'Brien SJ. The influence of HLA genotype on AIDS. Annu Rev Med 2003; 54:535–551.
2. Fowke KR, Nagelkerke NJ, Kimani J, Simonsen JN, Anzala AO, Bwayo JJ, et al
. Resistance to HIV-1 infection among persistently seronegative prostitutes in Nairobi, Kenya. Lancet 1996; 348:1347–1351.
3. Rowland-Jones S, Sutton J, Ariyoshi K, Dong T, Gotch F, McAdam S, et al
. HIV-specific cytotoxic T-cells in HIV-exposed but uninfected Gambian women. Nat Med 1995; 1:59–64.
4. Alimonti JB, Koesters SA, Kimani J, Matu L, Wachihi C, Plummer FA, et al
. CD4+ T cell responses in HIV-exposed seronegative women are qualitatively distinct from those in HIV-infected women. J Infect Dis 2005; 191:20–24.
5. Clerici M, Giorgi JV, Chou CC, Gudeman VK, Zack JA, Gupta P, et al
. Cell-mediated immune response to human immunodeficiency virus (HIV) type 1 in seronegative homosexual men with recent sexual exposure to HIV-1. J Infect Dis 1992; 165:1012–1019.
6. Kaul R, Rowland-Jones SL, Kimani J, Dong T, Yang HB, Kiama P, et al
. Late seroconversion in HIV-resistant Nairobi prostitutes despite preexisting HIV-specific CD8+ responses. J Clin Invest 2001; 107:341–349.
7. Kaul R, Thottingal P, Kimani J, Kiama P, Waigwa CW, Bwayo JJ, et al
. Quantitative ex vivo analysis of functional virus-specific CD8 T lymphocytes in the blood and genital tract of HIV-infected women. AIDS 2003; 17:1139–1144.
8. Kaul R, Plummer FA, Kimani J, Dong T, Kiama P, Rostron T, et al
. HIV-1-specific mucosal CD8+ lymphocyte responses in the cervix of HIV-1-resistant prostitutes in Nairobi. J Immunol 2000; 164:1602–1611.
9. Kaul R, Plummer F, Clerici M, Bomsel M, Lopalco L, Broliden K. Mucosal IgA in exposed, uninfected subjects: evidence for a role in protection against HIV infection. AIDS 2001; 15:431–432.
10. Huang Y, Paxton WA, Wolinsky SM, Neumann AU, Zhang L, He T, et al
. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat Med 1996; 2:1240–1243.
11. Smith MW, Dean M, Carrington M, Winkler C, Huttley GA, Lomb DA, et al
. Contrasting genetic influence of CCR2 and CCR5 variants on HIV-1 infection and disease progression. Hemophilia Growth and Development Study (HGDS), Multicenter AIDS Cohort Study (MACS), Multicenter Hemophilia Cohort Study (MHCS), San Francisco City Cohort (SFCC), ALIVE Study. Science 1997; 277:959–965.
12. Bird TG, Kaul R, Rostron T, Kimani J, Embree J, Dunn PP, et al
. HLA typing in a Kenyan cohort identifies novel class I alleles that restrict cytotoxic T-cell responses to local HIV-1 clades. AIDS 2002; 16:1899–1904.
13. Jeannet M, Sztajzel R, Carpentier N, Hirschel B, Tiercy JM. HLA antigens are risk factors for development of AIDS. J Acquir Immune Defic Syndr 1989; 2:28–32.
14. MacDonald KS, Fowke KR, Kimani J, Dunand VA, Nagelkerke NJ, Ball TB, et al
. Influence of HLA supertypes on susceptibility and resistance to human immunodeficiency virus type 1 infection. J Infect Dis 2000; 181:1581–1589.
15. Germain RN. MHC-dependent antigen processing and peptide presentation: providing ligands for T lymphocyte activation. Cell 1994; 76:287–299.
16. Braciale TJ, Braciale VL. Antigen presentation: structural themes and functional variations. Immunol Today 1991; 12:124–129.
17. McFarland BJ, Beeson C. Binding interactions between peptides and proteins of the class II major histocompatibility complex. Med Res Rev 2002; 22:168–203.
18. Vidales MC, Zubillaga P, Zubillaga I, Alfonso-Sanchez MA. Allele and haplotype frequencies for HLA class II (DQA1 and DQB1) loci in patients with celiac disease from Spain. Hum Immunol 2004; 65:352–358.
19. Arranz E, Telleria JJ, Sanz A, Martin JF, Alonso M, Calvo C, et al
. HLA-DQA1*0501 and DQB1*02 homozygosity and disease susceptibility in Spanish coeliac patients. Exp Clin Immunogenet 1997; 14:286–290.
20. Cintado A, Sorell L, Galvan JA, Martinez L, Castaneda C, Fragoso T, et al
. HLA DQA1*0501 and DQB1*02 in Cuban celiac patients. Hum Immunol 2006; 67:639–642.
21. Kotalova R, Vrana M, Dobrovolna M, Nevoral J, Loudova M. HLA-DRB1/DQA1/DQB1 alleles and haplotypes in Czech children with celiac sprue. Cas Lek Cesk 2002; 141:518–522.
22. Gebe JA, Swanson E, Kwok WW. HLA class II peptide-binding and autoimmunity. Tissue Antigens 2002; 59:78–87.
23. Saruhan-Direskeneli G, Esin S, Baykan-Kurt B, Ornek I, Vaughan R, Eraksoy M. HLA-DR and -DQ associations with multiple sclerosis in Turkey. Hum Immunol 1997; 55:59–65.
24. Marrosu MG, Muntoni F, Murru MR, Costa G, Congia M, Marrosu G, et al
. Role of predisposing and protective HLA-DQA and HLA-DQB alleles in Sardinian multiple sclerosis. Arch Neurol 1993; 50:256–260.
25. Van Autreve JE, Weets I, Gulbis B, Vertongen F, Gorus FK, Van der Auwera BJ. The rare HLA-DQA1*03-DQB1*02 haplotype confers susceptibility to type 1 diabetes in whites and is preferentially associated with early clinical disease onset in male subjects. Hum Immunol 2004; 65:729–736.
26. Shawkatova I, Michalkova D, Barak L, Fazekasova H, Kuba D, Buc M. HLA class II allele frequencies in type 1A diabetes mellitus Slovak patients. Bratisl Lek Listy 2006; 107:76–79.
27. Gao J, Lin Y, Qiu C, Liu Y, Ma Y, Liu Y. Association between HLA-DQA1, -DQB1 gene polymorphisms and susceptibility to asthma in northern Chinese subjects. Chin Med J (Engl) 2003; 116:1078–1082.
28. Sirikong M, Tsuchiya N, Chandanayingyong D, Bejrachandra S, Suthipinittharm P, Luangtrakool K, et al
. Association of HLA-DRB1*1502-DQB1*0501 haplotype with susceptibility to systemic lupus erythematosus in Thais. Tissue Antigens 2002; 59:113–117.
29. Davies EJ, Hillarby MC, Cooper RG, Hay EM, Green JR, Shah S, et al
. HLA-DQ, DR and complement C4 variants in systemic lupus erythematosus. Br J Rheumatol 1993; 32:870–875.
30. Skarsvag S, Hansen KE, Holst A, Moen T. Distribution of HLA class II alleles among Scandinavian patients with systemic lupus erythematosus (SLE): an increased risk of SLE among non[DRB1*03,DQA1*0501,DQB1*0201] class II homozygotes? Tissue Antigens 1992; 40:128–133.
31. Kanazawa S, Okamoto T, Peterlin BM. Tat competes with CIITA for the binding to P-TEFb and blocks the expression of MHC class II genes in HIV infection. Immunity 2000; 12:61–70.
32. Okamoto H, Asamitsu K, Nishimura H, Kamatani N, Okamoto T. Reciprocal modulation of transcriptional activities between HIV-1 Tat and MHC class II transactivator CIITA. Biochem Biophys Res Commun 2000; 279:494–499.
33. Motta P, Marinic K, Sorrentino A, Lopez R, Iliovich E. Habegger dS. Association of HLA-DQ and HLA-DR alleles with susceptibility or resistance to HIV-1 infection among the population of Chaco Province, Argentina. Medicina (B Aires) 2002; 62:245–248.
34. Ndung'u T, Gaseitsiwe S, Sepako E, Doualla-Bell F, Peter T, Kim S, et al
. Major histocompatibility complex class II (HLA-DRB and -DQB) allele frequencies in Botswana: association with human immunodeficiency virus type 1 infection. Clin Diagn Lab Immunol 2005; 12:1020–1028.
35. Achord AP, Lewis RE, Brackin MN, Henderson H, Cruse JM. HIV-1 disease association with HLA-DQ antigens in African Americans and Caucasians. Pathobiology 1996; 64:204–208.
36. Altfeld M, Rosenberg ES. The role of CD4(+) T helper cells in the cytotoxic T lymphocyte response to HIV-1. Curr Opin Immunol 2000; 12:375–380.
37. Rowland-Jones SL, Dong T, Dorrell L, Ogg G, Hansasuta P, Krausa P, et al
. Broadly cross-reactive HIV-specific cytotoxic T-lymphocytes in highly-exposed persistently seronegative donors. Immunol Lett 1999; 66(1–3):9–14.
38. Luo M, Blanchard J, Pan Y, Brunham K, Brunham RC. High-resolution sequence typing of HLA-DQA1 and -DQB1 exon 2 DNA with taxonomy-based sequence analysis (TBSA) allele assignment. Tissue Antigens 1999; 54:69–82.
39. Lancaster AK, Single RM, Solberg OD, Nelson MP, Thomson G. PyPop update - a software pipeline for large-scale multilocus population genomics. Tissue Antigens 2007; 69:192–197.
40. Hens N, Aerts M, Molenberghs G. Model selection for incomplete and design-based samples. Stat Med 2006; 25:2502–2520.
41. Plummer FA, Ball TB, Kimani J, Fowke KR. Resistance to HIV-1 infection among highly exposed sex workers in Nairobi: what mediates protection and why does it develop? Immunol Lett 1999; 66(1–3):27–34.
42. Fowke KR, Kaul R, Rosenthal KL, Oyugi J, Kimani J, Rutherford WJ, et al
. HIV-1-specific cellular immune responses among HIV-1-resistant sex workers. Immunol Cell Biol 2000; 78:586–595.
43. Kalams SA, Walker BD. The critical need for CD4 help in maintaining effective cytotoxic T lymphocyte responses. J Exp Med 1998; 188:2199–2204.
44. Roe DL, Lewis RE, Cruse JM. Association of HLA-DQ and -DR alleles with protection from or infection with HIV-1. Exp Mol Pathol 2000; 68:21–28.
45. Tang J, Penman-Aguilar A, Lobashevsky E, Allen S, Kaslow RA. HLA-DRB1 and -DQB1 alleles and haplotypes in Zambian couples and their associations with heterosexual transmission of HIV type 1. J Infect Dis 2004; 189:1696–1704.
46. Jones EY, Fugger L, Strominger JL, Siebold C. MHC class II proteins and disease: a structural perspective. Nat Rev Immunol 2006; 6:271–282.
47. Matsuki K, Grumet FC, Lin X, Gelb M, Guilleminault C, Dement WC, et al
. DQ (rather than DR) gene marks susceptibility to narcolepsy. Lancet 1992; 339:1052.
48. Fogdell A, Hillert J, Sachs C, Olerup O. The multiple sclerosis- and narcolepsy-associated HLA class II haplotype includes the DRB5*0101 allele. Tissue Antigens 1995; 46:333–336.
49. Baisch JM, Weeks T, Giles R, Hoover M, Stastny P, Capra JD. Analysis of HLA-DQ genotypes and susceptibility in insulin-dependent diabetes mellitus. N Engl J Med 1990; 322:1836–1841.
50. Todd JA, Bell JI, McDevitt HO. A molecular basis for genetic susceptibility to insulin-dependent diabetes mellitus. Trends Genet 1988; 4:129–134.
51. Yang S, Wang JY, Gao M, Liu HS, Sun LD, He PP, et al
. Association of HLA-DQA1 and DQB1 genes with vitiligo in Chinese Hans. Int J Dermatol 2005; 44:1022–1027.
52. Geng L, Wang Y, Zhai N, Lu YN, Song FJ, Chen HD. Association between pemphigus vulgaris and human leukocyte antigen in Han nation of northeast China. Chin Med Sci J 2005; 20:166–170.
53. Cinek O, Kolouskova S, Snajderova M, Sumnik Z, Sedlakova P, Drevinek P, et al
. HLA class II genetic association of type 1 diabetes mellitus in Czech children. Pediatr Diabetes 2001; 2:98–102.
54. Cavan DA, Jacobs KH, Penny MA, Kelly MA, Mijovic C, Jenkins D, et al
. Both DQA1 and DQB1 genes are implicated in HLA-associated protection from type 1 (insulin-dependent) diabetes mellitus in a British Caucasian population. Diabetologia 1993; 36:252–257.
55. Kwon OJ, Brautbar C, Weintrob N, Sprecher E, Saphirman C, Bloch K, et al
. Immunogenetics of HLA class II in Israeli Ashkenazi Jewish, Israeli non-Ashkenazi Jewish, and in Israeli Arab IDDM patients. Hum Immunol 2001; 62:85–91.
56. Kwok WW, Kovats S, Thurtle P, Nepom GT. HLA-DQ allelic polymorphisms constrain patterns of class II heterodimer formation. J Immunol 1993; 150:2263–2272.
57. Siebold C, Hansen BE, Wyer JR, Harlos K, Esnouf RE, Svejgaard A, et al
. Crystal structure of HLA-DQ0602 that protects against type 1 diabetes and confers strong susceptibility to narcolepsy. Proc Natl Acad Sci U S A 2004; 101:1999–2004.
58. Bondinas GP, Moustakas AK, Papadopoulos GK. The spectrum of HLA-DQ and HLA-DR alleles, 2006: a listing correlating sequence and structure with function. Immunogenetics 2007; 59:539–553.
59. Bordo D, Argos P. Evolution of protein cores. Constraints in point mutations as observed in globin tertiary structures. J Mol Biol 1990; 211:975–988.
60. Ogg GS, Jin X, Bonhoeffer S, Dunbar PR, Nowak MA, Monard S, et al
. Quantitation of HIV-1-specific cytotoxic T lymphocytes and plasma load of viral RNA. Science 1998; 279:2103–2106.
61. Safrit JT, Koup RA. The immunology of primary HIV infection: which immune responses control HIV replication? Curr Opin Immunol 1995; 7:456–461.