Human leukocyte antigen-DQ alleles and haplotypes and their associations with resistance and susceptibility to HIV-1 infection
Hardie, Rae-Annea; Luo, Maa; Bruneau, Brigitteb; Knight, Erinb; Nagelkerke, Nico JDc; Kimani, Joshuad; Wachihi, Charlese; Ngugi, Elizabeth Ne; Plummer, Francis Aa,b,d
From the aDepartment of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
bPublic Health Agency of Canada
cDepartment of Community Medicine, United Arab Emirates University, Al-Ain, United Arab Emirates
dDepartment of Medical Microbiology, Kenya
eDepartment of Community Health, University of Nairobi, Nairobi, Kenya.
Correspondence to Dr Ma Luo, Medical Microbiology, Room 507, Basic Medical Sciences Building, 730 William Avenue, Winnipeg, Manitoba, MB R3E 0W3, Canada. Tel: +1 204 789 5072; fax: +1 204 789 3926; e-mail: email@example.com
Objectives: To determine the association of DQ antigens with resistance and susceptibility to HIV-1.
Design: Despite repeated exposure to HIV-1, a subset of women in the Pumwani Sex Worker cohort established in Nairobi, Kenya in 1985 have remained HIV-1 negative for at least 3 years and are classified as resistant. Differential susceptibility to HIV-1 infection is associated with HIV-1 specific CD4+ and CD8+ T cell responses. As human leukocyte antigen-DQ antigens present viral peptides to CD4+ cells, we genotyped human leukocyte antigen -DQ alleles for 978 women enrolled in the cohort and performed cross-sectional and longitudinal analyses to identify associations of human leukocyte antigen -DQ with resistance/susceptibility to HIV-1.
Methods: DQA1 and DQB1 were genotyped using taxonomy-based sequence analysis. SPSS 13.0 was used to determine associations of DQ alleles/haplotypes with HIV-1 resistance, susceptibility, and seroconversion rates.
Results: Several DQB1 alleles and DQ haplotypes were associated with resistance to HIV-1 infection. These included DQB1*050301 (P = 0.055, Odds Ratio = 12.77, 95% Confidence Interval = 1.44–112), DQB1*0603 and DQB1*0609 (P = 0.037, Odds Ratio = 3.25, 95% Confidence Interval = 1.12–9.47), and DQA1*010201–DQB1*0603 (P = 0.044, Odds Ratio = 17.33, 95% Confidence Interval = 1.79–168). Conversely, DQB1*0602 (P = 0.048, Odds Ratio = 0.68, 95% Confidence Interval = 0.44–1.05) and DQA1*010201–DQB1*0602 (P = 0.039, Odds Ratio = 0.64, 95% Confidence Interval = 0.41–1.03) were overrepresented in the HIV-1 infected population. DQA1*0504-DQB1*0201, DQA1*010201–DQB1*0201, DQA1*0402-DQB1*0402 and DQA1*0402-DQB1*030101 genotypes were only found in HIV-1 positive subjects (Odds Ratio = 0.30-0.31, 95% Confidence Interval = 0.03–3.70), and these women seroconverted rapidly. The associations of these DQ alleles and haplotypes with resistance and susceptibility to HIV-1 were independent of the previously reported human leukocyte antigen-DRB*01, human leukocyte antigen A2/6802, and human leukocyte antigen-A*2301.
Conclusion: The associations of DQ alleles and haplotypes with resistance and susceptibility to HIV-1 emphasize the importance of human leukocyte antigen-DQ and CD4 in anti-HIV-1 immunity.
The global impact of HIV-1/AIDS is enormous, with 25 million deaths due to HIV-1/AIDS since it was first recognized in 1981 (www.unaids.org/en/knowledge centre/HIV Data/EpiUpdate/EpUpdArchive/2006). Sub-Saharan Africa has only 10% of the world's total population, but 67% of all people living with HIV-1/AIDS (www.unaids.org/en/knowledge centre/HIV Data/EpiUpdate/EpUpdArchive/2006). Unfortunately, this is also one of the world's poorest regions, and many people have no access to quality healthcare (www.unaids.org/en/knowledge centre/HIV Data/EpiUpdate/EpUpdArchive/2006). Although effective prevention programs have been developed, they have not been implemented at a large scale and the best hope of ending this pandemic is an effective vaccine. To achieve this, we need a better understanding of protective immunity against HIV-1.
Not every individual exposed to HIV-1 becomes infected with the virus. This variability in susceptibility to HIV-1 infection and disease has been documented in several cohort studies [1,2] and can be attributed to both host  and viral factors. Host factors that are correlated with susceptibility to infection and disease progression include HIV-specific CD8+ and CD4+ T-cell responses [3–7], mucosal immunity [8,9], chemokine receptor polymorphisms [10,11], and human leukocyte antigens (HLA) [1,12–14]. Polymorphisms in genes influencing the immune response to HIV-1 may account for the variation in susceptibility to HIV-1 infection between individuals with similar risk of exposure.
The HLA complex, located on the short arm of chromosome 6, is the most polymorphic system in the human genome. It is fundamental in the immune system's response to infectious agents, as HLA class I and II molecules restrict presentation of antigenic peptides to CD8+ and CD4+ T cells, respectively . HLA class II molecules are expressed on professional antigen presenting cells (APCs) and present exogenously derived epitopes to CD4+ helper T cells, which are important in antibody and cytokine production, help CD8+ mediated response, and are involved in other immune responses . Previous studies have shown that individuals may differ in their immune responses to HIV-1 due to differences in their HLA alleles, ability to present antigen to CD4+ T cells [12,14].
HLA-DQ consists of variable α and β chains that form membrane-anchored heterodimers. The DQ heterodimers form a nine pocket peptide binding cleft that opens at the ends to allow binding of peptides of various lengths . The combinations of DQ α1 (DQA1) and DQ β1 (DQB1) determine the DQ molecule's specificity and diversity for antigen presentation. This specificity is essential in distinguishing self and nonself antigens, making HLA-DQ an important determinant in transplant compatibility. In addition, DQ antigens have been associated with many autoimmune disorders such as celiac disease [18–21], multiple sclerosis (MS) [22–24], type 1 diabetes mellitus [25,26], asthma , and systemic lupus erythematosus (SLE) [28–30]. However, the roles of DQ alleles in infectious diseases have been less well studied. Given the significance of HLA class II in CD4+ immunity and its down regulation by HIV-1 Tat protein [31,32], the potential importance of DQ genes in the susceptibility to HIV-1 infection should not be ignored. HLA-DQ has been reported to correlate with susceptibility to HIV-1 infection and disease in several small cohort studies [33–35].
In this study, we investigated the role of DQ genes in the differential susceptibility to HIV-1 infection observed in Pumwani Sex Worker cohort in Nairobi, Kenya. A subgroup of women in this cohort remains seronegative and PCR negative to HIV-1, despite heavy exposure to HIV-1 infection through active sex work . As HIV-1 specific CD4+ T cell response is associated with relative resistance to HIV-1 infection [4,36,37], identifying DQ antigens and elucidating their roles in resistance/susceptibility to HIV-1 infection in the Pumwani cohort may contribute to the development of effective vaccines.
Materials and methods
The Pumwani Sex Worker cohort was established in Nairobi, Kenya in 1985. The present study was conducted among 978 women enrolled between 1985–2005. The overall HIV infection rate in the Pumwani cohort is greater than 70%. Women were classified as HIV-1 resistant if they remained HIV seronegative, PCR negative for at least 3 years while continuing active sex work, and were negative at the time of this study. The women classified as resistant in this study were all enrolled in the cohort before 1999 with an average follow-up time of 9.6 +/− 4.3 years. There were 978 women typed in this study. Some of the individuals were either new enrollees or their follow-up time was not long enough to meet the criteria for resistance. These individuals were excluded for comparisons between HIV-positive (susceptible) and HIV-resistant women (serology and PCR negative for at least 3 years, and negative at the time of study) in the analysis. The number of women typed differed slightly between the DQA1 (956) and DQB1 (978) groups due to a lack of high-quality DNA. This study has been approved by the Ethics Committee of the University of Manitoba and the Ethics and Research Committee of Kenyatta National Hospital, and informed consent was obtained from all women.
DNA was extracted from whole blood, buffy coat, B-cells and peripheral blood mononuclear cells (PBMC) using QIAmp DNA Mini Kit (QIAgen Inc., Mississauga, Ontario, Canada). The DNA was quantified by standard ultraviolet spectrophotometric analysis.
PCR amplification and sequencing DQ genes
PCR amplification of exon 2 of DQA1 and DQB1 followed the methods of Luo et al. . Five μl of PCR reaction was visualized on a 1.5% agarose gel stained with ethidium bromide to check for amplification of the correctly sized PCR products. The remaining PCR products were then purified using a MultiScreen HTS PCR filter plate (Millipore, Bedford, Massachussetts, USA) and vacuum apparatus. The purified PCR products were sequenced with BigDye cycle sequencing kits (Applied Biosystems, Foster City, California, USA) and analyzed using an ABI3100 Prism Genetic Analyzer.
Genotyping software CodonExpress based on a taxonomy-based sequence analysis  was used to genotype HLA-DQA1 and DQB1 genes. Since only exon 2 of DQA1 and DQB1 is involved in forming the peptide binding cleft and is the most polymorphic region of both genes, DQA1 and DQB1 were typed using exon 2 sequences only. When allele differences were in exons other than exon 2, we simplified the allele name expression, for example, DQA1*010101 includes DQA1*010101 or DQA1*010102. Quality control of the typing results was performed using Sequencher (Gene Codes Corporation).
Analyses were performed with SPSS 13.0 for Windows statistical analysis software package. Python for Populations (PyPop) 32-0.6.0 software for population genetics  was used to estimate HLA class II allele and haplotype frequencies, as well as Hardy–Weinberg equilibrium. The probability of being HLA typed may depend on HIV status and duration of follow up. Since we have not retained blood samples from all women enrolled during the first few years of the project, we carried out a sensitivity analysis that adjusted for this effects, using sampling weights based on the Hurvitz-Thompson theory . In this analysis the probability of being HLA typed was estimated using logistic regression with follow-up and HIV status as covariables and the inverse of this probability for each woman, after standardization, was used as a sample weight. The standard univariate Fisher's exact test (P value, odds ratio, confidence interval 95% [(Hutchon JR. http://www.hutchon.net/ConfidOR.htm. (Accessed 2007)] was utilized to determine the relationship between binary outcomes and explanatory variables. Kaplan–Meier plots with log rank tests were used to examine seroconversion rates. Only women enrolled before 2001 were included in the survival analysis. Multivariate binary logistic regression analyses were performed to determine potential linkage with the HLA alleles that were previously reported to associate with HIV-1 resistance or susceptibility .
Major DQA1 and DQB1 allele and haplotype frequencies in the Pumwani cohort
Sixteen DQA1 alleles were identified in the Pumwani cohort. The most common DQA1 alleles in the cohort were DQA1*010201 (31%), DQA1*050101 (22.6%), and DQA1*010101 (16.5%). These three DQA1 alleles account for 70% of all DQA1 alleles in the cohort. The DQA1 allele/genotype frequencies closely matched those expected for Hardy–Weinberg equilibrium with the exception of lower than expected heterozygotes for DQA1*010201 (P = 0.003) and DQA1*0402 (P = 0.048), as well as lower than expected frequencies for genotypes DQA1*010101–010201 (P = 0.045) and DQA1*010201–050101 (P = 0.027). Higher than expected homozygosity for DQA1*010201 was also observed (P = 0.002).
Although 37 DQB1 alleles were identified in the Pumwani cohort, the major DQB1 alleles in the cohort were DQB1*030101 (20.68%), DQB1*0602 (17.20%), DQB1*0201 (16.07%) and DQB1*050101 (16.17%). These four alleles account for 70% of all DQB1 alleles in the Pumwani cohort. The DQB1 allele and genotype frequencies matched those expected for Hardy–Weinberg equilibrium with the exception of lower than expected frequencies for DQB1*030101 heterozygotes (P = 0.032), genotypes DQB1*0201/030101 (P = 0.036) and DQB1*0602/0603 (P = 0.030). Higher than expected frequencies were observed for genotypes DQB1*0201/0402 (P = 0.012) and DQB1*030101 homozygotes (P = 0.003).
For alleles that did not match Hardy–Weinberg expected values, several checks were performed to exclude sources of error. All sequences were retyped, and confirmed with the original typing, thereby ruling out typing errors. We also examined the possibility of allele dropout, or uneven amplification of the two alleles due to quality/quantity of DNA, especially in cases where homozygote frequency was higher than expected. We also ruled this out as a source of error, due to the presence of polymorphisms in the intron regions of the samples. As the typing was found to be accurate, other factors might contribute to the deviations from Hardy–Weinberg equilibrium including nonrandom mating, selection by other diseases, migration, or the Wahlund effect.
The DQA1 and DQB1 heterodimers form a binding pocket that determines the specificity of the DQ molecule in antigen presentation. Therefore, the DQA1-DQB1 haplotype describes the full repertoire of antigen presentations by the DQA1 and DQB1 molecules in combination. Using PyPop 32-0.6.0, we estimated 216 distinct DQA1-DQB1 haplotypes in the Pumwani cohort. The most common DQ haplotypes were DQA1*010201-DQB1*0602 (13.56%), DQA1*010101-DQB1*050101 (13.28%), and DQA1*050101-DQB1*030101 (13.03%). These three major haplotypes accounted for almost 40% of all DQ haplotypes in the Pumwani cohort.
We compared DQA1 and DQB1 allele frequencies of the Pumwani cohort with those of other sub-Saharan African populations and observed very similar frequency distributions (data not shown) [http://www.ncbi.nlm.nih.gov/projects/mhc/ihwg.cgi. (Accessed 2006)].
Distributions of DQA1 and DQB1 alleles and haplotypes in HIV-1 resistant and infected women in the Pumwani cohort
We compared frequencies of DQA1 and DQB1 alleles and DQ haplotypes of HIV-1 resistant women with those of HIV-1 infected women in the cohort. We did not observe significant differences in DQA1 allele frequency distributions between HIV-1 resistant and HIV-1 positive women except that DQA1*0402 was only observed in the HIV-1 positive women (Table 1). Several significant differences in DQB1 allele frequency distributions were observed between HIV-1 resistant women and HIV-1 positive women (Table 1). The frequencies of DQB1*0609, DQB1*0603 and DQB1*050301 were significantly higher in HIV-1 resistant women than in HIV-1 positive women (P = 0.047, P = 0.039 and P = 0.055, respectively), whereas significantly higher frequencies of DQB1*0602 were observed in HIV-1 positive women (P = 0.036) (Table 1). We also observed that the frequencies of several DQA1-DQB1 haplotypes containing these differentially distributed DQB1 alleles were also significantly different between the HIV-1 resistant women and the HIV-1 positive group (Table 2). The frequency of DQA1*010201-DQB1*0603 haplotype was significantly higher in the HIV-1 resistant group (P = 0.044), whereas that of DQA1*010201-DQB1*0602 was significantly higher in the HIV-1 positive group (P = 0.024) (Table 2). Several haplotypes were only observed in the HIV-1 positive group including DQA1*0504-DQB1*0201, DQA1*010201-DQB1*0201, DQA1*0402-DQB1*0402 and DQA1*0402-DQB1*030101 (Table 2). These results are exploratory, and further studies should be carried out to verify these findings.
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).
Associations of DQ genotypes with resistance/susceptibility to HIV-1 infection
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.
DQ haplotypes with differential susceptibility to HIV-1 infection are independent of previously reported associations
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).
Many host factors are involved in natural resistance to HIV-1 [1–14,41,42]. Our study shows that HLA-DQ, a key factor in CD4+ T cell activation, is important in the protective immunity to HIV-1 infection in the highly exposed but uninfected female sex workers in the Pumwani cohort, providing further evidence that CD4+ T-helper cells play an integral role in HIV-1 infection and immunity [37,43].
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.
The DQ molecule's peptide binding groove presents peptides to CD4+ T cells, imparting its role in self-tolerance and adaptive response to pathogens . The αβ pairing at the DQ locus depends on polymorphisms in the allelic regions α44-53 and β85-90 [56–58]. Important amino acid residues have been identified in the HLA-DQ domains . Analysis of the protein products encoded by HLA will help elucidate why certain alleles associate with differential HIV-1 susceptibility. The associations of two DQ haplotypes, DQA1*010201-DQB1*0602 and DQA1*010201-DQB1*0603 with different outcomes of HIV-1 infection could be due to the amino acid differences between DQB1*0602 and DQB1*0603 as the two different DQB1 alleles pair with the same DQA1 alleles. DQB1*0602 and DQB1*0603 have differences at several important residues. At residue 9 on β strand 1, presumed to contact peptide pocket 9 , DQB1*0602 encoded Phe, whereas DQB1*0603 encoded Tyr. Although these amino acids are conserved substitutions , they may still convey some functional or structural differences in the DQ molecule. At residue 30 on β strand 2, presumed to contact peptide pocket 6 and hydrogen bonds to the peptide , DQB1*0602 encoded Val whereas DQB1*0603 encoded His. These amino acids are nonconserved substitutions , which may have functional consequences on the antigen presentation of the DQ molecule. DQB1*0602 and DQB1*0609, which are also associated with different outcomes of HIV-1 infection in the Pumwani cohort, also differed at residue 9, with DQB1*0609 encoding Tyr. Residue 57 on the helix is presumed to contact peptide pocket 9 and hydrogen bonds to the peptide . At this residue, DQB1*0602 encoded Asp whereas DQB*0609 encoded Val. Residue 70, which is on the helix and may contact peptide pocket 4 and the T-cell receptor , encodes Gly for DQB1*0602 and Arg for DQB1*0609. The differences at residues 57 and 70 are nonconserved substitutions  and may have significant effects on peptide binding. It will be important to determine the epitopes of these DQ haplotypes and subsequent immune responses after the differential antigen presentation by DQ haplotypes that are associated with resistance/susceptibility to HIV-1 infection.
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.
Sponsorship: This study was supported by a grant from the Bill and Melinda Gates Foundation and the Canadian Institutes of Health Research (HOP-43135) through the Grand Challenges in Global Health Initiative. This study was also supported through a grant from the NIH (R01 AI56980).
Conflict of interest: None.
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.
This article has been cited 10 time(s).
Plos OneA Small Set of Succinct Signature Patterns Distinguishes Chinese and Non-Chinese HIV-1 GenomesPlos One
Infection Genetics and EvolutionHLA-DQB1 and-DPB1 allele profile in HIV infected patients with and without pulmonary tuberculosis of south IndiaInfection Genetics and Evolution
ImmunogeneticsMhc haplotype H6 is associated with sustained control of SIVmac251 infection in Mauritian cynomolgus macaquesImmunogenetics
Canadian Medical Association JournalCorrelates of severe disease in patients with 2009 pandemic influenza (H1N1) virus infectionCanadian Medical Association Journal
Personalized MedicinePersonalizing antiretroviral therapy: is it a reality?Personalized Medicine
Human ImmunologyHLA-G and mother-child perinatal HIV transmissionHuman Immunology
Tissue AntigensHLA class I associations with rates of HIV-1 seroconversion and disease progression in the Pumwani Sex Worker CohortTissue Antigens
Expert Review of Clinical ImmunologyThe genetic basis of resistance to HIV infection and disease progressionExpert Review of Clinical Immunology
disease association; disease resistance; DNA sequence analysis; HIV-1; human leukocyte antigen-DQA1; human leukocyte antigen-DQB1; sex workers
© 2008 Lippincott Williams & Wilkins, Inc.
What does "Remember me" mean?
By checking this box, you'll stay logged in until you logout. You'll get easier access to your articles, collections,
media, and all your other content, even if you close your browser or shut down your
To protect your most sensitive data and activities (like changing your password),
we'll ask you to re-enter your password when you access these services.
What if I'm on a computer that I share with others?
If you're using a public computer or you share this computer with others, we recommend
that you uncheck the "Remember me" box.
Highlight selected keywords in the article text.
Data is temporarily unavailable. Please try again soon.