HIV control through a single nucleotide on the HLA-B locus

Journal of Virology

Volumn 86, Issue 21, 2012, Pages 11493-11500

  Kløverpris, Henrik N ^a   Harndahl, Mikkel ^b   Leslie, Alasdair J ^a   Carlson, Jonathan M ^h   Ismail, Nasreen ^c   van der Stok, Mary ^c   Gary Huang, Kuan Hsiang ^g   Chen, Fabian ^e   Riddell, Lynn ^f   Steyn, Dewald ⁱ   Goedhals, Dominique ⁱ   van Vuuren, Cloete ⁱ   Frater, John ^g   Walker, Bruce D ^c,d,j   Carrington, Mary ^d,k   Ndung'u, Thumbi ^c,d   Buus, Søren ^b   Goulder, Philip ^a,c,d  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c UNIVERSITY OF KWAZULU NATAL   (South Africa)

^d MASSACHUSETTS GENERAL HOSPITAL   (United States)

^e ROYAL BERKSHIRE HOSPITAL   (United Kingdom)

^f NORTHAMPTON GENERAL HOSPITAL   (United Kingdom)

^g UNIVERSITY OF OXFORD   (United Kingdom)

^h MICROSOFT RESEARCH   (United States)

ⁱ UNIVERSITY OF THE FREE STATE   (South Africa)

^j HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^k SAIC FREDERICK INC   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANTIRETROVIRUS AGENT; EPITOPE; GAG PROTEIN; GAMMA INTERFERON; HLA A ANTIGEN; HLA B ANTIGEN;

ALLELE; ARTICLE; COHORT ANALYSIS; CYTOTOXIC T LYMPHOCYTE; ENZYME LINKED IMMUNOSPOT ASSAY; EX VIVO STUDY; GENE LOCUS; GENE MUTATION; GENETIC VARIABILITY; HAPLOTYPE; HEREDITY; HUMAN; HUMAN CELL; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS 1 INFECTION; INFECTION CONTROL; MAJOR CLINICAL STUDY; NATURAL KILLER CELL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN EXPRESSION; PROTEIN FUNCTION; SINGLE NUCLEOTIDE POLYMORPHISM; SOUTH AFRICA; VIRUS LOAD;

ADULT; ALLELES; DISEASE RESISTANCE; HIV INFECTIONS; HIV-1; HLA-B27 ANTIGEN; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; VIRAL LOAD;

EID: 84866499912     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.01020-12     Document Type: Article

References (52)

1. Altfeld M, Goulder P. 2007. 'Unleashed' natural killers hinder HIV. Nat. Genet. 39:708-710.
2. Altman JD, et al. 1996. Phenotypic analysis of antigen-specific T lymphocytes. Science 274:94-96.
3. Archbold JK, et al. 2009. Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition. J.Exp. Med. 206:209-219.
4. Bade-Doding C, et al. 2010. The impact of human leukocyte antigen (HLA) micropolymorphism on ligand specificity within the HLA-B*41 allotypic family. Haematologicae 96:110-118.
5. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. 57: 289-300.
6. Brackenridge S, et al. 2011. An early HIV mutation within an HLA-B*57-restricted T cell epitope abrogates binding to the killer inhibitory receptor 3DL1. J. Virol. 85:5415-5422.
7. Burrows JM, et al. 2007. The impact of HLA-B micropolymorphism outside primary peptide anchor pockets on the CTL response to CMV. Eur. J. Immunol. 37:946-953.
8. Carlson J, Heckerman D, Shani G. 2009. Estimating false discovery rates for contingency tables. Microsoft, Redmond, WA.
9. Carlson JM, et al. 2012. Widespread impact of HLA restriction on immune control and escape pathways in HIV-1. J. Virol. 86:5230-5243.
10. Carrington M, Walker BD. 2012. Immunogenetics of spontaneous control of HIV. Annu. Rev. Med. 63:131-145.
11. Catano G, et al. 2008. HIV-1 disease-influencing effects associated with ZNRD1, HCP5 and HLA-C alleles are attributable mainly to either HLA A10 or HLA-B*57 alleles. PLoS One 3:e3636. doi:10.1371/journal.pone.0003636.
12. Crawford H, et al. 2007. Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. J. Virol. 81:8346-8351.
13. Erup Larsen M, et al. 2011. HLArestrictor-a tool for patient-specific predictions of HLA restriction elements and optimal epitopes within peptides. Immunogenetics 63:43-55.
14. Feeney ME, et al. 2004. Immune escape precedes breakthrough human immunodeficiency virus type 1 viremia and broadening of the cytotoxic T-lymphocyte response in an HLA-B27-positive long-termnonprogressing child. J. Virol. 78:8927-8930.
15. Fellay J, et al. 2009. Common genetic variation and the control of HIV-1 in humans. PLoS Genet. 5:e1000791. doi:10.1371/journal.pgen.1000791.
16. Fellay J, et al. 2007. A whole-genome association study of major determinants for host control of HIV-1. Science 317:944-947.
17. Flores-Villanueva PO, et al. 2001. Control of HIV-1 viremia and protection from AIDS are associated with HLA-Bw4 homozygosity. Proc. Natl. Acad. Sci. U.S.A. 98:5140-5145.
18. Gao X, et al. 2001. 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.
19. Goulder PJ, Watkins DI. 2008. Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat. Rev. Immunol. 8:619-630.
20. Green KJ, et al. 2004. Potent T cell response to a class I-binding 13-mer viral epitope and the influence ofHLAmicropolymorphism in controlling epitope length. Eur. J. Immunol. 34:2510-2519.
21. Harndahl M, et al. 2009. Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays. J. Biomol. Screen. 14:173-180.
22. Harndahl M, Rasmussen M, Roder G, Buus S. 2011. Real-time, highthroughput measurements of peptide-MHC-I dissociation using a scintillation proximity assay. J. Immunol. Methods 374:5-12.
23. Harndahl M, et al. 2012. Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity. Eur. J. Immunol. 42:1405-1416.
24. Honeyborne I, et al. 2007. Control of human immunodeficiency virus type 1 is associated with HLA-B*13 and targeting of multiple gag-specific CD8+ T-cell epitopes. J. Virol. 81:3667-3672.
25. Honeyborne I, et al. 2006. Motif inference reveals optimal CTL epitopes presented by HLA class I alleles highly prevalent in southern Africa. J. Immunol. 176:4699-4705.
26. Huang KH, et al. 2011. Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. PLoS One 6:e19018. doi:10.1371/journal.pone.0019018.
27. Jin X, et al. 2002. 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.
28. Kiepiela P, et al. 2004. Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature 432:769-775.
29. Kiepiela P, et al. 2007. CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat. Med. 13:46-53.
30. Kloverpris HN, et al. 2012. HLA-B*57 micropolymorphism shapes HLA allele-specific epitope immunogenicity, selection pressure and HIV immune control. J. Virol. 86:919-929.
31. Koehler RN, et al. 2010. Class I HLA-A*7401 is associated with protection from HIV-1 acquisition and disease progression in Mbeya, Tanzania. J. Infect. Dis. 202:1562-1566.
32. Kosmrlj A, et al. 2010. Effects of thymic selection of the T-cell repertoire on HLA class I-associated control of HIV infection. Nature 465: 350-354.
33. Kulkarni S, et al. 2011. Differential microRNA regulation of HLA-C expression and its association with HIV control. Nature 472:495-498.
34. Leslie A, et al. 2005. Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J. Exp. Med. 201:891-902.
35. Leslie A, et al. 2010. Additive contribution of HLA class I alleles in the immune control of HIV-1 infection. J. Virol. 84:9879-9888.
36. Leslie A, et al. 2006. Differential selection pressure exerted on HIV by CTL targeting identical epitopes but restricted by distinct HLA alleles from the same HLA supertype. J. Immunol. 177:4699-4708.
37. Macdonald WA, et al. 2003. A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition. J. Exp. Med. 198:679-691.
38. Marsh SGE, Parham P, Barber LD. 2000. The HLA facts book. Academic Press, London, United Kingdom.
39. Martin MP, et al. 2002. Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS. Nat. Genet. 31:429-434.
40. Martin MP, et al. 2007. Innate partnership of HLA-B and KIR3DL1 subtypes against HIV-1. Nat. Genet. 39:733-740.
41. Matthews PC, et al. 2011. HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703. J. Immunol. 186:5675-5686.
42. Matthews PC, et al. 2008. Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. J. Virol. 82: 8548-8559.
43. Mothe B, et al. 2011. Definition of the viral targets of protective HIV-1-specific T cell responses. J. Transl. Med. 9:208.
44. O'Brien SJ, Gao X, Carrington M. 2001. HLA and AIDS: a cautionary tale. Trends Mol. Med. 7:379-381.
45. Pelak K, et al. 2011. Copy number variation of KIR genes influences HIV-1 control. PLoS Biol. 9:e1001208. doi:10.1371/journal.pbio.1001208.
46. Pereyra F, et al. 2010. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 330:1551-1557.
47. Rapin N, Hoof I, Lund O, Nielsen M. 2008. MHC motif viewer. Immunogenetics 60:759-765.
48. Rousseau CM, et al. 2006. Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes. J. Virol. Methods 136:118-125.
49. Smith KD, Epperson DF, Lutz CT. 1996. Alloreactive cytotoxic T-lymphocyte defined HLA-B7 subtypes differ in peptide antigen presentation. Immunogenetics 43:27-37.
50. Stryhn A, et al. 1996. Peptide binding specificity of major histocompatibility complex class I resolved into an array of apparently independent subspecificities: quantitation by peptide libraries and improved prediction of binding. Eur. J. Immunol. 26:1911-1918.
51. Thomas R, et al. 2009. HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C. Nat. Genet. 41:1290-1294.
52. Zernich D, et al. 2004. Natural HLA class I polymorphism controls thepathway of antigen presentation and susceptibility to viral evasion. J. Exp.Med. 200:13-24.