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Host Genetics and HIV-1: The Final Phase?


This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches (siRNA screens, transcriptome or proteome analysis, comparative genomics) have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.


Vyšlo v časopise: Host Genetics and HIV-1: The Final Phase?. PLoS Pathog 6(10): e32767. doi:10.1371/journal.ppat.1001033
Kategorie: Review
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1001033

Souhrn

This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches (siRNA screens, transcriptome or proteome analysis, comparative genomics) have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.


Zdroje

1. KronerBL

RosenbergPS

AledortLM

AlvordWG

GoedertJJ

1994 HIV-1 infection incidence among persons with hemophilia in the United States and western Europe, 1978–1990. Multicenter Hemophilia Cohort Study. J Acquir Immune Defic Syndr 7 279 286

2. KulkarniPS

ButeraST

DuerrAC

2003 Resistance to HIV-1 infection: lessons learned from studies of highly exposed persistently seronegative (HEPS) individuals. AIDS Rev 5 87 103

3. FellayJ

ShiannaKV

GeD

ColomboS

LedergerberB

2007 A whole-genome association study of major determinants for host control of HIV-1. Science 317 944 947

4. LimouS

Le ClercS

CoulongesC

CarpentierW

DinaC

2009 Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). J Infect Dis 199 419 426

5. DalmassoC

CarpentierW

MeyerL

RouziouxC

GoujardC

2008 Distinct genetic loci control plasma HIV-RNA and cellular HIV-DNA levels in HIV-1 infection: the ANRS Genome Wide Association 01 study. PLoS ONE 3 e3907 doi:10.1371/journal.pone.0003907

6. Le ClercS

LimouS

CoulongesCd

CarpentierW

DinaC

2009 Genomewide association study of a rapid progression cohort identifies new susceptibility alleles for AIDS (ANRS Genomewide Association Study 03). J Infect Dis 200 1194 1201

7. FellayJ

GeD

ShiannaKV

ColomboS

LedergerberB

2009 Common genetic variation and the control of HIV-1 in humans. PLoS Genet 5 e1000791 doi:10.1371/journal.pgen.1000791

8. HerbeckJT

GottliebGS

WinklerCA

NelsonGW

AnP

2010 Multistage Genomewide Association Study Identifies a Locus at 1q41 Associated with Rate of HIV-1 Disease Progression to Clinical AIDS. J Infect Dis 201 618 626

9. PelakK

GoldsteinDB

WalleyNM

FellayJ

GeD

2010 Host determinants of HIV-1 control in African Americans. J Infect Dis 201 1141 1149

10. DetelsR

LiuZ

HennesseyK

KanJ

VisscherBR

1994 Resistance to HIV-1 infection. Multicenter AIDS Cohort Study. J Acquir Immune Defic Syndr 7 1263 1269

11. FowkeKR

NagelkerkeNJ

KimaniJ

SimonsenJN

AnzalaAO

1996 Resistance to HIV-1 infection among persistently seronegative prostitutes in Nairobi, Kenya. Lancet 348 1347 1351

12. MellorsJW

RinaldoCRJr

GuptaP

WhiteRM

ToddJA

1996 Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272 1167 1170

13. GeD

FellayJ

ThompsonAJ

SimonJS

ShiannaKV

2009 Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 461 399 401

14. FellayJ

ThompsonAJ

GeD

GumbsCE

UrbanTJ

2010 ITPA gene variants protect against anaemia in patients treated for chronic hepatitis C. Nature 464 405 408

15. GoulderPJ

WatkinsDI

2008 Impact of MHC class I diversity on immune control of immunodeficiency virus replication. Nat Rev Immunol 8 619 630

16. CarringtonM

NelsonGW

MartinMP

KissnerT

VlahovD

1999 HLA and HIV-1: heterozygote advantage and B*35-Cw*04 disadvantage. Science 283 1748 1752

17. GoulderPJ

BranderC

TangY

TremblayC

ColbertRA

2001 Evolution and transmission of stable CTL escape mutations in HIV infection. Nature 412 334 338

18. KiepielaP

LeslieAJ

HoneyborneI

RamduthD

ThobakgaleC

2004 Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature 432 769 775

19. KawashimaY

PfafferottK

FraterJ

MatthewsP

PayneR

2009 Adaptation of HIV-1 to human leukocyte antigen class I. Nature 458 641 645

20. CarringtonM

MartinMP

van BergenJ

2008 KIR-HLA intercourse in HIV disease. Trends Microbiol 16 620 627

21. ThomasR

AppsR

QiY

GaoX

MaleV

2009 HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C. Nat Genet 41 1290 1294

22. FellayJ

2009 Host genetics influences on HIV type-1 disease. Antivir Ther 14 731 738

23. DeanM

CarringtonM

WinklerC

HuttleyGA

SmithMW

1996 Genetic restriction of HIV-1 infection and progression to AIDS by a deletion allele of the CKR5 structural gene. Hemophilia Growth and Development Study, Multicenter AIDS Cohort Study, Multicenter Hemophilia Cohort Study, San Francisco City Cohort, ALIVE Study. Science 273 1856 1862

24. HuangY

PaxtonWA

WolinskySM

NeumannAU

ZhangL

1996 The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat Med 2 1240 1243

25. MartinMP

DeanM

SmithMW

WinklerC

GerrardB

1998 Genetic acceleration of AIDS progression by a promoter variant of CCR5. Science 282 1907 1911

26. MummidiS

AhujaSS

GonzalezE

AndersonSA

SantiagoEN

1998 Genealogy of the CCR5 locus and chemokine system gene variants associated with altered rates of HIV-1 disease progression. Nat Med 4 786 793

27. SmithMW

DeanM

CarringtonM

WinklerC

HuttleyGA

1997 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 277 959 965

28. IoannidisJP

RosenbergPS

GoedertJJ

AshtonLJ

BenfieldTL

2001 Effects of CCR5-Delta32, CCR2-64I, and SDF-1 3'A alleles on HIV-1 disease progression: an international meta-analysis of individual-patient data. Ann Intern Med 135 782 795

29. LiuR

PaxtonWA

ChoeS

CeradiniD

MartinSR

1996 Homozygous defect in HIV-1 coreceptor accounts for resistance of some multiply-exposed individuals to HIV-1 infection. Cell 86 367 377

30. SamsonM

LibertF

DoranzBJ

RuckerJ

LiesnardC

1996 Resistance to HIV-1 infection in caucasian individuals bearing mutant alleles of the CCR-5 chemokine receptor gene. Nature 382 722 725

31. QuillentC

OberlinE

BraunJ

RoussetD

Gonzalez-CanaliG

1998 HIV-1-resistance phenotype conferred by combination of two separate inherited mutations of CCR5 gene. Lancet 351 14 18

32. SheppardHW

CelumC

MichaelNL

O'BrienS

DeanM

2002 HIV-1 infection in individuals with the CCR5-Delta32/Delta32 genotype: acquisition of syncytium-inducing virus at seroconversion. J Acquir Immune Defic Syndr 29 307 313

33. GonzalezE

KulkarniH

BolivarH

ManganoA

SanchezR

2005 The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility. Science 307 1434 1440

34. UrbanTJ

WeintrobAC

FellayJ

ColomboS

ShiannaKV

2009 CCL3L1 and HIV/AIDS susceptibility. Nat Med 15 1110 1112

35. BhattacharyaT

StantonJ

KimEY

KunstmanKJ

PhairJP

2009 CCL3L1 and HIV/AIDS susceptibility. Nat Med 15 1112 1115

36. HeW

NeilS

KulkarniH

WrightE

AganBK

2008 Duffy antigen receptor for chemokines mediates trans-infection of HIV-1 from red blood cells to target cells and affects HIV-AIDS susceptibility. Cell Host Microbe 4 52 62

37. WalleyNM

JulgB

DicksonSP

FellayJ

GeD

2009 The Duffy antigen receptor for chemokines null promoter variant does not influence HIV-1 acquisition or disease progression. Cell Host Microbe 5 408 410; author reply 418–409

38. JulgB

ReddyS

van der StokM

KulkarniS

QiY

2009 Lack of Duffy antigen receptor for chemokines: no influence on HIV disease progression in an African treatment-naive population. Cell Host Microbe 5 413 415; author reply 418–419

39. HorneKC

LiX

JacobsonLP

PalellaF

JamiesonBD

2009 Duffy antigen polymorphisms do not alter progression of HIV in African Americans in the MACS cohort. Cell Host Microbe 5 415 417; author reply 418–419

40. WinklerCA

AnP

JohnsonR

NelsonGW

KirkG

2009 Expression of Duffy antigen receptor for chemokines (DARC) has no effect on HIV-1 acquisition or progression to AIDS in African Americans. Cell Host Microbe 5 411 413; author reply 418–419

41. SmithDM

RichmanDD

LittleSJ

2005 HIV superinfection. J Infect Dis 192 438 444

42. TangJ

TangS

LobashevskyE

ZuluI

AldrovandiG

2004 HLA allele sharing and HIV type 1 viremia in seroconverting Zambians with known transmitting partners. AIDS Res Hum Retroviruses 20 19 25

43. KannangaraS

DeSimoneJA

PomerantzRJ

2005 Attenuation of HIV-1 infection by other microbial agents. J Infect Dis 192 1003 1009

44. ManolioTA

CollinsFS

CoxNJ

GoldsteinDB

HindorffLA

2009 Finding the missing heritability of complex diseases. Nature 461 747 753

45. WilkinsonDA

OperskalskiEA

BuschMP

MosleyJW

KoupRA

1998 A 32-bp deletion within the CCR5 locus protects against transmission of parenterally acquired human immunodeficiency virus but does not affect progression to AIDS-defining illness. J Infect Dis 178 1163 1166

46. ZhangM

GoedertJJ

O'BrienTR

2003 High frequency of CCR5-delta32 homozygosity in HCV-infected, HIV-1-uninfected hemophiliacs results from resistance to HIV-1. Gastroenterology 124 867 868

47. KupferB

KaiserR

BrackmannHH

EffenbergerW

RockstrohJK

1999 Protection against parenteral HIV-1 infection by homozygous deletion in the C-C chemokine receptor 5 gene. AIDS 13 1025 1028

48. CirulliET

GoldsteinDB

2010 Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11 415 425

49. ChoiM

SchollUI

JiW

LiuT

TikhonovaIR

2009 Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proc Natl Acad Sci U S A 106 19096 19101

50. NgSB

TurnerEH

RobertsonPD

FlygareSD

BighamAW

2009 Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461 272 276

51. NgSB

BuckinghamKJ

LeeC

BighamAW

TaborHK

2009 Exome sequencing identifies the cause of a mendelian disorder. Nat Genet 42 30 35

52. PaiardiniM

PandreaI

ApetreiC

SilvestriG

2009 Lessons learned from the natural hosts of HIV-related viruses. Annu Rev Med 60 485 495

53. BrenchleyJM

PriceDA

SchackerTW

AsherTE

SilvestriG

2006 Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nat Med 12 1365 1371

54. BushmanFD

MalaniN

FernandesJ

D'OrsoI

CagneyG

2009 Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog 5 e1000437 doi:10.1371/journal.ppat.1000437

55. TelentiA

2009 HIV-1 host interactions - integration of large scale datasets. F1000 Biology Reports 1 71

56. SedaghatAR

GermanJ

TeslovichTM

CofrancescoJJr

JieCC

2008 Chronic CD4+ T-cell activation and depletion in human immunodeficiency virus type 1 infection: type I interferon-mediated disruption of T-cell dynamics. J Virol 82 1870 1883

57. HyrczaMD

KovacsC

LoutfyM

HalpennyR

HeislerL

2007 Distinct transcriptional profiles in ex vivo CD4+ and CD8+ T cells are established early in human immunodeficiency virus type 1 infection and are characterized by a chronic interferon response as well as extensive transcriptional changes in CD8+ T cells. J Virol 81 3477 3486

58. GiriMS

NebozyhnM

RaymondA

GekongeB

HancockA

2009 Circulating monocytes in HIV-1-infected viremic subjects exhibit an antiapoptosis gene signature and virus- and host-mediated apoptosis resistance. J Immunol 182 4459 4470

59. RotgerM

DangKK

FellayJ

HeinzenEL

FengS

2010 Genome-wide mRNA expression correlates of viral control in CD4+ T-cells from HIV-1-infected individuals. PLoS Pathog 6 e1000781 doi:10.1371/journal.ppat.1000781

60. GiriMS

NebozhynM

ShoweL

MontanerLJ

2006 Microarray data on gene modulation by HIV-1 in immune cells: 2000–2006. J Leukoc Biol 80 1031 1043

61. MandlJN

BarryAP

VanderfordTH

KozyrN

ChavanR

2008 Divergent TLR7 and TLR9 signaling and type I interferon production distinguish pathogenic and nonpathogenic AIDS virus infections. Nat Med 14 1077 1087

62. LedererS

FavreD

WaltersKA

ProllS

KanwarB

2009 Transcriptional profiling in pathogenic and non-pathogenic SIV infections reveals significant distinctions in kinetics and tissue compartmentalization. PLoS Pathog 5 e1000296 doi:10.1371/journal.ppat.1000296

63. BosingerSE

LiQ

GordonSN

KlattNR

DuanL

2009 Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys. J Clin Invest 119 3556 3572

64. JacquelinB

MayauV

TargatB

LiovatAS

KunkelD

2009 Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response. J Clin Invest 119 3544 3555

65. WangZ

GersteinM

SnyderM

2009 RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10 57 63

66. TangF

BarbacioruC

WangY

NordmanE

LeeC

2009 mRNA-Seq whole-transcriptome analysis of a single cell. Nat Meth 6 377 382

67. RingroseJH

JeeningaRE

BerkhoutB

SpeijerD

2008 Proteomic studies reveal coordinated changes in T-cell expression patterns upon infection with human immunodeficiency virus type 1. J Virol 82 4320 4330

68. ChanEY

QianWJ

DiamondDL

LiuT

GritsenkoMA

2007 Quantitative analysis of human immunodeficiency virus type 1-infected CD4+ cell proteome: dysregulated cell cycle progression and nuclear transport coincide with robust virus production. J Virol 81 7571 7583

69. FuW

Sanders-BeerBE

KatzKS

MaglottDR

PruittKD

2009 Human immunodeficiency virus type 1, human protein interaction database at NCBI. Nucleic Acids Res 37 D417 D422

70. DriscollT

DyerMD

MuraliTM

SobralBW

2009 PIG–the pathogen interaction gateway. Nucl Acids Res 37 D647 D650

71. DyerMD

MuraliTM

SobralBW

2008 The landscape of human proteins interacting with viruses and other pathogens. PLoS Pathog 4 e32 doi:10.1371/journal.ppat.0040032

72. BrassAL

DykxhoornDM

BenitaY

YanN

EngelmanA

2008 Identification of host proteins required for HIV infection through a functional genomic screen. Science 319 921 926

73. KonigR

ZhouY

EllederD

DiamondTL

BonamyGM

2008 Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 135 49 60

74. ZhouH

XuM

HuangQ

GatesAT

ZhangXD

2008 Genome-scale RNAi screen for host factors required for HIV replication. Cell Host Microbe 4 495 504

75. YeungML

HouzetL

YedavalliVS

JeangKT

2009 A genome-wide short hairpin RNA screening of jurkat T-cells for human proteins contributing to productive HIV-1 replication. J Biol Chem 284 19463 19473

76. NguyenDG

YinH

ZhouY

WolffKC

KuhenKL

2007 Identification of novel therapeutic targets for HIV infection through functional genomic cDNA screening. Virology 362 16 25

77. SabetiPC

SchaffnerSF

FryB

LohmuellerJ

VarillyP

2006 Positive natural selection in the human lineage. Science 312 1614 1620

78. SabetiPC

VarillyP

FryB

LohmuellerJ

HostetterE

2007 Genome-wide detection and characterization of positive selection in human populations. Nature 449 913 918

79. VoightBF

KudaravalliS

WenX

PritchardJK

2006 A map of recent positive selection in the human genome. PLoS Biol 4 e72 doi:10.1371/journal.pbio.0040072

80. BarreiroLB

LavalG

QuachH

PatinE

Quintana-MurciL

2008 Natural selection has driven population differentiation in modern humans. Nat Genet 40 340 345

81. BustamanteCD

Fledel-AlonA

WilliamsonS

NielsenR

HubiszMT

2005 Natural selection on protein-coding genes in the human genome. Nature 437 1153 1157

82. ClarkAG

GlanowskiS

NielsenR

ThomasPD

KejariwalA

2003 Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science 302 1960 1963

83. ConsortiumTCSaA

2005 Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437 69 87

84. KosiolC

VinarT

da FonsecaRR

HubiszMJ

BustamanteCD

2008 Patterns of positive selection in six mammalian genomes. PLoS Genet 4 e1000144 doi:10.1371/journal.pgen.1000144

85. SawyerSL

EmermanM

MalikHS

2004 Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G. PLoS Biol 2 e275 doi:10.1371/journal.pbio.0020275

86. SawyerSL

WuLI

EmermanM

MalikHS

2005 Positive selection of primate TRIM5alpha identifies a critical species-specific retroviral restriction domain. Proc Natl Acad Sci U S A 102 2832 2837

87. Quintana-MurciL

AlcaisA

AbelL

CasanovaJL

2007 Immunology in natura: clinical, epidemiological and evolutionary genetics of infectious diseases. Nat Immunol 8 1165 1171

88. EsnaultC

HeidmannO

DelebecqueF

DewannieuxM

RibetD

2005 APOBEC3G cytidine deaminase inhibits retrotransposition of endogenous retroviruses. Nature 433 430 433

89. StremlauM

OwensCM

PerronMJ

KiesslingM

AutissierP

2004 The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys. Nature 427 848 853

90. SheehyAM

GaddisNC

ChoiJD

MalimMH

2002 Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature 418 646 650

91. NeilSJ

ZangT

BieniaszPD

2008 Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu. Nature 451 425 430

92. OrtizM

GuexN

PatinE

MartinO

XenariosI

2009 Evolutionary trajectories of primate genes involved in HIV pathogenesis. Mol Biol Evol 26 2865 2875

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