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
Štítky
Hygiena a epidemiológia Infekčné lekárstvo LaboratóriumČlánok vyšiel v časopise
PLOS Pathogens
2010 Číslo 10
- Očkování proti virové hemoragické horečce Ebola experimentální vakcínou rVSVDG-ZEBOV-GP
- Parazitičtí červi v terapii Crohnovy choroby a dalších zánětlivých autoimunitních onemocnění
- Koronavirus hýbe světem: Víte jak se chránit a jak postupovat v případě podezření?
Najčítanejšie v tomto čísle
- Retroviral RNA Dimerization and Packaging: The What, How, When, Where, and Why
- Viral Replication Rate Regulates Clinical Outcome and CD8 T Cell Responses during Highly Pathogenic H5N1 Influenza Virus Infection in Mice
- Antimicrobial Peptides: Primeval Molecules or Future Drugs?
- Crystal Structure of DotD: Insights into the Relationship between Type IVB and Type II/III Secretion Systems