Host-pathogen interactions revealed by human genome-wide surveys

Trends in Genetics

Volumn 28, Issue 5, 2012, Pages 233-243

  Khor, Chiea Chuen ^a,b,c   Hibberd, Martin L ^a,b  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE RECRUITMENT DOMAIN PROTEIN 15; GAMMA INTERFERON RECEPTOR 1; HLA DP ANTIGEN; HLA DR ANTIGEN; INTERLEUKIN 12; INTERLEUKIN 23 RECEPTOR; INTERLEUKIN 28B; RECEPTOR INTERACTING PROTEIN SERINE THREONINE KINASE 2; TUMOR NECROSIS FACTOR RECEPTOR;

ACQUIRED IMMUNE DEFICIENCY SYNDROME; DENGUE; DENGUE VIRUS; DISEASE PREDISPOSITION; ENTERITIS; GENE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC ASSOCIATION; GENETIC CODE; GENETIC MARKER; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HEPATITIS B; HEPATITIS B VIRUS; HEPATITIS C; HEPATITIS C VIRUS; HOST PATHOGEN INTERACTION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; LEPROSY; MALARIA; MENINGOCOCCOSIS; MUCOCUTANEOUS LYMPH NODE SYNDROME; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM TUBERCULOSIS; NEISSERIA MENINGITIDIS; PLASMODIUM FALCIPARUM; PLASMODIUM VIVAX; PRIORITY JOURNAL; REVIEW; SIGNAL TRANSDUCTION; TUBERCULOSIS;

COMMUNICABLE DISEASES; DATA COLLECTION; GENETIC PREDISPOSITION TO DISEASE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HLA ANTIGENS; HOST-PATHOGEN INTERACTIONS; HUMANS; MODELS, BIOLOGICAL; RISK FACTORS;

EID: 84860251413     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2012.02.001     Document Type: Review

References (91)

1. Sorensen T.I., et al. Genetic and environmental influences on premature death in adult adoptees. N. Engl. J. Med. 1988, 318:727-732.
2. Walsh E.C., et al. Searching for signals of evolutionary selection in 168 genes related to immune function. Hum. Genet. 2006, 119:92-102.
3. Sabeti P.C., et al. Detecting recent positive selection in the human genome from haplotype structure. Nature 2002, 419:832-837.
4. Alcais A., et al. Human genetics of infectious diseases: between proof of principle and paradigm. J. Clin. Invest. 2009, 119:2506-2514.
5. Dean M., et al. 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 1996, 273:1856-1862.
6. Tournamille C., et al. Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals. Nat. Genet. 1995, 10:224-228.
7. Lindesmith L., et al. Human susceptibility and resistance to Norwalk virus infection. Nat. Med. 2003, 9:548-553.
8. Thorven M., et al. A homozygous nonsense mutation (428G→A) in the human secretor (FUT2) gene provides resistance to symptomatic norovirus (GGII) infections. J. Virol. 2005, 79:15351-15355.
9. Carlsson B., et al. The G428A nonsense mutation in FUT2 provides strong but not absolute protection against symptomatic GII.4 Norovirus infection. PLoS ONE 2009, 4:e5593.
10. Van Tyne D., et al. Identification and functional validation of the novel antimalarial resistance locus PF10_0355 in Plasmodium falciparum. PLoS Genet. 2011, 7:e1001383.
11. Filippi C.M., et al. Immunoregulatory mechanisms triggered by viral infections protect from type 1 diabetes in mice. J. Clin. Invest. 2009, 119:1515-1523.
12. Smyth D.J., et al. A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region. Nat. Genet. 2006, 38:617-619.
13. Larsen M., et al. Exhausted cytotoxic control of Epstein-Barr virus in human lupus. PLoS Pathog. 2011, 7:e1002328.
14. Harley J.B., et al. Genome-wide association scan in women with systemic lupus erythematosus identifies susceptibility variants in ITGAM, PXK, KIAA1542 and other loci. Nat. Genet. 2008, 40:204-210.
15. Rodrigues L.C., Lockwood D. Leprosy now: epidemiology, progress, challenges, and research gaps. Lancet Infect. Dis. 2011, 11:464-470.
16. Van Brakel W.H., et al. The allocation of leprosy patients into paucibacillary and multibacillary groups for multidrug therapy, taking into account the number of body areas affected by skin, or skin and nerve lesions. Lepr. Rev. 1992, 63:231-246.
17. Zhang F.R., et al. Genomewide association study of leprosy. N. Engl. J. Med. 2009, 361:2609-2618.
18. Zhang F., et al. Identification of two new loci at IL23R and RAB32 that influence susceptibility to leprosy. Nat. Genet. 2011, 43:1247-1251.
19. Modlin R.L. Th1-Th2 paradigm: insights from leprosy. J. Invest. Dermatol. 1994, 102:828-832.
20. Newport M.J., et al. A mutation in the interferon-gamma-receptor gene and susceptibility to mycobacterial infection. N. Engl. J. Med. 1996, 335:1941-1949.
21. Vogt G., et al. Gains of glycosylation comprise an unexpectedly large group of pathogenic mutations. Nat. Genet. 2005, 37:692-700.
22. de Jong R., et al. Severe mycobacterial and Salmonella infections in interleukin-12 receptor-deficient patients. Science 1998, 280:1435-1438.
23. Thye T., et al. Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2. Nat. Genet. 2010, 42:739-741.
24. Pereyra F., et al. The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science 2010, 330:1551-1557.
25. Davila S., et al. Genome-wide association study identifies variants in the CFH region associated with host susceptibility to meningococcal disease. Nat. Genet. 2010, 42:772-776.
26. Kamatani Y., et al. A genome-wide association study identifies variants in the HLA-DP locus associated with chronic hepatitis B in Asians. Nat. Genet. 2009, 41:591-595.
27. Kumar V., et al. Genome-wide association study identifies a susceptibility locus for HCV-induced hepatocellular carcinoma. Nat. Genet. 2011, 43:455-458.
28. Altare F., et al. Impairment of mycobacterial immunity in human interleukin-12 receptor deficiency. Science 1998, 280:1432-1435.
29. Menard D., et al. Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:5967-5971.
30. Miller L.H., et al. The resistance factor to Plasmodium vivax in blacks. The Duffy-blood-group genotype, FyFy. N. Engl. J. Med. 1976, 295:302-304.
31. Jallow M., et al. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat. Genet. 2009, 41:657-665.
32. Fry A.E., et al. Common variation in the ABO glycosyltransferase is associated with susceptibility to severe Plasmodium falciparum malaria. Hum. Mol. Genet. 2008, 17:567-576.
33. Boyle M.J., et al. Isolation of viable Plasmodium falciparum merozoites to define erythrocyte invasion events and advance vaccine and drug development. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:14378-14383.
34. Mu J., et al. Genome-wide variation and identification of vaccine targets in the Plasmodium falciparum genome. Nat. Genet. 2007, 39:126-130.
35. Mu J., et al. Plasmodium falciparum genome-wide scans for positive selection, recombination hot spots and resistance to antimalarial drugs. Nat. Genet. 2010, 42:268-271.
36. Richard D., et al. Interaction between Plasmodium falciparum apical membrane antigen 1 and the rhoptry neck protein complex defines a key step in the erythrocyte invasion process of malaria parasites. J. Biol. Chem. 2010, 285:14815-14822.
37. Ram S., et al. Meningococcal group W-135 and Y capsular polysaccharides paradoxically enhance activation of the alternative pathway of complement. J. Biol. Chem. 2011, 286:8297-8307.
38. Mathew S., Overturf G.D. Complement and properidin deficiencies in meningococcal disease. Pediatr. Infect. Dis. J. 2006, 25:255-256.
39. Fijen C.A., et al. Assessment of complement deficiency in patients with meningococcal disease in The Netherlands. Clin. Infect. Dis. 1999, 28:98-105.
40. Schneider M.C., et al. Functional significance of factor H binding to Neisseria meningitidis. J. Immunol. 2006, 176:7566-7575.
41. Tan L.K., et al. Advances in the development of vaccines against Neisseria meningitidis. N. Engl. J. Med. 2010, 362:1511-1520.
42. Klein R.J., et al. Complement factor H polymorphism in age-related macular degeneration. Science 2005, 308:385-389.
43. Gharavi A.G., et al. Genome-wide association study identifies susceptibility loci for IgA nephropathy. Nat. Genet. 2011, 43:321-327.
44. Anders K.L., et al. Epidemiological factors associated with dengue shock syndrome and mortality in hospitalized dengue patients in Ho Chi Minh City, Vietnam. Am. J. Trop. Med. Hyg. 2011, 84:127-134.
45. Stephens H.A., et al. HLA-A and -B allele associations with secondary dengue virus infections correlate with disease severity and the infecting viral serotype in ethnic Thais. Tissue Antigens 2002, 60:309-318.
46. Sakuntabhai A., et al. A variant in the CD209 promoter is associated with severity of dengue disease. Nat. Genet. 2005, 37:507-513.
47. Khor C.C., et al. Genome-wide association study identifies susceptibility loci for dengue shock syndrome at MICB and PLCE1. Nat. Genet. 2011, 43:1139-1141.
48. Field S.F., et al. Sequencing-based genotyping and association analysis of the MICA and MICB genes in type 1 diabetes. Diabetes 2008, 57:1753-1756.
49. Hinkes B., et al. Positional cloning uncovers mutations in PLCE1 responsible for a nephrotic syndrome variant that may be reversible. Nat. Genet. 2006, 38:1397-1405.
50. Petrovski S., et al. Common human genetic variants and HIV-1 susceptibility: a genome-wide survey in a homogeneous African population. AIDS 2011, 25:513-518.
51. Fellay J., et al. A whole-genome association study of major determinants for host control of HIV-1. Science 2007, 317:944-947.
52. Limou S., et al. Genomewide association study of an AIDS-nonprogression cohort emphasizes the role played by HLA genes (ANRS Genomewide Association Study 02). J. Infect. Dis. 2009, 199:419-426.
53. Huang Y., et al. The role of a mutant CCR5 allele in HIV-1 transmission and disease progression. Nat. Med. 1996, 2:1240-1243.
54. Deng H., et al. Identification of a major co-receptor for primary isolates of HIV-1. Nature 1996, 381:661-666.
55. + cells is mediated by the chemokine receptor CC-CKR-5. Nature 1996, 381:667-673.
56. Philpott S.M. HIV-1 coreceptor usage, transmission, and disease progression. Curr. HIV Res. 2003, 1:217-227.
57. Png E., et al. A genome-wide association study of hepatitis B vaccine response in an Indonesian population reveals multiple independent risk variants in the HLA region. Hum. Mol. Genet. 2011, 20:3893-3898.
58. Davila S., et al. New genetic associations detected in a host response study to hepatitis B vaccine. Genes Immun. 2010, 11:232-238.
59. Rauch A., et al. Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study. Gastroenterology 2010, 138:1338-1345.
60. Shiffman M.L., et al. Peginterferon alfa-2a and ribavirin for 16 or 24 weeks in HCV genotype 2 or 3. N. Engl. J. Med. 2007, 357:124-134.
61. Ge D., et al. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature 2009, 461:399-401.
62. Princen K., et al. Inhibition of human immunodeficiency virus replication by a dual CCR5/CXCR4 antagonist. J. Virol. 2004, 78:12996-13006.
63. Khor C.C., et al. Genome-wide association study identifies FCGR2A as a susceptibility locus for Kawasaki disease. Nat. Genet. 2011, 43:1241-1246.
64. McGovern D.P., et al. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat. Genet. 2010, 42:332-337.
65. Harnden A., et al. Kawasaki disease in England: ethnicity, deprivation, and respiratory pathogens. Pediatr. Infect. Dis. J. 2009, 28:21-24.
66. Rowley A.H., et al. Searching for the cause of Kawasaki disease - cytoplasmic inclusion bodies provide new insight. Nat. Rev. Microbiol. 2008, 6:394-401.
67. Onouchi Y., et al. ITPKC functional polymorphism associated with Kawasaki disease susceptibility and formation of coronary artery aneurysms. Nat. Genet. 2008, 40:35-42.
68. Bruhns P., et al. Specificity and affinity of human Fcgamma receptors and their polymorphic variants for human IgG subclasses. Blood 2009, 113:3716-3725.
69. Asano K., et al. A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in the Japanese population. Nat. Genet. 2009, 41:1325-1329.
70. Doerfer J., Wasser S. Kawasaki disease associated with ulcerative colitis. Eur. J. Pediatr. 1986, 145:448-449.
71. Rowley A.H., et al. Oligoclonal IgA response in the vascular wall in acute Kawasaki disease. J. Immunol. 2001, 166:1334-1343.
72. Rowley A.H. Kawasaki disease: novel insights into etiology and genetic susceptibility. Annu. Rev. Med. 2011, 62:69-77.
73. Barrett J.C., et al. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat. Genet. 2008, 40:955-962.
74. Behr M.A., Kapur V. The evidence for Mycobacterium paratuberculosis in Crohn's disease. Curr. Opin. Gastroenterol. 2008, 24:17-21.
75. Khor C.C., Hibberd M.L. Shared pathways to infectious disease susceptibility?. Genome Med. 2010, 2:52.
76. Manolio T.A., et al. Finding the missing heritability of complex diseases. Nature 2009, 461:747-753.
77. Li G., et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 2012, 148:84-98.
78. Handoko L., et al. CTCF-mediated functional chromatin interactome in pluripotent cells. Nat. Genet. 2011, 43:630-638.
79. Fehrmann R.S., et al. Trans-eQTLs reveal that independent genetic variants associated with a complex phenotype converge on intermediate genes, with a major role for the HLA. PLoS Genet. 2011, 7:e1002197.
80. Gardy J.L., et al. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak. N. Engl. J. Med. 2011, 364:730-739.
81. Pearson T.A., Manolio T.A. How to interpret a genome-wide association study. JAMA 2008, 299:1335-1344.
82. Galvan A., et al. Beyond genome-wide association studies: genetic heterogeneity and individual predisposition to cancer. Trends Genet. 2010, 26:132-141.
83. Nachman M.W., Crowell S.L. Estimate of the mutation rate per nucleotide in humans. Genetics 2000, 156:297-304.
84. Rivas M.A., et al. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat. Genet. 2011, 43:1066-1073.
85. Brand S. Crohn's disease: Th1, Th17 or both? The change of a paradigm: new immunological and genetic insights implicate Th17 cells in the pathogenesis of Crohn's disease. Gut 2009, 58:1152-1167.
86. Lees C.W., et al. New IBD genetics: common pathways with other diseases. Gut 2011, 60:1739-1753.
87. Glocker E.O., et al. A homozygous CARD9 mutation in a family with susceptibility to fungal infections. N. Engl. J. Med. 2009, 361:1727-1735.
88. Franke A., et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet. 2010, 42:1118-1125.
89. Gilks W.P., et al. A common LRRK2 mutation in idiopathic Parkinson's disease. Lancet 2005, 365:415-416.
90. Mira M.T., et al. Susceptibility to leprosy is associated with PARK2 and PACRG. Nature 2004, 427:636-640.
91. Lohmann E., et al. How much phenotypic variation can be attributed to parkin genotype?. Ann. Neurol. 2003, 54:176-185.