Risk of nontyphoidal Salmonella bacteraemia in African children is modified by STAT4

Nature Communications

Volumn 9, Issue 1, 2018, Pages

  Gilchrist, James J ^a,b   Rautanen, Anna ^a   Fairfax, Benjamin P ^a   Mills, Tara C ^a   Naranbhai, Vivek ^a   Trochet, Holly ^a   Pirinen, Matti ^a,c   Muthumbi, Esther ^d   Mwarumba, Salim ^d   Njuguna, Patricia ^d   Mturi, Neema ^d   Msefula, Chisomo L ^e   Gondwe, Esther N ^e   MacLennan, Jenny M ^e,f   Chapman, Stephen J ^a,g   Molyneux, Malcolm E ^e   Knight, Julian C ^a   Spencer, Chris C A ^a   Williams, Thomas N ^d,h   MacLennan, Calman A ^e,f   Scott, J Anthony G ^d,i   Hill, Adrian V S ^a,f   more..

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF HELSINKI   (Finland)

^d KEMRI WELLCOME TRUST RESEARCH PROGRAMME   (Kenya)

^e UNIVERSITY OF MALAWI   (Malawi)

^f UNIVERSITY OF OXFORD   (United Kingdom)

^g CHURCHILL HOSPITAL   (United Kingdom)

^h IMPERIAL COLLEGE LONDON   (United Kingdom)

ⁱ LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

GAMMA INTERFERON; INTERLEUKIN 12; STAT4 PROTEIN; STAT4 PROTEIN, HUMAN;

ALLELE; BACTERIAL DISEASE; BACTERIUM; CELL; CONCENTRATION (COMPOSITION); GENE EXPRESSION; GENOTYPE; HUMAN IMMUNODEFICIENCY VIRUS; IMMUNITY; MORBIDITY; MORTALITY;

ADULT; ALLELE; ARTICLE; BACTEREMIA; CELLULAR IMMUNITY; CHILD; CONTROLLED STUDY; CYTOKINE PRODUCTION; EXPRESSION QUANTITATIVE TRAIT LOCUS; FEMALE; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HUMAN; KENYAN; MAJOR CLINICAL STUDY; MALAWIAN; MALE; NATURAL KILLER CELL; NONTYPHOIDAL SALMONELLA; PROTEIN EXPRESSION; SALMONELLA; ADOLESCENT; AUTOIMMUNE DISEASE; BLOOD; CASE CONTROL STUDY; FOLLOW UP; GENETIC PREDISPOSITION; GENETICS; GENOTYPE; IMMUNOLOGY; INFANT; ISOLATION AND PURIFICATION; KENYA; MALAWI; METABOLISM; MICROBIOLOGY; NEWBORN; PATHOGENICITY; PRESCHOOL CHILD; QUANTITATIVE TRAIT LOCUS; RISK FACTOR; SALMONELLOSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

AFRICA;

SALMONELLA;

ADOLESCENT; ALLELES; AUTOIMMUNE DISEASES; BACTEREMIA; CASE-CONTROL STUDIES; CHILD; CHILD, PRESCHOOL; FEMALE; FOLLOW-UP STUDIES; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; IMMUNITY, CELLULAR; INFANT; INFANT, NEWBORN; INTERFERON-GAMMA; INTERLEUKIN-12; KENYA; KILLER CELLS, NATURAL; MALAWI; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; RISK FACTORS; SALMONELLA; SALMONELLA INFECTIONS; STAT4 TRANSCRIPTION FACTOR;

EID: 85043979423     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-017-02398-z     Document Type: Article

References (49)

1. Feasey, N. A., Dougan, G., Kingsley, R. A., Heyderman, R. S. &Gordon, M. A. Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa. Lancet 379, 2489-2499 (2012).
2. Ao, T. T. et al. Global burden of invasive nontyphoidal Salmonella disease, 2010 (1). Emerg. Infect. Dis. 21, 941-949 (2015).
3. Kariuki, S., Gordon, M. A., Feasey, N. &Parry, C. M. Antimicrobial resistance and management of invasive Salmonella disease. Vaccine 33, C21-C29 (2015).
4. MacLennan, C. A. &Levine, M. M. Invasive nontyphoidal Salmonella disease in Africa: current status. Expert. Rev. Anti. Infect. Ther. 11, 443-446 (2013).
5. Williams, T. N. et al. Bacteraemia in Kenyan children with sickle-cell anaemia: a retrospective cohort and case-control study. Lancet 374, 1364-1370 (2009).
6. Berkley, J. A. et al. Bacteremia among children admitted to a rural hospital in Kenya. N. Engl. J. Med. 352, 39-47 (2005).
7. Scott, J. A. G. et al. Relation between falciparum malaria and bacteraemia in Kenyan children: a population-based, case-control study and a longitudinal study. Lancet 378, 1316-1323 (2011).
8. Altshuler, D., Daly, M. J. &Lander, E. S. Genetic mapping in human disease. Science 322, 881-888 (2008).
9. Timmann, C. et al. Genome-wide association study indicates two novelresistance loci for severe malaria. Nature 489, 443-446 (2013).
10. Kenyan Bacteraemia Study Group et al. Polymorphism in a lincRNA associates with a doubled risk of Pneumococcal bacteremia in Kenyan children. Am. J. Hum. Genet. 98, 1092-1100 (2016).
11. McLaren, P. J. et al. Polymorphisms of large effect explain the majority of the host genetic contribution to variation of HIV-1 virus load. Proc. Natl. Acad. Sci. USA 112, 14658-14663 (2015).
12. Malaria Genomic Epidemiology Network, Band, G., Rockett, K. A., Spencer, C. C. A. &Kwiatkowski, D. P. A novel locus of resistance to severe malaria in a region of ancient balancing selection. Nature 526, 253-257 (2015).
13. Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190-1195 (2012).
14. Fairfax, B. P. et al. Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science 343, 1246949 (2014).
15. Fairfax, B. P. et al. Genetics of gene expression in primary immune cells identifies cell type-specific master regulators and roles of HLA alleles. Nat. Genet. 44, 502-510 (2012).
16. Naranbhai, V. et al. Genomic modulators of gene expression in human neutrophils. Nat. Commun. 6, 7545 (2015).
17. Brent, A. J. et al. Salmonella bacteremia in Kenyan children. Pediatr. Infect. Dis. J. 25, 230-236 (2006).
18. Liu, J. Z. et al. Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis. Nat. Genet. 44, 1137-1141 (2012).
19. Eyre, S. et al. High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis. Nat. Genet. 44, 1336-1340 (2012).
20. Trynka, G. et al. Dense genotyping identifies and localizes multiple common and rare variant association signals in celiac disease. Nat. Genet. 43, 1193-1201 (2011).
21. Onengut-Gumuscu, S. et al. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nat. Genet. 47, 381-386 (2015).
22. Watford, W. T. et al. Signaling by IL-12 and IL-23 and the immunoregulatory roles of STAT4. Immunol. Rev. 202, 139-156 (2004).
23. Jouanguy, E. et al. Interferon-gamma-receptor deficiency in an infant with fatal bacille Calmette-Guérin infection. N. Engl. J. Med. 335, 1956-1961 (1996).
24. Newport, M. J. et al. A mutation in the interferon-gamma-receptor gene and susceptibility to mycobacterial infection. N. Engl. J. Med. 335, 1941-1949 (1996).
25. de Beaucoudrey, L. et al. Revisiting human IL-12Rβ1 deficiency. Medicine 89, 381-402 (2010).
26. Dorman, S. E. et al. Clinical features of dominant and recessive interferon gamma receptor 1 deficiencies. Lancet 364, 2113-2121 (2004).
27. Prando, C. et al. Inherited IL-12p40 deficiency. Medicine 92, 109-122 (2013).
28. Bustamante, J., Boisson-Dupuis, S., Abel, L. &Casanova, J.-L. Mendelian susceptibility to mycobacterial disease: genetic, immunological, and clinical features of inborn errors of IFN-γ immunity. Semin. Immunol. 26, 454-470 (2014).
29. Gilchrist, J. J., MacLennan, C. A. &Hill, A. V. S. Genetic susceptibility to invasive Salmonella disease. Nat. Rev. Immunol. 15, 452-463 (2015).
30. Eva, M. M. et al. Altered IFN-γ-mediated immunity and transcriptional expression patterns in N-ethyl-N-nitrosourea-induced STAT4 mutants confer susceptibility to acute typhoid-like disease. J. Immunol. 192, 259-270 (2014).
31. Kupz, A. et al. Contribution of Thy1+NK cells to protective IFN-γ production during Salmonella typhimurium infections. Proc. Natl. Acad. Sci. USA 110, 2252-2257 (2013).
32. Nyirenda, T. S. et al. Sequential acquisition of T cells and antibodies to nontyphoidal Salmonella in Malawian children. J. Infect. Dis. 210, 56-64 (2014).
33. Jostins, L. et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491, 119-124 (2012).
34. Mandala, W. L. et al. Lymphocyte subsets in healthy Malawians: implications for immunologic assessment of HIV infection in Africa. J. Allergy Clin. Immunol. 125, 203-208 (2010).
35. UK IBD Genetics Consortium et al. Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region. Nat. Genet. 41, 1330-1334 (2009).
36. Delaneau, O., Marchini, J. &Zagury, J.-F. A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179-181 (2012).
37. Howie, B., Fuchsberger, C., Stephens, M., Marchini, J. &Abecasis, G. R. Fast and accurate genotype imputation in genome-wide association studies through pre-phasing. Nat. Genet. 44, 955-959 (2012).
38. Marchini, J., Howie, B., Myers, S., McVean, G. &Donnelly, P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39, 906-913 (2007).
39. Cortes, A. &Brown, M. A. Promise and pitfalls of the Immunochip. Arthritis Res. Ther. 13, 101 (2011).
40. Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559-575 (2007).
41. Zhou, X. &Stephens, M. Genome-wide efficient mixed-model analysis for association studies. Nat. Genet. 44, 821-824 (2012).
42. Wellcome Trust Case Control Consortium et al. Bayesian refinement of association signals for 14 loci in 3 common diseases. Nat. Genet. 44, 1294-1301 (2012).
43. Wakefield, J. Bayes factors for genome-wide association studies: comparison with P-values. Genet. Epidemiol. 33, 79-86 (2009).
44. Barrett, J. C., Fry, B., Maller, J. &Daly, M. J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263-265 (2005).
45. Ong, R. T.-H. &Teo, Y. Y. varLD: a program for quantifying variation in linkage disequilibrium patterns between populations. Bioinformatics 26, 1269-1270 (2010).
46. Hinks, A. et al. Dense genotyping of immune-related disease regions identifies 14 new susceptibility loci for juvenile idiopathic arthritis. Nat. Genet. 45, 664-669 (2013).
47. International Multiple Sclerosis Genetics Consortium (IMSGC) et al. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat. Genet. 45, 1353-1360 (2013).
48. Faraco, J. et al. ImmunoChip study implicates antigen presentation to T cells in narcolepsy. PLoS Genet. 9, e1003270 (2013).
49. Tsoi, L. C. et al. Identification of 15 new psoriasis susceptibility loci highlights the role of innate immunity. Nat. Genet. 44, 1341-1348 (2012).