Differential transcriptomic and metabolic profiles of M. africanum-and M. tuberculosis-infected patients after, but not before, drug treatment

Genes and Immunity

Volumn 16, Issue 5, 2015, Pages 347-355

  Tientcheu, L D ^a,b,c   Maertzdorf, J ^d   Weiner, J ^d   Adetifa, I M ^e   Mollenkopf, H J ^d   Sutherland, J S ^a   Donkor, S ^a   Kampmann, B ^a   Kaufmann, S H E ^d   Dockrell, H M ^b   Ota, M O ^a,f  

^a MEDICAL RESEARCH COUNCIL LABORATORIES   (Gambia)

^b LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^c UNIVERSITY OF YAOUNDÉ I   (Cameroon)

^d MAX PLANCK INSTITUTE FOR INFECTION BIOLOGY   (Germany)

^e Medical Research Council Unit The Gambia   (Gambia)

^f WORLD HEALTH ORGANIZATION   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; RAS PROTEIN; RETINOBLASTOMA BINDING PROTEIN 4; HEPATOCYTE NUCLEAR FACTOR 4; HNF4A PROTEIN, HUMAN; TRANSCRIPTOME; TUBERCULOSTATIC AGENT;

ADOLESCENT; ADULT; AGED; ARTICLE; BACTERIUM ISOLATE; BLOOD SAMPLING; CELL COMPOSITION; CLINICAL ARTICLE; EXPLORATORY RESEARCH; FEMALE; GENE EXPRESSION PROFILING; HUMAN; INFECTION SENSITIVITY; LUNG TUBERCULOSIS; MALE; METABOLIC DISORDER; MYCOBACTERIOSIS; MYCOBACTERIUM AFRICANUM; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; TRANSCRIPTOMICS; VENOUS BLOOD; DRUG EFFECTS; GENETICS; METABOLISM; METABOLOME; MICROBIOLOGY; MIDDLE AGED; PATHOGENICITY; TUBERCULOSIS;

MYCOBACTERIUM TUBERCULOSIS;

ADOLESCENT; ADULT; ANTITUBERCULAR AGENTS; FEMALE; HEPATOCYTE NUCLEAR FACTOR 4; HUMANS; MALE; METABOLOME; MIDDLE AGED; MYCOBACTERIUM TUBERCULOSIS; TRANSCRIPTOME; TUBERCULOSIS;

EID: 84937817451     PISSN: 14664879     EISSN: 14765470     Source Type: Journal    
DOI: 10.1038/gene.2015.21     Document Type: Article

References (49)

1. Gagneux S. Host-pathogen coevolution in human tuberculosis. Philos Trans R Soc Lond B Biol Sci 2012; 367: 850-859.
2. Comas I, Chakravartti J, Small PM, Galagan J, Niemann S, Kremer K et al. Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet 2010; 42: 498-503.
3. Niemann S, Kubica T, Bange FC, Adjei O, Browne EN, Chinbuah MA et al. The species Mycobacterium africanum in the light of new molecular markers. J Clin Microbiol 2004; 42: 3958-3962.
4. de Jong BC, Adetifa I, Walther B, Hill PC, Antonio M, Ota M et al. Differences between tuberculosis cases infected with Mycobacterium africanum, West African type 2, relative to Euro-American Mycobacterium tuberculosis: an update. FEMS Immunol Med Microbiol 2010; 58: 102-105.
5. Via LE, Weiner DM, Schimel D, Lin PL, Dayao E, Tankersley SL et al. Differential virulence and disease progression following Mycobacterium tuberculosis complex infection of the common marmoset (Callithrix jacchus). Infect Immun 2013; 81: 2909-2919.
6. Bentley SD, Comas I, Bryant JM, Walker D, Smith NH, Harris SR et al. The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. PLoS Negl Trop Dis 2012; 6: e1552.
7. Bold TD, Davis DC, Penberthy KK, Cox LM, Ernst JD, de Jong BC. Impaired fitness of Mycobacterium africanum despite secretion of ESAT-6. J Infect Dis 2012; 205: 984-990.
8. Gehre F, Otu J, DeRiemer K, de Sessions PF, Hibberd ML, Mulders W et al. Deciphering the growth behaviour of Mycobacterium africanum. PLoS Negl Trop Dis 2013; 7: e2220.
9. Varahram M, Farnia P, Nasiri MJ, Karahrudi MA, Dizagie MK, Velayati AA. Association of mycobacterium tuberculosis lineages with IFN-gamma and TNF-alpha gene polymorphisms among pulmonary tuberculosis patient. Mediterr J Hematol Infect Dis 2014; 6: e2014015.
10. Portevin D, Gagneux S, Comas I, Young D. Human macrophage responses to clinical isolates from the Mycobacterium tuberculosis complex discriminate between ancient and modern lineages. PLoS Pathog 2011; 7: e1001307.
11. Wang C, Peyron P, Mestre O, Kaplan G, van Soolingen D, Gao Q et al. Innate immune response to Mycobacterium tuberculosis Beijing and other genotypes. PLoS One 2010; 5: e13594.
12. Coussens AK, Wilkinson RJ, Nikolayevskyy V, Elkington PT, Hanifa Y, Islam K, et al. Ethnic variation in inflammatory profile in tuberculosis. PLoS Pathog 2013; 9: e1003468.
13. Pareek M, Evans J, Innes J, Smith G, Hingley-Wilson S, Lougheed KE et al. Ethnicity and mycobacterial lineage as determinants of tuberculosis disease phenotype. Thorax 2013; 68: 221-229.
14. Click ES, Winston CA, Oeltmann JE, Moonan PK, Mac Kenzie WR. Association between Mycobacterium tuberculosis lineage and time to sputum culture conversion. Int J Tuberc Lung Dis 2013; 17: 878-884.
15. Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T et al. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet 2013; 45: 784-790.
16. Gumbo T. Biological variability and the emergence of multidrug-resistant tuberculosis. Nat Genet 2013; 45: 720-721.
17. Tientcheu LD, Sutherland JS, de Jong BC, Kampmann B, Jafali J, Adetifa IM et al. Differences in T-cell responses between Mycobacterium tuberculosis and Mycobacterium africanum-infected patients. Eur J Immunol 2014; 44: 1387-1398.
18. Weiner J, Maertzdorf J, Kaufmann SH. The dual role of biomarkers for understanding basic principles and devising novel intervention strategies in tuberculosis. Ann NY Acad Sci 2013; 1283: 22-29.
19. Bloom CI, Graham CM, Berry MP, Wilkinson KA, Oni T, Rozakeas F et al. Detectable changes in the blood transcriptome are present after two weeks of antituberculosis therapy. PLoS One 2012; 7: e46191.
20. Anderson ST, Kaforou M, Brent AJ, Wright VJ, Banwell CM, Chagaluka G et al. Diagnosis of childhood tuberculosis and host RNA expression in Africa. N Engl J Med 2014; 370: 1712-1723.
21. Kaforou M, Wright VJ, Oni T, French N, Bangani N, Banwell CM et al. Detection of tuberculosis in HIV-infected and-uninfected African adults using whole blood RNA expression signatures: a case-control study. PLoS Med 2013; 10: e1001538.
22. Maertzdorf J, Weiner J 3rd, Mollenkopf HJ, Network TB, Bauer T, Prasse A et al. Common patterns and disease-related signatures in tuberculosis and sarcoidosis. Proc Natl Acad Sci USA 2012; 109: 7853-7858.
23. Berry MP, Graham CM, McNab FW, Xu Z, Bloch SA, Oni T et al. An interferoninducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 2010; 466: 973-977.
24. Maertzdorf J, Ota M, Repsilber D, Mollenkopf HJ, Weiner J, Hill PC et al. Functional correlations of pathogenesis-driven gene expression signatures in tuberculosis. PLoS One 2011; 6: e26938.
25. Maertzdorf J, Repsilber D, Parida SK, Stanley K, Roberts T, Black G et al. Human gene expression profiles of susceptibility and resistance in tuberculosis. Genes Immun 2011; 12: 15-22.
26. Cliff JM, Lee JS, Constantinou N, Cho JE, Clark TG, Ronacher K et al. Distinct phases of blood gene expression pattern through tuberculosis treatment reflect modulation of the humoral immune response. J Infect Dis 2013; 207: 18-29.
27. Joosten SA, Goeman JJ, Sutherland JS, Opmeer L, de Boer KG, Jacobsen M et al. Identification of biomarkers for tuberculosis disease using a novel dual-color RTMLPA assay. Genes Immun 2012; 13: 71-82.
28. Hwang-Verslues WW, Sladek FM. HNF4alpha-role in drug metabolism and potential drug target? Current opinion in pharmacology 2010; 10: 698-705.
29. Babeu JP, Boudreau F. Hepatocyte nuclear factor 4-alpha involvement in liver and intestinal inflammatory networks. World J Gastroenterol 2014; 20: 22-30.
30. Hayhurst GP, Lee YH, Lambert G, Ward JM, Gonzalez FJ. Hepatocyte nuclear factor 4alpha (nuclear receptor 2A1) is essential for maintenance of hepatic gene expression and lipid homeostasis. Mol Cell Biol 2001; 21: 1393-1403.
31. Jimenez-Corona ME, Cruz-Hervert LP, Garcia-Garcia L, Ferreyra-Reyes L, Delgado-Sanchez G, Bobadilla-Del-Valle M et al. Association of diabetes and tuberculosis: impact on treatment and post-treatment outcomes. Thorax 2013; 68: 214-220.
32. Restrepo BI, Schlesinger LS. Impact of diabetes on the natural history of tuberculosis. Diabetes Res Clin Pract 2014; 106: 191-199.
33. Mohlke KL, Boehnke M. The role of HNF4A variants in the risk of type 2 diabetes. Curr Diab Rep 2005; 5: 149-156.
34. Jafar-Mohammadi B, Groves CJ, Gjesing AP, Herrera BM, Winckler W, Stringham HM et al. A role for coding functional variants in HNF4A in type 2 diabetes susceptibility. Diabetologia 2011; 54: 111-119.
35. Crestani M, De Fabiani E, Caruso D, Mitro N, Gilardi F, Vigil Chacon AB et al. LXR (liver X receptor) and HNF-4 (hepatocyte nuclear factor-4): key regulators in reverse cholesterol transport. Biochem Soc Trans 2004; 32: 92-96.
36. Korf H, Vander Beken S, Romano M, Steffensen KR, Stijlemans B, Gustafsson JA et al. Liver X receptors contribute to the protective immune response against Mycobacterium tuberculosis in mice. J Clin Invest 2009; 119: 1626-1637.
37. Han M, Liang L, Liu LR, Yue J, Zhao YL, Xiao HP. Liver X receptor gene polymorphisms in tuberculosis: effect on susceptibility. PLoS One 2014; 9: e95954.
38. Weiner J 3rd, Parida SK, Maertzdorf J, Black GF, Repsilber D, Telaar A et al. Biomarkers of inflammation, immunosuppression and stress with active disease are revealed by metabolomic profiling of tuberculosis patients. PLoS One 2012; 7: e40221.
39. Suzuki Y, Suda T, Asada K, Miwa S, Suzuki M, Fujie M et al. Serum indoleamine 2, 3-dioxygenase activity predicts prognosis of pulmonary tuberculosis. Clin Vaccine Immunol 2012; 19: 436-442.
40. Blumenthal A, Nagalingam G, Huch JH, Walker L, Guillemin GJ, Smythe GA et al. M. tuberculosis induces potent activation of IDO-1, but this is not essential for the immunological control of infection. PLoS One 2012; 7: e37314.
41. Sedlmayr P, Blaschitz A, Stocker R. The role of placental tryptophan catabolism. Front Immunol 2014; 5: 230.
42. Renko M, Valkonen P, Tapiainen T, Kontiokari T, Mattila P, Knuuttila M et al. Xylitolsupplemented nutrition enhances bacterial killing and prolongs survival of rats in experimental pneumococcal sepsis. BMC Microbiol 2008; 8: 45.
43. Yin SY, Kim HJ, Kim HJ. Protective effect of dietary xylitol on influenza A virus infection. PLoS One 2014; 9: e84633.
44. Ammons MC, Copie V. Mini-review: Lactoferrin: a bioinspired, anti-biofilm therapeutic. Biofouling 2013; 29: 443-455.
45. de Jong BC, Hill PC, Aiken A, Jeffries DJ, Onipede A, Small PM et al. Clinical presentation and outcome of tuberculosis patients infected by M. africanum versus M. tuberculosis. Int J Tuberc Lung Dis 2007; 11: 450-456.
46. de Jong BC, Antonio M, Awine T, Ogungbemi K, de Jong YP, Gagneux S et al. Use of spoligotyping and large sequence polymorphisms to study the population structure of the Mycobacterium tuberculosis complex in a cohort study of consecutive smear-positive tuberculosis cases in The Gambia. J Clin Microbiol 2009; 47: 994-1001.
47. Evans AM, DeHaven CD, Barrett T, Mitchell M, Milgram E. Integrated, nontargeted ultrahigh performance liquid chromatography/electrospray ionization tandem mass spectrometry platform for the identification and relative quantification of the small-molecule complement of biological systems. Anal Chem 2009; 81: 6656-6667.
48. Smyth GK. Limma: linear models for microarray data. In: Gentleman R, Carey V, Irizarry R, Dudoit S, Huber W (eds). Bioinformatics and Computational Biology Solutions using R and Bioconductor. Springer: NY, USA, 2005; pp 397-420.
49. Liaw AWM. Classification and regression by random-forest. R News 2002; 2: 18-22.