Tuberculosis: Global approaches to a global disease

Current Opinion in Biotechnology

Volumn 21, Issue 4, 2010, Pages 524-531

  Kirschner, Denise E ^a   Young, Douglas ^b   Flynn, JoAnne L ^c  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

^c NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL MODEL; COMPUTATIONAL APPROACH; COMPUTATIONAL SYSTEM; GAIN INSIGHT; HOST-PATHOGEN INTERACTIONS; HUMAN PATHOGENS; IN-SILICO; MYCOBACTERIUM TUBERCULOSIS; SYSTEMS BIOLOGY;

BACTERIOLOGY;

MATHEMATICAL MODELS;

CYTOKINE; ETHIONAMIDE; ISONIAZID;

COMPUTER MODEL; DISEASE MODEL; GRANULOMA; HOST PATHOGEN INTERACTION; HUMAN; IMMUNE RESPONSE; IN VITRO STUDY; MATHEMATICAL MODEL; METABOLOMICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; SYSTEMS BIOLOGY; TUBERCULOSIS;

ANIMALS; DISEASE MODELS, ANIMAL; HOST-PATHOGEN INTERACTIONS; HUMANS; MYCOBACTERIUM TUBERCULOSIS; SYSTEMS BIOLOGY; TUBERCULOSIS;

ANIMALIA; MYCOBACTERIUM TUBERCULOSIS;

EID: 77956652501     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2010.06.002     Document Type: Review

References (75)

1. Cooper A.M. Cell-mediated immune responses in tuberculosis. Annu Rev Immunol 2009, 27:393-422.
2. Post F.A., Wood R., Pillay G.P. Pulmonary tuberculosis in HIV infection: radiographic appearance is related to CD4+ T-lymphocyte count. Tuber Lung Dis 1995, 76:518-521.
3. Keane J. Tumor necrosis factor blockers and reactivation of latent tuberculosis. Clin Infect Dis 2004, 39:300-302.
4. Casanova J.-L., Abel L. Genetic dissection of immunity to mycobacteria: the human model. Annu Rev Immunol 2002, 20:581-620.
5. Tailleux L., Waddell S.J., Pelizzola M., Mortellaro A., Withers M., Tanne A., Castagnoli P.R., Gicquel B., Stoker N.G., Butcher P.D., et al. Probing host-pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages. PLoS One 2008, 3:e1403.
6. Ehrt S., Schnappinger D., Bekiranov S., Drenkow J., Shi S., Gingeras T.R., Gaasterland T., Schoolnik G., Nathan C. Reprogramming of the macrophage transcriptome in response to interferon-gamma and Mycobacterium tuberculosis: signaling roles of nitric oxide synthase-2 and phagocyte oxidase. J Exp Med 2001, 194:1123-1140.
7. Nau G.J., Richmond J.F., Schlesinger A., Jennings E.G., Lander E.S., Young R.A. Human macrophage activation programs induced by bacterial pathogens. Proc Natl Acad Sci USA 2002, 99:1503-1508.
8. Shui W., Gilmore S.A., Sheu L., Liu J., Keasling J.D., Bertozzi C.R. Quantitative proteomic profiling of host-pathogen interactions: the macrophage response to Mycobacterium tuberculosis lipids. J Proteome Res 2009, 8:282-289.
9. Chaussabel D., Semnani R.T., McDowell M.A., Sacks D., Sher A., Nutman T.B. Unique gene expression profiles of human macrophages and dendritic cells to phylogenetically distinct parasites. Blood 2003, 102:672-681.
10. Fletcher H.A., Keyser A., Bowmaker M., Sayles P.C., Kaplan G., Hussey G., Hill A.V., Hanekom W.A. Transcriptional profiling of mycobacterial antigen-induced responses in infants vaccinated with BCG at birth. BMC Med Genomics 2009, 2:10.
11. Kim D.K., Park G.M., Hwang Y.I., Kim H.J., Han S.K., Shim Y.S., Yim J.J. Microarray analysis of gene expression associated with extrapulmonary dissemination of tuberculosis. Respirology 2006, 11:557-565.
12. Gonzalez-Juarrero M., Kingry L.C., Ordway D.J., Henao-Tamayo M., Harton M., Basaraba R.J., Hanneman W.H., Orme I.M., Slayden R.A. Immune response to Mycobacterium tuberculosis and identification of molecular markers of disease. Am J Respir Cell Mol Biol 2009, 40:398-409.
13. Beisiegel M., Mollenkopf H.J., Hahnke K., Koch M., Dietrich I., Reece S.T., Kaufmann S.H. Combination of host susceptibility and Mycobacterium tuberculosis virulence define gene expression profile in the host. Eur J Immunol 2009, 39:3369-3384.
14. Kumar D., Nath L., Kamal M.A., Varshney A., Jain A., Singh S., Rao K.V. Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell 2010, 140:731-743.
15. Chen C.Y., Huang D., Wang R.C., Shen L., Zeng G., Yao S., Shen Y., Halliday L., Fortman J., McAllister M., et al. A critical role for CD8 T cells in a nonhuman primate model of tuberculosis. PLoS Pathog 2009, 5:e1000392.
16. Diedrich C.R., Mattila J.T., Klein E., Janssen C., Phuah J., Sturgeon T.J., Montelaro R.C., Lin P.L., Flynn J.L. Reactivation of latent tuberculosis in cynomolgus macaques infected with SIV is associated with early peripheral T cell depletion and not virus load. PLoS One 2010, 5:e9611.
17. Lin P.L., Myers A., Smith L., Bigbee C., Bigbee M., Fuhrman C., Grieser H., Chiosea I., Voitenek N.N., Capuano S.V., et al. Tumor necrosis factor neutralization results in disseminated disease in acute and latent Mycobacterium tuberculosis infection with normal granuloma structure in a cynomolgus macaque model. Arthritis Rheum 2010, 62:340-350.
18. Lin P.L., Rodgers M., Smith L., Bigbee M., Myers A., Bigbee C., Chiosea I., Capuano S.V., Fuhrman C., Klein E., et al. Quantitative comparison of active and latent tuberculosis in the cynomolgus macaque model. Infect Immun 2009, 77:4631-4642.
19. Sharpe S.A., Eschelbach E., Basaraba R.J., Gleeson F., Hall G.A., McIntyre A., Williams A., Kraft S.L., Clark S., Gooch K., et al. Determination of lesion volume by MRI and stereology in a macaque model of tuberculosis. Tuberculosis (Edinb) 2009, 89:405-416.
20. Marino S., Hogue I.B., Ray C.J., Kirschner D.E. A methodology for performing global uncertainty and sensitivity analysis in systems biology. J Theor Biol 2008, 254:178-196.
21. Young D., Stark J., Kirschner D. Systems biology of persistent infection: tuberculosis as a case study. Nat Rev Microbiol 2008, 6:520-528.
22. Dietz K., Heesterbeek J.A.P. Bernoulli was ahead of modern epidemiology. Nature 2000, 408:513-514.
23. Farr W. On the Cattle Plague. J Soc Sci 1866, 349-351.
24. Perelson A.S. Viral kinetics and mathematical models. Am J Med 1999, 107:49S-52S.
25. Wigginton J.E., Kirschner D. A model to predict cell-mediated immune regulatory mechanisms during human infection with Mycobacterium tuberculosis. J Immunol 2001, 166:1951-1967.
26. Bauer A., Beauchemin C., Perelson A. Agent-based modeling of host-pathogen systems: the successes and challenges. Inform Sci 2009, 179:1379-1389.
27. Sud D., Bigbee C., Flynn J.L., Kirschner D.E. Contribution of CD8+ T cells to control of Mycobacterium tuberculosis infection. J Immunol 2006, 176:4296-4314.
28. Marino S., Pawar S., Fuller C.L., Reinhart T.A., Flynn J.L., Kirschner D.E. Dendritic cell trafficking and antigen presentation in the human immune response to Mycobacterium tuberculosis. J Immunol 2004, 173:494-506.
29. Grimm V., Railsback S.F. Individual-based modeling and ecology 2005, Princeton University Press, Princeton.
30. Chang S.T., Linderman J.J., Kirschner D.E. Multiple mechanisms allow Mycobacterium tuberculosis to continuously inhibit MHC class II-mediated antigen presentation by macrophages. Proc Natl Acad Sci USA 2005, 102:4530-4535.
31. Chang S.T., Linderman J.J., Kirschner D.E. Effect of multiple genetic polymorphisms on antigen presentation and susceptibility to Mycobacterium tuberculosis infection. Infect Immun 2008, 76:3221-3232.
32. Fallahi-Sichani M., Schaller M., Kirschner D., Kunkel S., Linderman J. Identification of key processes that control tumor necrosis factor availability in a tuberculosis granuloma. PLoS Comput Biol 2010, 6(5):e1000778.
33. Gammack D., Doering C.R., Kirschner D.E. Macrophage response to Mycobacterium tuberculosis infection. J Math Biol 2004, 48:218-242.
34. Kirschner D. The multi-scale immune response to pathogens: M. tuberculosis as an example. In silico Immunology 2006, Springer. D. Flower, J. Timmis (Eds.).
35. Kirschner D., Webb G.F., Cloyd M. Model of HIV-1 disease progression based on virus-induced lymph node homing and homing-induced apoptosis of CD4+ lymphocytes. J Acquir Immune Defic Syndr 2000, 24:352-362.
36. Kirschner D.E., Chang S.T., Riggs T.W., Perry N., Linderman J.J. Toward a multiscale model of antigen presentation in immunity. Immunol Rev 2007, 216:93-118.
37. Kirschner D.E., Linderman J.J. Mathematical and computational approaches can complement experimental studies of host-pathogen interactions. Cell Microbiol 2009, 11:531-539.
38. Linderman J.J., Riggs T., Pande M., Miller M., Marino S., Kirschner D.E. Characterizing the dynamics of CD4+ T cell priming within a lymph node. J Immunol 2010, 184:2873-2885.
39. Marino S., Kirschner D.E. The human immune response to Mycobacterium tuberculosis in lung and lymph node. J Theor Biol 2004, 227:463-486.
40. Marino S., Sud D., Plessner H., Lin P.L., Chan J., Flynn J.L., Kirschner D.E. Differences in reactivation of tuberculosis induced from anti-TNF treatments are based on bioavailability in granulomatous tissue. PLoS Comput Biol 2007, 3:1909-1924.
41. Ray J.C., Flynn J.L., Kirschner D.E. Synergy between individual TNF-dependent functions determines granuloma performance for controlling Mycobacterium tuberculosis infection. J Immunol 2009, 182:3706-3717.
42. Riggs T., Walts A., Perry N., Bickle L., Lynch J.N., Myers A., Flynn J., Linderman J.J., Miller M.J., Kirschner D.E. A comparison of random vs. chemotaxis-driven contacts of T cells with dendritic cells during repertoire scanning. J Theor Biol 2008, 250:732-751.
43. Segovia-Juarez J.L., Ganguli S., Kirschner D. Identifying control mechanisms of granuloma formation during M. tuberculosis infection using an agent-based model. J Theor Biol 2004, 231:357-376.
44. Warrender C., Forrest S., Koster F. Modeling intercellular interactions in early Mycobacterium infection. Bull Math Biol 2006, 68:2233-2261.
45. Marino S, Myers A, Flynn JL, Kirschner DE: TNF and IL-10 are major factors in modulation of the phagocytic cell environment in lung and lymph node in tuberculosis: A next-generation two-compartmental model. J Theor Biol, in press.
46. Day J., Friedman A., Schlesinger L.S. Modeling the immune rheostat of macrophages in the lung in response to infection. Proc Natl Acad Sci USA 2009, 106:11246-11251.
47. Magombedze G., Garira W., Mwenje E. In-vivo mathematical study of co-infection dynamics of HIV-1 and Mycobacterium tuberculosis. J Biol Syst 2008, 16:357-394.
48. Magombedze G., Garira W., Mwenje E. The role of dendritic cells and other immune mechanisms during human infection with Mycobacterium tuberculosis. J Biomath 2009, 2:69-105.
49. de Jong B.C., Hill P.C., Aiken A., Awine T., Antonio M., Adetifa I.M., Jackson-Sillah D.J., Fox A., Deriemer K., Gagneux S., et al. Progression to active tuberculosis, but not transmission, varies by Mycobacterium tuberculosis lineage in The Gambia. J Infect Dis 2008, 198:1037-1043.
50. Caws M., Thwaites G., Dunstan S., Hawn T.R., Lan N.T., Thuong N.T., Stepniewska K., Huyen M.N., Bang N.D., Loc T.H., et al. The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis. PLoS Pathog 2008, 4:e1000034.
51. Hershberg R., Lipatov M., Small P.M., Sheffer H., Niemann S., Homolka S., Roach J.C., Kremer K., Petrov D.A., Feldman M.W., et al. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 2008, 6:e311.
52. Chavadi S., Wooff E., Coldham N.G., Sritharan M., Hewinson R.G., Gordon S.V., Wheeler P.R. Global effects of inactivation of the pyruvate kinase gene in the Mycobacterium tuberculosis complex. J Bacteriol 2009, 191:7545-7553.
53. Mehaffy C., Hess A., Prenni J.E., Mathema B., Kreiswirth B., Dobos K.M. Descriptive proteomic analysis shows protein variability between closely related clinical isolates of Mycobacterium tuberculosis. Proteomics 2010, 10:1966-1984.
54. Garton N.J., Waddell S.J., Sherratt A.L., Lee S.M., Smith R.J., Senner C., Hinds J., Rajakumar K., Adegbola R.A., Besra G.S., et al. Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum. PLoS Med 2008, 5:e75.
55. Reddy T.B., Riley R., Wymore F., Montgomery P., DeCaprio D., Engels R., Gellesch M., Hubble J., Jen D., Jin H., et al. TB database: an integrated platform for tuberculosis research. Nucleic Acids Res 2009, 37:D499-508.
56. Krawczyk J., Kohl T.A., Goesmann A., Kalinowski J., Baumbach J. From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. Nucleic Acids Res 2009, 37:e97.
57. Balazsi G., Heath A.P., Shi L., Gennaro M.L. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol Syst Biol 2008, 4:225.
58. Sala C., Grainger D.C., Cole S.T. Dissecting regulatory networks in host-pathogen interaction using chIP-on-chip technology. Cell Host Microbe 2009, 5:430-437.
59. Lun D.S., Sherrid A., Weiner B., Sherman D.R., Galagan J.E. A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data. Genome Biol 2009, 10:R142.
60. Gordon B.R., Li Y., Wang L., Sintsova A., van Bakel H., Tian S., Navarre W.W., Xia B., Liu J. Lsr2 is a nucleoid-associated protein that targets AT-rich sequences and virulence genes in Mycobacterium tuberculosis. Proc Natl Acad Sci USA 2010, 107:5154-5159.
61. Arnvig K.B., Young D.B. Identification of small RNAs in Mycobacterium tuberculosis. Mol Microbiol 2009, 73:397-408.
62. Bitter W., Houben E.N., Bottai D., Brodin P., Brown E.J., Cox J.S., Derbyshire K., Fortune S.M., Gao L.Y., Liu J., et al. Systematic genetic nomenclature for type VII secretion systems. PLoS Pathog 2009, 5:e1000507.
63. Ramage H.R., Connolly L.E., Cox J.S. Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. PLoS Genet 2009, 5:e1000767.
64. Molle V., Kremer L. Division and cell envelope regulation by Ser/Thr phosphorylation: Mycobacterium shows the way. Mol Microbiol 2010, 5:1064-1077.
65. Rao P.K., Li Q. Protein turnover in mycobacterial proteomics. Molecules 2009, 14:3237-3258.
66. Rao P.K., Li Q. Principal component analysis of proteome dynamics in iron-starved Mycobacterium tuberculosis. J Proteomics Bioinform 2009, 2:19-31.
67. Raman K., Chandra N. Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance. BMC Microbiol 2008, 8:234.
68. Raman K., Yeturu K., Chandra N. targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC Syst Biol 2008, 2:109.
69. Cui T., Zhang L., Wang X., He Z.G. Uncovering new signaling proteins and potential drug targets through the interactome analysis of Mycobacterium tuberculosis. BMC Genomics 2009, 10:118.
70. Colijn C., Brandes A., Zucker J., Lun D.S., Weiner B., Farhat M.R., Cheng T.Y., Moody D.B., Murray M., Galagan J.E. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol 2009, 5:e1000489.
71. Raman K., Rajagopalan P., Chandra N. Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs. PLoS Comput Biol 2005, 1:e46.
72. Kim T.Y., Kim H.U., Lee S.Y. Metabolite-centric approaches for the discovery of antibacterials using genome-scale metabolic networks. Metab Eng 2010, 12:105-111.
73. Beste D.J., Hooper T., Stewart G., Bonde B., Avignone-Rossa C., Bushell M.E., Wheeler P., Klamt S., Kierzek A.M., McFadden J. GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism. Genome Biol 2007, 8:R89.
74. Jamshidi N., Palsson B.O. Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol 2007, 1:26.
75. Fang X., Wallqvist A., Reifman J. A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis. BMC Syst Biol 2009, 3:92.