Systems biology approaches to dissect mammalian innate immunity

Current Opinion in Immunology

Volumn 23, Issue 1, 2011, Pages 71-77

  Shapira, Sagi D ^a,b,c   Hacohen, Nir ^a,b,c  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA INTERFERON; COMPLEMENTARY DNA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; INTERLEUKIN 1BETA; MESSENGER RNA; TOLL LIKE RECEPTOR 4; TUMOR NECROSIS FACTOR ALPHA;

B LYMPHOCYTE; BACTERIAL INFECTION; CELL DIFFERENTIATION; CELLULAR IMMUNITY; CYTOKINE PRODUCTION; DENDRITIC CELL; DNA VIRUS; GENE ACTIVATION; GENE EXPRESSION; GENE FUNCTION; GENETIC VARIABILITY; HEPATITIS C VIRUS; HUMAN; IMMUNE RESPONSE; IMMUNE SYSTEM; INNATE IMMUNITY; MAMMAL CELL; NEWCASTLE DISEASE PARAMYXOVIRUS; NONHUMAN; REVIEW; SYSTEMS BIOLOGY; TUBERCULOSIS; VIRUS REPLICATION;

ANIMALS; GENE REGULATORY NETWORKS; GENETIC VARIATION; HUMANS; IMMUNITY, INNATE; MODELS, IMMUNOLOGICAL; SYSTEMS BIOLOGY;

EID: 79951676291     PISSN: 09527915     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.coi.2010.10.022     Document Type: Review

References (47)

1. Hartwell L.H. Cell division from a genetic perspective. J Cell Biol 1978, 77:627-637.
2. St Johnston D., Nusslein-Volhard C. The origin of pattern and polarity in the Drosophila embryo. Cell 1992, 68:201-219.
3. Irazoqui J.E., Urbach J.M., Ausubel F.M. Evolution of host innate defence: insights from Caenorhabditis elegans and primitive invertebrates. Nat Rev Immunol 2010, 10:47-58.
4. Cronin S.J., Nehme N.T., Limmer S., Liegeois S., Pospisilik J.A., Schramek D., Leibbrandt A., Simoes Rde M., Gruber S., Puc U., et al. Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Science 2009, 325:340-343.
5. Boudsocq M., Willmann M.R., McCormack M., Lee H., Shan L., He P., Bush J., Cheng S.H., Sheen J. Differential innate immune signalling via Ca(2+) sensor protein kinases. Nature 2010, 464:418-422.
6. Beutler B. Microbe sensing, positive feedback loops, and the pathogenesis of inflammatory diseases. Immunol Rev 2009, 227:248-263.
7. Echeverri C.J., Perrimon N. High-throughput RNAi screening in cultured cells: a user's guide. Nat Rev Genet 2006, 7:373-384.
8. Brummelkamp T.R., Nijman S.M., Dirac A.M., Bernards R. Loss of the cylindromatosis tumour suppressor inhibits apoptosis by activating NF-kappaB. Nature 2003, 424:797-801.
9. Hitomi J., Christofferson D.E., Ng A., Yao J., Degterev A., Xavier R.J., Yuan J. Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway. Cell 2008, 135:1311-1323.
10. Cho Y.S., Challa S., Moquin D., Genga R., Ray T.D., Guildford M., Chan F.K. Phosphorylation-driven assembly of the RIP1-RIP3 complex regulates programmed necrosis and virus-induced inflammation. Cell 2009, 137:1112-1123.
11. Brass A.L., Huang I.C., Benita Y., John S.P., Krishnan M.N., Feeley E.M., Ryan B.J., Weyer J.L., van der Weyden L., Fikrig E., et al. The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell 2009, 139:1243-1254.
12. Bouwmeester T., Bauch A., Ruffner H., Angrand P.O., Bergamini G., Croughton K., Cruciat C., Eberhard D., Gagneur J., Ghidelli S., et al. A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway. Nat Cell Biol 2004, 6:97-105.
13. Amit I., Garber M., Chevrier N., Leite A.P., Donner Y., Eisenhaure T., Guttman M., Grenier J.K., Li W., Zuk O., et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 2009, 326:257-263.
14. Shapira S.D., Gat-Viks I., Shum B.O., Dricot A., de Grace M.M., Wu L., Gupta P.B., Hao T., Silver S.J., Root D.E., et al. A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell 2009, 139:1255-1267.
15. Luo B., Cheung H.W., Subramanian A., Sharifnia T., Okamoto M., Yang X., Hinkle G., Boehm J.S., Beroukhim R., Weir B.A., et al. Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A 2008, 105:20380-20385.
16. Roguev A., Bandyopadhyay S., Zofall M., Zhang K., Fischer T., Collins S.R., Qu H., Shales M., Park H.O., Hayles J., et al. Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 2008, 322:405-410.
17. Ishikawa H., Barber G.N. STING is an endoplasmic reticulum adaptor that facilitates innate immune signalling. Nature 2008, 455:674-678.
18. Kim H., Seed B. The transcription factor MafB antagonizes antiviral responses by blocking recruitment of coactivators to the transcription factor IRF3. Nat Immunol 2010, 11:743-750.
19. Carette J.E., Guimaraes C.P., Varadarajan M., Park A.S., Wuethrich I., Godarova A., Kotecki M., Cochran B.H., Spooner E., Ploegh H.L., et al. Haploid genetic screens in human cells identify host factors used by pathogens. Science 2009, 326:1231-1235.
20. Vidal S.M., Malo D., Marquis J.F., Gros P. Forward genetic dissection of immunity to infection in the mouse. Annu Rev Immunol 2008, 26:81-132.
21. Fortin A., Abel L., Casanova J.L., Gros P. Host genetics of mycobacterial diseases in mice and men: forward genetic studies of BCG-osis and tuberculosis. Annu Rev Genomics Hum Genet 2007, 8:163-192.
22. Thye T., Vannberg F.O., Wong S.H., Owusu-Dabo E., Osei I., Gyapong J., Sirugo G., Sisay-Joof F., Enimil A., Chinbuah M.A., et al. Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2. Nat Genet 2010, 42:739-741.
23. Davila S., Wright V.J., Khor C.C., Sim K.S., Binder A., Breunis W.B., Inwald D., Nadel S., Betts H., Carrol E.D., 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.
24. Alcais A., Abel L., Casanova J.L. Human genetics of infectious diseases: between proof of principle and paradigm. J Clin Invest 2009, 119:2506-2514.
25. Calvo S.E., Mootha V.K. The mitochondrial proteome and human disease. Annu Rev Genomics Hum Genet 2010, 11:25-44.
26. Zak D.E., Aderem A. Systems biology of innate immunity. Immunol Rev 2009, 227:264-282.
27. Zaslavsky E, Hershberg U, Seto J, Pham AM, Marquez S, Duke JL, Wetmur JG, Tenoever BR, Sealfon SC, Kleinstein SH: Antiviral response dictated by choreographed cascade of transcription factors. J Immunol 2010, 184:2908-2917.
28. Berry MP, Graham CM, McNab FW, Xu Z, Bloch SA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, et al.: An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 2010, 466:973-977.
29. Cilloniz C., Shinya K., Peng X., Korth M.J., Proll S.C., Aicher L.D., Carter V.S., Chang J.H., Kobasa D., Feldmann F., et al. Lethal influenza virus infection in macaques is associated with early dysregulation of inflammatory related genes. PLoS Pathog 2009, 5:e1000604.
30. Kobasa D., Jones S.M., Shinya K., Kash J.C., Copps J., Ebihara H., Hatta Y., Kim J.H., Halfmann P., Hatta M., et al. Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus. Nature 2007, 445:319-323.
31. Querec T.D., Akondy R.S., Lee E.K., Cao W., Nakaya H.I., Teuwen D., Pirani A., Gernert K., Deng J., Marzolf B., et al. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol 2009, 10:116-125.
32. Diamond DL, Syder AJ, Jacobs JM, Sorensen CM, Walters KA, Proll SC, McDermott JE, Gritsenko MA, Zhang Q, Zhao R, et al.: Temporal proteome and lipidome profiles reveal hepatitis C virus-associated reprogramming of hepatocellular metabolism and bioenergetics. PLoS Pathog 2010, 6:e1000719.
33. Luber CA, Cox J, Lauterbach H, Fancke B, Selbach M, Tschopp J, Akira S, Wiegand M, Hochrein H, O'Keeffe M, et al.: Quantitative proteomics reveals subset-specific viral recognition in dendritic cells. Immunity 2010, 32:279-289.
34. Weintz G, Olsen JV, Fruhauf K, Niedzielska M, Amit I, Jantsch J, Mages J, Frech C, Dolken L, Mann M, et al.: The phosphoproteome of toll-like receptor-activated macrophages. Mol Syst Biol 2010, 6:371.
35. Burckstummer T., Baumann C., Bluml S., Dixit E., Durnberger G., Jahn H., Planyavsky M., Bilban M., Colinge J., Bennett K.L., et al. An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome. Nat Immunol 2009, 10:266-272.
36. Alexopoulos LG, Saez-Rodriguez J, Cosgrove BD, Lauffenburger DA, Sorger PK: Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Mol Cell Proteomics 2010, 9:1849-1865.
37. Litvak V., Ramsey S.A., Rust A.G., Zak D.E., Kennedy K.A., Lampano A.E., Nykter M., Shmulevich I., Aderem A. Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol 2009, 10:437-443.
38. Suzuki H., Forrest A.R., van Nimwegen E., Daub C.O., Balwierz P.J., Irvine K.M., Lassmann T., Ravasi T., Hasegawa Y., de Hoon M.J., et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet 2009, 41:553-562.
39. Konig R., Zhou Y., Elleder D., Diamond T.L., Bonamy G.M., Irelan J.T., Chiang C.Y., Tu B.P., De Jesus P.D., Lilley C.E., et al. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. Cell 2008, 135:49-60.
40. Watanabe T, Watanabe S, Kawaoka Y: Cellular networks involved in the influenza virus life cycle. Cell Host Microbe 2010, 7:427-439.
41. Kumar D, Nath L, Kamal MA, Varshney A, Jain A, Singh S, Rao KV: Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell 2010, 140:731-743.
42. Hughey JJ, Lee TK, Covert MW: Computational modeling of mammalian signaling networks. Wiley Interdiscip Rev Syst Biol Med 2010, 2:194-209.
43. Shih V.F., Kearns J.D., Basak S., Savinova O.V., Ghosh G., Hoffmann A. Kinetic control of negative feedback regulators of NF-kappaB/RelA determines their pathogen- and cytokine-receptor signaling specificity. Proc Natl Acad Sci U S A 2009, 106:9619-9624.
44. Cheong R., Hoffmann A., Levchenko A. Understanding NF-kappaB signaling via mathematical modeling. Mol Syst Biol 2008, 4:192.
45. Basak S., Kim H., Kearns J.D., Tergaonkar V., O'Dea E., Werner S.L., Benedict C.A., Ware C.F., Ghosh G., Verma I.M., et al. A fourth IkappaB protein within the NF-kappaB signaling module. Cell 2007, 128:369-381.
46. Tay S, Hughey JJ, Lee TK, Lipniacki T, Quake SR, Covert MW: Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature 2010, 466:267-271.
47. Lynn D.J., Winsor G.L., Chan C., Richard N., Laird M.R., Barsky A., Gardy J.L., Roche F.M., Chan T.H., Shah N., et al. InnateDB: facilitating systems-level analyses of the mammalian innate immune response. Mol Syst Biol 2008, 4:218.