Integrated microrna-mrna-analysis of human monocyte derived macrophages upon mycobacterium avium subsp. hominissuis infection

PLoS ONE

Volumn 6, Issue 5, 2011, Pages

  Sharbati, Jutta ^a   Lewin, Astrid ^b   Kutz Lohroff, Barbara ^a   Kamal, Elisabeth ^b   Einspanier, Ralf ^a   Sharbati, Soroush ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b ROBERT KOCH INSTITUTE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CASPASE 3; CASPASE 7; MESSENGER RNA; MICRORNA; PROTEIN BCL 2;

APOPTOSIS; ARTICLE; ATYPICAL MYCOBACTERIOSIS; BACTERIUM ISOLATION; CONTROLLED STUDY; DOWN REGULATION; ENZYME ACTIVITY; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE TARGETING; HUMAN; HUMAN CELL; MACROPHAGE; MICROARRAY ANALYSIS; MONOCYTE; MYCOBACTERIUM AVIUM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; RNA BINDING; TRANSCRIPTION REGULATION; UPREGULATION; 3' UNTRANSLATED REGION; CELL CULTURE; DNA MICROARRAY; GENETICS; METABOLISM; MICROBIOLOGY; PHYSIOLOGY; TUBERCULOSIS;

CORYNEBACTERINEAE; EUKARYOTA; MYCOBACTERIUM AVIUM;

3' UNTRANSLATED REGIONS; CELLS, CULTURED; HUMANS; MACROPHAGES; MICRORNAS; MYCOBACTERIUM AVIUM; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER; TUBERCULOSIS;

EID: 79956353001     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020258     Document Type: Article

References (63)

1. Corti M, Palmero DJ, (2008) Mycobacterium avium complex infection in HIV/AIDS patients. Expert Review of Anti-Infective Therapy 6: 351.
2. Haverkamp MH, Arend SM, Lindeboom JA, Hartwig NG, van Dissel JT, (2004) Nontuberculous mycobacterial infection in children: a 2-year prospective surveillance study in the Netherlands. Clin Infect Dis 39: 450-456.
3. Wittram C, Weisbrod GL, (2002) Mycobacterium avium complex lung disease in immunocompetent patients: radiography-CT correlation. Br J Radiol 75: 340-344.
4. Mijs W, de Haas P, Rossau R, Van der Laan T, Rigouts L, et al. (2002) Molecular evidence to support a proposal to reserve the designation Mycobacterium avium subsp. avium for bird-type isolates and 'M. avium subsp. hominissuis' for the human/porcine type of M. avium. Int J Syst Evol Microbiol 52: 1505-1518.
5. Appelberg R, (2006) Pathogenesis of Mycobacterium avium infection: typical responses to an atypical mycobacterium? Immunol Res 35: 179-190.
6. Greenwell-Wild T, Vazquez N, Sim D, Schito M, Chatterjee D, et al. (2002) Mycobacterium avium infection and modulation of human macrophage gene expression. Journal of Immunology 169: 6286.
7. Quesniaux V, Fremond C, Jacobs M, Parida S, Nicolle D, et al. (2004) Toll-like receptor pathways in the immune responses to mycobacteria. Microbes and Infection 6: 946.
8. Aki D, Minoda Y, Yoshida H, Watanabe S, Yoshida R, et al. (2008) Peptidoglycan and lipopolysaccharide activate PLCgamma2, leading to enhanced cytokine production in macrophages and dendritic cells. Genes Cells 13: 199-208.
9. Vazquez N, Greenwell-Wild T, Rekka S, Orenstein JM, Wahl SM, (2006) Mycobacterium avium-induced SOCS contributes to resistance to IFN-γ-mediated mycobactericidal activity in human macrophages. Journal of Leukocyte Biology 80: 1136.
10. Blumenthal A, Lauber J, Hoffmann R, Ernst M, Keller C, et al. (2005) Common and unique gene expression signatures of human macrophages in response to four strains of Mycobacterium avium that differ in their growth and persistence characteristics. Infection and Immunity 73: 3330.
11. Balcewicz-Sablinska MK, Gan H, Remold HG, (1999) Interleukin 10 produced by macrophages inoculated with Mycobacterium avium attenuates mycobacteria-induced apoptosis by reduction of TNF-alpha activity. J Infect Dis 180: 1230-1237.
12. Behar SM, Divangahi M, Remold HG, (2010) Evasion of innate immunity by Mycobacterium tuberculosis: is death an exit strategy? Nat Rev Microbiol 8: 668-674.
13. Behar SM, Martin CJ, Booty MG, Nishimura T, Zhao X, et al. (2011) Apoptosis is an innate defense function of macrophages against Mycobacterium tuberculosis. Mucosal Immunol.
14. McGarvey JA, Wagner D, Bermudez LE, (2004) Differential gene expression in mononuclear phagocytes infected with pathogenic and non-pathogenic mycobacteria. Clinical and Experimental Immunology 136: 490.
15. Kloosterman WP, Plasterk RH, (2006) The diverse functions of microRNAs in animal development and disease. Dev Cell 11: 441-450.
16. Lynam-Lennon N, Maher SG, Reynolds JV, (2009) The roles of microRNA in cancer and apoptosis. Biol Rev Camb Philos Soc 84: 55-71.
17. Tsang WP, Kwok TT, (2008) Let-7a microRNA suppresses therapeutics-induced cancer cell death by targeting caspase-3. Apoptosis 13: 1215-1222.
18. O'Connell RM, Rao DS, Chaudhuri AA, Baltimore D, (2010) Physiological and pathological roles for microRNAs in the immune system. Nat Rev Immunol 10: 111-122.
19. Sales G, Coppe A, Bisognin A, Biasiolo M, Bortoluzzi S, et al. (2010) MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. Nucleic Acids Res 38 (Suppl): 352-359.
20. Nam S, Li M, Choi K, Balch C, Kim S, et al. (2009) MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res 37: 356-362.
21. Horan KL, Freeman R, Weigel K, Semret M, Pfaller S, et al. (2006) Isolation of the genome sequence strain Mycobacterium avium 104 from multiple patients over a 17-year period. J Clin Microbiol 44: 783-789.
22. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382.
23. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, et al. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091-1093.
24. Shi S, Blumenthal A, Hickey CM, Gandotra S, Levy D, et al. (2005) Expression of many immunologically important genes in Mycobacterium tuberculosis-infected macrophages is independent of both TLR2 and TLR4 but dependent on IFN-alphabeta receptor and STAT1. J Immunol 175: 3318-3328.
25. Benoit M, Desnues B, Mege JL, (2008) Macrophage polarization in bacterial infections. J Immunol 181: 3733-3739.
26. Busca A, Saxena M, Kryworuchko M, Kumar A, (2009) Anti-apoptotic genes in the survival of monocytic cells during infection. Curr Genomics 10: 306-317.
27. Androulidaki A, Iliopoulos D, Arranz A, Doxaki C, Schworer S, et al. (2009) The kinase Akt1 controls macrophage response to lipopolysaccharide by regulating microRNAs. Immunity 31: 220-231.
28. Scharl M, Hruz P, McCole DF, (2010) Protein tyrosine phosphatase non-receptor Type 2 regulates IFN-gamma-induced cytokine signaling in THP-1 monocytes. Inflamm Bowel Dis 16: 2055-2064.
29. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: 355-360.
30. Sharbati-Tehrani S, Kutz-Lohroff B, Bergbauer R, Scholven J, Einspanier R, (2008) miR-Q: a novel quantitative RT-PCR approach for the expression profiling of small RNA molecules such as miRNAs in a complex sample. BMC Mol Biol 9: 34.
31. Kruger J, Rehmsmeier M, (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34: 451-454.
32. Dvorska L, Matlova L, Bartos M, Parmova I, Bartl J, et al. (2004) Study of Mycobacterium avium complex strains isolated from cattle in the Czech Republic between 1996 and 2000. Vet Microbiol 99: 239-250.
33. Semret M, Zhai G, Mostowy S, Cleto C, Alexander D, et al. (2004) Extensive genomic polymorphism within Mycobacterium avium. J Bacteriol 186: 6332-6334.
34. Hussain S, Zwilling BS, Lafuse WP, (1999) Mycobacterium avium infection of mouse macrophages inhibits IFN-gamma Janus kinase-STAT signaling and gene induction by down-regulation of the IFN-gamma receptor. J Immunol 163: 2041-2048.
35. Gehring AJ, Rojas RE, Canaday DH, Lakey DL, Harding CV, et al. (2003) The Mycobacterium tuberculosis 19-kilodalton lipoprotein inhibits gamma interferon-regulated HLA-DR and Fc gamma R1 on human macrophages through Toll-like receptor 2. Infect Immun 71: 4487-4497.
36. Tsuji S, Matsumoto M, Takeuchi O, Akira S, Azuma I, et al. (2000) Maturation of human dendritic cells by cell wall skeleton of Mycobacterium bovis bacillus Calmette-Guerin: involvement of toll-like receptors. Infect Immun 68: 6883-6890.
37. Jo EK, Yang CS, Choi CH, Harding CV, (2007) Intracellular signalling cascades regulating innate immune responses to Mycobacteria: branching out from Toll-like receptors. Cell Microbiol 9: 1087-1098.
38. Korbel DS, Schneider BE, Schaible UE, (2008) Innate immunity in tuberculosis: myths and truth. Microbes Infect 10: 995-1004.
39. Yamada H, Mizumo S, Horai R, Iwakura Y, Sugawara I, (2000) Protective role of interleukin-1 in mycobacterial infection in IL-1 alpha/beta double-knockout mice. Lab Invest 80: 759-767.
40. Parihar A, Eubank TD, Doseff AI, (2010) Monocytes and macrophages regulate immunity through dynamic networks of survival and cell death. J Innate Immun 2: 204-215.
41. Gey Van Pittius NC, Gamieldien J, Hide W, Brown GD, Siezen RJ, et al. (2001) The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria. Genome Biol 2: 44.
42. Koul A, Herget T, Klebl B, Ullrich A, (2004) Interplay between mycobacteria and host signalling pathways. Nat Rev Microbiol 2: 189-202.
43. Pathak SK, Basu S, Bhattacharyya A, Pathak S, Kundu M, et al. (2005) Mycobacterium tuberculosis lipoarabinomannan-mediated IRAK-M induction negatively regulates Toll-like receptor-dependent interleukin-12 p40 production in macrophages. J Biol Chem 280: 42794-42800.
44. Mott JL, Kurita S, Cazanave SC, Bronk SF, Werneburg NW, et al. (2010) Transcriptional suppression of mir-29b-1/mir-29a promoter by c-Myc, hedgehog, and NF-kappaB. J Cell Biochem 110: 1155-1164.
45. Ganguly N, Giang PH, Basu SK, Mir FA, Siddiqui I, et al. (2007) Mycobacterium tuberculosis 6-kDa early secreted antigenic target (ESAT-6) protein downregulates lipopolysaccharide induced c-myc expression by modulating the extracellular signal regulated kinases 1/2. BMC Immunol 8: 24.
46. Kapinas K, Kessler C, Ricks T, Gronowicz G, Delany AM, (2010) miR-29 modulates Wnt signaling in human osteoblasts through a positive feedback loop. J Biol Chem 285: 25221-25231.
47. Pereira CP, Bachli EB, Schoedon G, (2009) The wnt pathway: a macrophage effector molecule that triggers inflammation. Curr Atheroscler Rep 11: 236-242.
48. Wang A, Johnston SC, Chou J, Dean D, (2010) A systemic network for Chlamydia pneumoniae entry into human cells. J Bacteriol 192: 2809-2815.
49. Leemans JC, Florquin S, Heikens M, Pals ST, van der Neut R, et al. (2003) CD44 is a macrophage binding site for Mycobacterium tuberculosis that mediates macrophage recruitment and protective immunity against tuberculosis. J Clin Invest 111: 681-689.
50. Li JH, Xiao X, Zhang YN, Wang YM, Feng LM, et al. (2010) MicroRNA miR-886-5p inhibits apoptosis by down-regulating Bax expression in human cervical carcinoma cells. Gynecol Oncol 120: 145-151.
51. Shimizu S, Takehara T, Hikita H, Kodama T, Miyagi T, et al. (2010) The let-7 family of microRNAs inhibits Bcl-xL expression and potentiates sorafenib-induced apoptosis in human hepatocellular carcinoma. J Hepatol 52: 698-704.
52. Keane J, Remold HG, Kornfeld H, (2000) Virulent Mycobacterium tuberculosis strains evade apoptosis of infected alveolar macrophages. J Immunol 164: 2016-2020.
53. Zhang J, Jiang R, Takayama H, Tanaka Y, (2005) Survival of virulent Mycobacterium tuberculosis involves preventing apoptosis induced by Bcl-2 upregulation and release resulting from necrosis in J774 macrophages. Microbiol Immunol 49: 845-852.
54. Fratazzi C, Arbeit RD, Carini C, Remold HG, (1997) Programmed cell death of Mycobacterium avium serovar 4-infected human macrophages prevents the mycobacteria from spreading and induces mycobacterial growth inhibition by freshly added, uninfected macrophages. J Immunol 158: 4320-4327.
55. Bermudez LE, Parker A, Petrofsky M, (1999) Apoptosis of Mycobacterium avium-infected macrophages is mediated by both tumour necrosis factor (TNF) and Fas, and involves the activation of caspases. Clin Exp Immunol 116: 94-99.
56. Barry DP, Beaman BL, (2006) Modulation of eukaryotic cell apoptosis by members of the bacterial order Actinomycetales. Apoptosis 11: 1695-1707.
57. Sharbati S, Schramm K, Rempel S, Wang H, Andrich R, et al. (2009) Characterisation of porin genes from Mycobacterium fortuitum and their impact on growth. BMC Microbiol 9: 31.
58. Sharbati-Tehrani S, Stephan J, Holland G, Appel B, Niederweis M, et al. (2005) Porins limit the intracellular persistence of Mycobacterium smegmatis. Microbiology 151: 2403-2410.
59. Sharbati S, Friedlander MR, Sharbati J, Hoeke L, Chen W, et al. (2010) Deciphering the porcine intestinal microRNA transcriptome. BMC Genomics 11: 275.
60. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, et al. (2009) NCBI GEO: archive for high-throughput functional genomic data. Nucleic Acids Res 37: D885-890.
61. Scholven J, Taras D, Sharbati S, Schön J, Gabler C, et al. (2009) Intestinal expression of TFF and related genes during postnatal development in a piglet probiotic trial. Cellular Physiology and Biochemistry 23: 143-156.
62. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: 34.
63. Saeed AI, Sharov V, White J, Li J, Liang W, et al. (2003) TM4: a free, open-source system for microarray data management and analysis. Biotechniques 34: 374-378.