Differential gene expression segregates cattle confirmed positive for bovine tuberculosis from antemortem tuberculosis test-false positive cattle originating from herds free of bovine tuberculosis

Veterinary Medicine International

Volumn , Issue , 2012, Pages

  Lim, Ailam ^a   Steibel, Juan P ^a   Coussens, Paul M ^a   Grooms, Daniel L ^a   Bolin, Steven R ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); BOS; BOVINAE; MYCOBACTERIUM BOVIS;

EID: 84863649604     PISSN: None     EISSN: 20420048     Source Type: Journal    
DOI: 10.1155/2012/192926     Document Type: Article

References (56)

1. Garnier T., Eiglmeier K., Camus J. C., Medina N., Mansoor H., Pryor M., Duthoy S., Grondin S., Lacroix C., Monsempe C., Simon S., Harris B., Atkin R., Doggett J., Mayes R., Keating L., Wheeler P. R., Parkhill J., Barrell B. G., Cole S. T., Gordon S. V., Hewinson R. G., The complete genome sequence of Mycobacterium bovis Proceedings of the National Academy of Sciences of the United States of America 2003 100 13 7877 7882 (Pubitemid 36760063)
2. Schiller I., Oesch B., Vordermeier H. M., Palmer M. V., Harris B. N., Orloski K. A., Buddle B. M., Thacker T. C., Lyashchenko K. P., Waters W. R., Bovine tuberculosis: a review of current and emerging diagnostic techniques in view of their relevance for disease control and eradication Transboundary and Emerging Diseases 2010 57 4 205 220
3. O'Brien D. J., Schmitt S. M., Fitzgerald S. D., Berry D. E., Hickling G. J., Managing the wildlife reservoir of Mycobacterium bovis: The Michigan, USA, experience Veterinary Microbiology 2006 112 2-4 313 323 (Pubitemid 43182761)
4. Michel A. L., Bengis R. G., Keet D. F., Hofmeyr M., De Klerk L. M., Cross P. C., Jolles A. E., Cooper D., Whyte I. J., Buss P., Godfroid J., Wildlife tuberculosis in South African conservation areas: implications and challenges Veterinary Microbiology 2006 112 2-4 91 100 (Pubitemid 43182741)
5. de Kantor I. N., Ambroggi M., Poggi S., Morcillo N., Da Silva Telles M. A., Osrio Ribeiro M., Garzn Torres M. C., LLerena Polo C., Ribn W., Garca V., Kuffo D., Asencios L., Vsquez Campos L. M., Rivas C., de Waard J. H., Human Mycobacterium bovis infection in ten Latin American countries Tuberculosis 2008 88 4 358 365
6. WHO, The Control of Neglected Zoonotic Diseases. A route to poverty allevation 2006 Geneva, Switzerland WHO
7. Anon, A New Approach for Managing Bovine Tuberculosis: Veterinary Services Proposed Action Plan. USDA/APHIS/VS, July 2009
8. Monaghan M. L., Doherty M. L., Collins J. D., Kazda J. F., Quinn P. J., The tuberculin test Veterinary Microbiology 1994 40 1-2 111 124 (Pubitemid 24175295)
9. Anon, Michigan Bovine Tuberculosis Eradication Project Activities Report. Annual Report, Michigan, 2008
10. Boldrick J. C., Alizadeh A. A., Diehn M., Dudoit S., Liu C. L., Belcher C. E., Botstein D., Staudt L. M., Brown P. O., Relman D. A., Stereotyped and specific gene expression programs in human innate immune responses to bacteria Proceedings of the National Academy of Sciences of the United States of America 2002 99 2 972 977 (Pubitemid 34106620)
11. Jenner R. G., Young R. A., Insights into host responses against pathogens from transcriptional profiling Nature Reviews Microbiology 2005 3 4 281 294 (Pubitemid 40443722)
12. Ramilo O., Allman W., Chung W., Mejias A., Ardura M., Glaser C., Wittkowski K. M., Piqueras B., Banchereau J., Palucka A. K., Chaussabel D., Gene expression patterns in blood leukocytes discriminate patients with acute infections Blood 2007 109 5 2066 2077 (Pubitemid 46348207)
13. Sarmento L., Afonso C. L., Estevez C., Wasilenko J., Pantin-Jackwood M., Differential host gene expression in cells infected with highly pathogenic H5N1 avian influenza viruses Veterinary Immunology and Immunopathology 2008 125 3-4 291 302
14. Paranavitana C., Pittman P. R., Velauthapillai M., Zelazowska E., DaSilva L., Transcriptional profiling of Francisella tularensis infected peripheral blood mononuclear cells: a predictive tool for tularemia FEMS Immunology and Medical Microbiology 2008 54 1 92 103
15. Coussens P. M., Pudrith C. B., Skovgaard K., Ren X., Suchyta S. P., Stabel J. R., Heegaard P. M. H., Johne's disease in cattle is associated with enhanced expression of genes encoding IL-5, GATA-3, tissue inhibitors of matrix metalloproteinases 1 and 2, and factors promoting apoptosis in peripheral blood mononuclear cells Veterinary Immunology and Immunopathology 2005 105 3-4 221 234 (Pubitemid 40460947)
16. Meade K. G., Gormley E., O'Farrelly C., Park S. D., Costello E., Keane J., Zhao Y., MacHugh D. E., Antigen stimulation of peripheral blood mononuclear cells from Mycobacterium bovis infected cattle yields evidence for a novel gene expression program BMC Genomics 2008 9, article no. 447
17. Bejjani B. A., Shaffer L. G., Clinical utility of contemporary molecular cytogenetics Annual Review of Genomics and Human Genetics 2008 9 71 86
18. Stern J. N. H., Keskin D. B., Romero V., Zuniga J., Encinales L., Li C., Awad C., Yunis E. J., Molecular signatures distinguishing active from latent tuberculosis in peripheral blood mononuclear cells, after in vitro antigenic stimulation with purified protein derivative of tuberculin (PPD) or Candida: a preliminary report Immunologic Research 2009 45 1 1 12
19. Coussens P. M., Colvin C. J., Wiersma K., Abouzied A., Sipkovsky S., Gene expression profiling of peripheral blood mononuclear cells from cattle infected with Mycobacterium paratuberculosis Infection and Immunity 2002 70 10 5494 5502
20. Skovgaard K., Grell S. N., Heegaard P. M. H., Jungersen G., Pudrith C. B., Coussens P. M., Differential expression of genes encoding CD30L and P-selectin in cattle with Johne's disease: Progress toward a diagnostic gene expression signature Veterinary Immunology and Immunopathology 2006 112 3-4 210 224 (Pubitemid 43975143)
21. Meade K. G., Gormley E., Doyle M. B., Fitzsimons T., O'Farrelly C., Costello E., Keane J., Zhao Y., MacHugh D. E., Innate gene repression associated with Mycobacterium bovis infection in cattle: toward a gene signature of disease BMC Genomics 2007 8, article no. 400
22. Meade K. G., Gormley E., Park S. D. E., Fitzsimons T., Rosa G. J. M., Costello E., Keane J., Coussens P. M., MacHugh D. E., Gene expression profiling of peripheral blood mononuclear cells (PBMC) from Mycobacterium bovis infected cattle after in vitro antigenic stimulation with purified protein derivative of tuberculin (PPD) Veterinary Immunology and Immunopathology 2006 113 1-2 73 89 (Pubitemid 44131570)
23. MacHugh D. E., Gormley E., Park S. D. E., Browne J. A., Taraktsoglou M., O'Farrelly C., Meade K. G., Gene expression profiling of the host response to mycobacterium bovis infection in cattle Transboundary and Emerging Diseases 2009 56 6-7 204 214
24. Coussens P. M., Colvin C. J., Rosa G. J. M., Perez Laspiur J., Elftman M. D., Evidence for a novel gene expression program in peripheral blood mononuclear cells from Mycobacterium avium subsp paratuberculosis-infected cattle Infection and Immunity 2003 71 11 6487 6498 (Pubitemid 37337709)
25. Yao J., Burton J. L., Saama P., Sipkovsky S., Coussens P. M., Generation of EST and cDNA microarray resources for the study of bovine immunobiology Acta Veterinaria Scandinavica 2003 44 1 S89 S103
26. Coussens P. M., Nobis W., Bioinformatics and high throughput approach to create genomic resources for the study of bovine immunobiology Veterinary Immunology and Immunopathology 2002 86 3-4 229 244 (Pubitemid 34465753)
27. Steibel J. P., Rosa G. J. M., On reference designs for microarray experiments Statistical Applications in Genetics and Molecular Biology 2005 4 1, article no. 36
28. Churchill G. A., Fundamentals of experimental design for cDNA microarrays Nature Genetics 2002 32 5 490 495 (Pubitemid 35435151)
29. Dobbin K., Shih J. H., Simon R., Questions and answers on design of dual-label microarrays for identifying differentially expressed genes Journal of the National Cancer Institute 2003 95 18 1362 1369 (Pubitemid 37220455)
30. Smyth G. K., Gentleman V. C. R., Dudoit S., Irizarry R., Huber W., Limma: linear models for microarray data Bioinformatics and Computational Biology Solutions using R and Bioconductor 2005 New York, NY, USA Springer 397 420
31. Development Core Team R, R: A Language and Environment for Statistical Computing 2011 Vienna, Austria R Foundation for Statistical Computing
32. Ritchie M. E., Silver J., Oshlack A., Holmes M., Diyagama D., Holloway A., Smyth G. K., A comparison of background correction methods for two-colour microarrays Bioinformatics 2007 23 20 2700 2707 (Pubitemid 350048334)
33. Smyth G. K., Speed T., Normalization of cDNA microarray data Methods 2003 31 4 265 273 (Pubitemid 37338763)
34. Smyth G. K., Linear models and empirical bayes methods for assessing differential expression in microarray experiments Statistical Applications in Genetics and Molecular Biology 2004 3 1, article 3
35. Robinson T. L., Sutherland I. A., Sutherland J., Validation of candidate bovine reference genes for use with real-time PCR Veterinary Immunology and Immunopathology 2007 115 1-2 160 165 (Pubitemid 44908667)
36. Ramakers C., Ruijter J. M., Lekanne Deprez R. H., Moorman A. F. M., Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data Neuroscience Letters 2003 339 1 62 66 (Pubitemid 36263221)
37. Pfaffl M. W., A new mathematical model for relative quantification in real-time RT-PCR Nucleic Acids Research 2001 29 9, article e45
38. Steibel J. P., Poletto R., Coussens P. M., Rosa G. J. M., A powerful and flexible linear mixed model framework for the analysis of relative quantification RT-PCR data Genomics 2009 94 2 146 152
39. Wu H., Churchill G. A., R/MAANOVA: An Extensive R Environment for the Analysis of Microarray Experiments. 2008, http://churchill.jax.org/software/ rmaanova/maanova.pdf
40. Storey J. D., A direct approach to false discovery rates Journal of the Royal Statistical Society B 2002 64 3 479 498
41. Anon, Bovine Tuberculosis: Diagnostic techniques Manual of Diagnostic Tests and Vaccines for Terrestrial Animals 2008 chapter 2.4.7 OIE 686 689
42. de la Rua-Domenech R., Goodchild A. T., Vordermeier H. M., Hewinson R. G., Christiansen K. H., Clifton-Hadley R. S., Ante mortem diagnosis of tuberculosis in cattle: a review of the tuberculin tests, -interferon assay and other ancillary diagnostic techniques Research in Veterinary Science 2006 81 2 190 210 (Pubitemid 43905909)
43. Coad M., Downs S. H., Durr P. A., Clifton-Hadley R. S., Hewinson R. G., Vordermeier H. M., Whelan A. O., Blood-based assays to detect Mycobacterium bovis-infected cattle missed by tuberculin skin testing Veterinary Record 2008 162 12 382 384 (Pubitemid 351529844)
44. Schiller I., Vordermeier H. M., Waters W. R., Whelan A. O., Coad M., Gormley E., Buddle B. M., Palmer M., Thacker T., McNair J., Welsh M., Hewinson R. G., Oesch B., Bovine tuberculosis: effect of the tuberculin skin test on in vitro interferon gamma responses Veterinary Immunology and Immunopathology 2010 136 1-2 1 11
45. Coussens P. M., Jeffers A., Colvin C., Rapid and transient activation of gene expression in peripheral blood mononuclear cells from Johne's disease positive cows exposed to Mycobacterium paratuberculosis in vitro Microbial Pathogenesis 2004 36 2 93 108 (Pubitemid 37543701)
46. Bustin S. A., Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays Journal of Molecular Endocrinology 2000 25 2 169 193
47. Hendriks-Balk M. C., Michel M. C., Alewijnse A. E., Pitfalls in the normalization of real-time polymerase chain reaction data Basic Research in Cardiology 2007 102 3 195 197 (Pubitemid 46564068)
48. Wood P. R., Corner L. A., Plackett P., Development of a simple, rapid in vitro cellular assay for bovine tuberculosis based on the production of gamma interferon Research in veterinary science 1990 49 1 46 49
49. Phillips C. J. C., Foster C. R. W., Morris P. A., Teverson R., The transmission of Mycobacterium bovis infection to cattle Research in Veterinary Science 2003 74 1 1 15 (Pubitemid 36175763)
50. Pollock J. M., Girvin R. M., Lightbody K. A., Clements R. A., Neill S. D., Buddle B. M., Andersen P., Assessment of defined antigens for the diagnosis of bovine tuberculosis in skin test-reactor cattle Veterinary Record 2000 146 23 659 665
51. Morrison W. I., Bourne F. J., Cox D. R., Donnelly C. A., Gettinby G., Mcinerney J. P., Woodroffe R., Pathogenesis and diagnosis of infections with Mycobacterium bovis in cattle Veterinary Record 2000 146 9 236 242
52. Corner L. A., Post mortem diagnosis of Mycobacterium bovis infection in cattle Veterinary Microbiology 1994 40 1-2 53 63 (Pubitemid 24175291)
53. Pollock J. M., Neill S. D., Mycobacterium bovis infection and tuberculosis in cattle Veterinary Journal 2002 163 2 115 127 (Pubitemid 37555102)
54. Vordermeier H. A., Whelan A., Hewinson A. R. G., The scientific case for the gamma interferon BOVIGAM assay Government Veterinary Journal 2008 19 38 43
55. Morrison W. I., Bourne F. J., Cox D. R., Donnelly C. A., Gettinby G., Mcinerney J. P., Woodroffe R., Pathogenesis and diagnosis of infections with Mycobacterium bovis in cattle Cattle Practice 2005 13 351 360
56. Van Rhijn I., Godfroid J., Michel A., Rutten V., Bovine tuberculosis as a model for human tuberculosis: advantages over small animal models Microbes and Infection 2008 10 7 711 715