Deep sequencing of the innate immune transcriptomic response of zebrafish embryos to Salmonella infection

Fish and Shellfish Immunology

Volumn 31, Issue 5, 2011, Pages 716-724

  Ordas, Anita ^a,b   Hegedus, Zoltan ^c,d   Henkel, Christiaan V ^e   Stockhammer, Oliver W ^a   Butler, Derek ^f   Jansen, Hans J ^e   Racz, Peter ^a,b   Mink, Matyas ^b   Spaink, Herman P ^a   Meijer, Annemarie H ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

^b UNIVERSITY OF SZEGED   (Hungary)

^c Zenon Bio Ltd   (Hungary)

^d INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^e ZF Screens BV ^*  (Netherlands)

^f BaseClear BV   (Netherlands)

Author keywords

Innate immunity; RNA Seq; Salmonella typhimurium; Tag Seq; Zebrafish embryo

Indexed keywords

BACTERIA (MICROORGANISMS); DANIO RERIO; MYCOBACTERIUM MARINUM; SALMONELLA; SALMONELLA ENTERICA; SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM; SALMONELLA TYPHIMURIUM;

EID: 80053233587     PISSN: 10504648     EISSN: 10959947     Source Type: Journal    
DOI: 10.1016/j.fsi.2010.08.022     Document Type: Article

References (28)

1. Traver D., Herbomel P., Patton E.E., Murphey R.D., Yoder J.A., Litman G.W., et al. The zebrafish as a model organism to study development of the immune system. Adv Immunol 2003, 81:253-330.
2. Trede N.S., Langenau D.M., Traver D., Look A.T., Zon L.I. The use of zebrafish to understand immunity. Immunity 2004, 20(4):367-379.
3. Davidson A.J., Zon L.I. The 'definitive' (and 'primitive') guide to zebrafish hematopoiesis. Oncogene 2004, 23(43):7233-7246.
4. Herbomel P., Thisse B., Thisse C. Ontogeny and behaviour of early macrophages in the zebrafish embryo. Development 1999, 126(17):3735-3745.
5. Lam S.H., Chua H.L., Gong Z., Lam T.J., Sin Y.M. Development and maturation of the immune system in zebrafish, Danio rerio: a gene expression profiling, in situ hybridization and immunological study. Dev Comp Immunol 2004, 28(1):9-28.
6. Willett C.E., Cortes A., Zuasti A., Zapata A.G. Early hematopoiesis and developing lymphoid organs in the zebrafish. Dev Dyn 1999, 214(4):323-336.
7. Meijer A.H., Gabby Krens S.F., Medina Rodriguez I.A., He S., Bitter W., Ewa Snaar-Jagalska B., et al. Expression analysis of the Toll-like receptor and TIR domain adaptor families of zebrafish. Mol Immunol 2004, 40(11):773-783.
8. Stein C., Caccamo M., Laird G., Leptin M. Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish. Genome Biol 2007, 8(11):R251.
9. Meeker N.D., Trede N.S. Immunology and zebrafish: spawning new models of human disease. Dev Comp Immunol 2008, 32(7):745-757.
10. Santos R.L., Zhang S., Tsolis R.M., Kingsley R.A., Adams L.G., Baumler A.J. Animal models of Salmonella infections: enteritis versus typhoid fever. Microbes Infect 2001, 3(14-15):1335-1344.
11. van der Sar A.M., Musters R.J., van Eeden F.J., Appelmelk B.J., Vandenbroucke-Grauls C.M., Bitter W. Zebrafish embryos as a model host for the real time analysis of Salmonella typhimurium infections. Cell Microbiol 2003, 5(9):601-611.
12. Salazar-Gonzalez R.M., McSorley S.J. Salmonella flagellin, a microbial target of the innate and adaptive immune system. Immunol Lett 2005, 101(2):117-122.
13. van der Sar A.M., Stockhammer O.W., van der Laan C., Spaink H.P., Bitter W., Meijer A.H. MyD88 innate immune function in a zebrafish embryo infection model. Infect Immun 2006, 74(4):2436-2441.
14. Stockhammer O.W., Zakrzewska A., Hegedus Z., Spaink H.P., Meijer A.H. Transcriptome profiling and functional analyses of the zebrafish embryonic innate immune response to Salmonella infection. J Immunol 2009, 182(9):5641-5653.
15. Hegedus Z., Zakrzewska A., Agoston V.C., Ordas A., Racz P., Mink M., et al. Deep sequencing of the zebrafish transcriptome response to mycobacterium infection. Mol Immunol 2009, 46(15):2918-2930.
16. Hoen P.A., Ariyurek Y., Thygesen H.H., Vreugdenhil E., Vossen R.H., de Menezes R.X., et al. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res 2008, 36(21):e141.
17. Morrissy A.S., Morin R.D., Delaney A., Zeng T., McDonald H., Jones S., et al. Next-generation tag sequencing for cancer gene expression profiling. Genome Res 2009, 19(10):1825-1835.
18. Lash A.E., Tolstoshev C.M., Wagner L., Schuler G.D., Strausberg R.L., Riggins G.J., et al. SAGEmap: a public gene expression resource. Genome Res 2000, 10(7):1051-1060.
19. Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628.
20. Beisvag V., Junge F.K., Bergum H., Jolsum L., Lydersen S., Gunther C.C., et al. GeneTools - application for functional annotation and statistical hypothesis testing. BMC Bioinformatics 2006, 7:470.
21. Jenner R.G., Young R.A. Insights into host responses against pathogens from transcriptional profiling. Nat Rev Microbiol 2005, 3(4):281-294.
22. Meijer A.H., Verbeek F.J., Salas-Vidal E., Corredor-Adamez M., Bussman J., van der Sar A.M., et al. Transcriptome profiling of adult zebrafish at the late stage of chronic tuberculosis due to Mycobacterium marinum infection. Mol Immunol 2005, 42(10):1185-1203.
23. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10(1):57-63.
24. Beiter T., Reich E., Williams R.W., Simon P. Antisense transcription: a critical look in both directions. Cell Mol Life Sci 2009, 66(1):94-112.
25. Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., et al. The transcriptional landscape of the mammalian genome. Science 2005, 309(5740):1559-1563.
26. Katayama S., Tomaru Y., Kasukawa T., Waki K., Nakanishi M., Nakamura M., et al. Antisense transcription in the mammalian transcriptome. Science 2005, 309(5740):1564-1566.
27. van der Sar A.M., Spaink H.P., Zakrzewska A., Bitter W., Meijer A.H. Specificity of the zebrafish host transcriptome response to acute and chronic mycobacterial infection and the role of innate and adaptive immune components. Mol Immunol 2009, 46(11-12):2317-2332.
28. Stockhammer OW, Rauwerda H, Wittink FR, Breit TM, Meijer AH, Spaink HP. Transcriptome analysis of Traf6 function in the innate immune response of zebrafish embryos. Mol Immunol, in press, doi:10.1016/j.molimm.2010.08.011.