Whole blood transcriptome comparison of pigs with extreme production of in vivo dsRNA-induced serum IFN-a

Developmental and Comparative Immunology

Volumn 44, Issue 1, 2014, Pages 35-43

  Liu, Xiangdong ^a,b   Huang, Jing ^a,d   Yang, Songbai ^a   Zhao, Yunxia ^a   Xiang, Anjing ^a   Cao, Jianhua ^a   Fan, Bin ^a   Wu, Zhenfang ^c   Zhao, Junlong ^b   Zhao, Shuhong ^a   Zhu, Mengjin ^a  

^a Huazhong Agricultural University   (China)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^c SOUTH CHINA AGRICULTURAL UNIVERSITY   (China)

^d INSTITUTE OF PLANT PROTECTION AND MICROBIOLOGY   (China)

Author keywords

Blood; DsRNA; IFN a; Pig; Poly I:C; Transcriptome

Indexed keywords

ALPHA INTERFERON; DOUBLE STRANDED RNA; INTERFERON REGULATORY FACTOR 7; MEMBRANE PROTEIN; POLYINOSINIC POLYCYTIDYLIC ACID; PROTEIN MDA5; RETINOIC ACID INDUCIBLE PROTEIN I; TOLL LIKE RECEPTOR; TRANSCRIPTION FACTOR; TRANSCRIPTOME; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ANIMAL MODEL; ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; CYTOKINE PRODUCTION; CYTOKINE RESPONSE; GENE; GENE EXPRESSION; IMMUNE RESPONSE; IN VIVO STUDY; INTERFERON STIMULATED GENE; MICROARRAY ANALYSIS; NONHUMAN; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN BLOOD LEVEL; PROTEIN EXPRESSION; SIGNAL TRANSDUCTION; SWINE; TRANSCRIPTOMICS; VIRUS IMMUNITY; VIRUS INFECTION; VIRUS RESISTANCE;

SUIDAE;

BLOOD; DSRNA; IFN-A; PIG; POLY I:C; TRANSCRIPTOME;

ANIMALS; IMMUNITY, INNATE; INTERFERON REGULATORY FACTOR-7; INTERFERON-ALPHA; LEUKOCYTES, MONONUCLEAR; MICROARRAY ANALYSIS; POLY I-C; RNA, DOUBLE-STRANDED; SIGNAL TRANSDUCTION; SWINE; TRANSCRIPTOME; VIRUS DISEASES;

EID: 84890302377     PISSN: 0145305X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dci.2013.11.008     Document Type: Article

References (52)

1. Alexopoulou L., Holt A.C., Medzhitov R., Flavell R.A. Recognition of double-stranded RNA and activation of NF-kappaB by toll-like receptor 3. Nature 2001, 413:732-738.
2. Anderson S.L., Carton J.M., Lou J., Xing L., Rubin B.Y. Interferon-induced guanylate binding protein-1 (GBP-1) mediates an antiviral effect against vesicular stomatitis virus and encephalomyocarditis virus. Virology 1999, 256:8-14.
3. Balachandran S., Kim C.N., Yeh W.C., Mak T.W., Bhalla K., Barber G.N. Activation of the dsRNA-dependent protein kinase, PKR, induces apoptosis through FADD-mediated death signaling. EMBO J. 1998, 17:6888-6902.
4. Borden E.C., Sen G.C., Uze G., Silverman R.H., Ransohoff R.M., Foster G.R., Stark G.R. Interferons at age 50: past, current and future impact on biomedicine. Nat. Rev. Drug Discovery 2007, 6:975-990.
5. Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 2001, 29:365-372.
6. Brazma A., Parkinson H., Sarkans U., Shojatalab M., Vilo J., Abeygunawardena N., Holloway E., Kapushesky M., Kemmeren P., Lara G.G., Oezcimen A., Rocca-Serra P., Sansone S.A. ArrayExpress - a public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 2003, 31:68-71.
7. Chen H., Li C., Fang M., Zhu M., Li X., Zhou R., Li K., Zhao S. Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach. BMC Genomics. 2009, 10:64.
8. de La Motte C.A., Hascall V.C., Calabro A., Yen-Lieberman B., Strong S.A. Mononuclear leukocytes preferentially bind via CD44 to hyaluronan on human intestinal mucosal smooth muscle cells after virus infection or treatment with poly (I.C). J. Biol. Chem. 1999, 274:30747-30755.
9. Degols G., Eldin P., Mechti N. ISG20, an actor of the innate immune response. Biochimie 2007, 89:831-835.
10. Doyle S., Vaidya S., O'Connell R., Dadgostar H., Dempsey P., Wu T., Rao G., Sun R., Haberland M., Modlin R., Cheng G. IRF3 mediates a TLR3/TLR4-specific antiviral gene program. Immunity 2002, 17:251-263.
11. Edfors-Lilja I., Wattrang E., Magnusson U., Fossum C. Genetic variation in parameters reflecting immune competence of swine. Vet. Immunol. Immunop. 1994, 40:1-16.
12. Edfors-Lilja I., Wattrang E., Marklund L., Moller M., Andersson-Eklund L., Andersson L., Fossum C. Mapping quantitative trait loci for immune capacity in the pig. J. Immunol. 1998, 161:829-835.
13. Espert L., Degols G., Gongora C., Blondel D., Williams B.R., Silverman R.H., Mechti N. ISG20, a new interferon-induced RNase specific for single-stranded RNA, defines an alternative antiviral pathway against RNA genomic viruses. J. Biol. Chem. 2003, 278:16151-16158.
14. Espert L., Rey C., Gonzalez L., Degols G., Chelbi-Alix M.K., Mechti N., Gongora C. The exonuclease ISG20 is directly induced by synthetic dsRNA via NF-kappaB and IRF1 activation. Oncogene 2004, 23:4636-4640.
15. Fitzgerald-Bocarsly P., Dai J., Singh S. Plasmacytoid dendritic cells and type I IFN: 50 years of convergent history. Cytokine. Growth. Factor. Rev. 2008, 19:3-19.
16. Gautier L., Cope L., Bolstad B.M., Irizarry R.A. Affy - analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20:307-315.
17. Geiss G., Jin G., Guo J., Bumgarner R., Katze M.G., Sen G.C. A comprehensive view of regulation of gene expression by double-stranded RNA-mediated cell signaling. J. Biol. Chem. 2001, 276:30178-30182.
18. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
19. Gil J., Esteban M. Induction of apoptosis by the dsRNA-dependent protein kinase (PKR): mechanism of action. Apoptosis 2000, 5:107-114.
20. Gonzalez-Navajas J.M., Lee J., David M., Raz E. Immunomodulatory functions of type I interferons. Nat. Rev. Immunol. 2012, 12:125-135.
21. Honda K., Yanai H., Negishi H., Asagiri M., Sato M., Mizutani T., Shimada N., Ohba Y., Takaoka A., Yoshida N., Taniguchi T. IRF-7 is the master regulator of type-I interferon-dependent immune responses. Nature 2005, 434:772-777.
22. Huang da W., Sherman B.T., Lempicki R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37:1-13.
23. Huang da W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
24. Huang C.C., Duffy K.E., San Mateo L.R., Amegadzie B.Y., Sarisky R.T., Mbow M.L. A pathway analysis of poly (I:C)-induced global gene expression change in human peripheral blood mononuclear cells. Physiol. Genomics 2006, 26:125-133.
25. Huber W., Von Heydebreck A., Sültmann H., Poustka A., Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18:S96-S104.
26. Isaacs A., Lindenmann J. Virus interference. I. The interferon. Proc. R. Soc. Lond. B. Biol. Sci. 1957, 147:258-267.
27. Isaacs A., Lindenmann J., Valentine R.C. Virus interference. II. Some properties of interferon. Proc. R. Soc. Lond. B. Biol. Sci. 1957, 147:268-273.
28. Jacobs B.L., Langland J.O. When two strands are better than one: the mediators and modulators of the cellular responses to double-stranded RNA. Virology 1996, 219:339-349.
29. Jonasch E., Haluska F.G. Interferon in oncological practice: review of interferon biology, clinical applications, and toxicities. Oncologist 2001, 6:34-55.
30. Lai L., Prather R.S. Progress in producing knockout models for xenotransplantation by nuclear transfer. Ann. Med. 2002, 34:501-506.
31. Lai L., Kolber-Simonds D., Park K.W., Cheong H.T., Greenstein J.L., Im G.S., Samuel M., Bonk A., Rieke A., Day B.N., Murphy C.N., Carter D.B., Hawley R.J., Prather R.S. Production of alpha-1,3-galactosyltransferase knockout pigs by nuclear transfer cloning. Science 2002, 295:1089-1092.
32. Myers K.P., Olsen C.W., Gray G.C. Cases of swine influenza in humans: a review of the literature. Clin. Infect. Dis. 2007, 44:1084.
33. Nicholas F.W. Animal breeding and disease. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2005, 360:1529-1536.
34. Palm M., Garigliany M.M., Cornet F., Desmecht D. Interferon-induced Sus scrofa Mx1 blocks endocytic traffic of incoming influenza A virus particles. Vet. Res. 2010, 41:29.
35. Perry B.D., Grace D., Sones K. Current drivers and future directions of global livestock disease dynamics. Proc. Natl. Acad. Sci. USA 2011, 10.1073/pnas.1012953108.
36. Raj N.B., Cheung S.C., Rosztoczy I., Pitha P.M. Mouse genotype affects inducible expression of cytokine genes. J. Immunol. 1992, 148:1934-1940.
37. Saeed A.I., Sharov V., White J., Li J., Liang W., Bhagabati N., Braisted J., Klapa M., Currier T., Thiagarajan M., Sturn A., Snuffin M., Rezantsev A., Popov D., Ryltsov A., Kostukovich E., Borisovsky I., Liu Z., Vinsavich A., Trush V., Quackenbush J. TM4: a free, open-source system for microarray data management and analysis. Biotechniques 2003, 34:374-378.
38. Saeed A.I., Bhagabati N.K., Braisted J.C., Liang W., Sharov V., Howe E.A., Li J., Thiagarajan M., White J.A., Quackenbush J. TM4 microarray software suite. Methods Enzymol. 2006, 411:134-193.
39. Sarmiento U.M., Sarmiento J.I., Lunney J.K., Rishi S.S. Mapping of the porcine alpha interferon (IFNA) gene to chromosome 1 by fluorescence in situ hybridization. Mamm. Genome 1993, 4:62-63.
40. Sen G.C. Viruses and interferons. Annu. Rev. Microbiol. 2001, 55:255-281.
41. Sen G.C., Sarkar S.N. The interferon-stimulated genes: targets of direct signaling by interferons, double-stranded RNA, and viruses. Curr. Top. Microbiol. Immunol. 2007, 316:233-250.
42. Smyth G. Limma: linear models for microarray data. Bioinformatics and Computational Biology Solutions Using R and Bioconductor 2005, 397-420. Springer, New York. R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber (Eds.).
43. Stear M., Bishop S., Mallard B., Raadsma H. The sustainability, feasibility and desirability of breeding livestock for disease resistance. Res. Vet. Sci. 2001, 71:1-7.
44. Tamura T., Yanai H., Savitsky D., Taniguchi T. The IRF family transcription factors in immunity and oncogenesis. Annu. Rev. Immunol. 2008, 26:535-584.
45. Taniguchi T., Ogasawara K., Takaoka A., Tanaka N. IRF family of transcription factors as regulators of host defense. Annu. Rev. Immunol. 2001, 19:623-655.
46. Team R. R: a language and environment for statistical computing 2010, R Foundation for Statistical Computing, Vienna, Austria, http://www.R-project.org.
47. Thomas P.D., Kejariwal A., Campbell M.J., Mi H., Diemer K., Guo N., Ladunga I., Ulitsky-Lazareva B., Muruganujan A., Rabkin S., Vandergriff J.A., Doremieux O. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification. Nucleic Acids Res. 2003, 31:334-341.
48. Thomas P.D., Kejariwal A., Guo N., Mi H., Campbell M.J., Muruganujan A., Lazareva-Ulitsky B. Applications for protein sequence-function evolution data: mRNA/protein expression analysis and coding SNP scoring tools. Nucleic Acids Res. 2006, 34:W645-650.
49. Tsai S., Cassady J., Freking B., Nonneman D., Rohrer G., Piedrahita J. Annotation of the Affymetrix1 porcine genome microarray. Anim. Genet. 2006, 37:423-424.
50. van Iersel M.P., Kelder T., Pico A.R., Hanspers K., Coort S., Conklin B.R., Evelo C. Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics 2008, 9:399.
51. Wattrang E., Almqvist M., Johansson A., Fossum C., Wallgren P., Pielberg G., Andersson L., Edfors-Lilja I. Confirmation of QTL on porcine chromosomes 1 and 8 influencing leukocyte numbers, haematological parameters and leukocyte function. Anim. Genet. 2005, 36:337-345.
52. Williams B.R. PKR; a sentinel kinase for cellular stress. Oncogene 1999, 18:6112-6120.