Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines

Immunity

Volumn 38, Issue 4, 2013, Pages 831-844

  Obermoser, Gerlinde ^a   Presnell, Scott ^b   Domico, Kelly ^b   Xu, Hui ^c   Wang, Yuanyuan ^a   Anguiano, Esperanza ^a   Thompson Snipes, LuAnn ^a   Ranganathan, Rajaram ^a   Zeitner, Brad ^b   Bjork, Anna ^b   Anderson, David ^b   Speake, Cate ^b   Ruchaud, Emily ^a   Skinner, Jason ^a   Alsina, Laia ^a   Sharma, Mamta ^a   Dutartre, Helene ^a   Cepika, Alma ^a   Israelsson, Elisabeth ^b   Nguyen, Phuong ^a   Nguyen, Quynh Anh ^a   Harrod, A Carson ^a   Zurawski, Sandra M ^a   Pascual, Virginia ^a   Ueno, Hideki ^a   Nepom, Gerald T ^b   Quinn, Charlie ^a,b   Blankenship, Derek ^c   Palucka, Karolina ^a   Banchereau, Jacques ^a   Chaussabel, Damien ^a,b   more..

^a BAYLOR INSTITUTE FOR IMMUNOLOGY RESEARCH   (United States)

^b BENAROYA RESEARCH INSTITUTE   (United States)

^c BAYLOR HEALTH CARE SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INFLUENZA VACCINE; INTERFERON; PNEUMOCOCCUS VACCINE;

ADAPTIVE IMMUNITY; ANALYTIC METHOD; ARTICLE; BLOOD ANALYSIS; GENETIC PARAMETERS; GENETIC TRANSCRIPTION; HUMAN; IMMUNOLOGY; INFLUENZA VACCINATION; INNATE IMMUNITY; PNEUMOCOCCAL VACCINATION; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; SYSTEM SCALE INTERACTIVE EXPLORATION; TRANSCRIPTIONAL SIGNATURE; VACCINATION;

ADAPTIVE IMMUNITY; ANTIBODY FORMATION; CELL PROLIFERATION; HUMANS; IMMUNITY, INNATE; INFLAMMATION MEDIATORS; INFLUENZA VACCINES; INFLUENZA, HUMAN; INTERFERONS; MYELOID CELLS; NEUTROPHILS; ORTHOMYXOVIRIDAE; PNEUMOCOCCAL INFECTIONS; PNEUMOCOCCAL VACCINES; SOFTWARE; STREPTOCOCCUS PNEUMONIAE; VACCINATION;

EID: 84876745847     PISSN: 10747613     EISSN: 10974180     Source Type: Journal    
DOI: 10.1016/j.immuni.2012.12.008     Document Type: Article

References (22)

1. Alakulppi N., Seikku P., Jaatinen T., Holmberg C., Laine J. Feasibility of diagnosing subclinical renal allograft rejection in children by whole blood gene expression analysis. Transplantation 2008, 86:1222-1228.
2. Benjamini Y., Hochberg Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J.R. Stat. Soc. 1995, 57:289-300.
3. Bennett L., Palucka A.K., Arce E., Cantrell V., Borvak J., Banchereau J., Pascual V. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J. Exp. Med. 2003, 197:711-723.
4. Berry M.P., Graham C.M., McNab F.W., Xu Z., Bloch S.A., Oni T., Wilkinson K.A., Banchereau R., Skinner J., Wilkinson R.J., et al. An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 2010, 466:973-977.
5. Bucasas K.L., Franco L.M., Shaw C.A., Bray M.S., Wells J.M., Niño D., Arden N., Quarles J.M., Couch R.B., Belmont J.W. Early patterns of gene expression correlate with the humoral immune response to influenza vaccination in humans. J. Infect. Dis. 2011, 203:921-929.
6. Caskey M., Lefebvre F., Filali-Mouhim A., Cameron M.J., Goulet J.P., Haddad E.K., Breton G., Trumpfheller C., Pollak S., Shimeliovich I., et al. Synthetic double-stranded RNA induces innate immune responses similar to a live viral vaccine in humans. J. Exp. Med. 2011, 208:2357-2366.
7. Chaussabel D., Quinn C., Shen J., Patel P., Glaser C., Baldwin N., Stichweh D., Blankenship D., Li L., Munagala I., et al. A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 2008, 29:150-164.
8. Chaussabel D., Ueno H., Banchereau J., Quinn C. Data management: it starts at the bench. Nat. Immunol. 2009, 10:1225-1227.
9. FDA (2011). Complete List of Vaccines Licensed for Immunization and Distribution in the US. http://www.fda.gov/BiologicsBloodVaccines/Vaccines/ApprovedProducts/ucm093833.htm.
10. Gaucher D., Therrien R., Kettaf N., Angermann B.R., Boucher G., Filali-Mouhim A., Moser J.M., Mehta R.S., Drake D.R., Castro E., et al. Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J. Exp. Med. 2008, 205:3119-3131.
11. Germain R.N., Meier-Schellersheim M., Nita-Lazar A., Fraser I.D. Systems biology in immunology: a computational modeling perspective. Annu. Rev. Immunol. 2011, 29:527-585.
12. Maecker H.T., McCoy J.P., Nussenblatt R. Standardizing immunophenotyping for the Human Immunology Project. Nat. Rev. Immunol. 2012, 12:191-200.
13. Mallory R.M., Malkin E., Ambrose C.S., Bellamy T., Shi L., Yi T., Jones T., Kemble G., Dubovsky F. Safety and immunogenicity following administration of a live, attenuated monovalent 2009 H1N1 influenza vaccine to children and adults in two randomized controlled trials. PLoS ONE 2010, 5:e13755.
14. Nakaya H.I., Wrammert J., Lee E.K., Racioppi L., Marie-Kunze S., Haining W.N., Means A.R., Kasturi S.P., Khan N., Li G.-M., et al. Systems biology of vaccination for seasonal influenza in humans. Nat. Immunol. 2011, 12:786-795.
15. Ovcharenko D., Jarvis R., Hunicke-Smith S., Kelnar K., Brown D. High-throughput RNAi screening in vitro: from cell lines to primary cells. RNA: A Publication of the RNA Society 2005, 11:985-993.
16. Pascual V., Chaussabel D., Banchereau J. A genomic approach to human autoimmune diseases. Annu. Rev. Immunol. 2010, 28:535-571.
17. 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.
18. 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, 109:2066-2077.
19. Steel J., Lowen A.C., Pena L., Angel M., Solórzano A., Albrecht R., Perez D.R., García-Sastre A., Palese P. Live attenuated influenza viruses containing NS1 truncations as vaccine candidates against H5N1 highly pathogenic avian influenza. J. Virol. 2009, 83:1742-1753.
20. Tang B.M., McLean A.S., Dawes I.W., Huang S.J., Lin R.C. Gene-expression profiling of peripheral blood mononuclear cells in sepsis. Crit. Care Med. 2009, 37:882-888.
21. Whitley, P., Moturi, S., Santiago, J., Johnson, C., and Setterquist, R. Ambion, Inc. (2005). Improved Microarray Sensitivity using Whole Blood RNA Samples. In Applied Biosystems TechnicalNotes.
22. Wrammert J., Smith K., Miller J., Langley W.A., Kokko K., Larsen C., Zheng N.-Y., Mays I., Garman L., Helms C., et al. Rapid cloning of high-affinity human monoclonal antibodies against influenza virus. Nature 2008, 453:667-671.