Standardized Whole-Blood Transcriptional Profiling Enables the Deconvolution of Complex Induced Immune Responses

Cell Reports

Volumn 16, Issue 10, 2016, Pages 2777-2791

  Urrutia, Alejandra ^a,b,g   Duffy, Darragh ^a,b   Rouilly, Vincent ^a   Posseme, Céline ^a   Djebali, Raouf ^a   Illanes, Gabriel ^a,c   Libri, Valentina ^a   Albaud, Benoit ^d   Gentien, David ^d   Piasecka, Barbara ^a   Hasan, Milena ^a   Fontes, Magnus ^a,e   Quintana Murci, Lluis ^a,f,h   Albert, Matthew L ^a,b,g,h   Abel, Laurent ^h   Alcover, Andres ^h   Astrom, Kalla ^h   Bousso, Philippe ^h   Bruhns, Pierre ^h   Cumano, Ana ^h   Demangel, Caroline ^h   Deriano, Ludovic ^h   Di Santo, James ^h   Dromer, Françoise ^h   Eberl, Gérard ^h   Enninga, Jost ^h   Fellay, Jacques ^h   Freitas, Antonio ^h   Gelpi, Odile ^h   Gomperts Boneca, Ivo ^h   Hercberg, Serge ^h   Lantz, Olivier ^h   Leclerc, Claude ^h   Mouquet, Hugo ^h   Pellegrini, Sandra ^h   Pol, Stanislas ^h   Rogge, Lars ^h   Sakuntabhai, Anavaj ^h   Schwartz, Olivier ^h   Schwikowski, Benno ^h   Shorte, Spencer ^h   Soumelis, Vassili ^h   Tangy, Frédéric ^h   Tartour, Eric ^h   Toubert, Antoine ^h   Ungeheuer, Marie Noëlle ^h   more..

^a INSTITUT PASTEUR   (France)

^b INSTITUT PASTEUR   (France)

^c UNIVERSIDAD DE LA REPÚBLICA   (Uruguay)

^d INSTITUT CURIE   (France)

^e LUND UNIVERSITY   (Sweden)

^f CNRS   (France)

^g GENENTECH INC   (United States)

^h NONE

Author keywords

[No Author keywords available]

Indexed keywords

CYTOKINE; LIGAND; TOLL LIKE RECEPTOR;

ADULT; ARTICLE; BLOOD ANALYSIS; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; HUMAN; IMMUNOMODULATION; IMMUNOSTIMULATION; INNATE IMMUNITY; MACHINE LEARNING; MALE; PRIORITY JOURNAL; STANDARDIZATION; SUPPORT VECTOR MACHINE; BACTERIUM; BLOOD; DRUG EFFECTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; IMMUNITY; LYMPHOCYTE; METABOLISM; PROCEDURES;

ADULT; BACTERIA; BLOOD; CYTOKINES; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; IMMUNITY; LYMPHOCYTES; MALE; TOLL-LIKE RECEPTORS; TRANSCRIPTION, GENETIC;

EID: 85001720558     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2016.08.011     Document Type: Article

References (36)

1. Alter, O., Brown, P.O., Botstein, D., Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. USA 97 (2000), 10101–10106.
2. Amit, I., Garber, M., Chevrier, N., Leite, A.P., Donner, Y., Eisenhaure, T., Guttman, M., Grenier, J.K., Li, W., Zuk, O., et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326 (2009), 257–263.
3. Banchereau, R., Baldwin, N., Cepika, A.-M., Athale, S., Xue, Y., Yu, C.I., Metang, P., Cheruku, A., Berthier, I., Gayet, I., et al. Transcriptional specialization of human dendritic cell subsets in response to microbial vaccines. Nat. Commun., 5, 2014, 5283.
4. Barreiro, L.B., Ben-Ali, M., Quach, H., Laval, G., Patin, E., Pickrell, J.K., Bouchier, C., Tichit, M., Neyrolles, O., Gicquel, B., et al. Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense. PLoS Genet., 5, 2009, e1000562.
5. + T cell clones primed by pathogens or vaccines. Science 347 (2015), 400–406.
6. Benjamini, Y., Hochberg, Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J.R. Stat. Soc. Series B Stat. Methodol. 57 (1995), 289–300.
7. Bradski, G., Kaehler, A., Learning OpenCV: Computer Vision with the OpenCV Library. 2008, O'Reilly.
8. Burges, C.J.C., A tutorial on support vector machines for pattern recognition. Data Min. Knowl. Discov. 2 (1998), 121–167.
9. Chang, C.-C., Lin, C.-J., LIBSVM: A library for support vector machines. ACM Trans. Intell. Syst. Technol. TIST, 2, 2011.
10. Chaussabel, D., Pascual, V., Banchereau, J., Assessing the human immune system through blood transcriptomics. BMC Biol., 8, 2010, 84.
11. Chen, K.W., Groß, C.J., Sotomayor, F.V., Stacey, K.J., Tschopp, J., Sweet, M.J., Schroder, K., The neutrophil NLRC4 inflammasome selectively promotes IL-1β maturation without pyroptosis during acute Salmonella challenge. Cell Rep. 8 (2014), 570–582.
12. Dinarello, C.A., Ikejima, T., Warner, S.J., Orencole, S.F., Lonnemann, G., Cannon, J.G., Libby, P., Interleukin 1 induces interleukin 1. I. Induction of circulating interleukin 1 in rabbits in vivo and in human mononuclear cells in vitro. J. Immunol. 139 (1987), 1902–1910.
13. Duffy, D., Rouilly, V., Libri, V., Hasan, M., Beitz, B., David, M., Urrutia, A., Bisiaux, A., Labrie, S.T., Dubois, A., et al., Milieu Intérieur Consortium. Functional analysis via standardized whole-blood stimulation systems defines the boundaries of a healthy immune response to complex stimuli. Immunity 40 (2014), 436–450.
14. Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S., De Moor, B., Brazma, A., Huber, W., BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 21 (2005), 3439–3440.
15. Flicek, P., Amode, M.R., Barrell, D., Beal, K., Billis, K., Brent, S., Carvalho-Silva, D., Clapham, P., Coates, G., Fitzgerald, S., et al. Ensembl 2014. Nucleic Acids Res. 42 (2014), D749–D755.
16. Folds, J.D., Schmitz, J.L., 24. Clinical and laboratory assessment of immunity. J. Allergy Clin. Immunol. 111:2, Suppl (2003), S702–S711.
17. Fontes, M., Statistical and knowledge supported visualization of multivariate data. Åström, K., Persson, L.-E., Silvestrov, S.D., (eds.) Analysis for Science, Engineering and Beyond, 2012, Springer Berlin Heidelberg, 143–173.
18. Gay, N.J., Symmons, M.F., Gangloff, M., Bryant, C.E., Assembly and localization of Toll-like receptor signalling complexes. Nat. Rev. Immunol. 14 (2014), 546–558.
19. Geiger, R., Duhen, T., Lanzavecchia, A., Sallusto, F., Human naive and memory CD4+ T cell repertoires specific for naturally processed antigens analyzed using libraries of amplified T cells. J. Exp. Med. 206 (2009), 1525–1534.
20. Gibbons, L.J., Hyrich, K.L., Biologic therapy for rheumatoid arthritis: clinical efficacy and predictors of response. BioDrugs 23 (2009), 111–124.
21. Gorenshteyn, D., Zaslavsky, E., Fribourg, M., Park, C.Y., Wong, A.K., Tadych, A., Hartmann, B.M., Albrecht, R.A., García-Sastre, A., Kleinstein, S.H., et al. Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. Immunity 43 (2015), 605–614.
22. Hawn, T.R., Verbon, A., Lettinga, K.D., Zhao, L.P., Li, S.S., Laws, R.J., Skerrett, S.J., Beutler, B., Schroeder, L., Nachman, A., et al. A common dominant TLR5 stop codon polymorphism abolishes flagellin signaling and is associated with susceptibility to legionnaires’ disease. J. Exp. Med. 198 (2003), 1563–1572.
23. Hayashi, F., Means, T.K., Luster, A.D., Toll-like receptors stimulate human neutrophil function. Blood 102 (2003), 2660–2669.
24. Jovanovic, M., Rooney, M.S., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E.H., Fields, A.P., Schwartz, S., Raychowdhury, R., et al. Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens. Science, 347, 2015, 1259038.
25. Lee, M.N., Ye, C., Villani, A.-C., Raj, T., Li, W., Eisenhaure, T.M., Imboywa, S.H., Chipendo, P.I., Ran, F.A., Slowikowski, K., et al. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science, 343, 2014, 1246980.
26. Li, B., Cramer, D., Wagner, S., Hansen, R., King, C., Kakar, S., Ding, C., Yan, J., Yeast glucan particles activate murine resident macrophages to secrete proinflammatory cytokines via MyD88- and Syk kinase-dependent pathways. Clin. Immunol. 124 (2007), 170–181.
27. Li, S., Rouphael, N., Duraisingham, S., Romero-Steiner, S., Presnell, S., Davis, C., Schmidt, D.S., Johnson, S.E., Milton, A., Rajam, G., et al. Molecular signatures of antibody responses derived from a systems biology study of five human vaccines. Nat. Immunol. 15 (2014), 195–204.
28. Martinon, F., Pétrilli, V., Mayor, A., Tardivel, A., Tschopp, J., Gout-associated uric acid crystals activate the NALP3 inflammasome. Nature 440 (2006), 237–241.
29. McInnes, I.B., Schett, G., Cytokines in the pathogenesis of rheumatoid arthritis. Nat. Rev. Immunol. 7 (2007), 429–442.
30. Shin, H., Shannon, C.P., Fishbane, N., Ruan, J., Zhou, M., Balshaw, R., Wilson-McManus, J.E., Ng, R.T., McManus, B.M., Tebbutt, S.J., PROOF Centre of Excellence Team. Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion. PLoS ONE, 9, 2014, e91041.
31. Speake, C., Presnell, S., Domico, K., Zeitner, B., Bjork, A., Anderson, D., Mason, M.J., Whalen, E., Vargas, O., Popov, D., et al. An interactive web application for the dissemination of human systems immunology data. J. Transl. Med., 13, 2015, 196.
32. Steinhaus, H., Sur la division des corps matériels en parties. Bull. Acad. Pol. Sci. Fr. 4 (1956), 801–804.
33. Thomas, S., Rouilly, V., Patin, E., Alanio, C., Dubois, A., Delval, C., Marquier, L.-G., Fauchoux, N., Sayegrih, S., Vray, M., et al. The Milieu Intérieur study - an integrative approach for study of human immunological variance. Clin. Immunol. 157 (2015), 277–293.
34. Tsang, J.S., Schwartzberg, P.L., Kotliarov, Y., Biancotto, A., Xie, Z., Germain, R.N., Wang, E., Olnes, M.J., Narayanan, M., Golding, H., et al. Baylor HIPC Center, CHI Consortium. Global analyses of human immune variation reveal baseline predictors of postvaccination responses. Cell 157 (2014), 499–513.
35. Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., Speleman, F., Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol., 3, 2002 RESEARCH0034.
36. Wu, T.D., Nacu, S., Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26 (2010), 873–881.