Digital cell quantification identifies global immune cell dynamics during influenza infection

Molecular Systems Biology

Volumn 10, Issue 2, 2014, Pages

  Altboum, Zeev ^a   Steuerman, Yael ^b   David, Eyal ^b   Barnett Itzhaki, Zohar ^a   Valadarsky, Liran ^a   Keren Shaul, Hadas ^a   Meningher, Tal ^c,d   Mendelson, Ella ^b,c   Mandelboim, Michal ^c   Gat Viks, Irit ^b   Amit, Ido ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

^b TEL AVIV UNIVERSITY   (Israel)

^c SHEBA MEDICAL CENTER   (Israel)

^d BAR ILAN UNIVERSITY   (Israel)

Author keywords

cell quantification; deconvolution approach; dendritic cells; immune cell dynamics; influenza infection

Indexed keywords

CD103 ANTIGEN; CD11B ANTIGEN; CD8 ANTIGEN; ALPHA E INTEGRINS; ALPHA INTEGRIN; LEUKOCYTE ANTIGEN; TRANSCRIPTOME;

ALGORITHM; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CELL SUBPOPULATION; CONTROLLED STUDY; DENDRITIC CELL; DIGITAL CELL QUANTIFICATION; FEMALE; GENE EXPRESSION; GENOME WIDE GENE EXPRESSION; IMMUNOCOMPETENT CELL; INFLUENZA; LUNG; MACROPHAGE; MOUSE; NATURAL KILLER CELL; NONHUMAN; PRIORITY JOURNAL; ANIMAL; FLOW CYTOMETRY; HUMAN; IMMUNOLOGY; METABOLISM; PATHOLOGY;

MUS;

ANIMALS; ANTIGENS, CD; ANTIGENS, CD11B; CD8-POSITIVE T-LYMPHOCYTES; DENDRITIC CELLS; FLOW CYTOMETRY; HUMANS; INFLUENZA, HUMAN; INTEGRIN ALPHA CHAINS; LUNG; MICE; TRANSCRIPTOME;

EID: 84906930512     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.1002/msb.134947     Document Type: Article

References (46)

1. Abbas AR, Wolslegel K, Seshasayee D, Modrusan Z, Clark HF, (2009) Deconvolution of blood microarray data identifies cellular activation patterns in systemic lupus erythematosus. PLoS ONE 4: e6098
2. Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, et al, (2009) Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science 326: 257-263
3. Anders S, Huber W, (2010) Differential expression analysis for sequence count data. Genome Biol 11: R106
4. Bendall SC, Simonds EF, Qiu P, el Amir AD, Krutzik PO, Finck R, Bruggner RV, Melamed R, Trejo A, Ornatsky OI, Balderas RS, Plevritis SK, Sachs K, Pe'er D, Tanner SD, Nolan GP, (2011) Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 332: 687-696
5. Benoist C, Lanier L, Merad M, Mathis D, Immunological Genome P, (2012) Consortium biology in immunology: the perspective from the Immunological Genome Project. Nat Rev Immunol 12: 734-740
6. Bismarck D, Schütze N, Moore P, Büttner M, Alber G, Buttlar Hv, (2012) Canine CD4+ CD8+ double positive T cells in peripheral blood have features of activated T cells. Vet Immunol Immunopathol 149: 157-166
7. Brandes M, Klauschen F, Kuchen S, Germain RN, (2013) A systems analysis identifies a feedforward inflammatory circuit leading to lethal influenza infection. Cell 154: 197-212
8. Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, et al, (2011) Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 39: D691-697
9. Damjanovic D, Small CL, Jeyanathan M, McCormick S, Xing Z, (2012) Immunopathology in influenza virus infection: uncoupling the friend from foe. Clin Immunol 144: 57-69
10. Friedman J, Hastie T, Tibshirani R, (2010) Regularization Paths for Generalized Linear Models via Coordinate Descent. J Stat Softw 33: 1-22
11. Gat-Viks I, Chevrier N, Wilentzik R, Eisenhaure T, Raychowdhury R, Steuerman Y, Shalek AK, Hacohen N, Amit I, Regev A, (2013) Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli. Nat Biotechnol 31: 342-349
12. Geissmann F, Manz MG, Jung S, Sieweke MH, Merad M, Ley K, (2010) Development of monocytes, macrophages, and dendritic cells. Science 327: 656-661
13. Godfrey DI, MacDonald HR, Kronenberg M, Smyth MJ, Van Kaer L, (2004) NKT cells: what's in a name? Nat Rev Immunol 4: 231-237
14. Godfrey DI, Stankovic S, Baxter AG, (2010) Raising the NKT cell family. Nat Immunol 11: 197-206
15. Gordon S, Taylor PR, (2005) Monocyte and macrophage heterogeneity. Nat Rev Immunol 5: 953-964
16. Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A, (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 28: 503-510
17. Ho AW, Prabhu N, Betts RJ, Ge MQ, Dai X, Hutchinson PE, Lew FC, Wong KL, Hanson BJ, Macary PA, Kemeny DM, (2011) Lung CD103+ dendritic cells efficiently transport influenza virus to the lymph node and load viral antigen onto MHC class I for presentation to CD8 T cells. J Immunol 187: 6011-6021
18. Ibrahim SF, van den Engh G, (2007) Flow cytometry and cell sorting. Adv Biochem Eng Biotechnol 106: 19-39
19. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP, (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4: 249-264
20. Johns JL, Macnamara KC, Walker NJ, Winslow GM, Borjesson DL, (2009) Infection with Anaplasma phagocytophilum induces multilineage alterations in hematopoietic progenitor cells and peripheral blood cells. Infect Immun 77: 4070-4080
21. Jojic V, Shay T, Sylvia K, Zuk O, Sun X, Kang J, Regev A, Koller D, Best AJ, Knell J, Goldrath A, Jojic V, Koller D, Shay T, Regev A, Cohen N, Brennan P, Brenner M, Kim F, Rao TN, et al, (2013) Identification of transcriptional regulators in the mouse immune system. Nat Immunol 14: 633-643
22. Josset L, Belser JA, Pantin-Jackwood MJ, Chang JH, Chang ST, Belisle SE, Tumpey TM, Katze MG, (2012) Implication of inflammatory macrophages, nuclear receptors, and interferon regulatory factors in increased virulence of pandemic 2009 H1N1 influenza A virus after host adaptation. J Virol 86: 7192-7206
23. Kaji T, Ishige A, Hikida M, Taka J, Hijikata A, Kubo M, Nagashima T, Takahashi Y, Kurosaki T, Okada M, Ohara O, Rajewsky K, Takemori T, (2012) Distinct cellular pathways select germline-encoded and somatically mutated antibodies into immunological memory. J Exp Med 209: 2079-2097
24. Kenny E, Mason D, Pombo A, Ramírez F, (2000) Phenotypic analysis of peripheral CD4+ CD8+ T cells in the rat. Immunology 101: 178-184
25. th edn. New York, NY: WH Freeman.
26. Lu P, Nakorchevskiy A, Marcotte EM, (2003) Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci USA 100: 10370-10375
27. Luster AD, Alon R, von Andrian UH, (2005) Immune cell migration in inflammation: present and future therapeutic targets. Nat Immunol 6: 1182-1190
28. Massberg S, Schaerli P, Knezevic-Maramica I, Kollnberger M, Tubo N, Moseman EA, Huff IV, Junt T, Wagers AJ, Mazo IB, von Andrian UH, (2007) Immunosurveillance by hematopoietic progenitor cells trafficking through blood, lymph, and peripheral tissues. Cell 131: 994-1008
29. Moltedo B, Li W, Yount JS, Moran TM, (2011) Unique type I interferon responses determine the functional fate of migratory lung dendritic cells during influenza virus infection. PLoS Pathog 7: e1002345
30. th edn. New York, NY: Garland Science
31. Nakaya HI, Wrammert J, Lee EK, Racioppi L, Marie-Kunze S, Haining WN, Means AR, Kasturi SP, Khan N, Li GM, McCausland M, Kanchan V, Kokko KE, Li S, Elbein R, Mehta AK, Aderem A, Subbarao K, Ahmed R, Pulendran B, (2011) Systems biology of vaccination for seasonal influenza in humans. Nat Immunol 12: 786-795
32. Nascimbeni M, Shin E-C, Chiriboga L, Kleiner DE, Rehermann B, (2004) Peripheral CD4+ CD8+ T cells are differentiated effector memory cells with antiviral functions. Blood 104: 478-486
33. Newell EW, Sigal N, Bendall SC, Nolan GP, Davis MM, (2012) Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. Immunity 36: 142-152
34. Pang IK, Ichinohe T, Iwasaki A, (2013) IL-1R signaling in dendritic cells replaces pattern-recognition receptors in promoting CD8(+) T cell responses to influenza A virus. Nat Immunol 14: 246-253
35. Parnell GP, McLean AS, Booth DR, Armstrong NJ, Nalos M, Huang SJ, Manak J, Tang W, Tam OY, Chan S, Tang BM, (2012) A distinct influenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia. Crit Care 16: R157
36. Pommerenke C, Wilk E, Srivastava B, Schulze A, Novoselova N, Geffers R, Schughart K, (2012) Global transcriptome analysis in influenza-infected mouse lungs reveals the kinetics of innate and adaptive host immune responses. PLoS ONE 7: e41169
37. Rowe T, Leon AJ, Crevar CJ, Carter DM, Xu L, Ran L, Fang Y, Cameron CM, Cameron MJ, Banner D, Ng DC, Ran R, Weirback HK, Wiley CA, Kelvin DJ, Ross TM, (2010) Modeling host responses in ferrets during A/California/07/2009 influenza infection. Virology 401: 257-265
38. Stoll S, Delon J, Brotz TM, Germain RN, (2002) Dynamic imaging of T cell-dendritic cell interactions in lymph nodes. Science 296: 1873-1876
39. Tate MD, Brooks AG, Reading PC, Mintern JD, (2012) Neutrophils sustain effective CD8(+) T-cell responses in the respiratory tract following influenza infection. Immunol Cell Biol 90: 197-205
40. Tibshirani R, (1996) Regression shrinkage and selection via the lasso. J Roy Statist Soc B 58: 267-288
41. Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111
42. Wang M, Master SR, Chodosh LA, (2006) Computational expression deconvolution in a complex mammalian organ. BMC Bioinformatics 7: 328
43. Yeh TC, Shih LY, Chai IJ, Liu HC, Wang LY, Chiu NC, Chen SH, Chi H, Liang DC, (2007) Hematopoietic progenitor cells increase remarkably in the peripheral blood of children with infection. Acta Paediatr Taiwan 48: 10-14
44. Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y, Awasthi A, Wu C, Karwacz K, Xiao S, Jorgolli M, Gennert D, Satija R, Shakya A, Lu DY, Trombetta JJ, Pillai MR, Ratcliffe PJ, Coleman ML, Bix M, Tantin D, et al, (2013) Dynamic regulatory network controlling TH17 cell differentiation. Nature 496: 461-468
45. Zou H, Hastie T, (2005) Regularization and variable selection via the elastic net (vol B 67, pg 301, 2005). J Roy Stat Soc B 67: 768-768
46. Zuckermann FA, (1999) Extrathymic CD4/CD8 double positive T cells. Vet Immunol Immunopathol 72: 55-66