Expression profiling of human immune cell subsets identifies miRNA-mRNA regulatory relationships correlated with cell type specific expression

PLoS ONE

Volumn 7, Issue 1, 2012, Pages

  Allantaz, Florence ^a   Cheng, Donavan T ^b   Bergauer, Tobias ^a   Ravindran, Palanikumar ^b   Rossier, Michel F ^c   Ebeling, Martin ^a   Badi, Laura ^a   Reis, Bernhard ^a   Bitter, Hans ^b   D'Asaro, Matilde ^c   Chiappe, Alberto ^c   Sridhar, Sriram ^b   Pacheco, Gonzalo Duran ^a   Burczynski, Michael E ^b   Hochstrasser, Denis ^c   Vonderscher, Jacky ^b   Matthes, Thomas ^c  

^a F HOFFMANN LA ROCHE LTD   (Switzerland)

^b HOFFMANN LA ROCHE INC   (United States)

^c GENEVA UNIVERSITY HOSPITALS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA;

ABL2 GENE; ADOLESCENT; ADULT; ARTICLE; B LYMPHOCYTE; CD4+ T LYMPHOCYTE; CD8+ T LYMPHOCYTE; CELL LINEAGE; CELL SPECIFICITY; CELL TYPE; CONTROLLED STUDY; DOWN REGULATION; EIF4A2 GENE; EOSINOPHIL; EPC1 GENE; FEMALE; GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMAN; HUMAN CELL; IMMUNOCOMPETENT CELL; INO80D GENE; LYMPHOID CELL; MALE; MONOCYTE; MYELOID DENDRITIC CELL; NATURAL KILLER CELL; NEUTROPHIL; PLASMACYTOID DENDRITIC CELL; GENETICS; METABOLISM; METHODOLOGY; MIDDLE AGED;

ADOLESCENT; ADULT; B-LYMPHOCYTES; CD4-POSITIVE T-LYMPHOCYTES; CD8-POSITIVE T-LYMPHOCYTES; EOSINOPHILS; FEMALE; GENE EXPRESSION PROFILING; HUMANS; KILLER CELLS, NATURAL; MALE; MICRORNAS; MIDDLE AGED; MONOCYTES; NEUTROPHILS; RNA, MESSENGER; YOUNG ADULT;

EID: 84856065347     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0029979     Document Type: Article

References (37)

1. Wang M, Windgassen D, Papoutsakis ET, (2008) Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-cell activation. BMC Genomics 9: 225.
2. Lindstedt M, Lundberg K, Borrebaeck CA, (2005) Gene family clustering identifies functionally associated subsets of human in vivo blood and tonsillar dendritic cells. J Immunol 175: 4839-4846.
3. Zhao C, Zhang H, Wong WC, Sem X, Han H, et al. (2009) Identification of novel functional differences in monocyte subsets using proteomic and transcriptomic methods. J Proteome Res 8: 4028-4038.
4. Ehrhardt GR, Hijikata A, Kitamura H, Ohara O, Wang JY, et al. (2008) Discriminating gene expression profiles of memory B cell subpopulations. J Exp Med 205: 1807-1817.
5. Macaulay IC, Tijssen MR, Thijssen-Timmer DC, Gusnanto A, Steward M, et al. (2007) Comparative gene expression profiling of in vitro differentiated megakaryocytes and erythroblasts identifies novel activatory and inhibitory platelet membrane proteins. Blood 109: 3260-3269.
6. Abbas AR, Baldwin D, Ma Y, Ouyang W, Gurney A, et al. (2005) Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data. Genes Immun 6: 319-331.
7. Liu SM, Xavier R, Good KL, Chtanova T, Newton R, et al. (2006) Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes. J Allergy Clin Immunol 118: 496-503.
8. Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, et al. (2009) A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood 113: e1-9.
9. Chaussabel D, Pascual V, Banchereau J, (2010) Assessing the human immune system through blood transcriptomics. BMC Biol 8: 84.
10. Burczynski ME, Dorner AJ, (2006) Transcriptional profiling of peripheral blood cells in clinical pharmacogenomic studies. Pharmacogenomics 7: 187-202.
11. Darzacq X, Jady BE, Verheggen C, Kiss AM, Bertrand E, et al. (2002) Cajal body-specific small nuclear RNAs: a novel class of 2′-O-methylation and pseudouridylation guide RNAs. Embo J 21: 2746-2756.
12. Chen CZ, Li L, Lodish HF, Bartel DP, (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303: 83-86.
13. O'Connell RM, Chaudhuri AA, Rao DS, Gibson WS, Balazs AB, et al. (2010) MicroRNAs enriched in hematopoietic stem cells differentially regulate long-term hematopoietic output. Proc Natl Acad Sci USA 107: 14235-14240.
14. O'Connell RM, Rao DS, Chaudhuri AA, Baltimore D, (2010) Physiological and pathological roles for microRNAs in the immune system. Nat Rev Immunol 10: 111-122.
15. Basso K, Sumazin P, Morozov P, Schneider C, Maute RL, et al. (2009) Identification of the human mature B cell miRNome. Immunity 30: 744-752.
16. Bezman NA, Cedars E, Steiner DF, Blelloch R, Hesslein DG, et al. (2010) Distinct requirements of microRNAs in NK cell activation, survival, and function. J Immunol 185: 3835-3846.
17. Kuipers H, Schnorfeil FM, Brocker T, (2010) Differentially expressed microRNAs regulate plasmacytoid vs. conventional dendritic cell development. Mol Immunol.
18. Neilson JR, Zheng GX, Burge CB, Sharp PA, (2007) Dynamic regulation of miRNA expression in ordered stages of cellular development. Genes Dev 21: 578-589.
19. Wu H, Neilson JR, Kumar P, Manocha M, Shankar P, et al. (2007) miRNA profiling of naive, effector and memory CD8 T cells. PLoS One 2: e1020.
20. Guo H, Ingolia NT, Weissman JS, Bartel DP, (2010) Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835-840.
21. Volinia S, Galasso M, Costinean S, Tagliavini L, Gamberoni G, et al. (2011) Reprogramming of miRNA networks in cancer and leukemia. Genome Res 20: 589-599.
22. O'Connell RM, Kahn D, Gibson WS, Round JL, Scholz RL, et al. (2010) MicroRNA-155 promotes autoimmune inflammation by enhancing inflammatory T cell development. Immunity 33: 607-619.
23. Huttenhofer A, Kiefmann M, Meier-Ewert S, O'Brien J, Lehrach H, et al. (2001) RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. Embo J 20: 2943-2953.
24. Brameier M, Herwig A, Reinhardt R, Walter L, Gruber J, (2010) Human box C/D snoRNAs with miRNA like functions: expanding the range of regulatory RNAs. Nucleic Acids Res.
25. Baek D, Villen J, Shin C, Camargo FD, Gygi SP, et al. (2008) The impact of microRNAs on protein output. Nature 455: 64-71.
26. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382.
27. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13: 2498-2504.
28. Slezak S, Jin P, Caruccio L, Ren J, Bennett M, et al. (2009) Gene and microRNA analysis of neutrophils from patients with polycythemia vera and essential thrombocytosis: down-regulation of micro RNA-1 and-133a. J Transl Med 7: 39.
29. Cordes KR, Sheehy NT, White MP, Berry EC, Morton SU, et al. (2009) miR-145 and miR-143 regulate smooth muscle cell fate and plasticity. Nature 460: 705-710.
30. Rouas R, Fayyad-Kazan H, El Zein N, Lewalle P, Rothe F, et al. (2009) Human natural Treg microRNA signature: role of microRNA-31 and microRNA-21 in FOXP3 expression. Eur J Immunol 39: 1608-1618.
31. Johnnidis JB, Harris MH, Wheeler RT, Stehling-Sun S, Lam MH, et al. (2008) Regulation of progenitor cell proliferation and granulocyte function by microRNA-223. Nature 451: 1125-1129.
32. Zhou B, Wang S, Mayr C, Bartel DP, Lodish HF, (2007) miR-150, a microRNA expressed in mature B and T cells, blocks early B cell development when expressed prematurely. Proc Natl Acad Sci USA 104: 7080-7085.
33. Beaulieu AD, Paquin R, Rathanaswami P, McColl SR, (1992) Nuclear signaling in human neutrophils. Stimulation of RNA synthesis is a response to a limited number of proinflammatory agonists. J Biol Chem 267: 426-432.
34. Rossi RL, Rossetti G, Wenandy L, Curti S, Ripamonti A, et al. (2011) Distinct microRNA signatures in human lymphocyte subsets and enforcement of the naive state in CD4+ T cells by the microRNA miR-125b. Nat Immunol 12: 796-803.
35. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, et al. (2010) Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. Rna 16: 991-1006.
36. Griesinger F, Janke A, Podleschny M, Bohlander SK, (2002) Identification of an ETV6-ABL2 fusion transcript in combination with an ETV6 point mutation in a T-cell acute lymphoblastic leukaemia cell line. Br J Haematol 119: 454-458.
37. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 31: e15.