Genes that code for T cell signaling proteins establish transcriptional regulatory networks during thymus ontogeny

Molecular and Cellular Biochemistry

Volumn 318, Issue 1-2, 2008, Pages 63-71

  Macedo, Cláudia ^a   Magalhães, Danielle A ^a   Tonani, Monique ^a   Marques, Márcia C ^a   Junta, Cristina M ^a   Passos, Geraldo A S ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Gene expression; Gene networks; Microarray; Thymus development

Indexed keywords

CALCIUM; CALPASTATIN; CELL PROTEIN; COMPLEMENTARY DNA; CYCLIN DEPENDENT KINASE 4; GENE PRODUCT; PROTEIN ARGININE METHYLTRANSFERASE; PROTEIN PRRG2; PROTEIN STXBP3; SNARE PROTEIN; T CELL SIGNALING PROTEIN; UNCLASSIFIED DRUG;

ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CALCIUM SIGNALING; CELL DIFFERENTIATION; CELL MATURATION; DNA MICROARRAY; DNA SEQUENCE; FEMALE; FETUS; GENE EXPRESSION PROFILING; GENE INTERACTION; MALE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; ONTOGENY; PROTEIN TRANSPORT; SEQUENCE ANALYSIS; THYMOCYTE; THYMUS DEVELOPMENT; TRANSCRIPTION REGULATION;

ANIMALS; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; MICE; SIGNAL TRANSDUCTION; T-LYMPHOCYTES; THYMUS GLAND;

MURINAE;

EID: 54949156829     PISSN: 03008177     EISSN: 15734919     Source Type: Journal    
DOI: 10.1007/s11010-008-9857-7     Document Type: Article

References (43)

1. Anderson G, Moore NC, Owen JJT, Jenkinson EJ (1996) Cellular interactions in thymocyte development. Annu Rev Immunol 14:73-99. doi: 10.1146/annurev.immunol.14.1.73
2. Anderson G, Jenkinson EJ (2001) Lymphostromal interactions in thymic development and function. Nat Rev Immunol 1:31-40. doi: 10.1038/35095500
3. Kishimoto H, Sprent J (1999) Several different cell surface molecules control negative selection of medullary thymocytes. J Exp Med 190:65-73. doi: 10.1084/jem.190.1.65
4. Klein L, Kyewski B (2000) Self-antigen presentation by thymic stromal cells: A subtle division of labor. Curr Opin Immunol 12:179-186. doi: 10.1016/S0952-7915(99)00069-2
5. Kyewski B, Derbinski J (2004) Self-representation in the thymus: An extended view. Nat Rev Immunol 4:688-698. doi: 10.1038/nri1436
6. Puthier D, Joly F, Irla M, Saade M, Victorero G, Loriod B et al (2004) A general survey of thymocyte differentiation by transcriptional analysis of knockout mouse models. J Immunol 173:6109-6118
7. Magalhães DA, Macedo C, Junta CM, Mello SS, Marques MM, Cardoso RS et al (2005) Hybridization signatures during thymus ontogeny reveals modulation of genes coding for T-cell signaling proteins. Mol Immunol 42:1043-1048. doi: 10.1016/j.molimm.2004.09.031
8. Cardoso RS, Junta CM, Macedo C, Magalhães DA, Silveira EL, Paula MO, Marques MM, Mello SS, Zarate-Blades CR, Nguyen C, Houlgatte R, Donadi EA, Sakamoto-Hojo ET, Passos GA (2006) Hybridization signatures of gamma-irradiated murine fetal thymus organ culture (FTOC) reveal modulation of genes associated with T-cell receptor V(D)J recombination and DNA repair. Mol Immunol 43:464-472. doi: 10.1016/j.molimm.2005.03.010
9. Eisen MB, Spellmam PT, Brown PO, Botstein D (1998) Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863-14868. doi: 10.1073/pnas.95.25.14863
10. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to ionizing radiation response. Proc Natl Acad Sci USA 98:5126-5121. doi: 10.1073/pnas.091062498
11. Sousa-Cardoso R, Magalhães DA, Baião AM, Junta CM, Macedo C, Marques MM et al (2006) Onset of promiscuous gene expression in fetal thymus organ culture. Immunology 119:369-375. doi: 10.1111/ j.1365-2567.2006.02441.x
12. Wu CC, Huang HC, Juan HF, Chen ST (2004) GeneNetwork: An interactive tool for reconstruction of genetic network using microarray data. Bioinformatics 20:3691-3693. doi: 10.1093/bioinformatics/bth428
13. Schatz DG (2004) V(D)J recombination. Immunol Rev 200:5-11. doi: 10.1111/ j.0105-2896.2004.00173.x
14. Kishimoto H, Sprent J (2000) The thymus and negative selection. Immunol Res 21:315-323. doi: 10.1385/IR:21:2-3:315
15. Ghendler Y, Hussey RE, Witte T, Mizoguchi E, Clayton LK, Bhan AK et al (1997) Double-positive T cell receptor (high) thymocytes are resistant to peptide/major histocompatibility complex ligand induced negative selection. Eur J Immunol 27:2279-2289. doi: 10.1002/eji.1830270923
16. Shortman K, Wu L (1996) Early T lymphocytes progenitors. Annu Rev Immunol 14:29-47. doi: 10.1146/annurev.immunol.14.1.29
17. Junta CM, Passos GAS (1998) Emergence of TCR alpha/beta V(D)J recombination and transcription during ontogeny of inbred mouse strains. Mol Cell Biochem 187:67-72. doi: 10.1023/A:1006807021251
18. Macedo C, Junta CM, Passos GAS (1999) Onset of T-cell receptor VBeta8.1 and DBeta2.1 V(D)J recombination and transcription during ontogeny of inbred mouse strains. Immunol Lett 69:371-373. doi: 10.1016/ S0165-2478(99)00110-8
19. Espanhol AR, Macedo C, Junta CM, Cardoso RS, Victorero G, Loriod B et al (2003) Gene expression profiling during thymus ontogeny and its association with TCRVbeta8.1-Dbeta2.1 rearrangements of inbred mouse strains. Mol Cell Biochem 252:223-228. doi: 10.1023/A:1025556510001
20. DeRyckere D, Mann DL, DeGregori J (2003) Characterization of transcriptional regulation during negative selection in vivo. J Immunol 171:802-811
21. Hoffmann R, Bruno L, Seidl T, Rolink A, Melchers F (2003) Rules for gene usage inferred from a comparison of large-scale gene expression profiles of T and B lymphocytes development. J Immunol 170:1339-1353
22. Schmitz I, Clayton LK, Reinherz EL (2003) Gene expression analysis of thymocyte selection in vivo. Int Immunol 15:1237-1248. doi: 10.1093/ intimm/dxg125
23. Rugh R (1968) The mouse. Its reproduction and development, 1st edn. Burgess Publishing Company, Edina
24. Nguyen C, Rocha D, Granjeaud S, Baldit M, Bernard K, Naquet P et al (1995) Differential gene expression in murine thymus assayed by quantitative hybridization of arrayed cDNA clones. Genomics 29:207-215. doi: 10.1006/geno.1995.1233
25. Bertucci F, Houlgatte R, Granjeaud S, Nasser V, Loriod B, Beaudoing E et al (2002) Prognosis of breast cancer and gene expression profiling using DNA arrays. Ann N Y Acad Sci 975:217-231
26. Verdeil G, Puthier D, Nguyen C, Schmitt-Verhulst AM, Auphan-Anezin N (2002) Gene profiling approach to establish the molecular bases for partial versus full activation of naïve CD8 T lymphocytes. Ann NY Acad Sci 975:68-76
27. Honore P, Granjeaud S, Tagett R, Deraco S, Beaudoing E, Rougemont J et al (2006) MicroArray facility: A laboratory information management system with extended support for nylon based technologies. BMC Genomics 7:240. doi: 10.1186/1471-2164-7-240
28. Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32:496-501. doi: 10.1038/ng1032
29. Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A (2005) Reverse engineering of regulatory networks in human B cells. Nat Genet 37:382-390. doi: 10.1038/ng1532
30. Margolin A, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R et al (2006) Aracne: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics Suppl 1: S7
31. Gardner T, di Bernardo D, Lorenz D, Collins J (2003) Infering genetic networks and identifying compound mode of action via expression profiling. Science 301:102-105. doi: 10.1126/science.1081900
32. Di Bernardo D, Thomson M, Gardner T, Chobot S, Eastwood E, Wojtovich A et al (2005) Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol 23:377-383. doi: 10.1038/nbt1075
33. Bansal M, Della Gatta G, di Bernardo D (2006) Inference of gene regulatory networks and compound mode of action from time course gene expression profiles. Bioinformatics 22:815-822. doi: 10.1093/ bioinformatics/btl003
34. Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED (2004) Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics 20:3594-3603. doi: 10.1093/ bioinformatics/bth448
35. Soinov LA, Krestyaninova MA, Brazma A (2003) Towards reconstruction of gene networks from expression data by supervised learning. Genome Biol 4(1):R6.1-R6.10
36. Faith JJ, Hayete B, Thaden JT et al (2007) Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol 5:54-66. doi: 10.1371/ journal.pbio.0050008
37. Sandmann T, Girardot C, Brehme M et al (2007) A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev 21:436-449. doi: 10.1101/gad.1509007
38. Takaku T, Ohyashiki JH, Zhang Y, Ohyashikik K (2005) Estimating immunoregulatory gene networks in human herpesvirus type 6-infected T cells. Biochem Biophys Res Commun 336:469-477. doi: 10.1016/ j.bbrc.2005.08.104
39. Takasaki I, Takarada S, Fukuchi M, Yasuda M, Tsuda M, Tabuchi Y (2007) Identification of genetic networks involved in the cell growth arrest and proliferation of a rat astrocyte cell line RCG-12. J Cell Biochem 102:1472-1485. doi: 10.1002/jcb.21369
40. de La Fuente A, Brazhnik P, Mendes P (2002) Linking the genes: Inferring quantitative gene networks from microarray data. Trends Genet 18:395-398. doi: 10.1016/S0168-9525(02)02692-6
41. Feske S, Giltnane J, Dolmetsch R, Staudt LM, Rao A (2001) Gene regulation mediated by calcium signals in T lymphocytes. Nat Immunol 2:316-324. doi: 10.1038/86318
42. Feske S, Okamura H, Hogan PG, Rao A (2003) Ca+/calcineurin signalling in cells of the immune system. Biochem Biophys Res Commun 311:1117-1122. doi: 10.1016/j.bbrc.2003.09.174
43. Heissmeyer V, Macian F, Im SH, Varma R, Feske S, Venuprasad K et al (2004) Calcineurin imposes T cell unresponsiveness through targeted proteolysis of signaling proteins. Nat Immunol 5:255-265. doi: 10.1038/ ni1047