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Transcriptome project: large scale gene expression analysis using DNA-Arrays

Grant number: 99/12135-9
Support type:Research Projects - Thematic Grants
Duration: May 01, 2001 - December 31, 2005
Field of knowledge:Biological Sciences - Immunology - Immunogenetics
Principal Investigator:Geraldo Aleixo da Silva Passos Júnior
Grantee:Geraldo Aleixo da Silva Passos Júnior
Home Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
Co-Principal Investigators:Eduardo Antônio Donadi ; Elza Tiemi Sakamoto Hojo


The Transcriptome project is included in the field of functional genomics, i.e., the meaning of the DNA sequence function at the genomic level. Although much has been known in terms of human and non-human genomic DNA or cDNA sequencing data, few studies have been conducted on the function of these genes. The wide scale gene expression evaluation is the first step on the understanding of functional genomics. The availability of mouse, human and other organism cDNA libraries, together with recent advances of robotic methodology applied to molecular biology, have permitted the development of DNA-array technology. Large number of clones, inserts and oligonucleotides are hybridized with complex probes prepared with total RNA or mRNA extracted from cells or tissues. Under adequate conditions, the quantitative signal acquisition permits the measurement of the amount of mRNA in each specimen, and therefore, the gene expression. High density of cDNA clones (micro-arrays) blotted on glass slides and hybridized with fluorochrome-labeled complex probes prepared from total RNA will be used in this project. Three complex biological conditions will be studied by means of wide range gene expression. 1) Gene expression during thymus ontogeny. Since the thymus gland is the major source for T lymphocyte maturation, and the place where the T-cell receptor V(D)J recombination occurs, the aim of this project is the evaluation of clusters of thymus genes expressed during the late phase of pregnancy, when the T-cell receptor V(D)J recombination takes place. 2) Gene expression during the acute phases of autoimmune disorders. Although several mechanisms have been implicated in the pathogenesis of autoimmune diseases, most of the pathogenic events which occur in the acute phase of these diseases have not been completely elucidated. The gene expression in lymphomononuclear cells actively involved in the pathogenesis of systemic lupus erythematosus and type I diabetes mellitus will be studied. 3) Instability of the human genome induced by in vitro irradiation. The effects of ionizing radiation at molecular level have not been completely elucidated. This study is aimed to evaluate the differential gene expression profile induced during the in vitro irradiation of normal peripheral lymphocytes and fibroplast cell lines. (AU)

Scientific publications (15)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
MELLO, STEPHANO S.; FACHIN, ANA L.; JUNTA, CRISTINA M.; SANDRIN-GARCIA, PAULA; DONADI, EDUARDO A.; PASSOS, GERALDO A. S.; SAKAMOTO-HOJO, ELZA T. Delayed Effects of Exposure to a Moderate Radiation Dose on Transcription Profiles in Human Primary Fibroblasts. Environmental and Molecular Mutagenesis, v. 52, n. 2, p. 117-129, MAR 2011. Web of Science Citations: 8.
CARMINATI, PATRICIA OLIVEIRA; MELLO, STEPHANO SPANO; FACHIN, ANA LUCIA; JUNTA, CRISTINA MORAES; SANDRIN-GARCIA, PAULA; CARLOTTI, CARLOS GILBERTO; DONADI, EDUARDO ANTONIO; SILVA PASSOS, GERALDO ALEIXO; SAKAMOTO-HOJO, ELZA TIEMI. Alterations in gene expression profiles correlated with cisplatin cytotoxicity in the glioma U343 cell line. GENETICS AND MOLECULAR BIOLOGY, v. 33, n. 1, p. 159-168, 2010. Web of Science Citations: 6.
BASSI, C. L.; MELLO, S. S.; CARDOSO, R. S.; GODOY, P. D. V.; FACHIN, A. L.; JUNTA, C. M.; SANDRIN-GARCIA, P.; CARLOTTI, C. G.; FALCAO, R. P.; DONADI, E. A.; PASSOS, G. A. S.; SAKAMOTO-HOJO, E. T. Transcriptional changes in U343 MG-a glioblastoma cell line exposed to ionizing radiation. HUMAN & EXPERIMENTAL TOXICOLOGY, v. 27, n. 12, p. 919-929, DEC 2008. Web of Science Citations: 14.
FACHIN‚ A.L.; MELLO‚ S.S.; SANDRIN-GARCIA‚ P.; JUNTA‚ C.M.; DONADI‚ E.A.; PASSOS‚ G.A.S.; SAKAMOTO-HOJO‚ E.T. Gene expression profiles in human lymphocytes irradiated in vitro with low doses of gamma rays. RADIATION RESEARCH, v. 168, n. 6, p. 650-665, 2007.
SILVA‚ G.L.; JUNTA‚ C.M.; MELLO‚ S.S.; GARCIA‚ P.S.; RASSI‚ D.M.; SAKAMOTO-HOJO‚ E.T.; DONADI‚ E.A.; PASSOS‚ G.A.S. Profiling Meta-Analysis Reveals Primarily Gene Coexpression Concordance between Systemic Lupus Erythematosus and Rheumatoid Arthritis. Annals of the New York Academy of Sciences, v. 1110, n. 1, p. 33-46, 2007.
CARDOSO‚ R.S.; JUNTA‚ C.M.; MACEDO‚ C.; MAGALHÃES‚ D.A.R.; SILVEIRA‚ E.L.V.; PAULA‚ M.O.; MARQUES‚ M.; MELLO‚ S.S.; ZÁRATE-BLADÉS‚ C.R.; NGUYEN‚ C.; OTHERS. 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. Molecular Immunology, v. 43, n. 5, p. 464-472, 2006.
RASSI‚ D.M.; JUNTA‚ C.M.; FACHIN‚ A.N.A.L.; SANDRIN-GARCIA‚ P.; MELLO‚ S.; MARQUES‚ M.; FERNANDES‚ A.N.A.P.M.; FOSS-FREITAS‚ M.C.; FOSS‚ M.C.; SAKAMOTO-HOJO‚ E.T.; OTHERS. Metabolism genes are among the differentially expressed ones observed in lymphomononuclear cells of recently diagnosed type 1 diabetes mellitus patients. Annals of the New York Academy of Sciences, v. 1079, n. 1, p. 171-176, 2006.
RASSI‚ D.M.; JUNTA‚ C.M.; FACHIN‚ A.N.A.L.; SANDRIN-GARCIA‚ P.; MELLO‚ S.S.; FERNANDES‚ A.N.A.P.M.; DEGHAIDE‚ N.N.H.S.; FOSS-FREITAS‚ M.C.; FOSS‚ M.C.; SAKAMOTO-HOJO‚ E.T.; OTHERS. Is HLA Class II Profile Relevant for the Study of Large-Scale Differentially Expressed Genes in Type 1 Diabetes Mellitus Patients?. Annals of the New York Academy of Sciences, v. 1079, n. 1, p. 305-309, 2006.
SOUSA CARDOSO‚ R.; MAGALHÃES‚ D.A.R.; BAIÃO‚ A.M.T.; JUNTA‚ C.M.; MACEDO‚ C.; MARQUES‚ M.; SAKAMOTO-HOJO‚ E.T.; DONADI‚ E.A.; PASSOS‚ G.A.S. Onset of promiscuous gene expression in murine fetal thymus organ culture. Immunology, v. 119, n. 3, p. 369-375, 2006.
TREVISAN‚ G.L.; RASSI‚ D.M.; BAIÃO‚ A.M.T.; SANDRIN-GARCIA‚ P.; MELLO‚ S.S.; TAMIA-FERREIRA‚ M.C.; JUNTA‚ C.M.; FACHIN‚ A.L.; MARQUES‚ M.; SAKAMOTO-HOJO‚ E.T.; OTHERS. Using cDNA microarrays to identify human CD19+ B cell gene products (ESTs) originated from systemic lupus erythematosus susceptibility loci. AUTOIMMUNITY REVIEWS, v. 5, n. 5, p. 319-323, 2006.
MAGALHÃES, DANIELLE A. R.; MACEDO, CLAUDIA; JUNTA, CRISTINA M.; MELLO, STEPHANO S.; MARQUES, MÁRCIA M. C.; CARDOSO, RENATO S.; SAKAMOTO-HOJO, ELZA T.; DONADI, EDUARDO A.; PASSOS, GERALDO A. S. Hybridization signatures during thymus ontogeny reveals modulation of genes coding for T-cell signaling proteins. Molecular Immunology, v. 42, n. 9, p. 1043-1048, May 2005.
PEREIRA‚ E.; TAMIA-FERREIRA‚ M.C.; CARDOSO‚ R.S.; MELLO‚ S.S.; SAKAMOTO-HOJO‚ E.T.; PASSOS‚ G.A.S.; DONADI‚ E.A. Immunosuppressive therapy modulates T lymphocyte gene expression in patients with systemic lupus erythematosus. Immunology, v. 113, n. 1, p. 99-105, 2004.
TREVISAN, G. L.; TAMIA-FERREIRA, M. C.; PASSOS, G. A. S.; JUNTA, C. M. Immunoglobulin V-lambda transcription profiling of systemic lupus erythematosus patients reveals biased usage of genes located near the J lambda-C lambda segments. Scandinavian Journal of Immunology, v. 59, n. 4, p. 395-399, abr. 2004.
SAKAMOTO-HOJO, E. T.; PEREIRA, E.; FACHIN, A. L.; CARDOSO, R. S.; DONADI, E. A.; PASSOS, G. A. S.; MELLO, S. S.; JUNTA, C. M. Gene expression profiles in human cells submitted to genotoxic stress. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH, v. 544, n. 2-3, p. 403-413, Nov. 2003.

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