Generation of \Expressed sequence labels\ directed to coding portions of genes (Ores): identification of new human genes expressed in breast cancer

Author(s)

Ricardo Garcia Corrêa

• Document type: Doctoral Thesis
• Press: São Paulo.
• Institution: Universidade de São Paulo (USP). Conjunto das Químicas (IQ e FCF) (CQ/DBDCQ)
• Defense date: 2001-02-16

Examining board members

Ricardo Renzo Brentani; Elizabeth Angelica Leme Martins; Luis Eduardo Soares Netto; Mari Cleide Sogayar; Sergio Verjovski Almeida

• Advisor: Ricardo Renzo Brentani; Andrew John George Simpson
• Field of knowledge: Biological Sciences - Biochemistry
• Indexed in: Banco de Dados Bibliográficos da USP-DEDALUS; Biblioteca Digital de Teses e Dissertações - USP
• Location: Universidade de São Paulo. Biblioteca do Conjunto das Químicas; T 574.88; C824g

Abstract

Expressed sequence tags (ESTs) are of fundamental importance for the identification of genes within the human genome and defining gene expression characteristics. In this work, we describe a new approach for generating cDNA libraries using essentially arbitrary primers to construct PCR-based minilibraries from breast tumor mRNA. Clones from these libraries were sequenced to generate 6,029 ESTs. Using this approach, we were able to observe a significant normalization of the different mRNA subpopulations and a preferential amplification of the central portions of the genes. Bioinformatic analysis of these sequences shows that 3,350 ESTs (56%) have significant similarity to known DNA and/or cDNA sequences (annotated sequences) from different organisms and 1,509 ESTs (25%) show no similarity to any sequences on different databases. From the annotated sequences, we have identified some sequences with high similarity to known genes from different organisms, indicating the discovery of some homologous genes possibly correlated with carcinogenic processes. For instance, we have isolated and partially characterized (i) a new NABC1 (novel amplified sequence in breast carcinoma 1) isoform which is downregulated in colorectal tumors, (ii) a novel semaphorin member of axon guidance molecules that is down-regulated in glioblastoma cell lines treated with all-trans-retinoic acid, an anti-tumor agent and (iii) the ortolog Notch 2 human gene, apparenty overexpressed in breast tumors with higher malignancy. (AU)

• FAPESP's process: 97/04213-4 - Generation of expressed sequence tags by RAP-PCR: identification of new genes in human breast cancer model
• Grantee: Ricardo Garcia Corrêa
• Support Opportunities: Scholarships in Brazil - Doctorate