Transcriptomics

Dataset Information

29

Insights on PRAME and osteosarcoma by means of gene expression profiling


ABSTRACT: Abstract BACKGROUND: Osteosarcoma (OS) is the most frequent bone tumor in children and adolescents. Tumor antigens are encoded by genes that are expressed in many types of solid tumors but are silent in normal tissues, with the exception of placenta and male germ-line cells. It has been proposed that antigen tumors are potential tumor markers. OBJECTIVES: The premise of this study is that the identification of novel OS-associated transcripts will lead to a better understanding of the events involved in OS pathogenesis and biology. METHODS: We analyzed the expression of a panel of seven tumor antigens in OS samples to identify possible tumor markers. After selecting the tumor antigen expressed in most samples of the panel, gene expression profiling was used to identify osteosarcoma-associated molecular alterations. A microarray was employed because of its ability to accurately produce comprehensive expression profiles. RESULTS: PRAME was identified as the tumor antigen expressed in most OS samples; it was detected in 68% of the cases. Microarray results showed differences in expression for genes functioning in cell signaling and adhesion as well as extracellular matrix-related genes, implying that such tumors could indeed differ in regard to distinct patterns of tumorigenesis. CONCLUSIONS: The hypothesis inferred in this study was gathered mostly from available data concerning other kinds of tumors. There is circumstantial evidence that PRAME expression might be related to distinct patterns of tumorigenesis. Further investigation is needed to validate the differential expression of genes belonging to tumorigenesis-related pathways in PRAME-positive and PRAME-negative tumors. Overall design: Six tumor samples representing distinct histological classes of osteosarcoma (telangiectatic, giant cell, anaplastic, osteoblastic and chondroblastic) were included in this study. They were obtained from individual patients ranging from 5 to 29 years old. Microarray experiments were carried out using the microarray platform CodeLink (GE Healthcare). This platform utilizes bioarrays consisting of 30-base, single pre-validated oligonucleotide probe per gene target. CodeLink UniSet Human I bioarrays, containing 10,000 human transcripts, were used for all experiments. Hybridization procedures strictly followed protocols provided by the manufacturer (GE Healthcare). A total of 12 arrays were hybridized, including 6 tumor samples (3 PRAME-positive and 3 PRAME-negative) and their respective technical replicates. Arrays were scanned following the recommended scanning procedure and settings for use with CodeLink bioarrays (GE Healthcare) on GenePix 4000B Array Scanner/GenePix Pro 4.0 software (Axon Instruments).

INSTRUMENT(S): Codelink Uniset Human 1

ORGANISM(S): Homo sapiens  

SUBMITTER: Patricia Severino  

PROVIDER: GSE8079 | GEO |

SECONDARY ACCESSION(S): PRJNA100917

REPOSITORIES: GEO

Similar Datasets

2010-05-18 | E-GEOD-8079 | ArrayExpress
2010-05-15 | E-GEOD-9792 | ArrayExpress
| GSE9792 | GEO
2011-12-30 | E-GEOD-16072 | ArrayExpress
2015-12-31 | E-GEOD-22364 | ArrayExpress
| GSE12512 | GEO
2011-12-30 | GSE16072 | GEO
2013-03-28 | E-GEOD-38742 | ArrayExpress
| GSE22364 | GEO
| GSE38742 | GEO