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Transcription profiling by array of human BIN-67 small cell ovarian carcinoma to investigate gene expression

ABSTRACT: The biology of small cell ovarian carcinoma of the hypercalcemic type (SCCOHT), which is a rare and aggressive form of ovarian cancer, is poorly understood. Tumourigenicity, in vitro growth characteristics, genetic and genomic anomalies, and sensitivity to standard and novel chemotherapeutic treatments were investigated in the unique SCCOHT cell line, BIN-67, to provide further insight in the biology of this rare type of ovarian cancer. Microarray expression analysis was performed using the GeneChip? Human Genome U133 Plus 2.0 Array (Affymetrix?, Santa Clara, CA) with total RNA from BIN-67 cells. Hybridization and scanning were performed at the McGill University and Genome Quebec Innovation Centre (Montreal, QC). Gene expression levels were determined from the scanned images using Affymetrix? Microarray Suite (MAS) version 5.0 software expression algorithm (Affymetrix?, Santa Clara, CA). Gene expression profiles were compared with Affymetrix U133 Plus 2.0 (MAS5.0) generated expression profiles (similarly normalized) from 10 human normal ovarian surface epithelial (OSE) cell brushings available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress/), accession number E-GEOD-18520.

ORGANISM(S): Homo sapiens

SUBMITTER: Arcand Suzanna

PROVIDER: S-ECPF-MEXP-3872 | biostudies-other |

REPOSITORIES: biostudies-other

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Project description:Alternative pre-mRNA splicing critically contributes to the generation of protein variety in a tissue- and development-specific manner. Alterations in the normal pathways of alternative splicing (AS) have been associated with the growth and maintenance of several tumour types, and have been indicated as candidate bio-markers of tumour progression, metastasis and patient survival. In this study we applied genome-wide exon array technology to investigate AS events that may distinguish between human medulloblastoma and normal cerebellum. We initially investigated gene-level expression profiles to identify samples expressing gene signatures characteristic of previously described MB molecular subgroups. 3 medulloblastomas significantly over-expressed genes typically belonging to the Shh signalling pathway or associated with a granule cell progenitor status and were therefore classified as Shh-activated tumours (MB1). The remaining tumour samples were grouped together as medulloblastoma subset 2 (MB2). We then applied the Splicing Index algorithm and identified 1260 unique genes containing at least one candidate exon whose inclusion rate differed between different sample subgroups. Following the analysis of candidate event expression plots and gene structure annotation, we selected 14 examples of differential splicing of cassette exons and successfully validated 11 of them by semi-quantitative RT-PCR in a selection of the initial sample-set and subsequently in an independent set of 10 normal cerebellum and 20 medulloblastoma samples. Through the analysis of AS pathway in in vitro cultures of cerebellar granule cell progenitors (the putative cell of origin of least a subset of medulloblastomas), we showed that medulloblastoma-associated AS patterns could be indicative of a normal cerebellar undifferentiated phenotype and suggested that activation of oncogenic pathways during the development of the cerebellum may lead to a failure of neuronal differentiation also through the disruption of AS programs.

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Transcription profiling by array of human BIN-67 small cell ovarian carcinoma to investigate gene expression

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