Influence of monolayer, spheroid, and tumor growth conditions on chromosome 3 gene expression in tumorigenic epithelial ovarian cancer cell lines

Neal Al Cody,Ali Filali-Mouhim,Diane M Provencher,Magdalena Zietarska,Anne-Marie Mes-Masson,Patricia N Tonin

doi:10.1186/1755-8794-1-34

Abstract

BackgroundExpression microarray analyses of epithelial ovarian cancer (EOC) cell lines may be exploited to elucidate genetic and epigenetic events important in this disease. A possible variable is the influence of growth conditions on discerning candidates. The present study examined the influence of growth conditions on the expression of chromosome 3 genes in the tumorigenic EOC cell lines, OV-90, TOV-21G and TOV-112D using Affymetrix GeneChip® HG-U133A expression microarray analysis.MethodsChromosome 3 gene expression profiles (n = 1147 probe sets, representing 735 genes) were extracted from U133A expression microarray analyses of the EOC cell lines OV-90, TOV-21G and TOV-112D that were grown as monolayers, spheroids or nude mouse xenografts and monolayers derived from these tumors. Hierarchical cluster analysis was performed to compare chromosome 3 transcriptome patterns of each growth condition. Differentially expressed genes were identified and characterized by two-way comparative analyses of fold-differences in gene expression between monolayer cultures and each of the other growth conditions, and between the maximum and minimum values of expression of all growth conditions for each EOC cell line.ResultsAn overall high degree of similarity (> 90%) in gene expression was observed when expression values of alternative growth conditions were compared within each EOC cell line group. Two-way comparative analysis of each EOC cell line grown in an alternative condition relative to the monolayer culture showed that overall less than 15% of probe sets exhibited at least a 3-fold difference in expression profile. Less than 23% of probe sets exhibited greater than 3-fold differences in gene expression in comparisons of the maximum and minimum value of expression of all growth conditions within each EOC cell line group. The majority of these differences were less than 5-fold. There were 17 genes in common which were differentially expressed in all EOC cell lines. However, the patterns of expression of these genes were not necessarily the same for each growth condition when one cell line was compared with another.ConclusionThe various alternative in vivo and in vitro growth conditions of tumorigenic EOC cell lines appeared to modestly influence the global chromosome 3 transcriptome supporting the notion that the in vitro cell line models are a viable option for testing gene candidates.

Highlights

Expression microarray analyses of epithelial ovarian cancer (EOC) cell lines may be exploited to elucidate genetic and epigenetic events important in this disease
Hierarchical cluster analysis Hierarchical cluster analysis of chromosome 3 gene expression data from each EOC cell line grown in monolayer cultures (L) and alternative growth conditions such as spheroid cultures (S), nude mouse xenografts at subcutaneous (TSC) or intraperitoneal (TIP) sites, and monolayer cultures of subcutaneous (LSC) and intraperitoneal (LIP) xenografts is shown in Figures 1, 2 and 3
Hierarchical clustering of normalized chromosome 3 gene expression data sets derived from OV-90 grown as monolayer culture (L), and the alternative growth conditions consisting of spheroid cultures (S), tumors derived from xenograft tumors from subcutaneous (TSC) or intraperitoneal (TIP) injection sites in nude mice, and monolayer cultures derived from these tumors (LSC and LIP)

Summary

Introduction

Expression microarray analyses of epithelial ovarian cancer (EOC) cell lines may be exploited to elucidate genetic and epigenetic events important in this disease. The present study examined the influence of growth conditions on the expression of chromosome 3 genes in the tumorigenic EOC cell lines, OV-90, TOV-21G and TOV-112D using Affymetrix GeneChip® HG-U133A expression microarray analysis. We have studied the properties of three EOC cell lines derived from malignant ovarian tumors (TOV-21G and TOV112D) and ascites (OV-90) [2,3]. These EOC cell lines were derived from patient samples prior to chemotherapy They have been extensively characterized and shown to exhibit many of molecular genetic features, cytogenetic anomalies, and somatic mutations in tumor suppressor genes frequently associated with malignant ovarian cancers [2,3,4]. The application of various growth conditions to capture the full spectrum of the disease along with large-scale gene expression analyses could be important in our understanding of the biological and genetic factors that influence the phenotypic characteristics of the disease [1,12]

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Conclusion