Gene expression profiles of bladder cancers: evidence for a striking effect of in vitro cell models on gene patterns

Abstract

In order to assess the effect of in vitro models on the expression of key genes known to be implicated in the development or progression of cancer, we quantified by real-time quantitative PCR the expression of 28 key genes in three bladder cancer tissue specimens and in their derived cell lines, studied either as one-dimensional single cell suspensions, two-dimensional monolayers or three-dimensional spheroids. Global analysis of gene expression profiles showed that in vitro models had a dramatic impact upon gene expression. Remarkably, quantitative differences in gene expression of 2 -63-fold were observed in 24 out of 28 genes among the cell models. In addition, we observed that the in vitro model which most closely mimicked in vivo mRNA phenotype varied with both the gene and the patient. These results provide evidence that mRNA expression databases based on cancer cell lines, which are studied to provide a rationale for selection of therapy on the basis of molecular characteristics of a patient's tumour, must be carefully interpreted.

Comparison of hypoxia transcriptome in vitro with in vivo gene expression in human bladder cancer

“…The in vivo array, comparing as it does tumour samples to a panel of cell lines may be highlighting the more complex influences on gene expression present in the three-dimensional environment. Three-dimensional geometry of in vitro cell growth alone has been shown to have dramatic influences on biological function and gene expression profile (Dangles et al, 2002).…”

Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach

“…For example, Sabbah et al (1999) described a mechanism by which ERa regulates CCND1 gene transcription through a cyclic AMP response element (CRE); (b) Expression of genes in ERa-positive breast tumors can also reflect the presence of different types of epithelial cells in the mammary gland, independently of the presence of estrogen and ERa. In this regard, ERa-positive breast tumors have been suggested to exhibit the phenotype of luminal epithelial cells, whereas ERa-negative tumors resemble myoepithelial (basal) cells (Perou et al 2000); (c) Downregulation of genes in ERa-negative tumors may also simply reflect dedifferentiation of epithelial cells during malignant progression of ERanegative breast tumors evolving from ERa-positive precursors; (d) Finally, cultured cell lines (in vitro models) have lost many features that characterize tumor specimens in vivo (Welsh et al 2001, Dangles et al 2002. The mechanism that leads to in vivo gene overexpression in ERa-positive breast tumors involves several factors, including ERa and several known or unknown transcriptional coactivators, not all of, which present in classical in vitro models.…”

Establishment of Human Colon Cancer Cell Lines from Fresh Tumors versus Xenografts: Comparison of Success Rate and Cell Line Features

“…The commonality of these chromosomal aberrations cell lines is due to their common origin and not to specific features of colon cancer. It is noteworthy that CT320, CT320X6, CT329, and CT329X12 cells were studied at early in vitro passages (up to [10][11][12][13][14][15], reflecting the initial alterations in this tumor and not a genotypic diversity, which could have been attributed to long-term in vitro cell culture (30). Chemosensitivity tests underscored the fact that CT320 versus CT320X6 and CT329 versus CT329X12 were distinct cell lines.…”

“…The first 5-Am section was stained with H&E for histologic analysis to determine the ratio of viable cancer cells to normal contaminating cells. Steps of RNA extraction to reverse transcription-PCR were conducted as previously described (13). Standard curves were established using cDNA of five serial dilutions of the universal human reference RNA (20-0.032 ng per tube) from Stratagene (La Jolla, CA).…”