Choice of normal ovarian control influences determination of differentially expressed genes in ovarian cancer expression profiling studies.

PURPOSE As with many cancers thought to be of epithelial origin, expression profiling studies of ovarian cancer have relied on a variety of sources of normal cells for comparison with tumors, including whole ovary samples (WO), ovarian surface epithelium (OSE) exposed to short-term culture, and immortalized OSE cell lines (IOSE). Our purpose was to assess the impact of the use of different types of normal controls on the determination of gene expression alterations in ovarian cancer studies. EXPERIMENTAL DESIGN We compared the gene expression profiles generated on an 11,000-element cDNA microarray of OSE brushings, whole ovary samples, short-term cultures of normal OSE, SV40 large T antigen-immortalized OSE cell lines, and telomerase-immortalized OSE cell lines. The function of the groups as normal controls was then assessed by separate comparisons of each group to a set of 24 serous ovarian carcinoma samples. RESULTS The normal groups formed robust, distinct clusters in hierarchical clustering and multidimensional scaling. The Pearson correlation coefficient for all combinations of any two of the groups ranged from 0.04 to 0.54, emphasizing the disparity of the groups. In the gene lists produced by comparing each normal group with the ovarian cancer samples, the majority of genes were unique to that normal-cancer comparison, with no gene appearing on all five lists. CONCLUSIONS These results suggest that the selection of a normal control to compare with epithelial ovarian cancer samples in microarray studies strongly influences the genes that are identified as differentially expressed and complicates comparison with studies using a different normal control.

[1]  S K Libutti,et al.  Advantages of mRNA amplification for microarray analysis. , 2002, BioTechniques.

[2]  D. P. Singh,et al.  LEDGF, a survival factor, activates stress-related genes , 2002, Progress in Retinal and Eye Research.

[3]  M. Wells,et al.  Precursor lesions of ovarian epithelial malignancy , 2001, Histopathology.

[4]  L. Hood,et al.  Monitoring gene expression profile changes in ovarian carcinomas using cDNA microarray. , 1999, Gene.

[5]  E. Petricoin,et al.  Proteomic analysis of laser capture microdissected human prostate cancer and in vitro prostate cell lines , 2000, Electrophoresis.

[6]  T. Morgan,et al.  Transforming growth factor-β1 induces neuronal and astrocyte genes: Tubulin α1, glial fibrillary acidic protein and clusterin , 1994, Neuroscience.

[7]  P. Kruk,et al.  Simian virus 40-transformed human ovarian surface epithelial cells escape normal growth controls but retain morphogenetic responses to extracellular matrix. , 1992, American journal of obstetrics and gynecology.

[8]  E. Schmelz,et al.  Spontaneous malignant transformation of human ovarian surface epithelial cells in vitro. , 2001, Clinical cancer research : an official journal of the American Association for Cancer Research.

[9]  R. L. Baldwin,et al.  Gene expression in epithelial ovarian carcinoma , 2002, Oncogene.

[10]  A. C. Chinault,et al.  mRTVP-1, a Novel p53 Target Gene with Proapoptotic Activities , 2002, Molecular and Cellular Biology.

[11]  Kathleen R. Cho,et al.  Gene expression in ovarian cancer reflects both morphology and biological behavior, distinguishing clear cell from other poor-prognosis ovarian carcinomas. , 2002, Cancer research.

[12]  F. Marincola,et al.  High-fidelity mRNA amplification for gene profiling , 2000, Nature Biotechnology.

[13]  T. Hudson,et al.  Expression profiles of 290 ESTs mapped to chromosome 3 in human epithelial ovarian cancer cell lines using DNA expression oligonucleotide microarrays. , 2002, Genome research.

[14]  Anne-Marie Mes-Masson,et al.  Microarray analysis of gene expression mirrors the biology of an ovarian cancer model , 2001, Oncogene.

[15]  Ahmedin Jemal,et al.  Cancer Statistics, 2002 , 2002, CA: a cancer journal for clinicians.

[16]  Roger E Bumgarner,et al.  Comparative hybridization of an array of 21,500 ovarian cDNAs for the discovery of genes overexpressed in ovarian carcinomas. , 1999, Gene.

[17]  David B. Krizman,et al.  The genetics of cancer—a 3D model , 1999, Nature Genetics.

[18]  N. Dubrawsky.  Cancer statistics , 1989, CA: a cancer journal for clinicians.

[19]  R. Berkowitz,et al.  Characterization of human ovarian surface epithelial cells immortalized by human papilloma viral oncogenes (HPV-E6E7 ORFs). , 1995, Experimental cell research.

[20]  S. Tsao,et al.  Nonrandom chromosomal imbalances in human ovarian surface epithelial cells immortalized by HPV16-E6E7 viral oncogenes. , 2001, Cancer genetics and cytogenetics.

[21]  R. L. Baldwin,et al.  Differential gene expression between normal and tumor-derived ovarian epithelial cells. , 2000, Cancer research.

[22]  D. Lockhart,et al.  Analysis of gene expression profiles in normal and neoplastic ovarian tissue samples identifies candidate molecular markers of epithelial ovarian cancer. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Richard M. Simon,et al.  Methods for assessing reproducibility of clustering patterns observed in analyses of microarray data , 2002, Bioinform..

[24]  T Tanaka,et al.  Identification by cDNA microarray of genes involved in ovarian carcinogenesis. , 2000, Cancer research.

[25]  J. McDougall,et al.  Genetic and epigenetic changes in human epithelial cells immortalized by telomerase. , 2000, The American journal of pathology.

[26]  Christos Sotiriou,et al.  Gene expression profiles of BRCA1-linked, BRCA2-linked, and sporadic ovarian cancers. , 2002, Journal of the National Cancer Institute.

[27]  R. Moskowitz,et al.  Tumour necrosis factor alpha enhances the expression of hydroxyl lyase, cytoplasmic antiproteinase-2 and a dual specificity kinase TTK in human chondrocyte-like cells. , 2000, Cytokine.

[28]  A. Wellmann,et al.  Presence of genetic alterations in microdissected stroma of human colon and breast cancers. , 2001, Journal of molecular medicine.

[29]  R. Reddel,et al.  Comparison of human mammary epithelial cells immortalized by simian virus 40 T-Antigen or by the telomerase catalytic subunit , 2002, Oncogene.

[30]  G. Riggins,et al.  Large-scale serial analysis of gene expression reveals genes differentially expressed in ovarian cancer. , 2000, Cancer research.

[31]  R. L. Baldwin,et al.  Ovarian carcinoma cell cultures are resistant to TGF-beta1-mediated growth inhibition despite expression of functional receptors. , 1999, Gynecologic oncology.

[32]  S. Mok,et al.  Identification of differentially expressed genes from ovarian cancer cells by MICROMAX cDNA microarray system. , 2001, BioTechniques.