Expression scanning of an array of growth control genes in human tumor cell lines

Bertucci, François; Hulst, S Van; Bernard, Karine; Loriod, Béatrice; Granjeaud, Samuel; Tagett, Rebecca; Starkey, Mike; Nguyen, Catherine; Jordan, Bertrand; Birnbaum, Daniel

doi:10.1038/sj.onc.1202731

Cited by 52 publications

(44 citation statements)

References 22 publications

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“…Signal intensities were normalized for the amount of spotted DNA (Bertucci et al, 1999b) and the variability of experimental conditions (Bertucci et al, 1999a). Briefly, complex probe intensity of each spot ('C') was first corrected ('C/V') for the amount of target DNA accessible to hybridization as measured using vector hybridization ('V').…”

Section: Discussionmentioning

confidence: 99%

“…Amplification products were desiccated and resuspended in 50 ml of distilled water. They were then spotted as previously described (Bertucci et al, 1999b) onto Hybond-N þ 2 Â 7 cm 2 membranes (Amersham) stuck to glass slides using a 64-pin print head on a MicroGridII microarrayer (Apogent Discoveries, Cambridge, England). All membranes used in this study belonged to the same batch.…”

Section: Dna Microarrays Preparationmentioning

confidence: 99%

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Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters

et al. 2004

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Different diagnostic and prognostic groups of colorectal carcinoma (CRC) have been defined. However, accurate diagnosis and prediction of survival are sometimes difficult. Gene expression profiling might improve these classifications and bring new insights into underlying molecular mechanisms. We profiled 50 cancerous and noncancerous colon tissues using DNA microarrrays consisting of B8000 spotted human cDNA. Global hierarchical clustering was to some extent able to distinguish clinically relevant subgroups, normal versus cancer tissues and metastatic versus nonmetastatic tumours. Supervised analyses improved these segregations by identifying sets of genes that discriminated between normal and tumour tissues, tumours associated or not with lymph node invasion or genetic instability, and tumours from the right or left colon. A similar approach identified a gene set that divided patients with significantly different 5-year survival (100% in one group and 40% in the other group; P ¼ 0.005). Discriminator genes were associated with various cellular processes. An immunohistochemical study on 382 tumour and normal samples deposited onto a tissue microarray subsequently validated the upregulation of NM23 in CRC and a downregulation in poor prognosis tumours. These results suggest that microarrays may provide means to improve the classification of CRC, provide new potential targets against carcinogenesis and new diagnostic and/or prognostic markers and therapeutic targets.

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Section: Discussionmentioning

confidence: 99%

Section: Dna Microarrays Preparationmentioning

confidence: 99%

Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters

et al. 2004

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“…Nylon filter preparation with spotted polymerase chain reaction (PCR) products derived from ϳ1000 selected candidate cancer genes, 33 P radioactive hybridization, and data acquisition, normalization, and analysis have been described elsewhere 13,14 and can also be consulted on our web site (http:/tagc.univ-mrs.fr/pub/Cancer/). …”

Section: Dna Arraysmentioning

confidence: 99%

“…1,13,14,21 Nevertheless, we sought to further validate our data by comparing RNA expression levels of two genes, ERBB2 and MUC1, as measured by cDNA array, to those obtained by RQ-PCR.…”

Section: Validation Of Cdna Array Data With Rq-pcrmentioning

confidence: 99%

Distinct and Complementary Information Provided by Use of Tissue and DNA Microarrays in the Study of Breast Tumor Markers

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Charafe‐Jauffret

Bertucci

et al. 2002

The American Journal of Pathology

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Emerging high-throughput screening technologies are rapidly providing opportunities to identify new diagnostic and prognostic markers and new therapeutic targets in human cancer. Currently, cDNA arrays allow the quantitative measurement of thousands of mRNA expression levels simultaneously. Validation of this tool in hospital settings can be done on large series of archival paraffin-embedded tumor samples using the new technique of tissue microarray. On a series of 55 clinically and pathologically homogeneous breast tumors, we compared for 15 molecules with a proven or suspected role in breast cancer, the mRNA expression levels measured by cDNA array analysis with protein expression levels obtained using tumor tissue microarrays. The validity of cDNA array and tissue microarray data were first verified by comparison with quantitative reverse transcriptase-polymerase chain reaction measurements and immunohistochemistry on full tissue sections, respectively. We found a good correlation between cDNA and tissue array analyses in one-third of the 15 molecules, and no correlation in the remaining twothirds. Furthermore, protein but not RNA levels may have prognostic value; this was the case for MUC1 protein, which was studied further using a tissue microarray containing ϳ600 tumor samples. For THBS1 the opposite was observed because only RNA levels had prognostic value. Thus, differences extended to clinical prognostic information obtained by the two methods underlining their complementarity and the need for a global molecular analysis of tumors at both the RNA and protein levels.

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“…With suitable databases and bioinformatics tools, candidate genes can be selected following in silico analysis for favourable tissue distribution, secretion signals and other features, allowing empirical design of microarrays for candidate marker screening. Gene expression profiling is being increasingly used to analyse hundreds or thousands of genes simultaneously in cancer cell lines (Bertucci et al, 1999), and diseased and normal tissue (Zhang et al, 1997;Alon et al, 1999;Wang et al, 1999). Clustering analysis of gene expression data can provide novel insights into disease, for example molecular definition of subtypes of leukaemia, providing a tool for an important diagnostic problem (Golub et al, 1999).…”

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Identification of potential diagnostic markers of prostate cancer and prostatic intraepithelial neoplasia using cDNA microarray

et al. 2001

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The identification of novel genes or groups of genes expressed in prostate cancer may allow earlier diagnosis or more accurate staging of the disease. We describe the assembly and use of a 1877-member microarray representing cDNA clones from a range of prostate cancer stages and grades, precursor lesions and normal tissue. Using labelled cDNA from tumour samples obtained from TURP or radical prostatectomy, analysis of expression patterns identified many up-regulated transcripts. Cell lines were found to over-express fewer genes than diseased tissue samples. 17 known genes were found to over-express more than 4-fold in 4 or more cancers out of 15 cancers. Only 2 genes were over-expressed in 6 out of 15 cancers or more, whilst no genes were consistently found to be over-expressed in all cancer samples. Novel prostate cancer associations for several well characterized genes or full length cDNAs were identified, including PLRP1, JM27, human UbcM2, dynein light intermediate chain 2 and human homologue of rat sec61 . Novel associations with high-grade PIN include: breast carcinoma fatty acid synthase and cDNA DKFZp434B0335 . We shortlist and discuss the most significant over-expressed genes in prostate cancer and PIN, and highlight expression differences between malignant and benign samples. © 2001 Cancer Research Campaign http://www.bjcancer.com

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Expression scanning of an array of growth control genes in human tumor cell lines

Cited by 52 publications

References 22 publications

Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters

Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters

Distinct and Complementary Information Provided by Use of Tissue and DNA Microarrays in the Study of Breast Tumor Markers

Identification of potential diagnostic markers of prostate cancer and prostatic intraepithelial neoplasia using cDNA microarray

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