Hormone Therapy Failure in Human Prostate Cancer: Analysis by Complementary DNA and Tissue Microarrays

Bubendorf, Lukas; Kolmer, Meelis; Kononen, Juha; Koivisto, Pasi A.; Mousses, Spyro; Chen, Yidong; Mahlamäki, Eija; Schraml, Peter; Moch, Holger; Willi, Niels; Elkahloun, Abdel G.; Pretlow, Thomas G.; Gasser, Thomas C.; Mihatsch, Michael J.; Sauter, Guido; Kallioniemi, Olli

doi:10.1093/jnci/91.20.1758

Cited by 318 publications

(182 citation statements)

References 37 publications

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“…Using TMA of bladder tumors containing 2317 specimens from 1842 patients, Richter and colleagues 9 found a positive correlation between CCNE gene amplification measured by fluorescence in situ hybridization and cyclin-E protein overexpression measured by IHC. The combination of cDNA array and TMA allowed the identification of IGFBP2 and HSP27, 34 hepsin, 2 and AM-ACR 30 as significantly overexpressed in prostate cancer, suggesting their putative diagnostic interest. IGFBP2 was also found as a marker of poor prognosis in a series of 418 brain tumors arrayed onto a TMA.…”

Section: Discussionmentioning

confidence: 99%

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

Ginestier

Charafe‐Jauffret

Bertucci

et al. 2002

The American Journal of Pathology

135

126

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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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Section: Discussionmentioning

confidence: 99%

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

Ginestier

Charafe‐Jauffret

Bertucci

et al. 2002

The American Journal of Pathology

135

126

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“…The successful molecular classification of diverse tumors on the basis of gene expression profile indicates that cDNA microarray technology is potentially a powerful tool for the development of personalized treatment. 6,20 However, one of its restrictions for broader clinical utilization is the need of large amount of RNA required for its utilization, in the range of 50 to 100 g of total RNA. This limitation may be resolved by the application of different amplification approaches such as the T7-based Eberwine's procedure.…”

Section: Discussionmentioning

confidence: 99%

Core Biopsies Can Be Used to Distinguish Differences in Expression Profiling by cDNA Microarrays

Sotiriou

Khanna

Jazaeri

et al. 2002

The Journal of Molecular Diagnostics

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The primary focus of this work was to determine the feasibility of obtaining representative expression array profiles from clinical core biopsies. For this purpose we performed six 16-gauge needle core biopsies and an excision biopsy on each of two different human xenografts, one from an Ewing's sarcoma cell line and the second from neuroblastoma cell line grown in Beige-Scid mice. Three of the six core biopsies were processed separately and the remaining three were pooled and processed together. As the initial RNA material isolated from the core biopsies was not sufficient for microarray analysis, an amplification procedure using a modified Eberwine protocol was performed, and the amplified products applied onto a 6000-feature human cDNA microarray. Comparisons of the array results from core biopsies (amplified RNA) and surgical specimens (non-amplified RNA) showed maintenance of the expression profile as assessed by hierarchical clustering. Gene expression profiles obtained from microarray analysis clearly differentiated the Ewing's sarcoma from the neuroblastoma with both core and excisional biopsies as starting material. Pooling the core biopsies did not improve the concordance with excisional biopsies. In conclusion, our results suggest that core biopsies can be used as a suitable and reliable material for the determination of tumor genetic profiles.

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“…In this study, we describe a novel in silico approach to identify potential targets of methylation in prostate cancer. We employed transcriptomic databases and microarray experiments that provided detailed data summaries and focused on expression changes in early-stage disease (Chetcuti et al, 2001;Ashida et al, 2004) and in the progression to metastatic disease (Bubendorf et al, 1999;Dhanasekaran et al, 2001). Interestingly, a common finding between these studies was that downregulation rather than upregulation, accounted for the majority of differentially expressed genes in prostate cancer.…”

Section: Discussionmentioning

confidence: 99%

“…The Digital Differential Display (http:// www.ncbi.nlm.nih.gov/UniGene/ddd) was used to report on significant differences in gene expression between four different tissue pools, created from libraries of ESTs from normal prostate, primary and metastatic prostate cancer and PIN (Wheeler et al, 2001). The data from four independent, published microarray studies that quantified gene expression at different stages of prostate cancer were also examined (Bubendorf et al, 1999;Chetcuti et al, 2001;Dhanasekaran et al, 2001;Ashida et al, 2004).…”

Section: In Silico Mining To Identify Novel Targets Of Methylation Inmentioning

confidence: 99%

In silico mining identifies IGFBP3 as a novel target of methylation in prostate cancer

et al. 2007

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Promoter hypermethylation is central in deregulating gene expression in cancer. Identification of novel methylation targets in specific cancers provides a basis for their use as biomarkers of disease occurrence and progression. We developed an in silico strategy to globally identify potential targets of promoter hypermethylation in prostate cancer by screening for 5 0 CpG islands in 631 genes that were reported as downregulated in prostate cancer. A virtual archive of 338 potential targets of methylation was produced. One candidate, IGFBP3, was selected for investigation, along with glutathione-S-transferase pi (GSTP1), a well-known methylation target in prostate cancer. Methylation of IGFBP3 was detected by quantitative methylation-specific PCR in 49/79 primary prostate adenocarcinoma and 7/14 adjacent preinvasive high-grade prostatic intraepithelial neoplasia, but in only 5/37 benign prostatic hyperplasia (Po0.0001) and in 0/39 histologically normal adjacent prostate tissue, which implies that methylation of IGFBP3 may be involved in the early stages of prostate cancer development. Hypermethylation of IGFBP3 was only detected in samples that also demonstrated methylation of GSTP1 and was also correlated with Gleason score X7 (P ¼ 0.01), indicating that it has potential as a prognostic marker. In addition, pharmacological demethylation induced strong expression of IGFBP3 in LNCaP prostate cancer cells. Our concept of a methylation candidate gene bank was successful in identifying a novel target of frequent hypermethylation in earlystage prostate cancer. Evaluation of further relevant genes could contribute towards a methylation signature of this disease.

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Hormone Therapy Failure in Human Prostate Cancer: Analysis by Complementary DNA and Tissue Microarrays

Abstract: The combination of cDNA and tissue microarray technologies enables rapid identification of genes associated with progression of prostate cancer to the hormone-refractory state and may facilitate analysis of the role of the encoded gene products in the pathogenesis of human prostate cancer.

Cited by 318 publications

References 37 publications

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

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

Core Biopsies Can Be Used to Distinguish Differences in Expression Profiling by cDNA Microarrays

In silico mining identifies IGFBP3 as a novel target of methylation in prostate cancer

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