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Open Access item Co-regulation analysis of closely linked genes identifies a highly recurrent gain on chromosome 17q25.3 in prostate cancer

Authors:Bermudo, Raquel
Abia, David
Ferrer, Berta
Nayach, Iracema
Benguria, Alberto
Zaballos, Ángel
Rey, Javier del
Miró, Rosa
Campo, Elías
Martínez-Alonso, Carlos
Ramírez Ortiz, Miguel Ángel
Fernández, Pedro L.
Thomson, Timothy M.
Keywords:Prostate cancer, Transcriptional profiling, Markers of neoplasia, Chromosomal abnormalities, Chromosome 17q25.3, Copy number gain, Stromal tissue, Fluorescent in situ hybridization (FISH)
Issue Date:30-Oct-2008
Publisher:BioMed Central
Citation:BMC Cancer 2008, 8:315
Abstract:[Background] Transcriptional profiling of prostate cancer (PC) has unveiled new markers of neoplasia and allowed insights into mechanisms underlying this disease. Genomewide analyses have also identified new chromosomal abnormalities associated with PC. The combination of both classes of data for the same sample cohort might provide better criteria for identifying relevant factors involved in neoplasia. Here we describe transcriptional signatures identifying distinct normal and tumoral prostate tissue compartments, and the inference and demonstration of a new, highly recurrent copy number gain on chromosome 17q25.3.
[Methods] We have applied transcriptional profiling to tumoral and non-tumoral prostate samples with relatively homogeneous epithelial representations as well as pure stromal tissue from peripheral prostate and cultured cell lines, followed by quantitative RT-PCR validations and immunohistochemical analysis. In addition, we have performed in silico colocalization analysis of coregulated genes and validation by fluorescent in situ hybridization (FISH).
[Results] The transcriptomic analysis has allowed us to identify signatures corresponding to non-tumoral luminal and tumoral epithelium, basal epithelial cells, and prostate stromal tissue. In addition, in silico analysis of co-regulated expression of physically linked genes has allowed us to predict the occurrence of a copy number gain at chromosomal region 17q25.3. This computational inference was validated by fluorescent in situ hybridization, which showed gains in this region in over 65% of primary and metastatic tumoral samples.
[Conclusion] Our approach permits to directly link gene copy number variations with transcript co-regulation in association with neoplastic states. Therefore, transcriptomic studies of carefully selected samples can unveil new diagnostic markers and transcriptional signatures highly specific of PC, and lead to the discovery of novel genomic abnormalities that may provide additional insights into the causes and mechanisms of prostate cancer.
Description:12 pages, 4 figures.-- PMID: 18973659 [PubMed].-- PMCID: PMC2585097.-- Additional information available: File 1: Table showing FADA-selected genes information (58 pages).- File 2: Graphical representation of the genes selected by FADA (1 page).
The authors wish to dedicate this report to the memory of the late Ángel R. Ortiz, a key contributor to this report.
Publisher version (URL):http://dx.doi.org/10.1186/1471-2407-8-315
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