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Ena-DATASET-MUG-19-03-2013-14:14:47:994-92 - samples

ABSTRACT: In this study we analysed patients with metastatic prostate cancer to scan their tumor genomes noninvasively in plasma DNA. We enriched 1.3 Mbp of seven plasma DNAs (4 CRPC cases: CRPC1-3 and CRPC5; 3 CSPC cases: CSPC1-2 and CSPC4) including exonic sequences of 55 cancer genes and 38 introns of 18 genes, where fusion breakpoints have been described using Sure Select Custom DNA Kit.

PROVIDER: EGAD00001000365 | EGA |

REPOSITORIES: EGA

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Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing.

Heitzer Ellen E Ulz Peter P Belic Jelena J Gutschi Stefan S Quehenberger Franz F Fischereder Katja K Benezeder Theresa T Auer Martina M Pischler Carina C Mannweiler Sebastian S Pichler Martin M Eisner Florian F Haeusler Martin M Riethdorf Sabine S Pantel Klaus K Samonigg Hellmut H Hoefler Gerald G Augustin Herbert H Geigl Jochen B JB Speicher Michael R MR

Genome medicine 20130405 4

<h4>Background</h4>Patients with prostate cancer may present with metastatic or recurrent disease despite initial curative treatment. The propensity of metastatic prostate cancer to spread to the bone has limited repeated sampling of tumor deposits. Hence, considerably less is understood about this lethal metastatic disease, as it is not commonly studied. Here we explored whole-genome sequencing of plasma DNA to scan the tumor genomes of these patients non-invasively.<h4>Methods</h4>We wanted to ...[more]

PMID: 23561577

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Project description:Background: There is no cure for castration-recurrent prostate cancer (CRPC) and the mechanisms underlying this stage of the disease are unknown. Methods: We analyzed the transcriptome of human LNCaP prostate cancer cells as they progress to CRPC in vivo using replicate LongSAGE libraries. We refer to these libraries as the LNCaP atlas and compared these gene expression profiles with current suggested models of CRPC. Results: Three million tags were sequenced using in vivo samples at various stages of hormonal progression to reveal 96 novel genes differentially expressed in CRPC. Thirty-one genes encode proteins that are either secreted or are located at the plasma membrane, 21 genes changed levels of expression in response to androgen, and 8 genes have enriched expression in the prostate. Expression of 26, 6, 12, and 15 genes have previously been linked to prostate cancer, Gleason grade, progression, and metastasis, respectively. Expression profiles of genes in CRPC support a role for the transcriptional activity of the androgen receptor (CCNH, CUEDC2, FLNA, PSMA7), steroid synthesis and metabolism (DHCR24, DHRS7, ELOVL5, HSD17B4, OPRK1), neuroendocrine (ENO2, MAOA, OPRK1, S100A10, TRPM8), and proliferation (GAS5, GNB2L1, MT-ND3, NKX3-1, PCGEM1, PTGFR, STEAP1, TMEM30A), but neither supported nor discounted a role for cell survival genes. Conclusions: The in vivo gene expression atlas for LNCaP was sequenced and support a role for the androgen receptor in CRPC. BMC Medical Genomics 2010, 3:43 RNA from the hollow fibres of three mice (biological replicates) representing different stages of prostate cancer progression (AS, RAD, and CR) were used to make a total of nine LongSAGE libraries.

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