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Series GSE34174 Query DataSets for GSE34174
Status Public on Dec 06, 2011
Title Whole Genome Methylation Analysis of Metastatic Castration Resistant Prostate Cancer
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Methylation profiling by array
Summary Relatively little is known about how changes in gene copy number (CN) and gene CpG methylation interact to affect specific pathways in metastatic castration-resistant prostate cancer (CRPC). Oligonucleotide array comparative genomic hybridization (aCGH) was performed on DNA isolated from 15 metastatic CRPC samples. Commonly aberrant genes were evaluated in a confirmatory fashion using PCR, aCGH data from primary tumors, and existing CRPC expression data. Array-based comprehensive CpG methylation was assessed on the same sample set. A total of 495 genes (79 gained, 416 deleted) were CN aberrant in ≥66% of the samples by aCGH, and 77 (9 amplified, 68 deleted) had statistically concordant expression including gain of AR and loss of PTEN and RB1. Significant CN differences were seen between the genomes of patients with AR-amplified and AR-unamplified tumors, including common loss of AR repressors in AR-unamplified tumors. The majority of CRPC samples were hypermethylated compared to benign prostate tissue. Simultaneous methylation and heterozygous gene deletion occurred in the tumor suppressor RB1 and in HSD17B2, responsible for testosterone metabolism. Establishment of a comprehensive methylation signature and coupling of epigenomic and structural analyses sheds light on the alterations that allow CRPC to circumvent hormonal therapy and may provide new drug targets for what is currently an incurable disease state.
 
Overall design 15 tumor samples taken from 14 men with metastatic castration resistant prostate cancer were analyzed, including two samples from the same patient. No control samples were used for this experiment.
 
Contributor(s) Friedlander TW, Paris PL, Ngo V
Citation(s) 22158653
Submission date Dec 05, 2011
Last update date Oct 26, 2016
Contact name Terence Friedlander
E-mail(s) [email protected]
Phone 415-514-2559
Organization name UCSF
Department Hemotology-Oncology
Lab Paris Lab
Street address 1450 3rd Street
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platforms (2)
GPL4091 Agilent-014693 Human Genome CGH Microarray 244A (Feature number version)
GPL8490 Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)
Samples (30)
GSM843394 Met10_36M
GSM843395 Met17_18M
GSM843396 Met12_6M
Relations
BioProject PRJNA149609

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE34174_RAW.tar 1020.8 Mb (http)(custom) TAR (of TXT)
GSE34174_non-normalized.txt.gz 2.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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