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Series GSE7055 Query DataSets for GSE7055
Status Public on Jul 01, 2008
Title Expression of microRNAs and Protein-coding Genes Associated with Perineural Invasion in Prostate Cancer
Platform organisms Homo sapiens; Mus musculus
Sample organism Homo sapiens
Experiment type Expression profiling by array
Non-coding RNA profiling by array
Expression profiling by high throughput sequencing
Summary BACKGROUND. Perineural invasion (PNI) is the dominant pathway for local invasion in prostate cancer. To date, only few studies have investigated the molecular differences between prostate tumors with PNI and those without it.
METHODS. To evaluate the involvement of both microRNAs and protein-coding genes in PNI, we determined their genome-wide expression with a custom microRNA microarray and Affymetrix GeneChips in 50 prostate adenocarcinomas with PNI and 7 without it. In-situ hybridization and immunohistochemistry was used to validate candidate genes.
RESULTS. Unsupervised classification of the 57 adenocarcinomas revealed two clusters of tumors with distinct global microRNA expression. One cluster contained all non-PNI tumors and a subgroup of PNI tumors. Significance analysis of microarray data yielded a list of microRNAs associated with PNI. At a false discovery rate (FDR) < 10%, 19 microRNAs were higher expressed in PNI tumors than in non-PNI tumors. The most differently expressed microRNA was miR-224. In-situ hybridization showed that this microRNA is expressed by perineural cancer cells. The analysis of protein-coding genes identified 34 transcripts that were differently expressed by PNI status (FDR <10%). These transcripts were down-regulated in PNI tumors. Many of those encoded metallothioneins and proteins with mitochondrial localization and involvement in cell metabolism. Consistent with the microarray data, perineural cancer cells tended to have lower metallothionein expression by immunohistochemistry than nonperineural cancer cells.
CONCLUSIONS. Although preliminary, our findings suggest that alterations in microRNA expression, mitochondrial function, and cell metabolism occur at the transition from a non-invasive prostate tumor to a tumor with PNI.
Keywords: Disease State analysis
 
Overall design Frozen tumor specimens were obtained from the NCI Cooperative Prostate Cancer Tissue Resource (CPCTR). RNA from these patient, 7 of which had no Perineural invasion, were hybridized to both Affymetrix and miRNA microarrays to explore the underlying molecular events associated with perineural invasion.
 
Contributor(s) Ambs S, Hudson RS, Prueitt R, Yi M
Citation(s) 18459106, 23409773
Submission date Feb 16, 2007
Last update date Sep 17, 2019
Contact name Robert Scott Hudson
Organization name NIH
Department NCI
Lab The Laboratory of Human Carcinogenesis
Street address National Cancer Institute Room Blgd.37/3044
City Bethesda
State/province MD
ZIP/Postal code 20852
Country USA
 
Platforms (2)
GPL571 [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array
GPL4700 OSU-CCC MicroRNA Microarray Version 2.0
Samples (114)
GSM160343 Prostate tumor patient 1 (HG-U133A 2.0 Array)
GSM160344 Prostate tumor patient 2 (HG-U133A 2.0 Array)
GSM160345 Prostate tumor patient 3 (HG-U133A 2.0 Array)
Relations
BioProject PRJNA98497

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

Supplementary file Size Download File type/resource
GSE7055_RAW.tar 148.6 Mb (http)(custom) TAR (of CEL, GPR)
Processed data included within Sample table
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