Unknown,Transcriptomics,Genomics,Proteomics

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Gene Expression Changes Associated with the Progression of Intraductal Papillary Mucinous Neoplasms

ABSTRACT: Purpose: The diagnosis of high grade intraductal papillary mucinous neoplasm (IPMN) is difficult to distinguish from low grade IPMN. The aim of this study was to identify potential markers for the discrimination of high grade and invasive IPMN from low and moderate grade IPMN. Experimental Design: Laser capture microdissection was used to isolate distinct foci of low grade, moderate grade, high grade, and invasive IPMN from paraffin embedded archival tissue from 14 patients who underwent resection for IPMN. Most samples included multiple grades in the same specimen. Affymetrix Human Exon microarrays were used for gene expression analysis to compare low and moderate grade (LMD) IPMN to high grade and invasive (HgInv) IPMN. Results: When comparing samples of LMD dysplasia (n=15) to those demonstrating HgInv (n=13), 62 genes were identified as showing significant changes in expression (p≤0.05 and a 2-fold cutoff), with up-regulation of 41 in HgInv IPMN and down-regulation in 21. Changes in gene expression are associated with biological processes related to malignant behavior including cell motion, cell proliferation, response to hypoxia, and epithelial to mesenchymal transition. Hierarchical clustering analysis demonstrated the ability of these 62 differentially expressed genes to distinguish between LMD and HgInv samples. In addition, altered signaling in several TGFβ-related pathways was exhibited in the progression of IPMN to malignancy. Conclusions: This study identifies a set genes associated with the progression of IPMN to malignancy. These genes are potential markers that could be used to identify IPMN requiring surgical resection. Using laser capture microdissection, distinct foci of low (n=10), moderate (n=5), and high grade dysplasia (n=6) as well as invasive carcinoma (n=7) were isolated from paraffin embedded archival tissue of 14 patients who underwent resection for IPMN. Gene expression data from Affymetrix Human Exon 1.0ST microarrays was utilized to compare low and moderate grade IPMN to high and invasive IPMN.

ORGANISM(S): Homo sapiens

SUBMITTER: Bryan Thibodeau

PROVIDER: E-GEOD-26647 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:A comprehensive expression analysis of Wnt signaling genes was performed in a panel of prostate cancer cell lines and tissue specimens using TaqMan low density arrays. The effect of DNA methylation on gene expression was investigated using DNMT inhibitor 5-Aza-CdR. Tissue specimens from a range of disease states were used to represent the stepwise progression of prostate cancer, including benign prostatic hyperplasia (BPH), histologically benign epithelium adjacent to tumor (HB), pre-invasive high-grade prostatic intraepithelial neoplasia (HGPIN) and primary localized tumors categorized into low- and high-grade disease. Fifteen Wnt signaling related genes were idenified with significantly altered expression in prostate cancer; the majority of which were upregulated in tumors. Notably, histologically benign tissue from men with prostate cancer appeared more similar to tumour (r=0.76) than to BPH (r=0.57) (P<0.001). Overall, the expression profile was highly similar between tumors of high (M-bM-^IM-%7) and low (M-bM-^IM-$6) Gleason scores. Pharmacological demethylation of PC-3 cells reactivated 38 genes (M-bM-^IM-%2-fold); 40% of which inhibit Wnt signaling. qPCR gene expression profiling using TLDA Human Wnt Gene set v1.0 microfluidic card (Applied Biosystems, Foster City, CA).The TLDA consisted of 4 identical 96-gene sets preconfigured in a 384-well format. Three different malignant cell lines were profiled LNCaP, 22Rv1 and PC3 (+/- 5-Aza-2M-bM-^@M-^YDeoxycytidine). One benign cell line was included for comparative puposes: PWR1E. Patient samples were obtained from FFPE tissue sections from men who underwent radical prostatectomy or transrectal resection of the prostate. To overcome the limited amount of RNA obtained from FFPE tissues, RNA samples were pooled. Five different pools were generated: high grade prostate cancer (Gleason score M-bM-^IM-%7), low grade prostate cancer (Gleason score M-bM-^IM-$6), HGPIN, HB and BPH. Each pool consisted of DNase-treated total RNA (100ng), isolated from microdissected tissue from 4 individual cases, selected on the basis of similar histological and clinical features and previous epigenetic characterization in our laboratory. Two Biological replicates for each pool were prepared. The high capacity cDNA Archive Kit (Applied Biosystems) was used to reverse transcribe pooled RNA (400ng). TaqManM-BM-. reactions were performed in duplicate on a 7900HT Sequence Detection System. RQ data from TLDAs were analyzed using Real Time StatMinerM-BM-. v3.1 (Integromics, Granada, Spain).

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Gene Expression Changes Associated with the Progression of Intraductal Papillary Mucinous Neoplasms

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