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Genomic profiling of IPMN with an associated invasive carcinomas (IPMN-inv) and invasive ductal carcinomas (IDC) by array-based comparative genomic hybridization

ABSTRACT: In this study, we aimed to identify gene abnormalities necessary for the transformation from carcinoma in situ (CIS) of pancreas to invasive PC. We compared the genomic profiles of paired samples from invasive region and CIS region of the identical IPMN-inv. We further determined genomic profiles of IDC.

ORGANISM(S): Homo sapiens

PROVIDER: GSE65181 | GEO | 2016/01/22

SECONDARY ACCESSION(S): PRJNA273354

REPOSITORIES: GEO

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Project description: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.

Dataset Information

Genomic profiling of IPMN with an associated invasive carcinomas (IPMN-inv) and invasive ductal carcinomas (IDC) by array-based comparative genomic hybridization

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