Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human primary pancreatic tissue samples

ABSTRACT: Various primary pancreatic tissue samples as labelled.

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-3998 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Gene expression patterns in pancreatic tumors, cells and tissues.

Lowe Anson W AW Olsen Mari M Hao Ying Y Lee Sum P SP Taek Lee Kyu K Chen Xin X van de Rijn Matt M Brown Patrick O PO

PloS one 20070328 3

<h4>Background</h4>Cancers of the pancreas originate from both the endocrine and exocrine elements of the organ, and represent a major cause of cancer-related death. This study provides a comprehensive assessment of gene expression for pancreatic tumors, the normal pancreas, and nonneoplastic pancreatic disease.<h4>Methods/results</h4>DNA microarrays were used to assess the gene expression for surgically derived pancreatic adenocarcinomas, islet cell tumors, and mesenchymal tumors. The addition ...[more]

PMID: 17389914

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Project description:Insulinomas (INS) are rare pancreatic endocrine tumours (PETs), arising from tumoral beta-cells from the pancreatic islets of Langerhans. Canine INS are malignant in >95% of cases. This study aims to provide further insights on molecular pathways involved in INS pathogenesis and to identify prognostic genes. Canine specific cDNA microarray representing 20,313 genes was used to analyze expression profiles in a panel of ten primary INS and ten INS metastases. Eighty-four genes were found to be significantly down-regulated in the group of metastases in comparison to the group of primary INS. From the microarray analysis it also followed that primary INS, based on their gene expression profiles, can be divided into two groups, which differ in their malignancy potential. It was also demonstrated that canine INS have both endocrine and exocrine cell features. Furthermore, the present study has revealed pancreatic lipase and chymotrypsinogen B1 as candidate genes that can be followed up in prospective studies as prognostic markers for INS. Our findings add to the current knowledge of INS pathogenesis and tumor progression, which can be used for future therapeutic and prognostic strategies, for both dogs and humans. From 1993 to 2009, ten histologically confirmed primary insulinomas (INS) and their accompanying metastases were obtained from dogs that were presented at the Department of Clinical Sciences of Companion Animals of the Faculty of Veterinary Medicine of Utrecht University. Tumors were resected by experienced surgeons, and fragments (5-15 mm diameter) for RNA extraction were carefully removed from the central portion of the tumors to avoid contamination with normal adjacent tissue. Tissue specimens collected for RNA isolation were snap-frozen in liquid nitrogen immediately after surgical removal and stored at 70oC. Various clinical and pathological parameters were evaluated retrospectively for the dogs included in this study. Half of both the primary insulinoma samples, as well as half of the metastasis samples was labelled with Cy3, while the other half of both groups was labelled with Cy5. A common reference cRNA pool consisting of equal quantity of cRNA from all 20 tumor samples was used to hybridize against each sample on the array.

Project description:In recent years, the use of FFPE tissue in gene expression microarray (GEM) studies has become a topic of increased interest, because pathology departments worldwide contain an invaluable source of biological disease-specific FFPE- tissue material. Thus far, some published studies on FFPE tissue consider the processed tissue amenable, whereas other studies assert that the tissue is not useful in GEM. In general, pancreatic tissue is known to contain large amounts of nucleases, leading to high turnover rates and degradation of RNA in the tissue. This characteristic, in combination with FFPE processing time and its effect on the tissue, does not make FFPE pancreatic tissue the obvious choice for GEM. The basis for using FFPE pancreatic tissue in RNA-based assays seems suboptimal. Previous GEM studies have used different FFPE tissue types, but GEM studies on FFPE pancreatic tissue have not been published. In most studies, the tissue was specially processed for use with GEMs. Here we demonstrate the usefulness of randomly archived FFPE pancreatic tissues for GEMs. For this purpose we included FFPE pancreatic tissue from patients with congenital hyperinsulinism or insulinoma; In these patients, pancreas resection is performed when medical treatment is not adequate to prevent hyperinsulinemic hypoglycemia or when patients do not respond to medical treatment. Although ribonuclease-rich, we obtained biologically relevant and disease-specific, significant genes; cancer-related genes and genes involved in a) the regulation of insulin secretion and synthesis, b) amino acid metabolism, and c) calcium ion homeostasis. This application may extend the possibilities of gene expression studies to many tissue types, especially in rare diseases, for which fresh frozen tissue is not readily available. A total of 15 samples were included in this study using a 58K chip. 29,134 human 60mer oligonucleotide targets were arrayed on the chips in duplicates. Each chip is hybridized with sample material (labelled with Cy5) from one patient and reference material (labelled with Cy3). Reference material contains pooled RNA from four different cancer cell lines; HeLa (cervical epithelium), SK-BR-3 (mammary gland), HT29 (colon) and A431 (skin) cells. Seven patients with congenital hyperinsulinism (five FFPE and two frozen samples), one patient with insulinoma and five controls were included in the study. Inclusion criteria for controls was that their cause of death was not pancreas-related. Samples were obtained from archived FFPE pancreatic material. The insulinoma sample was included in the study, because the biopsy was originally divided with one part being frozen and the other part being routinely formalin-fixed and paraffin-embedded. In the study we therefore include a frozen insulinoma sample and a FFPE insulinoma sample that was processed in duplicate.

Dataset Information

Transcription profiling of human primary pancreatic tissue samples

Publications

Gene expression patterns in pancreatic tumors, cells and tissues.

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