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Molecular subtypes in pancreatic adenocarcinoma [tumors, normal and pancreatitis]

ABSTRACT: The goal of the study was to examine the transcriptional profile of pancreatic tumors to identify molecular subtypes in order to develop validated clinically useful gene expression signature with the potential to guide therapy decision. Tissue was obtained by snap freezing in liquid nitrogen as soon as removed. All tissue samples were stored at -80C. Samples were embedded in OCT and a 4ug section was taken for H/E staining. After QC procedure to ensure high quality RNA (RIN>7) and confirm PDAC histology, 78 samples were subjected to microarray analysis. All patients signed an Institutional Review Board approved consent for bio-banking, clinical data extraction and molecular analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE77858 | GEO | 2016/06/01

SECONDARY ACCESSION(S): PRJNA311748

REPOSITORIES: GEO

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Molecular subtypes in pancreatic adenocarcinoma [tumors, normal and pancreatitis]

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2016-06-01 | E-GEOD-77858 | biostudies-arrayexpress

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Project description:A set of 45 surgical specimens has been profiled for miRNA expression to validate miRNA alterations associated to early relapse in advanced stage ovarian cancer patients. Fresh frozen samples were collected from a series of consecutive patients with high-grade advanced stage ovarian cancer who underwent primary surgery at INT-Milan. After surgery all patients received postoperative platinum-based chemotherapy. All patients signed an Institutional Review Board approved consent for bio-banking, clinical data collection and molecular analysis. Clinical codes: Histotype: according to WHO classification guidelines Stage: according to International Federation of Gynecological and Obstetrics (FIGO) guidelines Grading: according to WHO classification guidelines Debulking: NED: not evident disease; mRD: minimal residual disease; GRD: gross residual disease Therapy code: P: Platinum without taxanes; PT: Platinum/paclitaxel

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Project description:Core needle biopsy (Cx) primary cancer specimens were collected at Okayama University Hospital in Japan from hormone receptor positive /HER2 negative patients that subsequently received two weeks of neoadjuvant hormone therapy. Thirty clinical TNM stage I and II women were enrolled in this study. The study was approved by the Institutional Review Board and all patients signed informed consent forms. Patients received preoperative hormone therapy daily for two weeks before surgery. Premenopausal patients received tamoxifen (40 mg) and postmenopausal patients received letrozole (2.5 mg). All patients underwent a mastectomy or breast-conserving surgery. Surgical samples after treatment were also collected. Hormone and HER2 receptor statuses were determined in the diagnostic Cx specimens before hormone therapy. Cases with ≥1% positive nuclear staining for estrogen receptors (ER) or progesterone receptors (PgR) with IHC were considered hormone receptor-positive. Cases with either 0 or 1 positive IHC staining for HER2 or with an HER2 gene copy number < 2.0 by fluorescent in situ hybridization (FISH) analysis were considered HER2−. Specimens for gene expression analysis were collected into RNA and later stored at -80°C. Gene expression profiling was performed using Affymetrix U133A gene chips. Expression data were normalized using the MAS5 algorithm, mean centered to 600, and log2 transformed before further analysis.

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