Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of ampullary carcinomas classifies ampullary carcinomas into biliary-like and intestinal-like subtypes that are prognostic of outcome

ABSTRACT: Adenocarcinomas of the ampulla of Vater are classified as biliary cancers, though the exact epithelium of origin for these cancers is not known. We sought to molecularly classify ampullary adenocarcinomas in comparison to known adenocarcinomas of the pancreas, extrahepatic bile duct, and duodenum by gene expression analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE39409 | GEO | 2013/01/01

SECONDARY ACCESSION(S): PRJNA170824

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiling of ampullary carcinomas classifies ampullary carcinomas into biliary-like and intestinal-like subtypes that are prognostic of outcome

Project description:Adenocarcinomas of the ampulla of Vater are classified as biliary cancers, though the exact epithelium of origin for these cancers is not known. We sought to molecularly classify ampullary adenocarcinomas in comparison to known adenocarcinomas of the pancreas, extrahepatic bile duct, and duodenum by gene expression analysis. We analyzed 32 fresh-frozen resected, untreated periampullary adenocarcinomas (8 pancreatic, 2 extrahepatic biliary, 8 duodenal, and 14 ampullary) using the Affymetrix U133 Plus 2.0 genome array.

2013-01-01 | E-GEOD-39409 | biostudies-arrayexpress

Integrated Genomic Analysis of Periampullary Tumors

Project description:<p>Adenocarcinomas arising in the complex environment of the ampulla of Vater constitute a histopathological heterogenous group, presumably originating from the different epithelial cellular constituents present at the site: pancreas, bile duct, and intestinal duodenum. These tumors have been described in many different ways: intra-ampullary, periampullary, intra-ampullary papillary-tubular neoplasm, ampullary-ductal, periampullary-duodenal, and ampullary-not otherwise specified. These varied classifications reflect the difficulty in classifying these tumors into specific groups. Only the tumors clearly localized in the bile duct or duodenum are identified as distal cholangiocarcinomas (CAC) or duodenal adenocarcinomas (DUOAC). The current classification is based on macroscopic features that may distinguish the epithelium of origin, microscopic features, clinicopathological criteria, histopathology and expression of differential markers. This classification is subjective and prone to inter-observer variability and significantly impacts on treatment selection and therapeutic development.</p> <p>In order to define subtypes of periampullary cancer with clinical relevance, we performed whole exome sequencing and copy number analysis of 160 cancers arising in the periampullary region, 62 of these clearly arising from either the bile duct (n = 44), or the duodenum (n = 18) and 98 periampullary cancers (AMPAC) where the epithelium of origin could not be clearly defined.</p>

| phs000895 | dbGaP

A postnatal network of co-hepato/pancreatic stem/progenitors in the biliary trees of pigs versus humans

Project description:A network of co-hepato/pancreatic stem/progenitors exists in pigs and humans in Brunner’s Glands (BGs) in the submucosa of the duodenum, in peribiliary glands (PBGs) of intrahepatic and extrahepatic biliary trees, and in pancreatic duct glands (PDGs) of intrapancreatic biliary trees, collectively supporting hepatic and pancreatic regeneration postnatally. The network is found in humans postnatally throughout life and, so far, has been demonstrated in pigs postnatally at least through to young adults. These stem/progenitors in vivo in pigs are in highest numbers in BGs and in PDGS nearest the duodenum, and in humans are in BGs and in PBGs in the hepato/pancreatic common duct, a duct missing postnatally in pigs. Elsewhere in PDGs in pigs and in all PDGs in humans are only committed unipotent or bipotent progenitors.

2023-08-02 | GSE229270 | GEO

Gene Expression of Single Extrahepatic Biliary Cells

Project description:These datasets look at the murine profile of extrahepatic biliary cells, primarily epithelial, in normal conditions and under mosaic Ctnnb1 gain of function.

2023-09-22 | GSE223099 | GEO

Simultaneous activation of Kras-Akt and Notch pathways induces extrahepatic biliary cancer via mTORC1 pathway

Project description:Biliary tract cancer (BTC) has poor prognosis. The Notch receptor is aberrantly expressed in extrahepatic cholangiocarcinoma (eCCA). However, the role of Notch signaling in the initiation and progression of eCCA and gallbladder (GB) cancer remains unknown. We investigated the functional role of Notch signaling during tumorigenesis of the extrahepatic bile duct and GB. We demonstrated that simultaneous activation of the Kras–Akt and Notch pathways in EHBD and GB resulted in the formation of BilINs and biliary cancer in a mouse model. Mechanistically, the Kras/Notch–Myc axis activates mTORC1 through phosphorylation of TSC2 in biliary tumorigenesis.

2023-05-04 | GSE231369 | GEO

Prominin-1 promotes restitution of the murine extrahepatic biliary luminal epithelium following cholestatic liver injury

Project description:Restitution of the extrahepatic biliary luminal epithelium in cholangiopathies is poorly understood. Prominin-1 (Prom1) is a key component of epithelial ciliary body of stem/progenitor cells. Given that intrahepatic Prom1-expressing progenitor cells undergo cholangiocyte differentiation, we hypothesized that Prom1 may promote restitution of the extrahepatic bile duct (EHBD) epithelium following injury. Utilizing various murine biliary injury models, we identified Prom1-expressing cells in the peribiliary glands (PBGs) of the EHBD. These Prom1-expressing cells are progenitor cells which give rise to cholangiocytes as part of the normal maintenance of the EHBD epithelium. Following injury, these cells proliferate significantly more rapidly to re-populate the biliary luminal epithelium. Null mutation of Prom1 leads to significantly more than ten-fold dilated PBGs following rhesus rotavirus-mediated biliary injury. Cultured organoids derived from Prom1 knockout mice are comprised of biliary progenitor cells with altered apical-basal cellular polarity, significantly fewer and shorter cilia, and decreased organoid proliferation dynamics consistent with impaired cell motility. We, therefore, conclude that Prom1 is involved in biliary epithelial restitution following biliary injury in part through its role in supporting cell polarity.

2022-12-05 | GSE220054 | GEO

Regional differences in human biliary tissues and corresponding in vitro derived organoids

Project description:RNA-Sequencing was performed on mechanically dissociated, epithelial-enriched samples, of human extrahepatic biliary tissue from Gallbladder, Common Bile Duct, and Pancreatic Duct tissues. Sequencing was also performed on in vitro cultures of Organoid cell lines at passage 5 that were derived from human Gallbladder, Common Bile Duct, Pancreatic Duct, or Intrahepatic Bile Ducts.

2019-01-20 | E-MTAB-7569 | biostudies-arrayexpress

mRNA and miRNA expression profiles for fresh frozen periampullary adenocarcinomas (pancreatobiliary and intestinal type) and adjacent normal tissues. [miRNA]

Project description:To study the molecular signatures of mRNAs and miRNAs which can potentially act as a prognostic biomarkers in pancreatobiliary and intestinal types of periampullary adenocarcinomas Total RNA was isolated from 10 x 20 Âµm sections of 83 fresh frozen tumor samples for miRNA expression profiling. A total of 51 PDAC, 8 bile duct adenocarcinoma, 8 ampulla of pancreatobiliary tye, 7 ampulla of intestinal type, 9 duodenum sample and 6 adjacent normal samples were used. These samples were analysed by microarray analysis using the 60K agilent platform. The expression profiles was RMA normalized for miRNA expression data. Filtering of controls, unannotated genes and low expressed probes was done.

2015-11-06 | E-GEOD-60978 | biostudies-arrayexpress

mRNA and miRNA expression profiles for fresh frozen periampullary adenocarcinomas (pancreatobiliary and intestinal type) and adjacent normal tissues. [mRNA]

Project description:To study the molecular signatures of mRNAs and miRNAs which can potentially act as a prognostic biomarkers in pancreatobiliary and intestinal types of periampullary adenocarcinomas Total RNA was isolated from 10 x 20 Âµm sections of 81 fresh frozen tumor samples for mRNA expression profiling. A total of 49 PDAC, 8 bile duct adenocarcinoma, 8 ampulla of pancreatobiliary tye, 7 ampulla of intestinal type, 9 duodenum sample and 12 adjacent normal samples were used. These samples were analysed by microarray analysis using the 60K agilent platform. The expression profiles were background corrected and quantile normalized for mRNA. Filtering of controls, unannotated genes and low expressed probes was done.

2015-11-06 | E-GEOD-60979 | biostudies-arrayexpress

Bulk RNA-seq of Sox9-deficient intrahepatic biliary epithelial cells

Project description:To define the regulatory role of Sox9 in intrahepatic biliary epithelium, we conducted bulk RNA-seq on biliary epithelial cells (BECs) from adult control (Sox9fl/fl) and conditional Sox9 knockout (Sox9cKO; Sox9fl/fl:Albumin-Cre) mice. Livers were dissociated to single cells and BECs isolated by FACS based on CD326 positivity. CD31+ and CD45+ cells were excluded by FACS. Gallbladder and extrahepatic tissues were excluded by dissection. RNA was isolated using Ambion RNAqueous Micro kit and libraries were made using Takara SMARTer Stranded Total RNA-seq Kit v3 Pico.

2024-01-01 | GSE249385 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data