Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms

ABSTRACT: Pancreatic neuroendocrine neoplasms (PNENs) are biologically and clinically heterogeneous neoplasms. We used quantitative global proteomic analysis on 40 PNENs to compliment paired transcriptome data.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Neuroendocrine Tumor Cell

DISEASE(S): Neuroendocrine Tumor

SUBMITTER: Sharon Gorski

LAB HEAD: Sharon Gorski

PROVIDER: PXD024175 | Pride | 2021-11-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Layout.xlsx	Xlsx
	Set1_1.raw	Raw
	Set1_10.raw	Raw
	Set1_11.raw	Raw
	Set1_12.raw	Raw

Items per page:

1 - 5 of 76

Publications

Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms.

Yang Kevin C KC Kalloger Steve E SE Aird John J JJ Lee Michael K C MKC Rushton Christopher C Mungall Karen L KL Mungall Andrew J AJ Gao Dongxia D Chow Christine C Xu Jing J Karasinska Joanna M JM Colborne Shane S Jones Steven J M SJM Schrader Jörg J Morin Ryan D RD Loree Jonathan M JM Marra Marco A MA Renouf Daniel J DJ Morin Gregg B GB Schaeffer David F DF Gorski Sharon M SM

Cell reports 20211001 2

Pancreatic neuroendocrine neoplasms (PNENs) are biologically and clinically heterogeneous. Here, we use a multi-omics approach to uncover the molecular factors underlying this heterogeneity. Transcriptomic analysis of 84 PNEN specimens, drawn from two cohorts, is substantiated with proteomic profiling and identifies four subgroups: Proliferative, PDX1-high, Alpha cell-like and Stromal/Mesenchymal. The Proliferative subgroup, consisting of both well- and poorly differentiated specimens, is associ ...[more]

PMID: 34644566

Similar Datasets

Proteomic Analysis of Canine Hepatobiliary Neuroendocrine Neoplasms

Project description:Neuroendocrine neoplasms of the gallbladder and liver occur rarely in dogs and humans. A recent reclassification of human neuroendocrine neoplasms by the World Health Organization has refined categorization of these tumors by morphology, replicative indices, and molecular signatures. In humans, these factors correlate with survival outcomes. Improved characterization of these tumors is needed in dogs to identify diagnostic biomarkers and determine therapeutic strategies. To achieve this objective, the proteome of 3 canine hepatobiliary neoplasms was compared to normal canine adrenal and liver tissue from formalin-fixed paraffin-embedded samples. Thirty-two upregulated and 121 downregulated differentially expressed proteins were identified in the hepatobiliary neuroendocrine neoplasm samples. Among the upregulated proteins is galectin-1, a multivalent carbohydrate binding protein known to play a role in lung and pancreatic neuroendocrine neoplasia development and progression in humans. Drugs targeting the galectin family have shown promise as anticancer therapeutics in cervical cancer, prostate cancer, lung and pancreatic neuroendocrine neoplasia in human medicine. Galectin-1 may represent a novel treatment target in hepatobiliary neuroendocrine neoplasia in both humans and dogs.

2023-03-11 | PXD028822 | Pride

Comprehensive Sequencing of High Grade Neuroendocrine Neoplasms

Project description:Comprehensive Sequencing of High Grade Neuroendocrine Neoplasms

| PRJNA648441 | ENA

Comprehensive Sequencing of High Grade Neuroendocrine Neoplasms

Project description:Comprehensive Sequencing of High Grade Neuroendocrine Neoplasms

| PRJNA648442 | ENA

CGH profiles of primary breast carcinomas from HBOC (Hereditary Breast and Ovarian Cancer) families

Project description:89 tumors from women that were eligible for, and subjected to, routine diagnostic testing according to the HBOC criteria but were negative for pathogenic BRCA1/2-mutations or carried an UV in either BRCA1/2 A BRCA2-classifier was built using array-CGH profiles of 28 BRCA2-mutated and 28 sporadic breast tumors. The classifier was validated on an independent group of 19 BRCA2-mutated and 19 sporadic breast tumors. Subsequently, we tested 89 breast tumors from suspected hereditary breast (and ovarian) cancer (HBOC) families, in which either no BRCA1/2 mutation or an UV had been found by routine diagnostics.

2010-07-05 | E-GEOD-22481 | biostudies-arrayexpress

Chloroquine-mediated lysosomal inhibition alters composition and function of cancer-derived extracellular vesicles

Project description:Extracellular vesicles (EV) are signaling entities that are released by most, if not all, eukaryotic cells. EV are of special interest in cancer due to their reported roles in modulating the cancer microenvironment and facilitating invasion. Macroautophagy is a catabolic process initially known for the recycling of cytosolic cargos through lysosomal degradation, while its non-degradative functions have only begun to emerge. To better understand the relationships between autophagy machinery and small EV (sEV) biogenesis, we utilized chloroquine (CQ) to inhibit lysosomal degradation and autophagy turnover in triple-negative breast cancer (TNBC) cell lines and characterized its effects on sEV content and function. We performed quantitative mass spectrometry analysis of the sEV proteome, and discovered a CQ-induced enrichment of mammalian ATG8 paralogs and their adaptor proteins that coincided with increased levels of K48-specific polyubiquitination in sEV, as well as with the co-localization of ATG8s and endolysosomal markers in the cytoplasm. Using ATG4B knockout cells, we established the lipidation-dependent luminal localization of sEV-associated ATG8s. We demonstrated CQ-mediated enrichment of MAP1LC3B and GABARAP in CD63-high but not CD9-high sEV subpopulations. sEV isolated from CQ treated versus untreated cells had differential effects on recipient cell growth and HMEC-1 tube formation, suggesting sEV are an avenue of CQ mediated non-cell-autonomous biological effects. Our study demonstrates the flexibility of sEV composition in response to perturbation of intracellular trafficking pathways, and has implications for CQ efficacy in therapeutic settings.

2023-03-10 | PXD015614 | Pride

Genetic lineage analysis in intramucosal gland-forming gastric neoplasms

Project description:To predict the progression risk of non-invasive gland-forming gastric neoplasms to invasive carcinoma, we assessed lineage continuity or discontinuity between the non-invasive and invasive neoplasms by applying hierarchical clustering analysis to the gene copy-number profiles of individual tumours. array-based Comparative Genomic Hybridization. Samples are including of 7 tumours of Vienna category 3, 12 tumours of Vienna category 4, 8 intramucosal cancers (Vienna category 5), 16 intramucosal lesions and 16 invasive parts (Vienna category 5); 40 reference for control, 19 control replicates

2014-08-06 | E-GEOD-60116 | biostudies-arrayexpress

Myelodysplastic/myeloproliferative neoplasms

Project description:This SuperSeries is composed of the following subset Series: GSE21948: High Density custom Agilent 44K CGH array analysis of 7q and TET2 region in myelodysplastic/myeloproliferative neoplasms GSE21990: Affymetrix SNP 6.0 array data for myelodysplastic/myeloproliferative neoplasms Refer to individual Series

2010-06-30 | E-GEOD-21991 | biostudies-arrayexpress

SmallRNAs profile in 60 Neuroendocrine Neoplasms (NEN) and 3 sera derived from NEN patients

Project description:We investigate the miRNA expression profiles with the attempt to identify deregulated molecules useful as NEN biomarkers. SmallRNA-Seq was performed allowing the identification of miRNAs commonly expressed in all samples. Three sera from the same samples were also sequenced.

2022-06-30 | E-MTAB-11598 | biostudies-arrayexpress

Genomic analysis of melanocytic neoplasms

Project description:Genomic analysis of melanocytic neoplasms

| PRJNA434347 | ENA

Genomic analysis of melanocytic neoplasms

Project description:Genomic analysis of melanocytic neoplasms

| PRJNA434348 | ENA