Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Quantitative proteomics of human pancreatic beta cells

ABSTRACT: Outline: using label-free alternate-scanning LC-MS/MS, we compared the proteomic architecture of core functional pathways in pancreatic beta cells of human origin. Results: we quantified the relative molar abundance of 707 proteins mainly composed of functional pathways of metabolism, protein synthesis and cytoskeleton.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, Pancreatic Islet Beta Cell

SUBMITTER: Gertjan Kramer

LAB HEAD: J.M.F.G. Aerts

PROVIDER: PXD001539 | Pride | 2015-08-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20111103_S16a.pride.mgf.gz	Mgf
	20111103_S16a.pride.mztab.gz	Mztab
	20111103_S16a.xml.gz	Xml
	20111103_s16b.pride.mgf.gz	Mgf
	20111103_s16b.pride.mztab.gz	Mztab

Items per page:

1 - 5 of 80

Publications

Quantitative proteomics of rat and human pancreatic beta cells.

Brackeva B B Kramer G G Vissers J P C JP Martens G A GA

Data in brief 20150310

Data set description: This data set is composed by label-free alternate-scanning LC-MS/MS proteomics analysis human and Wistar rat pancreatic islet endocrine cells. The mass spectrometry data of the human and rat pancreatic beta cells and the resulting proteome search output from ProteinLynx GlobalSERVER (PLGS) have been deposited to the ProteomeXchange Consortium [1] via the PRIDE partner repository with the dataset identifiers PXD001539 (human) and PXD001816 (rat). From these mass spectrometry ...[more]

PMID: 26217750

Similar Datasets

Genome-wide mRNA profiling of adult human pancreatic beta and duct cells in comparison to other human tissues

Project description:Aims: establishment of reference samples to investigate gene expression selective for endocrine or ductal-exocrine cells within the adult human pancreas. To this end, human islet endocrine cells, FACS-enriched in insulin+ cells, (n=3) and human exocrine ductal cells (n=2) are compared on Affymetrix HG133A platform with duplicate hybridizations of a panel of other primary human tissues. The microarray analysis was performed on 3 pools of human beta cell-enriched cell fractions, isolated from 10 non-selected donor organs, and 2 pools of duct cell-enriched fractions obtained from 6 non-selected donor pancreases. The cells were suspension-cultured for 2-3 weeks along standard procedures and with no specific treatment prior to FACS-sorting and RNA extraction. The average composition of human beta cell-preparations was 55 ± 13% insulin+ cells, 13±8% glucagon+ cells and 21 ±7% non-granulated cells. Pancreatic duct cells-enriched preparations contained 85 ±7% cytokeratin 19+ cells with 4 ± 1% insulin+ cells and 6 ±4% glucagon+ cells and were isolated as described by Heimberg H. et al.( Diabetes 2001,49: 571-579 ). Pancreatic cell mRNA profiles were compared to those of a panel of other human primary tissues (n=2 biological replicates). This dataset is part of the TransQST collection.

2011-07-21 | E-GEOD-30803 | biostudies-arrayexpress

Functional characteristics of neonatal rat beta cells With distinct markers

Project description:Neonatal beta cells are considered developmentally immature and hence less glucose-responsive. To study the acquisition of mature glucose-responsiveness, we compared glucose-regulated redox state, insulin synthesis and secretion of beta cells purified from neonatal or 10-weeks old rats to their transcriptomes and proteomes measured by oligonucleotide and LC-MS/MS profiling. Lower glucose-responsiveness of neonatal beta cells was explained by two distinct properties: higher activity at low glucose and lower activity at high glucose. Basal hyperactivity was associated with higher NAD(P)H, a higher fraction of neonatal beta cells actively incorporating 3H-Tyrosine, and persistently increased insulin secretion below 5 mM glucose. Neonatal beta cells lacked the steep glucose-responsive NAD(P)H rise between 5-10 mM glucose characteristic for adult beta cells, and accumulated less NAD(P)H at high glucose. They had 2-fold lower expression of malate/aspartate-NADH shuttle and most glycolytic enzymes. Genome-wide profiling situated neonatal beta cells at a developmental crossroad: they showed advanced endocrine differentiation when specifically analyzed for their mRNA/protein level of classical neuroendocrine markers. On the other hand, discrete neonatal beta cell subpopulations still expressed mRNAs/proteins typical for developing/proliferating tissues. One example, Delta-like 1 homolog (DLK1) was used to investigate if neonatal beta cells with basal hyperactivity corresponded to a more immature subset with high DLK1, but no association was found. In conclusion, the current study supports the importance of glycolytic NADH-shuttling in stimulus-function coupling, presents basal hyperactivity as novel property of neonatal beta cells, and provides potential markers to recognize intercellular developmental differences in the endocrine pancreas.

2014-12-12 | PXD001577 | Pride

Novel Observations from Next Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets

Project description:Understanding distinct gene expression patterns of normal adult and developing fetal human pancreatic a and b cells is crucial for developing stem cell therapies, islet regeneration strategies, and therapies designed to increase b cell function in patients with diabetes (type 1 or 2). Toward that end, we have developed methods to highly purify a, b, and d cells from human fetal and adult pancreata by intracellular staining for the cell-specific hormone content, sorting the sub-populations by flow cytometry and, using next generation RNA sequencing, we report on the detailed transcriptomes of fetal and adult a and b cells. We observed that human islet composition was not influenced by age, gender, or body mass index and transcripts for inflammatory gene products were noted in fetal b cells. In addition, within highly purified adult glucagon-expressing a cells, we observed surprisingly high insulin mRNA expression, but not insulin protein expression. This transcriptome analysis from highly purified islet a and b cell subsets from fetal and adult pancreata offers clear implications for strategies that seek to increase insulin expression in type 1 and type 2 diabetes. RNA-sequencing of highly purified human adult and fetal islet cell subset was performed using our newly developed method. Using this data, we can study and compare the detailed transcriptome or alpha and beta cells during development.

2015-06-08 | E-GEOD-67543 | biostudies-arrayexpress

The human and mouse islet peptidome: effects of obesity and type 2 diabetes

Project description:To characterise the impact of metabolic disease on the peptidome of human and mouse pancreatic islets and the contribution of intra-islet glucagon-like peptide 1 (GLP-1) receptor signalling.

2021-08-24 | PXD026095 | Pride

Human islet of Langerhans grown on nanosubstrates LC-MSMS

Project description:Intensive efforts are focused on identifying regulators of human pancreatic islet cell growth and maturation to accelerate development of therapies for diabetes. In the present study we evaluate the contribution of the physical properties of the extracellular matrix in supporting long term culture of human islets in vitro. We used metal oxide layers with tailored nanoscale roughness to fabricate scaffolds. Their suitability to support long term culture of human islets was investigated through assessment of β-cell survival, differentiation and function by using a proteomic approach to evaluate the molecular mechanisms involved. Proteomic analysis confirmed that ns-ZrOx promoted the activation of a transcriptional and translational program leading to activation of pro-survival and pro-differentiation signalling pathways. The process was driven by a mechanotransductive pathway driven by nanostructured topology, via remodelling of the actin cytoskeleton nuclear architecture and increase of oxygen sensor PDH2 Our data suggest that β-cells relay on nanotopography features to regulate their differentiation and survival. Tailored nanostructured substrates may provide a unique strategy to identify novel hints for tissue engineering and molecular /pharmacological targets of intervention to treat diabetes mellitus.

2018-07-11 | PXD007569 | Pride

SIK2 phosphorylation in response to glucagon or insulin in murine hepatocytes

Project description:The phosphorylation state of human HA-tagged-SIK2, adenovirally introduced in murine hepatocytes (C57/BL/6 strain) was analysed in unstimulated and in response to glucagon- or insulin- treated conditions. Background:- LKB1 is a master kinase that regulates metabolism and growth through AMPK and 12 other closely-related kinases. Liver-specific ablation of LKB1 causes increased glucose production in hepatocytes in vitro and hyperglycaemia in fasting mice in vivo. The salt-inducible kinases (SIK1, 2 and 3), members of the AMPK-related kinase family, play a key role as gluconeogenic suppressor downstream of LKB1 in the liver. A selective SIK inhibitor (HG-9-91-01) promotes dephosphorylation of transcriptional co-activators CRTC2/3 resulting in enhanced gluconeogenic gene expression and glucose production in hepatocytes, an effect that is abolished when an HG-9-91-01-insensitive-mutant-SIK is introduced or LKB1 is ablated. Although SIK2 was proposed as a key regulator of insulin-mediated suppression of gluconeogenesis, we provide genetic evidence that liver-specific ablation of SIK2 alone has no effect on gluconeogenesis and insulin does not modulate SIK2 phosphorylation/activity. Collectively, we demonstrate that the LKB1-SIK pathway functions as a key gluconeogenic gatekeeper in the liver.

2014-08-08 | PXD001032 | Pride

Drug-induced hepatotoxicity screening in primary mouse hepatocytes, an Omics approach.

Project description:Drug-induced hepatotoxicity is a leading cause of attrition of candidate drugs in drug development. Therefore new screening methods are necessary which predict these hazards more accurate and earlier in the drug development process. Of all in vitro hepatotoxicity models, primary human hepatocytes are considered as 'the gold standard'. However, the use of these hepatocytes is hindered by their scarcity and major inter-individual variation. These limitations may be overcome with use of primary mouse hepatocytes. Within this context changes in protein expressions in primary mouse hepatocytes, after exposure to cyclosporin A were studied using differential gel electrophoresis. Thereafter, the mRNA expression levels of these deregulated proteins from cyclosporin A-treated cells were analyzed. Cyclosporin A induced ER stress and altered the ER-Golgi transport, which may alter vesicle mediated transport and protein secretion. Moreover are the differentially expressed proteins observed upon challenge by cyclosporin A, associated with cholestatic mechanisms. For each biological experiment, one hybridization was conducted and one sample per array. In total, 6 arrays were used for 2 different conditions (Csa or control at 48 hours).

2013-04-01 | E-GEOD-33742 | biostudies-arrayexpress

The human pancreatic islet transcriptome: impact of pro-inflammatory cytokines

Project description:We have used RNA-seq to identify transcripts, including splice variants, expressed in human islets of Langerhans under control condition or following exposure to the pro-inflammatory cytokines interleukin-1β (IL-1β) and interferon-γ (IFN-γ). A total of 29,776 transcripts were identified as expressed in human islets. Expression of around 20% of these transcripts was modified by pro-inflammatory cytokines, including apoptosis- and inflammation-related genes. Chemokines were among the transcripts most modified by cytokines. Interestingly, 35% of the genes expressed in human islets undergo alternative splicing as annotated in RefSeq, and cytokines caused substantial changes in spliced transcripts. Nova1, previously considered a brain-specific regulator of mRNA splicing, is expressed in islets. 25/41 of the candidate genes for type 1 diabetes are expressed in islets, and cytokines modified expression of several of these transcripts. 5 human islet of Langerhans preparations examined under 2 conditions (control and cytokine treatment)

2012-03-09 | E-GEOD-35296 | biostudies-arrayexpress

Chromatin immunoprecipitation of mouse pancreatic beta-cells.

Project description:To gain insights into how pancreatic beta-cells are programmed in vivo, we profiled key histone methylations (H3K4/K27me3) in embryonic stem cells, multipotent progenitors of the nascent embryonic pancreas, purified beta-cells, and 10 other adult tissues (all under normal, untreated conditions). For these cells we also purified RNA to analyze tissue specfic genome wide transcription levels in relation to histone modifications. Corresponding RNA microarrays can be found under accession E-TABM-877.

2010-03-19 | E-TABM-906 | biostudies-arrayexpress

Detailed transcriptome atlas of the pancreatic beta cell

Project description:The aim of the present study was to explore the transcriptome of pancreatic islets and, based on this information, to prepare a comprehensive and open access inventory of insulin-producing ?-cell gene expression, the beta-Cell Gene Atlas (BCGA). INS-1 cells, primary rat beta-cells (>87% beta-cells) and non-beta-cells (<3% beta cells, mostly alpha) were isolated by FACS mediated purification of two different rat islet preparations.

2008-12-31 | E-GEOD-13381 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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