Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RAT liver OXYGEN-VENTILATED NMP LC-MS/MS

ABSTRACT: The project was to compare NMP on liver retrieval in DCD rats.

INSTRUMENT(S): LTQ

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Liver

SUBMITTER: Ji-Hua Shi

LAB HEAD: Shui-Jun Zhang

PROVIDER: PXD028641 | Pride | 2022-05-19

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Cytochrome P450 2E1 predicts liver functional recovery from donation after circulatory death using air-ventilated normothermic machine perfusion.

Shi Ji-Hua JH Yang Dong-Jing DJ Jin Qiang Q Cheng Nuo N Shi Yuan-Bin YB Bai Yang Y Yu Dong-Sheng DS Guo Wen-Zhi WZ Ge Guang-Bo GB Zhang Shui-Jun SJ

Scientific reports 20220506 1

The optimal oxygen concentration is unclear for normothermic machine perfusion (NMP) of livers from donation after circulatory death (DCD). Our purposes were to investigate the effect of air-ventilated NMP on the DCD liver, analyze the underlying mechanism and select the targets to predict liver functional recovery with NMP. NMP was performed using the NMP system with either air ventilation or oxygen ventilation for 2 h in the rat liver following warm ischemia and cold-storage preservation. Prot ...[more]

PMID: 35523980

Similar Datasets

LC-MS proteomics quantitative analysis of pancreatic cancer cells overexpressing NEK2

Project description:The NEK2 overexpression in pancreactic cancer cell (SW1990), and we performed LC-MS to further investigate the manner in which NEK2 regulates PD-L1.

2021-06-29 | PXD026877 | Pride

Urine recirculation prolongs normothermic kidney perfusion for via more optimal metabolic homeostasis – a proteomics study

Project description:We describe a proteomics analysis to determine the molecular differences between normothermically perfused (normothermic machine perfusion, NMP) human kidneys with urine recirculation (URC) and urine replacement (UR). Proteins were extracted from 16 kidney biopsies with URC (n=8 donors after brain death (DBD), n=8 donors after circulatory death (DCD)) and three with UR (n=2 DBD, n=1 DCD), followed by quantitative analysis by mass spectrometry. Damage-associated molecular patterns (DAMPs) were decreased in kidney tissue after six hours NMP with URC, suggesting reduced inflammation. Vasoconstriction was also attenuated in kidneys with URC as angiotensinogen levels were reduced. Strikingly, kidneys became metabolically active during NMP, which could be enhanced and prolonged by URC. For instance, mitochondrial succinate dehydrogenase enzyme levels as well as carbonic anhydrase were enhanced with URC, contributing to pH stabilisation. Levels of cytosolic and the mitochondrial phosphoenolpyruvate carboxykinase were elevated after 24 hours of NMP, more prevalent in DCD than DBD tissue. Key enzymes involved in glucose metabolism were also increased after twelve and 24 hours of NMP with URC, including mitochondrial malate dehydrogenase and glutamic-oxaloacetic transaminase, predominantly in DCD tissue. We conclude that NMP with URC permits prolonged preservation and revitalises metabolism to possibly minimize better cope with ischemia reperfusion injury in discarded kidneys.

2020-10-20 | PXD021507 | Pride

β-catenin-controlled tubular cell-derived exosomes play a key role in fibroblast activation via the OPN-CD44 axis

Project description:Tubular injury and peripheral fibroblast activation are the hallmarks of chronic kidney disease (CKD) and renal fibrosis, suggesting intimate communication between the two diseases. However, the underlying mechanisms remain to be determined. Exosomes play a role in shuttling proteins and other materials to recipient cells. In our study, we found that tubular cell-derived exosomes were aroused by β-catenin in kidney fibrogenesis. Osteopontin (OPN), especially its N-terminal fragments (N-OPN), was encapsulated in β-catenin-controlled tubular cell-derived exosome cargo, and subsequently passed to fibroblasts. Through binding with CD44, exosomal OPN promoted fibroblast proliferation and activation. Gene deletion of β-catenin in tubular cells (Ksp-β-catenin−/−) or gene ablation of CD44 (CD44−/−) greatly ameliorated renal fibrosis. Notably, N-OPN was secreted by exosome into the urine of patients with CKD, and negatively correlated with kidney function. The urinary exosomes from patients with CKD greatly accelerated renal fibrosis, which was blocked by CD44 deletion. These results suggest that exosome-mediated activation of the OPN/CD44 axis plays a key role in renal fibrosis, which is controlled by β-catenin.

2022-05-20 | PXD030696 | Pride

Expression data from an ex vivo ischaemia reperfusion model of renal deceased by cardiac death (DCD) donation in rat

Project description:In DCD organ donation one of the significant problems for the organ is the inflammatory response due to ischaemia reperfusion injury caused by warm ischaemia prior to retrieval followed by warm reoxygenation upon transplantation. We developed a model where a DCD kidney was retrieved and preserved using hypothermic machine perfusion with cold University of Wisconsin solution with/without the addition of heparinoids low molecular weight heparin and pentosan polysulfate (PPS) followed by warm oxygenated perfusion with modified Krebs-Henseleit buffer to simulate early ischaemia reperfusion injury (IRI). The donor rats consisted of a control group cold perfusion group compared to warm perfusion and groups treated with either low molecular weight heparin or PPS to assess their activity in ameliorating IRI. We used equimolar pooled RNA samples from each group to perform an exploratory microarray experiment Donor kidneys were harvested and preserved by hypothermic machine perfusion with University of Wisconsin (UW) Solution for 3 hours followed by warm oxygenated perfusion with modified Krebs-Henseleit buffer for 30 minutes to simulate transplantation and whole blood ischaemia reperfusion injury. The model was then used to test the anti-inflammatory properties of the glycosaminoglycan heparin and PPS when used as supplements into perfusate solutions. Half of the donor kidney was used to extract RNA using the Tri reagent and stored in RNA Later. The qualitative best three RNAs from each group were quantified by fluorimetry and mixed in an equimolar manner and used for microarray analysis.

2012-03-22 | E-GEOD-36671 | biostudies-arrayexpress

Viability of discarded human livers during normothermic machine perfusion is associated with activation of repair mechanisms

Project description:Background and Aims: Liver transplantation provides an effective cure for end-stage liver disease but is hampered by a severe organ shortage. Normothermic machine perfusion (NMP) of donor livers allows dynamic preservation in addition to viability assessment prior to transplantation. Little is known about the injury and repair mechanisms induced during NMP. Therefore, we examined gene and protein expression changes in a cohort of discarded human livers during NMP, stratified by liver viability. Approach and Results: 6 human livers from donation after circulatory death (DCD) underwent 12 hours of NMP, of which 3 met viability criteria. We applied bulk transcriptomics to evaluate differences in gene expression relating to injury, repair, and regenerative responses among livers based on viability. Viable livers demonstrated robust activation of innate immunity after 3 hours of NMP followed by enrichment of pro-repair and pro-survival mechanisms. Nonviable livers demonstrated delayed and persistent enrichment of innate immune responses. Viable livers demonstrated effective induction of autophagy, the cellular repair and homeostasis pathway, compared to nonviable livers. Enrichment of pro-survival signaling was also broader in these livers. Conclusions: NMP of discarded DCD human livers results in ischemia-reperfusion injury, but importantly activates autophagy as a means of cellular repair. More pronounced activation of autophagy was seen in livers that met viability criteria for transplantation. Therapeutic targeting of the autophagy mechanism may allow rehabilitation of nonviable livers for transplantation.

2022-01-25 | GSE165568 | GEO

Proteome analyses of sperm from wild type, Akap3 and Akap4 gene null mutant mice

Project description:PKA signaling plays important functions during mouse spermatogenesis and for the regulation of sperm motility. The efficiency of PKA signaling is regulated partly by its binding protein A-kinase anchoring protein (AKAP) family. Mature mouse sperm contain several AKAPs, of which AKAP3 and AKAP4 are localized in the principal piece of sperm tail and they are sperm-specific. Using gene knock-out mouse models, it was found that both AKAP3 and AKAP4 are essential for the formation of a complete fibrous sheath, the electron-dense sub-cellular structure within sperm flagellum that is important for the motility of sperm and male fertility. Lack of AKAP3 or AKAP4 caused aberrant sperm morphology and inmotility, leading to eventual male sterility. In the present study, we investigated the changes of cellular proteome in the absence of AKAP3 or AKAP4 in mature sperm, using quantitative mass spectrometry. It was found that global changes of sperm proteome occur in the absence of AKAP3 or AKAP4. In Akap3 null sperm, proteins related to flagella structure, PKA signaling and motility regulations are down-regulated, whereas proteins involved in RNA metabolism, protein translation and actin filaments formation are accumulated. Akap4 null sperm also displayed changes of sperm proteome at lesser extends. These results suggest that both AKAP3 and AKAP4 are essential for the formation of sperm sub-cellular structures, proper regulation of PKA activity and motility of sperm, providing new clues to elucidate the molecular pathways that underlie the coordinated synthesis and organization of sperm proteome and sperm morphology

2020-01-14 | PXD016928 | Pride

Bile proteome reveals biliary regeneration during normothermic preservation of human donor livers

Project description:Normothermic machine perfusion (NMP) after static cold storage is increasingly used for preservation and assessment of human donor livers prior to transplantation. Biliary viability assessment during NMP reduces the risk of post-transplant biliary complications. However, understanding molecular changes in the biliary system during NMP remains incomplete. Here, we performed RNA-seq analysis of donor livers undergoing NMP treatment and compared livers with biliary viability scores that were acceptable for transplantation vs those that were not.

2023-11-21 | E-MTAB-13501 | biostudies-arrayexpress

Ciona savignyi notochord LC-MS/MS based on 4D Mass Spectromete

Project description:Lumen formation and inflation are crucial for tubular organ morphogenesis, yet the underling mechanism remains largely unrevealed. Here, we applied 4D proteomics to screen the lumenogenesis-related proteins and reveal the potentially biological pathways that are involved in lumen inflation during notochord lumen formation in ascidian Ciona savignyi.

2023-05-10 | PXD037089 | Pride

Differential expression pattern of the proteome in response to cadmium stress based on proteomics analysis of wheat roots

Project description:Background: Heavy metal cadmium (Cd) is a common environmental pollutant in soils, which has an negative impacts on crop growth and development. At present, cadmium has become a major soil and water heavy metal pollutant, which not only causes permanent and irreversible health problems for humans, but also causes a significant reduction in crop yields. Results: This study examined the chemical forms of Cd in the roots of two wheat varieties (M1019 and Xinong20) by continuous extraction and analyzed differences in distribution characteristics of Cd in the root cell wall, cytoplasm, and organelles by elemental content determination and subcellular separation. Furthermore, we conducted proteomics analysis of the roots of the two varieties under Cd pollution using mass spectrometry quantitative proteomics techniques. A total of 11,651 proteins were identified, of which 10,532 proteins contained quantitative information. In addition, the differentially expressed proteins in the two varieties were related to DNA replication and repair, protein metabolism, and the glutathione metabolism pathway. Conclusion: The results of this study improve our understanding of the mechanism of plant responses to Cd stress.

2020-03-30 | PXD018179 | Pride

The microRNA expression profile in donation after cardiac death (DCD) livers and its ability to identify primary non function

Project description:The microRNA expression profile in donation after cardiac death (DCD) livers its ability to identify primary non function DCD livers are a marginal organ and their usein transplantation is associated with a higher risk of primary non function (PNF), or early graft dysfunction (EGD). We compared a three groups of DCD livers defined as PNF (n=7) retransplanted within a week, good functional outcome (n=7) AST < 1000IU/L and EGD (n=9) AST>2500IU/L . RNA was extracted from archived histology samples and miRNA expression was analysed using the affymetrix Genechip miRNA 2.0 assays.

2015-04-09 | E-GEOD-67689 | biostudies-arrayexpress

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