Browse
Submit Data
Databases
API
Help

Dataset Information

367 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury: Infarcted, Guanidine

ABSTRACT: The aim of the present study is to characterize ECM remodeling after myocardial infarction by applying a proteomics method based on ECM enrichment and MS analysis to a porcine model of ischemia/reperfusion injury. The human-like physiology and anatomy of pigs facilitate comparisons of different cardiac regions to establish an accurate temporal and spatial pattern of the ECM remodeling process.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Sus Scrofa (pig)

TISSUE(S): Heart

DISEASE(S): Myocardial Ischemia

SUBMITTER: Javier Barallobre-Barreiro

LAB HEAD: Manuel Mayr

PROVIDER: PXD003919 | Pride | 2016-04-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	RGIA_01.RAW	Raw
	RGIA_02.RAW	Raw
	RGIA_03.RAW	Raw
	RGIA_04.RAW	Raw
	RGIA_05.RAW	Raw

Items per page:

1 - 5 of 144

Publications

Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury.

Barallobre-Barreiro Javier J Didangelos Athanasios A Schoendube Friedrich A FA Drozdov Ignat I Yin Xiaoke X Fernández-Caggiano Mariana M Willeit Peter P Puntmann Valentina O VO Aldama-López Guillermo G Shah Ajay M AM Doménech Nieves N Mayr Manuel M

Circulation 20120118 6

<h4>Background</h4>After myocardial ischemia, extracellular matrix (ECM) deposition occurs at the site of the focal injury and at the border region.<h4>Methods and results</h4>We have applied a novel proteomic method for the analysis of ECM in cardiovascular tissues to a porcine model of ischemia/reperfusion injury. ECM proteins were sequentially extracted and identified by liquid chromatography tandem mass spectrometry. For the first time, ECM proteins such as cartilage intermediate layer prote ...[more]

PMID: 22261194

Similar Datasets

Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury: control, guanidine

Project description:The aim of the present study is to characterize ECM remodeling after myocardial infarction by applying a proteomics method based on ECM enrichment and MS analysis to a porcine model of ischemia/reperfusion injury. The human-like physiology and anatomy of pigs facilitate comparisons of different cardiac regions to establish an accurate temporal and spatial pattern of the ECM remodeling process.

2016-04-07 | PXD003918 | Pride

Proteomics analysis of cardiac extracellular matrix remodeling in a porcine model of ischemia/reperfusion injury Guanidine Infarct, focal area

2016-04-11 | PXD003926 | Pride

Extracellular matrix remodeling enhancing astrocyte lysosome pathway to reverse memory defected in Alzheimer’s disease

Project description:Extracellular matrix (ECM) remodeling is strongly linked to Alzheimer’s disease (AD) risk, but its functions are not fully understood. Here, we found that medial prefrontal cortex (mPFC) injection with chondroitinase ABC (ChABC) to remodel ECM reverses short-term memory loss and reduces Aβ deposition in 5xFAD mice. ECM remodeling also reactivates astrocytes, untangles aggrecan’s entanglement with amyloid-beta (Aβ) plaques, and encourages astrocyte recruitment to the surrounding plaques. ECM remodeling promotes astrocyte phagocytosis of Aβ plaque by activating the astrocyte phagocytosis receptor mertk and astrocytic vesicle circulation. Importantly, ECM remodeling enhances the autophagy-lysosome pathway in astrocytes to mediate Aβ clearance and alleviate AD pathology. Our work thus discovers a cellular mechanism to remodel the ECM to active astrocyte autophagic lysosomal pathway alleviation AD pathology. It may represent a potential therapeutic strategy and serve as a hallmark for treating AD.

2024-10-17 | PXD046784 | Pride

In depth quantification of extracellular matrix proteins from human pancreas

Project description:Extracellular matrix (ECM) is an important component of the pancreatic microenvironment which regulates β cell proliferation, differentiation and insulin secretion. Protocols have recently been developed for the decellularization of the human pancreas to generate functional scaffolds and hydrogels. In this work, we characterized human pancreatic ECM composition before and after decellularization using isobaric dimethylated leucine (DiLeu) labeling for relative quantification of ECM proteins. A novel correction factor was employed in the study to eliminate the bias introduced during sample preparation. In comparison to the commonly employed proteomic approaches (urea and FASP), a recently developed surfactant and chaotropic agent assisted sequential extraction/on pellet digestion (SCAD) protocol was proven to be a superior strategy for ECM protein extraction of human pancreatic ECM matrix. The quantitative proteomic results revealed the preservation of matrisome proteins while most of the cellular proteins were removed. This method was compared with a well-established label-free quantification (LFQ) approach which rendered similar expressions of different categories of proteins (collagens, ECM glycoproteins, proteoglycans, etc.). The distinct expression of ECM proteins was quantified comparing adult and fetal pancreas ECM, shedding light on the correlation between matrix composition and post-natal β cell maturation. Despite the distinct profiles of different subcategories in the native pancreas, the distribution of matrisome protein exhibited similar trends after the decellularization process. Our method generates the largest dataset of matrisome proteins from a single tissue type. These results provide valuable insight into the possibilities of constructing a bioengineered pancreas. It also facilitates an understanding of the significant roles that matrisome proteins play in post-natal cell maturation.

2019-06-17 | PXD012460 | Pride

Impact of fibrillar collagen scaffold on corneal stromal fibroblasts protein expression

Project description:The human cornea relies on its extracellular matrix (ECM) properties, with corneal stromal fibroblasts (CSFs) crucial for ECM remodeling. We studied the effects of nanofibrillar materials on CSFs using a decellularized human amniotic membrane (dHAM) and fibrillar collagen scaffold (FCS). FCS enhances focal adhesions (FAs), activating mechanotransduction signals through FAK autophosphorylation and YAP1 nuclear translocation. Nanofibrillar topography induces gene expression changes related to tissue remodeling and collagen production. Here, we performed shotgun proteomics analysis (DDA-PASEF in TimsToF Pro) to analyze the impact of FCS topography on CSFs protein expression.

2024-09-02 | PXD048096 | Pride

Distinct Combinatorial Cascade of Events Generated by ECM Proteolysis Dictates Cell Behavior

Project description:It is well established that the expression profiles of multiple and possibly redundant matrix remodeling proteases (e.g. collagenases) strongly differentiates in disease and development. Although enzymatic redundancy might be inferred from their close similarity in structure, their in-vivo activity can lead to extremely diverse tissue-remodeling outcomes. We observed that proteolysis of collagen, generated uniquely by individual homologous proteases, leads to a specific cascade of combinatorial events, which eventually affects overall extracellular matrix (ECM) topography, visco-elastic properties and composition. We reveal striking differences in the migratory and signaling patterns, morphology, and gene expression profiles of cells interacting with native collagen-rich ECM matrix degraded by different collagenases. Thus unlike envisioned before degradative matrix remodeling systems are not redundant and give rise to precise ECM-cell crosstalk. As ECM proteolysis is an abundant biochemical process critical to tissue homeostasis these results improve our fundamental understanding of systemic factors dictating cell behavior.

2016-09-27 | PXD003553 | Pride

Extracellular Matrix Proteomics Identifies Molecular Signature of Atherosclerotic Plaques from Symptomatic Patients

Project description:Recent findings have challenged the prevailing histology- or imaging-based definition of the “vulnerable plaque”. To investigate molecular characteristics associated with “clinical instability” of atherosclerosis, we performed a proteomics comparison of the vascular extracellular matrix and associated molecules in human carotid endarterectomy specimens from symptomatic versus asymptomatic patients. The proteomics data were integrated with gene expression profiling and an analysis of protein secretion by lipid-loaded human vascular smooth muscle cells. The molecular signature of plaques from symptomatic patients identified by proteomics and at least one of the other two approaches comprised matrix metalloproteinase-9, chitinase-3-like protein 1, S100A8/S100A9, cathepsin B, fibronectin and galectin-3-binding protein. These biomarker candidates were measured in 685 subjects of the Bruneck Study and found to significantly predict the progression to advanced atherosclerosis (as assessed by repeated carotid ultrasound) and the incidence of cardiovascular disease over a 10-year follow-up period, highlighting the strength of tissue-based proteomics for biomarker discovery.

2017-04-20 | PXD005130 | Pride

ECM deposition is driven by caveolin1-dependent regulation of exosomal biogenesis and cargo sorting

Project description:<p>The composition and physical properties of the extracellular matrix (ECM) critically influence tumor progression, but the molecular mechanisms underlying ECM layering are poorly understood. Tumor-stroma interaction is critically dependent on cell-cell communication mediated by exosomes, small vesicles generated within multivesicular bodies (MVBs). Here, we show that caveolin-1 (Cav1) is a central modulator of both exosome biogenesis and exosomal protein cargo sorting through the regulation of cholesterol content at the endosomal compartment/MVBs. Quantitative proteomics profiling revealed that Cav1 is required for exosomal sorting of ECM protein cargo subsets including tenascin-C (TnC), and for fibroblast-derived exosomes to efficiently depose ECM and promote tumor cell invasiveness. Cav1-driven exosomal ECM deposition not only promotes local stromal remodeling, but also the generation of distant ECM-enriched stromal niches. These results support a model by which Cav1 is a central regulatory hub for tumor-stroma interactions through a novel exosome-dependent ECM deposition mechanism.</p><p><br></p><p>Linked studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS1969' rel='noopener noreferrer' target='_blank'>MTBLS1969</a></p>

2020-10-07 | MTBLS1977 | MetaboLights

ECM deposition is driven by caveolin1-dependent regulation of exosomal biogenesis and cargo sorting

Project description:<p>The composition and physical properties of the extracellular matrix (ECM) critically influence tumor progression, but the molecular mechanisms underlying ECM layering are poorly understood. Tumor-stroma interaction is critically dependent on cell-cell communication mediated by exosomes, small vesicles generated within multivesicular bodies (MVBs). Here, we show that caveolin-1 (Cav1) is a central modulator of both exosome biogenesis and exosomal protein cargo sorting through the regulation of cholesterol content at the endosomal compartment/MVBs. Quantitative proteomics profiling revealed that Cav1 is required for exosomal sorting of ECM protein cargo subsets including tenascin-C (TnC), and for fibroblast-derived exosomes to efficiently depose ECM and promote tumor cell invasiveness. Cav1-driven exosomal ECM deposition not only promotes local stromal remodeling, but also the generation of distant ECM-enriched stromal niches. These results support a model by which Cav1 is a central regulatory hub for tumor-stroma interactions through a novel exosome-dependent ECM deposition mechanism.</p><p><br></p><p>Linked studies: <a href='https://www.ebi.ac.uk/metabolights/MTBLS1977' rel='noopener noreferrer' target='_blank'>MTBLS1977</a></p>

2020-10-07 | MTBLS1969 | MetaboLights

Integrin a5, aV, and aVb3 in zebrafish embryos at the 12 somite stage

Project description:Integrins are a major class of heterodimeric adhesion receptors composed of an a and b subunit that mediate cell adhesion to the extracellular matrix (ECM). The extracellular matrix protein fibronectin is important for early vertebrate development, and Integrin a5b1 and aVb3 are the two primary fibronectin receptors. To better define the integrin – ECM protein network at 10-13 somite stage of zebrafish development, we performed co-immunoprecipitation and Mass Spectrometry (MS) based proteomics using FLAG-tagged Integrin a5, aV, and aVb3 expressed in maternal zygotic a5 mutant (MZa5-/-) embryos. We found that Integrin a5b1 and aVb1 are the functional fibronectin receptors, whereas Integrin aVb3 displayed low affinity to both fibronectins (Fn1a and Fn1b). In addition, basement membrane ligands Laminins (lama1, lamb1a, lamc1) are roughly equal in all three datasets while Thrombospondins (thbs3b, thbs4b) and cartilage oligomeric matrix protein (comp/thbs5) are found exclusively in the aV dataset. Our results suggest a diverse role of aV class integrins in ECM protein recruitment.

2021-09-10 | PXD024665 | Pride

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