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ATOMS determination of MMP cleavage site locations in YRS

ABSTRACT: Recombinant human tyrosyl-tRNA synthetase (YRS) was cleaved using recombinant MMPs. Terminal amine oriented mass spectrometry of substrates (ATOMS) was used to identify MMP generated cleavage sites from these mixtures with LC-MS/MS analysis.

INSTRUMENT(S): impact II

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Parker Jobin

LAB HEAD: Christopher Mark Overall

PROVIDER: PXD013366 | Pride | 2019-05-29

REPOSITORIES: Pride

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ATOMS analyses of MMP cleavage sites in WRS

Project description:Human tryptophanyl-tRNA synthetase (WRS) was digested by human MMPs, and digestion mixtures were subjected to terminal amine oriented mass spectrometry of substrates (ATOMS) protocol and LC-MS/MS analysis to identify MMP cleavage sites in WRS.

2019-05-29 | PXD013367 | Pride

LC-MS/MS analyses of MMP cleavage fragments of tyrosyl-tRNA synthetase

Project description:Tyrosyl-tRNA synthetase was digested with MMPs after which cleavage fragments were resolved using SDS-PAGE. Major bands were digested with trypsin and analyzed by LC-MS/MS.

2019-05-30 | PXD013197 | Pride

Gel LC-MS/MS analyses of MMP cleavage of tryptophanyl-tRNA synthetase

Project description:Tryptophanyl-tRNA synthetase was incubated by MMPs, cleavage products were resolved on SDS-PAGE. Cleavage products were trypsin digested and analyzed by LC-MS/MS.

2019-05-29 | PXD013217 | Pride

Active Site Specificity Profiling of the Matrix Metalloproteinase Family: Proteomic Identification of 4,300 Cleavage Sites by MMPs 1, 2, 3, 7, 8, 9, 12, 13, and 14.

Project description:Background: The active site of matrix metalloproteinases (MMPs) is highly conserved, complicating the rational design of specific substrates and inhibitors for individual family members. Results: Active site specificity profiles of 9 MMPs were determined using high throughput Proteomic Identification of protease Cleavage Sites (PICS). Conclusion: Subtle specificity divergences distinguish individual MMP family members. Significance: Understanding individual MMP cleavage site specificities will bolster the design of MMP specific activity assays and targeted inhibitory drugs.

2015-09-29 | PXD002265 | Pride

Transcription profiling of mouse C57Bl6 MMP-7 and MMP-10 deficient mice Pseudomonas aeruginosa exposed airway epithelium.

Project description:Airway epithelium is the initial point of host-pathogen interaction in Pseudomonas aeruginosa infection, an important pathogen in cystic fibrosis and nosocomial pneumonia. We used global gene expression analysis to determine airway epithelial transcriptional responses dependent on matrilysin (MMP-7) and stromelysin-2 (MMP-10), two matrix metalloproteinases induced by acute P. aeruginosa pulmonary infection. Extraction of Differential Gene Expression (EDGE) analysis of gene expression changes in P. aeruginosa infected organotypic tracheal epithelial cell cultures from wildtype, Mmp7-/-, and Mmp10-/- mice identified 2,089 matrilysin-dependent and 1,628 stromelysin-2-dependent genes that were differentially expressed. Key node network analysis showed that these MMPs controlled distinct gene expression programs involved in proliferation, cell death, immune responses, and signal transduction, among other host defense processes. Our results demonstrate discrete roles for these MMPs in regulating epithelial responses to pseudomonas infection and show that a global genomics strategy can be used to assess MMP function. Experiment Overall Design: C57Bl6, Mmp7-/- and Mmp10-/- mouse epithelium at an organotypic air liquid interface culture was exposed to Pseudomonas aeruginosa for 1 and 24 h. RNA was collected from these samples as well as uninfected 0 h and assessed for expression changes using Affymetrix Mouse 430 2.0 Arrays. Triplicate samples were processed for each genotype at each time point.

2008-06-15 | E-GEOD-7957 | biostudies-arrayexpress

Expression data from Pseudomonas aeruginosa exposed airway epithelium from C57Bl6 and MMP-7 and MMP-10 deficient mice.

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Secretomics reveals gelatinase substrates at the blood-brain barrier that are implicated in astroglial barrier function

Project description:The[Q3] gelatinases, matrix metalloproteinase 2 (MMP-2) and MMP-9, are key for leukocyte penetration of the brain parenchymal border in neuroinflammation and the functional integrity of this barrier; however, it is unclear which MMP substrates are involved. Using a tailored, sensitive, label-free mass spectrometryÃ¢â‚¬â€œbased secretome approach, not previously applied to nonimmune cells, we identified 119 MMP-9 and 21 MMP-2 potential substrates at the cell surface of primary astrocytes, including known substrates (ÃŽÂ²-dystroglycan) and a broad spectrum of previously unknown MMP-dependent events involved in cell-cell and cell-matrix interactions. Using neuroinflammation as a model of assessing compromised astroglial barrier function, a selection of the potential MMP substrates were confirmed in vivo and verified in human samples, including vascular cell adhesion moleculeÃ¢â‚¬â€œ1 and neuronal cell adhesion molecule. We provide a unique resource of potential MMP-2/MMP-9 substrates specific for the astroglia barrier. Our data support a role for the gelatinases in the formation and maintenance of this barrier but also in astrocyte-neuron interactions.

2023-10-24 | PXD043521 | Pride

CELF1 upregulates MMP gene expression to regulate cataract development

Project description:As a multifunctional RBP, CELF1 is known to preferentially binds to GU-rich elements (GREs) predominantly located in 3’ untranslated regions(UTRs) of target mRNA to regulate various post-transcriptional process. However, the targeted genes that regulated by CELF1 during cataractogenesis remains unknown. In present study,the function of CELF1 in SRA01/04 cells was investigated with CELF1 overexpression, the expression of MMPs was regulated by CELF1.

2022-03-23 | GSE153022 | GEO

MiR-21 Promotes Glioma Invasion by Targeting MMP Regulators.

Project description:Substantial data indicate that microRNA-21 (miR-21) is significantly elevated in glioblastoma (GBM) and in many other tumors of various origins. This miRNA has been implicated in various aspects of carcinogenesis, including cellular proliferation, apoptosis and migration. We demonstrate that miR-21 regulates multiple genes associated with glioma cell apoptosis, migration, and invasiveness, including RECK and TIMP3, suppressors of malignancy and inhibitors of matrix metalloproteinases (MMPs). Specific inhibition of miR-21 with antisense olgonucleotides leads to elevated levels of RECK and TIMP3 and therefore reduces MMP activities in vitro and in a human model of glioma in nude mice. Moreover, down-regulation of miR-21 in glioma cells leads to decrease of their migratory and invasion abilities. Our data suggest that miR-21 contributes to the glioma malignancy by down-regulation of MMP inhibitors that leads to activation of MMPs thus promoting invasiveness of cancer cells. Our results also indicate that inhibition of a single oncomir like miR-21 with specific antisense molecules can provide a novel therapeutic approach for “physiological” modulation of multiple proteins whose expression is de-regulated in cancer.

2008-07-12 | GSE11778 | GEO

Genome-wide analysis of MCF-7 cells expressing or not MMP-14 (MT1-MMP) growing in monolayer cell culture conditions

Project description:In order to investigate the impact of MMP-14 (MT1-MMP) on the transcriptomes of a human breast adenocarcinoma cell line, we performed a microarray analysis from RNAs isolated from MCF-7 cells expressing either an empty vector (VEC) or human MMP-14 cDNA (MT1) in monolayer growth conditions. MCF-7 cells were stably transfected with either an empty vector (pcDNA3.1/Zeo) or human MMP-14 cDNA (pcDNA3.1-MMP-14/Zeo). Cells were grown for 48 hours in monolayer culture. Cells were then lysed in TRIzol and total RNA was isolated. For each experimental condition, total RNAs isolated from 3 independant biological replicates were pooled.

2015-12-11 | E-GEOD-64320 | biostudies-arrayexpress

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