References of "De Pauw, Edwin"
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See detailIdentification of proteins from wild cardoon flowers (Cynara cardunculus L.) by a proteomic approach
Ben Amira, Amal; Bauwens, Julien ULiege; De Pauw, Edwin ULiege et al

in Journal of Chemical Biology (2017), 10

Proteomic approach was applied to identify total proteins, particularly the enzymatic content, from wild cardoon flowers. As the selection of an appropriate sample preparation method is the key for ... [more ▼]

Proteomic approach was applied to identify total proteins, particularly the enzymatic content, from wild cardoon flowers. As the selection of an appropriate sample preparation method is the key for getting reliable results, two different extraction/precipitation methods (trichloroacetic acid and phenol/ammonium acetate) were tested on fresh and lyophilized flowers. After two-dimensional electrophoresis (2D–E) separations, a better protein pattern was obtained after phenol extraction from lyophilized flowers. Only 46 % of the total analyzed spots resulted in a protein identification by mass spectrometry MALDI-TOF. Four proteases (cardosins A, E, G, and H), which have become a subject of great interest in dairy technology, were identified. They presented molecular weights and isoelectric points very close and high levels of homology between matched peptides sequences. The absence of the other cardosins (B, C, D, and F) could be an advantage, as it reduces the excessive proteolytic activity that causes bitter flavors and texture defects, during cheese making. [less ▲]

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See detailProteomic signatures reveal a dualistic and clinically relevant classification of anal canal carcinoma
Herfs, Michael ULiege; Longuespée, Rémi ULiege; Quick, Charles et al

in Journal of Pathology (The) (2017), 241

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See detailEcotoxicoproteomic assessment of the functional alterations caused by chronic metallic exposures in gammarids
Gismondi, Eric ULiege; Thomé, Jean-Pierre ULiege; Urien, Nastassia et al

in Environmental Pollution (2017)

Very few ecotoxicological studies have been performed on long-term exposure under controlled conditions, hence limiting the assessment of the impact of chronic and diffuse chemical pressures on the health ... [more ▼]

Very few ecotoxicological studies have been performed on long-term exposure under controlled conditions, hence limiting the assessment of the impact of chronic and diffuse chemical pressures on the health of aquatic organisms. In this study, an ecotoxicoproteomic approach was used to assess the integrated response and possible acclimation mechanisms in Gammarus fossarum following chronic exposures to Cd, Cu or Pb, at environmentally realistic concentrations (i.e. 0.25, 1.5 and 5 µg/L respectively). After 10-week exposure, changes in protein expression were investigated in caeca of control and exposed males. Gel-free proteomic analyses allowed for the identification of 35 proteins involved in various biological functions, for which 23 were significantly deregulated by metal exposures. The protein deregulation profiles were specific to each metal, providing evidence for metal-specific action sites and responses of gammarids. Among the tested metals, Cu was the most toxic in terms of mortality, probably linked with persistent oxidative stress. Moulting and osmoregulation were the major biological functions affected by Cu in the long-term. In Pb-exposed gammarids, significant deregulations of proteins involved in immune response and cytoskeleton were observed. Reproduction appears to be strongly affected in gammarids chronically exposed to Cd or Pb. Besides, modified expressions of several proteins involved in energy transfer and metabolism highlighted important energetic reshuffling to cope with chronic metal exposures. These results support the fact that metallic pressures induce a functional and energetic cost for individuals of G. fossarum with potential repercussions on population dynamics. Furthermore, this ecotoxicoproteomic study offers promising lines of enquiry in the development of new biomarkers that could make evidence of long-term impacts of metals on the health of organisms. [less ▲]

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See detailIdentification and quantification of peptidoglycan cytoplasmic fragments by LC-MS
Boulanger, Madeleine ULiege; Raymackers, Alice ULiege; De Pauw, Edwin ULiege et al

Poster (2016, November 16)

In Bacillus licheniformis 749/I, the induction of BlaP beta-lactamase relies on a complex regulation system. During this process, the intracellular repressor BlaI is inactivated by a dipeptide coming from ... [more ▼]

In Bacillus licheniformis 749/I, the induction of BlaP beta-lactamase relies on a complex regulation system. During this process, the intracellular repressor BlaI is inactivated by a dipeptide coming from the peptidoglycan (PG) degradation via an “AND Gate” regulation. This regulation involves the cellular stress induced by the beta-lactam, the membrane receptor BlaR1 and the PG turnover. Briefly, the induction occurs when the extracellular domain of BlaR1 is acylated by the antibiotic which leads to a reorganization of the transmembrane segments and the receptor autocleavage. Simultaneously, the beta-lactam partially inhibits the penicillin-binding protein 1 (PBP1), triggering increased PG turnover and accumulation of PG fragments. Some of these fragments could enter in the cytoplasm and undergo enzymatic degradations which lead to the formation of the pro co-activator (tripeptide L-Ala-D-Glu-m-A2pm). This pro co-activator generates the co-activator, the dipeptide D-Glu-m-A2pm. Nowadays the nature and the concentration of PG fragments inside the cytoplasm are unknown. Therefore, the development and the validation of a zwitterionic hydrophilic interaction liquid chromatography coupled to electrospray ionization mass spectrometry method (ZIC-HILIC-MS) are required in order to identify and quantify those cytoplasmic fragments. [less ▲]

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See detailMyoferlin is a novel exosomal protein and functional regulator of cancer-derived exosomes
Blomme, Arnaud; Fahmy, Karim; Peulen, Olivier ULiege et al

in Oncotarget (2016)

Exosomes are communication mediators participating in the intercellular exchange of proteins, metabolites and nucleic acids. Recent studies have demonstrated that exosomes are characterized by a unique ... [more ▼]

Exosomes are communication mediators participating in the intercellular exchange of proteins, metabolites and nucleic acids. Recent studies have demonstrated that exosomes are characterized by a unique proteomic composition that is distinct from the cellular one. The mechanisms responsible for determining the proteome content of the exosomes remain however obscure. In the current study we employ ultrastructural approach to validate a novel exosomal protein myoferlin. This is a multiple C2-domain containing protein, known for its conserved physiological function in endocytosis and vesicle fusion biology. Emerging studies demonstrate that myoferlin is frequently overexpressed in cancer, where it promotes cancer cell migration and invasion. Our data expand these ndings by showing that myoferlin is a general component of cancer cell derived exosomes from different breast and pancreatic cancer cell lines. Using proteomic analysis, we demonstrate for the rst time that myoferlin depletion in cancer cells leads to a signi cantly modulated exosomal protein load. Such myoferlin-depleted exosomes were also functionally de cient as shown by their reduced capacity to transfer nucleic acids to human endothelial cells (HUVEC). Beyond this, myoferlin-depleted cancer exosomes also had a signi cantly reduced ability to induce migration and proliferation of HUVEC. The present study highlights myoferlin as a new functional player in exosome biology, calling for novel strategies to target this emerging oncogene in human cancer. [less ▲]

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See detailAccurate drift time determination by traveling wave ion mobility spectrometry: The concept of the diffusion calibration
Kune, Christopher ULiege; Far, Johann ULiege; De Pauw, Edwin ULiege

in Analytical Chemistry (2016), 88

Ion mobility spectrometry (IMS) is a gas phase separation technique which relies on differences in collision cross section (CCS) of ions. Ionic clouds of unresolved conformers overlap if the CCS ... [more ▼]

Ion mobility spectrometry (IMS) is a gas phase separation technique which relies on differences in collision cross section (CCS) of ions. Ionic clouds of unresolved conformers overlap if the CCS difference is below the instrumental resolution expressed as CCS/ΔCCS. The experimental arrival time distribution (ATD) peak is then a superimposition of the various contributions weighted by their relative intensities. This paper introduces a strategy for accurate drift time determination using traveling wave ion mobility spectrometry (TWIMS) of poorly resolved or unresolved conformers. This method implements through a calibration procedure the link between the peak full width at half maximum (FWHM) and the drift time of model compounds for wide range of settings for wave heights and velocities. We modified a Gaussian equation which achieves the deconvolution of ATD peaks where the FWHM is fixed according to our calibration procedure. The new fitting Gaussian equation only depends on two parameters: The apex of the peak (A) and the mean drift time value (μ). The standard deviation parameter (correlated to FWHM) becomes a function of the drift time. This correlation function between μ and FWHM is obtained using the TWIMS calibration procedure which determines the maximum instrumental ion beam diffusion under limited and controlled space charge effect using ionic compounds which are detected as single conformers in the gas phase. This deconvolution process has been used to highlight the presence of poorly resolved conformers of crown ether complexes and peptides leading to more accurate CCS determinations in better agreement with quantum chemistry predictions [less ▲]

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See detailSupramolecular influence on cis–trans isomerization probed by ion mobility spectrometry
Czerwinska, Izabella; Kulesza, Alexander; Choi, Changmin et al

in Physical Chemistry Chemical Physics [=PCCP] (2016), 18

We used tandem ion mobility spectrometry measurements to investigate how the photo-isomerization of a chromophore (a methylpyridinium derivative) is affected by the complexation with a crown ether. A ... [more ▼]

We used tandem ion mobility spectrometry measurements to investigate how the photo-isomerization of a chromophore (a methylpyridinium derivative) is affected by the complexation with a crown ether. A dramatic blue-shift of the photo-isomerization spectrum was observed upon complexation, which could be well reproduced by ab initio calculations. Our results support that the observed changes in the photo-physical properties of the chromophore originate from the charge-solvation of its pyridinium moiety by the host cage. [less ▲]

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See detailMyoferlin regulates cellular lipid metabolism and promotes metastases in triple-negative breast cancer
Blomme, Arnaud; Costanza, Brunella ULiege; De Tullio, Pascal ULiege et al

in Oncogene (2016)

Myoferlin is a multiple C2-domain-containing protein that regulates membrane repair, tyrosine kinase receptor function and endocytosis in myoblasts and endothelial cells. Recently it has been reported as ... [more ▼]

Myoferlin is a multiple C2-domain-containing protein that regulates membrane repair, tyrosine kinase receptor function and endocytosis in myoblasts and endothelial cells. Recently it has been reported as overexpressed in several cancers and shown to contribute to proliferation, migration and invasion of cancer cells. We have previously demonstrated that myoferlin regulates epidermal growth factor receptor activity in breast cancer. In the current study, we report a consistent overexpression of myoferlin in triple-negative breast cancer cells (TNBC) over cells originating from other breast cancer subtypes. Using a combination of proteomics, metabolomics and electron microscopy, we demonstrate that myoferlin depletion results in marked alteration of endosomal system and metabolism. Mechanistically, myoferlin depletion caused impaired vesicle traffic that led to a misbalance of saturated/unsaturated fatty acids. This provoked mitochondrial dysfunction in TNBC cells. As a consequence of the major metabolic stress, TNBC cells rapidly triggered AMP activated protein kinase-mediated metabolic reprogramming to glycolysis. This reduced their ability to balance between oxidative phosphorylation and glycolysis, rendering TNBC cells metabolically inflexible, and more sensitive to metabolic drug targeting in vitro. In line with this, our in vivo findings demonstrated a significantly reduced capacity of myoferlin-deficient TNBC cells to metastasise to lungs. The significance of this observation was further supported by clinical data, showing that TNBC patients whose tumors overexpress myoferlin have worst distant metastasis-free and overall survivals. This novel insight into myoferlin function establishes an important link between vesicle traffic, cancer metabolism and progression, offering new diagnostic and therapeutic concepts to develop treatments for TNBC patients. [less ▲]

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See detailAccurate drift time determination by traveling wave ion mobility spectrometry: The concept of the diffusion calibration
Kune, Christopher ULiege; Far, Johann ULiege; De Pauw, Edwin ULiege

Conference (2016, October 18)

Ion mobility spectrometry (IMS) is a gas phase separation technique which relies on differences in the collisional cross section (CCS) of ions. Ionic clouds of unresolved conformers overlapped if the CCS ... [more ▼]

Ion mobility spectrometry (IMS) is a gas phase separation technique which relies on differences in the collisional cross section (CCS) of ions. Ionic clouds of unresolved conformers overlapped if the CCS difference is below the instrumental resolution expressed as Ω/ΔΩ. The experimental arrival time distribution (ATD) peak is then a superimposition of the various contributions weighted by their relative intensities. We have developed a strategy for accurate drift time determination using traveling wave ion mobility spectrometry (TWIMS) of poorly and unresolved conformers. This method implements through a calibration procedure the link between the peak full width at half maximum (FWHM) and the drift time of model compounds for wide range of settings for wave heights and velocities. We modified a Gaussian equation which achieves the deconvolution of ATD peaks where the FWHM is fixed according to our calibration procedure. The new fitting Gaussian equation only depends on two parameters: The apex of the peak (A) and the mean drift time value (µ). The standard deviation parameter (correlated to FWHM) becomes a function of the drift time. This correlation function between µ and FWHM is obtained using the TWIMS calibration procedure which determines the maximum instrumental ion beam diffusion using ionic compounds which are detected as single conformers in the gas phase. This deconvolution process has been used to highlight the presence of poorly resolved conformers for couples of crown ethers and peptides leading to CCS determination in better agreement with quantum chemistry predictions. [less ▲]

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See detailThe concept of the diffusion calibration for accurate drift time measurement by traveling wave ion mobilty
Kune, Christopher ULiege; Far, Johann ULiege; De Pauw, Edwin ULiege

Poster (2016, October 13)

Ion mobility spectrometry (IMS) is a gas phase separation technique which relies on differences in the collisional cross section (CCS) of ions. Ionic clouds of unresolved conformers overlapped if the CCS ... [more ▼]

Ion mobility spectrometry (IMS) is a gas phase separation technique which relies on differences in the collisional cross section (CCS) of ions. Ionic clouds of unresolved conformers overlapped if the CCS difference is below the instrumental resolution expressed as Ω/ΔΩ. The experimental arrival time distribution (ATD) peak is then a superimposition of the various contributions weighted by their relative intensities. We have developed a strategy for accurate drift time determination using traveling wave ion mobility spectrometry (TWIMS) of poorly and unresolved conformers. This method implements through a calibration procedure the link between the peak full width at half maximum (FWHM) and the drift time of model compounds for wide range of settings for wave heights and velocities. We modified a Gaussian equation which achieves the deconvolution of ATD peaks where the FWHM is fixed according to our calibration procedure. The new fitting Gaussian equation only depends on two parameters: The apex of the peak (A) and the mean drift time value (µ). The standard deviation parameter (correlated to FWHM) becomes a function of the drift time. This correlation function between µ and FWHM is obtained using the TWIMS calibration procedure which determines the maximum instrumental ion beam diffusion using ionic compounds which are detected as single conformers in the gas phase. This deconvolution process has been used to highlight the presence of poorly resolved conformers for couples of crown ethers and peptides leading to CCS determination in better agreement with quantum chemistry predictions. [less ▲]

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See detailContribution of Cross-linking and Ion-mobility for the study of protein and complex structures
Baumans, France ULiege; Grifnée, Elodie ULiege; Hage, Christoph et al

Poster (2016, September 05)

The tridimensional structures of proteins and the mapping of protein-protein interactions are precious sources of information for the understanding of their function. Different techniques such as X-ray ... [more ▼]

The tridimensional structures of proteins and the mapping of protein-protein interactions are precious sources of information for the understanding of their function. Different techniques such as X-ray cristallography or nuclear magnetic resonance are usually used to achieve this goal. In the field of mass spectrometry, several tools were also developped. The one presented here is the chemical cross-linking in which two reactive residue side chains, spatially close, are linked thanks to a bifunctional chemical, called crosslinker. Ion-mobility coupled to mass spectrometry has also been investigated for the study of cross-linked products. The first results tend to show that cross-linkers allow to fix the shape of the protein in solution, leaving it intact when analysed in the gas phase. [less ▲]

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See detailDetecting organ-specific signals in Danio rerio by Mass Spectrometry Imaging
Tiquet, Mathieu ULiege; De Pauw, Edwin ULiege

Conference (2016, July 07)

The results shows the power of mass spectrometry imaging as an histological tool compared to classical manipulations.

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See detailPeptidoglycan fragments separation and identification by CE/LC-MS
Boulanger, Madeleine ULiege; Delvaux, Cédric ULiege; Far, Johann ULiege et al

Poster (2016, July 07)

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See detailMALDI-imaging guided microproteomics workflow for biomarker discovery of intra-tumor heterogeneity
Alberts, Deborah ULiege; Longuespée, Rémi ULiege; Smargiasso, Nicolas ULiege et al

Poster (2016, June 09)

Introduction A single tumoral tissue can bear phenotypically different cell populations. This phenomenon called intra-tumor heterogeneity can lead to differential behaviors regarding metastasis seeding ... [more ▼]

Introduction A single tumoral tissue can bear phenotypically different cell populations. This phenomenon called intra-tumor heterogeneity can lead to differential behaviors regarding metastasis seeding and therapy resistance [Zardavas et al., Nature Rev. Clin. Onc. 2015]. MALDI imaging has proven its efficiency for revealing hidden molecular features offering an insight into distinct cellular regions based on their molecular content. Further, proteomics applied to these regions could allow depicting the molecular context associated to particular cells groups and enable the collection of qualitative, quantitative and spatial information for each protein. Methods Breast cancer Formalin Fixed and Paraffin Embedded tissues, from patients whose outcome had been recorded over a period of 10 years, were provided by the department of Pathology of University of Liège. After Citric Acid Antigen Retrieval and trypsin digestion, images were obtained by MALDI-TOF/TOF-MS (Bruker, Germany). From the obtained datasets, segmentation and analytical data analysis were applied using SCiLS (Bruker, Germany) and the cloud software Multimaging (ImaBiotech, France). Small tissue areas were obtained by laser microdissection (LEICA LMD 700, Germany), upon which a combination of chemical processes was applied to ensure optimal protein antigen retrieval, extraction and digestion. Finally, the tissue pieces obtained were analyzed by LC-MS/MS using UPLC Waters Nanoacquity and Thermo Q-Exactive instruments. Preliminary data Based on mathematical calculations for the MALDI imaging datasets of the breast cancer FFPE tissues, Regions Of Interest (ROIs) were detected in a single tumor, revealing intra-tumoral heterogeneity, which can be correlated to the level of aggressiveness of the affliction and to the final prognosis of the patient. We aimed to compare the proteomic profiles of each of the small ROIs. Until today, proteomics applied to tissues composed by a restricted number of cells is quite tedious due to possible tissue losses during their handling. Recently, Longuespée [Longuespée et al., Methods 2015] published a method in order to retrieve the identification of 1400 proteins from microdissected tissue pieces containing only 2700 cells. This whole procedure allowed us to identify a panel of protein that characterizes tissue heterogeneity within a single tumor. This proves the applicability of the combination of MALDI imaging for the discovery of intra-tumoral heterogeneity without a priori, on a mathematical basis, and classical proteomics applied on laser-microdissected tissue samples of very restricted areas. This method will now be applied to several MALDI datasets in order to retrieve commune ROIs and to associate their presence with the information of each patient, such as their prognosis. Those ROIs will then be microdissected and subjected to microproteomic methods that will allow us to retrieve the extensive molecular context associated to bad patient prognosis and/or therapy resistance. The possibility to identify protein/peptide markers will have the power to predict the outcome of the breast cancer patient at the beginning of their treatment, and thus, improve the clinical care for the benefit of the patients. Novel aspect The workflow combines the unique advantages of MALDI imaging for de novo molecular features characterization and LMD-based microproteomics. [less ▲]

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See detailFirst Results Using TIMS on Systems Requiring High IMS Resolution
Haler, Jean ULiege; Massonnet, Philippe ULiege; Morsa, Denis ULiege et al

Conference (2016, June 05)

Detailed reference viewed: 29 (8 ULiège)