References of "Baiwir, Dominique"
     in
Bookmark and Share    
Peer Reviewed
See detailProteomic differential distribution of 53BP1 in serrated and conventional adenomas validated by histological characterisation
QUESADA-CALVO, Florence ULg; Merli, Angela-Maria ULg; MASSOT, Charlotte ULg et al

Poster (2017, February 10)

INTRODUCTION: Sessile serrated adenoma/polyp (SSA/p) is a precancerous lesion, mostly located in the right side of the colon (cecum, ascending and transverse colon). The difficulty is to visualize this ... [more ▼]

INTRODUCTION: Sessile serrated adenoma/polyp (SSA/p) is a precancerous lesion, mostly located in the right side of the colon (cecum, ascending and transverse colon). The difficulty is to visualize this lesion during colonoscopy because of its subtle appearance. MATERIAL AND METHOD: We compared proteomes of serrated polyps (SSA/p) and conventional adenomas using residual human formalin fixed paraffin embedded (FFPE) samples. FFPE-FASP method was applied on samples before label free proteomic analysis. Immunohistochemistry (IHC) characterisation of one candidate marker was performed for tissue validation on an independent set of samples including: conventional adenomas (low and high-grade dysplasia), serrated polyps (hyperplastic polyps, SSA/p and traditional serrated adenoma) and finally normal colon (taken at the margin of colorectal cancer (CRC) or of diverticular disease). RESULTS: Proteomics provided 765 proteins (out of 5992 proteins identified) significantly discriminating conventional adenomas from serrated lesions. We selected 53BP1 (Tumor suppressor p53-binding protein 1) among these for IHC validation, because of its tumor suppressor gene function and role as a mediator of DNA damage checkpoint. 53BP1 appeared significantly up-regulated in proteomes of low and high grade adenomas compared to these of normal tissue and SSA/p. 53BP1 IHC signal was located in the nucleus and the percentage of positive nucleus decreased in serrated polyps, especially in crypts and in the border epithelium, confirming part of the proteomic results. CONCLUSION: This study highlights potential marker proteins, including 53BP1 from which IHC signal was strongly decreased in some serrated polyps. The loss of 53BP1 has been associated with tumour progression and poor prognosis, while little is currently known about its involvement in precancerous CRC lesions. 53BP1 decrease of expression in the nucleus and therefore possible loss of function in some epithelial cells could reflect important changes occurring during dysplasia to neoplasia progression in serrated lesions. [less ▲]

Detailed reference viewed: 32 (6 ULg)
Full Text
Peer Reviewed
See detailIdentification of proteins discriminating inflammation induced dysplasia from simple inflammation in ulcerative colitis by laser capture microdissection and label free proteomics – a pilot study
Merli, Angela-Maria ULg; QUESADA-CALVO, Florence ULg; MASSOT, Charlotte ULg et al

Conference (2017, February 09)

Chronic colonic inflammation in ulcerative colitis (UC) may induce dysplasia, which can itself progress and transform into neoplasia. Diagnosis of dysplasia in UC remains difficult particularly when ... [more ▼]

Chronic colonic inflammation in ulcerative colitis (UC) may induce dysplasia, which can itself progress and transform into neoplasia. Diagnosis of dysplasia in UC remains difficult particularly when tissue inflammation is present. The aim of this retrospective pilot study was to highlight proteins specifically associated with inflammation induced dysplasia in UC. We performed a pilot experiment on 15 Formalin-Fixed, Paraffin-Embedded (FFPE) samples isolated from 5 cases of UC patients with a Polypoïd Pedunculated dysplasia (UC-PP). We compared the proteomes of the UC-PP, the inflammatory (UC-I) and the normal (UC-NL) tissues of each patient. We performed Laser Capture Microdissection (LCM) in order to collect only epithelial cells, avoiding inflammatory infiltrating ones. Label free proteomic analysis using a 2D-nanoUPLC coupled with a hybrid Quadrupole-Orbitrap was applied, as well as differential analysis on the paired samples. Immunohistochemistry (IHC) characterisation of one of the selected proteins of interest was used for validation. Out of 985 quantified proteins, 7 were found significantly more abundant in UC-PP compared to UC-I tissues, with 6 being only detected in UC-PP using proteomics. One of these is Solute Carrier Family 12 member 2 (SLC12A2), also known as Na-K-2Cl co-transporter 1 (NKCC1), a protein involved in ionic balance, in T-cell migration promotion and in some features involved in cancer development like proliferation, migration or invasion. IHC results obtained were in correlation with proteomic results and showed that SLC12A2 was more abundant in UC-PP tissue than in UC-I and UC-NL tissues, with a signal clearly delimiting the dysplastic region from the surrounding inflammatory tissue. This pilot experiment shows a different proteomic profile in inflammation-associated dysplasia and simple inflammation. This should be replicated using other types of dysplasia in IBD. SLC12A2 could be a potential biomarker of inflammation-associated dysplasia. [less ▲]

Detailed reference viewed: 28 (11 ULg)
Full Text
Peer Reviewed
See detailIdentification of proteins discriminating inflammation induced dysplasia from simple inflammation in ulcerative colitis by laser capture microdissection and label free proteomics – a pilot study
Merli, Angela-Maria ULg; QUESADA-CALVO, Florence ULg; MASSOT, Charlotte ULg et al

Poster (2017, February 01)

Chronic colonic inflammation in ulcerative colitis (UC) may induce dysplasia, which can itself progress and transform into neoplasia. Diagnosis of dysplasia in UC remains difficult particularly when ... [more ▼]

Chronic colonic inflammation in ulcerative colitis (UC) may induce dysplasia, which can itself progress and transform into neoplasia. Diagnosis of dysplasia in UC remains difficult particularly when tissue inflammation is present. The aim of this retrospective pilot study was to highlight proteins specifically associated with inflammation induced dysplasia in UC. We performed a pilot experiment on 15 Formalin-Fixed, Paraffin-Embedded (FFPE) samples isolated from 5 cases of UC patients with a Polypoïd Pedunculated dysplasia (UC-PP). We compared the proteomes of the UC-PP, the inflammatory (UC-I) and the normal (UC-NL) tissues of each patient. We performed Laser Capture Microdissection (LCM) in order to collect only epithelial cells, avoiding inflammatory infiltrating ones. Label free proteomic analysis using a 2D-nanoUPLC coupled with a hybrid Quadrupole-Orbitrap was applied, as well as differential analysis on the paired samples. Immunohistochemistry (IHC) characterisation of one of the selected proteins of interest was used for validation. Out of 985 quantified proteins, 7 were found significantly more abundant in UC-PP compared to UC-I tissues, with 6 being only detected in UC-PP using proteomics. One of these is Solute Carrier Family 12 member 2 (SLC12A2), also known as Na-K-2Cl co-transporter 1 (NKCC1), a protein involved in ionic balance, in T-cell migration promotion and in some features involved in cancer development like proliferation, migration or invasion. IHC results obtained were in correlation with proteomic results and showed that SLC12A2 was more abundant in UC-PP tissue than in UC-I and UC-NL tissues, with a signal clearly delimiting the dysplastic region from the surrounding inflammatory tissue. This pilot experiment shows a different proteomic profile in inflammation-associated dysplasia and simple inflammation. This should be replicated using other types of dysplasia in IBD. SLC12A2 could be a potential biomarker of inflammation-associated dysplasia. [less ▲]

Detailed reference viewed: 28 (4 ULg)
Full Text
Peer Reviewed
See detailEcotoxicoproteomic assessment of the functional alterations caused by chronic metallic exposures in gammarids
Gismondi, Eric ULg; Thomé, Jean-Pierre ULg; 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 ▲]

Detailed reference viewed: 14 (4 ULg)
Full Text
Peer Reviewed
See detailProteomic signatures reveal a dualistic and clinically relevant classification of anal canal carcinoma
Herfs, Michael ULg; Longuespée, Rémi ULg; Quick, Charles et al

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

Detailed reference viewed: 23 (3 ULg)
Full Text
Peer Reviewed
See detailMyoferlin is a novel exosomal protein and functional regulator of cancer-derived exosomes
Blomme, Arnaud; Fahmy, Karim; Peulen, Olivier ULg 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 ▲]

Detailed reference viewed: 46 (12 ULg)
Full Text
Peer Reviewed
See detailMALDI-imaging guided microproteomics workflow for biomarker discovery of intra-tumor heterogeneity
Alberts, Deborah ULg; Longuespée, Rémi ULg; Smargiasso, Nicolas ULg 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 ▲]

Detailed reference viewed: 65 (5 ULg)
Full Text
Peer Reviewed
See detailAnalysis of the Structure and Function of FOX-4 Cephamycinase
Lefurgy, S.T.; Malashkevich, V.N.; Aguilan, J.T. et al

in Antimicrobial Agents and Chemotherapy (2016), 60(2), 717-728

Class C β-lactamases poorly hydrolyze cephamycins (e.g., cefoxitin, cefotetan, and moxalactam). In the past 2 decades, a new family of plasmid-based AmpC β-lactamases conferring resistance to cefoxitin ... [more ▼]

Class C β-lactamases poorly hydrolyze cephamycins (e.g., cefoxitin, cefotetan, and moxalactam). In the past 2 decades, a new family of plasmid-based AmpC β-lactamases conferring resistance to cefoxitin, the FOX family, has grown to include nine unique members descended from the Aeromonas caviae chromosomal AmpC. To understand the basis for the unique cephamycinase activity in the FOX family, we determined the first X-ray crystal structures of FOX-4, apo enzyme and the acyl-enzyme with its namesake compound, cefoxitin, using the Y150F deacylation-deficient variant. Notably, recombinant expression of N-terminally tagged FOX-4 also yielded an inactive adenylylated enzyme form not previously observed in β-lactamases. The posttranslational modification (PTM), which occurs on the active site Ser64, would not seem to provide a selective advantage, yet might present an opportunity for the design of novel antibacterial drugs. Substantial ligand-induced changes in the enzyme are seen in the acyl-enzyme complex, particularly the R2 loop and helix H10 (P289 to N297), with movement of F293 by 10.3 Å. Taken together, this study provides the first picture of this highly proficient class C cephamycinase, uncovers a novel PTM, and suggests a possible cephamycin resistance mechanism involving repositioning of the substrate due to the presence of S153P, N289P, and N346I substitutions in the ligand binding pocket. [less ▲]

Detailed reference viewed: 22 (3 ULg)
Full Text
Peer Reviewed
See detailDe novo sequencing using MELD proteolysis coupled to a "sequence assembly" algorithm
Mazzucchelli, Gabriel ULg; Zimmerman, Tyler A; Smargiasso, Nicolas ULg et al

Poster (2016, January 22)

Detailed reference viewed: 44 (4 ULg)
Full Text
Peer Reviewed
See detailEffet inflammatoire des extraits de Cupressus sempervirens planté dans l’Est de l’Algérie : du modèle murin à la stimulation des cellules BEAS-2B par l’allergène majeur Cup s 1
Bouguenoun, Imene; De Pauw-Gillet, Marie-Claire ULg; Bensakhri, Z et al

in Revue Française d'Allergologie (2016), 56

Cupressus sempervirens est l’une des espèces les plus répandues en Algérie ayant une capacité allergénique très élevée. Nous avons étudié,d’abord, comment l’instillation nasale des différentes fractions ... [more ▼]

Cupressus sempervirens est l’une des espèces les plus répandues en Algérie ayant une capacité allergénique très élevée. Nous avons étudié,d’abord, comment l’instillation nasale des différentes fractions de l’extrait pollinique de cette espèce peut moduler la réponse immunitaire chez les souris, et, ensuite, la stimulation des cellules épithéliales bronchiques humaines (BEAS-2B) par l’allergène majeur, identifié par spectrométrie de masse et purifié par chromatographie échangeuse d’ions. La sensibilisation des souris a révélé, d’une part, une diminution du nombre de neutrophiles et une augmentation des éosinophiles, et, d’autre part, une augmentation significative du total cellulaire dans le liquide du lavage bronchoalvéolaire.L’étude histologique des poumons a montré une présence d’infiltrat inflammatoire et d’oedème péri-bronchique. La spectrométrie de masse nous a permis de mettre en évidence la présence de l’allergène majeur Cup s 1 dans toutes les fractions avec une présence spécifique du Cup s 3 et Cupa 1 dans la fraction 4. Cet allergène avait le potentiel pour stimuler la libération de l’IL-8 et l’IL-6 par la ligné cellulaire, BEAS-2B, in vitro d’une manière dose-dépendante [less ▲]

Detailed reference viewed: 43 (4 ULg)
Full Text
Peer Reviewed
See detailComparison of serum fractionation methods by data independent label-free proteomics
Baiwir, Dominique ULg; Mazzucchelli, Gabriel ULg; Smargiasso, Nicolas ULg et al

in EuPA Open Proteomics (2015), 9

Off-line sample prefractionations applied prior to biomarker discovery proteomics are options to enable more protein identifications and detect low-abundance proteins. This work compared five commercial ... [more ▼]

Off-line sample prefractionations applied prior to biomarker discovery proteomics are options to enable more protein identifications and detect low-abundance proteins. This work compared five commercial methods efficiency to raw serum analysis using label-free proteomics. The variability of the protein quantities determined for each process was similar to the unprefractionated serum. A 49% increase in protein identifications and 12.2% of reliable quantification were obtained. A 61 times lower limit of protein quantitation was reached compared to protein concentrations observed in raw serum. The concentrations of detected proteins were confronted to estimated reference values. [less ▲]

Detailed reference viewed: 111 (15 ULg)