0000000001046046
AUTHOR
Patrick Ducoroy
showing 36 related works from this author
Salivary protein profiles and sensitivity to the bitter taste of caffeine.
2011
WOS: 000298381900008; International audience; The interindividual variation in the sensitivity to bitterness is attributed in part to genetic polymorphism at the taste receptor level, but other factors, such as saliva composition, might be involved. In order to investigate this, 2 groups of subjects (hyposensitive, hypersensitive) were selected from 29 healthy male volunteers based on their detection thresholds for caffeine, and their salivary proteome composition was compared. Abundance of 26 of the 255 spots detected on saliva electrophoretic patterns was significantly different between hypo- and hypersensitive subjects. Saliva of hypersensitive subjects contained higher levels of amylase…
Multi-omics profiling reveals that eating difficulties developed consecutively to artificial nutrition in the neonatal period are associated to speci…
2015
Prolonged enteral or parenteral nutrition in neonatal periods sometimes results in eating difficulties persisting for years, with reduced food intake through the oral route and thereby reduced stimulation of the oral cavity. Aiming at describing the consequences on oral physiology, saliva of 21 children with eating difficulties (ED) was compared to that of 23 healthy controls, using various omics and targeted methods. Overall, despite heterogeneity within the groups (age, medication etc.), the three spectral methods (MALDI-TOF, SELDI-TOF, (1)H NMR) allowed discriminating ED and controls, confirming that oral stimulation by food intake plays a role in shaping the composition of saliva. Saliv…
Inter-individual variability of protein patterns in saliva of healthy adults
2009
International audience; In order to document inter-individual variability in salivary protein patterns, unstimulated whole saliva was obtained from 12 subjects at 10 am and 3 pm of the same day. Saliva proteins were separated using two-dimensional gel electrophoresis, and semi-quantified using image analysis. One-way ANOVA was used to test the effects “time of sampling” and “subject”. Data were further explored by multivariate analyses (PCA, hierarchical clustering). Spots of interest were identified by mass spectrometry (MALDI-TOF MS/MS and nanoLC ESI-IT MS/MS). A dataset of 509 spots matched in all gels was obtained. There was no diurnal statistical effect on salivary patterns while inter…
Immuno-MALDI-MS in Human Plasma and on-Chip Biomarker Characterizations at the Femtomole Level
2012
Immuno-SPR-MS is the combination of immuno-sensors in biochip format with mass spectrometry. This association of instrumentation allows the detection and the quantification of proteins of interest by SPR and their molecular characterization by additional MS analysis. However, two major bottlenecks must be overcome for a wide diffusion of the SPR-MS analytical platform: (i) To warrant all the potentialities of MS, an enzymatic digestion step must be developed taking into account the spot formats on the biochip and (ii) the biological relevancy of such an analytical solution requires that biosensing must be performed in complex media. In this study, we developed a procedure for the detection …
Human infant saliva peptidome is modified with age and diet transition.
2012
Abstract In order to describe developmental changes in human salivary peptidome, whole saliva was obtained from 98 infants followed longitudinally at 3 and 6 months of age. Data on teeth eruption and diet at the age of 6 months were also recorded. Salivary peptide extracts were characterised by label-free MALDI-MS. Peptides differentially expressed between the two ages, and those significantly affected by teeth eruption or introduction of solid foods were identified by MALDI TOF–TOF and LC ESI MS–MS. Out of 81 peaks retained for statistical analysis, 26 were overexpressed at the age of 6 months. Exposure to solid foods had a more pronounced effect on profiles (overexpression of nine peaks) …
Optimization of the preanalytical steps of matrix-assisted laser desorption ionization-time of flight mass spectrometry identification provides a fle…
2012
ABSTRACT We report here that modifications of the preanalytical steps of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) identification of yeasts, with regard to the original protocol provided by the manufacturers, appear to be efficient for the reliable routine identification of clinical yeast isolates in medical laboratories. Indeed, when one colony was sampled instead of five and the protein extraction protocol was modified, the performance of MALDI-TOF MS was superior to that of the API ID 32C method (discrepancies were confirmed by using molecular identification), allowing the correct identification of 94% of the 335 clinical isolates prospec…
Structure of MHC class I and class II cDNAs and possible immunodeficiency linked to class II expression in the Mexican axolotl
1998
Despite the fact that the axolotl (Ambystoma spp. a urodele amphibian) displays a large T-cell repertoire and a reasonable B-cell repertoire, its humoral immune response is slow (60 days), non-anamnestic, with a unique IgM class. The cytotoxic immune response is slow as well (21 days) with poor mixed lymphocyte reaction stimulation. Therefore, this amphibian can be considered as immunodeficient. The reason for this subdued immune response could be an altered antigenic presentation by major histocompatibility complex (MHC) molecules. This article summarizes our work on axolotl MHC genes. Class I genes have been characterized and the cDNA sequences show a good conservation of non-polymorphic …
Identification of HSP90 as a new GABARAPL1 (GEC1)-interacting protein
2011
GABARAPL1 belongs to the small family of GABARAP proteins (including GABARAP, GABARAPL1 and GABARAPL2/GATE-16), one of the two subfamilies of the yeast Atg8 orthologue. GABARAPL1 is involved in the intracellular transport of receptors, via an interaction with tubulin and GABA(A) or kappa opioid receptors, and also participates in autophagy and cell proliferation. In the present study, we identify the HSP90 protein as a novel interaction partner for GABARAPL1 using GST pull-down, mass spectrometry and coimmunoprecipitation experiments. GABARAPL1 and HSP90 partially colocalize in MCF-7 breast cancer cells overexpressed Dsred-GABARAPL1 and in rat brain. Moreover, treatment of MCF-7 cells overe…
Characterization of the Breast Cancer Marker Candidate LAG3 Protein in Human Plasma by Direct SPRi-MALDI-MS Analysis from Antibody Arrays
2013
Proteomics plays an important role in biomarker discovery as prerequisite for later utilization. In this study, we coupled Surface Plasmon Resonance imaging (SPRi) with MALDI-TOF mass spectrometry to permit the multiplexed quantification of binding by SPRi and the molecular characterization of interacting partners by subsequent MS analysis. Hyphenation of the two technologies is applied to the detection and characterization of LAG3 (potential breast cancer biomarker) in human serum1.
Méthodes multivariées combinant ondelettes et analyse en composantes principales pour le débruitage de données issues de spectrométrie de masse
2010
International audience; L'identification de nouveaux biomarqueurs diagnostiques ou pronostiques est un des objectifs majeurs en recherche clinique. L'utilisation des technologies à haut débit comme la spectrométrie de masse est prometteuse pour l'identification de tels marqueurs. A partir d'un prélèvement de sang ou de tumeur par exemple, cette technologie permet de traduire sous forme de spectres le profil protéique des individus. Le signal biologique observé dans les spectres est masqué par différentes sources de variabilités techniques, qu'une phase préalable de prétraitement doit permettre de retirer. La méthode classique permettant de retirer le bruit aléatoire de mesure de ce signal c…
Associations between food consumption patterns and saliva composition: Specificities of eating difficulties children
2017
Identifying objective markers of dietwould be beneficial to research fields such as nutritional epidemiology. As a preliminary study on the validity of using saliva for this purpose, and in order to explore the relationship between saliva and diet, we focused on clearly contrasted groups of children: children with eating difficulties (ED) receiving at least 50% of their energy intake through artificial nutrition vs healthy controls (C). Saliva of ED and C children was analyzed by various methods (targeted biochemical analyses, 2-D electrophoresis coupled to MS, 1H NMR) and their diet was characterized using food frequency questionnaires, considering 148 food items grouped into 13 categories…
Multivariate denoising methods combining wavelets and principal component analysis for mass spectrometry data
2010
The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. In recent years, there has been a growing interest in using mass spectrometry for the detection of such biomarkers. The MS signal resulting from MALDI-TOF measurements is contaminated by different sources of technical variations that can be removed by a prior pre-processing step. In particular, denoising makes it possible to remove the random noise contained in the signal. Wavelet methodology associated with thresholding is usually used for this purpose. In this study, we adapted two multivariate denoising methods that combine wavelets and PCA to MS data. The objective was to o…
Influence of a Thiolate Chemical Layer on GaAs (100) Biofunctionalization: An Original Approach Coupling Atomic Force Microscopy and Mass Spectrometr…
2013
International audience; Widely used in microelectronics and optoelectronics; Gallium Arsenide (GaAs) is a III-V crystal with several interesting properties for microsystem and biosensor applications. Among these; its piezoelectric properties and the ability to directly biofunctionalize the bare surface, offer an opportunity to combine a highly sensitive transducer with a specific bio-interface; which are the two essential parts of a biosensor. To optimize the biorecognition part; it is necessary to control protein coverage and the binding affinity of the protein layer on the GaAs surface. In this paper; we investigate the potential of a specific chemical interface composed of thiolate molec…
Technological innovation around protein and cell biochip for diagnosis: a translational research from nanoworld to patient
2009
International audience; A great challenge in biosensors and diagnosis devices relies on the way to reconstitute relevant biological mechanisms on surface of the biochips and which analytical tools are convenient to provide accurate and rapid information on the structures and function of molecules attached to this surface. A better control in the realization of biochips can be obtained in combining different complementary approaches while always keeping in mind the biological key point. Researches in CLIPP are focused towards this objective. Conception, realization and characterization of protein and cell chips are presented. We detail different strategies of materials engineering1,2,3, chem…
Natural and induced apoptosis during lymphocyte development in the axolotl
1999
Lymphocytes apoptosis was characterized in a urodele amphibian, the axolotl, by morphology using electron microscopy and by flow cytometry after propidium iodide staining, as well as by biochemical criteria with the detection of DNA ladders after glucocorticoid treatment. The morphological and biochemical features observed in treated axolotls are in accordance with the criteria of apoptosis found in different models of mammalian lymphocyte programmed cell death. The onset of natural apoptosis was then detected by DNA fragmentation in thymus and in spleen during lymphocyte development and ontogenesis. A typical DNA ladder characteristic of apoptosis is detectable in the thymus as early as 5 …
Reconstitution of a protein monolayer on thiolates functionalized gaas surface
2012
International audience; In the aim to realize an efficient resonant biosensor, gallium arsenide (GaAs) presents many advantages. In addition to its properties of transduction, GaAs is a crystal for which microfabrication processes were developed, conferring the possibility to miniaturize the device and integrate electronic circuit. Moreover, the biofunctionalization could be realized on the crystalline surface without layer deposition, constituting a real advantage to perform reusable sensor. The functionalization of GaAs surface was engaged in order to immobilize a protein monolayer on this substrate. Functionalization was done using a mixed self assembled monolayer of thiolate molecules. …
Alpha-defensins secreted by dysplastic granulocytes inhibit the differentiation of monocytes in chronic myelomonocytic leukemia.
2010
Abstract Chronic myelomonocytic leukemia (CMML) is a clonal hematopoietic disorder that occurs in elderly patients. One of the main diagnostic criteria is the accumulation of heterogeneous monocytes in the peripheral blood. We further explored this cellular heterogeneity and observed that part of the leukemic clone in the peripheral blood was made of immature dysplastic granulocytes with a CD14−/CD24+ phenotype. The proteome profile of these cells is dramatically distinct from that of CD14+/CD24− monocytes from CMML patients or healthy donors. More specifically, CD14−/CD24+ CMML cells synthesize and secrete large amounts of alpha-defensin 1-3 (HNP1-3). Recombinant HNPs inhibit macrophage co…
Axolotl MHC architecture and polymorphism.
1999
The MHC of the urodele amphibian Ambystoma mexicanum consists of multiple polymorphic class I loci linked, so far as yet known, to a single class II B locus. This architecture is very different from that of the anuran amphibian Xenopus. The number of class I loci in the axolotl can vary from 6 to 21 according to the haplotypes as shown by cDNA analysis and Southern blot studies in families. These loci can be classified into seven sequence groups with features ranging from the class Ia to the class Ib type. All individuals express genes from at least three of the seven groups, and all individuals possess the class Ia-like type.
Toward the Identification of Two Glycoproteins Involved in the Stomatal Deregulation of Downy Mildew–Infected Grapevine Leaves
2015
SPE Pôle IPM UB; International audience; Stomata remain abnormally opened and unresponsive to abscisic acid in grapevine leaves infected by downy mildew. This deregulation occurs from 3 days post inoculation and increases concomitantly with leaf colonization by the pathogen. Using epidermal peels, we demonstrated that the active compound involved in this deregulation is located in the apoplast. Biochemical assays showed that the active compound present in the apoplastic fluids isolated from Plasmopara viticola infected grapevine leaves (IAF) is a CysCys bridge-independent, thermostable and glycosylated protein. Fractionation guided assays based on chromatography / stomatal response and prot…
Children with eating disorders secondarily to artificial nutrition in the neonatal period have specific food preferences and saliva composition
2016
- Objectives and studyIn the neonatal period, some severe digestive diseases require the cessation of oral feeding and the use of enteral or parenteral nutrition for prolonged periods. In some cases, this by-pass of the oral cavity during the early stages of feeding results in the development of so-called oral disorders (OD). Oral disorders may persist for years after healing of the causal disease, and are expressed for example by an exacerbated gag reflex, difficulties in chewing and swallowing and high food selectivity.The aim of this study were to describe the consequences on oral physiology of oral by-pass and enteral nutrition in a population of 21 children who suffered oral disorder (…
Comparison of classification methods that combine clinical data and high-dimensional mass spectrometry data
2013
Background The identification of new diagnostic or prognostic biomarkers is one of the main aims of clinical cancer research. Technologies like mass spectrometry are commonly being used in proteomic research. Mass spectrometry signals show the proteomic profiles of the individuals under study at a given time. These profiles correspond to the recording of a large number of proteins, much larger than the number of individuals. These variables come in addition to or to complete classical clinical variables. The objective of this study is to evaluate and compare the predictive ability of new and existing models combining mass spectrometry data and classical clinical variables. This study was co…
Glycated albumin with loss of fatty acid binding capacity contributes to enhanced arachidonate oxygenation and platelet hyperactivity: relevance in p…
2014
High plasma concentrations of nonesterified fatty acids (NEFAs), transported bound to serum albumin, are associated with type 2 diabetes (T2D). The effects of albumin on platelet function were investigated in vitro. Modifications of albumin, such as those due to glycoxidation, were found in patients with T2D, and the consequences of these modifications on biological mechanisms related to NEFA handling were investigated. Mass spectrometry profiles of albumin from patients with T2D differed from those from healthy control subjects. Diabetic albumin showed impaired NEFA binding capacity, and both structural and functional alterations could be reproduced in vitro by incubating native albumin wi…
A Multicentre Pilot Study of a Two-Tier Newborn Sickle Cell Disease Screening Procedure with a First Tier Based on a Fully Automated MALDI-TOF MS Pla…
2019
The reference methods used for sickle cell disease (SCD) screening usually include two analytical steps: a first tier for differentiating haemoglobin S (HbS) heterozygotes, HbS homozygotes and β-thalassemia from other samples, and a confirmatory second tier. Here, we evaluated a first-tier approach based on a fully automated matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platform with automated sample processing, a laboratory information management system and NeoSickle® software for automatic data interpretation. A total of 6701 samples (with high proportions of phenotypes homozygous (FS) or heterozygous (FAS) for the inherited genes for sickle h…
Specific enrichment of 2-arachidonoyl-lysophosphatidylcholine in carotid atheroma plaque from type 2 diabetic patients
2016
IF 3.942; International audience; Background and aims: Diabetic patients are at high risk of stroke and coronary artery disease. Recent data suggest that arachidonic acid metabolism is altered in diabetic conditions and that these alterations contribute to accelerated atherosclerosis. Little is known about how these alterations affect the metabolism and the proportions of different lipid species within the atherosclerotic plaque. The aim of our study was to perform a targeted lipidomic analysis of human atherosclerotic lesions, with a specific focus on PUFA-containing lipid species, to reveal differences in the fatty-acid composition of plaque in diabetic patients compared with non-diabetic…
VARIABLE SELECTION FOR NOISY DATA APPLIED IN PROTEOMICS
2014
International audience; The paper proposes a variable selection method for pro-teomics. It aims at selecting, among a set of proteins, those (named biomarkers) which enable to discriminate between two groups of individuals (healthy and pathological). To this end, data is available for a cohort of individuals: the biological state and a measurement of concentrations for a list of proteins. The proposed approach is based on a Bayesian hierarchical model for the dependencies between biological and instrumental variables. The optimal selection function minimizes the Bayesian risk, that is to say the selected set of variables maximizes the posterior probability. The two main contributions are: (…
Proteomic analysis of sub-retinal deposits in age-related macular degeneration
2014
National audience
Statistical Approach for Biomarker Discovery Using Label-Free LC-MS Data: An Overview
2016
The identification of new diagnostic, prognostic, or theranostics biomarkers is one of the main aims of clinical research. Technologies like mass spectrometry (MS) focus on the discovery of proteins as biomarkers and are commonly being used for this purpose. Mass spectrometry consists in the separation by gas of charged molecules, based on their mass-over-charge. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) first involves a separation by liquid chromatography (LC) followed by mass spectrometry in the MS and MS/MS modes.
Sensitivity to bitterness: may in-mouth proteolysis be involved?
2011
Sensitivity to bitterness: may in-mouth proteolysis be involved?. 9. Pangborn sensory science symposium
Symplekin, a polyadenylation factor, prevents MOZ and MLL activity on HOXA9 in hematopoietic cells
2013
International audience; MOZ and MLL encoding a histone acetyltransferase and a histone methyltransferase, respectively, are targets for recurrent chromosomal translocations found in acute myeloblastic or lymphoblastic leukemia. We have previously shown that MOZ and MLL cooperate to activate HOXA9 gene expression in hematopoietic stem/progenitors cells. To dissect the mechanism of action of this complex, we decided to identify new proteins interacting with MOZ. We found that the scaffold protein Symplekin that supports the assembly of polyadenylation machinery was identified by mass spectrometry. Symplekin interacts and co-localizes with both MOZ and MLL in immature hematopoietic cells. Its …
Revisited BIA-MS combination: Entire "on-a-chip" processing leading to the proteins identification at low femtomole to sub-femtomole levels
2008
International audience; We present the results of a study in which biomolecular interaction analysis (BIA, Biacore 2000) was combined with mass spectrometry (MS) using entire "on-a-chip" procedure. Most BIA-MS studies included an elution step of the analyte prior MS analysis. Here, we report a low-cost approach combining Biacore analysis with homemade chips and MS in situ identification onto the chips without elution step. First experiments have been made with rat serum albumin to determine the sensitivity and validation of the concept has been obtained with an antibody/antigen couple. Our "on-a-chip" procedure allowed complete analysis by MS-MS of the biochip leading to protein identificat…
Automated Cancer Marker Characterization in Human Plasma Using SUrface PLASMON Resonance in Array combined with Mass Spectrometry (SUPRA-MS)
2012
International audience; The combination of Surface Plasmon Resonance technology with Mass Spectrometry becomes a key method for the characterization of targeted proteins in the fields of diagnosis and functional proteomics. We demonstrated in this work the ability of our SPRi-chip to capture targeted protein in biological fluids and in situ analyze by MS and MS/MS modes through automated procedure to go beyond classical immunoassays. Here, we established a proof of concept of SUPRA-MS for the detection, the identification and the characterization of a potential breast cancer marker.
Saliva electrophoretic protein profiles in infants: changes with age and impact of teeth eruption and diet transition.
2011
International audience; Objective : The objective of this study was to describe the changes in salivary protein profiles in infants between the ages of 3 and 6 months, and to evaluate the impact of teeth eruption and introduction of solid foods on such profiles. Design : 73 infants were followed longitudinally at 3 and 6 months of age. Their whole saliva proteins were separated by SDS–PAGE electrophoresis and semi-quantified by image analysis. Amylase activity was also measured on a sub-sample of the population (n=42 infants). Bands which abundance was significantly different between the two ages according to paired comparisons were identified by mass spectrometry techniques. Results : Out …
Variance component analysis to assess protein quantification in biomarker discovery. Application to MALDI-TOF mass spectrometry.
2017
International audience; Controlling the technological variability on an analytical chain is critical for biomarker discovery. The sources of technological variability should be modeled, which calls for specific experimental design, signal processing, and statistical analysis. Furthermore, with unbalanced data, the various components of variability cannot be estimated with the sequential or adjusted sums of squares of usual software programs. We propose a novel approach to variance component analysis with application to the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) technology and use this approach for protein quantification by a classical signal processing algori…
Consequences of a high sugar/high fat maternal diet on protein expression in young rat submandibular glands
2015
Consequences of a high sugar/high fat maternal diet on protein expression in young rat submandibular glands. Congrès français de Spectrométrie de Masse et d'Analyse Protéomique (SMAP 2015)
Saliva peptidome and taste preferences in infants: preliminary tests
2007
Saliva peptidome and taste preferences in infants: preliminary tests. Congrès français de spectrométrie de masse et d'analyse protéomique (SMAP 2007)
Oral sphere: salivary markers and food. A prospective study on children expressing oral disorders
2014
National audience