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…

Prognostic value of Thyroid Transcription Factor-1 expression in lung adenocarcinoma in patients treated with anti PD-1/PD-L1.

2021

ABSTRACT Anti-PD1/PD-L1-directed immune checkpoint inhibitors are game changers in advanced non-small-cell lung cancer, but biomarkers are lacking. The aim of our study was to find clinically relevant biomarkers of the efficacy of ICI in non-squamous NSCLC. We conducted a retrospective study of patients receiving ICI for advanced non squamous NSCLC in two cohorts. For a subset of patients, RNAseq data were generated on tumor biopsy taken before ICI. The primary end point was progression-free survival under ICI. Secondary end point was overall survival from ICI initiation. In the cohort, we studied 231 patients. Clinico-pathological characteristics included KRAS mutant status (n = 88), TTF1-…

Blood baseline neutrophil count predicts bevacizumab efficacy in glioblastoma

2016

// Aurelie Bertaut 1 , Caroline Truntzer 2 , Rachid Madkouri 3 , Coureche Guillaume Kaderbhai 4 , Valentin Derangere 5 , Julie Vincent 4 , Bruno Chauffert 6 , Marie Helene Aubriot-Lorton 7 , Wahlid Farah 3 , Klaus Luc Mourier 3 , Romain Boidot 5,8 and Francois Ghiringhelli 4,5,8,9 1 Biostatistics unit Georges Francois Leclerc Cancer Center, Dijon, France 2 CLIPP, Research Center, University of Burgundy, Dijon, France 3 Department of Neurosurgery, CHU, Dijon, France 4 Department of Medical Oncology, Georges Francois Leclerc Cancer Center, Dijon, France 5 Platform of Transfer in Cancer Biology Genetic and histology, Georges Francois Leclerc Cancer Center, Dijon, France 6 Department of Medical…

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) …

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…

Tumour mutational burden as a biomarker for immunotherapy: Current data and emerging concepts

2020

International audience; Treatment with immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) or its ligand (PD-L1) can generate durable responses in various cancer types, but only in a subset of patients. The use of predictive biomarkers for response to PD-1/PD-L1 inhibitors is critical for patient selection. Expression of PD-L1 has demonstrated utility in patient selection. Tumour mutational burden (TMB) is an emerging biomarker for response to PD-1/PD-L1 inhibitors. The evaluation of this biomarker is based on the hypothesis that a high number of mutations in somatic exonic regions will lead to an increase in neoantigen production, which could then be recognised by…

Cholesterol trafficking and raft-like membrane domain composition mediate scavenger receptor class B type 1-dependent lipid sensing in intestinal epi…

2018

IF 5.547; International audience; Scavenger receptor Class B type 1 (SR-B1) is a lipid transporter and sensor. In intestinal epithelial cells, SR-B1-dependent lipid sensing is associated with SR-B1 recruitment in raft-like/ detergent-resistant membrane domains and interaction of its C-terminal transmembrane domain with plasma membrane cholesterol. To clarify the initiating events occurring during lipid sensing by SR-B1, we analyzed cholesterol trafficking and raft-like domain composition in intestinal epithelial cells expressing wild-type SR-B1 or the mutated form SR-B1-Q445A, defective in membrane cholesterol binding and signal initiation. These features of SR-B1 were found to influence bo…

Analyse des infiltrats immunitaires CD3 et CD8 chez 1280 malades atteints de cancers coliques de stade III : approche par intelligence artificielle e…

2019

L’etude retrospective de tumeurs par immunohistochimie constitue un enjeu majeur dans l’amelioration de la prise en charge atteints de pathologies cancereuses. Cependant l’analyse est chronophage pour le pathologiste et reste le plus souvent semi-quantitative pouvant entrainer une perte d’information. L’intelligence artificielle, qui consiste en une approche d’analyse automatisee a haut debit, pourrait permettre de s’affranchir dans ce contexte du pathologiste en apportant de plus une information quantitative. Nous avons ainsi etudie deux parametres immunitaires, CD3 et CD8 sur 1280 lames de malades de la cohorte PETACC8 [1] , une etude europeenne de patients atteints de cancers coliques de…

Interplays between nitric oxide and reactive oxygen species in cryptogein signalling

2014

The cellular messenger nitric oxide (NO) has many functions in plants. In this study, we investigated its interplays with Reactive Oxygen Species (ROS) in the defense responses triggered by the elicitin cryptogein produced by the oomycete Phytophthora cryptogea. The production of NO induced by cryptogein in tobacco cell suspensions was partly regulated through a ROS-dependent pathway involving the NADPH oxidase NtRBOHD. In turn, NO down-regulated the level of H2O2 derived from NtRBOHD activity. Both NO and ROS synthesis appeared to be under the control of two redundant isoforms of histone deacetylases of type 2 acting as negative regulators of cell death. Occurrence of an interplay between …

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…

Does large NGS panel analysed using exome tumour sequencing improve the management of advanced non-small-cell lung cancers?

2020

Abstract Introduction Non-small-cell lung cancer (NSCLC) is one of the most common and deadly cancers. Several molecular drivers of oncogene addiction are now known to be strong predictive biomarkers for target therapies. Advances in large Next Generation Sequencing (LNGS) have improved the ability to detect potentially targetable mutations. However, the integration of LNGS into clinical management in an individualized manner remains challenging. Methods In this single-center observational study we included all patients with advanced NSCLC who underwent LNGS. Somatic and germline exome analysis was performed with a restriction on 323 cancer related genes. Variants were classified and Molecu…

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…

Genetic diversity and trait genomic prediction in a pea diversity panel

2014

Background Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. Resu…

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.

Evaluation of tumor immune contexture among intrinsic molecular subtypes helps to predict outcome in early breast cancer

2021

BackgroundThe prognosis of early breast cancer is linked to clinic-pathological stage and the molecular characteristics of intrinsic tumor cells. In some patients, the amount and quality of tumor-infiltrating immune cells appear to affect long term outcome. We aimed to propose a new tool to estimate immune infiltrate, and link these factors to patient prognosis according to breast cancer molecular subtypes.MethodsWe performed in silico analyses in more than 2800 early breast cancer transcriptomes with corresponding clinical annotations. We first developed a new gene expression deconvolution algorithm that accurately estimates the quantity of immune cell populations (tumor immune contexture,…

Effects of tumor mutation burden on the antigen presentation pathway

2021

AbstractTumor mutation burden (TMB) is used to select patients to receive immune checkpoint inhibitors (ICIs) but has mixed predictive capabilities. We hypothesized that inactivation of antigen presenting genes (APGs) that result from increased TMBs would result in inherent resistance to ICIs. We observed that somatic mutations in APGs were associated with increasing TMBs across 9,418 tumor samples of 33 different histological subtypes. In adenocarcinomas of the lung, ITGAX and CD1B were some of the most commonly mutated APGs. In 62 patients with non-small cell lung cancers treated with a PD-1 inhibitor in second or later lines of therapy, there was an association of increased TMB with muta…

Mixed-model of ANOVA for measurement reproducibility in proteomics

2009

This work is a statistical analysis of reproducibility of a MALDI-TOF mass spectrometry experiment. Its aim is to evaluate measurement variability and compare peak intensities from two types of MALDI-TOF platforms. We compared and commented on the abilities of Principal Component Analysis and mixed-model analysis of variance to evaluate the biological variability and the technical variability of peak intensities in different patients. The properties and hypotheses of both methods are summarized and applied to spectra from plasma of patients with Hodgkin lymphoma. Principal Component Analysis checks rapidly the balance between the two variabilities; however, a mixed-model analysis of varianc…

Seroprevalence of SARs-CoV-2 among the staff and patients of a French cancer centre after first lockdown: the canSEROcov study

2021

Abstract Background In view of the potential gravity of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection for patients with cancer, epidemiological data are vital to assess virus circulation among patients and staff of cancer centres. We performed a prospective study to investigate seroprevalence of SARS-CoV-2 antibodies among staff and patients with cancer at a large cancer centre, at the end of the period of first national lockdown in France and to determine factors associated with the risk of SARS-CoV-2 infection. Methods After the first lockdown, all medical and non-medical staff, as well as all patients attending the medical oncology department were invited to unde…

TCR Clonality and Genomic Instability Signatures as Prognostic Biomarkers in High Grade Serous Ovarian Cancer.

2021

Simple Summary High-grade serous ovarian carcinoma (HGSC) could be analyzed with a molecular stratification defined by different genomic instability signatures associated with specific mutational process and prognostic biomarkers. Immune infiltrate is known to be a robust biomarker in HGSC. We aimed to investigate immune parameters according to genomic instability signatures. We observed that homologous recombination deficiency positive, copy cumber variant signature 7 and TCR (T cells receptor) clonality are good prognostic biomarkers in HGSC. Combining TCR clonality and genomic instability signature or T cell infiltration improved the prognostic value compared to each variable taken alone…

Exome Analysis Reveals Genomic Markers Associated with Better Efficacy of Nivolumab in Lung Cancer Patients

2019

Abstract Purpose: Immune checkpoint inhibitors revolutionized the treatment of non-small cell lung cancer (NSCLC). However, only one-quarter of patients benefit from these new therapies. PD-L1 assessment and tumor mutational burden (TMB) are available tools to optimize use of checkpoint inhibitors but novel tools are needed. Exome sequencing could generate many variables but their role in identifying predictors of response is unknown. Experimental Design: We performed somatic and constitutional exome analyses for 77 patients with NSCLC treated with nivolumab. We studied: one-tumor-related characteristics: aneuploidy, CNA clonality, mutational signatures, TMB, mutations in WNT, AKT, MAPK, an…

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…

[Thu-P1-056] Is taste linked to oral microbiota?

2022

Taste perception varies strongly between individuals but the factors at the origin of this variability are not fully understood. For example, different events occurring at the vicinity of the taste receptors on the tongue can modulate taste perception. Our group has recently suggested that the microbiota at the surface of the tongue could be involved by controlling the taste compounds concentration in the lingual film (the biological material covering the tongue). The aim of this work is to evaluate the contribution of the oral microbiota to taste. To do this, taste sensitivity (5 basic tastes) was determined in 100 healthy adult subjects and the microbiota of their lingual film and saliva …

Oral sphere: salivary markers and food. A prospective study on children expressing oral disorders

2014

National audience

Is oral microbiota implicated in taste? A shotgun metagenomics approach

2023

Pea in the genomic era

2015

Pea in the genomic era. Séminaire IFR AIB (Agrobiosciences, Interactions & Biodiversité)

Is oral microbiota linked to taste perception in human?

2022