Expertise

Hub members Have many expertise, covering most of the fields in bioinformatics and biostatistics. You'll find below a non-exhaustive list of these expertise

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Searched keyword : Human

Related people (10)

Pascal CAMPAGNE

Group : Stats - Hub Core

Initially trained in evolutionary and environmental sciences, I studied population genetics and micro-evolutionary processes in a number of postdoctoral research projects. I recently joined the C3BI-Hub at the Institut Pasteur, where I work on various aspects involving Biostatistics and the analysis of genetic data.


Keywords
Association studiesGenomicsGenotypingBiostatisticsGeneticsEvolutionPopulation genetics
Organisms
BacteriaParasiteHumanInsect or arthropodOther animal
Projects (23)

Etienne KORNOBIS

Group : PLATEFORM - Detached : Epigenetic regulation

After a PhD in Biology in 2011 on population genetics and phylogeography on amazing little amphipods (Crangonyx, Crymostygius) at the University of Reykjavik (Iceland), I pursued my interest in Bioinformatics and Evolutionary Biology in various post-docs in Spain (MNCN Madrid, UB Barcelona). During this time, I investigated transcriptomic landscapes for various non-model species (groups Conus, Junco and Caecilians) using de novo assemblies and participated in the development of TRUFA, a web platform for de novo RNA-seq analysis. In July 2016, I integrated the Revive Consortium and the Epigenetic Regulation unit at Pasteur Institute, where my main focus were transcriptomic and epigenetic analyses on various thematics using short and long reads technologies, with a special interest in alternative splicing events detection. I joined the Bioinformatics and Biostatistics Hub in January 2018. My latest interests are long reads technologies, alternative splicing and achieving reproducibility in Bioinformatics using workflow managers, container technologies and literate programming.


Keywords
Data managementData VisualizationSequence analysisTranscriptomicsWeb developmentGenome analysisProgram developmentExploratory data analysisSofware development and engineeringGeneticsEvolutionRead mappingWorkflow and pipeline developmentPopulation geneticsMotifs and patterns detectionGrid and cloud computing
Organisms
HumanInsect or arthropodOther animalAnopheles gambiae (African malaria mosquito)Mouse
Projects (3)

Rachel LEGENDRE

Group : GORE - Hub Core

Rachel Legendre is a bioinformatics engineer. She completed her master degree in apprenticeship for two years at INRA in Jouy-en-Josas in the Genetic Animal department. She was involved in a project aiming at the detection and the expression analysis of micro-RNA involved in an equine disease. In 2012, she joined the Genomic, Structure and Translation Team at Paris-Sud (Paris XI) university. She worked principally on Ribosome Profiling data analysis, a new technique that allows to identify the position of the ribosome on the mRNA at the nucleotide level. Since november 2015, she worked at Institut Pasteur. During 4 years, she was detached to the Biomics Platform, where she was in charge of the bioinformatics analyses for transcriptomics and epigenomics projects. She was also involved in Long Reads (PacBio and Nanopore) developments with other bioinformaticians of Biomics. Since november 2019, she has joined the Hub of Bioinformatics and Biostatistics, et more precisely the Genome Organization Regulation and Expression group.


Keywords
AlgorithmicsChIP-seqEpigenomicsNon coding RNATranscriptomicsGenome analysisProgram developmentScientific computingSofware development and engineeringIllumina HiSeqRead mappingSequencingWorkflow and pipeline developmentChromatin accessibility assaysPac BioRibosome profiling
Organisms
BacteriaFungiParasiteHumanInsect or arthropodOther animal
Projects (24)

Christophe MALABAT

Group : HEAD - Hub Core

After a PhD in biochemistry of the rapeseed proteins, during which I developed my first automated scripts for handling data processing and analysis, I join Danone research facility center for developing multivariate models for the prediction of milk protein composition using infrared spectrometry.
As I was already developing my own informatics tools, I decided to join the course of informatic for biology of the Institut Pasteur in 2007. At the end of the course I was recruited by the Institute and integrate the unit of “génétique des interactions macromoléculaires” of Alain Jacquier. Within this group, I learn to handle sequencing data and I developed processing and analysis tools using python and R. I also create a genome browser and database system for storing, retrieving and visualizing microarray data. After 8 years within the Alain Jacquier’s lab, I join the Hub of bioinformatics and biostatistics as co-head of the team.


Keywords
ClusteringData managementSequence analysisTranscriptomicsWeb developmentDatabaseGenome analysisProgram developmentScientific computingExploratory data analysisData and text miningIllumina HiSeqRead mappingLIMSIllumina MiSeqHigh Throughput ScreeningMultidimensional data analysisWorkflow and pipeline developmentRibosome profilingMotifs and patterns detection
Organisms

Projects (10)

Violaine SAINT-ANDRÉ

Group : DETACHED - Detached : Labex milieu intérieur

After graduating from Paris VI University with a PhD in Genetics on the “Role of histone protein post-translational modifications in splicing regulation” that I performed in the Epigenetic Regulation unit at the Institut Pasteur, I carried out two post-doctoral experiences. I first worked for three years as a postdoctoral associate of the Whitehead Institute for Biomedical Research/MIT in Cambridge (USA). My main project consisted in the integration of genomic and epigenomic data in order to predict the transcription factors that are potentially at the core of the regulation of the cell-type specific gene expression programs. I then joined the Institut Curie where I deepened my experience in multi-omics data analyses and integration to identify non-coding RNAs involved in cancer progression. I have recently joined the HUB-C3BI of the Institut Pasteur where I am performing high-throughput data integration to better understand biological complexity and contribute to precision medicine development.


Keywords
ATAC-seqChIP-seqEpigenomicsNon coding RNAPathway AnalysisRNA-seqSingle CellSystems BiologyTool DevelopmentTranscriptomicsData integrationGraph theory and analysisCell biology and developmental biology
Organisms
Human
Projects (1)

Vincent LAVILLE


NA


Keywords
Biostatistics
Organisms
Human
Projects (0)

    Maguelonne ROUX


    to complete


    Keywords
    Comparative Genomics
    Organisms
    Human
    Projects (0)

      Nicolas TRAUT


      Neuroanatomie Appliquée et Théorique


      Keywords

      Organisms
      Human
      Projects (0)

        Related projects (131)

        Mapping the cell surface signature of the developing mouse heart

        Cell surface protein signatures have been successful to discriminate hematopoietic progenitor populations allowing major advances in understanding blood cell production, to define pathways in hematologic malignancies and to foster new therapeutic approaches. Limited knowledge on the phenotype of cells that participate in heart formation impairs our understanding of progenitors of the cardiac cell lineages and their eventual persistence in the adult organ. As a consequence, therapies to restore heart function after injury have been unsuccessful. A number of membrane proteins have been identified on cardiomyocytes; on cardiac fibroblasts; and on endothelial cells, however a multi-parametric analysis of the phenotype of the different cardiac cell compartments along development is still missing. We combined multi-parametric flow cytometry with transcriptional characterization, based on well-known gene expression patterns, to describe major cardiac cell-subsets. The expression of CD24, CD54, Sca-1 and CD90 allowed defining cardiac populations in the non-hematopoietic and non-endothelial cell fraction by flow cytometry. Transcriptional profiling of the sorted populations enabled the identification of cardiomyocytes, in the CD24+ population, while differential expression of CD54, Sca-1 and CD90 defined four cardiac stromal compartments. The identified subsets exhibited specific distributions in three analyzed regions (atria, auriculo-ventricular junction and ventricles). We have thus identified a panel of surface markers, some of which novel in the cardiac context, that allowed assigning surface signatures to different cellular fractions by their unique transcriptional profiles. This work is the foundation for comprehensive studies on the role of different cell fractions by their unique transcriptional profiles.



        Project status : Closed

        Characterisation of skeletal muscle stem cell properties in distinct physiological states

        Stem cells are defined by their is their capacity for self-renewal and differentiation. Some adult tissues maintain a reservoir of stem cells, that generally reside within specialized microenvironments, known as stem cell niches, that regulate their behaviour. Skeletal muscle stem (satellite) cells are quiescent in homeostatic conditions in adults, and they are activated after muscle injury, when they re-enter the cell cycle, proliferate and differentiate into myoblasts, which will then fuse to form new muscle fibers. Satellite cells express the paired/homeodomain gene Pax7, which plays a critical role in satellite cell maintenance postnatally. Numerous experiments have shown that the skeletal muscle stem cell population is heterogeneous, therefore like many other stem cell systems, characterising the stem cell states is a major objective. In our laboratory, a reversible dormant cell state was identified, correspondent to a Pax7Hi quiescent subpopulation (top 10% of the Pax7-nGFP+ cells isolated from the transgenic mouse model Tg:Pax7-nGFP) with a lower metabolic activity and longer lag for the first cell division compared to Pax7Lo cells [1]. Muscle stem cells that survive for extended periods post-mortem are also dormant, suggesting that this property, in addition to anoxia [2] contributes to their viability. Therefore, different physiological states are associated with distinct cell states of muscle stem cells. Metabolism could play a critical role in dictating whether a cell remains quiescent, proliferates or differentiates. Stem cell metabolic plasticity in homeostasis and differentiation, as well as during cell reprogramming, is well described in different cell systems. However, unanswered questions remain regarding the metabolic regulation of satellite cell biology and skeletal muscle regeneration. In this project, we will investigate the behaviour of muscle stem cells in distinct physiological states, especially post-mortem and aging.



        Project status : Closed

        Mise a disposition d'un(e) bioinformaticien(ne) du hub pour les analyses bioinformatiques du transcriptome et de l epigenome

        La PF Transcriptome et Epigenome développe des projets de séquençage à haut débit (collaboration et service) avec des équipes du Campus. Ceux-ci couvrent l'ensemble des thématiques du campus ainsi qu'une large gamme d'organismes (des virus aux mammifères). La plate-forme exerce des activités de biologie humide (construction des librairies et séquençage) et de biologie sèche (analyse bioinformatiques et statistiques). La personne mise a disposition interagira étroitement avec les autres bioinformaticiens du pôle BioMics et du Hub. Ses activités concerneront notamment: - La participation à la conception et à la mise en place des projets avec les équipes demandeuses, la prise en charge des analyses et le reporting aux utilisateurs - La mise en place d'un workflow d'analyse bioinformatique des données de transcriptome /épigénome en étroite collaboration avec le C3BI, la DSI et les autres bioinformaticiens du pole. Ce workflow permettra le contrôle qualité des données, leur prétraitement, le mapping des séquences sur les génomes/transcriptomes de réference, et le comptage des reads pour les différents éléments de l'annotation - L'adaptation du workflow d'analyse aux questions biologiques et aux organismes étudiés dans le cadre des activités de la PF - L'activité de veille technologique et bibliographique (test et validation de nouveaux outils d'analyse, updates d'outils existants...) - La mise en place et le développement d'outils d'analyse adaptés aux futurs projets de la PF: single cell RNAseq, métatranscriptome, ChIPseq, analyse des isoformes de splicing.. Ceci se fera notamment via la réalisation d'analyses dédiées avec certains utilisateurs. Les outils mis en place et validés dans ce cadre seront ensuite utilisés pour l'ensemble des projets. - L'activité de communication et de formation (participation aux réunions du consortium France Génomique,formation permanente à l' Institut Pasteur… - la participation a d autres projets du Pole BioMics (selon disponibilité) Bernd Jagla, qui était le bioinformaticien de la plateforme a rejoint le Hub au 1er janvier 2016. Rachel Legendre est mise a disposition depuis le 2 novembre 2015 et remplace Bernd Jagla. Je souhaite que Rachel Legendre soit mise à disposition de la plateforme pour une durée d'au moins 2 ans.



        Project status : Closed

        A long-term mission for an assigned CIH-embedded bioinformatician to provide bioinformatic support to the CIH community

        The Center for Human Immunology (CIH) supports researchers involved in translational research projects by providing access to 16 different cutting edge technologies. Currently, the CIH hosts over 60 scientific projects coming from 8 departments of the Institut Pastuer and 5 external teams. In order to respond to the growing needs of these projects in the area of single cell analysis, the CIH has introduced a significant number of single-cell/single-molecule technologies over the past 2-3 years. These new technologies, such as the Personal Genome Machine (PGM) and Ion Proton sequencers, iSCAN microarray scanner, Nanostring technology for transcriptomics profiling and real-time PCR machine BioMark, give rise to large datasets with high dimensionality. Such trend, in terms of data complexity, is also true for flow cytometry technologies (currently reaching over 20 parameters per cell). The exploration of this data is generally beyond the scope of scientists involved in translational research projects. In order to maximize the research outcomes obtained from the analysis of these rich datasets, and to ensure that the full potential of our technologies can be served to the users of the CIH, we would require a proximity bioinformatics support. A CIH-embedded bioinformatician would: 1) design and implement standard analysis pipelines for each of the data-rich technologies of the CIH; 2) provide regular ‘bioinformatics clinics’ to allow scientists the possibility to customize standard pipelines to their specific needs; 3) run trainings on the ‘R software’ platform and other data analysis tools (such as Qlucore) of interest for the CIH users. The objective would be to empower the users to run exploratory analysis by themselves, and to teach good practices in terms of data management and data analysis.    



        Project status : In Progress

        secretome analysis of human intestinal cells during shigella invasion



        Project status : Closed

        Transcriptional regulation of innate lymphoid cell plasticity versus differentiation

        Over the last years, innate lymphoid cells (ILC) have been increasingly investigated. Despite the absence of antigen specific receptors, they belong to the lymphoid lineage and represent important sentinels for tissue homeostasis and inflammation. They contribute to numerous homeostatic and pathophysiological situations via specific cytokine production. ILC are currently divided into three groups based on the expression of specific transcription factors and secretion of cytokines. We focus this study on fetal ILC3 development. We have observed that contrary to lymphocytes, ILC can migrate toward lymphoid organs, tissues and mucosal sites as lymphoid precusors and terminate their developmental program in situ. In the fetal spleen, we observe different stages of ILC3 with precursors that are already RORgt+ but could still give rise to other ILC fate. Hence, these splenic ILC3 precursors were sorted and analyzed by microarrays. The identification of gene expression differences was used to design a single cell transcriptomic assay. The single cell transcriptomic assay is based on this specific selection of primers for transcription factors and cytokine receptors. We evaluate their differential expression in single cells at different stages of their plasticity. The aim is to decipher the progression from an ILC precursor stage to an another in one cell. We are also using the new polaris technology to detect and evaluate at different early timepoints the sequence of molecular events for changing ILC cell fate. In this case, we chose to use the sc RNAseq technology. The single cell transcriptomic will be analyzed and bioinformatic programs will be applied in order to organize the sequential molecular events and to build a hierarchical developmental model in case of ILC cell fate decisions.



        Project status : In Progress

        Mapping the genomic architecture of human neuroanatomical diversity

        Our recent analyses suggest that the genetic determinants of human neuroanatomical diversity are massively polygenic. Like other quantitative traits such as height – but also IQ or ASD risk – neuroanatomical diversity seems to result from the aggregated effect of thousands of frequent variants, each of small effect. GWAS should then require populations of hundreds of thousands of individuals to start to detect the individual variants. GCTA (genomic complex trait analysis) offers an alternative approach to obtain valuable neurogenetic information despite the current impossibility to detect enough individual variants to explaining any substantial part of the variability. We are currently pooling together neuroimaging genomics data from multiple international projects (in particular, IMAGEN, ENIGMA, UK Biobank) to replicate and extend our earlier analyses. We aim to: (1) Compute the amount of variance captured by genome-wide SNPs (SNP-heritability) for the several brain regions: ICV, BV, Hip, Th, Ca, Pa, Pu, Amy and Acc, (2) Compute the matrix of SNP-based genetic correlation among structures, (3) Partition the variance captured by SNPs among structural and functional sets: per chromosome, genic vs non-genic, low/medium/high minor-allele frequency, positive/negative selection, involved or not in neurodevelopment, etc. (4) Compare our results with those obtained using GWAS-based estimations (for example, those used in ENIGMA2). GCTA requires the computation of matrices of genetic relationship among all individuals, and thus, direct access to the genotyping data. Once the matrices are computed, the genotyping data is no longer required, and it is not possible to reconstruct an individual's genome from the matrices. Our analysis of the IMAGEN cohort was based on 1,765 Individuals, which gave us sufficient statistical power (80%) to detect only strong heritabilities (h2~45%), and the estimations had very large standard errors (~20%). A cohort of 4,000 subjects should allow us to decrease the standard error to ~8% (80% power to detect h2=22%), and a cohort of 8,000 subjects should decrease it to ~4% (80% power to detect h2=11%). In this way, we could obtain more accurate estimates, but also detect eventually more subtle effects related to functional genomic partitions.   References Yang et al (2010) Common SNPs explain a large proportion of heritability for human height. Nature Genetics, doi: 10.1038/ng.608 Davies et al (2011) Genome-wide association studies establish that human intelligence is highly heritable and polygenic. Molecular Psychiatry, doi: 10.1038/mp.2011.85 Gaugler et al (2014) Most genetic risk for autism resides with common variation. Nature Genetics, doi: 10.1038/ng.3039 Wood et al (2014) Defining the role of common variation in the genomic and biological architecture of adult human height, doi: 10.1038/ng.3097



        Project status : Closed

        JASS: an online tool for the joint analysis of GWAS summary statistics

        In recent years, large genome-wide association studies (GWAS) have been successful in identifying thousands of significant genetic associations for multiple traits and diseases1. In the course of this endeavor, sample size has proven to be the key factor for identifying new variants. For example, GWAS of body mass index (BMI), now including up to 350,000 individuals from more than 100 cohorts, have been able to identify genetic variant that explain as low as 0.02% of BMI variance2. While standard approaches for detecting new genetic variants associated with traits and diseases will go on as sample size increases, multivariate analyses have been proposed as an alternative strategy for both improving detection of new variants and exploring the multidimensional components of complex traits and diseases. Intuitively, multivariate analysis can be used to improve detection of variants displaying a pleiotropic effect3 by accumulating moderate evidence of association across multiple traits and diseases. Several recent examples have been published about not only GWAS hit overlap across related traits4, but also of genome-wide shared genetic effect5. Multivariate analyses of GWAS have also proven useful to understand shared genetics between diseases5, and potential causal relationship between phenotypes using Mendelian randomization (MR)6. Importantly, most of existing multivariate methods are based on GWAS summary statistics, while approaches based on individual-level data have been seldom considered because of major practical and ethical issues. In the continuity of ongoing work on multi-phenotype analysis (Aschard et al 20147, Aschard et al 20158), we developed an effective and robust multivariate approach of GWAS summary statistics that addresses the major barriers of existing approaches, i.e. the presence of correlation between studies that would exists when GWAS analyzed share sample9-16. Our approach consists in a robust omnibus multivariate test of GWAS summary statis



        Project status : Closed

        Single cell analysis of HIV-specific CD4+ T cell differentiation



        Project status : Closed

        Genetic profile of patients with dyslexia

        Background: Dyslexia is characterized by difficulty with learning to read fluently and with accurate comprehension despite normal intelligence. It affects 5–10% of school-age children. Familial studies repeatedly showed that first-degree relatives of affected individuals have a 30–50% risk of developing the disorder. Twin studies showed that heritability was approximately 50% with a higher concordance rate for monozygotic twins compared to dizygotic twins. Although genetic factors contribute to dyslexia, very little is known on the genes associated with the condition. Preliminary data: Our project consists in the complementary analysis of (i) a cohort of 209 patients with dyslexia, 89 relatives and 95 very well phenotyped controls and (ii) an extended pedigree (Nantaise family) with 12 members diagnosed with dyslexia in three generations. For all the individuals of the project, we genotyped >600K SNPs in order to detect SNP association and copy-number variants (CNVs). For the extended pedigree, we also used linkage analysis and whole genome sequence (WGS). Our preliminary results indicate that a single region on chromosome 7q36 is segregating with dyslexia in the Nantaise family. The region is located within CNTNAP2, a gene previously proposed as a susceptibility gene, but without formal proof of its association. The WGS data of three affected and three unaffected individuals of the pedigree was performed to detect all the variants in the linkage region. Project: We proposed to use this unique resource in France to characterize the genetic profile of patients with dyslexia. We will (i) detect the CNVs present in the patients and (ii) detect the variants in the linkage region.



        Project status : In Progress

        ModeMood: Modeling Mood Disorders



        Project status : Closed

        Genotype to phenotype analysis of immune responses in chronic inflammatory diseases



        Project status : In Progress

        DNA encapsulation of human resources for research projects on immune system and inflammatory diseases

        Freezing is the most commonly used method for storing DNA extracts. However, that method is non-practical and expensive, since requiring freezers and back-up generators for storage, and specific conditions/reagents for transport. In addition, even when adequate procedures are followed, the frozen extracts integrity might suffer from repeated freeze-thaw cycles or residual microorganism activity. The Institut Pasteur’s ICAReB platform hosts the biological collection related to the CoSImmGEn cohorts (Cohort and Collection to Study the Immune System with its Genetic and Environmental determinants) since 2011 (see related team publication 1). Those cohorts have been designed for providing large, duly annotated, qualified blood-derived bio-resources such as blood peripheral mononuclear cells, DNA and RNA from healthy subjects or cases suffering from diseases such as Hidradenitis Suppurativa to support genetic studies linked to the immune system (see related team publication 2 et 3). To provide over the long term genomic DNA for any kind of future genetic studies searching for immune system etio-pathogenesis, the ICAReB platform has used a newly developed DNAshells® (Imagene) which ensure nondestructive, reliable and long-term stability of DNA at low-cost (Clermont et coll, Biopreserv Biobank, 2014). That technology involves encapsulation of the genomic material such that it can be stored dry at room temperature, in small, watertight, oxidation-proof metal capsules. The first aim of the present project is to determine if SNP genotyping allows the detection of DNA damage during storage in various conditions. The second aim of the project is to demonstrate that encapsulation allows an optimal storage of human blood derived DNA at room temperature.



        Project status : Closed

        Insight into the Immune System: A bioresource and data-sharing platform to study chronic inflammatory diseases (IsIShare)

        Chronic inflammatory systemic diseases (CIDs) are a burden to humans because of life-long debilitating illness, increased mortality and high therapy costs. CIDs’ increasing prevalence in western countries has indeed placed them at the third rank of morbi-mortality causes. Unfortunately, available treatments are poorly targeted and non-curative. That is partly linked to a complex and largely ununderstood pathophysiology. Genetic susceptibility clearly plays a role. Genes linked to the immune system have been identified, but causal genes remain mostly unknown and other factors such as intestinal microbiota have also been implicated. The complexity of CIDs’ pathophysiology suggests that a holistic approach is the most susceptible to help make significant progress. Our project intends to take advantage of recent technical progress and development of informatics tools to set up a transversal approach. High-resolution sequencing technology indeed quickly produces large amounts of accurate data. Besides, new integrative informatics tools allowing storage and integrative analysis of this resulting high amount of data are now available. We intend to set-up a CID’s network allowing the gathering and extensive analysis of data related to immuno-genetic determinants, immune repertoire and microbiota from individuals suffering from one of the three major interlinked CIDs, namely Hidradenitis Suppurativa (HS), Crohn’s disease (CD) and Spondyloarthropathy (SpA) as compared to healthy volunteers.



        Project status : Closed

        Identification of the mouse and/or rat orthologues of the human gene ANOS1, responsible for the X-chromosome-linked form of Kallmann syndrome



        Project status : Closed

        MOODel: Modeling Mood Disorders

        Mood disorders such as bipolar and major depressive illnesses are among the most severe psychiatric disorders. They have high prevalence and chronic course, and are associated with significant mental and somatic comorbidities and high personal and societal costs (lost productivity and increased medical expenses). Patients with bipolar disorder (BD), for example, exhibit a reduced lifespan compared with the general population, a finding that cannot only be explained by high suicide risk, reduced access to medical care and lifestyle factors. However, the pathophysiological mechanisms of BD are poorly understood, and patients often have incomplete treatment response. Advanced mathematical approaches such as machine learning techniques are increasingly being used to generate predictions based on complex data, and it has been successfully used to detect a number of clinical outcomes and to predict behaviours. In combination with mobile technologies (e.g. smartphones, wearables) to collect behavioural, physiological and environmental data, these big data predictive approaches may provide a much richer and deeper understanding of phenomenology and pathophysiological mechanisms of mood and bipolar disorders. By taking advantage of the high-standard bioinformatics expertise offered by the C3BI, this multidisciplinary, collaborative project aims to explore how clinical and biological factors, may contribute for better characterizing BD patients as well as to identify predictors of treatment response in BD. Our project also aims to explore how daily behavioural and physiological parameters may influence mood and behaviour in individuals at-risk or suffering from mood disorders.



        Project status : Closed

        Exploring immunological mechanisms of human graft-verus-host disease after hematopoietic stem cell transplantation

        Hematopoietic stem cell transplantation (HSCT) is a curative treatment for many hematologic malignancies. The main therapeutic benefit derives both from the ability to treat patients with intensive chemotherapy and from a potent graft-versus-leukemia (GVL) effect mediated by donor T lymphocytes. Unfortunately, in some patients, donor T cells also attack host normal tissues, giving rise to graft-versus-host disease (GVHD). GVHD prevalence is between 40-80% depending on patient and transplantation characteristics and GVHD remains the main cause of non-relapse morbidity and mortality. Despite the advances in the field of HSCT and GVHD prophylaxis, disease processes in humans remain poorly understood, and the lack of biomarkers for the early diagnosis and prognosis of GVHD contributes to the high mortality of the disease. The objective of the study is to investigate the cellular and molecular mechanisms involved in the immune reconstitution after transplantation and to explore the mechanisms of acute GVHD. For three independent cohorts of donor-recipient pairs, blood samples were collected from the all the donors before transplantation and for the respective recipients either at GVHD onset or at the Day 30 or Day 90 for recipients that did not develop GVHD. Donors and recipients’ samples were analyzed using different approaches: spectral flow cytometry to investigate the cellular correlates of immune reconstitution after HSCT and of GVHD onset, gene expression analysis by NanoString technology to assess the molecular profile of immune cell populations important for GVHD development (CD4+ T cells, CD8+ T cells, NK cells and monocytes) as well as a metabolomics profiling of serum samples using mass spectrometry.



        Project status : Closed

        The Flemmingsome: the proteome of intact cytokinetic midbodies

        The central part of the intercellular bridge connecting the two daughter cells during cytokinesis is a highly dense structure named the Midbody first described by Flemming in 1891. Work in the past ten years revealed that the midbody is a platform that concentrates essential proteins involved in cytokinetic abscission. After abscission, the midbody is cut on both sides, thus generating a midbody remnant (named MBR). The MBR usually interacts with the cell surface of one of the two daughter cells, before being engulfed in a phagocytic-like manner. We also found that the MBR can be easily released from cells before their engulfment by calcium chelation. Of note, MBRs at the cell surface might act as pro-proliferative, signalling entities but the proteins involved and the mechanisms of MBR anchoring are unknown. A previous proteomic study of the midbody conducted by Skop purified intercellular bridges from cell lysates recovered after cell synchronization, microtubule stabilization and detergent treatment. This pioneer proteomic study, although informative, did not allow the recovery of many key known proteins of the midbody. Here, we set up an experimental protocol to purify intact, detergent-free MBRs in order to have the full proteome of this organelle. Quantitative, label-free proteomics enabled us to identify 529 proteins enriched at least 2 times as compared to whole cell lysates, that we named the “Flemmingsome”. Besides known and well-established proteins of the midbody (MKLP1, MgcRacGAP, AuroraB, INCENP, MKLP2, Rab8, Rab11, Rab35, Citron Kinase, ESCRTs…), we identified new and promising candidates potentially involved in cytokinetic abscission. In addition, we identified 27 transmembrane proteins that are excellent candidates for mediating interactions between the MBR and the receiving daughter cells after cytokinetic abscission. We are also currently exploring whether newly identified candidates could participate in the signalling mediated by the MBRs. We would thus like to create a website that recapitulates the findings of our screen. The proteins discovered represent new candidates for the understanding of cytokinesis and tumorigenesis. This should be instrumental in the field as the previous websites are not updated (Microkits, Uniprot) and do not focus on this particular step of cytokinesis.



        Project status : Closed

        Identification of immune response signatures that correlate with therapeutic responses to TNF inhibitors using machine-learning algorithms

        Anti-TNF therapy has revolutionized treatment of many chronic inflammatory diseases, including rheumatoid arthritis, Crohn’s disease and spondyloarthritis (SpA). However, clinical efficacy of TNF-inhibitors (TNFi) is limited by a high rate of non-responsiveness (30-40%) both in SpA and other diseases, exposing a substantial fraction of patients to important side-effects without any clinical benefit. Despite the extensive use of TNFi since many years, it is still not possible to determine which patients will respond to TNFi before treatment initiation. In this study, we have tested the hypothesis that the functional analysis of immune responses may not only improve our understanding of the molecular mechanisms of TNF-blocker activity, but also identify correlates of therapeutic responses in SpA patients. To facilitate the potential translation of our findings into a clinical setting, we have used standardized whole-blood stimulation assays (“TruCulture” assays, Duffy et al., Immunity 2014), and have minimized sources of pre-analytical variability, implementing a highly sensitive and robust pipeline to assess immune functions in patients. To investigate the concept that the immune status of a patient will define their response to TNFi treatment, we have used machine-learning algorithms to identify, in whole-blood stimulation assays, immunological transcripts that correlate with clinical efficacy of TNFi. Our results obtained with a cohort of 67 SpA patients demonstrate that high expression, before treatment initiation, of molecules associated with leukocyte invasion/migration and inflammatory processes predisposes to favorable outcome of anti-TNF therapy, while high-level expression of cytotoxic molecules was associated with poor therapeutic responses to TNF-blockers. These findings may suggest that SpA patients whose immune response is characterized by strong, NF-kB-mediated inflammation are more likely to benefit from TNFi treatment than patients with an active T/NK-cell component. Unfortunately our manuscript describing these results has been rejected by Nature Medicine. However, in her letter the editor mentioned, “Should future experimental data allow you to demonstrate that the identified gene signatures predict response to treatment and outperform previously reported approaches in an independent cohort, we would be happy to look at a new submission…”. We have recruited additional SpA patients over the summer and we are currently in the process of performing the gene expression analysis. The goal of this bioinformatic analysis will be to identify transcripts in stimulated immune cells that predict therapeutic outcome in a training set of patients using machine-learning algorithms and validate the findings in a replication cohort.



        Project status : Closed

        High content screening of mitochondrial morphology defects in mitochondrial genetic diseases

        Mitochondria are double-membrane bound organelles that are essential in every tissue of the body. They are metabolic hubs and signalling platforms that are deeply integrated into cellular homeostasis. The functions of mitochondria are intimately linked to their form, which is regulated by a balance of membrane fusion and fission: dynamin-like GTPases OPA1 and MFN1/2 perform membrane fusion and DRP1 regulates membrane fission. Mutations in mitochondrial genes cause a pleiotropic spectrum of clinical disorders whose underlying genetic, morphological and biochemical defects can be easily studied in skin fibroblasts generated from patient biopsies. The morphology of mitochondria is inextricably linked to its many essential functions in the cell and we are interested in understanding the relationship between mitochondrial shape changes and metabolism in the context of acquired and inborn human diseases. Balanced fusion and fission events shape mitochondria to meet metabolic demands and to ensure removal of damaged organelles. Mitochondrial fragmentation occurs in response to nutrient excess and cellular dysfunction and has been observed in mitochondrial genetic diseases and is thought to play an important role in the development of disease. The physiological relevance of mitochondrial morphology and the mechanisms that regulate mitochondrial dynamics are incomplete and so we have set out to find ways to rebalance mitochondrial dynamics in genetic diseases. We recently developed imaging and informatics pipelines to allow for the automated, rapid, reliable quantification of mitochondrial morphology in human fibroblasts. We applied this new technology in the context of genome-wide siRNA screens in immortalized fibroblasts from an OPA1 patient with dominant optic atrophy and control fibroblasts to identify candidate genes able to reverse the mitochondrial fragmentation phenotype associated with mitochondrial dysfunction in patient cells. We have performed the same genome-wide screen in healthy immortalized control fibroblasts. Together, these studies will help us identify lists of genetic modifiers and therapeutic targets that can be investigated further using cell biology and biochemical tools in the lab.



        Project status : Closed

        Role of the Topoisomerase 1 and Guanine quadruplexes as transcriptional regulators

        DNA Topoisomerase 1 (Top1) is a major regulator of gene expression with great impact on genome stability. Similarly, Guanine quadruplexes (G4) have recently emerged as critical elements for transcription regulation and potential threats to the genome integrity. Studies of Top1 and G4 have many medical implications since their mutations or deregulations are associated with several pathologies, such as cancers, neurodegenerative diseases or viral infections. A few studies, including ours, have revealed physical and functional interactions between these two elements and their involvement in transcriptional regulation of viral and cellular genes. Our research hypothesis is that this Top1-G4 interaction is involved in a new mechanism of transcriptional regulation. This project aims to test this hypothesis and to determine, genome-wide, the contribution of this interaction on human gene transcriptional regulation. This will be tested using genomic and transcriptomic data obtained on the Top1-dependent transcriptional regulation of cellular genes (RNA-seq data), on the localization of Top1 along the cellular genome (ChIP data) and on the presence of G4 structures at specific foci of this genome (G4Hunter prediction and ChIP data). Results obtained by this bio-informatics analyses, should help us to design new experiments to test our hypothesis, on both retroviral and cellular promoters. In long-term perspectives, this project should reveal new mechanisms of gene transcriptional regulation that could serve for the development of new therapeutic strategies.



        Project status : Awaiting Publication

        Determination of host response elicited by different Salmonella lifestyles

        A number of mammalian cell types are susceptible to Salmonella Typhimurium infection, including epithelial cells, fibroblasts and macrophages. It has recently been demonstrated that Salmonella display specific lifestyles in a host cell type-specific manner, where these lifestyles are remarkable for the subcellular localization and replication rate of Salmonella. During epithelial cells infection, Salmonella are first uptaken by the host cell and being encapsulated in a unique endocytic compartment termed Salmonella-containing vacuole (SCV). Within the SCV, Salmonella could remodel the SCV into a viable replicative niche or rupture the SCV and hyper-replicate in the host cytosol. Salmonella replicate at distinct rates in the two localizations, the Salmonella replication in SCV commences from 5 hours post-infection (pi) and infected host cell harbors less then 10 bacteria at 8h pi. While the cytosolic Salmonella begins replication within the first hour of infection at a rate of 30 minutes per division and accumulates up to over 50 bacteria in the host at 8h pi. To understand how Salmonella achieves the two distinct intracellular lifestyles as well as the pathophysiological impacts of the two lifestyles, the primitive goal of my project is to develop a bacterial-borne fluorescent reporter that clearly depicts the subcellular localization and replication rate of Salmonella. With this multiplex fluorescent reporter, we will set to explore the fundamental biological questions: to determine the immune response of epithelial cells against the two Salmonella lifestyles.



        Project status : Declined

        Identification d’une mémoire épigénomique à Streptococcus pneumoniae

        Les modifications de la chromatine, au niveau de l’ADN ou des histones, jouent un rôle fondamental dans la régulation de l’expression des gènes chez les eucaryotes, en contrôlant l’accès de la machinerie transcriptionnelle aux séquences promotrices. Des études récentes ont mis en évidence que modifier la chromatine est l’un des moyens par lesquels les bactéries pathogènes interfèrent avec le programme transcriptionnel des cellules hôtes. Cependant, les mécanismes moléculaires sous-jacents sont très peu caractérisés. Ainsi que les rôles de ces modifications pour l’hôte ou pour la bactérie et l'impact à long terme des changements induits chez l’hôte restent mal définis. Les colonisateurs naturels ou les bactéries commensales n'ont pas été étudiés pour leur capacité à modifier les histones de l’hôte. Dans notre projet, nous utilisons le model bactérien, Streptococcus pneumoniae, pour nous focaliser sur les modifications d’histones importantes pour un colonisateur naturel de l’épithélium respiratoire et un pathogène opportuniste redoutable, dans le but de caractériser précisément les modifications des histones qui persistent après la colonisation afin d’évaluer la réponse de la mémoire. Nos résultats préliminaires montrent que cette bactérie induit bien des modifications d’histones qui sont conservés à long terme. Pour identifier les gènes affectés par ces modifications d’histones observées et comprendre leurs roles, nous voulons réaliser du ChIPseq.



        Project status : Awaiting Publication

        Gene expression and its regulation during and after inpatient detoxification of cocaine: a link to relapse?

        Cocaine is the most widely used illicit stimulant in Europe1, with a recent increase in use in the French general population. Cocaine addiction (CocAdd) is recognised as a public health priority worldwide, affecting 3% of the US general population, with high burden for individuals and societies1 (4 to 8-fold increase in standardised mortality rates). Clinically, (cocaine) addiction (or substance use disorder) is defined as the compulsive use of a substance causing clinically and functionally significant impairment (health problems, disability, and failure to meet major responsibilities at work, school, or home). These features constitute the basis of diagnostic criteria. There is no approved medication to treat CocAdd, despite significant advances regarding the mechanisms underpinning the neurobiology of chronic cocaine self-administration in rodents. CocAdd is defined as a maladaptive and compulsive reward-seeking behaviour related to cocaine. The loss-of-control over drug use and associated urges (craving) is such that 75-90% people with CocAdd report that they have relapsed within one year after inpatient detoxification. It is thus crucial to develop innovative and precise biomarkers to predict the liability to relapse if we are to develop efficient treatment strategies against this devastating disorder. Relapse is a key player in the chronicity of addiction in general and, as such, is the core therapeutic target of any therapy against addiction . Attached to an ongoing study of the neuroimaging signature of CocAdd relapse, we implemented an auxiliary study to draw blood samples from patients with CocAdd undergoing hospital detoxification and followed for up to three months after, so as to collect genetic material. The 'OBSCOC' protocol thus provides biological samples at entry and 15, 30 and 90 days after. These samples are aimed for characterising the whole RNome, miRNome and ChipSeq profile of these patients, who all provided written informed consent for the genetic study and for extensive clinical and sociodemographic assessment as well. We hypothesised that specific changes of gene expression between time points could either predict increased risk for/precocity of or announce imminent relapse. Thus they could serve, on the longer-term, as biomarkers and/or therapeutic targets.



        Project status : In Progress

        Afribiota-Neuro

        Globally one out of four children under 5 years is affected by linear growth delay (stunting). This syndrome has severe long-term sequelae including increased risk of illness and mortality and delayed psychomotor development. Stunting is a syndrome that is linked to poor nutrition and repeated infections. To date, the treatment of stunted children is challenging as the underlying etiology and pathophysiological mechanisms remain elusive. We hypothesize that pediatric environmental enteropathy (PEE), a chronic inflammation of the small intestine, plays a major role in the pathophysiology of stunting, failure of nutritional interventions and diminished response to oral vaccines, potentially via changes in the composition of the pro- and eukaryotic intestinal communities. The main objective of AFRIBIOTA is to describe the intestinal dysbiosis observed in the context of stunting and to link it to PEE. Secondary objectives include the identification of the broader socio-economic environment and biological and environmental risk factors for stunting and PEE as well as the testing of a set of easy-to-use candidate biomarkers for PEE. We also assess host outcomes including mucosal and systemic immunity and psychomotor development. AFRIBIOTA is a case-control study for stunting recruiting children in Bangui, Central African Republic and in Antananarivo, Madagascar. In each country, 460 children aged 2–5 years with no overt signs of gastrointestinal disease are recruited (260 with no growth delay, 100 moderately stunted and 100 severely stunted). We compare the intestinal microbiota composition (gastric and small intestinal aspirates; feces), the mucosal and systemic immune status and the psychomotor development of children with stunting and/or PEE compared to non-stunted controls. We also perform anthropological and epidemiological investigations of the children’s broader living conditions and assess risk factors using a standardized questionnaire. To date, the pathophysiology and risk factors of stunting and PEE have been insufficiently investigated. AFRIBIOTA will add new insights into the pathophysiology underlying stunting and PEE and in doing so will enable implementation of new biomarkers and design of evidence-based treatment strategies for these two syndromes. These analyses comprise the child development aspects of AFRIBIOTA.



        Project status : Closed

        Analyse transcriptionnelle du cellules cancéreuse intestinal vs normales après co-culture avec la bactérie associée au cancer Streptococcus gallolyticus

        Streptococcus gallolyticus sous espèce gallolyticus, autrefois dénommée Streptococcus bovis biotype I, est une bactérie de la flore intestinale qui constitue une cause émergente de septicémies et d’endocardites chez les personnes âgées. Depuis plus de 50 ans, les études épidémiologiques indiquent l’existence d’une forte association entre les infections invasives à S. gallolyticus et le CCR (cancer colorectal) (Pasquereau-Kotula et al., 2018). Néanmoins, le rôle exact de S.gallolyticus dans le développement du cancer colorectal n'est toujours pas déterminé. Dans notre projet, nous voulons déterminer si S.gallolyticus, une bactérie commensale du colon, est à l’origine du cancer colorectal comme Helicobacter pylori est l’agent étiologique du cancer de l’estomac. Précédemment, notre l’équipe a montré que cette bactérie est aussi capable de profiter de l’environnement tumoral pour se multiplier au détriment d’autres bactéries présentes dans le microbiote de souris comme Enterococcus faecalis (Aymeric et al., 2018). L'hypothèse alternative étant que cette bactérie profite de l’environnement tumoral pour se multiplier au détriment des autres populations bactériennes et provoquer des endocardites suite au relâchement de la barrière intestinale provoquée par la tumeur. L’objectif principal de ce projet de recherche est de mieux comprendre le rôle de S. gallolyticus dans les CCR. L’étude transcriptomique va nous permettre de déterminer impact de S. gallolyticus sur les cellules intestinalles non transformées vs cellules tumorales. Cette l’étude aidera à identifier les gènes altérés par S. gallolyticus qui pourraient à long terme contribuer à la progression de CCR et/ou à oncogénique des cellules normales. La réponse transcriptionnelle induite par S.gallolyticus sur les cellules humaines (normale et canceresuse) permettra de mieux comprendre les mécanismes moléculaires qui sous-tendent le rôle de S.gallolyticus dans le développement du cancer colorectal.



        Project status : Closed

        Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing

        Disruption of GABAergic inhibitory circuits is one of the common alteration responsible for several psychiatric developmental disorders. Gephyrin (GPHN) is the common and main molecular organizer of inhibitory synapses. It acts as a hub under the postsynaptic membrane for the multiple protein-protein interactions. Intriguingly, inhibitory synapses are highly heterogeneous, bearing various inhibitory postsynaptic potential (IPSP) properties and also specific subcellular localization on their target neuron. The molecular mechanism responsible of this diversity is still unknown although it could result, in part, of alternative splicing regulation that will produce specific GPHN isoforms carrying versatile properties. Interestingly, exons alternatively included in Gphn transcripts are proposed to change the binding of GPHN protein with inhibitory receptor as well as its oligomerization. Thus, alternative splicing regulation of Gphn expression intuitively provides a potential molecular mechanism to finely regulate several aspect of inhibitory synapse development, however this regulation step is still largely unexplored. In collaboration with Fabrice Ango (IGF-Montpellier), we have designed an experimental approach to sequence GPHN transcripts using the technologies from Pacific Bioscience and Oxford Nanopore. It was applied to samples prepared from mouse and human tissues. To date, we got sequences from Pacific Bioscience sequencing and our interaction with E. Kornobis allow us to get preliminary data that have revealed a high level of complexity in alternative transcripts expressed by GPHN in Mouse brain samples. However, we are fighting to cluster these sequences and pulling together alternative GPHN transcripts with a bioinformatic pipeline able to decipher properly between light variation of sequences and sequencing errors associated to long read sequencing. Results obtained from currently available solutions, such as PacBio IsoSeq3 analysis pipeline, led us to believe that a more suitable software solution is needed, especially to properly characterize Gephyrin splicing diversity. We propose to build a new bioinformatic pipeline to analyze our data and usable to long read sequencing obtained with Pacific Bioscience and Oxford Nanopore technologies.



        Project status : Closed

        Assessing the role of gut microbiota in spondyloarthritis patients and impact of anti-TNF treament on its composition

        Our hypothesis is that gut microbiota could define predictive markers of response and tolerance to biologics. A. Preliminary results: gut bacteria predicting response to TNF blockers. A proof-of-concept study has been performed on 58 patients who were recruited according to the following criteria: active disease despite NSAIDs intake; no history of inflammatory bowel disease; no antibiotics intake within 3 months prior recruitment. Bacterial 16S rRNA gene sequencing region was performed on stools samples before and after TNF-blocker treatment. Diversity metrics and custom LefSe were used to explore the relationship between the composition of the intestinal microbiota and the efficacy of TNF-blockers. A lower alpha diversity at baseline was unexpectedly associated with better treatment response, HLA-B27 genotype and smoking behavior. Meanwhile, beta diversity was associated with smoking behavior and HLA-B27 genotype before and after treatment. Beta diversity at baseline was associated with the BASDAI index after treatment, and the response to the treatment. These results indicate a potential regulatory role for the gut microbiota on the underlying mechanisms involved in the response to TNF-blockers. Moreover, a LefSe-like approach identified 6 bacterial species as potential biomarkers for the treatment response, despite the absence of global changes (beta diversity) in the microbiota composition following a 3-month TNF-blockers intake. B. Current project: ITS2 fungal rDNA sequencing analyses In order to establish a causal link between host-microbe interactions and clinical efficacy of anti-TNF, we expect the following research endpoints from our experimental and translation approach (cohorts/clinical trials): 1. Defining the impact of anti-TNF on fungal microbiota and on the relative representation of fungal/bacterial components 2. Defining correlations between gut fungal composition and clinical outcome, with the aim of identifying stool microbial fingerprint of durable responses and/or primary resistance to anti-TNFα in SpA patients. The analyses will be performed on the same 58 SpA patients that were previously analyzed for their 16S bacterial component. These patients perfectly described regarding their disease characteristics, demographics, ongoing treatments, response to anti-TNF after a 3-month treatment period.



        Project status : Closed

        Shigella targeting of human colonic Lamina Propria Mononuclear Cells



        Project status : Declined

        Modulation of cellular pathways involved in neuropathology of rabies infection

        Viruses have evolved powerful countermeasures to evade host innate immunity, which produces immediate, but non-specific, immune response during infection. Among viruses possessing RNA genomes, the order of negative-single-strand viruses (Mononegavirales) encompasses many human and animal pathogens that cause severe disease, including measles virus, mumps virus and rabies virus. Rabies virus is known for its neurotropic retrograde progression from the site of transmission to brain parenchyma, and towards salivary glands, different organs linked through parasympathetic nervous system. In the cases of human infection, the exhibited symptoms such as hallucination, diplopia, hydrophobia, unsteadiness or paralysis all indicate that there is causality between rabies virus infection and dysfunction of neural activity. However, lack of pathological brain lesions observed at the point of autopsy or noncytolytic propagation devoid of apoptosis suggest that rabies virus possesses mechanisms to evade or delay immune responses and cell death at least for the duration of replication and transmission. Even though the details in molecular perspective of these discoveries are well laid out now, how these proteins work in coordination or if there are hidden components which connect them all together leading toward deterioration of neural cells on the benefit of virus is largely unclear. Moreover, considering the complexity of brain cell composition and how important the neighboring cells are to shape one neuron’s specialization and dependency onto others in homeostasis, which result in the astounding heterogeneity of gene expression, an integrated and holistic approach is mandatory to get a fully comprehensive view of the mechanisms involved. Consequently, we performed an RNASeq analysis in human interneuron cells derived from induced pluripotent stem cells and infected by two recombinant rabies viruses (Tha virus, isolated from a dog in Thailand and Th4M, a less pathogenic virus which is mutated on 4 different residues of the M gene; this virus can no longer escape the NF-KB pathway) in order to obtain transcriptome data by comparison with uninfected cells, and to have an overview of the temporal dynamics of the genes expression.



        Project status : Closed

        Coaching in R

        Background : The Immunoregulation Unit is composed at present of: Lab Head, one senior staff scientists, two “ingegnieurs” (one IP, one Fondation APHP), two PhD students. The focus of the research is the study of immuno-mechanisms in the pathogenesis of chronic inflammatory diseases, and of the molecular basis of response to treatment. All members of the lab have expressed an interest in acquiring basic R skills for the analysis of large gene expression data sets, collected from the study of patients’ samples. Only one PhD student in the lab is currently using R tools for data analysis, the other members have all received some previous instructions in biostatistics and/or R, but have not been using R tools currently. Requirements : Lab members have expressed a specific need to be instructed in the following areas: 1.refresh basic notions of R language, with a particular focus on handling large gene expression data sets 2.introduction to graphic tools for data representation (ggplot) 3.introduction to tools for differential gene expression analysis (limma) 4.data exploration using Principal Component Analysis Constraints : 1. For the course, it has been decided to use data generated by the lab. Placing the course in the lab’s data context has the advantage of ensuring that the course content is adapted to the “real-life” situations that lab members face in the analysis of their own data. 2.The present situation of “confinement” due to the Covid19 pandemic offers some opportunities (time availability of all members to follow the instruction), but obvious restriction. To maintain interactivity, classes are held at a distance, using Skype group meetings.



        Project status : In Progress

        Phages - bacteria interactions network of the healthy human gut



        Project status : Closed

        Defining the effects of TNF-blockers and IL-17A-inhibitors on immune responses in spondyloarthritis patients, analysis of protein and gene expression signatures

        Anti-TNF therapy has proven effective to reduce inflammation and clinical symptoms in SpA, however, the high rate of non-responsiveness (30-40%) to TNFi exposes a substantial fraction of patients to side effects without clinical benefit, and it is still not possible to determine which patients will respond to TNF inhibitors (TNFi) before treatment initiation. The recent introduction of antibodies blocking IL-17A has expanded the therapeutic options for axial SpA (axSpA), as well as psoriasis and psoriatic arthritis. It is therefore important to develop tools to guide treatment decisions for patients affected by SpA and other chronic inflammatory diseases, to optimize clinical care and contain health care costs. This project builds on our recent work performed in collaboration with the Bioinfo Hub, in which we have defined the mechanisms of action of TNF-blockers and identified immune signatures correlating with therapeutic responses to anti-TNF therapy in SpA patients (Menegatti et al., 2020). We have measured whole blood immune responses to microbial and pathway-specific stimuli using TruCulture assays in 20 axSpA patients before or after treatment with IL-17A-inhibitors and 20 patients before and after anti-TNF therapy. Proteins in supernatants have been measured by Olink technology for protein profiling. Gene expression in cell pellets has been analyzed by RNA sequencing at the Biomics platform. A preliminary analysis of the RNA-Seq data has been performed by Etienne Kornobis and Thomas Cokelaer.



        Project status : In Progress

        Transcriptional profiling of the innate immune response of human fibroblasts of the LabEx Milieu interieur collection: interindividual variability and response to infection

        The LabEx Milieu interieur (MI) project is a clinical study aiming to define the natural variability of the human immune response. Fibroblasts were prepared from skin biopsies of 300 of the 1000 healthy donors (30 men and 30 women in each of 5 decades from 20 to 69 years) by Genethon. Each primary line is annotated by metadata derived from the systematic genotypic-phenotypic analysis Labex-MI (serology, genomic analyzes, proteomics, transcriptome, microbiota, clinical data and epidemiological selection criteria). The objective is to characterize the innate immune response of fibroblasts from healthy donors. We have developed approaches to obtain standardized measures of the immune response and to identify interindividual variance (Chansard et al., 2021) on a subset of sixteen primary fibroblast lines.. We observed that cell responses to LPS stimulation were distributed between “low” and “high” responders, while inter-donor variability of the response to poly I: C was very low. Poly I: C and LPS activate pathways from TLR3 and TLR4 receptors, respectively. We set up a real-time quantitative PCR assay of the 16 cells in parallel using the BioMark automated PCR system (Fluidigm) for comparative quantification of mRNAs baseline expression in the donors’ fibroblasts to check if low responses to LPS were due to a different expression of TLR4 and other factors of the pathway. We will extend the analysis to stimulated cells by Poly I: C ,LPS and other agonists of the innate immune response and also in parallel to cells infected by Leptospira interrogans.



        Project status : Pending

        Etude de l’évolution des Troubles Olfactifs chez les patients ayant une perte de l’odorat persistante des suites de la COVID-19

        La pandémie de la COVID-19 est un défi médical inédit en particulier du fait de la nature systémique de cette pathologie. En effet, la COVID-19 affecte à la fois plusieurs organes et systèmes. L’atteinte cérébrale s’effectue de plusieurs façons : infection directe des cellules nerveuses par le SRAS-CoV-2, inflammation du système nerveux central avec, entre autre, invasion de lymphocytes T et activation de la microglie, inflammation systémique sévère qui inonde le cerveau d'agents pro-inflammatoires et endommage ainsi les cellules nerveuses, ischémie cérébrale globale liée à une insuffisance respiratoire, accidents thromboemboliques liés à une augmentation de la coagulation intravasculaire et stress psychologique sévère. En conséquence, la COVID-19 se manifeste parfois par des symptômes neurologiques et neuropsychiatriques tels que des vertiges, des troubles du sommeil, des déficits cognitifs, un délire, ou une dépression sévère. La perte soudaine de l'odorat est un symptôme fréquemment associé à la COVID-19 et l'infection par le SARS-CoV-2 des neurones du système olfactif a été signalée à la fois chez le hamster et l'humain. La grande majorité des patients atteints de la COVID-19 retrouvent leur fonction olfactive en quelques semaines. Cependant une minorité significative de personnes infectées (1 sur 5 cas), souffre toujours de troubles olfactifs (anosmie, hyposmie et/ou parosmie) plusieurs mois après la primo-infection. Ces troubles olfactifs sont fréquemment associés à un comportement dépressif et à des plaintes cognitives. En TEP, il est même possible de corréler ce dysfonctionnement cognitif à un hypométabolisme de certaines régions cérébrales, y compris le gyrus olfactif. Ce projet propose d'évaluer et de suivre l’évolution, durant un an, des capacités olfactives de patients atteints de trouble persistant de l’odorat depuis un an (+/- 3 mois) des suites de la COVID-19. Il permettra de mieux distinguer si les troubles olfactifs de longue durée sont liés à une atteinte du système olfactif périphérique (en raison d’une persistance virale locale et/ou d’une inflammation chronique de l’épithélium olfactif nasal), ou du système nerveux central. En particulier, l’enregistrement des potentiels évoqués olfactifs permettra d'objectiver les capacités olfactives, de manière non déclarative. Cette étude pourra servir de base au développement d’études visant à évaluer les risques cliniques neurologiques et/ou psychiatriques associés à la forme chronique des troubles de l’odorat des suites de la COVID-19.



        Project status : Pending

        Clinical and biological characterisation of auto-antibodies to the nicotinic receptors in major psychiatric disorder patient

        In recent years, immune dysfunctions, including auto-immune mechanisms and peripheral inflammation, have been clearly associated with severe neuropsychiatric disorders like bipolar disorders (BD) and schizophrenia (SZ). These findings are supported by an extensive litterature highlighting a higher risk to develop neuropsychiatric disorders in patients suffering from auto-immune diseases and also the presence of low-grade inflammation and abnormal immunoglobulin rates in patients with psychosis. It is now well-established, since the description of paraneoplastic and auto-immune encephalitis, that antibodies targeting self-antigens such as membrane receptors or intracellular proteins could trigger psychiatric symptoms and severe inflammation. Therefore, an in-depth characterisation of circulating auto-antibodies and their clinical and/or biological implications has become a critical issue to stratify specific subgroups of patients with auto-immune psychosis in order to adjust and adapt the treatment and care, and develop novel approaches. Nicotinic acetylcholine receptors (nAChRs) have been linked to severe neuropsychiatric disorders by clinical and genome-wide association studies (GWAS). In addition to their key roles in neuronal function, nAChRs are also involved in the complex regulation of immuno-inflammatory processes both in the brain and the periphery, making them prime candidates to study the link between inflammation and major psychiatric disorders. Furthermore, nAChRs have already been identified as the target of autoimmune mechanisms leading to the destruction of the neuromuscular junction in the well-described autoimmune disease, myasthenia gravis. Based on these findings, we have started to dissect auto-immune mechanisms against nAChRs involved in SZ and BD. In brief, anti-nAChR auto-antibodies contribute to cognitive dysfunction and psychotic symptoms through peripheral inflammation. Here, our goals are (1) to extend the current knowledge by dissecting the relationship between clinical features and peripheral inflammation (cytokines, chemokines, ...) (2) to stratify patients with anti-nAChR auto-immune psychosis by using cluster analyse



        Project status : In Progress

        An online database of RNA-small molecules complexes for rational drug design

        The majority of approved drugs target proteins, which are encoded in a very small fraction of the human genome. When a pathology is associated with so-called undruggable proteins, an alternative strategy should be sought. In the last twenty years, non-coding RNA molecules have been shown to perform a variety of crucial biological functions, including regulating gene expression, protecting chromosomes from foreign nucleic acids, and guiding telomers synthesis. In this context, targeting either mRNA molecules that are translated into undruggable protein targets or biologically relevant non-coding RNA molecules with small molecules is emerging as a promising therapeutical approach in pathologies such as cancer, viral infections, and neurodegenerative disorders. However, the number of approved drugs that target RNA molecules is still very limited and the existing examples have mostly been found by costly and time-consuming screening experiments. In this project, we aim at building a computational framework to guide the rational design of drugs targeting RNA. To this end, we created a database containing all the experimentally-determined structures of RNA-small molecule complexes deposited in the PDB database. The entries containing drug-like compounds were selected and annotated based on the different biological entities interacting with the ligands. Our database, freely accessible via a web interface, will facilitate i) mapping the chemical space of the small molecules known to bind RNA, ii) understanding the nature of the interactions that drive ligand/RNA recognition, and iii) benchmarking existing tools for in silico protein drug design with RNA targets.



        Project status : Pending

        Regulation of HIV replication by cellular DNA topology

        HIV-1 replication requires the integration of the viral genome into the cell genome. A viral-encoded enzyme, integrase (IN), performs this critical step of infection and is a promising target for anti-viral therapeutics. If the catalytic properties of INs are well characterized, the mechanisms responsible for their site selectivity are still under investigation. Several cellular proteins, such as the LEDFGF/p75 transcription regulator, the RNA polymerase II machinery, nuclear pore proteins and specific modified histones have been proposed to be involved in IN selectivity at a genomic level. In addition, structural parameters of the target DNA helix (curvature, flexibility and topology) are proposed to regulate IN selectivity at a local level. Our team is studying the role and molecular mechanisms associated with these various parameters (Botbol et al., 2008; Lesbats et al., 2011; Morchikh et al., 2013; Benleulmi et al., 2015; Naughtin et al.,). This project aims to define the role of cellular DNA topology during HIV-1 integration. We will first compare already mapped integration sites and superhelicity profiles and search for possible correlations between these two parameters. We will then modify topoisomerases activity in infected cells and study the consequences on viral replication and integration. Finally, we will study in vitro, the direct effects on integration of two parameters of DNA topology, the twist and writhe of the DNA helix. This project relies on complementary in vivo, in vitro and in silico approaches. Bio-informatics tools are crucial for the correlative and statistical analyses of integration sites and superhelicity maps.



        Project status : Declined

        Identification of new cellular parameters involved in HIV-1 integration selectivity

        HIV-1 replication requires the integration of the viral genome into the cell genome. A viral-encoded enzyme, integrase (IN), performs this critical step of infection and is a promising target for anti-viral therapeutics. If the catalytic properties of INs are well characterized, the mechanisms responsible for their site selectivity are still under investigation. Several cellular proteins, such as the LEDFGF/p75 transcription co-activator, the RNA polymerase II machinery, nuclear pore proteins and specific modified histones have been proposed to be involved in IN selectivity at a genomic level but the underlying molecular mechanisms remain to be demonstrated. In addition, structural parameters of the target DNA helix (curvature, flexibility, topology) are proposed to regulate IN selectivity at a local level. Our aims are to study the role of these different parameters of IN selectivity, using both in vitro and in vivo approaches. In vitro, we will map integration sites on various target DNA substrates (naked DNA or chromatin, minicircles, plasmids with different topologies, transcribed templates) and will test the effect of purified proteins suspected to regulate IN selectivity. In vivo, integration sites will be mapped in cells depleted of these suspected regulators or in cells incubated with drugs targeting enzymes involved in transcription, DNA topology or histone modifications. Integration sites will be mapped using published or “home-made” protocols and the sites will be compared with DNA structural parameters, nucleosome positions, histone modifications or transcriptional parameters (published maps). Bio-informatics tools are crucial for these correlative and statistical analyses of integration sites. Our project relies on complementary in vivo, in vitro and in silico approaches. It should establish molecular and mechanistic rules of HIV-1 integration selectivity that could serve in the development of new antiviral strategies and of safer gene therapy vectors.



        Project status : Closed

        IgBlast on Galaxy

        We would like to be able to use IgBlast on the Galaxy platform. We are studying B cells in adaptive immune response, and are particularly interested in the antibodies termed as broadly neutralizing antibodies (bNAbs). By definition, these antibodies can neutralize most known HIV-1 strains, and are produced by rare infected individuals several years post-infection. We are currently investigating the bNabs immunoglobulin repertoire by focusing our NGS (454 pyrosequencing) analysis on  immunoglobulin sequences (V-domains) from HIV-infected patients who developed bNAbs. As immunoglobulin sequences result from the combinatorial rearrangement of 3 gene segments : V , (D) and J gene segments, we need a specific tool to analyze these sequences. Indentifying the germline genes which are involved in the rearrangment is an essential step. Two main tools are being widely used to analyze Immunoglobulins: IMGT and IgBlast. IgBlast has several advantages; it is based on BLAST (it is then possible for the user to build his own database), open source, can use protein or nucleotide sequences as input, and most of all, IgBlast is already installed on the Institut Pasteur's cluster as well as the germline genes database. As it would be very convenient for us to use the bic cluster and galaxy platform to run our analyzes, we would be grateful if IgBlast could be implemented in the Pasteur Galaxy Platform. In this regard, we are of course fully disposed to help in any ways. We also believe that it would be very useful to people working on immunoglobulin sequences in the immunology department by building specific pipelines. Thank you very much.



        Project status : Closed

        Regulation of HIV-1 integration selectivity by chromatin

        Integration of the viral reverse-transcribed genome into the genome of infected cells is an essential step of retroviral replication and is performed by a viral-encoded enzyme, named integrase (IN). In the case of HIV-1, IN is a new and efficient anti-viral target. The selectivity of this enzyme for its cellular genomic sites is also a major parameter of HIV replication and is regulated by several cellular parameters. One of them is chromatin, and different levels of this nucleoprotein complex are involved in the regulation of IN selectivity. Using in vitro integration assays, established by our team and collaborators, we have studied this regulation at two levels of chromatin architecture: large poly-nucleosome templates (Botbol et al., 2008; Lesbats et al., 2011; Benleulmi et al., 2015; Naughtin et al., 2015) or nucleosome-induced DNA curvature mimicked by DNA minicircles (Pasi et al., 2016). Our present project is to study IN selectivity into mononucleosomes (MN). These MNs will be used as target substrates of integration and the role of MN structure, histone modifications and IN cofactors will be studied. Results obtained in vitro, will be confronted to structural data obtained by molecular modeling and to integration sites observed in infected cells. This project will benefit from our expertise in integration in chromatin templates and a previous collaboration with the C3BI on the analysis of integration sites (Pasi, M., Mornico, D., S. Volant, S., et al., 2016). This project is funded by the ANRS.



        Project status : In Progress

        Utilize mouse models to study infection by HIV-1

        We previously showed that humanized immune system (HIS) mice generated in Balb/c Rag2-/-γc-/- SIRPNOD (BRGS) recipients are susceptible to HIV-1 infection (X4 and R5 isolates) and maintain circulating HIV-1 in the plasma, resulting in a dramatic depletion of human CD4+ T cells. We also characterized features of HIV physiopathology in this model. Human thymocyte subsets developing in the thymus of HIS mice appear phenotypically normal, but in the periphery the T cell repertoire is restricted compared with that of human peripheral blood T cells. This negatively impacts on the ability of HIS mice to generate antigen-specific human immune responses when mice are vaccinated with protein antigens or following infection with lymphotropic viruses such as HIV. One likely explanation for these functional deficiencies involves the fact that human T cells are selected intrathymically by mouse MHC molecules and that naïve T cells in peripheral lymphoid organs interact primarily with mouse DC (as human DC development in HIS mice is limited). As a first line of improvement, we recently generated a novel mouse model by crossing our BRGS mice with the HLA-A*02-HHD class I transgenic mice and the HLA-DRB1*15 class II transgenic mice, resulting in BRGS-A2DR2 mice. Following intra-hepatic injection of these mice with MHC-matched CD34+ stem cells we observed increased engraftment, with faster kinetics. Moreover BRGS-A2DR2 HIS mice have an increased T cell development leading to a more equilibrated B/T and CD4/CD8 phenotype. We showed that BRGS-A2DR2 HIS mice were able to sustain replication of HIV R5 virus as the BRGS hosts. Viremia was similar in a first phase and then lower in a second phase in BRGS-A2DR2 compared to BRGS HIS mice, which could be a consequence of a better quality of the immune response. However, the viremia reached a similar plateau in the last phase. We propose to study the impact of the immune res



        Project status : Closed

        Single cell analysis of HIV-specific CD4+ T cell differentiation



        Project status : Closed

        Study of the early pathogenesis during Lassa fever in cynomolgus monkeys and its correlation with the outcome

        Because of their increasing incidence, dramatic severity, lack of treatment or vaccine, complicated diagnosis, misreading of the pathogenesis, and need for a maximum containment, Viral Hemorrhagic Fevers (VHF) constitute a major public health problem. There is therefore an urgent need to further study VHF to understand the pathogenesis of the severe disease and the host responses involved in their control or in the dramatic damages. Among VHF, Lassa fever (LF) is probably the most worrying one because of its endemicity and the large number of cases. LF is caused by the Old-World arenavirus Lassa virus (LASV). It is endemic to West Africa and is responsible for 300,000 cases and 5,000 to 6,000 deaths each year. We propose here to study the pathogenesis of VHF by using LF in cynomolgus monkeys as a paradigm, with a particular emphasis on the very early events. The viral tropism, pathophysiological mechanisms, and immune responses will be studied during the course of infection, including the incubation period. Powerful approaches will be used to (1) identify early biological markers of infection, to be able to confirm infection and isolate patients; (2) determine the viral tropism and dynamics during the course of infection to understand the natural history of virus into its host. (3) characterize the early pathogenic events that lead to the severe hemorrhagic syndrome to fully understand the pathophysiogenesis of VHF and identify new therapeutic targets. (4) identify the immune responses involved in the control of infection or in the fatal outcome, to reveal the involvement of immunopathological mechanisms and help to design a vaccine approach. This ambitious and unprecedented project will allow to develop therapeutic and prophylactic approaches but also to identify early biological markers of infection and improve the early diagnosis to optimize the management of outbreaks in the field and increase the survival rate in patients.



        Project status : In Progress