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 : Mouse

Related people (2)

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)

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)

Related projects (54)

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

Gene ontology analysis of RNAseq data from uninfected and Leishmania-infected mouse macrophages

Gene ontology analysis of RNAseq data from uninfected and Leishmania-infected mouse macrophages.  Scientific context During the course of cutaneous or visceral disease in humans or experimental animal models, the resolution of leishmanial infections or the control of parasite growth is dependent on appropriate innate and adaptive immune responses developed by the parasitized host. Leishmania largely evades and subverts these responses by its intracellular life style inside the mammalian host, where the parasites develop into amastigotes mainly within macrophages (BMDMs). We have focused our interest in the BMDM inflammasome and the way Leishmania amastigotes interfere or subvert BMDM inflammatory responses. Our recent data are in favor of an absence of stimulation, even a down-regulation of the inflammasome in BMDMs harboring replicating amastigotes at the gene and protein expression levels. To go further on this, we have performed RNAseq experiments on uninfected and infected BMDMs. This project was done at the “Transcriptome and Epigenome” platform and in close collaboration with the C3BI for normalization and statistical analysis procedures. Objective In the present proposal we will perform a deep analysis of the repartition of modulated genes between the different conditions using these RNAseq data. Using C3Bi expertise we will classify known functions of modulated genes into GO aspects i.e. molecular function, cellular component and biological process, visualize gene annotations and perform statistical analyses for the distribution of the annotated genes over the GO hierarchy for the different gene lists analyzed. Hopefully, these analyses will bring us a better understanding of the mechanisms underlying the subversion of BMDM functions in the innate and adaptive immune response to Leishmania infection which is a prerequisite to design novel anti-parasitic intervention strategies targeting the infected host cell rather than the parasite.



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

Characterization of Yolk Sac Derived Progenitors in the Fetal Liver

Erythromyeloid progenitors (EMPs) originate from the yolk sac during early mouse development and migrate to the fetal liver via the circulation where they undergo massive expansion and differentiation into hematopoietic lineages. These events occur prior to the intraembryonic emergence of hematopoietic stem cells (HSCs). Unlike HSCs, EMPs cannot give rise to lymphoid lineages, nor can they provide long-term repopulation. As such, they are considered a transient fetal population, yet it is EMP-derived hematopoiesis that supports the growth and survival of the embryo prior to the establishment of long-term hematopoitic stem cells (HSCs). Hematopoietic cell differentiation occurs along a hierarchy of progenitors with either lymphoid or myeloid fates. Common myeloid progenitors (CMPs) give rise to further restricted granulocyte-monocyte progenitors (GMPs) and megakaryocyte-erythrocyte progenitors (MEPs). This hierarchy has been well documented in adult hematopoiesis, which occurs solely from HSCs. However, fetal hematopoiesis encompasses dual origins of myeloid lineages that can originate from either EMPs or HSCs. Using genetic pulse chase labeling, we are able to distinguish these two ontologies by positively labelling EMPs and their progeny. Currently, fetal liver progenitors have been characterised by direct comparison to markers and expression profiles that are established for adult hematopoiesis. Yet, fetal hematopoietic markers may not be regulated in the same manner as their adult counterparts. Furthermore, distinguishing EMP- versus HSC-derived progeny is technically challenging and has not been properly addressed with respect to fetal liver myelopoiesis. Therefore, using our genetic pulse chase labeling approach, we would like to rebuild the differentiation tree among myeloid fetal liver progenitors. We are using high parameter flow cytometry to re-evaluate progenitor sub-populations with an expanded repertoire of markers. Since heterogeneity among progenitors (in terms of gene expression and differentiation potential) can be misrepresented and difficult to characterize on the population level, we want to investigate this on the single cell level using MARS-Seq in combination with index sorting.



Project status : In Progress

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

3D PATH

Complex chronic diseases are caused by the accumulation of genetic, microbial and lifestyle factors. The number and complexity of such factors makes prediction of pathogenesis and therapy particularly difficult. Although a single factor is rarely sufficient to trigger pathology, genetic and environmental factors have so far been studied in isolation. Nevertheless, a substantial number of genetic variants have been associated with disease risk and the concomitant lifestyle shift and excessive hygiene are thought to contribute to the increased incidence in inflammatory diseases in industrialized countries. Moreover, clinical and experimental observations suggest a strong impact of gut microbiota on susceptibility to inflammatory diseases. The aim of 3D PATH is to explore the multiplicity and complexity of genetic, microbial and lifestyle factors associated with vulnerability to inflammatory pathology, using mice of the Collaborative Cross (CC), that model human genetic variability. Quantitative trait loci analyses, as well as integrative data analyses on metabolic and inflammatory outcomes will reveal new genetic variants and combinations of variants associated with disease susceptibility, and whether alterations of the gut microbiota in genetically susceptible mouse strains can trigger the phenotype. Moreover, the longitudinal design of experiments will allow us to identify early biomarkers that predict the pathology later in life. In a second step, validation of the identified risk factor combinations and exploration of the underlying molecular mechanisms will be performed taking advantage of the mouse model.



Project status : Closed

Early transcriptional signature of T-cell memory after dengue vaccination

Dengue virus (DENV) induces strong T and B cell responses upon infection. However, there is currently neither vaccine nor specific treatment against DENV, which is spreading worldwide causing 400 million new infections every year, of which 100 million cases are symptomatic, ranging from a self-limiting febrile illness named dengue fever (DF) to more severe life-threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). One of the major obstacles of dengue vaccine development is the cross-reactivity among antibodies against the different DENV serotypes (designed as DENV1-4) that are 67-75% identical at the amino acid level. Indeed, while a primary infection by one DENV serotype can induce a lifelong immunity against re-infection by the same serotype, subsequent infections by heterologous serotypes increase the risk of developing severe dengue, a phenomenon due to non-neutralizing or sub-neutralizing antibodies and called antibody-dependent enhancement (ADE). To avoid the induction of such enhancing antibodies, and given the identification of CD4+ and CD8+ T cell epitopes from previously dengue virus (DENV)-infected donors, we have designed a minimal DENV antigen (called DENV1-NS, patent EP14305984.8 filled on June 23 2014), which is enriched in conserved and highly antigenic epitopes. Using this minimal DENV1-NS antigen, we have first established in vivo its immunogenicity in transgenic mice expressing HLA class II and class I alleles (with the activation of DENV-specific CD4 and CD8 T cells). We have also shown that a prime-boost DNA immunization of these HLA transgenic mice induces a strong T cell immunity, with a significant protection against DENV1 infection, in the absence of neutralizing or sub-neutralizing anti-DENV antibodies (Roth et al., accepted for publication). Our proposal aims, therefore, to identify early transcriptional signatures correlated with the development of memory CD4 and CD8 T cells in vaccinated animals, which promote enhanced anti-dengue immunity.



Project status : Closed

Defining the differential contributions of CD4+ and CD8+ anti-CD19 CAR T cells to tumor outcome, immune recruitment and toxicity

Gene-modified T cells expressing a chimeric antigen receptor (CAR) targeting the CD19 molecule have demonstrated promising clinical efficacy in the treatment of B cell malignancies. However, the frequent relapses and toxic adverse events such as cytokine release syndrome represent hurdles to the success of CAR T cell therapies. In most clinical settings, CAR T cells are generated from a mixture of autologous CD4+ and CD8+ T cells before being infused into patients. This inter-patient heterogeneity within the composition of CAR T cell products renders the large variety of response efficacy and toxicity difficult to interpret. Using a model of B cell aggressive lymphoma developing in the bone marrow, we investigate the differential contributions of CD4+ and CD8+ anti-CD19 CAR T cells to tumor outcome and changes in the tumor microenvironment. Our first in vivo imaging and flow cytometry results suggest that CD4+ CAR T cells have poor cytotoxic potential compared to CD8+ CAR T cell. On the other hand, CD4+ CAR T cells were largely responsible for the cytokine release syndrome and have a unique role in boosting the accumulation of NK cells at the tumor site. Using single cell RNAseq, we aim to identify the changes in the bone marrow tumor microenvironment induced by CD4+ and CD8+ CAR T cells, focusing on the recruitment of host specific immune cell populations and their activation status. Identifying specific contributions of the CD4+ and CD8+ CAR T cells to immune cell recruitment and tumor outcome would help designing optimal CAR T cell products, with important clinical implications.



Project status : Awaiting Publication

Secretome Analysis of OIS IL6KO SASP

Cellular senescence is a stable cell cycle arrest that can be triggered by various biological stresses. Importantly, senescent cells remain metabolically active and secrete numerous molecules, such as cytokines, chemokines, proteases and growth factors. This secretome is called SASP (senescence associated secretory phenotype). Senescence plays a role in several processes, most notably in cancer, where it acts as an intrinsic tumor suppressor mechanism by inhibiting cell growth of premalignant cells. More recently, senescence has been shown to be involved in other biological responses, notably in tissue repair and aging. We recently showed that senescence upon tissue damage was promoting cellular reprogramming and cellular plasticity, notably via SASP. More precisely, we showed that IL-6 was an important mediator of SASP effect. Blocking IL-6 abolished beneficial effect of the SASP on reprogramming. Nonetheless, we speculate that other factors may be important for reprogramming. Indeed SASP factors have been previously shown to play redundant roles, notably in mediating senescence. Therefore we performed mass spectrometry analysis to identify other SASP factors in collaboration with proteomic platform of Institut Pasteur. We already identified promising candidates but we would also like to have a better global understanding of SASP complexity and which pathways it could activate in recipient cells. Thus, to investigate SASP effects more in details, we collaborate with C3BI platform of Institut Pasteur. Finally, understanding how SASP impact cellular plasticity in the context to tissue regeneration is essential for devising new strategies based on in vivo reprogramming.



Project status : In Progress

Functinal analysis of proteome and phopshoproteome changes in murin intestine – mechanism of Streptococcus gallolyticus-induced carcinogenesis



Project status : Declined

Identifying new population(s) of NK cells involved in memory to bacterial infection



Project status : In Progress

3DPATH

Complex chronic diseases such as type 1 and 2 diabetes are caused by the accumulation of genetic, microbial and lifestyle factors. The number and complexity of such factors makes prediction of pathogenesis and therapy particularly difficult. Although a single factor is rarely sufficient to trigger pathology, genetic and environmental factors have so far been studied in isolation. Nevertheless, a substantial number of genetic variants have been associated with disease risk and the concomitant lifestyle shift and excessive hygiene are thought to contribute to the increased incidence in inflammatory diseases in industrialized countries. Moreover, clinical and experimental observations suggest a strong impact of gut microbiota on susceptibility to inflammatory diseases. The aim of 3DPATH is to explore the multiplicity and complexity of genetic, microbial and lifestyle factors associated with vulnerability to inflammatory pathology, with a particular focus on type 1 and 2 diabetes, using mice of the Collaborative Cross (CC), that model human genetic variability. Quantitative trait loci analyses, as well as integrative data analyses on metabolic and inflammatory outcomes will reveal new genetic variants and combinations of variants associated with disease susceptibility, and whether alterations of the gut microbiota in genetically susceptible mouse strains can trigger the phenotype. Moreover, the longitudinal design of experiments will allow us to identify early biomarkers that predict the pathology later in life. In a second step, validation of the identified risk factor combinations and exploration of the underlying molecular mechanisms will be performed taking advantage of the mouse model.



Project status : In Progress

Role of the histone demethylase Kdm6b in ILC2 maturation and functional activation



Project status : Pending

A genome-wide RNAi screening for mitochondrial fission factors

Mitochondria are dynamic organelles that undergo constant morphological changes, resulting from fusion and fission events. Mitochondrial fission is crucial for mitochondrial function, apoptosis, mitophagy, and mitochondrial segregation during mitosis. While core mitochondrial fission factors have been elucidated and characterized, it is unclear if additional molecules participate or are main players of the fission process. To solve this question, we setup a genome wide, high content imaging (HCI) screening to identify suppressors of mitochondrial fragmentation in Opa1-/- cells. The principle is that using cells deficient for mitochondrial fusion (ablated for the core fusion protein Opa1), we may identify fission factors by screening for genes for which the loss of function is able to complement Opa1-/- phenotype. This was validated in preliminary experiments of silencing of the core fission protein Drp1, where confocal and electron microscopy confirmed that ablation of Drp1 resulted in mitochondrial elongation in Opa1-/- cells without causing mitochondrial fusion in a classic polyethylene glycol fusion assay. Following miniaturization of the assay, we set up an efficient pipeline to perform an automated HCI screening in Opa1-/- MEFs transfected with a pooled siRNAs library targeting >19,000 genes. Automated imaging and high content image quantification allowed us to generate a list of potential hits, that we aim to process in collaboration with the lab of Timothy Wai and the C3BI HUB, in order to identify promising genes that will be validated and investigated in the future.



Project status : Closed