NCube/papyrus huggingface dataset:
Intégration multisensorielle pour les mouvements de pointage chez les sujets sains et les patients avec ataxie optique

To execute reach movements, the central nervous system needs to combine information from different sensory modalities, a process knows as multisensory integration. The posterior parietal cortex is a sensorimotor interface implicated in multisensory integration processes. Patients with a damage to this region exhibit a visuomotor deficit called optic ataxia. Patients with optic ataxia present difficulties in performing hand visually-guided movements. To date, the mechanisms underlying multisensory integration are still not fully understood. The first aime of my thesis is to determine how visual and somatosensory information are integrated in healthy participants, during the planning of pointing movements. I will then focus on the sensorimotor deficits observed in optic ataxia which enable a better understanding of the functions of the posterior parietal cortex in motor planning and online control.

Keyphrases: Vision, Proprioception, Multisensory integration, Optic ataxia, Posterior parietal cortex
Étude des propriétés de signalisation et de trafic du récepteur delta opiacé : vers une meilleure compréhension des bases cellulaires de la tolérance analgésique aux opioïdes

Activation of G protein coupled receptors (GPCR) triggers a regulatory response in parallel with signaling processes. This response is initiated by receptor phosphorylation followed by β-arrestin (βarr) recruitment, receptor internalization, and subsequent sorting towards either the degradation pathway or recycling back to the membrane. Numerous reports have spoken of delta opioid receptor (DOPr) ligand-biased responses among signaling and regulation cascades. This functional selectivity may explain the differential profiles of these ligands to produce analgesic tolerance in vivo. Indeed, it has been shown that biased ligands that preferentially activate the signaling pathway over internalization produce less analgesic tolerance than those producing receptor internalization. On the other hand, the post-endocytic sorting mechanisms (recycling or degradation) of receptors have recently been the cornerstone for understanding the molecular basis of this analgesic tolerance. In this context, ligands producing receptor recycling following internalization have been shown to produce sustained analgesic action by comparing them to those sending the receptor to the degradation pathway. In the light of these observations, this study was conducted to better understand the molecular determinants underlying the loss of analgesic efficacy following prolonged opioid administration. We first wanted to evaluate how signaling versus internalization bias predicts analgesic tolerance in vivo, and secondly we are interested in describing the post-endocytic route of DOPr and how it prevents this tolerance. We then demonstrated that there is a measurable signaling versus internalization bias for some DOPr agonists using novel pharmacological tools for quantifying bias. This bias measured in HEK293 cells did not predict the analgesic tolerance in vivo and the DOPr internalization properties were different between HEK293 cells and neurons, where opioids exert their analgesic functions. This raises the question whether the observed bias would be maintained across the different biological systems. We were then interested to study the post-endocytic trafficking mechanisms as an alternative for understanding this analgesic tolerance. We established that the late endosome sorting mechanism involved the ALG-2-interacting Protein X (Alix) and the tail-interacting protein 47 (TIP47)/Rab9 retrieval complex, which support translocation of the receptor to the trans-Golgi network (TGN), from where it is subsequently recycled to the cell membrane. Preventing DOPr from completing this route precipitated acute analgesic tolerance, supporting the relevance of this recycling path in maintaining the analgesic response by this receptor. These results provide relevant insights for the process of screening new opioids with sustained analgesic activity.

Keyphrases: DOPr, TGN, Rab9, TIP47, ALIX, GPCR, Signaling, Internalization, Functional selectivity, Operational model, Recycling, Analgesic tolerance
Détection à grande échelle des réarrangements génomiques et élucidation de leurs mécanismes

Genome instability is defined as a high mutation rate in an organism, ranging from single nucleotide variations to rearrangements involving large chromosome segments. These mutations can occur following the repair of DNA damage by error-prone mechanisms, or even as a result of normal DNA metabolism processes. Some rearrangements at specific loci are linked to genetic diseases, whereas diseases like cancer exhibit generalized genomic instability. To study mechanisms leading to genome instability, we developed a new approach to detect DNA rearrangements from next-generation sequencing data. This approach differs from previous methods by its high sensitivity and base-pair resolution, which provide a more accurate portrait of the variations present in the genome of an organism. This has allowed us to characterize the genome instability present in the chloroplast of Arabidopsis thaliana and in the human mitochondrion. We thus discovered a high level of short-range inversions in these genomes, which can occur as a result of replication U-turns. U-turns are linked to replication fork stalling, but the steps and factors involved in this mechanism remain poorly understood. Using A. thaliana mutants, we have determined that the single-stranded DNA-binding Whirly proteins and the RecA family of recombinases both act to suppress replication U-turns. We then created a computer script to allow our approach to be used on larger genomes, and discovered the presence of U-turns in the nuclear genomes of humans and Saccharomyces cerevisiae. We compared DNA rearrangements in various yeast mutants under different conditions of replication stress, and established a correlation between stabilized stalled replication forks and replication U-turns. Our results highlight the importance of replication U-turns as a mechanism of genome instability in the genomes of several organisms. While U-turns appear mainly as an error-prone mechanism to restart stalled replication forks, it is interesting to note that it does not involve any double-strand break intermediates. We therefore propose that U-turns may also favor resistance to DNA damage when the homologous recombination machinery is not available.

Keyphrases: chloroplastes, mitochondries, DNA repair, genome rearrangements, stalled replication forks, double-strand breaks, next-generation sequencing, chloroplasts, nucleus
Mécanismes moléculaires de régulation de l’interaction SOCS1-p53 et leurs impacts sur la suppression tumorale

Tumor suppressor mechanisms are among the main processes that protect the organism against the development of malignant tumors. These mechanisms are numerous and each of them is regulated by a plethora of signaling pathways. These different signaling pathways, however, tend to converge towards the activation of a few central proteins, like p53, the so-called guardian of the genome for example, that are considered the main tumor suppressors of the cell. These proteins can themselves control many different mechanisms of tumor suppression. The specificity by which p53 controls one signaling pathway over another is still badly understood. Since this protein is involved in the malignant transformation of cells, the comprehension of how these functions are regulated is crucial in order to be eventually able to modulate their activities in specific contexts like cancer. Our laboratory has discovered that SOCS1 (Suppressor of Cytokine Signaling 1), a protein mainly considered as a tumor suppressor and a negative regulator of inflammatory signaling pathways, interacts with p53 in the context of cellular senescence and facilitates its phosphorylation by ATM (Ataxia Telangiectasia Mutated) and thus its activation. How SOCS1 controls the p53 signaling pathway, however, remained unknown. The goal of this thesis was to understand how SOCS1 regulates the p53 signaling pathway. First of all, we identified the transcriptional targets of p53 that are specifically modulated by SOCS1. P53 is known to regulate hundreds of targets and those important for tumors suppression still constitute a debate. One approach used to better understand how p53 functions is to identify which targets are important in which context. Knowing which p53 pathways are regulated by SOCS1 allowed us to discover that SOCS1 can regulate ferroptosis, a type of programmed cell death that seems very important for the tumor suppressor functions of p53. We then aimed our efforts at identifying the molecular components regulating the interaction between p53 and SOCS1. We determined that the amino acids tryptophan 53 and phenylalanine 54 of p53 TAD2 are crucial for the interaction with residues tyrosine 80 and tryptophan 81 within the SH2 domain of SOCS1. Mutating Y80 and W81 of SOCS1 results in a loss of interaction with p53 and the incapacity for SOCS1 to arrest the growth of cancer cells. We also discovered a new mode of regulation of SOCS1: the protein is phosphorylated on Y80 by the SRC family kinases. This phosphorylation seems to inhibit SOCS1’s tumor suppressor functions and is deregulated in the tissue samples of patients with lymphoma compared to normal lymph node samples. Finally, we discovered that SOCS1 can form dimers, both in vitro and in cells and it is the phosphorylated form of SOCS1 that dimerizes. This opens the door to a new biology for SOCS1.

Keyphrases: SOCS1, p53, Senescence, Phosphorylation, Kinases SRC, Cancer, YES1, SFK, Ferroptosis, Kinases, SFKs, SRC
Bayesian codon models for detecting convergent molecular adaptation

Modeling the interplay between mutation and selection at the molecular level is one of the primary goals in molecular evolution. Massive acquisition of genetic sequence data in recent years has provided a wealth of information for such empirically-driven studies. Codon-based models are increasingly used to give a realistic description of the substitution process in protein-coding genes. Among them, the mechanistic codon-based modeling approach distinctly parameterizes mutational and selective effects bearing on the overall substitution process. These mechanistic approaches characterize the selective pressure by relying on an explicit model of the amino acid fitness landscape over the sequence. Thus far, a constant fitness landscape has generally been assumed. Yet, there are some situations in which the fitness landscape experiences some environmental fluctuations through time. When the empirical knowledge about the systematic difference in selective pressures is available, regarding the fluctuating environment, it is possible to explicitly model condition-specific amino acid fitness modulations. In this thesis, we developed a codon-based model to capture these differential condition-specific selective effects on coding sequences. This model was implemented in a Bayesian framework and was first applied to HIV, which evolves under the selection pressure of the host immune system. Our Differential Selection (DS) model describes the detailed mechanisms of evolution of HIV under the constraints defined by host genetic backgrounds (e.g., Human Leukocyte Antigen). Therefore, it is possible to find associations between specific viral adaptations and specific HLA alleles of the hosts. Ultimately, our approach will enable us to understand better how the virus escapes from the host immune response, which will, in turn, provide a useful guideline for designing an efficient vaccine against AIDS. We also applied the DS model on Rubisco, an enzyme responsible for a major step in photosynthesis. The evolution of Rubisco has been shown to be different in C3 and C4 plants, as a consequence of differing environmental conditions. We used the DS model to reveal the consistent patterns of convergent adaptation in Rubisco in C4 plants, compared to C3 plants.  Finally, we contrasted our results from DS model with those obtained under classical codon models based on the estimation of dN/dS. This comparative analysis allows us to illustrate a fundamental conceptual difference between these two types of codon models, which are meant to detect different selective regimes: directional selection versus ongoing adaptation.

Keyphrases: Mutation, Rubisco, Evolution, Mutation, Codon Model, Selective Pressure, Bayesian Inference, Differential Selection, HIV, Rubisco
Epigenetic regulation of innate immune responses to infection

The importance of epigenetic modifications in the control of gene expression is widely accepted. Yet, it often remains unclear whether altered epigenetic patterns themselves invoke transcriptional modulation or are instead downstream consequences of regulatory factors. During my thesis, I investigated the role of DNA methylation in the regulation of innate immune responses. Specifically, I performed an integrated analysis of data on genome-wide DNA methylation, histone modifications, chromatin accessibility, and gene expression, in dendritic cells (DCs), before and after infection with Mycobacterium tuberculosis (MTB). I demonstrate that the immune response to infection is associated with loss of methylation at thousands of CpG sites, independent of cell proliferation. Active demethylation was specifically targeted to distal enhancer elements and was strongly associated with induction of nearby genes. However, time course analysis further indicates that most changes in gene expression in response to infection occur prior to detectable changes in DNA methylation. Footprinting analysis revealed that the recruitment of immune-related transcription factors, such as NF-κB/Rel, to these regions preceded the observed loss in methylation. Interestingly, levels of methylation at differentially methylated CpG sites never reverted back to higher levels during the course of infection, even among genes for which expression levels return to basal state. Collectively, these results show that DNA demethylation is likely not crucial for the establishment of the core regulatory program engaged by innate immune cells in response to a pathogen. Instead, it might play a role in the establishment of epigenetic memory, which allows for a faster response to a secondary infection. More generally, the results from this thesis opens the door for using DNA methylation marks as a predictive biomarker of past or present infection.

Keyphrases: Epigenetics, DNA methylation, Gene regulation, Infection
Analyse du rôle de l’interaction de VirB6 avec VirB10 dans le système de sécrétion de type IV

Infectious diseases are a major problem worldwide. Propagation and resistance to treatment are partly due to the fact that several bacterial pathogens use multiprotein complexes, such as type IV secretion systems (T4SSs), to deliver macromolecules directly to other cells. T4SSs are important for two fundamental reasons: the genetic exchange of plasmid DNA and the transfer of effectors in the target cell. These functions allow adaptation of pathogens to environmental changes and disruption of host defense mechanisms. T4SSs are typically composed of 12 proteins (VirB1-VirB11, VirD4) that can be divided into three groups, the pilus components, the central pore and the ATPases.  My Ph.D. research is focused on VirB6, an essential membrane protein of the T4SS, and in particular on its interaction with VirB10, to define its role for the structure and function of T4SS. In our first publication, we showed an interaction between these proteins leading to the main hypothesis: VirB6 interacts with VirB10 to deliver the substrates to the periplasmic components of the T4SS and to recruit VirB2/VirB5 complex, enabling pilus assembly and substrate transfer. To test this hypothesis, we used a three-pronged approach to obtain information on these interactions and on their functions. Firstly, site-directed mutagenesis was performed on VirB6 and we then evaluated the consequences on the interaction with VirB10 using the bacterial two-hybrid assay to identify the specific residues involved in the interaction. Then the effects of changes of these residues on complementation were tested using in vivo assays with the Agrobacterium tumefaciens and pKM101 T4SSs. Finally, we overexpressed and purified VirB6 for in vitro structural characterization, including SAXS, electron microscopy and various biochemical methods.  Understanding how these systems allow bacteria to invade hosts and survive is critical for the development of new antimicrobial treatments. It is essential to understand the molecular details of protein-protein interactions to evaluate their dynamics and their functions within these machineries. Better mechanistic insights into these systems will enable targeted inhibitor design that may lead to improved treatment of infectious diseases.

Keyphrases: Agrobacterium tumefaciens, VirB6, VirB10, Virulence, Type IV secretion system, Protein-protein interaction, Membranes proteins, Functionality
Arginine methylation by PRMT1 and PRMT5 regulates B cell activation, germinal center expansion and differentiation into plasma cells

Adaptive immunity relies in part on the ability of B cells to generate specific antibodies against foreign antigens. B cells develop in the bone marrow, and once they express a functional antibody at their surface, they reach secondary lymphoid organs where they will be exposed to foreign poly-peptides. Upon encounter with a cognate antigen, B cells proliferate rapidly, migrate to the border of the B cell follicle to receive T cell help and move back within the B cell follicle to form structures called germinal centers (GC). In GCs, B cells undergo affinity maturation, which increase the affinity of the antibodies, and antibody class switching to diversify their function. B cells exit GCs by differentiating into (i) memory B cells that can rapidly be activated following a second encounter with the pathogen or (ii) plasma cells that secrete antibodies in circulation to neutralize and clear pathogens. Post-translational modifications regulate several aspects of B cell biology such as B cell development, activation and differentiation. My thesis investigates the role of arginine methylation in B cells during T-dependant immune responses, focusing on two enzymes: the protein arginine methyltransferases 1 and 5 (PRMT1 and PRMT5), using mice as models. We have uncovered that Prmt5 is necessary during B cell development. In particular, Prmt5 is required at the pro-B cell stage in a p53-dependant manner and at the pre-B cell stage in a p53-independent fashion. Prmt5 is necessary for the expansion of the GC by promoting B cell proliferation and limiting plasma cell differentiation. These functions could originate, among other mechanisms, from the Prmt5 role in enforcing splicing fidelity and regulating gene expression. We have also discovered that Prmt1 is a major negative regulator of plasma cell differentiation, particularly following CD40 stimulation. Furthermore, we obtained evidence that Prmt1 and Prmt5 function synergistically to negatively regulate plasma cell differentiation. Overall arginine methylation by Prmt1 and Prmt5, via different mechanisms, influences GC B cell fate; by promoting B cells to remain in the GC reaction, at least in part by repressing plasma cell differentiation, thereby supporting antibody responses and enhancing affinity maturation.

Keyphrases: PRMT1, PRMT5, humoral immunity, B cell fate, germinal center, arginine methylation
Rôle et impact des protéines associées à la lame basale spécialisée dans l’attache gingivale et la maladie parodontale

The body is surrounded by an epithelial envelope to protect itself from the aggressive environment around it. The tooth is the only structure in the body that creates a breach of this epithelial barrier. It is also constantly exposed to a humid, warm and nutrient-rich environment that is a perfect medium for the growth of micro-organisms. To prevent and control the intrusion of external organisms such as bacteria, the body has developed the so-called dento-gingival junction. This epithelial attachment separates the underlying periodontal tissues from the septic oral medium by creating a seal around the tooth, thus forming a true barrier against bacteria. These are recognized as causative agents in the initiation and development of periodontal disease. Indeed, by their enzymatic activities, oral bacteria break the seal of the dento-gingival junction to expose underlying tissues to toxins and microorganisms leading to periodontal diseases. Periodontal diseases affect a large part of the population and their severity increases with age. Mild to moderate forms affect more than 80% of adults, while about 15% suffer from periodontitis. In the most severe cases, periodontal disease eventually leads to loss of tooth and bone. Beyond the serious consequences of this disease on the oral cavity, there is growing evidence that periodontal disease is related to various systemic diseases such as cardiovascular and respiratory diseases but also diabetes. Periodontal disease affects the quality of life but also represents a heavy financial and health burden for the patient and society. There is currently no cure for this widespread disease and the treatment is based on continuous and surgical management. It is then urgent and necessary to develop new treatments. It is crucial to understand precisely the architecture and composition of the extracellular matrix allowing sealing to open up new horizons for the fight against periodontal disease and for the development of preventive and / or therapeutic treatment.

Keyphrases: Junctional epithelium, Specialized basal lamina, Extracellular matrix, Periodontal diseases, Bacteria
Régulation de l’activité transcriptionnelle des récepteurs des estrogènes (ER) par le récepteur aux chimiokines CXCR7 et par la propyl isomérase Pin1

Estrogen receptors signaling, ERα and ERβ, is largely involved in the development, growth and progression of hormone-dependent cancers, including ovarian and breast cancer. In epithelial ovarian cancer, we identified a positive regulatory loop between the chemokine receptor CXCR7 and ERα. First, the expression of CXCR7 and its ligand I-TAC is upregulated in ovarian cancer cells ER + and this up-regulation is mediated by ERα and E2. Integrative analysis of TCGA gene data for high grade serous epithelial carcinoma reveals a positive correlation between CXCR7 and ERα expression. In addition, the chromatin immunoprecipitation and luciferase assays demonstrate that E2-ERα binds to an ERE located in the CXCR7 promoter and activates its expression. Next, CXCR7 in turn up-regulates ERα by increasing its E2-induced transcription through phosphorylation of pSer-118 of ERα. The phosphorylation of Ser-118 induced by E2 appears to be amplified by CXCR7. In addition, knockdown of CXCR7 alters the expression of epithelial-mesenchymal transition markers such as E-cadherin, N-cadherin, and Snail, suggesting that CXCR7 depletion might negatively regulate estrogen-induced EMT signaling pathways during the migration of ovarian cancer cells. In breast cancer, we have identified a mechanism by which Pin1 isomerase regulates the transcriptional activity of ERβ. We found that phosphorylated ERβ is a substrate for Pin1. In this context, Pin1 interacts with ERβ and this interaction is increased by E2. The effect of this interaction has the consequence of increasing the transcriptional activity of ERβ, and this through the phosphorylation of ERβ serine-87 which is targeted by ERK1/2. In addition, the interaction of Pin1 with ERβ promotes the stability of ERβ while increasing the migration of mammary cancer cells induced by E2-ERβ.

Keyphrases: ER, CXCR7, Activation, Pin1, Estrogen receptors, Estrogen, Target gene, Breast cancer, Ovarian cancer