NCube/papyrus huggingface dataset:
Le traitement non chirurgical du cancer du rein localisé : analyses populationnelles

The present thesis focus on the nonsurgical management of localized kidney cancer. Specifically, local tumor ablation and observation are studied under 4 chapters and six articles. In the first chapter, which contains two articles, we studied the complication profile of local tumor ablation. In the first study, using an american database of hospitalisations, we studied inpatient complications following local tumor ablation. We found that one patient out of six experienced a complication and that age, comorbidities and low hospital volume were independent predictors of complications. In the second study, we compared 30-day complication rates (both in- and outpatient) of percutaneous and laparoscopic local tumor ablation. We found similar complication (21% and 25%, respectively) and mortality rates. Moreover, no differences in multivariable analyses were recorded. In the second chapter, which also contains two studies, we focussed our attention on practice patterns of local tumor ablation in North America. In the first study, a survey was sent to canadian urologists to identify which type of ablation was more commonly used and in what context. Interestingly, we found that a important proportion of urologists did not have access to local tumor ablation and were also rarely involved in the procedure. In the second study, we evaluated sociodemographic disparities in the choice between observation and local tumor ablation for the treatment of localized kidney cancer. We found that several suggestive characteristics such as African-American ethnicity, male gender, low socioeconomical status or unmarried status were associated with lower acces to local tumor ablation compared to observation. In the third chapter (one study), we compared oncological outcomes (cancer- specific and other-cause mortality) following local tumor ablation and observation in a large american cancer registry. In multivariable competing-risks analyses, we found that local tumor ablation was associated with a 53% diminution in cancer- specific mortality compared to observation. In the fourth and last chapter (one study), we used preoperative characteristics to construct a model predicting cancer-specific and other-cause mortality following either surgery or observation for localized kidney cancer. This model can be used to help clinicians counsel their patients by providing them objective information.

Keyphrases: Observation, Patients âgés, Complications, Local tumour ablation, Nonsurgical management, Oncologic outcomes, Kidney cancer, Elderly patients, Practice patterns, Competing mortality
The Role of CBL Family Proteins in Dendritic Cell Development, Homeostasis, and Functional Quiescence

Dendritic cells (DCs) are innate immune cells that play an important role in immune recognition against foreign pathogens. They may also sense self-cues and prevent autoimmune diseases under the steady-state. Given the importance of DCs in immune regulation, it is conceivable that understanding how DCs development, homeostasis and functional quiescence are regulated under physiological and pathological conditions will not only bring insight into our knowledge how immune regulation is controlled but also some new approaches to treat infectious and autoimmune diseases and even cancers. Dr. Gu’s lab previously has shown that C-CBL and CBL-B, two members of the CBL family of E3 ubiquitin ligases, play a redundant negative regulatory role in both T cells and B cells development and activation. In the absence of CBL family of proteins in either T or B cells, mice develop severe autoimmune diseases, indicating that C-CBL and CBL-B restrain immune system against self. Based on these discoveries, we propose that C-CBL and CBL-B may also have a similar regulatory role in DC development and function. To study this possibility, we have generated DC-specific Cbl dKO mice. We have found that the Cbl dKO mutation results in an altered homeostasis of DC subsets, including a marked increase of CD8a+ cDCs and reduction of pDCs in the spleen (SP). This alteration is due to the enhanced proliferation of CD8a+ cDCs rather than the preferential lineage commitment to CD8a+ cDCs. In the mutant CD8a+ cDCs, both the PKB signaling pathway and ERK signaling pathways are constitutively activated. Blockage of MTOR signaling by Rapamycin significantly attenuates the hyperproliferation of CD8a+ cDCs both in vitro and in vivo, indicating that hyperactivation of MTOR is at least one of the reasons leading to CD8a+ cDC expansion. CBL proteins regulate ubiquitination and degradation of FLT3. Based on these results, we conclude that CBL proteins control CD8a+ cDC homeostasis through promoting FLT3 ubiquitination and degradation. In addition to the altered DC development, we have found that Cbl dKO mice develop severe liver and other organ inflammation characterized by massive leukocytes infiltration and profound peripheral T cell activation. Mutant mice produce high levels of inflammatory cytokines and chemokines including TNF-a, IL-6, CCL2, etc. Most strikingly, the mutant mice develop a similar liver inflammatory disease even in the absence of T and B cells. These findings together indicate that CBL proteins play an essential role in the maintenance of immune quiescence in mice. Since  Cbl dKO mice mainly develop severe liver inflammation, it will be interesting to study whether the pathways controlled by CBL proteins also contribute to the development of liver inflammation in humans.

Keyphrases: DC, Quiescence, Cbl-b, C-cbl, Flt3, Ubiquitination, Homeostasis, Chronic Inflammatory Disease
Mesure des changements de matière grise et de la connectivité cérébrale suite à un entrainement à des jeux vidéo

The aim of this work is to provide evidence in neuroimaging about the effect of video games on the brain. To this end, anatomical and behavioral characteristics of non-players were assessed before and after training in action (Call of duty)  and / or platform video games (Super Mario 64). The effect of these types of game has already been studied and their impact on the brain demonstrated at the striatal and hippocampal levels respectively. Taking into account the results present in the literature as to a possible interaction effect of a training to these types of video games and the navigation strategy adopted by the subject. This last one was evaluated beforehand and after the training through the "4/8" behavioral task .  The results indicate that training in an action video game reduces the amount of gray matter in the hippocampus and improves it in the amygdala in adults who use a so-called response or stimulus response strategy ", a strategy based on memorizing a series of actions from a stimulus. While there is an increase in gray matter among those using a spatial strategy, a strategy requiring the linking of elements of the environment to guide oneself and the elaboration of a cognitive map. The training of a platform-type video game shows an improvement of the gray matter in the hippocampus and the entorhinal cortex. These structural changes are reflected in the diffusion measures. An increase in the fractional anisotropy within the hippocampus and an increase in the connectivity between the hippocampus and the entorhinal cortex in adults using a spatial strategy are noted following the training in the platform video game. While in action video game players there is an improvement in fractional anisotropy within the amygdala. The latter using a spatial strategy have an improvement in this index in the hippocampus. Thus, it appears that a training in a video game can be beneficial or detrimental depending on the type of game but also on the navigation strategy used. The spatial navigation strategy appears to be protective, experience with action video games may be detrimental to the hippocampus of players using a response navigation strategy, and platform-type video games with a strong navigation component are beneficial to the hippocampus. Structure that is known plays a crucial role in learning, navigation and is particularly affected by neurodegenerative diseases. It has also been shown that training in a platform game enhanced the executive functions, more specifically oculomotor inhibition in older population (55-75 years) and gray matter in the frontal eye field. Thus, this type of game could counter the deleterious effects related to age (decrease of the inhibition) and improve the gray matter at the level of the hippocampus even if evidence remains to be done more specifically in this population.

Keyphrases: Striatum, Video game, Hippocampus, Striatum, Amygdala, Caudate nucleus, Navigation strategy, 4/8, Entorhinal cortex, Aging, Plasticity
Impact de la modification du métabolisme primaire des cellules CHO sur leur productivité

Antibody-based therapy is a promising approach for cancer treatment. Chinese hamster ovary (CHO) cells represents the most common and efficient antibody expression platform for large scale production. Their abilities to perform human-like glycosylation and produce high antibody titer make them the most suitable system compared to other continuous cell lines. In the past few years, advances in fed-batch process development led to significantly increase production yields. Nevertheless, the metabolic features of continuous cell lines constitute a hurdle to the improvement of process performances. Continuous cell lines typically exhibit a deregulated glycolysis and glutaminolysis causing the accumulation of toxic metabolites such as lactate and ammonia. Thus, only a small percentage of pyruvate, derived from glucose, is incorporated into the tricarboxylic acids (TCA) cycle explaining at least, in part the inefficient CHO cell metabolism. The mitochondrial pyruvate carboxylase, which catalyzes the conversion of pyruvate into oxaloacetate, is one of the key enzymes at the junction of the glycolysis and the TCA cycle. In CHO cells, only 5-10 % of the pyruvate pool is metabolized via this pathway. In this project, we hypothesized that counteracting the pyruvate carboxylase deficiency in CHO cells could alleviate in part, the deregulated glycolysis and consequently improve antibody production yield while maintaining satisfactory antibody glycosylation. In this work, a recombinant CHO cell line producing an antibody was further genetically modified with the insertion of a cytoplasmic yeast pyruvate carboxylase (PYC2) gene. Cultivated in fed-batch mode, PYC2 cells exhibited enhanced cell growth and antibody production yield compared to the parental cell line. Metabolic flux analysis using isotopic tracer led to a detailed characterisation of both cell line metabolism. The metabolic flux distribution obtained highlighted major differences in lactate and TCA fluxes. Comparative glycosylation analysis revealed that the metabolism alteration associated with the increase in antibody production did not significantly alter the product quality.  This work seems to corroborate the presumed existence of a link between metabolism and antibody productivity. The cell metabolism characterization and more precisely, lactate production contribute to gain knowledge in CHO cell metabolism and led to rationally improve cellular functions and culture conditions.

Keyphrases: glycosylation, CHO cells, antibody, fed-batch, metabolism, lactate, metabolic flux analysis, glycosylation
Décodage de l'expression de gènes cryptiques

Thanks to new high throughput sequencing technologies and automatic annotation pipelines, proceeding from an eppendorf tube to a genbank file can be achieved in a single mouse click or so, for some species. Others, however, fiercely resist bioinformaticians with their confounding genomic complexity. Diplonemids are one of them. My thesis is centered on the discovery of new strategies for encrypting genetic information in eukaryotes, and the identification of molecular decoding processes.  Diplonemids are a group of poorly studied marine protists. Unexpectedly, metagenomic studies have recently ranked this group as one of the most diverse in the oceans. Yet, their most distinctive feature is their multipartite mitochondrial genome with genes in pieces, and encryption by nucleotide deletions and substitutions. Genes are decrypted at the RNA level through three processes: (i) trans-splicing, (ii) polyuridylation at the junction of gene pieces and (iii) substitutions of A-to-I and C-to-T. Such a diverse arsenal of mitochondrial post-transcriptional processes is highly exceptional.  Using a bioinformatics approach, I have reconstructed the mitochondrial transcriptome from RNA-seq libraries. We have identified six new genes including one that presents alternative trans-splicing isoforms. In total, there are 216 uridines added in 14 genes with up to 29 U insertions, and 114 positions edited by deamination (A-to-I or C-to-T) among seven genes (nad4, nad7, rns, y1, y2, y3, y5).  In order to identify the machinery that processes mitochondrial RNAs, the nuclear genome has been sequenced. I have then assembled and annotated the genome. This machinery is probably unique and complex because no cis signal or trans actor typical for known splicing machineries have been found. I have identified promising protein candidates that are worth to be tested experimentally, notably RNA ligases, numerous members of the PPR family involved in plants RNA editing and deaminases.  During my thesis, we have identified new types of post-transcriptional RNA processing in diplonemid mitochondria and identified new promising candidates for the machinery. A system capable of joining precisely or editing RNAs could find biotechnological applications. From an evolutionary perspective, the discovery of new molecular systems gives insight into the process of gene recruitment, adaptation to new functions and establishment of complex molecular machineries.

Keyphrases: Annotation, Bioinformatics, Genomics, RNA editing, Trans-splicing, Genome assembly, Genome annotation
Vérification de la corrélation entre la fonction, la structure et la dynamique sur un chemin évolutif recombinant les β-lactamases TEM-1 et PSE-4

The link between enzyme structure and function is well established and has led to the description of many catalytic mechanisms. However, how enzymes accelerate the catalytic rate so drastically is still not fully understood. A growing amount of evidence linking protein dynamics to function, suggests that protein motions might have functional implications. This compels us to verify this correlation in an evolutionary context and to verify if protein dynamics should be considered to better engineer enzymes. Our studied enzymatic model is composed of two homologous and naturally evolved bacterial resistance enzymes, the TEM-1 and PSE-4 β-lactamases. By characterizing these structurally and functionally similar enzymes, we verified if protein dynamics are evolutionarily conserved. Our results show that TEM-1 and PSE-4 maintain similar patterns of restricted dynamics on timescales ranging from picoseconds to milliseconds. This supports the hypothesis that dynamics have been evolutionarily maintained in these enzymes and is consistent with a contribution of dynamics to enzyme function resulting in the evolutionary maintenance of dynamics. Various approaches are used to engineer proteins. Homologous recombination is extensively applied, as it mimics natural evolution. This technique allows the incorporation of many simultaneous sequence variations selected over the course of evolution. Our enzymatic model includes three chimeric enzymes, resulting from the recombination of TEM-1 and PSE-4. These represent intermediates over a hypothetical evolutionary path from TEM-1 to PSE-4. These artificially-evolved enzymes were selected to compose this system of evolutionarily related protein on the basis of their active site cavity having been recombined. A conservation of function, structure and fast dynamics was found in these chimeras. Striking variations of slow dynamics, occurring on a timescale coinciding with the catalytic turnover rate, were also observed. In silico exploration of the conformations adopted by the catalytic residue side-chains showed variations correlating with the functional diversification between TEM-1, PSE-4, and the chimeric β-lactamases. These results highlight the importance of probing motions on various timescales to fully comprehend their role in function. We propose that dynamics on the faster timescales are associated with the maintenance of reactivity in these enzymes, while modification of the slow dynamics may be associated with the high evolvability of these bacterial resistance enzymes.

Keyphrases: β-lactamases, chimeras, evolution, protein engineering, structure-function-dynamic analysis, X-ray crystallography, enzymatic kinetics, nuclear magnetic resonance, in silico molecular dynamic simulations
Caractérisation du rôle de Citron Kinase durant la cytokinèse

Cytokinesis is a multistep process that allows two sister cells to undergo complete separation following mitosis. Cytokinesis requires the formation of a contractile ring (CR) that will drive cleavage furrow ingression at the equator of the cell. One of the crucial steps in this process is the transition from a dynamic CR to a more stable structure named the midbody ring (MR), which directs the final separation or abscission. Our knowledge of the molecular mechanisms involved in the CR-to-MR transition would presumably improve our understanding of the molecular complexes involved throughout cytokinesis from initiation to abscission. Defects that occur during this transition can lead to the formation of bi-nucleate tetraploid cells that are often observed in pathological conditions such as cancer. I have used Drosophila melanogaster Schneider’s S2 cells to study the CR-to-MR transition. My findings have highlighted a previously uncharacterized maturation process essential for the transition. More specifically, I demonstrate that the Citron Kinase, Sticky, and the Septin, Peanut, have opposing actions on the scaffold protein Anillin to either retain or extrude, respectively, membrane-positive proteins during the CR-to-MR transition. Indeed, Sticky depletion by RNAi led to uncontrolled loss of membrane-associated Anillin at the MR. Conversely, Peanut depletion led to inhibition of MR maturation by membrane extrusion. Co-depletion of Sticky and Peanut led to oscillatory movements of the CR, typical of Anillin depletion. Sticky is a cortical protein during cytokinesis whose role and interacting partners are controversial. I have performed a structure/function analysis of Sticky to better define its role and regulation during cytokinesis. My work shows that Sticky has two mechanisms of cortical localization. The first is through an Anillin interaction and the second is through the small GTPase Rho1, a master regulator of cytokinesis. Sticky can localize to the cortex in the absence of either one of these mechanisms. However, loss of both inhibits its localization. Following the identification of the minimal interaction sites of Anillin and Sticky, I expressed an Anillin mutant that lacked part of this site and found that cells failed cytokinesis in a similar manner to cells depleted of Sticky. Mutation of the Rho1 binding site on Sticky produced similar cytokinesis failures. Altogether, the results suggest that Sticky interacts with Anillin and Rho1 at the cortex to guide the transition from dynamic CR to stable MR. This thesis advances our understanding of cytokinesis by highlighting a previously uncharacterized process of MR maturation and by defining the importance and regulation of Citron Kinase during this process.

Keyphrases: Citron Kinase, Anillin, Cytokinesis, Midbody ring, Contractile ring, Sticky, Peanut, Septin, RhoA, Rho1
L’immunoprotéasome : régulateur de transcription et promoteur de survie cellulaire

By regulating protein degradation, constitutive proteasomes (CP) control practically all cellular functions. In addition to CP, vertebrates express immunoproteasomes (IP), which display distinct substrate preferences. The first non-redundant role ascribed to IP is its enhanced ability to generate MHC I-associated antigens. However, deletion or inhibition of IP subunits can affect several immune cell functions independently of MHC-I antigen generation. Moreover, recent work has shown that IP can be expressed in non-immune cells to deal with cell stress. Thus, we wished to investigate the roles of IP that are not related to antigen generation and that are not redundant with the CP. Based on profiling of WT and IP-deficient maturing mouse dendritic cells (DCs), we report that IP regulate the expression of more than 8,000 transcripts. The broad impact of IP on gene expression is cell-autonomous, mediated mainly at the transcriptional level, and involves major signaling pathways including IRFs, NF-kB and STATs. Moreover, even when engineered to present optimal amounts of antigenic peptides, IP-deficient DCs are inefficient for in vivo T-cell priming. In addition, consistent with the fact that cancer cells endure proteotoxic stress, we report that acute myeloid leukemia (AML) cells from patients express high levels of IP genes. Expression of IP genes in AML is a cell-autonomous and IFN-independent feature that correlates with the methylation status of IP genes, and is particularly high in AML with a monocytic phenotype and/or MLL rearrangement. Notably, IP inhibition leads to accumulation of polyubiquitinated proteins and cell death in IPhigh but not IPlow AML cells. Co-clustering analysis reveals that genes correlated with IP subunits in monocytic AMLs are primarily implicated in cell metabolism and proliferation, mitochondrial activity and stress responses. Overall, our studies show that the role of IP is not limited to antigen processing and reveals major non-redundant roles for IP in transcription regulation and resistance to cell stress in AML.

Keyphrases: Ubiquitin-proteasome system, Immunoproteasome, RNA-Seq analyses, Gene regulation, Proteotoxic stress, Cancer, Acute myeloid leukemia, Proteasome inhibitors