The brain extracellular space (ECS) contains specified macromolecules forming the extracellular matrix (ECM), containing a high amount of negative charges that could bind water or other soluble ions and molecules diffusing within the ECS. In specific brain areas, the ECM molecules form a condensed, reticular-like structure of perineuronal nets (PNNs). It has been found that PNNs appear at the end of the critical period, when they stabilize the synapses and terminate their plasticity and may have also neuroprotective function. To study the role of brain link protein 2 (Bral2) in stabilizing the ECM complexes, we employed the real-time iontophoretic method and immunohistochemical analysis to show the difference in the ECS diffusion parameters and level of expression of the ECM molecules between the wild type and Bral2-deficient mice. We also compared changes in the ECS diffusion parameters induced by Bral2 deficiency with those appeared after enzymatic destruction of the ECM by the chondroitinase ABC (chABC). In the Bral2-deficient mice, we discovered significantly decreased values of tortuosity in the trapezoid body. This difference was age related and did not manifest itself in young mice. Immunohistochemical analysis showed that inferior colliculus does not contain Bral2-brevican based...

The extracellular matrix is a multi-functional environment that cells inhabit to form living tissue. To maintain the tissue, cells require constant telemetry with the matrix and respond to a variety of cues by remodeling matrix architecture. In this study the physical and biochemical manipulation of the matrix by resident cells is explored to better understand how these are used to remodel tissue. Cell-populated collagen hydrogels are used as a controllable in vitro tissue model. To directly measure mechanical forces involved with gel contraction, a culture force monitor was designed and built. Measuring dimensional changes together with contractile forces presents a method of separating mechanisms that influence tissue remodeling. Together, these techniques revealed a correlation between contractile force and gel deformation, suggesting a novel method for examining the material properties of the matrix. Limiting matrix metalloproteinase (MMP) activity altered the correlation as predicted, indicating a stiffer matrix. Contractile force was found to be regulated independent of MMP activity. In contrast, contractile force was found to be dependent on α2β1 integrin function. Collagen gel contraction correlated with both α2β1 function and MMP activity, and was significantly enhanced when combined. The results of this study indicate cells have the capacity to use multiple mechanisms for remodeling the extracellular matrix and may alternately use them together or independently to vary the rate of matrix contraction.

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La nétose du polynucléaire neutrophile (PN) correspond à la libération de filaments d’ADN recouverts de protéines appelés Neutrophil Extracellular Trap (NETs). Outre leur rôle anti-infectieux, les NETs représentent des acteurs émergents de nombreuses pathologies inflammatoires et nous avons souhaité évaluer leur implication au cours de réactions allergiques.Au cours d’une étude clinique multicentrique notre équipe a mis en évidence un mécanisme alternatif de l’anaphylaxie aux curares, impliquant les PN. La phase aiguë de ces réactions s’accompagne d’une libération de NETs dont la concentration est corrélée avec la sévérité et avec une diminution de l’expression des récepteurs activateurs des IgG à la surface des PN (FcγRs) ; ceci suggère un rôle des complexes immuns (CI) IgG/curares dans la formation des NETs au cours de ces réactions anaphylactiques.Pour confirmer cette hypothèse, la capacité d’activation de la nétose par les CI IgG a été étudiée, via la mise au point d’un modèle de stimulation in vitro des PN humains purifiés.Ce travail montre que 2 récepteurs aux IgG du PN (FcγRIIa et FcγRIIIB) contribuent à la libération de NETs en réponse à différents types de CI.En parallèle, la formation des NETs a été explorée dans un modèle de réaction allergique chronique, l’asthme. Au niveau systémique, la concentration de NETs est associée à la présence d’un asthme sévère mal contrôlé et d’une obstruction bronchique peu réversible. Inversement, la concentration de NETs dans le lavage broncho-alvéolaire est plus élevée au cours de l’asthme modéré et semble traduire un recrutement pulmonaire et une activation des PN en réponse à une colonisation microbienne.Au total nous montrons que les NETs sont libérés au cours des deux modèles de réactions allergiques choisis, aiguë (anaphylaxie aux curares) et chronique (asthme) et qu’ils pourraient représenter des biomarqueurs de sévérité. Des travaux complémentaires sont nécessaires pour déterminer dans quelle mesure les NETs contribuent à la physiopathologie des allergies. / Neutrophil netosis consists in the release of extracellular DNA filaments bound to granular proteins, called Neutrophil extracellular traps (NETs). In addition to their anti-infectious role, NETs are emerging actors of many inflammatory diseases and we decided to investigate their involvement during allergy.In a multicenter clinical study, our team highlighted an alternative mechanism of anaphylaxis to neuromuscular blocking agents (NMBA) involving neutrophils (PN). The acute phase of these reactions is characterized by NETs release which level is correlated with severity and with a decrease in IgG activating receptors (FcγRs) expression on PN; this suggests a role of immune complexes (IC) IgG / NMBA in NETs formation during these anaphylactic reactionsTo confirm this hypothesis, the ability of IgG ICs to activate netosis was studied through the development of an in vitro stimulation model of purified human PNs.This work shows that two PN IgG receptors (FcγRIIa and FcγRIIIB) contribute to NET release upon cellular activation by different ICsIn parallel, NETs formation has been explored in a model of chronic allergic reactions, asthma. At systemic level, NETs levels are associated with severe and poorly controlled asthma as well with the presence of low reversible bronchial obstruction. Conversely, NETs levels in bronchoalveolar lavage are higher in moderate asthma and appear to reflect pulmonary recruitment and activation of PN in response to microbial colonization.Taking together these results show that NETs are released during the two selected models of allergic reactions : acute (NMBA anaphylaxis) and chronic (asthma) and could be used as biomarkers of severity. Furthers works are needed to determine to what extent NETs contribute to the pathophysiology of allergy.

京都大学 / 新制・課程博士 / 博士(農学) / 甲第23952号 / 農博第2501号 / 新制||農||1091(附属図書館) / 学位論文||R4||N5387(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 栗原 達夫, 教授 小川 順, 教授 阪井 康能 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

Articular cartilage has a low propensity for self-repair, due to which 27 million people are affected by osteoarthritis every year in North America. The current repair techniques used for cartilage defects possess flaws that reduce long-term clinical success. Tissue engineering carries with it the promise of engineering hyaline-like cartilage with physical and biochemical properties, similar to that of native cartilage. This being said, the primary objective of my project was to engineer clinically relevant sized articular cartilage constructs. To achieve my objective, first, I investigated the effect of continuous culture on cartilaginous tissue growth. Constructs grown under continuous media flow significantly accumulated more collagen and glycosaminoglycan, and displayed a stratified morphology, similar to that found in native cartilage. The second goal was to further increase chondrocyte proliferation, and extracellular matrix (ECM) accumulation. To achieve this, constructs were grown in a bioreactor with media supplemented with 14 mM sodium bicarbonate (NaHCO3). Constructs cultivated in the bioreactor with NaHCO3 supplementation exhibited a significant (p<0.05) increase in ECM accumulation (a 98-fold increase in glycosaminoglycans and a 25-fold increase in collagen content), cell proliferation (a 13-fold increase), and thickness (a 28-fold increase) compared to all other conditions (static and reactor without NaHCO3 supplementation). The third goal was to engineer cartilage constructs with as little cells as possible, reducing donor site morbidity. From the results obtained, it was evident that the monolayer constructs outperformed all the other constructs (pellet, biopsy, and minced). The final goal was to understand the underlying reason for the increased proliferation. First, I investigated if there were any differences present in intracellular pH (pHi) and intracellular buffering capacity. Second, I determined the role of extracellular pH (pHe) on cell proliferation. In an effort to accurately achieve this, I, for the first time, have reported on measuring pHi of chondrocytes while still in culture (2D and 3D cultures) using a confocal microscope. This study demonstrated the importance of extracellular environments, such as pHe, extracellular buffering capacity, and the presence of carbon dioxide and bicarbonate ions for chondrocyte proliferation. / Thesis (Ph.D, Chemical Engineering) -- Queen's University, 2012-10-30 19:19:32.026

Les polynucléaires neutrophiles (PN) sont des cellules essentielles au cours de la réponse immunitaire innée ; recrutés rapidement au site inflammatoire où ils participent à la phase aigüe, ils vont aussi contribuer à la résolution de l’inflammation. Ils peuvent en effet moduler la réponse adaptative par interaction avec les lymphocytes (Ly) ou les cellules dendritiques (DC) via des médiateurs solubles ou des interactions cellulaires directes. Les Neutrophil Extracellular Traps (NETs) libérés par les PN activés pourraient jouer un rôle important dans ce contexte. Les NETs sont des filaments de chromatine décondensée associés à des protéines issues principalement des granulations et du cytoplasme. Ils sont essentiels dans la réponse anti-infectieuse mais semblent également impliqués dans la physiopathologie de certaines maladies auto-immunes et inflammatoires. L’objectif de ce travail a été d’évaluer les effets des NETs sur la maturation des DC dans un contexte inflammatoire au cours duquel les PN et les DC peuvent co-exister, assurant ainsi un pont entre immunité innée et immunité adaptative. La première partie de ce travail a consisté à développer un modèle de production, isolement et caractérisation des NETs issus de PN sanguins humains. L’ionophore de calcium A23187 a été choisi pour induire les NETs et l'enzyme de restriction AluI a permis la récupération de fragments de NETs de taille hétérogène. Certains des composants de ces NETs sont quantifiables (ADN, élastase, histone 3 en particulier), et nous avons montré qu’ils conservaient leurs capacités bactéricides in vitro. Ces échantillons de NETs constituent donc un outil biologique standardisé, permettant d’évaluer leurs effets sur des cellules ou des tissus. Dans la deuxième partie de ce travail, nous avons mis en évidence que ces NETs purifiés régulaient négativement la maturation de moDC induites par le LPS (expression de HLA-DR, CD80, CD83, CD86 et production de TNFα, IL-12, IL-6, IL-23). De plus, les NETs diminuent la capacité de ces moDC à induire la prolifération des LyT, et leur polarisation est modulée en favorisant la production de cytokines de type Th2 (IL-5 et IL-13) aux dépens de cytokines de types Th1 (INFγ) et Th17 (IL-17). De manière intéressante, la capacité de migration des moDC activées par le LPS n’est pas modifiée en présence de NETs. En résumé, ces résultats suggèrent que les NETs pourraient jouer un rôle immunorégulateur sur la maturation des moDC dans des conditions inflammatoires. Les NETs produits par les PN activés pourraient ainsi participer à la régulation indispensable de la réponse inflammatoire. / Polymorphonuclear neutrophils (PMN) are innate immune cells rapidly recruited to the inflammatory sites where they play a major role during the acute phase response but also contribute to resolution and repair. They can also modulate the adaptive response by interacting with lymphocytes (Ly) or dendritic cells (DC) via soluble mediators or cell-cell contacts. Activated PMN release Neutrophil Extracellular Traps (NETs) that could play a role in this context. NETs are decondensed chromatin fibers associated with granule and cytoplasmic proteins. As they are mainly involved in host defense against infection, they contribute to some autoimmune and inflammatory diseases. The aim of this work was to evaluate NET effects on DC maturation in an inflammatory context where PMN and DC co-exist, thus bridging innate and adaptive immunity. We first developed a model to induce, isolate and characterize NETs from human PMN. Calcium ionophore A23187 was chosen to induce NETs and the restriction enzyme AluI allowed the recovery of heterogeneous-sized fragments of NETs. Some of their components were quantified (DNA, elastase, histone 3, in particular) and we found that they retained their bactericidal activity. These NETs samples thus constitute a new and important biological tool to study their effects on immune cells or tissues. In the second part of this work, we found that isolated NETs were able to down-regulate LPS-induced moDC maturation as evidenced by the expressions of HLA-DR, CD80, CD83, CD86 and cytokine release (TNFα, Il-6, IL-12, Il-23). Moreover, the presence of NETs during moDC maturation lead to a decrease capacity of these moDC to induce T lymphocyte proliferation and modulated polarization by promoting the production of Th2 cytokines (IL-5 and IL-13) and decreasing Th1 cytokines (INFγ) and Th17 (IL- 17). Interestingly, moDC migration capacity was not modified when moDC maturation was done in the presence of NETs. In summary, these data suggest that NETs could downregulate DC activation. NETs produced by activated PMN could thus participate to the regulation of inflammation.

Le séquençage à haut débit est une technique très utile pour l’étude des ARN. Pendant mon doctorat, nous l’avons utilisé pour la caractérisation des ARN extracellulaire (ARNex) du plasma humain. Les ARNex du plasma sont retrouvés soit à l’état soluble sous forme de complexes ribonucléoprotéiques (RNP) ou encapsulés au sein de vésicules extracellulaires (VE) de diverses origines (exosomes, microvesicles, …). Dans ce projet, j’ai démontré que le plasma contenait principalement des micro ARN, le fragment hY4 et des ARN ribosomiques dégradés. Par ailleurs, après chromatographie à exclusion de tailles ou par traitement consécutif protéinase K/RNase A, des VE hautement purifiées peuvent être obtenus. Nous ne retrouvons plus en majorité les micro ARN et l’ARN hY4 dans ces échantillons mais plutôt des ARN du microbiote humain, montrant une composition différente entre les ARNex solubles et ceux des vésicules purifiées. Par ailleurs, j’ai également effectué une étude comparative de kits commerciaux qui sont supposés purifier les exosomes par précipitation. La composition en ARN de ces fractions est très similaire au plasma humain total, montrant une forte contamination par les RNP solubles. Ainsi, nous sommes en mesure de proposer un protocole pour l’étude des ARNex dans le cadre de biopsies liquides avec des échantillons cliniques afin de découvrir de potentiels biomarqueurs de diagnostic. Au-delà de la caractérisation d’ARN, le séquençage à haut-débit peut être utilisé pour la détection et quantification des modifications post-transcriptionnelles. Pendant ma thèse, j’ai utilisé le séquençage pour l’analyse des 2’O-méthylation des ARN de transfert chez E. coli par RiboMethSeq. Sous plusieurs conditions de stress (manque de nutriments ou des concentrations non létales d’antibiotiques), certaines 2’O-méthylations montrent une réponse adaptative. Alors que plus de la moitié des 2’O-méthylations en position 18 (Gm18) sont augmentées dans toutes les conditions de stress étudiées, les positions Nm34 montrent un effet opposé avec une diminution dans certains stress (chloramphénicol et streptomycine). Chacun de ces deux comportements peut être relié à un phénomène de régulation cellulaire en réponse au stress : un changement au niveau de la wobble base pourrait être un moyen de réguler la traduction en modifiant l’usage des codons. En ce qui concerne Gm18, son rôle dans l’évasion du système immunitaire inné lors de l’invasion d’un hôte est en cours d’élucidation. / For less than a decade, high-throughput sequencing became a very powerful, sensitive and precise technique for the study of ribonucleic acids. During my PhD thesis, I used this technology for in-depth characterization of the extracellular RNA (exRNA) content of human plasma. exRNA in plasma exists either in a “soluble state” as a component of ribonucleoprotein (RNP) complexes or encapsulated into extracellular vesicles (EV) of diverse origins (exosomes, microvesicles, …). In this project, I demonstrated that whole human plasma contains mostly micro RNA and the fragment of RNA hY4, as well as degraded ribosomal RNA. Moreover, using a rigorous strategy via size exclusion chromatography or consecutive proteinase K/RNase A treatments, highly purified EVs can be obtained. miRNAs and RNA hY4 fragments were not present in majority of samples, demonstrating a huge difference between soluble exRNA and exRNA from purified EVs. The RNA content of these EVs mainly reflects RNA composition of human microbiota. In addition, I also performed a comparative analysis of commercially available “exosome-enrichment” kits which are supposed to purify human exosomes by precipitation. Their RNA composition was found to be almost identical to human plasma, showing strong uncontrolled contamination by soluble RNPs. Based on this study, we were able to propose a protocol for studies in exRNA in the field of liquid biopsies with clinical sample in order to discover new diagnostic biomarkers. Apart from the characterization of RNA, high-throughput sequencing can be used for detection and quantification of RNA post-transcriptional modifications. During my PhD thesis I applied deep sequencing for analysis of transfer RNA (tRNA) 2’-O-methylations in model bacteria (E. coli) using RiboMethSeq. Under several stress conditions, such as starvation and non-lethal antibiotics concentrations, some 2’-O-methylated nucleotides show an adaptive response. While over than half of Gm18 show a global increase under all investigated stress conditions, ribomethylated residues at position 34 show an opposite effect for some antibiotic treatments (chloramphenicol and streptomycin). Each of these dynamic profiles can be linked to cell regulation in response to stress. Change at the tRNA wobble base (position 34) could be a way to regulate translation by modifying the codon usage. Concerning Gm18, its role in the escape from the human innate immune system during host invasion is currently elucidated.

Cell adhesion to the extracellular matrix (ECM) provides tissue structure and integrity as well as triggers signals that regulate complex biological processes such as cell cycle progression and tissue-specific cell differentiation. Hence, cell adhesion is critical to numerous physiological and pathological processes, including embryonic development, cancer metastasis, and wound healing, as well as biotechnological applications, such as host responses to implanted devices and integration of tissue-engineered constructs. During the adhesion process, integrin surface receptors bind ECM proteins, cluster, and associate with the actin cytoskeleton. Subsequent strengthening of the integrin/actin cytoskeleton interaction occurs via complexes of proteins known as focal adhesions. Due to the close association between biochemical and biophysical processes within adhesion complexes, mechanical analyses can provide important new insights into structure/function relationships involved in regulating the adhesion process. The objective of this project was to investigate the role of the protein tyrosine kinase FAK in cell adhesion strengthening. Our central hypothesis was that FAK regulates adhesion strengthening by modulating interactions between integrins and FA structural components. Using a novel combination of genetically engineered cells to control the interactions of FAK, a spinning disk adhesion assay with micropatterned substrates to obtain reproducible and sensitive measurements of adhesion strength, and quantitative biochemical assays for analyzing changes in adhesive complexes, we demonstrate that FAK modulates adhesion strengthening via two distinct mechanisms: (1) FAK expression results in elevated integrin activation leading to regulation of strengthening rate and (2) FAK regulates steady-state adhesion strength via vinculin recruitment to focal adhesions. We also show that the autophosphorylation and catalytic sites of FAK are critical to this regulation of adhesion strengthening. This work is significant because it both identifies functional mechanisms of FAK and provides the first evidence that focal adhesion signaling regulates the adhesion strengthening process. Furthermore, this research demonstrates that the dependency of migration on adhesion strength is highly complex and establishes a need for adhesion strengthening metrics in analyzing the functional mechanisms of molecules within adhesion complexes.

Stem cell synthesized extracellular matrix (ECM) may serve as a replacement for current bone grafting techniques. The overall goal of this thesis is to quantify the osteoinductivity of the ECM produced by human amniotic fluid stem cells (AFS cells), compare it to that of human mesenchymal stem cells (MSC), and assess its potential for use in bone tissue engineering therapies. Each stem cell type was cultured in osteogenic media to produce the ECM, which was then decellularized via freeze/thaw cycling and DNase treatment. The success of the decellularization was confirmed with live/dead staining and DNA quantification. A series of in vitro studies were performed to evaluate the characteristics of the ECM relevant to a bone tissue engineering therapy. Reseeded MSCs were able to attach to and proliferate on both ECM types in both 2D and 3D culture. In 2D, cells cultured on both ECM types showed increased levels of calcium deposition. Additionally, cells cultured on the MSC ECM showed increased alkaline phosphatase activity. A synergistic effect on osteogenic differentiation was observed when the osteoinductive factor dexamethasone was added to the culture. In 3D, both ECM types increased the mineralized matrix production of reseeded MSCs. The AFS ECM had a greater effect than the MSC ECM. When ECM was used to treat a rat femoral segmental defect in vivo, it was found that each ECM type increased the rate of bridging of the defect when compared to collagen coated scaffolds. However the ECM did not have a significant effect on the volume of mineralized matrix within the defect site in this study.