Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第15408号 / 工博第3287号 / 新制||工||1495(附属図書館) / 27886 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 森 泰生, 教授 濵地 格, 教授 跡見 晴幸 / 学位規則第4条第1項該当

The cardiac ryanodine receptor (RyR2) is a Ca2+ ion channel found in the sarcoplasmic reticulum (SR), an intracellular membranous Ca2+ storage system. It is well known that a destabilization of RyR2 can lead to a Ca2+ flux out of the SR, which results in an overload of intracellular Ca2+; this can also lead to arrhythmias and heart failure. The catecholamines play a large role in the regulation of RyR2; stimulation of the Beta-adrenergic receptor on the cell membrane can lead to a hyperphosphorylation of RyR2, making it more leaky to Ca2+. We have previously shown that strong electron donors will inhibit RyR2. It is hypothesized that the catecholamines, sharing a similar structure with other proven inhibitors of RyR2, will also inhibit RyR2. Here we confirm this hypothesis and show for the first time that the catecholamines, isoproterenol and epinephrine, act as strong electron donors and inhibit RyR2 activity at the single channel level. This data suggests that the catecholamines can influence RyR2 activity at two levels. This offers promising insight into the potential development of a new class of drugs to treat heart failure and arrhythmia; ones that can both prevent the hyperphosphorylation of RyR2 by blocking the Beta;-adrenergic receptor, but can also directly inhibit the release of Ca2+ from RyR2.

The principle calcium regulator in the muscle cell is the calcium ion release channel (RyR). Improper calcium homeostasis in the muscle cell is the foundation of many pathological states and has been targeted as a contributing factor to ventricular tachycardia, which is known to precede sudden cardiac arrest. Numerous endogenous and exogenous compounds can affect the way RyR regulates calcium. In this study the anthocyanidin Pelargonidin (Pg), an important natural colorant and dietary antioxidant, is evaluated for its effect on regulating the transport of calcium through the RyR1 of skeletal muscle sarcoplasmic reticulum. Pelargonidin undergoes time dependent structural changes in aqueous solutions at physiological pH and a mixture of up to seven forms of Pelargonidin are present in solution simultaneously. Pelargonidin is a unique RyR1 modulator. It can both stimulate and inhibit the RyR1 depending on the experimental conditions. In addition, when Pelargonidin is irradiated with white light, its inhibition properties on the RyR1 are essentially nullified. Proposed mechanisms include excited state charge shift within RyR1-Pg complexes.

Biological molecules, or molecular machines, visit a continuum of conformational states as they go through work cycles required for their metabolic functions. Single-molecule cryo-EM of suitable in vitro systems affords the ability to collect a large ensemble of projections depicting the continuum of structures. This information, however, comes buried among typically hundreds of thousands of unorganized images formed under extremely noisy conditions and microscopy aberrations. Through the use of machine-learning algorithms, it is possible to determine a low-dimensional conformational spectrum from such data, with leading coordinates of the embedding corresponding to each of the system’s degrees of freedom. By determining occupancies—or free energies—of the observed states, a free-energy landscape is formed, providing a complete mapping of a system’s configurations in state space while articulating its energetics topographically in the form of sprawling hills and valleys. Within this mapping, a minimum-energy path can be derived representing the most probable sequence of transitions taken by the machine between any two states in the landscape. Along this path, an accompanying sequence of 3D structures may be extracted for biophysical analysis, allowing the basis for molecular function to be elucidated. The ability to determine energy landscapes and minimum-energy paths experimentally from ensemble data opens a new horizon in structural biology and, by extension, molecular medicine. The present work is based on a geometric machine-learning approach using manifold embedding to obtain this desired information, which has been shown possible on two experimental systems—the 80S ribosome and ryanodine receptor—through a previously-established framework termed ManifoldEM. First, this framework is incorporated into an advanced graphic user interface for public release, and augmented with a new method, POLARIS, for determining minimum-energy pathways. ManifoldEM is next applied on two new systems: vacuolar ATPase and the SARS-CoV-2 spike protein, and for both systems, several novel aspects of the machine’s function are observed. During this exposition, critical limitations and uncertainties of the framework are also presented, as have been found throughout its extended development and use. However, in the absence of ground-truth data, testing and validation of ManifoldEM is infeasible. As recourse, a protocol is next proposed for generating simulated cryo-EM data from an atomic model subjected to multiple conformational changes and experimental conditions, with several Hsp90 synthetic ensembles generated for analysis by ManifoldEM. Guided by results of these ground-truth studies, new insights are made into the origin of longstanding ManifoldEM problems, further motivating and informing the development of a new, comprehensive method for correcting them, termed ESPER. The ESPER method operates within the ManifoldEM framework and, as will be shown using both synthetic and experimentally-obtained data, ultimately results in substantial improvements to the previous work. Finally, numerous recommendations are laid out for guiding future work on the ManifoldEM suite, particularly aimed at its next public release.

L’escarre est une pathologie liée à l’immobilité des patients, accidentelle ou associée à des comorbidités. Les premières lésions apparaissent dans le muscle avant de se développer en plaie cutanée sans que les mécanismes physiopathologiques de cette atteinte ne soient encore connus. L’objectif principal de cette thèse était d’identifier des voies de signalisation intervenant de manière précoce dans le développement des escarres au travers d’une étude transversale. Nous formulons l’hypothèse qu’une compression musculaire induit une altération de l’homéostasie calcique musculaire par atteinte des canaux calciques du réticulum sarcoplasmique (les récepteur de la ryanodine de type 1, RyR1) conduisant à la lésion du tissu musculaire et une inflammation du tissu sous-cutané.Sur un modèle animal de compression de 2 heures, à 100 mmHg, nous avons identifié une initiation des voies apoptotiques et une augmentation du stress oxydant des muscles de la paroi abdominale. Le RyR1 y est hyper-nitrosylé et hyper-oxidé et sa protéine régulatrice, calstabin1 se dissocie sous l’action de ce remodelage, ce qui entraîne une fuite calcique du réticulum sarcoplasmique vers le cytosol. Cette dysfonction n’est pas réversible à 3 jours post-compression mais il est possible de la prévenir en traitant les souris avec un rycal qui bloque la déplétion de la calstabin1. En clinique, chez une cohorte de patients paraplégiques, porteurs d’escarres, nous avons identifiés un remodelage du RyR1 dans les muscles paralysés (comparaison intra patient avec une biopsie saine) et une hypoxie des tissus sous la lésion médullaire. La dissociation de la calstabin1 au RyR1 a pu être corrélée à la pression moyenne et maximale exercée sur la peau de la zone sacrée du patient allongé en regard du muscle biopsié.Ce travail de thèse a permis de préciser les voies de signalisation intervenant de manière précoce dans le développement des escarres dans le muscle squelettique. Une compression mécanique induit une augmentation du stress oxydant, un remodelage du RyR1 et une dysfonction du canal à cause de la perte de l’interaction RyR1/calstabin1. Ces résultats ouvrent des perspectives intéressantes sur des traitements préventifs pharmacologiques et de suivi non-invasif qui permettront de retarder l’apparition des premières lésions musculaires. / Pressure ulcer is a pathology related to patient immobility, which can be either accidental or incidental to comorbidities. The first damage are located in muscle tissue before developing in cutaneous breakdown per an unclear pathophysiology. The core objective of my PhD was to identify the early signaling pathways involved in pressure ulcer development, through a transversal study. We hypothesized that muscle compression will induce a calcium imbalance in muscles by a dysfunction of calcium channels from the sarcoplasmic reticulum (Ryanodine receptor isoform 1, RyR1) which will lead to muscle damage and sub-cutaneous inflammation.Mice model of a 100 mmHg, 2 hours compression of abdominal muscles was used to identify the apoptotic pathway initiation and a rise of oxidative stress. RyR1 is hyper-nitrosylated and hyper-oxydated thus this remodeling induces depletion of RyR1 stabilizing protein, calstabin1, and the resulting leaky phenotype increases intracellular calcium concentration. This channel functional impairment was not reversible up to 3 days post-compression but it was possible to prevent it through rycal treatment, protecting the binding calstabin1/RyR1. In a clinical trial, we identified from a paraplegic population with existing pressure ulcers, a RyR1 remodeling in paralyzed muscles (intra patient comparison with a healthy muscle biopsy) and a hypoxia of tissues below the spinal cord injury. Calstabin1 dissociation was correlated to the mean and peak pressure intensity of interface pressure applied over the sacrum skin of the bedridden patient directly above the biopsy location.This thesis project focused on early signaling pathways participating in pressure ulcer in skeletal muscle. A mechanical strain induces an increase of the intracellular redox state, post translational RyR1 modifications and a channel dysfunction because of calstabin1 depletion. The significance of my work is to propose both pharmacology and non-invasive monitoring solutions to prevent first muscle damage in pressure ulcer development.

The tightly regulated openings of the cardiac ryanodine receptor (RyR2) help to ensure that intracellular Ca2+- release from the sarcoplasmic reticulum (SR) can only occur when heart contractions are required. Usually this process is self-regulatory, where Ca2+ both activates and inhibits release of further Ca2+ from the SR. In the progression of heart failure some of this control is lost and in rest periods Ca2+ can leak from the SR into the cytosol. Recent evidence has suggested that Zn2+- dyshomeostasis may contribute to SR Ca2+- leak but the underlying mechanism is unclear. Using single channel electrophysiological studies in combination with live cell imaging of HEK 293 and fibroblasts, this study reveals that Zn2+, along with Ca2+ and the inhibitor Mg2+, plays a physiological role in the grading of Ca2+- release via RyR2. Importantly the data reveal that pathophysiological concentrations of Zn2+ (> 100pM) within the cytosol remove the requirement of Ca2+ to activate RyR2, resulting in irregular channel activity even in the presence of Mg2+. This increase in channel open probability due to Zn2+ is known to be associated with increased Ca2+- release events such as Ca2+ sparks suggesting that Zn2+ is a regulator of the SR Ca2+-leak current. A potential source of releasable Zn2+, which could modulate RyR2 activity in cardiomyocytes, are the acidic organelles (endosomes and lysosomes). This study provides key evidence that the two pore channels (TPCs), which are expressed on the surface of these organelles, are candidate channels for ligand-gated release of Zn2+. Importantly this research demonstrates that dysregulated Zn2+ homeostasis, resulting in elevated Zn2+ within the lysosome, has severe consequences upon cellular Ca2+- release from fibroblasts, which is primarily the result of Zn2+ acting as a pore blocker of TPC2. Together these data reveal a key role of Zn2+ as a second messenger which can regulate intracellular Ca2+- release in both health and disease.

Activity of the Ryanodine Receptor (RyR2) (aka cardiac Ca2+ release channel) plays a pivotal role in contraction of the heart. S-adenosyl-l-methionine (SAM) is a biological methyl group donor that has close structural similarity to ATP, an important physiological regulator of RyR2. This work provides evidence that SAM can act as a RyR2 regulatory ligand in a manner independent from its recognized role as a biological methyl group donor. RyR2 activation appears to arise from the direct interaction of SAM, via its adenosyl moiety, with the RyR2 adenine nucleotide binding sites. Because uncertainty remains regarding the structural motifs involved in RyR2 modulation by ATP and its metabolites, this finding has important implications for clarifying the structural basis of ATP regulation of RyR2. During the course of this project, direct measurements of single RyR2 activity revealed that SAM has distinct effects on RyR2 conductance. From the cytosolic side of the channel, SAM produced a single clearly resolved subconductance state. The effects of SAM on channel conductance were dependent on SAM concentration and membrane holding potential. A second goal of this work was to distinguish between the two possible mechanisms by which SAM could reduce RyR2 conductance: i) SAM interfering directly with ion permeation via binding within the conduction pathway (pore block), or ii) SAM binding a regulatory (or allosteric) site thereby stabilizing or inducing a reduced conductance conformation of the channel. It was determined that SAM does not directly interact with the RyR2 conduction pathway. To account for these observations an allosteric model for the effect of SAM on RyR2 conductance is proposed. According to this model, SAM binding stabilizes an inherent RyR2 subconductance conformation. The voltage dependence of the SAM related subconductance state is accounted for by direct effects of voltage on channel conformation which indirectly alter the affinity of RyR2 for SAM. Patterns in the transitions between RyR2 conductance states in the presence of SAM may provide insight into the structure-activity relationship of RyR2 which can aid in the development of therapeutic strategies targeting this channel.

Le calcium (Ca2+) joue un rôle prépondérant dans la fonction de nos neurones et du système nerveux central. Différents travaux ont rapporté que la dérégulation de l’homéostasie calcique, est associée au développement de la Maladie d’Alzheimer (MA). Durant ma thèse, j’ai étudié l’implication de deux acteurs importants de l’homéostasie calcique du Réticulum Endoplasmique (RE) : 1) le Récepteur de la Ryanodine (RyR) faisant sortir le Ca2+ vers le cytosol et 2) l’isoforme tronquée de la Sarco-Endoplasmic Reticulum Ca2+ ATPase 1 (S1T), ayant perdu la fonction de pompe calcique et jouant un rôle dans la fuite passive du Ca2+ du RE. Au cours de ma thèse j’ai démontré le mécanisme moléculaire impliqué dans la dérégulation de l’activité de l’isoforme RyR2 dans des modèles d’étude in vitro et in vivo de la MA. Nous avons montré que le RyR2 subit des modifications post-traductionnelles (MPTs) (phosphorylation, oxydation, nitrosylation) dans le cerveau de patients atteints de la MA et dans des modèles murins de la maladie. Nous avons identifié une cascade dans laquelle l’Amyloïde β (Aβ) active les récepteurs β2-Adrénergiques, conduisant aux MPTs du RyR2 aboutissant à la dissociation de la protéine régulatrice Calstabine2 du macrocomplexe du RyR2 et à l’augmentation de la fuite de Ca2+ du RE. Nous avons aussi mis en évidence la possibilité de réduire les MPTs du RyR2 et de stabiliser la Calstabine2 sur le macrocomplexe RyR2 en inhibant pharmacologiquement la cascade β2-Adrénergique. Par ailleurs, nous avons également stabilisé la Calstabine2 par des moyens pharmacologiques (in vitro et in vivo) ou génétiques (in vivo). Nos résultats montrent que cela permet non seulement de limiter la fuite de Ca2+ mais également de réduire le métabolisme du Précurseur du Peptide Amyloïde (APP) et les dépôts d’Aβ in vitro et in vivo et le déficit cognitif et les défauts de plasticité synaptique dans deux modèles murins d’étude de la MA. Nos résultats ont également montré l’existence d’une boucle d’amplification de la pathologie dans laquelle la dérégulation calcique liée au RyR accroit la production de l’Aβ qui va en retour induire les modifications du RyR. Par ailleurs, je me suis également intéressé à l’implication potentielle de S1T dans la MA. Nos résultats révèlent : 1) l’expression de S1T dans les cerveaux de patients Alzheimer et dans un modèle in vitro de la MA ; 2) l’induction de S1T par l’Aβ, 3) l’impact de l’expression de S1T sur le métabolisme de l’APP et 4) l’impact de l’expression de S1T sur la neuroinflammation dans des modèles in vitro et in vivo. L’article issu de cette seconde étude est en cours de soumission. Ainsi l’augmentation de la fuite du Ca2+ du RE vers le cytosol semble être particulièrement impliquée dans la physiopathologie de la MA. Le canal RyR2 se révèlerait être un candidat intéressant à cibler pour des approches thérapeutiques visant à réguler son activité dans le but de prévenir ou guérir la MA. / Calcium (Ca2+) plays a major role in the function of our neurones and central nervous system. Various studies reported that the deregulation of Ca2+ homeostasis is associated with the development of Alzheimer’s Disease (AD). During my PhD, I studied the implication in two important actors of the Endoplasmic (ER) Ca2+ homeostasis. 1) The Ryanodine Receptor (RyR) which leads Ca2+ from the ER towards the cytosol and 2) the truncated isoform of the Sarco-Endoplasmic Reticulum Ca2+ ATPase 1 (S1T), which loses its Ca2+ pump function and plays a role in the ER passive Ca2+ leak. During my thesis I demonstrated the molecular mechanism involved in the deregulation of RyR2 isoform activity in in vitro and in vivo AD models. We have shown that RyR2 undergoes post-translational modifications (PTMs) (phosphorylation, oxidation, nitrosylation) in the brains of patients with AD and in murine models of the disease. We have identified a cascade in which Amyloid β (Aβ) activates β2-adrenergic receptors, leading to RyR2 PTMs resulting in dissociation of Calstabine2 regulatory protein from RyR2 macrocomplex and increased ER Ca2+ leakage. We have also demonstrated the possibility of reducing RyR2 PTMs and stabilizing Calstabine2 on the RyR2 macrocomplex by pharmacologically inhibiting the β2-adrenergic cascade. In addition, we have also stabilized Calstabine2 by pharmacological (in vitro and in vivo) or genetic (in vivo) means. Our results show that this is not only limiting Ca2+ leakage but also reducing the Amyloid Peptide Precursor (APP) metabolism and Aβ deposits in vitro and in vivo, and cognitive deficit and synaptic plasticity defects. two murine models of AD. Our results also showed the existence of a loop amplificating the pathology in which RyR-related calcium deregulation increases the production of Aβ, which in turn induces RyR modifications. In addition, I was also interested in the potential involvement of S1T in AD. Our results reveal: 1) the expression of S1T in the brains of Alzheimer patients and in an in vitro model of AD; 2) the induction of S1T by Aβ, 3) the impact of S1T expression on the metabolism of APP and 4) the impact of S1T expression on neuroinflammation in in vitro and in vivo models. The article from this second study is being submitted. Thus, the increase of the ER Ca2+ leakage towards the cytosol appears to be particularly involved in the pathophysiology of AD. The RyR2 channel would prove to be an interesting candidate to target for therapeutic approaches aimed at regulating its activity in order to prevent or cure AD.

La contraction des muscles striés est sous la dépendance du Complexe de Relâchement du Calcium (CRC). Ce complexe protéique est constitué principalement de deux canaux calciques, le récepteur des dihydropyridines, un canal sensible au voltage localisé dans la membrane des tubules-T et le récepteur de la ryanodine (RyR) situé dans la membrane du RS. Le CRC comprend également de nombreuses protéines régulatrices comme la triadine, la calséquestrine, la junctine et FKBP. Des mutations dans les gènes codant les protéines du CRC conduisent à des pathologies rares et souvent sévères. Cette thèse porte sur l'étude des mécanismes physiopathologiques induits par quelques unes de ces mutations pour décrypter les mécanismes pathologiques mis en œuvre mais également pour comprendre le fonctionnement global du CRC dans les muscles squelettique et cardiaque. La première partie de cette étude concerne RYR1, le gène codant l'isoforme squelettique du RyR qui est une cible importante de mutations chez des patients atteints de myopathies congénitales à cores. L'effet fonctionnel de ces mutations, réparties sur toute la séquence de RYR1, est peu connu. Ces mutations pourraient modifier la fonction canal de RyR1 mais également son adressage à la triade ou sa régulation par d'autres protéines du CRC. Parmi ces hypothèses, la modification de la localisation de RyR1 et sa régulation par une protéine régulatrice (la cavéoline-3) ont été révélées par l'étude de deux mutations de RyR1. La deuxième partie de cette étude concerne la tachycardie ventriculaire polymorphe catécholaminergique (TVPC), une pathologie liée à des défauts du CRC cardiaque, pour laquelle des recherches de mutations sont effectuées sur l'isoforme cardiaque du RyR, RYR2, puis dans les autres protéines du complexe. Nous avons identifié au laboratoire les premières mutations dans le gène de la triadine chez un de ces patients. L'impact d'une de ces mutations sur le fonctionnement du complexe a été étudié et nous avons pu caractériser le mécanisme physiopathologique mis en œuvre et conduisant à la TVPC chez ces patients. / The calcium release complex (CRC) plays a central role in both skeletal and cardiac muscle contraction. The composition of the complex is quite similar in both tissues, and differs only by tissue specific isoforms. The core of the complex is composed of the dihydropyridines receptor, a voltage sensor channel of the T-tubule and the ryanodine receptor, the sarcoplasmic reticulum calcium channel. A number of proteins are associated to this calcium channel like calsequestrin, triadin, junction and FKBP. Mutations in the skeletal CRC are responsible for rare and often severe diseases. This thesis work focuses on the study of physiopathological mechanisms induced by some of these mutations to decipher pathological mecanisms but also to understand the overall CRC functioning in skeletal and cardiac muscles. The first part of this study concerns RYR1, the skeletal RyR isoform coding gene. This gene is mostly the target of mutations resulting in core myopathies. The functional effect of these mutations spred on the entire RYR1 sequence is little known. These mutations could directly alter the calcium channel function but also its targeting to the triad or its regulation by other CRC proteins. Among these hypotheses, the modification of RyR1 localisation and regulation by a protein, Caveolin-3, have been highlighted with the study of two RyR1 mutations. The second part of this study concerns the catecholaminergic polymorphic ventricular tachycardia (CPVT), a rare fatal arrhythmia caused in part by mutations in RYR2 and CASQ2, both belonging to the cardiac CRC,. Recently, we have identified the first mutations in the human triadin gene, TRDN, in a CPVT patient. The goal of this project was to study the molecular and physiological consequences of one of these TRDN mutations allowing the analysis of the pathological mechanisms of this disease, but also a better understanding of the normal function of the cardiac CRC.

Les ions Ca2+ responsables de la contraction musculaire sont extrudés du réticulum sarcoplasmique (RS) via le récepteur de la ryanodine de type 1 (RyR1). Des mutations du gène de RyR1 sont responsables chez l’homme de l’hyperthermie maligne (HM) et de la myopathie à cores centraux (MCC). Nous avons caractérisé les altérations de l’efflux calcique du RS dues à de telles mutations dans la fibre musculaire de souris par électrophysiologie et imagerie confocale. L’expression des formes Y523S, R615C et R2163H de RyR1, associées à l’HM, provoque une hypersensibilité de l’efflux vis-à-vis du potentiel membranaire alors que les formes I4897T et G4896V associées à la MCC provoquent une réduction chronique de l’efflux sans modification de densité des RyR1 s ainsi que des protéines Cav1.1 et SERCA1. L’expression de la forme R4892W associée à la MCC ne modifie pas l’efflux calcique suggérant une plus faible pénétrance fonctionnelle de cette forme. Dans tous les cas, aucune indication de changement du contenu en calcium RS n’a été observée. Les résultats suggèrent que les modifications pathologiques de l’efflux calcique sont la conséquence directe de l’altération de fonction des canaux. Le deuxième objectif du travail s’est intéressé au rôle de certains phosphoinositides (PtdInsPs) dans la régulation de l’efflux calcique du RS. La surexpression de la PtdInsPs-phosphatase Mtm 1 n’a aucun effet sur l’efflux calcique alors que l’application intracellulaire de ses deux principaux substrats inhibe l’efflux, suggérant que leur accumulation dans les fibres musculaires déficientes en Mtm1 pourrait contribuer aux altérations pathologiques associées du couplage excitation-contraction / Ca2+ ions that trigger muscle contraction are released from the sarcoplasmic reticulum (SR) through the type 1 ryanodine receptor (RyR1) channel. Mutations of the gene encoding RyR1 are responsible for malignant hyperthermia (MH) and central core disease (CCD) in human. We characterized the alterations of SR Ca2+ release due to such mutations in mouse fibers using electrophysiology and confocal imaging. Expression of each of the MH-associated Y523S, R615C and R2163H mutant forms of RyR1 increases the sensitivity of Ca2+ release to membrane potential whereas forms I4897T and G4896V that are associated to CCD provoke a chronic depression of Ca2+ release with no concurrent alteration of RyR1, Cav1.1 and SERCA1 density. Expression of the CDD-associated R4892W form of RyR1 has no effect on Ca2+ release suggesting a weaker functional penetrance of this mutant form. In all cases we found no indication for a change in SR calcium content. Results suggest that pathological changes in Ca2+ release are the direct consequence of the functional alteration of the channels. The second goal of this work focused on the role of certain phosphoinositides (PtdInsPs) in the control of SR Ca2+ release. Over-expression of the PtdInsPs-phosphatase Mtm 1 does not affect Ca2+ release whereas intracellular application of its two main substrates inhibits Ca2+ release, suggesting that accumulation of these molecules in Mtm 1-deficient fibers could contribute to the associated alterations of excitation-contraction coupling