Projects & Collaborations 39 foundShow per page10 10 20 50 Investigating the Neuromuscular Involvement in Cachexia: Identifying Novel Target Genes and Therapeutic Targets Research Project | 2 Project MembersCancer cachexia is a severe and prevalent condition that affects up to 80% of cancer patients and causes muscle wasting and weakness, leading to frailty and reduced tolerance to cancer treatments. Despite its significant contribution to cancer-related morbidity and mortality, there are currently no effective treatment strategies to ameliorate cachexia. This highlights the need for further research to understand the mechanisms behind cachexia development. Recent studies indicate that changes in the connection between the nervous system and muscles, called the neuromuscular junction (NMJ), play a crucial role in developing cachexia. However, the specific mechanisms behind these alterations and how they mediate muscle wasting are not understood. The primary goal of this project is to use state-of-the-art techniques to investigate NMJs in both cachexia-susceptible and -protected muscles in mouse models of cachexia. Revealing the differences in different muscle types will provide novel information about the underlying causes of cachexia. Furthermore, we aim to genetically manipulate the factors revealed in this study to restore muscle wasting in mice with cancer. By this means, new potential therapeutic targets for treating cachexia will be identified. Ultimately, this research project aims to decipher the underlying neuromuscular causes of cancer cachexia and identify new treatment options that may enhance the quality of life and survival of cancer patients. Beitrag an die Fertigstellung der Dissertation "Transcriptional networks in skeletal muscle in response to acute exercise" Research Project | 2 Project MembersWestliche Gesellschaften leiden zunehmend unter Wohlstandskrankheiten die auf einen inaktiven Lebensstil und einen Überschuss an Kalorien zurückzuführen sind. Im Jahr 2020 gehörten Herz-Kreislauf-Erkrankungen, Diabetes und Demenz zu den häufigsten Todesursachen in der Schweiz; selbst während dem Höhepunkt der Covid19-Pandemie. Die Gemeinsamkeit all dieser Krankheiten ist die mögliche Prävention und Therapie durch körperliche Aktivität. Körperliche Fitness ist ein epidemiologischer Indikator für reduzierte Mortalität und Anfälligkeit für Krankheiten was regelmässiges Training zur absoluten Grundlage eines gesunden Lebensstils macht. Während wir aus physiologischer Sicht verstehen, wie sich die Muskulatur auf regelmässiges Training einstellt und dadurch die gesamte körperliche Gesundheit positiv beeinflusst, so sind die molekularen Prozesse die diese Veränderungen steuern weitgehend unbekannt. Das Ziel meines Doktorats ist es, genau diese molekularen Prozesse im Muskel besser zu verstehen und die wichtigsten Transkriptionsfaktoren in der Muskelanpassung zu identifizieren und charakterisieren. Structure-function analysis of the RNA-binding protein PGC-1a in skeletal muscle Research Project | 2 Project MembersPlasticity of cells, tissues and organs relies on sensing of external and internal cues, integration of the engaged signaling pathways, and orchestration of a pleiotropic response. For example, contractile patterns, ambient temperature and oxygen levels, nutrient availability and composition, as well as other factors result in a massive remodeling of biochemical pathways, cellular metabolism and mechanical properties of skeletal muscle cells, most notably in the context of repeated bouts of exercise, ultimately leading to training adaptations. In turn, such adaptations of skeletal muscle trigger internal and external changes that contribute to the systemic effects of exercise with many health benefits, and strong preventative and therapeutic outcomes in a number of pathologies. Surprisingly, even though the physiological and clinical contributions of exercise-linked muscle plasticity are well recognized, the molecular mechanisms that control the corresponding biological programs are still poorly understood. In recent years, the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) has emerged as a central regulatory nexus of plasticity in various cell types. PGC-1α integrates upstream signaling pathways to coordinate the complex transcriptional networks encoding biological programs involved in mitochondrial function, cellular metabolism and more. In the case of endurance exercise-mediated plasticity of muscle cells, most, if not all of the adaptations are evoked by this stimulus. Accordingly, muscle-specific overexpression or knockout of PGC-1α elicits high endurance and pathologically sedentary phenotypes, respectively. Our proposal aims at elucidating the molecular underpinnings of the complex transcriptional control that is exerted by PGC-1α in a spatio-temporal manner. We have recently discovered that the binding of RNAs to PGC-1α contributes to full transcriptional activity, and is central for the inclusion of PGC-1α-containing multiprotein complexes in liquid-liquid phase separated nuclear condensates for the sequestration of transcription. We now plan to determine the list and common features of PGC-1α-bound RNAs, interrogate how RNA binding is brought about in a structure-function analysis, study the consequences on multiprotein complex formation, and ultimately investigate the physiological relevance in skeletal muscle cells in vitro and in vivo . To do so, novel animal models will be leveraged for single-end enhanced crosslinking and immunoprecipitation (seCLIP) experiments to identify PGC-1α-bound RNAs, structural information will be obtained by NMR spectroscopy, and validated using site-directed mutagenesis of key amino acids and nucleotides in PGC-1α and RNAs, respectively, to study PGC-1α-dependent liquid-liquid phase separation. Then, PGC-1α-containing multiprotein complexes will be co-purified to perform cryo-electron microscopy-based single particle structural analysis. Finally, the functional consequence of targeted mutagenesis of key residues will be assessed in muscle cells in culture and mouse muscle in vivo with state-of-the-art myotropic adeno-associated viral vectors (AAVMYO). The research plan thus a.) highly synergizes in terms of interdisciplinary approaches between the groups involved and b.) will result in hitherto unprecedented insights into molecular mechanisms that underlie complex spatio-temporal control of transcriptional networks with important implications for the understanding of cellular and tissue plasticity in health and disease. A novel role of dysferlin in regulating skeletal muscle metabolism contributes to disease pathology in dysferlinopathies Research Project | 1 Project MembersDysferlin is a protein that is intimately involved in the control of membrane repair in damaged cells. Accordingly, mutations of the dysferlin gene cause progressive muscular dystrophies collectively referred to as dysferlinopathies. Unexpectedly though, therapeutic strategies aimed at restoring membrane resealing capabilities fail to prevent the muscular dystrophy in these diseases, indicating other, hitherto unknown molecular functions of dysferlin to contribute to the pathology in dysferlinopathy patients. We have now observed how the pathological progression in a mouse model for Limb-Girdle Muscular Dystrophy type 2B (LGMD2B) is closely linked to altered muscle cell metabolism, most notably an accumulation of glycogen. Moreover, exacerbation of glycogen storage by overexpression of the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) in these muscles results in a more severe muscle tissue damage, and impaired functionality. Our preliminary data thus indicate that abnormal muscle cell metabolism caused by mutations in the dysferlin gene contribute to the disease pathology, that dysferlinopathies recapitulate some of the aberrant changes observed in glycogen storage diseases such as McArdle's, and finally that dysferlin regulates cellular metabolism in an unknown manner, in addition to its role in controlling membrane repair. We therefore propose a research plan in this grant application that aims at a.) substantiating and validating these findings in different pre-clinical models, b.) obtaining proof-of-concept for therapeutic efficacy of normalization of muscle cell metabolism in LGMD2B, and c.) investigating the molecular underpinnings of the involvement of dysferlin in the regulation of muscle cell metabolism. The expected results will not only shed light on novel aspects of dysferlin function, but should also propose new therapeutic avenues to ameliorate this muscular dystrophies, complementing those targeting membrane repair. A new high-resolution LC-MS platform for high precision and throughput quantitative biology to support life science research at the Biozentrum of the University of Basel Research Project | 6 Project MembersLife science research is performed at many institutes and clinics at the University of Basel and encompasses areas from clinical studies to in-vitro studies with cellular systems or pathogens. Omics technologies are increasingly applied in these projects in order to gain detailed insights into biomolecular processes involved during homeostasis, regulation and perturbation of biological systems. Although genomics provides useful information on the genetic composition of a cell or organism, it is often insufficient to explain the observed biological phenotypes. These questions need to be answered by studying the protein complement (proteome) and cellular signalling by analysing post-translational modifications like phosphorylation (phosphoproteome). As outlined in this proposal, the different projects aim at a better understanding of complex processes involved in initiation and progression of diseases, including bacterial vaccination, malaria, cancer and muscle diseases, using proteomics data. Specifically, the following five projects of the proposal are described: Project 1 attempts to establish molecular mechanisms mediating responsiveness to targeted cancer therapy by generating proteome and phosphoproteome maps from serial biopsies of hepatocellular carcinoma patients (HCC) before and during drug treatment. We then take an 'multi-omics' approach to find molecular patterns predictive for treatment success. Project 2 focuses on the discovery of evasive signaling pathways in hepatocellular carcinoma (HCC) by quantitative proteome and phosphoproteome comparisons of patient-derived tumor organoids after Sorafenib treatment at different time points. Project 3 employs data-independent proteomics to define cellular protein concentrations of Staphylococcus aureus proteins in patient abscesses and lung secretions. We will then use a reverse translational approach to find key components for urgently needed protective vaccines. Projects 4 intends to gain novel important insights into the complex regulation of the biological program of muscle adaptation to exercise by integrating proteome, signaling and protein-protein interaction data obtained from LC-MS analyses. Project 5 will employ targeted proteomics to identify components of the molecular machinery that regulates singular gene choice, an intriguing transcriptional control mechanism that facilitates antigenic variation and immune evasion of malaria parasites. The proposed projects pose extremely challenging demands on protein sample analysis in terms of sensitivity, precision and throughput. Like in all clinical studies, due to the high interpatient variability, high sample numbers are required to achieve sufficient statistical power for confident target discovery and validation. Moreover, many proteins and modifications of interest are low abundant and very challenging to quantify consistently with high precision across large sample batches. After extensive evaluation, we found the Q Exactive HF-X mass spectrometer to be the only instrument on the market to have sufficient speed and sensitivity to meet these high analytical requirements. In particular, its compatibility with data-independent workflows and new on-the-fly acquisition software allows unprecedented proteome coverage in discovery and the highest sensitivity and throughput for targeted MS experiments. We are convinced that the new Q Exactive HF-X is the instrument of choice to fullfil the requirements of the projects listed above, and many more to come in the future. Treatment of sarcopenia with pulsatile, low-dose application of the myokine interleukin 6 (IL-6) Research Project | 1 Project MembersNo Description available Molecular mechanisms controlling the crosstalk between skeletal muscle and neurons Research Project | 1 Project MembersSkeletal muscle exhibits an enormous cellular plasticity to adapt to external and internal stimuli. For example, exercise triggers a pleiotropic adaptation in metabolic and contractile properties in muscle fibers, angiogenesis and increased vascularization within muscle tissue, as well as systemic metabolic remodeling in various other organs. Even though exercise exerts numerous health benefits, the molecular mechanisms that control muscle cell plasticity are still poorly understood. In particular, it is largely unclear how long-term adaptations of training are controlled, e.g. those related to the remodeling of the neuromuscular junction. Our grant aims at elucidating the transcriptional networks that control muscle cell identity in acute exercise and chronic exercise training. Preliminary data indicate that epigenetic adaptations in trained muscle might facilitate the gene expression changes elicited by individual exercise bouts. Besides a general analysis of these networks using a combination of next generation sequencing approaches and computational predictions, we will also specifically focus on potential mediators of a crosstalk between muscle fibers and neurons. We have previously published a hitherto unexpected retrograde effect of muscle on morphological and functional aspects of the motor neuron, mediated by so-far unknown effectors. Moreover, preliminary findings describing a potent effect of exercise and muscle peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α), a regulatory nexus of endurance exercise adaptation, on motor coordination and balance, and hence presumably proprioceptive and/or vestibular input indicate an even more extensive retrograde signaling between muscle and neuronal circuits. We thus plan to study the interaction of the neuromuscular, proprioceptive and vestibular systems, and to identify the respective mediators in this crosstalk. Retro- and anterograde mapping of proprioceptive and vestibular input on specific motor neuron pools will allow a fine-grained quantification of changes in these systems. These studies will not only contribute to a better understanding of neuromuscular physiology, but also help to identify factors that modulate neuromuscular junction stability, motor coordination and balance, all of which are affected in different pathological settings, e.g. in sarcopenia and aging. Exercise-based interventions in dysferlinopathies Research Project | 1 Project MembersDysferlin is a protein that is involved in different aspects of muscle cell biology, with a prominent role in damageinduced membrane repair. Mutations in the dysferlin gene result in muscular dystrophies collectively referred to as dysferlinopathies. To date, efficient interventions for the prevention and treatment of these pathologies remain elusive. Based on the known functions of dysferlin, exercise‐based interventions could be expected to alleviate many of the symptoms. However, since some specific exercise paradigms have been associated with a detrimental outcome, at least in mouse models for this disease, the adaptations linked to exercise might have to be achieved by alternative means to design safe therapeutic approaches. Our project aims at a better understanding of the function of dysferlin, the mechanisms that underlie the disease pathology and ultimately, the use of genetic and pharmacological interventions that elicit potential beneficial effects. These interventions are centered on the peroxisome proliferator‐activated receptor γ coactivator 1α (PGC‐1α), a key regulatory nexus of endurance exercise adaptation of skeletal muscle. A comprehensive analysis using in silico, in vitro and in vivo techniques will help to identify novel modalities to enhance membrane resealing, improve fiber repair, boost muscle regeneration and eventually enhance muscle function in dysferlinopathies. Effect of exercise and exercise factors on cancer cachexia Research Project | 1 Project MembersCachexia, defined as loss of muscle and fat mass, is a major complication in cancer that not only massively increases morbidity and mortality, but also reduces the tolerance to radio- and chemotherapy. In fact, cachexia is estimated to constitute the actual cause of death in 22%-40% of all cancer patients, and not the tumor itself. Despite this obvious clinical importance, the molecular mechanisms leading to cancer cachexia are poorly understood. Furthermore, no effective treatment exists for this pathology. Intriguingly however, many of the key symptoms of cachexia are highly reminiscent of the plastic changes observed in trained skeletal muscle, yet in an inversed manner. Therefore, exercise has been speculated to constitute a possible therapeutic intervention for cachexia. Unfortunately, cancer patients, in particular those undergoing radio- and chemotherapy or those already suffering from cachexia, often exhibit a relative exercise intolerance, e.g. due to frailty, fatigue, nausea or time-consuming and restricting cancer treatment regimes. To overcome these hurdles, a better understanding of exercise-mediated effects in cancer could help to identify specific factors that harbor an anti-cachectic potential. In addition, so-called "exercise mimetics", pharmacological agents that elicit training-like effects in muscle, could also benefit cancer patients. Our project is aimed to systematically assess the outcome of endurance exercise on cachexia in tumor-bearing mice. Second, we will study how the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) affects changes in body weight and muscle mass in sedentary and trained mice with ectopic tumors. PGC-1α is a key regulator of endurance training adaptation in skeletal muscle and sufficient to attenuate muscle wasting in various pathological contexts. Moreover, PGC-1α is thought to constitute the target for most currently described experimental exercise mimetics. Finally, state-of-the-art genomic and proteomic techniques will be combined with computational analysis methods to identify exercise and tumor-derived factors in cachectic animals in an unbiased manner. Collectively, the data will provide novel insights into the role of exercise in the treatment of cancer cachexia, and should reveal molecular mediators of such a therapeutic effect that could be used in the treatment of cancer patients. Molecular underpinning of age-related muscle loss Research Project | 9 Project MembersSkeletal muscle is the largest organ of the human body and thus, it has essential roles that include not only locomotion and breathing, but also in the regulation of energy and glucose homeostasis in the entire body. Skeletal muscle wasting is associated with a wide range of conditions, including heart and kidney failure, as well as cancer. Muscle wasting is also a hallmark of many, rare neuromuscular diseases. As the average life span in the human population increased, the loss of muscle mass and function at high age, called sarcopenia, has become an important socio-economic challenge of civilized countries. Sarcopenia is the main cause of frailty and leads to a high frequency of falls in the elderly. Sarcopenia is characterized by many morphological alterations of the skeletal muscle such as atrophy, changes in oxidative properties and degeneration combined with a poor regenerative capacity. Moreover, the site of contact between motor neurons and skeletal muscle fiber, called the neuromuscular junction, becomes fragmented indicating impaired function. Although multiple factors such as hormonal changes (e.g. testosterone, oestrogen, growth hormone, IGF-1), changes in muscle proteostasis (i.e. balance between anabolic and catabolic pathways) and in mitochondrial function have been implicated in sarcopenia, the underlying molecular mechanisms are not at all understood. In addition, extrinsic factors such as daily activity and nutritional habits have been shown to affect sarcopenia. In this Sinergia project, we aim to identify the core pathways underlying sarcopenia by conducting a multi-level analysis of mouse models that cover a broad range of rates at which the sarcopenic phenotype develops. Specifically, we will examine the aging process longitudinally in mice undergoing natural aging, two very distinct transgenic mouse models that both (muscle-specific TSC and Klotho knockouts) show accelerated sarcopenia, as well as mice that were subjected to treatments that were shown to prolong lifespan and delay sarcopenia. These are caloric restriction, exercise, treatment with rapamycin or transgenic expression of PGC-1a. With state-of-the-art methods for estimating mRNA transcription, mRNA translation and protein degradation rates we will evaluate proteostasis and signaling pathways implicated in sarcopenia in the muscles of all these mouse groups. We will extend this analysis to specific sub-cellular compartments such as the mitochondria and the neuromuscular junction, whose function has been found crucial for the maintenance of muscle functionality. In spite of a strong resurgence of interest in aging and aging-related conditions, the vast majority of the studies that have been done to date focused on a limited set of conditions or pathways. Substantial effort has been put in the physiological characterization of the animal models, but quantitative, genome-wide studies are scarce and largely limited to the transcriptomic level. The main strengths of our project are that 1. we will study in parallel mouse models in which the progression to sarcopenia is modulated through distinct, but presumably interlinked pathways; 2. we will apply a simultaneous and comprehensive analysis of all models, with a homogeneous set of state-of-the art methods that we have at our disposal through the highly complementary expertise of the groups involved. This will allow us to assess the relative contributions of individual pathways to the different phenotypes as well as distill a core signature of sarcopenia. Importantly, the comprehensiveness of the genome-wide data that we will obtain and analyze computationally will enable us to uncover novel regulators of muscle function in health and disease. 1234 1...4
Investigating the Neuromuscular Involvement in Cachexia: Identifying Novel Target Genes and Therapeutic Targets Research Project | 2 Project MembersCancer cachexia is a severe and prevalent condition that affects up to 80% of cancer patients and causes muscle wasting and weakness, leading to frailty and reduced tolerance to cancer treatments. Despite its significant contribution to cancer-related morbidity and mortality, there are currently no effective treatment strategies to ameliorate cachexia. This highlights the need for further research to understand the mechanisms behind cachexia development. Recent studies indicate that changes in the connection between the nervous system and muscles, called the neuromuscular junction (NMJ), play a crucial role in developing cachexia. However, the specific mechanisms behind these alterations and how they mediate muscle wasting are not understood. The primary goal of this project is to use state-of-the-art techniques to investigate NMJs in both cachexia-susceptible and -protected muscles in mouse models of cachexia. Revealing the differences in different muscle types will provide novel information about the underlying causes of cachexia. Furthermore, we aim to genetically manipulate the factors revealed in this study to restore muscle wasting in mice with cancer. By this means, new potential therapeutic targets for treating cachexia will be identified. Ultimately, this research project aims to decipher the underlying neuromuscular causes of cancer cachexia and identify new treatment options that may enhance the quality of life and survival of cancer patients.
Beitrag an die Fertigstellung der Dissertation "Transcriptional networks in skeletal muscle in response to acute exercise" Research Project | 2 Project MembersWestliche Gesellschaften leiden zunehmend unter Wohlstandskrankheiten die auf einen inaktiven Lebensstil und einen Überschuss an Kalorien zurückzuführen sind. Im Jahr 2020 gehörten Herz-Kreislauf-Erkrankungen, Diabetes und Demenz zu den häufigsten Todesursachen in der Schweiz; selbst während dem Höhepunkt der Covid19-Pandemie. Die Gemeinsamkeit all dieser Krankheiten ist die mögliche Prävention und Therapie durch körperliche Aktivität. Körperliche Fitness ist ein epidemiologischer Indikator für reduzierte Mortalität und Anfälligkeit für Krankheiten was regelmässiges Training zur absoluten Grundlage eines gesunden Lebensstils macht. Während wir aus physiologischer Sicht verstehen, wie sich die Muskulatur auf regelmässiges Training einstellt und dadurch die gesamte körperliche Gesundheit positiv beeinflusst, so sind die molekularen Prozesse die diese Veränderungen steuern weitgehend unbekannt. Das Ziel meines Doktorats ist es, genau diese molekularen Prozesse im Muskel besser zu verstehen und die wichtigsten Transkriptionsfaktoren in der Muskelanpassung zu identifizieren und charakterisieren.
Structure-function analysis of the RNA-binding protein PGC-1a in skeletal muscle Research Project | 2 Project MembersPlasticity of cells, tissues and organs relies on sensing of external and internal cues, integration of the engaged signaling pathways, and orchestration of a pleiotropic response. For example, contractile patterns, ambient temperature and oxygen levels, nutrient availability and composition, as well as other factors result in a massive remodeling of biochemical pathways, cellular metabolism and mechanical properties of skeletal muscle cells, most notably in the context of repeated bouts of exercise, ultimately leading to training adaptations. In turn, such adaptations of skeletal muscle trigger internal and external changes that contribute to the systemic effects of exercise with many health benefits, and strong preventative and therapeutic outcomes in a number of pathologies. Surprisingly, even though the physiological and clinical contributions of exercise-linked muscle plasticity are well recognized, the molecular mechanisms that control the corresponding biological programs are still poorly understood. In recent years, the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) has emerged as a central regulatory nexus of plasticity in various cell types. PGC-1α integrates upstream signaling pathways to coordinate the complex transcriptional networks encoding biological programs involved in mitochondrial function, cellular metabolism and more. In the case of endurance exercise-mediated plasticity of muscle cells, most, if not all of the adaptations are evoked by this stimulus. Accordingly, muscle-specific overexpression or knockout of PGC-1α elicits high endurance and pathologically sedentary phenotypes, respectively. Our proposal aims at elucidating the molecular underpinnings of the complex transcriptional control that is exerted by PGC-1α in a spatio-temporal manner. We have recently discovered that the binding of RNAs to PGC-1α contributes to full transcriptional activity, and is central for the inclusion of PGC-1α-containing multiprotein complexes in liquid-liquid phase separated nuclear condensates for the sequestration of transcription. We now plan to determine the list and common features of PGC-1α-bound RNAs, interrogate how RNA binding is brought about in a structure-function analysis, study the consequences on multiprotein complex formation, and ultimately investigate the physiological relevance in skeletal muscle cells in vitro and in vivo . To do so, novel animal models will be leveraged for single-end enhanced crosslinking and immunoprecipitation (seCLIP) experiments to identify PGC-1α-bound RNAs, structural information will be obtained by NMR spectroscopy, and validated using site-directed mutagenesis of key amino acids and nucleotides in PGC-1α and RNAs, respectively, to study PGC-1α-dependent liquid-liquid phase separation. Then, PGC-1α-containing multiprotein complexes will be co-purified to perform cryo-electron microscopy-based single particle structural analysis. Finally, the functional consequence of targeted mutagenesis of key residues will be assessed in muscle cells in culture and mouse muscle in vivo with state-of-the-art myotropic adeno-associated viral vectors (AAVMYO). The research plan thus a.) highly synergizes in terms of interdisciplinary approaches between the groups involved and b.) will result in hitherto unprecedented insights into molecular mechanisms that underlie complex spatio-temporal control of transcriptional networks with important implications for the understanding of cellular and tissue plasticity in health and disease.
A novel role of dysferlin in regulating skeletal muscle metabolism contributes to disease pathology in dysferlinopathies Research Project | 1 Project MembersDysferlin is a protein that is intimately involved in the control of membrane repair in damaged cells. Accordingly, mutations of the dysferlin gene cause progressive muscular dystrophies collectively referred to as dysferlinopathies. Unexpectedly though, therapeutic strategies aimed at restoring membrane resealing capabilities fail to prevent the muscular dystrophy in these diseases, indicating other, hitherto unknown molecular functions of dysferlin to contribute to the pathology in dysferlinopathy patients. We have now observed how the pathological progression in a mouse model for Limb-Girdle Muscular Dystrophy type 2B (LGMD2B) is closely linked to altered muscle cell metabolism, most notably an accumulation of glycogen. Moreover, exacerbation of glycogen storage by overexpression of the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) in these muscles results in a more severe muscle tissue damage, and impaired functionality. Our preliminary data thus indicate that abnormal muscle cell metabolism caused by mutations in the dysferlin gene contribute to the disease pathology, that dysferlinopathies recapitulate some of the aberrant changes observed in glycogen storage diseases such as McArdle's, and finally that dysferlin regulates cellular metabolism in an unknown manner, in addition to its role in controlling membrane repair. We therefore propose a research plan in this grant application that aims at a.) substantiating and validating these findings in different pre-clinical models, b.) obtaining proof-of-concept for therapeutic efficacy of normalization of muscle cell metabolism in LGMD2B, and c.) investigating the molecular underpinnings of the involvement of dysferlin in the regulation of muscle cell metabolism. The expected results will not only shed light on novel aspects of dysferlin function, but should also propose new therapeutic avenues to ameliorate this muscular dystrophies, complementing those targeting membrane repair.
A new high-resolution LC-MS platform for high precision and throughput quantitative biology to support life science research at the Biozentrum of the University of Basel Research Project | 6 Project MembersLife science research is performed at many institutes and clinics at the University of Basel and encompasses areas from clinical studies to in-vitro studies with cellular systems or pathogens. Omics technologies are increasingly applied in these projects in order to gain detailed insights into biomolecular processes involved during homeostasis, regulation and perturbation of biological systems. Although genomics provides useful information on the genetic composition of a cell or organism, it is often insufficient to explain the observed biological phenotypes. These questions need to be answered by studying the protein complement (proteome) and cellular signalling by analysing post-translational modifications like phosphorylation (phosphoproteome). As outlined in this proposal, the different projects aim at a better understanding of complex processes involved in initiation and progression of diseases, including bacterial vaccination, malaria, cancer and muscle diseases, using proteomics data. Specifically, the following five projects of the proposal are described: Project 1 attempts to establish molecular mechanisms mediating responsiveness to targeted cancer therapy by generating proteome and phosphoproteome maps from serial biopsies of hepatocellular carcinoma patients (HCC) before and during drug treatment. We then take an 'multi-omics' approach to find molecular patterns predictive for treatment success. Project 2 focuses on the discovery of evasive signaling pathways in hepatocellular carcinoma (HCC) by quantitative proteome and phosphoproteome comparisons of patient-derived tumor organoids after Sorafenib treatment at different time points. Project 3 employs data-independent proteomics to define cellular protein concentrations of Staphylococcus aureus proteins in patient abscesses and lung secretions. We will then use a reverse translational approach to find key components for urgently needed protective vaccines. Projects 4 intends to gain novel important insights into the complex regulation of the biological program of muscle adaptation to exercise by integrating proteome, signaling and protein-protein interaction data obtained from LC-MS analyses. Project 5 will employ targeted proteomics to identify components of the molecular machinery that regulates singular gene choice, an intriguing transcriptional control mechanism that facilitates antigenic variation and immune evasion of malaria parasites. The proposed projects pose extremely challenging demands on protein sample analysis in terms of sensitivity, precision and throughput. Like in all clinical studies, due to the high interpatient variability, high sample numbers are required to achieve sufficient statistical power for confident target discovery and validation. Moreover, many proteins and modifications of interest are low abundant and very challenging to quantify consistently with high precision across large sample batches. After extensive evaluation, we found the Q Exactive HF-X mass spectrometer to be the only instrument on the market to have sufficient speed and sensitivity to meet these high analytical requirements. In particular, its compatibility with data-independent workflows and new on-the-fly acquisition software allows unprecedented proteome coverage in discovery and the highest sensitivity and throughput for targeted MS experiments. We are convinced that the new Q Exactive HF-X is the instrument of choice to fullfil the requirements of the projects listed above, and many more to come in the future.
Treatment of sarcopenia with pulsatile, low-dose application of the myokine interleukin 6 (IL-6) Research Project | 1 Project MembersNo Description available
Molecular mechanisms controlling the crosstalk between skeletal muscle and neurons Research Project | 1 Project MembersSkeletal muscle exhibits an enormous cellular plasticity to adapt to external and internal stimuli. For example, exercise triggers a pleiotropic adaptation in metabolic and contractile properties in muscle fibers, angiogenesis and increased vascularization within muscle tissue, as well as systemic metabolic remodeling in various other organs. Even though exercise exerts numerous health benefits, the molecular mechanisms that control muscle cell plasticity are still poorly understood. In particular, it is largely unclear how long-term adaptations of training are controlled, e.g. those related to the remodeling of the neuromuscular junction. Our grant aims at elucidating the transcriptional networks that control muscle cell identity in acute exercise and chronic exercise training. Preliminary data indicate that epigenetic adaptations in trained muscle might facilitate the gene expression changes elicited by individual exercise bouts. Besides a general analysis of these networks using a combination of next generation sequencing approaches and computational predictions, we will also specifically focus on potential mediators of a crosstalk between muscle fibers and neurons. We have previously published a hitherto unexpected retrograde effect of muscle on morphological and functional aspects of the motor neuron, mediated by so-far unknown effectors. Moreover, preliminary findings describing a potent effect of exercise and muscle peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α), a regulatory nexus of endurance exercise adaptation, on motor coordination and balance, and hence presumably proprioceptive and/or vestibular input indicate an even more extensive retrograde signaling between muscle and neuronal circuits. We thus plan to study the interaction of the neuromuscular, proprioceptive and vestibular systems, and to identify the respective mediators in this crosstalk. Retro- and anterograde mapping of proprioceptive and vestibular input on specific motor neuron pools will allow a fine-grained quantification of changes in these systems. These studies will not only contribute to a better understanding of neuromuscular physiology, but also help to identify factors that modulate neuromuscular junction stability, motor coordination and balance, all of which are affected in different pathological settings, e.g. in sarcopenia and aging.
Exercise-based interventions in dysferlinopathies Research Project | 1 Project MembersDysferlin is a protein that is involved in different aspects of muscle cell biology, with a prominent role in damageinduced membrane repair. Mutations in the dysferlin gene result in muscular dystrophies collectively referred to as dysferlinopathies. To date, efficient interventions for the prevention and treatment of these pathologies remain elusive. Based on the known functions of dysferlin, exercise‐based interventions could be expected to alleviate many of the symptoms. However, since some specific exercise paradigms have been associated with a detrimental outcome, at least in mouse models for this disease, the adaptations linked to exercise might have to be achieved by alternative means to design safe therapeutic approaches. Our project aims at a better understanding of the function of dysferlin, the mechanisms that underlie the disease pathology and ultimately, the use of genetic and pharmacological interventions that elicit potential beneficial effects. These interventions are centered on the peroxisome proliferator‐activated receptor γ coactivator 1α (PGC‐1α), a key regulatory nexus of endurance exercise adaptation of skeletal muscle. A comprehensive analysis using in silico, in vitro and in vivo techniques will help to identify novel modalities to enhance membrane resealing, improve fiber repair, boost muscle regeneration and eventually enhance muscle function in dysferlinopathies.
Effect of exercise and exercise factors on cancer cachexia Research Project | 1 Project MembersCachexia, defined as loss of muscle and fat mass, is a major complication in cancer that not only massively increases morbidity and mortality, but also reduces the tolerance to radio- and chemotherapy. In fact, cachexia is estimated to constitute the actual cause of death in 22%-40% of all cancer patients, and not the tumor itself. Despite this obvious clinical importance, the molecular mechanisms leading to cancer cachexia are poorly understood. Furthermore, no effective treatment exists for this pathology. Intriguingly however, many of the key symptoms of cachexia are highly reminiscent of the plastic changes observed in trained skeletal muscle, yet in an inversed manner. Therefore, exercise has been speculated to constitute a possible therapeutic intervention for cachexia. Unfortunately, cancer patients, in particular those undergoing radio- and chemotherapy or those already suffering from cachexia, often exhibit a relative exercise intolerance, e.g. due to frailty, fatigue, nausea or time-consuming and restricting cancer treatment regimes. To overcome these hurdles, a better understanding of exercise-mediated effects in cancer could help to identify specific factors that harbor an anti-cachectic potential. In addition, so-called "exercise mimetics", pharmacological agents that elicit training-like effects in muscle, could also benefit cancer patients. Our project is aimed to systematically assess the outcome of endurance exercise on cachexia in tumor-bearing mice. Second, we will study how the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) affects changes in body weight and muscle mass in sedentary and trained mice with ectopic tumors. PGC-1α is a key regulator of endurance training adaptation in skeletal muscle and sufficient to attenuate muscle wasting in various pathological contexts. Moreover, PGC-1α is thought to constitute the target for most currently described experimental exercise mimetics. Finally, state-of-the-art genomic and proteomic techniques will be combined with computational analysis methods to identify exercise and tumor-derived factors in cachectic animals in an unbiased manner. Collectively, the data will provide novel insights into the role of exercise in the treatment of cancer cachexia, and should reveal molecular mediators of such a therapeutic effect that could be used in the treatment of cancer patients.
Molecular underpinning of age-related muscle loss Research Project | 9 Project MembersSkeletal muscle is the largest organ of the human body and thus, it has essential roles that include not only locomotion and breathing, but also in the regulation of energy and glucose homeostasis in the entire body. Skeletal muscle wasting is associated with a wide range of conditions, including heart and kidney failure, as well as cancer. Muscle wasting is also a hallmark of many, rare neuromuscular diseases. As the average life span in the human population increased, the loss of muscle mass and function at high age, called sarcopenia, has become an important socio-economic challenge of civilized countries. Sarcopenia is the main cause of frailty and leads to a high frequency of falls in the elderly. Sarcopenia is characterized by many morphological alterations of the skeletal muscle such as atrophy, changes in oxidative properties and degeneration combined with a poor regenerative capacity. Moreover, the site of contact between motor neurons and skeletal muscle fiber, called the neuromuscular junction, becomes fragmented indicating impaired function. Although multiple factors such as hormonal changes (e.g. testosterone, oestrogen, growth hormone, IGF-1), changes in muscle proteostasis (i.e. balance between anabolic and catabolic pathways) and in mitochondrial function have been implicated in sarcopenia, the underlying molecular mechanisms are not at all understood. In addition, extrinsic factors such as daily activity and nutritional habits have been shown to affect sarcopenia. In this Sinergia project, we aim to identify the core pathways underlying sarcopenia by conducting a multi-level analysis of mouse models that cover a broad range of rates at which the sarcopenic phenotype develops. Specifically, we will examine the aging process longitudinally in mice undergoing natural aging, two very distinct transgenic mouse models that both (muscle-specific TSC and Klotho knockouts) show accelerated sarcopenia, as well as mice that were subjected to treatments that were shown to prolong lifespan and delay sarcopenia. These are caloric restriction, exercise, treatment with rapamycin or transgenic expression of PGC-1a. With state-of-the-art methods for estimating mRNA transcription, mRNA translation and protein degradation rates we will evaluate proteostasis and signaling pathways implicated in sarcopenia in the muscles of all these mouse groups. We will extend this analysis to specific sub-cellular compartments such as the mitochondria and the neuromuscular junction, whose function has been found crucial for the maintenance of muscle functionality. In spite of a strong resurgence of interest in aging and aging-related conditions, the vast majority of the studies that have been done to date focused on a limited set of conditions or pathways. Substantial effort has been put in the physiological characterization of the animal models, but quantitative, genome-wide studies are scarce and largely limited to the transcriptomic level. The main strengths of our project are that 1. we will study in parallel mouse models in which the progression to sarcopenia is modulated through distinct, but presumably interlinked pathways; 2. we will apply a simultaneous and comprehensive analysis of all models, with a homogeneous set of state-of-the art methods that we have at our disposal through the highly complementary expertise of the groups involved. This will allow us to assess the relative contributions of individual pathways to the different phenotypes as well as distill a core signature of sarcopenia. Importantly, the comprehensiveness of the genome-wide data that we will obtain and analyze computationally will enable us to uncover novel regulators of muscle function in health and disease.
