Projects & Collaborations 21 foundShow per page10 10 20 50 Understanding processing body dynamics, composition and function under different stresses Research Project | 2 Project MembersImported from Grants Tool 4704182 Analysis of molecular changes of the nervous system in C. elegans upon circadian rhythm entrainment Research Project | 1 Project MembersImported from Grants Tool 4703218 Analysis and Regulation of Arf1-dependent compartmentalization Research Project | 1 Project MembersNo Description available Junk versus wholesome food: How dietary RNAs influence organismal proteostasis Research Project | 1 Project MembersVorbereitung eines ERC Advanced Grants Rektoratsbeschluss Nr. 21.03.52 CHF 50'000.00 PBStressERMCSs Research Project | 2 Project MembersOne of the first responses to eukaryotic cellular stress is the formation of cytoplasmic granules like processing bodies (PBs) and stress granules (SGs). PBs are membrane-less structures that are dynamic in their assembly/disassembly and composition depending on the type of stress that they encounter. While glucose starvation is the main stress applied to study PB formation and dynamics, much less is known about PBs under other stresses, especially endoplasmic reticulum (ER) and mitochondrial/lysosomal stresses. We propose to study the formation, content and dynamics of PBs under ER and mitochondrial/lysosomal stresses, together with their turnover (autophagy/dissolution) during stress recovery. I plan to use pharmacological and acute genetic interventions to induce stresses. PBs will be purified according to the established protocol in the laboratory, which enables subsequent Liquid hromatography-mass spectrometry (LC-MS) analysis for proteins and RNA-sequencing for the RNA content. Probing stress response further, we will also perform total RNA-sequencing and Ribosome-profiling. The fate of specific sets of mRNAs will be determined by FISH-IF and RNA decay analysis, thereby identifying the signals effectuating PB localization and fate (storage or decay) during ER and mitochondrial/lysosomal stress. The study will be extended to check conservation of PB stress response in mammalian cells. The proposed research will provide a holistic view on the pathways that are up- or down-regulated during ER and mitochondrial/lysosomal stress, the identification of common pathways between the different stresses and PB -mRNA and protein- turnover. This project will be of high impact in the fields of cancer, cell, and neuro biology. Junk versus wholesome food: Regulation of organismal proteostasis and well-being by dietary cues Research Project | 2 Project MembersThe average lifespan of humans has immensely increased over the past decades and with it the percentage of elderly in the population. Aging is associated with a progressive decline in numerous physiological processes, ultimately leading to a number of diseases. In particular neurodegenerative disorders such as Alzheimer's, Parkinson's and Huntington's disease are one of the most prevalent group of age-associated maladies. Huntington's disease is characterized by the aggregation of Huntingtin, a protein with a poly-glutamine (polyQ) stretch. A polyQ stretch above 35 is considered a high-risk factor for disease outbreak. Yet, human well-being is also chiefly dependent on environmental factors that interface with a variety of quality control mechanisms to sustain overall cellular homeostasis. A healthy lifestyle, including our eating habits, has a large impact on our health- and life-span. Increasing evidence provides a connection between aging, deregulated nutrient sensing and consumption as well as loss of protein homeostasis (or proteostasis for short). However, the role of diet in maintaining cellular and organismal proteostasis and the underlying mechanisms and pathways remain still largely elusive. With this project, we aim to bridge this gap and to identify individual dietary components that influence proteostasis and overall organismal physiology. In parallel, we also aim to identify the mechanisms involved. Our specific aims are to: identify the specific dietary cues that regulate proteostasis in C. elegans with impact on their health-span and life-span delineate the involved molecular and cellular mechanisms. To reach the goals, two distinct approaches will be pursued. First, we will use a combination of biochemical fractionation and 'omics' approaches to identify the dietary components that favorably (or even adversely) impacts proteostasis in C. elegans expressing different lengths of polyQ . Second, we will perform an RNAi screen using the same animal models reared on different diets to decipher the mechanisms in C. elegans that are regulating proteostasis during aging in relation to dietary cues . Finally, we will investigate the potential impact of the dietary cues and involved mechanisms on life- and health-span. Taken together, this project will reveal how dietary compounds affect organismal proteostasis and delineate the responsible mechanisms. Understanding the influence of diet in vivo and the affected evolutionary conserved pathways will open new avenues for future research on human physiology and the significance of specific dietary nutrients. Regulation of endosomal transport and maturation Research Project | 1 Project MembersEndocytosis is an essential pathway in eukaryotes to receive signals and regulate the protein composition of the plasma membrane. Proteins that are removed from the plasma membrane can either be recycled back, go to the trans-Golgi network (TGN) or be degraded in the lysosome. Inappropriate sorting at endosomes can lead to a variety of cancers, and many factors involved in these processes are oncogenes. In addition, the endosomal pathway is often highjacked by pathogens for their cell entry and infectivity. Moreover, a plethora of other diseases are linked to defects in the endosomal pathway. Therefore, understanding the endosomal pathway is of pivotal importance. Rather than concentrating on a specific disease, we work towards the elucidation of the regulation of the endosomal pathway. This knowledge can then be applied to many instances. Our starting point was the discovery of endosomal maturation. Even though, maturation had been proposed earlier, we were the first to show that endosomes mature from early to late before fusing with the lysosomes. Since then, we have been interested in understanding the regulation and coordination of processes that take place during maturation. Recently, we identified FERARI, a platform on sorting endosomes that recruits Rab11 recycling structures to the sorting endosomes, promotes fusion -without membrane flattening- and then fission of these Rab11 compartments from the sorting endosome. We surmise that during this process cargo destined for recycling is taken up. Thus, we discovered a kiss-and-run mechanism in endocytic recycling. Surprisingly, the residence time of recycling structures on sorting endosomes was quantal in 7 sec intervals, which we interpreted as the time of fusion pore opening and closing. To investigate this unexpected finding further, we propose to (1) determine the structure of FERARI by cryoEM and to reconstitute FERARI function in vitro. (2) to analyse the regulation of FERARI and sorting in vivo using mammalian cell lines and C. elegans as a model animal. (3) In order to better understand the regulation of endosome maturation, we have set up and in vivo assay system in mammalian cells, in which we can enlarge endosome about 40x without harming cells and follow endosome mature with ease under a widefield microscope. We want to explore this unpublished assay (manuscript in preparation) to first describe the coordination of different processes during endosome maturation and then use genetic engineering as well as acute perturbances to understand the regulation of endosome maturation. Thus, we use a balanced mix of high-risk, high-gain parts and very attainable goals to provide unprecedented data on endosomal transport. Elucidation of mechanisms of Arf1-dependent cellular processes Research Project | 1 Project MembersThe ability to communicate with and to sense the environment is essential for cells. Exo- and endocytosis are the processes promoting the discharge and uptake of proteins, lipids and other molecules at the plasma membrane, respectively. These processes are controlled by small GTPases mainly of the Arf and Rab family. At the same time signaling events occur at the plasma membrane that may drive the internalization of receptors and will subsequently lead to the termination of the initial signal transduction. Likewise, external cues read by receptors in the plasma membrane can influence membrane transport event. Thus, there is a crosstalk between membrane traffic and signaling. In recent years, however, it became clear that this crosstalk may be more complicated and intense and that small GTPases, such Arf1, may operate beyond their canonical functions We have been working on the elucidation of different Arf1 functions. One feature that stood out was that Arf1 is important for the subcellular localization of a subset of mRNAs, and that in an arf1 mutant, some RNAs became better translated, even though translation was generally attenuated, and processing body (PB) formation was increased. PBs are the major decay compartment in yeast. To gain more insights, we performed next generation sequencing (NGS) on total RNA and ribosome associated mRNA (Riboseq) in an arf1 mutant and wild type. The NGS analysis extended the knowledge on differentially translated mRNAs. More importantly, two processes stood out that were extremely affected in the arf1 mutant. Pathways that were the most strongly upregulated would yield an increase in methylation. We confirmed the hits and that the methyl donor (AdoMet) is increased in arf1 mutant cells. However, we do not know what molecular species are methylated. We can exclude so far lipids and histones. Nothing is known about the connection between Arf1 and methylation. Therefore, we will determine in the first aim the molecules that are methylated and the responsible methyltransferases. From there, we will determine the mechanism and signaling pathway that leads to the increase of methylation. The most downregulated pathways were connected to ribosome biogenesis and amino acid metabolism. The regulation of these pathways are hallmarks of TORC1 signaling. Therefore, we will determine in the second aim how Arf1 controls TORC1 signaling. Even though, it was proposed that Arf1 controls TORC1 signaling in Drosophila, the underlying mechanism remains unknown. In the third aim, we will aim to understand how mRNAs are recruited into PBs under various stress conditions and how the decision is made between storage and decay in PBs. In this aim, we will capitalize on our recently established method to purify PBs to determine the mRNA and protein content and combine this with Riboseq. This system-wide analysis will be followed up by in-depth mechanistic analyses. With this aim we will gain unprecedented molecular insights on how mRNA fate is determined. Interconnecting Proteotoxic Stress Research Project | 2 Project MembersInterconnecting Proteotoxic Stress Responses with Ageing and Cardiovascular Diseases Aging-proteostasis and CVD Research Project | 2 Project MembersThe average lifespan of humans has immensely increased over the past decades and with it the percentage of elderly. Aging is associated with a progressive decline in numerous physiological processes, leading to an increased risk of health complications and disease. Aging is the most important determinant of a person's cardiovascular health: aging remarkably affects the heart and arterial system and is considered one of the major risk factors for the development and progression of cardiovascular diseases (CVD) including atherosclerosis, hypertension, myocardial infarction and stroke. Another major risk factor for CVD is obesity , and evidence supports also that obesity may accelerate the aging process. A very important cellular process crucial to cardiovascular health is proteostasis . This refers to a collection of cellular processes handling protein folding, misfolding, unfolding, and degradation, and it is fundamental to cell survival and function. Both aging and obesity lead to gradual dysfunction and collapse of the proteostasis network. Thus, it is now clear that not only are aging, obesity and proteostasis malfunction per se pivotal in development and progression of CVD, they also profoundly impact each other (Fig. 1). Understanding fundamental mechanisms that dictate their interactions could lead to significant advancements in both preventative and therapeutic treatments of CVD. 123 123
Understanding processing body dynamics, composition and function under different stresses Research Project | 2 Project MembersImported from Grants Tool 4704182
Analysis of molecular changes of the nervous system in C. elegans upon circadian rhythm entrainment Research Project | 1 Project MembersImported from Grants Tool 4703218
Analysis and Regulation of Arf1-dependent compartmentalization Research Project | 1 Project MembersNo Description available
Junk versus wholesome food: How dietary RNAs influence organismal proteostasis Research Project | 1 Project MembersVorbereitung eines ERC Advanced Grants Rektoratsbeschluss Nr. 21.03.52 CHF 50'000.00
PBStressERMCSs Research Project | 2 Project MembersOne of the first responses to eukaryotic cellular stress is the formation of cytoplasmic granules like processing bodies (PBs) and stress granules (SGs). PBs are membrane-less structures that are dynamic in their assembly/disassembly and composition depending on the type of stress that they encounter. While glucose starvation is the main stress applied to study PB formation and dynamics, much less is known about PBs under other stresses, especially endoplasmic reticulum (ER) and mitochondrial/lysosomal stresses. We propose to study the formation, content and dynamics of PBs under ER and mitochondrial/lysosomal stresses, together with their turnover (autophagy/dissolution) during stress recovery. I plan to use pharmacological and acute genetic interventions to induce stresses. PBs will be purified according to the established protocol in the laboratory, which enables subsequent Liquid hromatography-mass spectrometry (LC-MS) analysis for proteins and RNA-sequencing for the RNA content. Probing stress response further, we will also perform total RNA-sequencing and Ribosome-profiling. The fate of specific sets of mRNAs will be determined by FISH-IF and RNA decay analysis, thereby identifying the signals effectuating PB localization and fate (storage or decay) during ER and mitochondrial/lysosomal stress. The study will be extended to check conservation of PB stress response in mammalian cells. The proposed research will provide a holistic view on the pathways that are up- or down-regulated during ER and mitochondrial/lysosomal stress, the identification of common pathways between the different stresses and PB -mRNA and protein- turnover. This project will be of high impact in the fields of cancer, cell, and neuro biology.
Junk versus wholesome food: Regulation of organismal proteostasis and well-being by dietary cues Research Project | 2 Project MembersThe average lifespan of humans has immensely increased over the past decades and with it the percentage of elderly in the population. Aging is associated with a progressive decline in numerous physiological processes, ultimately leading to a number of diseases. In particular neurodegenerative disorders such as Alzheimer's, Parkinson's and Huntington's disease are one of the most prevalent group of age-associated maladies. Huntington's disease is characterized by the aggregation of Huntingtin, a protein with a poly-glutamine (polyQ) stretch. A polyQ stretch above 35 is considered a high-risk factor for disease outbreak. Yet, human well-being is also chiefly dependent on environmental factors that interface with a variety of quality control mechanisms to sustain overall cellular homeostasis. A healthy lifestyle, including our eating habits, has a large impact on our health- and life-span. Increasing evidence provides a connection between aging, deregulated nutrient sensing and consumption as well as loss of protein homeostasis (or proteostasis for short). However, the role of diet in maintaining cellular and organismal proteostasis and the underlying mechanisms and pathways remain still largely elusive. With this project, we aim to bridge this gap and to identify individual dietary components that influence proteostasis and overall organismal physiology. In parallel, we also aim to identify the mechanisms involved. Our specific aims are to: identify the specific dietary cues that regulate proteostasis in C. elegans with impact on their health-span and life-span delineate the involved molecular and cellular mechanisms. To reach the goals, two distinct approaches will be pursued. First, we will use a combination of biochemical fractionation and 'omics' approaches to identify the dietary components that favorably (or even adversely) impacts proteostasis in C. elegans expressing different lengths of polyQ . Second, we will perform an RNAi screen using the same animal models reared on different diets to decipher the mechanisms in C. elegans that are regulating proteostasis during aging in relation to dietary cues . Finally, we will investigate the potential impact of the dietary cues and involved mechanisms on life- and health-span. Taken together, this project will reveal how dietary compounds affect organismal proteostasis and delineate the responsible mechanisms. Understanding the influence of diet in vivo and the affected evolutionary conserved pathways will open new avenues for future research on human physiology and the significance of specific dietary nutrients.
Regulation of endosomal transport and maturation Research Project | 1 Project MembersEndocytosis is an essential pathway in eukaryotes to receive signals and regulate the protein composition of the plasma membrane. Proteins that are removed from the plasma membrane can either be recycled back, go to the trans-Golgi network (TGN) or be degraded in the lysosome. Inappropriate sorting at endosomes can lead to a variety of cancers, and many factors involved in these processes are oncogenes. In addition, the endosomal pathway is often highjacked by pathogens for their cell entry and infectivity. Moreover, a plethora of other diseases are linked to defects in the endosomal pathway. Therefore, understanding the endosomal pathway is of pivotal importance. Rather than concentrating on a specific disease, we work towards the elucidation of the regulation of the endosomal pathway. This knowledge can then be applied to many instances. Our starting point was the discovery of endosomal maturation. Even though, maturation had been proposed earlier, we were the first to show that endosomes mature from early to late before fusing with the lysosomes. Since then, we have been interested in understanding the regulation and coordination of processes that take place during maturation. Recently, we identified FERARI, a platform on sorting endosomes that recruits Rab11 recycling structures to the sorting endosomes, promotes fusion -without membrane flattening- and then fission of these Rab11 compartments from the sorting endosome. We surmise that during this process cargo destined for recycling is taken up. Thus, we discovered a kiss-and-run mechanism in endocytic recycling. Surprisingly, the residence time of recycling structures on sorting endosomes was quantal in 7 sec intervals, which we interpreted as the time of fusion pore opening and closing. To investigate this unexpected finding further, we propose to (1) determine the structure of FERARI by cryoEM and to reconstitute FERARI function in vitro. (2) to analyse the regulation of FERARI and sorting in vivo using mammalian cell lines and C. elegans as a model animal. (3) In order to better understand the regulation of endosome maturation, we have set up and in vivo assay system in mammalian cells, in which we can enlarge endosome about 40x without harming cells and follow endosome mature with ease under a widefield microscope. We want to explore this unpublished assay (manuscript in preparation) to first describe the coordination of different processes during endosome maturation and then use genetic engineering as well as acute perturbances to understand the regulation of endosome maturation. Thus, we use a balanced mix of high-risk, high-gain parts and very attainable goals to provide unprecedented data on endosomal transport.
Elucidation of mechanisms of Arf1-dependent cellular processes Research Project | 1 Project MembersThe ability to communicate with and to sense the environment is essential for cells. Exo- and endocytosis are the processes promoting the discharge and uptake of proteins, lipids and other molecules at the plasma membrane, respectively. These processes are controlled by small GTPases mainly of the Arf and Rab family. At the same time signaling events occur at the plasma membrane that may drive the internalization of receptors and will subsequently lead to the termination of the initial signal transduction. Likewise, external cues read by receptors in the plasma membrane can influence membrane transport event. Thus, there is a crosstalk between membrane traffic and signaling. In recent years, however, it became clear that this crosstalk may be more complicated and intense and that small GTPases, such Arf1, may operate beyond their canonical functions We have been working on the elucidation of different Arf1 functions. One feature that stood out was that Arf1 is important for the subcellular localization of a subset of mRNAs, and that in an arf1 mutant, some RNAs became better translated, even though translation was generally attenuated, and processing body (PB) formation was increased. PBs are the major decay compartment in yeast. To gain more insights, we performed next generation sequencing (NGS) on total RNA and ribosome associated mRNA (Riboseq) in an arf1 mutant and wild type. The NGS analysis extended the knowledge on differentially translated mRNAs. More importantly, two processes stood out that were extremely affected in the arf1 mutant. Pathways that were the most strongly upregulated would yield an increase in methylation. We confirmed the hits and that the methyl donor (AdoMet) is increased in arf1 mutant cells. However, we do not know what molecular species are methylated. We can exclude so far lipids and histones. Nothing is known about the connection between Arf1 and methylation. Therefore, we will determine in the first aim the molecules that are methylated and the responsible methyltransferases. From there, we will determine the mechanism and signaling pathway that leads to the increase of methylation. The most downregulated pathways were connected to ribosome biogenesis and amino acid metabolism. The regulation of these pathways are hallmarks of TORC1 signaling. Therefore, we will determine in the second aim how Arf1 controls TORC1 signaling. Even though, it was proposed that Arf1 controls TORC1 signaling in Drosophila, the underlying mechanism remains unknown. In the third aim, we will aim to understand how mRNAs are recruited into PBs under various stress conditions and how the decision is made between storage and decay in PBs. In this aim, we will capitalize on our recently established method to purify PBs to determine the mRNA and protein content and combine this with Riboseq. This system-wide analysis will be followed up by in-depth mechanistic analyses. With this aim we will gain unprecedented molecular insights on how mRNA fate is determined.
Interconnecting Proteotoxic Stress Research Project | 2 Project MembersInterconnecting Proteotoxic Stress Responses with Ageing and Cardiovascular Diseases
Aging-proteostasis and CVD Research Project | 2 Project MembersThe average lifespan of humans has immensely increased over the past decades and with it the percentage of elderly. Aging is associated with a progressive decline in numerous physiological processes, leading to an increased risk of health complications and disease. Aging is the most important determinant of a person's cardiovascular health: aging remarkably affects the heart and arterial system and is considered one of the major risk factors for the development and progression of cardiovascular diseases (CVD) including atherosclerosis, hypertension, myocardial infarction and stroke. Another major risk factor for CVD is obesity , and evidence supports also that obesity may accelerate the aging process. A very important cellular process crucial to cardiovascular health is proteostasis . This refers to a collection of cellular processes handling protein folding, misfolding, unfolding, and degradation, and it is fundamental to cell survival and function. Both aging and obesity lead to gradual dysfunction and collapse of the proteostasis network. Thus, it is now clear that not only are aging, obesity and proteostasis malfunction per se pivotal in development and progression of CVD, they also profoundly impact each other (Fig. 1). Understanding fundamental mechanisms that dictate their interactions could lead to significant advancements in both preventative and therapeutic treatments of CVD.
