Proteomics (Schmidt)Head of Research UnitDr.Alexander SchmidtOverviewMembersPublicationsProjects & CollaborationsProjects & Collaborations OverviewMembersPublicationsProjects & Collaborations Projects & Collaborations 2 foundShow per page10 10 20 50 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. System-wide Proteomic Dissection of Molecular Diversity in the Nervous System Research Project | 4 Project MembersThe nervous system represents the most complex part of the body. It is estimated that in the human brain 10 11 neuronal cells are connected into networks through 10 13 synaptic connections, which are assembled with a stunning precision and reproducibility. Understanding the molecular mechanisms underlying neuron-specific functions and selective connectivity represents a major challenge. Disruptions in neuronal circuits are believed to underlie numerous neuropsychiatric disorders such as autism and schizophrenia, therefore, uncovering the mechanisms of synaptic specificity has important implications for human health. The use of molecular codes for cell and synapse-specific recognition in the nervous system has long been hypothesized to contribute to the functional and morphological diversification of neuronal cells. In fact, several gene families have been identified that encode highly polymorphic neuronal cell surface receptors, which may confer specific neuronal identities and mediate cellular recognition. Remarkable examples of such polymorphic proteins are the neurexins (NRXNs), transmembrane proteins potentially expressed in thousands of distinct variants in the mammalian nervous system. Importantly, NRXNs have emerged as important risk factors in neuropsychiatric disorders such as autism, schizophrenia, and drug abuse [1-7]. The goal of this proposal is to use the molecular diversity of neurexins as an entry point for dissecting functional and structural diversification of neurons. There are three neurexin genes, NRXN1, NRXN2 and NRXN3, each expressed from two alternative promoters. Transcription from the upstream promoter results in larger α-neurexin isoforms, whereas the downstream promoter yields shorter β-neurexins. The majority of NRXN molecular diversity results from extensive alternative splicing at five sites [8, 9], potentially resulting in more than three thousand different isoforms. An attractive model for the function of NRXNs is that they mediate splice isoform-specific biochemical interactions. Support for this idea has come from the analysis of certain alternative splice isoforms where isoform-specific ligands have been discovered (e.g. neuroligins, LRRTMs, Cbln1, and α-DG) [10-14]. However, neurexin variants have only been mapped on the mRNA level as the molecular complexity has hindered a quantitative analysis of the corresponding protein isoforms. In fact, a systematic mapping of any highly polymorphic protein family as not been performed. In this proposal we will use a systematic proteomics approach for comprehensive mapping of molecular diversity in neuronal cells. Specifically, we will address the following aims: Aim 1: We will perform a comprehensive isoform mapping of neurexin variants in developing and adult mouse brain. Aim 2: We will use the methods established for isoform mapping to probe modification of the neurexin proteome after learning paradigms and ablation of a mRNA splicing factor. Aim 3: We will probe the logic of neurexin isoform diversity by correlating it with protein levels of regulators of neuronal function and synaptic connectivity. 1 1 OverviewMembersPublicationsProjects & Collaborations
Projects & Collaborations 2 foundShow per page10 10 20 50 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. System-wide Proteomic Dissection of Molecular Diversity in the Nervous System Research Project | 4 Project MembersThe nervous system represents the most complex part of the body. It is estimated that in the human brain 10 11 neuronal cells are connected into networks through 10 13 synaptic connections, which are assembled with a stunning precision and reproducibility. Understanding the molecular mechanisms underlying neuron-specific functions and selective connectivity represents a major challenge. Disruptions in neuronal circuits are believed to underlie numerous neuropsychiatric disorders such as autism and schizophrenia, therefore, uncovering the mechanisms of synaptic specificity has important implications for human health. The use of molecular codes for cell and synapse-specific recognition in the nervous system has long been hypothesized to contribute to the functional and morphological diversification of neuronal cells. In fact, several gene families have been identified that encode highly polymorphic neuronal cell surface receptors, which may confer specific neuronal identities and mediate cellular recognition. Remarkable examples of such polymorphic proteins are the neurexins (NRXNs), transmembrane proteins potentially expressed in thousands of distinct variants in the mammalian nervous system. Importantly, NRXNs have emerged as important risk factors in neuropsychiatric disorders such as autism, schizophrenia, and drug abuse [1-7]. The goal of this proposal is to use the molecular diversity of neurexins as an entry point for dissecting functional and structural diversification of neurons. There are three neurexin genes, NRXN1, NRXN2 and NRXN3, each expressed from two alternative promoters. Transcription from the upstream promoter results in larger α-neurexin isoforms, whereas the downstream promoter yields shorter β-neurexins. The majority of NRXN molecular diversity results from extensive alternative splicing at five sites [8, 9], potentially resulting in more than three thousand different isoforms. An attractive model for the function of NRXNs is that they mediate splice isoform-specific biochemical interactions. Support for this idea has come from the analysis of certain alternative splice isoforms where isoform-specific ligands have been discovered (e.g. neuroligins, LRRTMs, Cbln1, and α-DG) [10-14]. However, neurexin variants have only been mapped on the mRNA level as the molecular complexity has hindered a quantitative analysis of the corresponding protein isoforms. In fact, a systematic mapping of any highly polymorphic protein family as not been performed. In this proposal we will use a systematic proteomics approach for comprehensive mapping of molecular diversity in neuronal cells. Specifically, we will address the following aims: Aim 1: We will perform a comprehensive isoform mapping of neurexin variants in developing and adult mouse brain. Aim 2: We will use the methods established for isoform mapping to probe modification of the neurexin proteome after learning paradigms and ablation of a mRNA splicing factor. Aim 3: We will probe the logic of neurexin isoform diversity by correlating it with protein levels of regulators of neuronal function and synaptic connectivity. 1 1
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.
System-wide Proteomic Dissection of Molecular Diversity in the Nervous System Research Project | 4 Project MembersThe nervous system represents the most complex part of the body. It is estimated that in the human brain 10 11 neuronal cells are connected into networks through 10 13 synaptic connections, which are assembled with a stunning precision and reproducibility. Understanding the molecular mechanisms underlying neuron-specific functions and selective connectivity represents a major challenge. Disruptions in neuronal circuits are believed to underlie numerous neuropsychiatric disorders such as autism and schizophrenia, therefore, uncovering the mechanisms of synaptic specificity has important implications for human health. The use of molecular codes for cell and synapse-specific recognition in the nervous system has long been hypothesized to contribute to the functional and morphological diversification of neuronal cells. In fact, several gene families have been identified that encode highly polymorphic neuronal cell surface receptors, which may confer specific neuronal identities and mediate cellular recognition. Remarkable examples of such polymorphic proteins are the neurexins (NRXNs), transmembrane proteins potentially expressed in thousands of distinct variants in the mammalian nervous system. Importantly, NRXNs have emerged as important risk factors in neuropsychiatric disorders such as autism, schizophrenia, and drug abuse [1-7]. The goal of this proposal is to use the molecular diversity of neurexins as an entry point for dissecting functional and structural diversification of neurons. There are three neurexin genes, NRXN1, NRXN2 and NRXN3, each expressed from two alternative promoters. Transcription from the upstream promoter results in larger α-neurexin isoforms, whereas the downstream promoter yields shorter β-neurexins. The majority of NRXN molecular diversity results from extensive alternative splicing at five sites [8, 9], potentially resulting in more than three thousand different isoforms. An attractive model for the function of NRXNs is that they mediate splice isoform-specific biochemical interactions. Support for this idea has come from the analysis of certain alternative splice isoforms where isoform-specific ligands have been discovered (e.g. neuroligins, LRRTMs, Cbln1, and α-DG) [10-14]. However, neurexin variants have only been mapped on the mRNA level as the molecular complexity has hindered a quantitative analysis of the corresponding protein isoforms. In fact, a systematic mapping of any highly polymorphic protein family as not been performed. In this proposal we will use a systematic proteomics approach for comprehensive mapping of molecular diversity in neuronal cells. Specifically, we will address the following aims: Aim 1: We will perform a comprehensive isoform mapping of neurexin variants in developing and adult mouse brain. Aim 2: We will use the methods established for isoform mapping to probe modification of the neurexin proteome after learning paradigms and ablation of a mRNA splicing factor. Aim 3: We will probe the logic of neurexin isoform diversity by correlating it with protein levels of regulators of neuronal function and synaptic connectivity.
