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This project serves as a centralized repository for unpublished omics datasets from ongoing research led by SyNergy group leaders. It includes sample metadata and assay information for studies currently in progress, grouped under investigations such as proteomics and transcriptomics. The project aims to facilitate collaboration and data management within the cluster while maintaining confidentiality for unpublished work.
To explore investigations and their associated studies in more detail, please ...
Public web page: Not specified
Organisms: Mus musculus, Rattus norvegicus, Homo sapiens, Macaca mulatta, Sus scrofa, Danio rerio
This project serves as a centralized repository for omics datasets published by research groups within the SyNergy Cluster. It encompasses investigations such as proteomics and transcriptomics, which are further divided into individual studies led by SyNergy members. Each study is linked to relevant publications, assays and data files (with links to external repositories).
To explore investigations and their associated studies in more detail, please visit the 'Related items' tab on the Project ...
Public web page: Not specified
Organisms: Mus musculus, Rattus norvegicus, Homo sapiens, Macaca mulatta, Sus scrofa, Danio rerio
Loss-of-function mutations in CLN3 cause juvenile Batten disease, featuring neurodegeneration and early-stage neuroinflammation. How loss of CLN3 function leads to early neuroinflammation is not yet understood. Here, we have comprehensively studied microglia from Cln3∆ex7/8 mice, a genetically accurate disease model. Loss of CLN3 function in microglia leads to lysosomal storage material accumulation and abnormal morphology of subcellular organelles. Moreover, pathological proteomic signatures are ...
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Ubiquitin carboxyl-terminal hydrolase 19 (USP19) is a unique deubiquitinase, characterized by multiple variants generated by alternative splicing. Several variants bear a C-terminal transmembrane domain that anchors them to the endoplasmic reticulum. Other than regulating protein stability by preventing proteasome degradation, USP19 has been reported to rescue substrates from endoplasmic reticulum-associated protein degradation in a catalytic-independent manner, promote autophagy, and address ...
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Ectodomain shedding, which is the proteolytic release of transmembrane proteins from the cell surface, is crucial for cell-to-cell communication and other biological processes. The metalloproteinase ADAM17 mediates ectodomain shedding of over 50 transmembrane proteins ranging from cytokines and growth factors, such as TNF and EGFR ligands, to signalling receptors and adhesion molecules. Yet, the ADAM17 sheddome is only partly defined and biological functions of the protease have not been fully ...
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Proteins delivered by endocytosis or autophagy to lysosomes are degraded by exo- and endoproteases. In humans 15 lysosomal cathepsins (CTS) act as important physiological regulators. The cysteine proteases CTSB and CTSL and the aspartic protease CTSD are the most abundant and functional important lysosomal proteinases. Whereas their general functions in proteolysis in the lysosome, their individual substrate, cleavage specificity, and their possible sequential action on substrate proteins have ...
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Loss-of-function mutations in the homotrimeric serine protease HTRA1 cause cerebral vasculopathy. Here, we establish independent approaches to achieve the functional correction of trimer assembly defects. Focusing on the prototypical R274Q mutation, we identify an HTRA1 variant that promotes trimer formation thus restoring enzymatic activity in vitro. Genetic experiments in Htra1R274Q mice further demonstrate that expression of this protein-based corrector in trans is sufficient to stabilize ...
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Submitter: Rainer Malik
Assay type: Proteomics
Technology type: Technology Type
Investigation: Proteomics (Published)
Organisms: Homo sapiens
SOPs: No SOPs
Data files: Trafficking and interactions upon loss of TECPR2
Snapshots: No snapshots
Submitter: Rainer Malik
Assay type: Proteomics
Technology type: Technology Type
Investigation: Proteomics (Published)
Organisms: Homo sapiens, Mus musculus
SOPs: No SOPs
Data files: DISCO-MS: Proteomics of spatially identified ti...
Snapshots: No snapshots
Submitter: Rainer Malik
Assay type: Proteomics
Technology type: Technology Type
Investigation: Proteomics (Published)
Organisms: Mus musculus
SOPs: No SOPs
Data files: CSF proteomics of the APPPS1 Alzheimer mouse mo...
Snapshots: No snapshots
Submitter: Rainer Malik
Assay type: Proteomics
Technology type: Technology Type
Investigation: Proteomics (Published)
Organisms: Mus musculus
SOPs: No SOPs
Data files: Cerebrospinal Fluid (CSF) Proteomics of A30P-αS..., Cerebrospinal Fluid (CSF) Proteomics of APPPS1 ...
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Submitter: Rainer Malik
Assay type: Proteomics
Technology type: Technology Type
Investigation: Proteomics (Published)
Organisms: Homo sapiens
SOPs: No SOPs
Data files: Proteome analysis of microvessels from CAA and ...
Snapshots: No snapshots
Signal peptide peptidase (SPP) and the four homologous SPP-like (SPPL) proteases constitute a family of intramembrane aspartyl proteases with selectivity for type II-oriented transmembrane segments. Here, we have analysed the physiological function of the orphan protease SPPL2c, previously considered to represent a non-expressed pseudogene. We identified proteolytic activity of SPPL2c towards selected tail-anchored proteins. Despite shared ER localization, SPPL2c and SPP exhibit distinct, though ...
Creators: Rainer Malik, Stephan Müller, Stefan Lichtenthaler
Submitter: Rainer Malik
Investigations: Proteomics (Published)
Studies: The intramembrane protease SPPL2c promotes male...
Assays: Shotgun proteomics (mouse)
Signal peptide peptidase-like 2c (SPPL2c) is the only member of the GxGD type intramembrane-cleaving aspartyl proteases that so far has not been assigned any substrates and thus its capability of proteolysis and its physiological function remain enigmatic. Based on a surprisingly high expression of SPPL2c in elongated spermatids we applied proteomics on a cellular model system with ectopic expression of SPPL2c and identified a variety of candidate substrates. The majority of these candidate ...
Creators: Rainer Malik, Stefan Lichtenthaler, Stephan Müller
Submitter: Rainer Malik
Investigations: Proteomics (Published)
Studies: Signal peptide peptidase-like 2c impairs vesicu...
Assays: Shotgun proteomics (human)
Acitretin has been shown to increase ADAM10 expression. In a phase II clinical trial, Alzheimer's disease patients were treated with acitretin or placebo to increase ADAM10 levels to counteract amyloid beta production. Analysis of the cerebrospinal fluid of from 18 AD patients treated with the synthetic retinoid acitretin or placebo were analyzed by label-free quantitative LC-MS/MS analysis.
Creators: Rainer Malik, Stefan Lichtenthaler, Stephan Müller
Submitter: Rainer Malik
Investigations: Proteomics (Published)
Studies: NrCAM is a marker for substrate-selective activ...
Assays: Shotgun proteomics (human)
Mitochondria vary in morphology and function in different tissues, however little is known about their molecular diversity among cell types. To investigate mitochondrial diversity in vivo, we developed an efficient protocol to isolate cell type-specific mitochondria based on a new MitoTag mouse. We profiled the mitochondrial proteome of three major neural cell types in cerebellum and identified a substantial number of differential mitochondrial markers for these cell types in mice and humans. ...
Creators: Rainer Malik, Stefan Lichtenthaler, Stephan Müller, Thomas Misgeld, Arthur Konnerth, Thomas Korn
Submitter: Rainer Malik
Investigations: Proteomics (Published)
Studies: Cell-type-specific profiling of brain mitochond...
Assays: Shotgun proteomics (mouse)
Mitochondria vary in morphology and function in different tissues, however little is known about their molecular diversity among cell types. To investigate mitochondrial diversity in vivo, we developed an efficient protocol to isolate cell type-specific mitochondria based on a new MitoTag mouse. We profiled the mitochondrial proteome of three major neural cell types in cerebellum and identified a substantial number of differential mitochondrial markers for these cell types in mice and humans. ...
Creators: Rainer Malik, Stephan Müller, Thomas Misgeld, Stefan Lichtenthaler, Arthur Konnerth, Thomas Korn
Submitter: Rainer Malik
Investigations: Proteomics (Published)
Studies: Cell-type-specific profiling of brain mitochond...
Assays: Shotgun proteomics (mouse)
Abstract (Expand)
Authors: Seda Yasa, Elisabeth S Butz, Alessio Colombo, Uma Chandrachud, Luca Montore, Sarah Tschirner, Matthias Prestel, Steven D Sheridan, Stephan A Müller, Janos Groh, Stefan F Lichtenthaler, Sabina Tahirovic, Susan L Cotman
Date Published: 22nd Oct 2024
Publication Type: Journal
Abstract (Expand)
Authors: Simone Bonelli, Margot Lo Pinto, Yihong Ye, Stephan A Müller, Stefan F Lichtenthaler, Simone Dario Scilabra
Date Published: 9th Oct 2024
Publication Type: Journal
PubMed ID: 39389361
DOI: 10.1016/j.mcpro.2024.100854
Citation: Molecular & cellular proteomics : MCP,23(11):100854
Abstract (Expand)
Authors: Matteo Calligaris, Donatella Pia Spanò, Maria Chiara Puccio, Stephan A Müller, Simone Bonelli, Margot Lo Pinto, Giovanni Zito, Carl P Blobel, Stefan F Lichtenthaler, Linda Troeberg, Simone Dario Scilabra
Date Published: 24th Sep 2024
Publication Type: Journal
Abstract (Expand)
Authors: Nathalie Beaufort, Linda Ingendahl, Melisa Merdanovic, Andree Schmidt, David Podlesainski, Tim Richter, Thorben Neumann, Michael Kuszner, Ingrid R Vetter, Patricia Stege, Steven G Burston, Anto Filipovic, Yasser B Ruiz-Blanco, Kenny Bravo-Rodriguez, Joel Mieres-Perez, Christine Beuck, Stephan Uebel, Monika Zobawa, Jasmin Schillinger, Rainer Malik, Katalin Todorov-Völgyi, Juliana Rey, Annabell Roberti, Birte Hagemeier, Benedikt Wefers, Stephan A Müller, Wolfgang Wurst, Elsa Sanchez-Garcia, Alexander Zimmermann, Xiao-Yu Hu, Tim Clausen, Robert Huber, Stefan F Lichtenthaler, Carsten Schmuck, Michael Giese, Markus Kaiser, Michael Ehrmann, Martin Dichgans
Date Published: 16th Jul 2024
Publication Type: Journal
Abstract (Expand)
Authors: A. Schmidt, B. Hrupka, F. van Bebber, S. Sunil Kumar, X. Feng, S. K. Tschirner, M. Assfalg, S. A. Muller, L. S. Hilger, L. I. Hofmann, M. Pigoni, G. Jocher, I. Voytyuk, E. L. Self, M. Ito, K. Hyakkoku, A. Yoshimura, N. Horiguchi, R. Feederle, B. De Strooper, S. Schulte-Merker, E. Lammert, D. Moechars, B. Schmid, S. F. Lichtenthaler
Date Published: 18th Jun 2024
Publication Type: Journal
PubMed ID: 38888964
Citation: J Clin Invest. 2024 Jun 18:e170550. doi: 10.1172/JCI170550.