338 results on '"Bernhard Kuster"'
Search Results
2. Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies
- Author
-
Qussai Abbas, Mathias Wilhelm, Bernhard Kuster, Brigitte Poppenberger, and Dmitrij Frishman
- Subjects
Crop genomics ,Genome annotation ,Gene prediction ,Plant evolution ,Peptide identification ,Bioinformatics algorithms ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease resistance, and stress tolerance. As the number of sequenced genomes grows and the accuracy and contiguity of genome assemblies improve, structural annotation of plant genomes continues to be a significant challenge due to their large size, polyploidy, and rich repeat content. In this paper, we present an overview of the current landscape in crop genomics research, highlighting the diversity of genomic characteristics across various crop species. We also assessed the accuracy of popular gene prediction tools in identifying genes within crop genomes and examined the factors that impact their performance. Our findings highlight the strengths and limitations of BRAKER2 and Helixer as leading structural genome annotation tools and underscore the impact of genome complexity, fragmentation, and repeat content on their performance. Furthermore, we evaluated the suitability of the predicted proteins as a reliable search space in proteomics studies using mass spectrometry data. Our results provide valuable insights for future efforts to refine and advance the field of structural genome annotation.
- Published
- 2024
- Full Text
- View/download PDF
3. A Novel AMPK Inhibitor Sensitizes Pancreatic Cancer Cells to Ferroptosis Induction
- Author
-
Carolin Schneider, Jorina Hilbert, Franziska Genevaux, Stefanie Höfer, Lukas Krauß, Felix Schicktanz, Constanza Tapia Contreras, Shaishavi Jansari, Aristeidis Papargyriou, Thorsten Richter, Abdallah M. Alfayomy, Chiara Falcomatà, Christian Schneeweis, Felix Orben, Ruppert Öllinger, Florian Wegwitz, Angela Boshnakovska, Peter Rehling, Denise Müller, Philipp Ströbel, Volker Ellenrieder, Lena Conradi, Elisabeth Hessmann, Michael Ghadimi, Marian Grade, Matthias Wirth, Katja Steiger, Roland Rad, Bernhard Kuster, Wolfgang Sippl, Maximilian Reichert, Dieter Saur, and Günter Schneider
- Subjects
AMPK ,ferroptosis ,pancreatic cancer ,Science - Abstract
Abstract Cancer cells must develop strategies to adapt to the dynamically changing stresses caused by intrinsic or extrinsic processes, or therapeutic agents. Metabolic adaptability is crucial to mitigate such challenges. Considering metabolism as a central node of adaptability, it is focused on an energy sensor, the AMP‐activated protein kinase (AMPK). In a subtype of pancreatic ductal adenocarcinoma (PDAC) elevated AMPK expression and phosphorylation is identified. Using drug repurposing that combined screening experiments and chemoproteomic affinity profiling, it is identified and characterized PF‐3758309, initially developed as an inhibitor of PAK4, as an AMPK inhibitor. PF‐3758309 shows activity in pre‐clinical PDAC models, including primary patient‐derived organoids. Genetic loss‐of‐function experiments showed that AMPK limits the induction of ferroptosis, and consequently, PF‐3758309 treatment restores the sensitivity toward ferroptosis inducers. The work established a chemical scaffold for the development of specific AMPK‐targeting compounds and deciphered the framework for the development of AMPK inhibitor‐based combination therapies tailored for PDAC.
- Published
- 2024
- Full Text
- View/download PDF
4. Decrypting lysine deacetylase inhibitor action and protein modifications by dose-resolved proteomics
- Author
-
Yun-Chien Chang, Christian Gnann, Raphael R. Steimbach, Florian P. Bayer, Severin Lechner, Amirhossein Sakhteman, Miriam Abele, Jana Zecha, Jakob Trendel, Matthew The, Emma Lundberg, Aubry K. Miller, and Bernhard Kuster
- Subjects
CP: Molecular biology ,Biology (General) ,QH301-705.5 - Abstract
Summary: Lysine deacetylase inhibitors (KDACis) are approved drugs for cutaneous T cell lymphoma (CTCL), peripheral T cell lymphoma (PTCL), and multiple myeloma, but many aspects of their cellular mechanism of action (MoA) and substantial toxicity are not well understood. To shed more light on how KDACis elicit cellular responses, we systematically measured dose-dependent changes in acetylation, phosphorylation, and protein expression in response to 21 clinical and pre-clinical KDACis. The resulting 862,000 dose-response curves revealed, for instance, limited cellular specificity of histone deacetylase (HDAC) 1, 2, 3, and 6 inhibitors; strong cross-talk between acetylation and phosphorylation pathways; localization of most drug-responsive acetylation sites to intrinsically disordered regions (IDRs); an underappreciated role of acetylation in protein structure; and a shift in EP300 protein abundance between the cytoplasm and the nucleus. This comprehensive dataset serves as a resource for the investigation of the molecular mechanisms underlying KDACi action in cells and can be interactively explored online in ProteomicsDB.
- Published
- 2024
- Full Text
- View/download PDF
5. CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose–response curves
- Author
-
Florian P. Bayer, Manuel Gander, Bernhard Kuster, and Matthew The
- Subjects
Science - Abstract
Abstract Dose-response curves are key metrics in pharmacology and biology to assess phenotypic or molecular actions of bioactive compounds in a quantitative fashion. Yet, it is often unclear whether or not a measured response significantly differs from a curve without regulation, particularly in high-throughput applications or unstable assays. Treating potency and effect size estimates from random and true curves with the same level of confidence can lead to incorrect hypotheses and issues in training machine learning models. Here, we present CurveCurator, an open-source software that provides reliable dose-response characteristics by computing p-values and false discovery rates based on a recalibrated F-statistic and a target-decoy procedure that considers dataset-specific effect size distributions. The application of CurveCurator to three large-scale datasets enables a systematic drug mode of action analysis and demonstrates its scalable utility across several application areas, facilitated by a performant, interactive dashboard for fast data exploration.
- Published
- 2023
- Full Text
- View/download PDF
6. Proteomic meta-study harmonization, mechanotyping and drug repurposing candidate prediction with ProHarMeD
- Author
-
Klaudia Adamowicz, Lis Arend, Andreas Maier, Johannes R. Schmidt, Bernhard Kuster, Olga Tsoy, Olga Zolotareva, Jan Baumbach, and Tanja Laske
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Abstract Proteomics technologies, which include a diverse range of approaches such as mass spectrometry-based, array-based, and others, are key technologies for the identification of biomarkers and disease mechanisms, referred to as mechanotyping. Despite over 15,000 published studies in 2022 alone, leveraging publicly available proteomics data for biomarker identification, mechanotyping and drug target identification is not readily possible. Proteomic data addressing similar biological/biomedical questions are made available by multiple research groups in different locations using different model organisms. Furthermore, not only various organisms are employed but different assay systems, such as in vitro and in vivo systems, are used. Finally, even though proteomics data are deposited in public databases, such as ProteomeXchange, they are provided at different levels of detail. Thus, data integration is hampered by non-harmonized usage of identifiers when reviewing the literature or performing meta-analyses to consolidate existing publications into a joint picture. To address this problem, we present ProHarMeD, a tool for harmonizing and comparing proteomics data gathered in multiple studies and for the extraction of disease mechanisms and putative drug repurposing candidates. It is available as a website, Python library and R package. ProHarMeD facilitates ID and name conversions between protein and gene levels, or organisms via ortholog mapping, and provides detailed logs on the loss and gain of IDs after each step. The web tool further determines IDs shared by different studies, proposes potential disease mechanisms as well as drug repurposing candidates automatically, and visualizes these results interactively. We apply ProHarMeD to a set of four studies on bone regeneration. First, we demonstrate the benefit of ID harmonization which increases the number of shared genes between studies by 50%. Second, we identify a potential disease mechanism, with five corresponding drug targets, and the top 20 putative drug repurposing candidates, of which Fondaparinux, the candidate with the highest score, and multiple others are known to have an impact on bone regeneration. Hence, ProHarMeD allows users to harmonize multi-centric proteomics research data in meta-analyses, evaluates the success of the ID conversions and remappings, and finally, it closes the gaps between proteomics, disease mechanism mining and drug repurposing. It is publicly available at https://apps.cosy.bio/proharmed/ .
- Published
- 2023
- Full Text
- View/download PDF
7. Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification
- Author
-
Celina Tretter, Niklas de Andrade Krätzig, Matteo Pecoraro, Sebastian Lange, Philipp Seifert, Clara von Frankenberg, Johannes Untch, Gabriela Zuleger, Mathias Wilhelm, Daniel P. Zolg, Florian S. Dreyer, Eva Bräunlein, Thomas Engleitner, Sebastian Uhrig, Melanie Boxberg, Katja Steiger, Julia Slotta-Huspenina, Sebastian Ochsenreither, Nikolas von Bubnoff, Sebastian Bauer, Melanie Boerries, Philipp J. Jost, Kristina Schenck, Iska Dresing, Florian Bassermann, Helmut Friess, Daniel Reim, Konrad Grützmann, Katrin Pfütze, Barbara Klink, Evelin Schröck, Bernhard Haller, Bernhard Kuster, Matthias Mann, Wilko Weichert, Stefan Fröhling, Roland Rad, Michael Hiltensperger, and Angela M. Krackhardt
- Subjects
Science - Abstract
Abstract Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types for proteogenomic-based discovery of neoantigens. By using an optimized computational approach, we discover a large number of tumor-specific and tumor-associated antigens. To create a pipeline for the identification of neoantigens in our cohort, we combine DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity and an in-depth validation process. We detect a broad variety of non-canonical HLA-binding peptides in the majority of patients demonstrating partially immunogenicity. Our validation process allows for the selection of 32 potential neoantigen candidates. The majority of neoantigen candidates originates from variants identified in the RNA data set, illustrating the relevance of RNA as a still understudied source of cancer antigens. This study underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.
- Published
- 2023
- Full Text
- View/download PDF
8. Chemoproteomic target deconvolution reveals Histone Deacetylases as targets of (R)-lipoic acid
- Author
-
Severin Lechner, Raphael R. Steimbach, Longlong Wang, Marshall L. Deline, Yun-Chien Chang, Tobias Fromme, Martin Klingenspor, Patrick Matthias, Aubry K. Miller, Guillaume Médard, and Bernhard Kuster
- Subjects
Science - Abstract
Abstract Lipoic acid is an essential enzyme cofactor in central metabolic pathways. Due to its claimed antioxidant properties, racemic (R/S)-lipoic acid is used as a food supplement but is also investigated as a pharmaceutical in over 180 clinical trials covering a broad range of diseases. Moreover, (R/S)-lipoic acid is an approved drug for the treatment of diabetic neuropathy. However, its mechanism of action remains elusive. Here, we performed chemoproteomics-aided target deconvolution of lipoic acid and its active close analog lipoamide. We find that histone deacetylases HDAC1, HDAC2, HDAC3, HDAC6, HDAC8, and HDAC10 are molecular targets of the reduced form of lipoic acid and lipoamide. Importantly, only the naturally occurring (R)-enantiomer inhibits HDACs at physiologically relevant concentrations and leads to hyperacetylation of HDAC substrates. The inhibition of HDACs by (R)-lipoic acid and lipoamide explain why both compounds prevent stress granule formation in cells and may also provide a molecular rationale for many other phenotypic effects elicited by lipoic acid.
- Published
- 2023
- Full Text
- View/download PDF
9. Author Correction: Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification
- Author
-
Celina Tretter, Niklas de Andrade Krätzig, Matteo Pecoraro, Sebastian Lange, Philipp Seifert, Clara von Frankenberg, Johannes Untch, Gabriela Zuleger, Mathias Wilhelm, Daniel P. Zolg, Florian S. Dreyer, Eva Bräunlein, Thomas Engleitner, Sebastian Uhrig, Melanie Boxberg, Katja Steiger, Julia Slotta-Huspenina, Sebastian Ochsenreither, Nikolas von Bubnoff, Sebastian Bauer, Melanie Boerries, Philipp J. Jost, Kristina Schenck, Iska Dresing, Florian Bassermann, Helmut Friess, Daniel Reim, Konrad Grützmann, Katrin Pfütze, Barbara Klink, Evelin Schröck, Bernhard Haller, Bernhard Kuster, Matthias Mann, Wilko Weichert, Stefan Fröhling, Roland Rad, Michael Hiltensperger, and Angela M. Krackhardt
- Subjects
Science - Published
- 2024
- Full Text
- View/download PDF
10. Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae
- Author
-
Ana Djukovic, María José Garzón, Cécile Canlet, Vitor Cabral, Rym Lalaoui, Marc García-Garcerá, Julia Rechenberger, Marie Tremblay-Franco, Iván Peñaranda, Leonor Puchades-Carrasco, Antonio Pineda-Lucena, Eva María González-Barberá, Miguel Salavert, José Luis López-Hontangas, Miguel Á. Sanz, Jaime Sanz, Bernhard Kuster, Jean-Marc Rolain, Laurent Debrauwer, Karina B. Xavier, Joao B. Xavier, and Carles Ubeda
- Subjects
Science - Abstract
Multidrug-resistant Enterobacteriaceae (MRE) represent a major threat for patients’ health. Here, the authors describe how cooperation between gut commensal bacteria (Lactobacillus spp. And Clostridiales) restrict MRE colonization in mice and patients
- Published
- 2022
- Full Text
- View/download PDF
11. A unified classification approach rating clinical utility of protein biomarkers across neurologic diseases
- Author
-
Alexander M. Bernhardt, Steffen Tiedt, Daniel Teupser, Martin Dichgans, Bernhard Meyer, Jens Gempt, Peer-Hendrik Kuhn, Mikael Simons, Carla Palleis, Endy Weidinger, Georg Nübling, Lesca Holdt, Lisa Hönikl, Christiane Gasperi, Pieter Giesbertz, Stephan A. Müller, Stephan Breimann, Stefan F. Lichtenthaler, Bernhard Kuster, Matthias Mann, Axel Imhof, Teresa Barth, Stefanie M. Hauck, Henrik Zetterberg, Markus Otto, Wilko Weichert, Bernhard Hemmer, and Johannes Levin
- Subjects
Biomarker ,Neurology ,Proteomics ,Protein ,Clinical utility ,Analytical validity ,Medicine ,Medicine (General) ,R5-920 - Abstract
Summary: A major evolution from purely clinical diagnoses to biomarker supported clinical diagnosing has been occurring over the past years in neurology. High-throughput methods, such as next-generation sequencing and mass spectrometry-based proteomics along with improved neuroimaging methods, are accelerating this development. This calls for a consensus framework that is broadly applicable and provides a spot-on overview of the clinical validity of novel biomarkers. We propose a harmonized terminology and a uniform concept that stratifies biomarkers according to clinical context of use and evidence levels, adapted from existing frameworks in oncology with a strong focus on (epi)genetic markers and treatment context. We demonstrate that this framework allows for a consistent assessment of clinical validity across disease entities and that sufficient evidence for many clinical applications of protein biomarkers is lacking. Our framework may help to identify promising biomarker candidates and classify their applications by clinical context, aiming for routine clinical use of (protein) biomarkers in neurology.
- Published
- 2023
- Full Text
- View/download PDF
12. Linking post-translational modifications and protein turnover by site-resolved protein turnover profiling
- Author
-
Jana Zecha, Wassim Gabriel, Ria Spallek, Yun-Chien Chang, Julia Mergner, Mathias Wilhelm, Florian Bassermann, and Bernhard Kuster
- Subjects
Science - Abstract
Post-translational modifications (PTMs) can regulate cellular protein function but their global impact on protein turnover is largely unknown. Here, the authors develop proteomic workflows to profile PTM-resolved protein turnover and analyze the effects of phosphorylation, acetylation and ubiquitination.
- Published
- 2022
- Full Text
- View/download PDF
13. Proteomic profiling in cerebral amyloid angiopathy reveals an overlap with CADASIL highlighting accumulation of HTRA1 and its substrates
- Author
-
Andreas Zellner, Stephan A. Müller, Barbara Lindner, Nathalie Beaufort, Annemieke J. M. Rozemuller, Thomas Arzberger, Nils C. Gassen, Stefan F. Lichtenthaler, Bernhard Kuster, Christof Haffner, and Martin Dichgans
- Subjects
Cerebral amyloid angiopathy ,Cerebral small vessel disease ,CADASIL ,Proteomics ,HTRA1 ,Proteostasis ,Neurology. Diseases of the nervous system ,RC346-429 - Abstract
Abstract Cerebral amyloid angiopathy (CAA) is an age-related condition and a major cause of intracerebral hemorrhage and cognitive decline that shows close links with Alzheimer's disease (AD). CAA is characterized by the aggregation of amyloid-β (Aβ) peptides and formation of Aβ deposits in the brain vasculature resulting in a disruption of the angioarchitecture. Capillaries are a critical site of Aβ pathology in CAA type 1 and become dysfunctional during disease progression. Here, applying an advanced protocol for the isolation of parenchymal microvessels from post-mortem brain tissue combined with liquid chromatography tandem mass spectrometry (LC–MS/MS), we determined the proteomes of CAA type 1 cases (n = 12) including a patient with hereditary cerebral hemorrhage with amyloidosis-Dutch type (HCHWA-D), and of AD cases without microvascular amyloid pathology (n = 13) in comparison to neurologically healthy controls (n = 12). ELISA measurements revealed microvascular Aβ1-40 levels to be exclusively enriched in CAA samples (mean: > 3000-fold compared to controls). The proteomic profile of CAA type 1 was characterized by massive enrichment of multiple predominantly secreted proteins and showed significant overlap with the recently reported brain microvascular proteome of patients with cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), a hereditary cerebral small vessel disease (SVD) characterized by the aggregation of the Notch3 extracellular domain. We found this overlap to be largely attributable to the accumulation of high-temperature requirement protein A1 (HTRA1), a serine protease with an established role in the brain vasculature, and several of its substrates. Notably, this signature was not present in AD cases. We further show that HTRA1 co-localizes with Aβ deposits in brain capillaries from CAA type 1 patients indicating a pathologic recruitment process. Together, these findings suggest a central role of HTRA1-dependent protein homeostasis in the CAA microvasculature and a molecular connection between multiple types of brain microvascular disease.
- Published
- 2022
- Full Text
- View/download PDF
14. Systematic analysis of migration factors by MigExpress identifies essential cell migration control genes in non‐small cell lung cancer
- Author
-
Jagriti Pal, Andrea C. Becker, Sonam Dhamija, Jeanette Seiler, Mahmoud Abdelkarim, Yogita Sharma, Jürgen Behr, Chen Meng, Christina Ludwig, Bernhard Kuster, and Sven Diederichs
- Subjects
cancer cell migration ,gene expression profiling ,metastasis ,non‐small cell lung cancer ,proteomics ,quantitative migration analysis ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Cell migration is an essential process in health and in disease, including cancer metastasis. A comprehensive inventory of migration factors is nonetheless lacking—in part due to the difficulty in assessing migration using high‐throughput technologies. Hence, there are currently very few screens that systematically reveal factors controlling cell migration. Here, we introduce MigExpress as a platform for the ‘identification of Migration control genes by differential Expression’. MigExpress exploits the combination of in‐depth molecular profiling and the robust quantitative analysis of migration capacity in a broad panel of samples and identifies migration‐associated genes by their differential expression in slow‐ versus fast‐migrating cells. We applied MigExpress to investigate non‐small cell lung cancer (NSCLC), which is the most frequent cause of cancer mortality mainly due to metastasis. In 54 NSCLC cell lines, we comprehensively determined mRNA and protein expression. Correlating the transcriptome and proteome profiles with the quantified migration properties led to the discovery and validation of FLNC, DSE, CPA4, TUBB6, and BICC1 as migration control factors in NSCLC cells, which were also negatively correlated with patient survival. Notably, FLNC was the least expressed filamin in NSCLC, but the only one controlling cell migration and correlating with patient survival and metastatic disease stage. In our study, we present MigExpress as a new method for the systematic analysis of migration factors and provide a comprehensive resource of transcriptomic and proteomic data of NSCLC cell lines related to cell migration.
- Published
- 2021
- Full Text
- View/download PDF
15. Stress-primed secretory autophagy promotes extracellular BDNF maturation by enhancing MMP9 secretion
- Author
-
Silvia Martinelli, Elmira A. Anderzhanova, Thomas Bajaj, Svenja Wiechmann, Frederik Dethloff, Katja Weckmann, Daniel E. Heinz, Tim Ebert, Jakob Hartmann, Thomas M. Geiger, Michael Döngi, Kathrin Hafner, Max L. Pöhlmann, Lee Jollans, Alexandra Philipsen, Susanne V. Schmidt, Ulrike Schmidt, Giuseppina Maccarrone, Valentin Stein, Felix Hausch, Christoph W. Turck, Mathias V. Schmidt, Anne-Kathrin Gellner, Bernhard Kuster, and Nils C. Gassen
- Subjects
Science - Abstract
Glucocorticoids are associated with stress. Here, the authors show that high levels of glucocorticoid stress promote secretory autophagy of matrix metalloproteinase 9 via a stress responsive chaperone, increasing brain-derived neurotrophic factor processing and potentially altering adult synaptic plasticity.
- Published
- 2021
- Full Text
- View/download PDF
16. Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics
- Author
-
Mathias Wilhelm, Daniel P. Zolg, Michael Graber, Siegfried Gessulat, Tobias Schmidt, Karsten Schnatbaum, Celina Schwencke-Westphal, Philipp Seifert, Niklas de Andrade Krätzig, Johannes Zerweck, Tobias Knaute, Eva Bräunlein, Patroklos Samaras, Ludwig Lautenbacher, Susan Klaeger, Holger Wenschuh, Roland Rad, Bernard Delanghe, Andreas Huhmer, Steven A. Carr, Karl R. Clauser, Angela M. Krackhardt, Ulf Reimer, and Bernhard Kuster
- Subjects
Science - Abstract
The identification of HLA peptides by mass spectrometry is non-trivial. Here, the authors extended and used the wealth of data from the ProteomeTools project to improve the prediction of non-tryptic peptides using deep learning, and show their approach enables a variety of immunological discoveries.
- Published
- 2021
- Full Text
- View/download PDF
17. Loss of UCP1 function augments recruitment of futile lipid cycling for thermogenesis in murine brown fat
- Author
-
Josef Oeckl, Petra Janovska, Katerina Adamcova, Kristina Bardova, Sarah Brunner, Sebastian Dieckmann, Josef Ecker, Tobias Fromme, Jiri Funda, Thomas Gantert, Piero Giansanti, Maria Soledad Hidrobo, Ondrej Kuda, Bernhard Kuster, Yongguo Li, Radek Pohl, Sabine Schmitt, Sabine Schweizer, Hans Zischka, Petr Zouhar, Jan Kopecky, and Martin Klingenspor
- Subjects
Brown adipose tissue ,UCP1-independent thermogenesis ,Futile substrate cycle ,Lipolysis ,Re-esterification ,Fatty acids ,Internal medicine ,RC31-1245 - Abstract
Objective: Classical ATP-independent non-shivering thermogenesis enabled by uncoupling protein 1 (UCP1) in brown adipose tissue (BAT) is activated, but not essential for survival, in the cold. It has long been suspected that futile ATP-consuming substrate cycles also contribute to thermogenesis and can partially compensate for the genetic ablation of UCP1 in mouse models. Futile ATP-dependent thermogenesis could thereby enable survival in the cold even when brown fat is less abundant or missing. Methods: In this study, we explore different potential sources of UCP1-independent thermogenesis and identify a futile ATP-consuming triglyceride/fatty acid cycle as the main contributor to cellular heat production in brown adipocytes lacking UCP1. We uncover the mechanism on a molecular level and pinpoint the key enzymes involved using pharmacological and genetic interference. Results: ATGL is the most important lipase in terms of releasing fatty acids from lipid droplets, while DGAT1 accounts for the majority of fatty acid re-esterification in UCP1-ablated brown adipocytes. Furthermore, we demonstrate that chronic cold exposure causes a pronounced remodeling of adipose tissues and leads to the recruitment of lipid cycling capacity specifically in BAT of UCP1-knockout mice, possibly fueled by fatty acids from white fat. Quantification of triglyceride/fatty acid cycling clearly shows that UCP1-ablated animals significantly increase turnover rates at room temperature and below. Conclusion: Our results suggest an important role for futile lipid cycling in adaptive thermogenesis and total energy expenditure.
- Published
- 2022
- Full Text
- View/download PDF
18. Epigenetic drug screening defines a PRMT5 inhibitor–sensitive pancreatic cancer subtype
- Author
-
Felix Orben, Katharina Lankes, Christian Schneeweis, Zonera Hassan, Hannah Jakubowsky, Lukas Krauß, Fabio Boniolo, Carolin Schneider, Arlett Schäfer, Janine Murr, Christoph Schlag, Bo Kong, Rupert Öllinger, Chengdong Wang, Georg Beyer, Ujjwal M. Mahajan, Yonggan Xue, Julia Mayerle, Roland M. Schmid, Bernhard Kuster, Roland Rad, Christian J. Braun, Matthias Wirth, Maximilian Reichert, Dieter Saur, and Günter Schneider
- Subjects
Cell biology ,Oncology ,Medicine - Abstract
Systemic therapies for pancreatic ductal adenocarcinoma (PDAC) remain unsatisfactory. Clinical prognosis is particularly poor for tumor subtypes with activating aberrations in the MYC pathway, creating an urgent need for novel therapeutic targets. To unbiasedly find MYC-associated epigenetic dependencies, we conducted a drug screen in pancreatic cancer cell lines. Here, we found that protein arginine N-methyltransferase 5 (PRMT5) inhibitors triggered an MYC-associated dependency. In human and murine PDACs, a robust connection of MYC and PRMT5 was detected. By the use of gain- and loss-of-function models, we confirmed the increased efficacy of PRMT5 inhibitors in MYC-deregulated PDACs. Although inhibition of PRMT5 was inducing DNA damage and arresting PDAC cells in the G2/M phase of the cell cycle, apoptotic cell death was executed predominantly in cells with high MYC expression. Experiments in primary patient-derived PDAC models demonstrated the existence of a highly PRMT5 inhibitor–sensitive subtype. Our work suggests developing PRMT5 inhibitor–based therapies for PDAC.
- Published
- 2022
- Full Text
- View/download PDF
19. Getting Ready for Large-Scale Proteomics in Crop Plants
- Author
-
Sarah Brajkovic, Nils Rugen, Carlos Agius, Nicola Berner, Stephan Eckert, Amirhossein Sakhteman, Claus Schwechheimer, and Bernhard Kuster
- Subjects
plant proteomics ,nutritional crop proteomics ,liquid chromatography mass spectrometry ,Nutrition. Foods and food supply ,TX341-641 - Abstract
Plants are an indispensable cornerstone of sustainable global food supply. While immense progress has been made in decoding the genomes of crops in recent decades, the composition of their proteomes, the entirety of all expressed proteins of a species, is virtually unknown. In contrast to the model plant Arabidopsis thaliana, proteomic analyses of crop plants have often been hindered by the presence of extreme concentrations of secondary metabolites such as pigments, phenolic compounds, lipids, carbohydrates or terpenes. As a consequence, crop proteomic experiments have, thus far, required individually optimized protein extraction protocols to obtain samples of acceptable quality for downstream analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS). In this article, we present a universal protein extraction protocol originally developed for gel-based experiments and combined it with an automated single-pot solid-phase-enhanced sample preparation (SP3) protocol on a liquid handling robot to prepare high-quality samples for proteomic analysis of crop plants. We also report an automated offline peptide separation protocol and optimized micro-LC-MS/MS conditions that enables the identification and quantification of ~10,000 proteins from plant tissue within 6 h of instrument time. We illustrate the utility of the workflow by analyzing the proteomes of mature tomato fruits to an unprecedented depth. The data demonstrate the robustness of the approach which we propose for use in upcoming large-scale projects that aim to map crop tissue proteomes.
- Published
- 2023
- Full Text
- View/download PDF
20. Dissecting the sequence determinants for dephosphorylation by the catalytic subunits of phosphatases PP1 and PP2A
- Author
-
Bernhard Hoermann, Thomas Kokot, Dominic Helm, Stephanie Heinzlmeir, Jeremy E. Chojnacki, Thomas Schubert, Christina Ludwig, Anna Berteotti, Nils Kurzawa, Bernhard Kuster, Mikhail M. Savitski, and Maja Köhn
- Subjects
Science - Abstract
The substrate specificity of phosphoprotein phosphatases PP1 and PP2A depends on their catalytic and regulatory subunits. Using proteomics approaches, the authors here provide insights into the sequence specificity of the catalytic subunits and their distinct contributions to PP1 and PP2A selectivity.
- Published
- 2020
- Full Text
- View/download PDF
21. Proteome activity landscapes of tumor cell lines determine drug responses
- Author
-
Martin Frejno, Chen Meng, Benjamin Ruprecht, Thomas Oellerich, Sebastian Scheich, Karin Kleigrewe, Enken Drecoll, Patroklos Samaras, Alexander Hogrebe, Dominic Helm, Julia Mergner, Jana Zecha, Stephanie Heinzlmeir, Mathias Wilhelm, Julia Dorn, Hans-Michael Kvasnicka, Hubert Serve, Wilko Weichert, and Bernhard Kuster
- Subjects
Science - Abstract
Proteome activity has a major role in cancer progression and response to drugs. Here, the authors use comprehensive proteomic and phosphoproteomic data, in conjunction with drug-sensitivity screens, to generate a community resource consisting of landscapes of pathway and kinase activity across different cell lines
- Published
- 2020
- Full Text
- View/download PDF
22. Wnt-driven LARGE2 mediates laminin-adhesive O-glycosylation in human colonic epithelial cells and colorectal cancer
- Author
-
Vanessa Dietinger, Cira R. García de Durango, Svenja Wiechmann, Sophie L. Boos, Marlies Michl, Jens Neumann, Heiko Hermeking, Bernhard Kuster, and Peter Jung
- Subjects
O-glycosylation ,LARGE2 ,Wnt signaling ,Colorectal cancer ,Organoid ,Colonic stem cell ,Medicine ,Cytology ,QH573-671 - Abstract
Abstract Background Wnt signaling drives epithelial self-renewal and disease progression in human colonic epithelium and colorectal cancer (CRC). Characterization of Wnt effector pathways is key for our understanding of these processes and for developing therapeutic strategies that aim to preserve tissue homeostasis. O-glycosylated cell surface proteins, such as α-dystroglycan (α-DG), mediate cellular adhesion to extracellular matrix components. We revealed a Wnt/LARGE2/α-DG signaling pathway which triggers this mode of colonic epithelial cell-to-matrix interaction in health and disease. Methods Next generation sequencing upon shRNA-mediated silencing of adenomatous polyposis coli (APC), and quantitative chromatin immunoprecipitation (qChIP) combined with CRISPR/Cas9-mediated transcription factor binding site targeting characterized LARGE2 as a Wnt target gene. Quantitative mass spectrometry analysis on size-fractionated, glycoprotein-enriched samples revealed functional O-glycosylation of α-DG by LARGE2 in CRC. The biology of Wnt/LARGE2/α-DG signaling was assessed by affinity-based glycoprotein enrichment, laminin overlay, CRC-to-endothelial cell adhesion, and transwell migration assays. Experiments on primary tissue, human colonic (tumor) organoids, and bioinformatic analysis of CRC cohort data confirmed the biological relevance of our findings. Results Next generation sequencing identified the LARGE2 O-glycosyltransferase encoding gene as differentially expressed upon Wnt activation in CRC. Silencing of APC, conditional expression of oncogenic β-catenin and endogenous β-catenin-sequestration affected LARGE2 expression. The first intron of LARGE2 contained a CTTTGATC motif essential for Wnt-driven LARGE2 expression, showed occupation by the Wnt transcription factor TCF7L2, and Wnt activation triggered LARGE2-dependent α-DG O-glycosylation and laminin-adhesion in CRC cells. Colonic crypts and organoids expressed LARGE2 mainly in stem cell-enriched subpopulations. In human adenoma organoids, activity of the LARGE2/α-DG axis was Wnt-dose dependent. LARGE2 expression was elevated in CRC and correlated with the Wnt-driven molecular subtype and intestinal stem cell features. O-glycosylated α-DG represented a Wnt/LARGE2-dependent feature in CRC cell lines and patient-derived tumor organoids. Modulation of LARGE2/α-DG signaling affected CRC cell migration through laminin-coated membranes and adhesion to endothelial cells. Conclusions We conclude that the LARGE2 O-glycosyltransferase-encoding gene represents a direct target of canonical Wnt signaling and mediates functional O-glycosylation of α-dystroglycan (α-DG) in human colonic stem/progenitor cells and Wnt-driven CRC. Our work implies that aberrant Wnt activation augments CRC cell-matrix adhesion by increasing LARGE/α-DG-mediated laminin-adhesiveness. Video abstract. Graphical abstract
- Published
- 2020
- Full Text
- View/download PDF
23. Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC–MS/MS
- Author
-
Yangyang Bian, Runsheng Zheng, Florian P. Bayer, Cassandra Wong, Yun-Chien Chang, Chen Meng, Daniel P. Zolg, Maria Reinecke, Jana Zecha, Svenja Wiechmann, Stephanie Heinzlmeir, Johannes Scherr, Bernhard Hemmer, Mike Baynham, Anne-Claude Gingras, Oleksandr Boychenko, and Bernhard Kuster
- Subjects
Science - Abstract
Mass spectrometry-based proteomics typically relies on highly sensitive nano-flow liquid chromatography (LC) but this can reduce robustness and reproducibility. Here, the authors show that micro-flow LC enables robust and reproducible high-throughput proteomics experiments at a very moderate loss of sensitivity.
- Published
- 2020
- Full Text
- View/download PDF
24. Posttranslational modification of the RHO of plants protein RACB by phosphorylation and cross-kingdom conserved ubiquitination.
- Author
-
Lukas Weiß, Lana Gaelings, Tina Reiner, Julia Mergner, Bernhard Kuster, Attila Fehér, Götz Hensel, Manfred Gahrtz, Jochen Kumlehn, Stefan Engelhardt, and Ralph Hückelhoven
- Subjects
Medicine ,Science - Abstract
Small RHO-type G-proteins act as signaling hubs and master regulators of polarity in eukaryotic cells. Their activity is tightly controlled, as defective RHO signaling leads to aberrant growth and developmental defects. Two major processes regulate G-protein activity: canonical shuttling between different nucleotide bound states and posttranslational modification (PTM), of which the latter can support or suppress RHO signaling, depending on the individual PTM. In plants, regulation of Rho of plants (ROPs) signaling activity has been shown to act through nucleotide exchange and GTP hydrolysis, as well as through lipid modification, but there is little data available on phosphorylation or ubiquitination of ROPs. Hence, we applied proteomic analyses to identify PTMs of the barley ROP RACB. We observed in vitro phosphorylation by barley ROP binding kinase 1 and in vivo ubiquitination of RACB. Comparative analyses of the newly identified RACB phosphosites and human RHO protein phosphosites revealed conservation of modified amino acid residues, but no overlap of actual phosphorylation patterns. However, the identified RACB ubiquitination site is conserved in all ROPs from Hordeum vulgare, Arabidopsis thaliana and Oryza sativa and in mammalian Rac1 and Rac3. Point mutation of this ubiquitination site leads to stabilization of RACB. Hence, this highly conserved lysine residue may regulate protein stability across different kingdoms.
- Published
- 2022
- Full Text
- View/download PDF
25. SARS‐CoV‐2 infection remodels the host protein thermal stability landscape
- Author
-
Joel Selkrig, Megan Stanifer, André Mateus, Karin Mitosch, Inigo Barrio‐Hernandez, Mandy Rettel, Heeyoung Kim, Carlos G P Voogdt, Philipp Walch, Carmon Kee, Nils Kurzawa, Frank Stein, Clément Potel, Anna Jarzab, Bernhard Kuster, Ralf Bartenschlager, Steeve Boulant, Pedro Beltrao, Athanasios Typas, and Mikhail M Savitski
- Subjects
aryl hydrocarbon hydroxylase ,heat shock chaperone ,rhapontigenin ,SARS‐CoV‐2 ,tanespimycin ,Biology (General) ,QH301-705.5 ,Medicine (General) ,R5-920 - Abstract
Abstract The severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) is a global threat to human health and has compromised economic stability. In addition to the development of an effective vaccine, it is imperative to understand how SARS‐CoV‐2 hijacks host cellular machineries on a system‐wide scale so that potential host‐directed therapies can be developed. In situ proteome‐wide abundance and thermal stability measurements using thermal proteome profiling (TPP) can inform on global changes in protein activity. Here we adapted TPP to high biosafety conditions amenable to SARS‐CoV‐2 handling. We discovered pronounced temporal alterations in host protein thermostability during infection, which converged on cellular processes including cell cycle, microtubule and RNA splicing regulation. Pharmacological inhibition of host proteins displaying altered thermal stability or abundance during infection suppressed SARS‐CoV‐2 replication. Overall, this work serves as a framework for expanding TPP workflows to globally important human pathogens that require high biosafety containment and provides deeper resolution into the molecular changes induced by SARS‐CoV‐2 infection.
- Published
- 2021
- Full Text
- View/download PDF
26. PTPN2 Deficiency Enhances Programmed T Cell Expansion and Survival Capacity of Activated T Cells
- Author
-
Markus Flosbach, Susanne G. Oberle, Stefanie Scherer, Jana Zecha, Madlaina von Hoesslin, Florian Wiede, Vijaykumar Chennupati, Jolie G. Cullen, Markus List, Josch K. Pauling, Jan Baumbach, Bernhard Kuster, Tony Tiganis, and Dietmar Zehn
- Subjects
Protein tyrosine phosphatase non‑receptor type 2 (PTPN2) ,T cell memory ,programmed T cell expansion ,adoptive T cell transfer ,immunotherapy ,effector T cells ,Biology (General) ,QH301-705.5 - Abstract
Summary: Manipulating molecules that impact T cell receptor (TCR) or cytokine signaling, such as the protein tyrosine phosphatase non-receptor type 2 (PTPN2), has significant potential for advancing T cell-based immunotherapies. Nonetheless, it remains unclear how PTPN2 impacts the activation, survival, and memory formation of T cells. We find that PTPN2 deficiency renders cells in vivo and in vitro less dependent on survival-promoting cytokines, such as interleukin (IL)-2 and IL-15. Remarkably, briefly ex vivo-activated PTPN2-deficient T cells accumulate in 3- to 11-fold higher numbers following transfer into unmanipulated, antigen-free mice. Moreover, the absence of PTPN2 augments the survival of short-lived effector T cells and allows them to robustly re-expand upon secondary challenge. Importantly, we find no evidence for impaired effector function or memory formation. Mechanistically, PTPN2 deficiency causes broad changes in the expression and phosphorylation of T cell expansion and survival-associated proteins. Altogether, our data underline the therapeutic potential of targeting PTPN2 in T cell-based therapies to augment the number and survival capacity of antigen-specific T cells.
- Published
- 2020
- Full Text
- View/download PDF
27. The Inflammasome Drives GSDMD-Independent Secondary Pyroptosis and IL-1 Release in the Absence of Caspase-1 Protease Activity
- Author
-
Katharina S. Schneider, Christina J. Groß, Roland F. Dreier, Benedikt S. Saller, Ritu Mishra, Oliver Gorka, Rosalie Heilig, Etienne Meunier, Mathias S. Dick, Tamara Ćiković, Jan Sodenkamp, Guillaume Médard, Ronald Naumann, Jürgen Ruland, Bernhard Kuster, Petr Broz, and Olaf Groß
- Subjects
caspase-1 ,IL-1 ,caspase-8 ,inflammasome ,ASC ,pyroptosis ,regulated necrosis ,gasdermin ,Biology (General) ,QH301-705.5 - Abstract
Inflammasomes activate the protease caspase-1, which cleaves interleukin-1β and interleukin-18 to generate the mature cytokines and controls their secretion and a form of inflammatory cell death called pyroptosis. By generating mice expressing enzymatically inactive caspase-1C284A, we provide genetic evidence that caspase-1 protease activity is required for canonical IL-1 secretion, pyroptosis, and inflammasome-mediated immunity. In caspase-1-deficient cells, caspase-8 can be activated at the inflammasome. Using mice either lacking the pyroptosis effector gasdermin D (GSDMD) or expressing caspase-1C284A, we found that GSDMD-dependent pyroptosis prevented caspase-8 activation at the inflammasome. In the absence of GSDMD-dependent pyroptosis, the inflammasome engaged a delayed, alternative form of lytic cell death that was accompanied by the release of large amounts of mature IL-1 and contributed to host protection. Features of this cell death modality distinguished it from apoptosis, suggesting it may represent a distinct form of pro-inflammatory regulated necrosis.
- Published
- 2017
- Full Text
- View/download PDF
28. Author Correction: Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics
- Author
-
Mathias Wilhelm, Daniel P. Zolg, Michael Graber, Siegfried Gessulat, Tobias Schmidt, Karsten Schnatbaum, Celina Schwencke-Westphal, Philipp Seifert, Niklas de Andrade Krätzig, Johannes Zerweck, Tobias Knaute, Eva Bräunlein, Patroklos Samaras, Ludwig Lautenbacher, Susan Klaeger, Holger Wenschuh, Roland Rad, Bernard Delanghe, Andreas Huhmer, Steven A. Carr, Karl R. Clauser, Angela M. Krackhardt, Ulf Reimer, and Bernhard Kuster
- Subjects
Science - Published
- 2021
- Full Text
- View/download PDF
29. A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
- Author
-
Dongxue Wang, Basak Eraslan, Thomas Wieland, Björn Hallström, Thomas Hopf, Daniel Paul Zolg, Jana Zecha, Anna Asplund, Li‐hua Li, Chen Meng, Martin Frejno, Tobias Schmidt, Karsten Schnatbaum, Mathias Wilhelm, Frederik Ponten, Mathias Uhlen, Julien Gagneur, Hannes Hahne, and Bernhard Kuster
- Subjects
human proteome ,human transcriptome ,proteogenomics ,quantitative mass spectrometry ,RNA‐Seq ,Biology (General) ,QH301-705.5 ,Medicine (General) ,R5-920 - Abstract
Abstract Genome‐, transcriptome‐ and proteome‐wide measurements provide insights into how biological systems are regulated. However, fundamental aspects relating to which human proteins exist, where they are expressed and in which quantities are not fully understood. Therefore, we generated a quantitative proteome and transcriptome abundance atlas of 29 paired healthy human tissues from the Human Protein Atlas project representing human genes by 18,072 transcripts and 13,640 proteins including 37 without prior protein‐level evidence. The analysis revealed that hundreds of proteins, particularly in testis, could not be detected even for highly expressed mRNAs, that few proteins show tissue‐specific expression, that strong differences between mRNA and protein quantities within and across tissues exist and that protein expression is often more stable across tissues than that of transcripts. Only 238 of 9,848 amino acid variants found by exome sequencing could be confidently detected at the protein level showing that proteogenomics remains challenging, needs better computational methods and requires rigorous validation. Many uses of this resource can be envisaged including the study of gene/protein expression regulation and biomarker specificity evaluation.
- Published
- 2019
- Full Text
- View/download PDF
30. Quantification and discovery of sequence determinants of protein‐per‐mRNA amount in 29 human tissues
- Author
-
Basak Eraslan, Dongxue Wang, Mirjana Gusic, Holger Prokisch, Björn M Hallström, Mathias Uhlén, Anna Asplund, Frederik Pontén, Thomas Wieland, Thomas Hopf, Hannes Hahne, Bernhard Kuster, and Julien Gagneur
- Subjects
codon usage ,mRNA sequence motifs ,proteomics ,transcriptomics ,translational control ,Biology (General) ,QH301-705.5 ,Medicine (General) ,R5-920 - Abstract
Abstract Despite their importance in determining protein abundance, a comprehensive catalogue of sequence features controlling protein‐to‐mRNA (PTR) ratios and a quantification of their effects are still lacking. Here, we quantified PTR ratios for 11,575 proteins across 29 human tissues using matched transcriptomes and proteomes. We estimated by regression the contribution of known sequence determinants of protein synthesis and degradation in addition to 45 mRNA and 3 protein sequence motifs that we found by association testing. While PTR ratios span more than 2 orders of magnitude, our integrative model predicts PTR ratios at a median precision of 3.2‐fold. A reporter assay provided functional support for two novel UTR motifs, and an immobilized mRNA affinity competition‐binding assay identified motif‐specific bound proteins for one motif. Moreover, our integrative model led to a new metric of codon optimality that captures the effects of codon frequency on protein synthesis and degradation. Altogether, this study shows that a large fraction of PTR ratio variation in human tissues can be predicted from sequence, and it identifies many new candidate post‐transcriptional regulatory elements.
- Published
- 2019
- Full Text
- View/download PDF
31. A bead-based western for high-throughput cellular signal transduction analyses
- Author
-
Fridolin Treindl, Benjamin Ruprecht, Yvonne Beiter, Silke Schultz, Anette Döttinger, Annette Staebler, Thomas O. Joos, Simon Kling, Oliver Poetz, Tanja Fehm, Hans Neubauer, Bernhard Kuster, and Markus F. Templin
- Subjects
Science - Abstract
Dissecting cellular signalling requires the analysis of large numbers of proteins. Here the authors describe DigiWest, a high-throughput protein detection method that combines the concept of western and widely-used bead array systems that allows rapid quantification of hundreds of specific proteins.
- Published
- 2016
- Full Text
- View/download PDF
32. Protease signaling through protease activated receptor 1 mediate nerve activation by mucosal supernatants from irritable bowel syndrome but not from ulcerative colitis patients.
- Author
-
Sabine Buhner, Hannes Hahne, Kerstin Hartwig, Qin Li, Sheila Vignali, Daniela Ostertag, Chen Meng, Gabriele Hörmannsperger, Breg Braak, Christian Pehl, Thomas Frieling, Giovanni Barbara, Roberto De Giorgio, Ihsan Ekin Demir, Güralp Onur Ceyhan, Florian Zeller, Guy Boeckxstaens, Dirk Haller, Bernhard Kuster, and Michael Schemann
- Subjects
Medicine ,Science - Abstract
The causes of gastrointestinal complaints in irritable bowel syndrome (IBS) remain poorly understood. Altered nerve function has emerged as an important pathogenic factor as IBS mucosal biopsy supernatants consistently activate enteric and sensory neurons. We investigated the neurally active molecular components of such supernatants from patients with IBS and quiescent ulcerative colitis (UC).Effects of supernatants from 7 healthy controls (HC), 20 IBS and 12 UC patients on human and guinea pig submucous neurons were studied with neuroimaging techniques. We identify differentially expressed proteins with proteome analysis.Nerve activation by IBS supernatants was prevented by the protease activated receptor 1 (PAR1) antagonist SCHE79797. UC supernatants also activated enteric neurons through protease dependent mechanisms but without PAR1 involvement. Proteome analysis of the supernatants identified 204 proteins, among them 17 proteases as differentially expressed between IBS, UC and HC. Of those the four proteases elastase 3a, chymotrypsin C, proteasome subunit type beta-2 and an unspecified isoform of complement C3 were significantly more abundant in IBS compared to HC and UC supernatants. Of eight proteases, which were upregulated in IBS, the combination of elastase 3a, cathepsin L and proteasome alpha subunit-4 showed the highest prediction accuracy of 98% to discriminate between IBS and HC groups. Elastase synergistically potentiated the effects of histamine and serotonin-the two other main neuroactive substances in the IBS supernatants. A serine protease inhibitor isolated from the probiotic Bifidobacterium longum NCC2705 (SERPINBL), known to inhibit elastase-like proteases, prevented nerve activation by IBS supernatants.Proteases in IBS and UC supernatants were responsible for nerve activation. Our data demonstrate that proteases, particularly those signalling through neuronal PAR1, are biomarker candidates for IBS, and protease profiling may be used to characterise IBS.
- Published
- 2018
- Full Text
- View/download PDF
33. Increased Pancreatic Protease Activity in Response to Antibiotics Impairs Gut Barrier and Triggers ColitisSummary
- Author
-
Hongsup Yoon, Monika Schaubeck, Ilias Lagkouvardos, Andreas Blesl, Stephanie Heinzlmeir, Hannes Hahne, Thomas Clavel, Suchita Panda, Christina Ludwig, Bernhard Kuster, Chaysavanh Manichanh, Patrizia Kump, Dirk Haller, and Gabriele Hörmannsperger
- Subjects
Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Background & Aims: Antibiotic (ABx) therapy is associated with increased risk for Crohn’s disease but underlying mechanisms are unknown. We observed high fecal serine protease activity (PA) to be a frequent side effect of ABx therapy. The aim of the present study was to unravel whether this rise in large intestinal PA may promote colitis development via detrimental effects on the large intestinal barrier. Methods: Transwell experiments were used to assess the impact of high PA in ABx-treated patients or vancomycin/metronidazole-treated mice on the epithelial barrier. Serine protease profiling was performed using liquid chromatography–mass spectrometry/mass spectrometry analysis. The impact of high large intestinal PA on the intestinal barrier in wild-type and interleukin (IL)10-/- mice and on colitis development in IL10-/- mice was investigated using vancomycin/metronidazole with or without oral serine protease inhibitor (AEBSF) treatment. Results: The ABx-induced, high large intestinal PA was caused by significantly increased levels of pancreatic proteases and impaired epithelial barrier integrity. In wild-type mice, the rise in PA caused a transient increase in intestinal permeability but did not affect susceptibility to chemically induced acute colitis. In IL10-/- mice, increased PA caused a consistent impairment of the intestinal barrier associated with inflammatory activation in the large intestinal tissue. In the long term, the vancomycin/metronidazole-induced lasting increase in PA aggravated colitis development in IL10-/- mice. Conclusions: High large intestinal PA is a frequent adverse effect of ABx therapy, which is detrimental to the large intestinal barrier and may contribute to the development of chronic intestinal inflammation in susceptible individuals. Keywords: Epithelial Barrier, Serine Proteases, Gut Microbiota, Inflammatory Bowel Diseases
- Published
- 2018
- Full Text
- View/download PDF
34. Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins
- Author
-
Yanqi Hao, Recep Colak, Joan Teyra, Carles Corbi-Verge, Alexander Ignatchenko, Hannes Hahne, Mathias Wilhelm, Bernhard Kuster, Pascal Braun, Daisuke Kaida, Thomas Kislinger, and Philip M. Kim
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Alternative splicing acts on transcripts from almost all human multi-exon genes. Notwithstanding its ubiquity, fundamental ramifications of splicing on protein expression remain unresolved. The number and identity of spliced transcripts that form stably folded proteins remain the sources of considerable debate, due largely to low coverage of experimental methods and the resulting absence of negative data. We circumvent this issue by developing a semi-supervised learning algorithm, positive unlabeled learning for splicing elucidation (PULSE; http://www.kimlab.org/software/pulse), which uses 48 features spanning various categories. We validated its accuracy on sets of bona fide protein isoforms and directly on mass spectrometry (MS) spectra for an overall AU-ROC of 0.85. We predict that around 32% of “exon skipping” alternative splicing events produce stable proteins, suggesting that the process engenders a significant number of previously uncharacterized proteins. We also provide insights into the distribution of positive isoforms in various functional classes and into the structural effects of alternative splicing.
- Published
- 2015
- Full Text
- View/download PDF
35. Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae
- Author
-
Julia Rechenberger, Patroklos Samaras, Anna Jarzab, Juergen Behr, Martin Frejno, Ana Djukovic, Jaime Sanz, Eva M. González-Barberá, Miguel Salavert, Jose Luis López-Hontangas, Karina B. Xavier, Laurent Debrauwer, Jean-Marc Rolain, Miguel Sanz, Marc Garcia-Garcera, Mathias Wilhelm, Carles Ubeda, and Bernhard Kuster
- Subjects
human gut microbiome ,metaproteome ,data analysis ,mass spectrometry ,proteomics ,clinical proteomics ,multi-omics ,multidrug-resistant Enterobacteriaceae ,Microbiology ,QR1-502 - Abstract
The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.
- Published
- 2019
- Full Text
- View/download PDF
36. Global Proteome Analysis of the NCI-60 Cell Line Panel
- Author
-
Amin Moghaddas Gholami, Hannes Hahne, Zhixiang Wu, Florian Johann Auer, Chen Meng, Mathias Wilhelm, and Bernhard Kuster
- Subjects
Biology (General) ,QH301-705.5 - Abstract
The NCI-60 cell line collection is a very widely used panel for the study of cellular mechanisms of cancer in general and in vitro drug action in particular. It is a model system for the tissue types and genetic diversity of human cancers and has been extensively molecularly characterized. Here, we present a quantitative proteome and kinome profile of the NCI-60 panel covering, in total, 10,350 proteins (including 375 protein kinases) and including a core cancer proteome of 5,578 proteins that were consistently quantified across all tissue types. Bioinformatic analysis revealed strong cell line clusters according to tissue type and disclosed hundreds of differentially regulated proteins representing potential biomarkers for numerous tumor properties. Integration with public transcriptome data showed considerable similarity between mRNA and protein expression. Modeling of proteome and drug-response profiles for 108 FDA-approved drugs identified known and potential protein markers for drug sensitivity and resistance. To enable community access to this unique resource, we incorporated it into a public database for comparative and integrative analysis (http://wzw.tum.de/proteomics/nci60).
- Published
- 2013
- Full Text
- View/download PDF
37. Auxin efflux by PIN-FORMED proteins is activated by two different protein kinases, D6 PROTEIN KINASE and PINOID
- Author
-
Melina Zourelidou, Birgit Absmanner, Benjamin Weller, Inês CR Barbosa, Björn C Willige, Astrid Fastner, Verena Streit, Sarah A Port, Jean Colcombet, Sergio de la Fuente van Bentem, Heribert Hirt, Bernhard Kuster, Waltraud X Schulze, Ulrich Z Hammes, and Claus Schwechheimer
- Subjects
AGC kinase ,protein kinase ,auxin ,auxin transport ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
The development and morphology of vascular plants is critically determined by synthesis and proper distribution of the phytohormone auxin. The directed cell-to-cell distribution of auxin is achieved through a system of auxin influx and efflux transporters. PIN-FORMED (PIN) proteins are proposed auxin efflux transporters, and auxin fluxes can seemingly be predicted based on the—in many cells—asymmetric plasma membrane distribution of PINs. Here, we show in a heterologous Xenopus oocyte system as well as in Arabidopsis thaliana inflorescence stems that PIN-mediated auxin transport is directly activated by D6 PROTEIN KINASE (D6PK) and PINOID (PID)/WAG kinases of the Arabidopsis AGCVIII kinase family. At the same time, we reveal that D6PKs and PID have differential phosphosite preferences. Our study suggests that PIN activation by protein kinases is a crucial component of auxin transport control that must be taken into account to understand auxin distribution within the plant.
- Published
- 2014
- Full Text
- View/download PDF
38. Merits of Diazirine Photo-Immobilization for Target Profiling of Natural Products and Cofactors
- Author
-
Polina Prokofeva, Stefanie Höfer, Maximilian Hornisch, Miriam Abele, Bernhard Kuster, and Guillaume Médard
- Subjects
Biological Products ,Proteome ,Diazomethane ,Flavin-Adenine Dinucleotide ,Molecular Medicine ,Humans ,General Medicine ,Biochemistry ,Mass Spectrometry - Abstract
Finding the targets of natural products is of key importance in both chemical biology and drug discovery, and deconvolution of cofactor interactomes contributes to the functional annotation of the proteome. Identifying the proteins that underlie natural compound activity in phenotypic screens helps to validate the respective targets and, potentially, expand the druggable proteome. Here, we present a generally applicable protocol for the photoactivated immobilization of unmodified and microgram quantities of natural products on diazirine-decorated beads and their use for systematic affinity-based proteome profiling. We show that among 31 molecules of very diverse reported activity and biosynthetic origin, 25 could indeed be immobilized. Dose-response competition binding experiments using lysates of human or bacterial cells followed by quantitative mass spectrometry recapitulated targets of 9 molecules with100 μM affinity. Among them, immobilization of coenzyme A produced a tool to interrogate proteins containing a HotDog domain. Surprisingly, immobilization of the cofactor flavin adenine dinucleotide (FAD) led to the identification of nanomolar interactions with dozens of RNA-binding proteins.
- Published
- 2023
39. Supplementary Figures from Adaptive Resistance to EGFR-Targeted Therapy by Calcium Signaling in NSCLC Cells
- Author
-
Simone Lemeer, Paul van Bergen en Henegouwen, Bernhard Kuster, Maria Reinecke, Sander van Doorn, Nadine Prust, and Celine Mulder
- Abstract
Supplementary Figures S1-S3
- Published
- 2023
40. Supplementary Table 1 from Adaptive Resistance to EGFR-Targeted Therapy by Calcium Signaling in NSCLC Cells
- Author
-
Simone Lemeer, Paul van Bergen en Henegouwen, Bernhard Kuster, Maria Reinecke, Sander van Doorn, Nadine Prust, and Celine Mulder
- Abstract
Raw Peptides
- Published
- 2023
41. Supplementary Material and Methods from Adaptive Resistance to EGFR-Targeted Therapy by Calcium Signaling in NSCLC Cells
- Author
-
Simone Lemeer, Paul van Bergen en Henegouwen, Bernhard Kuster, Maria Reinecke, Sander van Doorn, Nadine Prust, and Celine Mulder
- Abstract
Supplementary Material and Methods
- Published
- 2023
42. Supplementary Table 3 from Adaptive Resistance to EGFR-Targeted Therapy by Calcium Signaling in NSCLC Cells
- Author
-
Simone Lemeer, Paul van Bergen en Henegouwen, Bernhard Kuster, Maria Reinecke, Sander van Doorn, Nadine Prust, and Celine Mulder
- Abstract
Processed Proteins
- Published
- 2023
43. Supplementary Video 2 from Adaptive Resistance to EGFR-Targeted Therapy by Calcium Signaling in NSCLC Cells
- Author
-
Simone Lemeer, Paul van Bergen en Henegouwen, Bernhard Kuster, Maria Reinecke, Sander van Doorn, Nadine Prust, and Celine Mulder
- Abstract
Supplementary Video 2
- Published
- 2023
44. Supplementary Video 1 from Adaptive Resistance to EGFR-Targeted Therapy by Calcium Signaling in NSCLC Cells
- Author
-
Simone Lemeer, Paul van Bergen en Henegouwen, Bernhard Kuster, Maria Reinecke, Sander van Doorn, Nadine Prust, and Celine Mulder
- Abstract
Supplementary Video 1
- Published
- 2023
45. Raw proteome dataset from Lapatinib Resistance in Breast Cancer Cells Is Accompanied by Phosphorylation-Mediated Reprogramming of Glycolysis
- Author
-
Simone Lemeer, Bernhard Kuster, Celia R. Berkers, Wei Wu, Jana Zecha, Esther A. Zaal, and Benjamin Ruprecht
- Abstract
Proteome abundance dataset containing raw MaxQuant output.
- Published
- 2023
46. Supplementary Material and Methods from Lapatinib Resistance in Breast Cancer Cells Is Accompanied by Phosphorylation-Mediated Reprogramming of Glycolysis
- Author
-
Simone Lemeer, Bernhard Kuster, Celia R. Berkers, Wei Wu, Jana Zecha, Esther A. Zaal, and Benjamin Ruprecht
- Abstract
Supplementary Material and Methods
- Published
- 2023
47. Filtered and normalized proteome dataset from Lapatinib Resistance in Breast Cancer Cells Is Accompanied by Phosphorylation-Mediated Reprogramming of Glycolysis
- Author
-
Simone Lemeer, Bernhard Kuster, Celia R. Berkers, Wei Wu, Jana Zecha, Esther A. Zaal, and Benjamin Ruprecht
- Abstract
Phosphorylation site abundance dataset containing filtered, processed and annotated phosphorylation sites; STRING phosphoprotein input and output data for the lapatinib mode of action network and two dimensional enrichment analysis comparing lapatinib treatment of parental cells to phosphorylation changes in resistance (only significant terms).
- Published
- 2023
48. Kinome dataset from Lapatinib Resistance in Breast Cancer Cells Is Accompanied by Phosphorylation-Mediated Reprogramming of Glycolysis
- Author
-
Simone Lemeer, Bernhard Kuster, Celia R. Berkers, Wei Wu, Jana Zecha, Esther A. Zaal, and Benjamin Ruprecht
- Abstract
Kinome abundance dataset containing MaxQuant output for raw chemoproteomic data; the processed and filtered protein kinase dataset and the merged abundance of protein kinases identified in full and chemoproteome datasets.
- Published
- 2023
49. Supplementary Figures including Figure legends from Lapatinib Resistance in Breast Cancer Cells Is Accompanied by Phosphorylation-Mediated Reprogramming of Glycolysis
- Author
-
Simone Lemeer, Bernhard Kuster, Celia R. Berkers, Wei Wu, Jana Zecha, Esther A. Zaal, and Benjamin Ruprecht
- Abstract
Figure S1. Quality of phospho(proteomic) dataset acquired. Figure S2. (Phospho)proteomic analysis of lapatinib mode of action in parental cells. Figure S3. Signaling reprogramming in lapatinib resistance. Figure S4. Identification of pharmacologically actionable targets and phenotypes based on a breast cancer model of lapatinib resistance. Figure S5. Metabolic changes in lapatinib resistant cell line model.
- Published
- 2023
50. Cover Feature: Optimization of the Lead Compound NVP‐BHG712 as a Colorectal Cancer Inhibitor (Chem. Eur. J. 23/2023)
- Author
-
Alix Tröster, Michael DiPrima, Nathalie Jores, Denis Kudlinzki, Sridhar Sreeramulu, Santosh L. Gande, Verena Linhard, Damian Ludig, Alexander Schug, Krishna Saxena, Maria Reinecke, Stephanie Heinzlmeir, Matthias S. Leisegang, Jan Wollenhaupt, Frank Lennartz, Manfred S. Weiss, Bernhard Kuster, Giovanna Tosato, and Harald Schwalbe
- Subjects
Organic Chemistry ,General Chemistry ,Catalysis - Published
- 2023
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.