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Articles by Bernhard Kuster
A STRUBBELIG–NHL3 cell surface receptor complex mediates the response to cellulose deficiency in Arabidopsis
Abstract Plant cells are enclosed by a semi-rigid cell wall with a complex biochemical composition and architecture. The poorly understood process of remodelling the cell wall is crucial for controlling growth and development and for regulating abiotic and biotic stress responses. Cell wall remodelling upon disruption of cell wall integrity through inhibition of cellulose biosynthesis depends on the receptor kinase STRUBBELIG (SUB) and its binding partner QUIRKY (QKY).
Gut microbiota restricts intestinal lipid uptake via modulation of bile phosphatidylcholine metabolism in mice
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Abstract The gut microbiota influences host metabolism, but the mechanisms of lipid uptake from food remain mysterious. Here we used stable isotope-labelled tracers in gnotobiotic mouse models, which revealed that host uptake of dietary lipids depends on microbial colonization.
By Sarah Brunner, Maria Zimmermann-Kogadeeva, Marcus Höring, Gerhard Liebisch, Marijana Basic, Silvia Bolsega, Klaus-Peter Janssen, Emma Slack, Thomas Clavel, Michael T. Zimmermann, Joerg Heeren, Piero Giansanti, Anna Weiss, Aline Dupont, Anna-Lena Ullrich, Florian Jokisch, Claudine Seeliger, André Bleich, Bärbel Stecher, Olivia Coleman, Claudia Moresi, Giorgia Greter, Markus Arnoldini, Josef Scheiber, Martin Klingenspor, Bernhard Kuster, Dirk Haller, Ralph Burkhardt, Folkert Kuipers, Josef Ecker, Johannes Plagge, Sophia von Gamm, Alina Viehof-Beckmann, Sven Hermeling, Maria Hidrobo, Silke Matysik
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Nature
Verified
Pathogenesis of diffuse large B cell lymphoma proteogenotypes
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Keywords lymphoma genomics proteomics tumor microenvironment immune exhaustion multi-omics data integration MYC B cell receptor single cell sequencing protein translation Introduction Diffuse large B cell lymphoma (DLBCL) is a genetically and clinically heterogeneous disease. While about 60–70% of patients with DLCBL can be cured with R-CHOP chemoimmunotherapy, 30–40% relapse or are refractory to treatment.
By Julius C. Enssle, Björn Häupl, Arber Qoku, Boya Wang, George Wright Verified, Sharon Barrans, Yulai Zhou, Matthew A. Care, Cathy Burton, Caitlin Gribbin, Jennifer Ziello, Jason L. Weirather, Yibo Dai, Atish Kizhakeyil, Xubin Li, James Phelan, Smriti Kanangat, Stephan Eckert, Sebastian Scheich, Da Wei Huang, Josefine Jakob, Sebastian P. Perner, Andrea Di Fonzo, Martine Pape, Marion Bodach, Dominique Jahn, Uwe Plessmann, Annette M. Staiger, German Ott, Philipp Berning, Georg Lenz, Daniel Hodson, Bernhard Kuster, Roland Schmitz, Henning Urlaub, Michael Green, Ari M Melnick, Reuben M. Tooze, Coraline Mlynarczyk, Giorgio G. Inghirami, Florian Buettner, Louis M. Staudt, Thomas Oellerich
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Cell Press
Verified
Multi-layered molecular profiling informs the diagnosis and targeted therapy of desmoplastic small round cell tumor
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Abstract Desmoplastic small round cell tumor (DSRCT) is an ultra-rare sarcoma with limited treatment options. Here, we show that comprehensive molecular profiling informs diagnosis and individualized therapy in this disease. We report the results of whole-genome/exome, transcriptome, and DNA methylome analyses performed in 30 refractory DSRCT patients, complemented by (phospho)proteomic profiling in nine, within a nationwide precision oncology program.
By Marcus Renner, Nagarajan Paramasivam, Christoph E. Heilig, Annika Schneider, Jennifer Hüllein, Barbara Hutter, Cihan Erkut, Andreas Mock, Eva I. Krieghoff-Henning, Amirhossein Sakhteman, Matthew The, Tony Prinz, Panna Lajer, Katja Beck, Bettina Beuthien-Baumann, Leonidas Apostolidis, Sebastian Bauer, Melanie Boerries, Christian H. Brandts, Damian T. Rieke, Thomas Kindler, Frederick Klauschen, Klaus Schulze-Osthoff, Richard F. Schlenk, Guy Berchem, Michael Allgäuer, Gunhild Mechtersheimer, Albrecht Stenzinger, Daniel B. Lipka, Matthias Schlesner, Bernhard Kuster, Arne Jahn, Evelin Schröck, Christoph Heining, Peter Horak, Simon Kreutzfeldt, Daniel Hübschmann, Wolfgang Hartmann, Hanno Glimm, Stefan Fröhling, Małgorzata Oleś, Caroline Modugno, Catherine Herremans, Cecilia B. Jensen, Annika Baude-Müller, Maria-Veronica Teleanu
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Nature
Verified
Loss of GPRC5D enhances the proliferative capacity and competitive fitness of myeloma upon anti-GPRC5D immunotherapy
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Abstract Immunotherapies targeting surface antigens have transformed the treatment landscape of multiple myeloma (MM), with GPRC5D emerging as a promising therapeutic target. Monoallelic loss of GPRC5D is frequently observed in newly diagnosed MM patients, and the incidence of acquired GPRC5D alterations increases following exposure to GPRC5D-directed therapies.
By Umair Munawar, Thomas Nerreter, Alexander M. Leipold, Seungbin Han, Christina Verbruggen, Elena Gerhard-Hartmann, Cornelia Vogt, Sabine Roth, Julia Weingart, Patrick Eiring, Marietta Truger, Nazia Afrin, Torsten Steinbrunn, Xiang Zhou, Johanna Lehmann, Max Koppel, Andreas Rosenwald, Claudia Haferlach, Michael Hudecek, Antoine-Emmanuel Saliba, Leo Rasche, Markus Sauer, Hermann Einsele, Bernhard Kuster, Johannes M. Waldschmidt, K. Martin Kortüm, Johanna Thurner, Silvia Nerreter, Björn Grams, Shilpa Kurian, Emma Besant, Yoko Tamamushi, Nina Rein
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Nature
Verified
High-throughput chemical proteomics workflow for profiling protein citrullination dynamics - Nature Communications
Abstract Citrullination is a post-translational modification implicated in autoimmune and inflammatory diseases, yet its low abundance and lack of effective enrichment tools have limited proteome-wide analysis. Here, we develop a robust chemical proteomics workflow with improved specificity and throughput. This method builds upon glyoxal-based derivatization and incorporates a cleavable biotin linker for efficient peptide enrichment, release, and identification via mass spectrometry.
Inhibitors supercharge kinase turnover through native proteolytic circuits - Nature
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Abstract Targeted protein degradation is a pharmacological strategy that relies on small molecules such as proteolysis-targeting chimeras (PROTACs) or molecular glues, which induce proximity between a target protein and an E3 ubiquitin ligase to prompt target ubiquitination and proteasomal degradation1. Sporadic reports indicated that ligands designed to inhibit a target can also induce its destabilization2,3,4. Among others, this has repeatedly been observed for kinase inhibitors5,6,7.
By Natalie S. Scholes, Arnau Comajuncosa-Creus, Xuefei Guo, Fabian Frommelt, Matthias Hinterndorfer, Hlib Razumkov, Martin P. Schwalm, Hana Imrichova, Andrea Rukavina, Miriam Abele, Anna Koren, Stefan Kubicek, Stefan Knapp, Nathanael S. Gray, Giulio Superti-Furga, Bernhard Kuster, Yigong Shi, Patrick Aloy, Sandra Roehm, Eleonora Barone
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Nature
Verified
Computational Approaches for Pathway‐Centric Analysis of Protein Post‐Translational Modifications
API application programming interface FCS functional class scoring GSEA gene set enrichment analysis ORA overrepresentation analysis PCST prize-collecting Steiner tree PKN prior knowledge network PPI protein–protein interaction PSP PhosphoSitePlus PT pathway topology RWR random walk with restart SPIA signaling pathway impact analysis ssGSEA single sample gene set enrichment analysis TPS temporal pathway synthesizer 1 Introduction The study of post-translational modifications (PTMs) has...
Multicenter evaluation of label-free quantification in human plasma on a high dynamic range benchmark set - Nature Communications
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Abstract Human plasma is routinely collected during clinical care and constitutes a rich source of biomarkers for diagnostics and patient stratification. Liquid chromatography-mass spectrometry (LC-MS)-based proteomics is a key method for plasma biomarker discovery, but the high dynamic range of plasma proteins poses significant challenges for MS analysis and data processing.
By Ute Distler, David Gomez-Zepeda, Christine von Toerne, Juliane Merl-Pham, Johanna Tüshaus, Pieter Giesbertz, Henry Unger, Dario L. Frey, Dominic Helm, Luisa Schwarzmüller, Susanne I. Wudy, Ludwig Sinn, Julia Mergner, Christina Ludwig, Axel Imhof, Bernhard Kuster, Stefan F. Lichtenthaler, Philipp Mertins, Fabian Coscia, Markus Ralser, Michael Mülleder, Stefanie Hauck
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Nature
Verified
Privacy-preserving multicenter differential protein abundance analysis with FedProt - Nature Computational Science
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Abstract Quantitative mass spectrometry has revolutionized proteomics by enabling simultaneous quantification of thousands of proteins. Pooling patient-derived data from multiple institutions enhances statistical power but raises serious privacy concerns. Here we introduce FedProt, the first privacy-preserving tool for collaborative differential protein abundance analysis of distributed data, which utilizes federated learning and additive secret sharing.
By Yuliya Burankova, Mohammad Bakhtiari, Christine von Toerne, Lisa Schweizer, Pieter Giesbertz, Johannes Schmidt, Stefan Kalkhof, Janina Müller-Deile, Yassene Mohammed, Klaudia Adamowicz, Stefanie Hauck, Stefan F. Lichtenthaler, Axel Imhof, Matthias Mann, Christina Ludwig, Bernhard Kuster, Jan Baumbach, Tanja Laske
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Nature
Verified
Unifying the analysis of bottom-up proteomics data with CHIMERYS - Nature Methods
Abstract Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography–tandem mass spectrometry, creating thousands of spectra, most of which are chimeric and contain fragment ions from more than one peptide.
ProSIMSIt: The Best of Both Worlds in Data-Driven Rescoring and Identification Transfer
Special Issue Published as part of Journal of Proteome Research special issue “Software Tools and Resources 2025”. Introduction Click to copy section linkSection link copied! Isobaric labeling techniques such as tandem mass tags (TMTs) are frequently employed in proteomics to multiplex samples, allowing for the simultaneous measurement of up to 35 different conditions.
SWAPS: A Modular Deep-Learning Empowered Peptide Identity Propagation Framework Beyond Match-Between-Run
Special Issue Published as part of Journal of Proteome Research special issue “Software Tools and Resources 2025”. Introduction Click to copy section linkSection link copied! Mass spectrometry (MS)-based proteomics has been established as a key tool for addressing a wide range of questions about proteins, including but not limited to their sequences, abundance, subcellular localization, functional roles, structural conformations, chemical properties, and interactions with other proteins.
PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways - Nature Communications
Abstract Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how PTMs modulate cellular pathways on a molecular level.
Critical assessment of LC3/GABARAP ligands used for degrader development and ligandability of LC3/GABARAP binding pockets - Nature Communications
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Abstract Recent successes in developing small molecule degraders that act through the ubiquitin system have spurred efforts to extend this technology to other mechanisms, including the autophagosomal-lysosomal pathway. Therefore, reports of autophagosome tethering compounds (ATTECs) have received considerable attention from the drug development community.
By Martin P. Schwalm, Johannes Dopfer, Adarsh Kumar, Francesco Greco, Nicolas Bauer, Frank Lohr, Jan Heering, Severin Lechner, Thomas Hanke Verified, Viktoria Morasch Verified, Christopher G. Lenz, Daren Fearon, Peter Marples, Charles Tomlinson, Lorène Brunello, Krishna Saxena, Frank von Delft, Susanne Müller, Alexandra Stolz, Ewgenij Proschak, Bernhard Kuster, Stefan Knapp, Sara Cano-Franco, Ivana Jaser
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Nature
Verified
Exploring crop genomes: assembly features, gene prediction accuracy, and implications for proteomics studies - BMC Genomics
Among the 100 crops studied, we were able to retrieve genome assemblies and annotation data for 54 crops, classifying them under Group A. Group B consisted of 40 crops for which genome assemblies were available but lacked annotation data. Finally, Group C included 6 crops for which neither genome assemblies nor annotations were found (Fig. 1a). Our list of crops displays a remarkable spectrum of diversity within both the monocotyledons and dicotyledons classes (Fig.
Mapping the Human Proteome with Physical Access to DNA
Abstract In a human cell, DNA is packed in histones, RNA, and chromatin-associated proteins, forming a cohesive gel. At any given moment, only a specific subset of the proteome has physical access to the DNA and organizes its structure, transcription, replication, repair and other molecular functions essential to the way the genome is read and maintained. We have developed a zero-distance photo-crosslinking approach to quantify proteins in direct contact with DNA in living cells.
Author Correction: Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification - Nature Communications
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Correction to: Nature Communications https://doi.org/10.1038/s41467-023-39570-7, published online 02 August 2023 With respect to the original “Data availability” statement, since the publication of this work, to ensure patient data privacy protection per request of the authors’ institute Technical University of Munich, the RNA-seq dataset from sorted CD8+ TILs originally deposited to the European Nucleotide Archive (ENA) with study accession number PRJEB61429 has been transferred to the...
By Celina Tretter, Sebastian Lange, Johannes Untch, Gabriela Zuleger, Mathias Wilhelm, Katja Steiger, Sebastian Ochsenreither, Sebastian Bauer, Melanie Boerries, Florian Bassermann, Daniel Reim, Barbara Klink, Evelin Schröck, Bernhard Haller, Bernhard Kuster, Matthias Mann, Stefan Fröhling, Roland Rad, Michael Hiltensperger
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Nature
Verified
A new mass analyzer shakes up the proteomics field - Nature Biotechnology
A new mass analyzer enables protein identification at high speed and depth. In June 2023, the proteomics community was electrified by the launch of the first conceptually novel mass analyzer in a commercial instrument since 2005, announced at the annual meeting of the American Society for Mass Spectrometry. The addition of a so-called Asymmetric Track Lossless (Astral) mass analyzer into an Orbitrap instrument affords high data acquisition speed, sensitivity, resolution and mass accuracy.
D6PK plasma membrane polarity requires a repeated CXX(X)P motif and PDK1-dependent phosphorylation - Nature Plants
Abstract D6 PROTEIN KINASE (D6PK) is a polarly localized plasma-membrane-associated kinase from Arabidopsis thaliana that activates polarly distributed PIN-FORMED auxin transporters. D6PK moves rapidly to and from the plasma membrane, independent of its PIN-FORMED targets. The middle D6PK domain, an insertion between kinase subdomains VII and VIII, is required and sufficient for association and polarity of the D6PK plasma membrane.
CurveCurator: a recalibrated F-statistic to assess, classify, and explore significance of dose–response curves - Nature Communications
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.
Proteomic meta-study harmonization, mechanotyping and drug repurposing candidate prediction with ProHarMeD - npj Systems Biology and Applications
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.
PTMNavigator: Interactive Visualization of Differentially Regulated Post-Translational Modifications in Cellular Signaling Pathways
Abstract Post-translational modifications (PTMs) play a governing role in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how PTMs modulate cellular pathways on a molecular level.
CurveCurator: A recalibrated F-statistic to assess, classify, and explore significance of dose-response curves
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Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification - Nature Communications
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Human study The study was approved by the institutional review boards (Ethics Commission of the Medical Faculty of Technical University Munich (protocol 193/17S) and Ethics Committee of the Medical Faculty of Heidelberg University (protocol S-206/2011)) and all patients provided written informed consent under these protocols. The study was conducted in accordance with the Declaration of Helsinki.
By Sebastian Lange, Mathias Wilhelm, Katja Steiger, Sebastian Ochsenreither, Sebastian Bauer, Melanie Boerries, Florian Bassermann, Daniel Reim, Barbara Klink, Bernhard Haller, Bernhard Kuster, Matthias Mann, Stefan Fröhling, Roland Rad, Michael Hiltensperger, Celina Tretter, Johannes Untch, Gabriela Zuleger, Evelin Schröck
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Nature
Verified
Mass spectrometry-based draft of the mouse proteome - Nature Methods
Abstract The laboratory mouse ranks among the most important experimental systems for biomedical research and molecular reference maps of such models are essential informational tools. Here, we present a quantitative draft of the mouse proteome and phosphoproteome constructed from 41 healthy tissues and several lines of analyses exemplify which insights can be gleaned from the data.
Target deconvolution of HDAC pharmacopoeia reveals MBLAC2 as common off-target - Nature Chemical Biology
Abstract Drugs that target histone deacetylase (HDAC) entered the pharmacopoeia in the 2000s. However, some enigmatic phenotypes suggest off-target engagement. Here, we developed a quantitative chemical proteomics assay using immobilized HDAC inhibitors and mass spectrometry that we deployed to establish the target landscape of 53 drugs.
Selective multi-kinase inhibition sensitizes mesenchymal pancreatic cancer to immune checkpoint blockade by remodeling the tumor microenvironment - Nature Cancer
Abstract KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) is highly immunosuppressive and resistant to targeted and immunotherapies. Among the different PDAC subtypes, basal-like mesenchymal PDAC, which is driven by allelic imbalance, increased gene dosage and subsequent high expression levels of oncogenic KRAS, shows the most aggressive phenotype and strongest therapy resistance.
Robust, Reproducible, and Quantitative Analysis of Thousands of Proteomes by Micro-flow LC-MS/MS
Presentation Overview In this on-demand presentation, Prof.
Defining the carrier proteome limit for single-cell proteomics
Abstract Single-cell proteomics by mass spectrometry (SCoPE-MS) is a recently introduced method to quantify multiplexed single-cell proteomes. While this technique has generated great excitement, the underlying technologies (isobaric labeling and mass spectrometry (MS)) have technical limitations with the potential to affect data quality and biological interpretation.
Thermo Fisher Scientific: The Power of Omics
Major breakthrough in cancer treatment has been achieved by harnessing the capabilities of the immune system to both identify and eliminate cancer, even metastasized cancer. Mutations in cancer leading to altered proteins are well documented as cancer neoantigens.
Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning
Abstract In mass-spectrometry-based proteomics, the identification and quantification of peptides and proteins heavily rely on sequence database searching or spectral library matching. The lack of accurate predictive models for fragment ion intensities impairs the realization of the full potential of these approaches. Here, we extended the ProteomeTools synthetic peptide library to 550,000 tryptic peptides and 21 million high-quality tandem mass spectra.
Two serines in the distal C-terminus of the human ß1-adrenoceptor determine ß-arrestin2 recruitment
G protein-coupled receptors (GPCRs) undergo phosphorylation at several intracellular residues by G protein-coupled receptor kinases. The resulting phosphorylation pattern triggers arrestin recruitment and receptor desensitization. The exact sites of phosphorylation and their function remained largely unknown for the human ? -adrenoceptor (ADRB1), a key GPCR in adrenergic signal transduction and the target of widely used drugs such as ?-blockers.
DENEDDYLASE1 Protein Counters Automodification of Neddylating Enzymes to Maintain NEDD8 Protein Homeostasis in Arabidopsis
In eukaryotes, the conjugation of the ubiquitin-like protein NEDD8 onto protein targets is an important post-translational modification. The best understood neddylation targets are the cullins, scaffold subunits of E3 ubiquitin ligases, where neddylation as well as deneddylation, facilitated by the protease activity of the CSN (COP9 signalosome), are required to control ubiquitin ligase assembly, function, and ultimately substrate degradation.
DENEDDYLASE1 counters automodification of neddylating enzymes to maintain NEDD8 homeostasis in Arabidopsis
In eukaryotes, the conjugation of the ubiquitin-like protein NEDD8 onto protein targets is an important post-translational modification. The best understood neddylation targets are the cullins, scaffold subunits of E3 ubiquitin ligases, where neddylation as well as deneddylation, facilitated by the protease activity of the CSN (COP9 signalosome), are required to control ubiquitin ligase assembly, function and ultimately substrate degradation.
A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets
Calculating the number of confidently identified proteins and estimating false discovery rate (FDR) is a challenge when analyzing very large proteomic data sets such as entire human proteomes. Biological and technical heterogeneity in proteomic experiments further add to the challenge and there are strong differences in opinion regarding the conceptual validity of a protein FDR and no consensus regarding the methodology for protein FDR determination.
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