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Goetze S, van Drogen A, Albinus JB, Fort KL, Gandhi T, Robbiani D, Laforte V, Reiter L, Levesque MP, Xuan Y, Wollscheid B. Simultaneous targeted and discovery-driven clinical proteotyping using hybrid-PRM/DIA. Clin Proteomics 2024; 21:26. [PMID: 38565978 PMCID: PMC10988896 DOI: 10.1186/s12014-024-09478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Clinical samples are irreplaceable, and their transformation into searchable and reusable digital biobanks is critical for conducting statistically empowered retrospective and integrative research studies. Currently, mainly data-independent acquisition strategies are employed to digitize clinical sample cohorts comprehensively. However, the sensitivity of DIA is limited, which is why selected marker candidates are often additionally measured targeted by parallel reaction monitoring. METHODS Here, we applied the recently co-developed hybrid-PRM/DIA technology as a new intelligent data acquisition strategy that allows for the comprehensive digitization of rare clinical samples at the proteotype level. Hybrid-PRM/DIA enables enhanced measurement sensitivity for a specific set of analytes of current clinical interest by the intelligent triggering of multiplexed parallel reaction monitoring (MSxPRM) in combination with the discovery-driven digitization of the clinical biospecimen using DIA. Heavy-labeled reference peptides were utilized as triggers for MSxPRM and monitoring of endogenous peptides. RESULTS We first evaluated hybrid-PRM/DIA in a clinical context on a pool of 185 selected proteotypic peptides for tumor-associated antigens derived from 64 annotated human protein groups. We demonstrated improved reproducibility and sensitivity for the detection of endogenous peptides, even at lower concentrations near the detection limit. Up to 179 MSxPRM scans were shown not to affect the overall DIA performance. Next, we applied hybrid-PRM/DIA for the integrated digitization of biobanked melanoma samples using a set of 30 AQUA peptides against 28 biomarker candidates with relevance in molecular tumor board evaluations of melanoma patients. Within the DIA-detected approximately 6500 protein groups, the selected marker candidates such as UFO, CDK4, NF1, and PMEL could be monitored consistently and quantitatively using MSxPRM scans, providing additional confidence for supporting future clinical decision-making. CONCLUSIONS Combining PRM and DIA measurements provides a new strategy for the sensitive and reproducible detection of protein markers from patients currently being discussed in molecular tumor boards in combination with the opportunity to discover new biomarker candidates.
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Affiliation(s)
- Sandra Goetze
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology (D-HEST), ETH Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
- ETH PHRT Swiss Multi-Omics Center (SMOC), Zurich, Switzerland.
| | - Audrey van Drogen
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology (D-HEST), ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
- ETH PHRT Swiss Multi-Omics Center (SMOC), Zurich, Switzerland
| | - Jonas B Albinus
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology (D-HEST), ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Kyle L Fort
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | | | | | | | | | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Yue Xuan
- Thermo Fisher Scientific (Bremen) GmbH, Bremen, Germany
| | - Bernd Wollscheid
- Institute of Translational Medicine (ITM), Department of Health Sciences and Technology (D-HEST), ETH Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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2
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Wildschut MHE, Mena J, Dördelmann C, van Oostrum M, Hale BD, Settelmeier J, Festl Y, Lysenko V, Schürch PM, Ring A, Severin Y, Bader MS, Pedrioli PGA, Goetze S, van Drogen A, Balabanov S, Skoda RC, Lopes M, Wollscheid B, Theocharides APA, Snijder B. Proteogenetic drug response profiling elucidates targetable vulnerabilities of myelofibrosis. Nat Commun 2023; 14:6414. [PMID: 37828014 PMCID: PMC10570306 DOI: 10.1038/s41467-023-42101-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 09/25/2023] [Indexed: 10/14/2023] Open
Abstract
Myelofibrosis is a hematopoietic stem cell disorder belonging to the myeloproliferative neoplasms. Myelofibrosis patients frequently carry driver mutations in either JAK2 or Calreticulin (CALR) and have limited therapeutic options. Here, we integrate ex vivo drug response and proteotype analyses across myelofibrosis patient cohorts to discover targetable vulnerabilities and associated therapeutic strategies. Drug sensitivities of mutated and progenitor cells were measured in patient blood using high-content imaging and single-cell deep learning-based analyses. Integration with matched molecular profiling revealed three targetable vulnerabilities. First, CALR mutations drive BET and HDAC inhibitor sensitivity, particularly in the absence of high Ras pathway protein levels. Second, an MCM complex-high proliferative signature corresponds to advanced disease and sensitivity to drugs targeting pro-survival signaling and DNA replication. Third, homozygous CALR mutations result in high endoplasmic reticulum (ER) stress, responding to ER stressors and unfolded protein response inhibition. Overall, our integrated analyses provide a molecularly motivated roadmap for individualized myelofibrosis patient treatment.
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Affiliation(s)
- Mattheus H E Wildschut
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Department of Medical Oncology and Hematology, Division of Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Julien Mena
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Cyril Dördelmann
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Marc van Oostrum
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Benjamin D Hale
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jens Settelmeier
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yasmin Festl
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Veronika Lysenko
- Department of Medical Oncology and Hematology, Division of Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Patrick M Schürch
- Department of Medical Oncology and Hematology, Division of Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Alexander Ring
- Department of Medical Oncology and Hematology, Division of Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Yannik Severin
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Michael S Bader
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Patrick G A Pedrioli
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- ETH PHRT Swiss Multi-Omics Center (SMOC), Zurich, Switzerland
| | - Sandra Goetze
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- ETH PHRT Swiss Multi-Omics Center (SMOC), Zurich, Switzerland
| | - Audrey van Drogen
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- ETH PHRT Swiss Multi-Omics Center (SMOC), Zurich, Switzerland
| | - Stefan Balabanov
- Department of Medical Oncology and Hematology, Division of Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Radek C Skoda
- Department of Biomedicine, Experimental Hematology, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Alexandre P A Theocharides
- Department of Medical Oncology and Hematology, Division of Hematology, University Hospital Zurich, Zurich, Switzerland.
| | - Berend Snijder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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3
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Kropivsek K, Kachel P, Goetze S, Wegmann R, Festl Y, Severin Y, Hale BD, Mena J, van Drogen A, Dietliker N, Tchinda J, Wollscheid B, Manz MG, Snijder B. Ex vivo drug response heterogeneity reveals personalized therapeutic strategies for patients with multiple myeloma. Nat Cancer 2023; 4:734-753. [PMID: 37081258 DOI: 10.1038/s43018-023-00544-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 03/17/2023] [Indexed: 04/22/2023]
Abstract
Multiple myeloma (MM) is a plasma cell malignancy defined by complex genetics and extensive patient heterogeneity. Despite a growing arsenal of approved therapies, MM remains incurable and in need of guidelines to identify effective personalized treatments. Here, we survey the ex vivo drug and immunotherapy sensitivities across 101 bone marrow samples from 70 patients with MM using multiplexed immunofluorescence, automated microscopy and deep-learning-based single-cell phenotyping. Combined with sample-matched genetics, proteotyping and cytokine profiling, we map the molecular regulatory network of drug sensitivity, implicating the DNA repair pathway and EYA3 expression in proteasome inhibitor sensitivity and major histocompatibility complex class II expression in the response to elotuzumab. Globally, ex vivo drug sensitivity associated with bone marrow microenvironmental signatures reflecting treatment stage, clonality and inflammation. Furthermore, ex vivo drug sensitivity significantly stratified clinical treatment responses, including to immunotherapy. Taken together, our study provides molecular and actionable insights into diverse treatment strategies for patients with MM.
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Affiliation(s)
- Klara Kropivsek
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paul Kachel
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Sandra Goetze
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Multi-Omics Center, PHRT-CPAC, ETH Zurich, Zurich, Switzerland
| | - Rebekka Wegmann
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yasmin Festl
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Yannik Severin
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Benjamin D Hale
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Julien Mena
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Audrey van Drogen
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Multi-Omics Center, PHRT-CPAC, ETH Zurich, Zurich, Switzerland
| | - Nadja Dietliker
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Joëlle Tchinda
- Pediatric Oncology, Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland
| | - Bernd Wollscheid
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Translational Medicine, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
- Swiss Multi-Omics Center, PHRT-CPAC, ETH Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland.
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4
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Forny P, Bonilla X, Lamparter D, Shao W, Plessl T, Frei C, Bingisser A, Goetze S, van Drogen A, Harshman K, Pedrioli PGA, Howald C, Poms M, Traversi F, Bürer C, Cherkaoui S, Morscher RJ, Simmons L, Forny M, Xenarios I, Aebersold R, Zamboni N, Rätsch G, Dermitzakis ET, Wollscheid B, Baumgartner MR, Froese DS. Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency. Nat Metab 2023; 5:80-95. [PMID: 36717752 PMCID: PMC9886552 DOI: 10.1038/s42255-022-00720-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 12/01/2022] [Indexed: 01/31/2023]
Abstract
Methylmalonic aciduria (MMA) is an inborn error of metabolism with multiple monogenic causes and a poorly understood pathogenesis, leading to the absence of effective causal treatments. Here we employ multi-layered omics profiling combined with biochemical and clinical features of individuals with MMA to reveal a molecular diagnosis for 177 out of 210 (84%) cases, the majority (148) of whom display pathogenic variants in methylmalonyl-CoA mutase (MMUT). Stratification of these data layers by disease severity shows dysregulation of the tricarboxylic acid cycle and its replenishment (anaplerosis) by glutamine. The relevance of these disturbances is evidenced by multi-organ metabolomics of a hemizygous Mmut mouse model as well as through identification of physical interactions between MMUT and glutamine anaplerotic enzymes. Using stable-isotope tracing, we find that treatment with dimethyl-oxoglutarate restores deficient tricarboxylic acid cycling. Our work highlights glutamine anaplerosis as a potential therapeutic intervention point in MMA.
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Affiliation(s)
- Patrick Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ximena Bonilla
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - David Lamparter
- Health 2030 Genome Center, Geneva, Switzerland
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
| | - Wenguang Shao
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Tanja Plessl
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Caroline Frei
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anna Bingisser
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sandra Goetze
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Audrey van Drogen
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Keith Harshman
- Health 2030 Genome Center, Geneva, Switzerland
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
| | - Patrick G A Pedrioli
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | | | - Martin Poms
- Division of Clinical Chemistry, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Florian Traversi
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Céline Bürer
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sarah Cherkaoui
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif, France
| | - Raphael J Morscher
- Division of Oncology and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Luke Simmons
- Division of Child Neurology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Merima Forny
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Ioannis Xenarios
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Agora Center, Lausanne, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Nicola Zamboni
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
| | - Gunnar Rätsch
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Medical Informatics Unit, University Hospital Zurich, Zurich, Switzerland.
- AI Center, ETH Zurich, Zurich, Switzerland.
| | - Emmanouil T Dermitzakis
- Health 2030 Genome Center, Geneva, Switzerland.
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland.
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland.
| | - Bernd Wollscheid
- PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland.
- Institute of Translational Medicine, Department of Health Science and Technology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
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5
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Buljan M, Ciuffa R, van Drogen A, Vichalkovski A, Mehnert M, Rosenberger G, Lee S, Varjosalo M, Pernas LE, Spegg V, Snijder B, Aebersold R, Gstaiger M. Kinase Interaction Network Expands Functional and Disease Roles of Human Kinases. Mol Cell 2020; 79:504-520.e9. [PMID: 32707033 PMCID: PMC7427327 DOI: 10.1016/j.molcel.2020.07.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 02/14/2020] [Accepted: 06/30/2020] [Indexed: 12/30/2022]
Abstract
Protein kinases are essential for signal transduction and control of most cellular processes, including metabolism, membrane transport, motility, and cell cycle. Despite the critical role of kinases in cells and their strong association with diseases, good coverage of their interactions is available for only a fraction of the 535 human kinases. Here, we present a comprehensive mass-spectrometry-based analysis of a human kinase interaction network covering more than 300 kinases. The interaction dataset is a high-quality resource with more than 5,000 previously unreported interactions. We extensively characterized the obtained network and were able to identify previously described, as well as predict new, kinase functional associations, including those of the less well-studied kinases PIM3 and protein O-mannose kinase (POMK). Importantly, the presented interaction map is a valuable resource for assisting biomedical studies. We uncover dozens of kinase-disease associations spanning from genetic disorders to complex diseases, including cancer.
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Affiliation(s)
- Marija Buljan
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Empa, Swiss Federal Laboratories for Materials Science and Technology, 9014 St. Gallen, Switzerland
| | - Rodolfo Ciuffa
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Audrey van Drogen
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Anton Vichalkovski
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Martin Mehnert
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - George Rosenberger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Columbia University Department of Systems Biology, New York, NY 10032, USA
| | - Sohyon Lee
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Lucia Espona Pernas
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Vincent Spegg
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.
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6
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Mehnert M, Ciuffa R, Frommelt F, Uliana F, van Drogen A, Ruminski K, Gstaiger M, Aebersold R. Multi-layered proteomic analyses decode compositional and functional effects of cancer mutations on kinase complexes. Nat Commun 2020; 11:3563. [PMID: 32678104 PMCID: PMC7366679 DOI: 10.1038/s41467-020-17387-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/26/2020] [Indexed: 01/09/2023] Open
Abstract
Rapidly increasing availability of genomic data and ensuing identification of disease associated mutations allows for an unbiased insight into genetic drivers of disease development. However, determination of molecular mechanisms by which individual genomic changes affect biochemical processes remains a major challenge. Here, we develop a multilayered proteomic workflow to explore how genetic lesions modulate the proteome and are translated into molecular phenotypes. Using this workflow we determine how expression of a panel of disease-associated mutations in the Dyrk2 protein kinase alter the composition, topology and activity of this kinase complex as well as the phosphoproteomic state of the cell. The data show that altered protein-protein interactions caused by the mutations are associated with topological changes and affected phosphorylation of known cancer driver proteins, thus linking Dyrk2 mutations with cancer-related biochemical processes. Overall, we discover multiple mutation-specific functionally relevant changes, thus highlighting the extensive plasticity of molecular responses to genetic lesions.
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Affiliation(s)
- Martin Mehnert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
| | - Rodolfo Ciuffa
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Fabian Frommelt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Audrey van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
| | - Kilian Ruminski
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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7
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Mauracher AA, Eekels JJM, Woytschak J, van Drogen A, Bosch A, Prader S, Felber M, Heeg M, Opitz L, Trück J, Schroeder S, Adank E, Klocperk A, Haralambieva E, Zimmermann D, Tantou S, Kotsonis K, Stergiou A, Kanariou MG, Ehl S, Boyman O, Sediva A, Renella R, Schmugge M, Vavassori S, Pachlopnik Schmid J. Erythropoiesis defect observed in STAT3 GOF patients with severe anemia. J Allergy Clin Immunol 2019; 145:1297-1301. [PMID: 31857100 DOI: 10.1016/j.jaci.2019.11.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 01/29/2023]
Affiliation(s)
- Andrea A Mauracher
- Division of Immunology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Julia J M Eekels
- Division of Haematology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Janine Woytschak
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Audrey van Drogen
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Alessandra Bosch
- Division of Haematology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Seraina Prader
- Division of Immunology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Matthias Felber
- Division of Immunology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Division of Haematology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Maximillian Heeg
- Institute of Immunodeficiency and Center for Chronic Immunodeficiency, University Medical Center, Freiburg, Germany
| | - Lennart Opitz
- Division of Immunology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland; Functional Genomics Center Zürich, University of Zurich, ETH Zurich, Zurich, Switzerland
| | - Johannes Trück
- Division of Immunology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland
| | - Silke Schroeder
- Division of Rheumatology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Eva Adank
- Division of Rheumatology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Adam Klocperk
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Eugenia Haralambieva
- Department of Pathology University and University Hospital Zurich, Zurich, Switzerland
| | - Dieter Zimmermann
- Department of Pathology University and University Hospital Zurich, Zurich, Switzerland
| | - Sofia Tantou
- First Department of Paediatrics, Aghia Sophia Children's Hospital, Athens, Greece
| | - Kosmas Kotsonis
- First Department of Paediatrics, Aghia Sophia Children's Hospital, Athens, Greece
| | - Aikaterini Stergiou
- First Department of Paediatrics, Aghia Sophia Children's Hospital, Athens, Greece
| | - Maria G Kanariou
- First Department of Paediatrics, Aghia Sophia Children's Hospital, Athens, Greece
| | - Stephan Ehl
- Institute of Immunodeficiency and Center for Chronic Immunodeficiency, University Medical Center, Freiburg, Germany
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anna Sediva
- Department of Immunology, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Raffaele Renella
- Pediatric Hematology-Oncology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Markus Schmugge
- Division of Haematology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Stefano Vavassori
- Division of Immunology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Jana Pachlopnik Schmid
- Division of Immunology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland; University of Zurich, Zurich, Switzerland.
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8
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Bertran MT, Mouilleron S, Zhou Y, Bajaj R, Uliana F, Kumar GS, van Drogen A, Lee R, Banerjee JJ, Hauri S, O'Reilly N, Gstaiger M, Page R, Peti W, Tapon N. ASPP proteins discriminate between PP1 catalytic subunits through their SH3 domain and the PP1 C-tail. Nat Commun 2019; 10:771. [PMID: 30770806 PMCID: PMC6377682 DOI: 10.1038/s41467-019-08686-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/25/2019] [Indexed: 11/26/2022] Open
Abstract
Serine/threonine phosphatases such as PP1 lack substrate specificity and associate with a large array of targeting subunits to achieve the requisite selectivity. The tumour suppressor ASPP (apoptosis-stimulating protein of p53) proteins associate with PP1 catalytic subunits and are implicated in multiple functions from transcriptional regulation to cell junction remodelling. Here we show that Drosophila ASPP is part of a multiprotein PP1 complex and that PP1 association is necessary for several in vivo functions of Drosophila ASPP. We solve the crystal structure of the human ASPP2/PP1 complex and show that ASPP2 recruits PP1 using both its canonical RVxF motif, which binds the PP1 catalytic domain, and its SH3 domain, which engages the PP1 C-terminal tail. The ASPP2 SH3 domain can discriminate between PP1 isoforms using an acidic specificity pocket in the n-Src domain, providing an exquisite mechanism where multiple motifs are used combinatorially to tune binding affinity to PP1.
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Affiliation(s)
- M Teresa Bertran
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stéphane Mouilleron
- Structural Biology - Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - Yanxiang Zhou
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Rakhi Bajaj
- Chemistry and Biochemistry Department, University of Arizona, 1041 E. Lowell Street, Biosciences West, 517, Tucson, AZ, 85721, USA
| | - Federico Uliana
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Ganesan Senthil Kumar
- Chemistry and Biochemistry Department, University of Arizona, 1041 E. Lowell Street, Biosciences West, 517, Tucson, AZ, 85721, USA
| | - Audrey van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Rebecca Lee
- Structural Biology - Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Jennifer J Banerjee
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Simon Hauri
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Nicola O'Reilly
- Peptide Chemistry Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093, Zürich, Switzerland
| | - Rebecca Page
- Chemistry and Biochemistry Department, University of Arizona, 1041 E. Lowell Street, Biosciences West, 517, Tucson, AZ, 85721, USA
| | - Wolfgang Peti
- Chemistry and Biochemistry Department, University of Arizona, 1041 E. Lowell Street, Biosciences West, 517, Tucson, AZ, 85721, USA
| | - Nicolas Tapon
- Apoptosis and Proliferation Control Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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9
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Heusel M, Bludau I, Rosenberger G, Hafen R, Frank M, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R. Complex-centric proteome profiling by SEC-SWATH-MS. Mol Syst Biol 2019; 15:e8438. [PMID: 30642884 PMCID: PMC6346213 DOI: 10.15252/msb.20188438] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Proteins are major effectors and regulators of biological processes that can elicit multiple functions depending on their interaction with other proteins. The organization of proteins into macromolecular complexes and their quantitative distribution across these complexes is, therefore, of great biological and clinical significance. In this paper, we describe an integrated experimental and computational technique to quantify hundreds of protein complexes in a single operation. The method consists of size exclusion chromatography (SEC) to fractionate native protein complexes, SWATH/DIA mass spectrometry to precisely quantify the proteins in each SEC fraction, and the computational framework CCprofiler to detect and quantify protein complexes by error‐controlled, complex‐centric analysis using prior information from generic protein interaction maps. Our analysis of the HEK293 cell line proteome delineates 462 complexes composed of 2,127 protein subunits. The technique identifies novel sub‐complexes and assembly intermediates of central regulatory complexes while assessing the quantitative subunit distribution across them. We make the toolset CCprofiler freely accessible and provide a web platform, SECexplorer, for custom exploration of the HEK293 proteome modularity.
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Affiliation(s)
- Moritz Heusel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Molecular and Translational Biomedicine of the Competence Center Personalized Medicine UZH/ETH, Zurich, Switzerland
| | - Isabell Bludau
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Robin Hafen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Department of Computer Science, ETH Zurich, Zurich, Switzerland
| | - Max Frank
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Audrey van Drogen
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Matthias Gstaiger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland .,Faculty of Science, University of Zurich, Zurich, Switzerland
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10
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Yadav L, Tamene F, Göös H, van Drogen A, Katainen R, Aebersold R, Gstaiger M, Varjosalo M. Systematic Analysis of Human Protein Phosphatase Interactions and Dynamics. Cell Syst 2017; 4:430-444.e5. [PMID: 28330616 DOI: 10.1016/j.cels.2017.02.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/10/2017] [Accepted: 02/15/2017] [Indexed: 10/19/2022]
Abstract
Coordinated activities of protein kinases and phosphatases ensure phosphorylation homeostasis, which, when perturbed, can instigate diseases, including cancer. Yet, in contrast to kinases, much less is known about protein phosphatase functions and their interactions and complexes. Here, we used quantitative affinity proteomics to assay protein-protein interactions for 54 phosphatases distributed across the three major protein phosphatase families, with additional analysis of their 12 co-factors. We identified 838 high-confidence interactions, of which 631, to our knowledge, have not been reported before. We show that inhibiting the activity of phosphatases PP1 and PP2A by okadaic acid disrupts their specific interactions, supporting the potential of therapeutics that target these proteins. Additional analyses revealed candidate physical and functional interaction links to phosphatase-based regulation of several signaling pathways and to human cancer. Our study provides an initial glimpse of the protein interaction landscape of phosphatases and their functions in cellular regulation.
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Affiliation(s)
- Leena Yadav
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Helka Göös
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland
| | - Audrey van Drogen
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Riku Katainen
- Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki 00014, Finland
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Matthias Gstaiger
- Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki 00014, Finland.
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11
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Hauri S, Wepf A, van Drogen A, Varjosalo M, Tapon N, Aebersold R, Gstaiger M. Interaction proteome of human Hippo signaling: modular control of the co-activator YAP1. Mol Syst Biol 2013; 9:713. [PMID: 24366813 PMCID: PMC4019981 DOI: 10.1002/msb.201304750] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 11/13/2013] [Accepted: 11/20/2013] [Indexed: 12/11/2022] Open
Abstract
Tissue homeostasis is controlled by signaling systems that coordinate cell proliferation, cell growth and cell shape upon changes in the cellular environment. Deregulation of these processes is associated with human cancer and can occur at multiple levels of the underlying signaling systems. To gain an integrated view on signaling modules controlling tissue growth, we analyzed the interaction proteome of the human Hippo pathway, an established growth regulatory signaling system. The resulting high-resolution network model of 480 protein-protein interactions among 270 network components suggests participation of Hippo pathway components in three distinct modules that all converge on the transcriptional co-activator YAP1. One of the modules corresponds to the canonical Hippo kinase cassette whereas the other two both contain Hippo components in complexes with cell polarity proteins. Quantitative proteomic data suggests that complex formation with cell polarity proteins is dynamic and depends on the integrity of cell-cell contacts. Collectively, our systematic analysis greatly enhances our insights into the biochemical landscape underlying human Hippo signaling and emphasizes multifaceted roles of cell polarity complexes in Hippo-mediated tissue growth control.
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Affiliation(s)
- Simon Hauri
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Competence Center for Systems Physiology and Metabolic DiseasesETH ZürichZürichSwitzerland
| | | | | | - Markku Varjosalo
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
| | - Nic Tapon
- Cancer Research UKLondon Research InstituteLondonUK
| | - Ruedi Aebersold
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Competence Center for Systems Physiology and Metabolic DiseasesETH ZürichZürichSwitzerland
- Faculty of ScienceUniversity of ZürichZürichSwitzerland
| | - Matthias Gstaiger
- Institute of Molecular Systems BiologyETH ZürichZürichSwitzerland
- Competence Center for Systems Physiology and Metabolic DiseasesETH ZürichZürichSwitzerland
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12
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Varjosalo M, Sacco R, Stukalov A, van Drogen A, Planyavsky M, Hauri S, Aebersold R, Bennett KL, Colinge J, Gstaiger M, Superti-Furga G. Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS. Nat Methods 2013; 10:307-14. [DOI: 10.1038/nmeth.2400] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 01/29/2013] [Indexed: 12/19/2022]
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