1
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Jiang X, Yeung D, Liu Y, Spicer V, Afshari H, Lao Y, Lin F, Krokhin O, Zahedi RP. Accelerating Proteomics Using Broad Specificity Proteases. J Proteome Res 2024; 23:1360-1369. [PMID: 38457694 DOI: 10.1021/acs.jproteome.3c00852] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2024]
Abstract
Trypsin is the gold-standard protease in bottom-up proteomics, but many sequence stretches of the proteome are inaccessible to trypsin and standard LC-MS approaches. Thus, multienzyme strategies are used to maximize sequence coverage in post-translational modification profiling. We present fast and robust SP3- and STRAP-based protocols for the broad-specificity proteases subtilisin, proteinase K, and thermolysin. All three enzymes are remarkably fast, producing near-complete digests in 1-5 min, and cost 200-1000× less than proteomics-grade trypsin. Using FragPipe resolved a major challenge by drastically reducing the duration of the required "unspecific" searches. In-depth analyses of proteinase K, subtilisin, and thermolysin Jurkat digests identified 7374, 8178, and 8753 unique proteins with average sequence coverages of 21, 29, and 37%, including 10,000s of amino acids not reported in PeptideAtlas' >2400 experiments. While we could not identify distinct cleavage patterns, machine learning could distinguish true protease products from random cleavages, potentially enabling the prediction of cleavage products. Finally, proteinase K, subtilisin, and thermolysin enabled label-free quantitation of 3111, 3659, and 4196 unique Jurkat proteins, which in our hands is comparable to trypsin. Our data demonstrate that broad-specificity proteases enable quantitative proteomics of uncharted areas of the proteome. Their fast kinetics may allow "on-the-fly" digestion of samples in the future.
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Affiliation(s)
- Xuehui Jiang
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Darien Yeung
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Yang Liu
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Havva Afshari
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
| | - Ying Lao
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
| | - Francis Lin
- Department of Physics and Astronomy, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Oleg Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3A 1R9, Canada
| | - René P Zahedi
- Manitoba Centre for Proteomics and Systems Biology, Health Science Centre, Winnipeg, Manitoba R3E 3P4, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3E 0J9, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3A 1R9, Canada
- Paul Albrechtsen Research Institute, Cancer Care Manitoba, Winnipeg, Manitoba R3E 0 V9, Canada
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2
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Luo VM, Shen C, Worme S, Bhagrath A, Simo-Cheyou E, Findlay S, Hébert S, Wai Lam Poon W, Aryanpour Z, Zhang T, Zahedi RP, Boulais J, Buchwald ZS, Borchers CH, Côté JF, Kleinman CL, Mandl JN, Orthwein A. The Deubiquitylase Otub1 Regulates the Chemotactic Response of Splenic B Cells by Modulating the Stability of the γ-Subunit Gng2. Mol Cell Biol 2024; 44:1-16. [PMID: 38270191 PMCID: PMC10829841 DOI: 10.1080/10985549.2023.2290434] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/28/2023] [Indexed: 01/26/2024] Open
Abstract
The ubiquitin proteasome system performs the covalent attachment of lysine 48-linked polyubiquitin chains to substrate proteins, thereby targeting them for degradation, while deubiquitylating enzymes (DUBs) reverse this process. This posttranslational modification regulates key features both of innate and adaptative immunity, including antigen presentation, protein homeostasis and signal transduction. Here we show that loss of one of the most highly expressed DUBs, Otub1, results in changes in murine splenic B cell subsets, leading to a significant increase in marginal zone and transitional B cells and a concomitant decrease in follicular B cells. We demonstrate that Otub1 interacts with the γ-subunit of the heterotrimeric G protein, Gng2, and modulates its ubiquitylation status, thereby controlling Gng2 stability. Proximal mapping of Gng2 revealed an enrichment in partners associated with chemokine signaling, actin cytoskeleton and cell migration. In line with these findings, we show that Otub1-deficient B cells exhibit greater Ca2+ mobilization, F-actin polymerization and chemotactic responsiveness to Cxcl12, Cxcl13 and S1P in vitro, which manifests in vivo as altered localization of B cells within the spleen. Together, our data establishes Otub1 as a novel regulator of G-protein coupled receptor signaling in B cells, regulating their differentiation and positioning in the spleen.
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Affiliation(s)
- Vincent M. Luo
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Connie Shen
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- McGill Research Centre for Complex Traits, McGill University, Montréal, Québec, Canada
| | - Samantha Worme
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Aanya Bhagrath
- McGill Research Centre for Complex Traits, McGill University, Montréal, Québec, Canada
- Department of Physiology, McGill University, Montréal, Québec, Canada
| | - Estelle Simo-Cheyou
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Steven Findlay
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Steven Hébert
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - William Wai Lam Poon
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Zahra Aryanpour
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - Thomas Zhang
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
| | - René P. Zahedi
- Manitoba Centre for Proteomics & Systems Biology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- CancerCare Manitoba Research Institute, Winnipeg, Manitoba, Canada
| | - Jonathan Boulais
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Québec, Canada
| | - Zachary S. Buchwald
- Department of Radiation Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Christoph H. Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montréal, Québec, Canada
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Pathology, McGill University, Montreal, Québec, Canada
| | - Jean-Francois Côté
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, Québec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Québec, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, Québec, Canada
- Département de Médecine (Programmes de Biologie Moléculaire), Université de Montréal, Montreal, Québec, Canada
| | - Claudia L. Kleinman
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Judith N. Mandl
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- McGill Research Centre for Complex Traits, McGill University, Montréal, Québec, Canada
- Department of Physiology, McGill University, Montréal, Québec, Canada
| | - Alexandre Orthwein
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
- Department of Radiation Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
- Gerald Bronfman Department of Oncology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, Québec, Canada
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Dufault B, LeDuc RD, Zahedi RP. How to maximize power for differential expression analysis in discovery omics through experimental design. Expert Rev Proteomics 2023; 20:299-301. [PMID: 37990821 DOI: 10.1080/14789450.2023.2287054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/11/2023] [Indexed: 11/23/2023]
Affiliation(s)
- Brenden Dufault
- George & Fay Yee Centre for Healthcare Innovation, University of Manitoba, Winnipeg, MB, Canada
| | - Richard D LeDuc
- Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - René P Zahedi
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
- Paul Albrechtsen Research Institute, Cancer Care Manitoba, Winnipeg, MB, Canada
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Reboucas P, Fillebeen C, Botta A, Cleverdon R, Steele AP, Richard V, Zahedi RP, Borchers CH, Burelle Y, Hawke TJ, Pantopoulos K, Sweeney G. Discovery-Based Proteomics Identify Skeletal Muscle Mitochondrial Alterations as an Early Metabolic Defect in a Mouse Model of β-Thalassemia. Int J Mol Sci 2023; 24:ijms24054402. [PMID: 36901833 PMCID: PMC10002226 DOI: 10.3390/ijms24054402] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
Although metabolic complications are common in thalassemia patients, there is still an unmet need to better understand underlying mechanisms. We used unbiased global proteomics to reveal molecular differences between the th3/+ mouse model of thalassemia and wild-type control animals focusing on skeletal muscles at 8 weeks of age. Our data point toward a significantly impaired mitochondrial oxidative phosphorylation. Furthermore, we observed a shift from oxidative fibre types toward more glycolytic fibre types in these animals, which was further supported by larger fibre-type cross-sectional areas in the more oxidative type fibres (type I/type IIa/type IIax hybrid). We also observed an increase in capillary density in th3/+ mice, indicative of a compensatory response. Western blotting for mitochondrial oxidative phosphorylation complex proteins and PCR analysis of mitochondrial genes indicated reduced mitochondrial content in the skeletal muscle but not the hearts of th3/+ mice. The phenotypic manifestation of these alterations was a small but significant reduction in glucose handling capacity. Overall, this study identified many important alterations in the proteome of th3/+ mice, amongst which mitochondrial defects leading to skeletal muscle remodelling and metabolic dysfunction were paramount.
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Affiliation(s)
| | - Carine Fillebeen
- Lady Davis Institute for Medical Research, Department of Medicine, McGill University, Montreal, QC H3T 1E2, Canada
| | - Amy Botta
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
| | - Riley Cleverdon
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Alexandra P. Steele
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Vincent Richard
- Lady Davis Institute for Medical Research, Department of Medicine, McGill University, Montreal, QC H3T 1E2, Canada
- Segal Cancer Proteomics Centre, Lady Davis Institute, Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
| | - René P. Zahedi
- Lady Davis Institute for Medical Research, Department of Medicine, McGill University, Montreal, QC H3T 1E2, Canada
- Segal Cancer Proteomics Centre, Lady Davis Institute, Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
- Manitoba Centre for Proteomics & Systems Biology, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Christoph H. Borchers
- Lady Davis Institute for Medical Research, Department of Medicine, McGill University, Montreal, QC H3T 1E2, Canada
- Segal Cancer Proteomics Centre, Lady Davis Institute, Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H3T 1E2, Canada
- Manitoba Centre for Proteomics & Systems Biology, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Yan Burelle
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
| | - Thomas J. Hawke
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Kostas Pantopoulos
- Lady Davis Institute for Medical Research, Department of Medicine, McGill University, Montreal, QC H3T 1E2, Canada
| | - Gary Sweeney
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada
- Correspondence: ; Tel.: +1-416-736-2100 (ext. 66635)
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5
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Yeung D, Spicer V, Zahedi RP, Krokhin O. Exploring the variable space of shallow machine learning models for reversed-phase retention time prediction. Comput Struct Biotechnol J 2023; 21:2446-2453. [PMID: 37090433 PMCID: PMC10113922 DOI: 10.1016/j.csbj.2023.02.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/24/2023] [Accepted: 02/24/2023] [Indexed: 03/02/2023] Open
Abstract
Peptide retention time (RT) prediction algorithms are tools to study and identify the physicochemical properties that drive the peptide-sorbent interaction. Traditional RT algorithms use multiple linear regression with manually curated parameters to determine the degree of direct contribution for each parameter and improvements to RT prediction accuracies relied on superior feature engineering. Deep learning led to a significant increase in RT prediction accuracy and automated feature engineering via chaining multiple learning modules. However, the significance and the identity of these extracted variables are not well understood due to the inherent complexity when interpreting "relationships-of-relationships" found in deep learning variables. To achieve both accuracy and interpretability simultaneously, we isolated individual modules used in deep learning and the isolated modules are the shallow learners employed for RT prediction in this work. Using a shallow convolutional neural network (CNN) and gated recurrent unit (GRU), we find that the spatial features obtained via the CNN correlate with real-world physicochemical properties namely cross-collisional sections (CCS) and variations of assessable surface area (ASA). Furthermore, we determined that the discovered parameters are "micro-coefficients" that contribute to the "macro-coefficient" - hydrophobicity. Manually embedding CCS and the variations of ASA to the GRU model yielded an R2 = 0.981 using only 525 variables and can represent 88% of the ∼110,000 tryptic peptides used in our dataset. This work highlights the feature discovery process of our shallow learners can achieve beyond traditional RT models in performance and have better interpretability when compared with the deep learning RT algorithms found in the literature.
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Phan V, Hathazi D, Preuße C, Czech A, Freier E, Shema G, Zahedi RP, Roos A. Molecular mechanisms in chloroquine-exposed muscle cells elucidated by combined proteomic and microscopic studies. Neuropathol Appl Neurobiol 2023; 49:e12877. [PMID: 36633103 DOI: 10.1111/nan.12877] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/15/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023]
Abstract
OBJECTIVES Chloroquine (CQ) is an antimalarial drug with a growing number of applications as recently demonstrated in attempts to treat Covid-19. For decades, it has been well known that skeletal and cardiac muscle cells might display vulnerability against CQ exposure resulting in the clinical manifestation of a CQ-induced myopathy. In line with the known effect of CQ on inhibition of the lysosomal function and thus cellular protein clearance, the build-up of autophagic vacuoles along with protein aggregates is a histological hallmark of the disease. Given that protein targets of the perturbed proteostasis are still not fully discovered, we applied different proteomic and immunological-based studies to improve the current understanding of the biochemical nature of CQ-myopathy. METHODS To gain a comprehensive understanding of the molecular pathogenesis of this acquired myopathy and to define proteins targets as well as pathophysiological processes beyond impaired proteolysis, utilising CQ-treated C2C12 cells and muscle biopsies derived from CQ-myopathy patients, we performed different proteomic approaches and Coherent Anti-Stokes Raman Scattering (CARS) microscopy, in addition to immunohistochemical studies. RESULTS Our combined studies confirmed an impact of CQ-exposure on proper protein processing/folding and clearance, highlighted changes in the interactome of p62, a known aggregation marker and hereby identified the Rett syndrome protein MeCP2 as being affected. Moreover, our approach revealed-among others-a vulnerability of the extracellular matrix, cytoskeleton and lipid homeostasis. CONCLUSION We demonstrated that CQ exposure (secondarily) impacts biological processes beyond lysosomal function and linked a variety of proteins with known roles in the manifestation of other neuromuscular diseases.
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Affiliation(s)
- Vietxuan Phan
- Leibniz Institut für Analytische Wissenschaften -ISAS- e.V., Dortmund, Germany
| | - Denisa Hathazi
- Leibniz Institut für Analytische Wissenschaften -ISAS- e.V., Dortmund, Germany.,Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Corinna Preuße
- Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Berlin, Germany.,Department of Neurology with Institute for Translational Neurology, University Hospital Münster, Münster, Germany
| | - Artur Czech
- Leibniz Institut für Analytische Wissenschaften -ISAS- e.V., Dortmund, Germany
| | - Erik Freier
- Leibniz Institut für Analytische Wissenschaften -ISAS- e.V., Dortmund, Germany
| | - Gerta Shema
- Leibniz Institut für Analytische Wissenschaften -ISAS- e.V., Dortmund, Germany
| | - René P Zahedi
- Leibniz Institut für Analytische Wissenschaften -ISAS- e.V., Dortmund, Germany.,Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, Department of Biochemistry and Medical Genetics, CancerCare Manitoba Research Institute, University of Manitoba, Winnipeg, MB, Canada
| | - Andreas Roos
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, Centre for Neuromuscular Disorders in Children, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
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7
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Preston SEJ, Richard VR, Del Rincón SV, Borchers CH, Zahedi RP. Proteomic Assessment of the Murine Mammary Gland Extracellular Matrix. Methods Mol Biol 2023; 2614:261-271. [PMID: 36587130 DOI: 10.1007/978-1-0716-2914-7_16] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The extracellular matrix (ECM) is a molecular scaffold mainly comprising fibrous proteins, glycoproteins, proteoglycans, and polysaccharides. Aside from acting as a structural support, the ECM's composition dictates cell-matrix interactions at the biochemical and biophysical level. In the context of cancer, the ECM is a critical component of the tumor microenvironment (TME) and dysregulation of its deposition and remodelling has been shown to promote tumor onset, progression, and metastasis. Here, we describe a robust protocol for the isolation and subsequent proteomic analysis of the ECM of murine mammary glands, for downstream assays studying the role of the ECM in breast cancer. The protocol yields sufficient protein amounts to enable not only the global quantitation of protein expression but furthermore the enrichment and quantitative analysis of post-translationally modified peptides to study aberrant signalling.
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Affiliation(s)
- Samuel E J Preston
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.,Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Sonia V Del Rincón
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.,Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Christoph H Borchers
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada. .,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada. .,Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada. .,Department of Pathology, Jewish General Hospital, McGill University, Montreal, Canada. .,Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada.
| | - René P Zahedi
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada. .,Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
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8
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Gaither C, Popp R, Richard VR, Zahedi RP, Borchers CH. Offline Peptide Fractionation and Parallel Reaction Monitoring MS for the Quantitation of Low-Abundance Plasma Proteins. Methods Mol Biol 2023; 2628:353-364. [PMID: 36781797 DOI: 10.1007/978-1-0716-2978-9_23] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Mass spectrometry (MS)-based protein quantitation is an attractive means for research and diagnostics due to its high specificity, precision, sensitivity, versatility, and the ability to develop multiplexed assays for the "absolute" quantitation of virtually any protein target. However, due to the large dynamic range of protein concentrations in blood, high abundance proteins in blood plasma hinder the detectability and quantification of lower-abundance proteins which are often relevant in the context of different diseases. Here we outline a streamlined method involving offline high-pH reversed-phase fractionation of human plasma samples followed by the quantitative analysis of specific fractions using nanoLC-parallel reaction monitoring (PRM) on a Q Exactive Plus mass spectrometer for peptide detection and quantitation with increased sensitivity. Because we use a set of synthetic peptide standards, we can more efficiently determine the precise retention times of the target peptides in the first-dimensional separation and specifically collect eluting fractions of interest for the subsequent targeted MS quantitation, making the analysis faster and easier. An eight-point standard curve was generated by serial dilution of a mixture of previously validated unlabeled ("light") synthetic peptides of interest at known concentrations. The corresponding heavy stable-isotope-labeled standard (SIS) analogues were used as normalizers to account for losses during sample processing and analysis. Using this method, we were able to improve the sensitivity of plasma protein quantitation by up to 50-fold compared to using nanoLC-PRM alone.
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Affiliation(s)
| | | | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - René P Zahedi
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, QC, Canada.
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.
- Department of Pathology, McGill University, Montreal, QC, Canada.
- Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.
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9
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Jiang X, Lao Y, Spicer V, Zahedi RP. Improved Coverage of the N-Terminome by Combining ChaFRADIC with Alternative Proteases. Methods Mol Biol 2023; 2718:99-110. [PMID: 37665456 DOI: 10.1007/978-1-0716-3457-8_6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Many proteolytic cleavage events cannot be covered with conventional trypsin-based N-terminomics workflows. These typically involve the derivatization of protein N-termini and Lys residues as an initial step, such that trypsin will cleave C-terminal of arginine but not lysine residues (ArgC-like cleavage). From 20,422 reviewed human protein sequences in Uniprot, 3597 have known N-terminal signal peptides. An in silico ArgC-like digestion of the corresponding 3597 mature protein sequences reveals that-even for these well-known and well-studied proteolytic events-trypsin-based N-terminomics workflows may miss up to 50% of signaling cleavage events as the corresponding neo-N-terminal peptides will have an unfavorable length of <7 (875 peptides) or >30 (911 peptides) amino acids. In this chapter, we provide a protocol that can be applied to all kinds of samples to improve access to this "inaccessible" N-terminome, by making use of the alternative, broad-specificity protease subtilisin for fast and reproducible digestion of proteins.
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Affiliation(s)
- Xuehui Jiang
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Ying Lao
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada
| | - René P Zahedi
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada.
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada.
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
- CancerCare Manitoba Research Institute, Winnipeg, MB, Canada.
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Guettsches AK, Meyer N, Zahedi RP, Evangelista T, Muentefering T, Ruck T, Lacene E, Heute C, Gonczarowska-Jorge H, Schoser B, Krause S, Hentschel A, Vorgerd M, Roos A. FYCO1 Increase and Effect of Arimoclomol-Treatment in Human VCP-Pathology. Biomedicines 2022; 10:biomedicines10102443. [PMID: 36289705 PMCID: PMC9598455 DOI: 10.3390/biomedicines10102443] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
Dominant VCP–mutations cause a variety of neurological manifestations including inclusion body myopathy with early–onset Paget disease and frontotemporal dementia 1 (IBMPFD). VCP encodes a ubiquitously expressed multifunctional protein that is a member of the AAA+ protein family, implicated in multiple cellular functions ranging from organelle biogenesis to ubiquitin–dependent protein degradation. The latter function accords with the presence of protein aggregates in muscle biopsy specimens derived from VCP–patients. Studying the proteomic signature of VCP–mutant fibroblasts, we identified a (pathophysiological) increase of FYCO1, a protein involved in autophagosome transport. We confirmed this finding applying immunostaining also in muscle biopsies derived from VCP–patients. Treatment of fibroblasts with arimoclomol, an orphan drug thought to restore physiologic cellular protein repair pathways, ameliorated cellular cytotoxicity in VCP–patient derived cells. This finding was accompanied by increased abundance of proteins involved in immune response with a direct impact on protein clearaqnce as well as by elevation of pro–survival proteins as unravelled by untargeted proteomic profiling. Hence, the combined results of our study reveal a dysregulation of FYCO1 in the context of VCP–etiopathology, highlight arimoclomol as a potential drug and introduce proteins targeted by the pre–clinical testing of this drug in fibroblasts.
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Affiliation(s)
- Anne-Katrin Guettsches
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr University Bochum, 44789 Bochum, Germany
- Correspondence: (A.-K.G.); (A.R.); Tel.: +49-234-3020 (A.-K.G.); +49-201-723-6570 (A.R.)
| | - Nancy Meyer
- Department of Neuropediatrics and Neuromuscular Centre for Children and Adolescents, Center for Translational Neuro- and Behavioral Sciences, University Duisburg–Essen, 45147 Essen, Germany
| | - René P. Zahedi
- Manitoba Centre for Proteomics and Systems Biology, 715 McDermot Aveue, Winnipeg, MB R3E 3P4, Canada
- Department of Internal Medicine, University of Manitoba, 820 Sherbrook Street, Winnipeg, MB R3A 1R9, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, 745 Bannatyne Avenue, Winnipeg, MB R3E 0J9, Canada
- Leibniz–Institut für Analytische Wissenschaften—ISAS—e.V, 44227 Dortmund, Germany
| | - Teresinha Evangelista
- Nord/Est/Ile–de–France Neuromuscular Reference Center, Unité de Morphologie Neuromusculaire, Institute of Myology, Pitié–Salpêtrière Hospital, APHP, Sorbonne University, 75013 Paris, France
| | - Thomas Muentefering
- Department of Neurology, Medical Faculty, Heinrich–Heine–University Düsseldorf, 40225 Düsseldorf, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty, Heinrich–Heine–University Düsseldorf, 40225 Düsseldorf, Germany
| | - Emmanuelle Lacene
- Nord/Est/Ile–de–France Neuromuscular Reference Center, Unité de Morphologie Neuromusculaire, Institute of Myology, Pitié–Salpêtrière Hospital, APHP, Sorbonne University, 75013 Paris, France
| | - Christoph Heute
- Department of Neuropediatrics and Neuromuscular Centre for Children and Adolescents, Center for Translational Neuro- and Behavioral Sciences, University Duisburg–Essen, 45147 Essen, Germany
| | | | - Benedikt Schoser
- Department of Neurology, Friedrich–Baur–Institute, Ludwig–Maximilians–University Munich, Ziemssenstr. 1a, 80336 Munich, Germany
| | - Sabine Krause
- Department of Neurology, Friedrich–Baur–Institute, Ludwig–Maximilians–University Munich, Ziemssenstr. 1a, 80336 Munich, Germany
| | - Andreas Hentschel
- Leibniz–Institut für Analytische Wissenschaften—ISAS—e.V, 44227 Dortmund, Germany
| | - Matthias Vorgerd
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr University Bochum, 44789 Bochum, Germany
| | - Andreas Roos
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr University Bochum, 44789 Bochum, Germany
- Department of Neuropediatrics and Neuromuscular Centre for Children and Adolescents, Center for Translational Neuro- and Behavioral Sciences, University Duisburg–Essen, 45147 Essen, Germany
- Children’s Hospital of Eastern Ontario (CHEO) Research Institute, Ottawa, ON K1H 5B2, Canada
- Correspondence: (A.-K.G.); (A.R.); Tel.: +49-234-3020 (A.-K.G.); +49-201-723-6570 (A.R.)
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11
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Richard VR, Gaither C, Popp R, Chaplygina D, Brzhozovskiy A, Kononikhin A, Mohammed Y, Zahedi RP, Nikolaev EN, Borchers CH. Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning. Mol Cell Proteomics 2022; 21:100277. [PMID: 35931319 PMCID: PMC9345792 DOI: 10.1016/j.mcpro.2022.100277] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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] [Received: 11/25/2021] [Revised: 07/05/2022] [Accepted: 07/27/2022] [Indexed: 01/18/2023] Open
Abstract
The recent surge of coronavirus disease 2019 (COVID-19) hospitalizations severely challenges healthcare systems around the globe and has increased the demand for reliable tests predictive of disease severity and mortality. Using multiplexed targeted mass spectrometry assays on a robust triple quadrupole MS setup which is available in many clinical laboratories, we determined the precise concentrations of hundreds of proteins and metabolites in plasma from hospitalized COVID-19 patients. We observed a clear distinction between COVID-19 patients and controls and, strikingly, a significant difference between survivors and nonsurvivors. With increasing length of hospitalization, the survivors' samples showed a trend toward normal concentrations, indicating a potential sensitive readout of treatment success. Building a machine learning multi-omic model that considers the concentrations of 10 proteins and five metabolites, we could predict patient survival with 92% accuracy (area under the receiver operating characteristic curve: 0.97) on the day of hospitalization. Hence, our standardized assays represent a unique opportunity for the early stratification of hospitalized COVID-19 patients.
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Key Words
- acd, acid citrate dextrose
- acn, acetonitrile
- auc, area under the receiver operating characteristic curve
- bqc19, biobanque quebecoise de la covid-19
- bsa, bovine serum albumin covid-19
- cptac, clinical proteomic tumor analysis consortium
- dtt, dithiothreitol
- fa, formic acid
- fdr, false discovery rate
- icu, intensive care unit
- lc/mrm-ms, liquid chromatography/multiple reaction monitoring mass spectrometry
- lc-ms, liquid chromatography-mass spectrometry
- lloq, lower limit of quantitation
- lysopc, lysophosphatidylcholine
- maldi, matrix-assisted laser desorption ionization
- meoh, methanol
- ms, mass spectrometry
- pbs, phosphatase buffered saline
- pcr, polymerase chain reaction
- pitc, phenylisothiocyanate
- qc, quality control
- rp-uhplc, reversed phase ultrahigh performance liquid chromatography
- sis, stable-isotope-labeled internal standard
- spe, solid-phase extraction
- svm, support vector machine
- trishcl, tris (hydroxymethyl) aminomethane hydrochloride
- uniprot, the universal protein resource
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Affiliation(s)
- Vincent R. Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada
| | | | | | - Daria Chaplygina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexander Brzhozovskiy
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey Kononikhin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands,Genome BC Proteomics Centre, University of Victoria, Victoria, Canada
| | - René P. Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada,Manitoba Centre for Proteomics & Systems Biology, John Buhler Research Centre, University of Manitoba, Winnipeg, Canada,Department of Internal Medicine, University of Manitoba, Winnipeg, Canada
| | - Evgeny N. Nikolaev
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Christoph H. Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada,Gerald Bronfman Department of Oncology, Division of Experimental Medicine, Lady Davis Institute for Medical Research, McGill University, Montreal, Canada,Department of Pathology, McGill University, Montreal, Canada,For correspondence: Christoph H. Borchers
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12
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Gaither C, Popp R, Zahedi RP, Borchers CH. Multiple reaction monitoring-mass spectrometry enables robust quantitation of plasma proteins regardless of whole blood processing delays that may occur in the clinic. Mol Cell Proteomics 2022; 21:100212. [PMID: 35182769 PMCID: PMC9062485 DOI: 10.1016/j.mcpro.2022.100212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/24/2022] [Accepted: 02/13/2022] [Indexed: 12/23/2022] Open
Abstract
Plasma is an important biofluid for clinical research and diagnostics. In the clinic, unpredictable delays—from minutes to hours—between blood collection and plasma generation are often unavoidable. These delays can potentially lead to protein degradation and modification and might considerably affect intact protein measurement methods such as sandwich enzyme-linked immunosorbent assays that bind proteins on two epitopes to increase specificity, thus requiring largely intact protein structures. Here, we investigated, using multiple reaction monitoring mass spectrometry (MRM-MS), how delays in plasma processing affect peptide-centric “bottom-up” proteomics. We used validated assays for proteotypic peptide surrogates of 270 human proteins to analyze plasma generated after whole blood had been kept at room temperature from 0 to 40 h to mimic delays that occur in the clinic. Moreover, we evaluated the impact of different plasma-thawing conditions on MRM-based plasma protein quantitation. We demonstrate that >90% of protein concentration measurements were unaffected by the thawing procedure and by up to 40-h delayed plasma generation, reflected by relative standard deviations (RSDs) of <30%. Of the 159 MRM assays that yielded quantitative results in 60% of the measured time points, 139 enabled a stable protein quantitation (RSD <20%), 14 showed a slight variation (RSD 20–30%), and 6 appeared unstable/irreproducible (RSD > 30%). These results demonstrate the high robustness and thus the potential for MRM-based plasma-protein quantitation to be used in a clinical setting. In contrast to enzyme-linked immunosorbent assay, peptide-based MRM assays do not require intact three-dimensional protein structures for an accurate and precise quantitation of protein concentrations in the original sample. Delays in whole blood processing often cannot be avoided in the clinic. These delays might affect measurements by intact protein assays such as ELISA. The impact on LC/MRM was evaluated using validated assays to quantify 270 proteins. >95% of the measured concentrations had RSDs <30% between delays of 0 to 40 h. Protein quantitation by LC/MRM-MS is robust against pitfalls in the clinical setting.
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Affiliation(s)
| | - Robert Popp
- MRM Proteomics Inc, Montreal, Quebec, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.
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13
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Gaspar VP, Ibrahim S, Zahedi RP, Borchers CH. Utility, promise, and limitations of liquid chromatography-mass spectrometry-based therapeutic drug monitoring in precision medicine. J Mass Spectrom 2021; 56:e4788. [PMID: 34738286 PMCID: PMC8597589 DOI: 10.1002/jms.4788] [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] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 05/03/2023]
Abstract
Therapeutic drug monitoring (TDM) is typically referred to as the measurement of the concentration of drugs in patient blood. Although in the past, TDM was restricted to drugs with a narrow therapeutic range in order to avoid drug toxicity, TDM has recently become a major tool for precision medicine being applied to many more drugs. Through compensating for interindividual differences in a drug's pharmacokinetics, improved dosing of individual patients based on TDM ensures maximum drug effectiveness while minimizing side effects. This is especially relevant for individuals that present a particularly high intervariability in pharmacokinetics, such as newborns, or for critically/severely ill patients. In this article, we will review the applications for and limitations of TDM, discuss for which patients TDM is most beneficial and why, examine which techniques are being used for TDM, and demonstrate how mass spectrometry is increasingly becoming a reliable and convenient alternative for the TDM of different classes of drugs. We will also highlight the advances, challenges, and limitations of the existing repertoire of TDM methods and discuss future opportunities for TDM-based precision medicine.
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Affiliation(s)
- Vanessa P. Gaspar
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
| | - Sahar Ibrahim
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Division of Experimental MedicineMcGill UniversityMontrealQuebecCanada
- Clinical Pathology DepartmentMenoufia UniversityShibin el KomEgypt
| | - René P. Zahedi
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscowRussia
| | - Christoph H. Borchers
- Segal Cancer Proteomics CentreMcGill UniversityMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscowRussia
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14
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Froehlich BC, Popp R, Sobsey CA, Ibrahim S, LeBlanc A, Mohammed Y, Buchanan M, Aguilar-Mahecha A, Pötz O, Chen MX, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH. A multiplexed, automated immuno-matrix assisted laser desorption/ionization mass spectrometry assay for simultaneous and precise quantitation of PTEN and p110α in cell lines and tumor tissues. Analyst 2021; 146:6566-6575. [PMID: 34585690 DOI: 10.1039/d1an00165e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The PI3-kinase/AKT/mTOR pathway plays a central role in cancer signaling. While p110α is the catalytic α-subunit of PI3-kinase and a major drug target, PTEN is the main negative regulator of the PI3-kinase/AKT/mTOR pathway. PTEN is often down-regulated in cancer, and there are conflicting data on PTEN's role as breast cancer biomarker. PTEN and p110α protein expression in tumors is commonly analyzed by immunohistochemistry, which suffers from poor multiplexing capacity, poor standardization, and antibody crossreactivity, and which provides only semi-quantitative data. Here, we present an automated, and standardized immuno-matrix-assisted laser desorption/ionization mass spectrometry (iMALDI) assay that allows precise and multiplexed quantitation of PTEN and p110α concentrations, without the limitations of immunohistochemistry. Our iMALDI assay only requires a low-cost benchtop MALDI-TOF mass spectrometer, which simplifies clinical translation. We validated our assay's precision and accuracy, with simultaneous enrichment of both target proteins not significantly affecting the precision and accuracy of the quantitation when compared to the PTEN- and p110α-singleplex iMALDI assays (<15% difference). The multiplexed assay's linear range is from 0.6-20 fmol with accuracies of 90-112% for both target proteins, and the assay is free of matrix-related interferences. The inter-day reproducibility over 5-days was high, with an overall CV of 9%. PTEN and p110α protein concentrations can be quantified down to 1.4 fmol and 0.6 fmol per 10 μg of total tumor protein, respectively, in various tumor tissue samples, including fresh-frozen breast tumors and colorectal cancer liver metastases, and patient-derived xenograft (PDX) tumors.
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Affiliation(s)
- Bjoern C Froehlich
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada
| | - Robert Popp
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada
| | - Constance A Sobsey
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada
| | - Sahar Ibrahim
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada
| | - Andre LeBlanc
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada
| | - Yassene Mohammed
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada.,Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Marguerite Buchanan
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada
| | - Adriana Aguilar-Mahecha
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada
| | - Oliver Pötz
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany.,SIGNATOPE GmbH, Reutlingen 72770, Germany
| | - Michael X Chen
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, Canada
| | - Alan Spatz
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada
| | - Mark Basik
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada
| | - Gerald Batist
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A3T2, Canada.
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- University of Victoria - Genome BC Proteomics Centre, University of Victoria, Victoria, British Columbia V8Z 7X8, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC H3T1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC H4A3T2, Canada.
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15
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Beckmann L, Berg V, Dickhut C, Sun C, Merkel O, Bloehdorn J, Robrecht S, Seifert M, da Palma Guerreiro A, Claasen J, Loroch S, Oliverio M, Underbayev C, Vaughn L, Thomalla D, Hülsemann MF, Tausch E, Fischer K, Fink AM, Eichhorst B, Sickmann A, Wendtner CM, Stilgenbauer S, Hallek M, Wiestner A, Zahedi RP, Frenzel LP. MARCKS affects cell motility and response to BTK inhibitors in CLL. Blood 2021; 138:544-556. [PMID: 33735912 PMCID: PMC8377477 DOI: 10.1182/blood.2020009165] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/18/2021] [Accepted: 03/06/2021] [Indexed: 12/26/2022] Open
Abstract
Bruton tyrosine kinase (BTK) inhibitors are highly active drugs for the treatment of chronic lymphocytic leukemia (CLL). To understand the response to BTK inhibitors on a molecular level, we performed (phospho)proteomic analyses under ibrutinib treatment. We identified 3466 proteins and 9184 phosphopeptides (representing 2854 proteins) in CLL cells exhibiting a physiological ratio of phosphorylated serines (pS), threonines (pT), and tyrosines (pY) (pS:pT:pY). Expression of 83 proteins differed between unmutated immunoglobulin heavy-chain variable region (IGHV) CLL (UM-CLL) and mutated IGHV CLL (M-CLL). Strikingly, UM-CLL cells showed higher basal phosphorylation levels than M-CLL samples. Effects of ibrutinib on protein phosphorylation levels were stronger in UM-CLL, especially on phosphorylated tyrosines. The differentially regulated phosphopeptides and proteins clustered in pathways regulating cell migration, motility, cytoskeleton composition, and survival. One protein, myristoylated alanine-rich C-kinase substrate (MARCKS), showed striking differences in expression and phosphorylation level in UM-CLL vs M-CLL. MARCKS sequesters phosphatidylinositol-4,5-bisphosphate, thereby affecting central signaling pathways and clustering of the B-cell receptor (BCR). Genetically induced loss of MARCKS significantly increased AKT signaling and migratory capacity. CD40L stimulation increased expression of MARCKS. BCR stimulation induced phosphorylation of MARCKS, which was reduced by BTK inhibitors. In line with our in vitro findings, low MARCKS expression is associated with significantly higher treatment-induced leukocytosis and more pronounced decrease of nodal disease in patients with CLL treated with acalabrutinib.
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Affiliation(s)
- Laura Beckmann
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Valeska Berg
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Clarissa Dickhut
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Olaf Merkel
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Sandra Robrecht
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Marc Seifert
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Alexandra da Palma Guerreiro
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Julia Claasen
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
| | - Matteo Oliverio
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Chingiz Underbayev
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Lauren Vaughn
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Daniel Thomalla
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Malte F Hülsemann
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Kirsten Fischer
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Anna Maria Fink
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Barbara Eichhorst
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
| | - Clemens M Wendtner
- Department I of Internal Medicine and
- Munich Clinic Schwabing, Academic Teaching Hospital, Ludwig Maximilian University (LMU), Munich, Germany
| | - Stephan Stilgenbauer
- Department of Internal Medicine III, Ulm University, Ulm, Germany
- Department of Internal Medicine I, Saarland University, Homburg, Germany
| | - Michael Hallek
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute and
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, QC, Canada; and
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lukas P Frenzel
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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16
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Ibrahim S, Lan C, Chabot C, Mitsa G, Buchanan M, Aguilar-Mahecha A, Elchebly M, Poetz O, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH. Precise Quantitation of PTEN by Immuno-MRM: A Tool To Resolve the Breast Cancer Biomarker Controversy. Anal Chem 2021; 93:10816-10824. [PMID: 34324311 DOI: 10.1021/acs.analchem.1c00975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The tumor suppressor PTEN is the main negative regulator of PI3K/AKT/mTOR signaling and is commonly found downregulated in breast cancer (BC). Conflicting data from conventional immunoassays such as immunohistochemistry (IHC) has sparked controversy about PTEN's role as a prognostic and predictive biomarker in BC, which can be largely attributed to the lack of specificity, sensitivity, and interlaboratory standardization. Here, we present a fully standardized, highly sensitive, robust microflow immuno-MRM (iMRM) assay that enables precise quantitation of PTEN concentrations in cells and fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) tissues, down to 0.1 fmol/10 μg of extracted protein, with high interday and intraday precision (CV 6.3%). PTEN protein levels in BC PDX samples that were determined by iMRM correlate well with semiquantitative IHC and WB data. iMRM, however, allowed the precise quantitation of PTEN-even in samples that were deemed to be PTEN negative by IHC or western blot (WB)-while requiring substantially less tumor tissue than WB. This is particularly relevant because the extent of PTEN downregulation in tumors has been shown to correlate with severity. Our standardized and robust workflow includes an 11 min microflow LC-MRM analysis on a triple-quadrupole MS and thus provides a much needed tool for the study of PTEN as a potential biomarker for BC.
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Affiliation(s)
- Sahar Ibrahim
- Division of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1 Canada.,Clinical Pathology Department, Menoufia University, Shebeen, El Kom 32511, Egypt.,Segal Cancer Proteomics Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Cathy Lan
- Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Catherine Chabot
- Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Georgia Mitsa
- Division of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1 Canada.,Segal Cancer Proteomics Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | | | | | - Mounib Elchebly
- Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Oliver Poetz
- University of Tuebingen, Reutlingen 72770, Germany.,SIGNATOPE GmbH, Reutlingen 72770, Germany
| | - Alan Spatz
- Division of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1 Canada.,Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Department of Pathology, McGill University, Montréal, Quebec H3A 2B4, Canada.,OPTILAB-McGill University Health Centre, Montréal, Quebec H4A 3J1, Canada
| | - Mark Basik
- Division of Experimental Medicine, McGill University, Montréal, Quebec H4A 3J1 Canada.,Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - Gerald Batist
- Segal Cancer Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montréal, Quebec H3T 1E2, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, McGill University, Montréal, Quebec H3T 1E2, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montréal, Quebec H3T 1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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17
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Hathazi D, Cox D, D'Amico A, Tasca G, Charlton R, Carlier RY, Baumann J, Kollipara L, Zahedi RP, Feldmann I, Deleuze JF, Torella A, Cohn R, Robinson E, Ricci F, Jungbluth H, Fattori F, Boland A, O'Connor E, Horvath R, Barresi R, Lochmüller H, Urtizberea A, Jacquemont ML, Nelson I, Swan L, Bonne G, Roos A. INPP5K and SIL1 associated pathologies with overlapping clinical phenotypes converge through dysregulation of PHGDH. Brain 2021; 144:2427-2442. [PMID: 33792664 DOI: 10.1093/brain/awab133] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 04/28/2020] [Revised: 01/12/2021] [Accepted: 01/30/2021] [Indexed: 12/22/2022] Open
Abstract
Marinesco-Sjögren syndrome (MSS) is a rare human disorder caused by biallelic mutations in SIL1 characterized by cataracts in infancy, myopathy and ataxia, symptoms that are also associated with a novel disorder caused by mutations in INPP5K. While these phenotypic similarities may suggest commonalties at a molecular level, an overlapping pathomechanism has not been established yet. In this study, we present six new INPP5K patients and expand the current mutational and phenotypical spectrum of the disease showing the clinical overlap between MSS and the INPP5K-phenotype. We applied unbiased proteomic profiling on cells derived from MSS- and INPP5K-patients and identified alterations in D-3-phosphoglycerate dehydrogenase as a common molecular feature. D-3-phosphoglycerate dehydrogenase modulates the production of L-serine and mutations in this enzyme were previously associated with a neurological phenotype, which clinically overlaps with MSS and INPP5K-disease. As, L-serine administration represents a promising therapeutic strategy for D-3-phosphoglycerate dehydrogenase patients, we tested the effect of L-serine in generated sil1, phgdh and inpp5k a + b zebrafish models which showed an improvement in their neuronal phenotype. Thus our study defines a core phenotypical feature underpinning a key common molecular mechanism in three rare diseases and reveals a common and novel therapeutic target for these patients.
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Affiliation(s)
- Denisa Hathazi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e. V, Dortmund, Germany.,Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Dan Cox
- The John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Adele D'Amico
- Laboratory of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, Rome Italy
| | - Giorgio Tasca
- Unità Operativa Complessa di Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Richard Charlton
- The John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Robert-Yves Carlier
- AP-HP, Service d'Imagerie Médicale, Raymond Poincaré Hospital, Garches, France.,Inserm U 1179, University of Versailles Saint-Quentin-en-Yvelines (UVSQ), Versailles, France
| | - Jennifer Baumann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e. V, Dortmund, Germany
| | | | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e. V, Dortmund, Germany.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada
| | - Ingo Feldmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e. V, Dortmund, Germany
| | - Jean-Francois Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH) (A.B., J.F.D.), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Annalaura Torella
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy and Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Ronald Cohn
- SickKids Research Institute, Department of Paediatrics and Molecular Genetics, University of Toronto, Toronto, Canada
| | - Emily Robinson
- Department of molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Francesco Ricci
- Department of molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Heinz Jungbluth
- Guy's and St Thomas' NHS Trust and King's College London, London, UK
| | - Fabiana Fattori
- Laboratory of Molecular Medicine for Neuromuscular and Neurodegenerative Disorders, Bambino Gesù Children's Hospital, Rome Italy
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH) (A.B., J.F.D.), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Emily O'Connor
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Rita Barresi
- The John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
| | - Hanns Lochmüller
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | | | - Marie-Line Jacquemont
- Unité de Génétique Médicale, Pôle Femme-Mère-Enfant, Groupe Hospitalier Sud Réunion, CHU de La Réunion, La Réunion, France
| | - Isabelle Nelson
- Sorbonne Université, Inserm UMRS974, Centre de Recherche en Myologie, Institut de Myologie, Paris, France
| | - Laura Swan
- Department of molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, UK
| | - Gisèle Bonne
- Sorbonne Université, Inserm UMRS974, Centre de Recherche en Myologie, Institut de Myologie, Paris, France
| | - Andreas Roos
- Guy's and St Thomas' NHS Trust and King's College London, London, UK.,Department of Pediatric Neurology, University Hospital Essen, University of Duisburg-Essen, Faculty of Medicine, Essen, Germany
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18
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Gaspar VP, Ibrahim S, Sobsey CA, Richard VR, Spatz A, Zahedi RP, Borchers CH. Direct and Precise Measurement of Bevacizumab Levels in Human Plasma Based on Controlled Methionine Oxidation and Multiple Reaction Monitoring. ACS Pharmacol Transl Sci 2020; 3:1304-1309. [PMID: 33344903 DOI: 10.1021/acsptsci.0c00134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Indexed: 12/17/2022]
Abstract
Bevacizumab is a monoclonal antibody which targets vascular endothelial growth factor A (VEGF-A) and is used to treat various cancers and recently COVID-19. The dosage recommendations for bevacizumab are determined on the basis of body weight, and the drug is administered after defined time intervals, when it is presumed to still be above its minimum effective serum concentration. Interindividual and disease-stage-related variations in bevacizumab catabolism, however, can affect the proper dosing of patients, resulting in plasma concentrations which may not be within the optimal therapeutic window for the drug. Therapeutic drug monitoring (TDM) enables the assessment of patients' serum concentrations and allows personalized dosing which has the potential to improve efficacy and reduce side effects. While TMD is often performed using ligand-based assays, mass spectrometry (MS)-based TDM offers improved specificity. Here, we present a robust multiple reaction monitoring (MRM)-MS-based TDM method for the precise quantification of bevacizumab plasma concentrations, based on the controlled oxidation of the methionine-containing peptide, STAYLQMNSLR. The assay shows good linearity (r 2 = 0.9951), robustness, and precision (CVs < 20%) for the quantification of bevacizumab, with a lower limit of quantification (S/N > 10) of 1.8 μg/mL of plasma, without the need for enrichment and requiring less than 1 μL of plasma and less than 6 h from sampling to result.
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Affiliation(s)
- Vanessa P Gaspar
- Gerald Bronfman Department of Oncology, Jewish General Hospital, and Segal Cancer Proteomics Center, Lady Davis Institute, General Hospital, McGill University, Montreal, Quebec H3T1E2, Canada
| | - Sahar Ibrahim
- Gerald Bronfman Department of Oncology, Jewish General Hospital, and Segal Cancer Proteomics Center, Lady Davis Institute, General Hospital, McGill University, Montreal, Quebec H3T1E2, Canada
| | - Constance A Sobsey
- Gerald Bronfman Department of Oncology, Jewish General Hospital, and Segal Cancer Proteomics Center, Lady Davis Institute, General Hospital, McGill University, Montreal, Quebec H3T1E2, Canada
| | - Vincent R Richard
- Segal Cancer Proteomics Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T1E2, Canada
| | - Alan Spatz
- Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T1E2, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Center, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H Borchers
- Gerald Bronfman Department of Oncology, Jewish General Hospital, and Segal Cancer Proteomics Center, Lady Davis Institute, General Hospital, McGill University, Montreal, Quebec H3T1E2, Canada.,Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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19
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van Geffen JP, Swieringa F, van Kuijk K, Tullemans BME, Solari FA, Peng B, Clemetson KJ, Farndale RW, Dubois LJ, Sickmann A, Zahedi RP, Ahrends R, Biessen EAL, Sluimer JC, Heemskerk JWM, Kuijpers MJE. Mild hyperlipidemia in mice aggravates platelet responsiveness in thrombus formation and exploration of platelet proteome and lipidome. Sci Rep 2020; 10:21407. [PMID: 33293576 PMCID: PMC7722935 DOI: 10.1038/s41598-020-78522-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/23/2020] [Indexed: 01/21/2023] Open
Abstract
Hyperlipidemia is a well-established risk factor for cardiovascular diseases. Millions of people worldwide display mildly elevated levels of plasma lipids and cholesterol linked to diet and life-style. While the prothrombotic risk of severe hyperlipidemia has been established, the effects of moderate hyperlipidemia are less clear. Here, we studied platelet activation and arterial thrombus formation in Apoe-/- and Ldlr-/- mice fed a normal chow diet, resulting in mildly increased plasma cholesterol. In blood from both knockout mice, collagen-dependent thrombus and fibrin formation under flow were enhanced. These effects did not increase in severe hyperlipidemic blood from aged mice and upon feeding a high-fat diet (Apoe-/- mice). Bone marrow from wild-type or Ldlr-/- mice was transplanted into irradiated Ldlr-/- recipients. Markedly, thrombus formation was enhanced in blood from chimeric mice, suggesting that the hyperlipidemic environment altered the wild-type platelets, rather than the genetic modification. The platelet proteome revealed high similarity between the three genotypes, without clear indication for a common protein-based gain-of-function. The platelet lipidome revealed an altered lipid profile in mildly hyperlipidemic mice. In conclusion, in Apoe-/- and Ldlr-/- mice, modest elevation in plasma and platelet cholesterol increased platelet responsiveness in thrombus formation and ensuing fibrin formation, resulting in a prothrombotic phenotype.
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Affiliation(s)
- Johanna P van Geffen
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Frauke Swieringa
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.,Leibniz Institut für Analytische Wissenschaften - ISAS- e.V, Dortmund, Germany
| | - Kim van Kuijk
- Department of Pathology, CARIM, Maastricht University, Maastricht, The Netherlands
| | - Bibian M E Tullemans
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Fiorella A Solari
- Leibniz Institut für Analytische Wissenschaften - ISAS- e.V, Dortmund, Germany
| | - Bing Peng
- Leibniz Institut für Analytische Wissenschaften - ISAS- e.V, Dortmund, Germany
| | - Kenneth J Clemetson
- Department of Haematology, Inselspital, University of Bern, Bern, Switzerland
| | | | - Ludwig J Dubois
- The M-Lab, Department of Precision Medicine, School for Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, The Netherlands
| | - Albert Sickmann
- Leibniz Institut für Analytische Wissenschaften - ISAS- e.V, Dortmund, Germany
| | - René P Zahedi
- Leibniz Institut für Analytische Wissenschaften - ISAS- e.V, Dortmund, Germany.,Segal Cancer Proteomics Centre, Jewish General Hospital, McGill University, Montreal, Canada
| | - Robert Ahrends
- Leibniz Institut für Analytische Wissenschaften - ISAS- e.V, Dortmund, Germany.,Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Wien, Austria
| | - Erik A L Biessen
- Department of Pathology, CARIM, Maastricht University, Maastricht, The Netherlands.,Institute for Molecular Cardiovascular Research, RWTH Aachen University, Aachen, Germany
| | - Judith C Sluimer
- Department of Pathology, CARIM, Maastricht University, Maastricht, The Netherlands.,BHF Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Johan W M Heemskerk
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands
| | - Marijke J E Kuijpers
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, P.O. Box 616, 6200 MD, Maastricht, The Netherlands.
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20
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Kyselova A, Siragusa M, Anthes J, Solari FA, Loroch S, Zahedi RP, Walter U, Fleming I, Randriamboavonjy V. Cyclin Y is expressed in Platelets and Modulates Integrin Outside-in Signaling. Int J Mol Sci 2020; 21:ijms21218239. [PMID: 33153214 PMCID: PMC7662234 DOI: 10.3390/ijms21218239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 12/17/2022] Open
Abstract
Diabetes is associated with platelet hyper-reactivity and enhanced risk of thrombosis development. Here we compared protein expression in platelets from healthy donors and diabetic patients to identify differentially expressed proteins and their possible function in platelet activation. Mass spectrometry analyses identified cyclin Y (CCNY) in platelets and its reduced expression in platelets from diabetic patients, a phenomenon that could be attributed to the increased activity of calpains. To determine the role of CCNY in platelets, mice globally lacking the protein were studied. CCNY-/- mice demonstrated lower numbers of circulating platelets but platelet responsiveness to thrombin and a thromboxane A2 analogue were comparable with that of wild-type mice, as was agonist-induced α and dense granule secretion. CCNY-deficient platelets demonstrated enhanced adhesion to fibronectin and collagen as well as an attenuated spreading and clot retraction, indicating an alteration in "outside in" integrin signalling. This phenotype was accompanied by a significant reduction in the agonist-induced tyrosine phosphorylation of β3 integrin. Taken together we have shown that CCNY is present in anucleated platelets where it is involved in the regulation of integrin-mediated outside in signalling associated with thrombin stimulation.
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Affiliation(s)
- Anastasia Kyselova
- Institute for Vascular Signaling, Centre of Molecular Medicine, Goethe University, Frankfurt am Main, 60590 Frankfurt, Germany; (A.K.); (M.S.); (J.A.); (I.F.)
- German Center of Cardiovascular Research (DZHK), Partner site Rhein Main, 17475 Greifswald, Germany; (S.L.); (R.P.Z.); (U.W.)
| | - Mauro Siragusa
- Institute for Vascular Signaling, Centre of Molecular Medicine, Goethe University, Frankfurt am Main, 60590 Frankfurt, Germany; (A.K.); (M.S.); (J.A.); (I.F.)
- German Center of Cardiovascular Research (DZHK), Partner site Rhein Main, 17475 Greifswald, Germany; (S.L.); (R.P.Z.); (U.W.)
| | - Julian Anthes
- Institute for Vascular Signaling, Centre of Molecular Medicine, Goethe University, Frankfurt am Main, 60590 Frankfurt, Germany; (A.K.); (M.S.); (J.A.); (I.F.)
| | - Fiorella Andrea Solari
- Leibniz–Institute for Analytical Sciences (ISAS)- e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany;
| | - Stefan Loroch
- German Center of Cardiovascular Research (DZHK), Partner site Rhein Main, 17475 Greifswald, Germany; (S.L.); (R.P.Z.); (U.W.)
- Leibniz–Institute for Analytical Sciences (ISAS)- e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany;
| | - René P. Zahedi
- German Center of Cardiovascular Research (DZHK), Partner site Rhein Main, 17475 Greifswald, Germany; (S.L.); (R.P.Z.); (U.W.)
- Leibniz–Institute for Analytical Sciences (ISAS)- e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany;
| | - Ulrich Walter
- German Center of Cardiovascular Research (DZHK), Partner site Rhein Main, 17475 Greifswald, Germany; (S.L.); (R.P.Z.); (U.W.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center Mainz, 55131 Mainz, Germany
| | - Ingrid Fleming
- Institute for Vascular Signaling, Centre of Molecular Medicine, Goethe University, Frankfurt am Main, 60590 Frankfurt, Germany; (A.K.); (M.S.); (J.A.); (I.F.)
- German Center of Cardiovascular Research (DZHK), Partner site Rhein Main, 17475 Greifswald, Germany; (S.L.); (R.P.Z.); (U.W.)
| | - Voahanginirina Randriamboavonjy
- Institute for Vascular Signaling, Centre of Molecular Medicine, Goethe University, Frankfurt am Main, 60590 Frankfurt, Germany; (A.K.); (M.S.); (J.A.); (I.F.)
- German Center of Cardiovascular Research (DZHK), Partner site Rhein Main, 17475 Greifswald, Germany; (S.L.); (R.P.Z.); (U.W.)
- Correspondence: ; Tel.: +49-69-6301-6973; Fax: +49-69-6301-86880
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21
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Comer S, Nagy Z, Bolado A, von Kriegsheim A, Gambaryan S, Walter U, Pagel O, Zahedi RP, Jurk K, Smolenski A. The RhoA regulators Myo9b and GEF-H1 are targets of cyclic nucleotide-dependent kinases in platelets. J Thromb Haemost 2020; 18:3002-3012. [PMID: 32692911 DOI: 10.1111/jth.15028] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/15/2020] [Accepted: 07/13/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Circulating platelets are maintained in an inactive state by the endothelial lining of the vasculature. Endothelium-derived prostacyclin and nitric oxide stimulate cAMP- and cGMP-dependent kinases, PKA and PKG, to inhibit platelets. PKA and PKG effects include the inhibition of the GTPase RhoA, which has been suggested to involve the direct phosphorylation of RhoA on serine 188. OBJECTIVES We wanted to confirm RhoA S188 phosphorylation by cyclic nucleotide-dependent kinases and to identify possible alternative mechanisms of RhoA regulation in platelets. METHODS Phosphoproteomics data of human platelets were used to identify candidate PKA and PKG substrates. Phosphorylation of individual proteins was studied by Western blotting and Phos-tag gel electrophoresis in human platelets and transfected HEK293T cells. Pull-down assays were performed to analyze protein interaction and function. RESULTS Our data indicate that RhoA is not phosphorylated by PKA in platelets. Instead, we provide evidence that cyclic nucleotide effects are mediated through the phosphorylation of the RhoA-specific GTPase-activating protein Myo9b and the guanine nucleotide exchange factor GEF-H1. We identify Myo9b S1354 and guanine nucleotide exchange factor-H1 (GEF-H1) S886 as PKA and PKG phosphorylation sites. Myo9b S1354 phosphorylation enhances its GTPase activating protein function leading to reduced RhoA-GTP levels. GEF-H1 S886 phosphorylation stimulates binding of 14-3-3β and has been shown to inhibit GEF function by facilitating binding of GEF-H1 to microtubules. Microtubule disruption increases RhoA-GTP levels confirming the importance of GEF-H1 in platelets. CONCLUSION Phosphorylation of RhoA regulatory proteins Myo9b and GEF-H1, but not RhoA itself, is involved in cyclic nucleotide-mediated control of RhoA in human platelets.
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Affiliation(s)
- Shane Comer
- UCD School of Medicine and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin 2, Ireland
| | - Zoltan Nagy
- UCD School of Medicine and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Institute of Experimental Biomedicine, University Hospital and Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
| | - Alfonso Bolado
- Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | | | - Stepan Gambaryan
- Sechenov Institute for Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, St. Petersburg, Russia
| | - Ulrich Walter
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
| | - Oliver Pagel
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Kerstin Jurk
- Center for Thrombosis and Hemostasis, University Medical Center Mainz, Mainz, Germany
| | - Albert Smolenski
- UCD School of Medicine and Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin 2, Ireland
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22
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Kopczynski D, Hentschel A, Coman C, Schebb NH, Hornemann T, Mashek DG, Hartung NM, Shevchuk O, Schött HF, Lorenz K, Torta F, Burla B, Zahedi RP, Sickmann A, Kreutz MR, Ejsing CS, Medenbach J, Ahrends R. Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics. Anal Chem 2020; 92:13672-13676. [PMID: 32865986 PMCID: PMC7586293 DOI: 10.1021/acs.analchem.0c02793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
We
introduce STAMPS, a pathway-centric web service for the development
of targeted proteomics assays. STAMPS guides the user by providing
several intuitive interfaces for a rapid and simplified method design.
Applying our curated framework to signaling and metabolic pathways,
we reduced the average assay development time by a factor of ∼150
and revealed that the insulin signaling is actively controlled by
protein abundance changes in insulin-sensitive and -resistance states.
Although at the current state STAMPS primarily contains mouse data,
it was designed for easy extension with additional organisms.
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Affiliation(s)
- Dominik Kopczynski
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Cristina Coman
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
| | - Nils Helge Schebb
- Institute for Food Toxicology, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany.,Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gauss-Strasse 20, 42119 Wuppertal, Germany
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital Zürich, Wagistrasse 14 Schlieren, 8952 Zürich, Switzerland
| | - Douglas G Mashek
- Division of Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Minnesota, 401 East River Parkway, Minneapolis, Minnesota 55455, United States.,Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Nicole M Hartung
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gauss-Strasse 20, 42119 Wuppertal, Germany
| | - Olga Shevchuk
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Hans-Frieder Schött
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, 28 Medical Drive, #03-03, Singapore 117456, Singapore
| | - Kristina Lorenz
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, 28 Medical Drive, #03-03, Singapore 117456, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, 28 Medical Drive, #03-03, Singapore 117456, Singapore
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Cote Sainte Catherine Road, Montreal, Quebec H3T 1E2, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, Gesundheitscampus 4, 44801 Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, Scotland, United Kingdom
| | - Michael R Kreutz
- Leibniz Group "Dendritic Organelles and Synaptic Function", University Medical Center Hamburg-Eppendorf, Center for Molecular Neurobiology, ZMNH, Martinistrasse 52, 20251 Hamburg, Germany.,RG Neuroplasticity, Leibniz Institute for Neurobiology, Brenneckestraße 6, 39120 Magdeburg, Germany.,German Center for Neurodegenerative Diseases (DZNE), Leipziger Straße 44, 39120 Magdeburg, Germany
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, Odense M DK-5230, Denmark.,Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany.,Department of Analytical Chemistry, University of Vienna, Währinger Strasse 38, 1090 Vienna, Austria
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Richard VR, Zahedi RP, Eintracht S, Borchers CH. An LC-MRM assay for the quantification of metanephrines from dried blood spots for the diagnosis of pheochromocytomas and paragangliomas. Anal Chim Acta 2020; 1128:140-148. [PMID: 32825898 PMCID: PMC7346842 DOI: 10.1016/j.aca.2020.06.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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] [Received: 04/02/2020] [Revised: 05/23/2020] [Accepted: 06/09/2020] [Indexed: 12/19/2022]
Abstract
The quantitation of metanephrine (MN), normetanephrine (NMN), and 3-methoxytyramine (3-MT) – referred to as metanephrines -- by LC-MS/MS is the gold-standard for screening for pheochromocytoma and paragangliomas (PPGLs), tumours of the adrenal gland and the peripheral nervous system. An assay for metanephrines from dried blood spots (DBSs) would be of high clinical utility as it simplifies sample collection, enables remote sampling, and could increase compliance with the clinical recommendation for supine sampling. Moreover, DBS sampling facilitates the measurement of blood-derived metanephrines in pediatric patients – where DBSs are well-established – in order to diagnose neuroblastomas. Here, we adapted an established derivatization-based LC-MRM-MS assay for plasma catecholamines, and optimized the sample extraction, LC, and MS parameters to produce a fast, sensitive, and robust method for the measurement of metanephrines from DBSs, including 3-methoxytyramine. The DBS samples were excised, derivatized with phenyl isothiocyanate (PITC) on-spot, extracted, and measured by LC-MRM-MS. To validate assay suitability and performance, we assessed the linearity, precision, accuracy, recovery, and matrix effects of the method, and determined the stability of metanephrines in DBSs under different storage conditions. Assay performance for NMN, MN, and 3-MT was sufficient for quantitation from a single DBS within a linear range from 40 to 2000 pg/mL. MN and NMN were stable in DBSs for 2 weeks, whereas 3-MT was stable for one week regardless of storage temperature. Altogether, this work represents the first quantitative LC-MS/MS method for metanephrines from DBSs and provides a novel opportunity for the diagnosis of PPGLs and neuroblastomas in the future. Development and validation of an assay for metanephrines from dried blood spots. Method utilizes on-spot derivatization followed by LC-MRM-MS based quantitation. Method demonstrated high degree of sensitivity, precision, and accuracy. High relevance for the clinical diagnosis of pheochromocytomas and paragangliomas.
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Affiliation(s)
- Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, QC, Canada; Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia.
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, QC, Canada; Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia.
| | - Shaun Eintracht
- Department of Diagnostic Medicine, Jewish General Hospital, McGill University, Montreal, QC, Canada.
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University, Montreal, QC, Canada; Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC, Canada.
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24
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Froehlich BC, Popp R, Sobsey CA, Ibrahim S, LeBlanc AM, Mohammed Y, Aguilar‐Mahecha A, Poetz O, Chen MX, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH. Front Cover: Systematic Optimization of the iMALDI Workflow for the Robust and Straightforward Quantification of Signaling Proteins in Cancer Cells. Proteomics Clin Appl 2020. [DOI: 10.1002/prca.202070051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Froehlich BC, Popp R, Sobsey CA, Ibrahim S, LeBlanc AM, Mohammed Y, Aguilar‐Mahecha A, Poetz O, Chen MX, Spatz A, Basik M, Batist G, Zahedi RP, Borchers CH. Systematic Optimization of the iMALDI Workflow for the Robust and Straightforward Quantification of Signaling Proteins in Cancer Cells. Proteomics Clin Appl 2020; 14:e2000034. [PMID: 32643306 PMCID: PMC7539945 DOI: 10.1002/prca.202000034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 04/24/2020] [Revised: 06/13/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE Immuno-MALDI (iMALDI) combines immuno-enrichment of biomarkers with MALDI-MS for fast, precise, and specific quantitation, making it a valuable tool for developing clinical assays. iMALDI assays are optimized for the PI3-kinase signaling pathway members phosphatase and tensin homolog (PTEN) and PI3-kinase catalytic subunit alpha (p110α), with regard to sensitivity, robustness, and throughput. A standardized template for developing future iMALDI assays, including automation protocols to streamline assay development and translation, is provided. EXPERIMENTAL DESIGN Conditions for tryptic digestion and immuno-enrichment (beads, bead:antibody ratios, incubation times, direct vs. indirect immuno-enrichment) are rigorously tested. Different strategies for calibration and data readout are compared. RESULTS Digestion using 1:2 protein:trypsin (wt:wt) for 1 h yielded high and consistent peptide recoveries. Direct immuno-enrichment (antibody-bead coupling prior to antigen-enrichment) yielded 30% higher peptide recovery with a 1 h shorter incubation time than indirect enrichment. Immuno-enrichment incubation overnight yielded 1.5-fold higher sensitivities than 1 h incubation. Quantitation of the endogenous target proteins is not affected by the complexity of the calibration matrix, further simplifying the workflow. CONCLUSIONS AND CLINICAL RELEVANCE This optimized and automated workflow will facilitate the clinical translation of high-throughput sensitive iMALDI assays for quantifying cell-signaling proteins in individual tumor samples, thereby improving patient stratification for targeted treatment.
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Affiliation(s)
- Bjoern C. Froehlich
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCV8Z 7E8Canada
- Department of Biochemistry and MicrobiologyUniversity of VictoriaVictoriaBCV8P 5C2Canada
| | - Robert Popp
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCV8Z 7E8Canada
| | - Constance A. Sobsey
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Sahar Ibrahim
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Andre M. LeBlanc
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Yassene Mohammed
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCV8Z 7E8Canada
- Center for Proteomics and MetabolomicsLeiden University Medical CenterLeiden2333 ZAThe Netherlands
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscow121205Russia
| | - Adriana Aguilar‐Mahecha
- Segal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute University of TuebingenReutlingen72770Germany
- SIGNATOPE GmbHReutlingen72770Germany
| | - Michael X. Chen
- Department of Pathology and Laboratory MedicineFaculty of MedicineUniversity of British ColumbiaVancouverCanada
| | - Alan Spatz
- Segal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Mark Basik
- Segal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
| | - Gerald Batist
- Segal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill UniversityMontrealQCH4A3T2Canada
| | - René P. Zahedi
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscow121205Russia
| | - Christoph H. Borchers
- University of Victoria‐Genome BC Proteomics CentreUniversity of VictoriaVictoriaBCV8Z 7E8Canada
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQCH3T1E2Canada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill UniversityMontrealQCH4A3T2Canada
- Center for Computational and Data‐Intensive Science and EngineeringSkolkovo Institute of Science and TechnologyMoscow121205Russia
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Ibrahim S, Froehlich BC, Aguilar-Mahecha A, Aloyz R, Poetz O, Basik M, Batist G, Zahedi RP, Borchers CH. Using Two Peptide Isotopologues as Internal Standards for the Streamlined Quantification of Low-Abundance Proteins by Immuno-MRM and Immuno-MALDI. Anal Chem 2020; 92:12407-12414. [DOI: 10.1021/acs.analchem.0c02157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Sahar Ibrahim
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Bjoern C. Froehlich
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria V8Z 7X8, Canada
| | - Adriana Aguilar-Mahecha
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Raquel Aloyz
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
- SIGNATOPE GmbH, Reutlingen 72770, Germany
| | - Mark Basik
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Gerald Batist
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - René P. Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H. Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria V8Z 7X8, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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27
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Scheidt T, Alka O, Gonczarowska-Jorge H, Gruber W, Rathje F, Dell’Aica M, Rurik M, Kohlbacher O, Zahedi RP, Aberger F, Huber CG. Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells. Cell Commun Signal 2020; 18:99. [PMID: 32576205 PMCID: PMC7310537 DOI: 10.1186/s12964-020-00591-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/01/2019] [Accepted: 05/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Aberrant hedgehog (HH) signaling is implicated in the development of various cancer entities such as medulloblastoma. Activation of GLI transcription factors was revealed as the driving force upon pathway activation. Increased phosphorylation of essential effectors such as Smoothened (SMO) and GLI proteins by kinases including Protein Kinase A, Casein Kinase 1, and Glycogen Synthase Kinase 3 β controls effector activity, stability and processing. However, a deeper and more comprehensive understanding of phosphorylation in the signal transduction remains unclear, particularly during early response processes involved in SMO activation and preceding GLI target gene regulation. METHODS We applied temporal quantitative phosphoproteomics to reveal phosphorylation dynamics underlying the short-term chemical activation and inhibition of early hedgehog signaling in HH responsive human medulloblastoma cells. Medulloblastoma cells were treated for 5.0 and 15 min with Smoothened Agonist (SAG) to induce and with vismodegib to inhibit the HH pathway. RESULTS Our phosphoproteomic profiling resulted in the quantification of 7700 and 10,000 phosphosites after 5.0 and 15 min treatment, respectively. The data suggest a central role of phosphorylation in the regulation of ciliary assembly, trafficking, and signal transduction already after 5.0 min treatment. ERK/MAPK signaling, besides Protein Kinase A signaling and mTOR signaling, were differentially regulated after short-term treatment. Activation of Polo-like Kinase 1 and inhibition of Casein Kinase 2A1 were characteristic for vismodegib treatment, while SAG treatment induced Aurora Kinase A activity. Distinctive phosphorylation of central players of HH signaling such as SMO, SUFU, GLI2 and GLI3 was observed only after 15 min treatment. CONCLUSIONS This study provides evidence that phosphorylation triggered in response to SMO modulation dictates the localization of hedgehog pathway components within the primary cilium and affects the regulation of the SMO-SUFU-GLI axis. The data are relevant for the development of targeted therapies of HH-associated cancers including sonic HH-type medulloblastoma. A deeper understanding of the mechanisms of action of SMO inhibitors such as vismodegib may lead to the development of compounds causing fewer adverse effects and lower frequencies of drug resistance. Video Abstract.
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Affiliation(s)
- Tamara Scheidt
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Oliver Alka
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Humberto Gonczarowska-Jorge
- Leibniz-Institute of Analytical Sciences- ISAS - e.V, Dortmund, Germany
- Present address: CAPES Foundation, Ministry of Education of Brazil, Brasília, DF 70040-020 Brazil
| | - Wolfgang Gruber
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
- Present address: EVER Valinject GmbH, 4866 Unterach am Attersee, Austria
| | - Florian Rathje
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | | | - Marc Rurik
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Str. 9, 72076 Tübingen, Germany
- Applied Bioinformatics, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - René P. Zahedi
- Leibniz-Institute of Analytical Sciences- ISAS - e.V, Dortmund, Germany
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Canada
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada
| | - Fritz Aberger
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
| | - Christian G. Huber
- Department of Biosciences, Bioanalytical Research Laboratories and Molecular Cancer Research and Tumor Immunology, Cancer Cluster Salzburg, University of Salzburg, Hellbrunner Straße 34, 5020 Salzburg, Austria
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Grimmer J, Helm S, Dobritzsch D, Hause G, Shema G, Zahedi RP, Baginsky S. Mild proteasomal stress improves photosynthetic performance in Arabidopsis chloroplasts. Nat Commun 2020; 11:1662. [PMID: 32245955 PMCID: PMC7125294 DOI: 10.1038/s41467-020-15539-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 08/04/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
The proteasome is an essential protein-degradation machinery in eukaryotic cells that controls protein turnover and thereby the biogenesis and function of cell organelles. Chloroplasts import thousands of nuclear-encoded precursor proteins from the cytosol, suggesting that the bulk of plastid proteins is transiently exposed to the cytosolic proteasome complex. Therefore, there is a cytosolic equilibrium between chloroplast precursor protein import and proteasomal degradation. We show here that a shift in this equilibrium, induced by mild genetic proteasome impairment, results in elevated precursor protein abundance in the cytosol and significantly increased accumulation of functional photosynthetic complexes in protein import-deficient chloroplasts. Importantly, a proteasome lid mutant shows improved photosynthetic performance, even in the absence of an import defect, signifying that functional precursors are continuously degraded. Hence, turnover of plastid precursors in the cytosol represents a mechanism to constrain thylakoid membrane assembly and photosynthetic electron transport.
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Affiliation(s)
- Julia Grimmer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | - Dirk Dobritzsch
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany
| | - Gerd Hause
- Biocenter of the University, Martin-Luther-University Halle-Wittenberg, Weinbergweg 22, 06120, Halle, Saale, Germany
| | - Gerta Shema
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., Bunsen-Kirchhoff-Straße 11, 44139, Dortmund, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle, Saale, Germany.
- Biochemistry of Plants, Faculty for Biology and Biotechnology, Ruhr-University Bochum, Universitätsstrasse 150, 44801, Bochum, Germany.
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29
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Ibrahim S, Sobsey CA, Popp R, Zahedi RP, Batist G, Borchers CH. Abstract P4-10-20: Protein quantitation assays for AKT and PTEN to better understand sensitivity and resistance of breast cancer patients to treatment with AKT inhibitor capivasertib. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p4-10-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Context: The PI3K/AKT/PTEN pathway is frequently aberrantly activated in breast cancer (BC) and involved in resistance to hormonal therapy. Multiple drugs targeting this pathway are approved or in development, including the pan-AKT inhibitor capivasertib (AZD5363). Early phase studies of capivasertib as monotherapy for solid cancers (e.g. NCT01226316, NCT01625286) have used genetic testing to select patients considered most likely to respond based on AKT1, PIK3CA or PTEN mutations. However, not all selected patients responded. Randomised phase 2 studies on Capivasertib as combination treatment showed the importance of context; a more pronounced response in combination with paclitaxel was seen in TNBC patients whose tumors harboured an alteration on AKT1, PIK3CA or PTEN (Schmid et al. ASCO 2018), whereas the same combination in ER+ HER2- advanced/metastatic BC patients did not show a clinical benefit in the overall population nor in the PIK3CA-mutation subgroup (Turner et al. Ann Oncol 2019). The combination with fulvestrant demonstrated an effect in unselected ER+ HER2- advanced BC patients resistant to aromatase inhibitors irrespective of PIK3CA mutations or PTEN IHC status (Jones et al. ASCO 2019). DNA-based assays also have the limitation that potential responders may be missed, e.g., tumors with epigenetic pathway activation but no detectable mutations. Techniques such as IHC and Western Blot (WB) lack the sensitivity, reproducibility and standardization required to precisely quantify these proteins. We hypothesize that precise mass spectrometry (MS)-based methods may facilitate a better understanding of sensitivity and resistance to inhibitors of the PI3K/AKT pathway in future studies.
Methods: Protein extracted from tumor tissue lysate is subjected to proteolytic digestion to generate proteotypic peptides used for protein quantitation. Synthetic stable isotope-labeled peptides are added to the digest as an internal standard, after which the target peptides are immuno-enriched with antibodies coupled to magnetic beads. MS analysis is performed by either eluting peptides for measurement with liquid chromatography multiple reaction monitoring tandem MS (LC-MRM-MS/MS) or by spotting beads onto a plate for matrix-assisted laser desorption/ionization MS (MALDI-MS). Calibration curves enable accurate quantitation. A new method for PTEN was applied to 13 breast cancer PDXs. Results were compared to IHC and WB. In a retrospective study, we are applying these methods to test samples from HR+ metastatic breast or gynecological cancer patients (n=25 with PIK3CA-mutations, capivasertib monotherapy; n=26 with PTEN alterations, capivasertib + fulvestrant; n=9 with no PIK3CA, AKT1 or PTEN mutations, not receiving capivasertib). AKT and PTEN quantitation data will be analyzed for a relationship to treatment response as determined by RECIST guidelines (NCT01226316).
Results: We validated MS methods to precisely and reproducibly determine AKT and PTEN concentrations in tumor samples. AKT concentrations varied significantly between mutation-positive tumor samples (AKT1: 0.06-0.45, AKT2: 0.05-0.20 fmol/µg total protein). Significant phosphorylation of AKT1-Ser473 or AKT2-Ser474 was observed in 2 out of 17 tested samples. At least 1 mutation-negative sample had a high AKT1 concentration of 0.42 fmol/ug total protein. PTEN concentrations from PDXs were consistent across biological replicates and agreed with IHC and WB. Furthermore, we were able to detect and quantify PTEN from 3 samples that were negative by IHC and/or WB.
Conclusion: AKT and PTEN quantitative proteomics assays have the potential to enable more accurate assessment of PI3K/AKT/PTEN pathway activation in tumor tissues from patients treated with inhibitors of this key pathway.
Citation Format: Sahar Ibrahim, Constance A Sobsey, Robert Popp, René P. Zahedi, Gerald Batist, Christoph H. Borchers. Protein quantitation assays for AKT and PTEN to better understand sensitivity and resistance of breast cancer patients to treatment with AKT inhibitor capivasertib [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-10-20.
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Affiliation(s)
- Sahar Ibrahim
- 1Segal Cancer Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, QC, Canada
| | - Constance A Sobsey
- 1Segal Cancer Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, QC, Canada
| | | | - René P. Zahedi
- 1Segal Cancer Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, QC, Canada
| | - Gerald Batist
- 3Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Christoph H. Borchers
- 1Segal Cancer Proteomics Centre, Jewish General Hospital, Lady Davis Institute, McGill University, Montreal, QC, Canada
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Sobsey CA, Ibrahim S, Richard VR, Gaspar V, Mitsa G, Lacasse V, Zahedi RP, Batist G, Borchers CH. Targeted and Untargeted Proteomics Approaches in Biomarker Development. Proteomics 2020; 20:e1900029. [DOI: 10.1002/pmic.201900029] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/10/2019] [Indexed: 01/24/2023]
Affiliation(s)
- Constance A. Sobsey
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Sahar Ibrahim
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Vincent R. Richard
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Vanessa Gaspar
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Georgia Mitsa
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Vincent Lacasse
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - René P. Zahedi
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
| | - Gerald Batist
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill University Montreal Quebec H4A 3T2 Canada
| | - Christoph H. Borchers
- Segal Cancer Proteomics CentreLady Davis InstituteJewish General HospitalMcGill University Montreal Quebec H3T 1E2 Canada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill University Montreal Quebec H4A 3T2 Canada
- Department of Data Intensive Science and EngineeringSkolkovo Institute of Science and TechnologySkolkovo Innovation Center Moscow 143026 Russia
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31
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Lategahn J, Keul M, Klövekorn P, Tumbrink HL, Niggenaber J, Müller MP, Hodson L, Flaßhoff M, Hardick J, Grabe T, Engel J, Schultz-Fademrecht C, Baumann M, Ketzer J, Mühlenberg T, Hiller W, Günther G, Unger A, Müller H, Heimsoeth A, Golz C, Blank-Landeshammer B, Kollipara L, Zahedi RP, Strohmann C, Hengstler JG, van Otterlo WAL, Bauer S, Rauh D. Inhibition of osimertinib-resistant epidermal growth factor receptor EGFR-T790M/C797S. Chem Sci 2019; 10:10789-10801. [PMID: 31857889 PMCID: PMC6886544 DOI: 10.1039/c9sc03445e] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/03/2019] [Indexed: 11/21/2022] Open
Abstract
We present inhibitors of drug resistant mutants of EGFR including T790M and C797S. In addition, we present the first X-ray crystal structures of covalent inhibitors in complex with C797S-mutated EGFR to gain insight into their binding mode.
Precision medicine has revolutionized the treatment of patients in EGFR driven non-small cell lung cancer (NSCLC). Targeted drugs show high response rates in genetically defined subsets of cancer patients and markedly increase their progression-free survival as compared to conventional chemotherapy. However, recurrent acquired drug resistance limits the success of targeted drugs in long-term treatment and requires the constant development of novel efficient inhibitors of drug resistant cancer subtypes. Herein, we present covalent inhibitors of the drug resistant gatekeeper mutant EGFR-L858R/T790M based on the pyrrolopyrimidine scaffold. Biochemical and cellular characterization, as well as kinase selectivity profiling and western blot analysis, substantiate our approach. Moreover, the developed compounds possess high activity against multi drug resistant EGFR-L858R/T790M/C797S in biochemical assays due to their highly reversible binding character, that was revealed by characterization of the binding kinetics. In addition, we present the first X-ray crystal structures of covalent inhibitors in complex with C797S-mutated EGFR which provide detailed insight into their binding mode.
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Affiliation(s)
- Jonas Lategahn
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080.,Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) , 44227 Dortmund , Germany
| | - Marina Keul
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080.,Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) , 44227 Dortmund , Germany
| | - Philip Klövekorn
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080
| | - Hannah L Tumbrink
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080
| | - Janina Niggenaber
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080.,Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) , 44227 Dortmund , Germany
| | - Matthias P Müller
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080.,Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) , 44227 Dortmund , Germany
| | - Luke Hodson
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080.,Department of Chemistry and Polymer Science , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa
| | - Maren Flaßhoff
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080
| | - Julia Hardick
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080.,Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) , 44227 Dortmund , Germany
| | - Tobias Grabe
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080.,Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) , 44227 Dortmund , Germany
| | - Julian Engel
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080
| | | | - Matthias Baumann
- Lead Discovery Center GmbH , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany
| | - Julia Ketzer
- Department of Medical Oncology , Sarcoma Center , West German Cancer Center , University Duisburg-Essen , Medical School , Hufelandstrasse 55 , 45122 Essen , Germany.,German Cancer Consortium (DKTK) , 69120, Heidelberg , Germany
| | - Thomas Mühlenberg
- Department of Medical Oncology , Sarcoma Center , West German Cancer Center , University Duisburg-Essen , Medical School , Hufelandstrasse 55 , 45122 Essen , Germany.,German Cancer Consortium (DKTK) , 69120, Heidelberg , Germany
| | - Wolf Hiller
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080
| | - Georgia Günther
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) , TU Dortmund University , Ardeystrasse 67 , 44139 Dortmund , Germany
| | - Anke Unger
- Lead Discovery Center GmbH , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany
| | - Heiko Müller
- Lead Discovery Center GmbH , Otto-Hahn-Strasse 15 , 44227 Dortmund , Germany
| | - Alena Heimsoeth
- Molecular Pathology , Institute of Pathology , University Hospital of Cologne , Kerpener Strasse 62 , 50937 Cologne , Germany.,Department of Translational Genomics , Center of Integrated Oncology Cologne-Bonn , Medical Faculty , University of Cologne , Weyertal 115b , 50931 Cologne , Germany
| | - Christopher Golz
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080
| | - Bernhard Blank-Landeshammer
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , Otto-Hahn-Strasse 6b , 44227 Dortmund , Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , Otto-Hahn-Strasse 6b , 44227 Dortmund , Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , Otto-Hahn-Strasse 6b , 44227 Dortmund , Germany.,Segal Cancer Proteomics Centre , Lady Davis Institute , Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montreal , Quebec H3T 1E2 , Canada
| | - Carsten Strohmann
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo) , TU Dortmund University , Ardeystrasse 67 , 44139 Dortmund , Germany
| | - Willem A L van Otterlo
- Department of Chemistry and Polymer Science , Stellenbosch University , Private Bag X1 , Matieland 7602 , South Africa
| | - Sebastian Bauer
- Department of Medical Oncology , Sarcoma Center , West German Cancer Center , University Duisburg-Essen , Medical School , Hufelandstrasse 55 , 45122 Essen , Germany.,German Cancer Consortium (DKTK) , 69120, Heidelberg , Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Strasse 4a , 44227 Dortmund , Germany . ; www.twitter.com/DDHDortmund ; Tel: +49-231-755-7080.,Drug Discovery Hub Dortmund (DDHD), Zentrum für Integrierte Wirkstoffforschung (ZIW) , 44227 Dortmund , Germany
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Sirois I, Aguilar-Mahecha A, Lafleur J, Fowler E, Vu V, Scriver M, Buchanan M, Chabot C, Ramanathan A, Balachandran B, Légaré S, Przybytkowski E, Lan C, Krzemien U, Cavallone L, Aleynikova O, Ferrario C, Guilbert MC, Benlimame N, Saad A, Alaoui-Jamali M, Saragovi HU, Josephy S, O'Flanagan C, Hursting SD, Richard VR, Zahedi RP, Borchers CH, Bareke E, Nabavi S, Tonellato P, Roy JA, Robidoux A, Marcus EA, Mihalcioiu C, Majewski J, Basik M. A Unique Morphological Phenotype in Chemoresistant Triple-Negative Breast Cancer Reveals Metabolic Reprogramming and PLIN4 Expression as a Molecular Vulnerability. Mol Cancer Res 2019; 17:2492-2507. [PMID: 31537618 DOI: 10.1158/1541-7786.mcr-19-0264] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 06/18/2019] [Accepted: 09/16/2019] [Indexed: 11/16/2022]
Abstract
The major obstacle in successfully treating triple-negative breast cancer (TNBC) is resistance to cytotoxic chemotherapy, the mainstay of treatment in this disease. Previous preclinical models of chemoresistance in TNBC have suffered from a lack of clinical relevance. Using a single high dose chemotherapy treatment, we developed a novel MDA-MB-436 cell-based model of chemoresistance characterized by a unique and complex morphologic phenotype, which consists of polyploid giant cancer cells giving rise to neuron-like mononuclear daughter cells filled with smaller but functional mitochondria and numerous lipid droplets. This resistant phenotype is associated with metabolic reprogramming with a shift to a greater dependence on fatty acids and oxidative phosphorylation. We validated both the molecular and histologic features of this model in a clinical cohort of primary chemoresistant TNBCs and identified several metabolic vulnerabilities including a dependence on PLIN4, a perilipin coating the observed lipid droplets, expressed both in the TNBC-resistant cells and clinical chemoresistant tumors treated with neoadjuvant doxorubicin-based chemotherapy. These findings thus reveal a novel mechanism of chemotherapy resistance that has therapeutic implications in the treatment of drug-resistant cancer. IMPLICATIONS: These findings underlie the importance of a novel morphologic-metabolic phenotype associated with chemotherapy resistance in TNBC, and bring to light novel therapeutic targets resulting from vulnerabilities in this phenotype, including the expression of PLIN4 essential for stabilizing lipid droplets in resistant cells.
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Affiliation(s)
- Isabelle Sirois
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Adriana Aguilar-Mahecha
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Josiane Lafleur
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Emma Fowler
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Viet Vu
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Michelle Scriver
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Marguerite Buchanan
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Catherine Chabot
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Aparna Ramanathan
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Banujan Balachandran
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Stéphanie Légaré
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada
| | - Ewa Przybytkowski
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Cathy Lan
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Urszula Krzemien
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Luca Cavallone
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Olga Aleynikova
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Department of Oncology and Surgery, McGill University, Montréal, Québec, Canada
| | - Cristiano Ferrario
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Department of Oncology and Surgery, McGill University, Montréal, Québec, Canada
| | - Marie-Christine Guilbert
- Hôpital Maisonneuve Rosemont, Département de pathologie et biologie cellulaire, Université de Montréal, Québec, Canada
| | - Naciba Benlimame
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Amine Saad
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada.,Department of Oncology and Surgery, McGill University, Montréal, Québec, Canada
| | - Moulay Alaoui-Jamali
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada.,Department of Oncology and Surgery, McGill University, Montréal, Québec, Canada
| | - Horace Uri Saragovi
- Lady Davis Institute-Jewish General Hospital; Center for Translational Research, McGill University, Montréal, Québec, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada.,Integrated Program for Neuroscience, McGill University, Montréal, Québec, Canada
| | - Sylvia Josephy
- Lady Davis Institute-Jewish General Hospital; Center for Translational Research, McGill University, Montréal, Québec, Canada.,Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec, Canada.,Integrated Program for Neuroscience, McGill University, Montréal, Québec, Canada
| | - Ciara O'Flanagan
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Stephen D Hursting
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,University of North Carolina Nutrition Research Institute, Kannapolis, North Carolina
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec, Canada.,University of Victoria Genome British Columbia Proteomics Centre, University of Victoria, Victoria, Canada
| | - Eric Bareke
- McGill University and Genome Québec Innovation Center, Montréal, Québec, Canada
| | - Sheida Nabavi
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | - Peter Tonellato
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
| | | | - André Robidoux
- Centre Hospitalier de l'Université de Montreal, Montreal, Québec, Canada
| | | | | | - Jacek Majewski
- McGill University and Genome Québec Innovation Center, Montréal, Québec, Canada.,Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Mark Basik
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec, Canada. .,Division of Experimental Medicine, McGill University, Montréal, Québec, Canada.,Department of Oncology and Surgery, McGill University, Montréal, Québec, Canada
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Kösters M, Leufken J, Schulze S, Sugimoto K, Klein J, Zahedi RP, Hippler M, Leidel SA, Fufezan C. pymzML v2.0: introducing a highly compressed and seekable gzip format. Bioinformatics 2019; 34:2513-2514. [PMID: 29394323 DOI: 10.1093/bioinformatics/bty046] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 01/30/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation In the new release of pymzML (v2.0), we have optimized the speed of this established tool for mass spectrometry data analysis to adapt to increasing amounts of data in mass spectrometry. Thus, we integrated faster libraries for numerical calculations, improved data retrieving algorithms and have optimized the source code. Importantly, to adapt to rapidly growing file sizes, we developed a generalizable compression scheme for very fast random access and applied this concept to mzML files to retrieve spectral data. Results pymzML performs at par with established C programs when it comes to processing times. However, it offers the versatility of a scripting language, while adding unprecedented fast random access to compressed files. Additionally, we designed our compression scheme in such a general way that it can be applied to any field where fast random access to large data blocks in compressed files is desired. Availability and implementation pymzML is freely available on https://github.com/pymzML/pymzML under GPL license. pymzML requires Python3.4+ and optionally numpy. Documentation available on http://pymzml.readthedocs.io.
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Affiliation(s)
- M Kösters
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany
| | - J Leufken
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany.,Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - S Schulze
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany
| | - K Sugimoto
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany
| | - J Klein
- Bioinformatics Program, Boston University, One Silber Way, Boston, MA, USA
| | - R P Zahedi
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, 5100 de Maisonneuve Boulevard West, Suite 720, Montreal, Quebec, Canada.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte-Sainte-Catherine Road, Montreal, Quebec, Canada
| | - M Hippler
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany
| | - S A Leidel
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - C Fufezan
- Institute of Plant Biology and Biotechnology, WWU Münster, Münster, Germany.,Cellzome A GSK Company, Heidelberg, Germany
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34
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Mnatsakanyan R, Markoutsa S, Walbrunn K, Roos A, Verhelst SHL, Zahedi RP. Proteome-wide detection of S-nitrosylation targets and motifs using bioorthogonal cleavable-linker-based enrichment and switch technique. Nat Commun 2019; 10:2195. [PMID: 31097712 PMCID: PMC6522481 DOI: 10.1038/s41467-019-10182-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/18/2019] [Indexed: 01/03/2023] Open
Abstract
Cysteine modifications emerge as important players in cellular signaling and homeostasis. Here, we present a chemical proteomics strategy for quantitative analysis of reversibly modified Cysteines using bioorthogonal cleavable-linker and switch technique (Cys-BOOST). Compared to iodoTMT for total Cysteine analysis, Cys-BOOST shows a threefold higher sensitivity and considerably higher specificity and precision. Analyzing S-nitrosylation (SNO) in S-nitrosoglutathione (GSNO)-treated and non-treated HeLa extracts Cys-BOOST identifies 8,304 SNO sites on 3,632 proteins covering a wide dynamic range of the proteome. Consensus motifs of SNO sites with differential GSNO reactivity confirm the relevance of both acid-base catalysis and local hydrophobicity for NO targeting to particular Cysteines. Applying Cys-BOOST to SH-SY5Y cells, we identify 2,151 SNO sites under basal conditions and reveal significantly changed SNO levels as response to early nitrosative stress, involving neuro(axono)genesis, glutamatergic synaptic transmission, protein folding/translation, and DNA replication. Our work suggests SNO as a global regulator of protein function akin to phosphorylation and ubiquitination. Reversible cysteine modifications play important roles in cellular redox signaling. Here, the authors develop a chemical proteomics strategy that enables the quantitative analysis of endogenous cysteine nitrosylation sites and their dynamic regulation under nitrosative stress conditions.
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Affiliation(s)
- Ruzanna Mnatsakanyan
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
| | - Stavroula Markoutsa
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
| | - Kim Walbrunn
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227, Dortmund, Germany
| | - Andreas Roos
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227, Dortmund, Germany.,Department of Neuropediatrics, Centre for Neuromuscular Disorders in Children, University Hospital Essen, University of Duisburg-Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Steven H L Verhelst
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227, Dortmund, Germany.,Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, Box 802, 3000, Leuven, Belgium
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227, Dortmund, Germany. .,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, 5100 de Maisonneuve Blvd. West, Montreal, Quebec, H4A 3T2, Canada. .,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, 3755 Côte Ste-Catherine Road, Montreal, Quebec, H3T 1E2, Canada.
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35
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Mnatsakanyan R, Shema G, Basik M, Batist G, Borchers CH, Sickmann A, Zahedi RP. Detecting post-translational modification signatures as potential biomarkers in clinical mass spectrometry. Expert Rev Proteomics 2019; 15:515-535. [PMID: 29893147 DOI: 10.1080/14789450.2018.1483340] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Numerous diseases are caused by changes in post-translational modifications (PTMs). Therefore, the number of clinical proteomics studies that include the analysis of PTMs is increasing. Combining complementary information-for example changes in protein abundance, PTM levels, with the genome and transcriptome (proteogenomics)-holds great promise for discovering important drivers and markers of disease, as variations in copy number, expression levels, or mutations without spatial/functional/isoform information is often insufficient or even misleading. Areas covered: We discuss general considerations, requirements, pitfalls, and future perspectives in applying PTM-centric proteomics to clinical samples. This includes samples obtained from a human subject, for instance (i) bodily fluids such as plasma, urine, or cerebrospinal fluid, (ii) primary cells such as reproductive cells, blood cells, and (iii) tissue samples/biopsies. Expert commentary: PTM-centric discovery proteomics can substantially contribute to the understanding of disease mechanisms by identifying signatures with potential diagnostic or even therapeutic relevance but may require coordinated efforts of interdisciplinary and eventually multi-national consortia, such as initiated in the cancer moonshot program. Additionally, robust and standardized mass spectrometry (MS) assays-particularly targeted MS, MALDI imaging, and immuno-MALDI-may be transferred to the clinic to improve patient stratification for precision medicine, and guide therapies.
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Affiliation(s)
- Ruzanna Mnatsakanyan
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Gerta Shema
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany
| | - Mark Basik
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Gerald Batist
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada
| | - Christoph H Borchers
- b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,c University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria , Victoria , British Columbia V8Z 7X8 , Canada.,d Department of Biochemistry and Microbiology , University of Victoria , Victoria , British Columbia , V8P 5C2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
| | - Albert Sickmann
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,f Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum , 44801 Bochum , Germany.,g Department of Chemistry , College of Physical Sciences, University of Aberdeen , Aberdeen AB24 3FX , Scotland , United Kingdom
| | - René P Zahedi
- a Protein Dynamics , Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V , Dortmund , 44227 , Germany.,b Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,e Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
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Unsworth AJ, Bombik I, Pinto-Fernandez A, McGouran JF, Konietzny R, Zahedi RP, Watson SP, Kessler BM, Pears CJ. Human Platelet Protein Ubiquitylation and Changes following GPVI Activation. Thromb Haemost 2018; 119:104-116. [PMID: 30597505 PMCID: PMC6327716 DOI: 10.1055/s-0038-1676344] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Platelet activators stimulate post-translational modification of signalling proteins to change their activity or their molecular interactions leading to signal propagation. One covalent modification is attachment of the small protein ubiquitin to lysine residues in target proteins. Modification by ubiquitin can either target proteins for degradation by the proteasome or act as a scaffold for other proteins. Pharmacological inhibition of deubiquitylases or the proteasome inhibition of platelet activation by collagen, demonstrating a role for ubiquitylation, but relatively few substrates for ubiquitin have been identified and the molecular basis of inhibition is not established. Here, we report the ubiquitome of human platelets and changes in ubiquitylated proteins following stimulation by collagen-related peptide (CRP-XL). Using platelets from six individuals over three independent experiments, we identified 1,634 ubiquitylated peptides derived from 691 proteins, revealing extensive ubiquitylation in resting platelets. Note that 925 of these peptides show an increase of more than twofold following stimulation with CRP-XL. Multiple sites of ubiquitylation were identified on several proteins including Syk, filamin and integrin heterodimer sub-units. This work reveals extensive protein ubiquitylation during activation of human platelets and opens the possibility of novel therapeutic interventions targeting the ubiquitin machinery.
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Affiliation(s)
- Amanda J Unsworth
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.,Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, United Kingdom
| | - Izabela Bombik
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Adan Pinto-Fernandez
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Joanna F McGouran
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Rebecca Konietzny
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - René P Zahedi
- JGH Proteomics Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Steve P Watson
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.,Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, The Midlands, United Kingdom
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Catherine J Pears
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Affiliation(s)
- René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Carol E Parker
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada; .,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.,University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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Popp R, Zahedi RP, LeBlanc A, Mohammed Y, Aguilar-Mahecha A, Pötz O, Basik M, Batist G, Borchers CH. Abstract LB-177: Quantification of cell signaling proteins by immuno-MALDI. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-lb-177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction. To improve cancer patient stratification and overcome the drawbacks of currently used approaches to assess signaling pathway proteins, we set out to develop immuno-matrix assisted laser ionization/desorption (iMALDI) assays combined with a phosphatase-based phosphopeptide quantitation (PPQ) approach to measure PI3K/AKT/mTOR pathway activity. Specifically, we targeted the C-terminal tryptic peptides of AKT1 and AKT2 due to their involvement in full kinase activation.
Methods. Following trypsin digestion of cell lysate, stable isotope-labeled standard (SIS) peptides are added. After splitting the solution, one aliquot is treated with phosphatase. Bead-coupled antibodies enrich the non-phosphorylated target peptides, which are washed and spotted onto a MALDI plate, and acidic MALDI matrix elutes the peptides. The resulting light/heavy ratios of both aliquots allow the calculation of protein expression levels and peptide phosphorylation stoichiometry.
Results. The iMALDI assays were validated for linear range and accuracy, as well as interference screening, requiring only ~50 µg of total cell or tissue lysate protein to quantify both AKT1 and AKT2 expression levels and phosphorylation stoichiometry. CVs of technical replicates were found to consistently be below 10%. We were able to quantify AKT1 and AKT2 from various cell lines and fresh frozen tumor samples, including SW480 and HCT116 colon cancer cell lines, MDA-MB-231 breast cancer cells, and colon cancer and breast cancer tumor lysates. Further, a direct comparison of matched fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissues showed that the expression levels and phosphorylation stoichiometry quantified differ depending on the tissue preservation method, and that phosphorylation stoichiometries above 30% occur in only a small subset of samples. A direct comparison of four pairs of normal and adjacent tumor tissues showed elevated AKT1 phosphorylation stoichiometry of ~40% in a colorectal cancer liver metastasis, and significantly elevated AKT1 (3.6-fold) and AKT2 (2.2-fold) expression levels in a surgical breast tumor sample.
Future directions. In a next step, patient-derived mouse xenograft tissue samples, collected after specific drug treatment, will be analyzed, and the AKT results will be correlated to genomic data to answer the hypothesis whether the AKT expression levels and phosphorylation stoichiometries correlate with response to treatment.
Citation Format: Robert Popp, René P. Zahedi, André LeBlanc, Yassene Mohammed, Adriana Aguilar-Mahecha, Oliver Pötz, Mark Basik, Gerald Batist, Christoph H. Borchers. Quantification of cell signaling proteins by immuno-MALDI [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-177.
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Affiliation(s)
- Robert Popp
- 1University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia, Canada
| | - René P. Zahedi
- 2Proteogenomics Program, Segal Cancer Centre, Jewish General Hospital, Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - André LeBlanc
- 2Proteogenomics Program, Segal Cancer Centre, Jewish General Hospital, Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Yassene Mohammed
- 1University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia, Canada
| | - Adriana Aguilar-Mahecha
- 2Proteogenomics Program, Segal Cancer Centre, Jewish General Hospital, Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Oliver Pötz
- 3Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Reutlingen, Germany
| | - Mark Basik
- 2Proteogenomics Program, Segal Cancer Centre, Jewish General Hospital, Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Gerald Batist
- 2Proteogenomics Program, Segal Cancer Centre, Jewish General Hospital, Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Christoph H. Borchers
- 1University of Victoria - Genome BC Proteomics Centre, Victoria, British Columbia, Canada
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Pett C, Nasir W, Sihlbom C, Olsson BM, Caixeta V, Schorlemer M, Zahedi RP, Larson G, Nilsson J, Westerlind U. Effective Assignment of α2,3/α2,6-Sialic Acid Isomers by LC-MS/MS-Based Glycoproteomics. Angew Chem Int Ed Engl 2018; 57:9320-9324. [PMID: 29742324 DOI: 10.1002/anie.201803540] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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: 03/23/2018] [Revised: 05/08/2018] [Indexed: 11/07/2022]
Abstract
Distinct structural changes of the α2,3/α2,6-sialic acid glycosidic linkages on glycoproteins are of importance in cancer biology, inflammatory diseases, and virus tropism. Current glycoproteomic methodologies are, however, not amenable toward high-throughput characterization of sialic acid isomers. To enable such assignments, a mass spectrometry method utilizing synthetic model glycopeptides for the analysis of oxonium ion intensity ratios was developed. This method was successfully applied in large-scale glycoproteomics, thus allowing the site-specific structural characterization of sialic acid isomers.
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Affiliation(s)
- Christian Pett
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.,Department of Chemistry, Umeå University, 90187, Umeå, Sweden
| | - Waqas Nasir
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Thermo Fischer Scientific, Bremen, Germany
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Britt-Marie Olsson
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Vanessa Caixeta
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany
| | - Manuel Schorlemer
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.,Department of Chemistry, Umeå University, 90187, Umeå, Sweden
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Ulrika Westerlind
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44227, Dortmund, Germany.,Department of Chemistry, Umeå University, 90187, Umeå, Sweden
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40
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Pett C, Nasir W, Sihlbom C, Olsson BM, Caixeta V, Schorlemer M, Zahedi RP, Larson G, Nilsson J, Westerlind U. Effective Assignment of α2,3/α2,6-Sialic Acid Isomers by LC-MS/MS-Based Glycoproteomics. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Christian Pett
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.; 44227 Dortmund Germany
- Department of Chemistry; Umeå University; 90187 Umeå Sweden
| | - Waqas Nasir
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine; University of Gothenburg; Gothenburg Sweden
- Thermo Fischer Scientific; Bremen Germany
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy; University of Gothenburg; Gothenburg Sweden
| | - Britt-Marie Olsson
- Proteomics Core Facility, Sahlgrenska Academy; University of Gothenburg; Gothenburg Sweden
| | - Vanessa Caixeta
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.; 44227 Dortmund Germany
| | - Manuel Schorlemer
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.; 44227 Dortmund Germany
- Department of Chemistry; Umeå University; 90187 Umeå Sweden
| | - René P. Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.; 44227 Dortmund Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute; Jewish General Hospital; McGill University; Montreal Quebec Canada
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine; University of Gothenburg; Gothenburg Sweden
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine; University of Gothenburg; Gothenburg Sweden
| | - Ulrika Westerlind
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V.; 44227 Dortmund Germany
- Department of Chemistry; Umeå University; 90187 Umeå Sweden
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Boczonadi V, Meyer K, Gonczarowska-Jorge H, Griffin H, Roos A, Bartsakoulia M, Bansagi B, Ricci G, Palinkas F, Zahedi RP, Bruni F, Kaspar B, Lochmüller H, Boycott KM, Müller JS, Horvath R. Mutations in glycyl-tRNA synthetase impair mitochondrial metabolism in neurons. Hum Mol Genet 2018; 27:2187-2204. [PMID: 29648643 PMCID: PMC5985729 DOI: 10.1093/hmg/ddy127] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 03/27/2018] [Indexed: 12/30/2022] Open
Abstract
The nuclear-encoded glycyl-tRNA synthetase gene (GARS) is essential for protein translation in both cytoplasm and mitochondria. In contrast, different genes encode the mitochondrial and cytosolic forms of most other tRNA synthetases. Dominant GARS mutations were described in inherited neuropathies, while recessive mutations cause severe childhood-onset disorders affecting skeletal muscle and heart. The downstream events explaining tissue-specific phenotype-genotype relations remained unclear. We investigated the mitochondrial function of GARS in human cell lines and in the GarsC210R mouse model. Human-induced neuronal progenitor cells (iNPCs) carrying dominant and recessive GARS mutations showed alterations of mitochondrial proteins, which were more prominent in iNPCs with dominant, neuropathy-causing mutations. Although comparative proteomic analysis of iNPCs showed significant changes in mitochondrial respiratory chain complex subunits, assembly genes, Krebs cycle enzymes and transport proteins in both recessive and dominant mutations, proteins involved in fatty acid oxidation were only altered by recessive mutations causing mitochondrial cardiomyopathy. In contrast, significant alterations of the vesicle-associated membrane protein-associated protein B (VAPB) and its downstream pathways such as mitochondrial calcium uptake and autophagy were detected in dominant GARS mutations. The role of VAPB has been supported by similar results in the GarsC210R mice. Our data suggest that altered mitochondria-associated endoplasmic reticulum (ER) membranes (MAM) may be important disease mechanisms leading to neuropathy in this condition.
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Affiliation(s)
- Veronika Boczonadi
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK
| | - Kathrin Meyer
- The Research Institute, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Humberto Gonczarowska-Jorge
- Leibniz-Institute für Analytische Wissenschaften-ISAS-e.V., Dortmund 44139, Germany,CAPES Foundation, Ministry of Education of Brazil, Brazil
| | - Helen Griffin
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK
| | - Andreas Roos
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK,Leibniz-Institute für Analytische Wissenschaften-ISAS-e.V., Dortmund 44139, Germany
| | - Marina Bartsakoulia
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK
| | - Boglarka Bansagi
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK
| | - Giulia Ricci
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK,Department of Clinical and Experimental Medicine, University of Pisa, Pisa 56126, Italy
| | - Fanni Palinkas
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK
| | - René P Zahedi
- Leibniz-Institute für Analytische Wissenschaften-ISAS-e.V., Dortmund 44139, Germany
| | - Francesco Bruni
- Institute of Neuroscience, Wellcome Centre for Mitochondrial Research, Newcastle University, NE2 4HH Newcastle upon Tyne, UK,Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, 70121 Bari, Italy
| | - Brian Kaspar
- The Research Institute, Nationwide Children’s Hospital, Columbus, OH 43205, USA,Department of Neuroscience, Molecular, Cellular, and Developmental Biology Graduate Program and Integrated Biomedical Science Graduate Program, College of Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Hanns Lochmüller
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK,Department of Neuropediatrics and Muscle Disorders, Medical Center – University of Freiburg, Faculty of Medicine, Freiburg 79160, Germany,Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona 08028, Spain
| | - Kym M Boycott
- Department of Genetics, CHEO Research Institute, University of Ottawa, K1H 8L1 Ottawa, Canada
| | - Juliane S Müller
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK
| | - Rita Horvath
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, NE1 3BZ Newcastle upon Tyne, UK,To whom correspondence should be addressed at: Institute of Genetic Medicine, Newcastle University, Central Parkway, NE1 3BZ Newcastle upon Tyne, UK. Tel: +44 1912418855; Fax: +44 1912418666;
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Walter C, Gonczarowska-Jorge H, Sickmann A, Zahedi RP, Meisinger C, Schmidt O. Advanced tools for the analysis of protein phosphorylation in yeast mitochondria. Anal Biochem 2018; 554:23-27. [PMID: 29803787 DOI: 10.1016/j.ab.2018.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 04/05/2018] [Revised: 05/15/2018] [Accepted: 05/23/2018] [Indexed: 11/16/2022]
Abstract
The biochemical analysis of protein phosphorylation in mitochondria lags behind that of cytosolic signaling events. One reason is the poor stability of many phosphorylation sites during common isolation procedures for mitochondria. We present here an optimized, fast protocol for the purification of yeast mitochondria that greatly increases recovery of phosphorylated mitochondrial proteins. Moreover, we describe improved protocols for the biochemical analysis of mitochondrial protein phosphorylation by Zn2+-Phos-tag electrophoresis under both denaturing and - for the first time - native conditions, and demonstrate that they outperform previously applied methods.
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Affiliation(s)
- Corvin Walter
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany; Faculty of Biology, University of Freiburg, Germany
| | - Humberto Gonczarowska-Jorge
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany; CAPES Foundation, Ministry of Education of Brazil, Brasília, DF 70040-020, Brazil
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany; Medizinisches Proteom-Center (MPC), Medical Faculty, Ruhr-Universität Bochum, Bochum, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Canada
| | - Chris Meisinger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany.
| | - Oliver Schmidt
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria.
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43
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Rodrigues RM, Kollipara L, Chaudhari U, Sachinidis A, Zahedi RP, Sickmann A, Kopp-Schneider A, Jiang X, Keun H, Hengstler J, Oorts M, Annaert P, Hoeben E, Gijbels E, De Kock J, Vanhaecke T, Rogiers V, Vinken M. Omics-based responses induced by bosentan in human hepatoma HepaRG cell cultures. Arch Toxicol 2018; 92:1939-1952. [PMID: 29761207 DOI: 10.1007/s00204-018-2214-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 08/09/2017] [Accepted: 04/26/2018] [Indexed: 11/24/2022]
Abstract
Bosentan is well known to induce cholestatic liver toxicity in humans. The present study was set up to characterize the hepatotoxic effects of this drug at the transcriptomic, proteomic, and metabolomic levels. For this purpose, human hepatoma-derived HepaRG cells were exposed to a number of concentrations of bosentan during different periods of time. Bosentan was found to functionally and transcriptionally suppress the bile salt export pump as well as to alter bile acid levels. Pathway analysis of both transcriptomics and proteomics data identified cholestasis as a major toxicological event. Transcriptomics results further showed several gene changes related to the activation of the nuclear farnesoid X receptor. Induction of oxidative stress and inflammation were also observed. Metabolomics analysis indicated changes in the abundance of specific endogenous metabolites related to mitochondrial impairment. The outcome of this study may assist in the further optimization of adverse outcome pathway constructs that mechanistically describe the processes involved in cholestatic liver injury.
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Affiliation(s)
- Robim M Rodrigues
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | | | - Umesh Chaudhari
- Institute of Neurophysiology and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Agapios Sachinidis
- Institute of Neurophysiology and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, Scotland, UK.,Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, Bochum, Germany
| | | | - Xiaoqi Jiang
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
| | - Hector Keun
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Jan Hengstler
- Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund, Dortmund, Germany
| | - Marlies Oorts
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Pieter Annaert
- Drug Delivery and Disposition, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | - Eva Gijbels
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Joery De Kock
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Tamara Vanhaecke
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Vera Rogiers
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium
| | - Mathieu Vinken
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090, Brussels, Belgium.
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Nguyen MTN, Shema G, Zahedi RP, Verhelst SHL. Protease Specificity Profiling in a Pipet Tip Using "Charge-Synchronized" Proteome-Derived Peptide Libraries. J Proteome Res 2018; 17:1923-1933. [PMID: 29664642 DOI: 10.1021/acs.jproteome.8b00004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
About 2% of the genome of human and other organisms codes for proteases. An important step toward deciphering the biological function of a protease and designing inhibitors is the profiling of protease specificity. In this work we present a novel, label-free, proteomics-based protease specificity profiling method that only requires simple sample preparation steps. It uses proteome-derived peptide libraries and enriches the cleaved sequences using strong cation exchange chromatography (SCX) material in a pipet tip. As a demonstration of the method's versatility, we successfully determined the specificity of GluC, caspase-3, chymotrypsin, MMP-1 and cathepsin G from several hundreds to almost 2000 cleavage events per protease. Interestingly, we also found a novel intrinsic preference of cathepsin G for Asn at the P1 subsite, which we confirmed using synthetic peptides. Overall, this method is straightforward and requires so far the lowest investment in material and equipment for protease specificity profiling. Therefore, we think it will be applicable in any biochemistry laboratory and promote an increased understanding of protease specificity.
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Affiliation(s)
- Minh T N Nguyen
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Str. 6b , 44227 Dortmund , Germany
| | - Gerta Shema
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Str. 6b , 44227 Dortmund , Germany
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Str. 6b , 44227 Dortmund , Germany.,Gerald Bronfman Department of Oncology , Jewish General Hospital, McGill University , Montreal , Quebec H4A 3T2 , Canada.,Segal Cancer Proteomics Centre , Lady Davis Institute, Jewish General Hospital, McGill University , Montreal , Quebec H3T 1E2 , Canada
| | - Steven H L Verhelst
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V. , Otto-Hahn-Str. 6b , 44227 Dortmund , Germany.,Laboratory of Chemical Biology, Department of Cellular and Molecular Medicine , KU Leuven-University of Leuven , Herestraat 49 box 802, 3000 Leuven , Belgium
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Isensee J, Kaufholz M, Knape MJ, Hasenauer J, Hammerich H, Gonczarowska-Jorge H, Zahedi RP, Schwede F, Herberg FW, Hucho T. PKA-RII subunit phosphorylation precedes activation by cAMP and regulates activity termination. J Cell Biol 2018; 217:2167-2184. [PMID: 29615473 PMCID: PMC5987717 DOI: 10.1083/jcb.201708053] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 02/18/2018] [Accepted: 03/15/2018] [Indexed: 11/22/2022] Open
Abstract
Activity of endogenous protein kinase A (PKA) could never be analyzed directly in the cellular environment. Isensee et al. used antibodies to quantify conformational changes leading to an open conformation of endogenous PKA-II holoenzymes, which allowed them to analyze and model its activation cycle in primary sensory neurons. Type II isoforms of cyclic adenosine monophosphate (cAMP)–dependent protein kinase A (PKA-II) contain a phosphorylatable epitope within the inhibitory domain of RII subunits (pRII) with still unclear function. In vitro, RII phosphorylation occurs in the absence of cAMP, whereas staining of cells with pRII-specific antibodies revealed a cAMP-dependent pattern. In sensory neurons, we found that increased pRII immunoreactivity reflects increased accessibility of the already phosphorylated RII epitope during cAMP-induced opening of the tetrameric RII2:C2 holoenzyme. Accordingly, induction of pRII by cAMP was sensitive to novel inhibitors of dissociation, whereas blocking catalytic activity was ineffective. Also in vitro, cAMP increased the binding of pRII antibodies to RII2:C2 holoenzymes. Identification of an antibody specific for the glycine-rich loop of catalytic subunits facing the pRII-epitope confirmed activity-dependent binding with similar kinetics, proving that the reassociation is rapid and precisely controlled. Mechanistic modeling further supported that RII phosphorylation precedes cAMP binding and controls the inactivation by modulating the reassociation involving the coordinated action of phosphodiesterases and phosphatases.
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Affiliation(s)
- Jörg Isensee
- Department of Anesthesiology and Intensive Care Medicine, Experimental Anesthesiology and Pain Research, University Hospital of Cologne, Cologne, Germany
| | - Melanie Kaufholz
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Matthias J Knape
- Department of Biochemistry, University of Kassel, Kassel, Germany
| | - Jan Hasenauer
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.,Center for Mathematics, Technische Universität München, Garching, Germany
| | - Hanna Hammerich
- Department of Anesthesiology and Intensive Care Medicine, Experimental Anesthesiology and Pain Research, University Hospital of Cologne, Cologne, Germany
| | - Humberto Gonczarowska-Jorge
- ISAS, Leibniz-Institut für Analytische Wissenschaften, Dortmund, Germany.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - René P Zahedi
- ISAS, Leibniz-Institut für Analytische Wissenschaften, Dortmund, Germany
| | | | | | - Tim Hucho
- Department of Anesthesiology and Intensive Care Medicine, Experimental Anesthesiology and Pain Research, University Hospital of Cologne, Cologne, Germany
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Makhoul S, Walter E, Pagel O, Walter U, Sickmann A, Gambaryan S, Smolenski A, Zahedi RP, Jurk K. Effects of the NO/soluble guanylate cyclase/cGMP system on the functions of human platelets. Nitric Oxide 2018; 76:71-80. [PMID: 29550521 DOI: 10.1016/j.niox.2018.03.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/03/2018] [Accepted: 03/12/2018] [Indexed: 02/07/2023]
Abstract
Platelets are circulating sentinels of vascular integrity and are activated, inhibited, or modulated by multiple hormones, vasoactive substances or drugs. Endothelium- or drug-derived NO strongly inhibits platelet activation via activation of the soluble guanylate cyclase (sGC) and cGMP elevation, often in synergy with cAMP-elevation by prostacyclin. However, the molecular mechanisms and diversity of cGMP effects in platelets are poorly understood and sometimes controversial. Recently, we established the quantitative human platelet proteome, the iloprost/prostacyclin/cAMP/protein kinase A (PKA)-regulated phosphoproteome, and the interactions of the ADP- and iloprost/prostacyclin-affected phosphoproteome. We also showed that the sGC stimulator riociguat is in vitro a highly specific inhibitor, via cGMP, of various functions of human platelets. Here, we review the regulatory role of the cGMP/protein kinase G (PKG) system in human platelet function, and our current approaches to establish and analyze the phosphoproteome after selective stimulation of the sGC/cGMP pathway by NO donors and riociguat. Present data indicate an extensive and diverse NO/riociguat/cGMP phosphoproteome, which has to be compared with the cAMP phosphoproteome. In particular, sGC/cGMP-regulated phosphorylation of many membrane proteins, G-proteins and their regulators, signaling molecules, protein kinases, and proteins involved in Ca2+ regulation, suggests that the sGC/cGMP system targets multiple signaling networks rather than a limited number of PKG substrate proteins.
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Affiliation(s)
- Stephanie Makhoul
- University Medical Center Mainz, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany
| | - Elena Walter
- University Medical Center Mainz, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany
| | - Oliver Pagel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Dortmund, Germany
| | - Ulrich Walter
- University Medical Center Mainz, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Dortmund, Germany; Ruhr Universität Bochum, Medizinisches Proteom Center, Medizinische Fakultät, Bochum, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK
| | - Stepan Gambaryan
- University Medical Center Mainz, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany; Russian Academy of Sciences, Sechenov Institute of Evolutionary Physiology and Biochemistry, St. Petersburg, Russia; St. Petersburg State University, Department of Cytology and Histology, St. Petersburg, Russia
| | - Albert Smolenski
- Conway Institute of Biomolecular & Biomedical Research, Univ. College Dublin, Dublin, Ireland; Irish Centre for Vascular Biology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - René P Zahedi
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University , Montreal, Quebec H4A 3T2, Canada; Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal, Quebec H3T 1E2, Canada
| | - Kerstin Jurk
- University Medical Center Mainz, Center for Thrombosis and Hemostasis (CTH), Mainz, Germany.
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Gotru SK, Chen W, Kraft P, Becker IC, Wolf K, Stritt S, Zierler S, Hermanns HM, Rao D, Perraud AL, Schmitz C, Zahedi RP, Noy PJ, Tomlinson MG, Dandekar T, Matsushita M, Chubanov V, Gudermann T, Stoll G, Nieswandt B, Braun A. TRPM7 Kinase Controls Calcium Responses in Arterial Thrombosis and Stroke in Mice. Arterioscler Thromb Vasc Biol 2018; 38:344-352. [DOI: 10.1161/atvbaha.117.310391] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/30/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Sanjeev K. Gotru
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Wenchun Chen
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Peter Kraft
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Isabelle C. Becker
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Karen Wolf
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Simon Stritt
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Susanna Zierler
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Heike M. Hermanns
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Deviyani Rao
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Anne-Laure Perraud
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Carsten Schmitz
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - René P. Zahedi
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Peter J. Noy
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Michael G. Tomlinson
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Thomas Dandekar
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Masayuki Matsushita
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Vladimir Chubanov
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Thomas Gudermann
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Guido Stoll
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Bernhard Nieswandt
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
| | - Attila Braun
- From the Institute of Experimental Biomedicine, University Hospital of Würzburg (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), Rudolf Virchow Center (S.K.G., W.C., I.C.B., K.W., S.S., B.N., A.B.), and Institute of Clinical Epidemiology and Biometry, Comprehensive Heart Failure Center (P.K.), University of Würzburg, Germany; Department of Hepatology (H.M.H.) and Department of Neurology (P.K., G.S.), University Hospital of Würzburg, Germany; Walther-Straub-Institute for Pharmacology and Toxicology,
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Shema G, Nguyen MTN, Solari FA, Loroch S, Venne AS, Kollipara L, Sickmann A, Verhelst SHL, Zahedi RP. Simple, scalable, and ultrasensitive tip-based identification of protease substrates. Mol Cell Proteomics 2018; 17:826-834. [PMID: 29358340 DOI: 10.1074/mcp.tir117.000302] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 01/15/2018] [Indexed: 11/06/2022] Open
Abstract
Proteases are in the center of many diseases, and consequently, proteases and their substrates are important drug targets as represented by an estimated 5-10% of all drugs under development. Mass spectrometry has been an indispensable tool for the discovery of novel protease substrates, particularly through the proteome-scale enrichment of so-called N-terminal peptides representing endogenous protein N termini. Methods such as combined fractional diagonal chromatography (COFRADIC)1 and, later, terminal amine isotopic labeling of substrates (TAILS) have revealed numerous insights into protease substrates and consensus motifs. We present an alternative and simple protocol for N-terminal peptide enrichment, based on charge-based fractional diagonal chromatography (ChaFRADIC) and requiring only well-established protein chemistry and a pipette tip. Using iTRAQ-8-plex, we quantified on average 2,073 ± 52 unique N-terminal peptides from only 4.3 μg per sample/channel, allowing the identification of proteolytic targets and consensus motifs. This high sensitivity may even allow working with clinical samples such as needle biopsies in the future. We applied our method to study the dynamics of staurosporine-induced apoptosis. Our data demonstrate an orchestrated regulation of specific pathways after 1.5 h, 3 h, and 6 h of treatment, with many important players of homeostasis targeted already after 1.5 h. We additionally observed an early multilevel modulation of the splicing machinery both by proteolysis and phosphorylation. This may reflect the known role of alternative splicing variants for a variety of apoptotic genes, which seems to be a driving force of staurosporine-induced apoptosis.
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Affiliation(s)
- Gerta Shema
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Minh T N Nguyen
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Fiorella A Solari
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Stefan Loroch
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - A Saskia Venne
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Laxmikanth Kollipara
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Albert Sickmann
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.,§Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum, 44801 Bochum, Germany.,¶Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen AB24 3FX, Scotland, United Kingdom
| | - Steven H L Verhelst
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany.,‖Department of Cellular and Molecular Medicine, KU Leuven-University of Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - René P Zahedi
- From the ‡Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany; .,**Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec H4A 3T2, Canada.,‡‡Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec H3T 1E2, Canada
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O'Connor E, Töpf A, Zahedi RP, Spendiff S, Cox D, Roos A, Lochmüller H. Clinical and research strategies for limb-girdle congenital myasthenic syndromes. Ann N Y Acad Sci 2018; 1412:102-112. [PMID: 29315608 DOI: 10.1111/nyas.13520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 08/01/2017] [Revised: 09/05/2017] [Accepted: 09/12/2017] [Indexed: 12/21/2022]
Abstract
Congenital myasthenic syndromes (CMS) are a group of rare disorders that cause fatigable muscle weakness due to defective signal transmission at the neuromuscular junction, a specialized synapse between peripheral motor neurons and their target muscle fibers. There are now over 30 causative genes that have been reported for CMS. Of these, there are 10 that are associated with a limb-girdle pattern of muscle weakness and are thus classed as LG-CMS. Next-generation sequencing and advanced methods of data sharing are likely to uncover further genes that are associated with similar clinical phenotypes, contributing to better diagnosis and effective treatment of LG-CMS patients. This review highlights clinical and pathological hallmarks of LG-CMS in relation to the underlying genetic defects and pathways. Tailored animal and cell models are essential to elucidate the exact function and pathomechanisms at the neuromuscular synapse that underlie LG-CMS. The integration of genomics and proteomics data derived from these models and patients reveals new and often unexpected insights that are relevant beyond the rare genetic disorder of LG-CMS and may extend to the functioning of mammalian synapses in health and disease more generally.
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Affiliation(s)
- Emily O'Connor
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Ana Töpf
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften, ISAS e.V., Dortmund, Germany
| | - Sally Spendiff
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel Cox
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Andreas Roos
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Leibniz-Institut für Analytische Wissenschaften, ISAS e.V., Dortmund, Germany
| | - Hanns Lochmüller
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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Gonczarowska-Jorge H, Loroch S, Dell'Aica M, Sickmann A, Roos A, Zahedi RP. Quantifying Missing (Phospho)Proteome Regions with the Broad-Specificity Protease Subtilisin. Anal Chem 2017; 89:13137-13145. [PMID: 29136377 DOI: 10.1021/acs.analchem.7b02395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Despite huge efforts to map the human proteome using mass spectrometry the overall sequence coverage achieved to date is still below 50%. Reasons for missing areas of the proteome comprise protease-resistant domains including the lack/excess of enzymatic cleavage sites, nonunique peptide sequences, impaired peptide ionization/separation and low expression levels. To access novel areas of the proteome the beneficial use of enzymes complementary to trypsin, such as Glu-C, Asp-N, Lys-N, Arg-C, LysargiNase has been reported. Here, we present how the broad-specificity protease subtilisin enables mapping of previously hidden areas of the proteome. We systematically evaluated its digestion efficiency and reproducibility and compared it to the gold standard in the field, trypsin. Notably, subtilisin allows reproducible near-complete digestion of cells lysates in 1-5 min. As expected from its broad specificity the generation of overlapping peptide sequences reduces the number of identified proteins compared to trypsin (8363 vs 6807; 1% protein FDR). However, subtilisin considerably improved the coverage of missing and particularly proline-rich areas of the proteome. Along 14 628 high confidence phosphorylation sites identified in total, only 33% were shared between both enzymes, while 37% were exclusive to subtilisin. Notably, 926 of these were not even accessible by additional in silico digestion with either Asp-N, Arg-C, Glu-C, Lys-C, or Lys-N. Thus, subtilisin might be particularly beneficial for system-wide profiling of post-translational modification sites. Finally, we demonstrate that subtilisin can be used for reporter-ion based in-depth quantification, providing a precision comparable to trypsin-despite broad specificity and fast digestion that may increase technical variance.
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Affiliation(s)
- Humberto Gonczarowska-Jorge
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,CAPES Foundation, Ministry of Education of Brazil, Brasília Distrito Federal 70040-020, Brazil
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany
| | - Margherita Dell'Aica
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,Medizinische Fakultät, Medizinische Proteom-Center (MPC), Ruhr-Universität Bochum , 44801 Bochum, Germany.,Department of Chemistry, College of Physical Sciences, University of Aberdeen , Aberdeen, AB24 3FX, United Kingdom
| | - Andreas Roos
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Newcastle University , Newcastle upon Tyne, NE1 3BZ, United Kingdom
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. , 44227 Dortmund, Germany.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University , Montreal, Quebec H4A 3T2, Canada.,Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University , Montreal, Quebec H3T 1E2, Canada
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