1
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Ayagama T, Charles PD, Bose SJ, Boland B, Priestman DA, Aston D, Berridge G, Fischer R, Cribbs AP, Song Q, Mirams GR, Amponsah K, Heather L, Galione A, Herring N, Kramer H, Capel RA, Platt FM, Schotten U, Verheule S, Burton RA. Compartmentalization proteomics revealed endolysosomal protein network changes in a goat model of atrial fibrillation. iScience 2024; 27:109609. [PMID: 38827406 PMCID: PMC11141153 DOI: 10.1016/j.isci.2024.109609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 02/07/2024] [Accepted: 03/25/2024] [Indexed: 06/04/2024] Open
Abstract
Endolysosomes (EL) are known for their role in regulating both intracellular trafficking and proteostasis. EL facilitate the elimination of damaged membranes, protein aggregates, membranous organelles and play an important role in calcium signaling. The specific role of EL in cardiac atrial fibrillation (AF) is not well understood. We isolated atrial EL organelles from AF goat biopsies and conducted a comprehensive integrated omics analysis to study the EL-specific proteins and pathways. We also performed electron tomography, protein and enzyme assays on these biopsies. Our results revealed the upregulation of the AMPK pathway and the expression of EL-specific proteins that were not found in whole tissue lysates, including GAA, DYNLRB1, CLTB, SIRT3, CCT2, and muscle-specific HSPB2. We also observed structural anomalies, such as autophagic-vacuole formation, irregularly shaped mitochondria, and glycogen deposition. Our results provide molecular information suggesting EL play a role in AF disease process over extended time frames.
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Affiliation(s)
- Thamali Ayagama
- Department of Pharmacology, University of Oxford, Oxford, UK
| | | | - Samuel J. Bose
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Barry Boland
- Department of Pharmacology and Therapeutics, University College Cork, Cork, Ireland
| | | | - Daniel Aston
- Department of Anaesthesia and Critical Care, Royal Papworth Hospital NHS Foundation Trust, Papworth Road, Cambridge CB2 0AY, UK
| | | | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - Adam P. Cribbs
- Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Headington OX3 7LD, UK
| | - Qianqian Song
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Gary R. Mirams
- Centre for Mathematical Medicine & Biology, Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Kwabena Amponsah
- Centre for Mathematical Medicine & Biology, Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK
| | - Lisa Heather
- Department of Physiology, Anatomy and Genetics, , University of Oxford, South Park Road, Oxford OX1 3PT, UK
| | - Antony Galione
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Neil Herring
- Department of Physiology, Anatomy and Genetics, , University of Oxford, South Park Road, Oxford OX1 3PT, UK
| | - Holger Kramer
- Mass spectrometry Facility, The MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | | | - Ulrich Schotten
- Departments of Physiology and Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Sander Verheule
- Departments of Physiology and Cardiology, Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, the Netherlands
| | - Rebecca A.B. Burton
- Department of Pharmacology, University of Oxford, Oxford, UK
- University of Liverpool, Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, Liverpool, UK
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2
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Liang Z, Damianou A, Vendrell I, Jenkins E, Lassen FH, Washer SJ, Grigoriou A, Liu G, Yi G, Lou H, Cao F, Zheng X, Fernandes RA, Dong T, Tate EW, Di Daniel E, Kessler BM. Proximity proteomics reveals UCH-L1 as an essential regulator of NLRP3-mediated IL-1β production in human macrophages and microglia. Cell Rep 2024; 43:114152. [PMID: 38669140 DOI: 10.1016/j.celrep.2024.114152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/28/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Activation of the NACHT, LRR, and PYD domains-containing protein 3 (NLRP3) inflammasome complex is an essential innate immune signaling mechanism. To reveal how human NLRP3 inflammasome assembly and activation are controlled, in particular by components of the ubiquitin system, proximity labeling, affinity purification, and RNAi screening approaches were performed. Our study provides an intricate time-resolved molecular map of different phases of NLRP3 inflammasome activation. Also, we show that ubiquitin C-terminal hydrolase 1 (UCH-L1) interacts with the NACHT domain of NLRP3. Downregulation of UCH-L1 decreases pro-interleukin-1β (IL-1β) levels. UCH-L1 chemical inhibition with small molecules interfered with NLRP3 puncta formation and ASC oligomerization, leading to altered IL-1β cleavage and secretion, particularly in microglia cells, which exhibited elevated UCH-L1 expression as compared to monocytes/macrophages. Altogether, we profiled NLRP3 inflammasome activation dynamics and highlight UCH-L1 as an important modulator of NLRP3-mediated IL-1β production, suggesting that a pharmacological inhibitor of UCH-L1 may decrease inflammation-associated pathologies.
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Affiliation(s)
- Zhu Liang
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
| | - Andreas Damianou
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Iolanda Vendrell
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Edward Jenkins
- Kennedy Institute of Rheumatology, University of Oxford, Oxford OX3 7FY, UK
| | - Frederik H Lassen
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
| | - Sam J Washer
- James and Lillian Martin Centre for Stem Cell Research, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Athina Grigoriou
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Guihai Liu
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Gangshun Yi
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Hantao Lou
- Ludwig Institute for Cancer Research, University of Oxford, Oxford, UK
| | - Fangyuan Cao
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Xiaonan Zheng
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Ricardo A Fernandes
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Tao Dong
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Elena Di Daniel
- Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Benedikt M Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK.
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3
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Ye J, He X, Wang S, Dong MQ, Wu F, Lu S, Feng F. Test-Time Training for Deep MS/MS Spectrum Prediction Improves Peptide Identification. J Proteome Res 2024; 23:550-559. [PMID: 38153036 DOI: 10.1021/acs.jproteome.3c00229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
In bottom-up proteomics, peptide-spectrum matching is critical for peptide and protein identification. Recently, deep learning models have been used to predict tandem mass spectra of peptides, enabling the calculation of similarity scores between the predicted and experimental spectra for peptide-spectrum matching. These models follow the supervised learning paradigm, which trains a general model using paired peptides and spectra from standard data sets and directly employs the model on experimental data. However, this approach can lead to inaccurate predictions due to differences between the training data and the experimental data, such as sample types, enzyme specificity, and instrument calibration. To tackle this problem, we developed a test-time training paradigm that adapts the pretrained model to generate experimental data-specific models, namely, PepT3. PepT3 yields a 10-40% increase in peptide identification depending on the variability in training and experimental data. Intriguingly, when applied to a patient-derived immunopeptidomic sample, PepT3 increases the identification of tumor-specific immunopeptide candidates by 60%. Two-thirds of the newly identified candidates are predicted to bind to the patient's human leukocyte antigen isoforms. To facilitate access of the model and all the results, we have archived all the intermediate files in Zenodo.org with identifier 8231084.
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Affiliation(s)
- Jianbai Ye
- MoE Key Laboratory of Brain-inspired Intelligent Perception and Cognition, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Xiangnan He
- MoE Key Laboratory of Brain-inspired Intelligent Perception and Cognition, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shujuan Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Feng Wu
- MoE Key Laboratory of Brain-inspired Intelligent Perception and Cognition, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Shan Lu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, United States
| | - Fuli Feng
- MoE Key Laboratory of Brain-inspired Intelligent Perception and Cognition, University of Science and Technology of China, Hefei, Anhui 230026, China
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4
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Vasilyev N, Liu MMJ, Epshtein V, Shamovsky I, Nudler E. General transcription factor from Escherichia coli with a distinct mechanism of action. Nat Struct Mol Biol 2024; 31:141-149. [PMID: 38177674 PMCID: PMC10803263 DOI: 10.1038/s41594-023-01154-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 10/16/2023] [Indexed: 01/06/2024]
Abstract
Gene expression in Escherichia coli is controlled by well-established mechanisms that activate or repress transcription. Here, we identify CedA as an unconventional transcription factor specifically associated with the RNA polymerase (RNAP) σ70 holoenzyme. Structural and biochemical analysis of CedA bound to RNAP reveal that it bridges distant domains of β and σ70 subunits to stabilize an open-promoter complex. CedA does so without contacting DNA. We further show that cedA is strongly induced in response to amino acid starvation, oxidative stress and aminoglycosides. CedA provides a basal level of tolerance to these clinically relevant antibiotics, as well as to rifampicin and peroxide. Finally, we show that CedA modulates transcription of hundreds of bacterial genes, which explains its pleotropic effect on cell physiology and pathogenesis.
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Affiliation(s)
- Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Mengjie M J Liu
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Vitaly Epshtein
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, USA.
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5
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Li J, Krause GJ, Gui Q, Kaushik S, Rona G, Zhang Q, Liang FX, Dhabaria A, Anerillas C, Martindale JL, Vasilyev N, Askenazi M, Ueberheide B, Nudler E, Gorospe M, Cuervo AM, Pagano M. A noncanonical function of SKP1 regulates the switch between autophagy and unconventional secretion. SCIENCE ADVANCES 2023; 9:eadh1134. [PMID: 37831778 PMCID: PMC10575587 DOI: 10.1126/sciadv.adh1134] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
Intracellular degradation of proteins and organelles by the autophagy-lysosome system is essential for cellular quality control and energy homeostasis. Besides degradation, endolysosomal organelles can fuse with the plasma membrane and contribute to unconventional secretion. Here, we identify a function for mammalian SKP1 in endolysosomes that is independent of its established role as an essential component of the family of SCF/CRL1 ubiquitin ligases. We found that, under nutrient-poor conditions, SKP1 is phosphorylated on Thr131, allowing its interaction with V1 subunits of the vacuolar ATPase (V-ATPase). This event, in turn, promotes V-ATPase assembly to acidify late endosomes and enhance endolysosomal degradation. Under nutrient-rich conditions, SUMOylation of phosphorylated SKP1 allows its binding to and dephosphorylation by the PPM1B phosphatase. Dephosphorylated SKP1 interacts with SEC22B to promote unconventional secretion of the content of less acidified hybrid endosomal/autophagic compartments. Collectively, our study implicates SKP1 phosphorylation as a switch between autophagy and unconventional secretion in a manner dependent on cellular nutrient status.
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Affiliation(s)
- Jie Li
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gregory J. Krause
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qi Gui
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Susmita Kaushik
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Qingyue Zhang
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Avantika Dhabaria
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jennifer L. Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Manor Askenazi
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Biomedical Hosting LLC, 33 Lewis Avenue, Arlington, MA 02474, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
- Laura and Isaac Perlmutter NYU Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
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6
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Tamotsu H, Koizumi K, Briones AV, Komiya R. Spatial distribution of three ARGONAUTEs regulates the anther phasiRNA pathway. Nat Commun 2023; 14:3333. [PMID: 37286636 DOI: 10.1038/s41467-023-38881-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 05/16/2023] [Indexed: 06/09/2023] Open
Abstract
Argonaute protein (AGO) in association with small RNAs is the core machinery of RNA silencing, an essential mechanism for precise development and defense against pathogens in many organisms. Here, we identified two AGOs in rice anthers, AGO1b and AGO1d, that interact with phased small interfering RNAs (phasiRNAs) derived from numerous long non-coding RNAs. Moreover, 3D-immunoimaging and mutant analysis indicated that rice AGO1b and AGO1d cell type-specifically regulate anther development by acting as mobile carriers of these phasiRNAs from the somatic cell layers to the germ cells in anthers. Our study also highlights a new mode of reproductive RNA silencing via the specific nuclear and cytoplasmic localization of three AGOs, AGO1b, AGO1d, and MEL1, in rice pollen mother cells.
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Affiliation(s)
- Hinako Tamotsu
- Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Koji Koizumi
- Scientific Imaging Section, OIST, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | | | - Reina Komiya
- Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
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7
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Olie CS, Pinto-Fernández A, Damianou A, Vendrell I, Mei H, den Hamer B, van der Wal E, de Greef JC, Raz V, Kessler BM. USP18 is an essential regulator of muscle cell differentiation and maturation. Cell Death Dis 2023; 14:231. [PMID: 37002195 PMCID: PMC10066380 DOI: 10.1038/s41419-023-05725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/14/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023]
Abstract
The ubiquitin proteasomal system is a critical regulator of muscle physiology, and impaired UPS is key in many muscle pathologies. Yet, little is known about the function of deubiquitinating enzymes (DUBs) in the muscle cell context. We performed a genetic screen to identify DUBs as potential regulators of muscle cell differentiation. Surprisingly, we observed that the depletion of ubiquitin-specific protease 18 (USP18) affected the differentiation of muscle cells. USP18 depletion first stimulated differentiation initiation. Later, during differentiation, the absence of USP18 expression abrogated myotube maintenance. USP18 enzymatic function typically attenuates the immune response by removing interferon-stimulated gene 15 (ISG15) from protein substrates. However, in muscle cells, we found that USP18, predominantly nuclear, regulates differentiation independent of ISG15 and the ISG response. Exploring the pattern of RNA expression profiles and protein networks whose levels depend on USP18 expression, we found that differentiation initiation was concomitant with reduced expression of the cell-cycle gene network and altered expression of myogenic transcription (co) factors. We show that USP18 depletion altered the calcium channel gene network, resulting in reduced calcium flux in myotubes. Additionally, we show that reduced expression of sarcomeric proteins in the USP18 proteome was consistent with reduced contractile force in an engineered muscle model. Our results revealed nuclear USP18 as a critical regulator of differentiation initiation and maintenance, independent of ISG15 and its role in the ISG response.
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Affiliation(s)
- Cyriel Sebastiaan Olie
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andreas Damianou
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Iolanda Vendrell
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Bianca den Hamer
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Erik van der Wal
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Jessica C de Greef
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands
| | - Vered Raz
- Human Genetics department, Leiden University Medical Centre, 2333ZC, Leiden, The Netherlands.
| | - Benedikt M Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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8
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The Mechano-Ubiquitinome of Articular Cartilage: Differential Ubiquitination and Activation of a Group of ER-Associated DUBs and ER Stress Regulators. Mol Cell Proteomics 2022; 21:100419. [PMID: 36182100 PMCID: PMC9708921 DOI: 10.1016/j.mcpro.2022.100419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 01/18/2023] Open
Abstract
Understanding how connective tissue cells respond to mechanical stimulation is important to human health and disease processes in musculoskeletal diseases. Injury to articular cartilage is a key risk factor in predisposition to tissue damage and degenerative osteoarthritis. Recently, we have discovered that mechanical injury to connective tissues including murine and porcine articular cartilage causes a significant increase in lysine-63 polyubiquitination. Here, we identified the ubiquitin signature that is unique to injured articular cartilage tissue upon mechanical injury (the "mechano-ubiquitinome"). A total of 463 ubiquitinated peptides were identified, with an enrichment of ubiquitinated peptides of proteins involved in protein processing in the endoplasmic reticulum (ER), also known as the ER-associated degradation response, including YOD1, BRCC3, ATXN3, and USP5 as well as the ER stress regulators, RAD23B, VCP/p97, and Ubiquilin 1. Enrichment of these proteins suggested an injury-induced ER stress response and, for instance, ER stress markers DDIT3/CHOP and BIP/GRP78 were upregulated following cartilage injury on the protein and gene expression levels. Similar ER stress induction was also observed in response to tail fin injury in zebrafish larvae, suggesting a generic response to tissue injury. Furthermore, a rapid increase in global DUB activity following injury and significant activity in human osteoarthritic cartilage was observed using DUB-specific activity probes. Combined, these results implicate the involvement of ubiquitination events and activation of a set of DUBs and ER stress regulators in cellular responses to cartilage tissue injury and in osteoarthritic cartilage tissues. This link through the ER-associated degradation pathway makes this protein set attractive for further investigation in in vivo models of tissue injury and for targeting in osteoarthritis and related musculoskeletal diseases.
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9
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Hayakawa E, Guzman C, Horiguchi O, Kawano C, Shiraishi A, Mohri K, Lin MF, Nakamura R, Nakamura R, Kawai E, Komoto S, Jokura K, Shiba K, Shigenobu S, Satake H, Inaba K, Watanabe H. Mass spectrometry of short peptides reveals common features of metazoan peptidergic neurons. Nat Ecol Evol 2022; 6:1438-1448. [PMID: 35941202 PMCID: PMC9525235 DOI: 10.1038/s41559-022-01835-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/21/2022] [Indexed: 12/21/2022]
Abstract
The evolutionary origins of neurons remain unknown. Although recent genome data of extant early-branching animals have shown that neural genes existed in the common ancestor of animals, the physiological and genetic properties of neurons in the early evolutionary phase are still unclear. Here, we performed a mass spectrometry-based comprehensive survey of short peptides from early-branching lineages Cnidaria, Porifera and Ctenophora. We identified a number of mature ctenophore neuropeptides that are expressed in neurons associated with sensory, muscular and digestive systems. The ctenophore peptides are stored in vesicles in cell bodies and neurites, suggesting volume transmission similar to that of cnidarian and bilaterian peptidergic systems. A comparison of genetic characteristics revealed that the peptide-expressing cells of Cnidaria and Ctenophora express the vast majority of genes that have pivotal roles in maturation, secretion and degradation of neuropeptides in Bilateria. Functional analysis of neuropeptides and prediction of receptors with machine learning demonstrated peptide regulation of a wide range of target effector cells, including cells of muscular systems. The striking parallels between the peptidergic neuronal properties of Cnidaria and Bilateria and those of Ctenophora, the most basal neuron-bearing animals, suggest a common evolutionary origin of metazoan peptidergic nervous systems.
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Affiliation(s)
- Eisuke Hayakawa
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
| | - Christine Guzman
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Osamu Horiguchi
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Chihiro Kawano
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Akira Shiraishi
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Kurato Mohri
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Mei-Fang Lin
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- College of Marine Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Ryotaro Nakamura
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Ryo Nakamura
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Erina Kawai
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Marine Climate Change Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Shinya Komoto
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Imaging Section, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Kei Jokura
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Kogiku Shiba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Shuji Shigenobu
- Center for the Development of New Model Organisms, National Institute for Basic Biology, Okazaki, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Hiroshi Watanabe
- Evolutionary Neurobiology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan.
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10
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Cockman ME, Sugimoto Y, Pegg HB, Masson N, Salah E, Tumber A, Flynn HR, Kirkpatrick JM, Schofield CJ, Ratcliffe PJ. Widespread hydroxylation of unstructured lysine-rich protein domains by JMJD6. Proc Natl Acad Sci U S A 2022; 119:e2201483119. [PMID: 35930668 PMCID: PMC9371714 DOI: 10.1073/pnas.2201483119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
The Jumonji domain-containing protein JMJD6 is a 2-oxoglutarate-dependent dioxygenase associated with a broad range of biological functions. Cellular studies have implicated the enzyme in chromatin biology, transcription, DNA repair, mRNA splicing, and cotranscriptional processing. Although not all studies agree, JMJD6 has been reported to catalyze both hydroxylation of lysine residues and demethylation of arginine residues. However, despite extensive study and indirect evidence for JMJD6 catalysis in many cellular processes, direct assignment of JMJD6 catalytic substrates has been limited. Examination of a reported site of proline hydroxylation within a lysine-rich region of the tandem bromodomain protein BRD4 led us to conclude that hydroxylation was in fact on lysine and catalyzed by JMJD6. This prompted a wider search for JMJD6-catalyzed protein modifications deploying mass spectrometric methods designed to improve the analysis of such lysine-rich regions. Using lysine derivatization with propionic anhydride to improve the analysis of tryptic peptides and nontryptic proteolysis, we report 150 sites of JMJD6-catalyzed lysine hydroxylation on 48 protein substrates, including 19 sites of hydroxylation on BRD4. Most hydroxylations were within lysine-rich regions that are predicted to be unstructured; in some, multiple modifications were observed on adjacent lysine residues. Almost all of the JMJD6 substrates defined in these studies have been associated with membraneless organelle formation. Given the reported roles of lysine-rich regions in subcellular partitioning by liquid-liquid phase separation, our findings raise the possibility that JMJD6 may play a role in regulating such processes in response to stresses, including hypoxia.
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Affiliation(s)
- Matthew E. Cockman
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Yoichiro Sugimoto
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Hamish B. Pegg
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Norma Masson
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
| | - Eidarus Salah
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Helen R. Flynn
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Joanna M. Kirkpatrick
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Christopher J. Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Peter J. Ratcliffe
- Hypoxia Biology Laboratory, Francis Crick Institute, London, NW1 1AT, United Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, United Kingdom
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11
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Dearlove DJ, Soto Mota A, Hauton D, Pinnick K, Evans R, Miller J, Fischer R, Mccullagh JS, Hodson L, Clarke K, Cox PJ. The effects of endogenously- and exogenously-induced hyperketonemia on exercise performance and adaptation. Physiol Rep 2022; 10:e15309. [PMID: 35614576 PMCID: PMC9133544 DOI: 10.14814/phy2.15309] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/02/2022] [Accepted: 05/05/2022] [Indexed: 05/22/2023] Open
Abstract
Elevating blood ketones may enhance exercise capacity and modulate adaptations to exercise training; however, these effects may depend on whether hyperketonemia is induced endogenously through dietary carbohydrate restriction, or exogenously through ketone supplementation. To determine this, we compared the effects of endogenously- and exogenously-induced hyperketonemia on exercise capacity and adaptation. Trained endurance athletes undertook 6 days of laboratory based cycling ("race") whilst following either: a carbohydrate-rich control diet (n = 7; CHO); a carbohydrate-rich diet + ketone drink four-times daily (n = 7; Ex Ket); or a ketogenic diet (n = 7; End Ket). Exercise capacity was measured daily, and adaptations in exercise metabolism, exercise physiology and postprandial insulin sensitivity (via an oral glucose tolerance test) were measured before and after dietary interventions. Urinary β-hydroxybutyrate increased by ⁓150-fold and ⁓650-fold versus CHO with Ex Ket and End Ket, respectively. Exercise capacity was increased versus pre-intervention by ~5% on race day 1 with CHO (p < 0.05), by 6%-8% on days 1, 4, and 6 (all p < 0.05) with Ex Ket and decreased by 48%-57% on all race days (all p > 0.05) with End Ket. There was an ⁓3-fold increase in fat oxidation from pre- to post-intervention (p < 0.05) with End Ket and increased perceived exercise exertion (p < 0.05). No changes in exercise substrate metabolism occurred with Ex Ket, but participants had blunted postprandial insulin sensitivity (p < 0.05). Dietary carbohydrate restriction and ketone supplementation both induce hyperketonemia; however, these are distinct physiological conditions with contrasting effects on exercise capacity and adaptation to exercise training.
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Affiliation(s)
- David J. Dearlove
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordHeadingtonOxfordUnited Kingdom
| | - Adrian Soto Mota
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordHeadingtonOxfordUnited Kingdom
| | - David Hauton
- Chemistry Research LaboratoryUniversity of OxfordHeadingtonOxfordUnited Kingdom
| | - Katherine Pinnick
- Oxford Centre for Diabetes, Endocrinology and MetabolismChurchill Hospital and Oxford NIHRBiomedical Research CentreUniversity of OxfordHeadingtonOxfordUnited Kingdom
| | - Rhys Evans
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordHeadingtonOxfordUnited Kingdom
| | - Jack Miller
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordHeadingtonOxfordUnited Kingdom
- The PET Research Centre and The MR Research CentreAarhus UniversityHeadingtonOxfordUnited Kingdom
- Clarendon LaboratoryDepartment of PhysicsUniversity of OxfordHeadingtonOxfordUnited Kingdom
| | - Roman Fischer
- Target Discovery InstituteUniversity of OxfordHeadingtonOxfordUnited Kingdom
| | | | - Leanne Hodson
- Oxford Centre for Diabetes, Endocrinology and MetabolismChurchill Hospital and Oxford NIHRBiomedical Research CentreUniversity of OxfordHeadingtonOxfordUnited Kingdom
| | - Kieran Clarke
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordHeadingtonOxfordUnited Kingdom
| | - Pete J. Cox
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordHeadingtonOxfordUnited Kingdom
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12
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Escobar TM, Yu JR, Liu S, Lucero K, Vasilyev N, Nudler E, Reinberg D. Inheritance of repressed chromatin domains during S phase requires the histone chaperone NPM1. SCIENCE ADVANCES 2022; 8:eabm3945. [PMID: 35476441 PMCID: PMC9045712 DOI: 10.1126/sciadv.abm3945] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
The epigenetic process safeguards cell identity during cell division through the inheritance of appropriate gene expression profiles. We demonstrated previously that parental nucleosomes are inherited by the same chromatin domains during DNA replication only in the case of repressed chromatin. We now show that this specificity is conveyed by NPM1, a histone H3/H4 chaperone. Proteomic analyses of late S-phase chromatin revealed NPM1 in association with both H3K27me3, an integral component of facultative heterochromatin, and MCM2, an integral component of the DNA replication machinery; moreover, NPM1 interacts directly with PRC2 and with MCM2. Given that NPM1 is essential, the inheritance of repressed chromatin domains was examined anew using mESCs expressing an auxin-degradable version of endogenous NPM1. Upon NPM1 degradation, cells accumulated in the G1-S phase of the cell cycle and parental nucleosome inheritance from repressed chromatin domains was markedly compromised. NPM1 chaperone activity may contribute to the integrity of this process as appropriate inheritance required the NPM1 acidic patches.
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Affiliation(s)
- Thelma M. Escobar
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Jia-Ray Yu
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Sanxiong Liu
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Kimberly Lucero
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY, USA
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13
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Chen Z, Zhang J, Murillo-de-Ozores AR, Castañeda-Bueno M, D'Amico F, Heilig R, Manning CE, Sorrell FJ, D'Angiolella V, Fischer R, Mulder MPC, Gamba G, Alessi DR, Bullock AN. Sequence and structural variations determining the recruitment of WNK kinases to the KLHL3 E3 ligase. Biochem J 2022; 479:661-675. [PMID: 35179207 PMCID: PMC9022995 DOI: 10.1042/bcj20220019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/12/2022] [Accepted: 02/18/2022] [Indexed: 02/05/2023]
Abstract
The BTB-Kelch protein KLHL3 is a Cullin3-dependent E3 ligase that mediates the ubiquitin-dependent degradation of kinases WNK1-4 to control blood pressure and cell volume. A crystal structure of KLHL3 has defined its binding to an acidic degron motif containing a PXXP sequence that is strictly conserved in WNK1, WNK2 and WNK4. Mutations in the second proline abrograte the interaction causing the hypertension syndrome pseudohypoaldosteronism type II. WNK3 shows a diverged degron motif containing four amino acid substitutions that remove the PXXP motif raising questions as to the mechanism of its binding. To understand this atypical interaction, we determined the crystal structure of the KLHL3 Kelch domain in complex with a WNK3 peptide. The electron density enabled the complete 11-mer WNK-family degron motif to be traced for the first time revealing several conserved features not captured in previous work, including additional salt bridge and hydrogen bond interactions. Overall, the WNK3 peptide adopted a conserved binding pose except for a subtle shift to accommodate bulkier amino acid substitutions at the binding interface. At the centre, the second proline was substituted by WNK3 Thr541, providing a unique phosphorylatable residue among the WNK-family degrons. Fluorescence polarisation and structural modelling experiments revealed that its phosphorylation would abrogate the KLHL3 interaction similarly to hypertension-causing mutations. Together, these data reveal how the KLHL3 Kelch domain can accommodate the binding of multiple WNK isoforms and highlight a potential regulatory mechanism for the recruitment of WNK3.
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Affiliation(s)
- Zhuoyao Chen
- Centre for Medicines Discovery, New Biochemistry Building, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Jinwei Zhang
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD15EH, Scotland, U.K
| | - Adrián R. Murillo-de-Ozores
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, Mexico City, Mexico
| | - María Castañeda-Bueno
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, Mexico City, Mexico
| | - Francesca D'Amico
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Raphael Heilig
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Charlotte E. Manning
- Centre for Medicines Discovery, New Biochemistry Building, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Fiona J. Sorrell
- Centre for Medicines Discovery, New Biochemistry Building, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Vincenzo D'Angiolella
- Department of Oncology, Cancer Research U.K.. and Medical Research Council Institute for Radiation Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Monique P. C. Mulder
- Oncode Institute and Department of Cell and Chemical Biology, Leiden University Medical Center (LUMC), Einthovenweg 20, 2333, ZC, Leiden, The Netherlands
| | - Gerardo Gamba
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Tlalpan, Mexico City, Mexico
- Molecular Physiology Unit, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Tlalpan, Mexico City, Mexico
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD15EH, Scotland, U.K
| | - Alex N. Bullock
- Centre for Medicines Discovery, New Biochemistry Building, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
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14
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Muto T, Guillamot M, Yeung J, Fang J, Bennett J, Nadorp B, Lasry A, Redondo LZ, Choi K, Gong Y, Walker CS, Hueneman K, Bolanos LC, Barreyro L, Lee LH, Greis KD, Vasyliev N, Khodadadi-Jamayran A, Nudler E, Lujambio A, Lowe SW, Aifantis I, Starczynowski DT. TRAF6 functions as a tumor suppressor in myeloid malignancies by directly targeting MYC oncogenic activity. Cell Stem Cell 2022; 29:298-314.e9. [PMID: 35045331 PMCID: PMC8822959 DOI: 10.1016/j.stem.2021.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/05/2021] [Accepted: 12/15/2021] [Indexed: 02/05/2023]
Abstract
Clonal hematopoiesis (CH) is an aging-associated condition characterized by the clonal outgrowth of pre-leukemic cells that acquire specific mutations. Although individuals with CH are healthy, they are at an increased risk of developing myeloid malignancies, suggesting that additional alterations are needed for the transition from a pre-leukemia stage to frank leukemia. To identify signaling states that cooperate with pre-leukemic cells, we used an in vivo RNAi screening approach. One of the most prominent genes identified was the ubiquitin ligase TRAF6. Loss of TRAF6 in pre-leukemic cells results in overt myeloid leukemia and is associated with MYC-dependent stem cell signatures. TRAF6 is repressed in a subset of patients with myeloid malignancies, suggesting that subversion of TRAF6 signaling can lead to acute leukemia. Mechanistically, TRAF6 ubiquitinates MYC, an event that does not affect its protein stability but rather represses its functional activity by antagonizing an acetylation modification.
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Affiliation(s)
- Tomoya Muto
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA.,These authors contributed equally
| | - Maria Guillamot
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.,These authors contributed equally
| | - Jennifer Yeung
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, Columbia, SC 29208, USA
| | - Jing Fang
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, Columbia, SC 29208, USA
| | - Joshua Bennett
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina College of Pharmacy, Columbia, SC 29208, USA
| | - Bettina Nadorp
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Audrey Lasry
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Luna Zea Redondo
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Yixiao Gong
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Callum S. Walker
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Kathleen Hueneman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Lyndsey C. Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Laura Barreyro
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA
| | - Lynn H. Lee
- Division of Oncology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA
| | - Kenneth D. Greis
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45229 USA
| | - Nikita Vasyliev
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories and Genome Technology Center, NYU School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Amaia Lujambio
- Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Scott W. Lowe
- Department of Cancer Biology and Genetics, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 201815, USA
| | - Iannis Aifantis
- Department of Pathology and Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| | - Daniel T. Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229 USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229 USA.,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45229 USA.,Lead contact,Correspondence: (I.A.), (D.T.S.)
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15
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Proteomic analysis in primary T cells reveals IL-7 alters T cell receptor thresholding via CYTIP/cytohesin/LFA-1 localisation and activation. Biochem J 2022; 479:225-243. [PMID: 35015072 PMCID: PMC8883493 DOI: 10.1042/bcj20210313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 12/15/2021] [Accepted: 01/11/2022] [Indexed: 11/17/2022]
Abstract
The ability of the cellular immune system to discriminate self from foreign antigens depends on the appropriate calibration of the T cell receptor (TCR) signalling threshold. The lymphocyte homeostatic cytokine interleukin 7 (IL-7) is known to affect TCR thresholding, but the molecular mechanism is not fully elucidated. A better understanding of this process is highly relevant in the context of autoimmune disease therapy and cancer immunotherapy. We sought to characterise the early signalling events attributable to IL-7 priming; in particular, the altered phosphorylation of signal transduction proteins and their molecular localisation to the TCR. By integrating high-resolution proximity- phospho-proteomic and imaging approaches using primary T cells, rather than engineered cell lines or an in vitro expanded T cell population, we uncovered transduction events previously not linked to IL-7. We show that IL-7 leads to dephosphorylation of cytohesin interacting protein (CYTIP) at a hitherto undescribed phosphorylation site (pThr280) and alters the co-localisation of cytohesin-1 with the TCR and LFA-1 integrin. These results show that IL-7, acting via CYTIP and cytohesin-1, may impact TCR activation thresholds by enhancing the co-clustering of TCR and LFA-1 integrin.
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16
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Zhang J, Walker ME, Sanidad KZ, Zhang H, Liang Y, Zhao E, Chacon-Vargas K, Yeliseyev V, Parsonnet J, Haggerty TD, Wang G, Simpson JB, Jariwala PB, Beaty VV, Yang J, Yang H, Panigrahy A, Minter LM, Kim D, Gibbons JG, Liu L, Li Z, Xiao H, Borlandelli V, Overkleeft HS, Cloer EW, Major MB, Goldfarb D, Cai Z, Redinbo MR, Zhang G. Microbial enzymes induce colitis by reactivating triclosan in the mouse gastrointestinal tract. Nat Commun 2022; 13:136. [PMID: 35013263 PMCID: PMC8748916 DOI: 10.1038/s41467-021-27762-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 11/24/2021] [Indexed: 12/24/2022] Open
Abstract
Emerging research supports that triclosan (TCS), an antimicrobial agent found in thousands of consumer products, exacerbates colitis and colitis-associated colorectal tumorigenesis in animal models. While the intestinal toxicities of TCS require the presence of gut microbiota, the molecular mechanisms involved have not been defined. Here we show that intestinal commensal microbes mediate metabolic activation of TCS in the colon and drive its gut toxicology. Using a range of in vitro, ex vivo, and in vivo approaches, we identify specific microbial β-glucuronidase (GUS) enzymes involved and pinpoint molecular motifs required to metabolically activate TCS in the gut. Finally, we show that targeted inhibition of bacterial GUS enzymes abolishes the colitis-promoting effects of TCS, supporting an essential role of specific microbial proteins in TCS toxicity. Together, our results define a mechanism by which intestinal microbes contribute to the metabolic activation and gut toxicity of TCS, and highlight the importance of considering the contributions of the gut microbiota in evaluating the toxic potential of environmental chemicals.
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Affiliation(s)
- Jianan Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Morgan E Walker
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Hongna Zhang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, China
| | - Yanshan Liang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Ermin Zhao
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | | | - Vladimir Yeliseyev
- Massachusetts Host-Microbiota Center, Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Julie Parsonnet
- Department of Medicine and Department of Health Research and Policy, Stanford University, Stanford, CA, USA
| | - Thomas D Haggerty
- Department of Medicine and Department of Health Research and Policy, Stanford University, Stanford, CA, USA
| | - Guangqiang Wang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Joshua B Simpson
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Parth B Jariwala
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Violet V Beaty
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jun Yang
- Department of Entomology and Nematology, University of California, Davis, CA, USA
| | - Haixia Yang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Anand Panigrahy
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Lisa M Minter
- Department of Veterinary & Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Daeyoung Kim
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA, USA
| | - John G Gibbons
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - LinShu Liu
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, USA
| | - Zhengze Li
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Valentina Borlandelli
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Hermen S Overkleeft
- Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Erica W Cloer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, and Department of Otolaryngology, Washington University, St. Louis, MO, USA
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Institute for Informatics, Washington University, St. Louis, MO, USA
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China.
| | - Matthew R Redinbo
- Departments of Chemistry, Biochemistry, Microbiology and Genomics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Guodong Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA, USA.
- Department of Food Science and Technology, National University of Singapore, Singapore, Singapore.
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17
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Ryzhakov G, Almuttaqi H, Corbin AL, Berthold DL, Khoyratty T, Eames HL, Bullers S, Pearson C, Ai Z, Zec K, Bonham S, Fischer R, Jostins-Dean L, Travis SPL, Kessler BM, Udalova IA. Defactinib inhibits PYK2 phosphorylation of IRF5 and reduces intestinal inflammation. Nat Commun 2021; 12:6702. [PMID: 34795257 PMCID: PMC8602323 DOI: 10.1038/s41467-021-27038-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Interferon regulating factor 5 (IRF5) is a multifunctional regulator of immune responses, and has a key pathogenic function in gut inflammation, but how IRF5 is modulated is still unclear. Having performed a kinase inhibitor library screening in macrophages, here we identify protein-tyrosine kinase 2-beta (PTK2B/PYK2) as a putative IRF5 kinase. PYK2-deficient macrophages display impaired endogenous IRF5 activation, leading to reduction of inflammatory gene expression. Meanwhile, a PYK2 inhibitor, defactinib, has a similar effect on IRF5 activation in vitro, and induces a transcriptomic signature in macrophages similar to that caused by IRF5 deficiency. Finally, defactinib reduces pro-inflammatory cytokines in human colon biopsies from patients with ulcerative colitis, as well as in a mouse colitis model. Our results thus implicate a function of PYK2 in regulating the inflammatory response in the gut via the IRF5 innate sensing pathway, thereby opening opportunities for related therapeutic interventions for inflammatory bowel diseases and other inflammatory conditions.
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Affiliation(s)
- Grigory Ryzhakov
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, Basel, Switzerland
| | - Hannah Almuttaqi
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Alastair L Corbin
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Dorothée L Berthold
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Tariq Khoyratty
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Hayley L Eames
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Samuel Bullers
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Claire Pearson
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Zhichao Ai
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Kristina Zec
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Luke Jostins-Dean
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom
| | - Simon P L Travis
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Irina A Udalova
- University of Oxford, Kennedy Institute of Rheumatology, Oxford, United Kingdom.
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18
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Analysing the fitness cost of antibiotic resistance to identify targets for combination antimicrobials. Nat Microbiol 2021; 6:1410-1423. [PMID: 34697460 DOI: 10.1038/s41564-021-00973-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 09/03/2021] [Indexed: 11/09/2022]
Abstract
Mutations in the rifampicin (Rif)-binding site of RNA polymerase (RNAP) confer antibiotic resistance and often have global effects on transcription that compromise fitness and stress tolerance of resistant mutants. We suggested that the non-essential genome, through its impact on the bacterial transcription cycle, may represent an untapped source of targets for combination antimicrobial therapies. Using transposon sequencing, we carried out a genome-wide analysis of fitness cost in a clinically common rpoB H526Y mutant. We find that genes whose products enable increased transcription elongation rates compound the fitness costs of resistance whereas genes whose products function in cell wall synthesis and division mitigate it. We validate our findings by showing that the cell wall synthesis and division defects of rpoB H526Y result from an increased transcription elongation rate that is further exacerbated by the activity of the uracil salvage pathway and unresponsiveness of the mutant RNAP to the alarmone ppGpp. We applied our findings to identify drugs that inhibit more readily rpoB H526Y and other RifR alleles from the same phenotypic class. Thus, genome-wide analysis of fitness cost of antibiotic-resistant mutants should expedite the discovery of new combination therapies and delineate cellular pathways that underlie the molecular mechanisms of cost.
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19
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PIM1 phosphorylation of the androgen receptor and 14-3-3 ζ regulates gene transcription in prostate cancer. Commun Biol 2021; 4:1221. [PMID: 34697370 PMCID: PMC8546101 DOI: 10.1038/s42003-021-02723-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 09/21/2021] [Indexed: 11/19/2022] Open
Abstract
PIM1 is a serine/threonine kinase over-expressed in prostate cancer. We have previously shown that PIM1 phosphorylates the androgen receptor (AR), the primary therapeutic target in prostate cancer, at serine 213 (pS213), which alters expression of select AR target genes. Therefore, we sought to investigate the mechanism whereby PIM1 phosphorylation of AR alters its transcriptional activity. We previously identified the AR co-activator, 14-3-3 ζ, as an endogenous PIM1 substrate in LNCaP cells. Here, we show that PIM1 phosphorylation of AR and 14-3-3 ζ coordinates their interaction, and that they extensively occupy the same sites on chromatin in an AR-dependent manner. Their occupancy at a number of genes involved in cell migration and invasion results in a PIM1-dependent increase in the expression of these genes. We also use rapid immunoprecipitation and mass spectrometry of endogenous proteins on chromatin (RIME), to find that select AR co-regulators, such as hnRNPK and TRIM28, interact with both AR and 14-3-3 ζ in PIM1 over-expressing cells. We conclude that PIM1 phosphorylation of AR and 14-3-3 ζ coordinates their interaction, which in turn recruits additional co-regulatory proteins to alter AR transcriptional activity.
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20
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Kudriavtseva P, Kashkinov M, Kertész-Farkas A. Deep Convolutional Neural Networks Help Scoring Tandem Mass Spectrometry Data in Database-Searching Approaches. J Proteome Res 2021; 20:4708-4717. [PMID: 34449232 DOI: 10.1021/acs.jproteome.1c00315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Spectrum annotation is a challenging task due to the presence of unexpected peptide fragmentation ions as well as the inaccuracy of the detectors of the spectrometers. We present a deep convolutional neural network, called Slider, which learns an optimal feature extraction in its kernels for scoring mass spectrometry (MS)/MS spectra to increase the number of spectrum annotations with high confidence. Experimental results using publicly available data sets show that Slider can annotate slightly more spectra than the state-of-the-art methods (BoltzMatch, Res-EV, Prosit), albeit 2-10 times faster. More interestingly, Slider provides only 2-4% fewer spectrum annotations with low-resolution fragmentation information than other methods with high-resolution information. This means that Slider can exploit nearly as much information from the context of low-resolution spectrum peaks as the high-resolution fragmentation information can provide for other scoring methods. Thus, Slider can be an optimal choice for practitioners using old spectrometers with low-resolution detectors.
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Affiliation(s)
- Polina Kudriavtseva
- Laboratory on AI for Computational Biology, Faculty of Computer Science, HSE University, 11 Pokrovsky Bvld., Moscow 109028, Russian Federation
| | - Matvey Kashkinov
- Faculty of Computer Science, HSE University, 11 Pokrovsky Bvld., Moscow 109028, Russian Federation
| | - Attila Kertész-Farkas
- Laboratory on AI for Computational Biology, Faculty of Computer Science, HSE University, 11 Pokrovsky Bvld., Moscow 109028, Russian Federation
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21
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Ayagama T, Bose SJ, Capel RA, Priestman DA, Berridge G, Fischer R, Galione A, Platt FM, Kramer H, Burton RA. A modified density gradient proteomic-based method to analyze endolysosomal proteins in cardiac tissue. iScience 2021; 24:102949. [PMID: 34466782 PMCID: PMC8384914 DOI: 10.1016/j.isci.2021.102949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/04/2021] [Accepted: 08/02/2021] [Indexed: 11/22/2022] Open
Abstract
The importance of lysosomes in cardiac physiology and pathology is well established, and evidence for roles in calcium signaling is emerging. We describe a label-free proteomics method suitable for small cardiac tissue biopsies based on density-separated fractionation, which allows study of endolysosomal (EL) proteins. Density gradient fractions corresponding to tissue lysate; sarcoplasmic reticulum (SR), mitochondria (Mito) (1.3 g/mL); and EL with negligible contamination from SR or Mito (1.04 g/mL) were analyzed using Western blot, enzyme activity assay, and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis (adapted discontinuous Percoll and sucrose differential density gradient). Kyoto Encyclopedia of Genes and Genomes, Reactome, Panther, and Gene Ontology pathway analysis showed good coverage of RAB proteins and lysosomal cathepsins (including cardiac-specific cathepsin D) in the purified EL fraction. Significant EL proteins recovered included catalytic activity proteins. We thus present a comprehensive protocol and data set of guinea pig atrial EL organelle proteomics using techniques also applicable for non-cardiac tissue.
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Affiliation(s)
- Thamali Ayagama
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Samuel J. Bose
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Rebecca A. Capel
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | | | - Georgina Berridge
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ UK
| | - Antony Galione
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Frances M. Platt
- University of Oxford, Department of Pharmacology, Oxford, OX1 3QT UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, W12 0NN UK
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22
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Božič J, Motaln H, Janež AP, Markič L, Tripathi P, Yamoah A, Aronica E, Lee YB, Heilig R, Fischer R, Thompson AJ, Goswami A, Rogelj B. Interactome screening of C9orf72 dipeptide repeats reveals VCP sequestration and functional impairment by polyGA. Brain 2021; 145:684-699. [PMID: 34534264 PMCID: PMC9014755 DOI: 10.1093/brain/awab300] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 07/19/2021] [Accepted: 07/26/2021] [Indexed: 11/25/2022] Open
Abstract
Repeat expansions in the C9orf72 gene are a common cause of amyotrophic lateral sclerosis and frontotemporal lobar degeneration, two devastating neurodegenerative disorders. One of the proposed mechanisms of GGGGCC repeat expansion is their translation into non-canonical dipeptide repeats, which can then accumulate as aggregates and contribute to these pathologies. There are five different dipeptide repeat proteins (polyGA, polyGR, polyPR, polyPA and polyGP), some of which are known to be neurotoxic. In the present study, we used BioID2 proximity labelling to identify the interactomes of all five dipeptide repeat proteins consisting of 125 repeats each. We identified 113 interacting partners for polyGR, 90 for polyGA, 106 for polyPR, 25 for polyPA and 27 for polyGP. Gene Ontology enrichment analysis of the proteomic data revealed that these target interaction partners are involved in a variety of functions, including protein translation, signal transduction pathways, protein catabolic processes, amide metabolic processes and RNA-binding. Using autopsy brain tissue from patients with C9orf72 expansion complemented with cell culture analysis, we evaluated the interactions between polyGA and valosin containing protein (VCP). Functional analysis of this interaction revealed sequestration of VCP with polyGA aggregates, altering levels of soluble valosin-containing protein. VCP also functions in autophagy processes, and consistent with this, we observed altered autophagy in cells expressing polyGA. We also observed altered co-localization of polyGA aggregates and p62 in cells depleted of VCP. All together, these data suggest that sequestration of VCP with polyGA aggregates contributes to the loss of VCP function, and consequently to alterations in autophagy processes in C9orf72 expansion disorders.
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Affiliation(s)
- Janja Božič
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Helena Motaln
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Anja Pucer Janež
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Lara Markič
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Priyanka Tripathi
- Institute of Neuropathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Alfred Yamoah
- Institute of Neuropathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Eleonora Aronica
- Amsterdam UMC, University of Amsterdam, Department of (Neuro) Pathology, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Youn-Bok Lee
- Maurice Wohl Clinical Neuroscience Institute, King's College London, London, SE5 8AF, UK
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Anand Goswami
- Institute of Neuropathology, RWTH Aachen University Medical School, Aachen, Germany
| | - Boris Rogelj
- Department of Biotechnology, Jožef Stefan Institute, Ljubljana, Slovenia.,Biomedical Research Institute (BRIS), Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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23
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Clancy A, Heride C, Pinto-Fernández A, Elcocks H, Kallinos A, Kayser-Bricker KJ, Wang W, Smith V, Davis S, Fessler S, McKinnon C, Katz M, Hammonds T, Jones NP, O'Connell J, Follows B, Mischke S, Caravella JA, Ioannidis S, Dinsmore C, Kim S, Behrens A, Komander D, Kessler BM, Urbé S, Clague MJ. The deubiquitylase USP9X controls ribosomal stalling. J Cell Biol 2021; 220:211735. [PMID: 33507233 PMCID: PMC7849821 DOI: 10.1083/jcb.202004211] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 12/11/2020] [Indexed: 02/08/2023] Open
Abstract
When a ribosome stalls during translation, it runs the risk of collision with a trailing ribosome. Such an encounter leads to the formation of a stable di-ribosome complex, which needs to be resolved by a dedicated machinery. The initial stalling and the subsequent resolution of di-ribosomal complexes requires activity of Makorin and ZNF598 ubiquitin E3 ligases, respectively, through ubiquitylation of the eS10 and uS10 subunits of the ribosome. We have developed a specific small-molecule inhibitor of the deubiquitylase USP9X. Proteomics analysis, following inhibitor treatment of HCT116 cells, confirms previous reports linking USP9X with centrosome-associated protein stability but also reveals a loss of Makorin 2 and ZNF598. We show that USP9X interacts with both these ubiquitin E3 ligases, regulating their abundance through the control of protein stability. In the absence of USP9X or following chemical inhibition of its catalytic activity, levels of Makorins and ZNF598 are diminished, and the ribosomal quality control pathway is impaired.
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Affiliation(s)
- Anne Clancy
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Claire Heride
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,Cancer Research UK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London, UK
| | - Adán Pinto-Fernández
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah Elcocks
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Andreas Kallinos
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | | | | | - Victoria Smith
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | - Tim Hammonds
- Cancer Research UK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London, UK
| | - Neil P Jones
- Cancer Research UK Therapeutic Discovery Laboratories, London Bioscience Innovation Centre, London, UK
| | | | | | | | | | | | | | | | - Axel Behrens
- Adult Stem Cell Laboratory, Francis Crick Institute, London, UK
| | - David Komander
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sylvie Urbé
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Michael J Clague
- Department of Molecular Physiology and Cell Signaling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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24
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Briggs EM, Mita P, Sun X, Ha S, Vasilyev N, Leopold ZR, Nudler E, Boeke JD, Logan SK. Unbiased proteomic mapping of the LINE-1 promoter using CRISPR Cas9. Mob DNA 2021; 12:21. [PMID: 34425899 PMCID: PMC8381588 DOI: 10.1186/s13100-021-00249-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/12/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The autonomous retroelement Long Interspersed Element-1 (LINE-1) mobilizes though a copy and paste mechanism using an RNA intermediate (retrotransposition). Throughout human evolution, around 500,000 LINE-1 sequences have accumulated in the genome. Most of these sequences belong to ancestral LINE-1 subfamilies, including L1PA2-L1PA7, and can no longer mobilize. Only a small fraction of LINE-1 sequences, approximately 80 to 100 copies belonging to the L1Hs subfamily, are complete and still capable of retrotransposition. While silenced in most cells, many questions remain regarding LINE-1 dysregulation in cancer cells. RESULTS Here, we optimized CRISPR Cas9 gRNAs to specifically target the regulatory sequence of the L1Hs 5'UTR promoter. We identified three gRNAs that were more specific to L1Hs, with limited binding to older LINE-1 sequences (L1PA2-L1PA7). We also adapted the C-BERST method (dCas9-APEX2 Biotinylation at genomic Elements by Restricted Spatial Tagging) to identify LINE-1 transcriptional regulators in cancer cells. Our LINE-1 C-BERST screen revealed both known and novel LINE-1 transcriptional regulators, including CTCF, YY1 and DUSP1. CONCLUSION Our optimization and evaluation of gRNA specificity and application of the C-BERST method creates a tool for studying the regulatory mechanisms of LINE-1 in cancer. Further, we identified the dual specificity protein phosphatase, DUSP1, as a novel regulator of LINE-1 transcription.
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Affiliation(s)
- Erica M Briggs
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Present Address: Opentrons Labworks, Queens, NY, USA
| | - Paolo Mita
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Present Address: Opentrons Labworks, Queens, NY, USA
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Xiaoji Sun
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Cellarity, Cambridge, MA, USA
| | - Susan Ha
- Department of Urology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
| | - Zev R Leopold
- Department of Urology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA
| | - Jef D Boeke
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA
- Institute of Systems Genetics, NYU Grossman School of Medicine, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Susan K Logan
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA.
- Department of Urology, NYU Grossman School of Medicine, Alexandria Center for Life Sciences, 450 East 29th Street, Room 321, New York, NY, 10016, USA.
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25
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Kerr M, Dennis KMJH, Carr CA, Fuller W, Berridge G, Rohling S, Aitken CL, Lopez C, Fischer R, Miller JJ, Clarke K, Tyler DJ, Heather LC. Diabetic mitochondria are resistant to palmitoyl CoA inhibition of respiration, which is detrimental during ischemia. FASEB J 2021; 35:e21765. [PMID: 34318967 PMCID: PMC8662312 DOI: 10.1096/fj.202100394r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/24/2021] [Accepted: 06/14/2021] [Indexed: 01/07/2023]
Abstract
The bioactive lipid intermediate palmitoyl CoA (PCoA) can inhibit mitochondrial ADP/ATP transport, though the physiological relevance of this regulation remains unclear. We questioned whether myocardial ischemia provides a pathological setting in which PCoA regulation of ADP/ATP transport would be beneficial, and secondly, whether the chronically elevated lipid content within the diabetic heart could make mitochondria less sensitive to the effects of PCoA. PCoA acutely decreased ADP‐stimulated state 3 respiration and increased the apparent Km for ADP twofold. The half maximal inhibitory concentration (IC50) of PCoA in control mitochondria was 22 µM. This inhibitory effect of PCoA on respiration was blunted in diabetic mitochondria, with no significant difference in the Km for ADP in the presence of PCoA, and an increase in the IC50 to 32 µM PCoA. The competitive inhibition by PCoA was localised to the phosphorylation apparatus, particularly the ADP/ATP carrier (AAC). During ischemia, the AAC imports ATP into the mitochondria, where it is hydrolysed by reversal of the ATP synthase, regenerating the membrane potential. Addition of PCoA dose‐dependently prevented this wasteful ATP hydrolysis for membrane repolarisation during ischemia, however, this beneficial effect was blunted in diabetic mitochondria. Finally, using 31P‐magnetic resonance spectroscopy we demonstrated that diabetic hearts lose ATP more rapidly during ischemia, with a threefold higher ATP decay rate compared with control hearts. In conclusion, PCoA plays a role in protecting mitochondrial energetics during ischemia, by preventing wasteful ATP hydrolysis. However, this beneficial effect is blunted in diabetes, contributing to the impaired energy metabolism seen during myocardial ischemia in the diabetic heart.
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Affiliation(s)
- M Kerr
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - K M J H Dennis
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - C A Carr
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - W Fuller
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - G Berridge
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - S Rohling
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - C L Aitken
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - C Lopez
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - R Fischer
- Target Discovery Institute, University of Oxford, Oxford, UK
| | - J J Miller
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.,Department of Physics, University of Oxford, Oxford, UK.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - K Clarke
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - D J Tyler
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - L C Heather
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
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26
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Tan CMJ, Lewandowski AJ, Williamson W, Huckstep OJ, Yu GZ, Fischer R, Simon JN, Alsharqi M, Mohamed A, Leeson P, Bertagnolli M. Proteomic Signature of Dysfunctional Circulating Endothelial Colony-Forming Cells of Young Adults. J Am Heart Assoc 2021; 10:e021119. [PMID: 34275329 PMCID: PMC8475699 DOI: 10.1161/jaha.121.021119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/16/2021] [Indexed: 12/12/2022]
Abstract
Background A subpopulation of endothelial progenitor cells called endothelial colony-forming cells (ECFCs) may offer a platform for cellular assessment in clinical studies because of their remarkable angiogenic and expansion potentials in vitro. Despite endothelial cell function being influenced by cardiovascular risk factors, no studies have yet provided a comprehensive proteomic profile to distinguish functional (ie, more angiogenic and expansive cells) versus dysfunctional circulating ECFCs of young adults. The aim of this study was to provide a detailed proteomic comparison between functional and dysfunctional ECFCs. Methods and Results Peripheral blood ECFCs were isolated from 11 subjects (45% men, aged 27±5 years) using Ficoll density gradient centrifugation. ECFCs expressed endothelial and progenitor surface markers and displayed cobblestone-patterned morphology with clonal and angiogenic capacities in vitro. ECFCs were deemed dysfunctional if <1 closed tube formed during the in vitro tube formation assay and proliferation rate was <20%. Hierarchical functional clustering revealed distinct ECFC proteomic signatures between functional and dysfunctional ECFCs with changes in cellular mechanisms involved in exocytosis, vesicle transport, extracellular matrix organization, cell metabolism, and apoptosis. Targeted antiangiogenic proteins in dysfunctional ECFCs included SPARC (secreted protein acidic and rich in cysteine), CD36 (cluster of differentiation 36), LUM (lumican), and PTX3 (pentraxin-related protein PYX3). Conclusions Circulating ECFCs with impaired angiogenesis and expansion capacities have a distinct proteomic profile and significant phenotype changes compared with highly angiogenic endothelial cells. Impaired angiogenesis in dysfunctional ECFCs may underlie the link between endothelial dysfunction and cardiovascular disease risks in young adults.
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Affiliation(s)
- Cheryl M. J. Tan
- Oxford Cardiovascular Clinical Research Facility, Radcliffe Department of Medicine, Division of Cardiovascular MedicineUniversity of OxfordOxfordUK
| | - Adam J. Lewandowski
- Oxford Cardiovascular Clinical Research Facility, Radcliffe Department of Medicine, Division of Cardiovascular MedicineUniversity of OxfordOxfordUK
| | - Wilby Williamson
- Oxford Cardiovascular Clinical Research Facility, Radcliffe Department of Medicine, Division of Cardiovascular MedicineUniversity of OxfordOxfordUK
| | - Odaro J. Huckstep
- Oxford Cardiovascular Clinical Research Facility, Radcliffe Department of Medicine, Division of Cardiovascular MedicineUniversity of OxfordOxfordUK
- Department of BiologyUnited States Air Force AcademyColorado SpringsCOUSA
| | - Grace Z. Yu
- Oxford Cardiovascular Clinical Research Facility, Radcliffe Department of Medicine, Division of Cardiovascular MedicineUniversity of OxfordOxfordUK
- Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Roman Fischer
- Target Discovery Institute (TDI) Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of MedicineUniversity of OxfordOxfordUK
| | - Jillian N. Simon
- Division of Cardiovascular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Maryam Alsharqi
- Oxford Cardiovascular Clinical Research Facility, Radcliffe Department of Medicine, Division of Cardiovascular MedicineUniversity of OxfordOxfordUK
- Department of Cardiac TechnologyImam Abdulrahman Bin Faisal UniversityDammamSaudi Arabia
| | - Afifah Mohamed
- Oxford Cardiovascular Clinical Research Facility, Radcliffe Department of Medicine, Division of Cardiovascular MedicineUniversity of OxfordOxfordUK
- Department of Diagnostic Imaging & Applied Health Sciences, Faculty of Health SciencesUniversiti Kebangsaan MalaysiaKuala LumpurMalaysia
| | - Paul Leeson
- Oxford Cardiovascular Clinical Research Facility, Radcliffe Department of Medicine, Division of Cardiovascular MedicineUniversity of OxfordOxfordUK
| | - Mariane Bertagnolli
- Oxford Cardiovascular Clinical Research Facility, Radcliffe Department of Medicine, Division of Cardiovascular MedicineUniversity of OxfordOxfordUK
- Montreal Hospital Sacré‐Cœur Research CentreCentre Intégré Universitaire de Santé et de Services Sociaux du Nord‐de‐l'Île‐de‐MontréalMontréalQCCanada
- School of Physical and Occupational Therapy, Faculty of MedicineMcGill UniversityMontréalQCCanada
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27
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Shatalin K, Nuthanakanti A, Kaushik A, Shishov D, Peselis A, Shamovsky I, Pani B, Lechpammer M, Vasilyev N, Shatalina E, Rebatchouk D, Mironov A, Fedichev P, Serganov A, Nudler E. Inhibitors of bacterial H 2S biogenesis targeting antibiotic resistance and tolerance. Science 2021; 372:1169-1175. [PMID: 34112687 PMCID: PMC10723041 DOI: 10.1126/science.abd8377] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/09/2020] [Accepted: 04/30/2021] [Indexed: 12/20/2022]
Abstract
Emergent resistance to all clinical antibiotics calls for the next generation of therapeutics. Here we report an effective antimicrobial strategy targeting the bacterial hydrogen sulfide (H2S)-mediated defense system. We identified cystathionine γ-lyase (CSE) as the primary generator of H2S in two major human pathogens, Staphylococcus aureus and Pseudomonas aeruginosa, and discovered small molecules that inhibit bacterial CSE. These inhibitors potentiate bactericidal antibiotics against both pathogens in vitro and in mouse models of infection. CSE inhibitors also suppress bacterial tolerance, disrupting biofilm formation and substantially reducing the number of persister bacteria that survive antibiotic treatment. Our results establish bacterial H2S as a multifunctional defense factor and CSE as a drug target for versatile antibiotic enhancers.
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Affiliation(s)
- Konstantin Shatalin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ashok Nuthanakanti
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Abhishek Kaushik
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Alla Peselis
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Bibhusita Pani
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Mirna Lechpammer
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Nikita Vasilyev
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Elena Shatalina
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | | | - Alexander Mironov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119991, Russia
| | | | - Alexander Serganov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
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28
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Wilhelm M, Zolg DP, Graber M, Gessulat S, Schmidt T, Schnatbaum K, Schwencke-Westphal C, Seifert P, de Andrade Krätzig N, Zerweck J, Knaute T, Bräunlein E, Samaras P, Lautenbacher L, Klaeger S, Wenschuh H, Rad R, Delanghe B, Huhmer A, Carr SA, Clauser KR, Krackhardt AM, Reimer U, Kuster B. Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics. Nat Commun 2021; 12:3346. [PMID: 34099720 PMCID: PMC8184761 DOI: 10.1038/s41467-021-23713-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the identification of non-tryptic peptides presents substantial computational challenges. To address these, we synthesized and analyzed >300,000 peptides by multi-modal LC-MS/MS within the ProteomeTools project representing HLA class I & II ligands and products of the proteases AspN and LysN. The resulting data enabled training of a single model using the deep learning framework Prosit, allowing the accurate prediction of fragment ion spectra for tryptic and non-tryptic peptides. Applying Prosit demonstrates that the identification of HLA peptides can be improved up to 7-fold, that 87% of the proposed proteasomally spliced HLA peptides may be incorrect and that dozens of additional immunogenic neo-epitopes can be identified from patient tumors in published data. Together, the provided peptides, spectra and computational tools substantially expand the analytical depth of immunopeptidomics workflows.
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Affiliation(s)
- Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), Freising, Germany.
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.
| | - Daniel P Zolg
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Michael Graber
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Siegfried Gessulat
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | | | - Celina Schwencke-Westphal
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich; and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Philipp Seifert
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Niklas de Andrade Krätzig
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | | | | | - Eva Bräunlein
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Ludwig Lautenbacher
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany
| | - Susan Klaeger
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Roland Rad
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
- Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | | | | | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Angela M Krackhardt
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar, School of Medicine, Technical University of Munich (TUM), Munich, Germany
- German Cancer Consortium (DKTK), partner site Munich; and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich (TUM), Munich, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Germany.
- Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising, Germany.
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29
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Waters AM, Khatib TO, Papke B, Goodwin CM, Hobbs GA, Diehl JN, Yang R, Edwards AC, Walsh KH, Sulahian R, McFarland JM, Kapner KS, Gilbert TSK, Stalnecker CA, Javaid S, Barkovskaya A, Grover KR, Hibshman PS, Blake DR, Schaefer A, Nowak KM, Klomp JE, Hayes TK, Kassner M, Tang N, Tanaseichuk O, Chen K, Zhou Y, Kalkat M, Herring LE, Graves LM, Penn LZ, Yin HH, Aguirre AJ, Hahn WC, Cox AD, Der CJ. Targeting p130Cas- and microtubule-dependent MYC regulation sensitizes pancreatic cancer to ERK MAPK inhibition. Cell Rep 2021; 35:109291. [PMID: 34192548 PMCID: PMC8340308 DOI: 10.1016/j.celrep.2021.109291] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 01/31/2021] [Accepted: 06/03/2021] [Indexed: 12/28/2022] Open
Abstract
To identify therapeutic targets for KRAS mutant pancreatic cancer, we conduct a druggable genome small interfering RNA (siRNA) screen and determine that suppression of BCAR1 sensitizes pancreatic cancer cells to ERK inhibition. Integrative analysis of genome-scale CRISPR-Cas9 screens also identify BCAR1 as a top synthetic lethal interactor with mutant KRAS. BCAR1 encodes the SRC substrate p130Cas. We determine that SRC-inhibitor-mediated suppression of p130Cas phosphorylation impairs MYC transcription through a DOCK1-RAC1-β-catenin-dependent mechanism. Additionally, genetic suppression of TUBB3, encoding the βIII-tubulin subunit of microtubules, or pharmacological inhibition of microtubule function decreases levels of MYC protein in a calpain-dependent manner and potently sensitizes pancreatic cancer cells to ERK inhibition. Accordingly, the combination of a dual SRC/tubulin inhibitor with an ERK inhibitor cooperates to reduce MYC protein and synergistically suppress the growth of KRAS mutant pancreatic cancer. Thus, we demonstrate that mechanistically diverse combinations with ERK inhibition suppress MYC to impair pancreatic cancer proliferation.
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Affiliation(s)
- Andrew M Waters
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tala O Khatib
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bjoern Papke
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - G Aaron Hobbs
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Runying Yang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - A Cole Edwards
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Rita Sulahian
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Kevin S Kapner
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas S K Gilbert
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Clint A Stalnecker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sehrish Javaid
- Oral and Craniofacial Biomedicine PhD Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anna Barkovskaya
- Institute for Cancer Research, Oslo University Hospital, Oslo 0379, Norway
| | - Kajal R Grover
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Priya S Hibshman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Devon R Blake
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine M Nowak
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer E Klomp
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tikvah K Hayes
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michelle Kassner
- Cancer and Cell Biology Division, Translational Genomic Research Institute, Phoenix, AZ 85004, USA
| | - Nanyun Tang
- Cancer and Cell Biology Division, Translational Genomic Research Institute, Phoenix, AZ 85004, USA
| | - Olga Tanaseichuk
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Kaisheng Chen
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Yingyao Zhou
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA
| | - Manpreet Kalkat
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S, Canada
| | - Laura E Herring
- UNC Michael Hooker Proteomics Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lee M Graves
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Linda Z Penn
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5S, Canada
| | - Hongwei H Yin
- Cancer and Cell Biology Division, Translational Genomic Research Institute, Phoenix, AZ 85004, USA
| | - Andrew J Aguirre
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA; Brigham and Women's Hospital, Boston, MA 02215, USA
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02215, USA; Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Adrienne D Cox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Oral and Craniofacial Biomedicine PhD Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Channing J Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Oral and Craniofacial Biomedicine PhD Program, School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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30
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Na J, Newman JA, Then CK, Syed J, Vendrell I, Torrecilla I, Ellermann S, Ramadan K, Fischer R, Kiltie AE. SPRTN protease-cleaved MRE11 decreases DNA repair and radiosensitises cancer cells. Cell Death Dis 2021; 12:165. [PMID: 33558481 PMCID: PMC7870818 DOI: 10.1038/s41419-021-03437-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 12/21/2022]
Abstract
The human MRE11/RAD50/NBS1 (MRN) complex plays a crucial role in sensing and repairing DNA DSB. MRE11 possesses dual 3'-5' exonuclease and endonuclease activity and forms the core of the multifunctional MRN complex. We previously identified a C-terminally truncated form of MRE11 (TR-MRE11) associated with post-translational MRE11 degradation. Here we identified SPRTN as the essential protease for the formation of TR-MRE11 and characterised the role of this MRE11 form in its DNA damage response (DDR). Using tandem mass spectrometry and site-directed mutagenesis, the SPRTN-dependent cleavage site for MRE11 was identified between 559 and 580 amino acids. Despite the intact interaction of TR-MRE11 with its constitutive core complex proteins RAD50 and NBS1, both nuclease activities of truncated MRE11 were dramatically reduced due to its deficient binding to DNA. Furthermore, lack of the MRE11 C-terminal decreased HR repair efficiency, very likely due to abolished recruitment of TR-MRE11 to the sites of DNA damage, which consequently led to increased cellular radiosensitivity. The presence of this DNA repair-defective TR-MRE11 could explain our previous finding that the high MRE11 protein expression by immunohistochemistry correlates with improved survival following radical radiotherapy in bladder cancer patients.
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Affiliation(s)
- Juri Na
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Chee Kin Then
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Junetha Syed
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Iolanda Vendrell
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ignacio Torrecilla
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sophie Ellermann
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Kristijan Ramadan
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anne E Kiltie
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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31
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Deletion of the deISGylating enzyme USP18 enhances tumour cell antigenicity and radiosensitivity. Br J Cancer 2020; 124:817-830. [PMID: 33214684 PMCID: PMC7884788 DOI: 10.1038/s41416-020-01167-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 10/05/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Interferon (IFN) signalling pathways, a key element of the innate immune response, contribute to resistance to conventional chemotherapy, radiotherapy, and immunotherapy, and are often deregulated in cancer. The deubiquitylating enzyme USP18 is a major negative regulator of the IFN signalling cascade and is the predominant human protease that cleaves ISG15, a ubiquitin-like protein tightly regulated in the context of innate immunity, from its modified substrate proteins in vivo. METHODS In this study, using advanced proteomic techniques, we have significantly expanded the USP18-dependent ISGylome and proteome in a chronic myeloid leukaemia (CML)-derived cell line. USP18-dependent effects were explored further in CML and colorectal carcinoma cellular models. RESULTS Novel ISGylation targets were characterised that modulate the sensing of innate ligands, antigen presentation and secretion of cytokines. Consequently, CML USP18-deficient cells are more antigenic, driving increased activation of cytotoxic T lymphocytes (CTLs) and are more susceptible to irradiation. CONCLUSIONS Our results provide strong evidence for USP18 in regulating antigenicity and radiosensitivity, highlighting its potential as a cancer target.
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32
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Vere G, Kealy R, Kessler BM, Pinto-Fernandez A. Ubiquitomics: An Overview and Future. Biomolecules 2020; 10:E1453. [PMID: 33080838 PMCID: PMC7603029 DOI: 10.3390/biom10101453] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Covalent attachment of ubiquitin, a small globular polypeptide, to protein substrates is a key post-translational modification that determines the fate, function, and turnover of most cellular proteins. Ubiquitin modification exists as mono- or polyubiquitin chains involving multiple ways how ubiquitin C-termini are connected to lysine, perhaps other amino acid side chains, and N-termini of proteins, often including branching of the ubiquitin chains. Understanding this enormous complexity in protein ubiquitination, the so-called 'ubiquitin code', in combination with the ∼1000 enzymes involved in controlling ubiquitin recognition, conjugation, and deconjugation, calls for novel developments in analytical techniques. Here, we review different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as "ubiquitomics", aiming to understand this system's biological diversity.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
| | - Rachel Kealy
- St Anne’s College, University of Oxford, Oxford OX2 6HS, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Chinese Academy of Medical Sciences Oxford Institute (CAMS), Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
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33
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Pucciarelli D, Angus SP, Huang B, Zhang C, Nakaoka HJ, Krishnamurthi G, Bandyopadhyay S, Clapp DW, Shannon K, Johnson GL, Nakamura JL. Nf1-Mutant Tumors Undergo Transcriptome and Kinome Remodeling after Inhibition of either mTOR or MEK. Mol Cancer Ther 2020; 19:2382-2395. [PMID: 32847978 DOI: 10.1158/1535-7163.mct-19-1017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/18/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022]
Abstract
Loss of the tumor suppressor NF1 leads to activation of RAS effector pathways, which are therapeutically targeted by inhibition of mTOR (mTORi) or MEK (MEKi). However, therapeutic inhibition of RAS effectors leads to the development of drug resistance and ultimately disease progression. To investigate molecular signatures in the context of NF1 loss and subsequent acquired drug resistance, we analyzed the exomes, transcriptomes, and kinomes of Nf1-mutant mouse tumor cell lines and derivatives of these lines that acquired resistance to either MEKi or mTORi. Biochemical comparisons of this unique panel of tumor cells, all of which arose in Nf1+/- mice, indicate that loss of heterozygosity of Nf1 as an initial genetic event does not confer a common biochemical signature or response to kinase inhibition. Although acquired drug resistance by Nf1-mutant tumor cells was accompanied by altered kinomes and irreversibly altered transcriptomes, functionally in multiple Nf1-mutant tumor cell lines, MEKi resistance was a stable phenotype, in contrast to mTORi resistance, which was reversible. Collectively, these findings demonstrate that Nf1-mutant tumors represent a heterogeneous group biochemically and undergo broader remodeling of kinome activity and gene expression in response to targeted kinase inhibition.
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Affiliation(s)
- Daniela Pucciarelli
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Steven P Angus
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Benjamin Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Chi Zhang
- Department of Pediatrics, Indiana University, Indianapolis, Indiana
| | - Hiroki J Nakaoka
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Ganesh Krishnamurthi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Sourav Bandyopadhyay
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California
| | - D Wade Clapp
- Department of Pediatrics, Indiana University, Indianapolis, Indiana
| | - Kevin Shannon
- Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Gary L Johnson
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Jean L Nakamura
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California.
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Nazri HM, Imran M, Fischer R, Heilig R, Manek S, Dragovic RA, Kessler BM, Zondervan KT, Tapmeier TT, Becker CM. Characterization of exosomes in peritoneal fluid of endometriosis patients. Fertil Steril 2020; 113:364-373.e2. [PMID: 32106990 PMCID: PMC7057257 DOI: 10.1016/j.fertnstert.2019.09.032] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 09/11/2019] [Accepted: 09/23/2019] [Indexed: 12/12/2022]
Abstract
Objective To demonstrate the feasibility of studying exosomes directly from peritoneal fluid, we isolated exosomes from endometriosis patient samples and from controls, and characterized their cargo. Design Case-control experimental study. Setting Academic clinical center. Patient (s) Women with and without endometriosis who underwent laparoscopic surgery (n = 28 in total). Intervention (s) None. Main Outcome Measure (s) Concentration of exosomes within peritoneal fluid and protein content of the isolated exosomes. Result (s) Peritoneal fluid samples were pooled according to the cycle phase and disease stage to form six experimental groups, from which the exosomes were isolated. Exosomes were successfully isolated from peritoneal fluid in all the study groups. The concentration varied with cycle phase and disease stage. Proteomic analysis showed specific proteins in the exosomes derived from endometriosis patients that were absent in the controls. Five proteins were found exclusively in the endometriosis groups: PRDX1, H2A type 2-C, ANXA2, ITIH4, and the tubulin α-chain. Conclusion (s) Exosomes are present in peritoneal fluid. The characterization of endometriosis-specific exosomes opens up new avenues for the diagnosis and investigation of endometriosis.
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Affiliation(s)
- Hannah M Nazri
- Endometriosis CaRe Centre, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Maria Imran
- Endometriosis CaRe Centre, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Raphael Heilig
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sanjiv Manek
- Department of Cellular Pathology, Oxford University Hospitals, Oxford, United Kingdom
| | - Rebecca A Dragovic
- Endometriosis CaRe Centre, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Krina T Zondervan
- Endometriosis CaRe Centre, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, United Kingdom; Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Thomas T Tapmeier
- Endometriosis CaRe Centre, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, United Kingdom.
| | - Christian M Becker
- Endometriosis CaRe Centre, Nuffield Department of Women's & Reproductive Health, University of Oxford, Oxford, United Kingdom
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Rusilowicz-Jones EV, Jardine J, Kallinos A, Pinto-Fernandez A, Guenther F, Giurrandino M, Barone FG, McCarron K, Burke CJ, Murad A, Martinez A, Marcassa E, Gersch M, Buckmelter AJ, Kayser-Bricker KJ, Lamoliatte F, Gajbhiye A, Davis S, Scott HC, Murphy E, England K, Mortiboys H, Komander D, Trost M, Kessler BM, Ioannidis S, Ahlijanian MK, Urbé S, Clague MJ. USP30 sets a trigger threshold for PINK1-PARKIN amplification of mitochondrial ubiquitylation. Life Sci Alliance 2020; 3:3/8/e202000768. [PMID: 32636217 PMCID: PMC7362391 DOI: 10.26508/lsa.202000768] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
A new inhibitor of the deubiquitylase USP30, an actionable target relevant to Parkinson’s Disease, is introduced and characterised for parameters related to mitophagy. The mitochondrial deubiquitylase USP30 negatively regulates the selective autophagy of damaged mitochondria. We present the characterisation of an N-cyano pyrrolidine compound, FT3967385, with high selectivity for USP30. We demonstrate that ubiquitylation of TOM20, a component of the outer mitochondrial membrane import machinery, represents a robust biomarker for both USP30 loss and inhibition. A proteomics analysis, on a SHSY5Y neuroblastoma cell line model, directly compares the effects of genetic loss of USP30 with chemical inhibition. We have thereby identified a subset of ubiquitylation events consequent to mitochondrial depolarisation that are USP30 sensitive. Within responsive elements of the ubiquitylome, several components of the outer mitochondrial membrane transport (TOM) complex are prominent. Thus, our data support a model whereby USP30 can regulate the availability of ubiquitin at the specific site of mitochondrial PINK1 accumulation following membrane depolarisation. USP30 deubiquitylation of TOM complex components dampens the trigger for the Parkin-dependent amplification of mitochondrial ubiquitylation leading to mitophagy. Accordingly, PINK1 generation of phospho-Ser65 ubiquitin proceeds more rapidly in cells either lacking USP30 or subject to USP30 inhibition.
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Affiliation(s)
- Emma V Rusilowicz-Jones
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Jane Jardine
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Andreas Kallinos
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Franziska Guenther
- Alzheimer's Research UK, Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Mariacarmela Giurrandino
- Alzheimer's Research UK, Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Francesco G Barone
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Katy McCarron
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | | | | | - Aitor Martinez
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Elena Marcassa
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Malte Gersch
- Chemical Genomics Centre, Max-Planck-Institute of Molecular Physiology, Dortmund, Germany.,Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Dortmund, Germany
| | | | | | - Frederic Lamoliatte
- Laboratory for Biological Mass Spectrometry, Newcastle University Biosciences Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle, UK
| | - Akshada Gajbhiye
- Laboratory for Biological Mass Spectrometry, Newcastle University Biosciences Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle, UK
| | - Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah C Scott
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Emma Murphy
- Alzheimer's Research UK, Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katherine England
- Alzheimer's Research UK, Oxford Drug Discovery Institute, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - David Komander
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Matthias Trost
- Laboratory for Biological Mass Spectrometry, Newcastle University Biosciences Institute, Faculty of Medical Sciences, University of Newcastle, Newcastle, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | - Sylvie Urbé
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Michael J Clague
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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36
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Mei S, Ayala R, Ramarathinam SH, Illing PT, Faridi P, Song J, Purcell AW, Croft NP. Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors. Mol Cell Proteomics 2020; 19:1236-1247. [PMID: 32357974 PMCID: PMC7338083 DOI: 10.1074/mcp.ra119.001846] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
The presentation of post-translationally modified (PTM) peptides by cell surface HLA molecules has the potential to increase the diversity of targets for surveilling T cells. Although immunopeptidomics studies routinely identify thousands of HLA-bound peptides from cell lines and tissue samples, in-depth analyses of the proportion and nature of peptides bearing one or more PTMs remains challenging. Here we have analyzed HLA-bound peptides from a variety of allotypes and assessed the distribution of mass spectrometry-detected PTMs, finding deamidation of asparagine or glutamine to be highly prevalent. Given that asparagine deamidation may arise either spontaneously or through enzymatic reaction, we assessed allele-specific and global motifs flanking the modified residues. Notably, we found that the N-linked glycosylation motif NX(S/T) was highly abundant across asparagine-deamidated HLA-bound peptides. This finding, demonstrated previously for a handful of deamidated T cell epitopes, implicates a more global role for the retrograde transport of nascently N-glycosylated polypeptides from the ER and their subsequent degradation within the cytosol to form HLA-ligand precursors. Chemical inhibition of Peptide:N-Glycanase (PNGase), the endoglycosidase responsible for the removal of glycans from misfolded and retrotranslocated glycoproteins, greatly reduced presentation of this subset of deamidated HLA-bound peptides. Importantly, there was no impact of PNGase inhibition on peptides not containing a consensus NX(S/T) motif. This indicates that a large proportion of HLA-I bound asparagine deamidated peptides are generated from formerly glycosylated proteins that have undergone deglycosylation via the ER-associated protein degradation (ERAD) pathway. The information herein will help train deamidation prediction models for HLA-peptide repertoires and aid in the design of novel T cell therapeutic targets derived from glycoprotein antigens.
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Affiliation(s)
- Shutao Mei
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Rochelle Ayala
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Sri H Ramarathinam
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Patricia T Illing
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Pouya Faridi
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Jiangning Song
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Anthony W Purcell
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia.
| | - Nathan P Croft
- Biomedicine Discovery Institute and Department of Biochemistry & Molecular Biology, Monash University, Melbourne, VIC, Australia.
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Araki S, Le NT, Koizumi K, Villar-Briones A, Nonomura KI, Endo M, Inoue H, Saze H, Komiya R. miR2118-dependent U-rich phasiRNA production in rice anther wall development. Nat Commun 2020; 11:3115. [PMID: 32561756 PMCID: PMC7305157 DOI: 10.1038/s41467-020-16637-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 05/13/2020] [Indexed: 11/10/2022] Open
Abstract
Reproduction-specific small RNAs are vital regulators of germline development in animals and plants. MicroRNA2118 (miR2118) is conserved in plants and induces the production of phased small interfering RNAs (phasiRNAs). To reveal the biological functions of miR2118, we describe here rice mutants with large deletions of the miR2118 cluster. Our results demonstrate that the loss of miR2118 causes severe male and female sterility in rice, associated with marked morphological and developmental abnormalities in somatic anther wall cells. Small RNA profiling reveals that miR2118-dependent 21-nucleotide (nt) phasiRNAs in the anther wall are U-rich, distinct from the phasiRNAs in germ cells. Furthermore, the miR2118-dependent biogenesis of 21-nt phasiRNAs may involve the Argonaute proteins OsAGO1b/OsAGO1d, which are abundant in anther wall cell layers. Our study highlights the site-specific differences of phasiRNAs between somatic anther wall and germ cells, and demonstrates the significance of miR2118/U-phasiRNA functions in anther wall development and rice reproduction. MicroRNA2118 induces the production of phased small interfering RNAs (phaisRNAs) in plants. Here the authors show that rice miR2118 is required for both male and female fertility and supports the production of atypical U-rich 21 nt phasiRNAs that are abundant in anther walls.
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Affiliation(s)
- Saori Araki
- Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Ngoc Tu Le
- Plant Epigenetics Unit, OIST, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Koji Koizumi
- Imaging Section, OIST, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | | | - Ken-Ichi Nonomura
- Plant Cytogenetics, Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.,Department of Life Science, Graduate University for Advanced Studies/Sokendai, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Haruhiko Inoue
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan.,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, OIST, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Reina Komiya
- Science and Technology Group, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan. .,Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
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38
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Galardi A, Colletti M, Lavarello C, Di Paolo V, Mascio P, Russo I, Cozza R, Romanzo A, Valente P, De Vito R, Pascucci L, Peinado H, Carcaboso AM, Petretto A, Locatelli F, Di Giannatale A. Proteomic Profiling of Retinoblastoma-Derived Exosomes Reveals Potential Biomarkers of Vitreous Seeding. Cancers (Basel) 2020; 12:cancers12061555. [PMID: 32545553 PMCID: PMC7352325 DOI: 10.3390/cancers12061555] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/04/2020] [Accepted: 06/07/2020] [Indexed: 12/13/2022] Open
Abstract
Retinoblastoma (RB) is the most common tumor of the eye in early childhood. Although recent advances in conservative treatment have greatly improved the visual outcome, local tumor control remains difficult in the presence of massive vitreous seeding. Traditional biopsy has long been considered unsafe in RB, due to the risk of extraocular spread. Thus, the identification of new biomarkers is crucial to design safer diagnostic and more effective therapeutic approaches. Exosomes, membrane-derived nanovesicles that are secreted abundantly by aggressive tumor cells and that can be isolated from several biological fluids, represent an interesting alternative for the detection of tumor-associated biomarkers. In this study, we defined the protein signature of exosomes released by RB tumors (RBT) and vitreous seeding (RBVS) primary cell lines by high resolution mass spectrometry. A total of 5666 proteins were identified. Among these, 5223 and 3637 were expressed in exosomes RBT and one RBVS group, respectively. Gene enrichment analysis of exclusively and differentially expressed proteins and network analysis identified in RBVS exosomes upregulated proteins specifically related to invasion and metastasis, such as proteins involved in extracellular matrix (ECM) remodeling and interaction, resistance to anoikis and the metabolism/catabolism of glucose and amino acids.
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Affiliation(s)
- Angela Galardi
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (A.G.); (V.D.P.); (P.M.); (I.R.); (R.C.); (F.L.); (A.D.G.)
| | - Marta Colletti
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (A.G.); (V.D.P.); (P.M.); (I.R.); (R.C.); (F.L.); (A.D.G.)
- Correspondence: ; Tel.: +39-066859-3516
| | - Chiara Lavarello
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS, Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy; (C.L.); (A.P.)
| | - Virginia Di Paolo
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (A.G.); (V.D.P.); (P.M.); (I.R.); (R.C.); (F.L.); (A.D.G.)
| | - Paolo Mascio
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (A.G.); (V.D.P.); (P.M.); (I.R.); (R.C.); (F.L.); (A.D.G.)
| | - Ida Russo
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (A.G.); (V.D.P.); (P.M.); (I.R.); (R.C.); (F.L.); (A.D.G.)
| | - Raffaele Cozza
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (A.G.); (V.D.P.); (P.M.); (I.R.); (R.C.); (F.L.); (A.D.G.)
| | - Antonino Romanzo
- Ophtalmology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’ Onofrio 4, 00165 Rome, Italy; (A.R.); (P.V.)
| | - Paola Valente
- Ophtalmology Unit, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’ Onofrio 4, 00165 Rome, Italy; (A.R.); (P.V.)
| | - Rita De Vito
- Department of Pathology, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza di Sant’ Onofrio 4, 00165 Rome, Italy;
| | - Luisa Pascucci
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo 4, 06126 Perugia, Italy;
| | - Hector Peinado
- Microenvironment & Metastasis Group, Molecular Oncology Program, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro 3, 28029 Madrid, Spain;
| | - Angel M. Carcaboso
- Pediatric Hematology and Oncology, Hospital Sant Joan de Deu, Institut de Recerca Sant Joan de Deu, Barcelona, 08950 Esplugues de Llobregat, Spain;
| | - Andrea Petretto
- Core Facilities-Clinical Proteomics and Metabolomics, IRCCS, Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genoa, Italy; (C.L.); (A.P.)
| | - Franco Locatelli
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (A.G.); (V.D.P.); (P.M.); (I.R.); (R.C.); (F.L.); (A.D.G.)
- Department of Ginecology/Obstetrics & Pediatrics, Sapienza University of Rome, 00185 Roma, Italy
| | - Angela Di Giannatale
- Department of Pediatric Hematology/Oncology and Cell and Gene Therapy, IRCCS, Ospedale Pediatrico Bambino Gesù, Piazza Sant’Onofrio 4, 00165 Rome, Italy; (A.G.); (V.D.P.); (P.M.); (I.R.); (R.C.); (F.L.); (A.D.G.)
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Zurli V, Montecchi T, Heilig R, Poschke I, Volkmar M, Wimmer G, Boncompagni G, Turacchio G, D'Elios MM, Campoccia G, Resta N, Offringa R, Fischer R, Acuto O, Baldari CT, Kabanova A. Phosphoproteomics of CD2 signaling reveals AMPK-dependent regulation of lytic granule polarization in cytotoxic T cells. Sci Signal 2020; 13:13/631/eaaz1965. [PMID: 32398348 DOI: 10.1126/scisignal.aaz1965] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Understanding the costimulatory signaling that enhances the activity of cytotoxic T cells (CTLs) could identify potential targets for immunotherapy. Here, we report that CD2 costimulation plays a critical role in target cell killing by freshly isolated human CD8+ T cells, which represent a challenging but valuable model to gain insight into CTL biology. We found that CD2 stimulation critically enhanced signaling by the T cell receptor in the formation of functional immune synapses by promoting the polarization of lytic granules toward the microtubule-organizing center (MTOC). To gain insight into the underlying mechanism, we explored the CD2 signaling network by phosphoproteomics, which revealed 616 CD2-regulated phosphorylation events in 373 proteins implicated in the regulation of vesicular trafficking, cytoskeletal organization, autophagy, and metabolism. Signaling by the master metabolic regulator AMP-activated protein kinase (AMPK) was a critical node in the CD2 network, which promoted granule polarization toward the MTOC in CD8+ T cells. Granule trafficking was driven by active AMPK enriched on adjacent lysosomes, revealing previously uncharacterized signaling cross-talk between vesicular compartments in CD8+ T cells. Our results thus establish CD2 signaling as key for mediating cytotoxic killing and granule polarization in freshly isolated CD8+ T cells and strengthen the rationale to choose CD2 and AMPK as therapeutic targets to enhance CTL activity.
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Affiliation(s)
- Vanessa Zurli
- Department of Life Sciences, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | - Tommaso Montecchi
- Department of Life Sciences, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | - Raphael Heilig
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Isabel Poschke
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Michael Volkmar
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany
| | - Giuliana Wimmer
- Department of Life Sciences, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | - Gioia Boncompagni
- Department of Life Sciences, University of Siena, via Aldo Moro 2, Siena 53100, Italy
| | - Gabriele Turacchio
- Institute of Biochemistry and Cell Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Mario Milco D'Elios
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence 50134, Italy
| | - Giuseppe Campoccia
- Department of Immune Hematology and Transfusion Medicine, University Hospital of Siena, viale Bracci 16, Siena 53100, Italy
| | - Nicoletta Resta
- Medical Genetics Unit, Department of Biomedical Sciences and Human Oncology, University of Bari, Policlinico Hospital, Piazza Giulio Cesare 11, Bari 70124, Italy
| | - Rienk Offringa
- Division of Molecular Oncology of Gastrointestinal Tumors, German Cancer Research Center, Im Neuenheimer Feld 280, Heidelberg 69120, Germany.,Department of Surgery, Heidelberg University Hospital, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - Anna Kabanova
- Department of Life Sciences, University of Siena, via Aldo Moro 2, Siena 53100, Italy.
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40
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Bruschi M, Santucci L, Petretto A, Bartolocci M, Marchisio M, Ghiggeri GM, Verrina E, Ramenghi LA, Panfoli I, Candiano G. Association between maternal omega-3 polyunsaturated fatty acids supplementation and preterm delivery: A proteomic study. FASEB J 2020; 34:6322-6334. [PMID: 32162735 DOI: 10.1096/fj.201900738rr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 02/11/2020] [Accepted: 03/01/2020] [Indexed: 02/03/2023]
Abstract
Maternal nutrition during pregnancy influences offspring health. Dietary supplementation of pregnant women with (n-3) long-chain polyunsaturated fatty acids (PUFA) was shown to exert beneficial effects on offspring, through yet unknown mechanisms. Here, we conducted a dietary intervention study on a cohort of 10 women diagnosed with threatened preterm labor with a nutritional integration with eicosapentaenoic and docosahexaenoic acids. Microvesicles (MV) isolated form arterial cord blood of the treated cohort offspring and also of a randomized selection of 10 untreated preterm and 12 term newborns, were characterized by dynamic light scattering and analyzed by proteomic and statistical analysis. Glutathione synthetase was the protein bearing the highest discrimination ability between cohorts. ELISA assay showed that glutathione synthetase was more abundant in cord blood from untreated preterm compared to the other conditions. Assay of free SH-groups showed that serum of preterm subjects was oxidized. Data suggest that preterm suffer from oxidative stress, which was lower in the treated cohort. This study confirms that MV are a representative sample of the individual status and the efficacy of dietary intervention with PUFA in human pregnancy in terms of lowered inflammatory status, increased gestational age and weight at birth.
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Affiliation(s)
- Maurizio Bruschi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Laura Santucci
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Andrea Petretto
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Martina Bartolocci
- Core Facilities - Clinical Proteomics and Metabolomics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marco Marchisio
- Department of Medicine and Aging Science, School of Medicine and Health Sciences, Università G. d'Annunzio, Chieti-Pescara, Italy
| | - Gian Marco Ghiggeri
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy.,UO of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Enrico Verrina
- UO of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Luca A Ramenghi
- Neonatal Intensive Care Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Isabella Panfoli
- Dipartimento di Farmacia (DIFAR), Università di Genova, Genoa, Italy
| | - Giovanni Candiano
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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41
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Bocanegra JL, Fujita BM, Melton NR, Cowan JM, Schinski EL, Tamir TY, Major MB, Quintero OA. The MyMOMA domain of MYO19 encodes for distinct Miro-dependent and Miro-independent mechanisms of interaction with mitochondrial membranes. Cytoskeleton (Hoboken) 2020; 77:149-166. [PMID: 31479585 PMCID: PMC8556674 DOI: 10.1002/cm.21560] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/13/2019] [Accepted: 08/31/2019] [Indexed: 08/19/2023]
Abstract
MYO19 interacts with mitochondria through a C-terminal membrane association domain (MyMOMA). Specific mechanisms for localization of MYO19 to mitochondria are poorly understood. Using promiscuous biotinylation data in combination with existing affinity-capture databases, we have identified a number of putative MYO19-interacting proteins. We chose to explore the interaction between MYO19 and the mitochondrial GTPase Miro2 by expressing mchr-Miro2 in combination with GFP-tagged fragments of the MyMOMA domain and assaying for recruitment of MYO19-GFP to mitochondria. Coexpression of MYO19898-970 -GFP with mchr-Miro2 enhanced MYO19898-970 -GFP localization to mitochondria. Mislocalizing Miro2 to filopodial tips or the cytosolic face of the nuclear envelope did not recruit MYO19898-970 -GFP to either location. To address the kinetics of the Miro2/MYO19 interaction, we used FRAP analysis and permeabilization-activated reduction in fluorescence analysis. MyMOMA constructs containing a putative membrane-insertion motif but lacking the Miro2-interacting region displayed slow exchange kinetics. MYO19898-970 -GFP, which does not include the membrane-insertion motif, displayed rapid exchange kinetics, suggesting that MYO19 interacting with Miro2 has higher mobility than MYO19 inserted into the mitochondrial outer membrane. Mutation of well-conserved, charged residues within MYO19 or within the switch I and II regions of Miro2 abolished the enhancement of MYO19898-970 -GFP localization in cells ectopically expressing mchr-Miro2. Additionally, expressing mutant versions of Miro2 thought to represent particular nucleotide states indicated that the enhancement of MYO19898-970 -GFP localization is dependent on Miro2 nucleotide state. Taken together, these data suggest that membrane-inserted MYO19 is part of a larger complex, and that Miro2 plays a role in integration of actin- and microtubule-based mitochondrial activities.
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Affiliation(s)
| | | | | | - James M. Cowan
- Department of Biology, University of Richmond, Richmond, Virginia
| | | | - Tigist Y. Tamir
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | - Michael B. Major
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
- Department of Cell Biology and Physiology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina Chapel Hill, Chapel Hill, North Carolina
| | - Omar A. Quintero
- Department of Biology, University of Richmond, Richmond, Virginia
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42
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Vivas-García Y, Falletta P, Liebing J, Louphrasitthiphol P, Feng Y, Chauhan J, Scott DA, Glodde N, Chocarro-Calvo A, Bonham S, Osterman AL, Fischer R, Ronai Z, García-Jiménez C, Hölzel M, Goding CR. Lineage-Restricted Regulation of SCD and Fatty Acid Saturation by MITF Controls Melanoma Phenotypic Plasticity. Mol Cell 2019; 77:120-137.e9. [PMID: 31733993 DOI: 10.1016/j.molcel.2019.10.014] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 08/08/2019] [Accepted: 10/10/2019] [Indexed: 12/20/2022]
Abstract
Phenotypic and metabolic heterogeneity within tumors is a major barrier to effective cancer therapy. How metabolism is implicated in specific phenotypes and whether lineage-restricted mechanisms control key metabolic vulnerabilities remain poorly understood. In melanoma, downregulation of the lineage addiction oncogene microphthalmia-associated transcription factor (MITF) is a hallmark of the proliferative-to-invasive phenotype switch, although how MITF promotes proliferation and suppresses invasion is poorly defined. Here, we show that MITF is a lineage-restricted activator of the key lipogenic enzyme stearoyl-CoA desaturase (SCD) and that SCD is required for MITFHigh melanoma cell proliferation. By contrast MITFLow cells are insensitive to SCD inhibition. Significantly, the MITF-SCD axis suppresses metastasis, inflammatory signaling, and an ATF4-mediated feedback loop that maintains de-differentiation. Our results reveal that MITF is a lineage-specific regulator of metabolic reprogramming, whereby fatty acid composition is a driver of melanoma phenotype switching, and highlight that cell phenotype dictates the response to drugs targeting lipid metabolism.
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Affiliation(s)
- Yurena Vivas-García
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Paola Falletta
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Jana Liebing
- Institute of Experimental Oncology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Yongmei Feng
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Jagat Chauhan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - David A Scott
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Nicole Glodde
- Institute of Experimental Oncology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Ana Chocarro-Calvo
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK; Facultad de CC de la Salud, Edificio Dptal 1, Universidad Rey Juan Carlos, Avda Atenas s/n 28922, Alcorcón, Madrid, Spain
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford OX3 7FZ, UK
| | - Andrei L Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford OX3 7FZ, UK
| | - Ze'ev Ronai
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Custodia García-Jiménez
- Facultad de CC de la Salud, Edificio Dptal 1, Universidad Rey Juan Carlos, Avda Atenas s/n 28922, Alcorcón, Madrid, Spain
| | - Michael Hölzel
- Institute of Experimental Oncology, University Hospital Bonn, University of Bonn, 53127 Bonn, Germany
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK.
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43
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de Beyer JA, Szöllössi A, Byles E, Fischer R, Armitage JP. Mechanism of Signalling and Adaptation through the Rhodobacter sphaeroides Cytoplasmic Chemoreceptor Cluster. Int J Mol Sci 2019; 20:ijms20205095. [PMID: 31615130 PMCID: PMC6829392 DOI: 10.3390/ijms20205095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/05/2019] [Accepted: 10/07/2019] [Indexed: 11/16/2022] Open
Abstract
Rhodobacter sphaeroides has two chemotaxis clusters, an Escherichia coli-like cluster with membrane-spanning chemoreceptors and a less-understood cytoplasmic cluster. The cytoplasmic CheA is split into CheA4, a kinase, and CheA3, a His-domain phosphorylated by CheA4 and a phosphatase domain, which together phosphorylate and dephosphorylate motor-stopping CheY6. In bacterial two-hybrid analysis, one major cytoplasmic chemoreceptor, TlpT, interacted with CheA4, while the other, TlpC, interacted with CheA3. Both clusters have associated adaptation proteins. Deleting their methyltransferases and methylesterases singly and together removed chemotaxis, but with opposite effects. The cytoplasmic cluster signal overrode the membrane cluster signal. Methylation and demethylation of specific chemoreceptor glutamates controls adaptation. Tandem mass spectroscopy and bioinformatics identified four putative sites on TlpT, three glutamates and a glutamine. Mutating each glutamate to alanine resulted in smooth swimming and loss of chemotaxis, unlike similar mutations in E. coli chemoreceptors. Cells with two mutated glutamates were more stoppy than wild-type and responded and adapted to attractant addition, not removal. Mutating all four sites amplified the effect. Cells were non-motile, began smooth swimming on attractant addition, and rapidly adapted back to non-motile before attractant removal. We propose that TlpT responds and adapts to the cell's metabolic state, generating the steady-state concentration of motor-stopping CheY6~P. Membrane-cluster signalling produces a pulse of CheY3/CheY4~P that displaces CheY6~P and allows flagellar rotation and smooth swimming before both clusters adapt.
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Affiliation(s)
- Jennifer A. de Beyer
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.A.d.B.); (A.S.); (E.B.)
| | - Andrea Szöllössi
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.A.d.B.); (A.S.); (E.B.)
| | - Elaine Byles
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.A.d.B.); (A.S.); (E.B.)
| | - Roman Fischer
- Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK;
| | - Judith P. Armitage
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; (J.A.d.B.); (A.S.); (E.B.)
- Correspondence:
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44
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Cockman ME, Lippl K, Tian YM, Pegg HB, Figg WD, Abboud MI, Heilig R, Fischer R, Myllyharju J, Schofield CJ, Ratcliffe PJ. Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates. eLife 2019; 8:e46490. [PMID: 31500697 PMCID: PMC6739866 DOI: 10.7554/elife.46490] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/22/2019] [Indexed: 12/21/2022] Open
Abstract
Human and other animal cells deploy three closely related dioxygenases (PHD 1, 2 and 3) to signal oxygen levels by catalysing oxygen regulated prolyl hydroxylation of the transcription factor HIF. The discovery of the HIF prolyl-hydroxylase (PHD) enzymes as oxygen sensors raises a key question as to the existence and nature of non-HIF substrates, potentially transducing other biological responses to hypoxia. Over 20 such substrates are reported. We therefore sought to characterise their reactivity with recombinant PHD enzymes. Unexpectedly, we did not detect prolyl-hydroxylase activity on any reported non-HIF protein or peptide, using conditions supporting robust HIF-α hydroxylation. We cannot exclude PHD-catalysed prolyl hydroxylation occurring under conditions other than those we have examined. However, our findings using recombinant enzymes provide no support for the wide range of non-HIF PHD substrates that have been reported.
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Affiliation(s)
| | - Kerstin Lippl
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Ya-Min Tian
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | | | - William D Figg
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Martine I Abboud
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Raphael Heilig
- Target Discovery Institute, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Johanna Myllyharju
- Oulu Center for Cell-Matrix Research, Biocenter Oulu and Faculty of Biochemistry and Molecular MedicineUniversity of OuluOuluFinland
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of ChemistryUniversity of OxfordOxfordUnited Kingdom
| | - Peter J Ratcliffe
- The Francis Crick InstituteLondonUnited Kingdom
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUnited Kingdom
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45
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Pinto-Fernández A, Davis S, Schofield AB, Scott HC, Zhang P, Salah E, Mathea S, Charles PD, Damianou A, Bond G, Fischer R, Kessler BM. Comprehensive Landscape of Active Deubiquitinating Enzymes Profiled by Advanced Chemoproteomics. Front Chem 2019; 7:592. [PMID: 31555637 PMCID: PMC6727631 DOI: 10.3389/fchem.2019.00592] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
Enzymes that bind and process ubiquitin, a small 76-amino-acid protein, have been recognized as pharmacological targets in oncology, immunological disorders, and neurodegeneration. Mass spectrometry technology has now reached the capacity to cover the proteome with enough depth to interrogate entire biochemical pathways including those that contain DUBs and E3 ligase substrates. We have recently characterized the breast cancer cell (MCF7) deep proteome by detecting and quantifying ~10,000 proteins, and within this data set, we can detect endogenous expression of 65 deubiquitylating enzymes (DUBs), whereas matching transcriptomics detected 78 DUB mRNAs. Since enzyme activity provides another meaningful layer of information in addition to the expression levels, we have combined advanced mass spectrometry technology, pre-fractionation, and more potent/selective ubiquitin active-site probes with propargylic-based electrophiles to profile 74 DUBs including distinguishable isoforms for 5 DUBs in MCF7 crude extract material. Competition experiments with cysteine alkylating agents and pan-DUB inhibitors combined with probe labeling revealed the proportion of active cellular DUBs directly engaged with probes by label-free quantitative (LFQ) mass spectrometry. This demonstrated that USP13, 39, and 40 are non-reactive to probe, indicating restricted enzymatic activity under these cellular conditions. Our extended chemoproteomics workflow increases depth of covering the active DUBome, including isoform-specific resolution, and provides the framework for more comprehensive cell-based small-molecule DUB selectivity profiling.
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Affiliation(s)
- Adán Pinto-Fernández
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Davis
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Abigail B Schofield
- University of Oxford, Oxford, United Kingdom.,Christ Church, University of Oxford, Oxford, United Kingdom
| | - Hannah C Scott
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ping Zhang
- University of Oxford, Oxford, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Eidarus Salah
- University of Oxford, Oxford, United Kingdom.,Department of Chemistry, University of Oxford, Oxford, United Kingdom.,Structural Genomics Consortium (United Kingdom), Oxford, United Kingdom
| | - Sebastian Mathea
- Structural Genomics Consortium (United Kingdom), Oxford, United Kingdom.,Institute of Pharmaceutical Chemistry, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Philip D Charles
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andreas Damianou
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gareth Bond
- University of Oxford, Oxford, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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46
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Chapman TP, Corridoni D, Shiraishi S, Pandey S, Aulicino A, Wigfield S, do Carmo Costa M, Thézénas ML, Paulson H, Fischer R, Kessler BM, Simmons A. Ataxin-3 Links NOD2 and TLR2 Mediated Innate Immune Sensing and Metabolism in Myeloid Cells. Front Immunol 2019; 10:1495. [PMID: 31379806 PMCID: PMC6659470 DOI: 10.3389/fimmu.2019.01495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
The interplay between NOD2 and TLR2 following recognition of components of the bacterial cell wall peptidoglycan is well-established, however their role in redirecting metabolic pathways in myeloid cells to degrade pathogens and mount antigen presentation remains unclear. We show NOD2 and TLR2 mediate phosphorylation of the deubiquitinase ataxin-3 via RIPK2 and TBK1. In myeloid cells ataxin-3 associates with the mitochondrial cristae protein MIC60, and is required for oxidative phosphorylation. Depletion of ataxin-3 leads to impaired induction of mitochondrial reactive oxygen species (mROS) and defective bacterial killing. A mass spectrometry analysis of NOD2/TLR2 triggered ataxin-3 deubiquitination targets revealed immunometabolic regulators, including HIF-1α and LAMTOR1 that may contribute to these effects. Thus, we define how ataxin-3 plays an essential role in NOD2 and TLR2 sensing and effector functions in myeloid cells.
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Affiliation(s)
- Thomas P. Chapman
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Daniele Corridoni
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Seiji Shiraishi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Sumeet Pandey
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Anna Aulicino
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Simon Wigfield
- Department of Oncology, University of Oxford, Oxford, United Kingdom
| | | | - Marie-Laëtitia Thézénas
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Henry Paulson
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Benedikt M. Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Alison Simmons
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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47
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Prosit: proteome-wide prediction of peptide tandem mass spectra by deep learning. Nat Methods 2019; 16:509-518. [DOI: 10.1038/s41592-019-0426-7] [Citation(s) in RCA: 340] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/18/2019] [Indexed: 11/08/2022]
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48
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Leimbacher PA, Jones SE, Shorrocks AMK, de Marco Zompit M, Day M, Blaauwendraad J, Bundschuh D, Bonham S, Fischer R, Fink D, Kessler BM, Oliver AW, Pearl LH, Blackford AN, Stucki M. MDC1 Interacts with TOPBP1 to Maintain Chromosomal Stability during Mitosis. Mol Cell 2019; 74:571-583.e8. [PMID: 30898438 PMCID: PMC6509287 DOI: 10.1016/j.molcel.2019.02.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/30/2018] [Accepted: 02/11/2019] [Indexed: 12/29/2022]
Abstract
In mitosis, cells inactivate DNA double-strand break (DSB) repair pathways to preserve genome stability. However, some early signaling events still occur, such as recruitment of the scaffold protein MDC1 to phosphorylated histone H2AX at DSBs. Yet, it remains unclear whether these events are important for maintaining genome stability during mitosis. Here, we identify a highly conserved protein-interaction surface in MDC1 that is phosphorylated by CK2 and recognized by the DNA-damage response mediator protein TOPBP1. Disruption of MDC1-TOPBP1 binding causes a specific loss of TOPBP1 recruitment to DSBs in mitotic but not interphase cells, accompanied by mitotic radiosensitivity, increased micronuclei, and chromosomal instability. Mechanistically, we find that TOPBP1 forms filamentous structures capable of bridging MDC1 foci in mitosis, indicating that MDC1-TOPBP1 complexes tether DSBs until repair is reactivated in the following G1 phase. Thus, we reveal an important, hitherto-unnoticed cooperation between MDC1 and TOPBP1 in maintaining genome stability during cell division.
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Affiliation(s)
- Pia-Amata Leimbacher
- Department of Gynecology, University Hospital and University of Zurich, Wagistrasse 14, 8952 Schlieren, Switzerland
| | - Samuel E Jones
- Department of Oncology, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Ann-Marie K Shorrocks
- Department of Oncology, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Mara de Marco Zompit
- Department of Gynecology, University Hospital and University of Zurich, Wagistrasse 14, 8952 Schlieren, Switzerland
| | - Matthew Day
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, UK
| | - Jordy Blaauwendraad
- Department of Gynecology, University Hospital and University of Zurich, Wagistrasse 14, 8952 Schlieren, Switzerland
| | - Diana Bundschuh
- Department of Gynecology, University Hospital and University of Zurich, Wagistrasse 14, 8952 Schlieren, Switzerland
| | - Sarah Bonham
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Daniel Fink
- Department of Gynecology, University Hospital and University of Zurich, Wagistrasse 14, 8952 Schlieren, Switzerland
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer BN1 9RQ, UK
| | - Andrew N Blackford
- Department of Oncology, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK; Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, University of Oxford, Oxford OX3 7DQ, UK.
| | - Manuel Stucki
- Department of Gynecology, University Hospital and University of Zurich, Wagistrasse 14, 8952 Schlieren, Switzerland.
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49
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Abstract
We identify an ancient and atypical form of Paget’s disease of bone (PDB) in a collection of medieval skeletons exhibiting unusually extensive pathological changes, high disease prevalence, and low age-at-death estimations. Proteomic analysis of ancient bone-preserved proteins combined with analysis of small RNAs supports a retrospective diagnosis of PDB. Remains affected by other skeletal disorders may therefore hold a chemical memory amenable to similar molecular interrogation. Abnormalities in a contemporary PDB-linked protein detected in ancient tooth samples indicate that dentition may represent an unexplored storehouse for the study of skeletal disorders. Our work provides insights into the natural history of PDB and prompts a similar revaluation of other archaeological collections. Paget’s disease of bone (PDB) is a chronic skeletal disorder that can affect one or several bones in individuals older than 55 y of age. PDB-like changes have been reported in archaeological remains as old as Roman, although accurate diagnosis and natural history of the disease is lacking. Six skeletons from a collection of 130 excavated at Norton Priory in the North West of England, which dates to medieval times, show atypical and extensive pathological changes resembling contemporary PDB affecting as many as 75% of individual skeletons. Disease prevalence in the remaining collection is high, at least 16% of adults, with age at death estimations as low as 35 y. Despite these atypical features, paleoproteomic analysis identified sequestosome 1 (SQSTM1) or p62, a protein central to the pathological milieu of PDB, as one of the few noncollagenous human sequences preserved in skeletal samples. Targeted proteomic analysis detected >60% of the ancient p62 primary sequence, with Western blotting indicating p62 abnormalities, including in dentition. Direct sequencing of ancient DNA excluded contemporary PDB-associated SQSTM1 mutations. Our observations indicate that the ancient p62 protein is likely modified within its C-terminal ubiquitin-associated domain. Ancient miRNAs were remarkably preserved in an osteosarcoma from a skeleton with extensive disease, with miR-16 expression consistent with that reported in contemporary PDB-associated bone tumors. Our work displays the use of proteomics to inform diagnosis of ancient diseases such as atypical PDB, which has unusual features presumably potentiated by yet-unidentified environmental or genetic factors.
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Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination. Mol Cell 2019; 74:1010-1019.e6. [PMID: 30981630 DOI: 10.1016/j.molcel.2019.03.029] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/01/2019] [Accepted: 03/22/2019] [Indexed: 12/31/2022]
Abstract
The essential histone H3 lysine 79 methyltransferase Dot1L regulates transcription and genomic stability and is deregulated in leukemia. The activity of Dot1L is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120Ub); however, the detailed mechanism is not understood. We report cryo-EM structures of human Dot1L bound to (1) H2BK120Ub and (2) unmodified nucleosome substrates at 3.5 Å and 4.9 Å, respectively. Comparison of both structures, complemented with biochemical experiments, provides critical insights into the mechanism of Dot1L stimulation by H2BK120Ub. Both structures show Dot1L binding to the same extended surface of the histone octamer. In yeast, this surface is used by silencing proteins involved in heterochromatin formation, explaining the mechanism of their competition with Dot1. These results provide a strong foundation for understanding conserved crosstalk between histone modifications found at actively transcribed genes and offer a general model of how ubiquitin might regulate the activity of chromatin enzymes.
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