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Ellis MJ, Lekka C, Holden KL, Tulmin H, Seedat F, O'Brien DP, Dhayal S, Zeissler ML, Knudsen JG, Kessler BM, Morgan NG, Todd JA, Richardson SJ, Stefana MI. Identification of high-performing antibodies for the reliable detection of Tau proteoforms by Western blotting and immunohistochemistry. Acta Neuropathol 2024; 147:87. [PMID: 38761203 PMCID: PMC11102361 DOI: 10.1007/s00401-024-02729-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 05/20/2024]
Abstract
Antibodies are essential research tools whose performance directly impacts research conclusions and reproducibility. Owing to its central role in Alzheimer's disease and other dementias, hundreds of distinct antibody clones have been developed against the microtubule-associated protein Tau and its multiple proteoforms. Despite this breadth of offer, limited understanding of their performance and poor antibody selectivity have hindered research progress. Here, we validate a large panel of Tau antibodies by Western blot (79 reagents) and immunohistochemistry (35 reagents). We address the reagents' ability to detect the target proteoform, selectivity, the impact of protein phosphorylation on antibody binding and performance in human brain samples. While most antibodies detected Tau at high levels, many failed to detect it at lower, endogenous levels. By WB, non-selective binding to other proteins affected over half of the antibodies tested, with several cross-reacting with the related MAP2 protein, whereas the "oligomeric Tau" T22 antibody reacted with monomeric Tau by WB, thus calling into question its specificity to Tau oligomers. Despite the presumption that "total" Tau antibodies are agnostic to post-translational modifications, we found that phosphorylation partially inhibits binding for many such antibodies, including the popular Tau-5 clone. We further combine high-sensitivity reagents, mass-spectrometry proteomics and cDNA sequencing to demonstrate that presumptive Tau "knockout" human cells continue to express residual protein arising through exon skipping, providing evidence of previously unappreciated gene plasticity. Finally, probing of human brain samples with a large panel of antibodies revealed the presence of C-term-truncated versions of all main Tau brain isoforms in both control and tauopathy donors. Ultimately, we identify a validated panel of Tau antibodies that can be employed in Western blotting and/or immunohistochemistry to reliably detect even low levels of Tau expression with high selectivity. This work represents an extensive resource that will enable the re-interpretation of published data, improve reproducibility in Tau research, and overall accelerate scientific progress.
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Affiliation(s)
- Michael J Ellis
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Christiana Lekka
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - Katie L Holden
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Hanna Tulmin
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Faheem Seedat
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Nuffield Department of Women's and Reproductive Health, Women's Centre, University of Oxford, John Radcliffe Hospital, Level 3, Oxford, UK
| | - Darragh P O'Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Shalinee Dhayal
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - Marie-Louise Zeissler
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - Jakob G Knudsen
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Department of Medicine, University of Oxford, Radcliffe, UK
- Section for Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Noel G Morgan
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - John A Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Sarah J Richardson
- Islet Biology Group, Department of Clinical & Biomedical Sciences, Exeter Centre of Excellence in Diabetes (EXCEED), University of Exeter, RILD Building, Exeter, UK
| | - M Irina Stefana
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
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Damianou A, Liang Z, Lassen F, Vendrell I, Vere G, Hester S, Charles PD, Pinto-Fernandez A, Santos A, Fischer R, Kessler BM. Oncogenic mutations of KRAS modulate its turnover by the CUL3/LZTR1 E3 ligase complex. Life Sci Alliance 2024; 7:e202302245. [PMID: 38453365 PMCID: PMC10921066 DOI: 10.26508/lsa.202302245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
KRAS is a proto-oncogene encoding a small GTPase. Mutations contribute to ∼30% of human solid tumours, including lung adenocarcinoma, pancreatic, and colorectal carcinomas. Most KRAS activating mutations interfere with GTP hydrolysis, essential for its role as a molecular switch, leading to alterations in their molecular environment and oncogenic signalling. However, the precise signalling cascades these mutations affect are poorly understood. Here, APEX2 proximity labelling was used to profile the molecular environment of WT, G12D, G13D, and Q61H-activating KRAS mutants under starvation and stimulation conditions. Through quantitative proteomics, we demonstrate the presence of known KRAS interactors, including ARAF and LZTR1, which are differentially captured by WT and KRAS mutants. Notably, the KRAS mutations G12D, G13D, and Q61H abrogate their association with LZTR1, thereby affecting turnover. Elucidating the implications of LZTR1-mediated regulation of KRAS protein levels in cancer may offer insights into therapeutic strategies targeting KRAS-driven malignancies.
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Affiliation(s)
- Andreas Damianou
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zhu Liang
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Frederik Lassen
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Iolanda Vendrell
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Svenja Hester
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip D Charles
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adan Pinto-Fernandez
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alberto Santos
- https://ror.org/052gg0110 Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Center for Health Data Science, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roman Fischer
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- https://ror.org/052gg0110 Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- https://ror.org/052gg0110 Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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3
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Hamid MHBA, Cespedes PF, Jin C, Chen JL, Gileadi U, Antoun E, Liang Z, Gao F, Teague R, Manoharan N, Maldonado-Perez D, Khalid-Alham N, Cerundolo L, Ciaoca R, Hester SS, Pinto-Fernández A, Draganov SD, Vendrell I, Liu G, Yao X, Kvalvaag A, Dominey-Foy DCC, Nanayakkara C, Kanellakis N, Chen YL, Waugh C, Clark SA, Clark K, Sopp P, Rahman NM, Verrill C, Kessler BM, Ogg G, Fernandes RA, Fisher R, Peng Y, Dustin ML, Dong T. Unconventional human CD61 pairing with CD103 promotes TCR signaling and antigen-specific T cell cytotoxicity. Nat Immunol 2024; 25:834-846. [PMID: 38561495 PMCID: PMC11065694 DOI: 10.1038/s41590-024-01802-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/29/2024] [Indexed: 04/04/2024]
Abstract
Cancer remains one of the leading causes of mortality worldwide, leading to increased interest in utilizing immunotherapy strategies for better cancer treatments. In the past decade, CD103+ T cells have been associated with better clinical prognosis in patients with cancer. However, the specific immune mechanisms contributing toward CD103-mediated protective immunity remain unclear. Here, we show an unexpected and transient CD61 expression, which is paired with CD103 at the synaptic microclusters of T cells. CD61 colocalization with the T cell antigen receptor further modulates downstream T cell antigen receptor signaling, improving antitumor cytotoxicity and promoting physiological control of tumor growth. Clinically, the presence of CD61+ tumor-infiltrating T lymphocytes is associated with improved clinical outcomes, mediated through enhanced effector functions and phenotype with limited evidence of cellular exhaustion. In conclusion, this study identified an unconventional and transient CD61 expression and pairing with CD103 on human immune cells, which potentiates a new target for immune-based cellular therapies.
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MESH Headings
- Animals
- Humans
- Mice
- Antigens, CD/metabolism
- Antigens, CD/immunology
- Apyrase
- Cell Line, Tumor
- Cytotoxicity, Immunologic
- Integrin alpha Chains/metabolism
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Neoplasms/immunology
- Neoplasms/therapy
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/immunology
- Signal Transduction/immunology
- T-Lymphocytes, Cytotoxic/immunology
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Affiliation(s)
- Megat H B A Hamid
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Pablo F Cespedes
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Chen Jin
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ji-Li Chen
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Uzi Gileadi
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Elie Antoun
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Zhu Liang
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Fei Gao
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Renuka Teague
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Nikita Manoharan
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - David Maldonado-Perez
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Nasullah Khalid-Alham
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Lucia Cerundolo
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - Raul Ciaoca
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Svenja S Hester
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Adán Pinto-Fernández
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Simeon D Draganov
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Iolanda Vendrell
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Guihai Liu
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Xuan Yao
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Audun Kvalvaag
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Department of Molecular Cell Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
| | | | - Charunya Nanayakkara
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos Kanellakis
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Laboratory of Pleural and Lung Cancer Translational Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Respiratory Medicine, Churchill Hospital, Oxford University Hospitals, Oxford, UK
| | - Yi-Ling Chen
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Craig Waugh
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Sally-Ann Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Kevin Clark
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Paul Sopp
- Flow Cytometry Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Najib M Rahman
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
- Laboratory of Pleural and Lung Cancer Translational Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Oxford Centre for Respiratory Medicine, Churchill Hospital, Oxford University Hospitals, Oxford, UK
| | - Clare Verrill
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Oxford National Institute of Health Research (NIHR) Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Benedikt M Kessler
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Graham Ogg
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Ricardo A Fernandes
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fisher
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Yanchun Peng
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Michael L Dustin
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Tao Dong
- CAMS Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- MRC Translational Immune Discovery Unity, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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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5
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Blest HTW, Redmond A, Avissar J, Barker J, Bridgeman A, Fowler G, Chauveau L, Hertzog J, Vendrell I, Fischer R, Iversen MB, Jing L, Koelle DM, Paludan SR, Kessler BM, Crump CM, Rehwinkel J. HSV-1 employs UL56 to antagonize expression and function of cGAMP channels. Cell Rep 2024; 43:114122. [PMID: 38652659 DOI: 10.1016/j.celrep.2024.114122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 02/21/2024] [Accepted: 04/01/2024] [Indexed: 04/25/2024] Open
Abstract
DNA sensing is important for antiviral immunity. The DNA sensor cGAS synthesizes 2'3'-cyclic GMP-AMP (cGAMP), a second messenger that activates STING, which induces innate immunity. cGAMP not only activates STING in the cell where it is produced but cGAMP also transfers to other cells. Transporters, channels, and pores (including SLC19A1, SLC46A2, P2X7, ABCC1, and volume-regulated anion channels (VRACs)) release cGAMP into the extracellular space and/or import cGAMP. We report that infection with multiple human viruses depletes some of these cGAMP conduits. This includes herpes simplex virus 1 (HSV-1) that targets SLC46A2, P2X7, and the VRAC subunits LRRC8A and LRRC8C for degradation. The HSV-1 protein UL56 is necessary and sufficient for these effects that are mediated at least partially by proteasomal turnover. UL56 thereby inhibits cGAMP uptake via VRAC, SLC46A2, and P2X7. Taken together, HSV-1 antagonizes intercellular cGAMP transfer. We propose that this limits innate immunity by reducing cell-to-cell communication via the immunotransmitter cGAMP.
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Affiliation(s)
- Henry T W Blest
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Alexander Redmond
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jed Avissar
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jake Barker
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, UK
| | - Anne Bridgeman
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Gerissa Fowler
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Lise Chauveau
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Jonny Hertzog
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, 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; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marie B Iversen
- Department of Biomedicine, Aarhus University, Aarhus Aarhus C, Denmark
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - David M Koelle
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA; Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Global Health, University of Washington, Seattle, WA 98195, USA; Benaroya Research Institute, Seattle, WA 98101, USA
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University, Aarhus Aarhus C, Denmark
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Colin M Crump
- Department of Pathology, University of Cambridge, CB2 1QP Cambridge, UK
| | - Jan Rehwinkel
- Medical Research Council Translational Immune Discovery Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS Oxford, UK.
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6
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Jové V, Wheeler H, Lee CW, Healy DR, Levine K, Ralph EC, Yamaguchi M, Jiang ZK, Cabral E, Xu Y, Stock J, Yang B, Giddabasappa A, Loria P, Casimiro-Garcia A, Kessler BM, Pinto-Fernández A, Frattini V, Wes PD, Wang F. Type I interferon regulation by USP18 is a key vulnerability in cancer. iScience 2024; 27:109593. [PMID: 38632987 PMCID: PMC11022047 DOI: 10.1016/j.isci.2024.109593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 01/12/2024] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
Precise regulation of Type I interferon signaling is crucial for combating infection and cancer while avoiding autoimmunity. Type I interferon signaling is negatively regulated by USP18. USP18 cleaves ISG15, an interferon-induced ubiquitin-like modification, via its canonical catalytic function, and inhibits Type I interferon receptor activity through its scaffold role. USP18 loss-of-function dramatically impacts immune regulation, pathogen susceptibility, and tumor growth. However, prior studies have reached conflicting conclusions regarding the relative importance of catalytic versus scaffold function. Here, we develop biochemical and cellular methods to systematically define the physiological role of USP18. By comparing a patient-derived mutation impairing scaffold function (I60N) to a mutation disrupting catalytic activity (C64S), we demonstrate that scaffold function is critical for cancer cell vulnerability to Type I interferon. Surprisingly, we discovered that human USP18 exhibits minimal catalytic activity, in stark contrast to mouse USP18. These findings resolve human USP18's mechanism-of-action and enable USP18-targeted therapeutics.
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Affiliation(s)
- Veronica Jové
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Heather Wheeler
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - David R. Healy
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Kymberly Levine
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Erik C. Ralph
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Masaya Yamaguchi
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Edward Cabral
- Comparative Medicine, Pfizer, La Jolla, CA 92121, USA
| | - Yingrong Xu
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Jeffrey Stock
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | - Bing Yang
- Comparative Medicine, Pfizer, La Jolla, CA 92121, USA
| | | | - Paula Loria
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
| | | | - Benedikt M. Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Véronique Frattini
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Paul D. Wes
- Centers for Therapeutic Innovation, Pfizer, New York City, NY 10016, USA
| | - Feng Wang
- Discovery Sciences, Medicine Design, Pfizer, Groton, CT 06340, USA
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7
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Tsukada K, Jones SE, Bannister J, Durin MA, Vendrell I, Fawkes M, Fischer R, Kessler BM, Chapman JR, Blackford AN. BLM and BRCA1-BARD1 coordinate complementary mechanisms of joint DNA molecule resolution. Mol Cell 2024; 84:640-658.e10. [PMID: 38266639 DOI: 10.1016/j.molcel.2023.12.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 10/10/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The Bloom syndrome helicase BLM interacts with topoisomerase IIIα (TOP3A), RMI1, and RMI2 to form the BTR complex, which dissolves double Holliday junctions and DNA replication intermediates to promote sister chromatid disjunction before cell division. In its absence, structure-specific nucleases like the SMX complex (comprising SLX1-SLX4, MUS81-EME1, and XPF-ERCC1) can cleave joint DNA molecules instead, but cells deficient in both BTR and SMX are not viable. Here, we identify a negative genetic interaction between BLM loss and deficiency in the BRCA1-BARD1 tumor suppressor complex. We show that this is due to a previously overlooked role for BARD1 in recruiting SLX4 to resolve DNA intermediates left unprocessed by BLM in the preceding interphase. Consequently, cells with defective BLM and BRCA1-BARD1 accumulate catastrophic levels of chromosome breakage and micronucleation, leading to cell death. Thus, we reveal mechanistic insights into SLX4 recruitment to DNA lesions, with potential clinical implications for treating BRCA1-deficient tumors.
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Affiliation(s)
- Kaima Tsukada
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Samuel E Jones
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Julius Bannister
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Mary-Anne Durin
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Matthew Fawkes
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - J Ross Chapman
- MRC Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Andrew N Blackford
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
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8
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Dellar ER, Vendrell I, Talbot K, Kessler BM, Fischer R, Turner MR, Thompson AG. Data-independent acquisition proteomics of cerebrospinal fluid implicates endoplasmic reticulum and inflammatory mechanisms in amyotrophic lateral sclerosis. J Neurochem 2024; 168:115-127. [PMID: 38087504 PMCID: PMC10952667 DOI: 10.1111/jnc.16030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 01/26/2024]
Abstract
While unbiased proteomics of human cerebrospinal fluid (CSF) has been used successfully to identify biomarkers of amyotrophic lateral sclerosis (ALS), high-abundance proteins mask the presence of lower abundance proteins that may have diagnostic and prognostic value. However, developments in mass spectrometry (MS) proteomic data acquisition methods offer improved protein depth. In this study, MS with library-free data-independent acquisition (DIA) was used to compare the CSF proteome of people with ALS (n = 40), healthy (n = 15) and disease (n = 8) controls. Quantified protein groups were subsequently correlated with clinical variables. Univariate analysis identified 7 proteins, all significantly upregulated in ALS versus healthy controls, and 9 with altered abundance in ALS versus disease controls (FDR < 0.1). Elevated chitotriosidase-1 (CHIT1) was common to both comparisons and was proportional to ALS disability progression rate (Pearson r = 0.41, FDR-adjusted p = 0.035) but not overall survival. Ubiquitin carboxyl-terminal hydrolase isozyme L1 (UCHL1; upregulated in ALS versus healthy controls) was proportional to disability progression rate (Pearson r = 0.53, FDR-adjusted p = 0.003) and survival (Kaplan Meier log-rank p = 0.013) but not independently in multivariate proportional hazards models. Weighted correlation network analysis was used to identify functionally relevant modules of proteins. One module, enriched for inflammatory functions, was associated with age at symptom onset (Pearson r = 0.58, FDR-adjusted p = 0.005) and survival (Hazard Ratio = 1.78, FDR = 0.065), and a second module, enriched for endoplasmic reticulum proteins, was negatively correlated with disability progression rate (r = -0.42, FDR-adjusted p = 0.109). DIA acquisition methodology therefore strengthened the biomarker candidacy of CHIT1 and UCHL1 in ALS, while additionally highlighted inflammatory and endoplasmic reticulum proteins as novel sources of prognostic biomarkers.
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Affiliation(s)
| | - Iolanda Vendrell
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery InstituteUniversity of OxfordOxfordUK
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford InstituteUniversity of OxfordOxfordUK
| | - Kevin Talbot
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
- Kavli Institute for Nanoscience DiscoveryUniversity of OxfordOxfordUK
| | - Benedikt M. Kessler
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery InstituteUniversity of OxfordOxfordUK
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford InstituteUniversity of OxfordOxfordUK
| | - Roman Fischer
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery InstituteUniversity of OxfordOxfordUK
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford InstituteUniversity of OxfordOxfordUK
| | - Martin R. Turner
- Nuffield Department of Clinical NeurosciencesUniversity of OxfordOxfordUK
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9
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van Leeuwen LL, Ruigrok MJR, Kessler BM, Leuvenink HGD, Olinga P. Targeted delivery of galunisertib using machine perfusion reduces fibrogenesis in an integrated ex vivo renal transplant and fibrogenesis model. Br J Pharmacol 2024; 181:464-479. [PMID: 37596999 DOI: 10.1111/bph.16220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/23/2023] [Accepted: 08/09/2023] [Indexed: 08/21/2023] Open
Abstract
BACKGROUND AND PURPOSE Fibrosis in kidney allografts is a major post-transplant complication that contributes to graft failure. Lately, multiple potent inhibitors of fibrosis-related pathways have been developed such as galunisertib, an inhibitor of the transforming growth factor-beta (TGF-β/TGFβ1) signalling pathway. This drug, however, poses risks for adverse effects when administered systemically. Therefore, we devised a new repurposing strategy in which galunisertib is administered ex vivo. We combined machine perfusion and tissue slices to explore the antifibrotic effects of galunisertib in renal grafts. EXPERIMENTAL APPROACH Porcine kidneys were subjected to 30 min of warm ischaemia, 24 h of oxygenated hypothermic machine perfusion and 6 h of normothermic machine perfusion with various treatments (i.e. untreated control, TGFβ1, galunisertib or TGFβ1 + galunisertib; n = 8 kidneys per group). To determine whether effects persisted upon ceasing treatment, kidney slices were prepared from respective kidneys and incubated for 48 h. KEY RESULTS Galunisertib treatment improved general viability without negatively affecting renal function or elevating levels of injury markers or by-products of oxidative stress during perfusion. Galunisertib also reduced inflammation and, more importantly, reduced the onset of fibrosis after 48 h of incubation. CONCLUSIONS AND IMPLICATIONS Our findings demonstrate the value of using machine perfusion for administering antifibrotic drugs such as galunisertib, proving it to be an effective example of repurposing.
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Affiliation(s)
- L Leonie van Leeuwen
- Department of Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Nuffield Department of Medicine, Centre for Medicines Discovery, Target Discovery Institute, University of Oxford, Oxford, UK
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Mitchel J R Ruigrok
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Centre for Medicines Discovery, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Henri G D Leuvenink
- Department of Surgery, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
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10
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Bello C, Filipovic MG, Huber M, Flannery S, Kobel B, Fischer R, Kessler BM, Räber L, Stueber F, Luedi MM. Discovery of plasma proteome markers associated with clinical outcome and immunological stress after cardiac surgery. Front Cardiovasc Med 2023; 10:1287724. [PMID: 38379859 PMCID: PMC10876477 DOI: 10.3389/fcvm.2023.1287724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/20/2023] [Indexed: 02/22/2024] Open
Abstract
Background Molecular mechanisms underlying perioperative acute phase reactions in cardiac surgery are largely unknown. We aimed to characterise perioperative alterations of the acute phase plasma proteome in a cohort of adult patients undergoing on-pump cardiac surgery using high-throughput mass spectrometry and to identify candidate proteins potentially relevant to postoperative clinical outcome through a novel, multi-step approach. Methods This study is an analysis of the Bern Perioperative Biobank, a prospective cohort of adults who underwent cardiac surgery with the use of cardiopulmonary bypass (CPB) at Bern University Hospital between January and December 2019. Blood samples were taken before induction of anaesthesia and on postoperative day one. Proteomic analyses were performed by mass spectrometry. Through a multi-step, exploratory approach, hit-proteins were first identified according to their perioperative prevalence and dynamics. The set of hit-proteins were associated with predefined clinical outcome measures (all-cause one-year mortality, length of hospital stay, postoperative myocardial infarction and stroke until hospital discharge). Results 192 patients [75.5% male, median age 67.0 (IQR 60.0-73.0)] undergoing cardiac surgery with the use of CPB were included in this analysis. In total, we identified and quantified 402 proteins across all samples, whereof 30/402 (7%) proteins were identified as hit-proteins. Three hit-proteins-LDHB, VCAM1 and IGFBP2-demonstrated the strongest associations with clinical outcomes. After adjustment both for age, sex, BMI and for multiple comparisons, the scaled preoperative levels of IGFBP2 were associated with 1-year all-cause mortality (OR 10.63; 95% CI: 2.93-64.00; p = 0.046). Additionally, scaled preoperative levels of LDHB (OR 5.58; 95% CI: 2.58-8.57; p = 0.009) and VCAM1 (OR 2.32; 95% CI: 0.88-3.77; p = 0.05) were found to be associated with length of hospital stay. Conclusions We identified a subset of promising candidate plasma proteins relevant to outcome after on-pump cardiac surgery. IGFBP2 showed a strong association with clinical outcome measures and a significant association of preoperative levels with 1-year all-cause mortality. Other proteins strongly associated with outcome were LDHB and VCAM1, reflecting the dynamics in the acute phase response, inflammation and myocardial injury. We recommend further investigation of these proteins as potential outcome markers after cardiac surgery. Clinical Trial Registration ClinicalTrials.gov; NCT04767685, data are available via ProteomeXchange with identifier PXD046496.
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Affiliation(s)
- Corina Bello
- Department of Anaesthesiology and Pain Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Mark G. Filipovic
- Department of Anaesthesiology and Pain Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Markus Huber
- Department of Anaesthesiology and Pain Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Sarah Flannery
- Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Beatrice Kobel
- Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Benedikt M. Kessler
- Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
| | - Lorenz Räber
- Department of Cardiology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Frank Stueber
- Department of Anaesthesiology and Pain Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Markus M. Luedi
- Department of Anaesthesiology and Pain Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
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11
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Gan J, Pinto-Fernández A, Flierman D, Akkermans JJLL, O’Brien DP, Greenwood H, Scott HC, Fritz G, Knobeloch KP, Neefjes J, van Dam H, Ovaa H, Ploegh HL, Kessler BM, Geurink PP, Sapmaz A. USP16 is an ISG15 cross-reactive deubiquitinase that targets pro-ISG15 and ISGylated proteins involved in metabolism. Proc Natl Acad Sci U S A 2023; 120:e2315163120. [PMID: 38055744 PMCID: PMC10722975 DOI: 10.1073/pnas.2315163120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/02/2023] [Indexed: 12/08/2023] Open
Abstract
Interferon-induced ubiquitin (Ub)-like modifier ISG15 covalently modifies host and viral proteins to restrict viral infections. Its function is counteracted by the canonical deISGylase USP18 or Ub-specific protease 18. Notwithstanding indications for the existence of other ISG15 cross-reactive proteases, these remain to be identified. Here, we identify deubiquitinase USP16 as an ISG15 cross-reactive protease by means of ISG15 activity-based profiling. Recombinant USP16 cleaved pro-ISG15 and ISG15 isopeptide-linked model substrates in vitro, as well as ISGylated substrates from cell lysates. Moreover, interferon-induced stimulation of ISGylation was increased by depletion of USP16. The USP16-dependent ISG15 interactome indicated that the deISGylating function of USP16 may regulate metabolic pathways. Targeted enzymes include malate dehydrogenase, cytoplasmic superoxide dismutase 1, fructose-bisphosphate aldolase A, and cytoplasmic glutamic-oxaloacetic transaminase 1. USP16 may thus contribute to the regulation of a subset of metabolism-related proteins during type-I interferon responses.
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Affiliation(s)
- Jin Gan
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA02115
| | - Adán Pinto-Fernández
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Dennis Flierman
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Jimmy J. L. L. Akkermans
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Leiden2333 ZC, The Netherlands
| | - Darragh P. O’Brien
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Helene Greenwood
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Hannah Claire Scott
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - Günter Fritz
- Department of Cellular Microbiology, University of Hohenheim, Stuttgart70599, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, Department of Molecular Genetics, University of Freiburg, Freiburg79106, Germany
- Centre for Integrative Biological Signalling Studies, Department of Molecular Genetics, University of Freiburg, Freiburg79104, Germany
| | - Jacques Neefjes
- Department of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Leiden2333 ZC, The Netherlands
| | - Hans van Dam
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Huib Ovaa
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Hidde L. Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA02115
| | - Benedikt M. Kessler
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Target Discovery Institute, Nuffield Department of Medicine, Centre for Medicines Discovery, University of Oxford, OxfordOX3 7FZ, United Kingdom
| | - Paul P. Geurink
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
| | - Aysegul Sapmaz
- Department of Cell and Chemical Biology, Division of Chemical Biology and Drug Discovery, Leiden University Medical Center, Leiden2333 ZC, The Netherlands
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12
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Davis S, Scott C, Oetjen J, Charles PD, Kessler BM, Ansorge O, Fischer R. Deep topographic proteomics of a human brain tumour. Nat Commun 2023; 14:7710. [PMID: 38001067 PMCID: PMC10673928 DOI: 10.1038/s41467-023-43520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The spatial organisation of cellular protein expression profiles within tissue determines cellular function and is key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially-resolved, quantitative proteomics of tissue that generates maps of protein abundance across tissue slices derived from a human atypical teratoid-rhabdoid tumour at three spatial resolutions, the highest being 40 µm, to reveal distinct abundance patterns of thousands of proteins. We employ spatially-aware algorithms that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with spatial abundance patterns and correlate proteins in the context of tissue heterogeneity and cellular features such as extracellular matrix or proximity to blood vessels. We identify PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response-driven, spatially-organised protein networks of the extracellular tumour matrix. Overall, we demonstrate spatially-aware deep proteo-phenotyping of tissue heterogeneity, to re-define understanding tissue biology and pathology at the molecular level.
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Affiliation(s)
- Simon Davis
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Connor Scott
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Janina Oetjen
- Bruker Daltonics GmbH & Co. KG, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Philip D Charles
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Olaf Ansorge
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
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13
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Scott HC, Draganov SD, Yu Z, Kessler BM, Pinto-Fernández A. Targeted Mass Spectrometry Reveals Interferon-Dependent Eicosanoid and Fatty Acid Alterations in Chronic Myeloid Leukaemia. Int J Mol Sci 2023; 24:15513. [PMID: 37958498 PMCID: PMC10649737 DOI: 10.3390/ijms242115513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023] Open
Abstract
Bioactive lipids are involved in cellular signalling events with links to human disease. Many of these are involved in inflammation under normal and pathological conditions. Despite being attractive molecules from a pharmacological point of view, the detection and quantification of lipids has been a major challenge. Here, we have optimised a liquid chromatography-dynamic multiple reaction monitoring-targeted mass spectrometry (LC-dMRM-MS) approach to profile eicosanoids and fatty acids in biological samples. In particular, by applying this analytic workflow to study a cellular model of chronic myeloid leukaemia (CML), we found that the levels of intra- and extracellular 2-Arachidonoylglycerol (2-AG), intracellular Arachidonic Acid (AA), extracellular Prostaglandin F2α (PGF2α), extracellular 5-Hydroxyeicosatetraenoic acid (5-HETE), extracellular Palmitic acid (PA, C16:0) and extracellular Stearic acid (SA, C18:0), were altered in response to immunomodulation by type I interferon (IFN-I), a currently approved treatment for CML. Our observations indicate changes in eicosanoid and fatty acid metabolism, with potential relevance in the context of cancer inflammation and CML.
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Affiliation(s)
- Hannah C. Scott
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (S.D.D.); (Z.Y.); (B.M.K.)
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Simeon D. Draganov
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (S.D.D.); (Z.Y.); (B.M.K.)
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Zhanru Yu
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (S.D.D.); (Z.Y.); (B.M.K.)
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Benedikt M. Kessler
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (S.D.D.); (Z.Y.); (B.M.K.)
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adán Pinto-Fernández
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK; (S.D.D.); (Z.Y.); (B.M.K.)
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
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14
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Cao Y, Lin Y, Sun N, Du X, Dong Y, Mei S, Deng X, Li X, Guo S, Tang K, Liu J, Qiao X, Zhao D, Qin Y, Zhang C, Xin T, Shi X, Zhou C, Dong T, Guo DA, Kessler BM, Xu D, Song J, Huang F, Wang X, Jiang C. A comprehensive analysis of the Bencao (herbal) small RNA Atlas reveals novel RNA therapeutics for treating human diseases. Sci China Life Sci 2023; 66:2380-2398. [PMID: 37389760 DOI: 10.1007/s11427-022-2181-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 09/30/2022] [Indexed: 07/01/2023]
Abstract
Cross-kingdom herbal miRNA was first reported in 2012. Using a modified herbal extraction protocol, we obtained 73,677,287 sequences by RNA-seq from 245 traditional Chinese Medicine (TCM), of which 20,758,257 were unique sequences. We constructed a Bencao (herbal) small RNA (sRNA) Atlas ( http://bencao.bmicc.cn ), annotated the sequences by sequence-based clustering, and created a nomenclature system for Bencao sRNAs. The profiles of 21,757 miRNAs in the Atlas were highly consistent with those of plant miRNAs in miRBase. Using software tools, our results demonstrated that all human genes might be regulated by sRNAs from the Bencao sRNA Atlas, part of the predicted human target genes were experimentally validated, suggesting that Bencao sRNAs might be one of the main bioactive components of herbal medicines. We established roadmaps for oligonucleotide drugs development and optimization of TCM prescriptions. Moreover, the decoctosome, a lipo-nano particle consisting of 0.5%-2.5% of the decoction, demonstrated potent medical effects. We propose a Bencao (herbal) Index, including small-molecule compounds (SM), protein peptides (P), nucleic acid (N), non-nucleic and non-proteinogenic large-molecule compounds (LM) and elements from Mendeleev's periodic table (E), to quantitatively measure the medical effects of botanic medicine. The Bencao sRNA Atlas is a resource for developing gene-targeting oligonucleotide drugs and optimizing botanical medicine, and may provide potential remedies for the theory and practice of one medicine.
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Affiliation(s)
- Yinghao Cao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yexuan Lin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Na Sun
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xinyi Du
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yixin Dong
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Song Mei
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xingyu Deng
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xiaobei Li
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Shaoting Guo
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Kegong Tang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Jiaqi Liu
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Xiangyu Qiao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Dandan Zhao
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Yuhao Qin
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
| | - Cong Zhang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Tianyi Xin
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Xiaohu Shi
- Department of Traditional Chinese Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100005, China
| | - Congzhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Benedikt M Kessler
- Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Jingyuan Song
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of China, Engineering Research Center of Chinese Medicine Resource of Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, China
| | - Fengming Huang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
| | - Xiaoyue Wang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
| | - Chengyu Jiang
- State Key Laboratory of Common Mechanism Research for Major Diseases, Department of Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
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15
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Wellington D, Yin Z, Yu Z, Heilig R, Davis S, Fischer R, Felce SL, Antoun E, Hublitz P, Beveridge R, Dong D, Liu G, Yao X, Peng Y, Kessler BM, Dong T. SARS-CoV-2 mutations affect antigen processing by the proteasome to alter CD8 + T cell responses. Heliyon 2023; 9:e20076. [PMID: 37842619 PMCID: PMC10570596 DOI: 10.1016/j.heliyon.2023.e20076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 08/22/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Mutations within viral epitopes can result in escape from T cells, but the contribution of mutations in flanking regions of epitopes in SARS-CoV-2 has not been investigated. Focusing on two SARS-CoV-2 nucleoprotein CD8+ epitopes, we investigated the contribution of these flanking mutations to proteasomal processing and T cell activation. We found decreased NP9-17-B*27:05 CD8+ T cell responses to the NP-Q7K mutation, likely due to a lack of efficient epitope production by the proteasome, suggesting immune escape caused by this mutation. In contrast, NP-P6L and NP-D103 N/Y mutations flanking the NP9-17-B*27:05 and NP105-113-B*07:02 epitopes, respectively, increased CD8+ T cell responses associated with enhanced epitope production by the proteasome. Our results provide evidence that SARS-CoV-2 mutations outside the epitope could have a significant impact on proteasomal processing, either contributing to T cell escape or enhancement that may be exploited for future vaccine design.
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Affiliation(s)
- Dannielle Wellington
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zixi Yin
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Zhanru Yu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Simon Davis
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Suet Ling Felce
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Elie Antoun
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Philip Hublitz
- Genome Engineering Facility, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Ryan Beveridge
- Virus Screening Facility, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Danning Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Guihai Liu
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Xuan Yao
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Yanchun Peng
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Benedikt M. Kessler
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
| | - Tao Dong
- Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7FZ, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK
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16
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Leeuwen LV, Ruigrok MJR, Jaynes CL, Kessler BM, Leuvenink HGD, Olinga P. 211.5: Targeted delivery of galunisertib using machine perfusion reduces fibrogenesis in an integrated ex vivo renal transplant and fibrogenesis model. Transplantation 2023; 107:38. [PMID: 37845905 DOI: 10.1097/01.tp.0000993200.29197.1e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Affiliation(s)
- Leonie van Leeuwen
- Department of Surgery, University Medical Center Groningen, Groningen, Netherlands
- Nuffield Department of Medicine, Centre for Medicines Discovery, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Mitchel J R Ruigrok
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
| | - Chris L Jaynes
- Department of Surgery, University Medical Center Groningen, Groningen, Netherlands
- 34 Lives, West Lafayette, IN, United States
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Centre for Medicines Discovery, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Henri G D Leuvenink
- Department of Surgery, University Medical Center Groningen, Groningen, Netherlands
| | - Peter Olinga
- Department of Pharmaceutical Technology and Biopharmacy, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, Netherlands
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17
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O'Brien DP, Jones HBL, Guenther F, Murphy EJ, England KS, Vendrell I, Anderson M, Brennan PE, Davis JB, Pinto-Fernández A, Turnbull AP, Kessler BM. Structural Premise of Selective Deubiquitinase USP30 Inhibition by Small-Molecule Benzosulfonamides. Mol Cell Proteomics 2023; 22:100609. [PMID: 37385347 PMCID: PMC10400906 DOI: 10.1016/j.mcpro.2023.100609] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/07/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023] Open
Abstract
Dampening functional levels of the mitochondrial deubiquitylating enzyme Ubiquitin-specific protease 30 (USP30) has been suggested as an effective therapeutic strategy against neurodegenerative disorders such as Parkinson's Disease. USP30 inhibition may counteract the deleterious effects of impaired turnover of damaged mitochondria, which is inherent to both familial and sporadic forms of the disease. Small-molecule inhibitors targeting USP30 are currently in development, but little is known about their precise nature of binding to the protein. We have integrated biochemical and structural approaches to gain novel mechanistic insights into USP30 inhibition by a small-molecule benzosulfonamide-containing compound, USP30inh. Activity-based protein profiling mass spectrometry confirmed target engagement, high selectivity, and potency of USP30inh for USP30 against 49 other deubiquitylating enzymes in a neuroblastoma cell line. In vitro characterization of USP30inh enzyme kinetics inferred slow and tight binding behavior, which is comparable with features of covalent modification of USP30. Finally, we blended hydrogen-deuterium exchange mass spectrometry and computational docking to elucidate the molecular architecture and geometry of USP30 complex formation with USP30inh, identifying structural rearrangements at the cleft of the USP30 thumb and palm subdomains. These studies suggest that USP30inh binds to this thumb-palm cleft, which guides the ubiquitin C terminus into the active site, thereby preventing ubiquitin binding and isopeptide bond cleavage, and confirming its importance in the inhibitory process. Our data will pave the way for the design and development of next-generation inhibitors targeting USP30 and associated deubiquitinylases.
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Affiliation(s)
- Darragh P O'Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
| | - Hannah B L Jones
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Franziska Guenther
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Emma J Murphy
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Katherine S England
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Iolanda Vendrell
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | | | - Paul E Brennan
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - John B Davis
- ARUK-Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | | | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK; Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK.
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18
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Lassen FH, Venkatesh SS, Baya N, Zhou W, Bloemendal A, Neale BM, Kessler BM, Whiffin N, Lindgren CM, Palmer DS. Exome-wide evidence of compound heterozygous effects across common phenotypes in the UK Biobank. medRxiv 2023:2023.06.29.23291992. [PMID: 37461573 PMCID: PMC10350147 DOI: 10.1101/2023.06.29.23291992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Exome-sequencing association studies have successfully linked rare protein-coding variation to risk of thousands of diseases. However, the relationship between rare deleterious compound heterozygous (CH) variation and their phenotypic impact has not been fully investigated. Here, we leverage advances in statistical phasing to accurately phase rare variants (MAF ~ 0.001%) in exome sequencing data from 175,587 UK Biobank (UKBB) participants, which we then systematically annotate to identify putatively deleterious CH coding variation. We show that 6.5% of individuals carry such damaging variants in the CH state, with 90% of variants occurring at MAF < 0.34%. Using a logistic mixed model framework, systematically accounting for relatedness, polygenic risk, nearby common variants, and rare variant burden, we investigate recessive effects in common complex diseases. We find six exome-wide significant (P < 1.68 × 10 - 7 ) and 17 nominally significant (P < 5.25 × 10 - 5 ) gene-trait associations. Among these, only four would have been identified without accounting for CH variation in the gene. We further incorporate age-at-diagnosis information from primary care electronic health records, to show that genetic phase influences lifetime risk of disease across 20 gene-trait combinations (FDR < 5%). Using a permutation approach, we find evidence for genetic phase contributing to disease susceptibility for a collection of gene-trait pairs, including FLG-asthma (P = 0.00205 ) and USH2A-visual impairment (P = 0.0084 ). Taken together, we demonstrate the utility of phasing large-scale genetic sequencing cohorts for robust identification of the phenome-wide consequences of compound heterozygosity.
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Affiliation(s)
- Frederik H. Lassen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Samvida S. Venkatesh
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Nikolas Baya
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Wei Zhou
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital, Boston, MA, USA
| | - Alex Bloemendal
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Novo Nordisk Center for Genomic Mechanisms of Disease Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Data Sciences Platform Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M. Neale
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytical and Translational Genetics Unit, Department of Medicine Massachusetts General Hospital, Boston, MA, USA
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola Whiffin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Program in Medical and Population Genetics Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cecilia M. Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Population Health Health, Medical Sciences Division University of Oxford, Oxford, United Kingdom
| | - Duncan S. Palmer
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
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19
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Halner A, Hankey L, Liang Z, Pozzetti F, Szulc D, Mi E, Liu G, Kessler BM, Syed J, Liu PJ. DEcancer: Machine learning framework tailored to liquid biopsy based cancer detection and biomarker signature selection. iScience 2023; 26:106610. [PMID: 37168566 PMCID: PMC10165183 DOI: 10.1016/j.isci.2023.106610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/15/2022] [Accepted: 03/31/2023] [Indexed: 05/13/2023] Open
Abstract
Cancer is a leading cause of mortality worldwide. Over 50% of cancers are diagnosed late, rendering many treatments ineffective. Existing liquid biopsy studies demonstrate a minimally invasive and inexpensive approach for disease detection but lack parsimonious biomarker selection, exhibit poor cancer detection performance and lack appropriate validation and testing. We established a tailored machine learning pipeline, DEcancer, for liquid biopsy analysis that addresses these limitations and improved performance. In a test set from a published cohort of 1,005 patients including 8 cancer types and 812 cancer-free individuals, DEcancer increased stage 1 cancer detection sensitivity across cancer types from 48 to 90%. In addition, with a test set cohort of patients from a high dimensional proteomics dataset of 61 lung cancer patients and 80 cancer-free individuals, DEcancer's performance using a 14-43 protein panel was comparable to 1,000 original proteins. DEcancer is a promising tool which may facilitate improved cancer detection and management.
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Affiliation(s)
- Andreas Halner
- Oxford Cancer Analytics Ltd, 696, BioEscalator, Innovation Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, UK
- Corresponding author
| | - Luke Hankey
- Oxford Cancer Analytics Ltd, 696, BioEscalator, Innovation Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, UK
| | - Zhu Liang
- Oxford Cancer Analytics Ltd, 696, BioEscalator, Innovation Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, UK
| | - Francesco Pozzetti
- Oxford Cancer Analytics Ltd, 696, BioEscalator, Innovation Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, UK
| | - Daniel Szulc
- Oxford Cancer Analytics Ltd, 696, BioEscalator, Innovation Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, UK
| | - Ella Mi
- Oxford Cancer Analytics Ltd, 696, BioEscalator, Innovation Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, UK
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Benedikt M Kessler
- Target Discovery Institute, Center for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Junetha Syed
- Oxford Cancer Analytics Ltd, 696, BioEscalator, Innovation Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, UK
| | - Peter Jianrui Liu
- Oxford Cancer Analytics Ltd, 696, BioEscalator, Innovation Building, Old Road Campus, Roosevelt Drive, Headington, Oxford, UK
- Corresponding author
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [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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21
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Dietz L, Ellison CJ, Riechmann C, Cassidy CK, Felfoldi FD, Pinto-Fernández A, Kessler BM, Elliott PR. Structural basis for SMAC-mediated antagonism of caspase inhibition by the giant ubiquitin ligase BIRC6. Science 2023; 379:1112-1117. [PMID: 36758106 DOI: 10.1126/science.ade8840] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
Certain inhibitor of apoptosis (IAP) family members are sentinel proteins that prevent untimely cell death by inhibiting caspases. Antagonists, including second mitochondria-derived activator of caspases (SMAC), regulate IAPs and drive cell death. Baculoviral IAP repeat-containing protein 6 (BIRC6), a giant IAP with dual E2 and E3 ubiquitin ligase activity, regulates programmed cell death through unknown mechanisms. We show that BIRC6 directly restricts executioner caspase-3 and -7 and ubiquitinates caspase-3, -7, and -9, working exclusively with noncanonical E1, UBA6. Notably, we show that SMAC suppresses both mechanisms. Cryo-electron microscopy structures of BIRC6 alone and in complex with SMAC reveal that BIRC6 is an antiparallel dimer juxtaposing the substrate-binding module against the catalytic domain. Furthermore, we discover that SMAC multisite binding to BIRC6 results in a subnanomolar affinity interaction, enabling SMAC to competitively displace caspases, thus antagonizing BIRC6 anticaspase function.
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Affiliation(s)
- Larissa Dietz
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Cara J Ellison
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Carlos Riechmann
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - C Keith Cassidy
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - F Daniel Felfoldi
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Paul R Elliott
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
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22
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Jones HBL, Heilig R, Kessler BM, Pinto-Fernández A. Activity-Based Protein Profiling (ABPP) for Cellular Deubiquitinase (DUB) and Inhibitor Profiling at Deep and High-Throughput Levels. Methods Mol Biol 2023; 2591:101-122. [PMID: 36350545 DOI: 10.1007/978-1-0716-2803-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This chapter provides detailed methodology and materials required to profile deubiquitinases (DUBs) in a cellular matrix using specific activity-based probes, with immunoblotting and mass spectrometry proteomics-based readouts. Different types of activity-based protein profiling (ABPP) for studying the potency and selectivity of DUB inhibitors are outlined here, including the standard ABPP, the deep DUBome ABPP, and the ABPP-HT (high-throughput compatible).
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Affiliation(s)
- Hannah B L Jones
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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23
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Kessler BM. Nilabh Shastri - Towards understanding classical and non-classical MHC-I antigen processing and presentation. Cell Immunol 2022; 382:104638. [PMID: 36371991 DOI: 10.1016/j.cellimm.2022.104638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 10/31/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022]
Abstract
Major histocompatibility complex (MHC-I) peptide antigen processing and presentation has experienced a revived interest in the context of immuno oncology, immune surveillance escape by pathogen mutations and technical advances that accelerate vaccine design. This sheds new light on the discoveries made by Nilabh Shastri and colleagues that includes the characterisation of cryptic MHC-I peptide antigen epitopes derived from untranslated regions and the N-terminal trimming of peptide antigen precursors by the aminopeptidase ERAAP (ERAP1/2 / ARTS1/LRAP) in the endoplasmic reticulum (ER) prior to the complete assembly of MHC-I complexes and their subsequent exposure to the cell surface. These scientific findings have important implications for developing novel therapeutic approaches in immunotherapy and modern vaccine design.
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Affiliation(s)
- Benedikt M Kessler
- Chinese Academy of Medical Science Oxford Institute, Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK.
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24
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Chen Z, Ioris RM, Richardson S, Van Ess AN, Vendrell I, Kessler BM, Buffa FM, Busino L, Clifford SC, Bullock AN, D'Angiolella V. Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST degradation. Cell Death Differ 2022; 29:1955-1969. [PMID: 35379950 PMCID: PMC9525703 DOI: 10.1038/s41418-022-00983-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/30/2022] Open
Abstract
Medulloblastoma is the most common malignant brain tumour in children. Genomic studies have identified distinct disease subgroups: wnt/wingless (WNT), sonic hedgehog (SHH), and non-WNT/non-SHH, comprising group 3 and group 4. Alterations in WNT and SHH signalling form the pathogenetic basis for their subgroups, whereas those for non-WNT/non-SHH tumours remain largely elusive. Recent analyses have revealed recurrent in-frame insertions in the E3 ubiquitin ligase adaptor Kelch Repeat and BTB Domain Containing 4 (KBTBD4) in cases of group 3/4 medulloblastoma. Critically, group 3/4 tumours with KBTBD4 mutations typically lack other gene-specific alterations, such as MYC amplification, indicating KBTBD4 insertion mutations as the primary genetic driver. Delineating the role of KBTBD4 mutations thus offers significant opportunities to understand tumour pathogenesis and to exploit the underpinning mechanisms therapeutically. Here, we show a novel mechanism in cancer pathogenesis whereby indel mutations in KBTBD4 drive its recognition of neo-substrates for degradation. We observe that KBTBD4 mutants promote the recruitment and ubiquitylation of the REST Corepressor (CoREST), which forms a complex to modulate chromatin accessibility and transcriptional programmes. The degradation of CoREST promoted by KBTBD4 mutation diverts epigenetic programmes inducing significant alterations in transcription to promote increased stemness of cancer cells. Transcriptional analysis of >200 human group 3 and 4 medulloblastomas by RNA-seq, highlights the presence of CoREST and stem-like signatures in tumours with KBTBD4 mutations, which extend to a further sub-set of non-mutant tumours, suggesting CoREST alterations as a novel pathogenetic mechanism of wide relevance in groups 3 and 4. Our findings uncover KBTBD4 mutation as a novel driver of epigenetic reprogramming in non-WNT/non-SHH medulloblastoma, establish a novel mode of tumorigenesis through gain-of-function mutations in ubiquitin ligases (neo-substrate recruitment) and identify both mutant KBTBD4 and CoREST complexes as new druggable targets for improved tumour-specific therapies.
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Affiliation(s)
- Zhuoyao Chen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Rafael M Ioris
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Stacey Richardson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, NE1 7RU, UK
| | - Ava N Van Ess
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Iolanda Vendrell
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Cancer Research UK and Medical Research Council 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, OX3 7FZ, UK
| | - Benedikt M Kessler
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Francesca M Buffa
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Luca Busino
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, NE1 7RU, UK
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Vincenzo D'Angiolella
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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25
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Carroll TM, Chadwick JA, Owen RP, White MJ, Kaplinsky J, Peneva I, Frangou A, Chang J, Xie PF, Roth A, Amess B, Lou H, McCann KJ, Berridge G, Fischer R, Phetsouphanh C, Omiyale AO, Jacobs BA, Ahern D, Lord SR, Norris-Bulpitt S, Dobbie ST, Griffiths L, Ramirez KA, Ricciardi T, Macri MJ, Ryan A, Venhaus RR, Van den Eynde BJ, Karydis I, Kessler BM, Schuster-Böckler B, Middleton MR, Lu X. Abstract 1247: Comprehensive molecular profiling to predict first-line immunochemotherapy outcomes in inoperable esophageal adenocarcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
For patients with inoperable esophageal adenocarcinoma (EAC), prognosis on conventional chemotherapy (CTX) remains poor. In 2021, the FDA approved two αPD-1 immune checkpoint inhibitors (ICI) for addition to fluoropyrimidine/platinum-containing CTX in this first-line setting. As ICI+CTX enters the clinic, understanding ICI responses and predicting which patients will benefit from ICI addition are key challenges. To address these challenges, we assessed clinical and molecular profiles from the experimental LUD2015-005 trial (NCT02735239, EudraCT 2015-005298-19). Treatment consisted of an initial four-week ICI-only window with durvalumab (αPD-L1) with or without a single dose of tremelimumab (αCTLA-4), followed by 6 cycles of ICI+CTX (CapOx). 38 inoperable patients received treatment (35 EAC; 3 ESCC); median overall survival (OS) and progression-free survival (PFS) were 13.4 and 9.3 months, respectively. All patients reported at least one treatment emergent adverse event (TEAE), with 29 (76.3%) reporting grade 3 or higher TEAEs. EAC patients with available samples (n = 33) were taken forward for biomarker analysis, using tumor and adjacent normal biopsies collected at pre-treatment (PreTx), after four weeks of ICI-only (ICI-4W), and at the end of ICI+CTX (PostTx).
Transcriptomic comparison of paired PreTx and ICI-4W EAC biopsies (n = 28) revealed ICI-induced upregulation of a novel T-cell inflammation signature (termed INCITE). Stronger INCITE upregulation correlated with greater tumor shrinkage during the ICI-only window, and tumors with minimal INCITE upregulation showed markers of ICI resistance, including Innate PD-1 Resistance (IPRES). Despite correlation with ICI-only responses, INCITE changes were not associated with overall ICI+CTX outcomes.
To find predictive biomarkers of ICI+CTX outcomes, we conducted comprehensive genomic and transcriptomic profiling of PreTx EAC biopsies (n = 33). First, we generated a novel 65,000 cell scRNA-seq dataset and designed a deconvolution workflow to resolve tumor cell composition. Unexpectedly, monocyte composition was strongly linked with greater overall survival (OS) (HR: 0.40 [0.23-0.69]; p = 0.001; FDR = 0.047). Coding tumor mutational burden (TMB) was also associated with improved OS (HR: 0.50 [0.28-0.89]; p = 0.019). Multivariate modelling suggested monocyte composition and TMB were independent and complementary predictors of outcomes. Neither factor was associated with outcomes in a TCGA cohort of EAC patients not treated with ICI, suggesting these biomarkers may be specific to ICI or ICI+CTX.
Our findings suggest monocyte composition and TMB may identify EAC patients likely to benefit from ICI+CTX. INCITE upregulation may also serve as a useful monitor of ICI efficacy. These timely findings further our understanding of ICI response and resistance and may help inform patient selection for ICI+CTX.
Citation Format: Thomas M. Carroll, Joseph A. Chadwick, Richard P. Owen, Michael J. White, Joseph Kaplinsky, Iliana Peneva, Anna Frangou, Jaeho Chang, Phil F. Xie, Andrew Roth, Bob Amess, Hantao Lou, Katy J. McCann, Georgina Berridge, Roman Fischer, Chansavath Phetsouphanh, Ayo O. Omiyale, Brittany-Amber Jacobs, David Ahern, Simon R. Lord, Stewart Norris-Bulpitt, Sam T. Dobbie, Lucinda Griffiths, Kristen Aufiero Ramirez, Toni Ricciardi, Mary J. Macri, Aileen Ryan, Ralph R. Venhaus, Benoit J. Van den Eynde, Ioannis Karydis, Benedikt M. Kessler, Benjamin Schuster-Böckler, Mark R. Middleton, Xin Lu. Comprehensive molecular profiling to predict first-line immunochemotherapy outcomes in inoperable esophageal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1247.
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Affiliation(s)
- Thomas M. Carroll
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Joseph A. Chadwick
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Richard P. Owen
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Michael J. White
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Joseph Kaplinsky
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Iliana Peneva
- 2Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anna Frangou
- 3Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Jaeho Chang
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Phil F. Xie
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Andrew Roth
- 4Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Bob Amess
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Hantao Lou
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Katy J. McCann
- 5Cancer Research UK Southampton Experimental Cancer Medicine Centre, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Georgina Berridge
- 6Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- 6Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Ayo O. Omiyale
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
| | | | - David Ahern
- 7Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Simon R. Lord
- 8Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Stewart Norris-Bulpitt
- 9Early Phase Clinical Trials Unit, Cancer & Haematology Centre, Churchill Hospital, Oxford, United Kingdom
| | - Sam T. Dobbie
- 10Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Lucinda Griffiths
- 10Oncology Clinical Trials Office (OCTO), Department of Oncology, University of Oxford, Oxford, United Kingdom
| | | | | | | | | | | | | | - Ioannis Karydis
- 12Cancer Sciences Unit, University of Southampton and Cancer Care Group, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Benedikt M. Kessler
- 6Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Mark R. Middleton
- 8Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Xin Lu
- 1Ludwig Institute of Cancer Research, University of Oxford, Oxford, United Kingdom
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26
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Leissing TM, Hardy AP, Chan H, Wang Y, Tumber A, Chowdhury R, Feng T, Coleman ML, Cockman ME, Kramer HB, Berridge G, Fischer R, Kessler BM, Ratcliffe PJ, Lu X, Schofield CJ. Factor inhibiting HIF can catalyze two asparaginyl hydroxylations in VNVN motifs of ankyrin fold proteins. J Biol Chem 2022; 298:102020. [PMID: 35537551 PMCID: PMC9189129 DOI: 10.1016/j.jbc.2022.102020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/28/2022] [Accepted: 04/15/2022] [Indexed: 10/28/2022] Open
Abstract
The aspariginyl hydroxylase human factor inhibiting hypoxia-inducible factor (FIH) is an important regulator of the transcriptional activity of hypoxia-inducible factor. FIH also catalyzes the hydroxylation of asparaginyl and other residues in ankyrin repeat domain-containing proteins, including apoptosis stimulating of p53 protein (ASPP) family members. ASPP2 is reported to undergo a single FIH-catalyzed hydroxylation at Asn-986. We report biochemical and crystallographic evidence showing that FIH catalyzes the unprecedented post-translational hydroxylation of both asparaginyl residues in "VNVN" and related motifs of ankyrin repeat domains in ASPPs (i.e., ASPP1, ASPP2, and iASPP) and the related ASB11 and p18-INK4C proteins. Our biochemical results extend the substrate scope of FIH catalysis and may have implications for its biological roles, including in the hypoxic response and ASPP family function.
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Affiliation(s)
- Thomas M Leissing
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom; Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Adam P Hardy
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Hokfung Chan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Yihua Wang
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Rasheduzzaman Chowdhury
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Tianshu Feng
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; NDM Research Building, University of Oxford, Oxford, United Kingdom
| | - Mathew L Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Matthew E Cockman
- The Francis Crick Institute, Ratcliffe Laboratory, London, United Kingdom
| | - Holger B Kramer
- MRC London Institute of Medical Sciences, London, United Kingdom; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | | | - Roman Fischer
- NDM Research Building, University of Oxford, Oxford, United Kingdom
| | | | - Peter J Ratcliffe
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; The Francis Crick Institute, Ratcliffe Laboratory, London, United Kingdom.
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry and the Ineos Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom.
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27
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Vaughan RH, Kresse J, Farmer LK, Thézénas ML, Kessler BM, Lindeman JHN, Sharples EJ, Welsh GI, Nørregaard R, Ploeg RJ, Kaisar M. Cytoskeletal protein degradation in brain death donor kidneys associates with adverse posttransplant outcomes. Am J Transplant 2022; 22:1073-1087. [PMID: 34878723 PMCID: PMC9305475 DOI: 10.1111/ajt.16912] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 01/25/2023]
Abstract
In brain death, cerebral injury contributes to systemic biological dysregulation, causing significant cellular stress in donor kidneys adversely impacting the quality of grafts. Here, we hypothesized that donation after brain death (DBD) kidneys undergo proteolytic processes that may deem grafts susceptible to posttransplant dysfunction. Using mass spectrometry and immunoblotting, we mapped degradation profiles of cytoskeletal proteins in deceased and living donor kidney biopsies. We found that key cytoskeletal proteins in DBD kidneys were proteolytically cleaved, generating peptide fragments, predominantly in grafts with suboptimal posttransplant function. Interestingly, α-actinin-4 and talin-1 proteolytic fragments were detected in brain death but not in circulatory death or living donor kidneys with similar donor characteristics. As talin-1 is a specific proteolytic target of calpain-1, we investigated a potential trigger of calpain activation and talin-1 degradation using human ex vivo precision-cut kidney slices and in vitro podocytes. Notably, we showed that activation of calpain-1 by transforming growth factor-β generated proteolytic fragments of talin-1 that matched the degradation fragments detected in DBD preimplantation kidneys, also causing dysregulation of the actin cytoskeleton in human podocytes; events that were reversed by calpain-1 inhibition. Our data provide initial evidence that brain death donor kidneys are more susceptible to cytoskeletal protein degradation. Correlation to posttransplant outcomes may be established by future studies.
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Affiliation(s)
- Rebecca H. Vaughan
- Research and DevelopmentNHS Blood and TransplantBristol & OxfordUK,Nuffield Department of Surgical SciencesOxford University Hospital OxfordBiomedical Research CentreUniversity of OxfordOxfordUK
| | | | - Louise K. Farmer
- Bristol RenalBristol Medical SchoolUniversity of BristolBristolUK
| | - Marie L. Thézénas
- Nuffield Department of MedicineTarget Discovery InstituteUniversity of OxfordOxfordUK
| | - Benedikt M. Kessler
- Nuffield Department of MedicineTarget Discovery InstituteUniversity of OxfordOxfordUK
| | - Jan H. N. Lindeman
- Department of SurgeryLeiden University Medical CentreLeidenThe Netherlands
| | | | - Gavin I. Welsh
- Bristol RenalBristol Medical SchoolUniversity of BristolBristolUK
| | | | - Rutger J. Ploeg
- Research and DevelopmentNHS Blood and TransplantBristol & OxfordUK,Nuffield Department of Surgical SciencesOxford University Hospital OxfordBiomedical Research CentreUniversity of OxfordOxfordUK,Department of SurgeryLeiden University Medical CentreLeidenThe Netherlands
| | - Maria Kaisar
- Research and DevelopmentNHS Blood and TransplantBristol & OxfordUK,Nuffield Department of Surgical SciencesOxford University Hospital OxfordBiomedical Research CentreUniversity of OxfordOxfordUK
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28
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Jones HBL, Heilig R, Davis S, Fischer R, Kessler BM, Pinto-Fernández A. ABPP-HT*-Deep Meets Fast for Activity-Based Profiling of Deubiquitylating Enzymes Using Advanced DIA Mass Spectrometry Methods. Int J Mol Sci 2022; 23:ijms23063263. [PMID: 35328685 PMCID: PMC8955990 DOI: 10.3390/ijms23063263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/10/2022] [Accepted: 03/17/2022] [Indexed: 02/01/2023] Open
Abstract
Activity-based protein profiling (ABPP) uses a combination of activity-based chemical probes with mass spectrometry (MS) to selectively characterise a particular enzyme or enzyme class. ABPP has proven invaluable for profiling enzymatic inhibitors in drug discovery. When applied to cell extracts and cells, challenging the ABP-enzyme complex formation with a small molecule can simultaneously inform on potency, selectivity, reversibility/binding affinity, permeability, and stability. ABPP can also be applied to pharmacodynamic studies to inform on cellular target engagement within specific organs when applied to in vivo models. Recently, we established separate high depth and high throughput ABPP (ABPP-HT) protocols for the profiling of deubiquitylating enzymes (DUBs). However, the combination of the two, deep and fast, in one method has been elusive. To further increase the sensitivity of the current ABPP-HT workflow, we implemented state-of-the-art data-independent acquisition (DIA) and data-dependent acquisition (DDA) MS analysis tools. Hereby, we describe an improved methodology, ABPP-HT* (enhanced high-throughput-compatible activity-based protein profiling) that in combination with DIA MS methods, allowed for the consistent profiling of 35-40 DUBs and provided a reduced number of missing values, whilst maintaining a throughput of 100 samples per day.
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Affiliation(s)
- Hannah B. L. Jones
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
| | - Raphael Heilig
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
| | - Simon Davis
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (B.M.K.); (A.P.-F.)
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (H.B.L.J.); (R.H.); (S.D.); (R.F.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (B.M.K.); (A.P.-F.)
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29
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O'Brien DP, Thorne AM, Huang H, Pappalardo E, Yao X, Thyrrestrup PS, Ravlo K, Secher N, Norregaard R, Ploeg RJ, Jespersen B, Kessler BM. Integrative omics reveals subtle molecular perturbations following ischemic conditioning in a porcine kidney transplant model. Clin Proteomics 2022; 19:6. [PMID: 35164671 PMCID: PMC8903695 DOI: 10.1186/s12014-022-09343-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Remote Ischemic Conditioning (RIC) has been proposed as a therapeutic intervention to circumvent the ischemia/reperfusion injury (IRI) that is inherent to organ transplantation. Using a porcine kidney transplant model, we aimed to decipher the subclinical molecular effects of a RIC regime, compared to non-RIC controls. METHODS Kidney pairs (n = 8 + 8) were extracted from brain dead donor pigs and transplanted in juvenile recipient pigs following a period of cold ischemia. One of the two kidney recipients in each pair was subjected to RIC prior to kidney graft reperfusion, while the other served as non-RIC control. We designed an integrative Omics strategy combining transcriptomics, proteomics, and phosphoproteomics to deduce molecular signatures in kidney tissue that could be attributed to RIC. RESULTS In kidney grafts taken out 10 h after transplantation we detected minimal molecular perturbations following RIC compared to non-RIC at the transcriptome level, which was mirrored at the proteome level. In particular, we noted that RIC resulted in suppression of tissue inflammatory profiles. Furthermore, an accumulation of muscle extracellular matrix assembly proteins in kidney tissues was detected at the protein level, which may be in response to muscle tissue damage and/or fibrosis. However, the majority of these protein changes did not reach significance (p < 0.05). CONCLUSIONS Our data identifies subtle molecular phenotypes in porcine kidneys following RIC, and this knowledge could potentially aid optimization of remote ischemic conditioning protocols in renal transplantation.
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Affiliation(s)
- Darragh P O'Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - Adam M Thorne
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences and Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Honglei Huang
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Surgical Sciences and Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Elisa Pappalardo
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Xuan Yao
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Søndergaard Thyrrestrup
- Department of Renal Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Anaesthesiology, Aalborg University Hospital, Aalborg, Denmark
| | - Kristian Ravlo
- Department of Renal Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Niels Secher
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Anaesthesiology and Intensive Care Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Rikke Norregaard
- Department of Renal Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Rutger J Ploeg
- Nuffield Department of Surgical Sciences and Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.
| | - Bente Jespersen
- Department of Renal Medicine, Aarhus University Hospital, Aarhus, Denmark.
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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30
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Vere G, Alam MR, Farrar S, Kealy R, Kessler BM, O’Brien DP, Pinto-Fernández A. Targeting the Ubiquitylation and ISGylation Machinery for the Treatment of COVID-19. Biomolecules 2022; 12:biom12020300. [PMID: 35204803 PMCID: PMC8869442 DOI: 10.3390/biom12020300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Ubiquitylation and ISGylation are protein post-translational modifications (PTMs) and two of the main events involved in the activation of pattern recognition receptor (PRRs) signals allowing the host defense response to viruses. As with similar viruses, SARS-CoV-2, the virus causing COVID-19, hijacks these pathways by removing ubiquitin and/or ISG15 from proteins using a protease called PLpro, but also by interacting with enzymes involved in ubiquitin/ISG15 machinery. These enable viral replication and avoidance of the host immune system. In this review, we highlight potential points of therapeutic intervention in ubiquitin/ISG15 pathways involved in key host-pathogen interactions, such as PLpro, USP18, TRIM25, CYLD, A20, and others that could be targeted for the treatment of COVID-19, and which may prove effective in combatting current and future vaccine-resistant variants of the disease.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Md Rashadul Alam
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Sam Farrar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Rachel Kealy
- Environmental Futures & Big Data Impact Lab, University of Exeter, Stocker Rd., Exeter EX4 4PY, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Darragh P. O’Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Correspondence: (D.P.O.); (A.P.-F.)
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (D.P.O.); (A.P.-F.)
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31
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van Leeuwen L, Venema LH, Heilig R, Leuvenink HGD, Kessler BM. Doxycycline Alters the Porcine Renal Proteome and Degradome during Hypothermic Machine Perfusion. Curr Issues Mol Biol 2022; 44:559-577. [PMID: 35723325 PMCID: PMC8928973 DOI: 10.3390/cimb44020039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 11/16/2022] Open
Abstract
Ischemia-reperfusion injury (IRI) is a hallmark for tissue injury in donation after circulatory death (DCD) kidneys. The implementation of hypothermic machine perfusion (HMP) provides a platform for improved preservation of DCD kidneys. Doxycycline administration has shown protective effects during IRI. Therefore, we explored the impact of doxycycline on proteolytic degradation mechanisms and the urinary proteome of perfused kidney grafts. Porcine kidneys underwent 30 min of warm ischemia, 24 h of oxygenated HMP (control/doxycycline) and 240 min of ex vivo reperfusion. A proteomic analysis revealed distinctive clustering profiles between urine samples collected at T15 min and T240 min. High-efficiency undecanal-based N-termini (HUNTER) kidney tissue degradomics revealed significantly more proteolytic activity in the control group at T-10. At T240, significantly more proteolytic activity was observed in the doxycycline group, indicating that doxycycline alters protein degradation during HMP. In conclusion, doxycycline administration during HMP led to significant proteomic and proteolytic differences and protective effects by attenuating urinary NGAL levels. Ultimately, we unraveled metabolic, and complement and coagulation pathways that undergo alterations during machine perfusion and that could be targeted to attenuate IRI induced injury.
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Affiliation(s)
- Leonie van Leeuwen
- Department of Surgery, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (L.H.V.); (H.G.D.L.)
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK; (R.H.); (B.M.K.)
- Correspondence:
| | - Leonie H. Venema
- Department of Surgery, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (L.H.V.); (H.G.D.L.)
| | - Raphael Heilig
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK; (R.H.); (B.M.K.)
| | - Henri G. D. Leuvenink
- Department of Surgery, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; (L.H.V.); (H.G.D.L.)
| | - Benedikt M. Kessler
- Centre for Medicines Discovery, Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK; (R.H.); (B.M.K.)
- Nuffield Department of Medicine, Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford OX3 7FZ, UK
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32
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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: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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33
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Ruiz EJ, Pinto-Fernandez A, Turnbull AP, Lan L, Charlton TM, Scott HC, Damianou A, Vere G, Riising EM, Da Costa C, Krajewski WW, Guerin D, Kearns JD, Ioannidis S, Katz M, McKinnon C, O'Connell J, Moncaut N, Rosewell I, Nye E, Jones N, Heride C, Gersch M, Wu M, Dinsmore CJ, Hammonds TR, Kim S, Komander D, Urbe S, Clague MJ, Kessler BM, Behrens A. USP28 deletion and small-molecule inhibition destabilizes c-MYC and elicits regression of squamous cell lung carcinoma. eLife 2021; 10:71596. [PMID: 34636321 PMCID: PMC8553340 DOI: 10.7554/elife.71596] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/10/2021] [Indexed: 12/19/2022] Open
Abstract
Lung squamous cell carcinoma (LSCC) is a considerable global health burden, with an incidence of over 600,000 cases per year. Treatment options are limited, and patient’s 5-year survival rate is less than 5%. The ubiquitin-specific protease 28 (USP28) has been implicated in tumourigenesis through its stabilization of the oncoproteins c-MYC, c-JUN, and Δp63. Here, we show that genetic inactivation of Usp28-induced regression of established murine LSCC lung tumours. We developed a small molecule that inhibits USP28 activity in the low nanomole range. While displaying cross-reactivity against the closest homologue USP25, this inhibitor showed a high degree of selectivity over other deubiquitinases. USP28 inhibitor treatment resulted in a dramatic decrease in c-MYC, c-JUN, and Δp63 proteins levels and consequently induced substantial regression of autochthonous murine LSCC tumours and human LSCC xenografts, thereby phenocopying the effect observed by genetic deletion. Thus, USP28 may represent a promising therapeutic target for the treatment of squamous cell lung carcinoma.
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Affiliation(s)
- E Josue Ruiz
- Adult stem cell laboratory, The Francis Crick Institute, London, United Kingdom
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew P Turnbull
- London Bioscience Innovation Centre, CRUK Therapeutic Discovery Laboratories, London, United Kingdom
| | - Linxiang Lan
- Adult stem cell laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas M Charlton
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Hannah C Scott
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andreas Damianou
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - George Vere
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Eva M Riising
- Adult stem cell laboratory, The Francis Crick Institute, London, United Kingdom
| | - Clive Da Costa
- Adult stem cell laboratory, The Francis Crick Institute, London, United Kingdom
| | - Wojciech W Krajewski
- London Bioscience Innovation Centre, CRUK Therapeutic Discovery Laboratories, London, United Kingdom
| | | | | | | | - Marie Katz
- FORMA Therapeutics, Watertown, United Kingdom
| | | | | | - Natalia Moncaut
- Genetic Manipulation Service, The Francis Crick Institute, London, United States
| | - Ian Rosewell
- Genetic Manipulation Service, The Francis Crick Institute, London, United States
| | - Emma Nye
- Adult stem cell laboratory, The Francis Crick Institute, London, United Kingdom
| | - Neil Jones
- London Bioscience Innovation Centre, CRUK Therapeutic Discovery Laboratories, London, United Kingdom
| | - Claire Heride
- London Bioscience Innovation Centre, CRUK Therapeutic Discovery Laboratories, London, United Kingdom
| | - Malte Gersch
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Min Wu
- FORMA Therapeutics, Watertown, United Kingdom
| | | | - Tim R Hammonds
- London Bioscience Innovation Centre, CRUK Therapeutic Discovery Laboratories, London, United Kingdom
| | | | - David Komander
- Ubiquitin Signalling Division, Walter and Eliza Hall Institute of Medical Research, Royal Parade, and Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Sylvie Urbe
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Axel Behrens
- Adult stem cell laboratory, The Francis Crick Institute, London, United Kingdom.,Cancer Stem Cell Laboratory, Institute of Cancer Research, London, United Kingdom.,Imperial College, Division of Cancer, Department of Surgery and Cancer, London, United Kingdom.,Convergence Science Centre, Imperial College, London, United Kingdom
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34
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Wellington D, Yin Z, Kessler BM, Dong T. Immunodominance complexity: lessons yet to be learned from dominant T cell responses to SARS-COV-2. Curr Opin Virol 2021; 50:183-191. [PMID: 34534732 PMCID: PMC8424056 DOI: 10.1016/j.coviro.2021.08.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 11/14/2022]
Abstract
Immunodominance is a complex and highly debated topic of T cell biology. The current SARS-CoV-2 pandemic has provided the opportunity to profile adaptive immune responses and determine molecular factors contributing to emerging responses towards immunodominant viral epitopes. Here, we discuss parameters that alter the dynamics of CD8 viral epitope processing, generation and T-cell responses, and how immunodominance counteracts viral immune escape mechanisms that develop in the context of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Dannielle Wellington
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
| | - Zixi Yin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Benedikt M Kessler
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Target Discovery Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford University, Oxford, OX3 9DS, UK; Chinese Academy of Medical Sciences (CAMS) Oxford Institute, Nuffield Department of Medicine, Oxford University, Oxford, OX3 7BN, UK.
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35
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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36
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van Leeuwen LL, Spraakman NA, Brat A, Huang H, Thorne AM, Bonham S, van Balkom BWM, Ploeg RJ, Kessler BM, Leuvenink HGD. Proteomic analysis of machine perfusion solution from brain dead donor kidneys reveals that elevated complement, cytoskeleton and lipid metabolism proteins are associated with 1-year outcome. Transpl Int 2021; 34:1618-1629. [PMID: 34448265 PMCID: PMC9292651 DOI: 10.1111/tri.13984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/29/2022]
Abstract
Assessment of donor kidney quality is based on clinical scores or requires biopsies for histological assessment. Noninvasive strategies to identify and predict graft outcome at an early stage are, therefore, needed. We evaluated the perfusate of donation after brain death (DBD) kidneys during nonoxygenated hypothermic machine perfusion (HMP). In particular, we compared perfusate protein profiles of good outcome (GO) and suboptimal outcome (SO) 1‐year post‐transplantation. Samples taken 15 min after the start HMP (T1) and before the termination of HMP (T2) were analysed using quantitative liquid chromatography–tandem mass spectrometry (LC‐MS/MS). Hierarchical clustering of the 100 most abundant proteins showed discrimination between grafts with a GO and SO at T1. Elevated levels of proteins involved in classical complement cascades at both T1 and T2 and a reduced abundance of lipid metabolism at T1 and of cytoskeletal proteins at T2 in GO versus SO was observed. ATP‐citrate synthase and fatty acid‐binding protein 5 (T1) and immunoglobulin heavy variable 2‐26 and desmoplakin (T2) showed 91% and 86% predictive values, respectively, for transplant outcome. Taken together, DBD kidney HMP perfusate profiles can distinguish between outcome 1‐year post‐transplantation. Furthermore, it provides insights into mechanisms that could play a role in post‐transplant outcomes.
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Affiliation(s)
- L Leonie van Leeuwen
- Department of Surgery, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Nora A Spraakman
- Department of Anaesthesiology, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Aukje Brat
- Department of Surgery, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Honglei Huang
- Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK.,Nuffield Department of Surgical Sciences, University of Oxford, BRC Oxford and NHS Blood and Transplant, Oxford, UK
| | - Adam M Thorne
- Department of Surgery, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Sarah Bonham
- Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Bas W M van Balkom
- Department of Nephrology and Hypertension, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Rutger J Ploeg
- Department of Surgery, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.,Nuffield Department of Surgical Sciences, University of Oxford, BRC Oxford and NHS Blood and Transplant, Oxford, UK
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Henri G D Leuvenink
- Department of Surgery, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
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37
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Oftedal BE, Maio S, Handel AE, White MPJ, Howie D, Davis S, Prevot N, Rota IA, Deadman ME, Kessler BM, Fischer R, Trede NS, Sezgin E, Maizels RM, Holländer GA. The chaperonin CCT8 controls proteostasis essential for T cell maturation, selection, and function. Commun Biol 2021; 4:681. [PMID: 34083746 PMCID: PMC8175432 DOI: 10.1038/s42003-021-02203-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
T cells rely for their development and function on the correct folding and turnover of proteins generated in response to a broad range of molecular cues. In the absence of the eukaryotic type II chaperonin complex, CCT, T cell activation induced changes in the proteome are compromised including the formation of nuclear actin filaments and the formation of a normal cell stress response. Consequently, thymocyte maturation and selection, and T cell homeostatic maintenance and receptor-mediated activation are severely impaired. In the absence of CCT-controlled protein folding, Th2 polarization diverges from normal differentiation with paradoxical continued IFN-γ expression. As a result, CCT-deficient T cells fail to generate an efficient immune protection against helminths as they are unable to sustain a coordinated recruitment of the innate and adaptive immune systems. These findings thus demonstrate that normal T cell biology is critically dependent on CCT-controlled proteostasis and that its absence is incompatible with protective immunity.
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Affiliation(s)
- Bergithe E Oftedal
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Clinical Science, University of Bergen, Bergen, Norway, K.G. Jebsen Center for Autoimmune Disorders, Bergen, Norway
| | - Stefano Maio
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Adam E Handel
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Madeleine P J White
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Duncan Howie
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Nicolas Prevot
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Ioanna A Rota
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Mary E Deadman
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Benedikt M Kessler
- 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
| | - Nikolaus S Trede
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Rick M Maizels
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Georg A Holländer
- Developmental Immunology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
- Paediatric Immunology, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
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38
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Kilgas S, Singh AN, Paillas S, Then CK, Torrecilla I, Nicholson J, Browning L, Vendrell I, Konietzny R, Kessler BM, Kiltie AE, Ramadan K. p97/VCP inhibition causes excessive MRE11-dependent DNA end resection promoting cell killing after ionizing radiation. Cell Rep 2021; 35:109153. [PMID: 34038735 PMCID: PMC8170441 DOI: 10.1016/j.celrep.2021.109153] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/16/2021] [Accepted: 04/28/2021] [Indexed: 01/01/2023] Open
Abstract
The ATPase p97 is a central component of the ubiquitin-proteasome degradation system. p97 uses its ATPase activity and co-factors to extract ubiquitinated substrates from different cellular locations, including DNA lesions, thereby regulating DNA repair pathway choice. Here, we find that p97 physically and functionally interacts with the MRE11-RAD50-NBS1 (MRN) complex on chromatin and that inactivation of p97 blocks the disassembly of the MRN complex from the sites of DNA damage upon ionizing radiation (IR). The inhibition of p97 function results in excessive 5'-DNA end resection mediated by MRE11 that leads to defective DNA repair and radiosensitivity. In addition, p97 inhibition by the specific small-molecule inhibitor CB-5083 increases tumor cell killing following IR both in vitro and in vivo. Mechanistically, this is mediated via increased MRE11 nuclease accumulation. This suggests that p97 inhibitors might be exploited to improve outcomes for radiotherapy patients.
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Affiliation(s)
- Susan Kilgas
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Abhay Narayan Singh
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Salome Paillas
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Chee-Kin Then
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Ignacio Torrecilla
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Judith Nicholson
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals, NHS Foundation Trust, Oxford OX3 9DU, UK
| | - Iolanda Vendrell
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Rebecca Konietzny
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Anne E Kiltie
- 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.
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39
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Crump NT, Hadjinicolaou AV, Xia M, Walsby-Tickle J, Gileadi U, Chen JL, Setshedi M, Olsen LR, Lau IJ, Godfrey L, Quek L, Yu Z, Ballabio E, Barnkob MB, Napolitani G, Salio M, Koohy H, Kessler BM, Taylor S, Vyas P, McCullagh JSO, Milne TA, Cerundolo V. Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation. Cell Rep 2021; 35:109101. [PMID: 33979616 PMCID: PMC8131582 DOI: 10.1016/j.celrep.2021.109101] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 03/01/2021] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
Depleting the microenvironment of important nutrients such as arginine is a key strategy for immune evasion by cancer cells. Many tumors overexpress arginase, but it is unclear how these cancers, but not T cells, tolerate arginine depletion. In this study, we show that tumor cells synthesize arginine from citrulline by upregulating argininosuccinate synthetase 1 (ASS1). Under arginine starvation, ASS1 transcription is induced by ATF4 and CEBPβ binding to an enhancer within ASS1. T cells cannot induce ASS1, despite the presence of active ATF4 and CEBPβ, as the gene is repressed. Arginine starvation drives global chromatin compaction and repressive histone methylation, which disrupts ATF4/CEBPβ binding and target gene transcription. We find that T cell activation is impaired in arginine-depleted conditions, with significant metabolic perturbation linked to incomplete chromatin remodeling and misregulation of key genes. Our results highlight a T cell behavior mediated by nutritional stress, exploited by cancer cells to enable pathological immune evasion.
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Affiliation(s)
- Nicholas T Crump
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Andreas V Hadjinicolaou
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Meng Xia
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - John Walsby-Tickle
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Uzi Gileadi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ji-Li Chen
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mashiko Setshedi
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lars R Olsen
- Section for Bioinformatics, DTU Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - I-Jun Lau
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Laura Godfrey
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Lynn Quek
- School of Cancer and Pharmaceutical Sciences, King's College London, SGDP Centre, Memory Lane, London SE5 8AF, UK
| | - Zhanru Yu
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Erica Ballabio
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mike B Barnkob
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Giorgio Napolitani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Mariolina Salio
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Stephen Taylor
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Paresh Vyas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - James S O McCullagh
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Thomas A Milne
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, NIHR Oxford Biomedical Research Centre Haematology Theme, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, UK.
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
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40
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Weissenbacher A, Huang H, Surik T, Lo Faro ML, Ploeg RJ, Coussios CC, Friend PJ, Kessler BM. Urine recirculation prolongs normothermic kidney perfusion via more optimal metabolic homeostasis-a proteomics study. Am J Transplant 2021; 21:1740-1753. [PMID: 33021021 PMCID: PMC8246941 DOI: 10.1111/ajt.16334] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/27/2020] [Accepted: 09/20/2020] [Indexed: 01/25/2023]
Abstract
We describe a proteomics analysis to determine the molecular differences between normothermically perfused (normothermic machine perfusion, NMP) human kidneys with urine recirculation (URC) and urine replacement (UR). Proteins were extracted from 16 kidney biopsies with URC (n = 8 donors after brain death [DBD], n = 8 donors after circulatory death [DCD]) and three with UR (n = 2 DBD, n = 1 DCD), followed by quantitative analysis by mass spectrometry. Damage-associated molecular patterns (DAMPs) were decreased in kidney tissue after 6 hours NMP with URC, suggesting reduced inflammation. Vasoconstriction was also attenuated in kidneys with URC as angiotensinogen levels were reduced. Strikingly, kidneys became metabolically active during NMP, which could be enhanced and prolonged by URC. For instance, mitochondrial succinate dehydrogenase enzyme levels as well as carbonic anhydrase were enhanced with URC, contributing to pH stabilization. Levels of cytosolic and the mitochondrial phosphoenolpyruvate carboxykinase were elevated after 24 hours of NMP, more prevalent in DCD than DBD tissue. Key enzymes involved in glucose metabolism were also increased after 12 and 24 hours of NMP with URC, including mitochondrial malate dehydrogenase and glutamic-oxaloacetic transaminase, predominantly in DCD tissue. We conclude that NMP with URC permits prolonged preservation and revitalizes metabolism to possibly better cope with ischemia reperfusion injury in discarded kidneys.
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Affiliation(s)
- Annemarie Weissenbacher
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
- Present address:
Annemarie WeissenbacherDepartment of Visceral, Transplant and Thoracic SurgeryMedical University of InnsbruckInnsbruckAustria
| | - Honglei Huang
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordUK
- Present address:
Honglei HuangOxford BioMedica PlcOxfordUK
| | - Tomas Surik
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Maria L. Lo Faro
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Rutger J. Ploeg
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Constantin C. Coussios
- Institute of Biomedical EngineeringDepartment of Engineering ScienceUniversity of OxfordOxfordUK
| | - Peter J. Friend
- Nuffield Department of Surgical SciencesUniversity of OxfordOxfordUK
| | - Benedikt M. Kessler
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordUK
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41
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Thompson AG, Gray E, Charles PD, Hu MTM, Talbot K, Fischer R, Kessler BM, Turner MR. Network Analysis of the CSF Proteome Characterizes Convergent Pathways of Cellular Dysfunction in ALS. Front Neurosci 2021; 15:642324. [PMID: 33815045 PMCID: PMC8010303 DOI: 10.3389/fnins.2021.642324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/18/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis is a clinical syndrome with complex biological determinants, but which in most cases is characterized by TDP-43 pathology. The identification in CSF of a protein signature of TDP-43 network dysfunction would have the potential to inform the identification of new biomarkers and therapeutic targets. METHODS We compared CSF proteomic data from patients with ALS (n = 41), Parkinson's disease (n = 19) and healthy control participants (n = 20). Weighted correlation network analysis was used to identify modules within the CSF protein network and combined with gene ontology enrichment analysis to functionally annotate module proteins. Analysis of module eigenproteins and differential correlation analysis of the CSF protein network was used to compare ALS and Parkinson's disease protein co-correlation with healthy controls. In order to monitor temporal changes in the CSF proteome, we performed longitudinal analysis of the CSF proteome in a subset of ALS patients. RESULTS Weighted correlation network analysis identified 10 modules, including those enriched for terms involved in gene expression including nucleic acid binding, RNA metabolism and translation; humoral immune system function, including complement pathways; membrane proteins, axonal outgrowth and adherence; and glutamatergic synapses. Immune system module eigenproteins were increased in ALS, whilst axonal module eigenproteins were decreased in ALS. The 19 altered protein correlations in ALS were enriched for gene expression (OR 3.05, p = 0.017) and membrane protein modules (OR 17.48, p = 0.011), including intramodular hub proteins previously identified as TDP-43 interactors. Proteins decreasing over longitudinal analysis ALS were enriched in glutamatergic synapse and axonal outgrowth modules. Protein correlation network disruptions in Parkinson's disease showed no module enrichment. CONCLUSIONS Alterations in the co-correlation network in CSF samples identified a set of pathways known to be associated with TDP-43 dysfunction in the pathogenesis of ALS, with important implications for therapeutic targeting and biomarker development.
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Affiliation(s)
- Alexander G. Thompson
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Elizabeth Gray
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Philip D. Charles
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Michele T. M. Hu
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Martin R. Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
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42
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Olie CS, van der Wal E, Cikes D, Maton L, de Greef JC, Lin IH, Chen YF, Kareem E, Penninger JM, Kessler BM, Raz V. Author Correction: Cytoskeletal disorganization underlies PABPN1-mediated myogenic disability. Sci Rep 2021; 11:6429. [PMID: 33723339 PMCID: PMC7961016 DOI: 10.1038/s41598-021-85459-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
| | - Erik van der Wal
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - Domagoj Cikes
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Loes Maton
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - Jessica C de Greef
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands
| | - I-Hsuan Lin
- VYM Genome Research Center, National Yang-Ming University, Taipei, Taiwan
| | - Yi-Fan Chen
- College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Elsayad Kareem
- Advanced Microscopy Facility, Vienna Biocenter Core Facilities, Vienna Biocenter (VBC), Vienna, Austria
| | - Josef M Penninger
- IMBA-Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield, Department of Medicine, University of Oxford, Oxford, UK
| | - Vered Raz
- Human Genetics Department, Leiden University Medical Center, Leiden, The Netherlands.
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43
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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. Correction: The deubiquitylase USP9X controls ribosomal stalling. J Cell Biol 2021; 220:jcb.20200421102102021c. [PMID: 33600552 PMCID: PMC7888347 DOI: 10.1083/jcb.20200421102102021c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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44
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Jones HBL, Heilig R, Fischer R, Kessler BM, Pinto-Fernández A. ABPP-HT - High-Throughput Activity-Based Profiling of Deubiquitylating Enzyme Inhibitors in a Cellular Context. Front Chem 2021; 9:640105. [PMID: 33718328 PMCID: PMC7947856 DOI: 10.3389/fchem.2021.640105] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/18/2021] [Indexed: 01/21/2023] Open
Abstract
The potency and selectivity of a small molecule inhibitor are key parameters to assess during the early stages of drug discovery. In particular, it is very informative for characterizing compounds in a relevant cellular context in order to reveal potential off-target effects and drug efficacy. Activity-based probes are valuable tools for that purpose, however, obtaining cellular target engagement data in a high-throughput format has been particularly challenging. Here, we describe a new methodology named ABPP-HT (high-throughput-compatible activity-based protein profiling), implementing a semi-automated proteomic sample preparation workflow that increases the throughput capabilities of the classical ABPP workflow approximately ten times while preserving its enzyme profiling characteristics. Using a panel of deubiquitylating enzyme (DUB) inhibitors, we demonstrate the feasibility of ABPP-HT to provide compound selectivity profiles of endogenous DUBs in a cellular context at a fraction of time as compared to previous methodologies.
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Affiliation(s)
| | | | | | | | - Adán Pinto-Fernández
- Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
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45
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Liang Z, Damianou A, Di Daniel E, Kessler BM. Inflammasome activation controlled by the interplay between post-translational modifications: emerging drug target opportunities. Cell Commun Signal 2021; 19:23. [PMID: 33627128 PMCID: PMC7905589 DOI: 10.1186/s12964-020-00688-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 11/23/2020] [Indexed: 12/27/2022] Open
Abstract
Controlling the activation of the NLRP3 inflammasome by post-translational modifications (PTMs) of critical protein subunits has emerged as a key determinant in inflammatory processes as well as in pathophysiology. In this review, we put into context the kinases, ubiquitin processing and other PTM enzymes that modify NLRP3, ASC/PYCARD and caspase-1, leading to inflammasome regulation, activation and signal termination. Potential target therapeutic entry points for a number of inflammatory diseases focussed on PTM enzyme readers, writers and erasers, leading to the regulation of inflammasome function, are discussed. Video Abstract.
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Affiliation(s)
- Zhu Liang
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK. .,Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| | - Andreas Damianou
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Elena Di Daniel
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.,ARUK Oxford Drug Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK. .,Chinese Academy of Medical Sciences (CAMS), CAMS Oxford Institute (COI), Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
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46
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Wainwright SM, Hopkins BR, Mendes CC, Sekar A, Kroeger B, Hellberg JEEU, Fan SJ, Pavey A, Marie PP, Leiblich A, Sepil I, Charles PD, Thézénas ML, Fischer R, Kessler BM, Gandy C, Corrigan L, Patel R, Wigby S, Morris JF, Goberdhan DCI, Wilson C. Drosophila Sex Peptide controls the assembly of lipid microcarriers in seminal fluid. Proc Natl Acad Sci U S A 2021; 118:e2019622118. [PMID: 33495334 PMCID: PMC7865141 DOI: 10.1073/pnas.2019622118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Seminal fluid plays an essential role in promoting male reproductive success and modulating female physiology and behavior. In the fruit fly, Drosophila melanogaster, Sex Peptide (SP) is the best-characterized protein mediator of these effects. It is secreted from the paired male accessory glands (AGs), which, like the mammalian prostate and seminal vesicles, generate most of the seminal fluid contents. After mating, SP binds to spermatozoa and is retained in the female sperm storage organs. It is gradually released by proteolytic cleavage and induces several long-term postmating responses, including increased ovulation, elevated feeding, and reduced receptivity to remating, primarily signaling through the SP receptor (SPR). Here, we demonstrate a previously unsuspected SPR-independent function for SP. We show that, in the AG lumen, SP and secreted proteins with membrane-binding anchors are carried on abundant, large neutral lipid-containing microcarriers, also found in other SP-expressing Drosophila species. These microcarriers are transferred to females during mating where they rapidly disassemble. Remarkably, SP is a key microcarrier assembly and disassembly factor. Its absence leads to major changes in the seminal proteome transferred to females upon mating. Males expressing nonfunctional SP mutant proteins that affect SP's binding to and release from sperm in females also do not produce normal microcarriers, suggesting that this male-specific defect contributes to the resulting widespread abnormalities in ejaculate function. Our data therefore reveal a role for SP in formation of seminal macromolecular assemblies, which may explain the presence of SP in Drosophila species that lack the signaling functions seen in Dmelanogaster.
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Affiliation(s)
- S Mark Wainwright
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Ben R Hopkins
- Department of Zoology, University of Oxford, OX1 3PS Oxford, United Kingdom
- Department of Evolution and Ecology, University of California, Davis, CA 95616
| | - Cláudia C Mendes
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Aashika Sekar
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Benjamin Kroeger
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Josephine E E U Hellberg
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Shih-Jung Fan
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Abigail Pavey
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Pauline P Marie
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Aaron Leiblich
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Irem Sepil
- Department of Zoology, University of Oxford, OX1 3PS Oxford, United Kingdom
| | - Philip D Charles
- Target Discovery Institute Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - Marie L Thézénas
- Target Discovery Institute Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - Roman Fischer
- Target Discovery Institute Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7BN Oxford, United Kingdom
| | - Carina Gandy
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Laura Corrigan
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Rachel Patel
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Stuart Wigby
- Department of Zoology, University of Oxford, OX1 3PS Oxford, United Kingdom
- Applied Zoology, Faculty of Biology, Technische Universität Dresden, Dresden D-01069, Germany
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L69 7ZB Liverpool, United Kingdom
| | - John F Morris
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Deborah C I Goberdhan
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom
| | - Clive Wilson
- Department of Physiology, Anatomy and Genetics, University of Oxford, OX1 3QX Oxford, United Kingdom;
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47
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Feneberg E, Charles PD, Finelli MJ, Scott C, Kessler BM, Fischer R, Ansorge O, Gray E, Talbot K, Turner MR. Detection and quantification of novel C-terminal TDP-43 fragments in ALS-TDP. Brain Pathol 2021; 31:e12923. [PMID: 33300249 PMCID: PMC8412074 DOI: 10.1111/bpa.12923] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 12/25/2022] Open
Abstract
The pathological hallmark of amyotrophic lateral sclerosis (ALS) is the presence of cytoplasmic inclusions, containing C-terminal fragments of the protein TDP-43. Here, we tested the hypothesis that highly sensitive mass spectrometry with parallel reaction monitoring (MS-PRM) can generate a high-resolution map of pathological TDP-43 peptide ratios to form the basis for quantitation of abnormal C-terminal TDP-43 fragment enrichment. Human cortex and spinal cord, microscopically staged for the presence of p-TDP-43, p-tau, alpha-synuclein, and beta-amyloid pathology, were biochemically fractionated and analyzed by immunoblot and MS for the detection of full-length and truncated (disease-specific) TDP-43 peptides. This informed the synthesis of heavy isotope-labeled peptides for absolute quantification of TDP-43 by MS-PRM across 16 ALS, 8 Parkinson's, 8 Alzheimer's disease, and 8 aged control cases. We confirmed by immunoblot the previously described enrichment of pathological C-terminal fragments in ALS-TDP urea fractions. Subsequent MS analysis resolved specific TDP-43 N- and C-terminal peptides, including a novel N-terminal truncation site-specific peptide. Absolute quantification of peptides by MS-PRM showed an increased C:N-terminal TDP-43 peptide ratio in ALS-TDP brain compared to normal and disease controls. A C:N-terminal ratio >1.5 discriminated ALS from controls with a sensitivity of 100% (CI 79.6-100) and specificity of 100% (CI 68-100), and from Parkinson's and Alzheimer's disease with a sensitivity of 93% (CI 70-100) and specificity of 100% (CI 68-100). N-terminal truncation site-specific peptides were increased in ALS in line with C-terminal fragment enrichment, but were also found in a proportion of Alzheimer cases with normal C:N-terminal ratio but coexistent limbic TDP-43 neuropathological changes. In conclusion this is a novel, sensitive, and specific method to quantify the enrichment of pathological TDP-43 fragments in human brain, which could form the basis for an antibody-free assay. Our methodology has the potential to help clarify if specific pathological TDP-43 peptide signatures are associated with primary or secondary TDP-43 proteinopathies.
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Affiliation(s)
- Emily Feneberg
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Philip D Charles
- Nuffield Department of Medicine, Centre for Medicines Discovery, Target Discovery Institute, University of Oxford, Headington, UK
| | - Mattéa J Finelli
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Connor Scott
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Centre for Medicines Discovery, Target Discovery Institute, University of Oxford, Headington, UK
| | - Roman Fischer
- Nuffield Department of Medicine, Centre for Medicines Discovery, Target Discovery Institute, University of Oxford, Headington, UK
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Elizabeth Gray
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
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48
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Shorrocks AMK, Jones SE, Tsukada K, Morrow CA, Belblidia Z, Shen J, Vendrell I, Fischer R, Kessler BM, Blackford AN. The Bloom syndrome complex senses RPA-coated single-stranded DNA to restart stalled replication forks. Nat Commun 2021; 12:585. [PMID: 33500419 PMCID: PMC7838300 DOI: 10.1038/s41467-020-20818-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 12/22/2020] [Indexed: 01/30/2023] Open
Abstract
The Bloom syndrome helicase BLM interacts with topoisomerase IIIα (TOP3A), RMI1 and RMI2 to form the BTR complex, which dissolves double Holliday junctions to produce non-crossover homologous recombination (HR) products. BLM also promotes DNA-end resection, restart of stalled replication forks, and processing of ultra-fine DNA bridges in mitosis. How these activities of the BTR complex are regulated in cells is still unclear. Here, we identify multiple conserved motifs within the BTR complex that interact cooperatively with the single-stranded DNA (ssDNA)-binding protein RPA. Furthermore, we demonstrate that RPA-binding is required for stable BLM recruitment to sites of DNA replication stress and for fork restart, but not for its roles in HR or mitosis. Our findings suggest a model in which the BTR complex contains the intrinsic ability to sense levels of RPA-ssDNA at replication forks, which controls BLM recruitment and activation in response to replication stress.
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Affiliation(s)
- Ann-Marie K Shorrocks
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Samuel E Jones
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Kaima Tsukada
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Department of Transdisciplinary Science and Engineering, School of Environment and Society, Tokyo Institute of Technology, Tokyo, 152-8550, Japan
| | - Carl A Morrow
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Zoulikha Belblidia
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Johanna Shen
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, 06520, USA
| | - Iolanda Vendrell
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Andrew N Blackford
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DS, UK.
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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49
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Harris LD, Le Pen J, Scholz N, Mieszczanek J, Vaughan N, Davis S, Berridge G, Kessler BM, Bienz M, Licchesi JDF. The deubiquitinase TRABID stabilizes the K29/K48-specific E3 ubiquitin ligase HECTD1. J Biol Chem 2021; 296:100246. [PMID: 33853758 PMCID: PMC7948964 DOI: 10.1074/jbc.ra120.015162] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/18/2022] Open
Abstract
Ubiquitin is a versatile posttranslational modification, which is covalently attached to protein targets either as a single moiety or as a ubiquitin chain. In contrast to K48 and K63-linked chains, which have been extensively studied, the regulation and function of most atypical ubiquitin chains are only starting to emerge. The deubiquitinase TRABID/ZRANB1 is tuned for the recognition and cleavage of K29 and K33-linked chains. Yet, substrates of TRABID and the cellular functions of these atypical ubiquitin signals remain unclear. We determined the interactome of two TRABID constructs rendered catalytic dead either through a point mutation in the catalytic cysteine residue or through removal of the OTU catalytic domain. We identified 50 proteins trapped by both constructs and which therefore represent candidate substrates of TRABID. The E3 ubiquitin ligase HECTD1 was then validated as a substrate of TRABID and used UbiCREST and Ub-AQUA proteomics to show that HECTD1 preferentially assembles K29- and K48-linked ubiquitin chains. Further in vitro autoubiquitination assays using ubiquitin mutants established that while HECTD1 can assemble short homotypic K29 and K48-linked chains, it requires branching at K29/K48 in order to achieve its full ubiquitin ligase activity. We next used transient knockdown and genetic knockout of TRABID in mammalian cells in order to determine the functional relationship between TRABID and HECTD1. This revealed that upon TRABID depletion, HECTD1 is readily degraded. Thus, this study identifies HECTD1 as a mammalian E3 ligase that assembles branched K29/K48 chains and also establishes TRABID-HECTD1 as a DUB/E3 pair regulating K29 linkages.
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Affiliation(s)
- Lee D Harris
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Janic Le Pen
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nico Scholz
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Juliusz Mieszczanek
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Natalie Vaughan
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Simon Davis
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Georgina Berridge
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Mariann Bienz
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Julien D F Licchesi
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom.
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50
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Chen O, Manig F, Lehmann L, Sorour N, Löck S, Yu Z, Dubrovska A, Baumann M, Kessler BM, Stasyk O, Kunz-Schughart LA. Dual role of ER stress in response to metabolic co-targeting and radiosensitivity in head and neck cancer cells. Cell Mol Life Sci 2020; 78:3021-3044. [PMID: 33230565 PMCID: PMC8004506 DOI: 10.1007/s00018-020-03704-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/19/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022]
Abstract
Arginine deprivation therapy (ADT) is a new metabolic targeting approach with high therapeutic potential for various solid cancers. Combination of ADT with low doses of the natural arginine analog canavanine effectively sensitizes malignant cells to irradiation. However, the molecular mechanisms determining the sensitivity of intrinsically non-auxotrophic cancers to arginine deficiency are still poorly understood. We here show for the first time that arginine deficiency is accompanied by global metabolic changes and protein/membrane breakdown, and results in the induction of specific, more or less pronounced (severe vs. mild) ER stress responses in head and neck squamous cell carcinoma (HNSCC) cells that differ in their intrinsic ADT sensitivity. Combination of ADT with canavanine triggered catastrophic ER stress via the eIF2α-ATF4(GADD34)-CHOP pathway, thereby inducing apoptosis; the same signaling arm was irrelevant in ADT-related radiosensitization. The particular strong supra-additive effect of ADT, canavanine and irradiation in both intrinsically more and less sensitive cancer cells supports the rational of ER stress pathways as novel target for improving multi-modal metabolic anti-cancer therapy.
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Affiliation(s)
- Oleg Chen
- OncoRay, National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Fetscherstraße 74, 01307, Dresden, Germany.,Department of Cell Signaling, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine
| | - Friederike Manig
- OncoRay, National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Fetscherstraße 74, 01307, Dresden, Germany.,Chair of Food Chemistry, TU Dresden, Dresden, Germany
| | - Loreen Lehmann
- OncoRay, National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Fetscherstraße 74, 01307, Dresden, Germany
| | - Nagwa Sorour
- OncoRay, National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Fetscherstraße 74, 01307, Dresden, Germany
| | - Steffen Löck
- OncoRay, National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Fetscherstraße 74, 01307, Dresden, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Radiation Oncology, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Zhanru Yu
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Dubrovska
- OncoRay, National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Fetscherstraße 74, 01307, Dresden, Germany.,German Cancer Consortium (DKTK), Partner Site Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Radiooncology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Michael Baumann
- OncoRay, National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Fetscherstraße 74, 01307, Dresden, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Oleh Stasyk
- Department of Cell Signaling, Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine
| | - Leoni A Kunz-Schughart
- OncoRay, National Center for Radiation Research in Oncology, Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden and Helmholtz-Zentrum Dresden-Rossendorf, Fetscherstraße 74, 01307, Dresden, Germany. .,National Center for Tumor Diseases (NCT), Partner Site Dresden, Germany.
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