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Foster WS, Newman J, Thakur N, Spencer AJ, Davies S, Woods D, Godfrey L, Ross SH, Sharpe HJ, Richard AC, Bailey D, Lambe T, Linterman MA. ChAdOx1 nCoV-19 vaccination generates spike-specific CD8 + T cells in aged mice. Immunol Cell Biol 2023; 101:479-488. [PMID: 36975169 PMCID: PMC10952561 DOI: 10.1111/imcb.12645] [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: 02/20/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023]
Abstract
Effective vaccines have reduced the morbidity and mortality caused by severe acute respiratory syndrome coronavirus-2 infection; however, the elderly remain the most at risk. Understanding how vaccines generate protective immunity and how these mechanisms change with age is key for informing future vaccine design. Cytotoxic CD8+ T cells are important for killing virally infected cells, and vaccines that induce antigen-specific CD8+ T cells in addition to humoral immunity provide an extra layer of immune protection. This is particularly important in cases where antibody titers are suboptimal, as can occur in older individuals. Here, we show that in aged mice, spike epitope-specific CD8+ T cells are generated in comparable numbers to younger animals after ChAdOx1 nCoV-19 vaccination, although phenotypic differences exist. This demonstrates that ChAdOx1 nCoV-19 elicits a good CD8+ T-cell response in older bodies, but that typical age-associated features are evident on these vaccine reactive T cells.
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Affiliation(s)
- William S Foster
- Lymphocyte Signalling and DevelopmentBabraham Institute, Babraham Research CampusCambridgeUK
| | | | - Nazia Thakur
- The Pirbright InstitutePirbright, WokingUK
- The Jenner Institute, University of OxfordOxfordUK
| | - Alexandra J Spencer
- Lymphocyte Signalling and DevelopmentBabraham Institute, Babraham Research CampusCambridgeUK
- Oxford Vaccine Group, Medical Sciences Division, Department of PaediatricsUniversity of Oxford and Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of OxfordOxfordUK
- Present address:
School of Biomedical Sciences and PharmacyUniversity of NewcastleNewcastleNSWAustralia
| | | | - Danielle Woods
- Oxford Vaccine Group, Medical Sciences Division, Department of PaediatricsUniversity of Oxford and Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of OxfordOxfordUK
| | | | - Sarah H Ross
- Lymphocyte Signalling and DevelopmentBabraham Institute, Babraham Research CampusCambridgeUK
| | - Hayley J Sharpe
- Signalling Programme, Babraham Institute, Babraham Research CampusCambridgeUK
| | - Arianne C Richard
- Lymphocyte Signalling and DevelopmentBabraham Institute, Babraham Research CampusCambridgeUK
| | | | - Teresa Lambe
- The Jenner Institute, University of OxfordOxfordUK
| | - Michelle A Linterman
- Lymphocyte Signalling and DevelopmentBabraham Institute, Babraham Research CampusCambridgeUK
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2
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van der Klaauw AA, Horner EC, Pereyra-Gerber P, Agrawal U, Foster WS, Spencer S, Vergese B, Smith M, Henning E, Ramsay ID, Smith JA, Guillaume SM, Sharpe HJ, Hay IM, Thompson S, Innocentin S, Booth LH, Robertson C, McCowan C, Kerr S, Mulroney TE, O'Reilly MJ, Gurugama TP, Gurugama LP, Rust MA, Ferreira A, Ebrahimi S, Ceron-Gutierrez L, Scotucci J, Kronsteiner B, Dunachie SJ, Klenerman P, Park AJ, Rubino F, Lamikanra AA, Stark H, Kingston N, Estcourt L, Harvala H, Roberts DJ, Doffinger R, Linterman MA, Matheson NJ, Sheikh A, Farooqi IS, Thaventhiran JED. Accelerated waning of the humoral response to COVID-19 vaccines in obesity. Nat Med 2023; 29:1146-1154. [PMID: 37169862 PMCID: PMC10202802 DOI: 10.1038/s41591-023-02343-2] [Citation(s) in RCA: 15] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 04/07/2023] [Indexed: 05/13/2023]
Abstract
Obesity is associated with an increased risk of severe Coronavirus Disease 2019 (COVID-19) infection and mortality. COVID-19 vaccines reduce the risk of serious COVID-19 outcomes; however, their effectiveness in people with obesity is incompletely understood. We studied the relationship among body mass index (BMI), hospitalization and mortality due to COVID-19 among 3.6 million people in Scotland using the Early Pandemic Evaluation and Enhanced Surveillance of COVID-19 (EAVE II) surveillance platform. We found that vaccinated individuals with severe obesity (BMI > 40 kg/m2) were 76% more likely to experience hospitalization or death from COVID-19 (adjusted rate ratio of 1.76 (95% confidence interval (CI), 1.60-1.94). We also conducted a prospective longitudinal study of a cohort of 28 individuals with severe obesity compared to 41 control individuals with normal BMI (BMI 18.5-24.9 kg/m2). We found that 55% of individuals with severe obesity had unquantifiable titers of neutralizing antibody against authentic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus compared to 12% of individuals with normal BMI (P = 0.0003) 6 months after their second vaccine dose. Furthermore, we observed that, for individuals with severe obesity, at any given anti-spike and anti-receptor-binding domain (RBD) antibody level, neutralizing capacity was lower than that of individuals with a normal BMI. Neutralizing capacity was restored by a third dose of vaccine but again declined more rapidly in people with severe obesity. We demonstrate that waning of COVID-19 vaccine-induced humoral immunity is accelerated in individuals with severe obesity. As obesity is associated with increased hospitalization and mortality from breakthrough infections, our findings have implications for vaccine prioritization policies.
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Affiliation(s)
- Agatha A van der Klaauw
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Emily C Horner
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Pehuén Pereyra-Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Utkarsh Agrawal
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | | | - Sarah Spencer
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Bensi Vergese
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- NIHR Cambridge Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Miriam Smith
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Isobel D Ramsay
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jack A Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Iain M Hay
- Babraham Institute, Babraham Research Campus, Cambridge, UK
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Sam Thompson
- Babraham Institute, Babraham Research Campus, Cambridge, UK
| | | | - Lucy H Booth
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Chris Robertson
- Department of Mathematics and Statistics, University of Strathclyde, Glasgow, UK
| | - Colin McCowan
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK
| | - Steven Kerr
- Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | | | | | | | - Maria A Rust
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Alex Ferreira
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Soraya Ebrahimi
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lourdes Ceron-Gutierrez
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jacopo Scotucci
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Barbara Kronsteiner
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Adrian J Park
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Francesco Rubino
- Department of Diabetes, King's College London and King's College Hospital NHS Foundation Trust, London, UK
| | - Abigail A Lamikanra
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Hannah Stark
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lise Estcourt
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - David J Roberts
- NHS Blood and Transplant, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Rainer Doffinger
- Immunology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Clinical Biochemistry, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- NHS Blood and Transplant, Cambridge, UK
| | - Aziz Sheikh
- Usher Institute, University of Edinburgh, Edinburgh, UK.
| | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
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Foster WS, Lee JL, Thakur N, Newman J, Spencer AJ, Davies S, Woods D, Godfrey L, Hay IM, Innocentin S, Yam-Puc JC, Horner EC, Sharpe HJ, Thaventhiran JE, Bailey D, Lambe T, Linterman MA. Tfh cells and the germinal center are required for memory B cell formation & humoral immunity after ChAdOx1 nCoV-19 vaccination. Cell Rep Med 2022; 3:100845. [PMID: 36455555 PMCID: PMC9663747 DOI: 10.1016/j.xcrm.2022.100845] [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: 07/04/2022] [Revised: 10/19/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Emergence from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been facilitated by the rollout of effective vaccines. Successful vaccines generate high-affinity plasma blasts and long-lived protective memory B cells. Here, we show a requirement for T follicular helper (Tfh) cells and the germinal center reaction for optimal serum antibody and memory B cell formation after ChAdOx1 nCoV-19 vaccination. We found that Tfh cells play an important role in expanding antigen-specific B cells while identifying Tfh-cell-dependent and -independent memory B cell subsets. Upon secondary vaccination, germinal center B cells generated during primary immunizations can be recalled as germinal center B cells again. Likewise, primary immunization GC-Tfh cells can be recalled as either Tfh or Th1 cells, highlighting the pluripotent nature of Tfh cell memory. This study demonstrates that ChAdOx1 nCoV-19-induced germinal centers are a critical source of humoral immunity.
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Affiliation(s)
- William S Foster
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Jia Le Lee
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Nazia Thakur
- The Pirbright Institute, Ash Road, Pirbright GU24 0NF, UK; Oxford Vaccine Group, Department of Paediatrics, Medical Sciences Division, University of Oxford and Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), Oxford OX3 7BN, UK
| | - Joseph Newman
- The Pirbright Institute, Ash Road, Pirbright GU24 0NF, UK
| | - Alexandra J Spencer
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Sophie Davies
- Oxford Vaccine Group, Department of Paediatrics, Medical Sciences Division, University of Oxford and Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), Oxford OX3 7BN, UK
| | - Danielle Woods
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Leila Godfrey
- The Jenner Institute, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Iain M Hay
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 0XY, UK
| | - Silvia Innocentin
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Juan Carlos Yam-Puc
- MRC Toxicology Unit, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Emily C Horner
- MRC Toxicology Unit, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Hayley J Sharpe
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | | | - Dalan Bailey
- The Pirbright Institute, Ash Road, Pirbright GU24 0NF, UK
| | - Teresa Lambe
- Oxford Vaccine Group, Department of Paediatrics, Medical Sciences Division, University of Oxford and Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), Oxford OX3 7BN, UK.
| | - Michelle A Linterman
- Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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4
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Hay IM, Shamin M, Caroe ER, Mohammed ASA, Svergun DI, Jeffries CM, Graham SC, Sharpe HJ, Deane JE. Determinants of receptor tyrosine phosphatase homophilic adhesion: Structural comparison of PTPRK and PTPRM extracellular domains. J Biol Chem 2022; 299:102750. [PMID: 36436563 PMCID: PMC9800333 DOI: 10.1016/j.jbc.2022.102750] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022] Open
Abstract
Type IIB receptor protein tyrosine phosphatases are cell surface transmembrane proteins that engage in cell adhesion via their extracellular domains (ECDs) and cell signaling via their cytoplasmic phosphatase domains. The ECDs of type IIB receptor protein tyrosine phosphatases form stable, homophilic, and trans interactions between adjacent cell membranes. Previous work has demonstrated how one family member, PTPRM, forms head-to-tail homodimers. However, as the interface was composed of residues conserved across the family, the determinants of homophilic specificity remain unknown. Here, we have solved the X-ray crystal structure of the membrane-distal N-terminal domains of PTPRK that form a head-to-tail dimer consistent with intermembrane adhesion. Comparison with the PTPRM structure demonstrates interdomain conformational differences that may define homophilic specificity. Using small-angle X-ray scattering, we determined the solution structures of the full-length ECDs of PTPRM and PTPRK, identifying that both are rigid extended molecules that differ in their overall long-range conformation. Furthermore, we identified one residue, W351, within the interaction interface that differs between PTPRM and PTPRK and showed that mutation to glycine, the equivalent residue in PTPRM, abolishes PTPRK dimer formation in vitro. This comparison of two members of the receptor tyrosine phosphatase family suggests that homophilic specificity is driven by a combination of shape complementarity and specific but limited sequence differences.
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Affiliation(s)
- Iain M Hay
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Maria Shamin
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Eve R Caroe
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Ahmed S A Mohammed
- European Molecular Biology Laboratory (EMBL) Hamburg Site, Hamburg, Germany
| | - Dmitri I Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg Site, Hamburg, Germany
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL) Hamburg Site, Hamburg, Germany
| | - Stephen C Graham
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Hayley J Sharpe
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom.
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.
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5
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Hay IM, Mulholland KE, Lai T, Graham SC, Sharpe HJ, Deane JE. Molecular mechanism of Afadin substrate recruitment to the receptor phosphatase PTPRK via its pseudophosphatase domain. eLife 2022; 11:79855. [PMID: 36264065 PMCID: PMC9640194 DOI: 10.7554/elife.79855] [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: 04/29/2022] [Accepted: 10/19/2022] [Indexed: 12/05/2022] Open
Abstract
Protein tyrosine phosphatase receptor-type kappa (PTPRK) is a transmembrane receptor that links extracellular homophilic interactions to intracellular catalytic activity. Previously we showed that PTPRK promotes cell–cell adhesion by selectively dephosphorylating several cell junction regulators including the protein Afadin (Fearnley et al, 2019). Here, we demonstrate that Afadin is recruited for dephosphorylation by directly binding to the PTPRK D2 pseudophosphatase domain. We mapped this interaction to a putative coiled coil (CC) domain in Afadin that is separated by more than 100 amino acids from the substrate pTyr residue. We identify the residues that define PTP specificity, explaining how Afadin is selectively dephosphorylated by PTPRK yet not by the closely related receptor tyrosine phosphatase PTPRM. Our work demonstrates that PTP substrate specificity can be determined by protein–protein interactions distal to the active site. This explains how PTPRK and other PTPs achieve substrate specificity despite a lack of specific sequence context at the substrate pTyr. Furthermore, by demonstrating that these interactions are phosphorylation-independent and mediated via binding to a non-catalytic domain, we highlight how receptor PTPs could function as intracellular scaffolds in addition to catalyzing protein dephosphorylation.
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Affiliation(s)
- Iain M Hay
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | | | - Tiffany Lai
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | - Stephen C Graham
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Hayley J Sharpe
- Signalling Programme, Babraham Institute, Cambridge, United Kingdom
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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6
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Sharpe HJ, Hay IM, Deane JE. Protein Tyrosine Pseudophosphatase Signalling Mechanisms. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.0i117] [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: 11/11/2022]
Affiliation(s)
| | - Iain M. Hay
- SignallingBabraham InstituteCambridge
- Clinical BiochemistryCambridge Institute for Medical ResearchCambridge
| | - Janet E. Deane
- Clinical BiochemistryCambridge Institute for Medical ResearchCambridge
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7
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Yurchenko AA, Pop OT, Ighilahriz M, Padioleau I, Rajabi F, Sharpe HJ, Poulalhon N, Dreno B, Khammari A, Delord M, Alberti A, Soufir N, Battistella M, Mourah S, Bouquet F, Savina A, Besse A, Mendez-Lopez M, Grange F, Monestier S, Mortier L, Meyer N, Dutriaux C, Robert C, Saiag P, Herms F, Lambert J, de Sauvage FJ, Dumaz N, Flatz L, Basset-Seguin N, Nikolaev SI. Frequency and Genomic Aspects of Intrinsic Resistance to Vismodegib in Locally Advanced Basal Cell Carcinoma. Clin Cancer Res 2022; 28:1422-1432. [PMID: 35078858 PMCID: PMC9365352 DOI: 10.1158/1078-0432.ccr-21-3764] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/03/2021] [Accepted: 01/20/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE Vismodegib is approved for the treatment of locally advanced basal cell carcinoma (laBCC), but some cases demonstrate intrinsic resistance (IR) to the drug. We sought to assess the frequency of IR to vismodegib in laBCC and its underlying genomic mechanisms. EXPERIMENTAL DESIGN Response to vismodegib was evaluated in a cohort of 148 laBCC patients. Comprehensive genomic and transcriptomic profiling was performed in a subset of five intrinsically resistant BCC (IR-BCC). RESULTS We identified that IR-BCC represents 6.1% of laBCC in the studied cohort. Prior treatment with chemotherapy was associated with IR. Genetic events that were previously associated with acquired resistance (AR) in BCC or medulloblastoma were observed in three out of five IR-BCC. However, IR-BCCs were distinct by highly rearranged polyploid genomes. Functional analyses identified hyperactivation of the HIPPO-YAP and WNT pathways at RNA and protein levels in IR-BCC. In vitro assay on the BCC cell line further confirmed that YAP1 overexpression increases the cell proliferation rate. CONCLUSIONS IR to vismodegib is a rare event in laBCC. IR-BCCs frequently harbor resistance mutations in the Hh pathway, but also are characterized by hyperactivation of the HIPPO-YAP and WNT pathways.
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Affiliation(s)
- Andrey A. Yurchenko
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Oltin T. Pop
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | | | - Ismael Padioleau
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | - Fatemeh Rajabi
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France
| | | | - Nicolas Poulalhon
- Service de dermatologie, Hôpital Lyon Sud, Hospices Civils de Lyon, Pierre Bénite, France
| | - Brigitte Dreno
- Department of Dermato-Oncology, CHU Nantes, Nantes Université, CIC 1413, Inserm UMR 1302/EMR6001 INCIT, F-44000 Nantes, France
| | - Amir Khammari
- Department of Dermato-Oncology, CHU Nantes, Nantes Université, CIC 1413, Inserm UMR 1302/EMR6001 INCIT, F-44000 Nantes, France
| | - Marc Delord
- Université de Paris, Hôpital Saint-Louis, Paris, France.,Department of Population Health Sciences, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | | | | | - Maxime Battistella
- INSERM U976, Hôpital Saint-Louis, Paris, France.,Université de Paris, Hôpital Saint-Louis, Paris, France.,Service d'anatomie pathologique, Hôpital Saint-Louis, Claude Vellefaux, Paris, France
| | - Samia Mourah
- INSERM U976, Hôpital Saint-Louis, Paris, France.,Université de Paris, Hôpital Saint-Louis, Paris, France.,Département de Génomique des Tumeurs Solides, Hôpital Saint-Louis, Claude Vellefaux, Paris, France
| | | | | | - Andrej Besse
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Max Mendez-Lopez
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland
| | - Florent Grange
- Service de dermatologie, CHU Reims, Rue du general Koenig, Reims, France.,Service de Dermatologie, centre hospitalier de Valence, Valence, France
| | | | - Laurent Mortier
- Service de dermatologie, CHU Lille, Clin Dermato Hop Huriez, Rue Michel Polonovski, Lille, France
| | - Nicolas Meyer
- Service de dermatologie, Institut Univeristaire du Cancer et CHU de Toulouse, Hôpital Larrey, Toulouse, France
| | | | - Caroline Robert
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Department of Medical Oncology, Gustave Roussy and Paris-Saclay University, Villejuif, France
| | - Philippe Saiag
- Department of General and Oncologic Dermatology, Ambroise-Paré hospital, APHP, and EA 4340 “Biomarkers in Cancerology and Hemato-oncology,” UVSQ, Université Paris-Saclay, Boulogne-Billancourt, France
| | - Florian Herms
- Service de dermatologie, Hôpital Saint-Louis, Paris, France
| | - Jerome Lambert
- Université de Paris, Hôpital Saint-Louis, Paris, France.,Service de Biostatistique et Information Médicale, Hôpital Saint-Louis, Paris, France
| | | | | | - Lukas Flatz
- Institute of Immunobiology, Kantonsspital St. Gallen, St. Gallen, Switzerland.,Department of Dermatology, University Hospital Tübingen, Tübingen, Germany
| | - Nicole Basset-Seguin
- INSERM U976, Hôpital Saint-Louis, Paris, France.,Université de Paris, Hôpital Saint-Louis, Paris, France.,Service de dermatologie, Hôpital Saint-Louis, Paris, France.,Corresponding Authors: Sergey I. Nikolaev, U981 INSERM, Institut Gustave Roussy, 114 rue Edouard Vaillant, 94800 Villejuif, France. Phone: 33-142115775; E-mail: ; and Nicole Basset-Seguin, Service de dermatologie, unité d'oncodermatologie, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris. Phone: 33-153722066; Fax: 33-142355310; E-mail:
| | - Sergey I. Nikolaev
- INSERM U981, Gustave Roussy Cancer Campus, Université Paris-Saclay, Villejuif, France.,Corresponding Authors: Sergey I. Nikolaev, U981 INSERM, Institut Gustave Roussy, 114 rue Edouard Vaillant, 94800 Villejuif, France. Phone: 33-142115775; E-mail: ; and Nicole Basset-Seguin, Service de dermatologie, unité d'oncodermatologie, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75010 Paris. Phone: 33-153722066; Fax: 33-142355310; E-mail:
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Drissi I, Fletcher E, Shaheen R, Nahorski M, Alhashem AM, Lisgo S, Fernández-Jaén A, Schon K, Tlili-Graiess K, Smithson SF, Lindsay S, J Sharpe H, Alkuraya FS, Woods G. Mutations in phospholipase C eta-1 ( PLCH1) are associated with holoprosencephaly. J Med Genet 2021; 59:358-365. [PMID: 33820834 PMCID: PMC8961749 DOI: 10.1136/jmedgenet-2020-107237] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 01/08/2021] [Accepted: 01/24/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Holoprosencephaly is a spectrum of developmental disorder of the embryonic forebrain in which there is failed or incomplete separation of the prosencephalon into two cerebral hemispheres. To date, dominant mutations in sonic hedgehog (SHH) pathway genes are the predominant Mendelian causes, and have marked interfamilial and intrafamilial phenotypical variabilities. METHODS We describe two families in which offspring had holoprosencephaly spectrum and homozygous predicted-deleterious variants in phospholipase C eta-1 (PLCH1). Immunocytochemistry was used to examine the expression pattern of PLCH1 in human embryos. We used SHH as a marker of developmental stage and of early embryonic anatomy. RESULTS In the first family, two siblings had congenital hydrocephalus, significant developmental delay and a monoventricle or fused thalami with a homozygous PLCH1 c.2065C>T, p.(Arg689*) variant. In the second family, two siblings had alobar holoprosencephaly and cyclopia with a homozygous PLCH1 c.4235delA, p.(Cys1079ValfsTer16) variant. All parents were healthy carriers, with no holoprosencephaly spectrum features. We found that the subcellular localisation of PLCH1 is cytoplasmic, but the p.(Cys1079ValfsTer16) variant was predominantly nuclear. Human embryo immunohistochemistry showed PLCH1 to be expressed in the notorcord, developing spinal cord (in a ventral to dorsal gradient), dorsal root ganglia, cerebellum and dermatomyosome, all tissues producing or responding to SHH. Furthermore, the embryonic subcellular localisation of PLCH1 was exclusively cytoplasmic, supporting protein mislocalisation contributing to the pathogenicity of the p.(Cys1079ValfsTer16) variant. CONCLUSION Our data support the contention that PLCH1 has a role in prenatal mammalian neurodevelopment, and deleterious variants cause a clinically variable holoprosencephaly spectrum phenotype.
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Affiliation(s)
- Ichrak Drissi
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Emily Fletcher
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Ranad Shaheen
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Michael Nahorski
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Amal M Alhashem
- Pediatrics, Prince Sultan Military Medical City, Riyadh, Al Riyadh, Saudi Arabia
| | - Steve Lisgo
- Human Developmental Biology Resource, Newcastle Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Alberto Fernández-Jaén
- Especialista en Neurología Infantil, Hospital Universitario Quirónsalud de Madrid, Madrid, Spain
| | - Katherine Schon
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Kalthoum Tlili-Graiess
- Neuroradiology Section, Department of Radiology, Prince Sultan Military Medical, Riyadh, Saudi Arabia
| | - Sarah F Smithson
- Department of Clinical Genetics, St Michaels Hospital Bristol, Bristol, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Newcastle Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Hayley J Sharpe
- Signalling Programm, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Fowzan S Alkuraya
- Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Geoff Woods
- Cambridge Institute for Medical Research Cambridge, University of Cambridge, Cambridge, Cambridgeshire, UK
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9
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Abstract
Adhesive structures between cells and with the surrounding matrix are essential for the development of multicellular organisms. In addition to providing mechanical integrity, they are key signalling centres providing feedback on the extracellular environment to the cell interior, and vice versa. During development, mitosis and repair, cell adhesions must undergo extensive remodelling. Post-translational modifications of proteins within these complexes serve as switches for activity. Tyrosine phosphorylation is an important modification in cell adhesion that is dynamically regulated by the protein tyrosine phosphatases (PTPs) and protein tyrosine kinases. Several PTPs are implicated in the assembly and maintenance of cell adhesions, however, their signalling functions remain poorly defined. The PTPs can act by directly dephosphorylating adhesive complex components or function as scaffolds. In this review, we will focus on human PTPs and discuss their individual roles in major adhesion complexes, as well as Hippo signalling. We have collated PTP interactome and cell adhesome datasets, which reveal extensive connections between PTPs and cell adhesions that are relatively unexplored. Finally, we reflect on the dysregulation of PTPs and cell adhesions in disease.
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Affiliation(s)
- Katherine A. Young
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Laura Biggins
- Bioinformatics, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Hayley J. Sharpe
- Signalling Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, U.K
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10
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Abstract
The receptor-linked protein tyrosine phosphatases (RPTPs) are key regulators of cell-cell communication through the control of cellular phosphotyrosine levels. Most human RPTPs possess an extracellular receptor domain and tandem intracellular phosphatase domains: comprising an active membrane proximal (D1) domain and an inactive distal (D2) pseudophosphatase domain. Here we demonstrate that PTPRU is unique amongst the RPTPs in possessing two pseudophosphatase domains. The PTPRU-D1 displays no detectable catalytic activity against a range of phosphorylated substrates and we show that this is due to multiple structural rearrangements that destabilise the active site pocket and block the catalytic cysteine. Upon oxidation, this cysteine forms an intramolecular disulphide bond with a vicinal "backdoor" cysteine, a process thought to reversibly inactivate related phosphatases. Importantly, despite the absence of catalytic activity, PTPRU binds substrates of related phosphatases strongly suggesting that this pseudophosphatase functions in tyrosine phosphorylation by competing with active phosphatases for the binding of substrates.
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Affiliation(s)
- Iain M Hay
- Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK
- Signalling Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Gareth W Fearnley
- Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK
- Signalling Programme, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Pablo Rios
- Signalling Research Centres BIOSS and CIBSS, and Faculty of Biology, University of Freiburg, Schänzlestr. 18, Freiburg, D-79104, Germany
| | - Maja Köhn
- Signalling Research Centres BIOSS and CIBSS, and Faculty of Biology, University of Freiburg, Schänzlestr. 18, Freiburg, D-79104, Germany
| | - Hayley J Sharpe
- Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK.
- Signalling Programme, Babraham Institute, Cambridge, CB22 3AT, UK.
| | - Janet E Deane
- Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK.
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11
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Reiterer V, Pawłowski K, Desrochers G, Pause A, Sharpe HJ, Farhan H. The dead phosphatases society: a review of the emerging roles of pseudophosphatases. FEBS J 2020; 287:4198-4220. [PMID: 32484316 DOI: 10.1111/febs.15431] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/12/2020] [Accepted: 05/27/2020] [Indexed: 12/11/2022]
Abstract
Phosphatases are a diverse family of enzymes, comprising at least 10 distinct protein folds. Like most other enzyme families, many have sequence variations that predict an impairment or loss of catalytic activity classifying them as pseudophosphatases. Research on pseudoenzymes is an emerging area of interest, with new biological functions repurposed from catalytically active relatives. Here, we provide an overview of the pseudophosphatases identified to date in all major phosphatase families. We will highlight the degeneration of the various catalytic sequence motifs and discuss the challenges associated with the experimental determination of catalytic inactivity. We will also summarize the role of pseudophosphatases in various diseases and discuss the major challenges and future directions in this field.
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Affiliation(s)
| | | | - Guillaume Desrochers
- Department of Biochemistry, McGill University, Montréal, QC, Canada.,Goodman Cancer Research Centre, McGill University, Montréal, QC, Canada
| | - Arnim Pause
- Department of Biochemistry, McGill University, Montréal, QC, Canada.,Goodman Cancer Research Centre, McGill University, Montréal, QC, Canada
| | | | - Hesso Farhan
- Institute of Basic Medical Sciences, University of Oslo, Norway
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12
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Fearnley GW, Young KA, Edgar JR, Antrobus R, Hay IM, Liang WC, Martinez-Martin N, Lin W, Deane JE, Sharpe HJ. The homophilic receptor PTPRK selectively dephosphorylates multiple junctional regulators to promote cell-cell adhesion. eLife 2019; 8:44597. [PMID: 30924770 PMCID: PMC6440744 DOI: 10.7554/elife.44597] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 12/20/2018] [Accepted: 03/23/2019] [Indexed: 12/20/2022] Open
Abstract
Cell-cell communication in multicellular organisms depends on the dynamic and reversible phosphorylation of protein tyrosine residues. The receptor-linked protein tyrosine phosphatases (RPTPs) receive cues from the extracellular environment and are well placed to influence cell signaling. However, the direct events downstream of these receptors have been challenging to resolve. We report here that the homophilic receptor PTPRK is stabilized at cell-cell contacts in epithelial cells. By combining interaction studies, quantitative tyrosine phosphoproteomics, proximity labeling and dephosphorylation assays we identify high confidence PTPRK substrates. PTPRK directly and selectively dephosphorylates at least five substrates, including Afadin, PARD3 and δ-catenin family members, which are all important cell-cell adhesion regulators. In line with this, loss of PTPRK phosphatase activity leads to disrupted cell junctions and increased invasive characteristics. Thus, identifying PTPRK substrates provides insight into its downstream signaling and a potential molecular explanation for its proposed tumor suppressor function.
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Affiliation(s)
- Gareth W Fearnley
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Katherine A Young
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Iain M Hay
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Wei-Ching Liang
- Antibody Engineering Department, Genentech, South San Francisco, United States
| | - Nadia Martinez-Martin
- Microchemistry, Proteomics and Lipidomics Department, Genentech, South San Francisco, United States
| | - WeiYu Lin
- Antibody Engineering Department, Genentech, South San Francisco, United States
| | - Janet E Deane
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Hayley J Sharpe
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
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13
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Abstract
The kinase GRK2 has been linked to the clinically important Hedgehog (HH) signaling pathway, where it is paradoxically required for signal transduction yet also promotes internalization and degradation of the critical HH signal transducer Smoothened. Two reports by Li et al and Pusapati et al in this issue of Science Signaling provide new insights into the role of GRK2 in HH signaling.
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Affiliation(s)
- Hayley J Sharpe
- Cambridge Institute for Medical Research, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Frederic J de Sauvage
- Department of Molecular Oncology, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.
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14
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Bonilla X, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy VB, Sharpe HJ, McKee T, Letourneau A, Ribaux PG, Popadin K, Basset-Seguin N, Ben Chaabene R, Santoni FA, Andrianova MA, Guipponi M, Garieri M, Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage FJ, Antonarakis SE, Nikolaev SI. Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma. Nat Genet 2016; 48:398-406. [PMID: 26950094 DOI: 10.1038/ng.3525] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/11/2016] [Indexed: 12/13/2022]
Abstract
Basal cell carcinoma (BCC) of the skin is the most common malignant neoplasm in humans. BCC is primarily driven by the Sonic Hedgehog (Hh) pathway. However, its phenotypic variation remains unexplained. Our genetic profiling of 293 BCCs found the highest mutation rate in cancer (65 mutations/Mb). Eighty-five percent of the BCCs harbored mutations in Hh pathway genes (PTCH1, 73% or SMO, 20% (P = 6.6 × 10(-8)) and SUFU, 8%) and in TP53 (61%). However, 85% of the BCCs also harbored additional driver mutations in other cancer-related genes. We observed recurrent mutations in MYCN (30%), PPP6C (15%), STK19 (10%), LATS1 (8%), ERBB2 (4%), PIK3CA (2%), and NRAS, KRAS or HRAS (2%), and loss-of-function and deleterious missense mutations were present in PTPN14 (23%), RB1 (8%) and FBXW7 (5%). Consistent with the mutational profiles, N-Myc and Hippo-YAP pathway target genes were upregulated. Functional analysis of the mutations in MYCN, PTPN14 and LATS1 suggested their potential relevance in BCC tumorigenesis.
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Affiliation(s)
- Ximena Bonilla
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | - Bryan King
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - Fedor Bezrukov
- Department of Physics, University of Connecticut, Storrs, Connecticut, USA
- RIKEN BNL Research Center, Brookhaven National Laboratory, Upton, New York, USA
| | - Gürkan Kaya
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vladimir B Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Hayley J Sharpe
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, California, USA
| | - Thomas McKee
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - Audrey Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Pascale G Ribaux
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Konstantin Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Nicole Basset-Seguin
- Department of Dermatology, Saint Louis Hospital, Paris 7 University, Paris, France
| | - Rouaa Ben Chaabene
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Maria A Andrianova
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Michel Guipponi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Marco Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Carole Verdan
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - Kerstin Grosdemange
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - Olga Sumara
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Oncology, University of Lausanne and Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Frederic J de Sauvage
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, California, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
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15
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Sharpe HJ, Pau G, Dijkgraaf GJ, Basset-Seguin N, Modrusan Z, Januario T, Tsui V, Durham AB, Dlugosz AA, Haverty PM, Bourgon R, Tang JY, Sarin KY, Dirix L, Fisher DC, Rudin CM, Sofen H, Migden MR, Yauch RL, de Sauvage FJ. Genomic analysis of smoothened inhibitor resistance in basal cell carcinoma. Cancer Cell 2015; 27:327-41. [PMID: 25759019 PMCID: PMC5675004 DOI: 10.1016/j.ccell.2015.02.001] [Citation(s) in RCA: 229] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 11/12/2014] [Accepted: 02/05/2015] [Indexed: 01/01/2023]
Abstract
Smoothened (SMO) inhibitors are under clinical investigation for the treatment of several cancers. Vismodegib is approved for the treatment of locally advanced and metastatic basal cell carcinoma (BCC). Most BCC patients experience significant clinical benefit on vismodegib, but some develop resistance. Genomic analysis of tumor biopsies revealed that vismodegib resistance is associated with Hedgehog (Hh) pathway reactivation, predominantly through mutation of the drug target SMO and to a lesser extent through concurrent copy number changes in SUFU and GLI2. SMO mutations either directly impaired drug binding or activated SMO to varying levels. Furthermore, we found evidence for intra-tumor heterogeneity, suggesting that a combination of therapies targeting components at multiple levels of the Hh pathway is required to overcome resistance.
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Affiliation(s)
- Hayley J Sharpe
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Gregoire Pau
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Gerrit J Dijkgraaf
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | | | - Zora Modrusan
- Department of Molecular Biology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Thomas Januario
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Vickie Tsui
- Department of Discovery Chemistry, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Alison B Durham
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrzej A Dlugosz
- Department of Dermatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M Haverty
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Richard Bourgon
- Department of Bioinformatics and Computational Biology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Jean Y Tang
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kavita Y Sarin
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Luc Dirix
- Sint-Augustinus Cancer Center, Antwerp University Hospital, University of Antwerp, Antwerp 2610, Belgium
| | | | - Charles M Rudin
- Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Howard Sofen
- Department of Medicine/Dermatology, UCLA School of Medicine, Los Angeles, CA 90095, USA
| | | | - Robert L Yauch
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Frederic J de Sauvage
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, CA 94080, USA.
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16
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Basset-Seguin N, Sharpe HJ, de Sauvage FJ. Efficacy of Hedgehog pathway inhibitors in Basal cell carcinoma. Mol Cancer Ther 2015; 14:633-41. [PMID: 25585509 DOI: 10.1158/1535-7163.mct-14-0703] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 12/01/2014] [Indexed: 11/16/2022]
Abstract
Basal cell carcinoma (BCC) is the most commonly diagnosed cancer. While most BCCs are amenable to surgery, some tumors can reach a more advanced stage or metastasize, and become ineligible for surgical resection or radiotherapy. Abnormal activation of the Hedgehog (Hh) pathway is a key driver in BCC pathophysiology. Consequently, inhibitors of the Hh pathway have been developed. Molecules that inhibit the receptor protein Smoothened (SMO) are the most advanced in clinical development. Vismodegib is the first-in-class SMO inhibitor and has been approved in a number of countries for the treatment of metastatic or locally advanced BCC. Several molecules have demonstrated antitumoral activity, but treatment may be limited in duration by a number of side effects, and it is not yet established whether these agents are truly curative or whether continued treatment will be required. Resistance to SMO inhibition has been reported in the clinic for which incidence and mechanisms must be elucidated to inform future therapeutic strategies. Intermittent dosing regimens to improve tolerability, as well as neoadjuvant use of Hh pathway inhibitors, are currently under investigation. Here, we review the most recent outcomes obtained with Hh inhibitors under clinical investigation in BCC.
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Affiliation(s)
- Nicole Basset-Seguin
- Paris 7 Hôpital Saint-Louis, Paris, France. Department of Molecular Oncology, Genentech Inc., South San Francisco, California
| | - Hayley J Sharpe
- Department of Molecular Oncology, Genentech Inc., South San Francisco, California
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17
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Herzig Y, Sharpe HJ, Elbaz Y, Munro S, Schuldiner M. A systematic approach to pair secretory cargo receptors with their cargo suggests a mechanism for cargo selection by Erv14. PLoS Biol 2012; 10:e1001329. [PMID: 22629230 PMCID: PMC3358343 DOI: 10.1371/journal.pbio.1001329] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 04/03/2012] [Indexed: 11/29/2022] Open
Abstract
A systematic approach to visualize proteins exiting the endoplasmic reticulum paired with their cargo receptors identifies novel cargo for known receptors and reveals the mechanism of one conserved receptor, Erv14. The endoplasmic reticulum (ER) is the site of synthesis of secreted and membrane proteins. To exit the ER, proteins are packaged into COPII vesicles through direct interaction with the COPII coat or aided by specific cargo receptors. Despite the fundamental role of such cargo receptors in protein traffic, only a few have been identified; their cargo spectrum is unknown and the signals they recognize remain poorly understood. We present here an approach we term “PAIRS” (pairing analysis of cargo receptors), which combines systematic genetic manipulations of yeast with automated microscopy screening, to map the spectrum of cargo for a known receptor or to uncover a novel receptor for a particular cargo. Using PAIRS we followed the fate of ∼150 cargos on the background of mutations in nine putative cargo receptors and identified novel cargo for most of these receptors. Deletion of the Erv14 cargo receptor affected the widest range of cargo. Erv14 substrates have a wide array of functions and structures; however, they are all membrane-spanning proteins of the late secretory pathway or plasma membrane. Proteins residing in these organelles have longer transmembrane domains (TMDs). Detailed examination of one cargo supported the hypothesis that Erv14 dependency reflects the length rather than the sequence of the TMD. The PAIRS approach allowed us to uncover new cargo for known cargo receptors and to obtain an unbiased look at specificity in cargo selection. Obtaining the spectrum of cargo for a cargo receptor allows a novel perspective on its mode of action. The rules that appear to guide Erv14 substrate recognition suggest that sorting of membrane proteins at multiple points in the secretory pathway could depend on the physical properties of TMDs. Such a mechanism would allow diverse proteins to utilize a few receptors without the constraints of evolving location-specific sorting motifs. All cells sense their environment, respond to it, and communicate with neighboring cells. To perform these functions, cells use an impressive array of proteins that they display on their surface membranes and secrete into their external environment. Newly synthesized proteins destined for the surface of nucleated cells, or to be secreted into the environment must enter the secretory pathway through the endoplasmic reticulum. Those that reside there remain behind, but most leave for their next destination as cargo proteins in lipid vesicles. To be packaged into vesicles, many of them require a “cargo receptor,” which recognizes and tethers specific cargo proteins in the vesicles. Our study takes a systematic approach to identify the range of cargo proteins that bind to each of the known receptors in yeast. By using this approach, we both discover new cargo for known cargo receptors and delineate the rule that governs cargo selection for one cargo receptor, Erv14. Thus, our study demonstrates a novel approach to identify the cargo for any receptor or to discover new cargo receptors.
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Affiliation(s)
- Yonatan Herzig
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Yael Elbaz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- * E-mail: (SM); (MS)
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (SM); (MS)
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18
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Sharpe HJ, Stevens TJ, Munro S. A comprehensive comparison of transmembrane domains reveals organelle-specific properties. Cell 2010; 142:158-69. [PMID: 20603021 PMCID: PMC2928124 DOI: 10.1016/j.cell.2010.05.037] [Citation(s) in RCA: 583] [Impact Index Per Article: 41.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/15/2010] [Accepted: 05/10/2010] [Indexed: 11/25/2022]
Abstract
The various membranes of eukaryotic cells differ in composition, but it is at present unclear if this results in differences in physical properties. The sequences of transmembrane domains (TMDs) of integral membrane proteins should reflect the physical properties of the bilayers in which they reside. We used large datasets from both fungi and vertebrates to perform a comprehensive comparison of the TMDs of proteins from different organelles. We find that TMDs are not generic but have organelle-specific properties with a dichotomy in TMD length between the early and late parts of the secretory pathway. In addition, TMDs from post-ER organelles show striking asymmetries in amino acid compositions across the bilayer that is linked to residue size and varies between organelles. The pervasive presence of organelle-specific features among the TMDs of a particular organelle has implications for TMD prediction, regulation of protein activity by location, and sorting of proteins and lipids in the secretory pathway.
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Affiliation(s)
- Hayley J Sharpe
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Strisovsky K, Sharpe HJ, Freeman M. Sequence-specific intramembrane proteolysis: identification of a recognition motif in rhomboid substrates. Mol Cell 2009; 36:1048-59. [PMID: 20064469 PMCID: PMC2941825 DOI: 10.1016/j.molcel.2009.11.006] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 08/27/2009] [Accepted: 09/23/2009] [Indexed: 11/21/2022]
Abstract
Members of the widespread rhomboid family of intramembrane proteases cleave transmembrane domain (TMD) proteins to regulate processes as diverse as EGF receptor signaling, mitochondrial dynamics, and invasion by apicomplexan parasites. However, lack of information about their substrates means that the biological role of most rhomboids remains obscure. Knowledge of how rhomboids recognize their substrates would illuminate their mechanism and might also allow substrate prediction. Previous work has suggested that rhomboid substrates are specified by helical instability in their TMD. Here we demonstrate that rhomboids instead primarily recognize a specific sequence surrounding the cleavage site. This recognition motif is necessary for substrate cleavage, it determines the cleavage site, and it is more strictly required than TM helix-destabilizing residues. Our work demonstrates that intramembrane proteases can be sequence specific and that genome-wide substrate prediction based on their recognition motifs is feasible.
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Affiliation(s)
- Kvido Strisovsky
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Hayley J. Sharpe
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
| | - Matthew Freeman
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Abstract
Secretory proteins are transported from the endoplasmic reticulum to the Golgi apparatus via COPII-coated intermediates. Yeast Erv29p is a transmembrane protein cycling between these compartments. It is conserved across species, with one ortholog found in each genome studied, including the surf-4 protein in mammals. Yeast Erv29p acts as a receptor, loading a specific subset of soluble cargo, including glycosylated alpha factor pheromone precursor and carboxypeptidase Y, into vesicles. As the eukaryotic secretory pathway is highly conserved, mammalian surf-4 may perform a similar role in the transport of unknown substrates. Here we report the membrane topology of yeast Erv29p, which we solved by minimally invasive cysteine accessibility scanning using thiol-specific biotinylation and fluorescent labeling methods. Erv29p contains four transmembrane domains with both termini exposed to the cytosol. Two luminal loops may contain a recognition site for hydrophobic export signals on soluble cargo.
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Affiliation(s)
- Deirdre A Foley
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Illinois, USA
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