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Bravo F, Macpherson JA, Slack E, Patuto N, Cahenzli J, McCoy KD, Macpherson AJ, Juillerat P. Prospective Validation of CD-62L (L-Selectin) as Marker of Durable Response to Infliximab Treatment in Patients With Inflammatory Bowel Disease: A 5-Year Clinical Follow-up. Clin Transl Gastroenterol 2021; 12:e00298. [PMID: 33735154 PMCID: PMC7886452 DOI: 10.14309/ctg.0000000000000298] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
INTRODUCTION The development of biomarkers to guide management of anti-tumor necrosis factor (TNF) agents in patients with inflammatory bowel disease (IBD) is an unmet need. We developed an in vitro blood assay to predict patient long-term outcome with the anti-TNFα agent infliximab (IFX). METHODS Patients with IBD were classified according to the shedding of an L-selectin (CD62L) from the surface of their granulocytes in whole blood. CD62L shedding was quantified by flow cytometry before and after drug administration. A clinical data collection from June 2012 to August 2017 with blinded IFX management was aimed at validating the long-term predictive value of this test. RESULTS Among 33 patients with IBD (17 Crohn's disease and 5 ulcerative colitis), 22 were predicted functional responders (PFR) and 11 were predicted as nonresponders (NR) according to the in vitro test. Five years after study initiation, 72% of PFR were still treated with IFX (vs 27% in the NR group; P < 0.05), with a median time spent under IFX of 45 vs 12 months (P = 0.019), respectively. Thirty-five medicosurgical events occurred with a median time to first event of 3 vs 30 months (P = 0.023), respectively. Our assay was the best independent predictor of staying long term on IFX (P = 0.056). DISCUSSION An assay-based in vitro test for functional blockade of TNFα (CD62L shedding) provides an excellent long-term (at 3-5 years) independent predictor of durable use of IFX in patients with IBD. Testing patients could personalize decision making to significantly reduce costs and risk of adverse events and complications.
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Affiliation(s)
- Francisco Bravo
- Maurice E Müller Laboratories, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern, Switzerland
- Gastroenterology, Clinic for Visceral Surgery and Medicine, Bern University Hospital, Bern, Switzerland
| | - Jamie A. Macpherson
- Maurice E Müller Laboratories, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern, Switzerland
| | - Emma Slack
- Maurice E Müller Laboratories, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern, Switzerland
| | - Nicolas Patuto
- Gastroenterology, Clinic for Visceral Surgery and Medicine, Bern University Hospital, Bern, Switzerland
| | - Julia Cahenzli
- Maurice E Müller Laboratories, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern, Switzerland
| | - Kathy D. McCoy
- Maurice E Müller Laboratories, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern, Switzerland
| | - Andrew J. Macpherson
- Maurice E Müller Laboratories, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern, Switzerland
- Gastroenterology, Clinic for Visceral Surgery and Medicine, Bern University Hospital, Bern, Switzerland
| | - Pascal Juillerat
- Maurice E Müller Laboratories, Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, University of Bern, Bern, Switzerland
- Gastroenterology, Clinic for Visceral Surgery and Medicine, Bern University Hospital, Bern, Switzerland
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2
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Macpherson JA, Theisen A, Masino L, Fets L, Driscoll PC, Encheva V, Snijders AP, Martin SR, Kleinjung J, Barran PE, Fraternali F, Anastasiou D. Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation. eLife 2019; 8:e45068. [PMID: 31264961 PMCID: PMC6636998 DOI: 10.7554/elife.45068] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
Several enzymes can simultaneously interact with multiple intracellular metabolites, however, how the allosteric effects of distinct ligands are integrated to coordinately control enzymatic activity remains poorly understood. We addressed this question using, as a model system, the glycolytic enzyme pyruvate kinase M2 (PKM2). We show that the PKM2 activator fructose 1,6-bisphosphate (FBP) alone promotes tetramerisation and increases PKM2 activity, but addition of the inhibitor L-phenylalanine (Phe) prevents maximal activation of FBP-bound PKM2 tetramers. We developed a method, AlloHubMat, that uses eigenvalue decomposition of mutual information derived from molecular dynamics trajectories to identify residues that mediate FBP-induced allostery. Experimental mutagenesis of these residues identified PKM2 variants in which activation by FBP remains intact but cannot be attenuated by Phe. Our findings reveal residues involved in FBP-induced allostery that enable the integration of allosteric input from Phe and provide a paradigm for the coordinate regulation of enzymatic activity by simultaneous allosteric inputs.
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Affiliation(s)
- Jamie A Macpherson
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
- Randall Centre for Cell and Molecular BiophysicsKing’s College LondonLondonUnited Kingdom
| | - Alina Theisen
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of ChemistryUniversity of ManchesterManchesterUnited Kingdom
| | - Laura Masino
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Louise Fets
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
| | - Paul C Driscoll
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Vesela Encheva
- Proteomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Ambrosius P Snijders
- Proteomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Stephen R Martin
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Jens Kleinjung
- Computational Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of ChemistryUniversity of ManchesterManchesterUnited Kingdom
| | - Franca Fraternali
- Randall Centre for Cell and Molecular BiophysicsKing’s College LondonLondonUnited Kingdom
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Gehrig S, Macpherson JA, Driscoll PC, Symon A, Martin SR, MacRae JI, Kleinjung J, Fraternali F, Anastasiou D. An engineered photoswitchable mammalian pyruvate kinase. FEBS J 2017; 284:2955-2980. [PMID: 28715126 PMCID: PMC5637921 DOI: 10.1111/febs.14175] [Citation(s) in RCA: 23] [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] [Received: 04/29/2017] [Revised: 06/24/2017] [Accepted: 07/13/2017] [Indexed: 01/06/2023]
Abstract
Changes in allosteric regulation of glycolytic enzymes have been linked to metabolic reprogramming involved in cancer. Remarkably, allosteric mechanisms control enzyme function at significantly shorter time-scales compared to the long-term effects of metabolic reprogramming on cell proliferation. It remains unclear if and how the speed and reversibility afforded by rapid allosteric control of metabolic enzymes is important for cell proliferation. Tools that allow specific, dynamic modulation of enzymatic activities in mammalian cells would help address this question. Towards this goal, we have used molecular dynamics simulations to guide the design of mPKM2 internal light/oxygen/voltage-sensitive domain 2 (LOV2) fusion at position D24 (PiL[D24]), an engineered pyruvate kinase M2 (PKM2) variant that harbours an insertion of the light-sensing LOV2 domain from Avena Sativa within a region implicated in allosteric regulation by fructose 1,6-bisphosphate (FBP). The LOV2 photoreaction is preserved in the PiL[D24] chimera and causes secondary structure changes that are associated with a 30% decrease in the Km of the enzyme for phosphoenolpyruvate resulting in increased pyruvate kinase activity after light exposure. Importantly, this change in activity is reversible upon light withdrawal. Expression of PiL[D24] in cells leads to light-induced increase in labelling of pyruvate from glucose. PiL[D24] therefore could provide a means to modulate cellular glucose metabolism in a remote manner and paves the way for studying the importance of rapid allosteric phenomena in the regulation of metabolism and enzyme control.
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Affiliation(s)
- Stefanie Gehrig
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Paul C. Driscoll
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Alastair Symon
- Instrument Prototyping Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Stephen R. Martin
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - James I. MacRae
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Jens Kleinjung
- Computational BiologyThe Francis Crick InstituteLondonUK
| | - Franca Fraternali
- Randall Division of Cell and Molecular BiophysicsKing's CollegeLondonUK
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Schmidt C, Macpherson JA, Lau AM, Tan KW, Fraternali F, Politis A. Surface Accessibility and Dynamics of Macromolecular Assemblies Probed by Covalent Labeling Mass Spectrometry and Integrative Modeling. Anal Chem 2017; 89:1459-1468. [PMID: 28208298 PMCID: PMC5299547 DOI: 10.1021/acs.analchem.6b02875] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [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: 07/26/2016] [Accepted: 01/04/2017] [Indexed: 12/22/2022]
Abstract
Mass spectrometry (MS) has become an indispensable tool for investigating the architectures and dynamics of macromolecular assemblies. Here we show that covalent labeling of solvent accessible residues followed by their MS-based identification yields modeling restraints that allow mapping the location and orientation of subunits within protein assemblies. Together with complementary restraints derived from cross-linking and native MS, we built native-like models of four heterocomplexes with known subunit structures and compared them with available X-ray crystal structures. The results demonstrated that covalent labeling followed by MS markedly increased the predictive power of the integrative modeling strategy enabling more accurate protein assembly models. We applied this strategy to the F-type ATP synthase from spinach chloroplasts (cATPase) providing a structural basis for its function as a nanomotor. By subjecting the models generated by our restraint-based strategy to molecular dynamics (MD) simulations, we revealed the conformational states of the peripheral stalk and assigned flexible regions in the enzyme. Our strategy can readily incorporate complementary chemical labeling strategies and we anticipate that it will be applicable to many other systems providing new insights into the structure and function of protein complexes.
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Affiliation(s)
- Carla Schmidt
- Interdisciplinary
Research Center HALOmem, Martin Luther University
Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
| | - Jamie A. Macpherson
- Division
of Cell & Molecular Biophysics, King’s
College London, New Hunt’s
House, SE1 1UL, London, United Kingdom
| | - Andy M. Lau
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB, London, United Kingdom
| | - Ken Wei Tan
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB, London, United Kingdom
| | - Franca Fraternali
- Division
of Cell & Molecular Biophysics, King’s
College London, New Hunt’s
House, SE1 1UL, London, United Kingdom
| | - Argyris Politis
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB, London, United Kingdom
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Laffy JMJ, Dodev T, Macpherson JA, Townsend C, Lu HC, Dunn-Walters D, Fraternali F. Promiscuous antibodies characterised by their physico-chemical properties: From sequence to structure and back. Prog Biophys Mol Biol 2016; 128:47-56. [PMID: 27639634 PMCID: PMC6167913 DOI: 10.1016/j.pbiomolbio.2016.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 08/25/2016] [Accepted: 09/05/2016] [Indexed: 12/26/2022]
Abstract
Human B cells produce antibodies, which bind to their cognate antigen based on distinct molecular properties of the antibody CDR loop. We have analysed a set of 10 antibodies showing a clear difference in their binding properties to a panel of antigens, resulting in two subsets of antibodies with a distinct binding phenotype. We call the observed binding multiplicity ‘promiscuous’ and selected physico-chemical CDRH3 characteristics and conformational preferences may characterise these promiscuous antibodies. To classify CDRH3 physico-chemical properties playing a role in their binding properties, we used statistical analyses of the sequences annotated by Kidera factors. To characterise structure-function requirements for antigen binding multiplicity we employed Molecular Modelling and Monte Carlo based coarse-grained simulations. The ability to predict the molecular causes of promiscuous, multi-binding behaviour would greatly improve the efficiency of the therapeutic antibody discovery process.
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Affiliation(s)
- Julie M J Laffy
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Tihomir Dodev
- Department of Immunobiology, King's College London, UK
| | - Jamie A Macpherson
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | | | - Hui Chun Lu
- Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Deborah Dunn-Walters
- Department of Immunobiology, King's College London, UK; Faculty of Health and Medical Sciences, University of Surrey, UK
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, King's College London, UK.
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Macpherson JA. A Systems Approach to Understanding the Allosteric Mechanism of Pyruvate Kinase M2. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Li H, Limenitakis JP, Fuhrer T, Geuking MB, Lawson MA, Wyss M, Brugiroux S, Keller I, Macpherson JA, Rupp S, Stolp B, Stein JV, Stecher B, Sauer U, McCoy KD, Macpherson AJ. The outer mucus layer hosts a distinct intestinal microbial niche. Nat Commun 2015; 6:8292. [PMID: 26392213 PMCID: PMC4595636 DOI: 10.1038/ncomms9292] [Citation(s) in RCA: 301] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/06/2015] [Indexed: 12/22/2022] Open
Abstract
The overall composition of the mammalian intestinal microbiota varies between individuals: within each individual there are differences along the length of the intestinal tract related to host nutrition, intestinal motility and secretions. Mucus is a highly regenerative protective lubricant glycoprotein sheet secreted by host intestinal goblet cells; the inner mucus layer is nearly sterile. Here we show that the outer mucus of the large intestine forms a unique microbial niche with distinct communities, including bacteria without specialized mucolytic capability. Bacterial species present in the mucus show differential proliferation and resource utilization compared with the same species in the intestinal lumen, with high recovery of bioavailable iron and consumption of epithelial-derived carbon sources according to their genome-encoded metabolic repertoire. Functional competition for existence in this intimate layer is likely to be a major determinant of microbiota composition and microbial molecular exchange with the host.
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Affiliation(s)
- Hai Li
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Julien P. Limenitakis
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland
| | - Markus B. Geuking
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Melissa A. Lawson
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Madeleine Wyss
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Sandrine Brugiroux
- Max-von-Pettenkofer Institute, German Center for Infection Research (DZIF), Pettenkoferstrasse 9a, Partner site LMU Munich, D-80336 Munich, Germany
| | - Irene Keller
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Jamie A. Macpherson
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Sandra Rupp
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Bettina Stolp
- Theodor Kocher Institute, Freiestrasse 1, University of Bern, 3012 Bern, Switzerland
| | - Jens V. Stein
- Theodor Kocher Institute, Freiestrasse 1, University of Bern, 3012 Bern, Switzerland
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, German Center for Infection Research (DZIF), Pettenkoferstrasse 9a, Partner site LMU Munich, D-80336 Munich, Germany
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Auguste-Piccard-Hof 1, 8093 Zürich, Switzerland
| | - Kathy D. McCoy
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
| | - Andrew J. Macpherson
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Murtenstrasse 35, 3010 Bern, Switzerland
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Allam S, Anderson KJ, O'Brien C, Macpherson JA, Gambhir S, Leitch JA, Kenny GNC. Patient-maintained propofol sedation using reaction time monitoring: a volunteer safety study. Anaesthesia 2012; 68:154-8. [PMID: 23153106 DOI: 10.1111/anae.12036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Previous volunteer studies of an effect-site controlled, patient-maintained sedation system using propofol have demonstrated a risk of over-sedation. We have incorporated a reaction-time monitor into the handset of the patient-maintained sedation system to add an individualised patient-feedback mechanism. This study assessed if such reaction-time feedback modification would reduce the risk of over-sedation in 20 healthy volunteers deliberately attempting to over-administer themselves propofol. All the volunteers successfully sedated themselves without reaching any unsafe endpoints. All volunteers maintained verbal contact throughout, in accordance with the definition of conscious sedation. The mean (SD) lowest S(p) O(2) was 97 (1.7) % when breathing room air and no volunteer required supplementary oxygen. The mean (SD) maximum effect-site propofol concentration reached was 1.7 (0.4) μg.ml(-1) . The present system was found to be safer than its predecessors, allowing conscious sedation, but preventing over-sedation.
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Affiliation(s)
- S Allam
- Department of Anaesthesia, Forth Valley Royal Hospital, Larbert, UK.
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Greenwood ND, Hetherington C, Macpherson JA. Semi-automated system for the study of the release of drugs from solid dosage forms. Lab Pract 1974; 23:372-3. [PMID: 4854230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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