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Needham EJ, Ren AL, Digby RJ, Norton EJ, Ebrahimi S, Outtrim JG, Chatfield DA, Manktelow AE, Leibowitz MM, Newcombe VFJ, Doffinger R, Barcenas-Morales G, Fonseca C, Taussig MJ, Burnstein RM, Samanta RJ, Dunai C, Sithole N, Ashton NJ, Zetterberg H, Gisslén M, Edén A, Marklund E, Openshaw PJM, Dunning J, Griffiths MJ, Cavanagh J, Breen G, Irani SR, Elmer A, Kingston N, Summers C, Bradley JR, Taams LS, Michael BD, Bullmore ET, Smith KGC, Lyons PA, Coles AJ, Menon DK. Brain injury in COVID-19 is associated with dysregulated innate and adaptive immune responses. Brain 2022; 145:4097-4107. [PMID: 36065116 PMCID: PMC9494359 DOI: 10.1093/brain/awac321] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [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: 03/16/2022] [Revised: 06/24/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022] Open
Abstract
COVID-19 is associated with neurological complications including stroke, delirium and encephalitis. Furthermore, a post-viral syndrome dominated by neuropsychiatric symptoms is common, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of COVID-19 severity. We investigated the dynamics of, and relationship between, serum markers of brain injury [neurofilament light (NfL), glial fibrillary acidic protein (GFAP) and total tau] and markers of dysregulated host response (autoantibody production and cytokine profiles) in 175 patients admitted with COVID-19 and 45 patients with influenza. During hospitalization, sera from patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependent manner, with evidence of ongoing active brain injury at follow-up 4 months later. These biomarkers were associated with elevations of pro-inflammatory cytokines and the presence of autoantibodies to a large number of different antigens. Autoantibodies were commonly seen against lung surfactant proteins but also brain proteins such as myelin associated glycoprotein. Commensurate findings were seen in the influenza cohort. A distinct process characterized by elevation of serum total tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses unlike NfL and GFAP. These results demonstrate that brain injury is a common consequence of both COVID-19 and influenza, and is therefore likely to be a feature of severe viral infection more broadly. The brain injury occurs in the context of dysregulation of both innate and adaptive immune responses, with no single pathogenic mechanism clearly responsible.
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Affiliation(s)
- Edward J Needham
- Correspondence to: Edward Needham Department of Clinical Neurosciences University of Cambridge, Cambridge, UK E-mail:
| | - Alexander L Ren
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | - Richard J Digby
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | - Emma J Norton
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | - Soraya Ebrahimi
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | - Joanne G Outtrim
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | - Doris A Chatfield
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | - Anne E Manktelow
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | - Maya M Leibowitz
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | | | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke’s Hospital, Cambridge, UK
| | | | - Claudia Fonseca
- Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
| | - Michael J Taussig
- Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
| | - Rowan M Burnstein
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | - Romit J Samanta
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
| | - Cordelia Dunai
- Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK
| | - Nyarie Sithole
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
- Jeffrey Cheah Biomedical Centre, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Nicholas J Ashton
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, the Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Magnus Gisslén
- Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Arden Edén
- Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Emelie Marklund
- Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Jake Dunning
- Nuffield Department of Medicine, Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | - Michael J Griffiths
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jonathan Cavanagh
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Gerome Breen
- Department of Social Genetic and Developmental Psychiatry, King’s College London, London, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Department of Neurology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Anne Elmer
- Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Charlotte Summers
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK
| | - Leonie S Taams
- Centre for Inflammation Biology and Cancer Immunology (CIBCI) and Department Inflammation Biology, School of Immunology and Microbial Sciences, King’s College London, Guy's Campus, London, UK
| | - Benedict D Michael
- Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK
| | - Edward T Bullmore
- Department of Psychiatry, University of Cambridge, Herchel Smith Building for Brain and Mind Sciences, Cambridge Biomedical Campus, Cambridge, UK
| | - Kenneth G C Smith
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
- Jeffrey Cheah Biomedical Centre, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Paul A Lyons
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
- Jeffrey Cheah Biomedical Centre, Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Alasdair J Coles
- Department of Clinical Neurosciences, University of Cambridge, UK
| | - David K Menon
- Division of Anaesthesia, Department of Medicine, University of Cambridge, UK
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Do LD, Moritz CP, Muñiz-Castrillo S, Pinto AL, Tholance Y, Brugiere S, Couté Y, Stoevesandt O, Taussig MJ, Rogemond V, Vogrig A, Joubert B, Ferraud K, Camdessanché JP, Antoine JC, Honnorat J. Argonaute Autoantibodies as Biomarkers in Autoimmune Neurologic Diseases. Neurol Neuroimmunol Neuroinflamm 2021; 8:8/5/e1032. [PMID: 34321331 PMCID: PMC8362341 DOI: 10.1212/nxi.0000000000001032] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/26/2021] [Indexed: 11/15/2022]
Abstract
Objective To identify and characterize autoantibodies (Abs) as novel biomarkers for an autoimmune context in patients with central and peripheral neurologic diseases. Methods Two distinct approaches (immunoprecipitation/mass spectrometry–based proteomics and protein microarrays) and patients' sera and CSF were used. The specificity of the identified target was confirmed by cell-based assay (CBA) in 856 control samples. Results Using the 2 methods as well as sera and CSF of patients with central and peripheral neurologic involvement, we identified Abs against the family of Argonaute proteins (mainly AGO1 and AGO2), which were already reported in systemic autoimmunity. AGO-Abs were mostly of immunoglobulin G 1 subclass and conformation dependent. Using CBA, AGO-Abs were detected in 21 patients with a high suspicion of autoimmune neurologic diseases (71.4% were women; median age 57 years) and only in 4/856 (0.5%) controls analyzed by CBA (1 diagnosed with small-cell lung cancer and the other 3 with Sjögren syndrome). Among the 21 neurologic patients identified, the main clinical presentations were sensory neuronopathy (8/21, 38.1%) and limbic encephalitis (6/21, 28.6%). Fourteen patients (66.7%) had autoimmune comorbidities and/or co-occurring Abs, whereas AGO-Abs were the only autoimmune biomarker for the remaining 7/21 (33.3%). Thirteen (61.9%) patients were treated with immunotherapy; 8/13 (61.5%) improved, and 3/13 (23.1%) remained stable, suggesting an efficacy of these treatments. Conclusions AGO-Abs might be potential biomarkers of autoimmunity in patients with central and peripheral nonparaneoplastic neurologic diseases. In 7 patients, AGO-Abs were the only biomarkers; thus, their identification may be useful to suspect the autoimmune character of the neurologic disorder. Classification of Evidence This study provides Class III evidence that AGO-Abs are more frequent in patients with autoimmune neurologic diseases than controls.
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Affiliation(s)
- Le-Duy Do
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Christian P Moritz
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Sergio Muñiz-Castrillo
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Anne-Laurie Pinto
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Yannick Tholance
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Sabine Brugiere
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Yohann Couté
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Oda Stoevesandt
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Michael J Taussig
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Véronique Rogemond
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Alberto Vogrig
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Bastien Joubert
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Karine Ferraud
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Jean-Philippe Camdessanché
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Jean-Christophe Antoine
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France
| | - Jérôme Honnorat
- From French Reference Center on Paraneoplastic Neurological Syndrome (L.-D.D., S.M.-C., A.-L.P., V.R., A.V., B.J., J.-P.C., J.-C.A., J.H.), Hospices Civils de Lyon, Hôpital Neurologique, Bron, France; Institute NeuroMyoGène (L.-D.D., C.P.M., S.M.-C., A.-L.P., Y.T., V.R., A.V., B.J., K.F., J.-P.C., J.-C.A., J.H.), INSERM U1217/CNRS UMR 5310, Université de Lyon, Université Claude Bernard Lyon 1, France; University Jean Monnet (C.P.M., Y.T., J.-P.C., J.-C.A.), Saint-Étienne, France; Department of Biochemistry (Y.T.), University Hospital of Saint-Etienne, France; University Grenoble Alpes (S.B., Y.C.), CEA, INSERM, IRIG, BGE, France; Cambridge Protein Arrays Ltd. (O.S., M.J.T.), Babraham Research Campus, United Kingdom; and Department of Neurology (K.F., J.-P.C., J.-C.A.), University Hospital of Saint-Etienne, France.
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3
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Voskuil JL, Bandrowski A, Begley CG, Bradbury AR, Chalmers AD, Gomes AV, Hardcastle T, Lund-Johansen F, Plückthun A, Roncador G, Solache A, Taussig MJ, Trimmer JS, Williams C, Goodman SL. The Antibody Society's antibody validation webinar series. MAbs 2020; 12:1794421. [PMID: 32748696 PMCID: PMC7531563 DOI: 10.1080/19420862.2020.1794421] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 01/09/2023] Open
Abstract
In the wake of the reproducibility crisis and numerous discussions on how commercially available antibodies as research tool contribute to it, The Antibody Society developed a series of 10 webinars to address the issues involved. The webinars were delivered by speakers with both academic and commercial backgrounds. This report highlights the problems, and offers solutions to help the scientific community appropriately identify the right antibodies and to validate them for their research and development projects. Despite the various solutions proposed here, they must be applied on a case-by-case basis. Each antibody must be verified based on the content of the product sheet, and subsequently through experimentation to confirm integrity, specificity and selectivity. Verification needs to focus on the precise application and tissue/cell type for which the antibody will be used, and all verification data must be reported openly. The various approaches discussed here all have caveats, so a combination of solutions must be considered.
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Affiliation(s)
| | - Anita Bandrowski
- Center for Research in Biological Systems, University of California, La Jolla, CA, USA
| | | | | | - Andrew D. Chalmers
- Department of Biology and Biochemistry, University of Bath, Bath, UK
- CiteAb, Bath, UK
| | - Aldrin V. Gomes
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, Davis, CA, USA
| | | | | | - Andreas Plückthun
- Department. of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Giovanna Roncador
- Monoclonal Antibody Unit, Spanish National Cancer Research Center, Madrid, Spain
| | - Alejandra Solache
- Abcam Plc, Discovery Drive, Cambridge Biomedical Campus, Cambridge, UK
| | | | - James S. Trimmer
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA, USA
| | - Cecilia Williams
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Solna, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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4
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Abstract
Validation of antibodies and other protein binders is a subject of pressing concern for the research community and one which is uppermost in the minds of all who use antibodies as research and diagnostic reagents. Assessing an antibody's fitness for purpose includes accurate ascertainment of its target specificity and suitability for the envisaged task. Moreover, standardised procedures are essential to guarantee sample quality in testing procedures. The problem of defining precise standards for antibody validation has engendered much debate in recent publications and meetings, but gradually a consensus is emerging. At the 8th Alpbach Affinity Proteomics workshop (March 2017), a panel of leaders in the antibody field discussed suggestions which could bring this complex but essential issue a step nearer to a resolution. 'Alpbach recommendations' for best practice include tailoring binder validation processes according to the intended applications and promoting greater transparency in publications and in the information available from commercial antibody developers/providers. A single approach will not fit all applications and end users must ensure that the reported validation holds for their specific requirements, highlighting the need for adequate training in the fundamentals of antibody characterisation and validation across the user community.
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Affiliation(s)
- Michael J Taussig
- Cambridge Protein Arrays Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Cláudia Fonseca
- Cambridge Protein Arrays Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - James S Trimmer
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, CA, 95616, USA; Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Davis, CA, 95616, USA.
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5
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Taussig MJ. Affinity Proteomics in the mountains: Alpbach 2015. N Biotechnol 2016; 33:489-90. [PMID: 27118167 DOI: 10.1016/j.nbt.2016.04.003] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting.
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Affiliation(s)
- Michael J Taussig
- Cambridge Protein Arrays Ltd., Babraham Research Campus, Cambridge CB22 3AT, United Kingdom.
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6
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Galli J, Oelrich J, Taussig MJ, Andreasson U, Ortega-Paino E, Landegren U. The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples. Nucleic Acids Res 2014; 43:D1158-62. [PMID: 25336620 PMCID: PMC4383877 DOI: 10.1093/nar/gku1008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We report the development of a new database of technology services and products
for analysis of biobank samples in biomedical research. BARCdb, the Biobanking
Analysis Resource Catalogue, is a
freely available web resource, listing expertise and molecular resource
capabilities of research centres and biotechnology companies. The database is
designed for researchers who require information on how to make best use of
valuable biospecimens from biobanks and other sample collections, focusing on
the choice of analytical techniques and the demands they make on the type of
samples, pre-analytical sample preparation and amounts needed. BARCdb has been
developed as part of the Swedish biobanking infrastructure (BBMRI.se), but now
welcomes submissions from service providers throughout Europe. BARCdb can help
match resource providers with potential users, stimulating transnational
collaborations and ensuring compatibility of results from different labs. It can
promote a more optimal use of European resources in general, both with respect
to standard and more experimental technologies, as well as for valuable biobank
samples. This article describes how information on service and reagent providers
of relevant technologies is made available on BARCdb, and how this resource may
contribute to strengthening biomedical research in academia and in the
biotechnology and pharmaceutical industries.
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Affiliation(s)
- Joakim Galli
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Johan Oelrich
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
| | - Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ulrika Andreasson
- Department of Immunotechnology, Lund University, Medicon Village, SE-223 81 Lund, Sweden CREATE Health, Lund University Medicon Village, SE-223 81 Lund, Sweden
| | - Eva Ortega-Paino
- Department of Immunotechnology, Lund University, Medicon Village, SE-223 81 Lund, Sweden CREATE Health, Lund University Medicon Village, SE-223 81 Lund, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 08 Uppsala, Sweden
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7
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Abstract
Foreword to the special issue of New Biotechnology comprising review articles by former steering committee members to mark the end of the European Science Foundation Research Networking Programme in Functional Genomics.
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8
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Taussig MJ, Schmidt R, Cook EA, Stoevesandt O. Development of proteome-wide binding reagents for research and diagnostics. Proteomics Clin Appl 2014; 7:756-66. [PMID: 24178846 DOI: 10.1002/prca.201300060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [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: 07/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/11/2023]
Abstract
Alongside MS, antibodies and other specific protein-binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome-wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, 'next generation' methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well-characterised and quality-controlled pan-proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large-scale international collaboration.
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Affiliation(s)
- Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
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9
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Stoevesandt O, Taussig MJ. Affinity proteomics: the role of specific binding reagents in human proteome analysis. Expert Rev Proteomics 2014; 9:401-14. [DOI: 10.1586/epr.12.34] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Haynes MR, Lenz M, Taussig MJ, Wilson IA, Hilvert D. Sequence Similarity and Cross-Reactivity of a Diels-Alder Catalyst and an Anti-Progesterone Antibody. Isr J Chem 2013. [DOI: 10.1002/ijch.199600021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Schmidt R, Cook EA, Kastelic D, Taussig MJ, Stoevesandt O. Optimised 'on demand' protein arraying from DNA by cell free expression with the 'DNA to Protein Array' (DAPA) technology. J Proteomics 2013; 88:141-8. [PMID: 23454659 DOI: 10.1016/j.jprot.2013.02.002] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/28/2013] [Accepted: 02/04/2013] [Indexed: 12/16/2022]
Abstract
UNLABELLED We have previously described a protein arraying process based on cell free expression from DNA template arrays (DNA Array to Protein Array, DAPA). Here, we have investigated the influence of different array support coatings (Ni-NTA, Epoxy, 3D-Epoxy and Polyethylene glycol methacrylate (PEGMA)). Their optimal combination yields an increased amount of detected protein and an optimised spot morphology on the resulting protein array compared to the previously published protocol. The specificity of protein capture was improved using a tag-specific capture antibody on a protein repellent surface coating. The conditions for protein expression were optimised to yield the maximum amount of protein or the best detection results using specific monoclonal antibodies or a scaffold binder against the expressed targets. The optimised DAPA system was able to increase by threefold the expression of a representative model protein while conserving recognition by a specific antibody. The amount of expressed protein in DAPA was comparable to those of classically spotted protein arrays. Reaction conditions can be tailored to suit the application of interest. BIOLOGICAL SIGNIFICANCE DAPA represents a cost effective, easy and convenient way of producing protein arrays on demand. The reported work is expected to facilitate the application of DAPA for personalized medicine and screening purposes.
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Affiliation(s)
- Ronny Schmidt
- Protein Technology Group, Babraham Bioscience Technologies Ltd., Babraham Research Campus, Cambridge CB22 3AT, UK.
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12
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Abstract
In affinity proteomics, specific protein-binding molecules (a.k.a. binders), principally antibodies, are applied as reagents in proteome analysis. In recent years, advances in binder technologies have created the potential for an unprecedented view on protein expression and distribution patterns in plasma, cells and tissues and increasingly on protein function. Particular strengths of affinity proteomics methods include detecting proteins in their natural environments of cell or tissue, high sensitivity and selectivity for detection of low abundance proteins and exploiting binding actions such as functional interference in living cells. To maximise the use and impact of affinity reagents, it will be essential to create comprehensive, standardised binder collections. With this in mind, the EU FP7 programme AFFINOMICS (http://www.affinomics.org), together with the preceding EU programmes ProteomeBinders and AffinityProteome, aims to extend affinity proteomics research by generating a large-scale resource of validated protein-binding molecules for characterisation of the human proteome. Activity is directed at producing binders to about 1000 protein targets, primarily in signal transduction and cancer, by establishing a high throughput, coordinated production pipeline. An important aspect of AFFINOMICS is the development of highly efficient recombinant selection methods, based on phage, cell and ribosome display, capable of producing high quality binders at greater throughput and lower cost than hitherto. The programme also involves development of innovative and sensitive technologies for specific detection of target proteins and their interactions, and deployment of binders in proteomics studies of clinical relevance. The need for such binder generation programmes is now recognised internationally, with parallel initiatives in the USA for cancer (NCI) and transcription factors (NIH) and within the Human Proteome Organisation (HUPO). The papers in this volume of New Biotechnology are all contributed by participants at the 5th ESF Workshop on Affinity Proteomics organised by the AFFINOMICS consortium and held in Alpbach, Austria, in March 2011.
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13
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Klingström T, Soldatova L, Stevens R, Roos TE, Swertz MA, Müller KM, Kalaš M, Lambrix P, Taussig MJ, Litton JE, Landegren U, Bongcam-Rudloff E. Workshop on laboratory protocol standards for the Molecular Methods Database. N Biotechnol 2012; 30:109-13. [PMID: 22687389 DOI: 10.1016/j.nbt.2012.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 05/26/2012] [Accepted: 05/26/2012] [Indexed: 10/28/2022]
Abstract
Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (including the experimental constraints of the experiment), analysis and preservation, to peer-reviewed publication of results. Failure to recognise the issues at each level can lead to serious conflicts and mistakes; research may then be compromised as a result of the publication of non-coherent protocols, or the misinterpretation of published data. In this report, we present the results from a workshop that was organised to create an ontological data-modelling framework for Laboratory Protocol Standards for the Molecular Methods Database (MolMeth). The workshop provided a set of short- and long-term goals for the MolMeth database, the most important being the decision to use the established EXACT description of biomedical ontologies as a starting point.
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Affiliation(s)
- Tomas Klingström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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14
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Abstract
Ribosome display is a cell-free display technology for in vitro selection and optimisation of proteins from large diversified libraries. It operates through the formation of stable protein-ribosome-mRNA (PRM) complexes and selection of ligand-binding proteins, followed by DNA recovery from the selected genetic information. Both prokaryotic and eukaryotic ribosome display systems have been developed. In this chapter, we describe the eukaryotic rabbit reticulocyte method in which a distinct in situ single-primer RT-PCR procedure is used to recover DNA from the selected PRM complexes without the need for prior disruption of the ribosome.
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Affiliation(s)
- Mingyue He
- The Inositide Laboratory, The Babraham Institute, Cambridge, UK.
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15
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Wichmann HE, Kuhn KA, Waldenberger M, Schmelcher D, Schuffenhauer S, Meitinger T, Wurst SHR, Lamla G, Fortier I, Burton PR, Peltonen L, Perola M, Metspalu A, Riegman P, Landegren U, Taussig MJ, Litton JE, Fransson MN, Eder J, Cambon-Thomsen A, Bovenberg J, Dagher G, van Ommen GJ, Griffith M, Yuille M, Zatloukal K. Comprehensive catalog of European biobanks. Nat Biotechnol 2011; 29:795-7. [DOI: 10.1038/nbt.1958] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Abstract
The development of protein microarrays makes possible interaction-based protein assays in miniaturised, multiplexed formats. A major requirement determining their uptake and use is the availability and stability of purified, functional proteins for immobilisation. With conventional methods, involving individual expression and purification of recombinant proteins, the cost of commercial high-content protein arrays is often found to be prohibitively high. Moreover, due to the need for specialised microarray production equipment, custom-made protein arrays containing more focussed sets of proteins of interest are also in little use. In the DNA array to protein array technology described herein, repeated economical printing of protein microarrays from a reusable template DNA microarray is performed on demand by cell-free -protein synthesis. Once the template DNA microarray has been obtained, protein microarrays are made using purely macro-handling procedures, making protein arraying accessible without sophisticated microarraying apparatus.
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Affiliation(s)
- Oda Stoevesandt
- Protein Technology Group, Babraham Bioscience Technologies Ltd, Cambridge, UK.
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17
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Abrahams JP, Apweiler R, Balling R, Bertero MG, Bujnicki JM, Chayen NE, Chène P, Corthals GL, Dyląg T, Förster F, Heck AJR, Henderson PJF, Herwig R, Jehenson P, Kokalj SJ, Laue E, Legrain P, Martens L, Migliorini C, Musacchio A, Podobnik M, Schertler GFX, Schreiber G, Sixma TK, Smit AB, Stuart D, Svergun DI, Taussig MJ. "4D Biology for health and disease" workshop report. N Biotechnol 2010; 28:291-3. [PMID: 20951846 DOI: 10.1016/j.nbt.2010.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 10/08/2010] [Indexed: 10/18/2022]
Abstract
The "4D Biology Workshop for Health and Disease", held on 16-17th of March 2010 in Brussels, aimed at finding the best organising principles for large-scale proteomics, interactomics and structural genomics/biology initiatives, and setting the vision for future high-throughput research and large-scale data gathering in biological and medical science. Major conclusions of the workshop include the following. (i) Development of new technologies and approaches to data analysis is crucial. Biophysical methods should be developed that span a broad range of time/spatial resolution and characterise structures and kinetics of interactions. Mathematics, physics, computational and engineering tools need to be used more in biology and new tools need to be developed. (ii) Database efforts need to focus on improved definitions of ontologies and standards so that system-scale data and associated metadata can be understood and shared efficiently. (iii) Research infrastructures should play a key role in fostering multidisciplinary research, maximising knowledge exchange between disciplines and facilitating access to diverse technologies. (iv) Understanding disease on a molecular level is crucial. System approaches may represent a new paradigm in the search for biomarkers and new targets in human disease. (v) Appropriate education and training should be provided to help efficient exchange of knowledge between theoreticians, experimental biologists and clinicians. These conclusions provide a strong basis for creating major possibilities in advancing research and clinical applications towards personalised medicine.
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18
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Stoevesandt O, Vetter M, Kastelic D, Palmer EA, He M, Taussig MJ. Cell free expression put on the spot: advances in repeatable protein arraying from DNA (DAPA). N Biotechnol 2010; 28:282-90. [PMID: 20850573 DOI: 10.1016/j.nbt.2010.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 09/01/2010] [Indexed: 11/25/2022]
Abstract
We have previously described the 'DNA array to protein array' (DAPA) method for microarraying of proteins expressed by cell-free systems in situ on the array surface. In this technique, a DNA array on one slide acts as the template for generating a protein array on a second slide, mediated by a cell free lysate between the two juxtaposed slides. Here we explore the feature of the repeatability of the technology, in which the same DNA array is reused several times, and use the method to generate a microarray of 116 diverse proteins. The capabilities of DAPA technology in comparison with other protein array methods are discussed.
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Affiliation(s)
- Oda Stoevesandt
- Protein Technology Group, Babraham Bioscience Technologies, Cambridge CB22 3AT, UK.
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19
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Bourbeillon J, Orchard S, Benhar I, Borrebaeck C, de Daruvar A, Dübel S, Frank R, Gibson F, Gloriam D, Haslam N, Hiltker T, Humphrey-Smith I, Hust M, Juncker D, Koegl M, Konthur Z, Korn B, Krobitsch S, Muyldermans S, Nygren PÅ, Palcy S, Polic B, Rodriguez H, Sawyer A, Schlapshy M, Snyder M, Stoevesandt O, Taussig MJ, Templin M, Uhlen M, van der Maarel S, Wingren C, Hermjakob H, Sherman D. Minimum information about a protein affinity reagent (MIAPAR). Nat Biotechnol 2010; 28:650-3. [DOI: 10.1038/nbt0710-650] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Abstract
Protein arrays are fast becoming established as a means to monitor protein expression
levels and investigate protein interactions and function. They present particular technical
demands that will need to be solved in order to achieve the maximum capability of efficient
and sensitive protein analysis in the high throughput setting of functional genomics. The
following resumé of some major issues around this new technology was made as the
chairperson’s introduction to the workshop session on peptide and protein chips.
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Affiliation(s)
- M J Taussig
- ESF Programme in Integrated Approaches to Functional Genomics, The Babraham Institute, Cambridge CB2 4AT, UK.
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21
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Dübel S, Stoevesandt O, Taussig MJ, Hust M. Generating recombinant antibodies to the complete human proteome. Trends Biotechnol 2010; 28:333-9. [PMID: 20538360 DOI: 10.1016/j.tibtech.2010.05.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2010] [Revised: 04/29/2010] [Accepted: 05/03/2010] [Indexed: 10/19/2022]
Abstract
In vitro antibody generation technologies have now been available for two decades. Research reagents prepared via phage display are becoming available and several recent studies have demonstrated that these technologies are now sufficiently advanced to facilitate generation of a comprehensive renewable resource of antibodies for any protein encoded by the approximately 22,500 human protein-coding genes. Antibody selection in vitro offers properties not available in animal-based antibody generation methods. By adjusting the biochemical milieu during selection, it is possible to control the antigen conformation recognized, the antibody affinity or unwanted cross-reactivity. For larger-scale antibody generation projects, the handling, transport and storage logistics and bacterial production offer cost benefits. Because the DNA sequence encoding the antibody is available, modifications, such as site-specific in vivo biotinylation and multimerization, are only a cloning step away. This opinion article summarizes opportunities for the generation of antibodies for proteome research using in vitro technologies.
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Affiliation(s)
- Stefan Dübel
- Technische Universität Braunschweig, Institute of Biochemistry and Biotechnology, D-38106 Braunschweig, Germany.
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22
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Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CAK, Bourbeillon J, Bradbury ARM, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H. A community standard format for the representation of protein affinity reagents. Mol Cell Proteomics 2009; 9:1-10. [PMID: 19674966 DOI: 10.1074/mcp.m900185-mcp200] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cover only a fraction of the human proteome, and their cost is prohibitive for proteome scale applications. This situation has triggered several initiatives involving large scale generation and validation of antibodies, for example the Swedish Human Protein Atlas and the German Antibody Factory. Antibodies targeting specific subproteomes are being pursued by members of Human Proteome Organisation (plasma and liver proteome projects) and the United States National Cancer Institute (cancer-associated antigens). ProteomeBinders, a European consortium, aims to set up a resource of consistently quality-controlled protein-binding reagents for the whole human proteome. An ultimate PAR database resource would allow consumers to visit one on-line warehouse and find all available affinity reagents from different providers together with documentation that facilitates easy comparison of their cost and quality. However, in contrast to, for example, nucleotide databases among which data are synchronized between the major data providers, current PAR producers, quality control centers, and commercial companies all use incompatible formats, hindering data exchange. Here we propose Proteomics Standards Initiative (PSI)-PAR as a global community standard format for the representation and exchange of protein affinity reagent data. The PSI-PAR format is maintained by the Human Proteome Organisation PSI and was developed within the context of ProteomeBinders by building on a mature proteomics standard format, PSI-molecular interaction, which is a widely accepted and established community standard for molecular interaction data. Further information and documentation are available on the PSI-PAR web site.
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Affiliation(s)
- David E Gloriam
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.
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Abstract
Protein microarrays are versatile tools for parallel, miniaturized screening of binding events involving large numbers of immobilized proteins in a time- and cost-effective manner. They are increasingly applied for high-throughput protein analyses in many research areas, such as protein interactions, expression profiling and target discovery. While conventionally made by the spotting of purified proteins, recent advances in technology have made it possible to produce protein microarrays through in situ cell-free synthesis directly from corresponding DNA arrays. This article reviews recent developments in the generation of protein microarrays and their applications in proteomics and diagnostics.
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Affiliation(s)
- Oda Stoevesandt
- Babraham Bioscience Technologies Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
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Man AL, Lodi F, Bertelli E, Regoli M, Pin C, Mulholland F, Satoskar AR, Taussig MJ, Nicoletti C. Macrophage migration inhibitory factor plays a role in the regulation of microfold (M) cell-mediated transport in the gut. J Immunol 2008; 181:5673-80. [PMID: 18832726 DOI: 10.4049/jimmunol.181.8.5673] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
It has been shown previously that certain bacteria rapidly (3 h) up-regulated in vivo microfold cell (M cell)-mediated transport of Ag across the follicle-associated epithelium of intestinal Peyer's patch. Our aim was to determine whether soluble mediators secreted following host-bacteria interaction were involved in this event. A combination of proteomics and immunohistochemical analyses was used to identify molecules produced in the gut in response to bacterial challenge in vivo; their effects were then tested on human intestinal epithelial cells in vitro. Macrophage migration inhibitory factor (MIF) was the only cytokine produced rapidly after in vivo bacterial challenge by CD11c(+) cells located beneath the M cell-rich area of the follicle-associated epithelium of the Peyer's patch. Subsequently, in vitro experiments conducted using human Caco-2 cells showed that, within hours, MIF induced the appearance of cells that showed temperature-dependent transport of microparticles and M cell-specific bacterium Vibrio cholerae, and acquired biochemical features of M cells. Furthermore, using an established in vitro human M cell model, we showed that anti-MIF Ab blocked Raji B cell-mediated conversion of Caco-2 cells into Ag-sampling cells. Finally, we report that MIF(-/-) mice, in contrast to wild-type mice, failed to show increased M cell-mediated transport following in vivo bacterial challenge. These data show that MIF plays a role in M cell-mediated transport, and cross-talk between bacteria, gut epithelium, and immune system is instrumental in regulating key functions of the gut, including M cell-mediated Ag sampling.
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Affiliation(s)
- Angela L Man
- Programme of Gastrointestinal Tract Biology and Health, Institute of Food Research, Norwich, United Kingdom
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25
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Affiliation(s)
- Michael J Taussig
- ESF Programme in Integrated Approaches to Functional Genomics, The Babraham Institute, Cambridge CB2 4AT, UK.
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Taussig MJ, Suojanen C, Clark BFC. New Biotechnology and the European Federation of Biotechnology. N Biotechnol 2008; 25:1-2. [PMID: 18504001 DOI: 10.1016/j.nbt.2008.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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He M, Stoevesandt O, Palmer EA, Khan F, Ericsson O, Taussig MJ. Printing protein arrays from DNA arrays. Nat Methods 2008; 5:175-7. [DOI: 10.1038/nmeth.1178] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2007] [Accepted: 12/20/2007] [Indexed: 11/09/2022]
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Abstract
Protein arrays make possible the functional screening of large numbers of immobilized proteins in parallel. To facilitate the supply of proteins and to avoid their deterioration on storage, we describe our protein in situ array (PISA) method for production of protein arrays in a single step directly from PCR DNA, using cell-free transcription and translation. In PISA, the in vitro-generated proteins are immobilized, as they are formed, on the surface of wells, beads, or slides coated with a protein-capturing reagent. In our preferred method, proteins are tagged with a double-hexahistidine sequence that binds strongly to Ni-NTA-coated surfaces. Advantages of PISA include avoiding bacterial expression and protein purification and making functional protein arrays available as required from genetic information.
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Affiliation(s)
- Mingyue He
- Technology Research Group, The Babraham Institute, Cambridge, UK
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30
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Zou X, Osborn MJ, Bolland DJ, Smith JA, Corcos D, Hamon M, Oxley D, Hutchings A, Morgan G, Santos F, Kilshaw PJ, Taussig MJ, Corcoran AE, Brüggemann M. Heavy chain-only antibodies are spontaneously produced in light chain-deficient mice. ACTA ACUST UNITED AC 2007; 204:3271-83. [PMID: 18086860 PMCID: PMC2150980 DOI: 10.1084/jem.20071155] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In healthy mammals, maturation of B cells expressing heavy (H) chain immunoglobulin (Ig) without light (L) chain is prevented by chaperone association of the H chain in the endoplasmic reticulum. Camelids are an exception, expressing homodimeric IgGs, an antibody type that to date has not been found in mice or humans. In camelids, immunization with viral epitopes generates high affinity H chain–only antibodies, which, because of their smaller size, recognize clefts and protrusions not readily distinguished by typical antibodies. Developmental processes leading to H chain antibody expression are unknown. We show that L−/− (κ−/−λ−/−-deficient) mice, in which conventional B cell development is blocked at the immature B cell stage, produce diverse H chain–only antibodies in serum. The generation of H chain–only IgG is caused by the loss of constant (C) γ exon 1, which is accomplished by genomic alterations in CH1-circumventing chaperone association. These mutations can be attributed to errors in class switch recombination, which facilitate the generation of H chain–only Ig-secreting plasma cells. Surprisingly, transcripts with a similar deletion can be found in normal mice. Thus, naturally occurring H chain transcripts without CH1 (VHDJH-hinge-CH2-CH3) are selected for and lead to the formation of fully functional and diverse H chain–only antibodies in L−/− animals.
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Affiliation(s)
- Xiangang Zou
- The Babraham Institute, Babraham, Cambridge CB22 3AT, England, UK
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31
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Abstract
Essential to the ambition of characterising fully the human proteome are systematic and comprehensive collections of specific affinity reagents directed against all human proteins, including splice variants and modifications. Although a large number of affinity reagents are available commercially, their quality is often questionable and only a fraction of the proteome is covered. In order for more targets to be examined, there is a need for broad availability of panels of affinity reagents, including binders against proteins of unknown functions. The most familiar affinity reagents are antibodies and their fragments, but engineered forms of protein scaffolds and nucleic acid aptamers with similar diversity and binding properties are becoming viable alternatives. Recent initiatives in Europe and the USA have been established to improve both the availability and quality of reagents for affinity proteomics, with the ultimate aim of creating standardised collections of well-validated binding molecules for proteome analysis. As well as coordinating affinity reagent production through existing resources and technology providers, these projects aim to benchmark key molecular entities, tools, and applications, and establish the bioinformatics framework and databases needed. The benefits of such reagent resources will be seen in basic research, medicine and the biotechnology and pharmaceutical industries.
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Affiliation(s)
- Oda Stoevesandt
- Technology Research Group, The Babraham Institute, Cambridge, UK
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32
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He M, Taussig MJ. Erratum: Eukaryotic ribosome display with in situ DNA recovery. Nat Methods 2007. [DOI: 10.1038/nmeth0907-763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Yang YM, Barankiewicz TJ, He M, Taussig MJ, Chen SS. Selection of antigenic markers on a GFP-Cκ fusion scaffold with high sensitivity by eukaryotic ribosome display. Biochem Biophys Res Commun 2007; 359:251-7. [PMID: 17537405 DOI: 10.1016/j.bbrc.2007.05.083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 05/09/2007] [Accepted: 05/10/2007] [Indexed: 11/22/2022]
Abstract
Ribosome display is a cell-free system permitting gene selection through the physical association of genetic material (mRNA) and its phenotypic (protein) product. While often used to select single-chain antibodies from large libraries by panning against immobilized antigens, we have adapted ribosome display for use in the 'reverse' format in order to select high affinity antigenic determinants against solid-phase antibody. To create an antigenic scaffold, DNA encoding green fluorescent protein (GFP) was fused to a light chain constant domain (Ckappa) with stop codon deleted, and with 5' signals (T7 promoter, Kozak) enabling coupled transcription/translation in a eukaryotic cell-free system. Epitopes on either GFP (5') or Ckappa (3') were selected by anti-GFP or anti-Ckappa antibodies, respectively, coupled to magnetic beads. After selection, mRNA was amplified directly from protein-ribosome-mRNA (PRM) complexes by in situ PCR followed by internal amplification and reassembly PCR. As little as 10fg of the 1kb DNA construct, i.e. approximately 7500 molecules, could be recovered following a single round of interaction with solid-phase anti-GFP antibody. This platform is highly specific and sensitive for the antigen-antibody interaction and may permit selection and reshaping of high affinity antigenic variants of scaffold proteins.
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Affiliation(s)
- Yong-Min Yang
- The Institute of Genetics, San Diego, CA 92121-2233, USA
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34
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Duquerroy S, Stura EA, Bressanelli S, Fabiane SM, Vaney MC, Beale D, Hamon M, Casali P, Rey FA, Sutton BJ, Taussig MJ. Crystal structure of a human autoimmune complex between IgM rheumatoid factor RF61 and IgG1 Fc reveals a novel epitope and evidence for affinity maturation. J Mol Biol 2007; 368:1321-31. [PMID: 17395205 PMCID: PMC4625532 DOI: 10.1016/j.jmb.2007.02.085] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [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: 12/18/2006] [Revised: 02/19/2007] [Accepted: 02/21/2007] [Indexed: 01/07/2023]
Abstract
Rheumatoid factors (RF) are autoantibodies that recognize epitopes in the Fc region of immunoglobulin (Ig) G and that correlate with the clinical severity of rheumatoid arthritis (RA). Here we report the X-ray crystallographic structure, at 3 A resolution, of a complex between the Fc region of human IgG1 and the Fab fragment of a monoclonal IgM RF (RF61), derived from an RA patient and with a relatively high affinity for IgG Fc. In the complex, two Fab fragments bind to each Fc at epitopes close to the C terminus, and each epitope comprises residues from both Cgamma3 domains. A central role in the unusually hydrophilic epitope is played by the side-chain of Arg355, accounting for the subclass specificity of RF61, which recognizes IgG1,-2, and -3 in preference to IgG4, in which the corresponding residue is Gln355. Compared with a previously determined complex of a lower affinity RF (RF-AN) bound to IgG4 Fc, in which only residues at the very edge of the antibody combining site were involved in binding, the epitope bound by RF61 is centered in classic fashion on the axis of the V(H):V(L) beta-barrel. The complementarity determining region-H3 loop plays a key role, forming a pocket in which Arg355 is bound by two salt-bridges. The antibody contacts also involve two somatically mutated V(H) residues, reinforcing the suggestion of a process of antigen-driven maturation and selection for IgG Fc during the generation of this RF autoantibody.
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Affiliation(s)
- Stephane Duquerroy
- Virologie Moléculaire et Structurale, CNRS UMR 2472-INRA UMR 1157, 91198 Gif-sur-Yvette, France
- Unité de Virologie Structurale and URA 3015 CNRS, Département de Virologie, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
- Université Paris-Sud, Orsay Cedex, F-91405, France
| | - Enrico A. Stura
- Département d'Ingénierie et d'Études des Protéines, CEA de Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Stéphane Bressanelli
- Virologie Moléculaire et Structurale, CNRS UMR 2472-INRA UMR 1157, 91198 Gif-sur-Yvette, France
| | - Stella M. Fabiane
- The Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Marie C. Vaney
- Virologie Moléculaire et Structurale, CNRS UMR 2472-INRA UMR 1157, 91198 Gif-sur-Yvette, France
| | - Dennis Beale
- Technology Research Group, The Babraham Institute, Cambridge CB2 4AT, UK
| | - Maureen Hamon
- Technology Research Group, The Babraham Institute, Cambridge CB2 4AT, UK
| | - Paolo Casali
- Center for Immunology, School of Biological Sciences and School of Medicine, University of California, Irvine, CA 92657, USA
| | - Felix A. Rey
- Virologie Moléculaire et Structurale, CNRS UMR 2472-INRA UMR 1157, 91198 Gif-sur-Yvette, France
- Unité de Virologie Structurale and URA 3015 CNRS, Département de Virologie, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Brian J. Sutton
- The Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
- corresponding author:
| | - Michael J. Taussig
- Technology Research Group, The Babraham Institute, Cambridge CB2 4AT, UK
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35
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Abstract
While cell-free systems are increasingly used for protein expression in structural and functional studies, several proteins are difficult to express or expressed only at low levels in cell-free lysates. Here, we report that fusion of the human immunoglobulin kappa light chain constant domain (Ckappa) at the C terminus of four representative proteins dramatically improved their production in the Escherichia coli S30 system, suggesting that enhancement of cell-free protein expression by Ckappa fusion will be widely applicable.
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Affiliation(s)
- Elizabeth Palmer
- Technology Research Group, The Babraham Institute, Cambridge CB2 4AT, United Kingdom
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36
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Abstract
Ribosome display is a cell-free technology for the in vitro selection and evolution of proteins encoded by DNA libraries, in which individual nascent proteins (phenotypes) are linked physically to their corresponding mRNA (genotypes) in stable protein-ribosome-mRNA (PRM) complexes. Formation of the complexes can be achieved through deletion of the stop codon of the mRNA, stalling the ribosome at the end of translation; the nascent protein is extended by a spacer such as the immunoglobulin Ckappa domain or others to allow exit through the ribosome tunnel. Through affinity for a ligand, the protein-mRNA coupling permits simultaneous isolation of a functional nascent protein and its translated mRNA; the latter is then converted into cDNA by reverse transcription and amplified for further manipulation, repeated cycles or soluble protein expression. Through the use of PCR-generated libraries, avoiding the need for cloning, ribosome display can be used to both screen very large populations and continuously search for new diversity during subsequent rounds of selection. Additionally, the use of cell-free systems allows the selection of proteins that are toxic or unstable in cells, and proteins with chemical modifications. Ribosome display systems using both prokaryotic and eukaryotic cell extracts have been developed. Examples of the application of eukaryotic systems include the selection and evolution of antibody fragments, DNA binding domains, enzymes, interacting proteins and peptides among others. Here we describe the step-by-step procedure to perform our previously described eukaryotic ribosome display method, which has the distinctive feature of an in situ reverse transcription-PCR (RT-PCR) procedure for DNA recovery from ribosome-bound mRNA. We also introduce a recent, previously unpublished improvement to the procedure in which in situ reverse transcription is combined with sensitive single-primer PCR technology.
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Affiliation(s)
- Mingyue He
- Technology Research Group, The Babraham Institute, Cambridge CB22 4AT, UK
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37
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Taussig MJ, Stoevesandt O, Borrebaeck CAK, Bradbury AR, Cahill D, Cambillau C, de Daruvar A, Dübel S, Eichler J, Frank R, Gibson TJ, Gloriam D, Gold L, Herberg FW, Hermjakob H, Hoheisel JD, Joos TO, Kallioniemi O, Koegl M, Koegll M, Konthur Z, Korn B, Kremmer E, Krobitsch S, Landegren U, van der Maarel S, McCafferty J, Muyldermans S, Nygren PA, Palcy S, Plückthun A, Polic B, Przybylski M, Saviranta P, Sawyer A, Sherman DJ, Skerra A, Templin M, Ueffing M, Uhlén M. ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome. Nat Methods 2007; 4:13-7. [PMID: 17195019 DOI: 10.1038/nmeth0107-13] [Citation(s) in RCA: 189] [Impact Index Per Article: 11.1] [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: 11/09/2022]
Abstract
ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome. Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-European or even worldwide coordination.
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Affiliation(s)
- Michael J Taussig
- Technology Research Group, The Babraham Institute, Cambridge CB22 3AT, UK.
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He M, Hamon M, Liu H, Corper AL, Taussig MJ. Effects of mutation at the D-JH junction on affinity, specificity, and idiotypy of anti-progesterone antibody DB3. Protein Sci 2006; 15:2141-8. [PMID: 16882990 PMCID: PMC2242612 DOI: 10.1110/ps.062236806] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 10/24/2022]
Abstract
The crystal structures of the Fab' fragment of the anti-progesterone monoclonal antibody DB3 and its complexes with steroid haptens have shown that the D-JH junctional residue TrpH100 is a key contributor to binding site interactions with ligands. The indole group of TrpH100 also undergoes a significant conformational change between the bound and unliganded states, effectively opening and closing the combining site pocket. In order to explore the effect of substitutions at this position on steroid recognition, we have carried out mutagenesis on a construct encoding a three-domain single-chain fragment (VH/K) of DB3 expressed in Escherichia coli. TrpH100 was replaced by 13 different amino acids or deleted, and the functional and antigenic properties of the mutated fragments were analyzed. Most substitutions, including small, hydrophobic, hydrophilic, neutral, and negatively charged side chains, were reduced or abolished binding to free progesterone, although binding to progesterone-BSA was partially retained. The reduction in antigen binding was paralleled by alteration of the idiotype associated with the DB3 combining site. In contrast, the replacement of TrpH100 by Arg produced a mutant that retained wild-type antibody affinity and idiotype, but with altered specificity. Significant changes in this mutant included increased relative affinities of 10(4)-fold for progesterone-3-carboxymethyloxime and 10-fold for aetiocholanolone. Our results demonstrate an essential role for the junctional residue H100 in determining steroid-binding specificity and combining site idiotype and show that these properties can be changed by a single amino acid substitution at this position.
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Affiliation(s)
- Mingyue He
- Technology Research Group, The Babraham Institute, Cambridge, United Kingdom.
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Steinhauer C, Wingren C, Khan F, He M, Taussig MJ, Borrebaeck CAK. Improved affinity coupling for antibody microarrays: Engineering of double-(His)6-tagged single framework recombinant antibody fragments. Proteomics 2006; 6:4227-34. [PMID: 16826567 DOI: 10.1002/pmic.200600036] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [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: 11/06/2022]
Abstract
Antibody-based microarray is a novel technology with great promise in biomedicine that will provide unique means to perform global proteome analysis. In the process of designing the high-density antibody microarrays required, several critical key issues have been identified that remain to be resolved. In particular, there is a great need for specific and selective approaches enabling non-purified probes to be directly purified, orientated and coupled in a generic one-step procedure directly on the chip. In this study, we report on the successful design of affinity-tagged human recombinant single-chain fragment variable antibody fragments for improved affinity coupling in array applications. By replacing the standard single-histidine (His)(6)-tag with a consecutive double-(His)(6)-tag, the binding to Ni(2+)-nitrilotriacetic acid-coated substrates was significantly improved. Surface plasmon resonance analysis showed a significantly tighter binding with at least a threefold slower dissociation. The improved binding characteristics thus enabled non-purified probes even in the format of crude expression supernatants to be directly applied thereby eliminating the need for any time-consuming pre-purification step(s) prior to the immobilization. While the double-(His)(6)-tag probes were found to be expressed equally well as compared to the single-(His)(6)-tag probes, they displayed better long-term functional on-chip stability. Taken together, the results demonstrate the generic potential of double-(His)(6)-tag recombinant antibodies for the facile fabrication of high-density antibody microarrays.
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Khan F, He M, Taussig MJ. Double-Hexahistidine Tag with High-Affinity Binding for Protein Immobilization, Purification, and Detection on Ni−Nitrilotriacetic Acid Surfaces. Anal Chem 2006; 78:3072-9. [PMID: 16642995 DOI: 10.1021/ac060184l] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.3] [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: 11/28/2022]
Abstract
There is a particular need in protein analysis and purification for specific, functional, and generic methods of protein immobilization on solid supports. Here we describe a double-hexahistidine (His6) tag sequence, comprising two hexahistidines separated by an 11-amino acid spacer, which shows at least 1 order of magnitude stronger binding to Ni-NTA-modified surfaces than a conventional single-His6 tag or two single-His6 tags at N- and C-termini. Using, as a model, tagged versions of green fluorescent protein (GFP), stable and tight binding of the double-His6 tag/Ni-NTA interaction was demonstrated by competitive elution from Ni-NTA agarose beads, surface plasmon resonance on a Ni-NTA chip, and ELISA in Ni-NTA microwell plates. Protein purification by Ni-NTA chromatography was improved by a 6-8-fold increase in imidazole concentration required for elution, while the dissociation rate of double-His6 GFP from Ni-NTA chips in SPR (BIAcore) was 10 times slower than for single-His6-tagged proteins. ELISA assays and protein microarrays constructed with double-His6 GFP demonstrated greater detection sensitivity with anti-His antibodies and Ni-NTA conjugates. Moreover, the double-His6 tag could serve simultaneously both for protein immobilization and for detection on surfaces. The double-His6 peptide has the potential to be a universal tag for protein immobilization and detection on arrays and single-step purification of proteins from crude mixtures.
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Affiliation(s)
- Farid Khan
- Protein Technologies Laboratory, The Babraham Institute, Babraham Research Campus, Cambridge CB2 4AT, UK
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41
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He M, Taussig MJ. Ribosome display of antibodies: expression, specificity and recovery in a eukaryotic system. J Immunol Methods 2005; 297:73-82. [PMID: 15777932 DOI: 10.1016/j.jim.2004.11.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [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: 06/29/2004] [Revised: 10/04/2004] [Accepted: 11/30/2004] [Indexed: 10/26/2022]
Abstract
In ribosome display, proteins are linked to their encoding genetic material as protein-ribosome-mRNA complexes. The technology has been applied to the isolation of antibodies and other proteins from large PCR-derived libraries. Here we demonstrate the specificity of eukaryotic ribosome complexes and investigate recovery and display procedures using a single chain version of the anti-progesterone monoclonal antibody DB3. Complexes are formed by deletion of the 3' stop codon in a coupled rabbit reticulocyte system. Using inhibition with different steroid probes, we show that the fine specificity of the combining site expressed as a nascent protein is closely similar to the native monoclonal, indicating correct folding and function while bound to the ribosome. We have demonstrated that the 3' end of the mRNA is blocked by the stalled ribosome and unavailable to primers. Moreover, we show that an in situ RT-PCR recovery procedure, carried out on intact complexes, is more efficient than ribosome disruption and isolation of mRNA followed by RT-PCR. We also explore the Mg(2+) and DTT concentrations and time required for efficient production of complexes. Our findings confirm the effectiveness of the eukaryotic ribosome display system and define conditions for efficient selection of single chain antibodies.
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Affiliation(s)
- Mingyue He
- Protein Technologies Laboratory, The Babraham Institute, The Babraham Research Campus, Cambridge CB2 4AT, UK
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Taussig MJ, Landegren U. Progress in antibody arrays. Drug Discov Today 2004; 9:S53-S60. [PMID: 23573661] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Arrays of antibodies and of other types of ligand-binding molecule (e.g. protein scaffolds or aptamers) provide a means for rapid detection of proteins and other analytes in multiple samples and ultimately for screening the human proteome in health and disease. The chief reasons for using an array-based approach to diagnostics and proteomics relate to the advantages associated with parallelisation, miniaturisation and automation. The current generation of antibody microarrays promises to perform well as diagnostic tools and for limited protein profiling, using relatively small numbers of available antibodies. Sensitivity, specificity and signal-to-noise ratios in the multiplex format are major issues and will become more critical as the complexity of arrays is increased. This review describes progress in solving problems associated with the construction of antibody arrays.
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Affiliation(s)
- Michael J Taussig
- Technology Research Group, The Babraham Institute, Cambridge CB2 4AT, UK
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Affiliation(s)
- Mingyue He
- Discerna Ltd, Babraham Hall, Babraham, Cambridge, UK
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Abstract
Protein array technology offers a powerful tool to bridge genomics and proteomics. Currently, the bottleneck in the generation of protein arrays is the comprehensive production of functional proteins. We have developed a rapid cell-free method, DiscernArray, which creates functional protein arrays directly from PCR DNA by in vitro synthesis of individual tagged proteins on tag-binding surfaces, such that the tagged proteins are immobilized on a surface as they are synthesised. DiscernArray is particularly useful for arraying proteins and domains which cannot be functionally produced in heterologous expression systems or for which the cloned DNA is not available.
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Affiliation(s)
- Mingyue He
- Discerna Limited, Babraham Research Campus, Babraham, CB2 4AT, Cambridge, UK.
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Nordmark G, Rorsman F, Rönnblom L, Cajander S, Taussig MJ, Kämpe O, Winqvist O. Autoantibodies to alpha-fodrin in primary Sjögren's syndrome and SLE detected by an in vitro transcription and translation assay. Clin Exp Rheumatol 2003; 21:49-56. [PMID: 12673889] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
OBJECTIVE To investigate the prevalence of alpha-fodrin autoantibodies in primary Sjögren's syndrome (SS) and systemic lupus erythematosus (SLE) with and without secondary SS, using an in vitro transcription and translation assay (ITT). METHODS cDNA encoding JS-1, the amino-terminal portion of alpha-fodrin, was used for ITT. Immunoprecipitation was performed with sera from 56 primary SS patients and 67 SLE patients, 14 with and 53 without secondary SS. Correlations to RF, ANA, anti-dsDNA, anti-SS-A and anti-SS-B antibodies, hypergammaglobulinemia, labial salivary gland biopsy grade, extraglandular manifestations and a modified SLE disease activity index (mSLEDAI) were made. RESULTS Autoantibodies against alpha-fodrin were detected in 16/56 (29%) of primary SS patients and in 25/53 (47%) of sera from SLE patients without secondary SS. In SLE patients with secondary SS the prevalence was 3/14 (21%). None of the blood donors showed alpha-fodrin reactivity. Correlations were found to RF, ANA, anti-dsDNA antibodies and a positive mSLEDAI score. CONCLUSION The frequency of alpha-fodrin autoantibodies detected by this method is similar in sera from primary SS patients and SLE patients with or without secondary SS. The presence of alpha-fodrin autoantibodies seems to reflect non-organ-specific autoimmunity in primary SS and SLE and to be of limited discriminating value.
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Affiliation(s)
- G Nordmark
- Section of Rheumatology, Centre for Laboratory Medicine, University Hospital, Uppsala, Sweden.
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Graille M, Harrison S, Crump MP, Findlow SC, Housden NG, Muller BH, Battail-Poirot N, Sibaï G, Sutton BJ, Taussig MJ, Jolivet-Reynaud C, Gore MG, Stura EA. Evidence for plasticity and structural mimicry at the immunoglobulin light chain-protein L interface. J Biol Chem 2002; 277:47500-6. [PMID: 12221088 DOI: 10.1074/jbc.m206105200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The multidomain bacterial surface protein L (PpL) is a virulence factor expressed by only 10% of Peptostreptococcus magnus strains, and its expression is correlated with bacterial vaginosis. The molecular basis for its ability to recognize 60% of mammalian immunoglobulin light chain variable regions (V(L)) has been described recently by x-ray crystallography, which suggested the presence of two V(L) binding sites on each protein L domain (Graille, M., Stura, E. A., Housden, N. G., Beckingham, J. A., Bottomley, S. P., Beale, D., Taussig, M. J., Sutton, B. J., Gore, M. G., and Charbonnier, J. (2001) Structure 9, 679-687). Here, we report the crystal structure at 2.1 A resolution of a protein L mutant complexed to an Fab' fragment with only 50% of the V(L) residues interacting with PpL site 1 conserved. Comparison of the site 1 interface from both structures shows how protein L is able to accommodate these sequence differences and therefore bind to a large repertoire of Ig. The x-ray structure and NMR results confirm the existence of two V(L) binding sites on a single protein L domain. These sites exhibit a remarkable structural mimicry of growth factors binding to their receptors. This could explain the protein L superantigenic activity on human B lymphocytes.
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Affiliation(s)
- Marc Graille
- Laboratoire de Structure des Protéines, Département d'Ingénierie et d'Etudes des Protéines (DIEP), Commissariat à l'Energie Atomique, Centre d'Etudes de Saclay, Gif-sur-Yvette, France
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Stura EA, Taussig MJ, Sutton BJ, Duquerroy S, Bressanelli S, Minson AC, Rey FA. Scaffolds for protein crystallisation. Acta Crystallogr D Biol Crystallogr 2002; 58:1715-21. [PMID: 12351893 DOI: 10.1107/s0907444902012829] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2002] [Accepted: 07/16/2002] [Indexed: 11/10/2022]
Abstract
In the absence of a method to ensure that crystals can be obtained for any given protein, the possibility of developing scaffolds for protein crystallisation becomes attractive. Among several approaches that could yield scaffolds, two are particularly promising: the first is based on immunoglobulin Fab fragments and immunoglobulin binding proteins while the second is based on fusion proteins. In the Fab based scaffold, the protein of interest is the antigen recognised by the antibody. In the second case, it is a protein fused to one of the scaffold components. The operational difference between the two methods is the existence of a flexible covalent tether compared to a highly specific interaction. The relative merits and disadvantages of each approach are discussed here. We also describe a lattice obtained through a combinatorial approach which appears to have the required properties to be considered a scaffold. The system makes use of an Fab derived from a rheumatoid factor and an Fc-fusion protein. The Fc-fusion system is ideal for enhanced expression of glycoproteins in mammalian cells and provides a useful tag for their purification. The molecular replacement shows a mode of binding for this rheumatoid factor that is not competitive with bacterial Fc-binding proteins. Hence it may be possible to generalize the method to include bacterial expression of fusion proteins with either protein A or protein G as the fusion partner.
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Affiliation(s)
- Enrico A Stura
- CEA, Département d'Ingénierie des Protéines (DIEP), CE Saclay, 91191 Gif-sur-Yvette, France.
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Abstract
Ribosome display is a cell-free system for the in vitro selection of proteins and peptides from large libraries. It uses the principle of coupling individual nascent proteins (phenotypes) to their corresponding mRNA (genotypes), through the formation of stable protein-ribosome-mRNA (PRM) complexes. This permits the simultaneous isolation of a functional nascent protein, through affinity for a ligand, together with the encoding mRNA, which is then converted and amplified as DNA for further manipulation, including repeated cycles or protein expression. Ribosome display has a number of advantages over cell-based systems such as phage display; in particular, it can display very large libraries without the restriction of bacterial transformation. It is also suitable for generating toxic, proteolytically sensitive and unstable proteins, and allows the incorporation of modified amino acids at defined positions. In combination with polymerase chain reaction (PCR)-based methods, mutations can be introduced efficiently into the selected DNA pool in subsequent cycles, leading to continuous DNA diversification and protein selection (in vitro protein evolution). Both prokaryotic and eukaryotic ribosome display systems have been developed and each has its own distinctive features. In this paper, ribosome display systems and their application in selection and evolution of proteins are reviewed.
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Affiliation(s)
- Mingyue He
- Discerna Limited, Babraham, Cambridge, UK.
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Abstract
We describe a format for production of protein arrays termed 'protein in situ array' (PISA). A PISA is rapidly generated in one step directly from PCR-generated DNA fragments by cell-free protein expression and in situ immobilisation at a surface. The template for expression is DNA encoding individual proteins or domains, which is produced by PCR using primers designed from information in DNA databases. Coupled transcription and translation is carried out on a surface to which the tagged protein adheres as soon as it is synthesised. Because proteins generated by cell-free synthesis are usually soluble and functional, this method can overcome problems of insolubility or degradation associated with bacterial expression of recombinant proteins. Moreover, the use of PCR-generated DNA enables rapid production of proteins or domains based on genome information alone and will be particularly useful where cloned material is not available. Here we show that human single-chain antibody fragments (three domain, V(H)/K form) and an enzyme (luciferase) can be functionally arrayed by the PISA method.
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Affiliation(s)
- M He
- Technology Research Group, The Babraham Institute, Babraham, Cambridge CB2 4AT, UK.
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