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Cronin SJF, Yu W, Hale A, Licht-Mayer S, Crabtree MJ, Korecka JA, Tretiakov EO, Sealey-Cardona M, Somlyay M, Onji M, An M, Fox JD, Turnes BL, Gomez-Diaz C, da Luz Scheffer D, Cikes D, Nagy V, Weidinger A, Wolf A, Reither H, Chabloz A, Kavirayani A, Rao S, Andrews N, Latremoliere A, Costigan M, Douglas G, Freitas FC, Pifl C, Walz R, Konrat R, Mahad DJ, Koslov AV, Latini A, Isacson O, Harkany T, Hallett PJ, Bagby S, Woolf CJ, Channon KM, Je HS, Penninger JM. Crucial neuroprotective roles of the metabolite BH4 in dopaminergic neurons. bioRxiv 2023:2023.05.08.539795. [PMID: 37214873 PMCID: PMC10197517 DOI: 10.1101/2023.05.08.539795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Dopa-responsive dystonia (DRD) and Parkinson's disease (PD) are movement disorders caused by the dysfunction of nigrostriatal dopaminergic neurons. Identifying druggable pathways and biomarkers for guiding therapies is crucial due to the debilitating nature of these disorders. Recent genetic studies have identified variants of GTP cyclohydrolase-1 (GCH1), the rate-limiting enzyme in tetrahydrobiopterin (BH4) synthesis, as causative for these movement disorders. Here, we show that genetic and pharmacological inhibition of BH4 synthesis in mice and human midbrain-like organoids accurately recapitulates motor, behavioral and biochemical characteristics of these human diseases, with severity of the phenotype correlating with extent of BH4 deficiency. We also show that BH4 deficiency increases sensitivities to several PD-related stressors in mice and PD human cells, resulting in worse behavioral and physiological outcomes. Conversely, genetic and pharmacological augmentation of BH4 protects mice from genetically- and chemically induced PD-related stressors. Importantly, increasing BH4 levels also protects primary cells from PD-affected individuals and human midbrain-like organoids (hMLOs) from these stressors. Mechanistically, BH4 not only serves as an essential cofactor for dopamine synthesis, but also independently regulates tyrosine hydroxylase levels, protects against ferroptosis, scavenges mitochondrial ROS, maintains neuronal excitability and promotes mitochondrial ATP production, thereby enhancing mitochondrial fitness and cellular respiration in multiple preclinical PD animal models, human dopaminergic midbrain-like organoids and primary cells from PD-affected individuals. Our findings pinpoint the BH4 pathway as a key metabolic program at the intersection of multiple protective mechanisms for the health and function of midbrain dopaminergic neurons, identifying it as a potential therapeutic target for PD.
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Affiliation(s)
- Shane J F Cronin
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Weonjin Yu
- Signature Program in Neuroscience and Behavioural Disorders, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Ashley Hale
- Division of Cardiovascular Medicine, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Simon Licht-Mayer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Mark J Crabtree
- Division of Cardiovascular Medicine, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Joanna A Korecka
- Neurodegeneration Research Institute, Harvard Medical School/McLean Hospital, Belmont, MA, 02478, USA
| | - Evgenii O Tretiakov
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Marco Sealey-Cardona
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Mate Somlyay
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Masahiro Onji
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Meilin An
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Jesse D Fox
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Bruna Lenfers Turnes
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Carlos Gomez-Diaz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Débora da Luz Scheffer
- LABOX, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, SC 88037-100, Brazil
| | - Domagoj Cikes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Vanja Nagy
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases (LBI-RUD); Department of Neurology, Medical University of Vienna (MUW), 1090 Vienna, Austria
| | - Adelheid Weidinger
- Ludwig Boltzmann Institute for Traumatology. The Research Center in Cooperation with AUVA, Donaueschingen Str. 13, 1200 Vienna, Austria
| | - Alexandra Wolf
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Harald Reither
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Antoine Chabloz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Anoop Kavirayani
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Shuan Rao
- Department of Thoracic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Nick Andrews
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Alban Latremoliere
- Neurosurgery Department, Neurosurgery Pain Research Institute, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Michael Costigan
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Gillian Douglas
- Division of Cardiovascular Medicine, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Christian Pifl
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Roger Walz
- Center for Applied Neurocience, Universidade Federal de Santa Catarina (UFSC), Florianópolis, Brazil; Neurology Division, Internal Medicine Department, University Hospital of UFSC, Florianópolis, Brazil
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Labs, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Don J Mahad
- Centre for Clinical Brain Sciences, University of Edinburgh, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Andrey V Koslov
- Ludwig Boltzmann Institute for Traumatology. The Research Center in Cooperation with AUVA, Donaueschingen Str. 13, 1200 Vienna, Austria
| | - Alexandra Latini
- LABOX, Departamento de Bioquímica, Universidade Federal de Santa Catarina, Florianópolis, SC 88037-100, Brazil
| | - Ole Isacson
- Neurodegeneration Research Institute, Harvard Medical School/McLean Hospital, Belmont, MA, 02478, USA
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Neuroscience, Biomedicum 7D, Karolinska Institute, Solna, Sweden
| | - Penelope J Hallett
- Neurodegeneration Research Institute, Harvard Medical School/McLean Hospital, Belmont, MA, 02478, USA
| | - Stefan Bagby
- Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Clifford J Woolf
- FM Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA 02115, USA and Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Keith M Channon
- Division of Cardiovascular Medicine, British Heart Foundation Centre of Research Excellence, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Hyunsoo Shawn Je
- Signature Program in Neuroscience and Behavioural Disorders, Duke-National University of Singapore (NUS) Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, Canada
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2
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Chapman R, Jones L, D'Angelo A, Suliman A, Anwar M, Bagby S. Nanopore-Based Metagenomic Sequencing in Respiratory Tract Infection: A Developing Diagnostic Platform. Lung 2023; 201:171-179. [PMID: 37009923 PMCID: PMC10067523 DOI: 10.1007/s00408-023-00612-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 03/14/2023] [Indexed: 04/04/2023]
Abstract
Respiratory tract infection (RTI) remains a significant cause of morbidity and mortality across the globe. The optimal management of RTI relies upon timely pathogen identification via evaluation of respiratory samples, a process which utilises traditional culture-based methods to identify offending microorganisms. This process can be slow and often prolongs the use of broad-spectrum antimicrobial therapy, whilst also delaying the introduction of targeted therapy as a result. Nanopore sequencing (NPS) of respiratory samples has recently emerged as a potential diagnostic tool in RTI. NPS can identify pathogens and antimicrobial resistance profiles with greater speed and efficiency than traditional sputum culture-based methods. Increased speed to pathogen identification can improve antimicrobial stewardship by reducing the use of broad-spectrum antibiotic therapy, as well as improving overall clinical outcomes. This new technology is becoming more affordable and accessible, with some NPS platforms requiring minimal sample preparation and laboratory infrastructure. However, questions regarding clinical utility and how best to implement NPS technology within RTI diagnostic pathways remain unanswered. In this review, we introduce NPS as a technology and as a diagnostic tool in RTI in various settings, before discussing the advantages and limitations of NPS, and finally what the future might hold for NPS platforms in RTI diagnostics.
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Affiliation(s)
- Robert Chapman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK.
| | - Luke Jones
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Alberto D'Angelo
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
| | - Ahmed Suliman
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Muhammad Anwar
- Princess Alexandra Hospital, Hamstel Road, Harlow, CM20 1QX, UK
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, BA2 7AY, UK
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3
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D’Angelo A, Kilili H, Chapman R, Generali D, Tinhofer I, Luminari S, Donati B, Ciarrocchi A, Giannini R, Moretto R, Cremolini C, Pietrantonio F, Sobhani N, Bonazza D, Prins R, Song SG, Jeon YK, Pisignano G, Cinelli M, Bagby S, Urrutia AO. Immune-related pan-cancer gene expression signatures of patient survival revealed by NanoString-based analyses. PLoS One 2023; 18:e0280364. [PMID: 36649303 PMCID: PMC9844904 DOI: 10.1371/journal.pone.0280364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
The immune system plays a central role in the onset and progression of cancer. A better understanding of transcriptional changes in immune cell-related genes associated with cancer progression, and their significance in disease prognosis, is therefore needed. NanoString-based targeted gene expression profiling has advantages for deployment in a clinical setting over RNA-seq technologies. We analysed NanoString PanCancer Immune Profiling panel gene expression data encompassing 770 genes, and overall survival data, from multiple previous studies covering 10 different cancer types, including solid and blood malignancies, across 515 patients. This analysis revealed an immune gene signature comprising 39 genes that were upregulated in those patients with shorter overall survival; of these 39 genes, three (MAGEC2, SSX1 and ULBP2) were common to both solid and blood malignancies. Most of the genes identified have previously been reported as relevant in one or more cancer types. Using Cibersort, we investigated immune cell levels within individual cancer types and across groups of cancers, as well as in shorter and longer overall survival groups. Patients with shorter survival had a higher proportion of M2 macrophages and γδ T cells. Patients with longer overall survival had a higher proportion of CD8+ T cells, CD4+ T memory cells, NK cells and, unexpectedly, T regulatory cells. Using a transcriptomics platform with certain advantages for deployment in a clinical setting, our multi-cancer meta-analysis of immune gene expression and overall survival data has identified a specific transcriptional profile associated with poor overall survival.
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Affiliation(s)
- Alberto D’Angelo
- Department of Life Sciences, University of Bath, Bath, United Kingdom
- Oncology Department, Royal United Hospital, Bath, United Kingdom
- * E-mail:
| | - Huseyin Kilili
- Milner Centre, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Robert Chapman
- Department of Medicine, The Princess Alexandra Hospital, Harlow, United Kingdom
| | - Daniele Generali
- Multidisciplinary Unit of Breast Pathology and Translational Research, Cremona Hospital, Cremona, Italy
| | - Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy, Charite´ University Hospital, Berlin, Germany
| | - Stefano Luminari
- Hematology Unit, Azienda USL-IRCCS, Reggio Emilia, Italy
- Surgical, Medical and Dental Department of Morphological Sciences Related to Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Benedetta Donati
- Translational Research Laboratory, Azienda USL-IRCCS, Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Translational Research Laboratory, Azienda USL-IRCCS, Reggio Emilia, Italy
| | - Riccardo Giannini
- Department of Surgery, Clinical, Molecular and Critical Care Pathology, University of Pisa, Pisa, Italy
| | - Roberto Moretto
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Chiara Cremolini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | | | - Navid Sobhani
- Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Debora Bonazza
- Department of Medical, Surgical and Health Sciences, Cattinara Hospital, University of Trieste, Trieste, Italy
| | - Robert Prins
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Seung Geun Song
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | | | - Mattia Cinelli
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Araxi O. Urrutia
- Milner Centre, Department of Life Sciences, University of Bath, Bath, United Kingdom
- Instituto de Ecologia, UNAM, Ciudad de Mexico, Mexico
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4
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Chapman R, D'Angelo A, Bagby S. Nanopore-based metagenomic sequencing: a diagnostic tool in respiratory tract infection. ERJ Open Res 2022; 8:00461-2022. [PMID: 36545212 PMCID: PMC9761407 DOI: 10.1183/23120541.00461-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022] Open
Abstract
This correspondence highlights the burden of respiratory tract infection and focuses on nanopore sequencing as a promising approach in diagnostics https://bit.ly/3fgs8zg.
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Affiliation(s)
- Robert Chapman
- Princess Alexandra Hospital NHS Trust, Harlow, UK,Robert Chapman ()
| | | | - Stefan Bagby
- Department of Life Sciences, University of Bath, Bath, UK
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5
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D’Angelo A, Shibata K, Tokunaga M, Furutani-Seiki M, Bagby S. Corrigendum to "Generation of murine tumour-reactive T cells by co-culturing murine pancreatic cancer organoids and peripheral blood lymphocytes". Biochem Biophys Rep 2022; 33:101374. [PMID: 36861120 PMCID: PMC9969051 DOI: 10.1016/j.bbrep.2022.101374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
[This corrects the article DOI: 10.1016/j.bbrep.2022.101365.].
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Affiliation(s)
- Alberto D’Angelo
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom,Corresponding author.
| | - Kensuke Shibata
- Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan,Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan,Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan,Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan
| | - Masayuki Tokunaga
- Department of Obstetrics and Gynecology, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Makoto Furutani-Seiki
- Department of Systems Biochemistry in Regeneration and Pathology, Graduate School of Medicine, Yamaguchi University, 755-8505 Yamaguchi, Japan
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom
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D'Angelo A, Shibata K, Tokunaga M, Furutani-Seiki M, Bagby S. Generation of murine tumour-reactive T cells by co-culturing murine pancreatic cancer organoids and peripheral blood lymphocytes. Biochem Biophys Rep 2022; 32:101365. [PMID: 36237445 PMCID: PMC9552097 DOI: 10.1016/j.bbrep.2022.101365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed at a late stage and becomes resistant to several treatments. Significant clinical effects have been reported for cancer immunotherapies on a subset of patients diagnosed with epithelial cancers. Cancer organoid co-culture with autologous peripheral blood lymphocytes offers an innovative immunotherapeutic approach that is increasingly being tested, although there is a lack of cutting-edge platforms enabling the investigation of cancer-T cell interactions for individual patients. In this study, a pancreatic cancer organoid culture from a genetically engineered pancreatic cancer murine model was established and co-cultured with autologous peripheral blood lymphocytes to induce a tumour-specific T cell response to pancreatic cancer. Co-culturing autologous peripheral blood lymphocytes with cancer organoids can be an effective strategy to enrich tumour-reactive T cells from the peripheral blood of murine models; this approach could potentially be transferred to humans. Co-culture of peripheral blood lymphocytes and cancer organoids could provide an unbiased approach to evaluating the sensitivity of tumour cells to T cell-mediated priming on an individual patient level.
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Affiliation(s)
- Alberto D'Angelo
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom,Corresponding author.
| | - Kensuke Shibata
- Department of Biology and Biochemistry, University of Yamaguchi, Ube, Japan
| | - Masayuki Tokunaga
- Department of Biology and Biochemistry, University of Yamaguchi, Ube, Japan
| | | | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom
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Riddell V, Betteridge Z, Bowler E, Chinoy H, Gordon P, Wedderburn L, Bagby S, Mchugh N, Tansley S. P224 Anti-PARP1 as a novel autoantibody in myositis. Rheumatology (Oxford) 2022. [DOI: 10.1093/rheumatology/keac133.223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background/Aims
Idiopathic inflammatory myopathies (IIM) are multisystem diseases characterised by muscle inflammation. Over 60% of patients with IIM have a myositis-related autoantibody. Our laboratory specialises in autoantibody testing. We offer an extended spectrum autoantibody testing diagnostic service and have also screened over 3000 myositis patients enrolled in research studies for the presence of autoantibodies. We noticed a recurring pattern following K562 cell radio-immunoprecipitation that was present in several myositis patient sera and in a handful of samples that came to us via the diagnostic service. We set out to determine the antigenic target of this novel autoantibody.
Methods
We have previously screened 1319 serum/plasma samples from IIM patients enrolled in the UKMyoNet and 380 from patients with juvenile onset IIM enrolled in the JDCBS for autoantibodies by immunoprecipitation. Additional cohorts similarly investigated include >150 healthy control sera and >400 SLE patient sera. Patients with the novel autoantibody of interest were identified by a distinctive 120kDa band associated with a ‘smear’ on autoradiography following K562 cell immunoprecipitation and separation of autoantigens by SDS PAGE. ESI-QTOF mass spectrometry was used to identify the antigenic target in an example serum. Using a commercial anti-PARP1 antibody as a control, western blotting of K562 and PARP1 overexpressed cell lysate was used to confirm the antigenic target in remaining samples of interest. Indirect immunofluorescence was performed on HEp-2 cells according to manufacturers’ instructions.
Results
11 patient samples were identified as having the 120 complex ‘smear’ pattern of interest: six had been received via the diagnostic service and five were enrolled in UKMyoNet. Prevalence in the UKMyoNet cohort was 0.4%. Mass spectrometry identified PARP1 as the antigenic target. This was confirmed in all remaining samples by western blot. Table 1 shows available clinical data.
Conclusion
PARP1 is an autoantigen target in myositis patients in addition to those with other rheumatic diseases. Where data was available, patients with anti-PARP1 had features suggesting an anti-synthetase syndrome phenotype, but this may primarily relate to the other autoantibodies present. Further work is needed to determine the prevalence of anti-PARP1 in other cohorts and its clinical associations.
Disclosure
V. Riddell: Grants/research support; Bath Institute of Rheumatic Disease. Z. Betteridge: None. E. Bowler: None. H. Chinoy: None. P. Gordon: None. L. Wedderburn: None. S. Bagby: None. N. Mchugh: None. S. Tansley: None.
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Affiliation(s)
- Victoria Riddell
- Biology and Biochemistry, University of Bath, Bath, UNITED KINGDOM
| | - Zoe Betteridge
- Pharmacy and Pharmacology, University of Bath, Bath, UNITED KINGDOM
| | - Elizabeth Bowler
- Pharmacy and Pharmacology, University of Bath, Bath, UNITED KINGDOM
| | - Hector Chinoy
- Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UNITED KINGDOM
| | - Patrick Gordon
- NHS Foundation Trust, King's College London, London, UNITED KINGDOM
| | - Lucy Wedderburn
- Infection, Immunity and Inflammation, UCL GOS Institute of Child Health, London, UNITED KINGDOM
- Centre for Adolescent Rheumatology Versus Arthritis, UCL, London, UNITED KINGDOM
| | - Stefan Bagby
- Biology and Biochemistry, University of Bath, Bath, UNITED KINGDOM
| | - Neil Mchugh
- Pharmacy and Pharmacology, University of Bath, Bath, UNITED KINGDOM
| | - Sarah Tansley
- Pharmacy and Pharmacology, University of Bath, Bath, UNITED KINGDOM
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Wallis S, Wolska N, Englert H, Posner M, Upadhyay A, Renné T, Eggleston I, Bagby S, Pula G. A peptide from the staphylococcal protein Efb binds P-selectin and inhibits the interaction of platelets with leukocytes. J Thromb Haemost 2022; 20:729-741. [PMID: 34846792 DOI: 10.1111/jth.15613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/09/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022]
Abstract
AIMS P-selectin is a key surface adhesion molecule for the interaction of platelets with leukocytes. We have shown previously that the N-terminal domain of Staphylococcus aureus extracellular fibrinogen-binding protein (Efb) binds to P-selectin and interferes with platelet-leukocyte aggregate formation. Here, we aimed to identify the minimal Efb motif required for binding platelets and to characterize its ability to interfering with the formation of platelet-leukocyte aggregates. METHODS AND RESULTS Using a library of synthetic peptides, we mapped the platelet-binding site to a continuous 20 amino acid stretch. The peptide Efb68-87 was able to bind to resting and, to a greater extent, thrombin-stimulated platelets in the absence of fibrinogen. Dot blots, pull-down assays and P-selectin glycoprotein ligand-1 (PSGL-1) competitive binding experiments identified P-selectin as the cellular docking site mediating Efb68-87 platelet binding. Accordingly, Efb68-87 did not bind to other blood cells and captured platelets from human whole blood under low shear stress conditions. Efb68-87 did not affect platelet activation as tested by aggregometry, flow cytometry and immunoblotting, but inhibited the formation of platelet-leukocyte aggregates (PLAs). Efb68-87 also interfered with the platelet-dependent stimulation of neutrophil extracellular traps (NETs) formation in vitro. CONCLUSIONS We have identified Efb68-87 as a novel selective platelet-binding peptide. Efb68-87 binds directly to P-selectin and inhibits interactions of platelets with leukocytes that lead to PLA and NET formation. As PLAs and NETs play a key role in thromboinflammation, Efb68-87 is an exciting candidate for the development of novel selective inhibitors of the proinflammatory activity of platelets.
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Affiliation(s)
- Stuart Wallis
- Departments of Biology and Biochemistry, University of Bath, Bath, UK
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Eppendorf - Hamburg, Hamburg, Germany
| | - Nina Wolska
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Eppendorf - Hamburg, Hamburg, Germany
| | - Hanna Englert
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Eppendorf - Hamburg, Hamburg, Germany
| | - Mareike Posner
- Departments of Biology and Biochemistry, University of Bath, Bath, UK
- Department of Life Sciences, Manchester Metropolitan University, Manchester, UK
| | - Abhishek Upadhyay
- Departments of Biology and Biochemistry, University of Bath, Bath, UK
| | - Thomas Renné
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Eppendorf - Hamburg, Hamburg, Germany
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Ian Eggleston
- Department of Pharmacy and Pharmacology, University of Bath, Bath, UK
| | - Stefan Bagby
- Departments of Biology and Biochemistry, University of Bath, Bath, UK
| | - Giordano Pula
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Eppendorf - Hamburg, Hamburg, Germany
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Abrahams JS, Weigand MR, Ring N, MacArthur I, Etty J, Peng S, Williams MM, Bready B, Catalano AP, Davis JR, Kaiser MD, Oliver JS, Sage JM, Bagby S, Tondella ML, Gorringe AR, Preston A. Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis. Microb Genom 2022; 8:000761. [PMID: 35143385 PMCID: PMC8942028 DOI: 10.1099/mgen.0.000761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/11/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial genetic diversity is often described solely using base-pair changes despite a wide variety of other mutation types likely being major contributors. Tandem duplication/amplifications are thought to be widespread among bacteria but due to their often-intractable size and instability, comprehensive studies of these mutations are rare. We define a methodology to investigate amplifications in bacterial genomes based on read depth of genome sequence data as a proxy for copy number. We demonstrate the approach with Bordetella pertussis, whose insertion sequence element-rich genome provides extensive scope for amplifications to occur. Analysis of data for 2430 B. pertussis isolates identified 272 putative amplifications, of which 94 % were located at 11 hotspot loci. We demonstrate limited phylogenetic connection for the occurrence of amplifications, suggesting unstable and sporadic characteristics. Genome instability was further described in vitro using long-read sequencing via the Nanopore platform, which revealed that clonally derived laboratory cultures produced heterogenous populations rapidly. We extended this research to analyse a population of 1000 isolates of another important pathogen, Mycobacterium tuberculosis. We found 590 amplifications in M. tuberculosis, and like B. pertussis, these occurred primarily at hotspots. Genes amplified in B. pertussis include those involved in motility and respiration, whilst in M. tuberuclosis, functions included intracellular growth and regulation of virulence. Using publicly available short-read data we predicted previously unrecognized, large amplifications in B. pertussis and M. tuberculosis. This reveals the unrecognized and dynamic genetic diversity of B. pertussis and M. tuberculosis, highlighting the need for a more holistic understanding of bacterial genetics.
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Affiliation(s)
- Jonathan S. Abrahams
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Michael R. Weigand
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Natalie Ring
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Iain MacArthur
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Joss Etty
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - Scott Peng
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | | | | | | | | | - Stefan Bagby
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
| | - M. Lucia Tondella
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Andrew Preston
- Department of Biology and Biochemistry and Milner Centre for Evolution, University of Bath, Bath, UK
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10
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Ring N, Davies H, Morgan J, Sundaresan M, Tiong A, Preston A, Bagby S. Comparative genomics of Bordetella pertussis isolates from New Zealand, a country with an uncommonly high incidence of whooping cough. Microb Genom 2022; 8:000756. [PMID: 35084300 PMCID: PMC8914352 DOI: 10.1099/mgen.0.000756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/03/2021] [Indexed: 11/18/2022] Open
Abstract
Whooping cough, the respiratory disease caused by Bordetella pertussis, has undergone a wide-spread resurgence over the last several decades. Previously, we developed a pipeline to assemble the repetitive B. pertussis genome into closed sequences using hybrid nanopore and Illumina sequencing. Here, this sequencing pipeline was used to conduct a more high-throughput, longitudinal screen of 66 strains isolated between 1982 and 2018 in New Zealand. New Zealand has a higher incidence of whooping cough than many other countries; usually at least twice as many cases per 100000 people as the USA and UK and often even higher, despite similar rates of vaccine uptake. To the best of our knowledge, these strains are the first New Zealand B. pertussis isolates to be sequenced. The analyses here show that, on the whole, genomic trends in New Zealand B. pertussis isolates, such as changing allelic profile in vaccine-related genes and increasing pertactin deficiency, have paralleled those seen elsewhere in the world. At the same time, phylogenetic comparisons of the New Zealand isolates with global isolates suggest that a number of strains are circulating in New Zealand, which cluster separately from other global strains, but which are closely related to each other. The results of this study add to a growing body of knowledge regarding recent changes to the B. pertussis genome, and are the first genetic investigation into B. pertussis isolates from New Zealand.
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Affiliation(s)
- Natalie Ring
- Department of Biology and Biochemistry, University of Bath, UK
- Roslin Institute, University of Edinburgh, UK
| | - Heather Davies
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - Julie Morgan
- Institute of Environmental Science and Research, Porirua, New Zealand
| | | | - Audrey Tiong
- Institute of Environmental Science and Research, Porirua, New Zealand
| | - Andrew Preston
- Department of Biology and Biochemistry, University of Bath, UK
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath, UK
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11
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Riddell V, Mcmorrow F, Oldroyd A, Deakin C, Lamb J, Chinoy H, Wedderburn L, Bagby S, Mchugh N, Tansley S. POS0288 A KEY TIF1γ EPITOPE MAY FACILITATE THE IDENTIFICATION OF PATIENTS AT HIGHEST RISK OF CANCER ASSOCIATED MYOSITIS. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Background:The myositis specific autoantibody anti-TIF1γ targets TRIM33, a TRIM family proetin with a PHDBromo domain at the C terminal end. Anti-TIF1γ is strongly associated with malignancy in adult patients with idiopathic inflammatory myopathies (IIM). Intriguingly, anti-TIF1γ is also the most common autoantibody in juvenile-onset IIM but younger patients with anti-TIF1γ do not have an increased risk of cancer (1-3). Genetic studies have consistently shown human leukocyte antigen (HLA) to be the strongest risk factor for IIM. Adult and juvenile-onset patients with anti-TIF1γ have recently been shown to have different associations at the HLA-DQB1 locus (4). This could be due to differences in the key TIF1γ epitopes and may relate to differences in aetiology, such as malignancy in adults versus other environmental factors in juvenile onset disease.Objectives:To identify key epitopes targeted by anti-TIF1γ antibody in patients with IIM and establish if different TIF1γ epitopes are targeted in patients with and without malignancy.Methods:Patient plasma/serum samples were obtained from UK Juvenile Dermatomyositis Cohort and Biomarker and UKMyoNet studies. Autoantibody status had previously been determined by immunoprecipitation. Cancer data was collated from the UK Health and Social Care Information Centre and cancer associated IIM (CAM) defined as that occurring within 3 years of IIM diagnosis.An in house ELISA was developed using a purified TIF1γ fragment comprising residues 882-1090, produced in E.coli, corresponding to the PHDBromo protein domain. An ELISA cut-off of 5SD above the mean of 38 healthy control samples was used.Results:38 healthy controls, and 117 anti-TIF1γ IIM patient sera (60 juvenile onset) were analysed for reactivity to the TIF1γ PHDbromo domain.No healthy controls were positive. Anti-TIF1γPHDbromo was more common in JDM: 18 (30%) juvenile patients and 6 (10.5%) adult patients were positive, p=0.01.Additional data was available for 39 adult patients (82% female, median age 52 (IQR 38-64)). Anti-TIF1γPHDbromo was only found in CAM patients plus one young adult non-CAM patient aged 27 years at disease onset, p =0.07 (p=0.02 for patients >30 years at disease onset), see Table 1. No juvenile patients had a history of malignancy.Table 1.Anti-TIF1γPHDbromo in 39 adult patients with cancer data availableanti-TIF1γPHDbromo positiveanti-TIF1γPHDbromo negativeCancer associated myositis n(%)5a (83)12(36)Myositis not associated with cancer n(%)1b(17)21(64)Total633a. Median age 64 yearsb. Age 27 yearsConclusion:The TIF1γ PHDBromo domain is an important epitope and autoantibody reactivity is more common in patients with juvenile-onset disease and adults with CAM. The distinction between adult and juvenile-onset IIM is arbitrary and it is relevant that the only adult with anti-TIF1γPHDbromo not to have malignancy was just 27 years old. Our numbers are small and further work is needed to establish if anti-TIF1γPHDbromo, and indeed other TIF1γ epitopes, could help identify patients at highest risk of malignancy, and how this relates to our understanding of IIM aetiopathogenesis. Our findings may add weight to the theory that the development of IIM in younger patients occurs after immune-mediated resolution of a pre-cancer event.References:[1]Oldroyd A, Sergeant JC, New P et al. The temporal relationship between cancer and adult onset anti-transcriptional intermediary factor 1 antibody-positive dermatomyositis. Rheumatology. 2019;58(4):650-655[2]Tansley SL, Simou S, Shaddick G et al. Autoantibodies in juvenile-onset myositis: Their diagnostic value and associated clinical phenotype in a large UK cohort. J Autoimmun. 2017;84:55-64[3]Fujimoto M, Hamaguchi Y, Kaji K et al. Myositis-specific anti-155/140 autoantibodies target transcription intermediary factor 1 family proteins. Arthritis Rheum. 2012;64(2):513-22.[4]Rothwell S, Chinoy H, Lamb JA et al. Focused HLA analysis in Caucasians with myositis identifies significant associations with autoantibody subgroups. Ann Rheum Dis. 2019;78(7):996-1002.Disclosure of Interests:None declared
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12
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D'Angelo A, Bagby S, Galli IC, Bortoletti C, Roviello G. Overview of the clinical use of erdafitinib as a treatment option for the metastatic urothelial carcinoma: where do we stand. Expert Rev Clin Pharmacol 2020; 13:1139-1146. [PMID: 32935605 DOI: 10.1080/17512433.2020.1823830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Erdafitinib is the first orally administered pan-fibroblast growth factor receptor (FGFR) kinase inhibitor approved by the Food and Drug Administration (FDA). AREAS COVERED Specifically binding to FGFR family (FGFR-1 to FGFR-4), erdafitinib leads to reduced cell signaling and cellular apoptosis. Coupled with the ability to bind to vascular endothelial growth factor 2 (VEGFR-2), KIT, Fms-related tyrosine kinase 4 (FLT4), platelet-derived growth factor receptor α and β (PDGFR-α and PDGFR-β), RET and colony-stimulating factor 1 receptor (CSF-1 R), erdafitinib has further reported antitumor features causing cell killing. EXPERT OPINION In this review, we provide a comprehensive overview of erdafitinib chemical structure, pharmacologic properties, and current knowledge of clinical efficacy in the treatment of locally advanced or metastatic urothelial carcinoma. This treatment, recently approved in the U.S., is available for adult patients harboring FGFR2/FGFR3 genetic alterations who progressed within 12 months of an adjuvant or neoadjuvant chemotherapy regimen including platinum or progressed during or after prior a chemotherapy regimen including platinum.
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Affiliation(s)
- Alberto D'Angelo
- Department of Biology and Biochemistry, University of Bath , Bath, UK
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath , Bath, UK
| | - Ilaria Camilla Galli
- Department of Health Sciences, University of Florence, Section of Pathological Anatomy, University Hospital of Florence , Florence, Italy
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13
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D'Angelo A, Sobhani N, Bagby S, Casadei-Gardini A, Roviello G. Cabozantinib as a second-line treatment option in hepatocellular carcinoma. Expert Rev Clin Pharmacol 2020; 13:623-629. [PMID: 32394749 DOI: 10.1080/17512433.2020.1767591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is one of the most frequent tumors affecting the gastrointestinal tract and a universal cause of morbidity and mortality. Cabozantinib is a strong multi-inhibitor of receptor tyrosine kinases approved for renal cell carcinoma that could be useful also for the treatment of HCC. AREAS COVERED This review describes the chemical structure, the pharmacologic properties and current knowledge of the efficacy of cabozantinib in the treatment of HCC based on data available from first phase and later phase clinical trials. The ongoing studies testing cabozantinib, either alone or in combination with other drugs, are also described. EXPERT OPINION Despite the recent achievements in the use of cabozantinib for patients diagnosed with hepatocellular carcinoma, data are still needed to allow clinicians to make better decisions on how to treat specific patient subgroups.
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Affiliation(s)
- Alberto D'Angelo
- Department of Biology and Biochemistry, University of Bath , Bath, UK
| | - Navid Sobhani
- Department of Medicine, Baylor College , Houston, TX, USA
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath , Bath, UK
| | - Andrea Casadei-Gardini
- Division of Oncology, Department of Medical and Surgical Sciences for Children & Adults, University-Hospital of Modena and Reggio Emilia , Modena, Italy
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14
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Sobhani N, Corona SP, Roviello G, Bagby S, D'Angelo A, Iezzi G, Generali D. Immune-gene signature: a new tool for patient selection for checkpoint inhibitors? Future Oncol 2020; 16:1327-1330. [PMID: 32396404 DOI: 10.2217/fon-2020-0311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Navid Sobhani
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129 Trieste, Italy.,Section of Epidemiology and Population Science, Department of Medicine, Baylor College of Medicine, 77030 Houston, TX, USA
| | - Silvia P Corona
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129 Trieste, Italy
| | - Giandomenico Roviello
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129 Trieste, Italy
| | - Stefan Bagby
- Department of Biology & Biochemistry, University of Bath, BA2-7AX Bath, United Kingdom
| | - Alberto D'Angelo
- Department of Biology & Biochemistry, University of Bath, BA2-7AX Bath, United Kingdom
| | - Giandomenico Iezzi
- Institute for Research in Biomedicine (IRB), Murate Building, Via Murate 5A, 6500 Bellinzona, Switzerland
| | - Daniele Generali
- Department of Medical, Surgery & Health Sciences, University of Trieste, Piazza Ospitale 1, 34129 Trieste, Italy.,Breast Cancer Unit, ASST Cremona, Viale Concordia 1, 26100 Cremona, Italy
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15
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D'Angelo A, Bagby S, Di Pierro G, Chirra M, Nobili S, Mini E, Villari D, Roviello G. An overview of the clinical use of cabozantinib in the treatment of advanced non-clear-cell renal cell carcinoma (NCCRCC). Crit Rev Oncol Hematol 2020; 149:102921. [PMID: 32172222 DOI: 10.1016/j.critrevonc.2020.102921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 10/24/2022] Open
Abstract
Patients diagnosed with non-clear renal cell carcinoma have often been excluded from clinical trials due to the shortage of treatments available, the low incidence of tumours with non-clear histology, and the corresponding diversity of intrinsic molecular features. This approach led to a knowledge gap in finding the optimal treatment for patients diagnosed with non-clear cell renal carcinoma. Cabozantinib, a potent multiple tyrosine kinase receptor inhibitor, has been recently investigated in patients with non-clear cell histologies of renal cell cancer. In this review, we have summarized available data on the use of cabozantinib in non-clear renal cell carcinoma.
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Affiliation(s)
- Alberto D'Angelo
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom.
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, United Kingdom
| | - Giulia Di Pierro
- School of Human Health Sciences, University of Florence, Largo Brambilla 3, 50134, Florence, Italy
| | - Martina Chirra
- Department of Oncology, Medical Oncology Unit, University of Siena, Siena, 53100, Italy
| | - Stefania Nobili
- Department of Health Sciences, University of Florence, Viale Pieraccini, 6, 50139, Florence, Italy
| | - Enrico Mini
- Department of Health Sciences, University of Florence, Viale Pieraccini, 6, 50139, Florence, Italy
| | - Donata Villari
- Department of Urology, University of Florence, Florence, Italy
| | - Giandomenico Roviello
- Department of Health Sciences, University of Florence, Viale Pieraccini, 6, 50139, Florence, Italy
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16
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D’Angelo A, Sobhani N, Roviello G, Bagby S, Bonazza D, Bottin C, Giudici F, Zanconati F, De Manzini N, Guglielmi A, Generali D. Tumour infiltrating lymphocytes and immune-related genes as predictors of outcome in pancreatic adenocarcinoma. PLoS One 2019; 14:e0219566. [PMID: 31381571 PMCID: PMC6681957 DOI: 10.1371/journal.pone.0219566] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/26/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND We investigated the correlation between pancreatic ductal adenocarcinoma patient prognosis and the presence of tumour infiltrating lymphocytes and expression of 521 immune system genes. METHODS Intratumoural CD3+, CD8+, and CD20+ lymphocytes were examined by immunohistochemistry in 12 PDAC patients with different outcomes who underwent pancreaticoduodenectomy. The results were correlated with gene expression profile using the digital multiplexed NanoString nCounter analysis system (NanoString Technologies, Seattle, WA, USA). RESULTS Twenty immune system genes were significantly differentially expressed in patients with a good prognosis relative to patients with a worse prognosis: TLR2 and TLR7 (Toll-like receptor superfamily); CD4, CD37, FOXP3, PTPRC (B cell and T cell signalling); IRF5, IRF8, STAT1, TFE3 (transcription factors); ANP32B, CCND3 (cell cycle); BTK (B cell development); TNF, TNFRF1A (TNF superfamily); HCK (leukocyte function); C1QA (complement system); BAX, PNMA1 (apoptosis); IKBKE (NFκB pathway). Differential expression was more than twice log 2 for TLR7, TNF, C1QA, FOXP3, and CD37. DISCUSSION Tumour infiltrating lymphocytes were present at higher levels in samples from patients with better prognosis. Our findings indicate that tumour infiltrating lymphocyte levels and expression level of the immune system genes listed above influence pancreatic ductal adenocarcinoma prognosis. This information could be used to improve selection of best responders to immune inhibitors.
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Affiliation(s)
- Alberto D’Angelo
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
- Department of Medical, Surgical, & Health Sciences, University of Trieste, Piazza Ospitale, Trieste, Italy
| | - Navid Sobhani
- Department of Medical, Surgical, & Health Sciences, University of Trieste, Piazza Ospitale, Trieste, Italy
- Breast Cancer Unit, ASST Cremona, Cremona, Italy
| | - Giandomenico Roviello
- Department of Medical, Surgical, & Health Sciences, University of Trieste, Piazza Ospitale, Trieste, Italy
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Deborah Bonazza
- Department of Medical Sciences, Ospedale di Cattinara, Università degli Studi di Trieste, Strada di Fiume, Trieste, Italy
| | - Cristina Bottin
- Department of Medical Sciences, Ospedale di Cattinara, Università degli Studi di Trieste, Strada di Fiume, Trieste, Italy
| | - Fabiola Giudici
- Department of Medical Sciences, Ospedale di Cattinara, Università degli Studi di Trieste, Strada di Fiume, Trieste, Italy
| | - Fabrizio Zanconati
- Department of Medical Sciences, Ospedale di Cattinara, Università degli Studi di Trieste, Strada di Fiume, Trieste, Italy
| | - Nicolo De Manzini
- Department of Medical Sciences, Ospedale di Cattinara, Università degli Studi di Trieste, Strada di Fiume, Trieste, Italy
| | - Alessandra Guglielmi
- Department of Medical, Surgical, & Health Sciences, University of Trieste, Piazza Ospitale, Trieste, Italy
| | - Daniele Generali
- Department of Medical, Surgical, & Health Sciences, University of Trieste, Piazza Ospitale, Trieste, Italy
- Breast Cancer Unit, ASST Cremona, Cremona, Italy
- Department of Medical Sciences, Ospedale di Cattinara, Università degli Studi di Trieste, Strada di Fiume, Trieste, Italy
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17
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Abstract
The genome of Bordetella pertussis is complex, with high G+C content and many repeats, each longer than 1000 bp. Long-read sequencing offers the opportunity to produce single-contig B. pertussis assemblies using sequencing reads which are longer than the repetitive sections, with the potential to reveal genomic features which were previously unobservable in multi-contig assemblies produced by short-read sequencing alone. We used an R9.4 MinION flow cell and barcoding to sequence five B. pertussis strains in a single sequencing run. We then trialled combinations of the many nanopore user community-built long-read analysis tools to establish the current optimal assembly pipeline for B. pertussis genome sequences. This pipeline produced closed genome sequences for four strains, allowing visualization of inter-strain genomic rearrangement. Read mapping to the Tohama I reference genome suggests that the remaining strain contains an ultra-long duplicated region (almost 200 kbp), which was not resolved by our pipeline; further investigation also revealed that a second strain that was seemingly resolved by our pipeline may contain an even longer duplication, albeit in a small subset of cells. We have therefore demonstrated the ability to resolve the structure of several B. pertussis strains per single barcoded nanopore flow cell, but the genomes with highest complexity (e.g. very large duplicated regions) remain only partially resolved using the standard library preparation and will require an alternative library preparation method. For full strain characterization, we recommend hybrid assembly of long and short reads together; for comparison of genome arrangement, assembly using long reads alone is sufficient.
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Affiliation(s)
- Natalie Ring
- 1Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Jonathan S Abrahams
- 1Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Miten Jain
- 2UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Hugh Olsen
- 2UC Santa Cruz Genomics Institute, 1156 High Street, Santa Cruz, CA 95064, USA
| | - Andrew Preston
- 1Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
| | - Stefan Bagby
- 1Department of Biology and Biochemistry and the Milner Centre for Evolution, University of Bath, Bath, UK
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18
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Posner MG, Upadhyay A, Ishima R, Kalli AC, Harris G, Kremerskothen J, Sansom MSP, Crennell SJ, Bagby S. Distinctive phosphoinositide- and Ca 2+-binding properties of normal and cognitive performance-linked variant forms of KIBRA C2 domain. J Biol Chem 2018; 293:9335-9344. [PMID: 29724824 PMCID: PMC6005455 DOI: 10.1074/jbc.ra118.002279] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/03/2018] [Indexed: 01/07/2023] Open
Abstract
Kidney- and brain-expressed protein (KIBRA), a multifunctional scaffold protein with around 20 known binding partners, is involved in memory and cognition, organ size control via the Hippo pathway, cell polarity, and membrane trafficking. KIBRA includes tandem N-terminal WW domains, a C2 domain, and motifs for binding atypical PKC and PDZ domains. A naturally occurring human KIBRA variant involving residue changes at positions 734 (Met-to-Ile) and 735 (Ser-to-Ala) within the C2 domain affects cognitive performance. We have elucidated 3D structures and calcium- and phosphoinositide-binding properties of human KIBRA C2 domain. Both WT and variant C2 adopt a canonical type I topology C2 domain fold. Neither Ca2+ nor any other metal ion was bound to WT or variant KIBRA C2 in crystal structures, and Ca2+ titration produced no significant reproducible changes in NMR spectra. NMR and X-ray diffraction data indicate that KIBRA C2 binds phosphoinositides via an atypical site involving β-strands 5, 2, 1, and 8. Molecular dynamics simulations indicate that KIBRA C2 interacts with membranes via primary and secondary sites on the same domain face as the experimentally identified phosphoinositide-binding site. Our results indicate that KIBRA C2 domain association with membranes is calcium-independent and involves distinctive C2 domain-membrane relative orientations.
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Affiliation(s)
- Mareike G. Posner
- From the Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Abhishek Upadhyay
- From the Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15260
| | - Antreas C. Kalli
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, United Kingdom, ,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Gemma Harris
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, United Kingdom
| | - Joachim Kremerskothen
- Internal Medicine D, Department of Nephrology, Hypertension and Rheumatology, University Hospital Münster, D-48149 Münster, Germany, and
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Susan J. Crennell
- From the Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Stefan Bagby
- From the Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom, , To whom correspondence should be addressed. Tel.:
44-1225-386436; Fax:
44-1225-386779; E-mail:
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19
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Alshammari A, Posner MG, Upadhyay A, Marken F, Bagby S, Ilie A. A Modular Bioplatform Based on a Versatile Supramolecular Multienzyme Complex Directly Attached to Graphene. ACS Appl Mater Interfaces 2016; 8:21077-21088. [PMID: 27447357 DOI: 10.1021/acsami.6b05453] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Developing generic strategies for building adaptable or multifunctional bioplatforms is challenging, in particular because protein immobilization onto surfaces often causes loss of protein function and because multifunctionality usually necessitates specific combinations of heterogeneous elements. Here, we introduce a generic, modular bioplatform construction strategy that uses cage-like supramolecular multienzyme complexes as highly adaptable building blocks immobilized directly and noncovalently on graphene. Thermoplasma acidophilum dihydrolipoyl acyltransferase (E2) supramolecular complexes organize as a monolayer or can be controllably transferred onto graphene, preserving their supramolecular form with specific molecular recognition capability and capacity for engineering multifunctionality. This E2-graphene platform can bind enzymes (here, E1, E2's physiological partner) without loss of enzyme function; in this test case, E1 catalytic activity was detected on E2-graphene over 6 orders of magnitude in substrate concentration. The E2-graphene platform can be multiplexed via patterned cotransfer of differently modified E2 complexes. As the E2 complexes are robust and highly customizable, E2-graphene is a platform onto which multiple functionalities can be built.
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Affiliation(s)
- Abeer Alshammari
- Department of Physics, King Saud University , Riyadh 11451, Saudi Arabia
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20
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Zhou Q, Abraham AD, Li L, Babalmorad A, Bagby S, Arcaroli JJ, Hansen RJ, Valeriote FA, Gustafson DL, Schaack J, Messersmith WA, LaBarbera DV. Topoisomerase IIα mediates TCF-dependent epithelial-mesenchymal transition in colon cancer. Oncogene 2016; 35:4990-9. [PMID: 26947016 PMCID: PMC5036162 DOI: 10.1038/onc.2016.29] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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] [Received: 08/21/2015] [Revised: 12/16/2015] [Accepted: 01/06/2016] [Indexed: 12/23/2022]
Abstract
Aberrant T-cell factor (TCF) transcription is implicated in the majority of colorectal cancers (CRCs). TCF transcription induces epithelial–mesenchymal transition (EMT), promoting a tumor-initiating cell (TIC) phenotype characterized by increased proliferation, multidrug resistance (MDR), invasion and metastasis. The data presented herein characterize topoisomerase IIα (TopoIIα) as a required component of TCF transcription promoting EMT. Using chromatin immunoprecipitation (ChIP) and protein co-immunoprecipitation (co-IP) studies, we show that TopoIIα forms protein–protein interactions with β-catentin and TCF4 and interacts with Wnt response elements (WREs) and promoters of direct target genes of TCF transcription, including: MYC, vimentin, AXIN2 and LEF1. Moreover, both TopoIIα and TCF4 ChIP with the N-cadherin promoter, which is a new discovery indicating that TCF transcription may directly regulate N-cadherin expression. TopoIIα N-terminal ATP-competitive inhibitors, exemplified by the marine alkaloid neoamphimedine (neo), block TCF activity in vitro and in vivo. Neo effectively inhibits TopoIIα and TCF4 from binding WREs/promoter sites, whereas protein–protein interactions remain intact. Neo inhibition of TopoIIα-dependent TCF transcription also correlates with significant antitumor effects in vitro and in vivo, including the reversion of EMT, the loss of TIC-mediated clonogenic colony formation, and the loss of cell motility and invasion. Interestingly, non-ATP-competitive inhibitors of TopoIIα, etoposide and merbarone, were ineffective at preventing TopoIIα-dependent TCF transcription. Thus, we propose that TopoIIα participation in TCF transcription may convey a mechanism of MDR to conventional TopoIIα inhibitors. However, our results indicate that TopoIIα N-terminal ATP-binding sites remain conserved and available for drug targeting. This article defines a new strategy for targeted inhibition of TCF transcription that may lead to effective therapies for the treatment of CRC and potentially other Wnt-dependent cancers.
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Affiliation(s)
- Q Zhou
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - A D Abraham
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - L Li
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - A Babalmorad
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - S Bagby
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J J Arcaroli
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - R J Hansen
- Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - F A Valeriote
- Colorado State University, Flint Animal Cancer Center, Fort Collins, CO, USA
| | - D L Gustafson
- Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - J Schaack
- Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Josephine Ford Cancer Center, Henry Ford Health Systems, Detroit, MI, USA
| | - W A Messersmith
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - D V LaBarbera
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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21
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Posner MG, Upadhyay A, Abubaker AA, Fortunato TM, Vara D, Canobbio I, Bagby S, Pula G. Extracellular Fibrinogen-binding Protein (Efb) from Staphylococcus aureus Inhibits the Formation of Platelet-Leukocyte Complexes. J Biol Chem 2015; 291:2764-76. [PMID: 26627825 PMCID: PMC4742742 DOI: 10.1074/jbc.m115.678359] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Indexed: 12/13/2022] Open
Abstract
Extracellular fibrinogen-binding protein (Efb) from Staphylococcus aureus inhibits platelet activation, although its mechanism of action has not been established. In this study, we discovered that the N-terminal region of Efb (Efb-N) promotes platelet binding of fibrinogen and that Efb-N binding to platelets proceeds via two independent mechanisms: fibrinogen-mediated and fibrinogen-independent. By proteomic analysis of Efb-interacting proteins within platelets and confirmation by pulldown assays followed by immunoblotting, we identified P-selectin and multimerin-1 as novel Efb interaction partners. The interaction of both P-selectin and multimerin-1 with Efb is independent of fibrinogen. We focused on Efb interaction with P-selectin. Excess of P-selectin extracellular domain significantly impaired Efb binding by activated platelets, suggesting that P-selectin is the main receptor for Efb on the surface of activated platelets. Efb-N interaction with P-selectin inhibited P-selectin binding to its physiological ligand, P-selectin glycoprotein ligand-1 (PSGL-1), both in cell lysates and in cell-free assays. Because of the importance of P-selectin-PSGL-1 binding in the interaction between platelets and leukocytes, we tested human whole blood and found that Efb abolishes the formation of platelet-monocyte and platelet-granulocyte complexes. In summary, we present evidence that in addition to its documented antithrombotic activity, Efb can play an immunoregulatory role via inhibition of P-selectin-PSGL-1-dependent formation of platelet-leukocyte complexes.
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Affiliation(s)
| | | | | | - Tiago M Fortunato
- Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, United Kingdom and
| | - Dina Vara
- Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, United Kingdom and
| | - Ilaria Canobbio
- the Department of Biology and Biotechnology, University of Pavia, 27100 Pavia PV, Italy
| | - Stefan Bagby
- From the Departments of Biology and Biochemistry and
| | - Giordano Pula
- Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, United Kingdom and
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22
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Porazinski S, Wang H, Asaoka Y, Behrndt M, Miyamoto T, Morita H, Hata S, Sasaki T, Krens SG, Osada Y, Asaka S, Momoi A, Linton S, Miesfeld JB, Link BA, Senga T, Shimizu N, Nagase H, Matsuura S, Bagby S, Kondoh H, Nishina H, Heisenberg CP, Furutani-Seiki M. YAP is essential for tissue tension to ensure vertebrate 3D body shape. Nature 2015; 521:217-221. [PMID: 25778702 PMCID: PMC4720436 DOI: 10.1038/nature14215] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/29/2014] [Indexed: 01/08/2023]
Abstract
Vertebrates have a unique 3D body shape in which correct tissue and organ shape and alignment are essential for function. For example, vision requires the lens to be centred in the eye cup which must in turn be correctly positioned in the head. Tissue morphogenesis depends on force generation, force transmission through the tissue, and response of tissues and extracellular matrix to force. Although a century ago D'Arcy Thompson postulated that terrestrial animal body shapes are conditioned by gravity, there has been no animal model directly demonstrating how the aforementioned mechano-morphogenetic processes are coordinated to generate a body shape that withstands gravity. Here we report a unique medaka fish (Oryzias latipes) mutant, hirame (hir), which is sensitive to deformation by gravity. hir embryos display a markedly flattened body caused by mutation of YAP, a nuclear executor of Hippo signalling that regulates organ size. We show that actomyosin-mediated tissue tension is reduced in hir embryos, leading to tissue flattening and tissue misalignment, both of which contribute to body flattening. By analysing YAP function in 3D spheroids of human cells, we identify the Rho GTPase activating protein ARHGAP18 as an effector of YAP in controlling tissue tension. Together, these findings reveal a previously unrecognised function of YAP in regulating tissue shape and alignment required for proper 3D body shape. Understanding this morphogenetic function of YAP could facilitate the use of embryonic stem cells to generate complex organs requiring correct alignment of multiple tissues.
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Affiliation(s)
- Sean Porazinski
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Huijia Wang
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Yoichi Asaoka
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Martin Behrndt
- IST Austria, Am Campus 1, A-3400 Klosterneuburg, Austria
| | - Tatsuo Miyamoto
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Hitoshi Morita
- IST Austria, Am Campus 1, A-3400 Klosterneuburg, Austria
| | - Shoji Hata
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Takashi Sasaki
- Department of Molecular Biology, School of Medicine, Keio University, Tokyo 160-8582 Japan
| | | | - Yumi Osada
- Japan Science and Technology Agency (JST), ERATO-SORST Kondoh Differentiation Signaling Project, Kyoto, 606-8305, Japan
| | - Satoshi Asaka
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Akihiro Momoi
- Japan Science and Technology Agency (JST), ERATO-SORST Kondoh Differentiation Signaling Project, Kyoto, 606-8305, Japan
| | - Sarah Linton
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Joel B. Miesfeld
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Brian A. Link
- Department of Cell Biology, Neurobiology, and Anatomy, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Takeshi Senga
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Nobuyoshi Shimizu
- Department of Molecular Biology, School of Medicine, Keio University, Tokyo 160-8582 Japan
| | - Hideaki Nagase
- Matrix Biology Section, Kennedy Institute of Rheumatology, University of Oxford, Oxford, OX3 7FY, UK
| | - Shinya Matsuura
- Department of Genetics and Cell Biology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Hisato Kondoh
- Japan Science and Technology Agency (JST), ERATO-SORST Kondoh Differentiation Signaling Project, Kyoto, 606-8305, Japan
- Graduate School of Frontier Bioscience, Osaka University, Osaka 565-0871, Japan
| | - Hiroshi Nishina
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | | | - Makoto Furutani-Seiki
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
- Japan Science and Technology Agency (JST), ERATO-SORST Kondoh Differentiation Signaling Project, Kyoto, 606-8305, Japan
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23
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Nettleship JE, Watson PJ, Rahman-Huq N, Fairall L, Posner MG, Upadhyay A, Reddivari Y, Chamberlain JMG, Kolstoe SE, Bagby S, Schwabe JWR, Owens RJ. Transient expression in HEK 293 cells: an alternative to E. coli for the production of secreted and intracellular mammalian proteins. Methods Mol Biol 2015; 1258:209-22. [PMID: 25447866 DOI: 10.1007/978-1-4939-2205-5_11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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] [Indexed: 06/04/2023]
Abstract
Transient transfection of human embryonic kidney cells (HEK 293) enables the rapid and affordable lab-scale production of recombinant proteins. In this chapter protocols for the expression and purification of both secreted and intracellular proteins using transient expression in HEK 293 cells are described.
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Affiliation(s)
- Joanne E Nettleship
- OPPF-UK, Research Complex at Harwell, R92 Rutherford Appleton Laboratories, Harwell Oxford, Didcot, OX11 0FA, UK,
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24
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Borziak K, Posner MG, Upadhyay A, Danson MJ, Bagby S, Dorus S. Comparative genomic analysis reveals 2-oxoacid dehydrogenase complex lipoylation correlation with aerobiosis in archaea. PLoS One 2014; 9:e87063. [PMID: 24489835 PMCID: PMC3904984 DOI: 10.1371/journal.pone.0087063] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Accepted: 12/18/2013] [Indexed: 02/04/2023] Open
Abstract
Metagenomic analyses have advanced our understanding of ecological microbial diversity, but to what extent can metagenomic data be used to predict the metabolic capacity of difficult-to-study organisms and their abiotic environmental interactions? We tackle this question, using a comparative genomic approach, by considering the molecular basis of aerobiosis within archaea. Lipoylation, the covalent attachment of lipoic acid to 2-oxoacid dehydrogenase multienzyme complexes (OADHCs), is essential for metabolism in aerobic bacteria and eukarya. Lipoylation is catalysed either by lipoate protein ligase (LplA), which in archaea is typically encoded by two genes (LplA-N and LplA-C), or by a lipoyl(octanoyl) transferase (LipB or LipM) plus a lipoic acid synthetase (LipA). Does the genomic presence of lipoylation and OADHC genes across archaea from diverse habitats correlate with aerobiosis? First, analyses of 11,826 biotin protein ligase (BPL)-LplA-LipB transferase family members and 147 archaeal genomes identified 85 species with lipoylation capabilities and provided support for multiple ancestral acquisitions of lipoylation pathways during archaeal evolution. Second, with the exception of the Sulfolobales order, the majority of species possessing lipoylation systems exclusively retain LplA, or either LipB or LipM, consistent with archaeal genome streamlining. Third, obligate anaerobic archaea display widespread loss of lipoylation and OADHC genes. Conversely, a high level of correspondence is observed between aerobiosis and the presence of LplA/LipB/LipM, LipA and OADHC E2, consistent with the role of lipoylation in aerobic metabolism. This correspondence between OADHC lipoylation capacity and aerobiosis indicates that genomic pathway profiling in archaea is informative and that well characterized pathways may be predictive in relation to abiotic conditions in difficult-to-study extremophiles. Given the highly variable retention of gene repertoires across the archaea, the extension of comparative genomic pathway profiling to broader metabolic and homeostasis networks should be useful in revealing characteristics from metagenomic datasets related to adaptations to diverse environments.
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Affiliation(s)
- Kirill Borziak
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Mareike G. Posner
- Department of Biology & Biochemistry, University of Bath, Claverton Down, United Kingdom
| | - Abhishek Upadhyay
- Department of Biology & Biochemistry, University of Bath, Claverton Down, United Kingdom
| | - Michael J. Danson
- Department of Biology & Biochemistry, University of Bath, Claverton Down, United Kingdom
- Centre for Extremophile Research, University of Bath, Claverton Down, United Kingdom
| | - Stefan Bagby
- Department of Biology & Biochemistry, University of Bath, Claverton Down, United Kingdom
- * E-mail: (SB); (SD)
| | - Steve Dorus
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
- * E-mail: (SB); (SD)
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25
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Webb C, Upadhyay A, Giuntini F, Eggleston I, Furutani-Seiki M, Ishima R, Bagby S. Structural Features and Ligand Binding Properties of Tandem WW Domains from YAP and TAZ, Nuclear Effectors of the Hippo Pathway. Biochemistry 2011; 50:3300-9. [DOI: 10.1021/bi2001888] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | | | | | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
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26
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Clark EA, Crennell S, Upadhyay A, Zozulya AV, Mackay JD, Svergun DI, Bagby S, van den Elsen JM. A structural basis for Staphylococcal complement subversion: X-ray structure of the complement-binding domain of Staphylococcus aureus protein Sbi in complex with ligand C3d. Mol Immunol 2011; 48:452-62. [PMID: 21055811 PMCID: PMC3025320 DOI: 10.1016/j.molimm.2010.09.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2010] [Revised: 09/28/2010] [Accepted: 09/30/2010] [Indexed: 01/07/2023]
Abstract
The structure of the complement-binding domain of Staphylococcus aureus protein Sbi (Sbi-IV) in complex with ligand C3d is presented. The 1.7Å resolution structure reveals the molecular details of the recognition of thioester-containing fragment C3d of the central complement component C3, involving interactions between residues of Sbi-IV helix α2 and the acidic concave surface of C3d. The complex provides a structural basis for the binding preference of Sbi for native C3 over C3b and explains how Sbi-IV inhibits the interaction between C3d and complement receptor 2. A second C3d binding site on Sbi-IV is identified in the crystal structure that is not observed in related S. aureus C3 inhibitors Efb-C and Ehp. This binding mode perhaps hints as to how Sbi-IV, as part of Sbi, forms a C3b-Sbi adduct and causes futile consumption of C3, an extraordinary aspect of Sbi function that is not shared by any other known Staphylococcal complement inhibitor.
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Affiliation(s)
- Elizabeth A. Clark
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Susan Crennell
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Abhishek Upadhyay
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | | | - Julia D. Mackay
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | | | - Stefan Bagby
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom
| | - Jean M.H. van den Elsen
- University of Bath, Department of Biology and Biochemistry, Claverton Down, Bath BA2 7AY, United Kingdom,Corresponding author. Tel.: +44 1225 383639; fax: +44 1225 386779.
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Jones RT, Sanchez-Contreras M, Vlisidou I, Amos MR, Yang G, Muñoz-Berbel X, Upadhyay A, Potter UJ, Joyce SA, Ciche TA, Jenkins ATA, Bagby S, Ffrench-Constant RH, Waterfield NR. Photorhabdus adhesion modification protein (Pam) binds extracellular polysaccharide and alters bacterial attachment. BMC Microbiol 2010; 10:141. [PMID: 20462430 PMCID: PMC2878306 DOI: 10.1186/1471-2180-10-141] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 05/12/2010] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Photorhabdus are Gram-negative nematode-symbiotic and insect-pathogenic bacteria. The species Photorhabdus asymbiotica is able to infect humans as well as insects. We investigated the secreted proteome of a clinical isolate of P. asymbiotica at different temperatures in order to identify proteins relevant to the infection of the two different hosts. RESULTS A comparison of the proteins secreted by a clinical isolate of P. asymbiotica at simulated insect (28 degrees C) and human (37 degrees C) temperatures led to the identification of a small and highly abundant protein, designated Pam, that is only secreted at the lower temperature. The pam gene is present in all Photorhabdus strains tested and shows a high level of conservation across the whole genus, suggesting it is both ancestral to the genus and probably important to the biology of the bacterium. The Pam protein shows limited sequence similarity to the 13.6 kDa component of a binary toxin of Bacillus thuringiensis. Nevertheless, injection or feeding of heterologously produced Pam showed no insecticidal activity to either Galleria mellonella or Manduca sexta larvae. In bacterial colonies, Pam is associated with an extracellular polysaccharide (EPS)-like matrix, and modifies the ability of wild-type cells to attach to an artificial surface. Interestingly, Surface Plasmon Resonance (SPR) binding studies revealed that the Pam protein itself has adhesive properties. Although Pam is produced throughout insect infection, genetic knockout does not affect either insect virulence or the ability of P. luminescens to form a symbiotic association with its host nematode, Heterorhabditis bacteriophora. CONCLUSIONS We studied a highly abundant protein, Pam, which is secreted in a temperature-dependent manner in P. asymbiotica. Our findings indicate that Pam plays an important role in enhancing surface attachment in insect blood. Its association with exopolysaccharide suggests it may exert its effect through mediation of EPS properties. Despite its abundance and conservation in the genus, we find no evidence for a role of Pam in either virulence or symbiosis.
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Affiliation(s)
- Robert T Jones
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA27AY, UK
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Isenman DE, Leung E, Mackay JD, Bagby S, van den Elsen JMH. Mutational analyses reveal that the staphylococcal immune evasion molecule Sbi and complement receptor 2 (CR2) share overlapping contact residues on C3d: implications for the controversy regarding the CR2/C3d cocrystal structure. J Immunol 2010; 184:1946-55. [PMID: 20083651 DOI: 10.4049/jimmunol.0902919] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We recently characterized an interaction between the Staphylococcus aureus immune evasion molecule Staphylococcus aureus binder of Ig (Sbi) and complement C3, an interaction mediated primarily through the binding of C3d(g) to Sbi domain IV. Events related to these studies prompted us to investigate via mutagenesis the binding interface of C3d for Sbi domain IV (Sbi-IV), as well as to revisit the controversial issue of the complement receptor 2 (CR2) binding site of C3d. Specifically, we had shown that Sbi domains III and IV fragment binding to C3dg inhibited the latter's binding to CR2. Moreover, a published cocrystal structure of C3d bound to complement inhibitory C-terminal domain of extracellular fibrinogen-binding protein (Efb-C), a structural and functional homolog of Sbi-IV, showed Efb-C binding to a region on the concave face of C3d previously implicated in CR2 binding by our mutagenesis data but not confirmed in the CR2(short consensus repeat [SCR]1-2):C3d cocrystal structure. We have now analyzed by surface plasmon resonance the binding of a series of variant C3dg molecules to biosensor-bound Sbi-IV or CR2(SCR1-2). We found that mutations to the concave face acidic pocket of C3d significantly affected binding to both Sbi-IV and CR2, although there was divergence in which residues were most important in each case. By contrast, no binding defects were seen for mutations made to the sideface of C3d implicated from the cocrystal structure to be involved in binding CR2(SCR1-2). The results with Sbi-IV suggest a mode of binding highly similar to that visualized in the Efb-C:C3d complex. The results with CR2 confirm our earlier mapping studies and cast even further doubt on the physiologic relevance of the complex visualized in the C3d:CR2 cocrystal.
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Affiliation(s)
- David E Isenman
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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29
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Posner MG, Upadhyay A, Bagby S, Hough DW, Danson MJ. A unique lipoylation system in the Archaea. Lipoylation in Thermoplasma acidophilum requires two proteins. FEBS J 2009; 276:4012-22. [PMID: 19594830 DOI: 10.1111/j.1742-4658.2009.07110.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Members of the 2-oxoacid dehydrogenase multienzyme complex family play a key role in the pathways of central metabolism. Post-translational lipoylation of the dihydrolipoyl acyltransferase component of these complexes is essential for their activity, the lipoyllysine moiety performing the transfer of substrates and intermediates between the different active sites within these multienzyme systems. We have previously shown that the thermophilic archaeon, Thermoplasma acidophilum, has a four-gene cluster encoding the components of such a complex, which, when recombinantly expressed in Escherichia coli, can be assembled into an active multienzyme in vitro. Crucially, the E. coli host carries out the required lipoylation of the archaeal dihydrolipoyl acyltransferase component. Because active 2-oxoacid dehydrogenase multienzyme complexes have never been detected in any archaeon, the question arises as to whether Archaea possess a functional lipoylation system. In this study, we report the cloning and heterologous expression of two genes from Tp. acidophilum whose protein products together show significant sequence identity with the single lipoate protein ligase enzyme of bacteria. We demonstrate that both recombinantly expressed Tp. acidophilum proteins are required for lipoylation of the acyltransferase, and that the two proteins associate together to carry out this post-translational modification. From the published DNA sequences, we suggest the presence of functional transcriptional and translational regulatory elements, and furthermore we present preliminary evidence that lipoylation occurs in vivo in Tp. acidophilum. This is the first report of the lipoylation machinery in the Archaea, which is unique in that the catalytic activity is dependent on two separate gene products.
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31
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van den Elsen J, Upadhyay A, Burman J, Leung E, Clark E, Isenman D, Bagby S. Structure–function analysis of the novel Staphylococcus aureus immune subversion protein Sbi. Mol Immunol 2008. [DOI: 10.1016/j.molimm.2008.08.071] [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: 11/29/2022]
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Upadhyay A, Burman JD, Clark EA, Leung E, Isenman DE, van den Elsen JMH, Bagby S. Structure-function analysis of the C3 binding region of Staphylococcus aureus immune subversion protein Sbi. J Biol Chem 2008; 283:22113-20. [PMID: 18550524 PMCID: PMC2494919 DOI: 10.1074/jbc.m802636200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Revised: 05/19/2008] [Indexed: 11/11/2022] Open
Abstract
Among the recently discovered Staphylococcus aureus immune evasion proteins, Sbi is unique in its ability to interact with components of both the adaptive and innate immune systems of the host. Sbi domains I and II (Sbi-I and Sbi-II) bind IgG. Sbi domain IV (residues 198-266) binds the central complement protein C3. When linked to Sbi-III, Sbi-IV induces a futile consumption of complement via alternative pathway activation, whereas isolated Sbi-IV specifically inhibits the alternative pathway without complement consumption. Here we have determined the three-dimensional structure of Sbi-IV by NMR spectroscopy, showing that Sbi-IV adopts a three-helix bundle fold similar to those of the S. aureus complement inhibitors Efb-C, Ehp, and SCIN. The (1)H-(15)N HSQC spectrum of Sbi-III indicates that this domain, essential for futile complement consumption, is natively unfolded, at least when isolated from the rest of Sbi. Sbi-IV and Sbi-III-IV both bind C3dg with 1:1 stoichiometry and submicromolar affinity. Despite low overall sequence identity, Sbi possesses the same residues as Efb at two positions essential for Efb-C binding to C3d. Mutation to alanine of either of these residues, Arg-231 and Asn-238, abolishes both Sbi-IV binding to C3dg and Sbi-IV alternative pathway inhibition. The almost complete conservation of Sbi-III and Sbi-IV amino acid sequences across more than 30 strains isolated from human and animal hosts indicates that the unique mechanism of Sbi in complement system subversion is a feature of infections of both humans and economically important animals.
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Affiliation(s)
- Abhishek Upadhyay
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
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Burman JD, Leung E, Atkins KL, O'Seaghdha MN, Lango L, Bernadó P, Bagby S, Svergun DI, Foster TJ, Isenman DE, van den Elsen JMH. Interaction of human complement with Sbi, a staphylococcal immunoglobulin-binding protein: indications of a novel mechanism of complement evasion by Staphylococcus aureus. J Biol Chem 2008; 283:17579-93. [PMID: 18434316 DOI: 10.1074/jbc.m800265200] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Staphylococcal immunoglobulin-binding protein, Sbi, is a 436-residue protein produced by many strains of Staphylococcus aureus. It was previously characterized as being cell surface-associated and having binding capacity for human IgG and beta(2)-glycoprotein I. Here we show using small angle x-ray scattering that the proposed extracellular region of Sbi (Sbi-E) is an elongated molecule consisting of four globular domains, two immunoglobulin-binding domains (I and II) and two novel domains (III and IV). We further show that together domains III and IV (Sbi-III-IV), as well as domain IV on its own (Sbi-IV), bind complement component C3 via contacts involving both the C3dg fragment and the C3a anaphylatoxin domain. Preincubation of human serum with either Sbi-E or Sbi-III-IV is inhibitory to all complement pathways, whereas domain IV specifically inhibits the alternative pathway. Monitoring C3 activation in serum incubated with Sbi fragments reveals that Sbi-E and Sbi-III-IV both activate the alternative pathway, leading to consumption of C3. By contrast, inhibition of this pathway by Sbi-IV does not involve C3 consumption. The observation that Sbi-E activates the alternative pathway is counterintuitive to intact Sbi being cell wall-associated, as recruiting complement to the surface of S. aureus would be deleterious to the bacterium. Upon re-examination of this issue, we found that Sbi was not associated with the cell wall fraction, but rather was found in the growth medium, consistent with it being an excreted protein. As such, our data suggest that Sbi helps mediate bacterial evasion of complement via a novel mechanism, namely futile fluid-phase consumption.
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Affiliation(s)
- Julia D Burman
- Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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Atkins KL, Burman JD, Chamberlain ES, Cooper JE, Poutrel B, Bagby S, Jenkins ATA, Feil EJ, van den Elsen JMH. S. aureus IgG-binding proteins SpA and Sbi: host specificity and mechanisms of immune complex formation. Mol Immunol 2007; 45:1600-11. [PMID: 18061675 DOI: 10.1016/j.molimm.2007.10.021] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2007] [Revised: 10/03/2007] [Accepted: 10/04/2007] [Indexed: 10/22/2022]
Abstract
The evasion of the host immune response is central to the pathogenicity of Staphylococcus aureus, and is facilitated by the ability of the cell wall-associated protein A (SpA) to bind immunoglobulin G Fc fragments, thereby impeding phacocytosis and classical pathway complement fixation. SpA also acts as a B-cell superantigen through interactions with the heavy-chain variable part of Fab fragments, and sequesters immunoglobulins by forming large insoluble immune complexes with human IgG. Here we show that the formation of insoluble immune complexes is mediated by the binding of (VH3+) Fab fragments in addition to Fc, and that SpA forms soluble complexes with IgG Fc fragments. We compared these results with those for Sbi, a second staphylococcal immunoglobulin-binding protein, and note that this protein requires only the Fc fragment for precipitation with human IgG. Homology models of immunoglobulin-binding domains of SpA and Sbi in complex with Fc reveal the molecular basis of the Fab-independent formation of insoluble complexes by Sbi. Finally, we compared the sequences of the spa and sbi genes from human strains to those infecting a range of animal hosts to determine whether Sbi and SpA have acquired specificity for host IgG. We note remarkable sequence conservation within the IgG-binding domains of these genes, consistent with a lack of host specificity. The Fab-independent binding of IgG by Sbi could have significant clinical implications. The use of SpA in immunoadsorption therapy can cause severe side-effects, thought to be mediated by Fc gamma R recognition and complement fixation. The formation of insoluble immune complexes with Sbi occurs only via Fc binding and free Fc regions are unlikely to be available for Fc gamma R recognition and complement fixation.
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Affiliation(s)
- Karen L Atkins
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
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Wright AJ, Higginbottom A, Philippe D, Upadhyay A, Bagby S, Read RC, Monk PN, Partridge LJ. Characterisation of receptor binding by the chemotaxis inhibitory protein of Staphylococcus aureus and the effects of the host immune response. Mol Immunol 2007; 44:2507-17. [PMID: 17258808 PMCID: PMC2646901 DOI: 10.1016/j.molimm.2006.12.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 12/17/2006] [Indexed: 11/26/2022]
Abstract
The chemotaxis inhibitory protein of Staphylococcus aureus (CHIPS) is reported to bind to the receptors for C5a and formylated peptides and has been proposed as a promising lead for the development of new anti-inflammatory compounds. Here we have examined the receptor specificity and mode of action of recombinant CHIPS28–149 and also the immune response to CHIPS28–149 in patients with S. aureus infections and in uninfected controls. Recombinant CHIPS28–149 bound with high affinity to the human C5a receptor (C5aR), but had low affinity for the second C5a receptor, C5L2, and the formyl peptide receptor, FPR. Although ligand binding to C5aR was potently inhibited, CHIPS28–149 had much weaker effects on ligand binding to C5L2 and FPR. Similarly, CHIPS28–149 potently inhibited the ligand-induced activation of C5aR but was less potent at inhibition via FPR. NMR studies showed that CHIPS28–149 bound directly to the N-terminus of C5aR but not C5L2, and CHIPS28–149 residues involved in the interaction were identified by chemical shift analysis. All human sera examined contained high titres of IgG and IgA reactivity against CHIPS28–149, and no correlation was observed between infection status at the time of serum collection and antibody titre. Individual serum samples promoted or inhibited the binding of CHIPS28–149 to C5aR, or had no effect. IgG depletion of serum samples abrogated the effects on CHIPS binding, demonstrating that these were antibody mediated. Sera from infected individuals were more likely to inhibit CHIPS28–149 binding than sera from healthy controls. However, high antibody titres correlated well with both inhibition and enhancement of CHIPS28–149 binding to C5aR; this suggests that the inhibitory effect relates to epitope specificity rather than greater antibody binding. We conclude that CHIPS is likely to be too immunogenic to be used as an anti-inflammatory treatment but that some antibodies against CHIPS may be useful in the treatment of S. aureus infections.
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Affiliation(s)
- Andrew J. Wright
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - Adrian Higginbottom
- School of Medicine and Biomedical Science, University of Sheffield, Sheffield S10 2RX, UK
| | - Didier Philippe
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Abhishek Upadhyay
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Stefan Bagby
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Robert C. Read
- School of Medicine and Biomedical Science, University of Sheffield, Sheffield S10 2RX, UK
| | - Peter N. Monk
- School of Medicine and Biomedical Science, University of Sheffield, Sheffield S10 2RX, UK
- Corresponding author. Tel.: +44 114 226 1312; fax: +44 114 226 1201.
| | - Lynda J. Partridge
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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Abstract
Explaining the apparent non-random codon distribution and the nature and number of amino acids in the 'standard' genetic code remains a challenge, despite the various hypotheses so far proposed. In this paper we propose a simple new hypothesis for code evolution involving a progression from singlet to doublet to triplet codons with a reading mechanism that moves three bases each step. We suggest that triplet codons gradually evolved from two types of ambiguous doublet codons, those in which the first two bases of each three-base window were read ('prefix' codons) and those in which the last two bases of each window were read ('suffix' codons). This hypothesis explains multiple features of the genetic code such as the origin of the pattern of four-fold degenerate and two-fold degenerate triplet codons, the origin of its error minimising properties, and why there are only 20 amino acids.
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Affiliation(s)
- Huan-Lin Wu
- Department of Biology and Biochemistry, University of Bath, 4 South, Claverton Down, Bath BA2 7AY, UK
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Miles JH, Takahashi TN, Bagby S, Sahota PK, Vaslow DF, Wang CH, Hillman RE, Farmer JE. Essential versus complex autism: Definition of fundamental prognostic subtypes. Am J Med Genet A 2005; 135:171-80. [PMID: 15887228 DOI: 10.1002/ajmg.a.30590] [Citation(s) in RCA: 174] [Impact Index Per Article: 9.2] [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: 11/06/2022]
Abstract
Heterogeneity within the autism diagnosis obscures the genetic basis of the disorder and impedes our ability to develop effective treatments. We found that by using two readily available tests, autism can be divided into two subgroups, "essential autism" and "complex autism," with different outcomes and recurrence risks. Complex autism consists of individuals in whom there is evidence of some abnormality of early morphogenesis, manifested by either significant dysmorphology or microcephaly. The remainder have "essential autism." From 1995 to 2001, 260 individuals who met DSM-IV criteria for autistic disorder were examined. Five percent (13/260) were microcephalic and 16% (41/260) had significant physical anomalies. Individually, each trait predicted a poorer outcome. Together they define the "complex autism" subgroup, comprising 20% (46/233) of the total autism population. Individuals with complex autism have lower IQs (P=0.006), more seizures (P=0.0008), more abnormal EEGs (46% vs. 30%), more brain abnormalities by MRI (28% vs. 13%). Everyone with an identifiable syndrome was in the complex group. Essential autism defines the more heritable group with higher sib recurrence (4% vs. 0%), more relatives with autism (20% vs. 9%), and higher male to female ratio (6.5:1 vs. 3.2:1). Their outcome was better with higher IQs (P=0.02) and fewer seizures (P=0.0008). They were more apt to develop autism with a regressive onset (43% vs. 23%, P=0.02). Analysis of the features predictive of poor outcome (IQ<55, functionally non-verbal) showed that microcephaly was 100% specific but only 14% sensitive; the presence of physical anomalies was 86% specific and 34% sensitive. The two tests combined yielded 87% specificity, 47% sensitivity, and an odds ratio of 4.8:1 for poor outcome. Separating essential from complex autism should be the first diagnostic step for children with autism spectrum disorders as it allows better prognostication and counseling. Definition of more homogeneous populations should increase power of research analyses.
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Affiliation(s)
- J H Miles
- The Children's Hospital at the University of Missouri-Columbia, Columbia, Missouri 65212, USA.
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38
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Williams C, Galyov EE, Bagby S. solution structure, backbone dynamics, and interaction with Cdc42 of Salmonella guanine nucleotide exchange factor SopE2. Biochemistry 2004; 43:11998-2008. [PMID: 15379540 DOI: 10.1021/bi0490744] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [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] [Indexed: 11/30/2022]
Abstract
SopE and SopE2 are delivered by the Salmonella type III secretion system into eukaryotic cells to promote cell invasion. SopE and SopE2 are potent guanine nucleotide exchange factors (GEFs) for Rho GTPases Cdc42 and Rac1 and constitute a novel class of Rho GEFs. Although the sequence of SopE-like GEFs is not at all homologous to those of the Dbl homology domain-containing eukaryotic GEFs, the mechanism of nucleotide release seems to have significant similarities. We have determined the solution structure of the catalytic domain (residues 69-240) of SopE2, showing that SopE2(69-240) comprises two three-helix bundles (alpha1alpha4alpha5 and alpha2alpha3alpha6) arranged in a Lambda shape. Compared to the crystal structure of SopE(78-240) in complex with Cdc42, SopE2(69-240) exhibits a less open Lambda shape due to movement of SopE(78-240) helices alpha2 and alpha5 to accommodate binding to the Cdc42 switch regions. In an NMR titration to investigate the SopE2(69-240)-Cdc42 interaction, the SopE2(69-240) residues affected by binding Cdc42 were very similar to the SopE(78-240) residues that contact Cdc42 in the SopE(78-240)-Cdc42 complex. Analysis of the backbone (15)N dynamics of SopE2(69-240) revealed flexibility in residues that link the two three-helix bundles, including the alpha3-alpha4 linker that incorporates a beta-hairpin and the catalytic loop, and the alpha5-alpha6 loop, and flexibility in residues involved in interaction with Cdc42. Together, these observations provide experimental evidence of a previously proposed mechanism of GEF-mediated nucleotide exchange based on the Rac1-Tiam1 complex structure, with SopE/E2 flexibility, particularly in the interbundle loops, enabling conformational rearrangements of the nucleotide binding region of Cdc42 through an induced fit type of binding. Such flexibility in SopE/E2 may also facilitate interaction through adaptive binding with alternative target proteins such as Rab5, allograft inflammatory factor 1, and apolipoprotein A-1.
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39
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Wood MW, Williams C, Upadhyay A, Gill AC, Philippe DL, Galyov EE, van den Elsen JMH, Bagby S. Structural analysis of Salmonella enterica effector protein SopD. Biochim Biophys Acta 2004; 1698:219-26. [PMID: 15134655 DOI: 10.1016/j.bbapap.2003.12.003] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2003] [Revised: 11/28/2003] [Accepted: 12/01/2003] [Indexed: 10/26/2022]
Abstract
Salmonella outer protein D (SopD) is a type III secreted virulence effector protein from Salmonella enterica. Full-length SopD and SopD lacking 16 amino acids at the N-terminus (SopDDeltaN) have been expressed as fusions with GST in Escherichia coli, purified with a typical yield of 20-30 mg per litre of cell culture and crystallized. Biophysical characterization has been carried out mainly on SopDDeltaN. Analytical size exclusion chromatography shows that SopDDeltaN is monomeric and probably globular in aqueous solution. The secondary structure composition, calculated from the CD spectrum, is mixed (38% alpha-helix and 26% beta-strand). Sequence analysis indicates that SopD contains a coiled coil motif, as found in numerous other type III secretion system-associated proteins. This suggests that SopD has the potential for one or more heterotypic protein-protein interactions. Limited trypsin digestion of SopDDeltaN, monitored by both one-dimensional proton NMR spectroscopy and SDS-PAGE, shows that the protein has a large, protease-resistant core domain of 286 amino acid residues. This single-domain architecture suggests that SopD lacks a cognate chaperone. In crystallization trials, SopDDeltaN produced better crystals than either full-length SopD or trypsin-digested SopDDeltaN. Diffraction to 3.0 A resolution has so far been obtained from crystals of SopDDeltaN.
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Affiliation(s)
- Michael W Wood
- Division of Environmental Microbiology, Institute for Animal Health, Compton Laboratory, Berkshire RG20 7NN, UK
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40
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Wu HL, Williams C, Upadhyay A, Galyov EE, Bagby S. Assignment of the 1H, 13C and 15N resonances of the catalytic domain of guanine nucleotide exchange factor BopE from Burkholderia pseudomallei. J Biomol NMR 2004; 29:215-216. [PMID: 15014239 DOI: 10.1023/b:jnmr.0000019244.41446.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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41
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Upadhyay A, Williams C, Gill AC, Philippe DL, Davis K, Taylor LA, Stevens MP, Galyov EE, Bagby S. Biophysical characterization of the catalytic domain of guanine nucleotide exchange factor BopE from Burkholderia pseudomallei. Biochim Biophys Acta 2004; 1698:111-9. [PMID: 15063321 DOI: 10.1016/j.bbapap.2003.11.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2003] [Revised: 10/28/2003] [Accepted: 11/04/2003] [Indexed: 10/26/2022]
Abstract
BopE is a type III secreted protein from Burkholderia pseudomallei, the aetiological agent of melioidosis. Like its Salmonella homologues SopE and SopE2, BopE is a guanine nucleotide exchange factor for Rho GTPases. It is thought that, in order to be secreted by the type III system, proteins must be unfolded or only partially folded. As part of a study of B. pseudomallei virulence proteins, we have expressed, purified and characterized the catalytic domain of BopE (amino acids 78-261). Analytical ultracentrifugation experiments in conjunction with analytical size exclusion chromatography show that BopE(78-261) is monomeric in aqueous solution. CD spectroscopy indicates that the protein is predominantly alpha-helical, with predicted secondary structure composition of 59% alpha-helix and 7% beta-strand. NMR spectroscopy confirms that BopE(78-261) adopts a single, stable conformation. In differential scanning calorimetry experiments, thermal denaturation of BopE(78-261) (T(m) 52 degrees C) is reversible. Also, the secondary structure composition of BopE(78-261) changes little over a range of pH values from 3.5 to 10.5. BopE may therefore fold spontaneously to a functional form upon secretion into the host cell cytoplasm, and retains a native or native-like fold in varied environments. These properties are likely to be advantageous for a secreted bacterial effector protein.
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Affiliation(s)
- Abhishek Upadhyay
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
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42
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Williams C, Galyov EE, Bagby S. Assignment of the 1H, 13C and 15N resonances of the catalytic domain of guanine nucleotide exchange factor SopE2 from Salmonella dublin. J Biomol NMR 2003; 26:379-380. [PMID: 12815267 DOI: 10.1023/a:1024057108445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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Affiliation(s)
- Tapas K Mal
- Department of Medical Biophysics, Ontario Cancer Institute, University of Toronto, Toronto, ON, Canada
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44
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Abstract
The N-terminal domain of protein S, a Greek key calcium-binding protein from Myxococcus xanthus, forms an atypical molten globule in the calcium-free state. The structure of this state is characterized by significant conformational fluctuations, which are localized to a subdomain that is not contiguous along the polypeptide chain. The conformational instability of this subdomain appears to arise from repulsive electrostatic interactions of four acidic side chains that are clustered together but are removed from the calcium-binding sites. This domain can be induced to form a native-like state through two different routes, calcium binding or reduction of pH. Acid-induced folding stabilizes the locally unfolded subdomain by selectively removing repulsive interactions without significantly affecting global stability. In contrast, calcium binding appears to increase local stability indirectly by causing global stabilization.
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Affiliation(s)
- X F Qi
- Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Ontario, Canada
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45
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Affiliation(s)
- S Bagby
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, United Kingdom
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46
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Abstract
TATA box binding protein (TBP)-promoter interaction nucleates assembly of the RNA polymerase II transcription initiation complex. Transcription factor IIA (TFIIA) stabilizes the TBP-promoter complex whereas the N-terminal domain of the largest TAF(II) inhibits TBP-promoter interaction. We have mapped the interaction sites on TBP of Drosophila TAF(II)230 and yeast TFIIA (comprising two subunits, TOA1 and TOA2), using nuclear magnetic resonance (NMR), and also report structural evidence that subdomain II of the TAF(II)230 N-terminal inhibitory domain and TFIIA have overlapping binding sites on the convex surface of TBP. Together with previous mutational and biochemical data, our NMR results indicate that subdomain II augments subdomain I-mediated inhibition of TBP function by blocking TBP-TFIIA interaction.
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Affiliation(s)
- S Bagby
- Division of Molecular Biology, Ontario Cancer Institute, Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, Ont., Canada
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Bagby S, Arrowsmith CH, Ikura M. New perceptions of transcription factor properties from NMR. Biochem Cell Biol 1999; 76:368-78. [PMID: 9923706 DOI: 10.1139/bcb-76-2-3-368] [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: 11/22/2022] Open
Abstract
The complementarity of NMR and X-ray crystallography for biomacromolecular studies has been particularly evident in analysis of transcription factor structures and interactions. While X-ray crystallography can be used to tackle relatively complicated structural problems including multicomponent (three and higher) complexes, NMR studies have provided new insights into the nature of protein-DNA and protein-protein interactions that would be difficult to obtain by other biophysical methods. We describe herein some of the novel and important information recently derived from NMR studies of transcription factors.
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Affiliation(s)
- S Bagby
- Ontario Cancer Institute, and Department of Medical Biophysics, University of Toronto, Canada
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48
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Liu D, Ishima R, Tong KI, Bagby S, Kokubo T, Muhandiram DR, Kay LE, Nakatani Y, Ikura M. Solution structure of a TBP-TAF(II)230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP. Cell 1998; 94:573-83. [PMID: 9741622 DOI: 10.1016/s0092-8674(00)81599-8] [Citation(s) in RCA: 182] [Impact Index Per Article: 7.0] [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: 11/23/2022]
Abstract
General transcription factor TFIID consists of TATA box-binding protein (TBP) and TBP-associated factors (TAF(II)s), which together play a central role in both positive and negative regulation of transcription. The N-terminal region of the 230 kDa Drosophila TAF(II) (dTAF(II)230) binds directly to TBP and inhibits TBP binding to the TATA box. We report here the solution structure of the complex formed by dTAF(II)230 N-terminal region (residues 11-77) and TBP. dTAF(II)230(11-77) comprises three alpha helices and a beta hairpin, forming a core that occupies the concave DNA-binding surface of TBP. The TBP-binding surface of dTAF(II)230 markedly resembles the minor groove surface of the partially unwound TATA box in the TBP-TATA complex. This protein mimicry of the TATA element surface provides the structural basis of the mechanism by which dTAF(II)230 negatively controls the TATA box-binding activity within the TFIID complex.
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Affiliation(s)
- D Liu
- Department of Medical Biophysics, University of Toronto, Ontario, Canada
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49
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Hayashi F, Ishima R, Liu D, Tong KI, Kim S, Reinberg D, Bagby S, Ikura M. Human general transcription factor TFIIB: conformational variability and interaction with VP16 activation domain. Biochemistry 1998; 37:7941-51. [PMID: 9609687 DOI: 10.1021/bi9801098] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [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] [Indexed: 02/07/2023]
Abstract
Human TFIIB, an essential factor in transcription of protein-coding genes by RNA polymerase II, consists of an amino-terminal zinc binding domain (TFIIBn) connected by a linker of about 60 residues to a carboxy-terminal core domain (TFIIBc). The TFIIB core domain has two internally repeated motifs, each comprising five alpha-helices arranged as in the cyclin box. Compared to the crystal structure of TFIIBc in complex with TBP and a TATA-containing oligonucleotide, the NMR-derived solution structure of free TFIIBc is more compact, with a different repeat-repeat orientation and a significantly shorter first helix in the second repeat. Analysis of backbone 15N relaxation parameters indicates the presence of relatively large amplitude, nanosecond time-scale motions in the TFIIBc interrepeat linker and structural fluctuations throughout the backbone. Interaction of TFIIBc with the acidic activation domain of VP16 or with TFIIBn induces 1H-15N chemical shift and line width changes concentrated in the first repeat, interrepeat linker and the first helix of the second repeat. These results suggest that TFIIB is somewhat pliable and that the conformation of the C-terminal core domain can be modulated by interaction with the N-terminal zinc binding domain. Furthermore, binding of the VP16 activation domain may promote TFIIBc conformations primed for binding to a TBP-DNA complex.
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Affiliation(s)
- F Hayashi
- Division of Molecular and Structural Biology, Ontario Cancer Institute, University of Toronto, Canada
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50
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Abstract
The complementarity of NMR and X-ray crystallography for biomacromolecular studies has been particularly evident in analysis of transcription factor structures and interactions. While X-ray crystallography can be used to tackle relatively complicated structural problems including multicomponent (three and higher) complexes, NMR studies have provided new insights into the nature of protein-DNA and protein-protein interactions that would be difficult to obtain by other biophysical methods. We describe herein some of the novel and important information recently derived from NMR studies of transcription factors.Key words: protein-DNA interaction, protein-protein interaction, induced folding, conformational fluctuations, transcriptional regulation.
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