1
|
Middleton A, Niemiec E, Prainsack B, Bobe J, Farley L, Steed C, Smith J, Bevan P, Bonhomme N, Kleiderman E, Thorogood A, Schickhardt C, Garattini C, Vears D, Littler K, Banner N, Scott E, Kovalevskaya NV, Levin E, Morley KI, Howard HC. 'Your DNA, Your Say': global survey gathering attitudes toward genomics: design, delivery and methods. Per Med 2018; 15:311-318. [PMID: 29856292 DOI: 10.2217/pme-2018-0032] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [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: 01/13/2023]
Abstract
Our international study, 'Your DNA, Your Say', uses film and an online cross-sectional survey to gather public attitudes toward the donation, access and sharing of DNA information. We describe the methodological approach used to create an engaging and bespoke survey, suitable for translation into many different languages. We address some of the particular challenges in designing a survey on the subject of genomics. In order to understand the significance of a genomic result, researchers and clinicians alike use external databases containing DNA and medical information from thousands of people. We ask how publics would like their 'anonymous' data to be used (or not to be used) and whether they are concerned by the potential risks of reidentification; the results will be used to inform policy.
Collapse
Affiliation(s)
- Anna Middleton
- Society & Ethics Research, Connecting Science, Wellcome Genome Campus, Cambridge, UK.,Faculty of Education, University of Cambridge, Cambridge, UK
| | - Emilia Niemiec
- Centre for Research Ethics & Bioethics, Uppsala University, Uppsala, Sweden
| | - Barbara Prainsack
- Department of Global Health & Social Medicine, King's College London, London, UK
| | - Jason Bobe
- Department of Genetics & Genomic Sciences, Icahn Institute, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Lauren Farley
- Society & Ethics Research, Connecting Science, Wellcome Genome Campus, Cambridge, UK
| | - Claire Steed
- Web Team, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - James Smith
- Web Team, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Paul Bevan
- Web Team, Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Natasha Bonhomme
- Expecting Health, Genetic Alliance, Washington, DC 20008-2369, USA
| | - Erika Kleiderman
- Centre of Genomics & Policy, McGill University, Montreal, Quebec, Canada
| | - Adrian Thorogood
- Centre of Genomics & Policy, McGill University, Montreal, Quebec, Canada
| | - Christoph Schickhardt
- Department of Medical Oncology, National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Danya Vears
- Department of Public Health & Primary Care, Centre for Biomedical Ethics & Law, KU Leuven, Leuven, Belgium
| | | | | | - Erick Scott
- Department of Genetics & Genomic Sciences, Icahn Institute, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | | | - Elissa Levin
- Policy & Clinical Affairs, Helix OpCo LLC, San Francisco, CA 94158, USA
| | - Katherine I Morley
- Society & Ethics Research, Connecting Science, Wellcome Genome Campus, Cambridge, UK.,National Addiction Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.,Centre for Epidemiology & Biostatistics, Melbourne School of Global & Population Health, The University of Melbourne, Melbourne, Australia
| | - Heidi C Howard
- Society & Ethics Research, Connecting Science, Wellcome Genome Campus, Cambridge, UK.,Centre for Research Ethics & Bioethics, Uppsala University, Uppsala, Sweden
| |
Collapse
|
2
|
Bokhovchuk FM, Bate N, Kovalevskaya NV, Goult BT, Spronk CAEM, Vuister GW. The Structural Basis of Calcium-Dependent Inactivation of the Transient Receptor Potential Vanilloid 5 Channel. Biochemistry 2018; 57:2623-2635. [DOI: 10.1021/acs.biochem.7b01287] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fedir M. Bokhovchuk
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Neil Bate
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Nadezda V. Kovalevskaya
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Benjamin T. Goult
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| | - Chris A. E. M. Spronk
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
- JSC Spronk, Vilnius, Lithuania
| | - Geerten W. Vuister
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, United Kingdom
| |
Collapse
|
3
|
Abstract
It is generally acknowledged that, for reproducibility and progress of human genomic research, data sharing is critical. For every sharing transaction, a successful data exchange is produced between a data consumer and a data provider. Providers of human genomic data (e.g., publicly or privately funded repositories and data archives) fulfil their social contract with data donors when their shareable data conforms to FAIR (findable, accessible, interoperable, reusable) principles. Based on our experiences via Repositive (https://repositive.io), a leading discovery platform cataloguing all shared human genomic datasets, we propose guidelines for data providers wishing to maximise their shared data's FAIRness.
Collapse
Affiliation(s)
- Manuel Corpas
- Repositive Ltd, Betjeman House, Cambridge, United Kingdom
- * E-mail:
| | | | | | | |
Collapse
|
4
|
Kovalevskaya NV, Whicher C, Richardson TD, Smith C, Grajciarova J, Cardama X, Moreira J, Alexa A, McMurray AA, Nielsen FGG. DNAdigest and Repositive: Connecting the World of Genomic Data. PLoS Biol 2016; 14:e1002418. [PMID: 27011302 PMCID: PMC4807091 DOI: 10.1371/journal.pbio.1002418] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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] [Indexed: 11/18/2022] Open
Abstract
There is no unified place where genomics researchers can search through all available raw genomic data in a way similar to OMIM for genes or Uniprot for proteins. With the recent increase in the amount of genomic data that is being produced and the ever-growing promises of precision medicine, this is becoming more and more of a problem. DNAdigest is a charity working to promote efficient sharing of human genomic data to improve the outcome of genomic research and diagnostics for the benefit of patients. Repositive, a social enterprise spin-out of DNAdigest, is building an online platform that indexes genomic data stored in repositories and thus enables researchers to search for and access a range of human genomic data sources through a single, easy-to-use interface, free of charge. This Community Page article introduces the charity DNAdigest, which aims to promote best practices for ethical and efficient genomic data sharing, and the free online community platform Repositive, for easy search and access to genomic datasets.
Collapse
Affiliation(s)
- Nadezda V. Kovalevskaya
- DNAdigest, Future Business Centre, Cambridge, United Kingdom
- Repositive Ltd, Future Business Centre, Cambridge, United Kingdom
| | | | | | - Craig Smith
- DNAdigest, Future Business Centre, Cambridge, United Kingdom
- Repositive Ltd, Future Business Centre, Cambridge, United Kingdom
| | - Jana Grajciarova
- Repositive Ltd, Future Business Centre, Cambridge, United Kingdom
| | - Xocas Cardama
- Repositive Ltd, Future Business Centre, Cambridge, United Kingdom
| | - José Moreira
- Repositive Ltd, Future Business Centre, Cambridge, United Kingdom
| | - Adrian Alexa
- Repositive Ltd, Future Business Centre, Cambridge, United Kingdom
| | | | - Fiona G. G. Nielsen
- DNAdigest, Future Business Centre, Cambridge, United Kingdom
- Repositive Ltd, Future Business Centre, Cambridge, United Kingdom
- * E-mail:
| |
Collapse
|
5
|
Abstract
DNAdigest's mission is to investigate and address the issues hindering efficient and ethical genomic data sharing in the human genomics research community. We conducted contextual interviews with human genomics researchers in clinical, academic or industrial R&D settings about their experience with accessing and sharing human genomic data. The qualitative interviews were followed by an online survey which provided quantitative support for our findings. Here we present the generalised workflow for accessing human genomic data through both public and restricted-access repositories and discuss reported points of frustration and their possible improvements. We discuss how data discoverability and accessibility are lacking in current mechanisms and how these are the prerequisites for adoption of best practices in the research community. We summarise current initiatives related to genomic data discovery and present a new data discovery platform available at http://nucleobase.co.uk.
Collapse
Affiliation(s)
- Tempest A van Schaik
- DNAdigest, Future Business Centre, Kings Hedges Road, Cambridge CB4 2HY, United Kingdom
| | | | - Elena Protopapas
- DNAdigest, Future Business Centre, Kings Hedges Road, Cambridge CB4 2HY, United Kingdom
| | - Hamza Wahid
- DNAdigest, Future Business Centre, Kings Hedges Road, Cambridge CB4 2HY, United Kingdom
| | - Fiona G G Nielsen
- DNAdigest, Future Business Centre, Kings Hedges Road, Cambridge CB4 2HY, United Kingdom
| |
Collapse
|
6
|
Kovalevskaya NV, van de Waterbeemd M, Bokhovchuk FM, Bate N, Bindels RJM, Hoenderop JGJ, Vuister GW. Structural analysis of calmodulin binding to ion channels demonstrates the role of its plasticity in regulation. Pflugers Arch 2013; 465:1507-19. [PMID: 23609407 DOI: 10.1007/s00424-013-1278-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/18/2013] [Accepted: 04/02/2013] [Indexed: 12/17/2022]
Abstract
The Ca²⁺-binding protein calmodulin (CaM) is a well-known regulator of ion-channel activity. Consequently, the Protein Data Bank contains many structures of CaM in complex with different fragments of ion channels that together display a variety of binding modes. In addition to the canonical interaction, in which CaM engages its target with both its domains, many of the ion-channel-CaM complexes demonstrate alternative non-canonical binding modes that depend on the target and experimental conditions. Based on these findings, several mechanisms of ion-channel regulation by CaM have been proposed, all exploiting its plasticity and flexibility in interacting with its targets. In this review, we focus on complexes of CaM with either the voltage-gated calcium channels; the voltage-gated sodium channels or the small conductance calcium-activated potassium channels, for which both structural and functional data are available. For each channel, the functional relevance of these structural data and possible mechanism of calcium-dependent (in)activation and/or facilitation are discussed in detail.
Collapse
Affiliation(s)
- Nadezda V Kovalevskaya
- Department of Physiology, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Geert Grooteplein Zuid 26-28, Nijmegen, 6525, GA, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
7
|
Tudpor K, Laínez S, Kwakernaak AJ, Kovalevskaya NV, Verkaart S, van Genesen S, van der Kemp A, Navis G, Bindels RJM, Hoenderop JGJ. Urinary plasmin inhibits TRPV5 in nephrotic-range proteinuria. J Am Soc Nephrol 2012; 23:1824-34. [PMID: 23024298 DOI: 10.1681/asn.2011111126] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Urinary proteins that leak through the abnormal glomerulus in nephrotic syndrome may affect tubular transport by interacting with membrane transporters on the luminal side of tubular epithelial cells. Patients with nephrotic syndrome can develop nephrocalcinosis, which animal models suggest may develop from impaired transcellular Ca(2+) reabsorption via TRPV5 in the distal convoluted tubule (DCT). In nephrotic-range proteinuria, filtered plasminogen reaches the luminal side of DCT, where it is cleaved into active plasmin by urokinase. In this study, we found that plasmin purified from the urine of patients with nephrotic-range proteinuria inhibits Ca(2+) uptake in TRPV5-expressing human embryonic kidney 293 cells through the activation of protease-activated receptor-1 (PAR-1). Preincubation with a plasmin inhibitor, a PAR-1 antagonist, or a protein kinase C (PKC) inhibitor abolished the effect of plasmin on TRPV5. In addition, ablation of the PKC phosphorylation site S144 rendered TRPV5 resistant to the action of plasmin. Patch-clamp experiments showed that a decreased TRPV5 pore size and a reduced open probability accompany the plasmin-mediated reduction in Ca(2+) uptake. Furthermore, high-resolution nuclear magnetic resonance spectroscopy demonstrated specific interactions between calmodulin and residues 133-154 of the N-terminus of TRPV5 for both wild-type and phosphorylated (S144pS) peptides. In summary, PAR-1 activation by plasmin induces PKC-mediated phosphorylation of TRPV5, thereby altering calmodulin-TRPV5 binding, resulting in decreased channel activity. These results indicate that urinary plasmin could contribute to the downstream effects of proteinuria on the tubulointerstitium by negatively modulating TRPV5.
Collapse
Affiliation(s)
- Kukiat Tudpor
- Department of Physiology, Nijmegen Centre for Molecular Life Sciences, Radboud University, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Kovalevskaya NV, Bokhovchuk FM, Vuister GW. The TRPV5/6 calcium channels contain multiple calmodulin binding sites with differential binding properties. ACTA ACUST UNITED AC 2012; 13:91-100. [PMID: 22354706 PMCID: PMC3375010 DOI: 10.1007/s10969-012-9128-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [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: 08/31/2011] [Accepted: 02/02/2012] [Indexed: 11/26/2022]
Abstract
The epithelial Ca2+ channels TRPV5/6 (transient receptor potential vanilloid 5/6) are thoroughly regulated in order to fine-tune the amount of Ca2+ reabsorption. Calmodulin has been shown to be involved into calcium-dependent inactivation of TRPV5/6 channels by binding directly to the distal C-terminal fragment of the channels (de Groot et al. in Mol Cell Biol 31:2845–2853, 12). Here, we investigate this binding in detail and find significant differences between TRPV5 and TRPV6. We also identify and characterize in vitro four other CaM binding fragments of TRPV5/6, which likely are also involved in TRPV5/6 channel regulation. The five CaM binding sites display diversity in binding modes, binding stoichiometries and binding affinities, which may fine-tune the response of the channels to varying Ca2+-concentrations.
Collapse
Affiliation(s)
- Nadezda V Kovalevskaya
- Department of Protein Biophysics, IMM, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
| | | | | |
Collapse
|
9
|
Kovalevskaya NV, Schilderink N, Vuister GW. Expression and purification of the C-terminal fragments of TRPV5/6 channels. Protein Expr Purif 2011; 80:28-33. [DOI: 10.1016/j.pep.2011.05.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 05/25/2011] [Accepted: 05/26/2011] [Indexed: 02/02/2023]
|
10
|
Breukels V, Konijnenberg A, Nabuurs SM, Doreleijers JF, Kovalevskaya NV, Vuister GW. Overview on the use of NMR to examine protein structure. Curr Protoc Protein Sci 2011; Chapter 17:Unit17.5. [PMID: 21488042 DOI: 10.1002/0471140864.ps1705s64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Any protein structure determination process contains several steps, starting from obtaining a suitable sample, then moving on to acquiring data and spectral assignment, and lastly to the final steps of structure determination and validation. This unit describes all of these steps, starting with the basic physical principles behind NMR and some of the most commonly measured and observed phenomena such as chemical shift, scalar and residual coupling, and the nuclear Overhauser effect. Then, in somewhat more detail, the process of spectral assignment and structure elucidation is explained. Furthermore, the use of NMR to study protein-ligand interaction, protein dynamics, or protein folding is described.
Collapse
Affiliation(s)
- Vincent Breukels
- Protein Biophysics, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
| | | | | | | | | | | |
Collapse
|