1
|
Nadeu F, Royo R, Massoni-Badosa R, Playa-Albinyana H, Garcia-Torre B, Duran-Ferrer M, Dawson KJ, Kulis M, Diaz-Navarro A, Villamor N, Melero JL, Chapaprieta V, Dueso-Barroso A, Delgado J, Moia R, Ruiz-Gil S, Marchese D, Giró A, Verdaguer-Dot N, Romo M, Clot G, Rozman M, Frigola G, Rivas-Delgado A, Baumann T, Alcoceba M, González M, Climent F, Abrisqueta P, Castellví J, Bosch F, Aymerich M, Enjuanes A, Ruiz-Gaspà S, López-Guillermo A, Jares P, Beà S, Capella-Gutierrez S, Gelpí JL, López-Bigas N, Torrents D, Campbell PJ, Gut I, Rossi D, Gaidano G, Puente XS, Garcia-Roves PM, Colomer D, Heyn H, Maura F, Martín-Subero JI, Campo E. Detection of early seeding of Richter transformation in chronic lymphocytic leukemia. Nat Med 2022; 28:1662-1671. [PMID: 35953718 PMCID: PMC9388377 DOI: 10.1038/s41591-022-01927-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 07/01/2022] [Indexed: 02/06/2023]
Abstract
Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. We characterized the whole genome, epigenome and transcriptome, combined with single-cell DNA/RNA-sequencing analyses and functional experiments, of 19 cases of CLL developing RT. Studying 54 longitudinal samples covering up to 19 years of disease course, we uncovered minute subclones carrying genomic, immunogenetic and transcriptomic features of RT cells already at CLL diagnosis, which were dormant for up to 19 years before transformation. We also identified new driver alterations, discovered a new mutational signature (SBS-RT), recognized an oxidative phosphorylation (OXPHOS)high–B cell receptor (BCR)low-signaling transcriptional axis in RT and showed that OXPHOS inhibition reduces the proliferation of RT cells. These findings demonstrate the early seeding of subclones driving advanced stages of cancer evolution and uncover potential therapeutic targets for RT. Single-cell genomic and transcriptomic analyses of longitudinal samples of patients with Richter syndrome reveal the presence and dynamics of clones driving transformation from chronic lymphocytic leukemia years before clinical manifestation
Collapse
Affiliation(s)
- Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Romina Royo
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Ramon Massoni-Badosa
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Heribert Playa-Albinyana
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Beatriz Garcia-Torre
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Martí Duran-Ferrer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Marta Kulis
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ander Diaz-Navarro
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Neus Villamor
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Vicente Chapaprieta
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | | | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Riccardo Moia
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Sara Ruiz-Gil
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ariadna Giró
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Núria Verdaguer-Dot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Mónica Romo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Guillem Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maria Rozman
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | | | - Alfredo Rivas-Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Tycho Baumann
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Miguel Alcoceba
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Marcos González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Biología Molecular e Histocompatibilidad, IBSAL-Hospital Universitario, Centro de Investigación del Cáncer-IBMCC (USAL-CSIC), Salamanca, Spain
| | - Fina Climent
- Hospital Universitari de Bellvitge-Institut d'Investigació Biomédica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Pau Abrisqueta
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Josep Castellví
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Francesc Bosch
- Department of Hematology, Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Marta Aymerich
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain
| | - Anna Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Sílvia Ruiz-Gaspà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Armando López-Guillermo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Pedro Jares
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Sílvia Beà
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | | | - Josep Ll Gelpí
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Núria López-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - David Torrents
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Davide Rossi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Pablo M Garcia-Roves
- Universitat de Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Dolors Colomer
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Hospital Clínic of Barcelona, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Francesco Maura
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - José I Martín-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Universitat de Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain. .,Hospital Clínic of Barcelona, Barcelona, Spain. .,Universitat de Barcelona, Barcelona, Spain.
| |
Collapse
|
2
|
Royo R, Magnano L, Delgado J, Ruiz-Gil S, Gelpí JL, Heyn H, Taylor MA, Stankovic T, Puente XS, Nadeu F, Campo E. ATM germline variants in a young adult with chronic lymphocytic leukemia: 8 years of genomic evolution. Blood Cancer J 2022; 12:90. [PMID: 35672297 PMCID: PMC9174185 DOI: 10.1038/s41408-022-00686-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 01/14/2023] Open
Affiliation(s)
- Romina Royo
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Laura Magnano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
| | - Julio Delgado
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hospital Clínic of Barcelona, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Sara Ruiz-Gil
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Josep Ll Gelpí
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Malcom A Taylor
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, UK
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, UK
| | - Xose S Puente
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - Ferran Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Elías Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
- Hospital Clínic of Barcelona, Barcelona, Spain.
- Universitat de Barcelona, Barcelona, Spain.
| |
Collapse
|
3
|
López-Ferrando V, Gazzo A, de la Cruz X, Orozco M, Gelpí JL. PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update. Nucleic Acids Res 2019; 45:W222-W228. [PMID: 28453649 PMCID: PMC5793831 DOI: 10.1093/nar/gkx313] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [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: 02/19/2017] [Accepted: 04/18/2017] [Indexed: 12/18/2022] Open
Abstract
We present here a full update of the PMut predictor, active since 2005 and with a large acceptance in the field of predicting Mendelian pathological mutations. PMut internal engine has been renewed, and converted into a fully featured standalone training and prediction engine that not only powers PMut web portal, but that can generate custom predictors with alternative training sets or validation schemas. PMut Web portal allows the user to perform pathology predictions, to access a complete repository of pre-calculated predictions, and to generate and validate new predictors. The default predictor performs with good quality scores (MCC values of 0.61 on 10-fold cross validation, and 0.42 on a blind test with SwissVar 2016 mutations). The PMut portal is freely accessible at http://mmb.irbbarcelona.org/PMut. A complete help and tutorial is available at http://mmb.irbbarcelona.org/PMut/help.
Collapse
Affiliation(s)
- Víctor López-Ferrando
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Joint Program BSC-CRG-IRB Research Program for Computational Biology, Barcelona, Spain
| | - Andrea Gazzo
- Joint Program BSC-CRG-IRB Research Program for Computational Biology, Barcelona, Spain.,Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Barcelona. Spain
| | - Xavier de la Cruz
- Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Modesto Orozco
- Joint Program BSC-CRG-IRB Research Program for Computational Biology, Barcelona, Spain.,Institute for Research in Biomedicine (IRB) Barcelona, The Barcelona Institute of Science and Technology, Barcelona. Spain.,Dept. of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
| | - Josep Ll Gelpí
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Joint Program BSC-CRG-IRB Research Program for Computational Biology, Barcelona, Spain.,Dept. of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
| |
Collapse
|
4
|
Jiménez RC, Kuzak M, Alhamdoosh M, Barker M, Batut B, Borg M, Capella-Gutierrez S, Chue Hong N, Cook M, Corpas M, Flannery M, Garcia L, Gelpí JL, Gladman S, Goble C, González Ferreiro M, Gonzalez-Beltran A, Griffin PC, Grüning B, Hagberg J, Holub P, Hooft R, Ison J, Katz DS, Leskošek B, López Gómez F, Oliveira LJ, Mellor D, Mosbergen R, Mulder N, Perez-Riverol Y, Pergl R, Pichler H, Pope B, Sanz F, Schneider MV, Stodden V, Suchecki R, Svobodová Vařeková R, Talvik HA, Todorov I, Treloar A, Tyagi S, van Gompel M, Vaughan D, Via A, Wang X, Watson-Haigh NS, Crouch S. Four simple recommendations to encourage best practices in research software. F1000Res 2017; 6. [PMID: 28751965 PMCID: PMC5490478 DOI: 10.12688/f1000research.11407.1] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2017] [Indexed: 12/24/2022] Open
Abstract
Scientific research relies on computer software, yet software is not always developed following practices that ensure its quality and sustainability. This manuscript does not aim to propose new software development best practices, but rather to provide simple recommendations that encourage the adoption of existing best practices. Software development best practices promote better quality software, and better quality software improves the reproducibility and reusability of research. These recommendations are designed around Open Source values, and provide practical suggestions that contribute to making research software and its source code more discoverable, reusable and transparent. This manuscript is aimed at developers, but also at organisations, projects, journals and funders that can increase the quality and sustainability of research software by encouraging the adoption of these recommendations.
Collapse
Affiliation(s)
| | - Mateusz Kuzak
- Netherlands eScience Center, Science Park 140, Amsterdam, 1098 XG, Netherlands
| | - Monther Alhamdoosh
- CSL Limited, Bio21 Institute, 30 Flemington Road, Parkville, Victoria, 3010, Australia
| | - Michelle Barker
- National eResearch Collaboration Tools and Resources, Victoria, 3010, Australia
| | - Bérénice Batut
- ELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Mikael Borg
- ELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden
| | - Salvador Capella-Gutierrez
- ELIXIR-ES, Spanish National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, Madrid, 28029, Spain
| | - Neil Chue Hong
- Software Sustainability Institute, JCMB, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Martin Cook
- ELIXIR Hub, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Manuel Corpas
- Repositive Ltd, Future Business Centre, Cambridge, UK
| | - Madison Flannery
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Leyla Garcia
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Josep Ll Gelpí
- Barcelona Supercomputing Center, Barcelona, 08034, Spain.,Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, 08028, Spain
| | - Simon Gladman
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Carole Goble
- ELIXIR-UK, Software Sustainability Institute, School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | | | | | - Philippa C Griffin
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Björn Grüning
- ELIXIR-DE and de.NBI, Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Jonas Hagberg
- ELIXIR-SE, National Bioinformatics Infrastructure Sweden (NBIS), Scilifelab, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden
| | - Petr Holub
- BBMRI-ERIC, Neue Stiftingtalstraße 2/B/6, Graz, 8010, Austria
| | - Rob Hooft
- Dutch TechCenter for Life Sciences and ELIXIR-NL, Utrecht, Netherlands
| | - Jon Ison
- ELIXIR-DK, Technical University of Denmark, Denmark, Denmark
| | - Daniel S Katz
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,School of Information Sciences, University of Illinois Urbana Champaign, Urbana, IL, USA.,Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, Urbana, IL, USA.,Department of Computer Science, University of Illinois Urbana Champaign, Urbana, IL, USA
| | - Brane Leskošek
- ELIXIR-SI, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | | | | | - David Mellor
- Center for Open Science, Charlottesville, VA, USA
| | | | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Robert Pergl
- ELIXIR-CZ, Faculty of Information Technology, Czech Technical University in Prague, Prague, Czech Republic
| | - Horst Pichler
- BBMRI.at, Alpen-Adria-University Klagenfurt, Klagenfurt, Austria
| | - Bernard Pope
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Ferran Sanz
- GRIB, Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Universitat Pompeu Fabra, Barcelona, Spain
| | - Maria V Schneider
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia
| | - Victoria Stodden
- School of Information Sciences, University of Illinois Urbana Champaign, Urbana, IL, USA
| | - Radosław Suchecki
- School of Agriculture, Food & Wine, University of Adelaide, Adelaide, Australia
| | - Radka Svobodová Vařeková
- Central European Institute of Technology (CEITEC), Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Harry-Anton Talvik
- ELIXIR-EE, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ilian Todorov
- Science & Technologies Facilities Council, Swindon, UK
| | | | - Sonika Tyagi
- EMBL Australia Bioinformatics Resource, Lab-14, The University of Melbourne, 700 Swanston St, Parkville, Victoria, 3053, Australia.,Australian Genome Research Facility Ltd., Melbourne, Australia
| | - Maarten van Gompel
- Centre for Language and Speech Technology, Radboud University Nijmegen, Nijmegen, Netherlands
| | | | - Allegra Via
- IBPM-CNR, Department of Biochemical Sciences , Sapienza University of Rome, Rome, Italy
| | - Xiaochuan Wang
- Faculty of Information Technology, Monash University, Victoria, Australia
| | | | - Steve Crouch
- Software Sustainability Institute, Web and Internet Science, University of Southampton, Southampton, UK
| |
Collapse
|
5
|
Hospital A, Andrio P, Cugnasco C, Codo L, Becerra Y, Dans PD, Battistini F, Torres J, Goñi R, Orozco M, Gelpí JL. BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. Nucleic Acids Res 2015; 44:D272-8. [PMID: 26612862 PMCID: PMC4702913 DOI: 10.1093/nar/gkv1301] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [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: 08/27/2015] [Accepted: 11/02/2015] [Indexed: 12/25/2022] Open
Abstract
Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/.
Collapse
Affiliation(s)
- Adam Hospital
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Pau Andrio
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain
| | - Cesare Cugnasco
- Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Dept. Computer Architecture, Technical University of Catalonia (UPC-BarcelonaTech), 08034 Barcelona, Spain
| | - Laia Codo
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain
| | - Yolanda Becerra
- Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Dept. Computer Architecture, Technical University of Catalonia (UPC-BarcelonaTech), 08034 Barcelona, Spain
| | - Pablo D Dans
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Federica Battistini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Jordi Torres
- Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Dept. Computer Architecture, Technical University of Catalonia (UPC-BarcelonaTech), 08034 Barcelona, Spain
| | - Ramón Goñi
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Josep Ll Gelpí
- Joint BSC-IRB Research Program in Computational Biology, Baldiri Reixac 10-12, 08028 Barcelona, Spain Barcelona Supercomputing Center, Jordi Girona 29, 08034 Barcelona, Spain Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain
| |
Collapse
|
6
|
Orozco M, Orellana L, Hospital A, Naganathan AN, Emperador A, Carrillo O, Gelpí JL. Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings. Adv Protein Chem Struct Biol 2011; 85:183-215. [PMID: 21920324 DOI: 10.1016/b978-0-12-386485-7.00005-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Flexibility is the key magnitude to understand the variety of functions of proteins. Unfortunately, its experimental study is quite difficult, and in fact, most experimental procedures are designed to reduce flexibility and allow a better definition of the structure. Theoretical approaches have become then the alternative but face serious timescale problems, since many biologically relevant deformation movements happen in a timescale that is far beyond the possibility of current atomistic models. In this complex scenario, coarse-grained simulation methods have emerged as a powerful and inexpensive alternative. Along this chapter, we will review these coarse-grained methods, and explain their physical foundations and their range of applicability.
Collapse
Affiliation(s)
- Modesto Orozco
- Joint IRB-BSC Program on Computational Biology, Barcelona Supercomputing Center and Institute of Research in Biomedicine, Parc Científic de Barcelona, Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
7
|
Pineda M, Wagner CA, Bröer A, Stehberger PA, Kaltenbach S, Gelpí JL, Martín Del Río R, Zorzano A, Palacín M, Lang F, Bröer S. Cystinuria-specific rBAT(R365W) mutation reveals two translocation pathways in the amino acid transporter rBAT-b0,+AT. Biochem J 2004; 377:665-74. [PMID: 14561219 PMCID: PMC1223896 DOI: 10.1042/bj20030956] [Citation(s) in RCA: 39] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2003] [Revised: 10/09/2003] [Accepted: 10/15/2003] [Indexed: 11/17/2022]
Abstract
Apical reabsorption of dibasic amino acids and cystine in kidney is mediated by the heteromeric amino acid antiporter rBAT/b(0,+)AT (system b(0,+)). Mutations in rBAT cause cystinuria type A, whereas mutations in b(0,+)AT cause cystinuria type B. b(0,+)AT is the catalytic subunit, whereas it is believed that rBAT helps the routing of the rBAT/b(0,+)AT heterodimeric complex to the plasma membrane. In the present study, we have functionally characterized the cystinuria-specific R365W (Arg(365)-->Trp) mutation of human rBAT, which in addition to a trafficking defect, alters functional properties of the b(0,+) transporter. In oocytes, where human rBAT interacts with the endogenous b(0,+)AT subunit to form an active transporter, the rBAT(R365W) mutation caused a defect of arginine efflux without altering arginine influx or apparent affinities for intracellular or extracellular arginine. Transport of lysine or leucine remained unaffected. In HeLa cells, functional expression of rBAT(R365W)/b(0,+)AT was observed only at the permissive temperature of 33 degrees C. Under these conditions, the mutated transporter showed 50% reduction of arginine influx and a similar decreased accumulation of dibasic amino acids. Efflux of arginine through the rBAT(R365W)/b(0,+)AT holotransporter was completely abolished. This supports a two-translocation-pathway model for antiporter b(0,+), in which the efflux pathway in the rBAT(R365W)/b(0,+)AT holotransporter is defective for arginine translocation or dissociation. This is the first direct evidence that mutations in rBAT may modify transport properties of system b(0,+).
Collapse
Affiliation(s)
- Marta Pineda
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, Barcelona Science Park, Barcelona 08028, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Gelpí JL, Kalko SG, Barril X, Cirera J, de La Cruz X, Luque FJ, Orozco M. Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins. Proteins 2001; 45:428-37. [PMID: 11746690 DOI: 10.1002/prot.1159] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The latest version of the classical molecular interaction potential (CMIP) has the ability to predict the position of crystallographic waters in several proteins with great accuracy. This article analyzes the ability of the CMIP functional to improve the setup procedure of the molecular system in molecular dynamics (MD) simulations of proteins. To this end, the CMIP strategy is used to include both water molecules and counterions in different protein systems. The structural details of the configurations sampled from trajectories obtained using the CMIP setup procedure are compared with those obtained from trajectories derived from a standard equilibration process. The results show that standard MD simulations can lead to artifactual results, which are avoided using the CMIP setup procedure. Because the CMIP is easy to implement at a low computational cost, it can be very useful in obtaining reliable MD trajectories.
Collapse
Affiliation(s)
- J L Gelpí
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
9
|
Trejo F, Gelpí JL, Ferrer A, Boronat A, Busquets M, Cortés A. Contribution of engineered electrostatic interactions to the stability of cytosolic malate dehydrogenase. Protein Eng 2001; 14:911-7. [PMID: 11742111 DOI: 10.1093/protein/14.11.911] [Citation(s) in RCA: 10] [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: 11/13/2022]
Abstract
Protein engineering is a promising tool to obtain stable proteins. Comparison between homologous thermophilic and mesophilic enzymes from a given structural family can reveal structural features responsible for the enhanced stability of thermophilic proteins. Structures from pig heart cytosolic and Thermus flavus malate dehydrogenases (cMDH, Tf MDH), two proteins showing a 55% sequence homology, were compared with the aim of increasing cMDH stability using features from the Thermus flavus enzyme. Three potential salt bridges from Tf MDH were selected on the basis of their location in the protein (surface R176-D200, inter-subunit E57-K168 and intrasubunit R149-E275) and implemented on cMDH using site-directed mutagenesis. Mutants containing E275 were not produced in any detectable amount, which shows that the energy penalty of introducing a charge imbalance in a region that was not exposed to solvent was too unfavourable to allow proper folding of the protein. The salt bridge R149-E275, if formed, would not enhance stability enough to overcome this effect. The remaining mutants were expressed and active and no differences from wild-type other than stability were found. Of the mutants assayed, Q57E/L168K led to a stability increase of 0.4 kcal/mol, as determined by either guanidinium chloride denaturalization or thermal inactivation experiments. This results in a 15 degrees C shift in the optimal temperature, thus confirming that the inter-subunit salt bridge initially present in the T.flavus enzyme was formed in the cMDH structure and that the extra energy obtained is transformed into an increase in protein stability. These results indicate that the use of structural features of thermophilic enzymes, revealed by a detailed comparison of three-dimensional structures, is a valid strategy to improve the stability of mesophilic malate dehydrogenases.
Collapse
Affiliation(s)
- F Trejo
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franqués 1, Spain
| | | | | | | | | | | |
Collapse
|
10
|
Abstract
A variety of theoretical methods including classical molecular interaction potentials, classical molecular dynamics, and activated molecular dynamics have been used to analyze the substrate recognition mechanisms of peroxisomal catalase from Saccharomyces cerevisiae. Special attention is paid to the existence of channels connecting the heme group with the exterior of the protein. On the basis of these calculations a rationale is given for the unique catalytic properties of this enzyme, as well as for the change in enzyme efficiency related to key mutations. According to our calculations the water is expected to be a competitive inhibitor of the enzyme, blocking the access of hydrogen peroxide to the active site. The main channel is the preferred route for substrate access to the enzyme and shows a cooperative binding to hydrogen peroxide. However, the overall affinity of the main channel for H(2)O(2) is only slightly larger than that for H(2)O. Alternative channels connecting the heme group with the monomer interface and the NADP(H) binding site are detected. These secondary channels might be important for product release.
Collapse
Affiliation(s)
- S G Kalko
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
| | | | | | | |
Collapse
|
11
|
Calbó J, Marotta M, Cascalló M, Roig JM, Gelpí JL, Fueyo J, Mazo A. Adenovirus-mediated wt-p16 reintroduction induces cell cycle arrest or apoptosis in pancreatic cancer. Cancer Gene Ther 2001; 8:740-50. [PMID: 11687897 DOI: 10.1038/sj.cgt.7700374] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2001] [Indexed: 02/07/2023]
Abstract
Pancreatic cancer has long carried poor prognosis. The development of new therapeutic approaches is particularly urgent. Inactivation of the tumor-suppressor gene p16(INK4a/CDKN2), a specific inhibitor of the cyclin-dependent kinases CDK4 and CDK6, is the most common genetic alteration in human pancreatic cancer, making it an ideal target for gene replacement. Here we transfected tumor cells using a recombinant adenovirus containing the wt-p16 cDNA (Ad5RSV-p16). The overexpression of p16 decreased cell proliferation in all four human pancreatic tumor cell lines (NP-9, NP-18, NP-29, and NP-31). However, G1 arrest and senescence were observed in only three. In contrast, the fourth (NP-18) showed a significant increase in apoptosis. This differential behavior may be related to the differences found in the expression level of E2F-1. Experiments on subcutaneous pancreatic xenografts demonstrated the effectiveness of p16 in the inhibition of pancreatic tumor growth in vivo. Taken together, our results indicate that approaches involving p16 replacement are promising in pancreatic cancer treatment.
Collapse
Affiliation(s)
- J Calbó
- Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
12
|
Torras-Llort M, Torrents D, Soriano-García JF, Gelpí JL, Estévez R, Ferrer R, Palacín M, Moretó M. Sequential amino acid exchange across b(0,+)-like system in chicken brush border jejunum. J Membr Biol 2001; 180:213-20. [PMID: 11337893 DOI: 10.1007/s002320010072] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In the small intestine, cationic amino acids are transported by y(+)-like and b(0,+)-like systems present in the luminal side of the epithelium. Here, we report the characterization of a b(0,+)-like system in the apical membrane of the chicken jejunum, and its properties as an amino acid exchanger. Analysis of the brush border membrane by Western blot points out the presence of rBAT (protein related to b0,+ amino acid transport system) in these membranes. A functional mechanism for amino acid exchange across this system was established by kinetic analysis measuring fluxes at varying substrate concentrations both in internal (in) and external (out) vesicle compartments. This intestinal b(0,+)-like system functions for L-arginine as an obligatory exchanger since its transport capacity increases 100-200 fold in exchange conditions, thus suggesting an important role in the intestinal absorption of cationic amino acids. The kinetic analysis of Argin efflux velocities is compatible with the formation of a ternary complex and excludes a model involving a ping-pong mechanism. The binding affinity of Argout is higher than that of Argin, suggesting a possible order of binding (Argout first) for the formation of the ternary complex during the exchange cycle. A model of double translocation pathways with alternating access is discussed.
Collapse
Affiliation(s)
- M Torras-Llort
- Departament de Fisiologia-Divisió IV, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Busquets C, Merinero B, Christensen E, Gelpí JL, Campistol J, Pineda M, Fernández-Alvarez E, Prats JM, Sans A, Arteaga R, Martí M, Campos J, Martínez-Pardo M, Martínez-Bermejo A, Ruiz-Falcó ML, Vaquerizo J, Orozco M, Ugarte M, Coll MJ, Ribes A. Glutaryl-CoA dehydrogenase deficiency in Spain: evidence of two groups of patients, genetically, and biochemically distinct. Pediatr Res 2000; 48:315-22. [PMID: 10960496 DOI: 10.1203/00006450-200009000-00009] [Citation(s) in RCA: 97] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Glutaryl-CoA dehydrogenase (GCDH) deficiency causes glutaric aciduria type I (GA I), an inborn error of metabolism that is characterized clinically by dystonia and dyskinesia and pathologically by neural degeneration of the caudate and putamen. Studies of metabolite excretion allowed us to categorize 43 GA I Spanish patients into two groups: group 1 (26 patients), those presenting with high excretion of both glutarate and 3-hydroxyglutarate, and group 2 (17 patients), those who might not be detected by routine urine organic acid analysis because glutarate might be normal and 3-hydroxyglutarate only slightly higher than controls. Single-strand conformation polymorphism (SSCP) screening and sequence analysis of the 11 exons and the corresponding intron boundaries of the GCDH gene allowed us to identify 13 novel and 10 previously described mutations. The most frequent mutations in group 1 were A293T and R402W with an allele frequency of 30% and 28%, respectively. These two mutations were also found in group 2, but always in heterozygosity, in particular in combination with mutations V400M or R227P. Interestingly, mutations V400M and R227P were only found in group 2, and at least one of these mutations was found in 11 of 15 unrelated alleles, accounting together for 53% of the mutant alleles in group 2. Therefore, it seems clear that two genetically and biochemically distinct groups of patients exist. The severity of the clinical phenotype seems to be closely linked to the development of encephalopathic crises rather than to residual enzyme activity or genotype. Comparison of GCDH protein with other acyl-CoA dehydrogenases (whose x-ray crystal structure has been determined) reveals that most of the mutations identified in GCDH protein seem to affect folding and tetramerization, as has been described for a number of mutations affecting mitochondrial beta-oxidation acyl-CoA dehydrogenases.
Collapse
Affiliation(s)
- C Busquets
- Institut de Bioquímica Clinica, Barcelona, Spain
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Cascalló M, Calbó J, Gelpí JL, Mazo A. Modulation of drug cytotoxicity by reintroduction of wild-type p53 gene (Ad5CMV-p53) in human pancreatic cancer. Cancer Gene Ther 2000; 7:545-56. [PMID: 10811472 DOI: 10.1038/sj.cgt.7700150] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Chemotherapy does not significantly improve prognosis in pancreatic cancer. New therapeutical approaches involving p53 gene replacement appear to be very encouraging due to the key role of p53 in the cell response to DNA damage. Here, we have evaluated the effectiveness of combining wild-type p53 (wt-p53) gene reintroduction (Ad5CMV-p53) and exposure to two genotoxic drugs, gemcitabine and cisplatin, in several human pancreatic cell lines. The efficiency of the combinations was clearly dependent upon timing, as assessed by cell survival determinations. Although wt-p53 transduction before drug treatment induced chemoresistance, p53 transduction in cells treated previously with gemcitabine increased cytotoxicity. Cell cycle profiles showed significant decreases in the percentage of cells in the S phase as a consequence of arrests provoked by the expression of exogenous p53, reducing the number of cells susceptible to the drug. The sensitivity of cells to cisplatin, which has a lower degree of S-phase specificity, was not modified as much by p53 gene replacement. In contrast, the recognition of the previous drug-induced DNA damage by the newly expressed wt-p53 elicited increases in sub-G1 populations, consistent with the annexin determinations and bax/bcl-2 ratios observed. Experiments on subcutaneous pancreatic xenografts corroborated the effectiveness of this approach in vivo. Thus, the combination of p53 transduction and chemotherapy, under a correct schedule of administration, appears to be a very promising therapy for human pancreatic cancer.
Collapse
Affiliation(s)
- M Cascalló
- Department of Biochemistry and Molecular Biology, University of Barcelona, Spain
| | | | | | | |
Collapse
|
15
|
Ezquerra M, Carnero C, Blesa R, Gelpí JL, Ballesta F, Oliva R. A presenilin 1 mutation (Ser169Pro) associated with early-onset AD and myoclonic seizures. Neurology 1999; 52:566-70. [PMID: 10025789 DOI: 10.1212/wnl.52.3.566] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To characterize the mutation responsible for early-onset AD in a large Spanish kindred. BACKGROUND Mutations in the presenilin 1 (PS1) gene have been identified and are known to be responsible for 18 to 50% of familial early-onset AD cases. METHODS Patients were characterized clinically. The proband was further studied with EEG, CSF analysis, CT, brain biopsy, and histology. Other members were studied using EEG, CT, MRI, and SPECT. Genetic analysis of PS1 was performed using PCR amplification of PS1 exons and direct sequencing followed by PS1 modeling of the normal and mutant PS1 proteins. RESULTS A novel mutation (Ser169Pro) in exon 6 of the PS1 gene was identified in different affected members. The Ser169Pro mutation is located at a site of the PS1 protein that is not a cluster of mutations. The mutation was not present in 100 general population controls and in 50 unrelated sporadic AD cases. The Ser169Pro mutation is associated with generalized myoclonic seizures several years after the initial symptoms of AD, a very early AD onset (< or =35 years), and a rapidly progressive cognitive decline. CONCLUSIONS The absence of the PS1 Ser169Pro mutation in the general population and in sporadic AD cases together with its detection in the affected members of this kindred suggests that it is a pathogenic mutation. The serine to proline change predicts a kink in the alpha-helix of the transmembrane domain of the PS1 protein that could radically disrupt its normal structure. Further characterization of the effect of this mutation could help identify the function of the PS1 protein and the pathogenic mechanisms of AD.
Collapse
Affiliation(s)
- M Ezquerra
- Genetics Service, Institut de Investigació Biomédica Agustí Pi i Sunyer, Hospital Clinic and Faculty of Medicine, University of Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
16
|
Romero-Isart N, Cols N, Termansen MK, Gelpí JL, González-Duarte R, Atrian S, Capdevila M, González-Duarte P. Replacement of terminal cysteine with histidine in the metallothionein alpha and beta domains maintains its binding capacity. Eur J Biochem 1999; 259:519-27. [PMID: 9914535 DOI: 10.1046/j.1432-1327.1999.00074.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To generate novel forms of metal-binding proteins, six mutant mouse metallothionein (MT) 1 fragments, in which a terminal cysteine residue was replaced by histidine, were expressed in Escherichia coli. The spectroscopic and analytical results showed that the alphaMT (C33H, C36H, C41H, C57H) and betaMT (C5H, C13H) mutant forms bound 4 and 3 Zn(II) atoms per molecule of protein to the nearest integer, even though in C41H and C5H, species of lower stoichiometry were also detected. In Cd(II) titrations, all the Zn(II) ions bound to the mutant proteins were displaced from the binding sites, giving rise to Cd-mutated MT forms with 4 and 3 Cd(II), respectively. However, although Cys-to-His substitutions maintained the binding capacity of the MT fragments, they caused structural changes with respect to the wild-type proteins. While C13H, C36H and C57H seem to contain Zn(II)-aggregates that are closely related to those of the wild-type proteins, only C41H and C57H gave rise to Cd(II)-aggregates similar to those of Cd4-alphaMT, where the His residue plays the role of the substituted Cys. Despite the structural implications of the Cys-to-His replacement, the dissociation constants showed no major decrease in the Cd-binding affinity in any of the mutants assayed compared with the wild-type.
Collapse
Affiliation(s)
- N Romero-Isart
- Department de Química, Faculat de Ciénces, Universitat Autónoma de Barcelona, Spain
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Alvarez JA, Gelpí JL, Johnsen K, Bernard N, Delcour J, Clarke AR, Holbrook JJ, Cortés A. D-2-hydroxy-4-methylvalerate dehydrogenase from Lactobacillus delbrueckii subsp. bulgaricus. I. Kinetic mechanism and pH dependence of kinetic parameters, coenzyme binding and substrate inhibition. Eur J Biochem 1997; 244:203-12. [PMID: 9063465 DOI: 10.1111/j.1432-1033.1997.00203.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The steady-state kinetics of D-2-hydroxy-4-methylvalerate dehydrogenase have been studied at pH 8.0 by initial velocity, product inhibition, and dead-end inhibition techniques. The mechanism is rapid-equilibrium ordered in the NAD+ plus D-2-hydroxy-4-methylvalerate direction, and steady-state ordered in the other direction. In both cases coenzyme is the first substrate added and both the E-NADH-D-2-hydroxy-4-methylvalerate and E-NAD+-2-oxo-4-methylvalerate give rise to abortive complexes which cause excess substrate inhibition. Steady-state measurements show that the rate-limiting step in both directions at pH 8.0 is between formation of the enzyme-coenzyme-substrate ternary complex and the release of the first product of the reaction. Transient kinetics combined with primary kinetic deuterium isotope effects show that in the NADH-->NAD+ direction there is a slow, rate-limiting rearrangement of the E-NADH-oxoacid complex while hydride transfer is very fast. The release of NAD+ at pH 8.0 is 200-times faster than Kcat (NADH-->NAD+) whereas the release of NADH is only 5-times faster than Kcat (NAD+-->NADH). The pH dependence of NADH binding depends upon the presence of two ionizable residues with a pKa of about 5.9. The pH dependence of kinetic parameters is explained by a third ionizable residue with pKa values 7.2 (in the E-NADH complex) and < or = 6.4 (in the E-NAD+ complex) which may be the proton donor and acceptor for the chemical reaction. At pH 6.5 the mechanism changes in the NADH-->NAD+ direction to be partly limited by the chemical step with a measured primary kinetic isotope effect of 5.7 and partly by an only slightly faster dissociation of NAD+. In addition the inhibition by excess oxo-4-methylvalerate is more pronounced. The mechanism implies that removing the positive charges created by the two groups which control coenzyme affinity could both enhance the catalytic rate at pH 6.5 and diminish excess substrate inhibition to provide an enzyme better suited to the bulk synthesis of D-2-hydroxyacids.
Collapse
Affiliation(s)
- J A Alvarez
- Departament de Bioquímica i Biologia Molecular, Universitat de Barcelona, Spain
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Chillarón J, Estévez R, Mora C, Wagner CA, Suessbrich H, Lang F, Gelpí JL, Testar X, Busch AE, Zorzano A, Palacín M. Obligatory amino acid exchange via systems bo,+-like and y+L-like. A tertiary active transport mechanism for renal reabsorption of cystine and dibasic amino acids. J Biol Chem 1996; 271:17761-70. [PMID: 8663357 DOI: 10.1074/jbc.271.30.17761] [Citation(s) in RCA: 129] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mutations in the rBAT gene cause type I cystinuria, a common inherited aminoaciduria of cystine and dibasic amino acids due to their defective renal and intestinal reabsorption (Calonge, M. J., Gasparini, P., Chillarón, J., Chillón, M., Gallucci, M., Rousaud, F., Zelante, L., Testar, X., Dallapiccola, B., Di Silverio, F., Barceló, P., Estivill, X., Zorzano, A., Nunes, V., and Palacín, M. (1994) Nat. Genet. 6, 420-426; Calonge, M. J., Volipini, V., Bisceglia, L., Rousaud, F., De Sanctis, L., Beccia, E., Zelante, L., Testar, X., Zorzano, A., Estivill, X., Gasparini, P., Nunes, V., and Palacín, M.(1995) Proc. Natl. Acad. Sci. U. S. A. 92, 9667-9671). One important question that remains to be clarified is how the apparently non-concentrative system bo,+-like, associated with rBAT expression, participates in the active renal reabsorption of these amino acids. Several studies have demonstrated exchange of amino acids induced by rBAT in Xenopus oocytes. Here we offer evidence that system bo,+-like is an obligatory amino acid exchanger in oocytes and in the "renal proximal tubular" cell line OK. System bo, +-like showed a 1:1 stoichiometry of exchange, and the hetero-exchange dibasic (inward) with neutral (outward) amino acids were favored in oocytes. Obligatory exchange of amino acids via system bo,+-like fully explained the amino acid-induced current in rBAT-injected oocytes. Exchange via system bo,+-like is coupled enough to ensure a specific accumulation of substrates until the complete replacement of the internal oocyte substrates. Due to structural and functional analogies of the cell surface antigen 4F2hc to rBAT, we tested for amino acid exchange via system y+L-like. 4F2hc-injected oocytes accumulated substrates to a level higher than CAT1-injected oocytes (i.e. oocytes expressing system y+) and showed exchange of amino acids with the substrate specificity of system y+L and L-leucine-induced outward currents in the absence of extracellular sodium. In contrast to L-arginine, system y+L-like did not mediate measurable L-leucine efflux from the oocyte. We propose a role of systems bo,+-like and y+L-like in the renal reabsorption of cystine and dibasic amino acids that is based on their active tertiary transport mechanism and on the apical and basolateral localization of rBAT and 4F2hc, respectively, in the epithelial cells of the proximal tubule of the nephron.
Collapse
Affiliation(s)
- J Chillarón
- Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, Universitat de Barcelona, Avda, Diagonal 645, Barcelona 08028, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Trejo F, Costa M, Gelpí JL, Busquets M, Clarke AR, Holbrook JJ, Cortés A. Cloning, sequencing and functional expression of a DNA encoding pig cytosolic malate dehydrogenase: purification and characterization of the recombinant enzyme. Gene 1996; 172:303-8. [PMID: 8682322 DOI: 10.1016/0378-1119(96)00178-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Using the polymerase chain reaction, DNA encoding cytosolic malate dehydrogenase (cMDH) has been cloned from a pig heart cDNA library. Large amounts of the enzyme (30 mg per litre of original culture) have been produced in Escherichia coli using an inducible expression vector (pKK223-3) in which the 5'-non-coding region of the gene was replaced with the tac promoter. The complete nucleotide sequence of the DNA is reported for the first time. The recombinant cMDH purified was shown to be identical to the native enzyme according to: chromatographic behaviour, isoelectric point, N-terminal amino acid sequence, and physiochemical and catalytic properties.
Collapse
Affiliation(s)
- F Trejo
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
20
|
Abstract
Mitochondrial malate dehydrogenase shows a complex regulation pattern in the presence of citrate. Previously published results indicate that this enzyme is activated by citrate in the NAD(+)----NADH direction and inhibited in the opposite direction. Moreover, high concentrations of L-malate or oxaloacetate produce deviations from the Michaelis-Menten behaviour. Results reported in this paper clearly show that citrate both activates and inhibits mitochondrial malate dehydrogenase in the same direction (NAD(+)----NADH), and in the same reaction medium, depending on substrate concentration. This surprising effect has made it necessary to propose a new kinetic mechanism that extends those previously suggested and allows us to explain both the citrate effect (activating or inhibitory) and the effect of high concentrations of L-malate and oxaloacetate.
Collapse
Affiliation(s)
- J L Gelpí
- Department de Bioquímica i Fisiologia, Facultat de Química, Universitat de Barcelona, Spain
| | | | | | | | | |
Collapse
|
21
|
Gelpí JL, Gracia V, Imperial S, Mazo A, Cortés A. A rapid procedure for eliminating chromatofocusing buffer and concentrating minor active subforms of mitochondrial malate dehydrogenase. Biotechniques 1990; 9:616-8. [PMID: 2268429] [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: 12/31/2022] Open
Abstract
Mitochondrial malate dehydrogenase from several sources contains different molecular forms whose origin is still under discussion. Separation of these subforms has been achieved by chromatofocusing. A simple and rapid method, based on 5' AMP Sepharose chromatography, has been developed to concentrate mitochondrial malate dehydrogenase subforms and simultaneously remove chromatofocusing buffer.
Collapse
Affiliation(s)
- J L Gelpí
- Department de Bioqúimica i Fisiologia, Facultat de Química, Universitat de Barcelona, Spain
| | | | | | | | | |
Collapse
|
22
|
Mazo A, Forner A, Domènech C, Busquets M, Gelpí JL, Cortés A. Comparative analysis of the reduction of oxaloacetate by human hepatoma and normal liver extracts. Tumour Biol 1990; 11:120-8. [PMID: 2160721 DOI: 10.1159/000217646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
An apparent activation of the malate dehydrogenase activity is observed in the double-reciprocal plot at high oxaloacetate concentrations when human hepatoma extracts are analyzed. This phenomenon does not occur in healthy liver samples. In hepatoma extracts, the ratio of lactate dehydrogenase to malate dehydrogenase activities becomes five-fold higher than that of normal liver. Experiments performed with mixtures of both purified enzymes and, conversely, by using oxamate, a specific inhibitor of lactate dehydrogenase, reveal that the deviation in Michaelis-Menten behavior observed is due to the oxaloacetate reductase activity of lactate dehydrogenase instead of the presence of a novel malate dehydrogenase isoenzyme.
Collapse
Affiliation(s)
- A Mazo
- Departament de Bioquímica i Fisiologia, Facultat de Química, Universitat de Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
23
|
Gelpí JL, Domènech C, Mazo A, Cortés A, Bozal J. Purification of malate dehydrogenase from chicken liver mitochondria. Existence of a small quantity of cytosolic isoenzyme. Int J Biochem 1988; 20:989-96. [PMID: 3197911 DOI: 10.1016/0020-711x(88)90186-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
1. A new purification method for chicken liver mitochondrial malate dehydrogenase is described. The application of affinity chromatography through 5'AMP-Sepharose and Blue-Sepharose permits to obtain homogeneous preparations, with good yields (47%), in a short time (48 hr). 2. The 5'AMP-Sepharose chromatography reveals the presence of two malate dehydrogenase species in the mitochondrial extracts. 3. A comparative study of these forms point out the cytosolic nature of the minority form and suggests that its presence could be due to a slight interaction of the cytosolic malate dehydrogenase with mitochondrial membranes.
Collapse
Affiliation(s)
- J L Gelpí
- Departament de Bioquímica i Fisiologia, Facultat de Química, Universitat de Barcelona, Spain
| | | | | | | | | |
Collapse
|