1
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Waterhouse AM, Studer G, Robin X, Bienert S, Tauriello G, Schwede T. The structure assessment web server: for proteins, complexes and more. Nucleic Acids Res 2024:gkae270. [PMID: 38634802 DOI: 10.1093/nar/gkae270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/21/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
The 'structure assessment' web server is a one-stop shop for interactive evaluation and benchmarking of structural models of macromolecular complexes including proteins and nucleic acids. A user-friendly web dashboard links sequence with structure information and results from a variety of state-of-the-art tools, which facilitates the visual exploration and evaluation of structure models. The dashboard integrates stereochemistry information, secondary structure information, global and local model quality assessment of the tertiary structure of comparative protein models, as well as prediction of membrane location. In addition, a benchmarking mode is available where a model can be compared to a reference structure, providing easy access to scores that have been used in recent CASP experiments and CAMEO. The structure assessment web server is available at https://swissmodel.expasy.org/assess.
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Affiliation(s)
- Andrew M Waterhouse
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Gabriel Studer
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Xavier Robin
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Stefan Bienert
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Gerardo Tauriello
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Computational Structural Biology, Basel, Switzerland
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2
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Robin X, Studer G, Durairaj J, Eberhardt J, Schwede T, Walters WP. Assessment of protein-ligand complexes in CASP15. Proteins 2023; 91:1811-1821. [PMID: 37795762 DOI: 10.1002/prot.26601] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
CASP15 introduced a new category, ligand prediction, where participants were provided with a protein or nucleic acid sequence, SMILES line notation, and stoichiometry for ligands and tasked with generating computational models for the three-dimensional structure of the corresponding protein-ligand complex. These models were subsequently compared with experimental structures determined by x-ray crystallography or cryoEM. To assess these predictions, two novel scores were developed. The Binding-Site Superposed, Symmetry-Corrected Pose Root Mean Square Deviation (BiSyRMSD) evaluated the absolute deviations of the models from the experimental structures. At the same time, the Local Distance Difference Test for Protein-Ligand Interactions (lDDT-PLI) assessed the ability of models to reproduce the protein-ligand interactions in the experimental structures. The ligands evaluated in this challenge range from single-atom ions to large flexible organic molecules. More than 1800 submissions were evaluated for their ability to predict 23 different protein-ligand complexes. Overall, the best models could faithfully reproduce the geometries of more than half of the prediction targets. The ligands' size and flexibility were the primary factors influencing the predictions' quality. Small ions and organic molecules with limited flexibility were predicted with high fidelity, while reproducing the binding poses of larger, flexible ligands proved more challenging.
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Affiliation(s)
- Xavier Robin
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Gabriel Studer
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Janani Durairaj
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jerome Eberhardt
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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3
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Leemann M, Sagasta A, Eberhardt J, Schwede T, Robin X, Durairaj J. Automated benchmarking of combined protein structure and ligand conformation prediction. Proteins 2023; 91:1912-1924. [PMID: 37885318 DOI: 10.1002/prot.26605] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
The prediction of protein-ligand complexes (PLC), using both experimental and predicted structures, is an active and important area of research, underscored by the inclusion of the Protein-Ligand Interaction category in the latest round of the Critical Assessment of Protein Structure Prediction experiment CASP15. The prediction task in CASP15 consisted of predicting both the three-dimensional structure of the receptor protein as well as the position and conformation of the ligand. This paper addresses the challenges and proposed solutions for devising automated benchmarking techniques for PLC prediction. The reliability of experimentally solved PLC as ground truth reference structures is assessed using various validation criteria. Similarity of PLC to previously released complexes are employed to judge PLC diversity and the difficulty of a PLC as a prediction target. We show that the commonly used PDBBind time-split test-set is inappropriate for comprehensive PLC evaluation, with state-of-the-art tools showing conflicting results on a more representative and high quality dataset constructed for benchmarking purposes. We also show that redocking on crystal structures is a much simpler task than docking into predicted protein models, demonstrated by the two PLC-prediction-specific scoring metrics created. Finally, we introduce a fully automated pipeline that predicts PLC and evaluates the accuracy of the protein structure, ligand pose, and protein-ligand interactions.
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Affiliation(s)
- Michèle Leemann
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ander Sagasta
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jerome Eberhardt
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Xavier Robin
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Janani Durairaj
- Biozentrum, University of Basel, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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4
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Kryshtafovych A, Antczak M, Szachniuk M, Zok T, Kretsch RC, Rangan R, Pham P, Das R, Robin X, Studer G, Durairaj J, Eberhardt J, Sweeney A, Topf M, Schwede T, Fidelis K, Moult J. New prediction categories in CASP15. Proteins 2023; 91:1550-1557. [PMID: 37306011 PMCID: PMC10713864 DOI: 10.1002/prot.26515] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023]
Abstract
Prediction categories in the Critical Assessment of Structure Prediction (CASP) experiments change with the need to address specific problems in structure modeling. In CASP15, four new prediction categories were introduced: RNA structure, ligand-protein complexes, accuracy of oligomeric structures and their interfaces, and ensembles of alternative conformations. This paper lists technical specifications for these categories and describes their integration in the CASP data management system.
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Affiliation(s)
| | - Maciej Antczak
- Institute of Computing Science, Poznan University of TechnologyPoznanPoland
- Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznanPoland
| | - Marta Szachniuk
- Institute of Computing Science, Poznan University of TechnologyPoznanPoland
- Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznanPoland
| | - Tomasz Zok
- Institute of Computing Science, Poznan University of TechnologyPoznanPoland
- Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznanPoland
| | - Rachael C. Kretsch
- Biophysics Program, Stanford University School of MedicineStanfordCaliforniaUSA
| | - Ramya Rangan
- Biophysics Program, Stanford University School of MedicineStanfordCaliforniaUSA
| | - Phillip Pham
- Biochemistry DepartmentStanford University School of MedicineStanfordCaliforniaUSA
| | - Rhiju Das
- Biochemistry DepartmentStanford University School of MedicineStanfordCaliforniaUSA
- Howard Hughes Medical Institute, Stanford UniversityStanfordCaliforniaUSA
| | - Xavier Robin
- Biozentrum, University of BaselBaselSwitzerland
- SIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Gabriel Studer
- Biozentrum, University of BaselBaselSwitzerland
- SIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Janani Durairaj
- Biozentrum, University of BaselBaselSwitzerland
- SIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Jerome Eberhardt
- Biozentrum, University of BaselBaselSwitzerland
- SIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Aaron Sweeney
- Centre for Structural Systems Biology (CSSB), Leibniz‐Institut für Virologie (LIV)HamburgGermany
| | - Maya Topf
- Centre for Structural Systems Biology (CSSB), Leibniz‐Institut für Virologie (LIV)HamburgGermany
- Universitätsklinikum Hamburg Eppendorf (UKE)HamburgGermany
| | - Torsten Schwede
- Biozentrum, University of BaselBaselSwitzerland
- SIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | - John Moult
- Institute for Bioscience and Biotechnology Research, Department of Cell Biology and Molecular genetics, University of MarylandRockvilleMarylandUSA
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5
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Pereira J, Durairaj J, Pantolini L, Studer G, Robin X, Waterhouse A, Bienert S, Tauriello G, Schwede T. How predicted protein models help to illuminate the full protein universe. Acta Cryst Sect A 2022. [DOI: 10.1107/s2053273322096024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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6
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Madsen RR, Erickson EC, Rueda OM, Robin X, Caldas C, Toker A, Semple RK, Vanhaesebroeck B. Positive correlation between transcriptomic stemness and PI3K/AKT/mTOR signaling scores in breast cancer, and a counterintuitive relationship with PIK3CA genotype. PLoS Genet 2021; 17:e1009876. [PMID: 34762647 PMCID: PMC8584750 DOI: 10.1371/journal.pgen.1009876] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
A PI3Kα-selective inhibitor has recently been approved for use in breast tumors harboring mutations in PIK3CA, the gene encoding p110α. Preclinical studies have suggested that the PI3K/AKT/mTOR signaling pathway influences stemness, a dedifferentiation-related cellular phenotype associated with aggressive cancer. However, to date, no direct evidence for such a correlation has been demonstrated in human tumors. In two independent human breast cancer cohorts, encompassing nearly 3,000 tumor samples, transcriptional footprint-based analysis uncovered a positive linear association between transcriptionally-inferred PI3K/AKT/mTOR signaling scores and stemness scores. Unexpectedly, stratification of tumors according to PIK3CA genotype revealed a "biphasic" relationship of mutant PIK3CA allele dosage with these scores. Relative to tumor samples without PIK3CA mutations, the presence of a single copy of a hotspot PIK3CA variant was associated with lower PI3K/AKT/mTOR signaling and stemness scores, whereas the presence of multiple copies of PIK3CA hotspot mutations correlated with higher PI3K/AKT/mTOR signaling and stemness scores. This observation was recapitulated in a human cell model of heterozygous and homozygous PIK3CAH1047R expression. Collectively, our analysis (1) provides evidence for a signaling strength-dependent PI3K-stemness relationship in human breast cancer; (2) supports evaluation of the potential benefit of patient stratification based on a combination of conventional PI3K pathway genetic information with transcriptomic indices of PI3K signaling activation.
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Affiliation(s)
- Ralitsa R. Madsen
- University College London Cancer Institute, Paul O’Gorman Building, University College London, London, United Kingdom
| | - Emily C. Erickson
- Department of Pathology, Medicine and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Oscar M. Rueda
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Xavier Robin
- SIB Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Basel, Switzerland
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
- Cambridge Breast Unit, Addenbrooke’s Hospital, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre and Cambridge Experimental Cancer Medicine Centre, Cambridge University Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Alex Toker
- Department of Pathology, Medicine and Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert K. Semple
- Centre for Cardiovascular Science, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Bart Vanhaesebroeck
- University College London Cancer Institute, Paul O’Gorman Building, University College London, London, United Kingdom
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7
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Robin X, Haas J, Gumienny R, Smolinski A, Tauriello G, Schwede T. Continuous Automated Model EvaluatiOn (CAMEO)-Perspectives on the future of fully automated evaluation of structure prediction methods. Proteins 2021; 89:1977-1986. [PMID: 34387007 PMCID: PMC8673552 DOI: 10.1002/prot.26213] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 05/28/2021] [Revised: 08/05/2021] [Accepted: 08/07/2021] [Indexed: 11/18/2022]
Abstract
The Continuous Automated Model EvaluatiOn (CAMEO) platform complements the biennial CASP experiment by conducting fully automated blind evaluations of three‐dimensional protein prediction servers based on the weekly prerelease of sequences of those structures, which are going to be published in the upcoming release of the Protein Data Bank. While in CASP14, significant success was observed in predicting the structures of individual protein chains with high accuracy, significant challenges remain in correctly predicting the structures of complexes. By implementing fully automated evaluation of predictions for protein–protein complexes, as well as for proteins in complex with ligands, peptides, nucleic acids, or proteins containing noncanonical amino acid residues, CAMEO will assist new developments in those challenging areas of active research.
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Affiliation(s)
- Xavier Robin
- Biozentrum, University of Basel, Basel, Switzerland.,Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Juergen Haas
- Biozentrum, University of Basel, Basel, Switzerland.,Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Rafal Gumienny
- Biozentrum, University of Basel, Basel, Switzerland.,Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Anna Smolinski
- Biozentrum, University of Basel, Basel, Switzerland.,Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Gerardo Tauriello
- Biozentrum, University of Basel, Basel, Switzerland.,Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel, Basel, Switzerland.,Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Basel, Switzerland
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8
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Madsen RR, Longden J, Knox RG, Robin X, Völlmy F, Macleod KG, Moniz LS, Carragher NO, Linding R, Vanhaesebroeck B, Semple RK. NODAL/TGFβ signalling mediates the self-sustained stemness induced by PIK3CAH1047R homozygosity in pluripotent stem cells. Dis Model Mech 2021; 14:dmm048298. [PMID: 33514588 PMCID: PMC7969366 DOI: 10.1242/dmm.048298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
Activating PIK3CA mutations are known 'drivers' of human cancer and developmental overgrowth syndromes. We recently demonstrated that the 'hotspot' PIK3CAH1047R variant exerts unexpected allele dose-dependent effects on stemness in human pluripotent stem cells (hPSCs). In this study, we combine high-depth transcriptomics, total proteomics and reverse-phase protein arrays to reveal potentially disease-related alterations in heterozygous cells, and to assess the contribution of activated TGFβ signalling to the stemness phenotype of homozygous PIK3CAH1047R cells. We demonstrate signalling rewiring as a function of oncogenic PI3K signalling strength, and provide experimental evidence that self-sustained stemness is causally related to enhanced autocrine NODAL/TGFβ signalling. A significant transcriptomic signature of TGFβ pathway activation in heterozygous PIK3CAH1047R was observed but was modest and was not associated with the stemness phenotype seen in homozygous mutants. Notably, the stemness gene expression in homozygous PIK3CAH1047R hPSCs was reversed by pharmacological inhibition of NODAL/TGFβ signalling, but not by pharmacological PI3Kα pathway inhibition. Altogether, this provides the first in-depth analysis of PI3K signalling in hPSCs and directly links strong PI3K activation to developmental NODAL/TGFβ signalling. This work illustrates the importance of allele dosage and expression when artificial systems are used to model human genetic disease caused by activating PIK3CA mutations. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Ralitsa R. Madsen
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - James Longden
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, 10115Berlin, Germany
| | - Rachel G. Knox
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
- The National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Xavier Robin
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Franziska Völlmy
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Kenneth G. Macleod
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Larissa S. Moniz
- University College London Cancer Institute, Paul O'Gorman Building, University College London, London WC1E 6BT, UK
| | - Neil O. Carragher
- Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Rune Linding
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200 Copenhagen, Denmark
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, 10115Berlin, Germany
| | - Bart Vanhaesebroeck
- University College London Cancer Institute, Paul O'Gorman Building, University College London, London WC1E 6BT, UK
| | - Robert K. Semple
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
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9
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Longden J, Robin X, Engel M, Ferkinghoff-Borg J, Kjær I, Horak ID, Pedersen MW, Linding R. Deep neural networks identify signaling mechanisms of ErbB-family drug resistance from a continuous cell morphology space. Cell Rep 2021; 34:108657. [PMID: 33472071 DOI: 10.1016/j.celrep.2020.108657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 01/20/2020] [Accepted: 12/28/2020] [Indexed: 01/21/2023] Open
Abstract
It is well known that the development of drug resistance in cancer cells can lead to changes in cell morphology. Here, we describe the use of deep neural networks to analyze this relationship, demonstrating that complex cell morphologies can encode states of signaling networks and unravel cellular mechanisms hidden to conventional approaches. We perform high-content screening of 17 cancer cell lines, generating more than 500 billion data points from ∼850 million cells. We analyze these data using a deep learning model, resulting in the identification of a continuous 27-dimension space describing all of the observed cell morphologies. From its morphology alone, we could thus predict whether a cell was resistant to ErbB-family drugs, with an accuracy of 74%, and predict the potential mechanism of resistance, subsequently validating the role of MET and insulin-like growth factor 1 receptor (IGF1R) as drivers of cetuximab resistance in in vitro models of lung and head/neck cancer.
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Affiliation(s)
- James Longden
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark.
| | - Xavier Robin
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Mathias Engel
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark; Niels Bohr Institute, University of Copenhagen, Copenhagen, 2200, Denmark
| | | | - Ida Kjær
- Symphogen A/S, Ballerup, 2750, Denmark
| | | | | | - Rune Linding
- Biotech Research & Innovation Centre, University of Copenhagen, Copenhagen, 2200, Denmark; Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, 10115, Germany; Rewire Tx, Humboldt-Universität zu Berlin, Berlin, 10115, Germany.
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10
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Bonnardel F, Mariethoz J, Salentin S, Robin X, Schroeder M, Perez S, Lisacek F, Imberty A. UniLectin3D, a database of carbohydrate binding proteins with curated information on 3D structures and interacting ligands. Nucleic Acids Res 2020; 47:D1236-D1244. [PMID: 30239928 PMCID: PMC6323968 DOI: 10.1093/nar/gky832] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/07/2018] [Indexed: 01/02/2023] Open
Abstract
Lectins, and related receptors such as adhesins and toxins, are glycan-binding proteins from all origins that decipher the glycocode, i.e. the structural information encoded in the conformation of complex carbohydrates present on the surface of all cells. Lectins are still poorly classified and annotated, but since their functions are based on ligand recognition, their 3D-structures provide a solid foundation for characterization. UniLectin3D is a curated database that classifies lectins on origin and fold, with cross-links to literature, other databases in glycosciences and functional data such as known specificity. The database provides detailed information on lectins, their bound glycan ligands, and features their interactions using the Protein–Ligand Interaction Profiler (PLIP) server. Special care was devoted to the description of the bound glycan ligands with the use of simple graphical representation and numerical format for cross-linking to other databases in glycoscience. We conceived the design of the database architecture and the navigation tools to account for all organisms, as well as to search for oligosaccharide epitopes complexed within specified binding sites. UniLectin3D is accessible at https://www.unilectin.eu/unilectin3D.
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Affiliation(s)
- François Bonnardel
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France.,Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland
| | - Sebastian Salentin
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Xavier Robin
- Biozentrum, University of Basel, Klingelbergstrasse 50-70, CH-4056 Basel, Switzerland.,Computational Structural Biology Group, SIB Swiss Institute of Bioinformatics, CH-4056 Basel, Switzerland
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), TU Dresden, Tatzberg 47-49, 01307 Dresden, Germany
| | - Serge Perez
- Univ. Grenoble Alpes, CNRS, DPM, 38000 Grenoble, France
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, CH-1227 Geneva, Switzerland.,Department of Computer Science, University of Geneva, Route de Drize 7, CH-1227 Geneva, Switzerland.,Section of Biology, University of Geneva, CH-1205 Geneva, Switzerland
| | - Anne Imberty
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
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11
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Engel M, Longden J, Ferkinghoff-Borg J, Robin X, Saginc G, Linding R. Bowhead: Bayesian modelling of cell velocity during concerted cell migration. PLoS Comput Biol 2018; 14:e1005900. [PMID: 29309407 PMCID: PMC5774831 DOI: 10.1371/journal.pcbi.1005900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 01/19/2018] [Accepted: 11/27/2017] [Indexed: 11/28/2022] Open
Abstract
Cell migration is a central biological process that requires fine coordination of molecular events in time and space. A deregulation of the migratory phenotype is also associated with pathological conditions including cancer where cell motility has a causal role in tumor spreading and metastasis formation. Thus cell migration is of critical and strategic importance across the complex disease spectrum as well as for the basic understanding of cell phenotype. Experimental studies of the migration of cells in monolayers are often conducted with 'wound healing' assays. Analysis of these assays has traditionally relied on how the wound area changes over time. However this method does not take into account the shape of the wound. Given the many options for creating a wound healing assay and the fact that wound shape invariably changes as cells migrate this is a significant flaw. Here we present a novel software package for analyzing concerted cell velocity in wound healing assays. Our method encompasses a wound detection algorithm based on cell confluency thresholding and employs a Bayesian approach in order to estimate concerted cell velocity with an associated likelihood. We have applied this method to study the effect of siRNA knockdown on the migration of a breast cancer cell line and demonstrate that cell velocity can track wound healing independently of wound shape and provides a more robust quantification with significantly higher signal to noise ratios than conventional analyses of wound area. The software presented here will enable other researchers in any field of cell biology to quantitatively analyze and track live cell migratory processes and is therefore expected to have a significant impact on the study of cell migration, including cancer relevant processes. Installation instructions, documentation and source code can be found at http://bowhead.lindinglab.science licensed under GPLv3.
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Affiliation(s)
- Mathias Engel
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - James Longden
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Xavier Robin
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Gaye Saginc
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Rune Linding
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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Severino V, Dumonceau JM, Delhaye M, Moll S, Annessi-Ramseyer I, Robin X, Frossard JL, Farina A. Extracellular Vesicles in Bile as Markers of Malignant Biliary Stenoses. Gastroenterology 2017; 153:495-504.e8. [PMID: 28479376 DOI: 10.1053/j.gastro.2017.04.043] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 04/21/2017] [Accepted: 04/29/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Algorithms for diagnosis of malignant common bile duct (CBD) stenoses are complex and lack accuracy. Malignant tumors secrete large numbers of extracellular vesicles (EVs) into surrounding fluids; EVs might therefore serve as biomarkers for diagnosis. We investigated whether concentrations of EVs in bile could discriminate malignant from nonmalignant CBD stenoses. METHODS We collected bile and blood samples from 50 patients undergoing therapeutic endoscopic retrograde cholangiopancreatography at university hospitals in Europe for CBD stenosis of malignant (pancreatic cancer, n = 20 or cholangiocarcinoma, n = 5) or nonmalignant (chronic pancreatitis [CP], n = 15) origin. Ten patients with CBD obstruction due to biliary stones were included as controls. EV concentrations in samples were determined by nanoparticle tracking analyses. The discovery cohort comprised the first 10 patients with a diagnosis of pancreatic cancer, based on tissue analysis, and 10 consecutive controls. Using samples from these subjects, we identified a threshold concentration of bile EVs that could best discriminate between patients with pancreatic cancer from controls. We verified the diagnostic performance of bile EV concentration by analyzing samples from the 30 consecutive patients with a diagnosis of malignant (pancreatic cancer or cholangiocarcinoma, n = 15) or nonmalignant (CP, n = 15) CBD stenosis. Samples were compared using the Mann-Whitney test and nonparametric Spearman correlation analysis. Receiver operating characteristic area under the curve was used to determine diagnostic accuracy. RESULTS In both cohorts, the median concentration of EVs was significantly higher in bile samples from patients with malignant CBD stenoses than controls or nonmalignant CBD stenoses (2.41 × 1015 vs 1.60 × 1014 nanoparticles/L in the discovery cohort; P < .0001 and 4.00 × 1015 vs 1.26 × 1014 nanoparticles/L in the verification cohort; P < .0001). A threshold of 9.46 × 1014 nanoparticles/L in bile best distinguished patients with malignant CBD from controls in the discovery cohort. In the verification cohort, this threshold discriminated malignant from nonmalignant CBD stenoses with 100% accuracy. Serum concentration of EVs distinguished patients with malignant vs patients with nonmalignant CBD stenoses with 63.3% diagnostic accuracy. CONCLUSIONS Concentration of EVs in bile samples discriminates between patients with malignant vs nonmalignant CBD stenosis with 100% accuracy. Further studies are needed to confirm these findings. Clinical Trial registration no: ISRCTN66835592.
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Affiliation(s)
- Valeria Severino
- Department of Internal Medicine Specialties, University of Geneva, Geneva, Switzerland; Department of Human Protein Science, University of Geneva, Geneva, Switzerland
| | | | - Myriam Delhaye
- Department of Gastroenterology, Hepatopancreatology and GI Oncology, Erasme University Hospital, Brussels, Belgium
| | - Solange Moll
- Department of Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | | | - Xavier Robin
- Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Jean-Louis Frossard
- Department of Internal Medicine Specialties, University of Geneva, Geneva, Switzerland; Service of Gastroenterology and Hepatology, University Hospitals of Geneva, Switzerland
| | - Annarita Farina
- Department of Internal Medicine Specialties, University of Geneva, Geneva, Switzerland; Department of Human Protein Science, University of Geneva, Geneva, Switzerland.
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Calderón-Santiago M, Priego-Capote F, Turck N, Robin X, Jurado-Gámez B, Sanchez JC, Luque de Castro MD. Human sweat metabolomics for lung cancer screening. Anal Bioanal Chem 2015; 407:5381-92. [PMID: 25935675 DOI: 10.1007/s00216-015-8700-8] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/06/2015] [Accepted: 04/13/2015] [Indexed: 12/25/2022]
Abstract
Sweat is one of the less employed biofluids for discovery of markers in spite of its increased application in medicine for detection of drugs or for diagnostic of cystic fibrosis. In this research, human sweat was used as clinical sample to develop a screening tool for lung cancer, which is the carcinogenic disease with the highest mortality rate owing to the advanced stage at which it is usually detected. In this context, a method based on the metabolite analysis of sweat to discriminate between patients with lung cancer versus smokers as control individuals is proposed. The capability of the metabolites identified in sweat to discriminate between both groups of individuals was studied and, among them, a trisaccharide phosphate presented the best independent performance in terms of the specificity/sensitivity pair (80 and 72.7%, respectively). Additionally, two panels of metabolites were configured using the PanelomiX tool as an attempt to reduce false negatives (at least 80% specificity) and false positives (at least 80% sensitivity). The first panel (80% specificity and 69% sensitivity) was composed by suberic acid, a tetrahexose, and a trihexose, while the second panel (69% specificity and 80% sensitivity) included nonanedioic acid, a trihexose, and the monoglyceride MG(22:2). Thus, the combination of the five metabolites led to a single panel providing 80% specificity and 79% sensitivity, reducing the false positive and negative rates to almost 20%. The method was validated by estimation of within-day and between-days variability of the quantitative analysis of the five metabolites.
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Affiliation(s)
- Mónica Calderón-Santiago
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, 14071, Córdoba, Spain
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Walder B, Robin X, Rebetez MML, Copin JC, Gasche Y, Sanchez JC, Turck N. The prognostic significance of the serum biomarker heart-fatty acidic binding protein in comparison with s100b in severe traumatic brain injury. J Neurotrauma 2014; 30:1631-7. [PMID: 23590685 DOI: 10.1089/neu.2012.2791] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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
The outcome after severe traumatic brain injury (TBI) is largely unfavorable, with approximately two thirds of patients suffering from severe disabilities or dying during the first 6 months. Existing predictive models displayed only limited utility for outcome prediction in individual patients. Time courses of heart-fatty acidic binding protein (H-FABP) and their association with outcome were investigated and compared with S100b. Forty-nine consecutive patients with severe TBI (sTBI; Head component of the Abbreviated Injury Scale [HAIS] >3) with mono and multiple trauma were enrolled in this study. Enzyme-linked immunosorbent assay measured blood concentrations of H-FABP and S100b at 6, 12, 24, and 48 h after TBI. Outcome measures were conscious state at 14 days (Glasgow Coma Scale), disability (Glasgow Outcome Scale Extended; GOSE), and mortality at 3 months. Univariate logistic regression analysis and receiver operating characteristic curves analysis were carried out. Maximal H-FABP and S100b concentrations were observed at 6 h after TBI (34.4±34.0 and 0.64±0.99 ng/mL, respectively). Patients with multi-trauma had significantly higher H-FABP concentrations at 24 and 48 h (22.6±25.6 and 12.4±18.2 ng/mL, respectively), compared to patients with mono trauma (6.9±5.1 and 3.7±4.2 ng/mL, respectively). In the first 48 h, H-FABP and S100b were inversely correlated with the GOSE at 3 months; H-FABP at 48 h predicted mortality with 75% sensitivity and 93% specificity. Early blood levels of H-FABP after sTBI have prognostic significance for survival and disability.
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Affiliation(s)
- Bernhard Walder
- 1 Division of Anaesthesiology, University Hospitals of Geneva , Geneva, Switzerland
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Robin X, Creixell P, Radetskaya O, Santini CC, Longden J, Linding R. Personalized network-based treatments in oncology. Clin Pharmacol Ther 2013; 94:646-50. [PMID: 23995267 DOI: 10.1038/clpt.2013.171] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 08/16/2013] [Indexed: 11/09/2022]
Abstract
Network medicine aims at unraveling cell signaling networks to propose personalized treatments for patients suffering from complex diseases. In this short review, we show the relevance of network medicine to cancer treatment by outlining the potential convergence points of the most recent technological and scientific developments in both drug design and signaling network analysis.
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Affiliation(s)
- X Robin
- Cellular Signal Integration Group (C-SIG), Center for Biological Sequence Analysis (CBS), Department of Systems Biology, Technical University of Denmark (DTU), Lyngby, Denmark
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Tiberti N, Lejon V, Hainard A, Courtioux B, Robin X, Turck N, Kristensson K, Matovu E, Enyaru JC, Mumba Ngoyi D, Krishna S, Bisser S, Ndung′u JM, Büscher P, Sanchez JC. Neopterin is a cerebrospinal fluid marker for treatment outcome evaluation in patients affected by Trypanosoma brucei gambiense sleeping sickness. PLoS Negl Trop Dis 2013; 7:e2088. [PMID: 23469311 PMCID: PMC3585011 DOI: 10.1371/journal.pntd.0002088] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 10/03/2012] [Accepted: 01/19/2013] [Indexed: 11/30/2022] Open
Abstract
Background Post-therapeutic follow-up is essential to confirm cure and to detect early treatment failures in patients affected by sleeping sickness (HAT). Current methods, based on finding of parasites in blood and cerebrospinal fluid (CSF) and counting of white blood cells (WBC) in CSF, are imperfect. New markers for treatment outcome evaluation are needed. We hypothesized that alternative CSF markers, able to diagnose the meningo-encephalitic stage of the disease, could also be useful for the evaluation of treatment outcome. Methodology/Principal findings Cerebrospinal fluid from patients affected by Trypanosoma brucei gambiense HAT and followed for two years after treatment was investigated. The population comprised stage 2 (S2) patients either cured or experiencing treatment failure during the follow-up. IgM, neopterin, B2MG, MMP-9, ICAM-1, VCAM-1, CXCL10 and CXCL13 were first screened on a small number of HAT patients (n = 97). Neopterin and CXCL13 showed the highest accuracy in discriminating between S2 cured and S2 relapsed patients (AUC 99% and 94%, respectively). When verified on a larger cohort (n = 242), neopterin resulted to be the most efficient predictor of outcome. High levels of this molecule before treatment were already associated with an increased risk of treatment failure. At six months after treatment, neopterin discriminated between cured and relapsed S2 patients with 87% specificity and 92% sensitivity, showing a higher accuracy than white blood cell numbers. Conclusions/Significance In the present study, neopterin was highlighted as a useful marker for the evaluation of the post-therapeutic outcome in patients suffering from sleeping sickness. Detectable levels of this marker in the CSF have the potential to shorten the follow-up for HAT patients to six months after the end of the treatment. The reduction of the number of lumbar punctures performed during the follow-up of patients affected by sleeping sickness (HAT) is considered a research priority. Follow-up, consisting of the examination of cerebrospinal fluid (CSF) for presence of parasites and for the number of leukocytes, is necessary to assess treatment outcome. However, diagnosis of treatment failure is still imperfect and WHO encourages improvements in defining criteria. Many studies have attempted to standardize actual methods and to define a cut-off for the number of white blood cells in CSF to define relapses, while only few have proposed alternatives to current practice. Here we show that neopterin, already proven to be a powerful marker for staging T. b. gambiense HAT, is also useful in evaluating post-therapeutic outcome. The measurement of neopterin concentration in CSF during the follow-up may allow reduction in the number of lumbar punctures from five to three for the majority of cured patients.
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Affiliation(s)
- Natalia Tiberti
- Translational Biomarker Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | - Veerle Lejon
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Alexandre Hainard
- Translational Biomarker Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | - Bertrand Courtioux
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR1094, Tropical Neuroepidemiology, Limoges, France
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, Limoges, France
| | - Xavier Robin
- Translational Biomarker Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | - Natacha Turck
- Translational Biomarker Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | | | - Enock Matovu
- Department of Veterinary Parasitology and Microbiology, School of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - John Charles Enyaru
- Department of Biochemistry, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Dieudonné Mumba Ngoyi
- Department of Parasitology, Institut National de Recherche Biomédicale, Kinshasa, D. R. Congo
| | - Sanjeev Krishna
- Centre for Infection, Division of Cellular and Molecular Medicine, St. George's, University of London, London, United Kingdom
| | - Sylvie Bisser
- Institut National de la Santé et de la Recherche Médicale (INSERM), UMR1094, Tropical Neuroepidemiology, Limoges, France
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, Limoges, France
| | | | - Philippe Büscher
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Jean-Charles Sanchez
- Translational Biomarker Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
- * E-mail:
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Gluck F, Hoogland C, Antinori P, Robin X, Nikitin F, Zufferey A, Pasquarello C, Fétaud V, Dayon L, Müller M, Lisacek F, Geiser L, Hochstrasser D, Sanchez JC, Scherl A. EasyProt — An easy-to-use graphical platform for proteomics data analysis. J Proteomics 2013; 79:146-60. [DOI: 10.1016/j.jprot.2012.12.012] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 12/08/2012] [Accepted: 12/18/2012] [Indexed: 11/17/2022]
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Tiberti N, Matovu E, Hainard A, Enyaru JC, Lejon V, Robin X, Turck N, Ngoyi DM, Krishna S, Bisser S, Courtioux B, Büscher P, Kristensson K, Ndung'u JM, Sanchez JC. New biomarkers for stage determination in Trypanosoma brucei rhodesiense sleeping sickness patients. Clin Transl Med 2013; 2:1. [PMID: 23369533 PMCID: PMC3561069 DOI: 10.1186/2001-1326-2-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [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: 10/31/2012] [Accepted: 12/25/2012] [Indexed: 12/26/2022] Open
Abstract
Accurate stage determination is crucial in the choice of treatment for patients suffering from sleeping sickness, also known as human African trypanosomiasis (HAT). Current staging methods, based on the counting of white blood cells (WBC) and the detection of parasites in the cerebrospinal fluid (CSF) have limited accuracy. We hypothesized that immune mediators reliable for staging T. b. gambiense HAT could also be used to stratify T. b. rhodesiense patients, the less common form of HAT. A population comprising 85 T. b. rhodesiense patients, 14 stage 1 (S1) and 71 stage 2 (S2) enrolled in Malawi and Uganda, was investigated. The CSF levels of IgM, MMP-9, CXCL13, CXCL10, ICAM-1, VCAM-1, neopterin and B2MG were measured and their staging performances evaluated using receiver operating characteristic (ROC) analyses. IgM, MMP-9 and CXCL13 were the most accurate markers for stage determination (partial AUC 88%, 86% and 85%, respectively). The combination in panels of three molecules comprising CXCL13-CXCL10-MMP-9 or CXCL13-CXCL10-IgM significantly increased their staging ability to partial AUC 94% (p value < 0.01). The present study highlighted new potential markers for stage determination of T. b. rhodesiense patients. Further investigations are needed to better evaluate these molecules, alone or in panels, as alternatives to WBC to make reliable choice of treatment.
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Affiliation(s)
- Natalia Tiberti
- Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland.
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Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez JC, Müller M. PanelomiX: A threshold-based algorithm to create panels of biomarkers. Translational Proteomics 2013. [DOI: 10.1016/j.trprot.2013.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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Copin JC, Rebetez MML, Turck N, Robin X, Sanchez JC, Schaller K, Gasche Y, Walder B. Matrix metalloproteinase 9 and cellular fibronectin plasma concentrations are predictors of the composite endpoint of length of stay and death in the intensive care unit after severe traumatic brain injury. Scand J Trauma Resusc Emerg Med 2012; 20:83. [PMID: 23249478 PMCID: PMC3570325 DOI: 10.1186/1757-7241-20-83] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 12/16/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The relationship between severe traumatic brain injury (TBI) and blood levels of matrix metalloproteinase-9 (MMP-9) or cellular fibronectin (c-Fn) has never been reported. In this study, we aimed to assess whether plasma concentrations of MMP-9 and c-Fn could have predictive values for the composite endpoint of intensive care unit (ICU) length of stay (LOS) of survivors and mortality after severe TBI. Secondary outcomes were the state of consciousness measured with the Glasgow Coma Scale (GCS) of survivors at 14 days and Glasgow Outcome Scale Extended (GOSE) at 3 months. METHODS Forty-nine patients with abbreviated injury scores of the head region ≥ 4 were included. Blood was sampled at 6, 12, 24 and 48 hours after injury. MMP-9 and c-Fn concentrations were measured by ELISA. The values of MMP-9 and c-Fn, and, for comparison, the value of the GCS on the field of the accident (fGCS), as predictors of the composite outcome of ICU LOS and death were assessed by logistic regression. RESULTS There was a linear relationship between maximal MMP-9 concentration, measured during the 6-12-hour period, and maximal c-Fn concentration, measured during the 24-48-hour period. The risk of staying longer than 9 days in the ICU or of dying was increased in patients with a maximal early MMP-9 concentration ≥ 21.6 ng/ml (OR = 5.0; 95% CI: 1.3 to 18.6; p = 0.02) or with a maximal late c-Fn concentration ≥ 7.7 μg/ml (OR = 5.4; 95% CI: 1.4 to 20.8; p = 0.01). A similar risk association was observed with fGCS ≤8 (OR, 4.4; 95% CI, 1.2-15.8; p = 0.02). No relationship was observed between MMP-9, c-Fn concentrations or fGCS and the GCS at 14 days of survivors and GOSE at 3 months. CONCLUSIONS Plasma MMP-9 and c-Fn concentrations in the first 48 hours after injury are predictive for the composite endpoint of ICU LOS and death after severe TBI but not for consciousness at 14 days and outcome at 3 months.
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Affiliation(s)
- Jean-Christophe Copin
- Geneva Neuroscience Center, University of Geneva, Geneva, Switzerland
- Division of Intensive Care, University Hospitals of Geneva, Geneva, Switzerland
- Division of Neurosurgery, University Hospitals of Geneva, Geneva, Switzerland
- Centre Médical Universitaire, 1, rue Michel Servet, Genève 4, CH-1211, Switzerland
| | | | - Natacha Turck
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University of Geneva Medical Center, Geneva, Switzerland
| | - Xavier Robin
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University of Geneva Medical Center, Geneva, Switzerland
| | - Jean-Charles Sanchez
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University of Geneva Medical Center, Geneva, Switzerland
| | - Karl Schaller
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University of Geneva Medical Center, Geneva, Switzerland
| | - Yvan Gasche
- Geneva Neuroscience Center, University of Geneva, Geneva, Switzerland
- Division of Intensive Care, University Hospitals of Geneva, Geneva, Switzerland
| | - Bernhard Walder
- Division of Anaesthesiology, University Hospitals of Geneva, Geneva, Switzerland
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Turck N, Robin X, Walter N, Fouda C, Hainard A, Sztajzel R, Wagner G, Hochstrasser DF, Montaner J, Burkhard PR, Sanchez JC. Blood glutathione S-transferase-π as a time indicator of stroke onset. PLoS One 2012; 7:e43830. [PMID: 23028472 PMCID: PMC3444482 DOI: 10.1371/journal.pone.0043830] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [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: 04/20/2012] [Accepted: 07/30/2012] [Indexed: 11/18/2022] Open
Abstract
Background Ability to accurately determine time of stroke onset remains challenging. We hypothesized that an early biomarker characterized by a rapid increase in blood after stroke onset may help defining better the time window during which an acute stroke patient may be candidate for intravenous thrombolysis or other intravascular procedures. Methods The blood level of 29 proteins was measured by immunoassays on a prospective cohort of stroke patients (N = 103) and controls (N = 132). Mann-Whitney U tests, ROC curves and diagnostic odds ratios were applied to evaluate their clinical performances. Results Among the 29 molecules tested, GST-π concentration was the most significantly elevated marker in the blood of stroke patients (p<0.001). More importantly, GST-π displayed the best area under the curve (AUC, 0.79) and the best diagnostic odds ratios (10.0) for discriminating early (N = 22, <3 h of stroke onset) vs. late stroke patients (N = 81, >3 h after onset). According to goal-oriented distinct cut-offs (sensitivity(Se)-oriented: 17.7 or specificity(Sp)-oriented: 65.2 ug/L), the GST-π test obtained 91%Se/50%Sp and 50%Se/91%Sp, respectively. Moreover, GST-π showed also the highest AUC (0.83) and performances for detecting patients treated with tPA (N = 12) compared to ineligible patients (N = 103). Conclusions This study demonstrates that GST-π can accurately predict the time of stroke onset in over 50% of early stroke patients. The GST-π test could therefore complement current guidelines for tPA administration and potentially increase the number of patients accessing thrombolysis.
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Affiliation(s)
- Natacha Turck
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, Faculty of Medicine, Geneva, Switzerland.
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Tiberti N, Hainard A, Lejon V, Courtioux B, Matovu E, Enyaru JC, Robin X, Turck N, Kristensson K, Ngoyi DM, Vatunga GML, Krishna S, Büscher P, Bisser S, Ndung’u JM, Sanchez JC. Cerebrospinal fluid neopterin as marker of the meningo-encephalitic stage of Trypanosoma brucei gambiense sleeping sickness. PLoS One 2012; 7:e40909. [PMID: 22815865 PMCID: PMC3399808 DOI: 10.1371/journal.pone.0040909] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [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: 04/25/2012] [Accepted: 06/15/2012] [Indexed: 12/21/2022] Open
Abstract
Background Sleeping sickness, or human African trypanosomiasis (HAT), is a protozoan disease that affects rural communities in sub-Saharan Africa. Determination of the disease stage, essential for correct treatment, represents a key issue in the management of patients. In the present study we evaluated the potential of CXCL10, CXCL13, ICAM-1, VCAM-1, MMP-9, B2MG, neopterin and IgM to complement current methods for staging Trypanosoma brucei gambiense patients. Methods and Findings Five hundred and twelve T. b. gambiense HAT patients originated from Angola, Chad and the Democratic Republic of the Congo (D.R.C.). Their classification as stage 2 (S2) was based on the number of white blood cells (WBC) (>5/µL) or presence of parasites in the cerebrospinal fluid (CSF). The CSF concentration of the eight markers was first measured on a training cohort encompassing 100 patients (44 S1 and 56 S2). IgM and neopterin were the best in discriminating between the two stages of disease with 86.4% and 84.1% specificity respectively, at 100% sensitivity. When a validation cohort (412 patients) was tested, neopterin (14.3 nmol/L) correctly classified 88% of S1 and S2 patients, confirming its high staging power. On this second cohort, neopterin also predicted both the presence of parasites, and of neurological signs, with the same ability as IgM and WBC, the current reference for staging. Conclusions This study has demonstrated that neopterin is an excellent biomarker for staging T. b. gambiense HAT patients. A rapid diagnostic test for detecting this metabolite in CSF could help in more accurate stage determination.
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Affiliation(s)
- Natalia Tiberti
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | - Alexandre Hainard
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | - Veerle Lejon
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bertrand Courtioux
- INSERM UMR1094, Tropical Neuroepidemiology, Limoges, France
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, Limoges, France
| | - Enock Matovu
- Department of Veterinary Parasitology and Microbiology, School of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - John Charles Enyaru
- Department of Biochemistry, College of Natural Sciences, Makerere University, Kampala, Uganda
| | - Xavier Robin
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | - Natacha Turck
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
| | | | - Dieudonné Mumba Ngoyi
- Department of Parasitology, Institut National de Recherche Biomédicale, Kinshasa, D. R. Congo
| | | | - Sanjeev Krishna
- Division of Cellular and Molecular Medicine, Centre for Infection, St. George’s, University of London, London, Great Britain
| | - Philippe Büscher
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sylvie Bisser
- INSERM UMR1094, Tropical Neuroepidemiology, Limoges, France
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, Limoges, France
| | | | - Jean-Charles Sanchez
- Biomedical Proteomics Research Group, Department of Human Protein Sciences, University of Geneva, Geneva, Switzerland
- * E-mail:
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Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez JC, Müller M. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics 2011; 12:77. [PMID: 21414208 PMCID: PMC3068975 DOI: 10.1186/1471-2105-12-77] [Citation(s) in RCA: 6860] [Impact Index Per Article: 527.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 03/17/2011] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface. RESULTS With data previously imported into the R or S+ environment, the pROC package builds ROC curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing ROC curves. Intermediary and final results are visualised in user-friendly interfaces. A case study based on published clinical and biomarker data shows how to perform a typical ROC analysis with pROC. CONCLUSIONS pROC is a package for R and S+ specifically dedicated to ROC analysis. It proposes multiple statistical tests to compare ROC curves, and in particular partial areas under the curve, allowing proper ROC interpretation. pROC is available in two versions: in the R programming language or with a graphical user interface in the S+ statistical software. It is accessible at http://expasy.org/tools/pROC/ under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation.
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Affiliation(s)
- Xavier Robin
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Medical University Centre, Geneva, Switzerland
| | - Natacha Turck
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Medical University Centre, Geneva, Switzerland
| | - Alexandre Hainard
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Medical University Centre, Geneva, Switzerland
| | - Natalia Tiberti
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Medical University Centre, Geneva, Switzerland
| | - Frédérique Lisacek
- Swiss Institute of Bioinformatics, Medical University Centre, Geneva, Switzerland
| | - Jean-Charles Sanchez
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Medical University Centre, Geneva, Switzerland
| | - Markus Müller
- Swiss Institute of Bioinformatics, Medical University Centre, Geneva, Switzerland
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Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez JC, Müller M. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics 2011. [PMID: 21414208 DOI: 10.1186/1471-2105-12-77.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Receiver operating characteristic (ROC) curves are useful tools to evaluate classifiers in biomedical and bioinformatics applications. However, conclusions are often reached through inconsistent use or insufficient statistical analysis. To support researchers in their ROC curves analysis we developed pROC, a package for R and S+ that contains a set of tools displaying, analyzing, smoothing and comparing ROC curves in a user-friendly, object-oriented and flexible interface. RESULTS With data previously imported into the R or S+ environment, the pROC package builds ROC curves and includes functions for computing confidence intervals, statistical tests for comparing total or partial area under the curve or the operating points of different classifiers, and methods for smoothing ROC curves. Intermediary and final results are visualised in user-friendly interfaces. A case study based on published clinical and biomarker data shows how to perform a typical ROC analysis with pROC. CONCLUSIONS pROC is a package for R and S+ specifically dedicated to ROC analysis. It proposes multiple statistical tests to compare ROC curves, and in particular partial areas under the curve, allowing proper ROC interpretation. pROC is available in two versions: in the R programming language or with a graphical user interface in the S+ statistical software. It is accessible at http://expasy.org/tools/pROC/ under the GNU General Public License. It is also distributed through the CRAN and CSAN public repositories, facilitating its installation.
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Affiliation(s)
- Xavier Robin
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Medical University Centre, Geneva, Switzerland.
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Hainard A, Tiberti N, Robin X, Ngoyi DM, Matovu E, Enyaru JCK, Müller M, Turck N, Ndung’u JM, Lejon V, Sanchez JC. Matrix metalloproteinase-9 and intercellular adhesion molecule 1 are powerful staging markers for human African trypanosomiasis. Trop Med Int Health 2010; 16:119-26. [DOI: 10.1111/j.1365-3156.2010.02642.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Tiberti N, Hainard A, Lejon V, Robin X, Ngoyi DM, Turck N, Matovu E, Enyaru J, Ndung'u JM, Scherl A, Dayon L, Sanchez JC. Discovery and verification of osteopontin and Beta-2-microglobulin as promising markers for staging human African trypanosomiasis. Mol Cell Proteomics 2010; 9:2783-95. [PMID: 20724469 DOI: 10.1074/mcp.m110.001008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human African trypanosomiasis, or sleeping sickness, is a parasitic disease endemic in sub-Saharan Africa, transmitted to humans through the bite of a tsetse fly. The first or hemolymphatic stage of the disease is associated with presence of parasites in the bloodstream, lymphatic system, and body tissues. If patients are left untreated, parasites cross the blood-brain barrier and invade the cerebrospinal fluid and the brain parenchyma, giving rise to the second or meningoencephalitic stage. Stage determination is a crucial step in guiding the choice of treatment, as drugs used for S2 are potentially dangerous. Current staging methods, based on counting white blood cells and demonstrating trypanosomes in cerebrospinal fluid, lack specificity and/or sensitivity. In the present study, we used several proteomic strategies to discover new markers with potential for staging human African trypanosomiasis. Cerebrospinal fluid (CSF) samples were collected from patients infected with Trypanosoma brucei gambiense in the Democratic Republic of Congo. The stage was determined following the guidelines of the national control program. The proteome of the samples was analyzed by two-dimensional gel electrophoresis (n = 9), and by sixplex tandem mass tag (TMT) isobaric labeling (n = 6) quantitative mass spectrometry. Overall, 73 proteins were overexpressed in patients presenting the second stage of the disease. Two of these, osteopontin and β-2-microglobulin, were confirmed to be potential markers for staging human African trypanosomiasis (HAT) by Western blot and ELISA. The two proteins significantly discriminated between S1 and S2 patients with high sensitivity (68% and 78%, respectively) for 100% specificity, and a combination of both improved the sensitivity to 91%. The levels of osteopontin and β-2-microglobulin in CSF of S2 patients (μg/ml range), as well as the fold increased concentration in S2 compared with S1 (3.8 and 5.5 respectively) make the two markers good candidates for the development of a test for staging HAT patients.
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Affiliation(s)
- Natalia Tiberti
- Biomedical Proteomics Research Group, Medical University Centre, Geneva, Switzerland
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Robin X, Turck N, Hainard A, Lisacek F, Sanchez JC, Müller M. Bioinformatics for protein biomarker panel classification: what is needed to bring biomarker panels into in vitro diagnostics? Expert Rev Proteomics 2010; 6:675-89. [PMID: 19929612 DOI: 10.1586/epr.09.83] [Citation(s) in RCA: 44] [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] [Indexed: 12/21/2022]
Abstract
A large number of biomarkers have been discovered over the past few years using proteomics techniques. Unfortunately, most of them are neither specific nor sensitive enough to be translated into in vitro diagnostics and routine clinical practice. From this observation, the idea of combining several markers into panels to improve clinical performances has emerged. In this article, we present a discussion of the bioinformatics aspects of biomarker panels and the concomitant challenges, including high dimensionality and low patient number and reproducibility.
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Affiliation(s)
- Xavier Robin
- Biomedical Proteomics Research Group, Department of Structural Biology and Bioinformatics, Medical University Centre, Geneva, Switzerland
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Turck N, Vutskits L, Sanchez-Pena P, Robin X, Hainard A, Gex-Fabry M, Fouda C, Bassem H, Mueller M, Lisacek F, Puybasset L, Sanchez JC. A multiparameter panel method for outcome prediction following aneurysmal subarachnoid hemorrhage. Intensive Care Med 2009; 36:107-15. [DOI: 10.1007/s00134-009-1641-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 07/30/2009] [Accepted: 07/30/2009] [Indexed: 11/28/2022]
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Hainard A, Tiberti N, Robin X, Lejon V, Ngoyi DM, Matovu E, Enyaru JC, Fouda C, Ndung'u JM, Lisacek F, Müller M, Turck N, Sanchez JC. A combined CXCL10, CXCL8 and H-FABP panel for the staging of human African trypanosomiasis patients. PLoS Negl Trop Dis 2009; 3:e459. [PMID: 19554086 PMCID: PMC2696178 DOI: 10.1371/journal.pntd.0000459] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [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: 01/29/2009] [Accepted: 05/15/2009] [Indexed: 11/18/2022] Open
Abstract
Background Human African trypanosomiasis (HAT), also known as sleeping sickness, is a parasitic tropical disease. It progresses from the first, haemolymphatic stage to a neurological second stage due to invasion of parasites into the central nervous system (CNS). As treatment depends on the stage of disease, there is a critical need for tools that efficiently discriminate the two stages of HAT. We hypothesized that markers of brain damage discovered by proteomic strategies and inflammation-related proteins could individually or in combination indicate the CNS invasion by the parasite. Methods Cerebrospinal fluid (CSF) originated from parasitologically confirmed Trypanosoma brucei gambiense patients. Patients were staged on the basis of CSF white blood cell (WBC) count and presence of parasites in CSF. One hundred samples were analysed: 21 from stage 1 (no trypanosomes in CSF and ≤5 WBC/µL) and 79 from stage 2 (trypanosomes in CSF and/or >5 WBC/µL) patients. The concentration of H-FABP, GSTP-1 and S100β in CSF was measured by ELISA. The levels of thirteen inflammation-related proteins (IL-1ra, IL-1β, IL-6, IL-9, IL-10, G-CSF, VEGF, IFN-γ, TNF-α, CCL2, CCL4, CXCL8 and CXCL10) were determined by bead suspension arrays. Results CXCL10 most accurately distinguished stage 1 and stage 2 patients, with a sensitivity of 84% and specificity of 100%. Rule Induction Like (RIL) analysis defined a panel characterized by CXCL10, CXCL8 and H-FABP that improved the detection of stage 2 patients to 97% sensitivity and 100% specificity. Conclusion This study highlights the value of CXCL10 as a single biomarker for staging T. b. gambiense-infected HAT patients. Further combination of CXCL10 with H-FABP and CXCL8 results in a panel that efficiently rules in stage 2 HAT patients. As these molecules could potentially be markers of other CNS infections and disorders, these results should be validated in a larger multi-centric cohort including other inflammatory diseases such as cerebral malaria and active tuberculosis. The actual serological and parasitological tests used for the diagnosis of human African trypanosomiasis (HAT), also known as sleeping sickness, are not sensitive and specific enough. The card agglutination test for trypanosomiasis (CATT) assay, widely used for the diagnosis, is restricted to the gambiense form of the disease, and parasitological detection in the blood and cerebrospinal fluid (CSF) is often very difficult. Another very important problem is the difficulty of staging the disease, a crucial step in the decision of the treatment to be given. While eflornithine is difficult to administer, melarsoprol is highly toxic with incidences of reactive encephalopathy as high as 20%. Staging, which could be diagnosed as early (stage 1) or late (stage 2), relies on the examination of CSF for the presence of parasite and/or white blood cell (WBC) counting. However, the parasite is rarely found in CSF and WBC count is not standardised (cutoff set between 5 and 20 WBC per µL). In the present study, we hypothesized that an early detection of stage 2 patients with one or several proteins in association with clinical evaluation and WBC count would improve staging accuracy and allow more appropriate therapeutic interventions.
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Affiliation(s)
- Alexandre Hainard
- Biomedical Proteomics Research Group, Medical University Centre, Geneva, Switzerland
| | - Natalia Tiberti
- Biomedical Proteomics Research Group, Medical University Centre, Geneva, Switzerland
| | - Xavier Robin
- Biomedical Proteomics Research Group, Medical University Centre, Geneva, Switzerland
| | - Veerle Lejon
- Department of Parasitology, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Enock Matovu
- Department of Veterinary Parasitology and Microbiology, Faculty of Science, Makerere University, Kampala, Uganda
| | - John Charles Enyaru
- Department of Biochemistry, Faculty of Science, Makerere University, Kampala, Uganda
| | - Catherine Fouda
- Biomedical Proteomics Research Group, Medical University Centre, Geneva, Switzerland
| | | | - Frédérique Lisacek
- Swiss Institute of Bioinformatics, Medical University Centre, Geneva, Switzerland
| | - Markus Müller
- Swiss Institute of Bioinformatics, Medical University Centre, Geneva, Switzerland
| | - Natacha Turck
- Biomedical Proteomics Research Group, Medical University Centre, Geneva, Switzerland
| | - Jean-Charles Sanchez
- Biomedical Proteomics Research Group, Medical University Centre, Geneva, Switzerland
- * E-mail:
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Abstract
Bioinformatics tools may assist scientists in all steps of a typical 2-DE gel analysis workflow, that is, from the description of the sample preparation protocols, going through the gel image analysis and protein identification, to the publication of Internet-ready 2-DE gel databases. This short communication highlights in a single and summarised view, this workflow and the current bioinformatics solutions developed by the Proteome Informatics Group at the Swiss Institute of Bioinformatics.
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Affiliation(s)
- Christine Hoogland
- Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland.
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Hainard A, Robin X, Lejon V, Ngoy DM, Matovu E, Enyaru J, Tiberti N, Fouda C, Mueller M, Lisacek F, Turck N, Sanchez JC. A multiparameter panel for the staging of human African trypanosomiasis patients. BMC Proc 2008. [DOI: 10.1186/1753-6561-2-s1-p25] [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: 11/10/2022] Open
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Robin X, Hoogland C, Appel RD, Lisacek F. MIAPEGelDB, a web-based submission tool and public repository for MIAPE gel electrophoresis documents. J Proteomics 2008; 71:249-51. [PMID: 18590991 DOI: 10.1016/j.jprot.2008.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2008] [Revised: 06/06/2008] [Accepted: 06/09/2008] [Indexed: 10/21/2022]
Abstract
The HUPO Proteomics Standards Initiative (PSI) defines standards for data representation in proteomics to facilitate data exchange and comparison, and quality assessment. A set of minimum reporting requirements, called MIAPE (for Minimum Information About a Proteomics Experiment) is provided to ensure consistency of data set annotation. Like the MIAME reporting requirements for transcriptomics, it is anticipated that journal editors will soon require such annotation for published data sets, simplifying further mining of data. Therefore, tools for data entry and public repositories for long-term storage will be needed. MIAPEGelDB is a public repository and a web-based data entry tool for documents conforming to the MIAPE gel electrophoresis guidelines. It aims to guide authors through the publication of the minimal set of information for their proteomics experiments using a clear, sequential interface. After publication by their author, documents in MIAPEGelDB can be viewed in HTML or plain text formats, and further used through stable URL links from remote resources. MIAPEGelDB is accessible at: http://miapegeldb.expasy.org/.
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Affiliation(s)
- Xavier Robin
- Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Switzerland
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