1
|
Häussler U, Neres J, Vandenplas C, Eykens C, Kadiu I, Schramm C, Fleurance R, Stanley P, Godard P, de Mot L, van Eyll J, Knobeloch KP, Haas CA, Dedeurwaerdere S. Downregulation of Ubiquitin-Specific Protease 15 (USP15) Does Not Provide Therapeutic Benefit in Experimental Mesial Temporal Lobe Epilepsy. Mol Neurobiol 2024; 61:2367-2389. [PMID: 37874479 PMCID: PMC10973041 DOI: 10.1007/s12035-023-03692-2] [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: 07/11/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
Structural epilepsies display complex immune activation signatures. However, it is unclear which neuroinflammatory pathways drive pathobiology. Transcriptome studies of brain resections from mesial temporal lobe epilepsy (mTLE) patients revealed a dysregulation of transforming growth factor β, interferon α/β, and nuclear factor erythroid 2-related factor 2 pathways. Since these pathways are regulated by ubiquitin-specific proteases (USP), in particular USP15, we hypothesized that USP15 blockade may provide therapeutic relief in treatment-resistant epilepsies. For validation, transgenic mice which either constitutively or inducibly lack Usp15 gene expression underwent intrahippocampal kainate injections to induce mTLE. We show that the severity of status epilepticus is unaltered in mice constitutively lacking Usp15 compared to wild types. Cell death, reactive gliosis, and changes in the inflammatory transcriptome were pronounced at 4 days after kainate injection. However, these brain inflammation signatures did not differ between genotypes. Likewise, induced deletion of Usp15 in chronic epilepsy did not affect seizure generation, cell death, gliosis, or the transcriptome. Concordantly, siRNA-mediated knockdown of Usp15 in a microglial cell line did not impact inflammatory responses in the form of cytokine release. Our data show that a lack of USP15 is insufficient to modulate the expression of relevant neuroinflammatory pathways in an mTLE mouse model and do not support targeting USP15 as a therapeutic approach for pharmacoresistant epilepsy.
Collapse
Affiliation(s)
- Ute Häussler
- Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Strasse 64, 79106, Freiburg, Germany.
- BrainLinks-BrainTools Center, University of Freiburg, Georges-Koehler-Allee 201, 79110, Freiburg, Germany.
| | - João Neres
- Early Solutions, UCB Biopharma SRL, Chemin du Foriest, 1420, Braine L'Alleud, Belgium
| | - Catherine Vandenplas
- Early Solutions, UCB Biopharma SRL, Chemin du Foriest, 1420, Braine L'Alleud, Belgium
| | - Caroline Eykens
- Early Solutions, UCB Biopharma SRL, Chemin du Foriest, 1420, Braine L'Alleud, Belgium
| | - Irena Kadiu
- Early Solutions, UCB Biopharma SRL, Chemin du Foriest, 1420, Braine L'Alleud, Belgium
| | - Carolin Schramm
- Early Solutions, UCB Biopharma SRL, Chemin du Foriest, 1420, Braine L'Alleud, Belgium
| | - Renaud Fleurance
- Early Solutions, UCB Biopharma SRL, Chemin du Foriest, 1420, Braine L'Alleud, Belgium
| | - Phil Stanley
- Early Development Statistics, UCB Celltech, 208 Bath Road, Slough, Berkshire, SL1 3WE, UK
| | - Patrice Godard
- Early Solutions, UCB Biopharma SRL, Chemin du Foriest, 1420, Braine L'Alleud, Belgium
| | - Laurane de Mot
- Early Solutions, UCB Biopharma SRL, Chemin du Foriest, 1420, Braine L'Alleud, Belgium
| | - Jonathan van Eyll
- Early Solutions, UCB Biopharma SRL, Chemin du Foriest, 1420, Braine L'Alleud, Belgium
| | - Klaus-Peter Knobeloch
- Institute for Neuropathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Strasse 64, 79106, Freiburg, Germany.
- CIBSS - Centre for Integrative Biological Signalling Studies, Freiburg, Germany.
| | - Carola A Haas
- Experimental Epilepsy Research, Department of Neurosurgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacher Strasse 64, 79106, Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, Georges-Koehler-Allee 201, 79110, Freiburg, Germany
- Center for Basics in NeuroModulation, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
- Bernstein Center Freiburg, University of Freiburg, Hansastr. 9a, 79104, Freiburg, Germany
| | | |
Collapse
|
2
|
François L, Romagnolo A, Luinenburg MJ, Anink JJ, Godard P, Rajman M, van Eyll J, Mühlebner A, Skelton A, Mills JD, Dedeurwaerdere S, Aronica E. Identification of gene regulatory networks affected across drug-resistant epilepsies. Nat Commun 2024; 15:2180. [PMID: 38467626 PMCID: PMC10928184 DOI: 10.1038/s41467-024-46592-2] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/13/2024] Open
Abstract
Epilepsy is a chronic and heterogenous disease characterized by recurrent unprovoked seizures, that are commonly resistant to antiseizure medications. This study applies a transcriptome network-based approach across epilepsies aiming to improve understanding of molecular disease pathobiology, recognize affected biological mechanisms and apply causal reasoning to identify therapeutic hypotheses. This study included the most common drug-resistant epilepsies (DREs), such as temporal lobe epilepsy with hippocampal sclerosis (TLE-HS), and mTOR pathway-related malformations of cortical development (mTORopathies). This systematic comparison characterized the global molecular signature of epilepsies, elucidating the key underlying mechanisms of disease pathology including neurotransmission and synaptic plasticity, brain extracellular matrix and energy metabolism. In addition, specific dysregulations in neuroinflammation and oligodendrocyte function were observed in TLE-HS and mTORopathies, respectively. The aforementioned mechanisms are proposed as molecular hallmarks of DRE with the identified upstream regulators offering opportunities for drug-target discovery and development.
Collapse
Affiliation(s)
- Liesbeth François
- UCB Pharma, Early Solutions, Braine-l'Alleud, Belgium.
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands.
| | - Alessia Romagnolo
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Mark J Luinenburg
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Jasper J Anink
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | | | - Marek Rajman
- UCB Pharma, Early Solutions, Braine-l'Alleud, Belgium
| | | | - Angelika Mühlebner
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - James D Mills
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, Chalfont, UK
| | | | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands.
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands.
| |
Collapse
|
3
|
Zimmer TS, David B, Broekaart DWM, Schidlowski M, Ruffolo G, Korotkov A, van der Wel NN, van Rijen PC, Mühlebner A, van Hecke W, Baayen JC, Idema S, François L, van Eyll J, Dedeurwaerdere S, Kessels HW, Surges R, Rüber T, Gorter JA, Mills JD, van Vliet EA, Aronica E. Seizure-mediated iron accumulation and dysregulated iron metabolism after status epilepticus and in temporal lobe epilepsy. Acta Neuropathol 2021; 142:729-759. [PMID: 34292399 PMCID: PMC8423709 DOI: 10.1007/s00401-021-02348-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/02/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022]
Abstract
Neuronal dysfunction due to iron accumulation in conjunction with reactive oxygen species (ROS) could represent an important, yet underappreciated, component of the epileptogenic process. However, to date, alterations in iron metabolism in the epileptogenic brain have not been addressed in detail. Iron-related neuropathology and antioxidant metabolic processes were investigated in resected brain tissue from patients with temporal lobe epilepsy and hippocampal sclerosis (TLE-HS), post-mortem brain tissue from patients who died after status epilepticus (SE) as well as brain tissue from the electrically induced SE rat model of TLE. Magnetic susceptibility of the presumed seizure-onset zone from three patients with focal epilepsy was compared during and after seizure activity. Finally, the cellular effects of iron overload were studied in vitro using an acute mouse hippocampal slice preparation and cultured human fetal astrocytes. While iron-accumulating neurons had a pyknotic morphology, astrocytes appeared to acquire iron-sequestrating capacity as indicated by prominent ferritin expression and iron retention in the hippocampus of patients with SE or TLE. Interictal to postictal comparison revealed increased magnetic susceptibility in the seizure-onset zone of epilepsy patients. Post-SE rats had consistently higher hippocampal iron levels during the acute and chronic phase (when spontaneous recurrent seizures are evident). In vitro, in acute slices that were exposed to iron, neurons readily took up iron, which was exacerbated by induced epileptiform activity. Human astrocyte cultures challenged with iron and ROS increased their antioxidant and iron-binding capacity, but simultaneously developed a pro-inflammatory phenotype upon chronic exposure. These data suggest that seizure-mediated, chronic neuronal iron uptake might play a role in neuronal dysfunction/loss in TLE-HS. On the other hand, astrocytes sequester iron, specifically in chronic epilepsy. This function might transform astrocytes into a highly resistant, pro-inflammatory phenotype potentially contributing to pro-epileptogenic inflammatory processes.
Collapse
Affiliation(s)
- Till S Zimmer
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Bastian David
- Department of Epileptology, University Hospital Bonn, Bonn, Germany
| | - Diede W M Broekaart
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Martin Schidlowski
- Department of Epileptology, University Hospital Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Gabriele Ruffolo
- Laboratory affiliated to Istituto Pasteur Italia, Department of Physiology and Pharmacology, University of Rome Sapienza, Rome, Italy
| | - Anatoly Korotkov
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Nicole N van der Wel
- Department Cell Biology and Histology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department Electron Microscopy Center Amsterdam, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter C van Rijen
- Department of Neurosurgery, Brain Centre, Rudolf Magnus Institute for Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Angelika Mühlebner
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wim van Hecke
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johannes C Baayen
- Department of Neurosurgery, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sander Idema
- Department of Neurosurgery, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Liesbeth François
- Neurosciences Therapeutic Area, UCB Pharma, Braine-l'Alleud, Belgium
| | - Jonathan van Eyll
- Neurosciences Therapeutic Area, UCB Pharma, Braine-l'Alleud, Belgium
| | | | - Helmut W Kessels
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Rainer Surges
- Department of Epileptology, University Hospital Bonn, Bonn, Germany
| | - Theodor Rüber
- Department of Epileptology, University Hospital Bonn, Bonn, Germany
| | - Jan A Gorter
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - James D Mills
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Department of Clinical and Experimental Epilepsy, UCL, London, UK
- Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | - Erwin A van Vliet
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
- Center for Neuroscience, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
- Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands.
| |
Collapse
|
4
|
Zimmer TS, Broekaart DWM, Luinenburg M, Mijnsbergen C, Anink JJ, Sim NS, Michailidou I, Jansen FE, van Rijen PC, Lee JH, François L, van Eyll J, Dedeurwaerdere S, van Vliet EA, Mühlebner A, Mills JD, Aronica E. Balloon cells promote immune system activation in focal cortical dysplasia type 2b. Neuropathol Appl Neurobiol 2021; 47:826-839. [PMID: 34003514 PMCID: PMC8518746 DOI: 10.1111/nan.12736] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 05/12/2021] [Indexed: 11/29/2022]
Abstract
Aims Focal cortical dysplasia (FCD) type 2 is an epileptogenic malformation of the neocortex associated with somatic mutations in the mammalian target of rapamycin (mTOR) pathway. Histopathologically, FCD 2 is subdivided into FCD 2a and FCD 2b, the only discriminator being the presence of balloon cells (BCs) in FCD 2b. While pro‐epileptogenic immune system activation and inflammatory responses are commonly detected in both subtypes, it is unknown what contextual role BCs play. Methods The present study employed RNA sequencing of surgically resected brain tissue from FCD 2a (n = 11) and FCD 2b (n = 20) patients compared to autopsy control (n = 9) focusing on three immune system processes: adaptive immunity, innate immunity and cytokine production. This analysis was followed by immunohistochemistry on a clinically well‐characterised FCD 2 cohort. Results Differential expression analysis revealed stronger expression of components of innate immunity, adaptive immunity and cytokine production in FCD 2b than in FCD 2a, particularly complement activation and antigen presentation. Immunohistochemical analysis confirmed these findings, with strong expression of leukocyte antigen I and II in FCD 2b as compared to FCD 2a. Moreover, T‐lymphocyte tissue infiltration was elevated in FCD 2b. Expression of markers of immune system activation in FCD 2b was concentrated in subcortical white matter. Lastly, antigen presentation was strongly correlated with BC load in FCD 2b lesions. Conclusion We conclude that, next to mutation‐driven mTOR activation and seizure activity, BCs are crucial drivers of inflammation in FCD 2b. Our findings indicate that therapies targeting inflammation may be beneficial in FCD 2b.
Collapse
Affiliation(s)
- Till S Zimmer
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Diede W M Broekaart
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Mark Luinenburg
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Caroline Mijnsbergen
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Jasper J Anink
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Nam Suk Sim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Iliana Michailidou
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Floor E Jansen
- Department of Paediatric Neurology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Peter C van Rijen
- Department of Neurosurgery, Brain Center, Rudolf Magnus Institute for Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.,SoVarGen, Inc, Daejeon, Republic of Korea
| | - Liesbeth François
- Neurosciences Therapeutic Area, UCB Pharma, Braine-l'Alleud, Belgium
| | - Jonathan van Eyll
- Neurosciences Therapeutic Area, UCB Pharma, Braine-l'Alleud, Belgium
| | - Stefanie Dedeurwaerdere
- Neurosciences Therapeutic Area, UCB Pharma, Braine-l'Alleud, Belgium.,Department of Translational Neuroscience, University of Antwerp, Wilrijk, Belgium
| | - Erwin A van Vliet
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands.,Swammerdam Institute for Life Sciences, Center for Neuroscience, University of Amsterdam, Amsterdam, The Netherlands
| | - Angelika Mühlebner
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - James D Mills
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands.,Department of Clinical and Experimental Epilepsy, UCL, London, UK.,Chalfont Centre for Epilepsy, Chalfont St Peter, UK
| | - Eleonora Aronica
- Department of (Neuro)Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands.,Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, The Netherlands
| |
Collapse
|
5
|
Srivastava PK, van Eyll J, Godard P, Mazzuferi M, Delahaye-Duriez A, Van Steenwinckel J, Gressens P, Danis B, Vandenplas C, Foerch P, Leclercq K, Mairet-Coello G, Cardenas A, Vanclef F, Laaniste L, Niespodziany I, Keaney J, Gasser J, Gillet G, Shkura K, Chong SA, Behmoaras J, Kadiu I, Petretto E, Kaminski RM, Johnson MR. A systems-level framework for drug discovery identifies Csf1R as an anti-epileptic drug target. Nat Commun 2018; 9:3561. [PMID: 30177815 PMCID: PMC6120885 DOI: 10.1038/s41467-018-06008-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [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: 05/30/2018] [Accepted: 08/03/2018] [Indexed: 01/14/2023] Open
Abstract
The identification of drug targets is highly challenging, particularly for diseases of the brain. To address this problem, we developed and experimentally validated a general computational framework for drug target discovery that combines gene regulatory information with causal reasoning (“Causal Reasoning Analytical Framework for Target discovery”—CRAFT). Using a systems genetics approach and starting from gene expression data from the target tissue, CRAFT provides a predictive framework for identifying cell membrane receptors with a direction-specified influence over disease-related gene expression profiles. As proof of concept, we applied CRAFT to epilepsy and predicted the tyrosine kinase receptor Csf1R as a potential therapeutic target. The predicted effect of Csf1R blockade in attenuating epilepsy seizures was validated in three pre-clinical models of epilepsy. These results highlight CRAFT as a systems-level framework for target discovery and suggest Csf1R blockade as a novel therapeutic strategy in epilepsy. CRAFT is applicable to disease settings other than epilepsy. The identification of new drug targets is highly challenging, particularly for diseases of the brain. This study describes a general computational gene regulatory framework called CRAFT for drug target discovery, and the authors use CRAFT to identify the microglial membrane receptor Csf1R as a potential therapeutic target for epilepsy.
Collapse
Affiliation(s)
| | - Jonathan van Eyll
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Patrice Godard
- Clarivate Analytics (formerly the IP & Science Business of Thomson Reuters), 5901 Priestly Drive, #200, Carlsbad, CA, 92008, USA
| | - Manuela Mazzuferi
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK.,UFR de Santé, Médecine et Biologie Humaine, Sorbonne Paris Cité, Université Paris 13, Bobigny, France.,PROTECT, INSERM, Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | | | - Pierre Gressens
- PROTECT, INSERM, Sorbonne Paris Cité, Université Paris Diderot, Paris, France.,School of Biomedical Engineering & Imaging Sciences, Centre for the Developing Brain, King's College London, St. Thomas' Hospital, London, SE1 7EH, UK
| | - Benedicte Danis
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | | | - Patrik Foerch
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Karine Leclercq
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | | | - Alvaro Cardenas
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Frederic Vanclef
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Liisi Laaniste
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK
| | | | - James Keaney
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Julien Gasser
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Gaelle Gillet
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK
| | - Seon-Ah Chong
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK
| | - Irena Kadiu
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Enrico Petretto
- Duke-NUS Medical School, Centre for Computational Biology, 8 College Road, Singapore, 169857, Republic of Singapore. .,Faculty of Medicine, MRC Clinical Sciences Centre, Imperial College London, London, W12 0NN, UK.
| | - Rafal M Kaminski
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium.
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK.
| |
Collapse
|
6
|
Abstract
The understanding of molecular processes involved in a specific biological system can be significantly improved by combining and comparing different data sets and knowledge resources. However, these information sources often use different identification systems and an identifier conversion step is required before any integration effort. Mapping between identifiers is often provided by the reference information resources and several tools have been implemented to simplify their use. However, most of these tools do not combine the information provided by individual resources to increase the completeness of the mapping process. Also, deprecated identifiers from former versions of databases are not taken into account. Finally, finding automatically the most relevant path to map identifiers from one scope to the other is often not trivial. The Biological Entity Dictionary (BED) addresses these three challenges by relying on a graph data model describing possible relationships between entities and their identifiers. This model has been implemented using Neo4j and an R package provides functions to query the graph but also to create and feed a custom instance of the database. This design combined with a local installation of the graph database and a cache system make BED very efficient to convert large lists of identifiers.
Collapse
Affiliation(s)
- Patrice Godard
- Clarivate Analytics, Carlsbad, CA, 92008, USA.,UCB Pharma, Braine-l'Alleud, 1420, Belgium
| | | |
Collapse
|
7
|
De Meulder B, Lefaudeux D, Bansal AT, Mazein A, Chaiboonchoe A, Ahmed H, Balaur I, Saqi M, Pellet J, Ballereau S, Lemonnier N, Sun K, Pandis I, Yang X, Batuwitage M, Kretsos K, van Eyll J, Bedding A, Davison T, Dodson P, Larminie C, Postle A, Corfield J, Djukanovic R, Chung KF, Adcock IM, Guo YK, Sterk PJ, Manta A, Rowe A, Baribaud F, Auffray C. A computational framework for complex disease stratification from multiple large-scale datasets. BMC Syst Biol 2018; 12:60. [PMID: 29843806 PMCID: PMC5975674 DOI: 10.1186/s12918-018-0556-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 02/21/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND Multilevel data integration is becoming a major area of research in systems biology. Within this area, multi-'omics datasets on complex diseases are becoming more readily available and there is a need to set standards and good practices for integrated analysis of biological, clinical and environmental data. We present a framework to plan and generate single and multi-'omics signatures of disease states. METHODS The framework is divided into four major steps: dataset subsetting, feature filtering, 'omics-based clustering and biomarker identification. RESULTS We illustrate the usefulness of this framework by identifying potential patient clusters based on integrated multi-'omics signatures in a publicly available ovarian cystadenocarcinoma dataset. The analysis generated a higher number of stable and clinically relevant clusters than previously reported, and enabled the generation of predictive models of patient outcomes. CONCLUSIONS This framework will help health researchers plan and perform multi-'omics big data analyses to generate hypotheses and make sense of their rich, diverse and ever growing datasets, to enable implementation of translational P4 medicine.
Collapse
Affiliation(s)
- Bertrand De Meulder
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France.
| | - Diane Lefaudeux
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Aruna T Bansal
- Acclarogen Ltd, St John's Innovation Centre, Cambridge, CB4 OWS, UK
| | - Alexander Mazein
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Amphun Chaiboonchoe
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Hassan Ahmed
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Irina Balaur
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Mansoor Saqi
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Johann Pellet
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Stéphane Ballereau
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Nathanaël Lemonnier
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France
| | - Kai Sun
- Data Science Institute, Imperial College, London, SW7 2AZ, UK
| | - Ioannis Pandis
- Data Science Institute, Imperial College, London, SW7 2AZ, UK.,Janssen Research and Development Ltd, High Wycombe, HP12 4DP, UK
| | - Xian Yang
- Data Science Institute, Imperial College, London, SW7 2AZ, UK
| | | | | | | | | | - Timothy Davison
- Janssen Research and Development Ltd, High Wycombe, HP12 4DP, UK
| | - Paul Dodson
- AstraZeneca Ltd, Alderley Park, Macclesfield, SK10 4TG, UK
| | | | - Anthony Postle
- Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
| | - Julie Corfield
- AstraZeneca R & D, 43150, Mölndal, Sweden.,Arateva R & D Ltd, Nottingham, NG1 1GF, UK
| | - Ratko Djukanovic
- Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
| | - Kian Fan Chung
- National Hearth and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Ian M Adcock
- National Hearth and Lung Institute, Imperial College London, London, SW3 6LY, UK
| | - Yi-Ke Guo
- Data Science Institute, Imperial College, London, SW7 2AZ, UK
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, AZ1105, The Netherlands
| | - Alexander Manta
- Research Informatics, Roche Diagnostics GmbH, 82008, Unterhaching, Germany
| | - Anthony Rowe
- Janssen Research and Development Ltd, High Wycombe, HP12 4DP, UK
| | | | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL, EISBM, 50 Avenue Tony Garnier, 69007, Lyon, France.
| | | |
Collapse
|
8
|
Srivastava PK, Bagnati M, Delahaye-Duriez A, Ko JH, Rotival M, Langley SR, Shkura K, Mazzuferi M, Danis B, van Eyll J, Foerch P, Behmoaras J, Kaminski RM, Petretto E, Johnson MR. Genome-wide analysis of differential RNA editing in epilepsy. Genome Res 2018; 27:440-450. [PMID: 28250018 PMCID: PMC5340971 DOI: 10.1101/gr.210740.116] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [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: 05/31/2016] [Accepted: 01/10/2017] [Indexed: 02/03/2023]
Abstract
The recoding of genetic information through RNA editing contributes to proteomic diversity, but the extent and significance of RNA editing in disease is poorly understood. In particular, few studies have investigated the relationship between RNA editing and disease at a genome-wide level. Here, we developed a framework for the genome-wide detection of RNA sites that are differentially edited in disease. Using RNA-sequencing data from 100 hippocampi from mice with epilepsy (pilocarpine–temporal lobe epilepsy model) and 100 healthy control hippocampi, we identified 256 RNA sites (overlapping with 87 genes) that were significantly differentially edited between epileptic cases and controls. The degree of differential RNA editing in epileptic mice correlated with frequency of seizures, and the set of genes differentially RNA-edited between case and control mice were enriched for functional terms highly relevant to epilepsy, including “neuron projection” and “seizures.” Genes with differential RNA editing were preferentially enriched for genes with a genetic association to epilepsy. Indeed, we found that they are significantly enriched for genes that harbor nonsynonymous de novo mutations in patients with epileptic encephalopathy and for common susceptibility variants associated with generalized epilepsy. These analyses reveal a functional convergence between genes that are differentially RNA-edited in acquired symptomatic epilepsy and those that contribute risk for genetic epilepsy. Taken together, our results suggest a potential role for RNA editing in the epileptic hippocampus in the occurrence and severity of epileptic seizures.
Collapse
Affiliation(s)
| | - Marta Bagnati
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, United Kingdom
| | - Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom
| | - Jeong-Hun Ko
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, United Kingdom
| | - Maxime Rotival
- Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France
| | - Sarah R Langley
- Duke-NUS Medical School, Singapore 169857, Republic of Singapore
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom
| | | | | | | | - Patrik Foerch
- Neuroscience TA, UCB Pharma, 1420 Braine-l'Alleud, Belgium
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research (CCIR), Imperial College London, London W12 0NN, United Kingdom
| | | | - Enrico Petretto
- Duke-NUS Medical School, Singapore 169857, Republic of Singapore
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College Faculty of Medicine, London W12 0NN, United Kingdom
| |
Collapse
|
9
|
Godard P, van Eyll J. Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy. Nucleic Acids Res 2015; 43:3490-7. [PMID: 25800743 PMCID: PMC4402548 DOI: 10.1093/nar/gkv249] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [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: 12/17/2014] [Accepted: 03/10/2015] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs (miRNAs) are involved in the regulation of gene expression at a post-transcriptional level. As such, monitoring miRNA expression has been increasingly used to assess their role in regulatory mechanisms of biological processes. In large scale studies, once miRNAs of interest have been identified, the target genes they regulate are often inferred using algorithms or databases. A pathway analysis is then often performed in order to generate hypotheses about the relevant biological functions controlled by the miRNA signature. Here we show that the method widely used in scientific literature to identify these pathways is biased and leads to inaccurate results. In addition to describing the bias and its origin we present an alternative strategy to identify potential biological functions specifically impacted by a miRNA signature. More generally, our study exemplifies the crucial need of relevant negative controls when developing, and using, bioinformatics methods.
Collapse
Affiliation(s)
- Patrice Godard
- IP & Science, Thomson Reuters, 5901 Priestly Drive, #200, Carlsbad, CA 92008, USA
| | | |
Collapse
|
10
|
Mazzuferi M, Kumar G, van Eyll J, Danis B, Foerch P, Kaminski RM. Nrf2 defense pathway: Experimental evidence for its protective role in epilepsy. Ann Neurol 2013; 74:560-8. [DOI: 10.1002/ana.23940] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/27/2013] [Accepted: 05/10/2013] [Indexed: 12/12/2022]
|