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Chegraoui H, Guillemot V, Rebei A, Gloaguen A, Grill J, Philippe C, Frouin V. Integrating multiomics and prior knowledge: a study of the Graphnet penalty impact. Bioinformatics 2023; 39:btad454. [PMID: 37490467 PMCID: PMC10403429 DOI: 10.1093/bioinformatics/btad454] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 05/04/2023] [Accepted: 07/24/2023] [Indexed: 07/27/2023] Open
Abstract
MOTIVATION In the field of oncology, statistical models are used for the discovery of candidate factors that influence the development of the pathology or its outcome. These statistical models can be designed in a multiblock framework to study the relationship between different multiomic data, and variable selection is often achieved by imposing constraints on the model parameters. A priori graph constraints have been used in the literature as a way to improve feature selection in the model, yielding more interpretability. However, it is still unclear how these graphs interact with the models and how they impact the feature selection. Additionally, with the availability of different graphs encoding different information, one can wonder how the choice of the graph meaningfully impacts the results obtained. RESULTS We proposed to study the graph penalty impact on a multiblock model. Specifically, we used the SGCCA as the multiblock framework. We studied the effect of the penalty on the model using the TCGA-LGG dataset. Our findings are 3-fold. We showed that the graph penalty increases the number of selected genes from this dataset, while selecting genes already identified in other works as pertinent biomarkers in the pathology. We demonstrated that using different graphs leads to different though consistent results, but that graph density is the main factor influencing the obtained results. Finally, we showed that the graph penalty increases the performance of the survival prediction from the model-derived components and the interpretability of the results. AVAILABILITY AND IMPLEMENTATION Source code is freely available at https://github.com/neurospin/netSGCCA.
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Affiliation(s)
- Hamza Chegraoui
- Université Paris-Saclay, CEA, Neurospin, 91191 Gif-sur-Yvette, France
| | - Vincent Guillemot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015 Paris, France
| | - Amine Rebei
- Université Paris-Saclay, CEA, Neurospin, 91191 Gif-sur-Yvette, France
| | - Arnaud Gloaguen
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris-Saclay, 91000 Evry, France
| | - Jacques Grill
- Département Cancérologie de l’enfant et de l’adolescent, Gustave-Roussy, 94800 Villejuif, France
- Prédicteurs Moléculaires et Nouvelles Cibles en Oncologie—U981, Inserm, Université Paris-Saclay, 94800 Villejuif, France
| | - Cathy Philippe
- Université Paris-Saclay, CEA, Neurospin, 91191 Gif-sur-Yvette, France
| | - Vincent Frouin
- Université Paris-Saclay, CEA, Neurospin, 91191 Gif-sur-Yvette, France
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Tanguy D, Rametti-Lacroux A, Bouzigues A, Saracino D, Le Ber I, Godefroy V, Morandi X, Jannin P, Levy R, Batrancourt B, Migliaccio R, Azuar C, Dubois B, Lecouturier K, Araujo CM, Janvier E, Jourdain A, Rametti-Lacroux A, Coriou S, Brochard VB, Gaudebout C, Ferrand-Verdejo J, Bonnefous L, Pochan-Leva F, Jeanne L, Joulié M, Provost M, Renaud R, Hachemi S, Guillemot V, Bendetowicz D, Carle G, Socha J, Pineau F, Marin F, Liu Y, Mullot P, Mousli A, Blossier A, Visentin G, Tanguy D, Godefroy V, Sezer I, Boucly M, Cabrol-Douat B, Odobez R, Marque C, Tessereau-Barbot D, Raud A, Funkiewiez A, Chamayou C, Cognat E, Le Bozec M, Bouzigues A, Le Du V, Bombois S, Simard C, Fulcheri P, Guitton H, Peltier C, Lejeune FX, Jorgensen L, Mariani LL, Corvol JC, Valero-Cabre A, Garcin B, Volle E, Le Ber I, Migliaccio R, Levy R. Behavioural disinhibition in frontotemporal dementia investigated within an ecological framework. Cortex 2023; 160:152-166. [PMID: 36658040 DOI: 10.1016/j.cortex.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 09/29/2022] [Accepted: 11/09/2022] [Indexed: 12/29/2022]
Abstract
Disinhibition is a core symptom in behavioural variant frontotemporal dementia (bvFTD) particularly affecting the daily lives of both patients and caregivers. Yet, characterisation of inhibition disorders is still unclear and management options of these disorders are limited. Questionnaires currently used to investigate behavioural disinhibition do not differentiate between several subtypes of disinhibition, encompass observation biases and lack of ecological validity. In the present work, we explored disinhibition in an original semi-ecological situation, by distinguishing three categories of disinhibition: compulsivity, impulsivity and social disinhibition. First, we measured prevalence and frequency of these disorders in 23 bvFTD patients and 24 healthy controls (HC) in order to identify the phenotypical heterogeneity of disinhibition. Then, we examined the relationships between these metrics, the neuropsychological scores and the behavioural states to propose a more comprehensive view of these neuropsychiatric manifestations. Finally, we studied the context of occurrence of these disorders by investigating environmental factors potentially promoting or reducing them. As expected, we found that patients were more compulsive, impulsive and socially disinhibited than HC. We found that 48% of patients presented compulsivity (e.g., repetitive actions), 48% impulsivity (e.g., oral production) and 100% of the patients group showed social disinhibition (e.g., disregards for rules or investigator). Compulsivity was negatively related with emotions recognition. BvFTD patients were less active if not encouraged in an activity, and their social disinhibition decreased as activity increased. Finally, impulsivity and social disinhibition decreased when patients were asked to focus on a task. Summarising, this study underlines the importance to differentiate subtypes of disinhibition as well as the setting in which they are exhibited, and points to stimulating area for non-pharmacological management.
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Affiliation(s)
- Delphine Tanguy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, FrontLab, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France; Univ Rennes, CHU Rennes, Inserm, LTSI - UMR 1099, Rennes, France
| | - Armelle Rametti-Lacroux
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, FrontLab, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Arabella Bouzigues
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, FrontLab, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Dario Saracino
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, FrontLab, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France; AP-HP, Groupe Hospitalier Pitié-Salpêtriѐre, Department of Neurology, IM2A, Paris, France
| | - Isabelle Le Ber
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, FrontLab, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France; AP-HP, Groupe Hospitalier Pitié-Salpêtriѐre, Department of Neurology, IM2A, Paris, France
| | - Valérie Godefroy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, FrontLab, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France
| | - Xavier Morandi
- Univ Rennes, CHU Rennes, Inserm, LTSI - UMR 1099, Rennes, France
| | - Pierre Jannin
- Univ Rennes, CHU Rennes, Inserm, LTSI - UMR 1099, Rennes, France
| | - Richard Levy
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, FrontLab, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France; Univ Rennes, CHU Rennes, Inserm, LTSI - UMR 1099, Rennes, France; AP-HP, Groupe Hospitalier Pitié-Salpêtriѐre, Department of Neurology, IM2A, Paris, France
| | - Bénédicte Batrancourt
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, FrontLab, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France.
| | - Raffaella Migliaccio
- Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM, FrontLab, Inserm, CNRS, AP-HP, Hôpital de la Pitié Salpêtrière, Paris, France; AP-HP, Groupe Hospitalier Pitié-Salpêtriѐre, Department of Neurology, IM2A, Paris, France.
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Feige L, Kozaki T, Dias de Melo G, Guillemot V, Larrous F, Ginhoux F, Bourhy H. Susceptibilities of CNS Cells towards Rabies Virus Infection Is Linked to Cellular Innate Immune Responses. Viruses 2022; 15:88. [PMID: 36680128 PMCID: PMC9860954 DOI: 10.3390/v15010088] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022] Open
Abstract
Rabies is caused by neurotropic rabies virus (RABV), contributing to 60,000 human deaths annually. Even though rabies leads to major public health concerns worldwide, we still do not fully understand factors determining RABV tropism and why glial cells are unable to clear RABV from the infected brain. Here, we compare susceptibilities and immune responses of CNS cell types to infection with two RABV strains, Tha and its attenuated variant Th2P-4M, mutated on phospho- (P-protein) and matrix protein (M-protein). We demonstrate that RABV replicates in human stem cell-derived neurons and astrocytes but fails to infect human iPSC-derived microglia. Additionally, we observed major differences in transcription profiles and quantification of intracellular protein levels between antiviral immune responses mediated by neurons, astrocytes (IFNB1, CCL5, CXCL10, IL1B, IL6, and LIF), and microglia (CCL5, CXCL10, ISG15, MX1, and IL6) upon Tha infection. We also show that P- and M-proteins of Tha mediate evasion of NF-κB- and JAK-STAT-controlled antiviral host responses in neuronal cell types in contrast to glial cells, potentially explaining the strong neuron-specific tropism of RABV. Further, Tha-infected astrocytes and microglia protect neurons from Tha infection via a filtrable and transferable agent. Overall, our study provides novel insights into RABV tropism, showing the interest in studying the interplay of CNS cell types during RABV infection.
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Affiliation(s)
- Lena Feige
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology, 75015 Paris, France
| | - Tatsuya Kozaki
- Singapore Immunology Network, Agency for Science, Technology and Research, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
| | - Guilherme Dias de Melo
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology, 75015 Paris, France
| | - Vincent Guillemot
- Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Institut Pasteur, 75015 Paris, France
| | - Florence Larrous
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology, 75015 Paris, France
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, 8A Biomedical Grove, Immunos Building, Level 3, Singapore 138648, Singapore
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Center, 20 College Road, Discovery Tower Level 8, Singapore 169856, Singapore
- Inserm U1015, Gustave Roussy, Bâtiment de Médecine Moléculaire, 114 Rue Edouard Vaillant, 94800 Villejuif, France
| | - Hervé Bourhy
- Institut Pasteur, Université de Paris, Lyssavirus Epidemiology and Neuropathology, 75015 Paris, France
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Senol AD, Pinto G, Beau M, Guillemot V, Dupree JL, Stadelmann C, Ranft J, Lubetzki C, Davenne M. Alterations of the axon initial segment in multiple sclerosis grey matter. Brain Commun 2022; 4:fcac284. [PMID: 36451656 PMCID: PMC9700164 DOI: 10.1093/braincomms/fcac284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 07/14/2022] [Accepted: 11/02/2022] [Indexed: 07/22/2023] Open
Abstract
Grey matter damage has been established as a key contributor to disability progression in multiple sclerosis. Aside from neuronal loss and axonal transections, which predominate in cortical demyelinated lesions, synaptic alterations have been detected in both demyelinated plaques and normal-appearing grey matter, resulting in functional neuronal damage. The axon initial segment is a key element of neuronal function, responsible for action potential initiation and maintenance of neuronal polarity. Despite several reports of profound axon initial segment alterations in different pathological models, among which experimental auto-immune encephalomyelitis, whether the axon initial segment is affected in multiple sclerosis is still unknown. Using immunohistochemistry, we analysed axon initial segments from control and multiple sclerosis tissue, focusing on layer 5/6 pyramidal neurons in the neocortex and Purkinje cells in the cerebellum and performed analysis on the parameters known to control neuronal excitability, i.e. axon initial segment length and position. We found that the axon initial segment length was increased only in pyramidal neurons of inactive demyelinated lesions, compared with normal appearing grey matter tissue. In contrast, in both cell types, the axon initial segment position was altered, with an increased soma-axon initial segment gap, in both active and inactive demyelinated lesions. In addition, using a computational model, we show that this increased gap between soma and axon initial segment might increase neuronal excitability. Taken together, these results show, for the first time, changes of axon initial segments in multiple sclerosis, in active as well as inactive grey matter lesions in both neocortex and cerebellum, which might alter neuronal function.
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Affiliation(s)
- Aysegul Dilsizoglu Senol
- Sorbonne University, Paris Brain Institute—ICM, Inserm, CNRS, Pitié-Salpêtrière Hospital, Paris, France
| | - Giulia Pinto
- Sorbonne University, Paris Brain Institute—ICM, Inserm, CNRS, Pitié-Salpêtrière Hospital, Paris, France
| | - Maxime Beau
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Vincent Guillemot
- Sorbonne University, Paris Brain Institute—ICM, Inserm, CNRS, Pitié-Salpêtrière Hospital, Paris, France
- Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, Paris F-75015, France
| | - Jeffrey L Dupree
- Department of Anatomy and Neurobiology, Virginia Commonwealth University, Richmond, VA, USA
- Hunter Holmes McGuire VA Medical Center, Richmond, VA, USA
| | - Christine Stadelmann
- Institute of Neuropathology, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Jonas Ranft
- Institut de Biologie de l’École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, Inserm, PSL Research University, Paris, France
| | - Catherine Lubetzki
- Sorbonne University, Paris Brain Institute—ICM, Inserm, CNRS, Pitié-Salpêtrière Hospital, Paris, France
- Assistance Publique des Hôpitaux de Paris (APHP), Pitié-Salpêtrière Hospital, DMU Neurosciences, Paris, France
| | - Marc Davenne
- Correspondence to: Dr Marc Davenne Paris Brain Institute, Pitié-Salpêtrière Hospital 47, bd de l’hôpital, F-75013 Paris, France E-mail:
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Collard JM, Andrianonimiadana L, Habib A, Rakotondrainipiana M, Andriantsalama P, Randriamparany R, Rabenandrasana MAN, Weill FX, Sauvonnet N, Randremanana RV, Guillemot V, Vonaesch P, Sansonetti PJ. High prevalence of small intestine bacteria overgrowth and asymptomatic carriage of enteric pathogens in stunted children in Antananarivo, Madagascar. PLoS Negl Trop Dis 2022; 16:e0009849. [PMID: 35533199 PMCID: PMC9119516 DOI: 10.1371/journal.pntd.0009849] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 09/23/2021] [Revised: 05/19/2022] [Accepted: 04/01/2022] [Indexed: 11/26/2022] Open
Abstract
Environmental Enteric Dysfunction (EED) refers to an incompletely defined syndrome of inflammation, reduced absorptive capacity, and reduced barrier function in the small intestine. It is widespread among children and adults in low- and middle-income countries and is also associated with poor sanitation and certain gut infections possibly resulting in an abnormal gut microbiota, small intestinal bacterial overgrowth (SIBO) and stunting. We investigated bacterial pathogen exposure in stunted and non-stunted children in Antananarivo, Madagascar by collecting fecal samples from 464 children (96 severely stunted, 104 moderately stunted and 264 non-stunted) and the prevalence of SIBO in 109 duodenal aspirates from stunted children (61 from severely stunted and 48 from moderately stunted children). SIBO assessed by both aerobic and anaerobic plating techniques was very high: 85.3% when selecting a threshold of ≥105 CFU/ml of bacteria in the upper intestinal aspirates. Moreover, 58.7% of the children showed more than 106 bacteria/ml in these aspirates. The most prevalent cultivated genera recovered were Streptococcus, Neisseria, Staphylococcus, Rothia, Haemophilus, Pantoea and Branhamella. Feces screening by qPCR showed a high prevalence of bacterial enteropathogens, especially those categorized as being enteroinvasive or causing mucosal disruption, such as Shigella spp., enterotoxigenic Escherichia coli, enteropathogenic E. coli and enteroaggregative E. coli. These pathogens were detected at a similar rate in stunted children and controls, all showing no sign of severe diarrhea the day of inclusion but both living in a highly contaminated environment (slum-dwelling). Interestingly Shigella spp. was the most prevalent enteropathogen found in this study (83.3%) without overrepresentation in stunted children. About 2 million children under the age of 5 suffer from stunted growth in Madagascar. Although deficient diet is the major cause of undernutrition, impaired absorption or assimilation caused by Environmental Enteric dysfunction (EED) has been proposed to play an important role in stunting. EED is widespread among children and adults in low- and middle-income countries (LMIC) and is also associated with undernutrition, poor sanitation, certain gut infections resulting in an abnormal gut microbiota and small intestinal bacterial overgrowth (SIBO) although the role of SIBO in EED remains unclear. The current study highlights the presence at high concentrations of bacterial taxa usually found in the oro-pharyngeal sphere in a high number of duodenal fluids of stunted children. This uncommon presence suggests a decompartmentalization of the gastrointestinal tract and a possible pro-inflammatory effect due to the ectopic presence of some of these bacteria in the duodenum. The study also points to a high prevalence of enteropathogens (especially Shigella spp.) in the feces of both stunted and control children, hence preventing from proposing a direct association with stunting. This suggests that, beside combatting poverty and improving diet, environmental sanitation, quality of water sources, hygiene promotion and health education are key points to mitigate stunting and restore nutritional benefits.
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Affiliation(s)
- Jean-Marc Collard
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- * E-mail:
| | - Lova Andrianonimiadana
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Azimdine Habib
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Prisca Andriantsalama
- Unité d’Epidémiologie et de Recherche Clinique, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Ravaka Randriamparany
- Unité d’Epidémiologie et de Recherche Clinique, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - M. A. N. Rabenandrasana
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - François-Xavier Weill
- Centre National de Référence des Escherichia coli, Shigella et Salmonella, Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Nathalie Sauvonnet
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
| | | | - Vincent Guillemot
- Hub of Bioinformatics and Biostatistics, Institut Pasteur, Paris, France
| | - Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, Paris, France
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Mekki Y, Guillemot V, Lemaitre H, Carrion-Castillo A, Forkel S, Frouin V, Philippe C. The genetic architecture of language functional connectivity. Neuroimage 2021; 249:118795. [PMID: 34929384 DOI: 10.1016/j.neuroimage.2021.118795] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/11/2021] [Accepted: 12/08/2021] [Indexed: 02/08/2023] Open
Abstract
Language is a unique trait of the human species, of which the genetic architecture remains largely unknown. Through language disorders studies, many candidate genes were identified. However, such complex and multifactorial trait is unlikely to be driven by only few genes and case-control studies, suffering from a lack of power, struggle to uncover significant variants. In parallel, neuroimaging has significantly contributed to the understanding of structural and functional aspects of language in the human brain and the recent availability of large scale cohorts like UK Biobank have made possible to study language via image-derived endophenotypes in the general population. Because of its strong relationship with task-based fMRI (tbfMRI) activations and its easiness of acquisition, resting-state functional MRI (rsfMRI) have been more popularised, making it a good surrogate of functional neuronal processes. Taking advantage of such a synergistic system by aggregating effects across spatially distributed traits, we performed a multivariate genome-wide association study (mvGWAS) between genetic variations and resting-state functional connectivity (FC) of classical brain language areas in the inferior frontal (pars opercularis, triangularis and orbitalis), temporal and inferior parietal lobes (angular and supramarginal gyri), in 32,186 participants from UK Biobank. Twenty genomic loci were found associated with language FCs, out of which three were replicated in an independent replication sample. A locus in 3p11.1, regulating EPHA3 gene expression, is found associated with FCs of the semantic component of the language network, while a locus in 15q14, regulating THBS1 gene expression is found associated with FCs of the perceptual-motor language processing, bringing novel insights into the neurobiology of language.
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Affiliation(s)
- Yasmina Mekki
- NeuroSpin, Institut Joliot, CEA - Université Paris-Saclay, Gif-Sur-Yvette, 91191, France.
| | - Vincent Guillemot
- Hub de Bioinformatique et Biostatistique, Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Hervé Lemaitre
- Groupe d'Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives, CNRS UMR 5293, Université de Bordeaux, Centre Broca Nouvelle-Aquitaine, Bordeaux, France
| | | | - Stephanie Forkel
- Groupe d'Imagerie Neurofonctionnelle, Institut des Maladies Neurodégénératives, CNRS UMR 5293, Université de Bordeaux, Centre Broca Nouvelle-Aquitaine, Bordeaux, France; Brain Connectivity and Behaviour Laboratory, Sorbonne Universities, Paris, France; Department of Neuroimaging, Institute of Psychiatry, Psychology and Neurosciences, King's College London, UK
| | - Vincent Frouin
- NeuroSpin, Institut Joliot, CEA - Université Paris-Saclay, Gif-Sur-Yvette, 91191, France
| | - Cathy Philippe
- NeuroSpin, Institut Joliot, CEA - Université Paris-Saclay, Gif-Sur-Yvette, 91191, France.
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Peron C, Lacote C, Guillemot V, Attou S, Kuefouet S, Rebouh I, Blanchart K, Briet C, Roule V, Beygui F. Bedside assessment of dependence as an independent correlate of mortality in elderly patients admitted for Acute Coronary Syndromes. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.1140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Elderly patients are at high risk of dependence and mortality after acute coronary syndrome (ACS)
Purpose
To assess the impact of dependence detected by a simple bedside test in elderly patients admitted for ACS on 1-year mortality.
Methods
We compared mortality between patients with or without dependence based on an Activities of Daily Living (ADL) index <6 in a prospective, cohort of patients ≥75 years old admitted for an ACS to the cardiology department of our center using a Cox proportional survival model adjusted on pre-defined confounding variables (age, gender, revascularization, heart failure, left ventricular ejection fraction and admission GRACE and CRUSADE scores).
Results
In a cohort of 1011 consecutive patients, 946 underwent ADL assessment and completed one-year follow-up. Dependence was identified in 190 (20%). At 1 year follow-up 112 patients died, 52 (27.4%) in the dependent and 60 (7.9%) in the independent groups. Dependence was associated with higher rates of 1 year mortality both on undajusted (HR 3.79; 95% CI 2.62; 5.50], p<0.0001) and adjusted models (adj-HR 2.85; 95% CI 1.89; 4.33], p<0.0001). Other independent correlates of mortality were female gender (p<0.0001), CRUSADE score (p<0.0001) and coronary revascularization (p<0.001).
Conclusions
Dependence detected by a simple bedside test in patients ≥75 admitted for ACS is associated with a 2 to 3-fold increase of the risk of mortality independent of other predictors of poor outcome. Assessment of dependence should be performed in all elderly patients as a risk stratification tool and considered for the management of such patients.
Funding Acknowledgement
Type of funding sources: None.
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Affiliation(s)
- C Peron
- University Hospital of Caen, Department of Cardiology, Caen, France
| | - C Lacote
- University Hospital of Caen, Department of Cardiology, Caen, France
| | - V Guillemot
- University Hospital of Caen, Department of Cardiology, Caen, France
| | - S Attou
- University Hospital of Caen, Department of Cardiology, Caen, France
| | - S Kuefouet
- University Hospital of Caen, Department of Cardiology, Caen, France
| | - I Rebouh
- University Hospital of Caen, Department of Cardiology, Caen, France
| | - K Blanchart
- University Hospital of Caen, Department of Cardiology, Caen, France
| | - C Briet
- University Hospital of Caen, Department of Cardiology, Caen, France
| | - V Roule
- University Hospital of Caen, Department of Cardiology, Caen, France
| | - F Beygui
- University Hospital of Caen, Department of Cardiology, Caen, France
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8
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Julienne H, Laville V, McCaw ZR, He Z, Guillemot V, Lasry C, Ziyatdinov A, Nerin C, Vaysse A, Lechat P, Ménager H, Le Goff W, Dube MP, Kraft P, Ionita-Laza I, Vilhjálmsson BJ, Aschard H. Multitrait GWAS to connect disease variants and biological mechanisms. PLoS Genet 2021; 17:e1009713. [PMID: 34460823 PMCID: PMC8437297 DOI: 10.1371/journal.pgen.1009713] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 01/20/2021] [Revised: 09/13/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022] Open
Abstract
Genome-wide association studies (GWASs) have uncovered a wealth of associations between common variants and human phenotypes. Here, we present an integrative analysis of GWAS summary statistics from 36 phenotypes to decipher multitrait genetic architecture and its link with biological mechanisms. Our framework incorporates multitrait association mapping along with an investigation of the breakdown of genetic associations into clusters of variants harboring similar multitrait association profiles. Focusing on two subsets of immunity and metabolism phenotypes, we then demonstrate how genetic variants within clusters can be mapped to biological pathways and disease mechanisms. Finally, for the metabolism set, we investigate the link between gene cluster assignment and the success of drug targets in randomized controlled trials.
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Affiliation(s)
- Hanna Julienne
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Vincent Laville
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Zachary R. McCaw
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Zihuai He
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, United States of America
| | - Vincent Guillemot
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Carla Lasry
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Andrey Ziyatdinov
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Cyril Nerin
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Amaury Vaysse
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Pierre Lechat
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Hervé Ménager
- Department of Computational Biology, Institut Pasteur, Paris, France
| | - Wilfried Le Goff
- Sorbonne Université, INSERM, Institute of Cardiometabolism and Nutrition (ICAN), UMR_S 1166, Paris, France
| | - Marie-Pierre Dube
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Montreal, Canada
- Université de Montréal, Faculty of Medicine, Department of medicine, Université de Montréal, Montreal, Canada
| | - Peter Kraft
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Columbia University, New York, New York, United States of America
| | - Bjarni J. Vilhjálmsson
- National Centre for Register-based Research, Department of Economics and Business Economics, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Hugues Aschard
- Department of Computational Biology, Institut Pasteur, Paris, France
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
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9
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Surace L, Doisne JM, Croft CA, Thaller A, Escoll P, Marie S, Petrosemoli N, Guillemot V, Dardalhon V, Topazio D, Cama A, Buchrieser C, Taylor N, Amit I, Musumeci O, Di Santo JP. Dichotomous metabolic networks govern human ILC2 proliferation and function. Nat Immunol 2021; 22:1367-1374. [PMID: 34686862 PMCID: PMC8553616 DOI: 10.1038/s41590-021-01043-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 02/19/2021] [Accepted: 09/09/2021] [Indexed: 01/20/2023]
Abstract
Group 2 innate lymphoid cells (ILC2s) represent innate homologs of type 2 helper T cells (TH2) that participate in immune defense and tissue homeostasis through production of type 2 cytokines. While T lymphocytes metabolically adapt to microenvironmental changes, knowledge of human ILC2 metabolism is limited, and its key regulators are unknown. Here, we show that circulating 'naive' ILC2s have an unexpected metabolic profile with a higher level of oxidative phosphorylation (OXPHOS) than natural killer (NK) cells. Accordingly, ILC2s are severely reduced in individuals with mitochondrial disease (MD) and impaired OXPHOS. Metabolomic and nutrient receptor analysis revealed ILC2 uptake of amino acids to sustain OXPHOS at steady state. Following activation with interleukin-33 (IL-33), ILC2s became highly proliferative, relying on glycolysis and mammalian target of rapamycin (mTOR) to produce IL-13 while continuing to fuel OXPHOS with amino acids to maintain cellular fitness and proliferation. Our results suggest that proliferation and function are metabolically uncoupled in human ILC2s, offering new strategies to target ILC2s in disease settings.
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Affiliation(s)
- Laura Surace
- grid.428999.70000 0001 2353 6535Innate Immunity Unit, Institut Pasteur, Inserm U1223, Paris, France
| | - Jean-Marc Doisne
- grid.428999.70000 0001 2353 6535Innate Immunity Unit, Institut Pasteur, Inserm U1223, Paris, France
| | - Carys A. Croft
- grid.428999.70000 0001 2353 6535Innate Immunity Unit, Institut Pasteur, Inserm U1223, Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Anna Thaller
- grid.428999.70000 0001 2353 6535Innate Immunity Unit, Institut Pasteur, Inserm U1223, Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Pedro Escoll
- grid.428999.70000 0001 2353 6535Biology of Intracellular Bacteria Unit, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Solenne Marie
- grid.428999.70000 0001 2353 6535Innate Immunity Unit, Institut Pasteur, Inserm U1223, Paris, France
| | - Natalia Petrosemoli
- grid.428999.70000 0001 2353 6535Bioinformatics and Biostatistics Hub, Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, Paris, France
| | - Vincent Guillemot
- grid.428999.70000 0001 2353 6535Bioinformatics and Biostatistics Hub, Center of Bioinformatics, Biostatistics, and Integrative Biology, Institut Pasteur, Paris, France
| | - Valerie Dardalhon
- grid.121334.60000 0001 2097 0141Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Davide Topazio
- Department of Otolaryngology, Hospital ‘Mazzini’, Teramo, Italy
| | - Antonia Cama
- Department of Maxillofacial and Otolaryngology, Hospital ‘F. Renzetti’, Lanciano, Italy
| | - Carmen Buchrieser
- grid.428999.70000 0001 2353 6535Biology of Intracellular Bacteria Unit, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Naomi Taylor
- grid.121334.60000 0001 2097 0141Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Ido Amit
- grid.13992.300000 0004 0604 7563Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Olimpia Musumeci
- grid.10438.3e0000 0001 2178 8421Unit of Neurology and Neuromuscular Disorders, Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - James P. Di Santo
- grid.428999.70000 0001 2353 6535Innate Immunity Unit, Institut Pasteur, Inserm U1223, Paris, France
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10
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Menegatti S, Guillemot V, Latis E, Yahia-Cherbal H, Mittermüller D, Rouilly V, Mascia E, Rosine N, Koturan S, Millot GA, Leloup C, Duffy D, Gleizes A, Hacein-Bey-Abina S, Sellam J, Berenbaum F, Miceli-Richard C, Dougados M, Bianchi E, Rogge L. Immune response profiling of patients with spondyloarthritis reveals signalling networks mediating TNF-blocker function in vivo. Ann Rheum Dis 2020; 80:475-486. [PMID: 33268443 PMCID: PMC7958106 DOI: 10.1136/annrheumdis-2020-218304] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 06/17/2020] [Revised: 10/30/2020] [Accepted: 10/30/2020] [Indexed: 12/24/2022]
Abstract
Objectives Antitumour necrosis factor (TNF) therapy has revolutionised treatment of several chronic inflammatory diseases, including spondyloarthritis (SpA). However, TNF inhibitors (TNFi) are not effective in all patients and the biological basis for treatment failure remains unknown. We have analysed induced immune responses to define the mechanism of action of TNF blockers in SpA and to identify immunological correlates of responsiveness to TNFi. Methods Immune responses to microbial and pathway-specific stimuli were analysed in peripheral blood samples from 80 patients with axial SpA before and after TNFi treatment, using highly standardised whole-blood stimulation assays. Cytokines and chemokines were measured in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory, and gene expression was monitored using nCounter assays. Results Anti-TNF therapy induced profound changes in patients’ innate immune responses. TNFi action was selective, and had only minor effects on Th1/Th17 immunity. Modular transcriptional repertoire analysis identified prostaglandin E2 synthesis and signalling, leucocyte recirculation, macrophage polarisation, dectin and interleukin (IL)-1 signalling, as well as the nuclear factor kappa B (NF-kB) transcription factor family as key pathways targeted by TNF blockers in vivo. Analysis of induced immune responses before treatment initiation revealed that expression of molecules associated with leucocyte adhesion and invasion, chemotaxis and IL-1 signalling are correlated with therapeutic responses to anti-TNF. Conclusions We show that TNFi target multiple immune cell pathways that cooperate to resolve inflammation. We propose that immune response profiling provides new insight into the biology of TNF-blocker action in patients and can identify signalling pathways associated with therapeutic responses to biological therapies.
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Affiliation(s)
- Silvia Menegatti
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,INSERM U932, Institut Curie, PSL Research University, Paris, France
| | - Vincent Guillemot
- Bioinformatics and Biostatistics Hub-Département de Biologie Computationelle, Institut Pasteur, USR 3756 IP CNRS, Paris, France
| | - Eleonora Latis
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Hanane Yahia-Cherbal
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Daniela Mittermüller
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France
| | | | - Elena Mascia
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France
| | - Nicolas Rosine
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Surya Koturan
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Gael A Millot
- Bioinformatics and Biostatistics Hub-Département de Biologie Computationelle, Institut Pasteur, USR 3756 IP CNRS, Paris, France
| | - Claire Leloup
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France
| | - Darragh Duffy
- Institut Pasteur, Translational Immunology Laboratory, Department of Immunology, Paris, France
| | - Aude Gleizes
- Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, AP-HP, Le-Kremlin-Bicêtre, France.,UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | - Salima Hacein-Bey-Abina
- Clinical Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud, Hôpital Kremlin-Bicêtre, AP-HP, Le-Kremlin-Bicêtre, France.,UTCBS CNRS UMR 8258, INSERM U1267, Faculté de Pharmacie de Paris, Université de Paris, Paris, France
| | | | - Jérémie Sellam
- Sorbonne Université, Service de Rhumatologie, Hôpital Saint-Antoine, AP-HP, Paris, France.,Centre de Recherche Saint-Antoine, INSERM UMR_S 938, Paris, France
| | - Francis Berenbaum
- Sorbonne Université, Service de Rhumatologie, Hôpital Saint-Antoine, AP-HP, Paris, France.,Centre de Recherche Saint-Antoine, INSERM UMR_S 938, Paris, France
| | - Corinne Miceli-Richard
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Paris Descartes University, Rheumatology Department, Cochin Hospital, AP-HP, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
| | - Maxime Dougados
- Paris Descartes University, Rheumatology Department, Cochin Hospital, AP-HP, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France.,INSERM U1153 Clinical Epidemiology and Biostatistics, PRES Sorbonne Paris-Cité, Paris, France
| | - Elisabetta Bianchi
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France.,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
| | - Lars Rogge
- Immunoregulation Unit, Department of Immunology, Institut Pasteur, Paris, France .,Unité Mixte AP-HP/Institut Pasteur, Institut Pasteur, Paris, France
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11
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Julienne H, Lechat P, Guillemot V, Lasry C, Yao C, Araud R, Laville V, Vilhjalmsson B, Ménager H, Aschard H. JASS: command line and web interface for the joint analysis of GWAS results. NAR Genom Bioinform 2020; 2:lqaa003. [PMID: 32002517 PMCID: PMC6978790 DOI: 10.1093/nargab/lqaa003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 12/03/2019] [Accepted: 01/09/2020] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association study (GWAS) has been the driving force for identifying association between genetic variants and human phenotypes. Thousands of GWAS summary statistics covering a broad range of human traits and diseases are now publicly available. These GWAS have proven their utility for a range of secondary analyses, including in particular the joint analysis of multiple phenotypes to identify new associated genetic variants. However, although several methods have been proposed, there are very few large-scale applications published so far because of challenges in implementing these methods on real data. Here, we present JASS (Joint Analysis of Summary Statistics), a polyvalent Python package that addresses this need. Our package incorporates recently developed joint tests such as the omnibus approach and various weighted sum of Z-score tests while solving all practical and computational barriers for large-scale multivariate analysis of GWAS summary statistics. This includes data cleaning and harmonization tools, an efficient algorithm for fast derivation of joint statistics, an optimized data management process and a web interface for exploration purposes. Both benchmark analyses and real data applications demonstrated the robustness and strong potential of JASS for the detection of new associated genetic variants. Our package is freely available at https://gitlab.pasteur.fr/statistical-genetics/jass.
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Affiliation(s)
- Hanna Julienne
- Department of Computational Biology—USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Pierre Lechat
- Department of Computational Biology—USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Vincent Guillemot
- Department of Computational Biology—USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Carla Lasry
- Department of Computational Biology—USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Chunzi Yao
- Department of Computational Biology—USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Robinson Araud
- Department of Computational Biology—USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Vincent Laville
- Department of Computational Biology—USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Bjarni Vilhjalmsson
- National Center for Register-Based Research, Aarhus University, DK-8210 Aarhus, Denmark
| | - Hervé Ménager
- Department of Computational Biology—USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
| | - Hugues Aschard
- Department of Computational Biology—USR 3756 CNRS, Institut Pasteur, 75015 Paris, France
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 02115 Boston, MA, USA
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12
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Batrancourt B, Lecouturier K, Ferrand-Verdejo J, Guillemot V, Azuar C, Bendetowicz D, Migliaccio R, Rametti-Lacroux A, Dubois B, Levy R. Exploration Deficits Under Ecological Conditions as a Marker of Apathy in Frontotemporal Dementia. Front Neurol 2019; 10:941. [PMID: 31551908 PMCID: PMC6736613 DOI: 10.3389/fneur.2019.00941] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 02/03/2019] [Accepted: 08/14/2019] [Indexed: 11/13/2022] Open
Abstract
Apathy is one of the six clinical criteria for the behavioral variant of frontotemporal dementia (bvFTD), and it is almost universal in this disease. Although its consequences in everyday life are debilitating, its underlying mechanisms are poorly known, its assessment is biased by subjectivity and its care management is very limited. In this context, we have developed "ECOCAPTURE," a method aimed at providing quantifiable and objective signature(s) of apathy in order to assess it and identify its precise underlying mechanisms. ECOCAPTURE consists of the observation and recording of the patient's behavior when the participant is being submitted to a multiple-phase scenario reproducing a brief real-life situation. It is performed in a functional exploration platform transformed into a fully furnished waiting room equipped with a video and sensor-based data acquisition system. This multimodal method allowed video-based behavior analyses according to predefined behavioral categories (exploration behavior, sustained activities or inactivity) and actigraphy analyses from a 3D accelerometer. The data obtained were also correlated with behavioral/cognitive tests and scales assessing global cognitive efficiency, apathy, cognitive disinhibition, frontal syndrome, depression and anxiety. Here, bvFTD patients (n = 14) were compared to healthy participants (n = 14) during the very first minutes of the scenario, when the participants discovered the room and were encouraged to explore it. We showed that, in the context of facing a new environment, healthy participants first explored it and then engaged in sustained activities. By contrast, bvFTD patients were mostly inactive and eventually explored this new place, but in a more irregular and less efficient mode than normal subjects. This exploration deficit was correlated with apathy, disinhibition and cognitive and behavioral dysexecutive syndromes. These findings led us to discuss the presumed underlying mechanisms responsible for the exploration deficit (an inability to self-initiate actions, to integrate reward valuation and to inhibit involuntary behavior). Altogether, these results pave the way for simple and objective assessment of behavioral changes that represents a critical step for the evaluation of disease progression and efficacy of treatment in bvFTD.
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Affiliation(s)
- Bénédicte Batrancourt
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épiniére (ICM), FRONTlab, Paris, France
| | - Karen Lecouturier
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épiniére (ICM), FRONTlab, Paris, France
| | - Johan Ferrand-Verdejo
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épiniére (ICM), FRONTlab, Paris, France
| | - Vincent Guillemot
- Institut Pasteur, Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Paris, France
| | - Carole Azuar
- AP-HP, Groupe Hospitalier Pitiè-Salpêtrière, Département de Neurologie, Institut de la Mèmoire et de la Maladie d'Alzheimer (IM2A), Paris, France
| | - David Bendetowicz
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épiniére (ICM), FRONTlab, Paris, France.,AP-HP, Groupe Hospitalier Pitiè-Salpêtrière, Département de Neurologie, Institut de la Mèmoire et de la Maladie d'Alzheimer (IM2A), Paris, France.,AP-HP, Groupe Hospitalier Pitiè-Salpêtrière, Département de Neurologie, Behavioral Neuropsychiatry Unit, Paris, France
| | - Raffaella Migliaccio
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épiniére (ICM), FRONTlab, Paris, France.,AP-HP, Groupe Hospitalier Pitiè-Salpêtrière, Département de Neurologie, Institut de la Mèmoire et de la Maladie d'Alzheimer (IM2A), Paris, France.,AP-HP, Groupe Hospitalier Pitiè-Salpêtrière, Département de Neurologie, Behavioral Neuropsychiatry Unit, Paris, France
| | - Armelle Rametti-Lacroux
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épiniére (ICM), FRONTlab, Paris, France
| | - Bruno Dubois
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épiniére (ICM), FRONTlab, Paris, France.,AP-HP, Groupe Hospitalier Pitiè-Salpêtrière, Département de Neurologie, Institut de la Mèmoire et de la Maladie d'Alzheimer (IM2A), Paris, France
| | - Richard Levy
- Inserm U 1127, CNRS UMR 7225, Sorbonne Universités, UPMC Univ Paris 06, Institut du Cerveau et de la Moelle épiniére (ICM), FRONTlab, Paris, France.,AP-HP, Groupe Hospitalier Pitiè-Salpêtrière, Département de Neurologie, Institut de la Mèmoire et de la Maladie d'Alzheimer (IM2A), Paris, France.,AP-HP, Groupe Hospitalier Pitiè-Salpêtrière, Département de Neurologie, Behavioral Neuropsychiatry Unit, Paris, France
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13
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Dahl A, Guillemot V, Mefford J, Aschard H, Zaitlen N. Adjusting for Principal Components of Molecular Phenotypes Induces Replicating False Positives. Genetics 2019; 211:1179-1189. [PMID: 30692194 PMCID: PMC6456307 DOI: 10.1534/genetics.118.301768] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 11/04/2018] [Accepted: 01/23/2019] [Indexed: 12/20/2022] Open
Abstract
High-throughput measurements of molecular phenotypes provide an unprecedented opportunity to model cellular processes and their impact on disease. These highly structured datasets are usually strongly confounded, creating false positives and reducing power. This has motivated many approaches based on principal components analysis (PCA) to estimate and correct for confounders, which have become indispensable elements of association tests between molecular phenotypes and both genetic and nongenetic factors. Here, we show that these correction approaches induce a bias, and that it persists for large sample sizes and replicates out-of-sample. We prove this theoretically for PCA by deriving an analytic, deterministic, and intuitive bias approximation. We assess other methods with realistic simulations, which show that perturbing any of several basic parameters can cause false positive rate (FPR) inflation. Our experiments show the bias depends on covariate and confounder sparsity, effect sizes, and their correlation. Surprisingly, when the covariate and confounder have [Formula: see text], standard two-step methods all have [Formula: see text]-fold FPR inflation. Our analysis informs best practices for confounder correction in genomic studies, and suggests many false discoveries have been made and replicated in some differential expression analyses.
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Affiliation(s)
- Andy Dahl
- Department of Medicine, University of California San Francisco, 94158 California
| | - Vincent Guillemot
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur, Paris, 75015 France
| | - Joel Mefford
- Department of Medicine, University of California San Francisco, 94158 California
| | - Hugues Aschard
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur, Paris, 75015 France
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, 02115 Massachusetts
| | - Noah Zaitlen
- Department of Medicine, University of California San Francisco, 94158 California
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14
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Guillemot V, Beaton D, Gloaguen A, Löfstedt T, Levine B, Raymond N, Tenenhaus A, Abdi H. A constrained singular value decomposition method that integrates sparsity and orthogonality. PLoS One 2019; 14:e0211463. [PMID: 30865639 PMCID: PMC6415851 DOI: 10.1371/journal.pone.0211463] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 06/30/2018] [Accepted: 01/15/2019] [Indexed: 11/18/2022] Open
Abstract
We propose a new sparsification method for the singular value decomposition—called the constrained singular value decomposition (CSVD)—that can incorporate multiple constraints such as sparsification and orthogonality for the left and right singular vectors. The CSVD can combine different constraints because it implements each constraint as a projection onto a convex set, and because it integrates these constraints as projections onto the intersection of multiple convex sets. We show that, with appropriate sparsification constants, the algorithm is guaranteed to converge to a stable point. We also propose and analyze the convergence of an efficient algorithm for the specific case of the projection onto the balls defined by the norms L1 and L2. We illustrate the CSVD and compare it to the standard singular value decomposition and to a non-orthogonal related sparsification method with: 1) a simulated example, 2) a small set of face images (corresponding to a configuration with a number of variables much larger than the number of observations), and 3) a psychometric application with a large number of observations and a small number of variables. The companion R-package, csvd, that implements the algorithms described in this paper, along with reproducible examples, are available for download from https://github.com/vguillemot/csvd.
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Affiliation(s)
- Vincent Guillemot
- Bioinformatics and Biostatistics Hub, Institut Pasteur, Paris, France
- * E-mail: (VG); (HA)
| | - Derek Beaton
- The Rotman Research Institute Institution at Baycrest, Toronto, ON, Canada
| | - Arnaud Gloaguen
- L2S, UMR CNRS 8506, CNRS–CentraleSupélec–Université Paris-Sud, Université Paris-Saclay, 3 rue Joliot-Curie, 91192 Gif-sur-Yvette, France
| | - Tommy Löfstedt
- Department of Radiation Sciences, Umeå University, Umeå, Sweden
| | - Brian Levine
- The Rotman Research Institute Institution at Baycrest, Toronto, ON, Canada
| | | | - Arthur Tenenhaus
- L2S, UMR CNRS 8506, CNRS–CentraleSupélec–Université Paris-Sud, Université Paris-Saclay, 3 rue Joliot-Curie, 91192 Gif-sur-Yvette, France
| | - Hervé Abdi
- School of Behavioral and Brain Sciences, The University of Texas at Dallas, Richardson, TX, United States of America
- * E-mail: (VG); (HA)
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15
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Hadj-Selem F, Lofstedt T, Dohmatob E, Frouin V, Dubois M, Guillemot V, Duchesnay E. Continuation of Nesterov's Smoothing for Regression With Structured Sparsity in High-Dimensional Neuroimaging. IEEE Trans Med Imaging 2018; 37:2403-2413. [PMID: 29993684 DOI: 10.1109/tmi.2018.2829802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Predictive models can be used on high-dimensional brain images to decode cognitive states or diagnosis/prognosis of a clinical condition/evolution. Spatial regularization through structured sparsity offers new perspectives in this context and reduces the risk of overfitting the model while providing interpretable neuroimaging signatures by forcing the solution to adhere to domain-specific constraints. Total variation (TV) is a promising candidate for structured penalization: it enforces spatial smoothness of the solution while segmenting predictive regions from the background. We consider the problem of minimizing the sum of a smooth convex loss, a non-smooth convex penalty (whose proximal operator is known) and a wide range of possible complex, non-smooth convex structured penalties such as TV or overlapping group Lasso. Existing solvers are either limited in the functions they can minimize or in their practical capacity to scale to high-dimensional imaging data. Nesterov's smoothing technique can be used to minimize a large number of non-smooth convex structured penalties. However, reasonable precision requires a small smoothing parameter, which slows down the convergence speed to unacceptable levels. To benefit from the versatility of Nesterov's smoothing technique, we propose a first order continuation algorithm, CONESTA, which automatically generates a sequence of decreasing smoothing parameters. The generated sequence maintains the optimal convergence speed toward any globally desired precision. Our main contributions are: gap to probe the current distance to the global optimum in order to adapt the smoothing parameter and the To propose an expression of the duality convergence speed. This expression is applicable to many penalties and can be used with other solvers than CONESTA. We also propose an expression for the particular smoothing parameter that minimizes the number of iterations required to reach a given precision. Furthermore, we provide a convergence proof and its rate, which is an improvement over classical proximal gradient smoothing methods. We demonstrate on both simulated and high-dimensional structural neuroimaging data that CONESTA significantly outperforms many state-of-the-art solvers in regard to convergence speed and precision.
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16
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Löfstedt T, Guillemot V, Frouin V, Duchesnay E, Hadj-Selem F. Simulated Data for Linear Regression with Structured and Sparse Penalties: Introducing pylearn-simulate. J Stat Softw 2018. [DOI: 10.18637/jss.v087.i03] [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: 11/03/2022] Open
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Aschard H, Guillemot V, Vilhjalmsson B, Patel CJ, Skurnik D, Ye J, Wolpin B, Kraft P, Zaitlen N. Covariate selection for association screening in multiphenotype genetic studies. Nat Genet 2017; 49:1789-1795. [PMID: 29038595 PMCID: PMC5797835 DOI: 10.1038/ng.3975] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 07/14/2017] [Accepted: 09/21/2017] [Indexed: 12/13/2022]
Abstract
Testing for associations in big data faces the problem of multiple comparisons, wherein true signals are difficult to detect on the background of all associations queried. This difficulty is particularly salient in human genetic association studies, in which phenotypic variation is often driven by numerous variants of small effect. The current strategy to improve power to identify these weak associations consists of applying standard marginal statistical approaches and increasing study sample sizes. Although successful, this approach does not leverage the environmental and genetic factors shared among the multiple phenotypes collected in contemporary cohorts. Here we developed covariates for multiphenotype studies (CMS), an approach that improves power when correlated phenotypes are measured on the same samples. Our analyses of real and simulated data provide direct evidence that correlated phenotypes can be used to achieve increases in power to levels often surpassing the power gained by a twofold increase in sample size.
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Affiliation(s)
- Hugues Aschard
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vincent Guillemot
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, Paris, France
| | | | - Chirag J Patel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02215, USA
| | - David Skurnik
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Massachusetts Technology and Analytics, Brookline, Massachusetts, USA
| | - Jimmy Ye
- Department of Epidemiology and Biostatistics, Institute of Human Genetics, San Francisco, CA, USA
| | - Brian Wolpin
- Center for Gastrointestinal Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Noah Zaitlen
- Department of Medicine, University of California, San Francisco, CA, USA
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18
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Ibrahim EC, Guillemot V, Comte M, Tenenhaus A, Zendjidjian XY, Cancel A, Belzeaux R, Sauvanaud F, Blin O, Frouin V, Fakra E. Modeling a linkage between blood transcriptional expression and activity in brain regions to infer the phenotype of schizophrenia patients. NPJ Schizophr 2017; 3:25. [PMID: 28883405 PMCID: PMC5589880 DOI: 10.1038/s41537-017-0027-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/05/2017] [Accepted: 07/21/2017] [Indexed: 11/20/2022]
Abstract
Hundreds of genetic loci participate to schizophrenia liability. It is also known that impaired cerebral connectivity is directly related to the cognitive and affective disturbances in schizophrenia. How genetic susceptibility and brain neural networks interact to specify a pathological phenotype in schizophrenia remains elusive. Imaging genetics, highlighting brain variations, has proven effective to establish links between vulnerability loci and associated clinical traits. As previous imaging genetics works in schizophrenia have essentially focused on structural DNA variants, these findings could be blurred by epigenetic mechanisms taking place during gene expression. We explored the meaningful links between genetic data from peripheral blood tissues on one hand, and regional brain reactivity to emotion task assayed by blood oxygen level-dependent functional magnetic resonance imaging on the other hand, in schizophrenia patients and matched healthy volunteers. We applied Sparse Generalized Canonical Correlation Analysis to identify joint signals between two blocks of variables: (i) the transcriptional expression of 33 candidate genes, and (ii) the blood oxygen level-dependent activity in 16 region of interest. Results suggested that peripheral transcriptional expression is related to brain imaging variations through a sequential pathway, ending with the schizophrenia phenotype. Generalization of such an approach to larger data sets should thus help in outlining the pathways involved in psychiatric illnesses such as schizophrenia. IMAGING SEARCHING FOR LINKS TO AID DIAGNOSIS: Researchers explore links between the expression of genes associated with schizophrenia in blood cells and variations in brain activity during emotion processing. El Chérif Ibrahim and Eric Fakra at Aix-Marseille Université, France, and colleagues have developed a method to relate the expression levels of 33 schizophrenia susceptibility genes in blood cells and functional magnetic resonance imaging (fMRI) data obtained as individuals carry out a task that triggers emotional responses. Although they found no significant differences in the expression of genes between the 26 patients with schizophrenia and 26 healthy controls they examined, variations in activity in the superior temporal gyrus were strongly linked to schizophrenia-associated gene expression and presence of disease. Similar analyses of larger data sets will shed further light on the relationship between peripheral molecular changes and disease-related behaviors and ultimately, aid the diagnosis of neuropsychiatric disease.
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Affiliation(s)
- El Chérif Ibrahim
- Aix-Marseille Univ, CNRS, CRN2M, Marseille, France.
- Fondation FondaMental, Fondation de Recherche et de Soins en Santé Mentale, Créteil, France.
- Aix-Marseille Univ, CNRS, INT, Inst Neurosci Timone, Marseille, France.
| | - Vincent Guillemot
- INSERM, U 1127, Paris, France
- CNRS, 7225, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMRS_1127, Paris, France
- ICM, Département des maladies du système nerveux and Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Magali Comte
- Aix-Marseille Univ, CNRS, INT, Inst Neurosci Timone, Marseille, France
| | - Arthur Tenenhaus
- Laboratoire des Signaux et Systèmes (L2S, UMR CNRS 8506), CentraleSupélec-CNRS Université Paris-Sud, Gif-sur-Yvette, France
- Bioinformatics/Biostatistics Platform IHU-A-ICM, Brain and Spine Institute, Paris, France
| | - Xavier Yves Zendjidjian
- Pôle Psychiatrie centre, Hôpital de la Conception, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Aida Cancel
- Aix-Marseille Univ, CNRS, INT, Inst Neurosci Timone, Marseille, France
- Service Hospitalo-Universitaire de Psychiatrie Secteur Saint-Etienne, Hôpital Nord, Saint-Etienne, France
| | - Raoul Belzeaux
- Aix-Marseille Univ, CNRS, CRN2M, Marseille, France
- Fondation FondaMental, Fondation de Recherche et de Soins en Santé Mentale, Créteil, France
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec, Canada
| | - Florence Sauvanaud
- Service Hospitalo-Universitaire de Psychiatrie Secteur Saint-Etienne, Hôpital Nord, Saint-Etienne, France
| | - Olivier Blin
- Aix-Marseille Univ, CNRS, INT, Inst Neurosci Timone, Marseille, France
- CIC-UPCET et Pharmacologie Clinique, Hôpital de la Timone, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | | | - Eric Fakra
- Aix-Marseille Univ, CNRS, INT, Inst Neurosci Timone, Marseille, France.
- Service Hospitalo-Universitaire de Psychiatrie Secteur Saint-Etienne, Hôpital Nord, Saint-Etienne, France.
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Garali I, Adanyeguh IM, Ichou F, Perlbarg V, Seyer A, Colsch B, Moszer I, Guillemot V, Durr A, Mochel F, Tenenhaus A. A strategy for multimodal data integration: application to biomarkers identification in spinocerebellar ataxia. Brief Bioinform 2017; 19:1356-1369. [DOI: 10.1093/bib/bbx060] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Indexed: 11/14/2022] Open
Affiliation(s)
- Imene Garali
- Bioinformatics and Biostatistics Core Facility of the Brain and Spine Institute, La Pitié-Salpêtriére Hospital, Paris, France
| | | | - Farid Ichou
- ICANalytics department, institute of cardiometabolism and nutrition, Paris, France
| | - Vincent Perlbarg
- Bioinformatics and Biostatistics Core Facility of the Brain and Spine Institute, La Pitié-Salpêtriére Hospital, Paris, France
| | - Alexandre Seyer
- SpectMet platform of the MedDay Pharmaceuticals company, Paris, France
| | | | - Ivan Moszer
- Bioinformatics and Biostatistics Core Facility of the Brain and Spine Institute, La Pitié-Salpêtriére Hospital, Paris, France
| | - Vincent Guillemot
- Institut Pasteur, Statistical Genetics group, Bioinformatics/Biostatistics Core Facility
| | | | - Fanny Mochel
- University Pierre and Marie Curie (UPMC) and the Pitié-Salpêtriére University Hospital
| | - Arthur Tenenhaus
- Bioinformatics and Biostatistics Core Facility of the Brain and Spine Institute, La Pitié-Salpêtriére Hospital, Paris, France
- L2S Laboratory at CentraleSupélec, France
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20
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El Behi M, Sanson C, Bachelin C, Guillot-Noël L, Fransson J, Stankoff B, Maillart E, Sarrazin N, Guillemot V, Abdi H, Cournu-Rebeix I, Fontaine B, Zujovic V. Adaptive human immunity drives remyelination in a mouse model of demyelination. Brain 2017; 140:967-980. [PMID: 28334918 PMCID: PMC5382952 DOI: 10.1093/brain/awx008] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [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: 06/24/2016] [Accepted: 12/08/2016] [Indexed: 02/05/2023] Open
Abstract
One major challenge in multiple sclerosis is to understand the cellular and molecular mechanisms leading to disease severity progression. The recently demonstrated correlation between disease severity and remyelination emphasizes the importance of identifying factors leading to a favourable outcome. Why remyelination fails or succeeds in multiple sclerosis patients remains largely unknown, mainly because remyelination has never been studied within a humanized pathological context that would recapitulate major events in plaque formation such as infiltration of inflammatory cells. Therefore, we developed a new paradigm by grafting healthy donor or multiple sclerosis patient lymphocytes in the demyelinated lesion of nude mice spinal cord. We show that lymphocytes play a major role in remyelination whose efficacy is significantly decreased in mice grafted with multiple sclerosis lymphocytes compared to those grafted with healthy donors lymphocytes. Mechanistically, we demonstrated in vitro that lymphocyte-derived mediators influenced differentiation of oligodendrocyte precursor cells through a crosstalk with microglial cells. Among mice grafted with lymphocytes from different patients, we observed diverse remyelination patterns reproducing for the first time the heterogeneity observed in multiple sclerosis patients. Comparing lymphocyte secretory profile from patients exhibiting high and low remyelination ability, we identified novel molecules involved in oligodendrocyte precursor cell differentiation and validated CCL19 as a target to improve remyelination. Specifically, exogenous CCL19 abolished oligodendrocyte precursor cell differentiation observed in patients with high remyelination pattern. Multiple sclerosis lymphocytes exhibit intrinsic capacities to coordinate myelin repair and further investigation on patients with high remyelination capacities will provide new pro-regenerative strategies.
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Affiliation(s)
- Mohamed El Behi
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Charles Sanson
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Corinne Bachelin
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Léna Guillot-Noël
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Jennifer Fransson
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Bruno Stankoff
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France.,Assistance Publique-Hôpitaux de Paris, Neurology Service, Hôpital Saint Antoine-HUEP, Paris 12, France
| | - Elisabeth Maillart
- Assistance Publique-Hôpitaux de Paris, Neurology Department Pitié Salpétrière University Hospital Paris, France
| | - Nadège Sarrazin
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Vincent Guillemot
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Hervé Abdi
- School of Brain and Behavioral Sciences, The University of Texas, Dallas, USA
| | - Isabelle Cournu-Rebeix
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Bertrand Fontaine
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France.,Assistance Publique-Hôpitaux de Paris, Neurology Service, Hôpital Saint Antoine-HUEP, Paris 12, France.,Assistance Publique-Hôpitaux de Paris, Neurology Department Pitié Salpétrière University Hospital Paris, France
| | - Violetta Zujovic
- Sorbonne-Universités-UPMC 06, INSERM, CNRS, UMR ICM-75-1127-7225, 47 boulevard de l'Hôpital, 75013 Paris, France
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Kraemmer J, Smith K, Weintraub D, Guillemot V, Nalls MA, Cormier-Dequaire F, Moszer I, Brice A, Singleton AB, Corvol JC. Clinical-genetic model predicts incident impulse control disorders in Parkinson's disease. J Neurol Neurosurg Psychiatry 2016; 87:1106-11. [PMID: 27076492 PMCID: PMC5098340 DOI: 10.1136/jnnp-2015-312848] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 03/23/2016] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Impulse control disorders (ICD) are commonly associated with dopamine replacement therapy (DRT) in patients with Parkinson's disease (PD). Our aims were to estimate ICD heritability and to predict ICD by a candidate genetic multivariable panel in patients with PD. METHODS Data from de novo patients with PD, drug-naïve and free of ICD behaviour at baseline, were obtained from the Parkinson's Progression Markers Initiative cohort. Incident ICD behaviour was defined as positive score on the Questionnaire for Impulsive-Compulsive Disorders in PD. ICD heritability was estimated by restricted maximum likelihood analysis on whole exome sequencing data. 13 candidate variants were selected from the DRD2, DRD3, DAT1, COMT, DDC, GRIN2B, ADRA2C, SERT, TPH2, HTR2A, OPRK1 and OPRM1 genes. ICD prediction was evaluated by the area under the curve (AUC) of receiver operating characteristic (ROC) curves. RESULTS Among 276 patients with PD included in the analysis, 86% started DRT, 40% were on dopamine agonists (DA), 19% reported incident ICD behaviour during follow-up. We found heritability of this symptom to be 57%. Adding genotypes from the 13 candidate variants significantly increased ICD predictability (AUC=76%, 95% CI (70% to 83%)) compared to prediction based on clinical variables only (AUC=65%, 95% CI (58% to 73%), p=0.002). The clinical-genetic prediction model reached highest accuracy in patients initiating DA therapy (AUC=87%, 95% CI (80% to 93%)). OPRK1, HTR2A and DDC genotypes were the strongest genetic predictive factors. CONCLUSIONS Our results show that adding a candidate genetic panel increases ICD predictability, suggesting potential for developing clinical-genetic models to identify patients with PD at increased risk of ICD development and guide DRT management.
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Affiliation(s)
- Julia Kraemmer
- Sorbonne Universités, UPMC Univ Paris 06, and INSERM UMRS_1127 and CIC_1422, and CNRS UMR_7225, and AP-HP, and ICM, Département des maladies du système nerveux and Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France Medical University of Vienna, Vienna, Austria
| | - Kara Smith
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Weintraub
- Department of Neurology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA Corporal Michael J Crescenz Department of Veterans Affairs Medical Center, Philadelphia, Pennsylvania, USA
| | - Vincent Guillemot
- Sorbonne Universités, UPMC Univ Paris 06, and INSERM UMRS_1127 and CIC_1422, and CNRS UMR_7225, and AP-HP, and ICM, Département des maladies du système nerveux and Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institutes of Health, Bethesda, Maryland, USA
| | - Florence Cormier-Dequaire
- Sorbonne Universités, UPMC Univ Paris 06, and INSERM UMRS_1127 and CIC_1422, and CNRS UMR_7225, and AP-HP, and ICM, Département des maladies du système nerveux and Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Ivan Moszer
- Sorbonne Universités, UPMC Univ Paris 06, and INSERM UMRS_1127 and CIC_1422, and CNRS UMR_7225, and AP-HP, and ICM, Département des maladies du système nerveux and Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Alexis Brice
- Sorbonne Universités, UPMC Univ Paris 06, and INSERM UMRS_1127 and CIC_1422, and CNRS UMR_7225, and AP-HP, and ICM, Département des maladies du système nerveux and Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institutes of Health, Bethesda, Maryland, USA
| | - Jean-Christophe Corvol
- Sorbonne Universités, UPMC Univ Paris 06, and INSERM UMRS_1127 and CIC_1422, and CNRS UMR_7225, and AP-HP, and ICM, Département des maladies du système nerveux and Département de Génétique, Hôpital Pitié-Salpêtrière, Paris, France
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22
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Richard A, Corvol JC, Debs R, Reach P, Tahiri K, Carpentier W, Gueguen J, Guillemot V, Labeyrie C, Adams D, Viala K, Cohen Aubart F. Transcriptome Analysis of Peripheral Blood in Chronic Inflammatory Demyelinating Polyradiculoneuropathy Patients Identifies TNFR1 and TLR Pathways in the IVIg Response. Medicine (Baltimore) 2016; 95:e3370. [PMID: 27175635 PMCID: PMC4902477 DOI: 10.1097/md.0000000000003370] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We have studied the response to intravenous immunoglobulins (IVIg) by a transcriptomic approach in 11 chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) patients (CIDP duration = 6 [0.83-6.5] years). RNA was extracted from cells in whole blood collected before and 3 weeks after IVIg treatment, and hybridized on Illumina chips. After RNA quality controls, gene expression was analyzed using statistical tests fitted for microarrays (R software, limma package), and a pathway analysis was performed using DAVID software. We identified 52 genes with expression that varied significantly after IVIg (fold change [FC] > 1.2, P < 0.001, false discovery rate [FDR] <0.05). Among these 52 genes, 7 were related to immunity, 3 were related to the tumor necrosis factor (TNF)-α receptor 1 (TNFR1) pathway (inhibitor of caspase-activated DNase (ICAD): FC = 1.8, P = 1.7E-7, FDR = 0.004; p21 protein-activated kinase 2 [PAK2]: FC = 1.66, P = 2.6E-5, FDR = 0.03; TNF-α-induced protein 8-like protein 1 [TNFAIP8L1]: P = 1.00E-05, FDR = 0.026), and 2 were related to Toll-like receptors (TLRs), especially TLRs 7 and 9, and were implicated in autoimmunity. These genes were UNC93B1 (FC = 1.6, P = 2E-5, FDR = 0.03), which transports TLRs 7 and 9 to the endolysosomes, and RNF216 (FC = 1.5, P = 1E-05, FDR = 0.03), which promotes TLR 9 degradation. Pathway analysis showed that the TNFR1 pathway was significantly lessened by IVIg (enrichment score = 24, Fischer exact test = 0.003). TNF-α gene expression was higher in responder patients than in nonresponders; however, it decreased after IVIg in responders (P = 0.04), but remained stable in nonresponders. Our data suggest the actions of IVIg on the TNFR1 pathway and an original mechanism involving innate immunity through TLRs in CIDP pathophysiology and the response to IVIg. We conclude that responder patients have stronger inflammatory activity that is lessened by IVIg.
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Affiliation(s)
- Alexandra Richard
- From the Sorbonne Universités (AR, J-CC, KT), UPMC Univ Paris 06, INSERM UMRS_1127, CIC_1422, CNRS UMR_7225, AP-HP, and ICM, Hôpital Pitié-Salpêtrière, Département des maladies du système nerveux; Hôpital Pitié Salpêtrière (RD, PR, KV), Département de Neurophysiologie Clinique; Plateforme Post-génomique P3S (WC), UPMC, Site Pitié Salpêtrière; IHU-A-ICM Bioinformatics/Biostatistics Core Facility (JG, VG), Paris; Hôpital de Bicêtre (CL, DA), Centre de Référence des Neuropathies Amyloïdes et autres Neuropathies Périphériques Rares, Le Kremlin-Bicêtre; and AP-HP, Hôpital Pitié Salpêtrière, Service de Médecine Interne, Institut E3M, Centre National de Référence Maladies auto-immunes Systémiques Rares, et Université Paris VI Pierre et Marie Curie, Sorbonnes Université, Paris, France (FCA)
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23
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Allaïli N, Valabrègue R, Auerbach EJ, Guillemot V, Yahia-Cherif L, Bardinet E, Jabourian M, Fossati P, Lehéricy S, Marjańska M. Single-voxel (1)H spectroscopy in the human hippocampus at 3 T using the LASER sequence: characterization of neurochemical profile and reproducibility. NMR Biomed 2015; 28:1209-17. [PMID: 26282328 PMCID: PMC4573920 DOI: 10.1002/nbm.3364] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/17/2015] [Accepted: 06/18/2015] [Indexed: 05/22/2023]
Abstract
The hippocampus is crucial for long-term episodic memory and learning. It undergoes structural change in aging and is sensitive to neurodegenerative and psychiatric diseases. MRS studies have seldom been performed in the hippocampus due to technical challenges. The reproducibility of MRS in the hippocampus has not been evaluated at 3 T. The purpose of the present study was to quantify the concentration of metabolites in a small voxel placed in the hippocampus and evaluate the reproducibility of the quantification. Spectra were measured in a 2.4 mL voxel placed in the left hippocampus covering the body and most of the tail of the structure in 10 healthy subjects across three different sessions and quantified using LCModel. High-quality spectra were obtained, which allowed a reliable quantification of 10 metabolites including glutamate and glutamine. Reproducibility of MRS was evaluated with coefficient of variation, standard errors of measurement, and intraclass correlation coefficients. All of these measures showed improvement with increased number of averages. Changes of less than 5% in concentration of N-acetylaspartate, choline-containing compounds, and total creatine and of less than 10% in concentration of myo-inositol and the sum of glutamate and glutamine can be confidently detected between two measurements in a group of 20 subjects. A reliable and reproducible neurochemical profile of the human hippocampus was obtained using MRS at 3 T in a small hippocampal volume.
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Affiliation(s)
- Najib Allaïli
- Institut du cerveau et de la Moelle épinière – ICM, Centre de NeuroImagerie de Recherche – CENIR, Paris, France
- Inserm U 1127, Paris, France
- CNRS UMR 7225, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Paris, F-75013, France
- APHP – Département de Psychiatrie et de Médecine Addictologique, Groupe Hospitalier Saint-Louis – Lariboisière – Fernand-Widal, Paris, France
| | - Romain Valabrègue
- Institut du cerveau et de la Moelle épinière – ICM, Centre de NeuroImagerie de Recherche – CENIR, Paris, France
- Inserm U 1127, Paris, France
- CNRS UMR 7225, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Paris, France
| | - Edward J. Auerbach
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota, Minneapolis, USA
| | - Vincent Guillemot
- Inserm U 1127, Paris, France
- CNRS UMR 7225, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Paris, France
- ICM, Plate-forme de Bio-informatique/Biostatistique, F-75013, Paris, France
| | - Lydia Yahia-Cherif
- Institut du cerveau et de la Moelle épinière – ICM, Centre de NeuroImagerie de Recherche – CENIR, Paris, France
- Inserm U 1127, Paris, France
- CNRS UMR 7225, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Paris, France
| | - Eric Bardinet
- Institut du cerveau et de la Moelle épinière – ICM, Centre de NeuroImagerie de Recherche – CENIR, Paris, France
- Inserm U 1127, Paris, France
- CNRS UMR 7225, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Paris, France
| | | | - Philippe Fossati
- Department of Psychiatry, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Stéphane Lehéricy
- Institut du cerveau et de la Moelle épinière – ICM, Centre de NeuroImagerie de Recherche – CENIR, Paris, France
- Inserm U 1127, Paris, France
- CNRS UMR 7225, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06 UMR S 1127, Paris, France
- Department of Neuroradiology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Małgorzata Marjańska
- Center for Magnetic Resonance Research and Department of Radiology, University of Minnesota, Minneapolis, USA
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24
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Nava C, Rupp J, Boissel JP, Mignot C, Rastetter A, Amiet C, Jacquette A, Dupuits C, Bouteiller D, Keren B, Ruberg M, Faudet A, Doummar D, Philippe A, Périsse D, Laurent C, Lebrun N, Guillemot V, Chelly J, Cohen D, Héron D, Brice A, Closs EI, Depienne C. Hypomorphic variants of cationic amino acid transporter 3 in males with autism spectrum disorders. Amino Acids 2015. [PMID: 26215737 PMCID: PMC4633447 DOI: 10.1007/s00726-015-2057-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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] [Indexed: 12/27/2022]
Abstract
Cationic amino acid transporters (CATs) mediate the entry of L-type cationic amino acids (arginine, ornithine and lysine) into the cells including neurons. CAT-3, encoded by the SLC7A3 gene on chromosome X, is one of the three CATs present in the human genome, with selective expression in brain. SLC7A3 is highly intolerant to variation in humans, as attested by the low frequency of deleterious variants in available databases, but the impact on variants in this gene in humans remains undefined. In this study, we identified a missense variant in SLC7A3, encoding the CAT-3 cationic amino acid transporter, on chromosome X by exome sequencing in two brothers with autism spectrum disorder (ASD). We then sequenced the SLC7A3 coding sequence in 148 male patients with ASD and identified three additional rare missense variants in unrelated patients. Functional analyses of the mutant transporters showed that two of the four identified variants cause severe or moderate loss of CAT-3 function due to altered protein stability or abnormal trafficking to the plasma membrane. The patient with the most deleterious SLC7A3 variant had high-functioning autism and epilepsy, and also carries a de novo 16p11.2 duplication possibly contributing to his phenotype. This study shows that rare hypomorphic variants of SLC7A3 exist in male individuals and suggest that SLC7A3 variants possibly contribute to the etiology of ASD in male subjects in association with other genetic factors.
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Affiliation(s)
- Caroline Nava
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France.,Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Johanna Rupp
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Jean-Paul Boissel
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Cyril Mignot
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Centre de Référence "déficiences intellectuelles de causes rares", Paris, France.,Groupe de Recherche Clinique (GRC) "déficience intellectuelle et autisme" UPMC, Paris, France.,Service de neuropédiatrie, Hôpital Trousseau, AP-HP, Paris, France
| | - Agnès Rastetter
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France
| | - Claire Amiet
- Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Aurélia Jacquette
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Centre de Référence "déficiences intellectuelles de causes rares", Paris, France.,Groupe de Recherche Clinique (GRC) "déficience intellectuelle et autisme" UPMC, Paris, France
| | - Céline Dupuits
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France
| | - Delphine Bouteiller
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France
| | - Boris Keren
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Merle Ruberg
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France
| | - Anne Faudet
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Diane Doummar
- Service de neuropédiatrie, Hôpital Trousseau, AP-HP, Paris, France
| | - Anne Philippe
- Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Didier Périsse
- Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Centre Diagnostic Autisme de l'Hôpital Pitié-Salpêtrière, 75013, Paris, France
| | - Claudine Laurent
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France.,Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Nicolas Lebrun
- Institut Cochin, Inserm U567, UMR 8104, Université René Descartes, Paris 5, France
| | - Vincent Guillemot
- Bioinformatics and Biostatistics Core Facility (iCONICS), Institut du cerveau et de la moelle épinière (ICM), Paris, France
| | - Jamel Chelly
- Institut Cochin, Inserm U567, UMR 8104, Université René Descartes, Paris 5, France
| | - David Cohen
- Service de psychiatrie de l'enfant et de l'adolescent, Hôpital Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Institut des Systèmes Intelligents et Robotiques, CNRS UMR 7222, UPMC-Paris-6, Paris, France
| | - Delphine Héron
- Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France.,Centre de Référence "déficiences intellectuelles de causes rares", Paris, France.,Groupe de Recherche Clinique (GRC) "déficience intellectuelle et autisme" UPMC, Paris, France.,Service de neuropédiatrie, Hôpital Trousseau, AP-HP, Paris, France
| | - Alexis Brice
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France.,INSERM, U 1127, 75013, Paris, France.,CNRS, UMR 7225, 75013, Paris, France.,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France.,Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France
| | - Ellen I Closs
- Department of Pharmacology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Christel Depienne
- Sorbonne Universités, UPMC Univ Paris 06, UMR S 1127, ICM, 75013, Paris, France. .,INSERM, U 1127, 75013, Paris, France. .,CNRS, UMR 7225, 75013, Paris, France. .,Institut du cerveau et de la moelle épinière (ICM), 75013, Paris, France. .,Département de Génétique et de Cytogénétique, Hôpital de la Pitié-Salpêtrière, AP-HP, 75013, Paris, France.
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25
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Tenenhaus A, Philippe C, Guillemot V, Le Cao KA, Grill J, Frouin V. Variable selection for generalized canonical correlation analysis. Biostatistics 2014; 15:569-83. [DOI: 10.1093/biostatistics/kxu001] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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26
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Guillemot V, Bender A, Boulesteix AL. Iterative reconstruction of high-dimensional Gaussian Graphical Models based on a new method to estimate partial correlations under constraints. PLoS One 2013; 8:e60536. [PMID: 23593235 PMCID: PMC3623825 DOI: 10.1371/journal.pone.0060536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/27/2013] [Indexed: 11/19/2022] Open
Abstract
In the context of Gaussian Graphical Models (GGMs) with high-dimensional small sample data, we present a simple procedure, called PACOSE – standing for PArtial COrrelation SElection – to estimate partial correlations under the constraint that some of them are strictly zero. This method can also be extended to covariance selection. If the goal is to estimate a GGM, our new procedure can be applied to re-estimate the partial correlations after a first graph has been estimated in the hope to improve the estimation of non-zero coefficients. This iterated version of PACOSE is called iPACOSE. In a simulation study, we compare PACOSE to existing methods and show that the re-estimated partial correlation coefficients may be closer to the real values in important cases. Plus, we show on simulated and real data that iPACOSE shows very interesting properties with regards to sensitivity, positive predictive value and stability.
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Affiliation(s)
- Vincent Guillemot
- Department of Medical Informatics, Biometry and Epidemiology of the Faculty of Medicine, University of Munich, Munich, Germany
| | - Andreas Bender
- Department of Medical Informatics, Biometry and Epidemiology of the Faculty of Medicine, University of Munich, Munich, Germany
| | - Anne-Laure Boulesteix
- Department of Medical Informatics, Biometry and Epidemiology of the Faculty of Medicine, University of Munich, Munich, Germany
- * E-mail:
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27
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Le Floch E, Guillemot V, Frouin V, Pinel P, Lalanne C, Trinchera L, Tenenhaus A, Moreno A, Zilbovicius M, Bourgeron T, Dehaene S, Thirion B, Poline JB, Duchesnay E. Significant correlation between a set of genetic polymorphisms and a functional brain network revealed by feature selection and sparse Partial Least Squares. Neuroimage 2012; 63:11-24. [PMID: 22781162 DOI: 10.1016/j.neuroimage.2012.06.061] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 04/16/2012] [Accepted: 06/27/2012] [Indexed: 11/25/2022] Open
Abstract
Brain imaging is increasingly recognised as an intermediate phenotype to understand the complex path between genetics and behavioural or clinical phenotypes. In this context, a first goal is to propose methods to identify the part of genetic variability that explains some neuroimaging variability. Classical univariate approaches often ignore the potential joint effects that may exist between genes or the potential covariations between brain regions. In this paper, we propose instead to investigate an exploratory multivariate method in order to identify a set of Single Nucleotide Polymorphisms (SNPs) covarying with a set of neuroimaging phenotypes derived from functional Magnetic Resonance Imaging (fMRI). Recently, Partial Least Squares (PLS) regression or Canonical Correlation Analysis (CCA) have been proposed to analyse DNA and transcriptomics. Here, we propose to transpose this idea to the DNA vs. imaging context. However, in very high-dimensional settings like in imaging genetics studies, such multivariate methods may encounter overfitting issues. Thus we investigate the use of different strategies of regularisation and dimension reduction techniques combined with PLS or CCA to face the very high dimensionality of imaging genetics studies. We propose a comparison study of the different strategies on a simulated dataset first and then on a real dataset composed of 94 subjects, around 600,000 SNPs and 34 functional MRI lateralisation indexes computed from reading and speech comprehension contrast maps. We estimate the generalisability of the multivariate association with a cross-validation scheme and demonstrate the significance of this link, using a permutation procedure. Univariate selection appears to be necessary to reduce the dimensionality. However, the significant association uncovered by this two-step approach combining univariate filtering and L1-regularised PLS suggests that discovering meaningful genetic associations calls for a multivariate approach.
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Affiliation(s)
- Edith Le Floch
- Laboratoire de Neuroimagerie Assistée par Ordinateur, Neurospin Center, I2BM, DSV, CEA, Gif-sur-Yvette, France.
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28
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Guillemot V, Tenenhaus A, Le Brusquet L, Frouin V. Graph constrained discriminant analysis: a new method for the integration of a graph into a classification process. PLoS One 2011; 6:e26146. [PMID: 22022543 PMCID: PMC3195079 DOI: 10.1371/journal.pone.0026146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Accepted: 09/20/2011] [Indexed: 11/18/2022] Open
Abstract
Integrating gene regulatory networks (GRNs) into the classification process of DNA microarrays is an important issue in bioinformatics, both because this information has a true biological interest and because it helps in the interpretation of the final classifier. We present a method called graph-constrained discriminant analysis (gCDA), which aims to integrate the information contained in one or several GRNs into a classification procedure. We show that when the integrated graph includes erroneous information, gCDA's performance is only slightly worse, thus showing robustness to misspecifications in the given GRNs. The gCDA framework also allows the classification process to take into account as many a priori graphs as there are classes in the dataset. The gCDA procedure was applied to simulated data and to three publicly available microarray datasets. gCDA shows very interesting performance when compared to state-of-the-art classification methods. The software package gcda, along with the real datasets that were used in this study, are available online: http://biodev.cea.fr/gcda/.
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Affiliation(s)
- Vincent Guillemot
- Laboratory of Functional Genomics – CEA, DSV, IRCM, Evry, France
- Department of Signals and Electronics Systems – Supélec, Gif-sur-Yvette, France
- * E-mail: (VG); (VF)
| | - Arthur Tenenhaus
- Laboratory of Functional Genomics – CEA, DSV, IRCM, Evry, France
- Department of Signals and Electronics Systems – Supélec, Gif-sur-Yvette, France
| | - Laurent Le Brusquet
- Department of Signals and Electronics Systems – Supélec, Gif-sur-Yvette, France
| | - Vincent Frouin
- Laboratory of Functional Genomics – CEA, DSV, IRCM, Evry, France
- * E-mail: (VG); (VF)
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29
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Boulesteix AL, Guillemot V, Sauerbrei W. Use of pretransformation to cope with extreme values in important candidate features. Biom J 2011; 53:673-88. [DOI: 10.1002/bimj.201000189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 03/01/2011] [Accepted: 03/04/2011] [Indexed: 01/05/2023]
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30
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Heride C, Ricoul M, Kiêu K, von Hase J, Guillemot V, Cremer C, Dubrana K, Sabatier L. Distance between homologous chromosomes results from chromosome positioning constraints. J Cell Sci 2010; 123:4063-75. [DOI: 10.1242/jcs.066498] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The organization of chromosomes is important for various biological processes and is involved in the formation of rearrangements often observed in cancer. In mammals, chromosomes are organized in territories that are radially positioned in the nucleus. However, it remains unclear whether chromosomes are organized relative to each other. Here, we examine the nuclear arrangement of 10 chromosomes in human epithelial cancer cells by three-dimensional FISH analysis. We show that their radial position correlates with the ratio of their gene density to chromosome size. We also observe that inter-homologue distances are generally larger than inter-heterologue distances. Using numerical simulations taking radial position constraints into account, we demonstrate that, for some chromosomes, radial position is enough to justify the inter-homologue distance, whereas for others additional constraints are involved. Among these constraints, we propose that nucleolar organizer regions participate in the internal positioning of the acrocentric chromosome HSA21, possibly through interactions with nucleoli. Maintaining distance between homologous chromosomes in human cells could participate in regulating genome stability and gene expression, both mechanisms that are key players in tumorigenesis.
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Affiliation(s)
- Claire Heride
- Laboratoire de Radiobiologie et d'Oncologie (LRO), Commissariat à l'Energie Atomique, 92 265 Fontenay-aux-Roses Cedex, France
| | - Michelle Ricoul
- Laboratoire de Radiobiologie et d'Oncologie (LRO), Commissariat à l'Energie Atomique, 92 265 Fontenay-aux-Roses Cedex, France
| | - Kien Kiêu
- UR 341 Mathématiques et Informatique Appliquées, INRA, 78 350 Jouy-en-Josas, France
| | - Johann von Hase
- Kirchhoff Institute for Physics, University of Heidelberg, 69 120 Heidelberg, Germany
| | - Vincent Guillemot
- Laboratoire d'Exploration Fonctionnelle des Génomes (LEFG), Commissariat à l'Energie Atomique, 91 057 Evry, France
| | - Christoph Cremer
- Kirchhoff Institute for Physics, University of Heidelberg, 69 120 Heidelberg, Germany
| | - Karine Dubrana
- Laboratoire de Radiobiologie et d'Oncologie (LRO), Commissariat à l'Energie Atomique, 92 265 Fontenay-aux-Roses Cedex, France
| | - Laure Sabatier
- Laboratoire de Radiobiologie et d'Oncologie (LRO), Commissariat à l'Energie Atomique, 92 265 Fontenay-aux-Roses Cedex, France
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Abstract
MOTIVATION In statistical bioinformatics research, different optimization mechanisms potentially lead to 'over-optimism' in published papers. So far, however, a systematic critical study concerning the various sources underlying this over-optimism is lacking. RESULTS We present an empirical study on over-optimism using high-dimensional classification as example. Specifically, we consider a 'promising' new classification algorithm, namely linear discriminant analysis incorporating prior knowledge on gene functional groups through an appropriate shrinkage of the within-group covariance matrix. While this approach yields poor results in terms of error rate, we quantitatively demonstrate that it can artificially seem superior to existing approaches if we 'fish for significance'. The investigated sources of over-optimism include the optimization of datasets, of settings, of competing methods and, most importantly, of the method's characteristics. We conclude that, if the improvement of a quantitative criterion such as the error rate is the main contribution of a paper, the superiority of new algorithms should always be demonstrated on independent validation data. AVAILABILITY The R codes and relevant data can be downloaded from http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020_professuren/boulesteix/overoptimism/, such that the study is completely reproducible.
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Affiliation(s)
- Monika Jelizarow
- Department of Medical Informatics, Biometry and Epidemiology, University of Munich, Munich, Germany
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32
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Tenenhaus A, Guillemot V, Gidrol X, Frouin V. Gene association networks from microarray data using a regularized estimation of partial correlation based on PLS regression. IEEE/ACM Trans Comput Biol Bioinform 2010; 7:251-262. [PMID: 20431145 DOI: 10.1109/tcbb.2008.87] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Reconstruction of gene-gene interactions from large-scale data such as microarrays is a first step toward better understanding the mechanisms at work in the cell. Two main issues have to be managed in such a context: 1) choosing which measures have to be used to distinguish between direct and indirect interactions from high-dimensional microarray data and 2) constructing networks with a low proportion of false-positive edges. We present an efficient methodology for the reconstruction of gene interaction networks in a small-sample-size setting. The strength of independence of any two genes is measured, in such "high-dimensional network," by a regularized estimation of partial correlation based on Partial Least Squares Regression. We finally emphasize specific properties of the proposed method. To assess the sensitivity and specificity of the method, we carried out the reconstruction of networks from simulated data. We also tested PLS-based partial correlation network on static and dynamic real microarray data. An R implementation of the proposed algorithm is available from http://biodev.extra.cea.fr/plspcnetwork/.
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Affiliation(s)
- Arthur Tenenhaus
- Laboratoire d'Exploration Fonctionnelle des Genomes, Institut de Radiobiologie Cellulaire et Moléculaire, Commissariat à l'Energie Atomique, 2 rue Gaston Cremieux, F-91000 Evry, France.
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