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Corredor D, Segobin S, Hinault T, Eustache F, Dayan J, Guillery-Girard B, Naveau M. The multiscale topological organization of the functional brain network in adolescent PTSD. Cereb Cortex 2024; 34:bhae246. [PMID: 38864573 PMCID: PMC11167567 DOI: 10.1093/cercor/bhae246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/13/2024] Open
Abstract
The experience of an extremely aversive event can produce enduring deleterious behavioral, and neural consequences, among which posttraumatic stress disorder (PTSD) is a representative example. Although adolescence is a period of great exposure to potentially traumatic events, the effects of trauma during adolescence remain understudied in clinical neuroscience. In this exploratory work, we aim to study the whole-cortex functional organization of 14 adolescents with PTSD using a data-driven method tailored to our population of interest. To do so, we built on the network neuroscience framework and specifically on multilayer (multisubject) community analysis to study the functional connectivity of the brain. We show, across different topological scales (the number of communities composing the cortex), a hyper-colocalization between regions belonging to occipital and pericentral regions and hypo-colocalization in middle temporal, posterior-anterior medial, and frontal cortices in the adolescent PTSD group compared to a nontrauma exposed group of adolescents. These preliminary results raise the question of an altered large-scale cortical organization in adolescent PTSD, opening an interesting line of research for future investigations.
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Affiliation(s)
- David Corredor
- Centre Cyceron, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Normandie Université, UNICAEN, PSL Université Paris, EPHE, INSERM, U1077, Caen 14000, France
| | - Shailendra Segobin
- Centre Cyceron, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Normandie Université, UNICAEN, PSL Université Paris, EPHE, INSERM, U1077, Caen 14000, France
| | - Thomas Hinault
- Centre Cyceron, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Normandie Université, UNICAEN, PSL Université Paris, EPHE, INSERM, U1077, Caen 14000, France
| | - Francis Eustache
- Centre Cyceron, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Normandie Université, UNICAEN, PSL Université Paris, EPHE, INSERM, U1077, Caen 14000, France
| | - Jacques Dayan
- Centre Cyceron, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Normandie Université, UNICAEN, PSL Université Paris, EPHE, INSERM, U1077, Caen 14000, France
- Pôle Hospitalo-Universitaire de Psychiatrie de l’Enfant et de l’Adolescent, Centre Hospitalier Guillaume Régnier, Université Rennes 1, Rennes 35700, France
| | - Bérengère Guillery-Girard
- Centre Cyceron, CHU de Caen, Neuropsychologie et Imagerie de la Mémoire Humaine, Normandie Université, UNICAEN, PSL Université Paris, EPHE, INSERM, U1077, Caen 14000, France
| | - Mikaël Naveau
- UNICAEN, CNRS, INSERM, CEA, UAR3408 CYCERON, Normandie Université, Caen 14000, France
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Russell M, Aqi A, Saitou M, Gokcumen O, Masuda N. Gene communities in co-expression networks across different tissues. ARXIV 2023:arXiv:2305.12963v2. [PMID: 37292479 PMCID: PMC10246089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
With the recent availability of tissue-specific gene expression data, e.g., provided by the GTEx Consortium, there is interest in comparing gene co-expression patterns across tissues. One promising approach to this problem is to use a multilayer network analysis framework and perform multilayer community detection. Communities in gene co-expression networks reveal groups of genes similarly expressed across individuals, potentially involved in related biological processes responding to specific environmental stimuli or sharing common regulatory variations. We construct a multilayer network in which each of the four layers is an exocrine gland tissue-specific gene co-expression network. We develop methods for multilayer community detection with correlation matrix input and an appropriate null model. Our correlation matrix input method identifies five groups of genes that are similarly co-expressed in multiple tissues (a community that spans multiple layers, which we call a generalist community) and two groups of genes that are co-expressed in just one tissue (a community that lies primarily within just one layer, which we call a specialist community). We further found gene co-expression communities where the genes physically cluster across the genome significantly more than expected by chance (on chromosomes 1 and 11). This clustering hints at underlying regulatory elements determining similar expression patterns across individuals and cell types. We suggest that KRTAP3-1, KRTAP3-3, and KRTAP3-5 share regulatory elements in skin and pancreas. Furthermore, we find that CELA3A and CELA3B share associated expression quantitative trait loci in the pancreas. The results indicate that our multilayer community detection method for correlation matrix input extracts biologically interesting communities of genes.
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Affiliation(s)
| | - Alber Aqi
- Department of Biological Sciences, University at Buffalo
| | - Marie Saitou
- Faculty of Biosciences, Norwegian University of Life Sciences
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo
| | - Naoki Masuda
- Department of Mathematics, University at Buffalo
- Institute for Artificial Intelligence and Data Science, University at Buffalo
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Russell M, Aqil A, Saitou M, Gokcumen O, Masuda N. Gene communities in co-expression networks across different tissues. PLoS Comput Biol 2023; 19:e1011616. [PMID: 37976327 PMCID: PMC10691702 DOI: 10.1371/journal.pcbi.1011616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/01/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023] Open
Abstract
With the recent availability of tissue-specific gene expression data, e.g., provided by the GTEx Consortium, there is interest in comparing gene co-expression patterns across tissues. One promising approach to this problem is to use a multilayer network analysis framework and perform multilayer community detection. Communities in gene co-expression networks reveal groups of genes similarly expressed across individuals, potentially involved in related biological processes responding to specific environmental stimuli or sharing common regulatory variations. We construct a multilayer network in which each of the four layers is an exocrine gland tissue-specific gene co-expression network. We develop methods for multilayer community detection with correlation matrix input and an appropriate null model. Our correlation matrix input method identifies five groups of genes that are similarly co-expressed in multiple tissues (a community that spans multiple layers, which we call a generalist community) and two groups of genes that are co-expressed in just one tissue (a community that lies primarily within just one layer, which we call a specialist community). We further found gene co-expression communities where the genes physically cluster across the genome significantly more than expected by chance (on chromosomes 1 and 11). This clustering hints at underlying regulatory elements determining similar expression patterns across individuals and cell types. We suggest that KRTAP3-1, KRTAP3-3, and KRTAP3-5 share regulatory elements in skin and pancreas. Furthermore, we find that CELA3A and CELA3B share associated expression quantitative trait loci in the pancreas. The results indicate that our multilayer community detection method for correlation matrix input extracts biologically interesting communities of genes.
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Affiliation(s)
- Madison Russell
- Department of Mathematics, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Alber Aqil
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Marie Saitou
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Omer Gokcumen
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Naoki Masuda
- Department of Mathematics, State University of New York at Buffalo, Buffalo, New York, United States of America
- Institute for Artificial Intelligence and Data Science, State University of New York at Buffalo, Buffalo, New York, United States of America
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Alcantara DMC, Ikeda P, Souza CS, de Mello VVC, Torres JM, Lourenço EC, Bassini-Silva R, Herrera HM, Machado RZ, Barros-Battesti DM, Graciolli G, André MR. Multilayer Networks Assisting to Untangle Direct and Indirect Pathogen Transmission in Bats. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02108-3. [PMID: 36166070 DOI: 10.1007/s00248-022-02108-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
The importance of species that connect the different types of interactions is becoming increasingly recognized, and this role may be related to specific attributes of these species. Multilayer networks have two or more layers, which represent different types of interactions, for example, between different parasites and hosts that are nonetheless connected. The understanding of the ecological relationship between bats, ectoparasites, and vector-borne bacteria could shed some light on the complex transmission cycles of these pathogens. In this study, we investigated a multilayer network in Brazil formed by interactions between bat-bacteria, bat-ectoparasite, and ectoparasite-bacteria, and asked how these interactions overlap considering different groups and transmission modes. The multilayer network was composed of 31 nodes (12 bat species, 14 ectoparasite species, and five bacteria genera) and 334 links, distributed over three layers. The multilayer network has low modularity and shows a core-periphery organization, that is, composed of a few generalist species with many interactions and many specialist species participating in few interactions in the multilayer network. The three layers were needed to accurately describe the multilayer structure, while aggregation leads to loss of information. Our findings also demonstrated that the multilayer network is influenced by a specific set of species that can easily be connected to the behavior, life cycle, and type of existing interactions of these species. Four bat species (Artibeus lituratus, A. planirostris, Phyllostomus discolor, and Platyrrhinus lineatus), one ectoparasite species (Steatonyssus) and three bacteria genera (Ehrlichia, hemotropic Mycoplasma and Neorickettsia) are the most important species for the multilayer network structure. Finally, our study brings an ecological perspective under a multilayer network approach on the interactions between bats, ectoparasites, and pathogens. By using a multilayer approach (different types of interactions), it was possible to better understand these different ecological interactions and how they affect each other, advancing our knowledge on the role of bats and ectoparasites as potential pathogen vectors and reservoirs, as well as the modes of transmission of these pathogens.
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Affiliation(s)
| | - Priscila Ikeda
- Laboratório de Imunoparasitologia, Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
| | - Camila Silveira Souza
- Departamento de Biologia Geral, Programa de Pós-Graduação em Botânica Aplicada, Universidade Estadual de Montes Claros, Montes Claros, MG, Brazil
| | - Victória Valente Califre de Mello
- Laboratório de Imunoparasitologia, Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
| | - Jaire Marinho Torres
- Laboratório de Biologia Parasitária, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Elizabete Captivo Lourenço
- Laboratório de Ecologia de Mamíferos, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | | | - Heitor Miraglia Herrera
- Laboratório de Biologia Parasitária, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Rosangela Zacarias Machado
- Laboratório de Imunoparasitologia, Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil
| | - Darci Moraes Barros-Battesti
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Gustavo Graciolli
- Setor de Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Marcos Rogério André
- Laboratório de Imunoparasitologia, Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Jaboticabal, SP, Brazil.
- Laboratório de Imunoparasitologia, Departamento de Patologia, Reprodução e Saúde Única, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual "Júlio de Mesquita Filho" (UNESP), Campus de Jaboticabal, Via de Acesso Prof. Paulo Donato Castellane, s/n, CEP: 14884-900, Jaboticabal, SP, Brazil.
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Wilsenach JB, Warnaby CE, Deane CM, Reinert GD. Ranking of communities in multiplex spatiotemporal models of brain dynamics. APPLIED NETWORK SCIENCE 2022; 7:15. [PMID: 35308059 PMCID: PMC8921068 DOI: 10.1007/s41109-022-00454-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
UNLABELLED As a relatively new field, network neuroscience has tended to focus on aggregate behaviours of the brain averaged over many successive experiments or over long recordings in order to construct robust brain models. These models are limited in their ability to explain dynamic state changes in the brain which occurs spontaneously as a result of normal brain function. Hidden Markov Models (HMMs) trained on neuroimaging time series data have since arisen as a method to produce dynamical models that are easy to train but can be difficult to fully parametrise or analyse. We propose an interpretation of these neural HMMs as multiplex brain state graph models we term Hidden Markov Graph Models. This interpretation allows for dynamic brain activity to be analysed using the full repertoire of network analysis techniques. Furthermore, we propose a general method for selecting HMM hyperparameters in the absence of external data, based on the principle of maximum entropy, and use this to select the number of layers in the multiplex model. We produce a new tool for determining important communities of brain regions using a spatiotemporal random walk-based procedure that takes advantage of the underlying Markov structure of the model. Our analysis of real multi-subject fMRI data provides new results that corroborate the modular processing hypothesis of the brain at rest as well as contributing new evidence of functional overlap between and within dynamic brain state communities. Our analysis pipeline provides a way to characterise dynamic network activity of the brain under novel behaviours or conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s41109-022-00454-2.
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Affiliation(s)
- James B. Wilsenach
- Wellcome Centre for Human Neuroimaging, Institute of Neurology, University College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Catherine E. Warnaby
- Wellcome Centre for Integrative Neuroimaging, Nuffield Department of Clinical Neurosciences, FMRIB Centre, University of Oxford, Oxford, UK
| | | | - Gesine D. Reinert
- Department of Statistics, University of Oxford, Oxford, UK
- The Alan Turing Institute, London, UK
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