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Identification of gene co-expression modules from zebrafish brain data: Applications in psychiatry illustrated through alcohol-related traits.
Al-Soufi, Laila; Arana, Álvaro J; Facal, Fernando; Flórez, Gerardo; Vázquez, Fernando L; Arrojo, Manuel; Sánchez, Laura; Costas, Javier.
Afiliación
  • Al-Soufi L; Red de Investigación en Atención Primaria de Adicciones (RIAPAd), Psychiatric Genetics Group, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain; Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, University of
  • Arana ÁJ; Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain.
  • Facal F; Red de Investigación en Atención Primaria de Adicciones (RIAPAd), Psychiatric Genetics Group, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo
  • Flórez G; Addictive Treatment Unit, Ourense University Hospital, Ourense, Galicia, Spain; Centre for Biomedical Research in the Mental Health Network (CIBERSAM), Oviedo, Spain.
  • Vázquez FL; Department of Clinical Psychology and Psychobiology, University of Santiago de Compostela, Santiago de Compostela, Spain.
  • Arrojo M; Servizo de Psiquiatría, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Santiago de Compostela, Galicia, Spain.
  • Sánchez L; Department of Zoology, Genetics and Physical Anthropology, Faculty of Veterinary, University of Santiago de Compostela, Lugo, Spain.
  • Costas J; Red de Investigación en Atención Primaria de Adicciones (RIAPAd), Psychiatric Genetics Group, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain; Complexo Hospitalario Universitario de Santiago de Compostela (CHUS), Servizo Galego de Saúde (
Prog Neuropsychopharmacol Biol Psychiatry ; 135: 111136, 2024 Dec 20.
Article en En | MEDLINE | ID: mdl-39237023
ABSTRACT
Cumulative evidence suggests that zebrafish is a useful model in psychiatric research. Weighted Gene Co-expression Network Analysis (WGCNA) enables the reduction of genome-wide expression data to modules of highly co-expressed genes, which are hypothesized to interact within molecular networks. In this study, we first applied WGCNA to zebrafish brain expression data across different experimental conditions. Then, we characterized the different co-expression modules by gene-set enrichment analysis and hub gene-phenotype association. Finally, we analyzed association of polygenic risk scores (PRSs) based on genes of some interesting co-expression modules with alcohol dependence in 524 patients and 729 controls from Galicia, using competitive tests. Our approach revealed 34 co-expression modules in the zebrafish brain, with some showing enrichment in human synaptic genes, brain tissues, or brain developmental stages. Moreover, certain co-expression modules were enriched in psychiatry-related GWAS and comprised hub genes associated with psychiatry-related traits in both human GWAS and zebrafish models. Expression patterns of some co-expression modules were associated with the tested experimental conditions, mainly with substance withdrawal and cold stress. Notably, a PRS based on genes from co-expression modules exclusively associated with substance withdrawal in zebrafish showed a stronger association with human alcohol dependence than PRSs based on randomly selected brain-expressed genes. In conclusion, our analysis led to the identification of co-expressed gene modules that may model human brain gene networks involved in psychiatry-related traits. Specifically, we detected a cluster of co-expressed genes whose expression was exclusively associated with substance withdrawal in zebrafish, which significantly contributed to alcohol dependence susceptibility in humans.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Pez Cebra / Encéfalo / Alcoholismo / Redes Reguladoras de Genes / Estudio de Asociación del Genoma Completo Límite: Animals / Humans Idioma: En Revista: Prog Neuropsychopharmacol Biol Psychiatry Año: 2024 Tipo del documento: Article Pais de publicación: Reino Unido
Texto completo
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Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Pez Cebra / Encéfalo / Alcoholismo / Redes Reguladoras de Genes / Estudio de Asociación del Genoma Completo Límite: Animals / Humans Idioma: En Revista: Prog Neuropsychopharmacol Biol Psychiatry Año: 2024 Tipo del documento: Article Pais de publicación: Reino Unido