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      Meta-Analysis of Transcriptomic Data of Dorsolateral Prefrontal Cortex and of Peripheral Blood Mononuclear Cells Identifies Altered Pathways in Schizophrenia

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          Abstract

          Schizophrenia (SCZ) is a psychiatric disorder characterized by both positive and negative symptoms, including cognitive dysfunction, decline in motivation, delusion and hallucinations. Antipsychotic agents are currently the standard of care treatment for SCZ. However, only about one-third of SCZ patients respond to antipsychotic medications. In the current study, we have performed a meta-analysis of publicly available whole-genome expression datasets on Brodmann area 46 of the brain dorsolateral prefrontal cortex in order to prioritize potential pathways underlying SCZ pathology. Moreover, we have evaluated whether the differentially expressed genes in SCZ belong to specific subsets of cell types. Finally, a cross-tissue comparison at both the gene and functional level was performed by analyzing the transcriptomic pattern of peripheral blood mononuclear cells of SCZ patients. Our study identified a robust disease-specific set of dysfunctional biological pathways characterizing SCZ patients that could in the future be exploited as potential therapeutic targets.

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          Most cited references84

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          Schizophrenia: a concise overview of incidence, prevalence, and mortality.

          Recent systematic reviews have encouraged the psychiatric research community to reevaluate the contours of schizophrenia epidemiology. This paper provides a concise overview of three related systematic reviews on the incidence, prevalence, and mortality associated with schizophrenia. The reviews shared key methodological features regarding search strategies, analysis of the distribution of the frequency estimates, and exploration of the influence of key variables (sex, migrant status, urbanicity, secular trend, economic status, and latitude). Contrary to previous interpretations, the incidence of schizophrenia shows prominent variation between sites. The median incidence of schizophrenia was 15.2/100,000 persons, and the central 80% of estimates varied over a fivefold range (7.7-43.0/100,000). The rate ratio for males:females was 1.4:1. Prevalence estimates also show prominent variation. The median lifetime morbid risk for schizophrenia was 7.2/1,000 persons. On the basis of the standardized mortality ratio, people with schizophrenia have a two- to threefold increased risk of dying (median standardized mortality ratio = 2.6 for all-cause mortality), and this differential gap in mortality has increased over recent decades. Compared with native-born individuals, migrants have an increased incidence and prevalence of schizophrenia. Exposures related to urbanicity, economic status, and latitude are also associated with various frequency measures. In conclusion, the epidemiology of schizophrenia is characterized by prominent variability and gradients that can help guide future research.
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            Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

            Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic organization in diseased brains are limited. In this work, we integrated genotypes and RNA sequencing in brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, and bipolar disorder, as well as controls. More than 25% of the transcriptome exhibits differential splicing or expression, with isoform-level changes capturing the largest disease effects and genetic enrichments. Coexpression networks isolate disease-specific neuronal alterations, as well as microglial, astrocyte, and interferon-response modules defining previously unidentified neural-immune mechanisms. We integrated genetic and genomic data to perform a transcriptome-wide association study, prioritizing disease loci likely mediated by cis effects on brain expression. This transcriptome-wide characterization of the molecular pathology across three major psychiatric disorders provides a comprehensive resource for mechanistic insight and therapeutic development.
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              Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights

              Genome-wide association studies (GWAS) have identified over 100 risk loci for schizophrenia, but the causal mechanisms remain largely unknown. We performed a transcriptome-wide association study (TWAS) integrating a schizophrenia GWAS of 79,845 individuals from the Psychiatric Genomics Consortium with expression data from brain, blood, and adipose tissues across 3,693 primarily control individuals. We identified 157 TWAS significant genes, of which 35 did not overlap a known GWAS locus. 42/157 genes were associated to specific chromatin features measured in independent samples, highlighting potential regulatory targets for follow-up. Suppression of one identified susceptibility gene, MAPK3, in zebrafish showed a significant effect on neurodevelopmental phenotypes. Expression and splicing from brain captured the majority of the TWAS effect across all genes. This large-scale connection of associations to target genes, tissues, and regulatory features is an essential step in moving towards a mechanistic understanding of GWAS.
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                Author and article information

                Journal
                Genes (Basel)
                Genes (Basel)
                genes
                Genes
                MDPI
                2073-4425
                03 April 2020
                April 2020
                : 11
                : 4
                : 390
                Affiliations
                [1 ]Department of Educational Sciences, University of Catania, 95124 Catania, Italy; m.cristinapetralia@ 123456gmail.com
                [2 ]IRCCS Centro Neurolesi Bonino Pulejo, C.da Casazza, 98124 Messina, Italy; rossella.ciurleo@ 123456irccsme.it (R.C.); placido.bramanti@ 123456irccsme.it (P.B.)
                [3 ]Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; andresara96@ 123456gmail.com (A.S.); manuela.pennisi@ 123456unict.it (M.P.); sofiabasile@ 123456hotmail.it (M.S.B.); ferdinic@ 123456unict.it (F.N.); eugeniocavalli9@ 123456hotmail.it (E.C.)
                Author notes
                [* ]Correspondence: paolofagone@ 123456yahoo.it ; Tel.: +39-095-4781284
                Author information
                https://orcid.org/0000-0002-6694-1992
                https://orcid.org/0000-0002-4570-8462
                Article
                genes-11-00390
                10.3390/genes11040390
                7230488
                32260267
                e980e233-4082-4c11-b5a1-e265c82e3d7c
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 17 February 2020
                : 02 April 2020
                Categories
                Article

                schizophrenia,prefrontal cortex,transcriptomic meta-analysis,map kinases

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