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Joint-Tissue Integrative Analysis Identified Hundreds of Schizophrenia Risk Genes

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Abstract

Genome-wide association studies (GWAS) have identified a large number of schizophrenia risk variants, and most of them are mapped to noncoding regions. By leveraging multiple joint-tissue gene expression data and GWAS data, we herein performed a transcriptome-wide association study (TWAS) and Mendelian randomization (MR) analysis and identified 144 genes whose mRNA levels were related to genetic risk of schizophrenia. Most of these genes exhibited diametrically opposite trends of expression in prenatal and postnatal brain tissues, despite that their expression levels in dorsolateral prefrontal cortex (DLPFC) tissues did not significantly differ between schizophrenics and healthy controls. We then found significant enrichment of these genes in dopamine-related pathways that were repeatedly implicated in schizophrenia pathogenesis and in the action of antipsychotic drugs. Gene expression analysis using single cell RNA-sequencing (scRNA-seq) data of mid-gestation fetal brains further revealed enrichment of these genes in glutamatergic excitatory neurons and cycling progenitors. These lines of evidence, in consistency with previous findings, confirmed the polygenic nature of schizophrenia and highlighted involvement of early neurodevelopment aberrations in this disorder. Further investigations using advanced algorithms in both bulk brain tissues and in single cells and at different developmental stages are necessary to characterize transcriptomic features of schizophrenia pathogenesis along brain development.

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All data generated or analyzed in this study are included in the current manuscript and supplementary materials.

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Acknowledgements

For CMC data, data were generated as part of the CommonMind Consortium supported by funding from Takeda Pharmaceuticals Company Limited, F. Hoffmann-La Roche Ltd and NIH grants R01MH085542, R01MH093725, P50MH066392, P50MH080405, R01MH097276, RO1-MH-075916, P50M096891, P50MH084053S1, R37MH057881, AG02219, AG05138, MH06692, R01MH110921, R01MH109677, R01MH109897, U01MH103392, and contract HHSN271201300031C through IRP NIMH. Brain tissue for the study was obtained from the following brain bank collections: the Mount Sinai NIH Brain and Tissue Repository, the University of Pennsylvania Alzheimer’s Disease Core Center, the University of Pittsburgh NeuroBioBank and Brain and Tissue Repositories, and the NIMH Human Brain Collection Core. CMC Leadership: Panos Roussos, Joseph Buxbaum, Andrew Chess, Schahram Akbarian, Vahram Haroutunian (Icahn School of Medicine at Mount Sinai), Bernie Devlin, David Lewis (University of Pittsburgh), Raquel Gur, Chang-Gyu Hahn (University of Pennsylvania), Enrico Domenici (University of Trento), Mette A. Peters, Solveig Sieberts (Sage Bionetworks), Thomas Lehner, Stefano Marenco, Barbara K. Lipska (NIMH).

For PsychENCODE data, data were generated as part of the PsychENCODE Consortium, supported by: U01MH103392, U01MH103365, U01MH103346, U01MH103340, U01MH103339, R21MH109956, R21MH105881, R21MH105853, R21MH103877, R21MH102791, R01MH111721, R01MH110928, R01MH110927, R01MH110926, R01MH110921, R01MH110920, R01MH110905, R01MH109715, R01MH109677, R01MH105898, R01MH105898, R01MH094714, P50MH106934, U01MH116488, U01MH116487, U01MH116492, U01MH116489, U01MH116438, U01MH116441, U01MH116442, R01MH114911, R01MH114899, R01MH114901, R01MH117293, R01MH117291, R01MH117292 awarded to: Schahram Akbarian (Icahn School of Medicine at Mount Sinai), Gregory Crawford (Duke University), Stella Dracheva (Icahn School of Medicine at Mount Sinai), Peggy Farnham (University of Southern California), Mark Gerstein (Yale University), Daniel Geschwind (University of California, Los Angeles), Fernando Goes (Johns Hopkins University), Thomas M. Hyde (Lieber Institute for Brain Development), Andrew Jaffe (Lieber Institute for Brain Development), James A. Knowles (University of Southern California), Chunyu Liu (SUNY Upstate Medical University), Dalila Pinto (Icahn School of Medicine at Mount Sinai), Panos Roussos (Icahn School of Medicine at Mount Sinai), Stephan Sanders (University of California, San Francisco), Nenad Sestan (Yale University), Pamela Sklar (Icahn School of Medicine at Mount Sinai), Matthew State (University of California, San Francisco), Patrick Sullivan (University of North Carolina), Flora Vaccarino (Yale University), Daniel Weinberger (Lieber Institute for Brain Development), Sherman Weissman (Yale University), Kevin White (University of Chicago), Jeremy Willsey (University of California, San Francisco), and Peter Zandi (Johns Hopkins University).

The Genotype-Tissue Expression (GTEx) project was supported by the Common Fund of the Office of the Director of the National Institutes of Health and by NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS.

Funding

This study was supported by the Health Commission of Hubei Province scientific research project (WJ2021M025 to Y.W.) and Health Commission of Wuhan scientific research project (WX20Q02 to Y.W.).

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Y.W. and Y.L. designed the study and interpreted the results. Y.W. and X.L.Y. conducted all the data analysis. Y.W., M.L. and X.X. drafted the manuscript, and all authors contributed to the final version of the paper.

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Correspondence to Ming Li or Yi Li.

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Wu, Y., Yu, XL., Xiao, X. et al. Joint-Tissue Integrative Analysis Identified Hundreds of Schizophrenia Risk Genes. Mol Neurobiol 59, 107–116 (2022). https://doi.org/10.1007/s12035-021-02572-x

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