Rare coding variants as risk modifiers of the 22q11.2 deletion implicate postnatal cortical development in syndromic schizophrenia

Lin, Jhih-Rong, Zhao, Yingjie, Jabalameli, M Reza, Nguyen, Nha, Mitra, Joydeep, International 22q11.2DS Brain and Behavior Consortium*, Swillen, Ann, Vorstman, Jacob, Chow, Eva, van den Bree, Marianne ORCID: https://orcid.org/0000-0002-4426-3254, Emanuel, Beverly, Vermeesch, Joris, Owen, Michael ORCID: https://orcid.org/0000-0003-4798-0862, Williams, Nigel ORCID: https://orcid.org/0000-0003-1177-6931, Bassett, Anne, McDonald-McGinn, Donna, Gur, Raquel, Bearden, Carrie, Morrow, Bernice, Lachman, Herbert and Zhang, Zhengdong 2023. Rare coding variants as risk modifiers of the 22q11.2 deletion implicate postnatal cortical development in syndromic schizophrenia. Molecular Psychiatry 28 , pp. 2071-2080. 10.1038/s41380-023-02009-y

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Abstract

22q11.2 deletion is one of the strongest known genetic risk factors for schizophrenia. Recent whole-genome sequencing of schizophrenia cases and controls with this deletion provided an unprecedented opportunity to identify risk modifying genetic variants and investigate their contribution to the pathogenesis of schizophrenia in 22q11.2 deletion syndrome. Here, we apply a novel analytic framework that integrates gene network and phenotype data to investigate the aggregate effects of rare coding variants and identified modifier genes in this etiologically homogenous cohort (223 schizophrenia cases and 233 controls of European descent). Our analyses revealed significant additive genetic components of rare nonsynonymous variants in 110 modifier genes (adjusted P = 9.4E-04) that overall accounted for 4.6% of the variance in schizophrenia status in this cohort, of which 4.0% was independent of the common polygenic risk for schizophrenia. The modifier genes affected by rare coding variants were enriched with genes involved in synaptic function and developmental disorders. Spatiotemporal transcriptomic analyses identified an enrichment of coexpression between modifier and 22q11.2 genes in cortical brain regions from late infancy to young adulthood. Corresponding gene coexpression modules are enriched with brain-specific protein-protein interactions of SLC25A1, COMT, and PI4KA in the 22q11.2 deletion region. Overall, our study highlights the contribution of rare coding variants to the SCZ risk. They not only complement common variants in disease genetics but also pinpoint brain regions and developmental stages critical to the etiology of syndromic schizophrenia.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine MRC Centre for Neuropsychiatric Genetics and Genomics (CNGG)
Publisher:	Springer Nature
ISSN:	1359-4184
Date of First Compliant Deposit:	21 February 2023
Date of Acceptance:	21 February 2023
Last Modified:	09 Nov 2023 22:46
URI:	https://orca.cardiff.ac.uk/id/eprint/157200

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