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Single molecule in situ hybridization reveals distinct localizations of schizophrenia risk-related transcripts SNX19 and AS3MT in human brain

Molecular Psychiatry volume 26, pages 3536–3547 (2021)Cite this article

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Abstract

Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with schizophrenia risk. Integration of RNA-sequencing data from postmortem human brains with these risk SNPs identified transcripts associated with increased schizophrenia susceptibility, including a class of exon 9-spliced isoforms of Sorting nexin-19 (SNX19d9) and an isoform of Arsenic methyltransferase (AS3MT) splicing out exons 2 and 3 (AS3MTd2d3). However, the biological function of these transcript variants is unclear. Defining the cell types where these risk transcripts are dominantly expressed is an important step to understand function, in prioritizing specific cell types and/or neural pathways in subsequent studies. To identify the cell type-specific localization of SNX19 and AS3MT in the human dorsolateral prefrontal cortex (DLPFC), we used single-molecule in situ hybridization techniques combined with automated quantification and machine learning approaches to analyze 10 postmortem brains of neurotypical individuals. These analyses revealed that both pan-SNX19 and pan-AS3MT were more highly expressed in neurons than non-neurons in layers II/III and VI of DLPFC. Furthermore, pan-SNX19 was preferentially expressed in glutamatergic neurons, while pan-AS3MT was preferentially expressed in GABAergic neurons. Finally, we utilized duplex BaseScope technology, to delineate the localization of SNX19d9 and AS3MTd2d3 splice variants, revealing consistent trends in spatial gene expression among pan-transcripts and schizophrenia risk-related transcript variants. These findings demonstrate that schizophrenia risk transcripts have distinct localization patterns in the healthy human brains, and suggest that SNX19 transcripts might disrupt the normal function of glutamatergic neurons, while AS3MT may lead to disturbances in the GABAergic system in the pathophysiology of schizophrenia.

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Fig. 1: Proportion of cell types in human DLPFC.
Fig. 2: Distribution and quantification of pan-SNX19 transcripts in specific cell types.
Fig. 3: Distribution and quantification of pan-AS3MT transcripts in specific cell types.
Fig. 4: Distribution of SNX19 transcript variants in excitatory and inhibitory neurons.
Fig. 5: Distribution of AS3MT transcript variants in excitatory and inhibitory neurons.

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Acknowledgements

We are thankful for the contributions of the Clinical Brain Disorders Branch of the National Institute of Mental Health in assisting the Lieber Institute for Brain Development in the acquisition and curation of brain tissue donations. We are also thankful to Ran Tao and Richard Straub for their help with case selection. Funding for the study was provided by the Lieber Institute for Brain Development.

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Authors and Affiliations

  1. Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA

    Yoichiro Takahashi, Kristen R. Maynard, Madhavi Tippani, Andrew E. Jaffe, Keri Martinowich, Joel E. Kleinman, Daniel R. Weinberger & Thomas M. Hyde

  2. Department of Legal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan

    Yoichiro Takahashi

  3. Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA

    Andrew E. Jaffe, Keri Martinowich, Joel E. Kleinman, Daniel R. Weinberger & Thomas M. Hyde

  4. Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Andrew E. Jaffe, Keri Martinowich & Daniel R. Weinberger

  5. Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA

    Andrew E. Jaffe

  6. Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

    Andrew E. Jaffe

  7. Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA

    Daniel R. Weinberger & Thomas M. Hyde

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Takahashi, Y., Maynard, K.R., Tippani, M. et al. Single molecule in situ hybridization reveals distinct localizations of schizophrenia risk-related transcripts SNX19 and AS3MT in human brain. Mol Psychiatry 26, 3536–3547 (2021). https://doi.org/10.1038/s41380-021-01046-9

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