With few exceptions, the marked advances in knowledge about the genetic basis of schizophrenia have not converged on findings that can be confidently used for precise experimental modeling. By applying knowledge of the cellular taxonomy of the brain from single-cell RNA sequencing, we evaluated whether the genomic loci implicated in schizophrenia map onto specific brain cell types. We found that the common-variant genomic results consistently mapped to pyramidal cells, medium spiny neurons (MSNs) and certain interneurons, but far less consistently to embryonic, progenitor or glial cells. These enrichments were due to sets of genes that were specifically expressed in each of these cell types. We also found that many of the diverse gene sets previously associated with schizophrenia (genes involved in synaptic function, those encoding mRNAs that interact with FMRP, antipsychotic targets, etc.) generally implicated the same brain cell types. Our results suggest a parsimonious explanation: the common-variant genetic results for schizophrenia point at a limited set of neurons, and the gene sets point to the same cells. The genetic risk associated with MSNs did not overlap with that of glutamatergic pyramidal cells and interneurons, suggesting that different cell types have biologically distinct roles in schizophrenia.

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J.H.-L. was funded by the Swedish Research Council (Vetenskapsrådet, award 2014-3863), StratNeuro, the Wellcome Trust (108726/Z/15/Z) and the Swedish Brain Foundation (Hjärnfonden). P.F.S. gratefully acknowledges support from the Swedish Research Council (Vetenskapsrådet, award D0886501). N.G.S. was supported by the Wellcome Trust (108726/Z/15/Z). J.B. was supported by the Swiss National Science Foundation. The PGC has received major funding from the US National Institute of Mental Health (U01 MH109528 and U01 MH109532). H.A.G. was supported by PGC grant 1U01MH109514-01. Primary schizophrenia GWAS data were generated with support from the Medical Research Council (MRC) Centre (MR/L010305/1), program grant G0800509 and project grant MR/L011794/1, and funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 279227 (CRESTAR Consortium).

Author information

Author notes

  1. These authors contributed equally: Nathan G. Skene, Julien Bryois.

  2. A list of members and affiliations appears in the Supplementary Note.


  1. Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden

    • Nathan G. Skene
    • , Ana B. Muñoz-Manchado
    • , Sten Linnarsson
    •  & Jens Hjerling-Leffler
  2. UCL Institute of Neurology, Queen Square, London, UK

    • Nathan G. Skene
  3. Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden

    • Julien Bryois
    •  & Patrick F. Sullivan
  4. Allen Institute for Brain Science, Seattle, WA, USA

    • Trygve E. Bakken
    • , Rebecca D. Hodge
    • , Jeremy A. Miller
    •  & Ed S. Lein
  5. King’s College London, Institute of Psychiatry, Psychology and Neuroscience, MRC Social, Genetic and Developmental Psychiatry (SGDP) Centre, London, UK

    • Gerome Breen
    •  & Héléna A. Gaspar
  6. National Institute for Health Research Biomedical Research Centre, South London and Maudsley National Health Service Trust, London, UK

    • Gerome Breen
    •  & Héléna A. Gaspar
  7. Department of Genetics, University of North Carolina, Chapel Hill, NC, USA

    • James J. Crowley
    • , Paola Giusti-Rodriguez
    •  & Patrick F. Sullivan
  8. MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK

    • Michael C. O’Donovan
    • , Michael J. Owen
    • , Antonio F. Pardiñas
    •  & James T. R. Walters
  9. Brain Mind Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

    • Jesper Ryge


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  1. Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium


    N.G.S., J.B., P.F.S. and J.H.-L. designed the study and wrote and reviewed the manuscript; N.G.S. performed the LDSC analyses; J.B. performed the MAGMA analyses; T.E.B., R.D.H., J.A.M. and E.S.L. generated the human mid-temporal cortex data; A.B.M.-M., J.R., S.L. and J.H.-L. generated the KI single-cell data; the Major Depressive Disorder Working Group of the PGC performed the MDD GWAS; J.T.R.W., J.J.C., P.G.-R., M.C.O., M.J.O. and A.F.P. performed the schizophrenia CLOZUK GWAS; G.B. and H.A.G. analyzed the antipsychotic drug targets; and all authors read and approved the manuscript.

    Competing interests

    P.F.S. is on the advisory committee at Lundbeck, is a Scientific Advisory Board member at Pfizer and has received speaker reimbursement and grant funding from Roche. J.H.-L. is a Scientific Advisor at Cartana and has received grant funding from Roche.

    Corresponding authors

    Correspondence to Patrick F. Sullivan or Jens Hjerling-Leffler.

    Supplementary information

    1. Supplementary Text and Figures

      Supplementary Figures 1–21, Supplementary Note and Supplementary Tables 1–3

    2. Reporting Summary

    3. Supplementary Table 4

      Specificity values for Karolinska scRNA-seq superset

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