Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights
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Abstract
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. Of these 157 genes, 42 were associated with specific chromatin features measured in independent samples, thus 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 the brain captured most 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 toward a mechanistic understanding of GWAS.
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Consistent with previous findings, a substantial overlap was detected between H-MAGMA and eQTL-based gene mapping tools.
“Consistent with the previous finding3,11, we detected a substantial overlap.”
From A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles (2020) · cites this paper as [11]
Distinct data types derived in different laboratories and samples show significant overlap in regulatory predictions.
“These distinct data types – often derived in different laboratories in different samples- show significant overlap in regulatory predictions (Gusev et al., 2018).”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Gusev et al., 2018
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- Authors
- Gusev, A., Mancuso, N., Won, H., Kousi, M., Finucane, H. K., Reshef, Y., Song, L., Safi, A., Schizophrenia Working Group of the Psychiatric Genomics Consortium, McCarroll, S., Neale, B. M., Ophoff, R. A., O’Donovan, M. C., Crawford, G. E., Geschwind, D. H., Katsanis, N., Sullivan, P. F., Pasaniuc, B., & Price, A. L.
- Affiliations
- Broad Institute (US)
- University of California, Los Angeles (US)
- Duke Medical Center (US)
- Harvard University (US)
- Duke University (US)
- Cardiff University (GB)
- University of North Carolina at Chapel Hill (US)
- Corresponding author
- Gusev, Alexander
- Price, Alkes L.
- ORCID
- Venue
- Nature Genetics
- Published
- 2018-04
- Volume
- 50
- Issue
- 4
- Pages
- 538-548
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC5942893
- OpenAlex
- W2951325776
- Cited by
- 491
- References
- 58
- Citations by year
- 2026: 31 · 2025: 42 · 2024: 44 · 2023: 57 · 2022: 89 · 2021: 87 · 2020: 59 · 2019: 60 · 2018: 16 · 2017: 6
- FWCI
- 37.26
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institutes of Health (1s10od018164-01, 5r01mh080405-05, 5r01mh094714-04)
- Medical Research Council (MR/P005748/1, MR/L010305/1)
- National Institute on Aging (P50AG005138, P01AG002219)
- National Institute of Mental Health (P50MH084053, R01 MH‐080405, R01MH093725, R01MH107649, U01MH103339, U01MH109528, R01-MH094714, P50MH066392, R21MH105881, U01MH103365, R01MH110927, R01MH075916, R01MH109978, R01MH085542, R37MH057881, U01MH103340, R21MH102791, R01MH105472, R01MH097276, P50MH106934, U01MH103392, R01MH105898, R21MH103877, R00MH113823, U01MH103346, K99MH113823, P50MH094268)
- National Human Genome Research Institute (R01HG009120, U01HG009379)
- National Institute of General Medical Sciences (R01GM105857, F32GM106584, T32GM007753)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Medicine › Psychiatry and Mental health › Schizophrenia research and treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- schizophrenia, transcriptome-wide association study, chromatin activity, gene expression, susceptibility genes, ERK1, zebrafish, brain development, splicing, brain tissue, regulatory mechanisms, Psychiatric Genomics Consortium
- MeSH terms
- Animals, Brain, Chromatin, Humans, Microtubule-Associated Proteins, Schizophrenia, Zebrafish, Kinesins, Gene Dosage, Genetic Predisposition to Disease, Multifactorial Inheritance, Gene Expression Profiling, Zebrafish Proteins, Quantitative Trait Loci, Mitogen-Activated Protein Kinase 3, Protein Phosphatase 2, Genome-Wide Association Study
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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