Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types
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Abstract
Prioritizing disease-critical cell types by integrating genome-wide association studies (GWAS) with functional data is a fundamental goal. Single-cell chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) have characterized cell types at high resolution, and studies integrating GWAS with scRNA-seq have shown promise, but studies integrating GWAS with scATAC-seq have been limited. Here, we identify disease-critical fetal and adult brain cell types by integrating GWAS summary statistics from 28 brain-related diseases/traits (average N = 298 K) with 3.2 million scATAC-seq and scRNA-seq profiles from 83 cell types. We identified disease-critical fetal (respectively adult) brain cell types for 22 (respectively 23) of 28 traits using scATAC-seq, and for 8 (respectively 17) of 28 traits using scRNA-seq. Significant scATAC-seq enrichments included fetal photoreceptor cells for major depressive disorder, fetal ganglion cells for BMI, fetal astrocytes for ADHD, and adult VGLUT2 excitatory neurons for schizophrenia. Our findings improve our understanding of brain-related diseases/traits and inform future analyses.
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Epigenetic marks vary dramatically between neurons, glia, and other brain cells.
“Cell type specificity varies since epigenetic marks vary dramatically between neurons, glia, and other brain cells (45).”
From The clinical use of epigenetics in psychiatry: a narrative review of epigenetic mechanisms, key candidate genes, and precision psychiatry (2025) · cites this paper as [45]
The Methods section (page unavailable) describes cell-type-specific chromatin-accessibility peaks, and the Results compare annotations for astrocytes and neuronal cell types. This supports differences in chromatin accessibility between brain cell types, but the paper does not establish that epigenetic marks generally vary dramatically between neurons, glia, and other brain cells. (LLM, conf=0.80)
Experimental — accuracy not yet measuredGenetic risk for depression is enriched in adult BDNF-positive excitatory neurons as well as in specific developmental cell populations.
“Recent studies further indicate that genetic risk for depression is enriched in adult BDNF-positive excitatory neurons as well as in specific developmental cell populations, highlighting both cell-type specificity and developmental-stage vulnerability (Kim et al., 2024).”
From Histone modifications and depression: epigenetic mechanisms, therapeutic targets, and translational outlook (2026) · cites this paper as Kim et al., 2024
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- Authors
- Kim, S. S., Truong, B., Jagadeesh, K., Dey, K. K., Shen, A. Z., Raychaudhuri, S., Kellis, M., & Price, A. L.
- Affiliations
- Harvard University (US)
- Broad Institute (US)
- Memorial Sloan Kettering Cancer Center (US)
- Massachusetts Institute of Technology (US)
- Brigham and Women's Hospital (US)
- Corresponding author
- Kim, Samuel S.
- Truong, Buu
- Price, Alkes L.
- ORCID
- Venue
- Nature Communications
- Published
- 2024-01-17
- Volume
- 15
- Issue
- 1
- Pages
- 563-563
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC10794712
- OpenAlex
- W4390946851
- Cited by
- 56
- References
- 90
- Citations by year
- 2026: 22 · 2025: 20 · 2024: 7 · 2023: 3 · 2022: 1 · 2021: 3
- FWCI
- 6.65
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health (16549, CA008748, MH107649)
- National Institute of Mental Health (U01MH119509, R01MH109978, R37MH107649, R01MH101244, R01MH115676)
- National Human Genome Research Institute (HG009379, MH101244, F31HG010818, R01HG006399, HG006399, U01HG009379, R00HG012203, T32HG002295, U01HG012009, R56HG013083)
- National Cancer Institute (P30CA008748)
- National Institute of Allergy and Infectious Diseases (P01AI148102)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- brain cell types, chromatin accessibility, gene expression, GWAS summary statistics, fetal brain, adult brain, major depressive disorder, photoreceptors, ganglion cells, astrocytes, attention deficit hyperactivity disorder, schizophrenia, body mass index
- MeSH terms
- Chromatin Immunoprecipitation Sequencing, RNA-Seq, Brain, Chromatin, Major Depressive Disorder, Humans, Genome-Wide Association Study, Single-Cell Analysis
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