Single-cell genomics identifies cell type–specific molecular changes in autism
Open accessAbstract
Brain cell transcriptomes in autism: Autism manifests in many ways. Despite that diversity, the disorder seems to affect specific cellular pathways, including those observed in the neocortex of patients' brains. Velmeshev et al. analyzed the transcriptomes of single brain cells, including neurons and glia, from patients with autism. Single-nucleus RNA sequencing analysis suggested that affected pathways regulate synapse function as well as neural outgrowth and migration. Furthermore, in patient samples, specific sets of genes enriched in upper-layer projection neurons and microglia correlated with clinical severity. Science , this issue p. 685
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One study using single cell technologies on brain tissue from people with ASD demonstrated changes in transcription in multiple cell types including upper-layer cortical neurons.
“Of note, one study used single cell technologies to examine specific cell types and developmental stages using brain tissue from people with ASD 60 , and demonstrated changes in transcription in multiple cell types including upper-layer cortical neurons.”
From Autism spectrum disorder (2020) · cites this paper as [60]
The paper reports single-nucleus RNA sequencing of cortical tissue from people with ASD and identifies transcriptional changes in multiple cell types, including upper-layer L2/3 neurons (Abstract; study description and gene-expression results, page unavailable). The citing sentence also says the study examined developmental stages, but the passages describe samples aged 4–22 and developmental lineages, not an analysis of distinct developmental stages. (LLM, conf=0.85)
Experimental — accuracy not yet measuredOf the 121,451 cells in the Velmeshev et al. ASD snRNA-seq dataset, 20,249 were labeled as inhibitory neurons based on marker gene expression profiles.
“Of the 121,451 cells in this dataset, 20,249 were labeled as inhibitory neurons based on marker gene expression profiles.”
From hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data (2023) · cites this paper as Velmeshev et al.9
The paper’s clustering passage (section labeled Abstract; page unavailable) says it annotated cell types, including interneurons, using known cell-type markers. Its sequencing passage reports 104,559 ASD-and-control nuclei plus 21,984 additional epilepsy-and-control profiles; our copy does not establish the claimed total of 121,451 cells or the count of 20,249 inhibitory neurons. (LLM, conf=0.85)
Experimental — accuracy not yet measuredCell type-specific alterations have been observed in patients with autism spectrum disorder and brain organoid disease models.
“Cell type-specific alterations have been observed in patients with ASD and brain organoid disease models11,34.”
From Single-cell brain organoid screening identifies developmental defects in autism (2023) · cites this paper as [34]
The paper’s Abstract reports cell type-specific molecular changes in cortical tissue from patients with ASD, including changes in upper-layer excitatory neurons and microglia. The sentence also mentions brain organoid disease models, but our copy does not report findings from organoid models (searched: organoid). (LLM, conf=0.88)
Experimental — accuracy not yet measuredCHCHD2 encodes a mitochondrial protein, and its downregulation has been observed in neurons from postmortem brains of patients with autism spectrum disorder.
“CHCHD2 encodes a mitochondrial protein, and its downregulation has been observed in neurons from the postmortem brains of patients with ASD34.”
From Single-cell brain organoid screening identifies developmental defects in autism (2023) · cites this paper as [34]
The indexed text (section labeled Abstract; page unavailable) reports downregulated neuronal genes in postmortem ASD samples. It does not identify CHCHD2 among those genes or say that CHCHD2 encodes a mitochondrial protein, so it does not support the gene-specific claim. (LLM, conf=0.82)
Experimental — accuracy not yet measuredASD risk gene coexpression networks are enriched in upper-layer neurons during development and these neurons are preferentially affected in ASD patients.
“This aligns with the observation that ASD risk gene coexpression networks are enriched in upper-layer neurons during development and that these neurons are preferentially affected in ASD patients6,34.”
From Single-cell brain organoid screening identifies developmental defects in autism (2023) · cites this paper as [34]
The paper reports that ASD-associated genes and molecular changes are enriched in upper-layer cortical neurons, and that gene expression in layer 2/3 neurons is especially affected in ASD patients (Abstract; page not provided). It does not report an analysis showing that ASD risk-gene coexpression networks are enriched in those neurons during development; it refers more generally to previous studies of fetal cell-type convergence. (LLM, conf=0.87)
Experimental — accuracy not yet measured
Network analysis of inhibitory neurons from published single-nucleus RNA sequencing in autism spectrum disorder donors revealed modules disrupted in ASD containing key genetic risk genes such as SCN2A, TSC1, and SHANK2.
“Network analysis of inhibitory neurons from published single-nucleus RNA sequencing (snRNA-seq) in autism spectrum disorder (ASD) donors9 revealed modules disrupted in ASD containing key genetic risk genes such as SCN2A, TSC1, and SHANK2.”
From hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data (2023) · cites this paper as [9]
NRN1 in excitatory neurons showed decreased expression in ASD patients and was significantly decreased across the panel of 35 ASD risk gene perturbations at FDR < 0.1.
“From this analysis, we identified two genes, SST in interneurons and NRN1 in excitatory neurons, both of which showed decreased expression in ASD patients and were likewise significantly decreased in expression across our panel of perturbations (FDR < 0.1), albeit with different effect sizes (Fig. 4F, Table S10).”
From In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes (2020) · cites this paper as [31]
SST in interneurons showed decreased expression in ASD patients and was significantly decreased across the panel of 35 ASD risk gene perturbations at FDR < 0.1.
“From this analysis, we identified two genes, SST in interneurons and NRN1 in excitatory neurons, both of which showed decreased expression in ASD patients and were likewise significantly decreased in expression across our panel of perturbations (FDR < 0.1), albeit with different effect sizes (Fig. 4F, Table S10).”
From In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes (2020) · cites this paper as [31]
In postmortem snRNA-seq data from 15 ASD donors and 16 controls, 14 genes were differentially expressed between patients and controls in at least one of three major cell types (inhibitory neurons, excitatory neurons, or oligodendrocytes) at FDR < 0.2 and had 1:1 mouse orthologs.
“We identified genes that were differentially expressed between patients and controls in at least one of three major cell types (inhibitory neurons, excitatory neurons, or oligodendrocytes) with FDR < 0.2, and selected those that have 1:1 orthologs in mice, resulting in 14 genes (Fig. 4F, Table S10).”
From In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes (2020) · cites this paper as [31]
The human snRNA-seq differential expression analysis used a statistically conservative pseudobulk-based approach with DESeq2, correcting for age, sex, and patient-to-patient variability.
“Using a dataset of snRNA-seq profiles from 15 ASD donors and 16 controls (31), we defined differentially expressed (DE) genes in each cell type using a statistically conservative pseudobulk-based analysis with DESeq2 (35, 36), correcting for age, sex, and patient-to-patient variability.”
From In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes (2020) · cites this paper as [31]
A pattern of synaptic dysfunction in upper-layer cortical circuitry has previously been reported in autism and correlated with cognitive deficits.
“Such a pattern of dysfunction has previously been reported in an snRNA-seq study of autism and correlated with cognitive deficits8.”
From Dysregulation of brain and choroid plexus cell types in severe COVID-19 (2021) · cites this paper as [8]
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- Authors
- Velmeshev, D., Schirmer, L., Jung, D., Haeussler, M., Perez, Y., Mayer, S., Bhaduri, A., Goyal, N., Rowitch, D. H., & Kriegstein, A. R.
- Affiliations
- University of California, San Francisco (US)
- University of California, Santa Cruz (US)
- Corresponding author
- Velmeshev, Dmitry
- Kriegstein, Arnold R.
- ORCID
- Venue
- Science
- Published
- 2019-05-17
- Volume
- 364
- Issue
- 6441
- Pages
- 685-689
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC7678724
- OpenAlex
- W2946016273
- Cited by
- 927
- References
- 27
- Citations by year
- 2026: 110 · 2025: 131 · 2024: 150 · 2023: 147 · 2022: 138 · 2021: 117 · 2020: 113 · 2019: 18
- FWCI
- 56.21
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion)
- Apollo
- Funders
- National Institute of Mental Health (1U01MH114825-01)
- National Human Genome Research Institute (4U41HG002371)
- Simons Foundation (515488)
- California Institute for Regenerative Medicine (GC1R-06673-C)
- Silicon Valley Community Foundation (2018-182809)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- autism spectrum disorder, single-nucleus RNA sequencing, neocortex, excitatory neurons, microglia, synaptic signaling, clinical severity, cell type-specific transcriptomics, cortical circuits
- MeSH terms
- Adolescent, Autistic Disorder, Cell Nucleus, Child, Child, Preschool, Female, Gene Expression Regulation, Humans, Male, Neurons, Sequence Analysis, RNA, Microglia, Neocortex, Gene Expression Profiling, Genomics, Young Adult, Single-Cell Analysis
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