Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism
Open accessAbstract
Autism spectrum disorder (ASD) is a complex developmental syndrome of unknown etiology. Recent studies employing exome- and genome-wide sequencing have identified nine high-confidence ASD (hcASD) genes. Working from the hypothesis that ASD-associated mutations in these biologically pleiotropic genes will disrupt intersecting developmental processes to contribute to a common phenotype, we have attempted to identify time periods, brain regions, and cell types in which these genes converge. We have constructed coexpression networks based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood. By assessing enrichment of an independent set of probable ASD (pASD) genes, derived from the same sequencing studies, we demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons. This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology.
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Prior analyses have implicated excitatory glutamatergic neurons in the cortex and medium spiny neurons in the striatum in ASD.
“Prior analyses have implicated excitatory glutamatergic neurons in the cortex and medium spiny neurons in the striatum in ASD (Chang et al., 2015; Parikshak et al., 2013; Willsey et al., 2013; Xu et al., 2014).”
From Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism (2020) · cites this paper as Willsey et al., 2013
The Results section, “Gene-Marker-Based Analysis Implicates Layer 5/6 Glutamatergic Projection Neurons in ASD” (page not provided), reports an ASD-associated signal in cortical glutamatergic projection neurons. The cited passages do not support the sentence’s additional claim about medium spiny neurons in the striatum. (LLM, conf=0.87)
Experimental — accuracy not yet measuredASD genes are expressed at high levels in the human cortex and early in development.
“Thus, in keeping with prior analyses (Chang et al., 2015; Parikshak et al., 2013; Willsey et al., 2013; Xuet al., 2014), ASD genes are expressed at high levels in the human cortex and early in development.”
From Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism (2020) · cites this paper as Willsey et al., 2013
The Results section, “Expression Profiling Confirms the Expression of hcASD Genes in Midfetal Cortical Projection Neurons” (page unavailable), reports robust expression of five representative high-confidence ASD genes in human midfetal frontal-cortex projection neurons. This supports expression in the cortex early in development, but does not establish high expression levels for ASD genes generally across the human cortex. (LLM, conf=0.85)
Experimental — accuracy not yet measuredMicroarray probes for CHD8 do not perform well.
“Because the microarray probes for CHD8 , one of the genes with the lowest p values for ASD association (De Rubeis et al., 2014), do not perform well (Willsey et al., 2013; Cotney et al., 2015)”
From Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism (2020) · cites this paper as Willsey et al., 2013
The Experimental Procedures section (Construction of Spatiotemporal Coexpression Networks; page unavailable) says CHD8 was an exception to the usual use of core microarray probes: its expression data came from the extended probe set. That supports unusual handling of CHD8 probes, but the paper does not say that the probes performed poorly or explain why the exception was made. (LLM, conf=0.75)
Experimental — accuracy not yet measuredThe PFC of individuals with ASD shows structural and functional changes, specifically in the ACC, oFC and lPFC.
“It has been described that the PFC of individuals with ASD show structural and functional changes, specifically in the ACC, oFC and lPFC [367, 368].”
From Development of prefrontal cortex (2022) · cites this paper as [367]
The Introduction reports convergence of ASD risk genes in midfetal prefrontal cortical neurons, and the Results include orbitofrontal cortex in the analyzed PFC-MSC cluster. These passages support a link between prefrontal cortex and ASD, but they do not establish structural and functional changes in individuals with ASD, specifically in the ACC, oFC and lPFC. (LLM, conf=0.82)
Experimental — accuracy not yet measuredSeveral studies have supported a nexus in mid-fetal, glutamatergic neurons during cortical development, with modestly divergent findings regarding deep versus superficial cortical layers.
“several studies have supported a nexus in mid-fetal, glutamatergic neurons during cortical development, with modestly divergent findings regarding deep 56 versus”
From Autism spectrum disorder (2020) · cites this paper as [56]
Midfetal development in the prefrontal cortex was previously implicated for ASD risk.
“We extracted the subset of the data for a spatio-temporal window that was previously implicated for ASD risk: midfetal development in the prefrontal cortex (PFC) (Willsey et al., 2013).”
From Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism (2020) · cites this paper as Willsey et al., 2013
Coexpression network analyses of autism spectrum disorder genes indicate that developmental defects associated with autism spectrum disorder may arise during fetal stages.
“Moreover, coexpression network analyses of ASD genes indicate that the developmental defects associated with ASD may arise during fetal stages5,6, periods that are difficult to investigate.”
From Single-cell brain organoid screening identifies developmental defects in autism (2023) · cites this paper as [5]
ASD candidate gene expression converges on transcriptional regulation in pyramidal, glutamatergic cortical neurons during mid-fetal human development.
“Recent studies integrating ASD candidate genes with spatiotemporal coexpression networks demonstrate that gene expression converge on the transcriptional regulation in pyramidal, glutamatergic cortical neurons during mid-fetal human development8, 9.”
From Altered proliferation and networks in neural cells derived from idiopathic autistic individuals (2017) · cites this paper as [9]
Some of these networks are particularly involved during pre-natal cortical development while others are associated with post-natal down-regulation of synaptic density.
“Some of these networks are particularly involved during pre-natal cortical development (Willsey et al., 2013) while others were associated with post-natal down-regulation of synaptic density (Tsai et al., 2013).”
From From early markers to neuro-developmental mechanisms of autism (2014) · cites this paper as Willsey et al., 2013
Autism spectrum disorder risk variants are enriched in cortical glutamatergic neurons expressed during neurogenesis and neuronal migration during fetal cortical development in human and mouse.
“ASD risk variants are enriched in cortical glutamatergic neurons expressed during neurogenesis and neuronal migration during fetal cortical development in human and mouse (Parikshak et al., 2013; Willsey et al., 2013).”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Willsey et al., 2013
ASD genes as a group are preferentially expressed in late mid-fetal prefrontal cortex, concentrated in layer 5/6 cortical projection neurons.
“Analysis of spatiotemporal expression of genes has revealed that ASD genes as a group are preferentially expressed in late mid-fetal prefrontal cortex, with a concentration in layer 5/6 cortical projection neurons (Willsey et al., 2013).”
From Getting to the cores of autism (2019) · cites this paper as Willsey et al., 2013
lncRNAs will be important targets for investigation in ASD.
“Remarkably, CTX.M24 was significantly enriched for lncRNAs, genes expressed highly during fetal cortical development, and genes harbouring protein-disrupting mutations found in ASD, suggesting that lncRNAs will be important targets for investigation in ASD10,25 (FDR < 0.05, Extended Data Fig. 9a, g).”
From Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism (2016) · cites this paper as [25]
A complementary study identified developmental co-expression networks enriched for ASD risk genes seeded around nine genes with the highest ASD association signal from whole-exome sequencing.
“A complementary study identified developmental co-expression networks enriched for ASD risk genes seeded around nine genes with the highest ASD association signal from whole-exome sequencing112.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [112]
Both of these studies found convergence for rare de novo ASD-associated mutations during early fetal and mid-fetal development, with greatest enrichment for risk in genes found in cortical glutamatergic neurons.
“Importantly, both of these studies found convergence for rare de novo ASD-associated mutations during early fetal and mid-fetal development, with the greatest enrichment for risk in genes found in cortical glutamatergic neurons.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [112]
That study identified three spatiotemporal combinations that passed stringent correction for multiple testing: frontal cortical regions during the fetal period, and thalamic and cerebellar regions from birth to 6 years of postnatal age.
“They identified three spatiotemporal combinations that passed stringent correction for multiple testing: frontal cortical regions during the fetal period, and thalamic and cerebellar regions from birth to 6 years of postnatal age.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [112]
This overlap suggests involvement of autism risk factors in early development of excitatory cortical neurons.
“This suggests involvement of autism risk factors in early development of excitatory cortical neurons, consistent with other recent studies39,40.”
From Transcriptional landscape of the prenatal human brain (2014) · cites this paper as [40]
ANK2 has been consistently associated with ASD and also with cardiac arrhythmia.
“ANK2 has been consistently associated with ASD (22,26,80) and also with cardiac arrhythmia (OMIM no.600919) (78).”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [80]
Genetic and non-genetic factors and their interaction may act at very early periods of fetal brain development and potentially alter protein or gene expression regulation leading to shared pathways for complex ASD-related phenotypes.
“Recent evidence11, 12, 13, 14, 15, 16, 17, 18, 19, 20 has also catalyzed the concept that genetic and non-genetic factors and their interaction, may act at very early periods of fetal brain development and potentially alter protein or gene expression regulation leading to shared pathways for complex ASD-related phenotypes.”
From Maternal immune activation dysregulation of the fetal brain transcriptome and relevance to the pathophysiology of autism spectrum disorder (2018) · cites this paper as [13]
Ank2 exhibited decreased inclusion of a MXE in the STR of oASD mice, compared to oTD controls.
“Ank2, necessary for neuronal migration (Kordeli and Bennett, 1991; Willsey et al., 2013), exhibited decreased inclusion of a MXE in the STR of oASD mice, compared to oTD controls (Figure 3F).”
From Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice (2019) · cites this paper as Willsey et al., 2013
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- Authors
- Willsey, A. J., Sanders, S. J., Li, M., Dong, S., Tebbenkamp, A. T., Muhle, R. A., Reilly, S. K., Lin, L., Fertuzinhos, S., Miller, J. A., Murtha, M. T., Bichsel, C., Niu, W., Cotney, J., Ercan-Sencicek, A. G., Gockley, J., Gupta, A. R., Han, W., He, X., Hoffman, E. J., Klei, L., Lei, J., Liu, W., Liu, L., Lu, C., Xu, X., Zhu, Y., Mane, S. M., Lein, E. S., Wei, L., Noonan, J. P., Roeder, K., Devlin, B., Sestan, N., & State, M. W.
- Affiliations
- University of California, San Francisco (US)
- Yale University (US)
- Peking University (CN)
- Allen Institute for Brain Science (US)
- Carnegie Mellon University (US)
- University of Pittsburgh (US)
- Corresponding author
- Devlin, Bernie
- State, Matthew W.
- ORCID
- Willsey, A. Jeremy
- Sanders, Stephan J.
- Li, Mingfeng
- Dong, Shan
- Tebbenkamp, Andrew T.
- Muhle, Rebecca A.
- Reilly, Steven K.
- Lin, Leon
- Fertuzinhos, Sofia
- Miller, Jeremy A.
- Niu, Wei
- Cotney, Justin
- Gockley, Jake
- Gupta, Abha R.
- He, Xin
- Hoffman, Ellen J.
- Klei, Lambertus
- Lei, Jing
- Liu, Wenzhong
- Liu, Li
- Lu, Cong
- Xu, Xuming
- Zhu, Ying
- Mane, Shrikant M.
- Lein, Ed S.
- Wei, Liping
- Noonan, James P.
- Roeder, Kathryn
- Devlin, Bernie
- State, Matthew W.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-11
- Volume
- 155
- Issue
- 5
- Pages
- 997-1007
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3995413
- OpenAlex
- W2009742334
- Cited by
- 934
- References
- 35
- Citations by year
- 2026: 48 · 2025: 59 · 2024: 61 · 2023: 57 · 2022: 69 · 2021: 77 · 2020: 112 · 2019: 83 · 2018: 76 · 2017: 82 · 2016: 81 · 2015: 66 · 2014: 59 · 2013: 2
- FWCI
- 37.35
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Simons Foundation Autism Research Initiative
- Canadian Institutes of Health Research
- National Institute of Mental Health (RC2MH089956, R37MH057881, U01MH081896, R25MH077823, T32MH018268)
- National Institute of General Medical Sciences (R01GM094780)
- 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 › Bioinformatics and Genomic Networks
- Keywords
- autism spectrum disorder, co-expression network, ASD pathogenesis
- MeSH terms
- Animals, Brain, Child Development Disorders, Pervasive, Female, Fetus, Humans, Male, Mutation, Neurons, Prefrontal Cortex, Sequence Analysis, DNA, Genetic Predisposition to Disease, Gene Expression Profiling, Mice, Genome-Wide Association Study, Exome
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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