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Research
An Intronic Variant of CHD7 Identified in Autism Patients Interferes With Neuronal Differentiation and Development
Zilong Qiu
Institute of Neuroscience, Chinese Academy of Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4286-3288
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This work is licensed under a CC BY 4.0 License. Read Full License
Background: Genetic compositions play critical roles in pathogenesis of autism spectrum disorders (ASD). Inherited and de novo intronic variants are often seen in patients with ASD. However, the biological significance of intronic variants are difficult to address. Here, we identified a recurrent inherited intronic variant in the CHD7 gene among Chinese ASD cohort, which is specifically enriched in East Asian populations. CHD7 has been implicated in numerous developmental disorders including CHARGE syndrome and ASD. Here, we use differentiated human embryonic stem cells to investigate whether the ASD-associated CHD7 intronic variant may affect neural development.
Methods: 167 ASD probands and their parents performed whole-exome sequencing and a recurrent inherited intronic variant was selected for functional research. We established human embryonic stem cells carrying this intronic variant using CRISPR/Cas methods and differentiated to neural progenitor cells and neurons for analysis.
Results: The level of CHD7 mRNA significantly decreased in cell lines carrying homozygous mutants compared to control. Upon differentiation towards the forebrain neuronal lineage, neural cells carrying the CHD7 intronic variant exhibited developmental delay in neuronal differentiation and maturation. Importantly, TBR1, a gene also implicated in ASD, significantly increased in neurons carrying the CHD7 intronic variant, suggesting the intrinsic relevance among ASD genes. Furthermore, the morphological defects found in neurons carrying CHD7 intronic mutations could be rescued by knocking down TBR1, indicating that TBR1 may be responsible for defects in CHD7-related disorders. Finally, the CHD7 intronic variant generates three abnormal forms of transcripts through alternative splicing, which all exhibited loss-of-function manners in functional assays.
Limitations: The probands with CHD7 intronic variant were heterozygous while both cell lines established were homozygous, so the phenotype of the disease could not be completely simulated.
Conclusions: Our study provides the crucial evidences for supporting the notion that intronic variant site of CHD7 is a potentially autism susceptible site, shedding new light on identifying functions of intronic variants in autism genetic studies.
Keywords
Autism, CHD7, Intronic variant, Inherited variant
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Research
An Intronic Variant of CHD7 Identified in Autism Patients Interferes With Neuronal Differentiation and Development
Zilong Qiu
Institute of Neuroscience, Chinese Academy of Sciences
Corresponding Author
ORCiD: https://orcid.org/0000-0003-4286-3288
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 17 Aug, 2020
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Cellular & Molecular Neuroscience
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Genetic compositions play critical roles in pathogenesis of autism spectrum disorders (ASD). Inherited and de novo intronic variants are often seen in patients with ASD. However, the biological significance of intronic variants are difficult to address. Here, we identified a recurrent inherited intronic variant in the CHD7 gene among Chinese ASD cohort, which is specifically enriched in East Asian populations. CHD7 has been implicated in numerous developmental disorders including CHARGE syndrome and ASD. Here, we use differentiated human embryonic stem cells to investigate whether the ASD-associated CHD7 intronic variant may affect neural development.
Methods: 167 ASD probands and their parents performed whole-exome sequencing and a recurrent inherited intronic variant was selected for functional research. We established human embryonic stem cells carrying this intronic variant using CRISPR/Cas methods and differentiated to neural progenitor cells and neurons for analysis.
Results: The level of CHD7 mRNA significantly decreased in cell lines carrying homozygous mutants compared to control. Upon differentiation towards the forebrain neuronal lineage, neural cells carrying the CHD7 intronic variant exhibited developmental delay in neuronal differentiation and maturation. Importantly, TBR1, a gene also implicated in ASD, significantly increased in neurons carrying the CHD7 intronic variant, suggesting the intrinsic relevance among ASD genes. Furthermore, the morphological defects found in neurons carrying CHD7 intronic mutations could be rescued by knocking down TBR1, indicating that TBR1 may be responsible for defects in CHD7-related disorders. Finally, the CHD7 intronic variant generates three abnormal forms of transcripts through alternative splicing, which all exhibited loss-of-function manners in functional assays.
Limitations: The probands with CHD7 intronic variant were heterozygous while both cell lines established were homozygous, so the phenotype of the disease could not be completely simulated.
Conclusions: Our study provides the crucial evidences for supporting the notion that intronic variant site of CHD7 is a potentially autism susceptible site, shedding new light on identifying functions of intronic variants in autism genetic studies.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5