Detection of autism spectrum disorder-related pathogenic trio variants by a novel structure-based approach
Abstract Background Glutamatergic synapse dysfunction is believed to underlie the development of Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) in many individuals. However, identification of genetic markers that contribute to synaptic dysfunction in these individuals is notoriously...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-04-01
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| Series: | Molecular Autism |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13229-024-00590-9 |
| _version_ | 1797219831479533568 |
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| author | Sadhna Rao Anastasiia Sadybekov David C. DeWitt Joanna Lipka Vsevolod Katritch Bruce E. Herring |
| author_facet | Sadhna Rao Anastasiia Sadybekov David C. DeWitt Joanna Lipka Vsevolod Katritch Bruce E. Herring |
| author_sort | Sadhna Rao |
| collection | DOAJ |
| description | Abstract Background Glutamatergic synapse dysfunction is believed to underlie the development of Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) in many individuals. However, identification of genetic markers that contribute to synaptic dysfunction in these individuals is notoriously difficult. Based on genomic analysis, structural modeling, and functional data, we recently established the involvement of the TRIO-RAC1 pathway in ASD and ID. Furthermore, we identified a pathological de novo missense mutation hotspot in TRIO’s GEF1 domain. ASD/ID-related missense mutations within this domain compromise glutamatergic synapse function and likely contribute to the development of ASD/ID. The number of ASD/ID cases with mutations identified within TRIO’s GEF1 domain is increasing. However, tools for accurately predicting whether such mutations are detrimental to protein function are lacking. Methods Here we deployed advanced protein structural modeling techniques to predict potential de novo pathogenic and benign mutations within TRIO’s GEF1 domain. Mutant TRIO-9 constructs were generated and expressed in CA1 pyramidal neurons of organotypic cultured hippocampal slices. AMPA receptor-mediated postsynaptic currents were examined in these neurons using dual whole-cell patch clamp electrophysiology. We also validated these findings using orthogonal co-immunoprecipitation and fluorescence lifetime imaging (FLIM-FRET) experiments to assay TRIO mutant overexpression effects on TRIO-RAC1 binding and on RAC1 activity in HEK293/T cells. Results Missense mutations in TRIO’s GEF1 domain that were predicted to disrupt TRIO-RAC1 binding or stability were tested experimentally and found to greatly impair TRIO-9’s influence on glutamatergic synapse function. In contrast, missense mutations in TRIO’s GEF1 domain that were predicted to have minimal effect on TRIO-RAC1 binding or stability did not impair TRIO-9’s influence on glutamatergic synapse function in our experimental assays. In orthogonal assays, we find most of the mutations predicted to disrupt binding display loss of function but mutants predicted to disrupt stability do not reflect our results from neuronal electrophysiological data. Limitations We present a method to predict missense mutations in TRIO’s GEF1 domain that may compromise TRIO function and test for effects in a limited number of assays. Possible limitations arising from the model systems employed here can be addressed in future studies. Our method does not provide evidence for whether these mutations confer ASD/ID risk or the likelihood that such mutations will result in the development of ASD/ID. Conclusions Here we show that a combination of structure-based computational predictions and experimental validation can be employed to reliably predict whether missense mutations in the human TRIO gene impede TRIO protein function and compromise TRIO’s role in glutamatergic synapse regulation. With the growing accessibility of genome sequencing, the use of such tools in the accurate identification of pathological mutations will be instrumental in diagnostics of ASD/ID. |
| first_indexed | 2024-04-24T12:39:54Z |
| format | Article |
| id | doaj.art-e04f25582550489b9b9369030d6873fe |
| institution | Directory Open Access Journal |
| issn | 2040-2392 |
| language | English |
| last_indexed | 2024-04-24T12:39:54Z |
| publishDate | 2024-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Molecular Autism |
| spelling | doaj.art-e04f25582550489b9b9369030d6873fe2024-04-07T11:20:48ZengBMCMolecular Autism2040-23922024-04-0115111510.1186/s13229-024-00590-9Detection of autism spectrum disorder-related pathogenic trio variants by a novel structure-based approachSadhna Rao0Anastasiia Sadybekov1David C. DeWitt2Joanna Lipka3Vsevolod Katritch4Bruce E. Herring5Department of Biological Sciences, Neurobiology Section, Dornsife College of Letters, Arts and Sciences, University of Southern CaliforniaQuantitative and Computational Biology, University of Southern CaliforniaDepartment of Pathology, Genentech, Inc.Department of Neuroscience, Genentech, Inc.Quantitative and Computational Biology, University of Southern CaliforniaDepartment of Biological Sciences, Neurobiology Section, Dornsife College of Letters, Arts and Sciences, University of Southern CaliforniaAbstract Background Glutamatergic synapse dysfunction is believed to underlie the development of Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) in many individuals. However, identification of genetic markers that contribute to synaptic dysfunction in these individuals is notoriously difficult. Based on genomic analysis, structural modeling, and functional data, we recently established the involvement of the TRIO-RAC1 pathway in ASD and ID. Furthermore, we identified a pathological de novo missense mutation hotspot in TRIO’s GEF1 domain. ASD/ID-related missense mutations within this domain compromise glutamatergic synapse function and likely contribute to the development of ASD/ID. The number of ASD/ID cases with mutations identified within TRIO’s GEF1 domain is increasing. However, tools for accurately predicting whether such mutations are detrimental to protein function are lacking. Methods Here we deployed advanced protein structural modeling techniques to predict potential de novo pathogenic and benign mutations within TRIO’s GEF1 domain. Mutant TRIO-9 constructs were generated and expressed in CA1 pyramidal neurons of organotypic cultured hippocampal slices. AMPA receptor-mediated postsynaptic currents were examined in these neurons using dual whole-cell patch clamp electrophysiology. We also validated these findings using orthogonal co-immunoprecipitation and fluorescence lifetime imaging (FLIM-FRET) experiments to assay TRIO mutant overexpression effects on TRIO-RAC1 binding and on RAC1 activity in HEK293/T cells. Results Missense mutations in TRIO’s GEF1 domain that were predicted to disrupt TRIO-RAC1 binding or stability were tested experimentally and found to greatly impair TRIO-9’s influence on glutamatergic synapse function. In contrast, missense mutations in TRIO’s GEF1 domain that were predicted to have minimal effect on TRIO-RAC1 binding or stability did not impair TRIO-9’s influence on glutamatergic synapse function in our experimental assays. In orthogonal assays, we find most of the mutations predicted to disrupt binding display loss of function but mutants predicted to disrupt stability do not reflect our results from neuronal electrophysiological data. Limitations We present a method to predict missense mutations in TRIO’s GEF1 domain that may compromise TRIO function and test for effects in a limited number of assays. Possible limitations arising from the model systems employed here can be addressed in future studies. Our method does not provide evidence for whether these mutations confer ASD/ID risk or the likelihood that such mutations will result in the development of ASD/ID. Conclusions Here we show that a combination of structure-based computational predictions and experimental validation can be employed to reliably predict whether missense mutations in the human TRIO gene impede TRIO protein function and compromise TRIO’s role in glutamatergic synapse regulation. With the growing accessibility of genome sequencing, the use of such tools in the accurate identification of pathological mutations will be instrumental in diagnostics of ASD/ID.https://doi.org/10.1186/s13229-024-00590-9Glutamatergic neurotransmissionAutism spectrum disordersSynaptic dysfunctionMissense mutationsTRIO-related disordersMutation modeling |
| spellingShingle | Sadhna Rao Anastasiia Sadybekov David C. DeWitt Joanna Lipka Vsevolod Katritch Bruce E. Herring Detection of autism spectrum disorder-related pathogenic trio variants by a novel structure-based approach Molecular Autism Glutamatergic neurotransmission Autism spectrum disorders Synaptic dysfunction Missense mutations TRIO-related disorders Mutation modeling |
| title | Detection of autism spectrum disorder-related pathogenic trio variants by a novel structure-based approach |
| title_full | Detection of autism spectrum disorder-related pathogenic trio variants by a novel structure-based approach |
| title_fullStr | Detection of autism spectrum disorder-related pathogenic trio variants by a novel structure-based approach |
| title_full_unstemmed | Detection of autism spectrum disorder-related pathogenic trio variants by a novel structure-based approach |
| title_short | Detection of autism spectrum disorder-related pathogenic trio variants by a novel structure-based approach |
| title_sort | detection of autism spectrum disorder related pathogenic trio variants by a novel structure based approach |
| topic | Glutamatergic neurotransmission Autism spectrum disorders Synaptic dysfunction Missense mutations TRIO-related disorders Mutation modeling |
| url | https://doi.org/10.1186/s13229-024-00590-9 |
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