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Lu X, Ni P, Suarez-Meade P, Ma Y, Forrest EN, Wang G, Wang Y, Quiñones-Hinojosa A, Gerstein M, Jiang YH. Transcriptional determinism and stochasticity contribute to the complexity of autism-associated SHANK family genes. Cell Rep 2024; 43:114376. [PMID: 38900637 DOI: 10.1016/j.celrep.2024.114376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/08/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Precision of transcription is critical because transcriptional dysregulation is disease causing. Traditional methods of transcriptional profiling are inadequate to elucidate the full spectrum of the transcriptome, particularly for longer and less abundant mRNAs. SHANK3 is one of the most common autism causative genes. Twenty-four Shank3-mutant animal lines have been developed for autism modeling. However, their preclinical validity has been questioned due to incomplete Shank3 transcript structure. We apply an integrative approach combining cDNA-capture and long-read sequencing to profile the SHANK3 transcriptome in humans and mice. We unexpectedly discover an extremely complex SHANK3 transcriptome. Specific SHANK3 transcripts are altered in Shank3-mutant mice and postmortem brain tissues from individuals with autism spectrum disorder. The enhanced SHANK3 transcriptome significantly improves the detection rate for potential deleterious variants from genomics studies of neuropsychiatric disorders. Our findings suggest that both deterministic and stochastic transcription of the genome is associated with SHANK family genes.
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Affiliation(s)
- Xiaona Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Yu Ma
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Emily Niemitz Forrest
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guilin Wang
- Keck Microarray Shared Resource, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA; Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT 06520, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA; Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA.
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Lu X, Ni P, Suarez-Meade P, Ma Y, Forrest EN, Wang G, Wang Y, Quiñones-Hinojosa A, Gerstein M, Jiang YH. Transcriptional Determinism and Stochasticity Contribute to the Complexity of Autism Associated SHANK Family Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585480. [PMID: 38562714 PMCID: PMC10983920 DOI: 10.1101/2024.03.18.585480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Precision of transcription is critical because transcriptional dysregulation is disease causing. Traditional methods of transcriptional profiling are inadequate to elucidate the full spectrum of the transcriptome, particularly for longer and less abundant mRNAs. SHANK3 is one of the most common autism causative genes. Twenty-four Shank3 mutant animal lines have been developed for autism modeling. However, their preclinical validity has been questioned due to incomplete Shank3 transcript structure. We applied an integrative approach combining cDNA-capture and long-read sequencing to profile the SHANK3 transcriptome in human and mice. We unexpectedly discovered an extremely complex SHANK3 transcriptome. Specific SHANK3 transcripts were altered in Shank3 mutant mice and postmortem brains tissues from individuals with ASD. The enhanced SHANK3 transcriptome significantly improved the detection rate for potential deleterious variants from genomics studies of neuropsychiatric disorders. Our findings suggest the stochastic transcription of genome associated with SHANK family genes.
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Affiliation(s)
- Xiaona Lu
- Department of Genetics, Yale University School of Medicine New Haven, CT, 06520 USA
| | - Pengyu Ni
- Biomedical Informatics & Data Science, Yale University School of Medicine New Haven, CT, 06520 USA
| | | | - Yu Ma
- Department of Neurology, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | | | - Guilin Wang
- Yale Center for Genome Analysis, Yale University School of Medicine New Haven, CT, 06520 USA
| | - Yi Wang
- Department of Neurology, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | | | - Mark Gerstein
- Biomedical Informatics & Data Science, Yale University School of Medicine New Haven, CT, 06520 USA
- Yale Center for Genome Analysis, Yale University School of Medicine New Haven, CT, 06520 USA
| | - Yong-hui Jiang
- Department of Genetics, Yale University School of Medicine New Haven, CT, 06520 USA
- Neuroscienc, Yale University School of Medicine New Haven, CT, 06520 USA
- Pediatrics, Yale University School of Medicine New Haven, CT, 06520 USA
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Zhu F, Shi Q, Jiang YH, Zhang YQ, Zhao H. Impaired synaptic function and hyperexcitability of the pyramidal neurons in the prefrontal cortex of autism-associated Shank3 mutant dogs. Mol Autism 2024; 15:9. [PMID: 38297387 PMCID: PMC10829216 DOI: 10.1186/s13229-024-00587-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/22/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND SHANK3 gene is a highly replicated causative gene for autism spectrum disorder and has been well characterized in multiple Shank3 mutant rodent models. When compared to rodents, domestic dogs are excellent animal models in which to study social cognition as they closely interact with humans and exhibit similar social behaviors. Using CRISPR/Cas9 editing, we recently generated a dog model carrying Shank3 mutations, which displayed a spectrum of autism-like behaviors, such as social impairment and heightened anxiety. However, the neural mechanism underlying these abnormal behaviors remains to be identified. METHODS We used Shank3 mutant dog models to examine possible relationships between Shank3 mutations and neuronal dysfunction. We studied electrophysiological properties and the synaptic transmission of pyramidal neurons from acute brain slices of the prefrontal cortex (PFC). We also examined dendrite elaboration and dendritic spine morphology in the PFC using biocytin staining and Golgi staining. We analyzed the postsynaptic density using electron microscopy. RESULTS We established a protocol for the electrophysiological recording of canine brain slices and revealed that excitatory synaptic transmission onto PFC layer 2/3 pyramidal neurons in Shank3 heterozygote dogs was impaired, and this was accompanied by reduced dendrite complexity and spine density when compared to wild-type dogs. Postsynaptic density structures were also impaired in Shank3 mutants; however, pyramidal neurons exhibited hyperexcitability. LIMITATIONS Causal links between impaired PFC pyramidal neuron function and behavioral alterations remain unclear. Further experiments such as manipulating PFC neuronal activity or restoring synaptic transmission in Shank3 mutant dogs are required to assess PFC roles in altered social behaviors. CONCLUSIONS Our study demonstrated the feasibility of using canine brain slices as a model system to study neuronal circuitry and disease. Shank3 haploinsufficiency causes morphological and functional abnormalities in PFC pyramidal neurons, supporting the notion that Shank3 mutant dogs are new and valid animal models for autism research.
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Affiliation(s)
- Feipeng Zhu
- State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Shi
- State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Hui Jiang
- Department of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, 06510, USA
| | - Yong Q Zhang
- State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Sciences, Hubei University, Wuhan, 430415, China.
| | - Hui Zhao
- State Key Laboratory for Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Department of Neurobiology, School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
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