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Xie CTY, Pastore SF, Vincent JB, Frankland PW, Hamel PA. Nonsynonymous Mutations in Intellectual Disability and Autism Spectrum Disorder Gene PTCHD1 Disrupt N-Glycosylation and Reduce Protein Stability. Cells 2024; 13:199. [PMID: 38275824 PMCID: PMC10814814 DOI: 10.3390/cells13020199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
PTCHD1 has been implicated in Autism Spectrum Disorders (ASDs) and/or intellectual disability, where copy-number-variant losses or loss-of-function coding mutations segregate with disease in an X-linked recessive fashion. Missense variants of PTCHD1 have also been reported in patients. However, the significance of these mutations remains undetermined since the activities, subcellular localization, and regulation of the PTCHD1 protein are currently unknown. This paucity of data concerning PTCHD1 prevents the effective evaluation of sequence variants identified during diagnostic screening. Here, we characterize PTCHD1 protein binding partners, extending previously reported interactions with postsynaptic scaffolding protein, SAP102. Six rare missense variants of PTCHD1 were also identified from patients with neurodevelopmental disorders. After modelling these variants on a hypothetical three-dimensional structure of PTCHD1, based on the solved structure of NPC1, PTCHD1 variants harboring these mutations were assessed for protein stability, post-translational processing, and protein trafficking. We show here that the wild-type PTCHD1 post-translational modification includes complex N-glycosylation and that specific mutant proteins disrupt normal N-link glycosylation processing. However, regardless of their processing, these mutants still localized to PSD95-containing dendritic processes and remained competent for complexing SAP102.
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Affiliation(s)
- Connie T. Y. Xie
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Stephen F. Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1RS, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - John B. Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1RS, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
| | - Paul W. Frankland
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Psychology, University of Toronto, Toronto, ON M5S 3G3, Canada
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Paul A. Hamel
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
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Farley KO, Forbes CA, Shaw NC, Kuzminski E, Ward M, Baynam G, Lassmann T, Fear VS. CRISPR-Cas9-generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural induction. HGG Adv 2024; 5:100257. [PMID: 38007613 PMCID: PMC10787298 DOI: 10.1016/j.xhgg.2023.100257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023] Open
Abstract
An estimated 3.5%-5.9% of the global population live with rare diseases, and approximately 80% of these diseases have a genetic cause. Rare genetic diseases are difficult to diagnose, with some affected individuals experiencing diagnostic delays of 5-30 years. Next-generation sequencing has improved clinical diagnostic rates to 33%-48%. In a majority of cases, novel variants potentially causing the disease are discovered. These variants require functional validation in specialist laboratories, resulting in a diagnostic delay. In the interim, the finding is classified as a genetic variant of uncertain significance (VUS) and the affected individual remains undiagnosed. A VUS (PTCHD1 c. 2489T>G) was identified in a child with autistic behavior, global developmental delay, and hypotonia. Loss of function mutations in PTCHD1 are associated with autism spectrum disorder and intellectual disability; however, the molecular function of PTCHD1 and its role in neurodevelopmental disease is unknown. Here, we apply CRISPR gene editing and induced pluripotent stem cell (iPSC) neural disease modeling to assess the variant. During differentiation from iPSCs to neural progenitors, we detect subtle but significant gene signatures in synaptic transmission and muscle contraction pathways. Our work supports the causal link between the genetic variant and the child's phenotype, providing evidence for the variant to be considered a pathogenic variant according to the American College of Medical Genetics and Genomics guidelines. In addition, our study provides molecular data on the role of PTCHD1 in the context of other neurodevelopmental disorders.
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Affiliation(s)
- Kathryn O Farley
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia.
| | - Catherine A Forbes
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Nicole C Shaw
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Emma Kuzminski
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Michelle Ward
- Undiagnosed Diseases Program, Genetic Services of WA, Subiaco WA 6008, Australia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, King Edward Memorial Hospital, Subiaco, WA 6008, Australia; Undiagnosed Diseases Program, Genetic Services of WA, Subiaco WA 6008, Australia; Rare Care Centre, Perth Children's Hospital, Nedlands, WA 6009, Australia
| | - Timo Lassmann
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Vanessa S Fear
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA 6009, Australia; Centre for Child Health Research, University of Western Australia, Nedlands, WA 6009, Australia
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Kiral FR, Cakir B, Tanaka Y, Kim J, Yang WS, Wehbe F, Kang YJ, Zhong M, Sancer G, Lee SH, Xiang Y, Park IH. Generation of ventralized human thalamic organoids with thalamic reticular nucleus. Cell Stem Cell 2023; 30:677-688.e5. [PMID: 37019105 PMCID: PMC10329908 DOI: 10.1016/j.stem.2023.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/06/2023] [Accepted: 03/09/2023] [Indexed: 04/07/2023]
Abstract
Human brain organoids provide unique platforms for modeling several aspects of human brain development and pathology. However, current brain organoid systems mostly lack the resolution to recapitulate the development of finer brain structures with subregional identity, including functionally distinct nuclei in the thalamus. Here, we report a method for converting human embryonic stem cells (hESCs) into ventral thalamic organoids (vThOs) with transcriptionally diverse nuclei identities. Notably, single-cell RNA sequencing revealed previously unachieved thalamic patterning with a thalamic reticular nucleus (TRN) signature, a GABAergic nucleus located in the ventral thalamus. Using vThOs, we explored the functions of TRN-specific, disease-associated genes patched domain containing 1 (PTCHD1) and receptor tyrosine-protein kinase (ERBB4) during human thalamic development. Perturbations in PTCHD1 or ERBB4 impaired neuronal functions in vThOs, albeit not affecting the overall thalamic lineage development. Together, vThOs present an experimental model for understanding nuclei-specific development and pathology in the thalamus of the human brain.
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Affiliation(s)
- Ferdi Ridvan Kiral
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Bilal Cakir
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yoshiaki Tanaka
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, QC H1T 2M4, Canada
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Woo Sub Yang
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Fabien Wehbe
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Centre, University of Montreal, Montreal, QC H1T 2M4, Canada
| | - Young-Jin Kang
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Mei Zhong
- Department of Cell Biology, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gizem Sancer
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sang-Hun Lee
- Department of Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Yangfei Xiang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA.
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Pastore SF, Ko SY, Frankland PW, Hamel PA, Vincent JB. PTCHD1: Identification and Neurodevelopmental Contributions of an Autism Spectrum Disorder and Intellectual Disability Susceptibility Gene. Genes (Basel) 2022; 13:527. [PMID: 35328080 PMCID: PMC8953913 DOI: 10.3390/genes13030527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/01/2022] [Accepted: 03/03/2022] [Indexed: 11/24/2022] Open
Abstract
Over the last one and a half decades, copy number variation and whole-genome sequencing studies have illuminated the considerable genetic heterogeneity that underlies the etiologies of autism spectrum disorder (ASD) and intellectual disability (ID). These investigations support the idea that ASD may result from complex interactions between susceptibility-related genetic variants (single nucleotide variants or copy number variants) and the environment. This review outlines the identification and neurobiological characterization of two such genes located in Xp22.11, Patched domain-containing 1 (PTCHD1), and its antisense lncRNA PTCHD1-AS. Animal models of Ptchd1 disruption have recapitulated a subset of clinical symptoms related to ASD as well as to ID. Furthermore, these Ptchd1 mouse knockout studies implicate the expression of Ptchd1 in both the thalamic and the hippocampal brain regions as being crucial for proper neurodevelopment and cognitive function. Altered kynurenine metabolic signalling has been postulated as a disease mechanism in one of these animal studies. Additionally, ASD patient-derived induced pluripotent stem cells (iPSCs) carrying a copy number loss impacting the antisense non-coding RNA PTCHD1-AS have been used to generate 2D neuronal cultures. While copy number loss of PTCHD1-AS does not affect the transcription of PTCHD1, the neurons exhibit diminished miniature excitatory postsynaptic current frequency, supporting its role in ASD etiology. A more thorough understanding of risk factor genes, such as PTCHD1 and PTCHD1-AS, will help to clarify the intricate genetic and biological mechanisms that underlie ASD and ID, providing a foundation for meaningful therapeutic interventions to enhance the quality of life of individuals who experience these conditions.
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Affiliation(s)
- Stephen F. Pastore
- Molecular Neuropsychiatry and Development (MiND) Lab, Molecular Brain Science Research Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1RS, Canada;
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Sangyoon Y. Ko
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Paul W. Frankland
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada;
- Department of Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Psychology, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Paul A. Hamel
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - John B. Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Molecular Brain Science Research Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1RS, Canada;
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada
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