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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 ADVANCES 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] [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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Fear VS, Forbes CA, Shaw NC, Farley KO, Mantegna JL, Htun JP, Syn G, Viola H, Cserne Szappanos H, Hool L, Ward M, Baynam G, Lassmann T. Gene editing and cardiac disease modelling for the interpretation of genetic variants of uncertain significance in congenital heart disease. Stem Cell Res Ther 2023; 14:345. [PMID: 38049901 PMCID: PMC10696868 DOI: 10.1186/s13287-023-03592-1] [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: 02/23/2023] [Accepted: 11/29/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Genomic sequencing in congenital heart disease (CHD) patients often discovers novel genetic variants, which are classified as variants of uncertain significance (VUS). Functional analysis of each VUS is required in specialised laboratories, to determine whether the VUS is disease causative or not, leading to lengthy diagnostic delays. We investigated stem cell cardiac disease modelling and transcriptomics for the purpose of genetic variant classification using a GATA4 (p.Arg283Cys) VUS in a patient with CHD. METHODS We performed high efficiency CRISPR gene editing with homology directed repair in induced pluripotent stem cells (iPSCs), followed by rapid clonal selection with amplicon sequencing. Genetic variant and healthy matched control cells were compared using cardiomyocyte disease modelling and transcriptomics. RESULTS Genetic variant and healthy cardiomyocytes similarly expressed Troponin T (cTNNT), and GATA4. Transcriptomics analysis of cardiomyocyte differentiation identified changes consistent with the patient's clinical human phenotype ontology terms. Further, transcriptomics revealed changes in calcium signalling, and cardiomyocyte adrenergic signalling in the variant cells. Functional testing demonstrated, altered action potentials in GATA4 genetic variant cardiomyocytes were consistent with patient cardiac abnormalities. CONCLUSIONS This work provides in vivo functional studies supportive of a damaging effect on the gene or gene product. Furthermore, we demonstrate the utility of iPSCs, CRISPR gene editing and cardiac disease modelling for genetic variant interpretation. The method can readily be applied to other genetic variants in GATA4 or other genes in cardiac disease, providing a centralised assessment pathway for patient genetic variant interpretation.
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Affiliation(s)
- 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, Crawley, Australia.
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, 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
| | - Kathryn O Farley
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Jessica L Mantegna
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Jasmin P Htun
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Genevieve Syn
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
| | - Helena Viola
- University of Western Australia, Crawley, Australia
| | | | - Livia Hool
- University of Western Australia, Crawley, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Michelle Ward
- Undiagnosed Diseases Program, Genetic Services of WA, Subiaco, 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, Australia
| | - Timo Lassmann
- Translational Genetics, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
- Computational Biology, Precision Health, Telethon Kids Institute, Perth Children's Hospital, Nedlands, WA, 6009, Australia
- Centre for Child Health Research, University of Western Australia, Crawley, Australia
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Kubota N, Takeda R, Kobayashi J, Hidaka E, Nishi E, Takano K, Wakui K. Reanalysis of Chromosomal Microarray Data Using a Smaller Copy Number Variant Call Threshold Identifies Four Cases with Heterozygous Multiexon Deletions of ARID1B, EHMT1, and FOXP1 Genes. Mol Syndromol 2023; 14:394-404. [PMID: 37901861 PMCID: PMC10601822 DOI: 10.1159/000530252] [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: 10/22/2022] [Accepted: 03/16/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Chromosomal microarray (CMA) is a highly accurate and established method for detecting copy number variations (CNVs) in clinical genetic testing. CNVs are important etiological factors for disorders such as intellectual disability, developmental delay, and multiple congenital anomalies. Recently developed analytical methods have facilitated the identification of smaller CNVs. Therefore, reanalyzing CMA data using a smaller CNV calling threshold may yield useful information. However, this method was left to the discretion of each institution. Methods We reanalyzed the CMA data of 131 patients using a smaller CNV call threshold: 50 kb 50 probes for gain and 25 kb 25 probes for loss. We interpreted the reanalyzed CNVs based on the most recently available information. In the reanalysis, we filtered the data using the Clinical Genome Resource dosage sensitivity gene list as an index to quickly and efficiently check morbid genes. Results The number of copy number loss was approximately 20 times greater, and copy number gain was approximately three times greater compared to those in the previous analysis. We detected new likely pathogenic CNVs in four participants: a 236.5 kb loss within ARID1B, a 50.6 kb loss including EHMT1, a 46.5 kb loss including EHMT1, and an 89.1 kb loss within the FOXP1 gene. Conclusion The method employed in this study is simple and effective for CMA data reanalysis using a smaller CNV call threshold. Thus, this method is efficient for both ongoing and repeated analyses. This study may stimulate further discussion of reanalysis methodology in clinical laboratories.
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Affiliation(s)
- Noriko Kubota
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Ryojun Takeda
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
| | - Jun Kobayashi
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Eiko Hidaka
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
| | - Eriko Nishi
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
| | - Kyoko Takano
- Division of Medical Genetics, Nagano Children’s Hospital, Azumino, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Keiko Wakui
- Life Science Research Center, Nagano Children’s Hospital, Azumino, Japan
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
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Rwandamuriye FX, Evans CW, Wylie B, Norret M, Vitali B, Ho D, Nguyen D, Roper EA, Wang T, Hepburn MS, Sanderson RW, Pfirrmann M, Fear VS, Forbes CA, Wyatt K, Ryan AL, Johns TG, Phillips MB, Hodder R, Leslie C, Kennedy BF, Zemek RM, Iyer KS, Lesterhuis WJ. A surgically optimized intraoperative poly(I:C)-releasing hydrogel prevents cancer recurrence. Cell Rep Med 2023; 4:101113. [PMID: 37467718 PMCID: PMC10394259 DOI: 10.1016/j.xcrm.2023.101113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/10/2023] [Accepted: 06/18/2023] [Indexed: 07/21/2023]
Abstract
Recurrences frequently occur following surgical removal of primary tumors. In many cancers, adjuvant therapies have limited efficacy. Surgery provides access to the tumor microenvironment, creating an opportunity for local therapy, in particular immunotherapy, which can induce local and systemic anti-cancer effects. Here, we develop a surgically optimized biodegradable hyaluronic acid-based hydrogel for sustained intraoperative delivery of Toll-like receptor 3 agonist poly(I:C) and demonstrate that it significantly reduces tumor recurrence after surgery in multiple mouse models. Mechanistically, poly(I:C) induces a transient interferon alpha (IFNα) response, reshaping the tumor/wound microenvironment by attracting inflammatory monocytes and depleting regulatory T cells. We demonstrate that a pre-existing IFN signature predicts response to the poly(I:C) hydrogel, which sensitizes tumors to immune checkpoint therapy. The safety, immunogenicity, and surgical feasibility are confirmed in a veterinary trial in canine soft tissue tumors. The surgically optimized poly(I:C)-loaded hydrogel provides a safe and effective approach to prevent cancer recurrence.
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Affiliation(s)
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Ben Wylie
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Marck Norret
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Breana Vitali
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Diwei Ho
- School of Molecular Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Dat Nguyen
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Ellise A Roper
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Tao Wang
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Matt S Hepburn
- BRITElab, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia; Department of Electrical, Electronic and Computer Engineering, School of Engineering, The University of Western Australia, Crawley, WA, Australia
| | - Rowan W Sanderson
- BRITElab, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia; Department of Electrical, Electronic and Computer Engineering, School of Engineering, The University of Western Australia, Crawley, WA, Australia
| | - Maren Pfirrmann
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia; Department of Medical BioSciences, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Vanessa S Fear
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Catherine A Forbes
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Ken Wyatt
- Perth Veterinary Specialists, Osborne Park, WA, Australia; Murdoch Veterinary School, Murdoch University, Murdoch, WA, Australia
| | - Anne L Ryan
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia; Department of Oncology, Hematology and Tissue and Cellular Therapies, Perth Children's Hospital, Perth, WA, Australia
| | - Terrance G Johns
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
| | - Marianne B Phillips
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia; Department of Oncology, Hematology and Tissue and Cellular Therapies, Perth Children's Hospital, Perth, WA, Australia
| | - Rupert Hodder
- Department of Surgery, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | - Connull Leslie
- Department of Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia
| | - Brendan F Kennedy
- BRITElab, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA, Australia; Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia; Department of Electrical, Electronic and Computer Engineering, School of Engineering, The University of Western Australia, Crawley, WA, Australia
| | - Rachael M Zemek
- Telethon Kids Institute, The University of Western Australia, Nedlands, WA, Australia
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Roth C, Kilpinen H, Kurian MA, Barral S. Histone lysine methyltransferase-related neurodevelopmental disorders: current knowledge and saRNA future therapies. Front Cell Dev Biol 2023; 11:1090046. [PMID: 36923252 PMCID: PMC10009263 DOI: 10.3389/fcell.2023.1090046] [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: 12/07/2022] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
Neurodevelopmental disorders encompass a group of debilitating diseases presenting with motor and cognitive dysfunction, with variable age of onset and disease severity. Advances in genetic diagnostic tools have facilitated the identification of several monogenic chromatin remodeling diseases that cause Neurodevelopmental disorders. Chromatin remodelers play a key role in the neuro-epigenetic landscape and regulation of brain development; it is therefore not surprising that mutations, leading to loss of protein function, result in aberrant neurodevelopment. Heterozygous, usually de novo mutations in histone lysine methyltransferases have been described in patients leading to haploinsufficiency, dysregulated protein levels and impaired protein function. Studies in animal models and patient-derived cell lines, have highlighted the role of histone lysine methyltransferases in the regulation of cell self-renewal, cell fate specification and apoptosis. To date, in depth studies of histone lysine methyltransferases in oncology have provided strong evidence of histone lysine methyltransferase dysregulation as a determinant of cancer progression and drug resistance. As a result, histone lysine methyltransferases have become an important therapeutic target for the treatment of different cancer forms. Despite recent advances, we still lack knowledge about the role of histone lysine methyltransferases in neuronal development. This has hampered both the study and development of precision therapies for histone lysine methyltransferases-related Neurodevelopmental disorders. In this review, we will discuss the current knowledge of the role of histone lysine methyltransferases in neuronal development and disease progression. We will also discuss how RNA-based technologies using small-activating RNAs could potentially provide a novel therapeutic approach for the future treatment of histone lysine methyltransferase haploinsufficiency in these Neurodevelopmental disorders, and how they could be first tested in state-of-the-art patient-derived neuronal models.
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Affiliation(s)
- Charlotte Roth
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Helena Kilpinen
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland.,Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Manju A Kurian
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Department of Neurology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Serena Barral
- Molecular Neurosciences, Developmental Neurosciences Programme, Zayed Centre for Research into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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