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Cheerie D, Meserve MM, Beijer D, Kaiwar C, Newton L, Taylor Tavares AL, Verran AS, Sherrill E, Leonard S, Sanders SJ, Blake E, Elkhateeb N, Gandhi A, Liang NSY, Morgan JT, Verwillow A, Verheijen J, Giles A, Williams S, Chopra M, Croft L, Dafsari HS, Davidson AE, Friedman J, Gregor A, Haque B, Lechner R, Montgomery KA, Ryten M, Schober E, Siegel G, Sullivan PJ, Whittle EF, Zardetto B, Yu TW, Synofzik M, Aartsma-Rus A, Costain G, Lauffer MC, N=1 Collaborative. Consensus guidelines for assessing eligibility of pathogenic DNA variants for antisense oligonucleotide treatments. Am J Hum Genet 2025; 112:975-983. [PMID: 40139194 PMCID: PMC12120168 DOI: 10.1016/j.ajhg.2025.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 02/19/2025] [Accepted: 02/19/2025] [Indexed: 03/29/2025] Open
Abstract
Of the around 7,000 known rare diseases worldwide, disease-modifying treatments are available for fewer than 5%, leaving millions of individuals without specialized therapeutic strategies. In recent years, antisense oligonucleotides (ASOs) have shown promise as individualized genetic interventions for rare genetic diseases. However, there is currently no consensus on which disease-causing DNA variants are suitable candidates for this type of genetic therapy. The patient identification working group of the N=1 Collaborative (N1C), alongside an international group of volunteer assessors, has developed and piloted consensus guidelines for assessing the eligibility of pathogenic DNA variants for ASO treatments. We herein present the N1C VARIANT (variant assessments toward eligibility for antisense oligonucleotide treatment) guidelines, including the guiding scientific principles and our approach to consensus building. Pathogenic, disease-causing variants can be assessed for the three currently best-established ASO treatment approaches: splice correction, exon skipping, and downregulation of RNA transcripts. A genetic variant is classified as "eligible," "likely eligible," "unlikely eligible," or "not eligible" in relation to the different approaches or as "unable to assess." We also review key considerations related to assessing the upregulation of transcripts from the wild-type allele, an emerging ASO therapeutic strategy. We provide additional tools and training materials to enable clinicians and researchers to use these guidelines for their eligibility assessments. With this initial edition of our N1C VARIANT guidelines, we provide the rare genetic disease community with guidance on how to identify suitable candidates for variant-specific ASO-based therapies and the possibility of integrating such assessments into routine clinical practice.
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Affiliation(s)
- David Cheerie
- Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Margaret M Meserve
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Danique Beijer
- Division of Translational Genomics of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany; German Center of Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - Charu Kaiwar
- Clinical Molecular Geneticist, Department of Pathology and Laboratory Medicine, Precision Diagnostics Laboratory, Children's Hospital Colorado, Aurora, CO 80045, USA
| | - Logan Newton
- Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ana Lisa Taylor Tavares
- Genomics England, London E14 5AB, UK; Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire CB2 0QQ, UK
| | - Aubrie Soucy Verran
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Emma Sherrill
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Pediatrics, University of Oxford, Oxford OX3 7TY, UK; Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; New York Genome Center, New York, NY 10013, USA
| | - Emily Blake
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55902, USA
| | - Nour Elkhateeb
- Genomics England, London E14 5AB, UK; Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire CB2 0QQ, UK
| | - Aastha Gandhi
- Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Nicole S Y Liang
- Division of Clinical & Metabolic Genetics, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Genetic Counselling, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Jack T Morgan
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Anna Verwillow
- Center for Genomic Medicine, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Jan Verheijen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55902, USA; Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA; ARUP Laboratories, Salt Lake City, UT 84108, USA
| | - Andrew Giles
- Ambry Genetics, 1 Enterprise, Aliso Viejo, CA 92656, USA
| | - Sean Williams
- Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Laura Croft
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Hormos Salimi Dafsari
- Department of Pediatrics and Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Max-Planck-Institute for Biology of Ageing and Cologne Excellence Cluster for Ageing-associated Diseases, 50931 Cologne, Germany; Randall Division of Cell and Molecular Biophysics, Muscle Signaling Section, King's College London, London WC2R 2LS, UK
| | - Alice E Davidson
- University College London Institute of Ophthalmology, London EC1V 9EL, UK; UK Platform for Nucleic Acid Therapies (UpNAT), London, UK
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California, San Diego, San Diego, CA 92093, USA; Division of Neurology, Rady Children's Hospital, Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Anne Gregor
- Department of Human Genetics, Inselspital University Hospital Bern, University of Bern, 3010 Bern, Switzerland; Department for Biomedical Research, University of Bern, 3010 Bern, Switzerland
| | - Bushra Haque
- Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON M5G 0A4, Canada
| | - Rosan Lechner
- Department of Clinical Genetics, Erasmus MC, Rotterdam 3015 CN, the Netherlands; Center of Expertise for Neurodevelopmental Disorders (ENCORE), Erasmus MC, Rotterdam 3015 CN, the Netherlands
| | - Kylie-Ann Montgomery
- UK Platform for Nucleic Acid Therapies (UpNAT), London, UK; Great Ormond Institute of Child Health and Queen Square Institute of Neurology, University College London, London WC1N 1EH, UK
| | - Mina Ryten
- UK Platform for Nucleic Acid Therapies (UpNAT), London, UK; Dementia Research Institute, University of Cambridge, Cambridge CB2 0AH, UK
| | - Emil Schober
- Department of Pediatrics and Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Max-Planck-Institute for Biology of Ageing and Cologne Excellence Cluster for Ageing-associated Diseases, 50931 Cologne, Germany
| | - Gabriele Siegel
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Patricia J Sullivan
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2033, Australia
| | - Ella F Whittle
- UK Platform for Nucleic Acid Therapies (UpNAT), London, UK; Genetics and Genomic Medicine Research and Teaching Department, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Bianca Zardetto
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Timothy W Yu
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Matthis Synofzik
- Division of Translational Genomics of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research and Center of Neurology, University of Tübingen, 72076 Tübingen, Germany; German Center of Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - Annemieke Aartsma-Rus
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Gregory Costain
- Program in Genetics & Genome Biology, SickKids Research Institute, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Division of Clinical & Metabolic Genetics, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Marlen C Lauffer
- Dutch Center for RNA Therapeutics, Department of Human Genetics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands.
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Neil CR, Schaening-Burgos C, Alexis MS, Reynolds DJ, Smith PG, Seiler MW, Vaillancourt FH, Agrawal AA. Poison exons: tuning RNA splicing for targeted gene regulation. Trends Pharmacol Sci 2025; 46:264-278. [PMID: 39915130 DOI: 10.1016/j.tips.2025.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2024] [Revised: 12/20/2024] [Accepted: 01/02/2025] [Indexed: 03/09/2025]
Abstract
Poison exons (PEs) are a class of alternatively spliced exons whose inclusion targets mRNA transcripts for degradation via the nonsense-mediated decay (NMD) pathway. Although a role for NMD as an essential mRNA quality control pathway has long been appreciated, recent advances in RNA sequencing (RNA-seq) strategies and analyses have revealed that its coupling to RNA splicing is broadly used to regulate mRNA stability and abundance. Regulation of PE splicing affects patterns of targeted degradation across the transcriptome and influences gene expression in both healthy and disease states. Importantly, PEs represent a novel therapeutic opportunity to modulate the expression of disease-relevant genes with sequence-specific resolution. We review the emergence of PE splicing in endogenous gene regulation, its misregulation in disease, and the ways in which it can be leveraged for therapeutic benefit.
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Ma R, Kim US, Chung Y, Kang HR, Zhang Y, Han K. Recent advances in CYFIP2-associated neurodevelopmental disorders: From human genetics to molecular mechanisms and mouse models. Brain Dev 2025; 47:104302. [PMID: 39603202 DOI: 10.1016/j.braindev.2024.104302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2024] [Revised: 10/29/2024] [Accepted: 11/04/2024] [Indexed: 11/29/2024]
Abstract
Cytoplasmic FMR1-interacting protein 2 (CYFIP2) is an evolutionarily conserved protein with a critical role in brain development and function. As a key component of the WAVE regulatory complex, CYFIP2 regulates actin cytoskeleton dynamics, essential for maintaining proper neuronal morphology and circuit formation. Recent studies have also shown that CYFIP2 interacts with various RNA-binding proteins, suggesting its involvement in mRNA processing and translation in neurons. Since 2018, de novo CYFIP2 variants have been identified in patients with neurodevelopmental disorders, particularly developmental and epileptic encephalopathy and West syndrome, characterized by early-onset intractable seizures, intellectual disability, microcephaly, and developmental delay. This review summarizes these CYFIP2 variants and examines their potential impact on the molecular functions of CYFIP2, focusing on its roles in regulating actin dynamics and mRNA processing/translation. Additionally, we review various Cyfip2 mouse models, highlighting the insights they offer into CYFIP2 function, dysfunction, and clinical relevance. Finally, we discuss future research directions aimed at better understanding CYFIP2-associated neurodevelopmental disorders and potential therapeutic strategies.
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Affiliation(s)
- Ruiying Ma
- Department of Neuroscience, Korea University College of Medicine, Seoul 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - U Suk Kim
- Department of Neuroscience, Korea University College of Medicine, Seoul 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Yousun Chung
- Department of Laboratory Medicine, Kangdong Sacred Heart Hospital, Seoul 05355, Republic of Korea
| | - Hyae Rim Kang
- Department of Neuroscience, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Yinhua Zhang
- Department of Neuroscience, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Kihoon Han
- Department of Neuroscience, Korea University College of Medicine, Seoul 02841, Republic of Korea; BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea.
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Iida N, Okada A, Kobayashi Y, Chiba K, Yatabe Y, Shiraishi Y. Systematically developing a registry of splice-site creating variants utilizing massive publicly available transcriptome sequence data. Nat Commun 2025; 16:426. [PMID: 39788962 PMCID: PMC11718197 DOI: 10.1038/s41467-024-55185-y] [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: 04/10/2024] [Accepted: 12/04/2024] [Indexed: 01/12/2025] Open
Abstract
Genomic variants causing abnormal splicing play important roles in genetic disorders and cancer development. Among them, variants that cause the formation of novel splice-sites (splice-site creating variants, SSCVs) are particularly difficult to identify and often overlooked in genomic studies. Additionally, these SSCVs are frequently considered promising candidates for treatment with splice-switching antisense oligonucleotides (ASOs). To leverage massive transcriptome sequence data such as those available from the Sequence Read Archive, we develop a novel framework to screen for SSCVs solely using transcriptome data. We apply it to 322,072 publicly available transcriptomes and identify 30,130 SSCVs. Among them, 5121 SSCVs affect disease-causing variants. By utilizing this extensive collection of SSCVs, we reveal the characteristics of Alu exonization via SSCVs, especially the hotspots of SSCVs within Alu sequences and their evolutionary relationships. We discover novel gain-of-function SSCVs in the deep intronic region of the NOTCH1 gene and demonstrate that their activation can be suppressed using splice-switching ASOs. Collectively, we provide a systematic approach for automatically acquiring a registry of SSCVs, which facilitates the elucidation of novel biological mechanisms underlying splicing and serves as a valuable resource for drug discovery. The catalogs of SSCVs identified in this study are accessible on the SSCV DB ( https://sscvdb.io ).
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Affiliation(s)
- Naoko Iida
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Ai Okada
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Yoshihisa Kobayashi
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichi Chiba
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Yatabe
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.
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5
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Kohli S, Saxena R, Puri RD, Bijarnia Mahay S, Pal S, Dubey S, Arora V, Verma I. The molecular landscape of oculocutaneous albinism in India and its therapeutic implications. Eur J Hum Genet 2024; 32:1267-1277. [PMID: 38030918 PMCID: PMC11500089 DOI: 10.1038/s41431-023-01496-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/14/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023] Open
Abstract
Oculocutaneous albinism is an inherited disorder of melanin biosynthesis, characterized by absent or reduced pigmentation of the skin, hair, and eyes. Molecular alterations of genes that cause non-syndromic albinism in Asian Indians are poorly characterized. This information would be useful for developing therapies for this disorder. We analyzed 164 persons with non-syndromic albinism, belonging to unrelated families from all parts of India, for molecular changes in the causative genes. Subjects with white hair, white skin, and red iris had their tyrosinase gene sequenced and were also tested by MLPA for deletions/duplications. Subjects with negative results or with darker skin, golden/brown or darker hair had sequencing of TYR, P, TYRP1, SLC45A2 and GPR143 genes. Pathogenic variants in TYR (OCA1) were observed in 139 (84.7%) patients, in the P gene (OCA2) in 20 (12.2%), in TYRP1 (OCA3) in two (1.2%), in SLC45A2 (OCA 4) in one (0.61%), and in GPR143 (X-linked ocular albinism) in two (1.2%) patients. Of 278 alleles with variants in TYR, 179 (64.3%) alleles had (p.R278*) alteration, suggesting the possibility of therapy with a stop codon readthrough molecule. We report 20 patients with 13 disease associated variants in the P gene and 18 novel pathogenic variants in TYR, P, TYRP1, SLC45A2 and GPR143 genes. The data are compared with those reported from India, Pakistan and rest of the world. The therapeutic options in albinism are briefly described, opening this field for future therapies.
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Affiliation(s)
- Sudha Kohli
- Institute of Medical Genetics and Genomics, Ganga Ram Institute of Postgraduate Medical Education and Research, Sir Ganga Ram Hospital, New Delhi, 110060, India.
| | - Renu Saxena
- Institute of Medical Genetics and Genomics, Ganga Ram Institute of Postgraduate Medical Education and Research, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Ratna Dua Puri
- Institute of Medical Genetics and Genomics, Ganga Ram Institute of Postgraduate Medical Education and Research, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Sunita Bijarnia Mahay
- Institute of Medical Genetics and Genomics, Ganga Ram Institute of Postgraduate Medical Education and Research, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Swasti Pal
- Institute of Medical Genetics and Genomics, Ganga Ram Institute of Postgraduate Medical Education and Research, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Sudhisha Dubey
- Institute of Medical Genetics and Genomics, Ganga Ram Institute of Postgraduate Medical Education and Research, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Veronica Arora
- Institute of Medical Genetics and Genomics, Ganga Ram Institute of Postgraduate Medical Education and Research, Sir Ganga Ram Hospital, New Delhi, 110060, India
| | - Ishwar Verma
- Institute of Medical Genetics and Genomics, Ganga Ram Institute of Postgraduate Medical Education and Research, Sir Ganga Ram Hospital, New Delhi, 110060, India.
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6
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Nicolas-Martinez EC, Robinson O, Pflueger C, Gardner A, Corbett MA, Ritchie T, Kroes T, van Eyk CL, Scheffer IE, Hildebrand MS, Barnier JV, Rousseau V, Genevieve D, Haushalter V, Piton A, Denommé-Pichon AS, Bruel AL, Nambot S, Isidor B, Grigg J, Gonzalez T, Ghedia S, Marchant RG, Bournazos A, Wong WK, Webster RI, Evesson FJ, Jones KJ, Cooper ST, Lister R, Gecz J, Jolly LA. RNA variant assessment using transactivation and transdifferentiation. Am J Hum Genet 2024; 111:1673-1699. [PMID: 39084224 PMCID: PMC11339655 DOI: 10.1016/j.ajhg.2024.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 08/02/2024] Open
Abstract
Understanding the impact of splicing and nonsense variants on RNA is crucial for the resolution of variant classification as well as their suitability for precision medicine interventions. This is primarily enabled through RNA studies involving transcriptomics followed by targeted assays using RNA isolated from clinically accessible tissues (CATs) such as blood or skin of affected individuals. Insufficient disease gene expression in CATs does however pose a major barrier to RNA based investigations, which we show is relevant to 1,436 Mendelian disease genes. We term these "silent" Mendelian genes (SMGs), the largest portion (36%) of which are associated with neurological disorders. We developed two approaches to induce SMG expression in human dermal fibroblasts (HDFs) to overcome this limitation, including CRISPR-activation-based gene transactivation and fibroblast-to-neuron transdifferentiation. Initial transactivation screens involving 40 SMGs stimulated our development of a highly multiplexed transactivation system culminating in the 6- to 90,000-fold induction of expression of 20/20 (100%) SMGs tested in HDFs. Transdifferentiation of HDFs directly to neurons led to expression of 193/516 (37.4%) of SMGs implicated in neurological disease. The magnitude and isoform diversity of SMG expression following either transactivation or transdifferentiation was comparable to clinically relevant tissues. We apply transdifferentiation and/or gene transactivation combined with short- and long-read RNA sequencing to investigate the impact that variants in USH2A, SCN1A, DMD, and PAK3 have on RNA using HDFs derived from affected individuals. Transactivation and transdifferentiation represent rapid, scalable functional genomic solutions to investigate variants impacting SMGs in the patient cell and genomic context.
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Affiliation(s)
- Emmylou C Nicolas-Martinez
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Olivia Robinson
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Christian Pflueger
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Alison Gardner
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Mark A Corbett
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Tarin Ritchie
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Thessa Kroes
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Clare L van Eyk
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia; Murdoch Children's Research Institute, Parkville, VIC 3052, Australia; Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia; The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jean-Vianney Barnier
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - Véronique Rousseau
- Institut des Neurosciences Paris-Saclay, UMR 9197, CNRS, Université Paris-Saclay, Saclay, France
| | - David Genevieve
- Montpellier University, Inserm U1183, Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndromes, Genetics Department, Montpellier Hospital, Montpellier, France
| | - Virginie Haushalter
- Genetic Diagnosis Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Amélie Piton
- Genetic Diagnosis Laboratory, Strasbourg University Hospital, Strasbourg, France
| | - Anne-Sophie Denommé-Pichon
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Ange-Line Bruel
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Sophie Nambot
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Bertrand Isidor
- CRMRs "Anomalies du Développement et syndromes malformatifs" et "Déficiences Intellectuelles de causes rares", Centre de Génétique, CHU Dijon, Dijon, France; INSERM UMR1231, GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - John Grigg
- Speciality of Ophthalmology, Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia
| | - Tina Gonzalez
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Sondhya Ghedia
- Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Rhett G Marchant
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia
| | - Adam Bournazos
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Wui-Kwan Wong
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia; Department of Paediatric Neurology, Children's Hospital at Westmead, Sydney, NSW 2000, Australia
| | - Richard I Webster
- Department of Paediatric Neurology, Children's Hospital at Westmead, Sydney, NSW 2000, Australia
| | - Frances J Evesson
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Kristi J Jones
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia; Department of Clinical Genetics, Children's Hospital at Westmead, Sydney, NSW 2000, Australia
| | - Sandra T Cooper
- Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2000, Australia; Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Ryan Lister
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jozef Gecz
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
| | - Lachlan A Jolly
- The Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia; School of Biomedicine, University of Adelaide, Adelaide, SA 5005, Australia.
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Zhang X. Splice-switching antisense oligonucleotides for pediatric neurological disorders. Front Mol Neurosci 2024; 17:1412964. [PMID: 39119251 PMCID: PMC11306167 DOI: 10.3389/fnmol.2024.1412964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024] Open
Abstract
Pediatric neurological disorders are frequently devastating and present unmet needs for effective medicine. The successful treatment of spinal muscular atrophy with splice-switching antisense oligonucleotides (SSO) indicates a feasible path to targeting neurological disorders by redirecting pre-mRNA splicing. One direct outcome is the development of SSOs to treat haploinsufficient disorders by targeting naturally occurring non-productive splice isoforms. The development of personalized SSO treatment further inspired the therapeutic exploration of rare diseases. This review will discuss the recent advances that utilize SSOs to treat pediatric neurological disorders.
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Affiliation(s)
- Xiaochang Zhang
- Department of Human Genetics, The Neuroscience Institute, University of Chicago, Chicago, IL, United States
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8
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Zardetto B, van Roon-Mom W, Aartsma-Rus A, Lauffer MC. Treatability of the KMT2-Associated Neurodevelopmental Disorders Using Antisense Oligonucleotide-Based Treatments. Hum Mutat 2024; 2024:9933129. [PMID: 40225946 PMCID: PMC11925151 DOI: 10.1155/2024/9933129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/26/2024] [Accepted: 04/15/2024] [Indexed: 04/15/2025]
Abstract
Neurodevelopmental disorders (NDDs) of genetic origin are a group of early-onset neurological diseases with highly heterogeneous etiology and a symptomatic spectrum that includes intellectual disability, autism spectrum disorder, and learning and language disorders. One group of rare NDDs is associated with dysregulation of the KMT2 protein family. Members of this family share a common methyl transferase function and are involved in the etiology of rare haploinsufficiency disorders. For each of the KMT2 genes, at least one distinct disorder has been reported, yet clinical manifestations often overlap for multiple of these individually very rare disorders. Clinical care is currently focused on the management of symptoms with no targeted treatments available, illustrating a high unmet medical need and the urgency of developing disease-modifying therapeutic strategies. Antisense oligonucleotides (ASOs) are one option to treat some of these rare genetic disorders. ASOs are RNA-based treatments that can be employed to modulate gene expression through various mechanisms. In this work, we discuss the phenotypic features across the KMT2-associated NDDs and which ASO approaches are most suited for the treatment of each associated disorder. We hereby address variant-specific strategies as well as options applicable to larger groups of patients.
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Affiliation(s)
- Bianca Zardetto
- Dutch Center for RNA TherapeuticsDepartment of Human GeneticsLeiden University Medical CenterLeiden, Netherlands
| | - Willeke van Roon-Mom
- Dutch Center for RNA TherapeuticsDepartment of Human GeneticsLeiden University Medical CenterLeiden, Netherlands
| | - Annemieke Aartsma-Rus
- Dutch Center for RNA TherapeuticsDepartment of Human GeneticsLeiden University Medical CenterLeiden, Netherlands
| | - Marlen C. Lauffer
- Dutch Center for RNA TherapeuticsDepartment of Human GeneticsLeiden University Medical CenterLeiden, Netherlands
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Yuan Y, Lopez-Santiago L, Denomme N, Chen C, O'Malley HA, Hodges SL, Ji S, Han Z, Christiansen A, Isom LL. Antisense oligonucleotides restore excitability, GABA signalling and sodium current density in a Dravet syndrome model. Brain 2024; 147:1231-1246. [PMID: 37812817 PMCID: PMC10994531 DOI: 10.1093/brain/awad349] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/13/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023] Open
Abstract
Dravet syndrome is an intractable developmental and epileptic encephalopathy caused by de novo variants in SCN1A resulting in haploinsufficiency of the voltage-gated sodium channel Nav1.1. We showed previously that administration of the antisense oligonucleotide STK-001, also called ASO-22, generated using targeted augmentation of nuclear gene output technology to prevent inclusion of the nonsense-mediated decay, or poison, exon 20N in human SCN1A, increased productive Scn1a transcript and Nav1.1 expression and reduced the incidence of electrographic seizures and sudden unexpected death in epilepsy in a mouse model of Dravet syndrome. Here, we investigated the mechanism of action of ASO-84, a surrogate for ASO-22 that also targets splicing of SCN1A exon 20N, in Scn1a+/- Dravet syndrome mouse brain. Scn1a +/- Dravet syndrome and wild-type mice received a single intracerebroventricular injection of antisense oligonucleotide or vehicle at postnatal Day 2. We examined the electrophysiological properties of cortical pyramidal neurons and parvalbumin-positive fast-spiking interneurons in brain slices at postnatal Days 21-25 and measured sodium currents in parvalbumin-positive interneurons acutely dissociated from postnatal Day 21-25 brain slices. We show that, in untreated Dravet syndrome mice, intrinsic cortical pyramidal neuron excitability was unchanged while cortical parvalbumin-positive interneurons showed biphasic excitability with initial hyperexcitability followed by hypoexcitability and depolarization block. Dravet syndrome parvalbumin-positive interneuron sodium current density was decreased compared to wild-type. GABAergic signalling to cortical pyramidal neurons was reduced in Dravet syndrome mice, suggesting decreased GABA release from interneurons. ASO-84 treatment restored action potential firing, sodium current density and GABAergic signalling in Dravet syndrome parvalbumin-positive interneurons. Our work suggests that interneuron excitability is selectively affected by ASO-84. This new work provides critical insights into the mechanism of action of this antisense oligonucleotide and supports the potential of antisense oligonucleotide-mediated upregulation of Nav1.1 as a successful strategy to treat Dravet syndrome.
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Affiliation(s)
- Yukun Yuan
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Luis Lopez-Santiago
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nicholas Denomme
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chunling Chen
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Heather A O'Malley
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Samantha L Hodges
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sophina Ji
- Stoke Therapeutics, Inc., Bedford, MA 01730, USA
| | - Zhou Han
- Stoke Therapeutics, Inc., Bedford, MA 01730, USA
| | | | - Lori L Isom
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
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10
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Gleeson JG, Bennett CF, Carroll JB, Cole T, Douville J, Glass S, Tekendo-Ngongang C, Williford AC, Crooke ST. Personalized antisense oligonucleotides 'for free, for life' - the n-Lorem Foundation. Nat Med 2023:10.1038/s41591-023-02335-2. [PMID: 37169866 DOI: 10.1038/s41591-023-02335-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Affiliation(s)
- Joseph G Gleeson
- n-Lorem Foundation, Carlsbad, CA, USA.
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
| | - C Frank Bennett
- n-Lorem Foundation, Carlsbad, CA, USA
- Ionis Pharmaceutical, Carlsbad, CA, USA
| | - Jeffrey B Carroll
- n-Lorem Foundation, Carlsbad, CA, USA
- Department of Neurology, University of Washington, Seattle, WA, USA
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