1
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Jiang Y, Xia Z, Zhou Y, Lu X, Du X, Guo Q. Comparison of the accuracy of multiplex digital PCR versus multiplex ligation-dependent probe amplification in quantification of the survival of motor neuron genes copy numbers. Clin Chim Acta 2024; 553:117708. [PMID: 38097128 DOI: 10.1016/j.cca.2023.117708] [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: 11/06/2023] [Revised: 11/28/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
For over two decades, multiplex ligation-dependent probe amplification (MLPA) has served as the gold standard for genetic testing of spinal muscular atrophy. However, there is emerging evidence questioning the reliability of MLPA in determining the copy numbers (CNs) of the survival of motor neuron (SMN) gene in certain cases. Recently, digital polymerase chain reaction (dPCR) has shown potential for better performance in copy number variant detection. This study aimed to compare MLPA and dPCR in quantifying SMN1 and SMN2 CNs, identify reasons for observed discrepancies, and explore the clinical implications of false results. A total of 733 DNA samples, previously subjected to MLPA analysis, were tested using multiplex droplet dPCR assays. Samples exhibiting inconsistent results between the two methods underwent repeated dPCR assays. When inconsistencies persisted, a third method was employed for verification. Digital PCR yielded results consistent with those of MLPA in 94.4% (692/733) of samples. Forty-one cases exhibited quantitative disparities in SMN1 and/or SMN2 CNs between the two methods. Confirmatory tests revealed that 37 inaccurate results were produced by the MLPA analysis, whereas four were attributed to the dPCR method. The dPCR technique exhibits better accuracy than MLPA and is qualified for SMA genetic testing across various clinical scenarios.
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Affiliation(s)
- Yu Jiang
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China; Biobank, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, PR China.
| | - Zhongmin Xia
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China
| | - Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China; Biobank, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, PR China
| | - Xingxiu Lu
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China
| | - Xiaohan Du
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China
| | - Qiwei Guo
- United Diagnostic and Research Center for Clinical Genetics, Women and Children's Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, PR China.
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2
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Abiusi E, Costa-Roger M, Bertini ES, Tiziano FD, Tizzano EF, Abiusi E, Baranello G, Bertini E, Boemer F, Burghes A, Codina-Solà M, Costa-Roger M, Dangouloff T, Groen E, Gos M, Jędrzejowska M, Kirschner J, Lemmink HH, Müller-Felber W, Ouillade MC, Quijano-Roy S, Rucinski K, Saugier-Veber P, Tiziano FD, Tizzano EF, Wirth B. 270th ENMC International Workshop: Consensus for SMN2 genetic analysis in SMA patients 10-12 March, 2023, Hoofddorp, the Netherlands. Neuromuscul Disord 2024; 34:114-122. [PMID: 38183850 DOI: 10.1016/j.nmd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
The 270th ENMC workshop aimed to develop a common procedure to optimize the reliability of SMN2 gene copy number determination and to reinforce collaborative networks between molecular scientists and clinicians. The workshop involved neuromuscular and clinical experts and representatives of patient advocacy groups and industry. SMN2 copy number is currently one of the main determinants for therapeutic decision in SMA patients: participants discussed the issues that laboratories may encounter in this molecular test and the cruciality of the accurate determination, due the implications as prognostic factor in symptomatic patients and in individuals identified through newborn screening programmes. At the end of the workshop, the attendees defined a set of recommendations divided into four topics: SMA molecular prognosis assessment, newborn screening for SMA, SMN2 copies and treatments, and modifiers and biomarkers. Moreover, the group draw up a series of recommendations for the companies manufacturing laboratory kits, that will help to minimize the risk of errors, regardless of the laboratories' expertise.
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Affiliation(s)
- Emanuela Abiusi
- Section of Genomic Medicine, Department of Public Health and Life Sciences, Università Cattolica del Sacro Cuore, Roma, Italy
| | - Mar Costa-Roger
- Clinical and Molecular Genetics Area, Vall d'Hebron Hospital; Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Enrico Silvio Bertini
- Research Unit of Neuromuscular Disease, Bambino Gesu’ Children's Hospital, IRCCS, Roma, Italy
| | - Francesco Danilo Tiziano
- Section of Genomic Medicine, Department of Public Health and Life Sciences, Università Cattolica del Sacro Cuore, Roma, Italy
- Complex Unit of Medical Genetics, Fondazione Policlinico Universitario IRCCS “A. Gemelli”, Roma, Italy
| | - Eduardo F Tizzano
- Clinical and Molecular Genetics Area, Vall d'Hebron Hospital; Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Emanuela Abiusi
- Section of Genomic Medicine, Dept. of Life Sciences and Public Health, Catholic University of the Sacred Heart, Roma, Italy
| | - Giovanni Baranello
- The Dubowitz Neuromuscular Centre, Developmental Neuroscience Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, NIHR Great Ormond Street Hospital Biomedical Research Centre & Great Ormond Street Hospital NHS Foundation Trust, 30 Guilford Street, London WC1N 1EH, UK
| | - Enrico Bertini
- Italy, Research Unit of Neuromuscular Disease, Bambino Gesù Children's Hospital, IRCCS, Roma, Italy
| | - François Boemer
- Biochemical Genetics Lab, Department of Human Genetics, University Hospital, University of Liège, 4000 Liège, Belgium
| | - Arthur Burghes
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Marta Codina-Solà
- Neuromuscular Reference Center, Department of Paediatrics, University Hospital Liege & University of Liege, Belgium
| | - Mar Costa-Roger
- Department of Neurology & Neurosurgery, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Tamara Dangouloff
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Ewout Groen
- Department of Neurology, Medical University of Warsaw, Warsaw, Poland
| | - Monika Gos
- Department of Neuropediatrics and Muscle Disorders, Medical Center University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Maria Jędrzejowska
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Janbernd Kirschner
- Centre for Neuromuscular Disorders, Center for Translational Neuro and Behavioral Sciences, Department of Pediatric Neurology, University Duisburg-Essen, 45147 Essen, Germany
| | - Henny H Lemmink
- AFM Téléthon, Évry, France; SMA Europe; European Alliance for Newborn Screening in Spinal Muscular Atrophy
| | - Wolfgang Müller-Felber
- Pediatric Neuromuscular Unit (NEIDF Reference Center at FILNEMUS & Euro-NMD), Child Neurology Department, Raymond Poincaré Hospital (UVSQ), APHP Université Paris Saclay, Garches France
| | - Marie-Christine Ouillade
- Fundacja SMA, Warsaw, Poland; SMA Europe; European Alliance for Newborn Screening in Spinal Muscular Atrophy
| | - Susana Quijano-Roy
- Univ Rouen Normandie, Inserm U1245, Normandie Univ and CHU Rouen, Department of Genetics and Nord/Est/Ile de France Neuromuscular Reference Center, F-76000 Rouen, France
| | - Kacper Rucinski
- Institute of Medical Genomics, Dept. of Life Sciences and Public Health, Catholic University of the Sacred Heart, and Complex Unit of Medical Genetics, Fondazione Policlinico Universitario IRCCS “A. Gemelli”, Roma, Italy
| | - Pascale Saugier-Veber
- Institute of Human Genetics, University Hospital of Cologne, Center for Molecular Medicine, University of Cologne and Center for Rare Diseases Cologne, University Hopsital of Cologne, Cologne, Germany
| | - Francesco Danilo Tiziano
- Institute of Medical Genomics, Dept. of Life Sciences and Public Health, Catholic University of the Sacred Heart, and Complex Unit of Medical Genetics, Fondazione Policlinico Universitario IRCCS “A. Gemelli”, Roma, Italy
| | - Eduardo Fidel Tizzano
- Clinical and Molecular Genetics Area, Vall d'Hebron Hospital; Medicine Genetics Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Brunhilde Wirth
- Institute of Human Genetics, University Hospital of Cologne, Center for Molecular Medicine, University of Cologne and Center for Rare Diseases Cologne, University Hopsital of Cologne, Cologne, Germany
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3
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Votsi C, Koutsou P, Ververis A, Georghiou A, Nicolaou P, Tanteles G, Christodoulou K. Spinal muscular atrophy type I associated with a novel SMN1 splicing variant that disrupts the expression of the functional transcript. Front Neurol 2023; 14:1241195. [PMID: 37799281 PMCID: PMC10548546 DOI: 10.3389/fneur.2023.1241195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/31/2023] [Indexed: 10/07/2023] Open
Abstract
Introduction Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by pathogenic variants in the SMN1 gene. The majority of SMA patients harbor a homozygous deletion of SMN1 exon 7 (95%). Heterozygosity for a conventional variant and a deletion is rare (5%) and not easily detected, due to the highly homologous SMN2 gene interference. SMN2 mainly produces a truncated non-functional protein (SMN-d7) instead of the full-length functional (SMN-FL). We hereby report a novel SMN1 splicing variant in an infant with severe SMA. Methods MLPA was used for SMN1/2 exon dosage determination. Sanger sequencing approaches and long-range PCR were employed to search for an SMN1 variant. Conventional and improved Real-time PCR assays were developed for the qualitative and quantitative SMN1/2 RNA analysis. Results The novel SMN1 splice-site variant c.835-8_835-5delinsG, was identified in compound heterozygosity with SMN1 exons 7/8 deletion. RNA studies revealed complete absence of SMN1 exon 7, thus confirming a disruptive effect of the variant on SMN1 splicing. No expression of the functional SMN1-FL transcript, remarkable expression of the SMN1-d7 and increased levels of the SMN2-FL/SMN2-d7 transcripts were observed. Discussion We verified the occurrence of a non-deletion SMN1 variant and supported its pathogenicity, thus expanding the SMN1 variants spectrum. We discuss the updated SMA genetic findings in the Cypriot population, highlighting an increased percentage of intragenic variants compared to other populations.
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Affiliation(s)
- Christina Votsi
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Pantelitsa Koutsou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Antonis Ververis
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Anthi Georghiou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Paschalis Nicolaou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - George Tanteles
- Clinical Genetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Kyproula Christodoulou
- Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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4
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Nadal M, Anton R, Dorca‐Arévalo J, Estébanez‐Perpiñá E, Tizzano EF, Fuentes‐Prior P. Structure and function analysis of Sam68 and hnRNP A1 synergy in the exclusion of exon 7 from SMN2 transcripts. Protein Sci 2023; 32:e4553. [PMID: 36560896 PMCID: PMC10031812 DOI: 10.1002/pro.4553] [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: 08/03/2022] [Revised: 12/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022]
Abstract
Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by the absence of a functional copy of the Survival of Motor Neuron 1 gene (SMN1). The nearly identical paralog, SMN2, cannot compensate for the loss of SMN1 because exon 7 is aberrantly skipped from most SMN2 transcripts, a process mediated by synergistic activities of Src-associated during mitosis, 68 kDa (Sam68/KHDRBS1) and heterogeneous nuclear ribonucleoprotein (hnRNP) A1. This results in the production of a truncated, nonfunctional protein that is rapidly degraded. Here, we present several crystal structures of Sam68 RNA-binding domain (RBD). Sam68-RBD forms stable symmetric homodimers by antiparallel association of helices α3 from two monomers. However, the details of domain organization and the dimerization interface differ significantly from previously characterized homologs. We demonstrate that Sam68 and hnRNP A1 can simultaneously bind proximal motifs within the central region of SMN2 (ex7). Furthermore, we show that the RNA-binding pockets of the two proteins are close to each other in their heterodimeric complex and identify contact residues using crosslinking-mass spectrometry. We present a model of the ternary Sam68·SMN2 (ex7)·hnRNP A1 complex that reconciles all available information on SMN1/2 splicing. Our findings have important implications for the etiology of SMA and open new avenues for the design of novel therapeutics to treat splicing diseases.
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Affiliation(s)
- Marta Nadal
- Molecular Bases of DiseaseBiomedical Research Institute Sant Pau (IIB Sant Pau)BarcelonaSpain
| | - Rosa Anton
- Molecular Bases of DiseaseBiomedical Research Institute Sant Pau (IIB Sant Pau)BarcelonaSpain
| | - Jonatan Dorca‐Arévalo
- Molecular Bases of DiseaseBiomedical Research Institute Sant Pau (IIB Sant Pau)BarcelonaSpain
- Present address:
Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, Campus of BellvitgeHospitalet de Llobregat, University of BarcelonaBarcelonaSpain
| | - Eva Estébanez‐Perpiñá
- Structural Biology of Nuclear Receptors, Department of Biochemistry and Molecular Biomedicine, Faculty of BiologyInstitute of Biomedicine (IBUB) of the University of Barcelona (UB)BarcelonaSpain
| | - Eduardo F. Tizzano
- Medicine Genetics GroupVall d'Hebron Research Institute (VHIR)BarcelonaSpain
- Department of Clinical and Molecular GeneticsHospital Vall d'HebronBarcelonaSpain
| | - Pablo Fuentes‐Prior
- Molecular Bases of DiseaseBiomedical Research Institute Sant Pau (IIB Sant Pau)BarcelonaSpain
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5
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Bai J, Qu Y, OuYang S, Jiao H, Wang Y, Li J, Huang W, Zhao Y, Peng X, Wang D, Jin Y, Wang H, Song F. Novel Alu-mediated deletions of the SMN1 gene were identified by ultra-long read sequencing technology in patients with spinal muscular atrophy. Neuromuscul Disord 2023; 33:382-390. [PMID: 37023488 DOI: 10.1016/j.nmd.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/20/2023] [Accepted: 03/01/2023] [Indexed: 03/11/2023]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disease caused by biallelic variants of the survival motor neuron 1 (SMN1) gene. In this study, our aim was to make a molecular diagnosis in two patients with SMA carrying only one SMN1 copy number. Using ultra-long read sequencing (Ultra-LRS), 1415 bp deletion and 3348 bp deletion of the SMN1 gene were identified in patient 1 and the father of patient 2, respectively. Ultra-LRS revealed two novel deletions, starting from the SMN1 promoter to intron 1. It also accurately provided the location of the deletion breakpoints in the SMN1 gene: chr5 g.70,924,798-70,926,212 for a 1415 bp deletion; chr5 g.70,922,695-70,926,042 for a 3348 bp deletion. By analyzing the breakpoint junctions, we identified that these genomic sequences were composed of Alu sequences, including AluJb, AluYm1, AluSq, and AluYm1, indicating that Alu-mediated rearrangements are a mechanism of SMN1 deletion events. In addition, full-length SMN1 transcripts and SMN protein in patient 1 were significantly decreased (p < 0.01), suggesting that a 1415 bp deletion that included the transcription and translation initiation sites of the SMN1 gene had severe consequences for SMN expression. Ultra-LRS can easily distinguish highly homozygous genes compared to other detection technologies, which is useful for detecting SMN1 intragenic mutations, to quickly discover structural rearrangements and to precisely present the breakpoint positions.
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6
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Milligan JN, Blasco-Pérez L, Costa-Roger M, Codina-Solà M, Tizzano EF. Recommendations for Interpreting and Reporting Silent Carrier and Disease-Modifying Variants in SMA Testing Workflows. Genes (Basel) 2022; 13:1657. [PMID: 36140824 PMCID: PMC9498682 DOI: 10.3390/genes13091657] [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: 09/01/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Genetic testing for SMA diagnosis, newborn screening, and carrier screening has become a significant public health interest worldwide, driven largely by the development of novel and effective molecular therapies for the treatment of spinal muscular atrophy (SMA) and the corresponding updates to testing guidelines. Concurrently, understanding of the underlying genetics of SMA and their correlation with a broad range of phenotypes and risk factors has also advanced, particularly with respect to variants that modulate disease severity or impact residual carrier risks. While testing guidelines are beginning to emphasize the importance of these variants, there are no clear guidelines on how to utilize them in a real-world setting. Given the need for clarity in practice, this review summarizes several clinically relevant variants in the SMN1 and SMN2 genes, including how they inform outcomes for spinal muscular atrophy carrier risk and disease prognosis.
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Affiliation(s)
| | - Laura Blasco-Pérez
- Department of Clinical and Molecular Genetics, University Hospital Vall d’Hebron, 08035 Barcelona, Spain
| | - Mar Costa-Roger
- Department of Clinical and Molecular Genetics, University Hospital Vall d’Hebron, 08035 Barcelona, Spain
| | - Marta Codina-Solà
- Department of Clinical and Molecular Genetics, University Hospital Vall d’Hebron, 08035 Barcelona, Spain
| | - Eduardo F. Tizzano
- Department of Clinical and Molecular Genetics, University Hospital Vall d’Hebron, 08035 Barcelona, Spain
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7
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Abstract
Onasemnogene abeparvovec (Zolgensma®) is a gene therapy approved for the treatment of spinal muscular atrophy (SMA). Administered as a one-time intravenous infusion, onasemnogene abeparvovec uses the adeno-associated virus vector to deliver a functional copy of the human survival motor neuron (SMN) gene to motor neuron cells. SMN1 encodes survival motor neuron protein, which is responsible for the maintenance and function of motor neurons. In clinical trials, onasemnogene abeparvovec improved event-free survival, motor function and motor milestone outcomes in patients with SMA, with these improvements maintained over the longer term (up to a median of ≈ 5 years). Onasemnogene abeparvovec was also associated with rapid age-appropriate achievement of motor milestones and improvements in motor function in children with pre-symptomatic SMA, indicating the benefit of early treatment. Onasemnogene abeparvovec was generally well tolerated. Hepatotoxicity is a known risk that can generally be mitigated with prophylactic prednisolone. In conclusion, onasemnogene abeparvovec represents an important treatment option for patients with SMA, particularly when initiated early in the course of the disease.
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Affiliation(s)
- Hannah A Blair
- Springer Nature, Private Bag 65901, Mairangi Bay, Auckland, 0754, New Zealand.
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8
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Ramos-Platt L, Elman L, Shieh PB. Experience and Perspectives in the US on the Evolving Treatment Landscape in Spinal Muscular Atrophy. Int J Gen Med 2022; 15:7341-7353. [PMID: 36157294 PMCID: PMC9491367 DOI: 10.2147/ijgm.s369021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/10/2022] [Indexed: 12/02/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a rare, progressive neuromuscular disorder that, until recently, was the most common inherited cause of infant mortality. Since 2016, three disease-modifying therapies have emerged, nusinersen, onasemnogene abeparvovec-xioi, and risdiplam, leading to a transformation in the SMA treatment landscape, changes in disease trajectories, and a profound impact on clinical care. This environment poses a challenge to making informed treatment decisions, including initial treatment choice, treatment changes, and potential use of combination therapies as new data emerge. To better understand factors that influence physician-patient decision-making, a roundtable discussion was convened by Biogen (sponsor) with a panel of four US SMA experts. This report shares the panel’s opinions and clinical experiences, with the goals of helping clinicians and people with SMA and their families to better understand the factors influencing real-world treatment decisions and stimulating a broader discussion in the SMA community. The panelists highlighted that patients are often heavily involved in treatment decisions, and physicians must be aware of current data to guide patients in making the best decisions. Thus, in the absence of data from head-to-head treatment comparisons, physicians’ roles include reviewing treatment options and describing what is known of the benefits, challenges, and potential side effects of each therapy with patients and families. For infants and young children, the panelists expressed a sense of urgency for early intervention to minimize motor function loss, whereas the goal for adults is long-term disease stabilization. In the panelists’ experience, factors that influence patients’ decisions to change to an alternative therapy include convenience, administration route, novelty of therapy, and hope for improved function, while reasons for returning to a previous therapy include a perception of decreased efficacy and side effects. Ongoing clinical trials and analyses of real-world experiences should further inform treatment decisions and optimize patient outcomes.
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Affiliation(s)
- Leigh Ramos-Platt
- Department of Pediatrics, Keck School of Medicine, University of Southern California and Children’s Hospital of Los Angeles, Los Angeles, CA, USA
| | - Lauren Elman
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Perry B Shieh
- Department of Neurology and Pediatrics, University of California Los Angeles, Los Angeles, CA, USA
- Correspondence: Perry B Shieh, Department of Neurology and Pediatrics, University of California Los Angeles, Los Angeles, CA, USA, Email
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9
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Chen L, Roake CM, Maccallini P, Bavasso F, Dehghannasiri R, Santonicola P, Mendoza-Ferreira N, Scatolini L, Rizzuti L, Esposito A, Gallotta I, Francia S, Cacchione S, Galati A, Palumbo V, Kobin MA, Tartaglia G, Colantoni A, Proietti G, Wu Y, Hammerschmidt M, De Pittà C, Sales G, Salzman J, Pellizzoni L, Wirth B, Di Schiavi E, Gatti M, Artandi S, Raffa GD. TGS1 impacts snRNA 3'-end processing, ameliorates survival motor neuron-dependent neurological phenotypes in vivo and prevents neurodegeneration. Nucleic Acids Res 2022; 50:12400-12424. [PMID: 35947650 PMCID: PMC9757054 DOI: 10.1093/nar/gkac659] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
Trimethylguanosine synthase 1 (TGS1) is a highly conserved enzyme that converts the 5'-monomethylguanosine cap of small nuclear RNAs (snRNAs) to a trimethylguanosine cap. Here, we show that loss of TGS1 in Caenorhabditis elegans, Drosophila melanogaster and Danio rerio results in neurological phenotypes similar to those caused by survival motor neuron (SMN) deficiency. Importantly, expression of human TGS1 ameliorates the SMN-dependent neurological phenotypes in both flies and worms, revealing that TGS1 can partly counteract the effects of SMN deficiency. TGS1 loss in HeLa cells leads to the accumulation of immature U2 and U4atac snRNAs with long 3' tails that are often uridylated. snRNAs with defective 3' terminations also accumulate in Drosophila Tgs1 mutants. Consistent with defective snRNA maturation, TGS1 and SMN mutant cells also exhibit partially overlapping transcriptome alterations that include aberrantly spliced and readthrough transcripts. Together, these results identify a neuroprotective function for TGS1 and reinforce the view that defective snRNA maturation affects neuronal viability and function.
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Affiliation(s)
- Lu Chen
- Correspondence may also be addressed to Lu Chen.
| | | | - Paolo Maccallini
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Francesca Bavasso
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | | | - Natalia Mendoza-Ferreira
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute for Genetics, University of Cologne, 50931 Cologne, Germany
| | - Livia Scatolini
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Ludovico Rizzuti
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | | | - Ivan Gallotta
- Institute of Genetics and Biophysics, IGB-ABT, CNR, Naples, Italy
| | - Sofia Francia
- IFOM-The FIRC Institute of Molecular Oncology, Milan, Italy,Istituto di Genetica Molecolare, CNR-Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Stefano Cacchione
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Alessandra Galati
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Valeria Palumbo
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy
| | - Marie A Kobin
- Cancer Signaling and Epigenetics Program and Cancer Epigenetics Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Gian Gaetano Tartaglia
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy,Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy,Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Alessio Colantoni
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy,Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy,Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Gabriele Proietti
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome 00161, Italy,Center for Human Technology, Fondazione Istituto Italiano di Tecnologia (IIT), Genoa 16152, Italy
| | - Yunming Wu
- Cancer Signaling and Epigenetics Program and Cancer Epigenetics Institute, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA 19111, USA,Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Matthias Hammerschmidt
- Institute for Zoology, Developmental Biology, University of Cologne, 50674 Cologne, Germany
| | | | - Gabriele Sales
- Department of Biology, University of Padova, Padua, Italy
| | - Julia Salzman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Columbia University, NY 10032, USA,Department of Pathology and Cell Biology, Columbia University, NY 10032, USA,Department of Neurology, Columbia University, NY 10032, USA
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Institute for Genetics, University of Cologne, 50931 Cologne, Germany,Center for Rare Diseases, University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Elia Di Schiavi
- Institute of Biosciences and BioResources, IBBR, CNR, Naples, Italy,Institute of Genetics and Biophysics, IGB-ABT, CNR, Naples, Italy
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie, Sapienza University of Rome, Rome, Italy,Istituto di Biologia e Patologia Molecolari (IBPM) del CNR, Rome, Italy
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Deep Molecular Characterization of Milder Spinal Muscular Atrophy Patients Carrying the c.859G>C Variant in SMN2. Int J Mol Sci 2022; 23:ijms23158289. [PMID: 35955418 PMCID: PMC9368089 DOI: 10.3390/ijms23158289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 02/01/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a severe neuromuscular disorder caused by biallelic loss or pathogenic variants in the SMN1 gene. Copy number and modifier intragenic variants in SMN2, an almost identical paralog gene of SMN1, are known to influence the amount of complete SMN proteins. Therefore, SMN2 is considered the main phenotypic modifier of SMA, although genotype−phenotype correlation is not absolute. We present eleven unrelated SMA patients with milder phenotypes carrying the c.859G>C-positive modifier variant in SMN2. All were studied by a specific NGS method to allow a deep characterization of the entire SMN region. Analysis of two homozygous cases for the variant allowed us to identify a specific haplotype, Smn2-859C.1, in association with c.859G>C. Two other cases with the c.859G>C variant in their two SMN2 copies showed a second haplotype, Smn2-859C.2, in cis with Smn2-859C.1, assembling a more complex allele. We also identified a previously unreported variant in intron 2a exclusively linked to the Smn2-859C.1 haplotype (c.154-1141G>A), further suggesting that this region has been ancestrally conserved. The deep molecular characterization of SMN2 in our cohort highlights the importance of testing c.859G>C, as well as accurately assessing the SMN2 region in SMA patients to gain insight into the complex genotype−phenotype correlations and improve prognostic outcomes.
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