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Staszewski J, Lazarewicz N, Konczak J, Migdal I, Maciaszczyk-Dziubinska E. UPF1-From mRNA Degradation to Human Disorders. Cells 2023; 12:cells12030419. [PMID: 36766761 PMCID: PMC9914065 DOI: 10.3390/cells12030419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/07/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Up-frameshift protein 1 (UPF1) plays the role of a vital controller for transcripts, ready to react in the event of an incorrect translation mechanism. It is well known as one of the key elements involved in mRNA decay pathways and participates in transcript and protein quality control in several different aspects. Firstly, UPF1 specifically degrades premature termination codon (PTC)-containing products in a nonsense-mediated mRNA decay (NMD)-coupled manner. Additionally, UPF1 can potentially act as an E3 ligase and degrade target proteins independently from mRNA decay pathways. Thus, UPF1 protects cells against the accumulation of misfolded polypeptides. However, this multitasking protein may still hide many of its functions and abilities. In this article, we summarize important discoveries in the context of UPF1, its involvement in various cellular pathways, as well as its structural importance and mutational changes related to the emergence of various pathologies and disease states. Even though the state of knowledge about this protein has significantly increased over the years, there are still many intriguing aspects that remain unresolved.
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Affiliation(s)
- Jacek Staszewski
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
| | - Natalia Lazarewicz
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Institute of Genetics and Development of Rennes, CNRS UMR 6290, University of Rennes 1, 35000 Rennes, France
| | - Julia Konczak
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Iwona Migdal
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland
- Correspondence: (J.S.); (E.M.-D.)
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Dai M, Xu Y, Sun Y, Xiao B, Ying X, Liu Y, Jiang W, Zhang J, Liu X, Ji X. Revealing diverse alternative splicing variants of the highly homologous SMN1 and SMN2 genes by targeted long-read sequencing. Mol Genet Genomics 2022; 297:1039-1048. [PMID: 35612622 DOI: 10.1007/s00438-022-01874-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022]
Abstract
The survival of motor neuron (SMN) genes, SMN1 and SMN2, are two highly homologous genes related to spinal muscular atrophy (SMA). Different patterns of alternative splicing have been observed in the SMN genes. In this study, the long-read sequencing technique for distinguishing SMN1 and SMN2 without any assembly were developed and applied to reveal multiple alternative splicing patterns and to comprehensively identify transcript variants of the SMN genes. In total, 36 types of transcript variants were identified, with an equal number of variants generated from both SMN1 and SMN2. Of these, 18 were novel SMN transcripts that have never been reported. The structures of SMN transcripts were revealed to be much more complicated and diverse than previously discovered. These novel transcripts were derived from diverse splicing events, including skipping of one or more exons, intron retention, and exon shortening or addition. SMN1 mainly produces FL-SMN1, SMN1Δ7, SMN1Δ5 and SMN1Δ3. The distribution of SMN2 transcripts was significantly different from those of SMN1, with the majority transcripts to be SMN2Δ7, followed by FL-SMN2, SMN2Δ3,5 and SMN2Δ5,7. Targeted long-read sequencing approach could accurately distinguish sequences of SMN1 from those of SMN2. Our study comprehensively addressed naturally occurring SMN1 and SMN2 transcript variants and splicing patterns in peripheral blood mononuclear cells (PBMCs). The novel transcripts identified in our study expanded knowledge of the diversity of transcript variants generated from the SMN genes and showed a much more comprehensive profile of the SMN splicing spectrum. Results in our study will provide valuable information for the study of low expression level of SMN proteins and SMA pathogenesis based on transcript levels.
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Affiliation(s)
- Mengyao Dai
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China
- National Research Center for Translational Medicine, National Key Scientific Infrastructure for Translational Medicine (Shanghai), Shanghai Jiaotong University, Shanghai, China
- National Clinical Research Centre for Metabolic Diseases, State Key Laboratory of Medical Genomics, Shanghai Clinical Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yan Xu
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Sun
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China
| | - Bing Xiao
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China
| | - Xiaomin Ying
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China
| | - Yu Liu
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China
| | - Wenting Jiang
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China
| | - Jingmin Zhang
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China
| | - Xiaoqing Liu
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China
| | - Xing Ji
- Department of Paediatric Endocrinology/Genetics, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Molecular Genetics Group, Shanghai Institute for Paediatric Research, Shanghai, China.
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Zhang M, Lin Y, Zhang X, Lan F, Zeng J. Premature termination codons in SMN1 leading to spinal muscular atrophy trigger nonsense-mediated mRNA decay. Clin Chim Acta 2022; 530:45-49. [DOI: 10.1016/j.cca.2022.02.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 02/28/2022] [Indexed: 11/03/2022]
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Gaweda-Walerych K, Sitek EJ, Borczyk M, Berdyński M, Narożańska E, Brockhuis B, Korostyński M, Sławek J, Zekanowski C. Two Rare Variants in PLAU and BACE1 Genes-Do They Contribute to Semantic Dementia Clinical Phenotype? Genes (Basel) 2021; 12:genes12111806. [PMID: 34828412 PMCID: PMC8624613 DOI: 10.3390/genes12111806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
We have performed whole-genome sequencing to identify the genetic variants potentially contributing to the early-onset semantic dementia phenotype in a patient with family history of dementia and episodic memory deficit accompanied with profound semantic loss. Only very rare variants of unknown significance (VUS) have been identified: a nonsense variant c.366C>A/p.Cys122* in plasminogen activator, urokinase (PLAU) and a missense variant c.944C>T/p.Thr315Met in β-site APP-cleaving enzyme 1 (BACE1)-along with known disease-modifying variants of moderate penetrance. Patient-derived fibroblasts showed reduced PLAU and elevated BACE1 mRNA and protein levels compared to control fibroblasts. Successful rescue of PLAU mRNA levels by nonsense-mediated mRNA decay (NMD) inhibitor (puromycin) confirmed NMD as the underlying mechanism. This is the first report of the PLAU variant with the confirmed haploinsufficiency, associated with semantic dementia phenotype. Our results suggest that rare variants in the PLAU and BACE1 genes should be considered in future studies on early-onset dementias.
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Affiliation(s)
- Katarzyna Gaweda-Walerych
- Laboratory of Neurogenetics, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland; (M.B.); (C.Z.)
- Correspondence: (K.G.-W.); (E.J.S.)
| | - Emilia J. Sitek
- Neurology Department, St. Adalbert Hospital, Copernicus PL, 80-462 Gdansk, Poland; (E.N.); (J.S.)
- Division of Neurological and Psychiatric Nursing, Faculty of Health Sciences, Medical University of Gdansk, 80-462 Gdansk, Poland
- Correspondence: (K.G.-W.); (E.J.S.)
| | - Małgorzata Borczyk
- Laboratory of Pharmacogenomics, Department of Molecular Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Krakow, Poland; (M.B.); (M.K.)
| | - Mariusz Berdyński
- Laboratory of Neurogenetics, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland; (M.B.); (C.Z.)
| | - Ewa Narożańska
- Neurology Department, St. Adalbert Hospital, Copernicus PL, 80-462 Gdansk, Poland; (E.N.); (J.S.)
| | - Bogna Brockhuis
- Division of Nuclear Medicine, Faculty of Health Sciences, Medical University of Gdansk, 80-214 Gdansk, Poland;
| | - Michał Korostyński
- Laboratory of Pharmacogenomics, Department of Molecular Pharmacology, Maj Institute of Pharmacology Polish Academy of Sciences, 31-343 Krakow, Poland; (M.B.); (M.K.)
| | - Jarosław Sławek
- Neurology Department, St. Adalbert Hospital, Copernicus PL, 80-462 Gdansk, Poland; (E.N.); (J.S.)
- Division of Neurological and Psychiatric Nursing, Faculty of Health Sciences, Medical University of Gdansk, 80-462 Gdansk, Poland
| | - Cezary Zekanowski
- Laboratory of Neurogenetics, Mossakowski Medical Research Institute, Polish Academy of Sciences, 02-106 Warsaw, Poland; (M.B.); (C.Z.)
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Canosa A, Lomartire A, De Marco G, Grassano M, Brunetti M, Manera U, Vasta R, Salamone P, Fuda G, Sbaiz L, Gallone S, Moglia C, Calvo A, Chiò A. A novel splice site FUS mutation in a familial ALS case: effects on protein expression. Amyotroph Lateral Scler Frontotemporal Degener 2021; 23:128-136. [PMID: 33879000 DOI: 10.1080/21678421.2021.1909065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Objective: To investigate the impact of a novel heterozygous FUS mutation in the acceptor splice site of intron 14 (c.1542 - 1 g > t) on protein expression in Peripheral Blood Mononuclear Cells (PBMC) from a familial ALS patient. Methods: PBMC were isolated for mRNA analysis (cDNA synthesis, sequencing and one-step RT-PCR), Western Immunoblot (WI), and Immunofluorescence (IF). Results: cDNA analysis revealed the skipping of exon 15 and a premature stop codon at c.228. RT-PCR showed reduced FUS mRNA by more than half compared to a healthy control (HC) and an ALS patient without genetic mutations (wtALS). In WI FUS band intensity in the proband was 30-50% compared to HC and wtALS. An antibody expected to detect only the wild-type protein did not reveal any reduction of FUS band intensity compared to the other antibodies. IF showed no difference among HC, wtALS, and the proband. Discussion: The reduction of FUS mRNA and protein in PBMC suggests the absence of the truncated protein, probably due to nonsense-mediated decay, leading to loss of function.
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Affiliation(s)
- Antonio Canosa
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy
| | - Annarosa Lomartire
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Giovanni De Marco
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy
| | - Maurizio Grassano
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Maura Brunetti
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Umberto Manera
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Rosario Vasta
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Paolina Salamone
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Giuseppe Fuda
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy
| | - Luca Sbaiz
- Department of Clinical Pathology, Laboratory of Genetics, Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Turin, Italy
| | - Salvatore Gallone
- Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy
| | - Cristina Moglia
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy
| | - Andrea Calvo
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy.,Neuroscience Institute of Turin (NIT), Turin, Italy, and
| | - Adriano Chiò
- "Rita Levi Montalcini" Department of Neuroscience, ALS Centre, University of Turin, Turin, Italy.,Azienda Ospedaliero-Universitaria Città della Salute e della Scienza di Torino, Neurology Unit 1, Turin, Italy.,Neuroscience Institute of Turin (NIT), Turin, Italy, and.,Institute of Cognitive Sciences and Technologies, C.N.R., Rome, Italy
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6
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Michaels WE, Bridges RJ, Hastings ML. Antisense oligonucleotide-mediated correction of CFTR splicing improves chloride secretion in cystic fibrosis patient-derived bronchial epithelial cells. Nucleic Acids Res 2020; 48:7454-7467. [PMID: 32520327 PMCID: PMC7367209 DOI: 10.1093/nar/gkaa490] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 05/22/2020] [Accepted: 06/05/2020] [Indexed: 12/27/2022] Open
Abstract
Cystic fibrosis (CF) is an autosomal recessive disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene, encoding an anion channel that conducts chloride and bicarbonate across epithelial membranes. Mutations that disrupt pre-mRNA splicing occur in >15% of CF cases. One common CFTR splicing mutation is CFTR c.3718-2477C>T (3849+10 kb C>T), which creates a new 5′ splice site, resulting in splicing to a cryptic exon with a premature termination codon. Splice-switching antisense oligonucleotides (ASOs) have emerged as an effective therapeutic strategy to block aberrant splicing. We test an ASO targeting the CFTR c.3718-2477C>T mutation and show that it effectively blocks aberrant splicing in primary bronchial epithelial (hBE) cells from CF patients with the mutation. ASO treatment results in long-term improvement in CFTR activity in hBE cells, as demonstrated by a recovery of chloride secretion and apical membrane conductance. We also show that the ASO is more effective at recovering chloride secretion in our assay than ivacaftor, the potentiator treatment currently available to these patients. Our findings demonstrate the utility of ASOs in correcting CFTR expression and channel activity in a manner expected to be therapeutic in patients.
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Affiliation(s)
- Wren E Michaels
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA.,School of Graduate and Postdoctoral Studies, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Robert J Bridges
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Michelle L Hastings
- Center for Genetic Diseases, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
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Bai J, Qu Y, Song F, Cao Y, Cheng M, Wang J, Jin Y, Wang H. Dual Mechanism of a New SMN1 Variant (c.835G>C, p.Gly279Arg) by Interrupting Exon 7 Skipping and YG Oligomerization in Causation of Spinal Muscular Atrophy. J Mol Neurosci 2021; 71:112-21. [PMID: 32812185 DOI: 10.1007/s12031-020-01631-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/08/2020] [Indexed: 10/23/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by deletion or subtle variant of survival motor neuron 1 (SMN1) gene. By multiplex ligation-dependent probe amplification, genomic sequencing, and T-A cloning on cDNA level, we identified one novel SMN1 subtle variant c.835G>C (p.Gly279Arg) in a non-homozygous patient with type 1 SMA. Full-length SMN1 (fl-SMN1) transcripts in the peripheral bloods of the patient were significantly decreased compared with those in healthy individuals and the carries (p < 0.05). And two fragments of SMN1 transcripts including fl-SMN1 and △7-SMN1 were observed by RT-PCR, which indicated Exon 7 skipping of SMN1 gene. To further evaluate its splicing effects on Exon 7, we performed ex vivo splicing analysis, which showed that the mutant mini gene with c.835G>C reduced Exon 7 inclusion to 54%. In addition, self-oligomerization between mutant SMN protein with the c.835G>C (p.Gly279Arg) and wild SMN was decreased in self-interaction assays. Our study clearly demonstrates that the c.835G>C (p.Gly279Arg) variant can lead to a decrease in fl-SMN1 transcripts by interrupting correct splicing of SMN1. What is more, the variant also affects SMN self-oligomerization via amino acid substitution from Gly to Arg at amino acid position of 279. This work presents the first evidence that it does exit double-hit events for the novel variant, which is crucial to understanding a severe SMA phenotype (type 1).
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Xu Y, Xiao B, Liu Y, Qu XX, Dai MY, Ying XM, Jiang WT, Zhang JM, Liu XQ, Chen YW, Ji X. Identification of novel SMN1 subtle mutations using an allelic-specific RT-PCR. Neuromuscul Disord 2019; 30:219-226. [PMID: 32169315 DOI: 10.1016/j.nmd.2019.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 11/12/2019] [Accepted: 11/22/2019] [Indexed: 01/18/2023]
Abstract
Spinal muscular atrophy (SMA) is caused by homozygous deletions of the SMN1 gene in approximately 95% of patients. The remaining 5% of patients with SMA retain at least one copy of the SMN1 gene carrying insertions, deletions, or point mutations. Although molecular genetic testing for most SMA patients is quite easy, diagnosing "nondeletion" SMA patients is still compromised by the presence of a highly homologous SMN2 gene. In this study, we analyzed the SMN1/SMN2 copy number by quantitative PCR and multiplex ligation-dependent probe amplification (MLPA). Further, common primers for both SMN1 and SMN2 sequences were used to screen DNA intragenic mutations. To confirm whether the identified mutations occurred in SMN1 or SMN2, we improved the traditional RT-PCR method by only amplifying SMN1 transcripts using an allelic-specific PCR (AS-RT-PCR) strategy. We identified six SMN1 point mutations and small indels in 8 families, which included c.683T>A, c.22dupA, c.815A>G, c.19delG, c.551_552insA and c.401_402delAG. To the best of our knowledge, the latter three have never been previously reported. The most common mutation in Chinese patients is c.22dupA, which was identified in three families. In this work, we demonstrated AS-RT-PCR to be reliable for identifying SMN1 subtle mutations, especially the prevalent mutation c.22dupA in Chinese SMA patients. By reviewing published papers and summarizing reported SMN1 mutations, a distinct ethnic specificity was found in SMA patients from China. Our research extends the SMN1 mutation spectrum.
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Affiliation(s)
- Yan Xu
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China; Department of Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Bing Xiao
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China; Department of Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yu Liu
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China; Department of Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xiao-Xing Qu
- Department of Fetal Medicine Center, Shanghai First Maternity and Infant Hospital Affiliated to Shanghai Tongji University, Shanghai, China
| | - Meng-Yao Dai
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China; Department of Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xiao-Min Ying
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China; Department of Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Wen-Ting Jiang
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China; Department of Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Jing-Min Zhang
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China; Department of Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Xiao-Qing Liu
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China; Department of Endocrinology and Genetics, Shanghai Institute for Pediatric Research, Shanghai, China
| | - Ying-Wei Chen
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China
| | - Xing Ji
- Department of Genetic Counseling, Shanghai Institute for Pediatric Research, Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai 200092, China.
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9
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Strunk A, Abbes A, Stuitje AR, Hettinga C, Sepers EM, Snetselaar R, Schouten J, Asselman FL, Cuppen I, Lemmink H, van der Pol WL, Engel H. Validation of a Fast, Robust, Inexpensive, Two-Tiered Neonatal Screening Test algorithm on Dried Blood Spots for Spinal Muscular Atrophy. Int J Neonatal Screen 2019; 5:21. [PMID: 33072980 PMCID: PMC7510214 DOI: 10.3390/ijns5020021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022] Open
Abstract
Spinal muscular atrophy (SMA) is one of the leading genetic causes of infant mortality with an incidence of 1:10,000. The recently-introduced antisense oligonucleotide treatment improves the outcome of this disease, in particular when applied at an early stage of progression. The genetic cause of SMA is, in >95% of cases, a homozygous deletion of the survival motor neuron 1 (SMN1) gene, which makes the low-cost detection of SMA cases as part of newborn screening programs feasible. We developed and validated a new SALSA MC002 melting curve assay that detects the absence of the SMN1 exon 7 DNA sequence without detecting asymptomatic carriers and reliably discriminates SMN1 from its genetic homolog SMN2 using crude extracts from newborn screening cards. Melting curve analysis shows peaks specific for both the SMN1 gene and the disease modifying SMN2 homolog. The detection of the SMN2 homolog, of which the only clinically relevant difference from the SMN1 gene is a single nucleotide in exon 7, was only used to confirm a correct reaction in samples that lacked the SMN1 gene, and not for SMN2 quantification. We retrieved 47 DBS samples from children with genetically-confirmed SMA, after informed consent from parents, and 375 controls from the national archive of the Dutch National Institute for Public Health and the Environment (RIVM). The assay correctly identified all anonymized and randomized SMA and control samples (i.e., sensitivity and specificity of 100%), without the detection of carriers, on the three most commonly-used PCR platforms with melting curve analysis. This test's concordance with the second-tier 'golden standard' P021 SMA MLPA test was 100%. Using the new P021-B1 version, crude extracts from DBS cards could also be used to determine the SMN2 copy number of SMA patients with a high level of accuracy. The MC002 test showed the feasibility and accuracy of SMA screening in a neonatal screening program.
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Affiliation(s)
- Annuska Strunk
- Department of Clinical Chemistry and Neonatal Screening, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | - Andre Abbes
- Department of Clinical Chemistry and Neonatal Screening, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
| | - Antoine R. Stuitje
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Chris Hettinga
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Eline M. Sepers
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Reinier Snetselaar
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Jan Schouten
- MRC-Holland, Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Fay-Lynn Asselman
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Inge Cuppen
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Henny Lemmink
- Department of Genetics, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - W. Ludo van der Pol
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands
| | - Henk Engel
- Department of Clinical Chemistry and Neonatal Screening, Isala Hospital, Dokter van Heesweg 2, 8025 AB Zwolle, The Netherlands
- Correspondence: ; Tel.: +31-38-424-7190
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