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Jiang Y, Luo Z, Wang W, Lu X, Xia Z, Xie J, Lu M, Wu L, Zhou Y, Guo Q. Development of a low-cost and accurate carrier screening method for spinal muscular atrophy in developing countries. Eur J Med Genet 2024; 68:104921. [PMID: 38325644 DOI: 10.1016/j.ejmg.2024.104921] [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: 05/31/2023] [Revised: 11/29/2023] [Accepted: 02/04/2024] [Indexed: 02/09/2024]
Abstract
Heterozygous carriers of the survival of motor neuron 1 (SMN1) gene deletion in parents account for approximately 95% of neonatal spinal muscular atrophy cases. Given the severity of the disease, professional organizations have recommended periconceptional spinal muscular atrophy carrier screening to all couples, regardless of race or ethnicity. However, the prevalence of screening activities in mainland China remains suboptimal, mainly attributed to the limitations of the existing carrier screening methods. Herein, we aimed to develop a low-cost, accessible, and accurate carrier screening method based on duplex droplet digital PCR (ddPCR), to cover a wider population in developing countries, including China. The receiver operating characteristic curve was used to determine the cut-off value of SMN1 copy numbers. Performance validation was conducted for linearity, precision, and accuracy. In total, 482 cases were considered to validate the concordance between the developed ddPCR assay and multiplex ligation-dependent probe amplification. Linear correlations were excellent between the expected concentration of the reference gene and the observed values (R2 > 0.99). Both the intra- and inter-assay precision of our ddPCR assays were less than 6.0%. The multiplex ligation-dependent probe amplification and ddPCR results were consistent in 480 of the 482 cases (99.6%). Two cases with multiplex ligation-dependent probe amplification, suggestive of two copies of SMN1 exon 7, were classified into three copies by ddPCR analysis. The overall correct classification of the samples included in our ddPCR assay was 100%. This study demonstrates that an appropriate cut-off value is an important prerequisite for establishing a semi-quantitative method to determine the SMN1 copy numbers. Compared to conventional methods, our ddPCR assay is low-cost, highly accurate, and has full potential for application in population spinal muscular atrophy carriers screening.
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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.
| | - Zhenyu Luo
- Department of Family Planning, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, 361003, PR China
| | - Wenrong Wang
- Department of Family Planning, 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
| | - 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
| | - Jieqiong Xie
- 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
| | - Mei Lu
- Department of Pediatrics, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian, 361003, PR China
| | - Lili Wu
- Department of Obstetrics and Gynecology, Women and Children's Hospital, School of Medicine, 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
| | - 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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Xing Y, Wang Y, Li X, Pang S. Digital microfluidics methods for nucleic acid detection: A mini review. BIOMICROFLUIDICS 2024; 18:021501. [PMID: 38456173 PMCID: PMC10917463 DOI: 10.1063/5.0180125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/09/2024]
Abstract
Many serious infectious diseases have occurred throughout human history. Rapid and accurate detection as well as the isolation of infected individuals, through nucleic acid testing, are effective means of containing the spread of these viruses. However, traditional nucleic acid testing methods rely on complex machines and specialized personnel, making it difficult to achieve large-scale, high-throughput, and rapid detection. In recent years, digital microfluidics has emerged as a promising technology that integrates various fields, including electrokinetics, acoustics, optics, magnetism, and mechanics. By leveraging the advantages of these different technologies, digital microfluidic chips offer several benefits, such as high detection throughput, integration of multiple functions, low reagent consumption, and portability. This rapid and efficient testing is crucial in the timely detection and isolation of infected individuals to prevent the virus spread. Another advantage is the low reagent consumption of digital microfluidic chips. Compared to traditional methods, these chips require smaller volumes of reagents, resulting in cost savings and reduced waste. Furthermore, digital microfluidic chips are portable and can be easily integrated into point-of-care testing devices. This enables testing to be conducted in remote or resource-limited areas, where access to complex laboratory equipment may be limited. Onsite testing reduces the time and cost associated with sample transportation. In conclusion, bioassay technologies based on digital microfluidic principles have the potential to significantly improve infectious disease detection and control. By enabling rapid, high-throughput, and portable testing, these technologies enhance our ability to contain the spread of infectious diseases and effectively manage public health outbreaks.
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Affiliation(s)
- Youqiang Xing
- School of Mechanical Engineering, Southeast University, Nanjing 211189, Jiangsu Province, People’s Republic of China
| | - Yan Wang
- Clinical Laboratory, Yantai Yuhuangding Hospital, Yantai 264000, Shandong Province, People’s Republic of China
| | - Xiang Li
- Bio-manufacturing Engineering Laboratory, Tsinghua Shenzhen International Graduate School, Tsinghua University, Guangdong 518000, Shenzhen, People’s Republic of China
| | - Shangran Pang
- Jinzhong Normal Junior College, 189 Guang'an Street, Yuci District, Jinzhong 030600, Shanxi Province, People’s Republic of China
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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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4
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Zhou Y, Jiang Y. Current Advances in Genetic Testing for Spinal Muscular Atrophy. Curr Genomics 2023; 24:273-286. [PMID: 38235355 PMCID: PMC10790334 DOI: 10.2174/0113892029273388231023072050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/19/2024] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most common genetic disorders worldwide, and genetic testing plays a key role in its diagnosis and prevention. The last decade has seen a continuous flow of new methods for SMA genetic testing that, along with traditional approaches, have affected clinical practice patterns to some degree. Targeting different application scenarios and selecting the appropriate technique for genetic testing have become priorities for optimizing the clinical pathway for SMA. In this review, we summarize the latest technological innovations in genetic testing for SMA, including MassArray®, digital PCR (dPCR), next-generation sequencing (NGS), and third-generation sequencing (TGS). Implementation recommendations for rationally choosing different technical strategies in the tertiary prevention of SMA are also explored.
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Affiliation(s)
- 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, P.R. China
- Biobank, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
| | - 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, P.R. China
- Biobank, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
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5
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Ibrahim F, Velayutham D, Alsharshani M, AlAlami U, AlDewik M, Abuarja T, Al Rifai H, Al‐Dewik NI. Studying carrier frequency of spinal muscular atrophy in the State of Qatar and comparison to other ethnic groups: Pilot study. Mol Genet Genomic Med 2023; 11:e2184. [PMID: 37964750 PMCID: PMC10724519 DOI: 10.1002/mgg3.2184] [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: 01/08/2023] [Revised: 03/29/2023] [Accepted: 04/04/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is an autosomal recessive disease caused by mutations and deletions in SMN1 at exon 7. The carrier frequency for SMN1 mutations ranges from 2 to 4% in the general population. METHODS We examined allelic, genotypic relatedness and copy number (CN) variations and frequencies of SMN1 and SMN2, in 13,426 samples from Qatar biobank (QBB) to provide a precise estimation of SMA carrier frequency in Qatar in comparison to other populations. RESULTS The SMA carrier frequency was found to be (2.8%) and the rs143838139 was found in 491/13426 (3.66%) of individuals. The SNP rs121909192, which is a pathogenic risk factor, was found in 321/13500 (2.38%). In Addition 242/11379 (2.13%) had two copies of SMN1 and the rs143838139, which may explain the (2 + 0) silent carrier. Additionally, two participants were found to be SMA type 4 with 0 and 4 copy numbers in SMN1 and SMN2, respectively. CONCLUSION The SMA carrier frequency in Qatar was found to be comparable to Saudi Arabia and Caucasians. The likely pathogenic variant, rs121909192, was found to be significantly higher when compering with other in our study. The rs143838139 variant, which has a strong association with the silent carrier genotype, has been found. Consequently, testing for this SNP may enhance the precision of evaluating the likelihood of a patient having an affected child. We conclude that the frequency of SMA carriers varies within the Qatar population and other ethnic groups.
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Affiliation(s)
- Faisal Ibrahim
- Diagnostic Genetics Division (DGD), Department of Laboratory Medicine and Pathology (DLMP)Hamad Medical Corporation (HMC)DohaQatar
| | - Dinesh Velayutham
- Liberal Arts and ScienceHamad Bin Khalifa University (HBKU)DohaQatar
| | - Mohamed Alsharshani
- Diagnostic Genetics Division (DGD), Department of Laboratory Medicine and Pathology (DLMP)Hamad Medical Corporation (HMC)DohaQatar
| | - Usama AlAlami
- School of Life ScienceManipal Academy of Higher Education (MAHE)DubaiUAE
| | - Manar AlDewik
- Department of Research and Translational and Precision Medicine Research LabWomen's Wellness and Research Center, Hamad Medical CorporationDohaQatar
| | - Tala Abuarja
- Department of Research and Translational and Precision Medicine Research LabWomen's Wellness and Research Center, Hamad Medical CorporationDohaQatar
| | - Hilal Al Rifai
- Department of Pediatrics and Neonatology, Neonatal Intensive Care Unit, Newborn Screening Unit, Women's Wellness and Research CenterHamad Medical CorporationDohaQatar
| | - Nader I. Al‐Dewik
- Department of Research and Translational and Precision Medicine Research LabWomen's Wellness and Research Center, Hamad Medical CorporationDohaQatar
- Department of Pediatrics and Neonatology, Neonatal Intensive Care Unit, Newborn Screening Unit, Women's Wellness and Research CenterHamad Medical CorporationDohaQatar
- Translational Research Institute (TRI)Hamad Medical Corporation (HMC)DohaQatar
- Genomics and Precision Medicine (GPM), College of Health & Life Science (CHLS)Hamad Bin Khalifa University (HBKU)DohaQatar
- College of Health and Life SciencesHamad Bin Khalifa University, Education CityDohaQatar
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Fortuna TR, Kour S, Chimata AV, Muiños-Bühl A, Anderson EN, Nelson Iv CH, Ward C, Chauhan O, O'Brien C, Rajasundaram D, Rajan DS, Wirth B, Singh A, Pandey UB. SMN regulates GEMIN5 expression and acts as a modifier of GEMIN5-mediated neurodegeneration. Acta Neuropathol 2023; 146:477-498. [PMID: 37369805 DOI: 10.1007/s00401-023-02607-8] [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: 05/17/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023]
Abstract
GEMIN5 is essential for core assembly of small nuclear Ribonucleoproteins (snRNPs), the building blocks of spliceosome formation. Loss-of-function mutations in GEMIN5 lead to a neurodevelopmental syndrome among patients presenting with developmental delay, motor dysfunction, and cerebellar atrophy by perturbing SMN complex protein expression and assembly. Currently, molecular determinants of GEMIN5-mediated disease have yet to be explored. Here, we identified SMN as a genetic suppressor of GEMIN5-mediated neurodegeneration in vivo. We discovered that an increase in SMN expression by either SMN gene therapy replacement or the antisense oligonucleotide (ASO), Nusinersen, significantly upregulated the endogenous levels of GEMIN5 in mammalian cells and mutant GEMIN5-derived iPSC neurons. Further, we identified a strong functional association between the expression patterns of SMN and GEMIN5 in patient Spinal Muscular Atrophy (SMA)-derived motor neurons harboring loss-of-function mutations in the SMN gene. Interestingly, SMN binds to the C-terminus of GEMIN5 and requires the Tudor domain for GEMIN5 binding and expression regulation. Finally, we show that SMN upregulation ameliorates defective snRNP biogenesis and alternative splicing defects caused by loss of GEMIN5 in iPSC neurons and in vivo. Collectively, these studies indicate that SMN acts as a regulator of GEMIN5 expression and neuropathologies.
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Affiliation(s)
- Tyler R Fortuna
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Sukhleen Kour
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | | | - Anixa Muiños-Bühl
- Institute of Human Genetics, Center for Molecular Medicine, Center for Rare Disorders, University of Cologne, Cologne, Germany
| | - Eric N Anderson
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Charlie H Nelson Iv
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Caroline Ward
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Om Chauhan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Casey O'Brien
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Deepa S Rajan
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine, Center for Rare Disorders, University of Cologne, Cologne, Germany
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, USA
| | - Udai Bhan Pandey
- Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
- Children's Neuroscience Institute, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA.
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7
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Lumpkin CJ, Harris AW, Connell AJ, Kirk RW, Whiting JA, Saieva L, Pellizzoni L, Burghes AHM, Butchbach MER. Evaluation of the orally bioavailable 4-phenylbutyrate-tethered trichostatin A analogue AR42 in models of spinal muscular atrophy. Sci Rep 2023; 13:10374. [PMID: 37365234 PMCID: PMC10293174 DOI: 10.1038/s41598-023-37496-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 06/22/2023] [Indexed: 06/28/2023] Open
Abstract
Proximal spinal muscular atrophy (SMA) is a leading genetic cause for infant death in the world and results from the selective loss of motor neurons in the spinal cord. SMA is a consequence of low levels of SMN protein and small molecules that can increase SMN expression are of considerable interest as potential therapeutics. Previous studies have shown that both 4-phenylbutyrate (4PBA) and trichostatin A (TSA) increase SMN expression in dermal fibroblasts derived from SMA patients. AR42 is a 4PBA-tethered TSA derivative that is a very potent histone deacetylase inhibitor. SMA patient fibroblasts were treated with either AR42, AR19 (a related analogue), 4PBA, TSA or vehicle for 5 days and then immunostained for SMN localization. AR42 as well as 4PBA and TSA increased the number of SMN-positive nuclear gems in a dose-dependent manner while AR19 did not show marked changes in gem numbers. While gem number was increased in AR42-treated SMA fibroblasts, there were no significant changes in FL-SMN mRNA or SMN protein. The neuroprotective effect of this compound was then assessed in SMNΔ7 SMA (SMN2+/+;SMNΔ7+/+;mSmn-/-) mice. Oral administration of AR42 prior to disease onset increased the average lifespan of SMNΔ7 SMA mice by ~ 27% (20.1 ± 1.6 days for AR42-treated mice vs. 15.8 ± 0.4 days for vehicle-treated mice). AR42 treatment also improved motor function in these mice. AR42 treatment inhibited histone deacetylase (HDAC) activity in treated spinal cord although it did not affect SMN protein expression in these mice. AKT and GSK3β phosphorylation were both significantly increased in SMNΔ7 SMA mouse spinal cords. In conclusion, presymptomatic administration of the HDAC inhibitor AR42 ameliorates the disease phenotype in SMNΔ7 SMA mice in a SMN-independent manner possibly by increasing AKT neuroprotective signaling.
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Affiliation(s)
- Casey J Lumpkin
- Division of Neurology, Nemours Children's Hospital Delaware, 4462 E400 DuPont Experimental Station, 200 Powder Mill Road, Wilmington, DE, 19803, USA
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Ashlee W Harris
- Division of Neurology, Nemours Children's Hospital Delaware, 4462 E400 DuPont Experimental Station, 200 Powder Mill Road, Wilmington, DE, 19803, USA
| | - Andrew J Connell
- Division of Neurology, Nemours Children's Hospital Delaware, 4462 E400 DuPont Experimental Station, 200 Powder Mill Road, Wilmington, DE, 19803, USA
| | - Ryan W Kirk
- Division of Neurology, Nemours Children's Hospital Delaware, 4462 E400 DuPont Experimental Station, 200 Powder Mill Road, Wilmington, DE, 19803, USA
| | - Joshua A Whiting
- Division of Neurology, Nemours Children's Hospital Delaware, 4462 E400 DuPont Experimental Station, 200 Powder Mill Road, Wilmington, DE, 19803, USA
| | - Luciano Saieva
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Livio Pellizzoni
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University, New York, NY, USA
| | - Arthur H M Burghes
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Matthew E R Butchbach
- Division of Neurology, Nemours Children's Hospital Delaware, 4462 E400 DuPont Experimental Station, 200 Powder Mill Road, Wilmington, DE, 19803, USA.
- Department of Biological Sciences, University of Delaware, Newark, DE, USA.
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA.
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8
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Shin HJ, Na JH, Lee H, Lee YM. Nusinersen for spinal muscular atrophy types II and III: a retrospective single-center study in South Korea. World J Pediatr 2023; 19:450-459. [PMID: 36441395 DOI: 10.1007/s12519-022-00638-x] [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: 07/08/2022] [Accepted: 10/11/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND This study investigated the efficacy and safety of nusinersen, an antisense oligonucleotide, in patients with spinal muscular atrophy (SMA) types II (OMIM: 253,550) or III (OMIM: 253,400), including those with severe scoliosis or requiring respiratory support via mechanical ventilation. METHODS Data from 40 patients with genetically confirmed SMA who were treated with nusinersen at our institute from March 2019 to April 2022 were retrospectively analyzed. Of these, 30 patients with an age of onset < 3 years and not on permanent ventilation were selected. Clinical and genetic characteristics were investigated, and motor function was evaluated based on the Hammersmith Functional Motor Scale-Expanded (HFMSE) score. RESULTS The mean age of symptom onset was 1.2 years. Most patients were diagnosed with SMA type II (27/30, 90%). Nusinersen was administered via computed tomography-guided or direct intrathecal injection in 87% (26/30) and 13% (4/30) of the patients, respectively. At the 6-, 14-, 22-, and 26-month follow-ups, 72%, 71%, 88%, and 86% of patients showed motor improvement, respectively, with mean changes in HFMSE scores of 2.10, 2.88, 4.21, and 5.29, respectively. Multivariable analysis showed that the use of noninvasive ventilation was associated with poorer outcomes of motor function. CONCLUSIONS Patients with SMA type II or III who received nusinersen treatment showed significant improvement in motor function. A longer treatment duration led to a higher number of patients with improved motor function. No significant side effects of nusinersen were observed. Patients with SMA, even those with severe scoliosis or on respiratory support, can be safely treated using nusinersen.
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Affiliation(s)
- Hui Jin Shin
- Department of Pediatrics, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 135-720, Korea
| | - Ji-Hoon Na
- Department of Pediatrics, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 135-720, Korea
| | - Hyunjoo Lee
- Department of Pediatrics, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 135-720, Korea
| | - Young-Mock Lee
- Department of Pediatrics, Gangnam Severance Hospital, Yonsei University College of Medicine, 211 Eonju-Ro, Gangnam-Gu, Seoul, 135-720, Korea.
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9
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Chen X, Harting J, Farrow E, Thiffault I, Kasperaviciute D, Hoischen A, Gilissen C, Pastinen T, Eberle MA. Comprehensive SMN1 and SMN2 profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing. Am J Hum Genet 2023; 110:240-250. [PMID: 36669496 PMCID: PMC9943720 DOI: 10.1016/j.ajhg.2023.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/20/2022] [Indexed: 01/21/2023] Open
Abstract
Spinal muscular atrophy, a leading cause of early infant death, is caused by bi-allelic mutations of SMN1. Sequence analysis of SMN1 is challenging due to high sequence similarity with its paralog SMN2. Both genes have variable copy numbers across populations. Furthermore, without pedigree information, it is currently not possible to identify silent carriers (2+0) with two copies of SMN1 on one chromosome and zero copies on the other. We developed Paraphase, an informatics method that identifies full-length SMN1 and SMN2 haplotypes, determines the gene copy numbers, and calls phased variants using long-read PacBio HiFi data. The SMN1 and SMN2 copy-number calls by Paraphase are highly concordant with orthogonal methods (99.2% for SMN1 and 100% for SMN2). We applied Paraphase to 438 samples across 5 ethnic populations to conduct a population-wide haplotype analysis of these highly homologous genes. We identified major SMN1 and SMN2 haplogroups and characterized their co-segregation through pedigree-based analyses. We identified two SMN1 haplotypes that form a common two-copy SMN1 allele in African populations. Testing positive for these two haplotypes in an individual with two copies of SMN1 gives a silent carrier risk of 88.5%, which is significantly higher than the currently used marker (1.7%-3.0%). Extending beyond simple copy-number testing, Paraphase can detect pathogenic variants and enable potential haplotype-based screening of silent carriers through statistical phasing of haplotypes into alleles. Future analysis of larger population data will allow identification of more diverse haplotypes and genetic markers for silent carriers.
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Affiliation(s)
| | | | - Emily Farrow
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA,UMKC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA,Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA,UMKC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA,Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | | | | | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA,UMKC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
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10
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Chavda VP, Raval N, Sheta S, Vora LK, Elrashdy F, Redwan EM, Uversky VN, Ertas YN. Blood filtering system for COVID-19 management: novel modality of the cytokine storm therapeutics. Front Immunol 2023; 14:1064459. [PMID: 37153613 PMCID: PMC10160615 DOI: 10.3389/fimmu.2023.1064459] [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: 10/08/2022] [Accepted: 03/24/2023] [Indexed: 05/09/2023] Open
Abstract
The newly emerged coronavirus (SARS-CoV-2) is virulent, contagious, and has rapidly gained many mutations, which makes it highly infectious and swiftly transmissible around the world. SARS-CoV-2 infects people of all ages and targets all body organs and their cellular compartments, starting from the respiratory system, where it shows many deleterious effects, to other tissues and organs. Systemic infection can lead to severe cases that require intensive intervention. Multiple approaches were elaborated, approved, and successfully used in the intervention of the SARS-CoV-2 infection. These approaches range from the utilization of single and/or mixed medications to specialized supportive devices. For critically ill COVID-19 patients with acute respiratory distress syndrome, both extracorporeal membrane oxygenation (ECMO) and hemadsorption are utilized in combination or individually to support and release the etiological factors responsible for the "cytokine storm" underlying this condition. The current report discusses hemadsorption devices that can be used as part of supportive treatment for the COVID-19-associated cytokine storm.
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Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutic and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad, India
| | - Nidhi Raval
- National Institute of Pharmaceutical Education and Research (NIPER) – Ahmedabad, Gandhinagar, Gujarat, India
| | - Soham Sheta
- Formulation and Development, Zydus Lifesciences Ltd., Ahmedabad, Gujrat, India
| | - Lalitkumar K. Vora
- School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
- *Correspondence: Lalitkumar K. Vora, ; Vladimir N. Uversky, ; Yavuz Nuri Ertas,
| | - Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Cairo University, Cairo, Egypt
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer’s Research Institure, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- *Correspondence: Lalitkumar K. Vora, ; Vladimir N. Uversky, ; Yavuz Nuri Ertas,
| | - Yavuz Nuri Ertas
- ERNAM - Nanotechnology Research and Application Center, Erciyes University, Kayseri, Türkiye
- Department of Biomedical Engineering, Erciyes University, Kayseri, Türkiye
- *Correspondence: Lalitkumar K. Vora, ; Vladimir N. Uversky, ; Yavuz Nuri Ertas,
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11
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A high-throughput newborn screening approach for SCID, SMA, and SCD combining multiplex qPCR and tandem mass spectrometry. PLoS One 2023; 18:e0283024. [PMID: 36897914 PMCID: PMC10004496 DOI: 10.1371/journal.pone.0283024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/28/2023] [Indexed: 03/11/2023] Open
Abstract
Early diagnosis of severe combined immunodeficiency (SCID), spinal muscular atrophy (SMA), and sickle cell disease (SCD) improves health outcomes by providing a specific treatment before the onset of symptoms. A high-throughput nucleic acid-based method in newborn screening (NBS) has been shown to be fast and cost-effective in the early detection of these diseases. Screening for SCD has been included in Germany's NBS Program since Fall 2021 and typically requires high-throughput NBS laboratories to adopt analytical platforms that are demanding in terms of instrumentation and personnel. Thus, we developed a combined approach applying a multiplexed quantitative real-time PCR (qPCR) assay for simultaneous SCID, SMA, and 1st-tier SCD screening, followed by a tandem mass spectrometry (MS/MS) assay for 2nd-tier SCD screening. DNA is extracted from a 3.2-mm dried blood spot from which we simultaneously quantify T-cell receptor excision circles for SCID screening, identify the homozygous SMN1 exon 7 deletion for SMA screening, and determine the integrity of the DNA extraction through the quantification of a housekeeping gene. In our two-tier SCD screening strategy, our multiplex qPCR identifies samples carrying the HBB: c.20A>T allele that is coding for sickle cell hemoglobin (HbS). Subsequently, the 2nd tier MS/MS assay is used to distinguish heterozygous HbS/A carriers from samples of patients with homozygous or compound heterozygous SCD. Between July 2021 and March 2022, 96,015 samples were screened by applying the newly implemented assay. The screening revealed two positive SCID cases, while 14 newborns with SMA were detected. Concurrently, the qPCR assay registered HbS in 431 samples which were submitted to 2nd-tier SCD screening, resulting in 17 HbS/S, five HbS/C, and two HbS/β thalassemia patients. The results of our quadruplex qPCR assay demonstrate a cost-effective and fast approach for a combined screening of three diseases that benefit from nucleic-acid based methods in high-throughput NBS laboratories.
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12
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Rojahn S, Hambuch T, Adrian J, Gafni E, Gileta A, Hatchell H, Johnson B, Kallman B, Karfilis K, Kautzer C, Kennemer M, Kirk L, Kvitek D, Lettes J, Macrae F, Mendez F, Paul J, Pellegrino M, Preciado R, Risinger J, Schultz M, Spurka L, Swamy S, Truty R, Usem N, Velenich A, Aradhya S. Scalable detection of technically challenging variants through modified next-generation sequencing. Mol Genet Genomic Med 2022; 10:e2072. [PMID: 36251442 PMCID: PMC9747563 DOI: 10.1002/mgg3.2072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Some clinically important genetic variants are not easily evaluated with next-generation sequencing (NGS) methods due to technical challenges arising from high- similarity copies (e.g., PMS2, SMN1/SMN2, GBA1, HBA1/HBA2, CYP21A2), repetitive short sequences (e.g., ARX polyalanine repeats, FMR1 AGG interruptions in CGG repeats, CFTR poly-T/TG repeats), and other complexities (e.g., MSH2 Boland inversions). METHODS We customized our NGS processes to detect the technically challenging variants mentioned above with adaptations including target enrichment and bioinformatic masking of similar sequences. Adaptations were validated with samples of known genotypes. RESULTS Our adaptations provided high-sensitivity and high-specificity detection for most of the variants and provided a high-sensitivity primary assay to be followed with orthogonal disambiguation for the others. The sensitivity of the NGS adaptations was 100% for all of the technically challenging variants. Specificity was 100% for those in PMS2, GBA1, SMN1/SMN2, and HBA1/HBA2, and for the MSH2 Boland inversion; 97.8%-100% for CYP21A2 variants; and 85.7% for ARX polyalanine repeats. CONCLUSIONS NGS assays can detect technically challenging variants when chemistries and bioinformatics are jointly refined. The adaptations described support a scalable, cost-effective path to identifying all clinically relevant variants within a single sample.
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13
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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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14
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Emerging digital PCR technology in precision medicine. Biosens Bioelectron 2022; 211:114344. [DOI: 10.1016/j.bios.2022.114344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022]
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15
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Kanda S, Moulton E, Butchbach MER. Effects of inhibitors of SLC9A-type sodium-protein exchangers on Survival Motor Neuron 2 ( SMN2) mRNA splicing and expression. Mol Pharmacol 2022; 102:92-105. [PMID: 35667685 PMCID: PMC9341265 DOI: 10.1124/molpharm.122.000529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/09/2022] [Indexed: 11/22/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive, pediatric-onset disorder caused by the loss of spinal motor neurons thereby leading to muscle atrophy. SMA is caused by the loss of or mutations in the survival motor neuron 1 (SMN1) gene. SMN1 is duplicated in humans to give rise to the paralogous SMN2 gene. This paralog is nearly identical except for a cytosine to thymine (C-to-T) transition within an exonic splicing enhancer (ESE) element within exon 7. As a result, the majority of SMN2 transcripts lack exon 7 (SMNΔ7) which produces a truncated and unstable SMN protein. Since SMN2 copy number is inversely related to disease severity, it is a well-established target for SMA therapeutics development. 5-(N-ethyl-N-isopropyl)amiloride (EIPA), an inhibitor of sodium/proton exchangers (NHEs), has previously been shown to increase exon 7 inclusion and SMN protein levels in SMA cells. In this study, NHE inhibitors were evaluated for their ability to modulate SMN2 expression. EIPA as well as 5-(N,N-hexamethylene)amiloride (HMA) increase exon 7 inclusion in SMN2 splicing reporter lines as well as in SMA fibroblasts. The EIPA-induced exon 7 inclusion occurs via a unique mechanism that does not involve previously identified splicing factors. Transcriptome analysis identified novel targets, including TIA1 and FABP3, for further characterization. EIPA and HMA are more selective at inhibiting the NHE5 isoform, which is expressed in fibroblasts as well as in neuronal cells. These results show that NHE5 inhibition increases SMN2 expression and may be a novel target for therapeutics development. Significance Statement This study demonstrates a molecular mechanism by which inhibitors of the sodium-protein exchanger increase the alternative splicing of SMN2 in spinal muscular atrophy cells. NHE5 selective inhibitors increase the inclusion of full-length SMN2 mRNAs by targeting TIA1 and FABP3 expression, which is distinct from other small molecule regulators of SMN2 alternative splicing. This study provides a novel means to increase full-length SMN2 expression and a novel target for therapeutics development.
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Affiliation(s)
- Sambee Kanda
- Biological Sciences, University of Delaware, United States
| | - Emily Moulton
- Biomedical Research, Nemours Children's Hospital Delaware, United States
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16
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Pinto A, Cunha C, Chaves R, Butchbach MER, Adega F. Comprehensive In Silico Analysis of Retrotransposon Insertions within the Survival Motor Neuron Genes Involved in Spinal Muscular Atrophy. BIOLOGY 2022; 11:824. [PMID: 35741345 PMCID: PMC9219815 DOI: 10.3390/biology11060824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are interspersed repetitive and mobile DNA sequences within the genome. Better tools for evaluating TE-derived sequences have provided insights into the contribution of TEs to human development and disease. Spinal muscular atrophy (SMA) is an autosomal recessive motor neuron disease that is caused by deletions or mutations in the Survival Motor Neuron 1 (SMN1) gene but retention of its nearly perfect orthologue SMN2. Both genes are highly enriched in TEs. To establish a link between TEs and SMA, we conducted a comprehensive, in silico analysis of TE insertions within the SMN1/2 loci of SMA, carrier and healthy genomes. We found an Alu insertion in the promoter region and one L1 element in the 3'UTR that may play an important role in alternative promoter as well as in alternative transcriptional termination. Additionally, several intronic Alu repeats may influence alternative splicing via RNA circularization and causes the presence of new alternative exons. These Alu repeats present throughout the genes are also prone to recombination events that could lead to SMN1 exons deletions and, ultimately, SMA. TE characterization of the SMA genomic region could provide for a better understanding of the implications of TEs on human disease and genomic evolution.
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Affiliation(s)
- Albano Pinto
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Catarina Cunha
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
| | - Matthew E. R. Butchbach
- Division of Neurology, Nemours Children’s Hospital Delaware, Wilmington, DE 19803, USA;
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Filomena Adega
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (A.P.); (C.C.); (R.C.)
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal
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17
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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18
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Next generation sequencing is a highly reliable method to analyze exon 7 deletion of survival motor neuron 1 (SMN1) gene. Sci Rep 2022; 12:223. [PMID: 34997153 PMCID: PMC8741787 DOI: 10.1038/s41598-021-04325-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/28/2021] [Indexed: 12/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most common and severe genetic diseases. SMA carrier screening is an effective way to identify couples at risk of having affected children. Next-generation sequencing (NGS)-based expanded carrier screening could detect SMN1 gene copy number without extra experiment and with high cost performance. However, its performance has not been fully evaluated. Here we conducted a systematic comparative study to evaluate the performance of three common methods. 478 samples were analyzed with multiplex ligation probe amplification (MLPA), real-time quantitative polymerase chain reaction (qPCR) and NGS, simultaneously. Taking MLPA-based results as the reference, for 0 copy, 1 copy and ≥ 2 copy SMN1 analysis with NGS, the sensitivity, specificity and precision were all 100%. Using qPCR method, the sensitivity was 100%, 97.52% and 94.30%, respectively; 98.63%, 95.48% and 100% for specificity; and 72.72%, 88.72% and 100% for precision. NGS repeatability was higher than that of qPCR. Moreover, among three methods, NGS had the lowest retest rate. Thus, NGS is a relatively more reliable method for SMN1 gene copy number detection. In expanded carrier screening, compared with the combination of multiple methods, NGS method could reduce the test cost and simplify the screening process.
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19
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Alternative Splicing Role in New Therapies of Spinal Muscular Atrophy. Genes (Basel) 2021; 12:genes12091346. [PMID: 34573328 PMCID: PMC8468182 DOI: 10.3390/genes12091346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
It has been estimated that 80% of the pre-mRNA undergoes alternative splicing, which exponentially increases the flow of biological information in cellular processes and can be an attractive therapeutic target. It is a crucial mechanism to increase genetic diversity. Disturbed alternative splicing is observed in many disorders, including neuromuscular diseases and carcinomas. Spinal Muscular Atrophy (SMA) is an autosomal recessive neurodegenerative disease. Homozygous deletion in 5q13 (the region coding for the motor neuron survival gene (SMN1)) is responsible for 95% of SMA cases. The nearly identical SMN2 gene does not compensate for SMN loss caused by SMN1 gene mutation due to different splicing of exon 7. A pathologically low level of survival motor neuron protein (SMN) causes degeneration of the anterior horn cells in the spinal cord with associated destruction of α-motor cells and manifested by muscle weakness and loss. Understanding the regulation of the SMN2 pre-mRNA splicing process has allowed for innovative treatment and the introduction of new medicines for SMA. After describing the concept of splicing modulation, this review will cover the progress achieved in this field, by highlighting the breakthrough accomplished recently for the treatment of SMA using the mechanism of alternative splicing.
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20
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Butchbach MER. Genomic Variability in the Survival Motor Neuron Genes ( SMN1 and SMN2): Implications for Spinal Muscular Atrophy Phenotype and Therapeutics Development. Int J Mol Sci 2021; 22:ijms22157896. [PMID: 34360669 PMCID: PMC8348669 DOI: 10.3390/ijms22157896] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a leading genetic cause of infant death worldwide that is characterized by loss of spinal motor neurons leading to muscle weakness and atrophy. SMA results from the loss of survival motor neuron 1 (SMN1) gene but retention of its paralog SMN2. The copy numbers of SMN1 and SMN2 are variable within the human population with SMN2 copy number inversely correlating with SMA severity. Current therapeutic options for SMA focus on increasing SMN2 expression and alternative splicing so as to increase the amount of SMN protein. Recent work has demonstrated that not all SMN2, or SMN1, genes are equivalent and there is a high degree of genomic heterogeneity with respect to the SMN genes. Because SMA is now an actionable disease with SMN2 being the primary target, it is imperative to have a comprehensive understanding of this genomic heterogeneity with respect to hybrid SMN1–SMN2 genes generated by gene conversion events as well as partial deletions of the SMN genes. This review will describe this genetic heterogeneity in SMA and its impact on disease phenotype as well as therapeutic efficacy.
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Affiliation(s)
- Matthew E. R. Butchbach
- Center for Applied Clinical Genomics, Nemours Children’s Health Delaware, Wilmington, DE 19803, USA;
- Center for Pediatric Research, Nemours Children’s Health Delaware, Wilmington, DE 19803, USA
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
- Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA 19107, USA
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21
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Detection of SMN1 to SMN2 gene conversion events and partial SMN1 gene deletions using array digital PCR. Neurogenetics 2021; 22:53-64. [PMID: 33415588 DOI: 10.1007/s10048-020-00630-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/26/2020] [Indexed: 12/15/2022]
Abstract
Proximal spinal muscular atrophy (SMA), a leading genetic cause of infant death worldwide, is an early-onset motor neuron disease characterized by loss of α-motor neurons and associated muscle atrophy. SMA is caused by deletion or other disabling mutations of survival motor neuron 1 (SMN1) but retention of one or more copies of the paralog SMN2. Within the SMA population, there is substantial variation in SMN2 copy number (CN); in general, those individuals with SMA who have a high SMN2 CN have a milder disease. Because SMN2 functions as a disease modifier, its accurate CN determination may have clinical relevance. In this study, we describe the development of array digital PCR (dPCR) to quantify SMN1 and SMN2 CNs in DNA samples using probes that can distinguish the single nucleotide difference between SMN1 and SMN2 in exon 8. This set of dPCR assays can accurately and reliably measure the number of SMN1 and SMN2 copies in DNA samples. In a cohort of SMA patient-derived cell lines, the assay confirmed a strong inverse correlation between SMN2 CN and disease severity. We can detect SMN1-SMN2 gene conversion events in DNA samples by comparing CNs at exon 7 and exon 8. Partial deletions of SMN1 can also be detected with dPCR by comparing CNs at exon 7 or exon 8 with those at intron 1. Array dPCR is a practical technique to determine, accurately and reliably, SMN1 and SMN2 CNs from SMA samples as well as identify gene conversion events and partial deletions of SMN1.
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22
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Rouzier C, Chaussenot A, Paquis-Flucklinger V. Molecular diagnosis and genetic counseling for spinal muscular atrophy (SMA). Arch Pediatr 2020; 27:7S9-7S14. [DOI: 10.1016/s0929-693x(20)30270-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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23
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Cuscó I, Bernal S, Blasco-Pérez L, Calucho M, Alias L, Fuentes-Prior P, Tizzano EF. Practical guidelines to manage discordant situations of SMN2 copy number in patients with spinal muscular atrophy. NEUROLOGY-GENETICS 2020; 6:e530. [PMID: 33324756 PMCID: PMC7713720 DOI: 10.1212/nxg.0000000000000530] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/29/2020] [Indexed: 12/26/2022]
Abstract
Objective Assessment of SMN2 copy number in patients with spinal muscular atrophy (SMA) is essential to establish careful genotype-phenotype correlations and predict disease evolution. This issue is becoming crucial in the present scenario of therapeutic advances with the perspective of SMA neonatal screening and early diagnosis to initiate treatment, as this value is critical to stratify patients for clinical trials and to define those eligible to receive medication. Several technical pitfalls and interindividual variations may account for reported discrepancies in the estimation of SMN2 copy number and establishment of phenotype-genotype correlations. Methods We propose a management guide based on a sequence of specified actions once SMN2 copy number is determined for a given patient. Regardless of the method used to estimate the number of SMN2 copies, our approach focuses on the manifestations of the patient to recommend how to proceed in each case. Results We defined situations according to SMN2 copy number in a presymptomatic scenario of screening, in which we predict the possible evolution, and when a symptomatic patient is genetically confirmed. Unexpected discordant cases include patients having a single SMN2 copy but noncongenital disease forms, 2 SMN2 copies compatible with type II or III SMA, and 3 or 4 copies of the gene showing more severe disease than expected. Conclusions Our proposed guideline would help to systematically identify discordant SMA cases that warrant further genetic investigation. The SMN2 gene, as the main modifier of SMA phenotype, deserves a more in-depth study to provide more accurate genotype-phenotype correlations.
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Affiliation(s)
- Ivon Cuscó
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Sara Bernal
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Laura Blasco-Pérez
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Maite Calucho
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Laura Alias
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Pablo Fuentes-Prior
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Eduardo F Tizzano
- Medicine Genetics Group (I.C., L.B.-P., M.C., E.F.T.), Vall dHebron Research Institute (VHIR), Barcelona; Department of Clinical and Molecular Genetics (I.C., L.B.-P., M.C., E.F.T.), Hospital Vall dHebron, Barcelona; Department of Genetics (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Biomedical Research Institute Sant Pau (IIB Sant Pau) (S.B., L.A.), Hospital de la Santa Creu i Sant Pau, Barcelona; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER-ISCIII, U-705 Barcelona) (S.B., L.A.), Madrid; Molecular Bases of Disease (P.F.-P.), Biomedical Research Institute Sant Pau (IIB Sant Pau), Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
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24
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Müller-Felber W, Vill K, Schwartz O, Gläser D, Nennstiel U, Wirth B, Burggraf S, Röschinger W, Becker M, Durner J, Eggermann K, Müller C, Hannibal I, Olgemöller B, Schara U, Blaschek A, Kölbel H. Infants Diagnosed with Spinal Muscular Atrophy and 4 SMN2 Copies through Newborn Screening - Opportunity or Burden? J Neuromuscul Dis 2020; 7:109-117. [PMID: 32144995 PMCID: PMC7175938 DOI: 10.3233/jnd-200475] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Although the value of newborn screening (NBS) for early detection and treatment opportunity in SMA patients is generally accepted, there is still an ongoing discussion about the best strategy in children with 4 and more copies of the SMN2 gene. This gene is known to be the most important but not the only disease modifier. In our SMA-NBS pilot project in Germany comprising 278,970 infants screened between January 2018 and November 2019 were 38 positive cases with a homozygous SMN1 deletion. 40% of them had 4 or more SMN2 copies. The incidence for homozygous SMN1 deletion was 1 : 7350, which is within the known range of SMA incidence in Germany. Of the 15 SMA children with 4 SMN2 copies, one child developed physical signs of SMA by the age of 8 months. Reanalysis of the SMN2 copy number by a different test method revealed 3 copies. Two children had affected siblings with SMA Type III, who were diagnosed only after detection of the index patient in the NBS. One had a positive family history with an affected aunt (onset of disease at the age of 3 years). Three families were lost to medical follow up; two because of socioeconomic reasons and one to avoid the psychological stress associated with the appointments. Decisions on how to handle patients with 4 SMN2 copies are discussed in the light of the experience gathered from our NBS pilot SMA program.
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Affiliation(s)
- Wolfgang Müller-Felber
- Dr. v. Hauner Children's Hospital, Department of Pediatric Neurology and Developmental Medicine, LMU - University of Munich, Munich, Germany
| | - Katharina Vill
- Dr. v. Hauner Children's Hospital, Department of Pediatric Neurology and Developmental Medicine, LMU - University of Munich, Munich, Germany
| | - Oliver Schwartz
- Department of Pediatric Neurology, Muenster University Hospital, Münster, Germany
| | - Dieter Gläser
- Genetikum ®, Center for Human Genetics, Neu-Ulm, Germany
| | - Uta Nennstiel
- Screening Center of the Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Genetics Cologne and Center for Rare Diseases Cologne, University of Cologne, Cologne, Germany
| | | | | | | | - Jürgen Durner
- Labor Becker und Kollegen, Munich, Germany.,Department of Operative/Restorative Dentistry, Periodontology and Pedodontics, Ludwig-Maximilians-Universität München, Goethestr. 70, 80336 Munich, Germany
| | - Katja Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Christine Müller
- Dr. v. Hauner Children's Hospital, Department of Pediatric Neurology and Developmental Medicine, LMU - University of Munich, Munich, Germany
| | - Iris Hannibal
- Dr. v. Hauner Children's Hospital, Department of Pediatric Neurology and Developmental Medicine, LMU - University of Munich, Munich, Germany
| | | | - Ulrike Schara
- Department of Pediatric Neurology, Developmental Neurology and Social Pediatrics, University of Essen, Germany
| | - Astrid Blaschek
- Dr. v. Hauner Children's Hospital, Department of Pediatric Neurology and Developmental Medicine, LMU - University of Munich, Munich, Germany
| | - Heike Kölbel
- Department of Pediatric Neurology, Developmental Neurology and Social Pediatrics, University of Essen, Germany
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25
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Jiang L, Lin R, Gallagher S, Zayac A, Butchbach MER, Hung P. Development and validation of a 4-color multiplexing spinal muscular atrophy (SMA) genotyping assay on a novel integrated digital PCR instrument. Sci Rep 2020; 10:19892. [PMID: 33199817 PMCID: PMC7670453 DOI: 10.1038/s41598-020-76893-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 11/02/2020] [Indexed: 01/30/2023] Open
Abstract
Digital PCR (dPCR) technology has been proven to be highly sensitive and accurate in detecting copy number variations (CNV). However, a higher-order multiplexing dPCR assay for measuring SMN1 and SMN2 copy numbers in spinal muscular atrophy (SMA) samples has not been reported. Described here is a rapid multiplex SMA dPCR genotyping assay run on a fully integrated dPCR instrument with five optical channels. The hydrolysis probe-based multiplex dPCR assay quantifies SMN1, SMN2, and the total SMN (SMN1 + SMN2) while using RPPH1 gene as an internal reference control. The quadruplex assay was evaluated with characterized control DNA samples and validated with 15 blinded clinical samples from a previously published study. SMN1 and SMN2 copy numbers were completely concordant with previous results for both the control and blinded samples. The dPCR-based SMA copy number determination was accomplished in 90 min with a walk-away workflow identical to real-time quantitative PCR (qPCR). In summary, presented here is a simple higher-order multiplexing solution on a novel digital PCR platform to meet the growing demand for SMA genotyping and prognostics.
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Affiliation(s)
- Lingxia Jiang
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA.
| | - Robert Lin
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA
| | - Steve Gallagher
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA
| | - Andrew Zayac
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA
| | - Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Department of Pediatrics, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Paul Hung
- Combinati Inc., 2450 Embarcadero Way, Palo Alto, CA, 94303, USA
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26
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Zhang R, Gu C, Pu L, Meng Y, Shu J, Cai C. High-throughput screening reveals novel mutations in spinal muscular atrophy patients. Ital J Pediatr 2020; 46:166. [PMID: 33148303 PMCID: PMC7641840 DOI: 10.1186/s13052-020-00925-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 10/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is an autosomal recessive hereditary disease associated with severe muscle atrophy and weakness in the limbs and trunk. The discovery of mutated genes is helpful in diagnosis and treatment for SMA. METHODS Eighty-three whole blood samples were collected from 28 core families of clinically suspected SMA, and multiplex ligation probe amplification (MLPA) was performed. Afterwards, the complete gene sequence of SMN1 gene was detected. Furthermore, 20 SMA patients were selected from the 28 probands, and 5 non SMA children as controls. The Life Technologies SOLiD™ technology with mate-pair chemistry was utilized to conduct the whole exome high-throughput sequencing. RESULTS Twenty-two probands were SMA patients, 3 probands carriers, and 3 probands normal individuals. Moreover, 2 parents from 2 SMA families were with 3 SMN1 exon7 copies. Six SMN1 single nucleotide variants (SNVs) were identified in the 83 samples, and c.[84C > T], c.[271C > T], c.[-39A > G] and g.[70240639G > C] were novel. Compared with control group, 9102 mutation were selected out in SMA patients. SPTA1 mutation c.[-41_-40insCTCT], FUT5 SNV c.[1001A > G], and MCCC2 SNV c.[-117A > G] were the 3 most frequent mutations in SMA group (95, 85 and 75%, respectively). CONCLUSIONS We identified some mutations in both SMN1 and other genes, and c.[271C > T], c.[-41_-40insCTCT], c.[1001A > G] and c.[-117A > G] might be associated with the onset of SMA.
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Affiliation(s)
- Ruiping Zhang
- Department of Pediatric, Tianjin Children's Hospital, Tianjin, 300134, China
| | - Chunyu Gu
- Graduate School, Tianjin Medical University, Tianjin, 300070, China
| | - Linjie Pu
- Graduate School, Tianjin Medical University, Tianjin, 300070, China
| | - Yingtao Meng
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, 238 Longyan Road, Beichen District, Tianjin, 300134, China
| | - Jianbo Shu
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, 238 Longyan Road, Beichen District, Tianjin, 300134, China. .,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China.
| | - Chunquan Cai
- Tianjin Pediatric Research Institute, Tianjin Children's Hospital, 238 Longyan Road, Beichen District, Tianjin, 300134, China. .,Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, 300134, China. .,Department of Neurosurgery, Tianjin Children's Hospital, 238 Longyan Road, Beichen District, Tianjin, 300134, China.
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27
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Kannan A, Jiang X, He L, Ahmad S, Gangwani L. ZPR1 prevents R-loop accumulation, upregulates SMN2 expression and rescues spinal muscular atrophy. Brain 2020; 143:69-93. [PMID: 31828288 PMCID: PMC6935747 DOI: 10.1093/brain/awz373] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/08/2019] [Accepted: 10/07/2019] [Indexed: 12/21/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by homozygous mutation or deletion of the survival motor neuron 1 (SMN1) gene. A second copy, SMN2, is similar to SMN1 but produces ∼10% SMN protein because of a single-point mutation that causes splicing defects. Chronic low levels of SMN cause accumulation of co-transcriptional R-loops and DNA damage leading to genomic instability and neurodegeneration in SMA. Severity of SMA disease correlates inversely with SMN levels. SMN2 is a promising target to produce higher levels of SMN by enhancing its expression. Mechanisms that regulate expression of SMN genes are largely unknown. We report that zinc finger protein ZPR1 binds to RNA polymerase II, interacts in vivo with SMN locus and upregulates SMN2 expression in SMA mice and patient cells. Modulation of ZPR1 levels directly correlates and influences SMN2 expression levels in SMA patient cells. ZPR1 overexpression in vivo results in a systemic increase of SMN levels and rescues severe to moderate disease in SMA mice. ZPR1-dependent rescue improves growth and motor function and increases the lifespan of male and female SMA mice. ZPR1 reduces neurodegeneration in SMA mice and prevents degeneration of cultured primary spinal cord neurons derived from SMA mice. Further, we show that the low levels of ZPR1 associated with SMA pathogenesis cause accumulation of co-transcriptional RNA-DNA hybrids (R-loops) and DNA damage leading to genomic instability in SMA mice and patient cells. Complementation with ZPR1 elevates senataxin levels, reduces R-loop accumulation and rescues DNA damage in SMA mice, motor neurons and patient cells. In conclusion, ZPR1 is critical for preventing accumulation of co-transcriptional R-loops and DNA damage to avert genomic instability and neurodegeneration in SMA. ZPR1 enhances SMN2 expression and leads to SMN-dependent rescue of SMA. ZPR1 represents a protective modifier and a therapeutic target for developing a new method for the treatment of SMA.
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Affiliation(s)
- Annapoorna Kannan
- Center of Emphasis in Neurosciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA.,Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Xiaoting Jiang
- Center of Emphasis in Neurosciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA.,Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Lan He
- Center of Emphasis in Neurosciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA.,Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Saif Ahmad
- Center of Emphasis in Neurosciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA.,Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
| | - Laxman Gangwani
- Center of Emphasis in Neurosciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA.,Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA.,Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, USA
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28
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Smeriglio P, Langard P, Querin G, Biferi MG. The Identification of Novel Biomarkers Is Required to Improve Adult SMA Patient Stratification, Diagnosis and Treatment. J Pers Med 2020; 10:jpm10030075. [PMID: 32751151 PMCID: PMC7564782 DOI: 10.3390/jpm10030075] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
Spinal muscular atrophy (SMA) is currently classified into five different subtypes, from the most severe (type 0) to the mildest (type 4) depending on age at onset, best motor function achieved, and copy number of the SMN2 gene. The two recent approved treatments for SMA patients revolutionized their life quality and perspectives. However, upon treatment with Nusinersen, the most widely administered therapy up to date, a high degree of variability in therapeutic response was observed in adult SMA patients. These data, together with the lack of natural history information and the wide spectrum of disease phenotypes, suggest that further efforts are needed to develop precision medicine approaches for all SMA patients. Here, we compile the current methods for functional evaluation of adult SMA patients treated with Nusinersen. We also present an overview of the known molecular changes underpinning disease heterogeneity. We finally highlight the need for novel techniques, i.e., -omics approaches, to capture phenotypic differences and to understand the biological signature in order to revise the disease classification and device personalized treatments.
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Affiliation(s)
- Piera Smeriglio
- Centre of Research in Myology, Institute of Myology, Sorbonne Université, INSERM, 75013 Paris, France; (P.L.); (G.Q.)
- Correspondence: (P.S.); (M.G.B.)
| | - Paul Langard
- Centre of Research in Myology, Institute of Myology, Sorbonne Université, INSERM, 75013 Paris, France; (P.L.); (G.Q.)
| | - Giorgia Querin
- Centre of Research in Myology, Institute of Myology, Sorbonne Université, INSERM, 75013 Paris, France; (P.L.); (G.Q.)
- Association Institut de Myologie, Plateforme Essais Cliniques Adultes, 75013 Paris, France
- APHP, Service de Neuromyologie, Hôpital Pitié-Salpêtrière, 75013 Paris, France
| | - Maria Grazia Biferi
- Centre of Research in Myology, Institute of Myology, Sorbonne Université, INSERM, 75013 Paris, France; (P.L.); (G.Q.)
- Correspondence: (P.S.); (M.G.B.)
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29
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Hryshchenko NV, Yurchenko AA, Karaman HS, Livshits LA. Genetic Modifiers of the Spinal Muscular Atrophy Phenotype. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720020073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Chen X, Sanchis-Juan A, French CE, Connell AJ, Delon I, Kingsbury Z, Chawla A, Halpern AL, Taft RJ, Bentley DR, Butchbach MER, Raymond FL, Eberle MA. Spinal muscular atrophy diagnosis and carrier screening from genome sequencing data. Genet Med 2020; 22:945-953. [PMID: 32066871 PMCID: PMC7200598 DOI: 10.1038/s41436-020-0754-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 11/21/2022] Open
Abstract
Purpose Spinal muscular atrophy (SMA), caused by loss of the SMN1 gene, is a leading cause of early childhood death. Due to the near identical sequences of SMN1 and SMN2, analysis of this region is challenging. Population-wide SMA screening to quantify the SMN1 copy number (CN) is recommended by the American College of Medical Genetics and Genomics. Methods We developed a method that accurately identifies the CN of SMN1 and SMN2 using genome sequencing (GS) data by analyzing read depth and eight informative reference genome differences between SMN1/2. Results We characterized SMN1/2 in 12,747 genomes, identified 1568 samples with SMN1 gains or losses and 6615 samples with SMN2 gains or losses, and calculated a pan-ethnic carrier frequency of 2%, consistent with previous studies. Additionally, 99.8% of our SMN1 and 99.7% of SMN2 CN calls agreed with orthogonal methods, with a recall of 100% for SMA and 97.8% for carriers, and a precision of 100% for both SMA and carriers. Conclusion This SMN copy-number caller can be used to identify both carrier and affected status of SMA, enabling SMA testing to be offered as a comprehensive test in neonatal care and an accurate carrier screening tool in GS sequencing projects.
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Affiliation(s)
| | - Alba Sanchis-Juan
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Courtney E French
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Andrew J Connell
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Isabelle Delon
- East Midlands and East of England NHS Genomic Laboratory Hub, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | | | | | | | - Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA.,Department of Pediatrics, Sidney Kimmel College of Medicine, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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31
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Mao X, Liu C, Tong H, Chen Y, Liu K. Principles of digital PCR and its applications in current obstetrical and gynecological diseases. Am J Transl Res 2019; 11:7209-7222. [PMID: 31934273 PMCID: PMC6943456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
Digital PCR (dPCR) is a revolutionary technique to precisely quantify nucleic acids. For its high sensitivity and specificity, this technique has been widely replicated worldwide. To verify its applicability, we reviewed all the related articles in PubMed database published before May 10, 2019. Original articles and reviews on the topics were selected. Entered key words included "digital PCR/dPCR", "advantage", "combined use", "microfluidic chip", "gynecological cancer/tumor". We found that dPCR has shown great potential in clinical operations, like tumor liquid biopsy, non-invasive prenatal diagnosis, microorganism detection, and next-generation sequencing library quality-control.
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Affiliation(s)
- Xiaodong Mao
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Chao Liu
- Department of Endocrinology, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese MedicineNanjing 210028, Jiangsu, China
| | - Hua Tong
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Yajun Chen
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
| | - Kangsheng Liu
- Department of Clinical Laboratory, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care HospitalNanjing 210029, Jiangsu, China
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32
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Zhao M, Lian M, Cheah FSH, Tan ASC, Agarwal A, Chong SS. Identification of Novel Microsatellite Markers Flanking the SMN1 and SMN2 Duplicated Region and Inclusion Into a Single-Tube Tridecaplex Panel for Haplotype-Based Preimplantation Genetic Testing of Spinal Muscular Atrophy. Front Genet 2019; 10:1105. [PMID: 31781167 PMCID: PMC6851269 DOI: 10.3389/fgene.2019.01105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Preimplantation genetic testing for the monogenic disorder (PGT-M) spinal muscular atrophy (SMA) is significantly improved by supplementation of SMN1 deletion detection with marker-based linkage analysis. To expand the availability of informative markers for PGT-M of SMA, we identified novel non-duplicated and highly polymorphic microsatellite markers closely flanking the SMN1 and SMN2 duplicated region. Six of the novel markers within 0.5 Mb of the 1.7 Mb duplicated region containing SMN1 and SMN2 (SMA6863, SMA6873, SMA6877, SMA7093, SMA7115, and SMA7120) and seven established markers (D5S1417, D5S1413, D5S1370, D5S1408, D5S610, D5S1999, and D5S637), all with predicted high heterozygosity values, were selected and optimized in a tridecaplex PCR panel, and their polymorphism indices were determined in two populations. Observed marker heterozygosities in the Chinese and Caucasian populations ranged from 0.54 to 0.86, and 98.4% of genotyped individuals (185 of 188) were heterozygous for ≥2 markers on either side of SMN1. The marker panel was evaluated for disease haplotype phasing using single cells from two parent–child trios after whole-genome amplification, and applied to a clinical IVF (in vitro fertilization) PGT-M cycle in an at-risk couple, in parallel with SMN1 deletion detection. Both direct and indirect test methods determined that none of five tested embryos were at risk for SMA, with haplotype analysis further identifying one embryo as unaffected and four as carriers. Fresh transfer of the unaffected embryo did not lead to implantation, but subsequent frozen-thaw transfer of a carrier embryo produced a pregnancy, with fetal genotype confirmed by amniocentesis, and a live birth at term.
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Affiliation(s)
- Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mulias Lian
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Felicia S H Cheah
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Arnold S C Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Anupriya Agarwal
- Clinic for Human Reproduction, Department of Obstetrics and Gynecology, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore.,Molecular Diagnosis Center and Clinical Cytogenetics Service, Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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Kariyawasam DST, D'Silva A, Lin C, Ryan MM, Farrar MA. Biomarkers and the Development of a Personalized Medicine Approach in Spinal Muscular Atrophy. Front Neurol 2019; 10:898. [PMID: 31481927 PMCID: PMC6709682 DOI: 10.3389/fneur.2019.00898] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022] Open
Abstract
Recent unprecedented advances in treatment for spinal muscular atrophy (SMA) enabled patients to access the first approved disease modifying therapy for the condition. There are however many uncertainties, regarding timing of treatment initiation, response to intervention, treatment effects and long-term outcomes, which are complicated by the evolving phenotypes seen in the post-treatment era for patients with SMA. Biomarkers of disease, with diagnostic, prognostic, predictive, and pharmacodynamic value are thus urgently required, to facilitate a wider understanding in this dynamic landscape. A spectrum of these candidate biomarkers, will be evaluated in this review, including genetic, epigenetic, proteomic, electrophysiological, and imaging measures. Of these, SMN2 appears to be the most significant modifier of phenotype to date, and its use in prognostication shows considerable clinical utility. Longitudinal studies in patients with SMA highlight an emerging role of circulatory markers such as neurofilament, in tracking disease progression and response to treatment. Furthermore, neurophysiological biomarkers such as CMAP and MUNE values show considerable promise in the real word setting, in following the dynamic response and output of the motor unit to therapeutic intervention. The specific value for these possible biomarkers across diagnosis, prognosis, prediction of treatment response, efficacy, and safety will be central to guide future patient-targeted treatments, the design of clinical trials, and understanding of the pathophysiological mechanisms of disease and intervention.
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Affiliation(s)
- Didu S T Kariyawasam
- Department of Neurology, Sydney Children's Hospital, Sydney, NSW, Australia.,School of Women's and Children's Health, University of New South Wales Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Arlene D'Silva
- School of Women's and Children's Health, University of New South Wales Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Cindy Lin
- Department of Neurophysiology, Brain and Mind Center, University of Sydney, Sydney, NSW, Australia
| | - Monique M Ryan
- Department of Neurology, Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Michelle A Farrar
- Department of Neurology, Sydney Children's Hospital, Sydney, NSW, Australia.,School of Women's and Children's Health, University of New South Wales Medicine, University of New South Wales, Sydney, NSW, Australia
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Kollmer J, Hilgenfeld T, Ziegler A, Saffari A, Sam G, Hayes JM, Pietsch A, Jost M, Heiland S, Bendszus M, Wick W, Weiler M. Quantitative MR neurography biomarkers in 5q-linked spinal muscular atrophy. Neurology 2019; 93:e653-e664. [PMID: 31292223 DOI: 10.1212/wnl.0000000000007945] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/21/2019] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVE To characterize and quantify peripheral nerve lesions and muscle degeneration in clinically, genetically, and electrophysiologically well-classified, nonpediatric patients with 5q-linked spinal muscular atrophy (SMA) by high-resolution magnetic resonance neurography (MRN). METHODS Thirty-one adult patients with genetically confirmed 5q-linked SMA types II, IIIa, and IIIb and 31 age- and sex-matched healthy volunteers were prospectively investigated. All patients received neurologic, physiotherapeutic, and electrophysiologic assessments. MRN at 3.0T with anatomic coverage from the lumbosacral plexus and proximal thigh down to the tibiotalar joint was performed with dual-echo 2D relaxometry sequences with spectral fat saturation and a 3D T2-weighted inversion recovery sequence. Detailed quantification of nerve injury by morphometric and microstructural MRN markers and qualitative classification of fatty muscle degeneration were conducted. RESULTS Established clinical scores and compound muscle action potentials discriminated well between the 3 SMA types. MRN revealed that peroneal and tibial nerve cross-sectional area (CSA) at the thigh and lower leg level as well as spinal nerve CSA were markedly decreased throughout all 3 groups, indicating severe generalized peripheral nerve atrophy. While peroneal and tibial nerve T2 relaxation time was distinctly increased at all analyzed anatomic regions, the proton spin density was clearly decreased. Marked differences in fatty muscle degeneration were found between the 3 groups and for all analyzed compartments. CONCLUSIONS MRN detects and quantifies peripheral nerve involvement in SMA types II, IIIa, and IIIb with high sensitivity in vivo. Quantitative MRN parameters (T2 relaxation time, proton spin density, CSA) might serve as novel imaging biomarkers in SMA to indicate early microstructural nerve tissue changes in response to treatment.
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Affiliation(s)
- Jennifer Kollmer
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany.
| | - Tim Hilgenfeld
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - Andreas Ziegler
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - Afshin Saffari
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - Georges Sam
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - John M Hayes
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - Adriana Pietsch
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - Marie Jost
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - Sabine Heiland
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - Martin Bendszus
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - Wolfgang Wick
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany
| | - Markus Weiler
- From the Department of Neuroradiology (J.K., T.H., A.P., M.J., S.H., M.B.), Division of Child Neurology and Metabolic Medicine (A.Z., A.S.), Center for Child and Adolescent Medicine, Department of Neurology (G.S., W.W., M.W.), and Department of Neuroradiology (S.H.), Division of Experimental Radiology, Heidelberg University Hospital, Germany; Department of Neurology (J.M.H.), University of Michigan, Ann Arbor; Medical Faculty (M.J.), University of Tübingen; and German Cancer Consortium (DKTK) within the German Cancer Research Center (DKFZ) (W.W.), Heidelberg, Germany.
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AAV9 Vector: a Novel modality in gene therapy for spinal muscular atrophy. Gene Ther 2019; 26:287-295. [PMID: 31243392 DOI: 10.1038/s41434-019-0085-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 05/03/2019] [Accepted: 05/20/2019] [Indexed: 12/30/2022]
Abstract
Spinal muscular atrophy (SMA), the leading genetic cause of infant mortality, is characterized by the deterioration of alpha motor neurons in the brainstem and spinal cord. Currently, there is no cure for SMA, which calls for an urgent need to explore affordable and effective therapies and to maximize patients' independence and quality of life. Adeno-associated virus (AAV) vector, one of the most promising and well-investigated vehicles for delivering transgenes, is a compelling candidate for gene therapy. Some of the hallmarks of AAVs are their nonpathogenicity, inability to incur an immune response, potential to achieve robust transgene expression, and varied tropism for several tissues of the body. Recently, these features were harnessed in a clinical trial conducted by AveXis in SMA patients, where AAV9 was employed as a vehicle for one-time administration of the SMN gene, the causative gene in SMA. The trial demonstrated remarkable improvements in motor milestones and rates of survival in the patients. This review focuses on the advent of SMA gene therapy and summarizes different preclinical studies that were conducted leading up to the AAV9-SMA trial in SMA patients.
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36
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Carrier screening for spinal muscular atrophy with a simple test based on melting analysis. J Hum Genet 2019; 64:387-396. [DOI: 10.1038/s10038-019-0576-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/04/2019] [Accepted: 01/30/2019] [Indexed: 11/08/2022]
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Impaired myogenic development, differentiation and function in hESC-derived SMA myoblasts and myotubes. PLoS One 2018; 13:e0205589. [PMID: 30304024 PMCID: PMC6179271 DOI: 10.1371/journal.pone.0205589] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/27/2018] [Indexed: 12/11/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a severe genetic disorder that manifests in progressive neuromuscular degeneration. SMA originates from loss-of-function mutations of the SMN1 (Survival of Motor Neuron 1) gene. Recent evidence has implicated peripheral deficits, especially in skeletal muscle, as key contributors to disease progression in SMA. In this study we generated myogenic cells from two SMA-affected human embryonic stem cell (hESC) lines with deletion of SMN1 bearing two copies of the SMN2 gene and recapitulating the molecular phenotype of Type 1 SMA. We characterized myoblasts and myotubes by comparing them to two unaffected, control hESC lines and demonstrate that SMA myoblasts and myotubes showed altered expression of various myogenic markers, which translated into an impaired in vitro myogenic maturation and development process. Additionally, we provide evidence that these SMN1 deficient cells display functional deficits in cholinergic calcium signaling response, glycolysis and oxidative phosphorylation. Our data describe a novel human myogenic SMA model that might be used for interrogating the effect of SMN depletion during skeletal muscle development, and as model to investigate biological mechanisms targeting myogenic differentiation, mitochondrial respiration and calcium signaling processes in SMA muscle cells.
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Ziemka-Nalecz M, Jaworska J, Sypecka J, Zalewska T. Histone Deacetylase Inhibitors: A Therapeutic Key in Neurological Disorders? J Neuropathol Exp Neurol 2018; 77:855-870. [DOI: 10.1093/jnen/nly073] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Malgorzata Ziemka-Nalecz
- NeuroRepair Department, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Jaworska
- NeuroRepair Department, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Sypecka
- NeuroRepair Department, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
| | - Teresa Zalewska
- NeuroRepair Department, Mossakowski Medical Research Centre, Polish Academy of Sciences, Warsaw, Poland
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Correlation between SMA type and SMN2 copy number revisited: An analysis of 625 unrelated Spanish patients and a compilation of 2834 reported cases. Neuromuscul Disord 2018; 28:208-215. [PMID: 29433793 DOI: 10.1016/j.nmd.2018.01.003] [Citation(s) in RCA: 247] [Impact Index Per Article: 41.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 11/30/2017] [Accepted: 01/07/2018] [Indexed: 01/01/2023]
Abstract
Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by loss or mutations in SMN1. According to age of onset, achieved motor abilities, and life span, SMA patients are classified into type I (never sit), II (never walk unaided) or III (achieve independent walking abilities). SMN2, the highly homologous copy of SMN1, is considered the most important phenotypic modifier of the disease. Determination of SMN2 copy number is essential to establish careful genotype-phenotype correlations, predict disease evolution, and to stratify patients for clinical trials. We have determined SMN2 copy numbers in 625 unrelated Spanish SMA patients with loss or mutation of both copies of SMN1 and a clear assignation of the SMA type by clinical criteria. Furthermore, we compiled data from relevant worldwide reports that link SMN2 copy number with SMA severity published from 1999 to date (2834 patients with different ethnic and geographic backgrounds). Altogether, we have assembled a database with a total of 3459 patients to delineate more universal prognostic rules regarding the influence of SMN2 copy number on SMA phenotype. This issue is crucial in the present scenario of therapeutic advances with the perspective of SMA neonatal screening and early diagnosis to initiate treatments.
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40
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The effects of C5-substituted 2,4-diaminoquinazolines on selected transcript expression in spinal muscular atrophy cells. PLoS One 2017; 12:e0180657. [PMID: 28662219 PMCID: PMC5491266 DOI: 10.1371/journal.pone.0180657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/19/2017] [Indexed: 02/03/2023] Open
Abstract
C5-substituted 2,4-diaminoquinazolines (2,4-DAQs) ameliorate disease severity in SMA mice. It is uncertain, however, that these compounds increase SMN protein levels in vivo even though they were identified as activators of the SMN2 promoter. These compounds also regulate the expression of other transcripts in neuroblastoma cells. In this study, we investigate the mechanism by which the 2,4-DAQs regulate the expression of SMN2 as well as other targets. D156844, D158872, D157161 and D157495 (RG3039) increased SMN2 promoter-driven reporter gene activity by at least 3-fold in NSC-34 cells. These compounds, however, did not significantly increase SMN2 mRNA levels in type II SMA fibroblasts nor in NSC-34 cells, although there was a trend for these compounds increasing SMN protein in SMA fibroblasts. The number of SMN-containing gems was increased in SMA fibroblasts in response to 2,4-DAQ treatment in a dose-dependent manner. ATOH7 mRNA levels were significantly lower in type II SMA fibroblasts. 2,4-DAQs significantly increased ATOH7, DRNT1 and DRTN2 transcript levels in type II SMA fibroblasts and restored ATOH7 levels to those observed in healthy fibroblasts. These compounds also increase Atoh7 mRNA expression in NSC-34 cells. In conclusion, 2,4-DAQs regulate SMN2 by increasing protein levels and gem localization. They also increase ATOH7, DRNT1 and DRNT2 transcript levels. This study reveals that the protective effects of 2,4-DAQs in SMA may be independent of SMN2 gene regulation. These compounds could be used in concert with a proven SMN2 inducer to develop a multi-faceted approach to treating SMA.
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Stabley DL, Holbrook J, Harris AW, Swoboda KJ, Crawford TO, Sol-Church K, Butchbach MER. Establishing a reference dataset for the authentication of spinal muscular atrophy cell lines using STR profiling and digital PCR. Neuromuscul Disord 2017; 27:439-446. [PMID: 28284873 PMCID: PMC5403612 DOI: 10.1016/j.nmd.2017.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/23/2017] [Accepted: 02/03/2017] [Indexed: 12/31/2022]
Abstract
Fibroblasts and lymphoblastoid cell lines (LCLs) derived from individuals with spinal muscular atrophy (SMA) have been and continue to be essential for translational SMA research. Authentication of cell lines helps ensure reproducibility and rigor in biomedical research. This quality control measure identifies mislabeling or cross-contamination of cell lines and prevents misinterpretation of data. Unfortunately, authentication of SMA cell lines used in various studies has not been possible because of a lack of a reference. In this study, we provide said reference so that SMA cell lines can be subsequently authenticated. We use short tandem repeat (STR) profiling and digital PCR (dPCR), which quantifies SMN1 and SMN2 copy numbers, to generate molecular identity codes for fibroblasts and LCLs that are commonly used in SMA research. Using these molecular identity codes, we clarify the familial relationships within a set of fibroblasts commonly used in SMA research. This study presents the first cell line reference set for the SMA research community and demonstrates its usefulness for re-identification and authentication of lines commonly used as in vitro models for future studies.
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Affiliation(s)
- Deborah L Stabley
- Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Jennifer Holbrook
- Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Ashlee W Harris
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Kathryn J Swoboda
- Neurogenetics Research Program, Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA, USA
| | - Thomas O Crawford
- Department of Neurology, Johns Hopkins University, Baltimore, MD, USA; Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
| | - Katia Sol-Church
- Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA
| | - Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA.
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Santos C, Duarte S, Tedesco S, Fevereiro P, Costa RL. Expression Profiling of Castanea Genes during Resistant and Susceptible Interactions with the Oomycete Pathogen Phytophthora cinnamomi Reveal Possible Mechanisms of Immunity. FRONTIERS IN PLANT SCIENCE 2017; 8:515. [PMID: 28443110 PMCID: PMC5387079 DOI: 10.3389/fpls.2017.00515] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/23/2017] [Indexed: 05/28/2023]
Abstract
The most dangerous pathogen affecting the production of chestnuts is Phytophthora cinnamomi a hemibiotrophic that causes root rot, also known as ink disease. Little information has been acquired in chestnut on the molecular defense strategies against this pathogen. The expression of eight candidate genes potentially involved in the defense to P. cinnamomi was quantified by digital PCR in Castanea genotypes showing different susceptibility to the pathogen. Seven of the eight candidate genes displayed differentially expressed levels depending on genotype and time-point after inoculation. Cast_Gnk2-like revealed to be the most expressed gene across all experiments and the one that best discriminates between susceptible and resistant genotypes. Our data suggest that the pre-formed defenses are crucial for the resistance of C. crenata to P. cinnamomi. A lower and delayed expression of the eight studied genes was found in the susceptible Castanea sativa, which may be related with the establishment and spread of the disease in this species. A working model integrating the obtained results is presented.
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Affiliation(s)
- Carmen Santos
- Molecular Biology Lab, Instituto Nacional de Investigação Agrária e Veterinária, I.P.Oeiras, Portugal
- Plant Cell Biotechnology Lab, Instituto de Tecnologia Química e Biológica António Xavier (Green-it Unit), Universidade Nova de LisboaOeiras, Portugal
| | - Sofia Duarte
- Molecular Biology Lab, Instituto Nacional de Investigação Agrária e Veterinária, I.P.Oeiras, Portugal
| | - Sara Tedesco
- Molecular Biology Lab, Instituto Nacional de Investigação Agrária e Veterinária, I.P.Oeiras, Portugal
| | - Pedro Fevereiro
- Plant Cell Biotechnology Lab, Instituto de Tecnologia Química e Biológica António Xavier (Green-it Unit), Universidade Nova de LisboaOeiras, Portugal
- Departamento Biologia Vegetal, Faculdade de Ciências da Universidade de LisboaCampo Grande, Portugal
| | - Rita L. Costa
- Molecular Biology Lab, Instituto Nacional de Investigação Agrária e Veterinária, I.P.Oeiras, Portugal
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa - Tapada da AjudaLisboa, Portugal
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Cao L, Cui X, Hu J, Li Z, Choi JR, Yang Q, Lin M, Ying Hui L, Xu F. Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications. Biosens Bioelectron 2016; 90:459-474. [PMID: 27818047 DOI: 10.1016/j.bios.2016.09.082] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/18/2022]
Abstract
Since the invention of polymerase chain reaction (PCR) in 1985, PCR has played a significant role in molecular diagnostics for genetic diseases, pathogens, oncogenes and forensic identification. In the past three decades, PCR has evolved from end-point PCR, through real-time PCR, to its current version, which is the absolute quantitive digital PCR (dPCR). In this review, we first discuss the principles of all key steps of dPCR, i.e., sample dispersion, amplification, and quantification, covering commercialized apparatuses and other devices still under lab development. We highlight the advantages and disadvantages of different technologies based on these steps, and discuss the emerging biomedical applications of dPCR. Finally, we provide a glimpse of the existing challenges and future perspectives for dPCR.
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Affiliation(s)
- Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Xingye Cui
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Jie Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Jane Ru Choi
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Qingzhen Yang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Min Lin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Li Ying Hui
- Foundation of State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing 100094, PR China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
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Liu Z, Zhang P, He X, Liu S, Tang S, Zhang R, Wang X, Tan J, Peng B, Jiang L, Hong S, Zou L. New multiplex real-time PCR approach to detect gene mutations for spinal muscular atrophy. BMC Neurol 2016; 16:141. [PMID: 27534852 PMCID: PMC4989483 DOI: 10.1186/s12883-016-0651-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/29/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is the most common autosomal recessive disease in children, and the diagnosis is complicated and difficult, especially at early stage. Early diagnosis of SMA is able to improve the outcome of SMA patients. In our study, Real-time PCR was developed to measure the gene mutation or deletion of key genes for SMA and to further analyse genotype-phenotype correlation. METHODS The multiple real-time PCR for detecting the mutations of survival of motor neuron (SMN), apoptosis inhibitory protein (NAIP) and general transcription factor IIH, polypeptide 2 gene (GTF2H2) was established and confirmed by DNA sequencing and multiplex ligation-dependent probe amplification (MLPA). The diagnosis and prognosis of 141 hospitalized children, 100 normal children and further 2000 cases of dry blood spot (DBS) samples were analysed by this multiple real-time PCR. RESULTS The multiple real-time PCR was established and the accuracy of it to detect the mutations of SMN, NAIP and GTF2H2 was at least 98.8 % comparing with DNA sequencing and MLPA. Among 141 limb movement disorders children, 75 cases were SMA. 71 cases of SMA (94.67 %) were with SMN c.840 mutation, 9 cases (12 %) with NAIP deletion and 3 cases (4 %) with GTF2H2 deletion. The multiple real-time PCR was able to diagnose and predict the prognosis of SMA patients. Simultaneously, the real-time PCR was applied to detect trace DNA from DBS and able to make an early diagnosis of SMA. CONCLUSION The clinical and molecular characteristics of SMA in Southwest of China were presented. Our work provides a novel way for detecting SMA in children by using real-time PCR and the potential usage in newborn screening for early diagnosis of SMA.
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Affiliation(s)
- Zhidai Liu
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Penghui Zhang
- Center for Clinical Laboratory, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Xiaoyan He
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Shan Liu
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Shi Tang
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Rong Zhang
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Xinbin Wang
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Junjie Tan
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Bin Peng
- Department of Health Statistics, School of Public Health, Chongqing Medical University, Yuzhong District, Chongqing, China
| | - Li Jiang
- Department of Neurology, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Siqi Hong
- Department of Neurology, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China
| | - Lin Zou
- Center for Clinical Molecular Medicine, Children's Hospital, Chongqing Medical University, 136 Zhongshan Er Road, Yuzhong District, Chongqing, 400014, China. .,Ministry of Education Key Laboratory of Development and Disorders, Children's Hospital, Chongqing Medical University, Yuzhong District, Chongqing, China. .,Key Laboratory of Pediatrics in Chongqing, Children's Hospital, Chongqing Medical University, Chongqing, China.
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Butchbach MER. Applicability of digital PCR to the investigation of pediatric-onset genetic disorders. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:9-14. [PMID: 27990344 PMCID: PMC5154671 DOI: 10.1016/j.bdq.2016.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/08/2016] [Accepted: 06/21/2016] [Indexed: 12/12/2022]
Abstract
Early-onset rare diseases have a strong impact on child healthcare even though the incidence of each of these diseases is relatively low. In order to better manage the care of these children, it is imperative to quickly diagnose the molecular bases for these disorders as well as to develop technologies with prognostic potential. Digital PCR (dPCR) is well suited for this role by providing an absolute quantification of the target DNA within a sample. This review illustrates how dPCR can be used to identify genes associated with pediatric-onset disorders, to identify copy number status of important disease-causing genes and variants and to quantify modifier genes. It is also a powerful technology to track changes in genomic biomarkers with disease progression. Based on its capability to accurately and reliably detect genomic alterations with high sensitivity and a large dynamic detection range, dPCR has the potential to become the tool of choice for the verification of pediatric disease-associated mutations identified by next generation sequencing, copy number determination and noninvasive prenatal screening.
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Affiliation(s)
- Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA
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Butchbach MER, Lumpkin CJ, Harris AW, Saieva L, Edwards JD, Workman E, Simard LR, Pellizzoni L, Burghes AHM. Protective effects of butyrate-based compounds on a mouse model for spinal muscular atrophy. Exp Neurol 2016; 279:13-26. [PMID: 26892876 PMCID: PMC4834225 DOI: 10.1016/j.expneurol.2016.02.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/11/2016] [Accepted: 02/13/2016] [Indexed: 11/17/2022]
Abstract
Proximal spinal muscular atrophy (SMA) is a childhood-onset degenerative disease resulting from the selective loss of motor neurons in the spinal cord. SMA is caused by the loss of SMN1 (survival motor neuron 1) but retention of SMN2. The number of copies of SMN2 modifies disease severity in SMA patients as well as in mouse models, making SMN2 a target for therapeutics development. Sodium butyrate (BA) and its analog (4PBA) have been shown to increase SMN2 expression in SMA cultured cells. In this study, we examined the effects of BA, 4PBA as well as two BA prodrugs-glyceryl tributyrate (BA3G) and VX563-on the phenotype of SMNΔ7 SMA mice. Treatment with 4PBA, BA3G and VX563 but not BA beginning at PND04 significantly improved the lifespan and delayed disease end stage, with administration of VX563 also improving the growth rate of these mice. 4PBA and VX563 improved the motor phenotype of SMNΔ7 SMA mice and prevented spinal motor neuron loss. Interestingly, neither 4PBA nor VX563 had an effect on SMN expression in the spinal cords of treated SMNΔ7 SMA mice; however, they inhibited histone deacetylase (HDAC) activity and restored the normal phosphorylation states of Akt and glycogen synthase kinase 3β, both of which are altered by SMN deficiency in vivo. These observations show that BA-based compounds with favorable pharmacokinetics ameliorate SMA pathology possibly by modulating HDAC and Akt signaling.
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Affiliation(s)
- Matthew E R Butchbach
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Department of Pediatrics, Thomas Jefferson University, Philadelphia, PA, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA.
| | - Casey J Lumpkin
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Ashlee W Harris
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for Children, Wilmington, DE, USA
| | - Luciano Saieva
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Jonathan D Edwards
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Eileen Workman
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Louise R Simard
- Department of Biochemistry and Medical Genetics, University of Manitoba Faculty of Health Sciences, Winnipeg, Manitoba, Canada
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Arthur H M Burghes
- Department of Biological Chemistry and Pharmacology, The Ohio State University Wexner Medical Center, Columbus, OH, USA; Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, USA.
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Butchbach MER. Copy Number Variations in the Survival Motor Neuron Genes: Implications for Spinal Muscular Atrophy and Other Neurodegenerative Diseases. Front Mol Biosci 2016; 3:7. [PMID: 27014701 PMCID: PMC4785180 DOI: 10.3389/fmolb.2016.00007] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/25/2016] [Indexed: 12/11/2022] Open
Abstract
Proximal spinal muscular atrophy (SMA), a leading genetic cause of infant death worldwide, is an early-onset, autosomal recessive neurodegenerative disease characterized by the loss of spinal α-motor neurons. This loss of α-motor neurons is associated with muscle weakness and atrophy. SMA can be classified into five clinical grades based on age of onset and severity of the disease. Regardless of clinical grade, proximal SMA results from the loss or mutation of SMN1 (survival motor neuron 1) on chromosome 5q13. In humans a large tandem chromosomal duplication has lead to a second copy of the SMN gene locus known as SMN2. SMN2 is distinguishable from SMN1 by a single nucleotide difference that disrupts an exonic splice enhancer in exon 7. As a result, most of SMN2 mRNAs lack exon 7 (SMNΔ7) and produce a protein that is both unstable and less than fully functional. Although only 10–20% of the SMN2 gene product is fully functional, increased genomic copies of SMN2 inversely correlates with disease severity among individuals with SMA. Because SMN2 copy number influences disease severity in SMA, there is prognostic value in accurate measurement of SMN2 copy number from patients being evaluated for SMA. This prognostic value is especially important given that SMN2 copy number is now being used as an inclusion criterion for SMA clinical trials. In addition to SMA, copy number variations (CNVs) in the SMN genes can affect the clinical severity of other neurological disorders including amyotrophic lateral sclerosis (ALS) and progressive muscular atrophy (PMA). This review will discuss how SMN1 and SMN2 CNVs are detected and why accurate measurement of SMN1 and SMN2 copy numbers is relevant for SMA and other neurodegenerative diseases.
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Affiliation(s)
- Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, DE, USA; Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, DE, USA; Department of Biological Sciences, University of DelawareNewark, DE, USA; Department of Pediatrics, Thomas Jefferson UniversityPhiladelphia, PA, USA
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