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Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
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2
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Kiselev A, Maretina M, Shtykalova S, Al-Hilal H, Maslyanyuk N, Plokhih M, Serebryakova E, Frolova M, Shved N, Krylova N, Il’ina A, Freund S, Osinovskaya N, Sultanov I, Egorova A, Lobenskaya A, Koroteev A, Sosnina I, Gorelik Y, Bespalova O, Baranov V, Kogan I, Glotov A. Establishment of a Pilot Newborn Screening Program for Spinal Muscular Atrophy in Saint Petersburg. Int J Neonatal Screen 2024; 10:9. [PMID: 38390973 PMCID: PMC10885106 DOI: 10.3390/ijns10010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Spinal muscular atrophy 5q (SMA) is one of the most common neuromuscular inherited diseases and is the most common genetic cause of infant mortality. SMA is associated with homozygous deletion of exon 7 in the SMN1 gene. Recently developed drugs can improve the motor functions of infants with SMA when they are treated in the pre-symptomatic stage. With aim of providing an early diagnosis, newborn screening (NBS) for SMA using a real-time PCR assay with dried blood spots (DBS) was performed from January 2022 through November 2022 in Saint Petersburg, which is a representative Russian megapolis. Here, 36,140 newborns were screened by the GenomeX real-time PCR-based screening test, and three genotypes were identified: homozygous deletion carriers (4 newborns), heterozygous carriers (772 newborns), and wild-type individuals (35,364 newborns). The disease status of all four newborns that screened positive for the homozygous SMN1 deletion was confirmed by alternate methods. Two of the newborns had two copies of SMN2, and two of the newborns had three copies. We determined the incidence of spinal muscular atrophy in Saint Petersburg to be 1 in 9035 and the SMA carrier frequency to be 1 in 47. In conclusion, providing timely information regarding SMN1, confirmation of disease status, and SMN2 copy number as part of the SMA newborn-screening algorithm can significantly improve clinical follow-up, testing of family members, and treatment of patients with SMA.
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Affiliation(s)
- Anton Kiselev
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Marianna Maretina
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Sofia Shtykalova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Haya Al-Hilal
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Natalia Maslyanyuk
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Mariya Plokhih
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Elena Serebryakova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Marina Frolova
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Natalia Shved
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Nadezhda Krylova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Arina Il’ina
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Svetlana Freund
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Natalia Osinovskaya
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Iskender Sultanov
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Anna Egorova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Anastasia Lobenskaya
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Alexander Koroteev
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Irina Sosnina
- Saint Petersburg State Budgetary Healthcare Institution “Consulting and Diagnostic Center for Children”, Aleksa Dundić Street 36/2, 192289 Saint Petersburg, Russia;
| | - Yulia Gorelik
- Children’s City Multidisciplinary Clinical Specialized Center of High Medical Technologies, Avangardnaya Street 14, 198205 Saint Petersburg, Russia;
| | - Olesya Bespalova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Vladislav Baranov
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Igor Kogan
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Andrey Glotov
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
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3
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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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4
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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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5
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Kianifard L, Rafiqi AM, Akcakir O, Aly ASI, Billingsley PF, Uysal S. A recombinant Aspergillus oryzae fungus transmitted from larvae to adults of Anopheles stephensi mosquitoes inhibits malaria parasite oocyst development. Sci Rep 2023; 13:12177. [PMID: 37500682 PMCID: PMC10374630 DOI: 10.1038/s41598-023-38654-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
The control of malaria parasite transmission from mosquitoes to humans is hampered by decreasing efficacies of insecticides, development of drug resistance against the last-resort antimalarials, and the absence of effective vaccines. Herein, the anti-plasmodial transmission blocking activity of a recombinant Aspergillus oryzae (A. oryzae-R) fungus strain, which is used in human food industry, was investigated in laboratory-reared Anopheles stephensi mosquitoes. The recombinant fungus strain was genetically modified to secrete two anti-plasmodial effector peptides, MP2 (midgut peptide 2) and EPIP (enolase-plasminogen interaction peptide) peptides. The transstadial transmission of the fungus from larvae to adult mosquitoes was confirmed following inoculation of A. oryzae-R in the water trays used for larval rearing. Secretion of the anti-plasmodial effector peptides inside the mosquito midguts inhibited oocyst formation of P. berghei parasites. These results indicate that A. oryzae can be used as a paratransgenesis model carrying effector proteins to inhibit malaria parasite development in An. stephensi. Further studies are needed to determine if this recombinant fungus can be adapted under natural conditions, with a minimal or no impact on the environment, to target mosquito-borne infectious disease agents inside their vectors.
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Affiliation(s)
- Leila Kianifard
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820, Istanbul, Turkey
| | - Ab Matteen Rafiqi
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820, Istanbul, Turkey
| | - Osman Akcakir
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820, Istanbul, Turkey
| | - Ahmed S I Aly
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820, Istanbul, Turkey
- School of Science and Engineering, Al Akhawayn University, Ifrane, 53000, Morocco
| | - Peter F Billingsley
- Sanaria Inc., 9800 Medical Center Dr., Suite A209, Rockville, MD, 20850, USA
| | - Serdar Uysal
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, 34820, Istanbul, Turkey.
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6
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Rey F, Berardo C, Maghraby E, Mauri A, Messa L, Esposito L, Casili G, Ottolenghi S, Bonaventura E, Cuzzocrea S, Zuccotti G, Tonduti D, Esposito E, Paterniti I, Cereda C, Carelli S. Redox Imbalance in Neurological Disorders in Adults and Children. Antioxidants (Basel) 2023; 12:antiox12040965. [PMID: 37107340 PMCID: PMC10135575 DOI: 10.3390/antiox12040965] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/03/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Oxygen is a central molecule for numerous metabolic and cytophysiological processes, and, indeed, its imbalance can lead to numerous pathological consequences. In the human body, the brain is an aerobic organ and for this reason, it is very sensitive to oxygen equilibrium. The consequences of oxygen imbalance are especially devastating when occurring in this organ. Indeed, oxygen imbalance can lead to hypoxia, hyperoxia, protein misfolding, mitochondria dysfunction, alterations in heme metabolism and neuroinflammation. Consequently, these dysfunctions can cause numerous neurological alterations, both in the pediatric life and in the adult ages. These disorders share numerous common pathways, most of which are consequent to redox imbalance. In this review, we will focus on the dysfunctions present in neurodegenerative disorders (specifically Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis) and pediatric neurological disorders (X-adrenoleukodystrophies, spinal muscular atrophy, mucopolysaccharidoses and Pelizaeus-Merzbacher Disease), highlighting their underlining dysfunction in redox and identifying potential therapeutic strategies.
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Affiliation(s)
- Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Erika Maghraby
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Letizia Messa
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milano, Italy
| | - Letizia Esposito
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Giovanna Casili
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Sara Ottolenghi
- Department of Medicine and Surgery, University of Milano Bicocca, 20126 Milano, Italy
| | - Eleonora Bonaventura
- Child Neurology Unit, Buzzi Children's Hospital, 20154 Milano, Italy
- Center for Diagnosis and Treatment of Leukodystrophies and Genetic Leukoencephalopathies (COALA), Buzzi Children's Hospital, 20154 Milano, Italy
| | - Salvatore Cuzzocrea
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Gianvincenzo Zuccotti
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Davide Tonduti
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Child Neurology Unit, Buzzi Children's Hospital, 20154 Milano, Italy
- Center for Diagnosis and Treatment of Leukodystrophies and Genetic Leukoencephalopathies (COALA), Buzzi Children's Hospital, 20154 Milano, Italy
| | - Emanuela Esposito
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Irene Paterniti
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98166 Messina, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences, University of Milano, 20157 Milano, Italy
- Center of Functional Genomics and Rare diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milano, Italy
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7
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Tan C, Yan Y, Guo N, Wang F, Wang S, Zhu L, Wang Y, Ma Y, Guo Y. Single-Tube Multiplex Digital Polymerase Chain Reaction Assay for Molecular Diagnosis and Prediction of Severity of Spinal Muscular Atrophy. Anal Chem 2022; 94:3517-3525. [PMID: 35137581 DOI: 10.1021/acs.analchem.1c04403] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disease characterized by the degeneration of motor neurons and progressive muscle atrophy. Accurate detection of SMN1 and SMN2 copy numbers is essential for SMA diagnosis, carrier screening, disease severity prediction, therapy, and prognosis. However, a method for SMN1 and SMN2 copy number determination that is simultaneously accurate, simple, rapid, multitargeted, and applicable to various samples has not previously been reported. Here, we developed a single-tube multiplex digital polymerase chain reaction (dPCR) assay for simultaneous determination of the copy numbers of SMN1 exons 7 and 8 and SMN2 exons 7 and 8. A total of 317 clinical samples, including peripheral blood, amniotic fluid, chorionic villus, buccal swabs, and dried blood spots, were collected to evaluate the performance of this dPCR-based assay. The test results were accurate for all the clinical samples. Our assay is accurate, rapid, easy to handle, and applicable to many types of samples and uses a small amount of DNA; it is a powerful tool for SMA molecular diagnosis, large-scale screening, and disease severity assessment.
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Affiliation(s)
- Chianru Tan
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Na Guo
- TargetingOne Corporation, Beijing 100190, China
| | - Fang Wang
- TargetingOne Corporation, Beijing 100190, China
| | - Songtao Wang
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | | | - Yipeng Wang
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing 100026, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
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8
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Sicko RJ, Romitti PA, Browne ML, Brody LC, Stevens CF, Mills JL, Caggana M, Kay DM. Rare Variants in RPPH1 Real-Time Quantitative PCR Control Assay Binding Sites Result in Incorrect Copy Number Calls. J Mol Diagn 2022; 24:33-40. [PMID: 34656763 PMCID: PMC8802765 DOI: 10.1016/j.jmoldx.2021.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/21/2021] [Accepted: 09/15/2021] [Indexed: 01/03/2023] Open
Abstract
Real-time quantitative PCR (qPCR) using RPPH1 as a reference gene is a standard method for assessment and validation of genomic copy number variations. However, variants in the reference amplicon may cause errors, which was investigated herein. While conducting copy number variation validations for birth defects research studies, 13 of 1634 specimens with multiple loci that appeared to be present as three copies were unexpectedly detected. This apparent trisomy was hypothesized to be an amplification artifact caused by a variant in the RPPH1 amplicon. Sequencing revealed all 13 individuals carried one of the four different variants within the RPPH1 amplicon. These variants could produce allelic dropout or altered reaction efficiency, causing an inaccurate measurement of copy number. Additional genotyping predicted a low frequency of the most common variant (rs3093876; 14/3562 alleles; minor allele frequency, 0.39%). Laboratories should recognize the potential for inaccurate results when using a single qPCR control assay. Overestimated CFTR and SMN2 copy numbers identified during newborn screening that otherwise would have been incorrectly called were also detected. Variants in reference loci may produce false-negative normal results for test loci when real deletions are present. For clinical laboratories screening for heterozygous deletions for diagnostic testing or prenatal/carrier screening via qPCR, the most cost-effective solution to maximize sensitivity is to run triplex reactions targeting the region of interest with two control genes.
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Affiliation(s)
- Robert J Sicko
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, The University of Iowa, Iowa City, Iowa
| | - Marilyn L Browne
- Birth Defects Registry, New York State Department of Health, Albany, New York; University at Albany School of Public Health, Rensselaer, New York
| | - Lawrence C Brody
- Genetics and Environment Interaction Section, National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Colleen F Stevens
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - James L Mills
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Michele Caggana
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Denise M Kay
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, New York.
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9
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Romanelli Tavares VL, Monfardini F, Lourenço NCV, da Rocha KM, Weinmann K, Pavanello R, Zatz M. Newborn Screening for 5q Spinal Muscular Atrophy: Comparisons between Real-Time PCR Methodologies and Cost Estimations for Future Implementation Programs. Int J Neonatal Screen 2021; 7:ijns7030053. [PMID: 34449526 PMCID: PMC8396021 DOI: 10.3390/ijns7030053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/15/2021] [Accepted: 08/05/2021] [Indexed: 01/09/2023] Open
Abstract
Since the approval of modifying therapies for Spinal Muscular Atrophy (SMA), several protocols aiming to screen SMN1 homozygous deletion in a neonatal context have been published. However, no work has compared different methodologies along with detailed implementation costs for centers where the neonatal screening of SMA has not yet been implemented. Therefore, our work compared different qualitative real-time PCR approaches for SMA screening and the estimated costs of test implementation. Using Brazilian blood samples, the presence and absence (P/A) and melt curve protocols were analyzed. MLPA was used as a confirmatory test. The costs were calculated for the simplex and multiplex tests plus equipment. The test workflow was based on the present experience and literature report. The accuracy of the P/A protocol was 1 (95% CI 0.8677-1) using dried blood spots (DBS). The melt curve protocol also achieved 100% concordance. The consumable costs ranged from USD 1.68 to 4.42 and from USD 2.04 to 12.76 per reaction, for the simplex and multiplex tests, respectively. The equipment acquisition costs ranged from USD 44,817.07 to 467,253.10, with several factors influencing this value presented. Our work presents a framework for decision-making, with a project demonstration of the different assays that will be useful in dealing with the issues of cost and availability of reagents. Moreover, we present a literature review and discussion of important concerns regarding treatment policies. We take the first step towards a future SMA NBS pilot program where it is not yet a reality.
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10
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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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11
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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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12
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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: 34] [Impact Index Per Article: 8.5] [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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13
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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: 25] [Impact Index Per Article: 6.3] [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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14
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Wijaya YOS, Purevsuren J, Harahap NIF, Niba ETE, Bouike Y, Nurputra DK, Rochmah MA, Thursina C, Hapsara S, Yamaguchi S, Nishio H, Shinohara M. Assessment of Spinal Muscular Atrophy Carrier Status by Determining SMN1 Copy Number Using Dried Blood Spots. Int J Neonatal Screen 2020; 6:43. [PMID: 33073034 PMCID: PMC7423012 DOI: 10.3390/ijns6020043] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 05/27/2020] [Indexed: 01/16/2023] Open
Abstract
Spinal muscular atrophy (SMA) is a common neuromuscular disease with autosomal recessive inheritance. The disease gene, SMN1, is homozygously deleted in 95% of SMA patients. Although SMA has been an incurable disease, treatment in infancy with newly developed drugs has dramatically improved the disease severity. Thus, there is a strong rationale for newborn and carrier screening for SMA, although implementing SMA carrier screening in the general population is controversial. We previously developed a simple, accurate newborn SMA screening system to detect homozygous SMN1 deletions using dried blood spots (DBS) on filter paper. Here, we modified our previous system to detect the heterozygous deletions of SMN1, which indicates SMA carrier status. The system involves a calibrator-normalized relative quantification method using quantitative nested PCR technology. Our system clearly separated the DBS samples with one SMN1 copy (carrier status with a heterozygous deletion of SMN1) from the DBS samples with two SMN1 copies (non-carrier status with no deletion of SMN1). We also analyzed DBS samples from SMA families, confirmed SMA in the affected children, and determined the carrier status of their parents based on the SMN1 copy number. In conclusion, our system will provide essential information for risk assessment and genetic counseling, at least for SMA families.
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Affiliation(s)
- Yogik Onky Silvana Wijaya
- Department of Community Medicine and Social Healthcare Science, Division of Epidemiology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.O.S.W.); (E.T.E.N.); (M.S.)
| | - Jamiyan Purevsuren
- Medical Genetics Laboratory, National Center for Maternal and Child Health, Khuvisgalchdyn Street, Bayangol District, Ulaanbaatar 16060, Mongolia;
| | - Nur Imma Fatimah Harahap
- Department of Clinical Pathology and Laboratory Medicine, Faculty of Medicine, Universitas Gadjah Mada, Radiopoetro Building 5th floor, Jl. Farmako, Sekip Utara, Yogyakarta 55281, Indonesia;
| | - Emma Tabe Eko Niba
- Department of Community Medicine and Social Healthcare Science, Division of Epidemiology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.O.S.W.); (E.T.E.N.); (M.S.)
| | - Yoshihiro Bouike
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan;
| | - Dian Kesumapramudya Nurputra
- Department of Pediatrics, Faculty of Medicine, Universitas Gadjah Mada, Jl. Kesehatan No.1, Sekip, Yogyakarta 55281, Indonesia; (D.K.N.); (S.H.)
| | - Mawaddah Ar Rochmah
- Department of Neurology, Faculty of Medicine, Universitas Gadjah Mada, Jl. Kesehatan No.1, Sekip, Yogyakarta 55281, Indonesia; (M.A.R.); (C.T.)
| | - Cempaka Thursina
- Department of Neurology, Faculty of Medicine, Universitas Gadjah Mada, Jl. Kesehatan No.1, Sekip, Yogyakarta 55281, Indonesia; (M.A.R.); (C.T.)
| | - Sunartini Hapsara
- Department of Pediatrics, Faculty of Medicine, Universitas Gadjah Mada, Jl. Kesehatan No.1, Sekip, Yogyakarta 55281, Indonesia; (D.K.N.); (S.H.)
| | - Seiji Yamaguchi
- Department of Pediatrics, Shimane University School of Medicine, 89-1 Enya, Izumo, Shimane 693-8501, Japan;
| | - Hisahide Nishio
- Department of Community Medicine and Social Healthcare Science, Division of Epidemiology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.O.S.W.); (E.T.E.N.); (M.S.)
- Faculty of Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe 651-2180, Japan
| | - Masakazu Shinohara
- Department of Community Medicine and Social Healthcare Science, Division of Epidemiology, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (Y.O.S.W.); (E.T.E.N.); (M.S.)
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15
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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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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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17
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Nery FC, Siranosian JJ, Rosales I, Deguise MO, Sharma A, Muhtaseb AW, Nwe P, Johnstone AJ, Zhang R, Fatouraei M, Huemer N, Alves CRR, Kothary R, Swoboda KJ. Impaired kidney structure and function in spinal muscular atrophy. NEUROLOGY-GENETICS 2019; 5:e353. [PMID: 31517062 PMCID: PMC6705648 DOI: 10.1212/nxg.0000000000000353] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/25/2019] [Indexed: 01/24/2023]
Abstract
Objective To determine changes in serum profiles and kidney tissues from patients with spinal muscular atrophy (SMA) type 1 compared with age- and sex-matched controls. Methods In this cohort study, we investigated renal structure and function in infants and children with SMA type 1 in comparison with age- and sex-matched controls. Results Patients with SMA had alterations in serum creatinine, cystatin C, sodium, glucose, and calcium concentrations, granular casts and crystals in urine, and nephrocalcinosis and fibrosis. Nephrotoxicity and polycystic kidney disease PCR arrays revealed multiple differentially expressed genes, and immunoblot analysis showed decreased calcium-sensing receptors and calbindin and increased insulin-like growth factor-binding proteins in kidneys from patients with SMA. Conclusions These findings demonstrate that patients with SMA type 1, in the absence of disease-modifying therapies, frequently manifest impaired renal function as a primary or secondary consequence of their disease. This study provides new insights into systemic contributions to SMA disease pathogenesis and the need to identify coadjuvant therapies.
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Affiliation(s)
- Flávia C Nery
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer J Siranosian
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Ivy Rosales
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Marc-Olivier Deguise
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Amita Sharma
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Abdurrahman W Muhtaseb
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Pann Nwe
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Alec J Johnstone
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Ren Zhang
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Maryam Fatouraei
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Natassja Huemer
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Christiano R R Alves
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Rashmi Kothary
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
| | - Kathryn J Swoboda
- Department of Neurology (F.C.N., J.J.S., A.W.M., P.N., A.J.J., R.Z., M.F., N.H., C.R.R.A., K.J.S.), Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Department of Pathology (I.R.), Massachusetts General Hospital, Boston, MA; Regenerative Medicine Program (M.-O.D., R.K.), Ottawa Hospital Research, Institute Ottawa, Ontario, Canada; Department of Cellular and Molecular Medicine (M.-O.D., R.K.), University of Ottawa, Canada; Centre for Neuromuscular Disease (M.-O.D., R.K.), University of Ottawa, Ottawa, Ontario, Canada; Division of Pediatric Nephrology (A.S.), Massachusetts General Hospital, Boston, MA; Department of Biology (N.H.), Federal University of São Carlos, Sorocaba, Sao Paulo, SP, Brazil; and Department of Medicine (R.K.), University of Ottawa, Ottawa, Ontario, Canada
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Ruhno C, McGovern VL, Avenarius MR, Snyder PJ, Prior TW, Nery FC, Muhtaseb A, Roggenbuck JS, Kissel JT, Sansone VA, Siranosian JJ, Johnstone AJ, Nwe PH, Zhang RZ, Swoboda KJ, Burghes AHM. Complete sequencing of the SMN2 gene in SMA patients detects SMN gene deletion junctions and variants in SMN2 that modify the SMA phenotype. Hum Genet 2019; 138:241-256. [PMID: 30788592 PMCID: PMC6503527 DOI: 10.1007/s00439-019-01983-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/14/2019] [Indexed: 12/11/2022]
Abstract
Spinal muscular atrophy (SMA) is a progressive motor neuron disease caused by loss or mutation of the survival motor neuron 1 (SMN1) gene and retention of SMN2. We performed targeted capture and sequencing of the SMN2, CFTR, and PLS3 genes in 217 SMA patients. We identified a 6.3 kilobase deletion that occurred in both SMN1 and SMN2 (SMN1/2) and removed exons 7 and 8. The deletion junction was flanked by a 21 bp repeat that occurred 15 times in the SMN1/2 gene. We screened for its presence in 466 individuals with the known SMN1 and SMN2 copy numbers. In individuals with 1 SMN1 and 0 SMN2 copies, the deletion occurred in 63% of cases. We modeled the deletion junction frequency and determined that the deletion occurred in both SMN1 and SMN2. We have identified the first deletion junction where the deletion removes exons 7 and 8 of SMN1/2. As it occurred in SMN1, it is a pathogenic mutation. We called variants in the PLS3 and SMN2 genes, and tested for association with mild or severe exception patients. The variants A-44G, A-549G, and C-1897T in intron 6 of SMN2 were significantly associated with mild exception patients, but no PLS3 variants correlated with severity. The variants occurred in 14 out of 58 of our mild exception patients, indicating that mild exception patients with an intact SMN2 gene and without modifying variants occur. This sample set can be used in the association analysis of candidate genes outside of SMN2 that modify the SMA phenotype.
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Affiliation(s)
- Corey Ruhno
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | - Vicki L McGovern
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA
| | | | - Pamela J Snyder
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Thomas W Prior
- Department of Pathology, Case Western Reserve Medical Center, Cleveland, OH, USA
| | - Flavia C Nery
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Abdurrahman Muhtaseb
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - John T Kissel
- Department of Neurology, The Ohio State University, Columbus, OH, USA
| | | | - Jennifer J Siranosian
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Alec J Johnstone
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Pann H Nwe
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ren Z Zhang
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kathryn J Swoboda
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Arthur H M Burghes
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, USA.
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Characterization and evolutionary dynamics of complex regions in eukaryotic genomes. SCIENCE CHINA-LIFE SCIENCES 2019; 62:467-488. [PMID: 30810961 DOI: 10.1007/s11427-018-9458-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/05/2018] [Indexed: 01/07/2023]
Abstract
Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless, the repetitive nature of these regions, together with the often high sequence identity among repeats, have made complex regions particularly recalcitrant to proper molecular characterization, often being misassembled or completely absent in genome assemblies. This limitation has prevented accurate functional and evolutionary analyses of these regions. This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across phyla. With the advent of long-read sequencing technologies and suitable assemblers, the development of algorithms that can accommodate sample heterozygosity, and the adoption of a pangenomic-like view of these regions, accurate reconstructions of complex regions are now within reach. These reconstructions will finally allow for accurate functional and evolutionary studies of complex genomic regions, underlying the generation of genotype-phenotype maps of unprecedented resolution.
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Pilot study of population-based newborn screening for spinal muscular atrophy in New York state. Genet Med 2017; 20:608-613. [PMID: 29758563 DOI: 10.1038/gim.2017.152] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/26/2017] [Indexed: 12/28/2022] Open
Abstract
PurposeTo determine feasibility and utility of newborn screening for spinal muscular atrophy (SMA) in New York State.MethodsWe validated a multiplex TaqMan real-time quantitative polymerase chain reaction assay using dried blood spots for SMA. From January 2016 to January 2017, we offered, consented, and screened 3,826 newborns at three hospitals in New York City and tested newborns for the deletion in exon 7 of SMN1.ResultsNinety-three percent of parents opted in for SMA screening. Overall the SMA carrier frequency was 1.5%. We identified one newborn with a homozygous SMN1 deletion and two copies of SMN2, which strongly suggests the severe type 1 SMA phenotype. The infant was enrolled in the NURTURE clinical trial and was first treated with Spinraza at age 15 days. She is now age 12 months, meeting all developmental milestones, and free of any respiratory issues.ConclusionOur pilot study demonstrates the feasibility of population-based screening, the acceptance by families, and the benefit of newborn screening for SMA. We suggest that SMA be considered for addition to the national recommended uniform screening panel.
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Verhaart IEC, Robertson A, Wilson IJ, Aartsma-Rus A, Cameron S, Jones CC, Cook SF, Lochmüller H. Prevalence, incidence and carrier frequency of 5q-linked spinal muscular atrophy - a literature review. Orphanet J Rare Dis 2017; 12:124. [PMID: 28676062 PMCID: PMC5496354 DOI: 10.1186/s13023-017-0671-8] [Citation(s) in RCA: 356] [Impact Index Per Article: 50.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/13/2017] [Indexed: 12/14/2022] Open
Abstract
Spinal muscular atrophy linked to chromosome 5q (SMA) is a recessive, progressive, neuromuscular disorder caused by bi-allelic mutations in the SMN1 gene, resulting in motor neuron degeneration and variable presentation in relation to onset and severity. A prevalence of approximately 1-2 per 100,000 persons and incidence around 1 in 10,000 live births have been estimated with SMA type I accounting for around 60% of all cases. Since SMA is a relatively rare condition, studies of its prevalence and incidence are challenging. Most published studies are outdated and therefore rely on clinical rather than genetic diagnosis. Furthermore they are performed in small cohorts in small geographical regions and only study European populations. In addition, the heterogeneity of the condition can lead to delays and difficulties in diagnosing the condition, especially outside of specialist clinics, and contributes to the challenges in understanding the epidemiology of the disease. The frequency of unaffected, heterozygous carriers of the SMN1 mutations appears to be higher among Caucasian and Asian populations compared to the Black (Sub-Saharan African ancestry) population. However, carrier frequencies cannot directly be translated into incidence and prevalence, as very severe (death in utero) and very mild (symptom free in adults) phenotypes carrying bi-allelic SMN1 mutations exist, and their frequency is unknown. More robust epidemiological data on SMA covering larger populations based on accurate genetic diagnosis or newborn screening would be helpful to support planning of clinical studies, provision of care and therapies and evaluation of outcomes.
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Affiliation(s)
- Ingrid E. C. Verhaart
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Agata Robertson
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Ian J. Wilson
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Annemieke Aartsma-Rus
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Shona Cameron
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Hanns Lochmüller
- John Walton Muscular Dystrophy Research Centre, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
- John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ UK
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Li L, Zhou WJ, Fang P, Zhong ZY, Xie JS, Yan TZ, Zeng J, Tan XH, Xu XM. Evaluation and comparison of three assays for molecular detection of spinal muscular atrophy. Clin Chem Lab Med 2017; 55:358-367. [PMID: 27754957 DOI: 10.1515/cclm-2016-0275] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/29/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is mainly caused by deletions in SMA-related genes. The objective of this study was to develop gene-dosage assays for diagnosing SMA. METHODS A multiplex, quantitative PCR assay and a CNVplex assay were developed for determining the copy number of SMN1, SMN2, and NAIP. Reproducibility and specificity of the two assays were compared to a multiple ligation-dependent probe amplification (MLPA) assay. To evaluate reproducibility, 30 samples were analyzed three times using the three assays. A total of 317 samples were used to assess the specificity of the two assays. RESULTS The multiplex quantitative PCR (qPCR) assay had higher reproducibility. Intra-assay CVs were 3.01%-8.52% and inter-assay CVs were 4.12%-6.24%. The CNVplex assay had ratios that were closer to expected (0.49-0.5 for one copy, 1.03-1.0 for two copies, and 1.50-1.50 for three copies). Diagnostic accuracy rates for the two assays were 100%. CONCLUSIONS The multiplex qPCR assay was a simple, rapid, and cost-effective method for routine SMA diagnosis and carrier screening. The CNVplex assay could be used to detect SMAs with complicated gene structures. The assays were reliable and could be used as alternative methods for clinical diagnosis of SMA.
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Lee TG, Diers BW, Hudson ME. An efficient method for measuring copy number variation applied to improvement of nematode resistance in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:143-153. [PMID: 27310152 DOI: 10.1111/tpj.13240] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 05/22/2023]
Abstract
Copy number variation (CNV) is implicated in important traits in multiple crop plants, but can be challenging to genotype using conventional methods. The Rhg1 locus of soybean, which confers resistance to soybean cyst nematode (SCN), is a CNV of multiple 31.2-kb genomic units each containing four genes. Reliable, high-throughput methods to quantify Rhg1 and other CNVs for selective breeding were developed. The CNV genotyping assay described here uses a homeologous gene copy within the paleopolyploid soybean genome to provide the internal control for a single-tube TaqMan copy number assay. Using this assay, CNV in breeding populations can be tracked with high precision. We also show that extensive CNV exists within Fayette, a released, inbred SCN-resistant soybean cultivar with a high copy number at Rhg1 derived from a single donor parent. Copy number at Rhg1 is therefore unstable within a released variety over a relatively small number of generations. Using this assay to select for individuals with altered copy number, plants were obtained with both increased copy number and increased SCN resistance relative to control plants. Thus, CNV genotyping technologies can be used as a new type of marker-assisted selection to select for desirable traits in breeding populations, and to control for undesirable variation within cultivars.
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Affiliation(s)
- Tong Geon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brian W Diers
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, 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: 110] [Impact Index Per Article: 13.8] [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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Prior TW, Nagan N. Spinal Muscular Atrophy: Overview of Molecular Diagnostic Approaches. ACTA ACUST UNITED AC 2016; 88:9.27.1-9.27.13. [PMID: 26724723 DOI: 10.1002/0471142905.hg0927s88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disease and the most common genetic cause of infant mortality, affecting ∼1 in 10,000 live births. The disease is characterized by progressive symmetrical muscle weakness resulting from the degeneration and loss of anterior horn cells in the spinal cord and brain stem nuclei. The disease is classified on the basis of age of onset and clinical course. SMA is caused by mutations in the telomeric copy of the survival motor neuron 1 (SMN1) gene, but all patients retain a centromeric copy of the gene, SMN2. The homozygous absence of the SMN1 exon 7 has been observed in the majority of patients and is being utilized as a reliable and sensitive SMA diagnostic test. In the majority of cases, the disease severity correlates inversely with an increased SMN2 gene copy number. Carrier detection, in the deletion cases, relies on the accurate determination of the SMN1 gene copies. Since SMA is one of the most common lethal genetic disorders, with a carrier frequency of 1 in 40 to 1 in 60, direct carrier dosage testing has been beneficial to many families. This unit attempts to highlight the molecular genetics of SMA with a focus on the advantages and limitations of the current molecular technologies.
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Affiliation(s)
- Thomas W Prior
- Department of Pathology, The Ohio State University, Columbus, Ohio
| | - Narasimhan Nagan
- Integrated Genetics, Laboratory Corporation of America Holdings, Westborough, Massachusetts
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Larson JL, Silver AJ, Chan D, Borroto C, Spurrier B, Silver LM. Validation of a high resolution NGS method for detecting spinal muscular atrophy carriers among phase 3 participants in the 1000 Genomes Project. BMC MEDICAL GENETICS 2015; 16:100. [PMID: 26510457 PMCID: PMC4625734 DOI: 10.1186/s12881-015-0246-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 10/22/2015] [Indexed: 11/10/2022]
Abstract
Background Spinal muscular atrophy (SMA) is the most common pan-ethnic cause of early childhood death due to mutations in a single gene, SMN1. Most chromosome 5 homologs have a functional gene and dysfunctional copy, SMN2, with a single synonymous base substitution that results in faulty RNA splicing. However, the copy number of SMN1 and SMN2 is highly variable, and one in 60 adults worldwide are SMA carriers. Although population-wide screening is recommended, current SMA carrier tests have not been incorporated into targeted gene panels. Methods Here we describe a novel computational protocol for determining SMA carrier status based solely on individual exome data. Our method utilizes a Bayesian hierarchical model to quantify an individual’s carrier probability given only his or her SMN1 and SMN2 reads at six loci of interest. Results We find complete concordance with results obtained with the current qPCR-based testing standard in known SMA carriers and affecteds. We applied our protocol to the phase 3 cohort of the 1,000 Genomes Project and found carrier frequencies in multiple populations consistent with the present literature. Conclusion Our process is a convenient, robust alternative to qPCR, which can easily be integrated into the analysis of large multi-gene NGS carrier screens. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0246-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Ari J Silver
- GenePeeks, Inc., Cambridge, MA, USA. .,GenePeeks, Inc., New York, NY, USA.
| | | | | | | | - Lee M Silver
- GenePeeks, Inc., Cambridge, MA, USA. .,GenePeeks, Inc., New York, NY, USA. .,Department of Molecular Biology and the Woodrow Wilson School of Public and International Affairs, Princeton University, Princeton, NJ, USA.
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Stabley DL, Harris AW, Holbrook J, Chubbs NJ, Lozo KW, Crawford TO, Swoboda KJ, Funanage VL, Wang W, Mackenzie W, Scavina M, Sol-Church K, Butchbach MER. SMN1 and SMN2 copy numbers in cell lines derived from patients with spinal muscular atrophy as measured by array digital PCR. Mol Genet Genomic Med 2015; 3:248-57. [PMID: 26247043 PMCID: PMC4521962 DOI: 10.1002/mgg3.141] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 02/22/2015] [Accepted: 02/26/2015] [Indexed: 11/22/2022] Open
Abstract
Proximal spinal muscular atrophy (SMA) 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 mutation of survival motor neuron 1 (SMN1). In the human genome, a large duplication of the SMN-containing region gives rise to a second copy of this gene (SMN2) that is distinguishable by a single nucleotide change in exon 7. Within the SMA population, there is substantial variation in SMN2 copy number; in general, those individuals with SMA who have a high SMN2 copy number have a milder disease. Because SMN2 functions as a disease modifier, its accurate copy number determination may have clinical relevance. In this study, we describe the development of an assay to assess SMN1 and SMN2 copy numbers in DNA samples using an array-based digital PCR (dPCR) system. This dPCR assay 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 copy number and disease severity. Array dPCR is a practical technique to determine, accurately and reliably, SMN1 and SMN2 copy numbers from SMA samples.
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Affiliation(s)
- Deborah L Stabley
- Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Ashlee W Harris
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Jennifer Holbrook
- Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Nicholas J Chubbs
- Department of Biological Sciences, University of DelawareNewark, Delaware
| | - Kevin W Lozo
- Department of Biological Sciences, University of DelawareNewark, Delaware
| | - Thomas O Crawford
- Department of Neurology, Johns Hopkins UniversityBaltimore, Maryland
- Department of Pediatrics, Johns Hopkins UniversityBaltimore, Maryland
| | - Kathryn J Swoboda
- Neurogenetics Research Program, Center for Human Genetics Research, Massachusetts General HospitalBoston, Massachusetts
| | - Vicky L Funanage
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Department of Pediatrics, Thomas Jefferson UniversityPhiladelphia, Pennsylvania
| | - Wenlan Wang
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Department of Pediatrics, Thomas Jefferson UniversityPhiladelphia, Pennsylvania
| | - William Mackenzie
- Division of Orthopedics, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Mena Scavina
- Division of Neurology, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Katia Sol-Church
- Nemours Biomolecular Core Laboratory, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
| | - Matthew E R Butchbach
- Center for Applied Clinical Genomics, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Department of Biological Sciences, University of DelawareNewark, Delaware
- Center for Pediatric Research, Nemours Biomedical Research, Nemours Alfred I. duPont Hospital for ChildrenWilmington, Delaware
- Department of Pediatrics, Thomas Jefferson UniversityPhiladelphia, Pennsylvania
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Clinical utility gene card for: Proximal spinal muscular atrophy (SMA) - update 2015. Eur J Hum Genet 2015; 23:ejhg201590. [PMID: 25990799 DOI: 10.1038/ejhg.2015.90] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 03/03/2015] [Accepted: 03/19/2015] [Indexed: 11/08/2022] Open
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Contreras-Capetillo SN, Blanco HLG, Cerda-Flores RM, Lugo-Trampe J, Torres-Muñoz I, Bravo-Oro A, Esmer C, DE Villarreal LEM. Frequency of SMN1 deletion carriers in a Mestizo population of central and northeastern Mexico: A pilot study. Exp Ther Med 2015; 9:2053-2058. [PMID: 26136935 DOI: 10.3892/etm.2015.2436] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 03/16/2015] [Indexed: 11/05/2022] Open
Abstract
Individuals who suffer from spinal muscular atrophy (SMA) exhibit progressive muscle weakness that frequently results in mortality in the most severe forms of the disease. In 98% of cases, there is a homozygous deletion of the survival of motor neuron 1 (SMN1) gene, and both parents carry the same heterozygous genetic abnormality in the majority of cases. Various population studies have been conducted to estimate the frequency of carriers and thereby identify the communities or countries in which children are at a high risk of being affected by SMA. However, the prevalence of SMA in Mexican populations has not yet been established. In the present pilot study, the frequency of the heterozygous deletion of the SMN1 gene was determined in two groups from northeastern (n=287) and central (n=133) Mexican Mestizo populations and compared with other ethnic populations. Amplification refractory mutation system polymerase chain reaction analysis yielded a disease carrier frequency of 11/420 (2.62%) healthy individuals, comprising 9/287 (3.14%) northeastern and 2/133 (1.5%) central Mexican individuals. In summary, no significant differences were identified between the northeastern and central populations of Mexico and other ethnic populations, with the exception of the general worldwide Hispanic population, which exhibited the lowest carrier frequency of 8/1,030. The results of the present study may be used to improve the evaluation procedure, and appear to justify further studies involving larger sample populations.
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Affiliation(s)
- Silvina Noemi Contreras-Capetillo
- Department of Genetics, Dr. Hideyo Noguchi Regional Research Center, Autonomous University of Yucatan, Mérida, Yucatán CP 97225, Mexico
| | | | | | - José Lugo-Trampe
- Department of Genetics, School of Medicine, Monterrey, Nuevo León CP 64460, Mexico
| | - Iris Torres-Muñoz
- Department of Genetics, School of Medicine, Monterrey, Nuevo León CP 64460, Mexico
| | - Antonio Bravo-Oro
- Neuropediatrics, Central Hospital 'Dr. Ignacio Morones Prieto', San Luis Potosí CP 78240, Mexico
| | - Carmen Esmer
- Department of Genetics, Central Hospital 'Dr. Ignacio Morones Prieto', San Luis Potosí CP 78240, Mexico
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Phan HC, Taylor JL, Hannon H, Howell R. Newborn screening for spinal muscular atrophy: Anticipating an imminent need. Semin Perinatol 2015; 39:217-29. [PMID: 25979781 DOI: 10.1053/j.semperi.2015.03.006] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality. Children with type I SMA typically die by the age of 2 years. Recent progress in gene modification and other innovative therapies suggest that improved outcomes may soon be forthcoming. In animal models, therapeutic intervention initiated before the loss of motor neurons alters SMA phenotype and increases lifespan. Presently, supportive care including respiratory, nutritional, physiatry, and orthopedic management can ameliorate clinical symptoms and improve survival rates if SMA is diagnosed early in life. Newborn screening could help optimize these potential benefits. A recent report demonstrated that SMA detection can be multiplexed at minimal additional cost with the assay for severe combined immunodeficiency, already implemented by many newborn screening programs. The public health community should remain alert to the rapidly changing developments in early detection and treatment of SMA.
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Affiliation(s)
- Han C Phan
- Department of Pediatrics, Emory University, Atlanta, GA.
| | | | - Harry Hannon
- Newborn Screening Consensus Committee, Clinical and Laboratory Standards Institute (CLSI), Wayne, PA
| | - Rodney Howell
- Miller School of Medicine, University of Miami, Miami, FL
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31
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Taylor JL, Lee FK, Yazdanpanah GK, Staropoli JF, Liu M, Carulli JP, Sun C, Dobrowolski SF, Hannon WH, Vogt RF. Newborn blood spot screening test using multiplexed real-time PCR to simultaneously screen for spinal muscular atrophy and severe combined immunodeficiency. Clin Chem 2015; 61:412-9. [PMID: 25502182 PMCID: PMC7906865 DOI: 10.1373/clinchem.2014.231019] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a motor neuron disorder caused by the absence of a functional survival of motor neuron 1, telomeric (SMN1) gene. Type I SMA, a lethal disease of infancy, accounts for the majority of cases. Newborn blood spot screening (NBS) to detect severe combined immunodeficiency (SCID) has been implemented in public health laboratories in the last 5 years. SCID detection is based on real-time PCR assays to measure T-cell receptor excision circles (TREC), a byproduct of T-cell development. We modified a multiplexed real-time PCR TREC assay to simultaneously determine the presence or absence of the SMN1 gene from a dried blood spot (DBS) punch in a single reaction well. METHOD An SMN1 assay using a locked nucleic acid probe was initially developed with cell culture and umbilical cord blood (UCB) DNA extracts, and then integrated into the TREC assay. DBS punches were placed in 96-well arrays, washed, and amplified directly using reagents specific for TREC, a reference gene [ribonuclease P/MRP 30kDa subunit (RPP30)], and the SMN1 gene. The assay was tested on DBS made from UCB units and from peripheral blood samples of SMA-affected individuals and their family members. RESULTS DBS made from SMA-affected individuals showed no SMN1-specific amplification, whereas DBS made from all unaffected carriers and UCB showed SMN1 amplification above a well-defined threshold. TREC and RPP30 content in all DBS were within the age-adjusted expected range. CONCLUSIONS SMA caused by the absence of SMN1 can be detected from the same DBS punch used to screen newborns for SCID.
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Affiliation(s)
- Jennifer L Taylor
- Newborn Screening and Molecular Biology Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA
| | - Francis K Lee
- Newborn Screening and Molecular Biology Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA
| | | | | | - Mei Liu
- Genetics and Genomics, Biogen Idec, Cambridge, MA
| | | | - Chao Sun
- Genetics and Genomics, Biogen Idec, Cambridge, MA
| | - Steven F Dobrowolski
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - W Harry Hannon
- Newborn Screening Translation Research Initiative, CDC Foundation, Atlanta, GA
| | - Robert F Vogt
- Newborn Screening and Molecular Biology Branch, Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA;
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MacDonald WK, Hamilton D, Kuhle S. SMA carrier testing: a meta-analysis of differences in test performance by ethnic group. Prenat Diagn 2014; 34:1219-26. [DOI: 10.1002/pd.4459] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 07/03/2014] [Accepted: 07/07/2014] [Indexed: 02/05/2023]
Affiliation(s)
| | - David Hamilton
- Department of Mathematics and Statistics; Dalhousie University; Halifax NS Canada
| | - Stefan Kuhle
- Department of Obstetrics & Gynaecology; Dalhousie University; Halifax NS Canada
- Department of Pediatrics; Dalhousie University; Halifax NS Canada
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Kariya S, Sampson JB, Northrop LE, Luccarelli CM, Naini AB, Re DB, Hirano M, Mitsumoto H. Nuclear localization of SMN and FUS is not altered in fibroblasts from patients with sporadic ALS. Amyotroph Lateral Scler Frontotemporal Degener 2014; 15:581-7. [PMID: 24809826 DOI: 10.3109/21678421.2014.907319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Abstract Sporadic amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no established biological marker. Recent observation of a reduced number of gems (survival motor neuron protein (SMN)-positive nuclear bodies) in cells from patients with familial ALS and the mouse models suggests an involvement of SMN in ALS pathology. At a molecular level, fused in sarcoma (FUS), one of the familial ALS-linked proteins, has been demonstrated to directly interact with SMN, while impaired nuclear localization of mutated FUS causes defective gem formation. Our objective was to determine whether gems and/or nuclear FUS levels in skin derived fibroblasts from sporadic ALS patients are consistently reduced and thus could constitute a novel and readily available biomarker of the disease. Fibroblasts from 20 patients and 17 age-matched healthy controls were cultured and co-immunostained for SMN and FUS. Results showed that no difference was detected between the two groups in the number of gems and in expression pattern of FUS. The number of gems negatively correlated with the age at biopsy in both ALS and control subjects. In conclusion, the expression pattern of SMN and FUS in fibroblasts cannot serve as a biomarker for sporadic ALS. Donor age-dependent gem reduction is a novel observation that links SMN with cellular senescence.
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Affiliation(s)
- Shingo Kariya
- Department of Pathology and Cell Biology, Center for Motor Neuron Biology and Disease and the Columbia Translational Neuroscience Initiative, Columbia University Medical Center , New York
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Sangaré M, Hendrickson B, Sango HA, Chen K, Nofziger J, Amara A, Dutra A, Schindler AB, Guindo A, Traoré M, Harmison G, Pak E, Yaro FN, Bricceno K, Grunseich C, Chen G, Boehm M, Zukosky K, Bocoum N, Meilleur KG, Daou F, Bagayogo K, Coulibaly YI, Diakité M, Fay MP, Lee HS, Saad A, Gribaa M, Singleton AB, Maiga Y, Auh S, Landouré G, Fairhurst RM, Burnett BG, Scholl T, Fischbeck KH. Genetics of low spinal muscular atrophy carrier frequency in sub-Saharan Africa. Ann Neurol 2014; 75:525-32. [PMID: 24515897 PMCID: PMC4112719 DOI: 10.1002/ana.24114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/27/2014] [Accepted: 01/30/2014] [Indexed: 12/14/2022]
Abstract
Objective Spinal muscular atrophy (SMA) is one of the most common severe hereditary diseases of infancy and early childhood in North America, Europe, and Asia. SMA is usually caused by deletions of the survival motor neuron 1 (SMN1) gene. A closely related gene, SMN2, modifies the disease severity. SMA carriers have only 1 copy of SMN1 and are relatively common (1 in 30–50) in populations of European and Asian descent. SMN copy numbers and SMA carrier frequencies have not been reliably estimated in Malians and other sub‐Saharan Africans. Methods We used a quantitative polymerase chain reaction assay to determine SMN1 and SMN2 copy numbers in 628 Malians, 120 Nigerians, and 120 Kenyans. We also explored possible mechanisms for SMN1 and SMN2 copy number differences in Malians, and investigated their effects on SMN mRNA and protein levels. Results The SMA carrier frequency in Malians is 1 in 209, lower than in Eurasians. Malians and other sub‐Saharan Africans are more likely to have ≥3 copies of SMN1 than Eurasians, and more likely to lack SMN2 than Europeans. There was no evidence of gene conversion, gene locus duplication, or natural selection from malaria resistance to account for the higher SMN1 copy numbers in Malians. High SMN1 copy numbers were not associated with increased SMN mRNA or protein levels in human cell lines. Interpretation SMA carrier frequencies are much lower in sub‐Saharan Africans than in Eurasians. This finding is important to consider in SMA genetic counseling in individuals with black African ancestry. Ann Neurol 2014;75:525–532
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Affiliation(s)
- Modibo Sangaré
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD; Institute of Biomedical Sciences, George Washington University, Washington, DC
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Ma L, Chung WK. Quantitative analysis of copy number variants based on real-time LightCycler PCR. CURRENT PROTOCOLS IN HUMAN GENETICS 2014; 80:7.21.1-7.21.8. [PMID: 24510682 PMCID: PMC3949243 DOI: 10.1002/0471142905.hg0721s80] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Quantitative real-time PCR is PCR visualized in real time by the use of fluorescent or intercalating dyes, which are employed to measure gene expression or gene quantification including contiguous gene deletions or duplications. A simple method is described here to quantify DNA copy number from human samples.
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Affiliation(s)
- Lijiang Ma
- Department of Pediatrics, Columbia University, New York, New York
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University, New York, New York,Department of Medicine, Columbia University, New York, New York
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Genetisches Modell der autosomal-rezessiv erblichen proximalen spinalen Muskelatrophie. MED GENET-BERLIN 2013. [DOI: 10.1007/s11825-013-0402-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Zusammenfassung
Die proximale infantile und juvenile spinale Muskelatrophie (SMA) ist eine der häufigsten autosomal-rezessive Erbkrankheiten. Man unterteilt die Patienten in 3 Gruppen, SMA Typ I-III, abhängig von der Schwere der Erkrankung (den erreichten Meilensteinen). Das hauptsächlich verantwortliche Gen, das Survival-motor-neuron(SMN1)-Gen, ist auf Chromosom 5 lokalisiert. Während das Normalallel meist mit einer oder 2 SMN1-Kopien vorliegt, sind die Defektallele bei den meisten Patienten von einer Deletion betroffen; bei einigen liegen Punktmutationen vor. Bei den Deletionen wiederum unterscheidet man zwischen einfacher und großer Deletion, die über das SMN1-Gen hinausgeht. Ein homozygotes Auftreten letzterer führt zu pränataler Letalität.
Für die vorliegende Arbeit wurden zahlreiche in der Literatur verfügbare Daten zur SMA Typ I-III zusammengetragen und in ihrer Abhängigkeit in einem genetischen Modell zusammengefasst. So war es möglich, fehlende Parameter zu schätzen, um genauere Aussagen über Genotypen machen zu können. Die einzelnen Allelfrequenzen konnten wie folgt geschätzt werden:
Normalallel b (1 SMN1-Kopie): ≈ 0,9527; Normalallel c (2 SMN1-Kopien): ≈ 0,0362; einfache Deletion a (0 SMN1-Kopien): ≈ 0,0104; Punktmutation d (1 SMN1-Kopie): ≈ 0,0003; große Deletion g (0 SMN1-Kopien): ≈ 0,0004. Die Genhäufigkeit beträgt etwa 1:90 mit einer Heterozygtenfrequenz von 1:46.
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Nurputra DK, Lai PS, Harahap NIF, Morikawa S, Yamamoto T, Nishimura N, Kubo Y, Takeuchi A, Saito T, Takeshima Y, Tohyama Y, Tay SKH, Low PS, Saito K, Nishio H. Spinal muscular atrophy: from gene discovery to clinical trials. Ann Hum Genet 2013; 77:435-63. [PMID: 23879295 DOI: 10.1111/ahg.12031] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 04/26/2013] [Indexed: 12/25/2022]
Abstract
Spinal muscular atrophy (SMA) is a common neuromuscular disorder with autosomal recessive inheritance, resulting in the degeneration of motor neurons. The incidence of the disease has been estimated at 1 in 6000-10,000 newborns with a carrier frequency of 1 in 40-60. SMA is caused by mutations of the SMN1 gene, located on chromosome 5q13. The gene product, survival motor neuron (SMN) plays critical roles in a variety of cellular activities. SMN2, a homologue of SMN1, is retained in all SMA patients and generates low levels of SMN, but does not compensate for the mutated SMN1. Genetic analysis demonstrates the presence of homozygous deletion of SMN1 in most patients, and allows screening of heterozygous carriers in affected families. Considering high incidence of carrier frequency in SMA, population-wide newborn and carrier screening has been proposed. Although no effective treatment is currently available, some treatment strategies have already been developed based on the molecular pathophysiology of this disease. Current treatment strategies can be classified into three major groups: SMN2-targeting, SMN1-introduction, and non-SMN targeting. Here, we provide a comprehensive and up-to-date review integrating advances in molecular pathophysiology and diagnostic testing with therapeutic developments for this disease including promising candidates from recent clinical trials.
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Affiliation(s)
- Dian K Nurputra
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
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Luo M, Liu L, Peter I, Zhu J, Scott SA, Zhao G, Eversley C, Kornreich R, Desnick RJ, Edelmann L. An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular atrophy. Genet Med 2013; 16:149-56. [PMID: 23788250 DOI: 10.1038/gim.2013.84] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 05/02/2013] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Spinal muscular atrophy is a common autosomal-recessive disorder caused by mutations of the SMN1 gene. Spinal muscular atrophy carrier screening uses dosage-sensitive methods that determine SMN1 copy number, and the frequency of carriers varies by ethnicity, with detection rates ranging from 71 to 94% due to the inability to identify silent (2 + 0) carriers with two copies of SMN1 on one chromosome 5 and deletion on the other. We hypothesized that identification of deletion and/or duplication founder alleles might provide an approach to identify silent carriers in various ethnic groups. METHODS SMN1 founder alleles were investigated in the Ashkenazi Jewish population by microsatellite analysis and next-generation sequencing. RESULTS An extended haplotype block, specific to Ashkenazi Jewish SMN1 duplications, was identified by microsatellite analysis, and next-generation sequencing of SMN1 further defined a more localized haplotype. Of note, six novel SMN1 sequence variants were identified that were specific to duplications and not present on single-copy alleles. The haplotype was also identified on SMN1 duplication alleles in additional ethnic groups. CONCLUSION Identification of these novel variants in an individual with two copies of SMN1 significantly improves the accuracy of residual risk estimates and has important implications for spinal muscular atrophy carrier screening.
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Affiliation(s)
- Minjie Luo
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Liu Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Geping Zhao
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | | | - Ruth Kornreich
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine of New York University, New York, New York, USA
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Wieme MH, Monia Ben H, Yosr B, Sihem S, Nawel T, Ines MA, Wajdi B, Najla K, Houda N, Faycal H, Rim A. Confirmation of the spinal motor neuron gene 2 (SMN2) copy numbers by real-time PCR. DIAGNOSTIC MOLECULAR PATHOLOGY : THE AMERICAN JOURNAL OF SURGICAL PATHOLOGY, PART B 2012; 21:172-175. [PMID: 22847162 DOI: 10.1097/pdm.0b013e31824696b6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive disease caused by mutation or deletion of the survival motor neuron gene 1 (SMN1). SMN2, a copy gene, influences the severity of SMA and may be used in somatic gene therapy of patients with SMA in the future. The SMA carrier analysis developed at the Institute of Medical Genetics, Catholic University (Rome), on the Applied Biosystems real-time PCR instruments by Dr Danilo Tiziano and his group, provides a robust workflow to evaluate SMA carrier status. In this study, the SMN2 copy number was confirmed on 22 patients by developing our own assay on the basis of a relative real-time PCR system using the 7500 Fast Real-Time PCR System.
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Affiliation(s)
- Maamouri-Hicheri Wieme
- Department of Molecular Neurobiology and Neuropathology, La Rabta, National Institute of Neurology, Tunis, Tunisia.
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Zabnenkova VV, Dadali EL, Spiridonova MG, Zinchenko RA, Polyakov AV. Heterozygous carrier rate for type I–IV proximal spinal muscular atrophy in Chuvashes, Udmurts, and residents of the Moscow region. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412080091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rudnik-Schöneborn S, Eggermann T, Kress W, Lemmink HH, Cobben JM, Zerres K. Clinical utility gene card for: proximal spinal muscular atrophy. Eur J Hum Genet 2012; 20:ejhg201262. [PMID: 22510849 DOI: 10.1038/ejhg.2012.62] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Stuppia L, Antonucci I, Palka G, Gatta V. Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases. Int J Mol Sci 2012; 13:3245-3276. [PMID: 22489151 PMCID: PMC3317712 DOI: 10.3390/ijms13033245] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/16/2022] Open
Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA) assay is a recently developed technique able to evidence variations in the copy number of several human genes. Due to this ability, MLPA can be used in the molecular diagnosis of several genetic diseases whose pathogenesis is related to the presence of deletions or duplications of specific genes. Moreover, MLPA assay can also be used in the molecular diagnosis of genetic diseases characterized by the presence of abnormal DNA methylation. Due to the large number of genes that can be analyzed by a single technique, MLPA assay represents the gold standard for molecular analysis of all pathologies derived from the presence of gene copy number variation. In this review, the main applications of the MLPA technique for the molecular diagnosis of human diseases are described.
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Affiliation(s)
- Liborio Stuppia
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Ivana Antonucci
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Giandomenico Palka
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Valentina Gatta
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
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Abstract
Spinal muscular atrophy is a common autosomal recessive neuromuscular disorder caused by mutations in the survival motor neuron (SMN1) gene, affecting approximately 1 in 10,000 live births. The disease is characterized by progressive symmetrical muscle weakness resulting from the degeneration and loss of anterior horn cells in the spinal cord and brainstem nuclei. The disease is classified on the basis of age of onset and clinical course. Two almost identical SMN genes are present on 5q13: the SMN1 gene, which is the spinal muscular atrophy-determining gene, and the SMN2 gene. The homozygous absence of the SMN1 exon 7 has been observed in the majority of patients and is being used as a reliable and sensitive spinal muscular atrophy diagnostic test. Although SMN2 produces less full-length transcript than SMN1, the number of SMN2 copies has been shown to modulate the clinical phenotype. Carrier detection relies on the accurate determination of the SMN1 gene copies. This document follows the outline format of the general Standards and Guidelines for Clinical Laboratories. It is designed to be a checklist for genetic testing professionals who are already familiar with the disease and methods of analysis.
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Maranda B, Fan L, Soucy JF, Simard L, Mitchell GA. Spinal muscular atrophy: clinical validation of a single-tube multiplex real time PCR assay for determination of SMN1 and SMN2 copy numbers. Clin Biochem 2011; 45:88-91. [PMID: 22085534 DOI: 10.1016/j.clinbiochem.2011.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Revised: 10/22/2011] [Accepted: 10/30/2011] [Indexed: 01/07/2023]
Abstract
OBJECTIVES To describe and validate a new protocol for molecular diagnosis of spinal muscular atrophy (SMA), a frequent neuromuscular disease of childhood. DESIGN AND METHODS SMA is caused in most cases by homozygous deletion of the SMN1 gene. We describe a triplex quantitative real-time PCR method in which fragments of SMN1, SMN2 (a nearly-identical neighboring gene with markedly reduced function) and of a control gene, CFTR, are amplified in the same tube. RESULTS We validated this method in three ways. First, testing the same samples ten times yielded CV values <4.6%. Second, in 104 previously-genotyped individuals, SMN copy numbers identical to those of the previously-determined genotype was unambiguously obtained in all cases. Finally, results using the technique in practice are described and analyzed for reproducibility of amplification efficiency and for inter-run variability. CONCLUSIONS In over 1200 samples, this technique has proven accurate, fast, economical and reproducible.
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Affiliation(s)
- Bruno Maranda
- Department of Genetics, CHUS and Université de Sherbrooke, Sherbrooke, Québec, Canada
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Pan-ethnic carrier screening and prenatal diagnosis for spinal muscular atrophy: clinical laboratory analysis of >72,400 specimens. Eur J Hum Genet 2011; 20:27-32. [PMID: 21811307 PMCID: PMC3234503 DOI: 10.1038/ejhg.2011.134] [Citation(s) in RCA: 420] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Spinal muscular atrophy (SMA) is a leading inherited cause of infant death with a reported incidence of ∼1 in 10 000 live births and is second to cystic fibrosis as a common, life-shortening autosomal recessive disorder. The American College of Medical Genetics has recommended population carrier screening for SMA, regardless of race or ethnicity, to facilitate informed reproductive options, although other organizations have cited the need for additional large-scale studies before widespread implementation. We report our data from carrier testing (n=72 453) and prenatal diagnosis (n=121) for this condition. Our analysis of large-scale population carrier screening data (n=68 471) demonstrates the technical feasibility of high throughput testing and provides mutation carrier and allele frequencies at a level of accuracy afforded by large data sets. In our United States pan-ethnic population, the calculated a priori carrier frequency of SMA is 1/54 with a detection rate of 91.2%, and the pan-ethnic disease incidence is calculated to be 1/11 000. Carrier frequency and detection rates provided for six major ethnic groups in the United States range from 1/47 and 94.8% in the Caucasian population to 1/72 and 70.5% in the African American population, respectively. This collective experience can be utilized to facilitate accurate pre- and post-test counseling in the settings of carrier screening and prenatal diagnosis for SMA.
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Genetic and expression studies of SMN2 gene in Russian patients with spinal muscular atrophy type II and III. BMC MEDICAL GENETICS 2011; 12:96. [PMID: 21762474 PMCID: PMC3146920 DOI: 10.1186/1471-2350-12-96] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 07/15/2011] [Indexed: 11/30/2022]
Abstract
Background Spinal muscular atrophy (SMA type I, II and III) is an autosomal recessive neuromuscular disorder caused by mutations in the survival motor neuron gene (SMN1). SMN2 is a centromeric copy gene that has been characterized as a major modifier of SMA severity. SMA type I patients have one or two SMN2 copies while most SMA type II patients carry three SMN2 copies and SMA III patients have three or four SMN2 copies. The SMN1 gene produces a full-length transcript (FL-SMN) while SMN2 is only able to produce a small portion of the FL-SMN because of a splice mutation which results in the production of abnormal SMNΔ7 mRNA. Methods In this study we performed quantification of the SMN2 gene copy number in Russian patients affected by SMA type II and III (42 and 19 patients, respectively) by means of real-time PCR. Moreover, we present two families consisting of asymptomatic carriers of a homozygous absence of the SMN1 gene. We also developed a novel RT-qPCR-based assay to determine the FL-SMN/SMNΔ7 mRNA ratio as SMA biomarker. Results Comparison of the SMN2 copy number and clinical features revealed a significant correlation between mild clinical phenotype (SMA type III) and presence of four copies of the SMN2 gene. In both asymptomatic cases we found an increased number of SMN2 copies in the healthy carriers and a biallelic SMN1 absence. Furthermore, the novel assay revealed a difference between SMA patients and healthy controls. Conclusions We suggest that the SMN2 gene copy quantification in SMA patients could be used as a prognostic tool for discrimination between the SMA type II and SMA type III diagnoses, whereas the FL-SMN/SMNΔ7 mRNA ratio could be a useful biomarker for detecting changes during SMA pharmacotherapy.
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Zhong Q, Bhattacharya S, Kotsopoulos S, Olson J, Taly V, Griffiths AD, Link DR, Larson JW. Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR. LAB ON A CHIP 2011; 11:2167-74. [PMID: 21584334 DOI: 10.1039/c1lc20126c] [Citation(s) in RCA: 220] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Quantitative polymerase chain reactions (qPCR) based on real-time PCR constitute a powerful and sensitive method for the analysis of nucleic acids. However, in qPCR, the ability to multiplex targets using differently colored fluorescent probes is typically limited to 4-fold by the spectral overlap of the fluorophores. Furthermore, multiplexing qPCR assays requires expensive instrumentation and most often lengthy assay development cycles. Digital PCR (dPCR), which is based on the amplification of single target DNA molecules in many separate reactions, is an attractive alternative to qPCR. Here we report a novel and easy method for multiplexing dPCR in picolitre droplets within emulsions-generated and read out in microfluidic devices-that takes advantage of both the very high numbers of reactions possible within emulsions (>10(6)) as well as the high likelihood that the amplification of only a single target DNA molecule will initiate within each droplet. By varying the concentration of different fluorogenic probes of the same color, it is possible to identify the different probes on the basis of fluorescence intensity. Adding multiple colors increases the number of possible reactions geometrically, rather than linearly as with qPCR. Accurate and precise copy numbers of up to sixteen per cell were measured using a model system. A 5-plex assay for spinal muscular atrophy was demonstrated with just two fluorophores to simultaneously measure the copy number of two genes (SMN1 and SMN2) and to genotype a single nucleotide polymorphism (c.815A>G, SMN1). Results of a pilot study with SMA patients are presented.
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Affiliation(s)
- Qun Zhong
- RainDance Technologies, Inc., 44 Hartwell Ave., Lexington, MA 02150, USA.
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Alías L, Bernal S, Barceló MJ, Also-Rallo E, Martínez-Hernández R, Rodríguez-Alvarez FJ, Hernández-Chico C, Baiget M, Tizzano EF. Accuracy of marker analysis, quantitative real-time polymerase chain reaction, and multiple ligation-dependent probe amplification to determine SMN2 copy number in patients with spinal muscular atrophy. Genet Test Mol Biomarkers 2011; 15:587-94. [PMID: 21548796 DOI: 10.1089/gtmb.2010.0253] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder caused by absence of or mutations in the survival motor neuron1 gene (SMN1). All SMA patients have a highly homologous copy of SMN1, the SMN2 gene. Severe (type I) SMA patients present one or two SMN2 copies, whereas milder chronic forms (type II-III) usually have three or four SMN2 copies. SMN2 dosage is important to stratify patients for motor function tests and clinical trials. Our aim was to compare three methods, marker analysis, real-time quantitative polymerase chain reaction using the LightCycler instrument, and multiple ligation-dependent probe amplification (MLPA), to characterize their accuracy in quantifying SMN2 genes. We studied a group of 62 genetically confirmed SMA patients, 54 with homozygous absence of exons 7 and 8 of SMN1 and 8 with SMN2-SMN1 hybrid genes. A complete correlation using the three methods was observed in 32 patients (51.6%). In the remaining 30 patients, discordances between the three methods were found, including under or overestimation of SMN2 copies by marker analysis with respect to the quantitative methods (LightCycler and MLPA) because of lack of informativeness of markers, 3' deletions of SMN genes, and breakpoints in SMN2-SMN1 hybrid genes. The technical limitations and advantages and disadvantages of these methods are discussed. We conclude that the three methods complement each other in estimating the SMN2 copy number in most cases. However, MLPA offers additional information to characterize SMA cases with particular rearrangements such as partial deletions and hybrid genes.
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Affiliation(s)
- Laura Alías
- Servicio de Genética, Hospital de la Santa Creu i Sant Pau, CIBERER (U705), Barcelona, Spain
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Carrier screening for spinal muscular atrophy (SMA) in 107,611 pregnant women during the period 2005-2009: a prospective population-based cohort study. PLoS One 2011; 6:e17067. [PMID: 21364876 PMCID: PMC3045421 DOI: 10.1371/journal.pone.0017067] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 01/14/2011] [Indexed: 11/20/2022] Open
Abstract
Background Spinal muscular atrophy (SMA) is the most common neuromuscular autosomal recessive disorder. The American College of Medical Genetics has recently recommended routine carrier screening for SMA because of the high carrier frequency (1 in 25–50) as well as the severity of that genetic disease. Large studies are needed to determine the feasibility, benefits, and costs of such a program. Methods and Findings This is a prospective population-based cohort study of 107,611 pregnant women from 25 counties in Taiwan conducted during the period January 2005 to June 2009. A three-stage screening program was used: (1) pregnant women were tested for SMA heterozygosity; (2) if the mother was determined to be heterozygous for SMA (carrier status), the paternal partner was then tested; (3) if both partners were SMA carriers, prenatal diagnostic testing was performed. During the study period, a total of 2,262 SMA carriers with one copy of the SMN1 gene were identified among the 107,611 pregnant women that were screened. The carrier rate was approximately 1 in 48 (2.10%). The negative predictive value of DHPLC coupled with MLPA was 99.87%. The combined method could detect approximately 94% of carriers because most of the cases resulted from a common single deletion event. In addition, 2,038 spouses were determined to be SMA carriers. Among those individuals, 47 couples were determined to be at high risk for having offspring with SMA. Prenatal diagnostic testing was performed in 43 pregnant women (91.49%) and SMA was diagnosed in 12 (27.91%) fetuses. The prevalence of SMA in our population was 1 in 8,968. Conclusion The main benefit of SMA carrier screening is to reduce the burden associated with giving birth to an affected child. In this study, we determined the carrier frequency and genetic risk and provided carrier couples with genetic services, knowledge, and genetic counseling.
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Bueno KC, Gouvea SP, Genari AB, Funayama CA, Zanette DL, Silva WA, Oliveira AB, Scola RH, Werneck LC, Marques W. Detection of spinal muscular atrophy carriers in a sample of the Brazilian population. Neuroepidemiology 2011; 36:105-8. [PMID: 21335981 DOI: 10.1159/000324156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 01/03/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Spinal muscular atrophy is a common autosomal recessive neuromuscular disorder caused by mutations in the SMN1 gene. Identification of spinal muscular atrophy carriers has important implications for individuals with a family history of the disorder and for genetic counseling. The aim of this study was to determine the frequency of carriers in a sample of the nonconsanguineous Brazilian population by denaturing high-performance liquid chromatography (DHPLC). METHODS To validate the method, we initially determined the relative quantification of DHPLC in 28 affected patients (DHPLC values: 0.00) and 65 parents (DHPLC values: 0.49-0.69). Following quantification, we studied 150 unrelated nonconsanguineous healthy individuals from the general population. RESULTS Four of the 150 healthy individuals tested (with no family history of a neuromuscular disorder) presented a DHPLC value in the range of heterozygous carriers (0.6-0.68). CONCLUSIONS Based on these results, we estimated there is a carrier frequency of 2.7% in the nonconsanguineous Brazilian population, which is very similar to other areas of the world where consanguineous marriage is not common. This should be considered in the process of genetic counseling and risk calculations.
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Affiliation(s)
- K C Bueno
- Departments of Neurosciences and Behavior Sciences, University of São Paulo, Ribeirão Preto, Brazil
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