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WIJAYA YOGIKONKYSILVANA, NIBA EMMATABEEKO, YABUSHITA RYO, BOUIKE YOSHIHIRO, NISHIO HISAHIDE, AWANO HIROYUKI. Glycogen Storage Disease Type Ia Screening Using Dried Blood Spots on Filter Paper: Application of COP-PCR for Detection of the c.648G>T G6PC Gene Mutation. Kobe J Med Sci 2021; 67:E71-E78. [PMID: 34795158 PMCID: PMC8622217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Glycogen storage disease type Ia (GSDIa, OMIM #232200) is an autosomal recessive metabolic disease characterized by impaired glucose homeostasis and has a long-term complication of hepatocellular adenoma/carcinoma. GSDIa is caused by deleterious mutations in the glucose-6-phosphatase gene (G6PC). Recent studies have suggested that early treatment by gene replacement therapy may be a good solution to correct the glucose metabolism and prevent serious late complications. Early treatment of the disease needs an early disease detection system. Thus, we aimed to develop a screening system for GSDIa using dried blood spots (DBS) to detect the c.648G>T mutation in G6PC, which is a frequent mutation in the East Asian population. In this study, a total of 51 DBS samples (50 healthy controls and one patient with c.648G>T) were tested by modified competitive oligonucleotide priming PCR (mCOP-PCR). In control DBS samples, the c.648G allele was amplified at lower Cq (quantification cycle) values (<11), while the c.648T allele was amplified at higher Cq values (>14). In the patient DBS sample, the c.648T allele was amplified at a lower Cq value (<11), and the c.648G allele was amplified at a higher Cq value (>14). Based on these findings, we concluded that our mCOP-PCR system clearly differentiated the wild-type and mutant alleles, and may be applicable for screening for GSDIa with the c.648G>T mutation in G6PC.
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Affiliation(s)
- YOGIK ONKY SILVANA WIJAYA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - EMMA TABE EKO NIBA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - RYO YABUSHITA
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe, Hyogo 651-2180, Japan
| | - YOSHIHIRO BOUIKE
- Faculty of Nutrition, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe, Hyogo 651-2180, Japan
| | - HISAHIDE NISHIO
- Faculty of Medical Rehabilitation, Kobe Gakuin University, 518 Arise, Ikawadani-cho, Nishi-ku, Kobe, Hyogo 651-2180, Japan
| | - HIROYUKI AWANO
- Department of Pediatrics, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan
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ROCHMAH MAWADDAHAR, WIJAYA YOGIKONKYSILVANA, HARAHAP NURIMMAFATIMAH, TODE CHISATO, TAKEUCHI ATSUKO, OHUCHI KAZUKI, SHIMAZAWA MASAMITSU, HARA HIDEAKI, FUNATO MICHINORI, SAITO TOSHIO, SAITO KAYOKO, LAI POHSAN, AWANO HIROYUKI, SHINOHARA MASAKAZU, NISHIO HISAHIDE, NIBA EMMATABEEKO. Phosphoethanolamine Elevation in Plasma of Spinal Muscular Atrophy Type 1 Patients. Kobe J Med Sci 2020; 66:E1-E11. [PMID: 32814752 PMCID: PMC7447103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder characterized by degeneration or loss of lower motor neurons. The survival of motor neuron (SMN) 1 gene, which produces the SMN protein, has been identified as a responsible gene for the disease. SMN is ubiquitously expressed in any tissue and may play an important role on the metabolism in the human body. However, no appropriate biomarkers reflecting the alteration in the metabolism in SMA have been identified. METHODS Low-molecular-weight metabolites were extracted from plasma of 20 human infants (9 SMA type 1 patients and 11 controls) and 9 infant mice (5 SMA-model mice, 4 control mice), and derivatized with N-methyl-N-trimethylsilyltrifluoroacetamide. Finally, the derivatized products were applied to Gas Chromatography/Mass Spectrometry apparatus. To confirm the metabolite abnormality in SMA type 1 patients, we performed SMN-silencing experiment using a hepatocyte-derived cell line (HepG2). RESULTS We performed a comprehensive metabolomics analysis of plasma from the patients with SMA type 1 and controls, and found that phosphoethanolamine (PEA) was significantly higher in the patients than in the controls. HepG2 experiment also showed that SMN-silencing increased PEA levels. However, comprehensive metabolomics analysis of plasma from SMA-model mice and control mice showed different profile compared to human plasma; there was no increase of PEA even in the SMA-model mice plasma. CONCLUSION Our data suggested that PEA was one of the possible biomarkers of human SMA reflecting metabolic abnormalities due to the SMN protein deficiency.
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Affiliation(s)
- MAWADDAH AR ROCHMAH
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Neurology, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - YOGIK ONKY SILVANA WIJAYA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - NUR IMMA FATIMAH HARAHAP
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Clinical Pathology, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - CHISATO TODE
- Instrumental Analysis Center, Kobe Pharmaceutical University, Kobe, Japan
| | - ATSUKO TAKEUCHI
- Instrumental Analysis Center, Kobe Pharmaceutical University, Kobe, Japan
| | - KAZUKI OHUCHI
- Department of Molecular Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
| | - MASAMITSU SHIMAZAWA
- Department of Molecular Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
| | - HIDEAKI HARA
- Department of Molecular Pharmacology, Gifu Pharmaceutical University, Gifu, Japan
| | - MICHINORI FUNATO
- Department of Clinical Research, National Hospital Organization, Nagara Medical Center, Gifu, Japan
| | - TOSHIO SAITO
- Division of Child Neurology, Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Japan
| | - KAYOKO SAITO
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | - POH SAN LAI
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - HIROYUKI AWANO
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MASAKAZU SHINOHARA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - HISAHIDE NISHIO
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
- Faculty of Medical Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - EMMA TABE EKO NIBA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
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3
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TAKEUCHI ATSUKO, TODE CHISATO, NISHINO MASAYOSHI, WIJAYA YOGIKONKYSILVANA, NIBA EMMATABEEKO, AWANO HIROYUKI, TAKESHIMA YASUHIRO, SAITO TOSHIO, SAITO KAYOKO, LAI POHSAN, BOUIKE YOSHIHIRO, NISHIO HISAHIDE, SHINOHARA MASAKAZU. Newborn Screening for Spinal Muscular Atrophy: DNA Preparation from Dried Blood Spot and DNA Polymerase Selection in PCR. Kobe J Med Sci 2019; 65:E95-E99. [PMID: 32029694 PMCID: PMC7012323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Polymerase chain reaction (PCR) analysis using DNA from dried blood spot (DBS) samples on filter paper is a critical technique for spinal muscular atrophy (SMA) newborn screening. However, DNA extraction from DBS is time-consuming, and elimination of PCR inhibitors from DBS is almost impossible. METHODS Exon 7 of the two homologous SMA-related genes, survival motor neuron (SMN) 1 and SMN2, of five SMA patients and five controls were amplified by PCR with a punched-out circle of the DBS paper. Two types of DNA preparation methods were tested; DNA-extraction (extracted DNA was added in a PCR tube) and non-DNA-extraction (a punched-out DBS circle was placed in a PCR tube). As for the DNA polymerases, two different enzymes were compared; TaKaRa Ex Taq™ and KOD FX Neo™. To test the diagnostic quality of PCR products, RFLP (Restriction fragment length polymorphism) analysis with DraI digestion was performed, differentiating SMN1 and SMN2. RESULTS In PCR using extracted DNA, sufficient amplification was achieved with TaKaRa Ex Taq™ and KOD FX Neo™, and there was no significant difference in amplification efficiency between them. In direct PCR with a punched-out DBS circle, sufficient amplification was achieved when KOD FX Neo™ polymerase was used, while there was no amplification with TaKaRa Ex Taq™. RFLP analysis of the direct PCR products with KOD FX Neo™ clearly separated SMN1 and SMN2 sequences and proved the presence of both of SMN1 and SMN2 in controls, and only SMN2 in SMA patients, suggesting that the direct PCR products with KOD FX Neo™ were of sufficient diagnostic quality for SMA testing. CONCLUSION Direct PCR with DNA polymerases like KOD FX NeoTM has potential to be widely used in SMA newborn screening in the near future as it obviates the DNA extraction process from DBS and can precisely amplify the target sequences in spite of the presence of PCR inhibitors.
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Affiliation(s)
- ATSUKO TAKEUCHI
- Instrumental Analysis Center, Kobe Pharmaceutical University, Kobe, Japan
| | - CHISATO TODE
- Instrumental Analysis Center, Kobe Pharmaceutical University, Kobe, Japan
| | - MASAYOSHI NISHINO
- Instrumental Analysis Center, Kobe Pharmaceutical University, Kobe, Japan
| | - YOGIK ONKY SILVANA WIJAYA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - EMMA TABE EKO NIBA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - HIROYUKI AWANO
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - TOSHIO SAITO
- Division of Child Neurology, Department of Neurology, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Japan
| | - KAYOKO SAITO
- Director, Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | - POH SAN LAI
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - HISAHIDE NISHIO
- Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - MASAKAZU SHINOHARA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
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NIBA EMMATABEEKO, ROCHMAH MAWADDAHAR, HARAHAP NURIMMAFATIMAH, AWANO HIROYUKI, MORIOKA ICHIRO, IIJIMA KAZUMOTO, TAKESHIMA YASUHIRO, SAITO TOSHIO, SAITO KAYOKO, TAKEUCHI ATSUKO, LAI POHSAN, BOUIKE YOSHIHIRO, MATSUO MASAFUMI, NISHIO HISAHIDE, SHINOHARA MASAKAZU. Spinal Muscular Atrophy: Advanced Version of Screening System with Real-Time mCOP-PCR and PCR-RFLP for SMN1 Deletion. Kobe J Med Sci 2019; 65:E49-E53. [PMID: 31956256 PMCID: PMC7012194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Spinal Muscular Atrophy (SMA) is a common autosomal recessive neuromuscular disease characterized by defects of lower motor neurons. More than 95% of SMA patients show homozygous deletion for the survival motor neuron 1 (SMN1) gene. For the screening of SMN1 deletion using dried blood spot (DBS), we developed a new combined system with real-time "modified competitive oligonucleotide priming"-polymerase chain reaction (mCOP-PCR) and PCR restriction fragment length polymorphism (PCR-RFLP). Although our real-time mCOP-PCR method is secured enough to be gene-specific, its amplification efficiency is not as good because the reverse primers carry a nucleotide mismatched with the sequence of the pre-amplified product. The mismatch has consequently been generated in the process of introducing a restriction enzyme site in the pre-amplified products for PCR-RFLP. METHOD DBS samples of the subjects were stored at room temperature for a period of less than one year. Each subject had already been genotyped by the first PCR-RFLP using fresh blood DNA. SMN1/SMN2 exon 7 was collectively amplified using conventional PCR (targeted pre-amplification). Pre-amplified products were used as template in the real-time mCOP-PCR, and, on the other hand, were digested with DraI enzyme (PCR-RFLP). To improve the amplification efficiency of mCOP-PCR, one nucleotide change was introduced in the original reverse primers (SMN1-COP and SMN2-COP) to eliminate the mismatched nucleotide. RESULTS The real-time mCOP-PCR with a new primer (SMN1-COP-DRA or SMN2-COP-DRA) more rapidly and specifically amplified SMN1 and SMN2, and clearly demonstrated SMN1 deletion in an SMA patient. With the new primers, the amplification efficiencies of real-time mCOP-PCR were improved and the Cq values of SMN1 (+) and SMN2 (+) samples were significantly lowered. CONCLUSION In the advanced version of our screening system for homozygous SMN1 deletion using DBS, the real-time mCOP-PCR with newly-designed reverse primers demonstrated the presence or absence of SMN1 and SMN2 within a shorter time, and the results were easily tested by PCR-RFLP. This rapid and accurate screening system will be useful for detection of newborn infants with SMA.
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Affiliation(s)
- EMMA TABE EKO NIBA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MAWADDAH AR ROCHMAH
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - NUR IMMA FATIMAH HARAHAP
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - HIROYUKI AWANO
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - ICHIRO MORIOKA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - KAZUMOTO IIJIMA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - TOSHIO SAITO
- Division of Child Neurology, Department of Neurology, National Hospital Organization Toneyama National Hospital, Toneyama, Japan
| | - KAYOKO SAITO
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | | | - POH SAN LAI
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - MASAFUMI MATSUO
- Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - HISAHIDE NISHIO
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
- Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - MASAKAZU SHINOHARA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
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NIBA EMMATABEEKO, ROCHMAH MAWADDAHAR, HARAHAP NURIMMAFATIMAH, AWANO HIROYUKI, MORIOKA ICHIRO, IIJIMA KAZUMOTO, TAKESHIMA YASUHIRO, SAITO TOSHIO, SAITO KAYOKO, TAKEUCHI ATSUKO, LAI POHSAN, BOUIKE YOSHIHIRO, MATSUO MASAFUMI, NISHIO HISAHIDE, SHINOHARA MASAKAZU. Spinal Muscular Atrophy: New Screening System with Real-Time mCOP-PCR and PCR-RFLP for SMN1 Deletion. Kobe J Med Sci 2019; 65:E44-E48. [PMID: 31956255 PMCID: PMC7012196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Spinal Muscular Atrophy (SMA) is a common autosomal recessive neuromuscular disorder characterized by degeneration or loss of lower motor neurons. More than 95% of SMA patients show homozygous deletion for the survival motor neuron 1 (SMN1) gene. For the screening of SMN1 deletion, it is necessary to differentiate SMN1 from its highly homologous gene, SMN2. We developed a modified competitive oligonucleotide priming-PCR (mCOP-PCR) method using dried blood spot (DBS)-DNA, in which SMN1 and SMN2-specific PCR products are detected with gel-electrophoresis. Next, we added a targeted pre-amplification step prior to the mCOP-PCR step, to avoid unexpected, non-specific amplification. The pre-amplification step enabled us to combine mCOP-PCR and real-time PCR. In this study, we combined real-time mCOP-PCR and PCR-restriction fragment length polymorphism (PCR-RFLP) to develop a new screening system for detection of SMN1 deletion. METHODS DBS samples of the subjects were stored at room temperature for a period of less than one year. Each subject had already been genotyped by the first PCR-RFLP using fresh blood DNA. SMN1/SMN2 exon 7 was collectively amplified using conventional PCR (targeted pre-amplification), the products of which were then used as a template in the real-time PCR with mCOP-primer sets. To confirm the results, the pre-amplified products were subject to the second PCR-RFLP. RESULTS The real-time mCOP-PCR separately amplified SMN1 and SMN2 exon7, and clearly demonstrated SMN1 deletion in an SMA patient. The results of the real-time mCOP-PCR using DBS-DNA were completely consistent with those of the first and second PCR-RFLP analysis. CONCLUSION In our new system for detection of SMN1 deletion, real-time mCOP-PCR rapidly proved the presence or absence of SMN1 and SMN2, and the results were easily tested by PCR-RFLP. This solid genotyping system will be useful for SMA screening.
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Affiliation(s)
- EMMA TABE EKO NIBA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MAWADDAH AR ROCHMAH
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - NUR IMMA FATIMAH HARAHAP
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - HIROYUKI AWANO
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - ICHIRO MORIOKA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - KAZUMOTO IIJIMA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - TOSHIO SAITO
- Division of Child Neurology, Department of Neurology, National Hospital Organization Toneyama National Hospital, Toneyama, Japan
| | - KAYOKO SAITO
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | | | - POH SAN LAI
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - MASAFUMI MATSUO
- Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - HISAHIDE NISHIO
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
- Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - MASAKAZU SHINOHARA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
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WIJAYA YOGIKONKYSILVANA, NIBA EMMATABEEKO, ROCHMAH MAWADDAHAR, HARAHAP NURIMMAFATIMAH, AWANO HIROYUKI, TAKESHIMA YASUHIRO, SAITO TOSHIO, SAITO KAYOKO, TAKEUCHI ATSUKO, LAI POHSAN, BOUIKE YOSHIHIRO, NISHIO HISAHIDE, SHINOHARA MASAKAZU. Nested PCR Amplification Secures DNA Template Quality and Quantity in Real-time mCOP-PCR Screening for SMA. Kobe J Med Sci 2019; 65:E54-E58. [PMID: 31956257 PMCID: PMC7012193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 05/27/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Spinal Muscular Atrophy (SMA) is a common autosomal recessive disorder caused by SMN1 gene deletion. SMA has been considered an incurable disease. However, a newly-developed antisense oligonucleotide drug, nusinersen, brings about a good outcome to SMA patients in the clinical trials. Now, a screening for SMA is required for early diagnosis and early treatment so as to give a better clinical outcome to the patients. We have invented a new technology, mCOP-PCR, for SMA screening using dried blood spot (DBS) on the filter paper. One of the problems encountered in SMA screening is poor quality and quantity of DNA extracted from DBS. METHODS DNA was extracted from DBS of six individuals. Fresh blood DNA of each individual had already been genotyped using PCR/RFLP. The fragments including the sequence of SMN1/SMN2 exon 7 were pre-amplified with conventional PCR. To determine which pre-amplified product is a better template for the real-time mCOP-PCR, we did pre-amplification with a single PCR or pre-amplification with a nested PCR. RESULTS The real-time mCOP-PCR using pre-amplified products with a single PCR brought about ambiguous results in some SMN1-carrying individuals. However, the results of real-time mCOP-PCR following pre-amplification with a nested PCR were completely matched with those of PCR-RFLP. CONCLUSION In our study on the real-time mCOP-PCR screening system for SMA, a nested PCR secured the DNA template quality and quantity, leading to unambiguous results of SMA screening.
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Affiliation(s)
- YOGIK ONKY SILVANA WIJAYA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - EMMA TABE EKO NIBA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MAWADDAH AR ROCHMAH
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - NUR IMMA FATIMAH HARAHAP
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - HIROYUKI AWANO
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - TOSHIO SAITO
- Division of Child Neurology, Department of Neurology, National Hospital Organization Toneyama National Hospital, Toneyama, Japan
| | - KAYOKO SAITO
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | | | - POH SAN LAI
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - HISAHIDE NISHIO
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
- Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - MASAKAZU SHINOHARA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
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NIBA EMMATABEEKO, ROCHMAH MAWADDAHAR, HARAHAP NURIMMAFATIMAH, AWANO HIROYUKI, MORIOKA ICHIRO, IIJIMA KAZUMOTO, SAITO TOSHIO, SAITO KAYOKO, TAKEUCHI ATSUKO, LAI POHSAN, BOUIKE YOSHIHIRO, NISHIO HISAHIDE, SHINOHARA MASAKAZU. SMA Diagnosis: Detection of SMN1 Deletion with Real-Time mCOP-PCR System Using Fresh Blood DNA. Kobe J Med Sci 2017; 63:E80-E83. [PMID: 29434179 PMCID: PMC5826024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 08/21/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is one of the most common autosomal recessive disorders. The symptoms are caused by defects of lower motor neurons in the spinal cord. More than 95% of SMA patients are homozygous for survival motor neuron 1 (SMN1) deletion. We previously developed a screening system for SMN1 deletion based on a modified competitive oligonucleotide priming-PCR (mCOP-PCR) technique using dried blood spot (DBS) on filter paper. This system is convenient for mass screening in the large population and/or first-tier diagnostic method of the patients in the remote areas. However, this system was still time-consuming and effort-taking, because it required pre-amplification procedure to avoid non-specific amplification and gel-electrophoresis to detect the presence or absence of SMN1 deletion. When the fresh blood samples are used instead of DBS, or when the gel-electrophoresis is replaced by real-time PCR, we may have a simpler and more rapid diagnostic method for SMA. AIM To establish a simpler and more rapid diagnostic method of SMN1 deletion using fresh blood DNA. METHODS DNA samples extracted from fresh blood and stored at 4 ℃ for 1 month. The samples were assayed using a real-time mCOP-PCR system without pre-amplification procedures. DNA samples had already been genotyped by PCR-restriction fragment length polymorphism (PCR-RFLP), showing the presence or absence of SMN1 exon 7. The DNA samples were directly subjected to the mCOP-PCR step. The amplification of mCOP-PCR was monitored in a real-time PCR apparatus. RESULTS The genotyping results of the real-time mCOP-PCR system using fresh blood DNA were completely matched with those of PCR-RFLP. In this real-time mCOP-PCR system using fresh blood-DNA, it took only four hours from extraction of DNA to detection of the presence or absence of SMN1 deletion, while it took more than 12 hours in PCR-RFLP. CONCLUSION Our real-time mCOP-PCR system using fresh blood DNA was rapid and accurate, suggesting it may be useful for the first-tier diagnostic method of SMA.
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Affiliation(s)
- EMMA TABE EKO NIBA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MAWADDAH AR ROCHMAH
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - NUR IMMA FATIMAH HARAHAP
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - HIROYUKI AWANO
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - ICHIRO MORIOKA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - KAZUMOTO IIJIMA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - TOSHIO SAITO
- Division of Child Neurology, Department of Neurology, National Hospital Organization Toneyama National Hospital, Toneyama, Japan
| | - KAYOKO SAITO
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | | | - POH SAN LAI
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - HISAHIDE NISHIO
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MASAKAZU SHINOHARA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
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ROCHMAH MAWADDAHAR, SHIMA AI, HARAHAP NURIMMAFATIMAH, NIBA EMMATABEEKO, MORISADA NAOYA, YANAGISAWA SHINICHIRO, SAITO TOSHIO, KANEKO KAORI, SAITO KAYOKO, MORIOKA ICHIRO, IIJIMA KAZUMOTO, LAI POHSAN, BOUIKE YOSHIHIRO, NISHIO HISAHIDE, SHINOHARA MASAKAZU. Gender Effects on the Clinical Phenotype in Japanese Patients with Spinal Muscular Atrophy. Kobe J Med Sci 2017; 63:E41-E44. [PMID: 29434173 PMCID: PMC5826018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 06/20/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a neuromuscular disease caused by a mutation in SMN1. SMA is classified into three subtypes (types 1, 2, 3) based on achieved motor milestones. Although NAIP and SMN2 are widely accepted as SMA-modifying factors, gender-related modifying factors or gender effects on the clinical phenotype are still controversial. METHODS A total of 122 Japanese patients with SMA, of which SMN1 was homozygously deleted, were analyzed from the perspective of the achieved motor milestone, NAIP status and SMN2 copy number. RESULTS A predominance of male patients was observed in SMA type 3 (the walker group) without NAIP-deletion or with high SMN2 copy number (3 or 4 copies). CONCLUSION We suggest the presence of gender-related modifiers on disease severity in SMA patients. The modifiers may contribute only in the presence of NAIP and a high copy number of SMN2.
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Affiliation(s)
- MAWADDAH AR ROCHMAH
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
| | - AI SHIMA
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
- Institute of Industrial Science, University of Tokyo, Tokyo, Japan
| | - NUR IMMA FATIMAH HARAHAP
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
| | - EMMA TABE EKO NIBA
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
| | - NAOYA MORISADA
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Clinical Genetics, Hyogo Prefectural Kobe Children’s Hospital, Kobe, Japan
| | | | - TOSHIO SAITO
- Division of Child Neurology, Department of Neurology, National Hospital Organization Toneyama National Hospital, Toyonaka, Japan
| | - KAORI KANEKO
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | - KAYOKO SAITO
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | - ICHIRO MORIOKA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - KAZUMOTO IIJIMA
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - POH SAN LAI
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | - HISAHIDE NISHIO
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MASAKAZU SHINOHARA
- Department of Community Medicine and Social Health Care, Kobe University Graduate School of Medicine, Kobe, Japan
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SHINOHARA MASAKAZU, ROCHMAH MAWADDAHAR, NAKANISHI KENTA, HARAHAP NURIMMAFATIMAH, NIBA EMMATABEEKO, SAITO TOSHIO, SAITO KAYOKO, TAKEUCHI ATSUKO, BOUIKE YOSHIHIRO, NISHIO HISAHIDE. New, Improved Version of the mCOP-PCR Screening System for Detection of Spinal Muscular Atrophy Gene (SMN1) Deletion. Kobe J Med Sci 2017; 63:E37-E40. [PMID: 29434172 PMCID: PMC5826017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/01/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a frequent autosomal recessive disorder, characterized by lower motor neuron loss in the spinal cord. More than 95% of SMA patients show homozygous survival motor neuron 1 (SMN1) deletion. We previously developed a screening system for SMN1 deletion based on a modified competitive oligonucleotide priming-PCR (mCOP-PCR) technique. However, non-specific amplification products were observed with mCOP-PCR, which might lead to erroneous interpretation of the screening results. AIM To establish an improved version of the mCOP-PCR screening system without non-specific amplification. METHODS DNA samples were assayed using a new version of the mCOP-PCR screening system. DNA samples had already been genotyped by PCR-restriction fragment length polymorphism (PCR-RFLP), showing the presence or absence of SMN1 exon 7. The new mCOP-PCR method contained a targeted pre-amplification step of the region, including an SMN1-specific nucleotide, prior to the mCOP-PCR step. mCOP-PCR products were electrophoresed on agarose gels. RESULTS No non-specific amplification products were detected in electrophoresis gels with the new mCOP-PCR screening system. CONCLUSION An additional targeted pre-amplification step eliminated non-specific amplification from mCOP-PCR screening.
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Affiliation(s)
- MASAKAZU SHINOHARA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - MAWADDAH AR ROCHMAH
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - KENTA NAKANISHI
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - NUR IMMA FATIMAH HARAHAP
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - EMMA TABE EKO NIBA
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - TOSHIO SAITO
- Division of Child Neurology, Department of Neurology, National Hospital Organization Toneyama National Hospital, Toneyama, Japan
| | - KAYOKO SAITO
- Institute of Medical Genetics, Tokyo Women’s Medical University, Tokyo, Japan
| | | | | | - HISAHIDE NISHIO
- Department of Community Medicine and Social Healthcare Science, Kobe University Graduate School of Medicine, Kobe, Japan
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HARTOMO TRIBUDI, KOZAKI AIKO, HASEGAWA DAIICHIRO, VAN HUYEN PHAM THI, YAMAMOTO NOBUYUKI, SAITOH ATSURO, ISHIDA TOSHIAKI, KAWASAKI KEIICHIRO, KOSAKA YOSHIYUKI, OHASHI HIROKI, YAMAMOTO TOMOTO, MORIKAWA SATORU, HIRASE SATOSHI, KUBOKAWA IKUKO, MORI TAKESHI, YANAI TOMOKO, HAYAKAWA AKIRA, TAKESHIMA YASUHIRO, IIJIMA KAZUMOTO, MATSUO MASAFUMI, NISHIO HISAHIDE, NISHIMURA NORIYUKI. Minimal residual disease monitoring in neuroblastoma patients based on the expression of a set of real-time RT-PCR markers in tumor-initiating cells. Oncol Rep 2013; 29:1629-36. [DOI: 10.3892/or.2013.2286] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 12/28/2012] [Indexed: 11/06/2022] Open
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