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Yang Y, Ma B, Chen J, Liu D, Ma J, Li B, Hao J, Zhou X. Epigenetic regulation and factors that influence the effect of iPSCs-derived neural stem/progenitor cells (NS/PCs) in the treatment of spinal cord injury. Clin Epigenetics 2024; 16:30. [PMID: 38383473 PMCID: PMC10880347 DOI: 10.1186/s13148-024-01639-5] [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: 10/19/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024] Open
Abstract
Spinal cord injury (SCI) is a severe neurological disorder that causes neurological impairment and disability. Neural stem/progenitor cells (NS/PCs) derived from induced pluripotent stem cells (iPSCs) represent a promising cell therapy strategy for spinal cord regeneration and repair. However, iPSC-derived NS/PCs face many challenges and issues in SCI therapy; one of the most significant challenges is epigenetic regulation and that factors that influence this mechanism. Epigenetics refers to the regulation of gene expression and function by DNA methylation, histone modification, and chromatin structure without changing the DNA sequence. Previous research has shown that epigenetics plays a crucial role in the generation, differentiation, and transplantation of iPSCs, and can influence the quality, safety, and outcome of transplanted cells. In this study, we review the effects of epigenetic regulation and various influencing factors on the role of iPSC-derived NS/PCs in SCI therapy at multiple levels, including epigenetic reprogramming, regulation, and the adaptation of iPSCs during generation, differentiation, and transplantation, as well as the impact of other therapeutic tools (e.g., drugs, electrical stimulation, and scaffolds) on the epigenetic status of transplanted cells. We summarize our main findings and insights in this field and identify future challenges and directions that need to be addressed and explored.
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Affiliation(s)
- Yubiao Yang
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Boyuan Ma
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China
| | - Jinyu Chen
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China
| | - Derong Liu
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Jun Ma
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, People's Republic of China
| | - Bo Li
- Department of Orthopedics, Beijing Luhe Hospital, Capital Medical University, Beijing, People's Republic of China
| | - Jian Hao
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China.
| | - Xianhu Zhou
- The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510260, People's Republic of China.
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Khan T, Becker TM, Po JW, Chua W, Ma Y. Single-Circulating Tumor Cell Whole Genome Amplification to Unravel Cancer Heterogeneity and Actionable Biomarkers. Int J Mol Sci 2022; 23:ijms23158386. [PMID: 35955517 PMCID: PMC9369222 DOI: 10.3390/ijms23158386] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 12/04/2022] Open
Abstract
The field of single-cell analysis has advanced rapidly in the last decade and is providing new insights into the characterization of intercellular genetic heterogeneity and complexity, especially in human cancer. In this regard, analyzing single circulating tumor cells (CTCs) is becoming particularly attractive due to the easy access to CTCs from simple blood samples called “liquid biopsies”. Analysis of multiple single CTCs has the potential to allow the identification and characterization of cancer heterogeneity to guide best therapy and predict therapeutic response. However, single-CTC analysis is restricted by the low amounts of DNA in a single cell genome. Whole genome amplification (WGA) techniques have emerged as a key step, enabling single-cell downstream molecular analysis. Here, we provide an overview of recent advances in WGA and their applications in the genetic analysis of single CTCs, along with prospective views towards clinical applications. First, we focus on the technical challenges of isolating and recovering single CTCs and then explore different WGA methodologies and recent developments which have been utilized to amplify single cell genomes for further downstream analysis. Lastly, we list a portfolio of CTC studies which employ WGA and single-cell analysis for genetic heterogeneity and biomarker detection.
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Affiliation(s)
- Tanzila Khan
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (T.K.); (T.M.B.); (W.C.)
- Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia
- Centre of Circulating Tumor Cells Diagnostics & Research, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia;
| | - Therese M. Becker
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (T.K.); (T.M.B.); (W.C.)
- Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia
- Centre of Circulating Tumor Cells Diagnostics & Research, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia;
- South West Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia
| | - Joseph W. Po
- Centre of Circulating Tumor Cells Diagnostics & Research, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia;
- Surgical Innovations Unit, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Wei Chua
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (T.K.); (T.M.B.); (W.C.)
- Medical Oncology, Liverpool Hospital, Liverpool, NSW 2170, Australia
| | - Yafeng Ma
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia; (T.K.); (T.M.B.); (W.C.)
- Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia
- Centre of Circulating Tumor Cells Diagnostics & Research, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia;
- South West Sydney Clinical School, University of New South Wales, Liverpool, NSW 2170, Australia
- Correspondence:
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Kojima M, Harada T, Fukazawa T, Kurihara S, Saeki I, Takahashi S, Hiyama E. Single-cell DNA and RNA sequencing of circulating tumor cells. Sci Rep 2021; 11:22864. [PMID: 34819539 PMCID: PMC8613180 DOI: 10.1038/s41598-021-02165-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/03/2021] [Indexed: 01/02/2023] Open
Abstract
Single-cell sequencing of circulating tumor cells can precisely represent tumor heterogeneity and provide useful information for cancer treatment and research. After spiking TGW neuroblastoma cells into blood derived from healthy volunteer, the cells were isolated by fluorescence-activated cell sorting. DNA and mRNA were amplified by four different whole-genome amplifications (WGA) and three whole-transcriptome amplifications (WTA) methods, followed by single-cell DNA and RNA sequencing. Multiple displacement amplification (MDA)-based WGA methods showed higher amplification efficiency than other methods with a comparable depth of coverage as the bulk sample. The uniformity of coverage greatly differed among samples (12.5–89.2%), with some samples evaluated by the MDA-based WGA method using phi29 DNA polymerase and random primers showing a high (> 80%) uniformity of coverage. The MDA-based WTA method less effectively amplified mRNA and showed non-specific gene expression patterns. The PCR-based WTA using template switching with locked nucleic acid technology accurately amplified mRNA from a single cell. Taken together, our results present a more reliable and adaptable approach for CTC profiling at the single-cell level. Such molecular information on CTCs derived from clinical patients will promote cancer treatment and research.
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Affiliation(s)
- Masato Kojima
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.,Natural Science Center for Basic Research and Development (N-BARD), Hiroshima University, Hiroshima, Japan
| | - Takanori Harada
- Natural Science Center for Basic Research and Development (N-BARD), Hiroshima University, Hiroshima, Japan
| | - Takahiro Fukazawa
- Natural Science Center for Basic Research and Development (N-BARD), Hiroshima University, Hiroshima, Japan
| | - Sho Kurihara
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Isamu Saeki
- Department of Pediatric Surgery, Hiroshima University Hospital, Hiroshima, Japan
| | - Shinya Takahashi
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Eiso Hiyama
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan. .,Natural Science Center for Basic Research and Development (N-BARD), Hiroshima University, Hiroshima, Japan.
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Verdyck P, Berckmoes V, Van Laere S, Keymolen K, Olsen C, De Rycke M. Analysis of parental contribution for aneuploidy detection (APCAD): a novel method to detect aneuploidy and mosaicism in preimplantation embryos. Reprod Biomed Online 2021; 44:459-468. [PMID: 34930679 DOI: 10.1016/j.rbmo.2021.10.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/03/2021] [Accepted: 10/29/2021] [Indexed: 12/27/2022]
Abstract
RESEARCH QUESTION Can (mosaic) aneuploidy be reliably detected in preimplantation embryos after multiple displacement amplification and single nucleotide polymorphism detection, independent of haplotyping and copy number detection, with a new method 'analysis of parental contribution for aneuploidy detection' or 'APCAD'? DESIGN This method is based on the maternal contribution, a parameter that reflects the proportion of DNA that is of maternal origin for a given chromosome or chromosome segment. A maternal contribution deviating from 50% for autosomes is strongly indicative of a (mosaic) chromosomal anomaly. The method was optimized using cell mixtures with varying ratios of euploid and aneuploid (47,XY,+21) lymphocytes. Next, the maternal contribution was retrospectively measured for all chromosomes from 349 Karyomapping samples. RESULTS Retrospective analysis showed a skewed maternal contribution (<36.4 or >63.6%) in 57 out of 59 autosome meiotic trisomies and all autosome monosomies (n = 57), with values close to theoretical expectation. Thirty-two out of 7436 chromosomes, for which no anomalies had been observed with Karyomapping, showed a similarly skewed maternal contribution. CONCLUSIONS APCAD was used to measure the maternal contribution, which is an intuitive parameter independent of copy number detection. This method is useful for detecting copy number neutral anomalies and can confirm diagnosis of (mosaic) aneuploidy detected based on copy number. Mosaic and complete aneuploidy can be distinguished and the parent of origin for (mosaic) chromosome anomalies can be determined. Because of these benefits, the APCAD method has the potential to improve aneuploidy detection carried out by comprehensive preimplantation genetic testing methods.
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Affiliation(s)
- Pieter Verdyck
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium.
| | - Veerle Berckmoes
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Sven Van Laere
- Vrije Universiteit Brussel (VUB), Interfaculty Center Data Processing and Statistics, Laarbeeklaan 103, Brussels 1090, Belgium
| | - Kathelijn Keymolen
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Catharina Olsen
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium; Brussels Interuniversity Genomics High Throughput core (BRIGHTcore), VUB-ULB, Laarbeeklaan 101, Brussels 1090, Belgium
| | - Martine De Rycke
- Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Centrum Medische Genetica, Laarbeeklaan 101, Brussels 1090, Belgium
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Long N, Qiao Y, Xu Z, Tu J, Lu Z. Recent advances and application in whole-genome multiple displacement amplification. QUANTITATIVE BIOLOGY 2020. [DOI: 10.1007/s40484-020-0217-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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De Rycke M, Berckmoes V. Preimplantation Genetic Testing for Monogenic Disorders. Genes (Basel) 2020; 11:E871. [PMID: 32752000 PMCID: PMC7463885 DOI: 10.3390/genes11080871] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/17/2022] Open
Abstract
Preimplantation genetic testing (PGT) has evolved into a well-established alternative to invasive prenatal diagnosis, even though genetic testing of single or few cells is quite challenging. PGT-M is in theory available for any monogenic disorder for which the disease-causing locus has been unequivocally identified. In practice, the list of indications for which PGT is allowed may vary substantially from country to country, depending on PGT regulation. Technically, the switch from multiplex PCR to robust generic workflows with whole genome amplification followed by SNP array or NGS represents a major improvement of the last decade: the waiting time for the couples has been substantially reduced since the customized preclinical workup can be omitted and the workload for the laboratories has decreased. Another evolution is that the generic methods now allow for concurrent analysis of PGT-M and PGT-A. As innovative algorithms are being developed and the cost of sequencing continues to decline, the field of PGT moves forward to a sequencing-based, all-in-one solution for PGT-M, PGT-SR, and PGT-A. This will generate a vast amount of complex genetic data entailing new challenges for genetic counseling. In this review, we summarize the state-of-the-art for PGT-M and reflect on its future.
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Affiliation(s)
- Martine De Rycke
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Laarbeeklaan 101, 1090 Brussels, Belgium;
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Lu S, Chang CJ, Guan Y, Szafer-Glusman E, Punnoose E, Do A, Suttmann B, Gagnon R, Rodriguez A, Landers M, Spoerke J, Lackner MR, Xiao W, Wang Y. Genomic Analysis of Circulating Tumor Cells at the Single-Cell Level. J Mol Diagn 2020; 22:770-781. [PMID: 32247862 PMCID: PMC8351127 DOI: 10.1016/j.jmoldx.2020.02.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/20/2019] [Accepted: 02/28/2020] [Indexed: 01/22/2023] Open
Abstract
Circulating tumor cells (CTCs) have a great potential for noninvasive diagnosis and real-time monitoring of cancer. A comprehensive evaluation of four whole genome amplification (WGA)/next-generation sequencing workflows for genomic analysis of single CTCs, including PCR-based (GenomePlex and Ampli1), multiple displacement amplification (Repli-g), and hybrid PCR- and multiple displacement amplification–based [multiple annealing and loop-based amplification cycling (MALBAC)] is reported herein. To demonstrate clinical utilities, copy number variations (CNVs) in single CTCs isolated from four patients with squamous non–small-cell lung cancer were profiled. Results indicate that MALBAC and Repli-g WGA have significantly broader genomic coverage compared with GenomePlex and Ampli1. Furthermore, MALBAC coupled with low-pass whole genome sequencing has better coverage breadth, uniformity, and reproducibility and is superior to Repli-g for genome-wide CNV profiling and detecting focal oncogenic amplifications. For mutation analysis, none of the WGA methods were found to achieve sufficient sensitivity and specificity by whole exome sequencing. Finally, profiling of single CTCs from patients with non–small-cell lung cancer revealed potentially clinically relevant CNVs. In conclusion, MALBAC WGA coupled with low-pass whole genome sequencing is a robust workflow for genome-wide CNV profiling at single-cell level and has great potential to be applied in clinical investigations. Nevertheless, data suggest that none of the evaluated single-cell sequencing workflows can reach sufficient sensitivity or specificity for mutation detection required for clinical applications.
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Affiliation(s)
- Shan Lu
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California; Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, California
| | - Chia-Jung Chang
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, California
| | - Yinghui Guan
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California
| | - Edith Szafer-Glusman
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California
| | - Elizabeth Punnoose
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California
| | - An Do
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California
| | - Becky Suttmann
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California
| | - Ross Gagnon
- Division of Expression Analysis Genomics, Q2 Solutions, Morrisville, North Carolina
| | - Angel Rodriguez
- Department of Translational Research, Epic Sciences Inc., San Diego, California
| | - Mark Landers
- Department of Translational Research, Epic Sciences Inc., San Diego, California
| | - Jill Spoerke
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California
| | - Mark R Lackner
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, California.
| | - Yulei Wang
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, California.
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Hong S, Wang L, Zhao D, Zhang Y, Chen Y, Tan J, Liang L, Zhu T. Clinical utility in infants with suspected monogenic conditions through next-generation sequencing. Mol Genet Genomic Med 2019; 7:e684. [PMID: 30968598 PMCID: PMC6565546 DOI: 10.1002/mgg3.684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/06/2019] [Accepted: 03/04/2019] [Indexed: 12/14/2022] Open
Abstract
Background Rare diseases are complex disorders with huge variability in clinical manifestations. Decreasing cost of next‐generation sequencing (NGS) tests in recent years made it affordable. We witnessed the diagnostic yield and clinical use of different NGS strategies on a myriad of monogenic disorders in a pediatric setting. Methods Next‐generation sequencing tests are performed for 98 unrelated Chinese patients within their first year of life, who were admitted to Xin Hua Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, during a 2‐year period. Results Clinical indications for NGS tests included a range of medical concerns. The mean age was 4.4 ± 4.2 months of age for infants undergoing targeting specific (known) disease‐causing genes (TRS) analysis, and 4.4 ± 4.3 months of age for whole‐exome sequencing (WES) (p > 0.05). A molecular diagnosis is done in 72 infants (73.47%), which finds a relatively high yield with phenotypes of metabolism/homeostasis abnormality (HP: 0001939) (odds ratio, 1.83; 95% CI, 0.56–6.04; p = 0.32) and a significantly low yield with atypical symptoms (without a definite HPO term) (odds ratio, 0.08; 95% CI, 0.01–0.73; p = 0.03). TRS analysis provides molecular yields higher than WES (p = 0.01). Ninety‐eight different mutations are discovered in 72 patients. Twenty‐seven of them have not been reported previously. Nearly half (43.06%, 31/72) of the patients are found to carry 11 common disorders, mostly being inborn errors of metabolism (IEM) and neurogenetic disorders and all of them are observed through TRS analysis. Eight positive cases are identified through WES, and all of them are sporadic, of highly variable phenotypes and severity. There are 26 patients with negative findings in this study. Conclusion This study provides evidence that NGS can yield high success rates in a tertiary pediatric setting, but suggests that the scope of known Mendelian conditions may be considerably broader than currently recognized.
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Affiliation(s)
- Sha Hong
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Wang
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongying Zhao
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yonghong Zhang
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Chen
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jintong Tan
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lili Liang
- Department of Endocrinology and Genetic Metabolism, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tianwen Zhu
- Department of Neonatal Medicine, Xin-Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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