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Araki R, Suga T, Hoki Y, Imadome K, Sunayama M, Kamimura S, Fujita M, Abe M. iPS cell generation-associated point mutations include many C > T substitutions via different cytosine modification mechanisms. Nat Commun 2024; 15:4946. [PMID: 38862540 PMCID: PMC11166658 DOI: 10.1038/s41467-024-49335-5] [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: 04/17/2023] [Accepted: 05/31/2024] [Indexed: 06/13/2024] Open
Abstract
Genomic aberrations are a critical impediment for the safe medical use of iPSCs and their origin and developmental mechanisms remain unknown. Here we find through WGS analysis of human and mouse iPSC lines that genomic mutations are de novo events and that, in addition to unmodified cytosine base prone to deamination, the DNA methylation sequence CpG represents a significant mutation-prone site. CGI and TSS regions show increased mutations in iPSCs and elevated mutations are observed in retrotransposons, especially in the AluY subfamily. Furthermore, increased cytosine to thymine mutations are observed in differentially methylated regions. These results indicate that in addition to deamination of cytosine, demethylation of methylated cytosine, which plays a central role in genome reprogramming, may act mutagenically during iPSC generation.
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Affiliation(s)
- Ryoko Araki
- Stem Cell Biology Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan.
- Department of Radiation Regulatory Science Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan.
| | - Tomo Suga
- Stem Cell Biology Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Radiation Regulatory Science Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Yuko Hoki
- Stem Cell Biology Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Radiation Regulatory Science Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Kaori Imadome
- Stem Cell Biology Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Radiation Regulatory Science Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Misato Sunayama
- Stem Cell Biology Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Radiation Regulatory Science Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Satoshi Kamimura
- Stem Cell Biology Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Radiation Regulatory Science Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Mayumi Fujita
- Stem Cell Biology Team, Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
- Department of Radiation Regulatory Science Research, Institute for Radiological Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Masumi Abe
- Institute for Quantum Medical Science, National Institutes for Quantum Science and Technology, Chiba, Japan.
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Alowaysi M, Lehmann R, Al-Shehri M, Baadhaim M, Alzahrani H, Aboalola D, Zia A, Malibari D, Daghestani M, Alghamdi K, Haneef A, Jawdat D, Hakami F, Gomez-Cabrero D, Tegner J, Alsayegh K. HLA-based banking of induced pluripotent stem cells in Saudi Arabia. Stem Cell Res Ther 2023; 14:374. [PMID: 38111036 PMCID: PMC10729375 DOI: 10.1186/s13287-023-03612-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/07/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Human iPSCs' derivation and use in clinical studies are transforming medicine. Yet, there is a high cost and long waiting time associated with autologous iPS-based cellular therapy, and the genetic engineering of hypo-immunogenic iPS cell lines is hampered with numerous hurdles. Therefore, it is increasingly interesting to create cell stocks based on HLA haplotype distribution in a given population. This study aimed to assess the potential of HLA-based iPS banking for the Saudi population. METHODS In this study, we interrogated the HLA database of the Saudi Stem Cell Donor Registry (SSCDR), containing high-resolution HLA genotype data from 64,315 registered Saudi donors at the time of analysis. This database was considered to be a representative sample of the Saudi population. The most frequent HLA haplotypes in the Saudi population were determined, and an in-house developed iterative algorithm was used to identify their HLA matching percentages in the SSCDR database and cumulative coverage. Subsequently, to develop a clinically relevant protocol for iPSCs generation, and to illustrate the applicability of the concept of HLA-based banking for cell therapy purposes, the first HLA-based iPS cell line in Saudi Arabia was generated. Clinically relevant methods were employed to generate the two iPS clones from a homozygous donor for the most prevalent HLA haplotype in the Saudi population. The generated lines were then assessed for pluripotency markers, and their ability to differentiate into all three germ layers, beating cardiomyocytes, and neural progenitors was examined. Additionally, the genetic stability of the HLA-iPS cell lines was verified by comparing the mutational burden in the clones and the original blood sample, using whole-genome sequencing. The standards set by the American College of Medical Genetics and Genomics (ACMG) were used to determine the clinical significance of identified variants. RESULTS The analysis revealed that the establishment of only 13 iPSC lines would match 30% of the Saudi population, 39 lines would attain 50% coverage, and 596 lines would be necessary for over 90% coverage. The proof-of-concept HLA-iPSCs, which cover 6.1% of the Saudi population, successfully demonstrated pluripotency and the ability to differentiate into various cell types including beating cardiomyocytes and neuronal progenitors. The comprehensive genetic analysis corroborated that all identified variants in the derived iPSCs were inherently present in the original donor sample and were classified as benign according to the standards set by the ACMG. CONCLUSIONS Our study sets a road map for introducing iPS-based cell therapy in the Kingdom of Saudi Arabia. It underscores the pragmatic approach of HLA-based iPSC banking which circumvents the limitations of autologous iPS-based cellular therapies. The successful generation and validation of iPSC lines based on the most prevalent HLA haplotype in the Saudi population signify a promising step toward broadening the accessibility and applicability of stem cell therapies and regenerative medicine in Saudi Arabia.
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Affiliation(s)
- Maryam Alowaysi
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard for Health Affairs, Jeddah, Saudi Arabia
| | - Robert Lehmann
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohammad Al-Shehri
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard for Health Affairs, Jeddah, Saudi Arabia
| | - Moayad Baadhaim
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard for Health Affairs, Jeddah, Saudi Arabia
| | - Hajar Alzahrani
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard for Health Affairs, Jeddah, Saudi Arabia
| | - Doaa Aboalola
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard for Health Affairs, Jeddah, Saudi Arabia
| | - Asima Zia
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dalal Malibari
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard for Health Affairs, Jeddah, Saudi Arabia
| | - Mustafa Daghestani
- Molecular Medicine Section, Department of Pathology and Laboratory Medicine, Ministry of the National Guard - Health Affairs, Jeddah, Saudi Arabia
| | - Khaled Alghamdi
- Forensic Laboratories, Criminal Evidence Department, Jeddah, Saudi Arabia
| | - Ali Haneef
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard for Health Affairs, Jeddah, Saudi Arabia
| | - Dunia Jawdat
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard for Health Affairs, Jeddah, Saudi Arabia
| | - Fahad Hakami
- Molecular Medicine Section, Department of Pathology and Laboratory Medicine, Ministry of the National Guard - Health Affairs, Jeddah, Saudi Arabia
| | - David Gomez-Cabrero
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jesper Tegner
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Khaled Alsayegh
- King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard for Health Affairs, Jeddah, Saudi Arabia.
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