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Park CS, Habib O, Lee Y, Hur JK. Applications of CRISPR technologies to the development of gene and cell therapy. BMB Rep 2024; 57:2-11. [PMID: 38178651 PMCID: PMC10828430] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 01/06/2024] Open
Abstract
Advancements in gene and cell therapy have resulted in novel therapeutics for diseases previously considered incurable or challenging to treat. Among the various contributing technologies, genome editing stands out as one of the most crucial for the progress in gene and cell therapy. The discovery of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and the subsequent evolution of genetic engineering technology have markedly expanded the field of target-specific gene editing. Originally studied in the immune systems of bacteria and archaea, the CRISPR system has demonstrated wide applicability to effective genome editing of various biological systems including human cells. The development of CRISPR-based base editing has enabled directional cytosine-tothymine and adenine-to-guanine substitutions of select DNA bases at the target locus. Subsequent advances in prime editing further elevated the flexibility of the edit multiple consecutive bases to desired sequences. The recent CRISPR technologies also have been actively utilized for the development of in vivo and ex vivo gene and cell therapies. We anticipate that the medical applications of CRISPR will rapidly progress to provide unprecedented possibilities to develop novel therapeutics towards various diseases. [BMB Reports 2024; 57(1): 2-11].
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Affiliation(s)
- Chul-Sung Park
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
| | - Omer Habib
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Younsu Lee
- Division of R&D, RedGene Inc., Seoul 08790, Korea
| | - Junho K. Hur
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea
- Department of Genetics, College of Medicine, Hanyang University, Seoul 04763, Korea
- Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Korea
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2
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Seo BJ, Na SB, Choi J, Ahn B, Habib O, Park C, Hong K, Do JT. Metabolic and cell cycle shift induced by the deletion of Dnm1l attenuates the dissolution of pluripotency in mouse embryonic stem cells. Cell Mol Life Sci 2023; 80:302. [PMID: 37747543 DOI: 10.1007/s00018-023-04962-x] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/26/2023]
Abstract
Mitochondria are versatile organelles that continuously change their morphology via fission and fusion. However, the detailed functions of mitochondrial dynamics-related genes in pluripotent stem cells remain largely unclear. Here, we aimed to determine the effects on energy metabolism and differentiation ability of mouse embryonic stem cells (ESCs) following deletion of the mitochondrial fission-related gene Dnml1. Resultant Dnm1l-/- ESCs maintained major pluripotency characteristics. However, Dnm1l-/- ESCs showed several phenotypic changes, including the inhibition of differentiation ability (dissolution of pluripotency). Notably, Dnm1l-/- ESCs maintained the expression of the pluripotency marker Oct4 and undifferentiated colony types upon differentiation induction. RNA sequencing analysis revealed that the most frequently differentially expressed genes were enriched in the glutathione metabolic pathway. Our data suggested that differentiation inhibition of Dnm1l-/- ESCs was primarily due to metabolic shift from glycolysis to OXPHOS, G2/M phase retardation, and high level of Nanog and 2-cell-specific gene expression.
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Affiliation(s)
- Bong Jong Seo
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seung Bin Na
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Joonhyuk Choi
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Byeongyong Ahn
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Omer Habib
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Chankyu Park
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jeong Tae Do
- Department of Stem Cell and Regenerative Biotechnology, Konkuk Institute of Technology, Konkuk University, Seoul, 05029, Republic of Korea.
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Shin HY, Jang S, Woo HJ, Chung JH, Kim WH, Kim D, Kang M, Lim Y, Habib O, Lee J, Yang S, Lee DH, Kim MS. Cytokine engineered NK-92 therapy to improve persistence and anti-tumor activity. Theranostics 2023; 13:1506-1519. [PMID: 37056568 PMCID: PMC10086201 DOI: 10.7150/thno.79942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/25/2023] [Indexed: 03/13/2023] Open
Abstract
Natural killer (NK) cells are an attractive cell source in cancer immunotherapy due to their potent antitumor ability and promising safety for allogenic applications. However, the clinical outcome of NK cell therapy has been limited due to poor persistence and loss of activity in the cytokine-deficient tumor microenvironment. Benefits from exogenous administration of soluble interleukin-2 (IL-2) to stimulate the activity of NK cells have not been significant due to cytokine consumption and activation of other immune cells, compromising both efficacy and safety. Methods: To overcome these drawbacks, we developed a novel membrane-bound protein (MBP) technology to express IL-2 on the surface of NK-92 cells (MBP NK) inducing autocrine signal for proliferation without IL-2 supplementation. Results: The MBP NK cells exhibited not only improved proliferation in IL-2 deficient conditions but also stronger secretion of cytolytic granules leading to enhanced anti-tumor activity both in vitro and in vivo. Furthermore, the experiment with a spheroid solid tumor model exhibited enhanced infiltration by MBP NK cells creating higher local effector-to-target ratio for efficient tumor killing. These results suggest MBP technology can be an effective utility for NK-92 cell engineering to increase anti-tumor activity and reduce potential adverse effects, providing a higher therapeutic index in clinical applications.
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4
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Habib O, Habib G, Hwang GH, Bae S. Comprehensive analysis of prime editing outcomes in human embryonic stem cells. Nucleic Acids Res 2022; 50:1187-1197. [PMID: 35018468 PMCID: PMC8789035 DOI: 10.1093/nar/gkab1295] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
Abstract
Prime editing is a versatile and precise genome editing technique that can directly copy desired genetic modifications into target DNA sites without the need for donor DNA. This technique holds great promise for the analysis of gene function, disease modeling, and the correction of pathogenic mutations in clinically relevant cells such as human pluripotent stem cells (hPSCs). Here, we comprehensively tested prime editing in hPSCs by generating a doxycycline-inducible prime editing platform. Prime editing successfully induced all types of nucleotide substitutions and small insertions and deletions, similar to observations in other human cell types. Moreover, we compared prime editing and base editing for correcting a disease-related mutation in induced pluripotent stem cells derived form a patient with α 1-antitrypsin (A1AT) deficiency. Finally, whole-genome sequencing showed that, unlike the cytidine deaminase domain of cytosine base editors, the reverse transcriptase domain of a prime editor does not lead to guide RNA-independent off-target mutations in the genome. Our results demonstrate that prime editing in hPSCs has great potential for complementing previously developed CRISPR genome editing tools.
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Affiliation(s)
- Omer Habib
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| | - Gizem Habib
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| | - Gue-Ho Hwang
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
| | - Sangsu Bae
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 08826, South Korea
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5
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Hwang GH, Jeong YK, Habib O, Hong SA, Lim K, Kim JS, Bae S. PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing. Nucleic Acids Res 2021; 49:W499-W504. [PMID: 33939828 PMCID: PMC8265102 DOI: 10.1093/nar/gkab319] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/24/2021] [Accepted: 04/20/2021] [Indexed: 12/26/2022] Open
Abstract
Prime editing technology is capable of generating targeted insertions, deletions, and base conversions. However, the process of designing prime editing guide RNAs (pegRNAs), which contain a primer binding site and a reverse-transcription template at the 3′ end, is more complex than that for the single guide RNAs used with CRISPR nucleases or base editors. Furthermore, the assessment of high-throughput sequencing data after prime editors (PEs) have been employed should consider the unique feature of PEs; thus, pre-existing assessment tools cannot directly be adopted for PEs. Here, we present two user-friendly web-based tools for PEs, named PE-Designer and PE-Analyzer. PE-Designer, a dedicated tool for pegRNA selection, provides all possible target sequences, pegRNA extension sequences, and nicking guide RNA sequences together with useful information, and displays the results in an interactive image. PE-Analyzer, a dedicated tool for PE outcome analysis, accepts high-throughput sequencing data, summarizes mutation-related information in a table, and provides interactive graphs. PE-Analyzer was mainly written using JavaScript so that it can analyze several data sets without requiring that huge sequencing data (>100MB) be uploaded to the server, reducing analysis time and increasing personal security. PE-Designer and PE-Analyzer are freely available at http://www.rgenome.net/pe-designer/ and http://www.rgenome.net/pe-analyzer/ without a login process.
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Affiliation(s)
- Gue-Ho Hwang
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea
| | - You Kyeong Jeong
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea
| | - Omer Habib
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea
| | - Sung-Ah Hong
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea
| | - Kayeong Lim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Daejeon, South Korea.,Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Sangsu Bae
- Department of Chemistry and Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul, South Korea
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6
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Kim A, Lee KG, Kwon Y, Lee KI, Yang HM, Habib O, Kim J, Kim ST, Kim SJ, Kim JS, Hwang DY. Off-the-Shelf, Immune-Compatible Human Embryonic Stem Cells Generated Via CRISPR-Mediated Genome Editing. Stem Cell Rev Rep 2021; 17:1053-1067. [PMID: 33423156 PMCID: PMC8166669 DOI: 10.1007/s12015-020-10113-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/26/2020] [Indexed: 10/27/2022]
Abstract
Human embryonic stem cells (hESCs) hold promise in regenerative medicine but allogeneic immune rejections caused by highly polymorphic human leukocyte antigens (HLAs) remain a barrier to their clinical applications. Here, we used a CRISPR/Cas9-mediated HLA-editing strategy to generate a variety of HLA homozygous-like hESC lines from pre-established hESC lines. We edited four pre-established HLA-heterozygous hESC lines and created a mini library of 14 HLA-edited hESC lines in which single HLA-A and HLA-B alleles and both HLA-DR alleles are disrupted. The HLA-edited hESC derivatives elicited both low T cell- and low NK cell-mediated immune responses. Our library would cover about 40% of the Asian-Pacific population. We estimate that HLA-editing of only 19 pre-established hESC lines would give rise to 46 different hESC lines to cover 90% of the Asian-Pacific population. This study offers an opportunity to generate an off-the-shelf HLA-compatible hESC bank, available for immune-compatible cell transplantation, without embryo destruction. Graphical Abstract.
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Affiliation(s)
- Annie Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul, Republic of Korea
| | - Kun-Gu Lee
- Department of Biomedical Science, Graduate School of CHA University, Seongnam, South Korea
| | - Yeongbeen Kwon
- Samsung Advanced Institute for Health Sciences & Technology(SAIHST), Graduate School, Department of Health Sciences & Technology, Sungkyunkwan University, Seoul, South Korea.,Transplantation Research Center, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Kang-In Lee
- Department of Biomedical Science, Graduate School of CHA University, Seongnam, South Korea.,ToolGen, Inc., Seoul, South Korea
| | - Heung-Mo Yang
- Transplantation Research Center, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea.,GenNbio Inc., Seoul, South Korea.,Department of Medicine, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Omer Habib
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea.,Department of Chemistry, Hanyang University, Seoul, Republic of Korea
| | | | - Sang-Tae Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, Republic of Korea.,Department of Life Sciences, The Catholic University of Korea, Bucheon-si, Gyeonggi-do, South Korea
| | - Sung Joo Kim
- Transplantation Research Center, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea.,GenNbio Inc., Seoul, South Korea.,Department of Medicine, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science, Seoul, Republic of Korea. .,Department of Chemistry, Seoul National University, Seoul, Republic of Korea.
| | - Dong-Youn Hwang
- Department of Biomedical Science, Graduate School of CHA University, Seongnam, South Korea.
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7
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Wu Q, Ferry QRV, Baeumler TA, Michaels YS, Vitsios DM, Habib O, Arnold R, Jiang X, Maio S, Steinkraus BR, Tapia M, Piazza P, Xu N, Holländer GA, Milne TA, Kim JS, Enright AJ, Bassett AR, Fulga TA. In situ functional dissection of RNA cis-regulatory elements by multiplex CRISPR-Cas9 genome engineering. Nat Commun 2017; 8:2109. [PMID: 29235467 PMCID: PMC5727397 DOI: 10.1038/s41467-017-00686-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022] Open
Abstract
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs. We use GenERA to survey the entire regulatory landscape of a 3′UTR, and apply it in a multiplex fashion to analyse combinatorial interactions between sets of miRNA response elements (MREs), providing strong evidence for cooperative activity. We also employ this technology to probe the functionality of an entire MRE network under cellular homeostasis, and show that high-resolution analysis of the GenERA dataset can be used to extract functional features of MREs. This study provides a genome editing-based multiplex strategy for direct functional interrogation of RNA cis-regulatory elements in a native cellular environment. RNA regulatory elements (RREs) are important post-transcriptional control features but studying them requires disrupting their activity without disturbing cellular homeostasis. Here the authors present GenERA, a CRISPR-Cas9 screening platform of in situ analysis of native RREs.
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Affiliation(s)
- Qianxin Wu
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Quentin R V Ferry
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Toni A Baeumler
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Yale S Michaels
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Dimitrios M Vitsios
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Omer Habib
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Roland Arnold
- Molecular and Population Genetics Laboratory, Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Xiaowei Jiang
- Molecular and Population Genetics Laboratory, Oxford Centre for Cancer Gene Research, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Stefano Maio
- Weatherall Institute of Molecular Medicine, Developmental Immunology, University of Oxford, Oxford, OX3 9DS, UK
| | - Bruno R Steinkraus
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Marta Tapia
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Oxford, OX3 9DS, UK
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Ni Xu
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Georg A Holländer
- Weatherall Institute of Molecular Medicine, Developmental Immunology, University of Oxford, Oxford, OX3 9DS, UK.,Department of Biomedicine, Laboratory of Paediatric Immunology, University of Basel, CH-4058, Basel, Switzerland
| | - Thomas A Milne
- Weatherall Institute of Molecular Medicine, MRC Molecular Haematology Unit, NIHR Oxford Biomedical Research Centre Programme, University of Oxford, Oxford, OX3 9DS, UK
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Seoul, 08826, Republic of Korea.,Department of Chemistry, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Anton J Enright
- European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew R Bassett
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RF, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Tudor A Fulga
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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8
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Kim SJ, Habib O, Kim JS, Han HW, Koo SK, Kim JH. A homozygous Keap1-knockout human embryonic stem cell line generated using CRISPR/Cas9 mediates gene targeting. Stem Cell Res 2017; 19:52-54. [DOI: 10.1016/j.scr.2016.12.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 12/21/2016] [Indexed: 11/27/2022] Open
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Kim SJ, Habib O, Kim JS, Han HW, Koo SK, Kim JH. Generation of a Nrf2 homozygous knockout human embryonic stem cell line using CRISPR/Cas9. Stem Cell Res 2017; 19:46-48. [DOI: 10.1016/j.scr.2016.12.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022] Open
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Habib O, Habib G, Moon SH, Hong KS, Do JT, Choi Y, Chang SW, Chung HM. Ground-state conditions promote robust Prdm14 reactivation and maintain an active Dlk1-Dio3 region during reprogramming. Mol Cells 2014; 37:31-5. [PMID: 24552707 PMCID: PMC3907008 DOI: 10.14348/molcells.2014.2212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 11/06/2013] [Accepted: 11/15/2013] [Indexed: 11/27/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) are capable of unlimited self-renewal and can give rise to all three germ layers, thereby providing a new platform with which to study mammalian development and epigenetic reprogramming. However, iPSC generation may result in subtle epigenetic variations, such as the aberrant methylation of the Dlk1-Dio3 locus, among the clones, and this heterogeneity constitutes a major drawback to harnessing the full potential of iPSCs. Vitamin C has recently emerged as a safeguard to ensure the normal imprinting of the Dlk1-Dio3 locus during reprogramming. Here, we show that vitamin C exerts its effect in a manner that is independent of the reprogramming kinetics. Moreover, we demonstrate that reprogramming cells under 2i conditions leads to the early upregulation of Prdm14, which in turn results in a highly homogeneous population of authentic pluripotent colonies and prevents the abnormal silencing of the Dlk1-Dio3 locus.
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Affiliation(s)
- Omer Habib
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 143-701,
Korea
- Stem Cell Research Laboratory, CHA Stem Cell Institute, CHA University, Seoul 135-907,
Korea
| | - Gizem Habib
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 143-701,
Korea
| | - Sung-Hwan Moon
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 143-701,
Korea
| | - Ki-Sung Hong
- Stem Cell Research Laboratory, CHA Stem Cell Institute, CHA University, Seoul 135-907,
Korea
| | - Jeong Tae Do
- Laboratory of Stem Cell and Developmental Biology Department of Animal Biotechnology, College of Animal Bioscience and Technology, Konkuk University, Seoul 143-701,
Korea
| | - Youngsok Choi
- Department of Biomedical Science, CHA University, Seoul 135-907,
Korea
| | - Sung Woon Chang
- Department of Obstetrics and Gynecology, Bundang CHA General Hospital, Seoul 463-836,
Korea
| | - Hyung-Min Chung
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul 143-701,
Korea
- Stem Cell Research Laboratory, CHA Stem Cell Institute, CHA University, Seoul 135-907,
Korea
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11
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Habib O, Habib G, Do JT, Moon SH, Chung HM. Activation-induced deaminase-coupled DNA demethylation is not crucial for the generation of induced pluripotent stem cells. Stem Cells Dev 2013; 23:209-18. [PMID: 24083501 DOI: 10.1089/scd.2013.0337] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA methylation constitutes a major obstacle in the reprogramming of cells to pluripotency. Although little is known regarding the molecular mechanisms of DNA demethylation, activation-induced deaminase (AID), which is known to function in antibody diversification, has been implicated in DNA demethylation through a base excision repair (BER)-mediated pathway. Here we comprehensively examine the plausibility of coupled AID-BER demethylation in the generation of induced pluripotent stem cells (iPSCs) and show that AID is dispensable for reprogramming cells into iPSCs. Additionally, the overexpression of AID and other factors involved in AID-coupled DNA demethylation does not increase the efficiency of reprogramming. Moreover, BER is not likely to play a role in this process. Our results indicate that the reactivation of key genes governing the pluripotency circuitry occurs through a mechanism that is independent of deamination-coupled demethylation.
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Affiliation(s)
- Omer Habib
- 1 School of Medicine, Konkuk University , Seoul, South Korea
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12
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Okutucu B, Dinçer A, Habib O, Zihnioglu F. Comparison of five methods for determination of total plasma protein concentration. ACTA ACUST UNITED AC 2007; 70:709-11. [PMID: 17597224 DOI: 10.1016/j.jbbm.2007.05.009] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Revised: 05/23/2007] [Accepted: 05/23/2007] [Indexed: 11/20/2022]
Abstract
Quantitation of exact total protein content is often a key step and is common to many applications in general biochemistry research and routine clinical laboratory practice. Before embarking on any type of protein analysis, particularly comparative techniques, it is important to accurately quantitate the amount of protein in the sample. In order to assess the quality of total protein estimation results, five methods were tested and were applied to the same pooled plasma sample. For this aim, Bradford (Coomassie Brilliant Blue), Lowry (Folin-Ciocalteau), Biüret, Pesce and Strande (Ponceau-S/TCA), and modified method of Schaffner-Weismann (Amido Black 10B) were used. The last two methods employ simultaneous precipitation of proteins with the acid containing dye solutions followed by dissolution of precipitate in a NaOH solution. It is shown that each assay has advantages and disadvantages relative to sensitivity, ease of performance, acceptance in literature, accuracy and reproducibility/coefficient of variation. All of the methods tested show a CV %<6. Besides pooled plasma, a known concentration of human serum albumin was also analyzed and discussed by means of standardization of plasma total protein content.
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Affiliation(s)
- Burcu Okutucu
- Ege University, Faculty of Science, Biochemistry Department, 35100-Bornova, Izmir, Turkey.
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13
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el Kholy A, Habib O, Abdel-Monem MH, Abu Safia S. Septal mucoperichondrial flap for closure of nostril in atrophic rhinitis. Rhinology 1998; 36:202-3. [PMID: 9923066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The aetiology of primary atrophic rhinitis is still unknown. Treatment of this disease is conservative in the first place. Surgery is indicated if the medical treatment fails. The aim of surgery is either to narrow the nasal cavity or in special cases to close the nostril. Closure of the nostril (Young's operation), is achieved by raising a circular skin flap. Raising the skin flap is difficult, the suture line may break down and an excessive scar tissue may form resulting in vestibular stenosis. We therefore developed a septal mucoperichondrial flap to close the nostril. This new and easy technique has been used to treat 17 patients with excellent results. The description of this technique and the results of surgery will be discussed.
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Affiliation(s)
- A el Kholy
- Department of Otorhinolaryngology, Al Hada Military Hospital, Taif, Saudi Arabia
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