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Kim J, Kwon EJ, Kim YJ, Kim D, Shin YZ, Gil D, Kim JH, Shin HD, Kim LH, Lee MO, Go YH, Cha HJ. Epigenetic repression of CHCHD2 enhances survival from single cell dissociation through attenuated Rho A kinase activity. Cell Mol Life Sci 2024; 81:38. [PMID: 38214772 PMCID: PMC10787008 DOI: 10.1007/s00018-023-05060-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/18/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024]
Abstract
During in vitro culture, human pluripotent stem cells (hPSCs) often acquire survival advantages characterized by decreased susceptibility to mitochondrial cell death, known as "culture adaptation." This adaptation is associated with genetic and epigenetic abnormalities, including TP53 mutations, copy number variations, trisomy, and methylation changes. Understanding the molecular mechanisms underlying this acquired survival advantage is crucial for safe hPSC-based cell therapies. Through transcriptome and methylome analysis, we discovered that the epigenetic repression of CHCHD2, a mitochondrial protein, is a common occurrence during in vitro culture using enzymatic dissociation. We confirmed this finding through genetic perturbation and reconstitution experiments in normal human embryonic stem cells (hESCs). Loss of CHCHD2 expression conferred resistance to single cell dissociation-induced cell death, a common stress encountered during in vitro culture. Importantly, we found that the downregulation of CHCHD2 significantly attenuates the activity of Rho-associated protein kinase (ROCK), which is responsible for inducing single cell death in hESCs. This suggests that hESCs may survive routine enzyme-based cell dissociation by downregulating CHCHD2 and thereby attenuating ROCK activity. These findings provide insights into the mechanisms by which hPSCs acquire survival advantages and adapt to in vitro culture conditions.
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Affiliation(s)
- Jumee Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eun-Ji Kwon
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yun-Jeong Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dayeon Kim
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yoon-Ze Shin
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Dayeon Gil
- Korea National Stem Cell Bank, Osong, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex 202, Osong, Republic of Korea
| | - Jung-Hyun Kim
- Korea National Stem Cell Bank, Osong, Republic of Korea
- Division of Intractable Disease Research, Department of Chronic Disease Convergence Research, Korea National Institute of Health, Osong Health Technology Administration Complex 202, Osong, Republic of Korea
| | - Hyoung Doo Shin
- Department of Life Science, Sogang University, Seoul, Republic of Korea
- Research Institute for Basic Science, Sogang University, Seoul, Republic of Korea
| | - Lyoung Hyo Kim
- Research Institute for Life Science, GW Vitek, Inc., Seoul, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Young-Hyun Go
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Hyuk-Jin Cha
- College of Pharmacy, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
- Research Institute of Pharmaceutical Science, Seoul National University, 1 Gwanak-ro Gwanak-gu, Seoul, 08826, Republic of Korea.
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Viner-Breuer R, Golan-Lev T, Benvenisty N, Goldberg M. Genome-Wide Screening in Human Embryonic Stem Cells Highlights the Hippo Signaling Pathway as Granting Synthetic Viability in ATM Deficiency. Cells 2023; 12:1503. [PMID: 37296624 PMCID: PMC10253227 DOI: 10.3390/cells12111503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/18/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
ATM depletion is associated with the multisystemic neurodegenerative syndrome ataxia-telangiectasia (A-T). The exact linkage between neurodegeneration and ATM deficiency has not been established yet, and no treatment is currently available. In this study, we aimed to identify synthetic viable genes in ATM deficiency to highlight potential targets for the treatment of neurodegeneration in A-T. We inhibited ATM kinase activity using the background of a genome-wide haploid pluripotent CRISPR/Cas9 loss-of-function library and examined which mutations confer a growth advantage on ATM-deficient cells specifically. Pathway enrichment analysis of the results revealed the Hippo signaling pathway as a major negative regulator of cellular growth upon ATM inhibition. Indeed, genetic perturbation of the Hippo pathway genes SAV1 and NF2, as well as chemical inhibition of this pathway, specifically promoted the growth of ATM-knockout cells. This effect was demonstrated in both human embryonic stem cells and neural progenitor cells. Therefore, we suggest the Hippo pathway as a candidate target for the treatment of the devastating cerebellar atrophy associated with A-T. In addition to the Hippo pathway, our work points out additional genes, such as the apoptotic regulator BAG6, as synthetic viable with ATM-deficiency. These genes may help to develop drugs for the treatment of A-T patients as well as to define biomarkers for resistance to ATM inhibition-based chemotherapies and to gain new insights into the ATM genetic network.
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Affiliation(s)
- Ruth Viner-Breuer
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Givat-Ram, Jerusalem 9190401, Israel; (R.V.-B.); (T.G.-L.)
- Department of Genetics, Institute of Life Sciences, The Hebrew University, Givat-Ram, Jerusalem 9190401, Israel
| | - Tamar Golan-Lev
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Givat-Ram, Jerusalem 9190401, Israel; (R.V.-B.); (T.G.-L.)
- Department of Genetics, Institute of Life Sciences, The Hebrew University, Givat-Ram, Jerusalem 9190401, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, The Hebrew University, Givat-Ram, Jerusalem 9190401, Israel; (R.V.-B.); (T.G.-L.)
- Department of Genetics, Institute of Life Sciences, The Hebrew University, Givat-Ram, Jerusalem 9190401, Israel
| | - Michal Goldberg
- Department of Genetics, Institute of Life Sciences, The Hebrew University, Givat-Ram, Jerusalem 9190401, Israel
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Applications of piggyBac Transposons for Genome Manipulation in Stem Cells. Stem Cells Int 2021; 2021:3829286. [PMID: 34567130 PMCID: PMC8460389 DOI: 10.1155/2021/3829286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022] Open
Abstract
Transposons are mobile genetic elements in the genome. The piggyBac (PB) transposon system is increasingly being used for stem cell research due to its high transposition efficiency and seamless excision capacity. Over the past few decades, forward genetic screens based on PB transposons have been successfully established to identify genes associated with drug resistance and stem cell-related characteristics. Moreover, PB transposon is regarded as a promising gene therapy vector and has been used in some clinically relevant stem cells. Here, we review the recent progress on the basic biology of PB, highlight its applications in current stem cell research, and discuss its advantages and challenges.
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Bower OJ, McCarthy A, Lea RA, Alanis-Lobato G, Zohren J, Gerri C, Turner JMA, Niakan KK. Generating CRISPR-Cas9-Mediated Null Mutations and Screening Targeting Efficiency in Human Pluripotent Stem Cells. Curr Protoc 2021; 1:e232. [PMID: 34432381 DOI: 10.1002/cpz1.232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
CRISPR-Cas9 mutagenesis facilitates the investigation of gene function in a number of developmental and cellular contexts. Human pluripotent stem cells (hPSCs), either embryonic or induced, are a tractable cellular model to investigate molecular mechanisms involved in early human development and cell fate decisions. hPSCs also have broad potential in regenerative medicine to model, investigate, and ameliorate diseases. Here, we provide an optimized protocol for efficient CRISPR-Cas9 genome editing of hPSCs to investigate the functional role of genes by engineering null mutations. We emphasize the importance of screening single guide RNAs (sgRNAs) to identify those with high targeting efficiency for generation of clonally derived null mutant hPSC lines. We provide important considerations for targeting genes that may have a role in hPSC maintenance. We also present methods to evaluate the on-target mutation spectrum and unintended karyotypic changes. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Selecting and ligating sgRNAs into expression plasmids Basic Protocol 2: Validation of sgRNA via in vitro transcription and cleavage assay Basic Protocol 3: Nucleofection of primed human embryonic stem cells Basic Protocol 4: MiSeq analysis of indel mutations Basic Protocol 5: Single cell cloning of targeted hPSCs Basic Protocol 6: Karyotyping of targeted hPSCs.
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Affiliation(s)
- Oliver J Bower
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Afshan McCarthy
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Rebecca A Lea
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Gregorio Alanis-Lobato
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Jasmin Zohren
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Claudia Gerri
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, London, United Kingdom
- The Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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Zaaijer S, Groen SC, Sanjana NE. Tracking cell lineages to improve research reproducibility. Nat Biotechnol 2021; 39:666-670. [PMID: 34012093 PMCID: PMC9644290 DOI: 10.1038/s41587-021-00928-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Sophie Zaaijer
- Cornell Tech, New York, NY, USA,FIND Genomics, New York, NY, USA
| | - Simon C. Groen
- Department of Biology, New York University, New York, NY, USA
| | - Neville E. Sanjana
- Department of Biology, New York University, New York, NY, USA,New York Genome Center, New York, NY, USA
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Abranches E, Spyrou S, Ludwig T. GMP Banking of Human Pluripotent Stem Cells: A US and UK perspective. Stem Cell Res 2020; 45:101805. [PMID: 32413790 DOI: 10.1016/j.scr.2020.101805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/20/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Elsa Abranches
- UK Stem Cell Bank, Advanced Therapies Division, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK.
| | - Sofia Spyrou
- UK Stem Cell Bank, Advanced Therapies Division, National Institute for Biological Standards and Control (NIBSC), Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Tenneille Ludwig
- WiCell Research Institute, 504 S. Rosa Rd Suite 101, Madison, WI, 53719, USA
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