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Nie S, Zhang W, Jin X, Li X, Sun S, Zhao Y, Jia Q, Li L, Liu Y, Liu D, Gao Q. Genetic Screening of Haploid Neural Stem Cells Reveals that Nfkbia and Atp2b4 are Key Regulators of Oxidative Stress in Neural Precursors. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309292. [PMID: 38666459 PMCID: PMC11304298 DOI: 10.1002/advs.202309292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 03/31/2024] [Indexed: 08/09/2024]
Abstract
Neurological diseases are expected to become the leading cause of death in the next decade. Although little is known about it, the interaction between oxidative stress and inflammation is harmful to the nervous system. To find an advanced tool for neural genetics, mouse haploid neural stem cells (haNSCs) from the somite of chimeric mouse embryos at E8.5 is established. The haNSCs present a haploid neural progenitor identity for long-term culture, promising to robustly differentiate into neural subtypes and being able to form cerebral organoids efficiently. Thereafter, haNSC mutants via a high-throughput approach and screened targets of oxidative stress is generated using the specific mutant library. Deletion of Nfkbia (the top hit among the insertion mutants) reduces damage from reactive oxygen species (ROS) in NSCs exposed to H2O2. Transcriptome analysis revealed that Atp2b4 is upregulated significantly in Nfkbia-null NSCs and is probably responsible for the observed resistance. Additionally, overexpression of Atp2b4 itself can increase the survival of NSCs in the presence of H2O2, suggesting that Atp2b4 is closely involved in this resistance. Herein, a powerful haploid system is presented to study functional genetics in neural lineages, shedding light on the screening of critical genes and drugs for neurological diseases.
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Affiliation(s)
- Shaochen Nie
- Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University School of stomatologyTianjin Medical University School of StomatologyTianjin300070China
| | - Wenhao Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of PharmacyNankai UniversityTianjin300350China
| | - Xin Jin
- School of MedicineNankai UniversityTianjin300071China
| | - Xiaoyan Li
- Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University School of stomatologyTianjin Medical University School of StomatologyTianjin300070China
| | - Shengyi Sun
- State Key Laboratory of Medicinal Chemical Biology and College of PharmacyNankai UniversityTianjin300350China
| | - Yiding Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of PharmacyNankai UniversityTianjin300350China
| | - Qingshen Jia
- State Key Laboratory of Medicinal Chemical Biology and College of PharmacyNankai UniversityTianjin300350China
| | - Luyuan Li
- State Key Laboratory of Medicinal Chemical Biology and College of PharmacyNankai UniversityTianjin300350China
| | - Yan Liu
- Department of ObstetricsTianjin First Central HospitalNankai UniversityTianjin300192China
| | - Dayong Liu
- Tianjin Key Laboratory of Oral Soft and Hard Tissues Restoration and Regeneration, Tianjin Medical University School of stomatologyTianjin Medical University School of StomatologyTianjin300070China
| | - Qian Gao
- State Key Laboratory of Medicinal Chemical Biology and College of PharmacyNankai UniversityTianjin300350China
- Tianjin Key Laboratory of Animal and Plant ResistanceCollege of Life SciencesTianjin Normal UniversityTianjin300387China
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Liu S, Xu J, Ai Y, Zhang Y, Li S, Li J, Li Y. Derivation of zebrafish heart-related haploid cells. J Mol Cell Biol 2024; 15:mjad077. [PMID: 38049373 PMCID: PMC11004926 DOI: 10.1093/jmcb/mjad077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023] Open
Affiliation(s)
- Siqi Liu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jia Xu
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yirui Ai
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunbin Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shifeng Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yiping Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Geng K, Merino LG, Veiga RG, Sommerauer C, Epperlein J, Brinkman EK, Kutter C. Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles. Life Sci Alliance 2024; 7:e202302128. [PMID: 37984988 PMCID: PMC10662290 DOI: 10.26508/lsa.202302128] [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: 05/02/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/22/2023] Open
Abstract
The CRISPR-Cas9 system is a powerful tool for studying gene functions and holds potential for disease treatment. However, precise genome editing requires thorough assessments to minimize unintended on- and off-target effects. Here, we report an unexpected 283-kb deletion on Chromosome 10 (10q23.31) in chronic myelogenous leukemia-derived HAP1 cells, which are frequently used in CRISPR screens. The deleted region encodes regulatory genes, including PAPSS2, ATAD1, KLLN, and PTEN We found that this deletion was not a direct consequence of CRISPR-Cas9 off-targeting but rather occurred frequently during the generation of CRISPR-Cas9-modified cells. The deletion was associated with global changes in histone acetylation and gene expression, affecting fundamental cellular processes such as cell cycle and DNA replication. We detected this deletion in cancer patient genomes. As in HAP1 cells, the deletion contributed to similar gene expression patterns among cancer patients despite interindividual differences. Our findings suggest that the unintended deletion of 10q23.31 can confound CRISPR-Cas9 studies and underscore the importance to assess unintended genomic changes in CRISPR-Cas9-modified cells, which could impact cancer research.
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Affiliation(s)
- Keyi Geng
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Lara G Merino
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Raül G Veiga
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Christian Sommerauer
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Janine Epperlein
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Eva K Brinkman
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Claudia Kutter
- https://ror.org/056d84691 Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
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Sun S, Zhao Q, Zhao Y, Geng M, Wang Q, Gao Q, Zhang X, Zhang W, Shuai L. BCL2 is a major regulator of haploidy maintenance in murine embryonic stem cells. Cell Prolif 2023; 56:e13498. [PMID: 37144356 PMCID: PMC10693186 DOI: 10.1111/cpr.13498] [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: 01/27/2023] [Revised: 04/19/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
Mammalian haploid cells are important resources for forward genetic screening and are important in genetic medicine and drug development. However, the self-diploidization of murine haploid embryonic stem cells (haESCs) during daily culture or differentiation jeopardizes their use in genetic approaches. Here, we show that overexpression (OE) of an antiapoptosis gene, BCL2, in haESCs robustly ensures their haploidy maintenance in various situations, even under strict differentiation in vivo (embryonic 10.5 chimeric fetus or 21-day teratoma). Haploid cell lines of many lineages, including epiblasts, trophectodermal lineages, and neuroectodermal lineages, can be easily derived by the differentiation of BCL2-OE haESCs in vitro. Transcriptome analysis revealed that BCL2-OE activates another regulatory gene, Has2, which is also sufficient for haploidy maintenance. Together, our findings provide an effective and secure strategy to reduce diploidization during differentiation, which will contribute to the generation of haploid cell lines of the desired lineage and related genetic screening.
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Affiliation(s)
- Shengyi Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive RegulationNankai UniversityTianjinChina
| | - Qin Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive RegulationNankai UniversityTianjinChina
| | - Yiding Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive RegulationNankai UniversityTianjinChina
| | - Mengyang Geng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive RegulationNankai UniversityTianjinChina
| | - Qing Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive RegulationNankai UniversityTianjinChina
| | - Qian Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive RegulationNankai UniversityTianjinChina
| | - Xiao‐Ou Zhang
- Shanghai Key Laboratory of Maternal and Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life and Science and TechnologyTongji UniversityShanghaiChina
| | - Wenhao Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive RegulationNankai UniversityTianjinChina
- Chongqing Key Laboratory of Human Embryo EngineeringChongqing Health Center for Women and ChildrenChongqingChina
| | - Ling Shuai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive RegulationNankai UniversityTianjinChina
- National Clinical Research Center for Obstetrics and GynecologyPeking University Third HospitalBeijingChina
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5
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Xu M, Zhang W, Geng M, Zhao Y, Sun S, Gao Q, Liu Y, Shuai L. Rapid generation of murine haploid-induced trophoblast stem cells via a Tet-on system. STAR Protoc 2021; 2:100881. [PMID: 34806042 PMCID: PMC8585661 DOI: 10.1016/j.xpro.2021.100881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Haploid trophoblast stem cells (TSCs) are advanced in studying placental development for their placental precursor and homozygous features. Here, we describe how to generate haploid-induced TSCs (haiTSCs) from haploid embryonic stem cells with a Tet-on system. Our haiTSCs can maintain haploidy long-term and can produce genome-wide mutants combined with transposons. It is promising in high-throughput genetic screening of trophoblast-specific modulators. For complete details on the use and execution of this protocol, please refer to Peng et al. (2019). Protocol for inducing a Cdx2-OE Tet-on system into haploid ESCs Protocol for conversion and purification of haploid induced TSCs from haploid ESCs Protocol for construction of genome-wide mutated homozygous TSCs by piggyBac transposon
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Affiliation(s)
- Mei Xu
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Wenhao Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Mengyang Geng
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Yiding Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Shengyi Sun
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Qian Gao
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China
| | - Yan Liu
- Department of Obstetrics, Tianjin First Central Hospital, Nankai University, Tianjin 300192, China
| | - Ling Shuai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin 300350, China.,National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
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