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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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2
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Zhang R, He Z, Shi Y, Sun X, Chen X, Wang G, Zhang Y, Gao P, Wu Y, Lu S, Duan J, Sun S, Yang N, Fan W, Zhao K, Yang B, Xia Y, Zhang Y, Zhang Y, Yin H. Amplification editing enables efficient and precise duplication of DNA from short sequence to megabase and chromosomal scale. Cell 2024; 187:3936-3952.e19. [PMID: 38936359 DOI: 10.1016/j.cell.2024.05.056] [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: 12/25/2023] [Revised: 03/24/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024]
Abstract
Duplication is a foundation of molecular evolution and a driver of genomic and complex diseases. Here, we develop a genome editing tool named Amplification Editing (AE) that enables programmable DNA duplication with precision at chromosomal scale. AE can duplicate human genomes ranging from 20 bp to 100 Mb, a size comparable to human chromosomes. AE exhibits activity across various cell types, encompassing diploid, haploid, and primary cells. AE exhibited up to 73.0% efficiency for 1 Mb and 3.4% for 100 Mb duplications, respectively. Whole-genome sequencing and deep sequencing of the junctions of edited sequences confirm the precision of duplication. AE can create chromosomal microduplications within disease-relevant regions in embryonic stem cells, indicating its potential for generating cellular and animal models. AE is a precise and efficient tool for chromosomal engineering and DNA duplication, broadening the landscape of precision genome editing from an individual genetic locus to the chromosomal scale.
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Affiliation(s)
- Ruiwen Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China; Department of Rheumatology and Immunology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Zhou He
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yajing Shi
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xiangkun Sun
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xinyu Chen
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Guoquan Wang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yizhou Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Pan Gao
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Ying Wu
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Shuhan Lu
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Junyi Duan
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Shangwu Sun
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Na Yang
- Center for Gene Diagnosis and Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Wei Fan
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan 430071, China
| | - Yan Zhang
- Department of Clinical Laboratory, Institute of Translational Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ying Zhang
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China; Department of Rheumatology and Immunology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, China
| | - Hao Yin
- Departments of Urology and Laboratory Medicine, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, State Key Laboratory of Virology, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430071, China.
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3
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Mu A, Okamoto Y, Katsuki Y, Takata M. The role of SLFN11 in DNA replication stress response and its implications for the Fanconi anemia pathway. DNA Repair (Amst) 2024; 141:103733. [PMID: 39096698 DOI: 10.1016/j.dnarep.2024.103733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/26/2024] [Accepted: 07/19/2024] [Indexed: 08/05/2024]
Abstract
Fanconi anemia (FA) is a hereditary disorder characterized by a deficiency in the repair of DNA interstrand crosslinks and the response to replication stress. Endogenous DNA damage, most likely caused by aldehydes, severely affects hematopoietic stem cells in FA, resulting in progressive bone marrow failure and the development of leukemia. Recent studies revealed that expression levels of SLFN11 affect the replication stress response and are a strong determinant in cell killing by DNA-damaging cancer chemotherapy. Because SLFN11 is highly expressed in the hematopoietic system, we speculated that SLFN11 may have a significant role in FA pathophysiology. Indeed, we found that DNA damage sensitivity in FA cells is significantly mitigated by the loss of SLFN11 expression. Mechanistically, we demonstrated that SLFN11 destabilizes the nascent DNA strands upon replication fork stalling. In this review, we summarize our work regarding an interplay between SLFN11 and the FA pathway, and the role of SLFN11 in the response to replication stress.
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Affiliation(s)
- Anfeng Mu
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan; Multilayer Network Research Unit, Research Coordination Alliance, Kyoto University, Kyoto, Japan.
| | - Yusuke Okamoto
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoko Katsuki
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan; Multilayer Network Research Unit, Research Coordination Alliance, Kyoto University, Kyoto, Japan.
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4
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He W, Tang H, Li Y, Wang M, Li Y, Chen J, Gao S, Han Z. Overexpression of Let-7a mitigates diploidization in mouse androgenetic haploid embryonic stem cells. iScience 2024; 27:109769. [PMID: 38711447 PMCID: PMC11070717 DOI: 10.1016/j.isci.2024.109769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/23/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024] Open
Abstract
Mouse androgenetic haploid embryonic stem cells (mAG-haESCs) can be utilized to uncover gene functions, especially those of genes with recessive effects, and to produce semicloned mice when injected into mature oocytes. However, mouse haploid cells undergo rapid diploidization during long-term culture in vitro and subsequently lose the advantages of haploidy, and the factors that drive diploidization are poorly understood. In this study, we compared the small RNAs (sRNAs) of mAG-haESCs, normal embryonic stem cells (ESCs), and mouse round spermatids by high-throughput sequencing and identified distinct sRNA profiles. Several let-7 family members and miR-290-295 cluster microRNAs (miRNAs) were found significantly differentially transcribed. Knockdown and overexpression experiments showed that let-7a and let-7g suppress diploidization while miR-290a facilitates diploidization. Our study revealed the unique sRNA profile of mAG-haESCs and demonstrated that let-7a overexpression can mitigate diploidization in mAG-haESCs. These findings will help us to better understand mAG-haESCs and utilize them as tools in the future.
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Affiliation(s)
- Wenteng He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Hongming Tang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yuanyuan Li
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Mingzhu Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
| | - Yuanyuan Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayu Chen
- Clinical and Translation Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200120, China
- Clinical and Translation Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiming Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
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5
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Sirozh O, Saez-Mas A, Jung B, Sanchez-Burgos L, Zarzuela E, Rodrigo-Perez S, Ventoso I, Lafarga V, Fernandez-Capetillo O. Nucleolar stress caused by arginine-rich peptides triggers a ribosomopathy and accelerates aging in mice. Mol Cell 2024; 84:1527-1540.e7. [PMID: 38521064 DOI: 10.1016/j.molcel.2024.02.031] [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: 09/15/2023] [Revised: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 03/25/2024]
Abstract
Nucleolar stress (NS) has been associated with age-related diseases such as cancer or neurodegeneration. To investigate how NS triggers toxicity, we used (PR)n arginine-rich peptides present in some neurodegenerative diseases as inducers of this perturbation. We here reveal that whereas (PR)n expression leads to a decrease in translation, this occurs concomitant with an accumulation of free ribosomal (r) proteins. Conversely, (PR)n-resistant cells have lower rates of r-protein synthesis, and targeting ribosome biogenesis by mTOR inhibition or MYC depletion alleviates (PR)n toxicity in vitro. In mice, systemic expression of (PR)97 drives widespread NS and accelerated aging, which is alleviated by rapamycin. Notably, the generalized accumulation of orphan r-proteins is a common outcome of chemical or genetic perturbations that induce NS. Together, our study presents a general model to explain how NS induces cellular toxicity and provides in vivo evidence supporting a role for NS as a driver of aging in mammals.
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Affiliation(s)
- Oleksandra Sirozh
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Anabel Saez-Mas
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Bomi Jung
- Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 21 Stockholm, Sweden
| | - Laura Sanchez-Burgos
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Eduardo Zarzuela
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Sara Rodrigo-Perez
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Ivan Ventoso
- Centro de Biologia Molecular Severo Ochoa (CSIC-UAM), Departamento de Biologia Molecular, Universidad Autonoma de Madrid (UAM), Madrid, Spain
| | - Vanesa Lafarga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 21 Stockholm, Sweden.
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6
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Tokugawa M, Inoue Y, Aoki H, Miyajima C, Ishiuchi K, Tsurumi K, Kujirai C, Morishita D, Matsuno M, Mizukami H, Ri M, Iida S, Makino T, Aoyama M, Hayashi H. Involvement of cardiac glycosides targeting Na/K-ATPase in their inhibitory effects on c-Myc expression via its transcription, translation and proteasomal degradation. J Biochem 2024; 175:253-263. [PMID: 37948630 DOI: 10.1093/jb/mvad085] [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: 05/16/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
Cardiac glycosides (CGs) have been used for decades to treat heart failure and arrhythmic diseases. Recent non-clinical and epidemiological findings have suggested that CGs exhibit anti-tumor activities. Therefore, CGs may be repositioned as drugs for the treatment of cancer. A detailed understanding of the anti-cancer mechanisms of CGs is essential for their application to the treatment of targetable cancer types. To elucidate the factors associated with the anti-tumor effects of CGs, we performed transcriptome profiling on human multiple myeloma AMO1 cells treated with periplocin, one of the CGs. Periplocin significantly down-regulated the transcription of MYC (c-Myc), a well-established oncogene. Periplocin also suppressed c-Myc expression at the protein levels. This repression of c-Myc was also observed in several cell lines. To identify target proteins for the inhibition of c-Myc, we generated CG-resistant (C9) cells using a sustained treatment with digoxin. We confirmed that C9 cells acquired resistance to the inhibition of c-Myc expression and cell proliferation by CGs. Moreover, the sequencing of genomic DNA in C9 cells revealed the mutation of D128N in α1-Na/K-ATPase, indicating the target protein. These results suggest that CGs suppress c-Myc expression in cancer cells via α1-Na/K-ATPase, which provides further support for the anti-tumor activities of CGs.
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Affiliation(s)
- Muneshige Tokugawa
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Yasumichi Inoue
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Hiromasa Aoki
- Department of Pathobiology, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Chiharu Miyajima
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Kan'ichiro Ishiuchi
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Kento Tsurumi
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Chisane Kujirai
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Daisuke Morishita
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
- Chordia Therapeutics Inc., 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Michiyo Matsuno
- Plant research section, The Kochi Prefectural Makino Botanical Garden, 4200-6 Godaiyama, Kochi 781-8125, Japan
| | - Hajime Mizukami
- Plant research section, The Kochi Prefectural Makino Botanical Garden, 4200-6 Godaiyama, Kochi 781-8125, Japan
| | - Masaki Ri
- Department of Hematology and Oncology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Shinsuke Iida
- Department of Hematology and Oncology, Graduate School of Medical Sciences, Nagoya City University, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Toshiaki Makino
- Department of Pharmacognosy, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Mineyoshi Aoyama
- Department of Pathobiology, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
| | - Hidetoshi Hayashi
- Department of Cell Signaling, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
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7
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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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8
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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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9
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Muñoz-Pujol G, Ugarteburu O, Segur-Bailach E, Moliner S, Jurado S, Garrabou G, Guitart-Mampel M, García-Villoria J, Artuch R, Fons C, Ribes A, Tort F. CRISPR/Cas9-based functional genomics strategy to decipher the pathogenicity of genetic variants in inherited metabolic disorders. J Inherit Metab Dis 2023; 46:1029-1042. [PMID: 37718653 DOI: 10.1002/jimd.12681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/19/2023]
Abstract
The determination of the functional impact of variants of uncertain significance (VUS) is one of the major bottlenecks in the diagnostic workflow of inherited genetic diseases. To face this problem, we set up a CRISPR/Cas9-based strategy for knock-in cellular model generation, focusing on inherited metabolic disorders (IMDs). We selected variants in seven IMD-associated genes, including seven reported disease-causing variants and four benign/likely benign variants. Overall, 11 knock-in cell models were generated via homology-directed repair in HAP1 haploid cells using CRISPR/Cas9. The functional impact of the variants was determined by analyzing the characteristic biochemical alterations of each disorder. Functional studies performed in knock-in cell models showed that our approach accurately distinguished the functional effect of pathogenic from non-pathogenic variants in a reliable manner in a wide range of IMDs. Our study provides a generic approach to assess the functional impact of genetic variants to improve IMD diagnosis and this tool could emerge as a promising alternative to invasive tests, such as muscular or skin biopsies. Although the study has been performed only in IMDs, this strategy is generic and could be applied to other genetic disorders.
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Affiliation(s)
- Gerard Muñoz-Pujol
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Olatz Ugarteburu
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Eulàlia Segur-Bailach
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Sonia Moliner
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Susana Jurado
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Glòria Garrabou
- Inherited Metabolic diseases and Muscle Disorder's lab, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Service-Hospital Clinic of Barcelona and CIBERER, Barcelona, Spain
| | - Mariona Guitart-Mampel
- Inherited Metabolic diseases and Muscle Disorder's lab, Cellex-IDIBAPS, Faculty of Medicine and Health Sciences, University of Barcelona, Internal Medicine Service-Hospital Clinic of Barcelona and CIBERER, Barcelona, Spain
| | - Judit García-Villoria
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry and Molecular Medicine and Genetics Departments, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, and CIBERER, Esplúgues de Llobregat, Barcelona, Spain
| | - Carme Fons
- Neurology Department, Fetal, Neonatal Neurology and Early Epilepsy Unit, Institut de Recerca, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Antonia Ribes
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
| | - Frederic Tort
- Secció d'Errors Congènits del Metabolisme-IBC, Servei de Bioquímica i Genètica Molecular, Hospital Clínic de Barcelona, IDIBAPS, CIBERER, Barcelona, Spain
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10
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Zheng W, Wang L, He W, Hu X, Zhu Q, Gu L, Jiang C. Transcriptome profiles and chromatin states in mouse androgenetic haploid embryonic stem cells. Cell Prolif 2023; 56:e13436. [PMID: 36855927 PMCID: PMC10472531 DOI: 10.1111/cpr.13436] [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: 11/14/2022] [Revised: 02/12/2023] [Accepted: 02/17/2023] [Indexed: 03/02/2023] Open
Abstract
Haploid embryonic stem cells (haESCs) are derived from the inner cell mass of the haploid blastocyst, containing only one set of chromosomes. Extensive and accurate chromatin remodelling occurs during haESC derivation, but the intrinsic transcriptome profiles and chromatin structure of haESCs have not been fully explored. We profiled the transcriptomes, nucleosome positioning, and key histone modifications of four mouse haESC lines, and compared these profiles with those of other closely-related stem cell lines, MII oocytes, round spermatids, sperm, and mouse embryonic fibroblasts. haESCs had transcriptome profiles closer to those of naïve pluripotent stem cells. Consistent with the one X chromosome in haESCs, Xist was repressed, indicating no X chromosome inactivation. haESCs and ESCs shared a similar global chromatin structure. However, a nucleosome depletion region was identified in 2056 promoters in ESCs, which was absent in haESCs. Furthermore, three characteristic spatial relationships were formed between transcription factor motifs and nucleosomes in both haESCs and ESCs, specifically in the linker region, on the nucleosome central surface, and nucleosome borders. Furthermore, the chromatin state of 4259 enhancers was off in haESCs but active in ESCs. Functional annotation of these enhancers revealed enrichment in regulation of the cell cycle, a predominantly reported mechanism of haESC self-diploidization. Notably, the transcriptome profiles and chromatin structure of haESCs were highly preserved during passaging but different from those of differentiated cell types.
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Affiliation(s)
- Weisheng Zheng
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Wenteng He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Xinjie Hu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and TechnologyTongji UniversityShanghaiChina
- Frontier Science Center for Stem Cell ResearchTongji UniversityShanghaiChina
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11
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Delhomme TM, Munteanu M, Buonanno M, Grilj V, Biayna J, Supek F. Proton and alpha radiation-induced mutational profiles in human cells. Sci Rep 2023; 13:9791. [PMID: 37328655 PMCID: PMC10275862 DOI: 10.1038/s41598-023-36845-3] [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: 10/10/2022] [Accepted: 06/11/2023] [Indexed: 06/18/2023] Open
Abstract
Ionizing radiation is known to be DNA damaging and mutagenic, however less is known about which mutational footprints result from exposures of human cells to different types of radiation. We were interested in the mutagenic effects of particle radiation exposures on genomes of various human cell types, in order to gauge the genotoxic risks of galactic cosmic radiation, and of certain types of tumor radiotherapy. To this end, we exposed cultured cell lines from the human blood, breast and lung to fractionated proton and alpha particle (helium nuclei) beams at doses sufficient to considerably affect cell viability. Whole-genome sequencing revealed that mutation rates were not overall markedly increased upon proton and alpha exposures. However, there were modest changes in mutation spectra and distributions, such as the increases in clustered mutations and of certain types of indels and structural variants. The spectrum of mutagenic effects of particle beams may be cell-type and/or genetic background specific. Overall, the mutational effects of repeated exposures to proton and alpha radiation on human cells in culture appear subtle, however further work is warranted to understand effects of long-term exposures on various human tissues.
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Affiliation(s)
- Tiffany M Delhomme
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Maia Munteanu
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Manuela Buonanno
- Radiological Research Accelerator Facility (RARAF), Columbia University, New York, USA
| | - Veljko Grilj
- Radiological Research Accelerator Facility (RARAF), Columbia University, New York, USA
| | - Josep Biayna
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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12
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Liu-Lupo Y, Ham JD, Jeewajee SKA, Nguyen L, Delorey T, Ramos A, Weinstock DM, Regev A, Hemann MT. Integrated multi-omics analyses reveal homology-directed repair pathway as a unique dependency in near-haploid leukemia. Blood Cancer J 2023; 13:92. [PMID: 37286545 PMCID: PMC10247733 DOI: 10.1038/s41408-023-00863-1] [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: 11/16/2022] [Accepted: 05/22/2023] [Indexed: 06/09/2023] Open
Abstract
Whole chromosome losses resulting in near-haploid karyotypes are found in a rare subgroup of treatment-refractory acute lymphoblastic leukemia. To systematically dissect the unique physiology and uncover susceptibilities that can be exploited in near-haploid leukemia, we leveraged single-cell RNA-Seq and computational inference of cell cycle stages to pinpoint key differences between near-haploid and diploid leukemia cells. Combining cell cycle stage-specific differential expression with gene essentiality scores from a genome-wide CRISPR-Cas9-mediated knockout screen, we identified the homologous recombination pathway component RAD51B as an essential gene in near-haploid leukemia. DNA damage analyses revealed significantly increased sensitivity of RAD51-mediated repair to RAD51B loss in the G2/M stage of near-haploid cells, suggesting a unique role of RAD51B in the homologous recombination pathway. Elevated G2/M and G1/S checkpoint signaling was part of a RAD51B signature expression program in response to chemotherapy in a xenograft model of human near-haploid B-ALL, and RAD51B and its associated programs were overexpressed in a large panel of near-haploid B-ALL patients. These data highlight a unique genetic dependency on DNA repair machinery in near-haploid leukemia and demarcate RAD51B as a promising candidate for targeted therapy in this treatment-resistant disease.
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Affiliation(s)
- Yunpeng Liu-Lupo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
- MIT Koch Institute for Integrative Cancer Research, Cambridge, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - James Dongjoo Ham
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
- MIT Koch Institute for Integrative Cancer Research, Cambridge, USA
| | - Swarna K A Jeewajee
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
- MIT Koch Institute for Integrative Cancer Research, Cambridge, USA
| | - Lan Nguyen
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Toni Delorey
- Broad Institute of MIT and Harvard, Cambridge, USA
| | - Azucena Ramos
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
- MIT Koch Institute for Integrative Cancer Research, Cambridge, USA
| | - David M Weinstock
- Broad Institute of MIT and Harvard, Cambridge, USA
- Dana Farber Cancer Institute, Boston, USA
| | - Aviv Regev
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
- MIT Koch Institute for Integrative Cancer Research, Cambridge, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- Genentech, 1 DNA Way, South San Francisco, USA
| | - Michael T Hemann
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA.
- MIT Koch Institute for Integrative Cancer Research, Cambridge, USA.
- Broad Institute of MIT and Harvard, Cambridge, USA.
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13
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Xi J, Zheng W, Chen M, Zou Q, Tang C, Zhou X. Genetically engineered pigs for xenotransplantation: Hopes and challenges. Front Cell Dev Biol 2023; 10:1093534. [PMID: 36712969 PMCID: PMC9878146 DOI: 10.3389/fcell.2022.1093534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/31/2022] [Indexed: 01/14/2023] Open
Abstract
The shortage of donor resources has greatly limited the application of clinical xenotransplantation. As such, genetically engineered pigs are expected to be an ideal organ source for xenotransplantation. Most current studies mainly focus on genetically modifying organs or tissues from donor pigs to reduce or prevent attack by the human immune system. Another potential organ source is interspecies chimeras. In this paper, we reviewed the progress of the genetically engineered pigs from the view of immunologic barriers and strategies, and discussed the possibility and challenges of the interspecies chimeras.
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14
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Llargués-Sistac G, Bonjoch L, Castellvi-Bel S. HAP1, a new revolutionary cell model for gene editing using CRISPR-Cas9. Front Cell Dev Biol 2023; 11:1111488. [PMID: 36936678 PMCID: PMC10020200 DOI: 10.3389/fcell.2023.1111488] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
The use of next-generation sequencing (NGS) technologies has been instrumental in the characterization of the mutational landscape of complex human diseases like cancer. But despite the enormous rise in the identification of disease candidate genetic variants, their functionality is yet to be fully elucidated in order to have a clear implication in patient care. Haploid human cell models have become the tool of choice for functional gene studies, since they only contain one copy of the genome and can therefore show the unmasked phenotype of genetic variants. Over the past few years, the human near-haploid cell line HAP1 has widely been consolidated as one of the favorite cell line models for functional genetic studies. Its rapid turnover coupled with the fact that only one allele needs to be modified in order to express the subsequent desired phenotype has made this human cell line a valuable tool for gene editing by CRISPR-Cas9 technologies. This review examines the recent uses of the HAP1 cell line model in functional genetic studies and high-throughput genetic screens using the CRISPR-Cas9 system. It covers its use in an attempt to develop new and relevant disease models to further elucidate gene function, and create new ways to understand the genetic basis of human diseases. We will cover the advantages and potential of the use of CRISPR-Cas9 technology on HAP1 to easily and efficiently study the functional interpretation of gene function and human single-nucleotide genetic variants of unknown significance identified through NGS technologies, and its implications for changes in clinical practice and patient care.
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15
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Hess L, Moos V, Seiser C. Development of a Cellular Model Mimicking Specific HDAC Inhibitors. Methods Mol Biol 2023; 2589:51-73. [PMID: 36255617 DOI: 10.1007/978-1-0716-2788-4_4] [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] [Indexed: 06/16/2023]
Abstract
Class I histone deacetylases (HDACs) are important regulators of cellular functions in health and disease. HDAC1, HDAC2, HDAC3, and HDAC8 are promising targets for the treatment of cancer, neurological, and immunological disorders. These enzymes have both catalytic and non-catalytic functions in the regulation of gene expression. We here describe the generation of a genetic toolbox by the CRISPR/Cas9 methodology in nearly haploid human tumor cells. This novel model system allows to discriminate between catalytic and structural functions of class I HDAC enzymes and to mimic the treatment with specific HDAC inhibitors.
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Affiliation(s)
- Lena Hess
- Center for Anatomy and Cell Biology, Division for Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Verena Moos
- Center for Anatomy and Cell Biology, Division for Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Christian Seiser
- Center for Anatomy and Cell Biology, Division for Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria.
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16
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Banerjee R, Sotero-Caio CG, Fu B, Yang F. Chromosomal instability (CIN) in HAP1 cell lines revealed by multiplex fluorescence in situ hybridisation (M-FISH). Mol Cytogenet 2022; 15:46. [PMID: 36289492 PMCID: PMC9609465 DOI: 10.1186/s13039-022-00625-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HAP1, a near-haploid human leukemic cancer cell line is often used in combination with CRISPR-Cas9 gene editing technology for genetic screens. HAP1 carries the Philadelphia chromosome (Ph) and an additional ~ 30 Mb fragment of chromosome 15 inserted into chromosome 19. The potential use of an in vitro cell line as a model system in biomedical research studies depends on its ability to maintain genome stability. Being a cancer cell line with a near-haploid genome, HAP1 is prone to genetic instability, which is further compounded by its tendency to diploidise in culture spontaneously. Moreover, CRISPR-Cas9 gene editing coupled with prolonged in-vitro cell culturing has the potential to induce unintended 'off-target' cytogenetic mutations. To gain an insight into chromosomal instability (CIN) and karyotype heterogeneity, 19 HAP1 cell lines were cytogenetically characterised, 17 of which were near-haploids and two double-haploids, using multiplex fluorescence in situ hybridisation (M-FISH), at single cell resolution. We focused on novel numerical (N) and structural (S) CIN and discussed the potential causal factors for the observed instability. For each cell line we examined its ploidy, gene editing status and its length of in-vitro cell culturing. RESULTS Sixteen of the 19 cell lines had been gene edited with passage numbers ranging from 10 to 35. Diploidisation in 17 near-haploid cell lines ranged from 4 to 35% and percentage of N- and S-CIN in [1n] and [2n] metaphases ranged from 7 to 50% with two cell lines showing no CIN. Percentage of cells with CIN in the two double-haploid cell lines were 96% and 100% respectively. The most common S-CIN observed was deletion followed by translocation of both types, non-reciprocal and Robertsonian. Interestingly, we observed a prevalence of S-CIN associated with chromosome 13 in both near-and double-haploid cell lines, with a high incidence of Robertsonian translocation involving chromosome 13. Furthermore, locus-specific BAC (bacterial artificial chromosome) FISH enabled us to show for the first time that the additional chromosome 15 fragment is inserted into the p-arm rather than the q-arm of chromosome 19 of the HAP1 genome. CONCLUSION Our study revealed a high incidence of CIN leading to karyotype heterogeneity in majority of the HAP1 cell lines with the number of chromosomal aberrations varying between cell lines. A noteworthy observation was the high frequency of structural chromosomal aberrations associated with chromosome 13. We showed that CRISPR-Cas9 gene editing technology in combination with spontaneous diploidisation and prolonged in-vitro cell culturing is potentially instrumental in inducing further chromosomal rearrangements in the HAP1 cell lines with existing CIN. We highlight the importance of maintaining cell lines at low passage and the need for regular monitoring to prevent implications in downstream applications. Our study also established that the additional fragment of chromosome 15 in the HAP1 genome is inserted into chromosome 19p rather than 19q.
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Affiliation(s)
- Ruby Banerjee
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Cibele G. Sotero-Caio
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Beiyuan Fu
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK
| | - Fengtang Yang
- grid.10306.340000 0004 0606 5382Molecular Cytogenetics Core Facility, Wellcome Sanger Institute, Cambridge, CB10 1SA UK ,grid.412509.b0000 0004 1808 3414School of Life Sciences and Medicine, Shandong University of Technology, Zibo, Shandong People’s Republic of China
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17
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Geng K, Merino LG, Wedemann L, Martens A, Sobota M, Sanchez YP, Søndergaard JN, White RJ, Kutter C. Target-enriched nanopore sequencing and de novo assembly reveals co-occurrences of complex on-target genomic rearrangements induced by CRISPR-Cas9 in human cells. Genome Res 2022; 32:1876-1891. [PMID: 36180232 PMCID: PMC9712622 DOI: 10.1101/gr.276901.122] [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: 05/05/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022]
Abstract
The CRISPR-Cas9 system is widely used to permanently delete genomic regions via dual guide RNAs. Genomic rearrangements induced by CRISPR-Cas9 can occur, but continuous technical developments make it possible to characterize complex on-target effects. We combined an innovative droplet-based target enrichment approach with long-read sequencing and coupled it to a customized de novo sequence assembly. This approach enabled us to dissect the sequence content at kilobase scale within an on-target genomic locus. We here describe extensive genomic disruptions by Cas9, involving the allelic co-occurrence of a genomic duplication and inversion of the target region, as well as integrations of exogenous DNA and clustered interchromosomal DNA fragment rearrangements. Furthermore, we found that these genomic alterations led to functional aberrant DNA fragments and can alter cell proliferation. Our findings broaden the consequential spectrum of the Cas9 deletion system, reinforce the necessity of meticulous genomic validations, and introduce a data-driven workflow enabling detailed dissection of the on-target sequence content with superior resolution.
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Affiliation(s)
- Keyi Geng
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Lara G Merino
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Linda Wedemann
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Aniek Martens
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Małgorzata Sobota
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Yerma P Sanchez
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Jonas Nørskov Søndergaard
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
| | - Robert J White
- Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Claudia Kutter
- Department of Microbiology, Tumor, and Cell Biology, Karolinska Institute, Science for Life Laboratory, 171 65, Stockholm, Sweden
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18
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Liu C, Li W. Advances in haploid embryonic stem cell research. Biol Reprod 2022; 107:250-260. [PMID: 35639627 DOI: 10.1093/biolre/ioac110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/12/2022] [Accepted: 05/25/2022] [Indexed: 11/14/2022] Open
Abstract
Haploid embryonic stem cells are embryonic stem cells of a special type. Their nuclei contain one complete set of genetic material, and they are capable of self-renewal and differentiation. The emergence of haploid embryonic stem cells has aided research in functional genomics, genetic imprinting, parthenogenesis, genetic screening, and somatic cell nuclear transfer. This article reviews current issues in haploid stem cell research based on reports published in recent years and assesses the potential applications of these cells in somatic cell nuclear transfer, genome imprinting, and parthenogenesis.
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Affiliation(s)
- Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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19
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Consequences of Chromosome Loss: Why Do Cells Need Each Chromosome Twice? Cells 2022; 11:cells11091530. [PMID: 35563836 PMCID: PMC9101035 DOI: 10.3390/cells11091530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
Aneuploidy is a cellular state with an unbalanced chromosome number that deviates from the usual euploid status. During evolution, elaborate cellular mechanisms have evolved to maintain the correct chromosome content over generations. The rare errors often lead to cell death, cell cycle arrest, or impaired proliferation. At the same time, aneuploidy can provide a growth advantage under selective conditions in a stressful, frequently changing environment. This is likely why aneuploidy is commonly found in cancer cells, where it correlates with malignancy, drug resistance, and poor prognosis. To understand this “aneuploidy paradox”, model systems have been established and analyzed to investigate the consequences of aneuploidy. Most of the evidence to date has been based on models with chromosomes gains, but chromosome losses and recurrent monosomies can also be found in cancer. We summarize the current models of chromosome loss and our understanding of its consequences, particularly in comparison to chromosome gains.
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20
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Kulicke CA, De Zan E, Hein Z, Gonzalez-Lopez C, Ghanwat S, Veerapen N, Besra GS, Klenerman P, Christianson JC, Springer S, Nijman SM, Cerundolo V, Salio M. The P5-type ATPase ATP13A1 modulates major histocompatibility complex I-related protein 1 (MR1)-mediated antigen presentation. J Biol Chem 2022; 298:101542. [PMID: 34968463 PMCID: PMC8808182 DOI: 10.1016/j.jbc.2021.101542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/08/2022] Open
Abstract
The monomorphic antigen-presenting molecule major histocompatibility complex-I-related protein 1 (MR1) presents small-molecule metabolites to mucosal-associated invariant T (MAIT) cells. The MR1-MAIT cell axis has been implicated in a variety of infectious and noncommunicable diseases, and recent studies have begun to develop an understanding of the molecular mechanisms underlying this specialized antigen presentation pathway. However, proteins regulating MR1 folding, loading, stability, and surface expression remain to be identified. Here, we performed a gene trap screen to discover novel modulators of MR1 surface expression through insertional mutagenesis of an MR1-overexpressing clone derived from the near-haploid human cell line HAP1 (HAP1.MR1). The most significant positive regulators identified included β2-microglobulin, a known regulator of MR1 surface expression, and ATP13A1, a P5-type ATPase in the endoplasmic reticulum (ER) not previously known to be associated with MR1-mediated antigen presentation. CRISPR/Cas9-mediated knockout of ATP13A1 in both HAP1.MR1 and THP-1 cell lines revealed a profound reduction in MR1 protein levels and a concomitant functional defect specific to MR1-mediated antigen presentation. Collectively, these data are consistent with the ER-resident ATP13A1 being a key posttranscriptional determinant of MR1 surface expression.
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Affiliation(s)
- Corinna A Kulicke
- MRC Human Immunology Unit, Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.
| | - Erica De Zan
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research Ltd and Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Zeynep Hein
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Claudia Gonzalez-Lopez
- MRC Human Immunology Unit, Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Swapnil Ghanwat
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Natacha Veerapen
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Gurdyal S Besra
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - John C Christianson
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Sebastian Springer
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Sebastian M Nijman
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research Ltd and Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Mariolina Salio
- MRC Human Immunology Unit, Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.
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21
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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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22
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Powell G, Pavlovic Djuranovic S, Djuranovic S. Gene dosage effects of poly(A) track-engineered hypomorphs. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:865-878. [PMID: 34729253 PMCID: PMC8536507 DOI: 10.1016/j.omtn.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/29/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022]
Abstract
Manipulation of gene activity through creation of hypomorphic mutants has been a long-standing tool in examining gene function. Our previous studies have indicated that hypomorphic mutants could be created by inserting cis-regulatory sequences composed of consecutive adenosine nucleotides called poly(A) tracks. Here we use poly(A) tracks to create hypomorphic mutants and functional characterization of membrane, secretory, and endogenous proteins. Insertion of poly(A) tracks into the sequences of interleukin-2 and membrane protein CD20 results in a programmable reduction of mRNA stability and attenuation of protein expression regardless of the presence of a signaling sequence. Likewise, CRISPR-Cas9 targeted insertion of poly(A) tracks into the coding sequence of the endogenous human genes AUF1 and TP53 results in a programmable reduction of targeted protein and mRNA levels. Functional analyses of AUF1-engineered hypomorphs indicate a direct correlation between AUF1 gene levels and the stability of AUF1-regulated mRNAs. Hypomorphs of TP53 affect expression of the target genes differentially depending on the severity of the hypomorphic mutation. Finally, decreases in TP53 protein affect the same cellular pathways in poly(A) track-engineered cells as in cancer cells, indicating these variants’ biological relevance. These results highlight this technology’s power to create predictable, stable hypomorphs in recombinant or endogenous genes in combination with CRISPR-Cas9 engineering tools.
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Affiliation(s)
- Geralle Powell
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
- Correspondence: Sergej Djuranovic, Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA.
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23
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Aizawa E, Kaufmann C, Sting S, Boigner S, Freimann R, Di Minin G, Wutz A. Haploid mouse germ cell precursors from embryonic stem cells reveal Xist activation from a single X chromosome. Stem Cell Reports 2021; 17:43-52. [PMID: 34919812 PMCID: PMC8758942 DOI: 10.1016/j.stemcr.2021.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/03/2022] Open
Abstract
Mammalian haploid cells have applications for genetic screening and substituting gametic genomes. Here, we characterize a culture system for obtaining haploid primordial germ cell-like cells (PGCLCs) from haploid mouse embryonic stem cells (ESCs). We find that haploid cells show predisposition for PGCLCs, whereas a large fraction of somatic cells becomes diploid. Characterization of the differentiating haploid ESCs (haESCs) reveals that Xist is activated from and colocalizes with the single X chromosome. This observation suggests that X chromosome inactivation (XCI) is initiated in haploid cells consistent with a model where autosomal blocking factors set a threshold for X-linked activators. We further find that Xist expression is lost at later timepoints in differentiation, which likely reflects the loss of X-linked activators. In vitro differentiation of haploid PGCLCs can be a useful approach for future studies of potential X-linked activators of Xist. A culture system for obtaining haploid PGCLCs Predisposition of haploid cells in the germline over somatic lineages A single X chromosome in haploid cells leads to activation of Xist Mutation of Xist is insufficient to prevent diploidization of haESCs
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Affiliation(s)
- Eishi Aizawa
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Corinne Kaufmann
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Sarah Sting
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Sarah Boigner
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Remo Freimann
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Giulio Di Minin
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland
| | - Anton Wutz
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zurich, Zurich, Switzerland.
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24
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Yunusova A, Smirnov A, Shnaider T, Lukyanchikova V, Afonnikova S, Battulin N. Evaluation of the OsTIR1 and AtAFB2 AID Systems for Genome Architectural Protein Degradation in Mammalian Cells. Front Mol Biosci 2021; 8:757394. [PMID: 34805274 PMCID: PMC8599953 DOI: 10.3389/fmolb.2021.757394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 09/28/2021] [Indexed: 01/26/2023] Open
Abstract
The auxin-inducible degron (AID) system is a promising tool for dynamic protein degradation. In mammalian cells, this approach has become indispensable to study fundamental molecular functions, such as replication, chromatin dynamics, or transcription, which are otherwise difficult to dissect. We present evaluation of the two prominent AID systems based on OsTIR1 and AtAFB2 auxin receptor F-box proteins (AFBs). We analyzed degradation dynamics of cohesin/condensin complex subunits in mouse embryonic stem cells (Rad21, Smc2, Ncaph, and Ncaph2) and human haploid HAP1 line (RAD21, SMC2). Double antibiotic selection helped achieve high homozygous AID tagging of an endogenous gene for all genes using CRISPR/Cas9. We found that the main challenge for successful protein degradation is obtaining cell clones with high and stable AFB expression levels due to the mosaic expression of AFBs. AFB expression from a transgene tends to decline with passages in the absence of constant antibiotic selection, preventing epigenetic silencing of a transgene, even at the AAVS1 safe-harbor locus. Comparing two AFBs, we found that the OsTIR1 system showed weak dynamics of protein degradation. At the same time, the AtAFB2 approach was very efficient even in random integration of AFB-expressed transgenes. Other factors such as degradation dynamics and low basal depletion were also in favor of the AtAFB2 system.
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Affiliation(s)
| | | | | | | | - Svetlana Afonnikova
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Nariman Battulin
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
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25
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Abstract
The development of CRISPR-Cas9 screening techniques coupled with chemical inhibition of specific biological processes enables high-throughput investigation into many areas of molecular biology. We present a protocol to conduct ubiquitin proteasome system-specific chemical-genetic CRISPR-Cas9 screens in the human HAP1 cell line. This protocol can be adapted for use in other cell lines, with other compounds and types of treatments, and with any other sgRNA library. For complete details on the use and execution of this protocol, please refer to Hundley et al. (2021).
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Affiliation(s)
- Frances V. Hundley
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
- Present address: Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115, USA
| | - David P. Toczyski
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
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26
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Haas OA. Somatic Sex: On the Origin of Neoplasms With Chromosome Counts in Uneven Ploidy Ranges. Front Cell Dev Biol 2021; 9:631946. [PMID: 34422788 PMCID: PMC8373647 DOI: 10.3389/fcell.2021.631946] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 06/22/2021] [Indexed: 01/09/2023] Open
Abstract
Stable aneuploid genomes with nonrandom numerical changes in uneven ploidy ranges define distinct subsets of hematologic malignancies and solid tumors. The idea put forward herein suggests that they emerge from interactions between diploid mitotic and G0/G1 cells, which can in a single step produce all combinations of mono-, di-, tri-, tetra- and pentasomic paternal/maternal homologue configurations that define such genomes. A nanotube-mediated influx of interphase cell cytoplasm into mitotic cells would thus be responsible for the critical nondisjunction and segregation errors by physically impeding the proper formation of the cell division machinery, whereas only a complete cell fusion can simultaneously generate pentasomies, uniparental trisomies as well as biclonal hypo- and hyperdiploid cell populations. The term "somatic sex" was devised to accentuate the similarities between germ cell and somatic cell fusions. A somatic cell fusion, in particular, recapitulates many processes that are also instrumental in the formation of an abnormal zygote that involves a diploid oocyte and a haploid sperm, which then may further develop into a digynic triploid embryo. Despite their somehow deceptive differences and consequences, the resemblance of these two routes may go far beyond of what has hitherto been appreciated. Based on the arguments put forward herein, I propose that embryonic malignancies of mesenchymal origin with these particular types of aneuploidies can thus be viewed as the kind of flawed somatic equivalent of a digynic triploid embryo.
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Affiliation(s)
- Oskar A Haas
- St. Anna Children's Cancer Research Institute, Vienna, Austria
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27
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Martín I, Villamón E, Abellán R, Calasanz MJ, Irigoyen A, Sanz G, Such E, Mora E, Gutiérrez M, Collado R, García-Serra R, Vara M, Blanco ML, Oiartzabal I, Álvarez S, Bernal T, Granada I, Xicoy B, Jerez A, Calabuig M, Diez R, Gil Á, Díez-Campelo M, Solano C, Tormo M. Myelodysplastic syndromes with 20q deletion: incidence, prognostic value and impact on response to azacitidine of ASXL1 chromosomal deletion and genetic mutations. Br J Haematol 2021; 194:708-717. [PMID: 34296432 DOI: 10.1111/bjh.17675] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/05/2021] [Accepted: 06/09/2021] [Indexed: 11/28/2022]
Abstract
In myelodysplastic syndromes (MDS), the 20q deletion [del(20q)] may cause deletion of the ASXL1 gene. We studied 153 patients with MDS and del(20q) to assess the incidence, prognostic value and impact on response to azacitidine (AZA) of ASXL1 chromosomal alterations and genetic mutations. Additionally, in vitro assay of the response to AZA in HAP1 (HAP1WT ) and HAP1 ASXL1 knockout (HAP1KN ) cells was performed. ASXL1 chromosomal alterations were detected in 44 patients (28·5%): 34 patients (22%) with a gene deletion (ASXL1DEL ) and 10 patients (6·5%) with additional gene copies. ASXL1DEL was associated with a lower platelet count. The most frequently mutated genes were U2AF1 (16%), ASXL1 (14%), SF3B1 (11%), TP53 (7%) and SRSF2 (6%). ASXL1 alteration due to chromosomal deletion or genetic mutation (ASXL1DEL /ASXL1MUT ) was linked by multivariable analysis with shorter overall survival [hazard ratio, (HR) 1·84; 95% confidence interval, (CI): 1·11-3·04; P = 0·018] and a higher rate for acute myeloid leukaemia progression (HR 2·47; 95% CI: 1·07-5·70, P = 0·034). ASXL1DEL /ASXL1MUT patients were correlated by univariable analysis with a worse response to AZA. HAP1KN cells showed more resistance to AZA compared to HAP1WT cells. In conclusion, ASXL1 alteration exerts a negative impact on MDS with del(20q) and could become useful for prognostic risk stratification and treatment decisions.
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Affiliation(s)
- Iván Martín
- Hematology Department, Hospital Clínico Universitario de Valencia, INCLIVA Research Institute, University of Valencia, Valencia, Spain
| | - Eva Villamón
- Hematology Department, Hospital Clínico Universitario de Valencia, INCLIVA Research Institute, University of Valencia, Valencia, Spain
| | - Rosario Abellán
- Biochemistry and Molecular Pathology Department, Hospital Clínico Universitario de Valencia, INCLIVA Research Institute, Valencia, Spain
| | | | - Aroa Irigoyen
- CIMA LAB Diagnostics, Universidad de Navarra, Pamplona, Spain
| | - Guillermo Sanz
- Hematology Department, Hospital Universitario y Politécnico La Fe, Health Research Institute Hospital La Fe, IIS La Fe, Valencia, Spain
| | - Esperanza Such
- Hematology Department, Hospital Universitario y Politécnico La Fe, Health Research Institute Hospital La Fe, IIS La Fe, Valencia, Spain
| | - Elvira Mora
- Hematology Department, Hospital Universitario y Politécnico La Fe, Health Research Institute Hospital La Fe, IIS La Fe, Valencia, Spain
| | - Míriam Gutiérrez
- Genetics Department, Hospital Universitario Infanta Sofía, Madrid, Spain
| | - Rosa Collado
- Hematology Department, Consorcio Hospital General Universitario de Valencia, Research Foundation of the General University Hospital of Valencia, Valencia, Spain
| | - Rocío García-Serra
- Hematology Department, Consorcio Hospital General Universitario de Valencia, Research Foundation of the General University Hospital of Valencia, Valencia, Spain
| | - Míriam Vara
- Hematology Department, Hospital Universitario de Cruces, Barakaldo, Spain
| | - Mª Laura Blanco
- Hematology Department, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Itziar Oiartzabal
- Hematology Department, Hospital de Txagorritxu, Vitoria-Gasteiz, Spain
| | - Sara Álvarez
- NIMGenetics, Genómica y Medicina, Madrid, Spain.,Hematology Department, Hospital HM Sanchinarro, Madrid, Spain
| | - Teresa Bernal
- Hematology Department, Hospital Universidad de Asturias, IISPA, IUOPA, Oviedo, Spain
| | - Isabel Granada
- Hematology Department, Hospital Germans Trias i Pujol, Institut Català d'Oncologia, Josep Carreras Leukaemia Research Institute (IJC), Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Blanca Xicoy
- Hematology Department, Hospital Germans Trias i Pujol, Institut Català d'Oncologia, Josep Carreras Leukaemia Research Institute (IJC), Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Andrés Jerez
- Hematology Department, Hospital Universitario Morales Meseguer, Murcia, Spain
| | - Marisa Calabuig
- Hematology Department, Hospital Clínico Universitario de Valencia, INCLIVA Research Institute, University of Valencia, Valencia, Spain
| | - Rosana Diez
- Hematology Department, Hospital Universitario Miguel Servet de Zaragoza, Zaragoza, Spain
| | - Ángela Gil
- Hematology Department, Hospital Universitario de Guadalajara, Guadalajara, Spain
| | - María Díez-Campelo
- Hematology Department, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Carlos Solano
- Hematology Department, Hospital Clínico Universitario de Valencia, INCLIVA Research Institute, University of Valencia, Valencia, Spain.,Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - Mar Tormo
- Hematology Department, Hospital Clínico Universitario de Valencia, INCLIVA Research Institute, University of Valencia, Valencia, Spain
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28
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Atkinson SP. A preview of selected articles. Stem Cells Transl Med 2021; 10:643-646. [PMID: 33852778 PMCID: PMC8046101 DOI: 10.1002/sctm.21-0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 11/21/2022] Open
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29
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The actin nucleation factors JMY and WHAMM enable a rapid Arp2/3 complex-mediated intrinsic pathway of apoptosis. PLoS Genet 2021; 17:e1009512. [PMID: 33872315 PMCID: PMC8084344 DOI: 10.1371/journal.pgen.1009512] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 04/29/2021] [Accepted: 03/28/2021] [Indexed: 01/02/2023] Open
Abstract
The actin cytoskeleton is a well-known player in most vital cellular processes, but comparably little is understood about how the actin assembly machinery impacts programmed cell death pathways. In the current study, we explored roles for the human Wiskott-Aldrich Syndrome Protein (WASP) family of actin nucleation factors in DNA damage-induced apoptosis. Inactivation of each WASP-family gene revealed that two of them, JMY and WHAMM, are necessary for rapid apoptotic responses. JMY and WHAMM participate in a p53-dependent cell death pathway by enhancing mitochondrial permeabilization, initiator caspase cleavage, and executioner caspase activation. JMY-mediated apoptosis requires actin nucleation via the Arp2/3 complex, and actin filaments are assembled in cytoplasmic territories containing clusters of cytochrome c and active caspase-3. The loss of JMY additionally results in significant changes in gene expression, including upregulation of the WHAMM-interacting G-protein RhoD. Depletion or deletion of RHOD increases cell death, suggesting that RhoD normally contributes to cell survival. These results give rise to a model in which JMY and WHAMM promote intrinsic cell death responses that can be opposed by RhoD.
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30
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Gao Q, Zhang W, Zhao Y, Tian Y, Wang Y, Zhang J, Geng M, Xu M, Yao C, Wang H, Li L, Liu Y, Shuai L. High-throughput screening in postimplantation haploid epiblast stem cells reveals Hs3st3b1 as a modulator for reprogramming. Stem Cells Transl Med 2021; 10:743-755. [PMID: 33511777 PMCID: PMC8046116 DOI: 10.1002/sctm.20-0468] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/12/2020] [Accepted: 01/03/2021] [Indexed: 12/15/2022] Open
Abstract
Epiblast stem cells (EpiSCs) derived from postimplantation epiblast are pluripotent stem cells, epigenetically distinct from embryonic stem cells (ESCs), which are widely used in reprogramming studies. Recent achieved haploid cell lines in mammalian species open a new era for high-throughput genetic screening, due to their homozygous phenotypes. Here, we report the generation of mouse haploid EpiSCs (haEpiSCs) from postimplantation chimeric embryos at embryonic day 6.5 (E6.5). These cells maintain one set of chromosomes, express EpiSC-specific genes, and have potentials to differentiate into three germ layers. We also develop a massive mutagenesis protocol with haEpiSCs, and subsequently perform reprogramming selection using this genome-wide mutation library. Multiple modules related to various pathways are implicated. The validation experiments prove that knockout of Hst3st3b1 (one of the candidates) can promote reprogramming of EpiSCs to the ground state efficiently. Our results open the feasibility of utilizing haEpiSCs to elucidate fundamental biological processes including cell fate alternations.
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Affiliation(s)
- Qian Gao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Wenhao Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Yiding Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Yaru Tian
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Yuna Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Jinxin Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Mengyang Geng
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Mei Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Chunmeng Yao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Haoyu Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Luyuan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China
| | - Yan Liu
- Department of Obstetrics, Tianjin First Central Hospital, Nankai University, Tianjin, People's Republic of China
| | - Ling Shuai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, People's Republic of China.,Nankai Animal Resource Center, Nankai University, Tianjin, People's Republic of China.,Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin, People's Republic of China
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31
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Zhang G, Li X, Sun Y, Wang X, Liu G, Huang Y. A Genetic Screen Identifies Etl4-Deficiency Capable of Stabilizing the Haploidy in Embryonic Stem Cells. Stem Cell Reports 2021; 16:29-38. [PMID: 33440180 PMCID: PMC7815943 DOI: 10.1016/j.stemcr.2020.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 01/05/2023] Open
Abstract
Mammalian haploid embryonic stem cells (haESCs) hold great promise for functional genetic studies and forward screening. However, all established haploid cells are prone to spontaneous diploidization during long-term culture, rendering application challenging. Here, we report a genome-wide loss-of-function screening that identified gene mutations that could significantly reduce the rate of self-diploidization in haESCs. We further demonstrated that CRISPR/Cas9-mediated Etl4 knockout (KO) stabilizes the haploid state in different haESC lines. More interestingly, Etl4 deficiency increases mitochondrial oxidative phosphorylation (OXPHOS) capacity and decreases glycolysis in haESCs. Mimicking this effect by regulating the energy metabolism with drugs decreased the rate of self-diploidization. Collectively, our study identified Etl4 as a novel haploidy-related factor linked to an energy metabolism transition occurring during self-diploidization of haESCs. A genome-wide genetic screen identifies several haploidy-related factors in haESCs Etl4-deficiency stabilizes the haploid state in different haESC lines Etl4-deficiency increases mitochondrial OXPHOS and decrease glycolysis in haESCs Energy metabolism regulation with drugs decreased the rate of self-diploidization
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Affiliation(s)
- Guozhong Zhang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Xiaowen Li
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Yi Sun
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Xue Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China
| | - Guang Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
| | - Yue Huang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China; Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100005, China.
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Abstract
Functional characterizations and molecular dissections of long noncoding RNAs (lncRNAs) are critical to understand their involvement in the cellular regulatory network. LncRNAs exert their effects through functional RNA domains that interact with other molecules, including proteins, DNA, and RNA. Here, we describe experimental procedures for generating genomic deletions in a human haploid cell line using the CRISPR/Cas9 system. This method can be applied to examine functions of lncRNAs and their domains by establishing knockout and partial deletion mutant cell lines. In addition, we describe a CRISPR-mediated knockin method for artificial tethering of partner RNA-binding proteins to lncRNAs and its use to validate lncRNA-mediated functions.
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Henkel L, Rauscher B, Schmitt B, Winter J, Boutros M. Genome-scale CRISPR screening at high sensitivity with an empirically designed sgRNA library. BMC Biol 2020; 18:174. [PMID: 33228647 PMCID: PMC7686728 DOI: 10.1186/s12915-020-00905-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/20/2020] [Indexed: 12/22/2022] Open
Abstract
Background In recent years, large-scale genetic screens using the CRISPR/Cas9 system have emerged as scalable approaches able to interrogate gene function with unprecedented efficiency and specificity in various biological contexts. By this means, functional dependencies on both the protein-coding and noncoding genome of numerous cell types in different organisms have been interrogated. However, screening designs vary greatly and criteria for optimal experimental implementation and library composition are still emerging. Given their broad utility in functionally annotating genomes, the application and interpretation of genome-scale CRISPR screens would greatly benefit from consistent and optimal design criteria. Results We report advantages of conducting viability screens in selected Cas9 single-cell clones in contrast to Cas9 bulk populations. We further systematically analyzed published CRISPR screens in human cells to identify single-guide (sg) RNAs with consistent high on-target and low off-target activity. Selected guides were collected in a novel genome-scale sgRNA library, which efficiently identifies core and context-dependent essential genes. Conclusion We show how empirically designed libraries in combination with an optimized experimental design increase the dynamic range in gene essentiality screens at reduced library coverage. Supplementary information The online version contains supplementary material available at 10.1186/s12915-020-00905-1.
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Affiliation(s)
- Luisa Henkel
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany
| | - Benedikt Rauscher
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany
| | - Barbara Schmitt
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany
| | - Jan Winter
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, D-69120, Heidelberg, Germany.
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Beigl TB, Kjosås I, Seljeseth E, Glomnes N, Aksnes H. Efficient and crucial quality control of HAP1 cell ploidy status. Biol Open 2020; 9:9/11/bio057174. [PMID: 33184093 PMCID: PMC7673356 DOI: 10.1242/bio.057174] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The near-haploid human cell line HAP1 recently became a popular subject for CRISPR/Cas9 editing, since only one allele requires modification. Through the gene-editing service at Horizon Discovery, there are at present more than 7500 edited cell lines available and the number continuously increases. The haploid nature of HAP1 is unstable as cultures become diploid with time. Here, we demonstrated some fundamental differences between haploid and diploid HAP1 cells, hence underlining the need for taking control over ploidy status in HAP1 cultures prior to phenotyping. Consequently, we optimized a procedure to determine the ploidy of HAP1 by flow cytometry in order to obtain diploid cultures and avoid ploidy status as an interfering variable in experiments. Furthermore, in order to facilitate this quality control, we validated a size-based cell sorting procedure to obtain the diploid culture more rapidly. Hence, we provide here two streamlined protocols for quality controlling the ploidy of HAP1 cells and document their validity and necessity. This article has an associated First Person interview with the co-first authors of the paper. Summary: Sharing an effective procedure to quality control the near-haploid HAP1 cells for standardized comparison to CRISPR/Cas9 modified versions and demonstrating the need for controlling the spontaneous diploidization of HAP1 cultures.
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Affiliation(s)
- Tobias B Beigl
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.,Institute of cell biology and immunology, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Ine Kjosås
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway
| | - Emilie Seljeseth
- Department of Biological Sciences, University of Bergen, 5020 Bergen, Norway
| | - Nina Glomnes
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway.,Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Henriette Aksnes
- Department of Biomedicine, University of Bergen, 5020 Bergen, Norway
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Sun S, Zhao Y, Shuai L. The milestone of genetic screening: Mammalian haploid cells. Comput Struct Biotechnol J 2020; 18:2471-2479. [PMID: 33005309 PMCID: PMC7509586 DOI: 10.1016/j.csbj.2020.09.006] [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] [Received: 04/26/2020] [Revised: 09/04/2020] [Accepted: 09/05/2020] [Indexed: 12/30/2022] Open
Abstract
Mammalian haploid cells provide insights into multiple genetics approaches as have been proved by advances in homozygous phenotypes and function as gametes. Recent achievements make ploidy of mammalian haploid cells stable and improve the developmental efficiency of embryos derived from mammalian haploid cells intracytoplasmic microinjection, which promise great potentials for using mammalian haploid cells in forward and reverse genetic screening. In this review, we introduce breakthroughs of mammalian haploid cells involving in mechanisms of self-diploidization, forward genetics for various targeting genes and imprinted genes related development.
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Affiliation(s)
- Shengyi Sun
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Yiding Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Ling Shuai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
- Tate Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Tianjin Central Hospital of Gynecology Obstetrics / Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin 300052, China
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Olbrich T, Vega-Sendino M, Murga M, de Carcer G, Malumbres M, Ortega S, Ruiz S, Fernandez-Capetillo O. A Chemical Screen Identifies Compounds Capable of Selecting for Haploidy in Mammalian Cells. Cell Rep 2020; 28:597-604.e4. [PMID: 31315040 PMCID: PMC6656781 DOI: 10.1016/j.celrep.2019.06.060] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/24/2019] [Accepted: 06/15/2019] [Indexed: 12/24/2022] Open
Abstract
The recent availability of somatic haploid cell lines has provided a unique tool for genetic studies in mammals. However, the percentage of haploid cells rapidly decreases in these cell lines, which we recently showed is due to their overgrowth by diploid cells present in the cultures. Based on this property, we have now performed a phenotypic chemical screen in human haploid HAP1 cells aiming to identify compounds that facilitate the maintenance of haploid cells. Our top hit was 10-Deacetyl-baccatin-III (DAB), a chemical precursor in the synthesis of Taxol, which selects for haploid cells in HAP1 and mouse haploid embryonic stem cultures. Interestingly, DAB also enriches for diploid cells in mixed cultures of diploid and tetraploid cells, including in the colon cancer cell line DLD-1, revealing a general strategy for selecting cells with lower ploidy in mixed populations of mammalian cells. Mammalian haploid cell cultures become progressively enriched in diploid cells DAB, a precursor of Taxol, facilitates the maintenance of haploidy DAB selects for cells with lower ploidy in mixed cultures of mammalian cells Statins accelerate the gradual loss of haploid cells in culture
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Affiliation(s)
- Teresa Olbrich
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Maria Vega-Sendino
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Matilde Murga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Guillermo de Carcer
- Chromosome Dynamics Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Marcos Malumbres
- Chromosome Dynamics Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Sagrario Ortega
- Transgenics Unit, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Sergio Ruiz
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain; Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 21 Stockholm, Sweden.
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37
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Yoshizawa K, Yaguchi K, Uehara R. Uncoupling of DNA Replication and Centrosome Duplication Cycles Is a Primary Cause of Haploid Instability in Mammalian Somatic Cells. Front Cell Dev Biol 2020; 8:721. [PMID: 32850837 PMCID: PMC7408703 DOI: 10.3389/fcell.2020.00721] [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] [Received: 06/02/2020] [Accepted: 07/14/2020] [Indexed: 11/13/2022] Open
Abstract
Mammalian haploid somatic cells are unstable and prone to diploidize, but the cause of haploid instability remains largely unknown. Previously, we found that mammalian haploid somatic cells suffer chronic centrosome loss stemming from the uncoupling of DNA replication and centrosome duplication cycles. However, the lack of methodology to restore the coupling between DNA replication and centrosome duplication has precluded us from investigating the potential contribution of the haploidy-linked centrosome loss to haploid instability. In this study, we developed an experimental method that allows the re-coupling of DNA and centrosome cycles through the chronic extension of the G1/S phase without compromising cell proliferation using thymidine treatment/release cycles. Chronic extension of G1/S restored normal mitotic centrosome number and mitotic control, substantially improving the stability of the haploid state in HAP1 cells. Stabilization of the haploid state was compromised when cdk2 was inhibited during the extended G1/S, or when early G1 was chronically extended instead of G1/S, showing that the coupling of DNA and centrosome cycles rather than a general extension of the cell cycle is required for haploid stability. Our data indicate the chronic centriole loss arising from the uncoupling of centrosome and DNA cycles as a direct cause of genome instability in haploid somatic cells, and also demonstrate the feasibility of modulation of haploid stability through artificial coordination between DNA and centrosome cycles in mammalian somatic cells.
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Affiliation(s)
- Koya Yoshizawa
- Graduate School of Life Science, Hokkaido University, Hokkaido, Japan
| | - Kan Yaguchi
- Graduate School of Life Science, Hokkaido University, Hokkaido, Japan
| | - Ryota Uehara
- Graduate School of Life Science, Hokkaido University, Hokkaido, Japan
- Faculty of Advanced Life Science, Hokkaido University, Hokkaido, Japan
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38
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Li Y, Li W, Zhou Q. Haploid pluripotent stem cells: twofold benefits with half the effort in genetic screening and reproduction. Curr Opin Genet Dev 2020; 64:6-12. [PMID: 32563751 DOI: 10.1016/j.gde.2020.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 11/30/2022]
Abstract
Haploid pluripotent stem cells, which are capable of self-renewal and differentiation into other cell types with only one set of chromosomes, have been established in several species from haploid embryos. Compared with diploid embryonic stem cells (ESCs), haploid embryonic stem cells (haESCs) are smaller in size, have a prolonged metaphase, and undergo self-doubling during culture. The monoallelic expression of haESCs provides great convenience for recessive inheritance research. Genetically modified haESCs also provide benefits in replacement of the gamete genomes, which not only facilitates the study of the function of imprinted genes but also potentially removes barriers to same-sex reproduction. In this review, we focus on strategies for obtaining haESCs and their potential applications in genetic screening, genomic imprinting, and unisexual reproduction.
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Affiliation(s)
- Yufei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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39
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Zhang S, Yan L, Cui C, Wang Z, Wu J, Zhao M, Dong B, Guan X, Tian X, Hao C. Identification of TYMS as a promoting factor of retroperitoneal liposarcoma progression: Bioinformatics analysis and biological evidence. Oncol Rep 2020; 44:565-576. [PMID: 32627015 PMCID: PMC7336505 DOI: 10.3892/or.2020.7635] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 05/14/2020] [Indexed: 12/24/2022] Open
Abstract
Retroperitoneal liposarcoma (RLPS) is one of the most common types of retroperitoneal sarcomas, and has a high recurrence rate. There is an urgent need to further explore its pathogenesis and develop more effective treatment strategies. The aim of the present study was to identify potential driver genes of RLPS through bioinformatics analysis and molecular biology to elucidate potential targets that are suitable for further analysis for the treatment of RLPS. Differentially expressed genes (DEGs) between liposarcoma and normal fatty (NF) tissues were identified based on microarray data through bioinformatics analysis, and thymidylate synthase (TYMS) was selected from the DEGs, based on high content screening (HCS). TYMS expression was evaluated in RLPS tumor tissues and cell lines. A total of 21 RLPS tissues and 10 NF frozen tissues were used for reverse transcription-quantitative PCR, and 47 RLPS formalin-fixed specimens were used for immunohistochemical analysis. The effect of TYMS downregulation on cell proliferation, apoptosis, cell cycle progression, and cell migration and invasion were evaluated using lentivirus-mediated short hairpin RNA. The underlying mechanisms of TYMS in RLPS were examined by protein microarray and verified by western blotting. A total of 855 DEGs were identified. TYMS knockdown had the most notable effect on the proliferative capacity of RLPS cells according to the HCS results. TYMS mRNA expression levels were higher in RLPS tissues compared with NF tissues (P<0.001). TYMS expression was higher in high-grade RLPS tissues compared with low-grade RLPS tissues (P=0.003). The patients with positive TYMS expression had a worse overall survival (OS) and disease-free survival (DFS) compared with the patients with negative TYMS expression (OS, P=0.024; DFS, P=0.030). The knockdown of TYMS reduced proliferation, promoted apoptosis, facilitated cell cycle progression from G1 to S phase, and reduced cell migration and invasion of RLPS cells. Protein microarray analysis and western blotting showed that the Janus Kinase/Signal transducers and activators of transcription pathway was downregulated following TYMS knockdown. In conclusion, TYMS expression is upregulated in RLPS tissues, and downregulation of TYMS reduces RLPS progression.
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Affiliation(s)
- Sha Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Liang Yan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Can Cui
- Department of Breast Oncology, Tianjin Medical University Cancer Institute and Hospital, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Zhen Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Jianhui Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Min Zhao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Bin Dong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Central Laboratory, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Xiaoya Guan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Xiuyun Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Chunyi Hao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Hepato‑Pancreato‑Biliary Surgery, Peking University Cancer Hospital and Institute, Beijing 100142, P.R. China
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40
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Zhang W, Tian Y, Gao Q, Li X, Li Y, Zhang J, Yao C, Wang Y, Wang H, Zhao Y, Zhang Q, Li L, Yu Y, Fan Y, Shuai L. Inhibition of Apoptosis Reduces Diploidization of Haploid Mouse Embryonic Stem Cells during Differentiation. Stem Cell Reports 2020; 15:185-197. [PMID: 32502463 PMCID: PMC7363743 DOI: 10.1016/j.stemcr.2020.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 01/19/2023] Open
Abstract
Phenotypes of haploid embryonic stem cells (haESCs) are dominant for recessive traits in mice. However, one major obstacle to their use is self-diploidization in daily culture. Although haESCs maintain haploidy well by deleting p53, whether they can sustain haploidy in differentiated status and the mechanism behind it remain unknown. To address this, we induced p53-deficient haESCs into multiple differentiated lineages maintain haploid status in vitro. Haploid cells also remained in chimeric embryos and teratomas arising from p53-null haESCs. Transcriptome analysis revealed that apoptosis genes were downregulated in p53-null haESCs compared with that in wild-type haESCs. Finally, we knocked out p73, another apoptosis-related gene, and observed stabilization of haploidy in haESCs. These results indicated that the main mechanism of diploidization was apoptosis-related gene-triggered cell death in haploid cell cultures. Thus, we can derive haploid somatic cells by manipulating the apoptosis gene, facilitating genetic screens of lineage-specific development. haEpiLCs and haNSCLCs differentiated from p53-null haESCs in vitro p53-null haESCs contributed to chimeric embryos and teratoma Downregulation of apoptosis genes resulted in haploidy stabilization Deletion of p73 was also of benefit for haploidy sustenance
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Affiliation(s)
- Wenhao Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Yaru Tian
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Qian Gao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China; Reproductive Medical Center, Department of Gynecology and Obstetrics, Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Xu Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Yanni Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Jinxin Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Chunmeng Yao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Yuna Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Haoyu Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Yiding Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Qian Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Luyuan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China
| | - Yang Yu
- Reproductive Medical Center, Department of Gynecology and Obstetrics, Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing 100191, China.
| | - Yong Fan
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China.
| | - Ling Shuai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin 300350, China.
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41
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Koh G, Zou X, Nik-Zainal S. Mutational signatures: experimental design and analytical framework. Genome Biol 2020; 21:37. [PMID: 32059681 PMCID: PMC7023746 DOI: 10.1186/s13059-020-1951-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 01/30/2020] [Indexed: 12/21/2022] Open
Abstract
Mutational signatures provide a powerful alternative for understanding the pathophysiology of cancer. Currently, experimental efforts aimed at validating and understanding the etiologies of cancer-derived mutational signatures are underway. In this review, we highlight key aspects of mutational signature experimental design and describe the analytical framework. We suggest guidelines and quality control measures for handling whole-genome sequencing data for mutational signature analyses and discuss pitfalls in interpretation. We envision that improved next-generation sequencing technologies and molecular cell biology approaches will usher in the next generation of studies into the etiologies and mechanisms of mutational patterns uncovered in cancers.
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Affiliation(s)
- Gene Koh
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Xueqing Zou
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Serena Nik-Zainal
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK.
- MRC Cancer Unit, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0XZ, UK.
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42
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Ji L, Lu B, Zamponi R, Charlat O, Aversa R, Yang Z, Sigoillot F, Zhu X, Hu T, Reece-Hoyes JS, Russ C, Michaud G, Tchorz JS, Jiang X, Cong F. USP7 inhibits Wnt/β-catenin signaling through promoting stabilization of Axin. Nat Commun 2019; 10:4184. [PMID: 31519875 PMCID: PMC6744515 DOI: 10.1038/s41467-019-12143-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
Axin is a key scaffolding protein responsible for the formation of the β-catenin destruction complex. Stability of Axin protein is regulated by the ubiquitin-proteasome system, and modulation of cellular concentration of Axin protein has a profound effect on Wnt/β-catenin signaling. Although E3s promoting Axin ubiquitination have been identified, the deubiquitinase responsible for Axin deubiquitination and stabilization remains unknown. Here, we identify USP7 as a potent negative regulator of Wnt/β-catenin signaling through CRISPR screens. Genetic ablation or pharmacological inhibition of USP7 robustly increases Wnt/β-catenin signaling in multiple cellular systems. USP7 directly interacts with Axin through its TRAF domain, and promotes deubiquitination and stabilization of Axin. Inhibition of USP7 regulates osteoblast differentiation and adipocyte differentiation through increasing Wnt/β-catenin signaling. Our study reveals a critical mechanism that prevents excessive degradation of Axin and identifies USP7 as a target for sensitizing cells to Wnt/β-catenin signaling. Axin is a scaffolding protein known for its role in Wnt signalling that can be marked with a variety of post-translational modifications. Here, Cong et al. demonstrate that USP7 de-ubiquinates Axin and that canonical Wnt signaling output can be increased with USP7 inhibitors.
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Affiliation(s)
- Lei Ji
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Bo Lu
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Raffaella Zamponi
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA.,Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123, Reggio Emila, Italy
| | - Olga Charlat
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Robert Aversa
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Zinger Yang
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Frederic Sigoillot
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Xiaoping Zhu
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Tiancen Hu
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - John S Reece-Hoyes
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Carsten Russ
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Gregory Michaud
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Jan S Tchorz
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Basel, Switzerland
| | - Xiaomo Jiang
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA
| | - Feng Cong
- Novartis Institutes for Biomedical Research, Novartis Pharma AG, Cambridge, MA, USA.
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43
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Serebrenik YV, Sansbury SE, Kumar SS, Henao-Mejia J, Shalem O. Efficient and flexible tagging of endogenous genes by homology-independent intron targeting. Genome Res 2019; 29:1322-1328. [PMID: 31239279 PMCID: PMC6673721 DOI: 10.1101/gr.246413.118] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/12/2019] [Indexed: 01/28/2023]
Abstract
Genome editing tools have simplified the generation of knock-in gene fusions, yet the prevalent use of gene-specific homology-directed repair (HDR) templates still hinders scalability. Consequently, realization of large-scale gene tagging requires further development of approaches to generate knock-in protein fusions via generic donors that do not require locus-specific homology sequences. Here, we combine intron-based protein trapping with homology-independent repair-based integration of a generic donor and demonstrate precise, scalable, and efficient gene tagging. Because editing is performed in introns using a synthetic exon, this approach tolerates mutations in the unedited allele, indels at the integration site, and the addition of resistance genes that do not disrupt the target gene coding sequence, resulting in easy and flexible gene tagging.
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Affiliation(s)
- Yevgeniy V Serebrenik
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Stephanie E Sansbury
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Saranya Santhosh Kumar
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Division of Protective Immunity, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Ophir Shalem
- Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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44
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Elling U, Woods M, Forment JV, Fu B, Yang F, Ng BL, Vicente JR, Adams DJ, Doe B, Jackson SP, Penninger JM, Balmus G. Derivation and maintenance of mouse haploid embryonic stem cells. Nat Protoc 2019; 14:1991-2014. [PMID: 31160788 PMCID: PMC6997032 DOI: 10.1038/s41596-019-0169-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/21/2019] [Indexed: 01/05/2023]
Abstract
Ploidy represents the number of chromosome sets in a cell. Although gametes have a haploid genome (n), most mammalian cells have diploid genomes (2n). The diploid status of most cells correlates with the number of probable alleles for each autosomal gene and makes it difficult to target these genes via mutagenesis techniques. Here, we describe a 7-week protocol for the derivation of mouse haploid embryonic stem cells (hESCs) from female gametes that also outlines how to maintain the cells once derived. We detail additional procedures that can be used with cell lines obtained from the mouse Haplobank, a biobank of >100,000 individual mouse hESC lines with targeted mutations in 16,970 genes. hESCs can spontaneously diploidize and can be maintained in both haploid and diploid states. Mouse hESCs are genomically and karyotypically stable, are innately immortal and isogenic, and can be derived in an array of differentiated cell types; they are thus highly amenable to genetic screens and to defining molecular connectivity pathways.
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Affiliation(s)
- Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Michael Woods
- UK Dementia Research Institute at University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Josep V Forment
- DNA Damage Response Biology, Oncology Innovative Medicines, AstraZeneca, Cambridge, UK
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Cambridge, UK
| | | | - Bee Ling Ng
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Jose R Vicente
- UK Dementia Research Institute at University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - Brendan Doe
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Stephen P Jackson
- The Wellcome Trust CRUK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Josef M Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna Biocenter (VBC), Vienna, Austria.
- Department of Medical Genetics, Life Science Institute, University of British Columbia, Vancouver, BC, Canada.
| | - Gabriel Balmus
- UK Dementia Research Institute at University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
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45
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He W, Chen J, Gao S. Mammalian haploid stem cells: establishment, engineering and applications. Cell Mol Life Sci 2019; 76:2349-2367. [PMID: 30888429 PMCID: PMC11105600 DOI: 10.1007/s00018-019-03069-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/23/2019] [Accepted: 03/13/2019] [Indexed: 12/19/2022]
Abstract
Haploid embryonic stem cells (haESCs) contain only one set of genomes inherited from the sperm or egg and are termed AG- or PG-haESCs, respectively. Mammalian haESCs show genome-wide hypomethylation and dysregulated imprinting, whereas they can sustain genome integrity during derivation and long-term propagation. In addition, haESCs exhibit similar pluripotency to traditional diploid ESCs but are unique because they function as gametes and have been used to produce semi-cloned animals. More strikingly, unisexual reproduction has been achieved in mice by using haESCs. In combination with a gene editing or screening system, haESCs represent a powerful tool for studies of underlying gene functions and explorations of mechanisms of genetic and epigenetic regulation not only at the cellular level in vitro but also at the animal level in vivo. More importantly, genetically edited AG-haESC lines may further serve as an ideal candidate for the establishment of a sperm bank, which is a highly cost-effective approach, and a wide range of engineered semi-cloned mice have been produced. Here, we review the historical development, characteristics, advantages and disadvantages of haESCs. Additionally, we present an in-depth discussion of the recent advances in haESCs and their potential applications.
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Affiliation(s)
- Wenteng He
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China
| | - Jiayu Chen
- Clinical and Translation Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200120, China.
- Clinical and Translation Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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46
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Cui T, Li Z, Zhou Q, Li W. Current advances in haploid stem cells. Protein Cell 2019; 11:23-33. [PMID: 31004328 PMCID: PMC6949308 DOI: 10.1007/s13238-019-0625-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/29/2019] [Indexed: 12/14/2022] Open
Abstract
Diploidy is the typical genomic mode in all mammals. Haploid stem cells are artificial cell lines experimentally derived in vitro in the form of different types of stem cells, which combine the characteristics of haploidy with a broad developmental potential and open the possibility to uncover biological mysteries at a genomic scale. To date, a multitude of haploid stem cell types from mouse, rat, monkey and humans have been derived, as more are in development. They have been applied in high-throughput genetic screens and mammalian assisted reproduction. Here, we review the generation, unique properties and broad applications of these remarkable cells.
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Affiliation(s)
- Tongtong Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhikun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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47
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Kneissig M, Bernhard S, Storchova Z. Modelling chromosome structural and copy number changes to understand cancer genomes. Curr Opin Genet Dev 2019; 54:25-32. [PMID: 30921673 DOI: 10.1016/j.gde.2019.02.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 02/18/2019] [Indexed: 12/26/2022]
Abstract
Cancer cells differ from healthy cells by genetic information that is massively altered not only by point mutations and small insertions and deletions, but also by large scale changes such as chromosomal rearrangements as well as gains and losses of individual chromosomes or entire chromosome sets. How exactly large-scale chromosomal abnormalities contribute to tumorigenesis has been difficult to study. Remarkable progress has been recently made thanks to in vitro models that mimic large-scale chromosomal aberrations and allow their systematic analysis. The obtained findings reveal that genomic alterations strongly affect the cellular physiology and, importantly, instigate further genomic instability. This suggests that these model systems might provide novel insights by recapitulating the processes that occur during tumorigenesis.
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Affiliation(s)
- Maja Kneissig
- Department of Molecular Genetics, University of Kaiserslautern, Germany
| | - Sara Bernhard
- Department of Molecular Genetics, University of Kaiserslautern, Germany
| | - Zuzana Storchova
- Department of Molecular Genetics, University of Kaiserslautern, Germany.
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48
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Derivation of Haploid Trophoblast Stem Cells via Conversion In Vitro. iScience 2019; 11:508-518. [PMID: 30635215 PMCID: PMC6354440 DOI: 10.1016/j.isci.2018.12.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/11/2018] [Accepted: 12/17/2018] [Indexed: 11/22/2022] Open
Abstract
Owing to their single genome, haploid cells are powerful to uncover unknown genes by performing genetic screening in mammals. However, no haploid cell line from an extraembryonic lineage has been achieved yet, which limits the application of haploid cells in placental genetic screening. Here, we show that overexpression of Cdx2 can convert haploid embryonic stem cells to trophoblast stem cells (TSCs). p53 deletion reduces diploidization during the conversion and guarantees the generation of haploid-induced TSCs (haiTSCs). haiTSCs not only share the same molecular characterization with trophoderm-derived TSCs but also possess multipotency to placental lineages in various procedures. In addition, haiTSCs can maintain haploidy in the long term, assisted by periodic sorting and with reliance on FGF4 and heparin. Finally, we perform piggyBac-mediated high-throughput mutation in haiTSCs and use them in trophoblast lineage genetic screening. Deep sequencing analysis and validation experiments prove that Htra1 is a blocker for spongiotrophoblast specification. A haploid cell line of extraembryonic lineages with self-renewal ability haiTSCs have multipotency to functional trophoblast lineages both in vitro and in vivo High-throughput screening of spongiotrophoblast specification-related genes in haiTSCs Htra1 is a blocker for spongiotrophoblast-specific differentiation
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49
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Felley-Bosco E, MacFarlane M. Asbestos: Modern Insights for Toxicology in the Era of Engineered Nanomaterials. Chem Res Toxicol 2018; 31:994-1008. [PMID: 30156102 DOI: 10.1021/acs.chemrestox.8b00146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Asbestos fibers are naturally occurring silicates that have been extensively used in the past, including house construction, but because of their toxicity, their use has been banned in 63 countries. Despite this, more than one million metric tons of asbestos are still consumed annually in countries where asbestos use has not been banned. Asbestos-related disease incidence is still increasing in several countries, including those countries that banned the use of asbestos more than 30 years ago. We highlight here recent knowledge obtained in experimental models about the mechanisms leading to tumor development following asbestos exposure, including genetic and epigenetic changes. Importantly, the landscape of alterations observed experimentally in tumor samples is consistent with alterations observed in clinical tumor samples; therefore, studies performed on early/precancer stages should help inform secondary prevention, which remains crucial in the absence of an efficient primary prevention. Knowledge gathered on asbestos should also help address future challenges, especially in view of the increased production of new materials that may behave similarly to asbestos fibers.
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Affiliation(s)
- Emanuela Felley-Bosco
- Laboratory of Molecular Oncology , University Hospital Zurich , Sternwartstrasse 14 , 8091 Zürich , Switzerland
| | - Marion MacFarlane
- MRC Toxicology Unit , University of Cambridge , Hodgkin Building, Leicester LE1 9HN , United Kingdom
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50
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Ploidy-dependent change in cyclin D2 expression and sensitization to cdk4/6 inhibition in human somatic haploid cells. Biochem Biophys Res Commun 2018; 504:231-237. [DOI: 10.1016/j.bbrc.2018.08.160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 08/26/2018] [Indexed: 01/22/2023]
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