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Chialastri A, Sarkar S, Schauer EE, Lamba S, Dey SS. Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity. Nat Struct Mol Biol 2024:10.1038/s41594-024-01291-w. [PMID: 38671229 DOI: 10.1038/s41594-024-01291-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
Inheritance of 5-methylcytosine from one cell generation to the next by DNA methyltransferase 1 (DNMT1) plays a key role in regulating cellular identity. While recent work has shown that the activity of DNMT1 is imprecise, it remains unclear how the fidelity of DNMT1 is tuned in different genomic and cell state contexts. Here we describe Dyad-seq, a method to quantify the genome-wide methylation status of cytosines at the resolution of individual CpG dinucleotides to find that the fidelity of DNMT1-mediated maintenance methylation is related to the local density of DNA methylation and the landscape of histone modifications. To gain deeper insights into methylation/demethylation turnover dynamics, we first extended Dyad-seq to quantify all combinations of 5-methylcytosine and 5-hydroxymethylcytosine at individual CpG dyads. Next, to understand how cell state transitions impact maintenance methylation, we scaled the method down to jointly profile genome-wide methylation levels, maintenance methylation fidelity and the transcriptome from single cells (scDyad&T-seq). Using scDyad&T-seq, we demonstrate that, while distinct cell states can substantially impact the activity of the maintenance methylation machinery, locally there exists an intrinsic relationship between DNA methylation density, histone modifications and DNMT1-mediated maintenance methylation fidelity that is independent of cell state.
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Affiliation(s)
- Alex Chialastri
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Saumya Sarkar
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Elizabeth E Schauer
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Shyl Lamba
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA, USA
| | - Siddharth S Dey
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA, USA.
- Department of Bioengineering, University of California Santa Barbara, Santa Barbara, CA, USA.
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
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2
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Chi P, Ou G, Qin D, Han Z, Li J, Xiao Q, Gao Z, Xu C, Qi Q, Liu Q, Liu S, Li J, Guo L, Lu Y, Chen J, Wang X, Shi H, Li L, Deng D. Structural basis of the subcortical maternal complex and its implications in reproductive disorders. Nat Struct Mol Biol 2024; 31:115-124. [PMID: 38177687 DOI: 10.1038/s41594-023-01153-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/16/2023] [Indexed: 01/06/2024]
Abstract
The subcortical maternal complex (SCMC) plays a crucial role in early embryonic development. Malfunction of SCMC leads to reproductive diseases in women. However, the molecular function and assembly basis for SCMC remain elusive. Here we reconstituted mouse SCMC and solved the structure at atomic resolution using single-particle cryo-electron microscopy. The core complex of SCMC was formed by MATER, TLE6 and FLOPED, and MATER embraced TLE6 and FLOPED via its NACHT and LRR domains. Two core complexes further dimerize through interactions between two LRR domains of MATERs in vitro. FILIA integrates into SCMC by interacting with the carboxyl-terminal region of FLOPED. Zygotes from mice with Floped C-terminus truncation showed delayed development and resembled the phenotype of zygotes from Filia knockout mice. More importantly, the assembly of mouse SCMC was affected by corresponding clinical variants associated with female reproductive diseases and corresponded with a prediction based on the mouse SCMC structure. Our study paves the way for further investigations on SCMC functions during mammalian preimplantation embryonic development and reveals underlying causes of female reproductive diseases related to SCMC mutations, providing a new strategy for the diagnosis of female reproductive disorders.
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Affiliation(s)
- Pengliang Chi
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Guojin Ou
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
- Clinical Laboratory, West China Second Hospital, Sichuan University, Chengdu, China
| | - Dandan Qin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhuo Han
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, China
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Jialu Li
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, China
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Qingjie Xiao
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Zheng Gao
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Chengpeng Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Qianqian Qi
- Clinical Laboratory, West China Second Hospital, Sichuan University, Chengdu, China
| | - Qingting Liu
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Sibei Liu
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Jinhong Li
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Li Guo
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
| | - Yuechao Lu
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
- Department of Reproductive Medicine, West China Second Hospital, Sichuan University, Chengdu, China
| | - Jing Chen
- Laboratory of Pediatric Surgery, Department of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Xiang Wang
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, China
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China
| | - Hubing Shi
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Stem Cell and Regeneration, Beijing Institute of Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China.
| | - Dong Deng
- Department of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu, China.
- NHC Key Laboratory of Chronobiology, Sichuan University, Chengdu, China.
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Sichuan University, Chengdu, China.
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Li C, Bi R, Wang L, Ma YH, Yao YG, Zheng P. Characterization of long-term ex vivo expansion of tree shrew spermatogonial stem cells. Zool Res 2023; 44:1080-1094. [PMID: 37914523 PMCID: PMC10802108 DOI: 10.24272/j.issn.2095-8137.2023.317] [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: 09/30/2023] [Accepted: 10/30/2023] [Indexed: 11/03/2023] Open
Abstract
Tree shrews ( Tupaia belangeri chinensis) share a close relationship to primates and have been widely used in biomedical research. We previously established a spermatogonial stem cell (SSC)-based gene editing platform to generate transgenic tree shrews. However, the influences of long-term expansion on tree shrew SSC spermatogenesis potential remain unclear. Here, we examined the in vivo spermatogenesis potential of tree shrew SSCs cultured across different passages. We found that SSCs lost spermatogenesis ability after long-term expansion (>50 passages), as indicated by the failure to colonize the seminiferous epithelium and generate donor spermatogonia (SPG)-derived spermatocytes or spermatids marking spermatogenesis. RNA sequencing (RNA-seq) analysis of undifferentiated SPGs across different passages revealed significant gene expression changes after sub-culturing primary SPG lines for more than 40 passages on feeder layers. Specifically, DNA damage response and repair genes (e.g., MRE11, SMC3, BLM, and GEN1) were down-regulated, whereas genes associated with mitochondrial function (e.g., NDUFA9, NDUFA8, NDUFA13, and NDUFB8) were up-regulated after expansion. The DNA damage accumulation and mitochondrial dysfunction were experimentally validated in high-passage cells. Supplementation with nicotinamide adenine dinucleotide (NAD +) precursor nicotinamide riboside (NR) exhibited beneficial effects by reducing DNA damage accumulation and mitochondrial dysfunction in SPG elicited by long-term culture. Our research presents a comprehensive analysis of the genetic and physiological attributes critical for the sustained expansion of undifferentiated SSCs in tree shrews and proposes an effective strategy for extended in vitro maintenance.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yu-Hua Ma
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650204, China. E-mail:
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650204, China. E-mail:
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4
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Fleifel D, Cook JG. G1 Dynamics at the Crossroads of Pluripotency and Cancer. Cancers (Basel) 2023; 15:4559. [PMID: 37760529 PMCID: PMC10526231 DOI: 10.3390/cancers15184559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
G1 cell cycle phase dynamics are regulated by intricate networks involving cyclins, cyclin-dependent kinases (CDKs), and CDK inhibitors, which control G1 progression and ensure proper cell cycle transitions. Moreover, adequate origin licensing in G1 phase, the first committed step of DNA replication in the subsequent S phase, is essential to maintain genome integrity. In this review, we highlight the intriguing parallels and disparities in G1 dynamics between stem cells and cancer cells, focusing on their regulatory mechanisms and functional outcomes. Notably, SOX2, OCT4, KLF4, and the pluripotency reprogramming facilitator c-MYC, known for their role in establishing and maintaining stem cell pluripotency, are also aberrantly expressed in certain cancer cells. In this review, we discuss recent advances in understanding the regulatory role of these pluripotency factors in G1 dynamics in the context of stem cells and cancer cells, which may offer new insights into the interconnections between pluripotency and tumorigenesis.
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Affiliation(s)
| | - Jeanette Gowen Cook
- Department of Biochemistry & Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
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5
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Jiang F, Wang L, Dong Y, Nie W, Zhou H, Gao J, Zheng P. DPPA5A suppresses the mutagenic TLS and MMEJ pathways by modulating the cryptic splicing of Rev1 and Polq in mouse embryonic stem cells. Proc Natl Acad Sci U S A 2023; 120:e2305187120. [PMID: 37459543 PMCID: PMC10372678 DOI: 10.1073/pnas.2305187120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
Genetic alterations are often acquired during prolonged propagation of pluripotent stem cells (PSCs). This ruins the stem cell quality and hampers their full applications. Understanding how PSCs maintain genomic integrity would provide the clues to overcome the hurdle. It has been known that embryonic stem cells (ESCs) utilize high-fidelity pathways to ensure genomic stability, but the underlying mechanisms remain largely elusive. Here, we show that many DNA damage response and repair genes display differential alternative splicing in mouse ESCs compared to differentiated cells. Particularly, Rev1 and Polq, two key genes for mutagenic translesion DNA synthesis (TLS) and microhomology-mediated end joining (MMEJ) repair pathways, respectively, display a significantly higher rate of cryptic exon (CE) inclusion in ESCs. The frequent CE inclusion disrupts the normal protein expressions of REV1 and POLθ, thereby suppressing the mutagenic TLS and MMEJ. Further, we identify an ESC-specific RNA binding protein DPPA5A which stimulates the CE inclusion in Rev1 and Polq. Depletion of DPPA5A in mouse ESCs decreased the CE inclusion of Rev1 and Polq, induced the protein expression, and stimulated the TLS and MMEJ activity. Enforced expression of DPPA5A in NIH3T3 cells displayed reverse effects. Mechanistically, we found that DPPA5A directly regulated CE splicing of Rev1. DPPA5A associates with U2 small nuclear ribonucleoprotein of the spliceosome and binds to the GA-rich motif in the CE of Rev1 to promote CE inclusion. Thus, our study uncovers a mechanism to suppress mutagenic TLS and MMEJ pathways in ESCs.
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Affiliation(s)
- Fangjie Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- University of Chinese Academy of Sciences, Beijing101408, China
- Department of Reproductive Medicine, The Second Affiliated Hospital of Kunming Medical University,Kunming650101, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Yuping Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- University of Chinese Academy of Sciences, Beijing101408, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Wenhui Nie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
| | - Hu Zhou
- Department of Analytical Chemistry and Key Laboratory of Receptor Research of Chinese Academy of Sciences, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Jing Gao
- Department of Analytical Chemistry and Key Laboratory of Receptor Research of Chinese Academy of Sciences, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai201203, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
- The Chinese University of Hong Kong and Kunming Institute of Zoology Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan650223, China
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6
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Wang ZX, Liu Y, Li YL, Wei Q, Lin RR, Kang R, Ruan Y, Lin ZH, Xue NJ, Zhang BR, Pu JL. Nuclear DJ-1 Regulates DNA Damage Repair via the Regulation of PARP1 Activity. Int J Mol Sci 2023; 24:ijms24108651. [PMID: 37239999 DOI: 10.3390/ijms24108651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 05/28/2023] Open
Abstract
DNA damage and defective DNA repair are extensively linked to neurodegeneration in Parkinson's disease (PD), but the underlying molecular mechanisms remain poorly understood. Here, we determined that the PD-associated protein DJ-1 plays an essential role in modulating DNA double-strand break (DSB) repair. Specifically, DJ-1 is a DNA damage response (DDR) protein that can be recruited to DNA damage sites, where it promotes DSB repair through both homologous recombination and nonhomologous end joining. Mechanistically, DJ-1 interacts directly with PARP1, a nuclear enzyme essential for genomic stability, and stimulates its enzymatic activity during DNA repair. Importantly, cells from PD patients with the DJ-1 mutation also have defective PARP1 activity and impaired repair of DSBs. In summary, our findings uncover a novel function of nuclear DJ-1 in DNA repair and genome stability maintenance, and suggest that defective DNA repair may contribute to the pathogenesis of PD linked to DJ-1 mutations.
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Affiliation(s)
- Zhong-Xuan Wang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yi Liu
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yao-Lin Li
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Qiao Wei
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Rong-Rong Lin
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Ruiqing Kang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Yang Ruan
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Zhi-Hao Lin
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Nai-Jia Xue
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Bao-Rong Zhang
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
| | - Jia-Li Pu
- Department of Neurology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
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7
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Chialastri A, Sarkar S, Schauer EE, Lamba S, Dey SS. Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.539708. [PMID: 37205524 PMCID: PMC10187321 DOI: 10.1101/2023.05.06.539708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Transmission of 5-methylcytosine (5mC) from one cell generation to the next plays a key role in regulating cellular identity in mammalian development and diseases. While recent work has shown that the activity of DNMT1, the protein responsible for the stable inheritance of 5mC from mother to daughter cells, is imprecise; it remains unclear how the fidelity of DNMT1 is tuned in different genomic and cell state contexts. Here we describe Dyad-seq, a method that combines enzymatic detection of modified cytosines with nucleobase conversion techniques to quantify the genome-wide methylation status of cytosines at the resolution of individual CpG dinucleotides. We find that the fidelity of DNMT1-mediated maintenance methylation is directly related to the local density of DNA methylation, and for genomic regions that are lowly methylated, histone modifications can dramatically alter the maintenance methylation activity. Further, to gain deeper insights into the methylation and demethylation turnover dynamics, we extended Dyad-seq to quantify all combinations of 5mC and 5-hydroxymethylcytosine (5hmC) at individual CpG dyads to show that TET proteins preferentially hydroxymethylate only one of the two 5mC sites in a symmetrically methylated CpG dyad rather than sequentially convert both 5mC to 5hmC. To understand how cell state transitions impact DNMT1-mediated maintenance methylation, we scaled the method down and combined it with the measurement of mRNA to simultaneously quantify genome-wide methylation levels, maintenance methylation fidelity and the transcriptome from the same cell (scDyad&T-seq). Applying scDyad&T-seq to mouse embryonic stem cells transitioning from serum to 2i conditions, we observe dramatic and heterogenous demethylation and the emergence of transcriptionally distinct subpopulations that are closely linked to the cell-to-cell variability in loss of DNMT1-mediated maintenance methylation activity, with regions of the genome that escape 5mC reprogramming retaining high levels of maintenance methylation fidelity. Overall, our results demonstrate that while distinct cell states can substantially impact the genome-wide activity of the DNA methylation maintenance machinery, locally there exists an intrinsic relationship between DNA methylation density, histone modifications and DNMT1-mediated maintenance methylation fidelity that is independent of cell state.
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Affiliation(s)
- Alex Chialastri
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Saumya Sarkar
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elizabeth E. Schauer
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Shyl Lamba
- Department of Mathematics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Siddharth S. Dey
- Department of Chemical Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Biological Engineering Program, University of California Santa Barbara, Santa Barbara, CA 93106, USA
- Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA 93106, USA
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8
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Gong D, Wang L, Zhou H, Gao J, Zhang W, Zheng P. Long noncoding RNA Lnc530 localizes on R-loops and regulates R-loop formation and genomic stability in mouse embryonic stem cells. Stem Cell Reports 2023; 18:952-968. [PMID: 36931280 PMCID: PMC10147553 DOI: 10.1016/j.stemcr.2023.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 03/18/2023] Open
Abstract
Embryonic stem cells (ESCs) are superior to differentiated cells to maintain genome stability, but the underlying mechanisms remain largely elusive. R-loops are constantly formed during transcription and are inducers of DNA damage if not resolved. Here we report that mouse ESCs (mESCs) can efficiently prevent unscheduled R-loop formation, and a long noncoding RNA Lnc530 plays regulatory role. Lnc530 is expressed in mESCs and localizes on R-loops. Depletion of Lnc530 in mESCs causes R-loop accumulation and DNA damage, whereas forced expression of Lnc530 in differentiated cells suppresses the R-loop formation. Mechanistically, Lnc530 associates with DDX5 and TDP-43 in an inter-dependent manner on R-loops. Formation of Lnc530-DDX5-TDP-43 complex substantially increases the local protein levels of DDX5 and TDP-43, both of which play critical roles in R-loop regulation. This study uncovers an efficient strategy to prevent R-loop accumulation and preserve genomic stability in mESCs and possibly other stem cell types.
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Affiliation(s)
- Daohua Gong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; University of Chinese Academy of Sciences, Beijing 101408, China; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China; Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650203, China.
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9
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PARP-1 Expression Influences Cancer Stem Cell Phenotype in Colorectal Cancer Depending on p53. Int J Mol Sci 2023; 24:ijms24054787. [PMID: 36902215 PMCID: PMC10002521 DOI: 10.3390/ijms24054787] [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: 01/16/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a protein involved in multiple physiological processes. Elevated PARP-1 expression has been found in several tumours, being associated with stemness and tumorigenesis. In colorectal cancer (CRC), some controversy among studies has been described. In this study, we analysed the expression of PARP-1 and cancer stem cell (CSC) markers in CRC patients with different p53 status. In addition, we used an in vitro model to evaluate the influence of PARP-1 in CSC phenotype regarding p53. In CRC patients, PARP-1 expression correlated with the differentiation grade, but this association was only maintained for tumours harbouring wild-type p53. Additionally, in those tumours, PARP-1 and CSC markers were positively correlated. In mutated p53 tumours, no associations were found, but PARP-1 was an independent factor for survival. According to our in vitro model, PARP-1 regulates CSC phenotype depending on p53 status. PARP-1 overexpression in a wild type p53 context increases CSC markers and sphere forming ability. By contrast, those features were reduced in mutated p53 cells. These results could implicate that patients with elevated PARP-1 expression and wild type p53 could benefit from PARP-1 inhibition therapies, meanwhile it could have adverse effects for those carrying mutated p53 tumours.
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10
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Tichy ED. Specialized Circuitry of Embryonic Stem Cells Promotes Genomic Integrity. Crit Rev Oncog 2023; 27:1-15. [PMID: 36734869 DOI: 10.1615/critrevoncog.2022042332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Embryonic stem cells (ESCs) give rise to all cell types of the organism. Given the importance of these cells in this process, ESCs must employ robust mechanisms to protect genomic integrity or risk catastrophic propagation of mutations throughout the organism. Should such an event occur in daughter cells that will eventually contribute to the germline, the overall species health could dramatically decline. This review describes several key mechanisms employed by ESCs that are unique to these cells, in order to maintain their genomic integrity. Additionally, the contributions of cell cycle regulators in modulating ESC differentiation, after DNA damage exposure, are also examined. Where data are available, findings reported in ESCs are extended to include observations described in induced pluripotent stem cells (IPSCs).
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Affiliation(s)
- Elisia D Tichy
- Department of Orthopaedic Surgery, Perelman School of Medicine, The University of Pennsylvania, 371 Stemmler Hall, 3450 Hamilton Walk, Philadelphia, PA 19104-6081
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11
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Zhang W, Tang M, Wang L, Zhou H, Gao J, Chen Z, Zhao B, Zheng P. Lnc956-TRIM28-HSP90B1 complex on replication forks promotes CMG helicase retention to ensure stem cell genomic stability and embryogenesis. SCIENCE ADVANCES 2023; 9:eadf6277. [PMID: 36706191 PMCID: PMC9882984 DOI: 10.1126/sciadv.adf6277] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Replication stress is a major source of endogenous DNA damage. Despite the identification of numerous proteins on replication forks to modulate fork or replication machinery activities, it remains unexplored whether noncoding RNAs can localize on stalled forks and play critical regulatory roles. Here, we identify an uncharacterized long noncoding RNA NONMMUT028956 (Lnc956 for short) predominantly expressed in mouse embryonic stem cells. Lnc956 is accumulated on replication forks to prevent fork collapse and preserve genomic stability and is essential for mouse embryogenesis. Mechanistically, it drives assembly of the Lnc956-TRIM28-HSP90B1 complex on stalled forks in an interdependent manner downstream of ataxia telangiectasia and Rad3-related (ATR) signaling. Lnc956-TRIM28-HSP90B1 complex physically associates with minichromosome maintenance proteins 2 (MCM2) to minichromosome maintenance proteins 7 (MCM7) hexamer via TRIM28 and directly regulates the CDC45-MCM-GINS (CMG) helicase retention on chromatin. The regulation of Lnc956-TRIM28-HSP90B1 on CMG retention is mediated by HSP90B1's chaperoning function. These findings reveal a player that actively regulates replisome retention to prevent fork collapse.
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Affiliation(s)
- Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Min Tang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhongliang Chen
- Key Laboratory of Adult Stem Cell Translational Research (Chinese Academy of Medical Sciences), Guizhou Medical University, Guiyang, China
- National Joint Local Engineering Laboratory for Cell Engineering and Biomedicine Technique, Guizhou Medical University, Guiyang, China
| | - Bo Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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12
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Ma H, Ning Y, Wang L, Zhang W, Zheng P. Lnc956 regulates mouse embryonic stem cell differentiation in response to DNA damage in a p53-independent pathway. SCIENCE ADVANCES 2023; 9:eade9742. [PMID: 36662856 PMCID: PMC9858519 DOI: 10.1126/sciadv.ade9742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Maintaining genomic stability is crucial for embryonic stem cells (ESCs). ESCs with unrepaired DNA damage are eliminated through differentiation and apoptosis. To date, only tumor suppressor p53 is known to be implicated in this quality control process. Here, we identified a p53-independent quality control factor lncRNA NONMMUT028956 (Lnc956 for short) in mouse ESCs. Lnc956 is prevalently expressed in ESCs and regulates the differentiation of ESCs after DNA damage. Mechanistically, Ataxia telangiectasia mutated (ATM) activation drives m6A methylation of Lnc956, which promotes its interaction with Krüppel-like factor 4 (KLF4). Lnc956-KLF4 association sequestrates the KLF4 protein and prevents KLF4's transcriptional regulation on pluripotency. This posttranslational mechanism favors the rapid shutdown of the regulatory circuitry of pluripotency. Thus, ATM signaling in ESCs can activate two pathways mediated by p53 and Lnc956, respectively, which act together to ensure robust differentiation and apoptosis in response to unrepaired DNA damage.
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Affiliation(s)
- Huaixiao Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Yuqi Ning
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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13
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Zhao Q, Liu K, Zhang L, Li Z, Wang L, Cao J, Xu Y, Zheng A, Chen Q, Zhao T. BNIP3-dependent mitophagy safeguards ESC genomic integrity via preventing oxidative stress-induced DNA damage and protecting homologous recombination. Cell Death Dis 2022; 13:976. [PMID: 36402748 PMCID: PMC9675825 DOI: 10.1038/s41419-022-05413-4] [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: 02/14/2022] [Revised: 11/03/2022] [Accepted: 11/07/2022] [Indexed: 11/21/2022]
Abstract
Embryonic stem cells (ESCs) have a significantly lower mutation load compared to somatic cells, but the mechanisms that guard genomic integrity in ESCs remain largely unknown. Here we show that BNIP3-dependent mitophagy protects genomic integrity in mouse ESCs. Deletion of Bnip3 increases cellular reactive oxygen species (ROS) and decreases ATP generation. Increased ROS in Bnip3-/- ESCs compromised self-renewal and were partially rescued by either NAC treatment or p53 depletion. The decreased cellular ATP in Bnip3-/- ESCs induced AMPK activation and deteriorated homologous recombination, leading to elevated mutation load during long-term propagation. Whereas activation of AMPK in X-ray-treated Bnip3+/+ ESCs dramatically ascended mutation rates, inactivation of AMPK in Bnip3-/- ESCs under X-ray stress remarkably decreased the mutation load. In addition, enhancement of BNIP3-dependent mitophagy during reprogramming markedly decreased mutation accumulation in established iPSCs. In conclusion, we demonstrated a novel pathway in which BNIP3-dependent mitophagy safeguards ESC genomic stability, and that could potentially be targeted to improve pluripotent stem cell genomic integrity for regenerative medicine.
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Affiliation(s)
- Qian Zhao
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Kun Liu
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Lin Zhang
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zheng Li
- grid.24696.3f0000 0004 0369 153XDepartment of Gastroenterology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070 China
| | - Liang Wang
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Jiani Cao
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China
| | - Youqing Xu
- grid.24696.3f0000 0004 0369 153XDepartment of Gastroenterology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070 China
| | - Aihua Zheng
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Quan Chen
- grid.216938.70000 0000 9878 7032College of Life Sciences, Nankai University, Tianjin, 300073 China
| | - Tongbiao Zhao
- grid.9227.e0000000119573309State Key Laboratory of Stem Cell and Reproductive Biology, Institute for Stem Cell and Regeneration, Institute of Zoology, Chinese Academy of Sciences Beijing, Beijing, 100101 China ,grid.512959.3Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
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14
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Georges RO, Sepulveda H, Angel JC, Johnson E, Palomino S, Nowak RB, Desai A, López-Moyado IF, Rao A. Acute deletion of TET enzymes results in aneuploidy in mouse embryonic stem cells through decreased expression of Khdc3. Nat Commun 2022; 13:6230. [PMID: 36266342 PMCID: PMC9584922 DOI: 10.1038/s41467-022-33742-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 09/29/2022] [Indexed: 02/06/2023] Open
Abstract
TET (Ten-Eleven Translocation) dioxygenases effect DNA demethylation through successive oxidation of the methyl group of 5-methylcytosine (5mC) in DNA. In humans and in mouse models, TET loss-of-function has been linked to DNA damage, genome instability and oncogenesis. Here we show that acute deletion of all three Tet genes, after brief exposure of triple-floxed, Cre-ERT2-expressing mouse embryonic stem cells (mESC) to 4-hydroxytamoxifen, results in chromosome mis-segregation and aneuploidy; moreover, embryos lacking all three TET proteins showed striking variation in blastomere numbers and nuclear morphology at the 8-cell stage. Transcriptional profiling revealed that mRNA encoding a KH-domain protein, Khdc3 (Filia), was downregulated in triple TET-deficient mESC, concomitantly with increased methylation of CpG dinucleotides in the vicinity of the Khdc3 gene. Restoring KHDC3 levels in triple Tet-deficient mESC prevented aneuploidy. Thus, TET proteins regulate Khdc3 gene expression, and TET deficiency results in mitotic infidelity and genome instability in mESC at least partly through decreased expression of KHDC3.
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Affiliation(s)
- Romain O Georges
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Hugo Sepulveda
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - J Carlos Angel
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Eric Johnson
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Susan Palomino
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Roberta B Nowak
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Arshad Desai
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Isaac F López-Moyado
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA
| | - Anjana Rao
- Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
- Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA.
- Department of Pharmacology and Moores Cancer Center, University of California, San Diego; 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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15
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Tu Q, Liu X, Yao X, Li R, Liu G, Jiang H, Li K, Chen Q, Huang X, Chang Q, Xu G, Zhu H, Shi P, Zhao B. RETSAT associates with DDX39B to promote fork restarting and resistance to gemcitabine based chemotherapy in pancreatic ductal adenocarcinoma. J Exp Clin Cancer Res 2022; 41:274. [PMID: 36109793 PMCID: PMC9476698 DOI: 10.1186/s13046-022-02490-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/07/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Severe hypoxia is a prominent character of pancreatic ductal adenocarcinoma (PDAC) microenvironment. In the process of gemcitabine based chemotherapy, PDAC cells are insulted from replication stresses co-induced by hypoxia and gemcitabine. However, PDAC cells get outstanding abilities to resist to such harsh conditions and keep proliferating, causing a major obstacle for current therapy. RETSAT (Retinol Saturase) is defined as a hypoxia convergent gene recently, with high expression in PDAC hypoxic sectors. This study aimed to explore the roles of RETSAT in replication stress resistance and hypoxia adaptation in PDAC cells, and decipher the underlying mechanism.
Methods
The expression of RETSAT was examined in TCGA (The Cancer Genome Atlas), human pancreatic cancer microarray, clinical specimens and cell lines. Functions of RETSAT were studied by means of DNA fiber assay and comet assay in monolayer cultured PDAC cell lines, three dimensional spheroids, patient derived organoids and cell derived xenograft mouse models. Mechanism was investigated by using iPOND (isolate proteins on nascent DNA) combined with mass spectrometry, immunoprecipitation and immunoblotting.
Results
First, we found the converse relationship of RETSAT expression and PDAC chemotherapy. That is, PDAC patients with high RETSAT expression correlated with poor survival, while ones holding low RETSAT expression were benefitted more in Gemcitabine based chemotherapy. Second, we identified RETSAT as a novel replication fork associated protein. HIF-1α signaling promotes RETSAT expression under hypoxia. Functionally, RETSAT promoted fork restarting under replication stress and maintained genomic stability. Third, we uncovered the interaction of RETSAT and R-loop unwinding helicase DDX39B. RETSAT detained DDX39B on forks to resolve R-loops, through which avoided fork damage and CHK1 initiated apoptosis. Targeting DDX39B using chemical CCT018159 sensitized PDAC cells and organoids to gemcitabine induced apoptosis, highlighting the synergetic application of CCT018159 and gemcitabine in PDAC chemotherapy.
Conclusions
This study identified RETSAT as a novel replication fork protein, which functions through interacting with DDX39B mediated R-loop clearance to promote fork restarting, leading to cellular resistance to replication stresses co-induced by tumor environmental hypoxia and gemcitabine in pancreatic ductal adenocarcinoma.
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16
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Current understanding of genomic stability maintenancein pluripotent stem cells. Acta Biochim Biophys Sin (Shanghai) 2022; 54:858-863. [PMID: 35713312 PMCID: PMC9828662 DOI: 10.3724/abbs.2022064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Pluripotent stem cells (PSCs) are able to generate all cell types in the body and have wide applications in basic research and cell-based regenerative medicine. Maintaining stable genome in culture is the first priority for stem cell application in clinics. In addition, genomic instability in PSCs can cause developmental failure or abnormalities. Understanding how PSCs maintain genome stability is of critical importance. Due to their fundamental role in organism development, PSCs must maintain superior stable genome than differentiated cells. However, the underlying mechanisms are far from clear. Very limited studies suggest that PSCs utilize specific strategies and regulators to robustly improve genome stability. In this review, we summarize the current understandings of the unique properties of genome stability maintenance in PSCs.
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17
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Wang L, Li J, Zhou H, Zhang W, Gao J, Zheng P. A novel lncRNA Discn fine-tunes replication protein A (RPA) availability to promote genomic stability. Nat Commun 2021; 12:5572. [PMID: 34552092 PMCID: PMC8458541 DOI: 10.1038/s41467-021-25827-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
RPA is a master regulator of DNA metabolism and RPA availability acts as a rate-limiting factor. While numerous studies focused on the post-translational regulations of RPA for its functions, little is known regarding how RPA availability is controlled. Here we identify a novel lncRNA Discn as the guardian of RPA availability in stem cells. Discn is induced upon genotoxic stress and binds to neucleolin (NCL) in the nucleolus. This prevents NCL from translocation into nucleoplasm and avoids undesirable NCL-mediated RPA sequestration. Thus, Discn-NCL-RPA pathway preserves a sufficient RPA pool for DNA replication stress response and repair. Discn loss causes massive genome instability in mouse embryonic stem cells and neural stem/progenigor cells. Mice depleted of Discn display newborn death and brain dysfunctions due to DNA damage accumulation and associated inflammatory reactions. Our findings uncover a key regulator of DNA metabolism and provide new clue to understand the chemoresistance in cancer treatment.
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Affiliation(s)
- Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jingzheng Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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18
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Novo CL. A Tale of Two States: Pluripotency Regulation of Telomeres. Front Cell Dev Biol 2021; 9:703466. [PMID: 34307383 PMCID: PMC8300013 DOI: 10.3389/fcell.2021.703466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/08/2021] [Indexed: 01/01/2023] Open
Abstract
Inside the nucleus, chromatin is functionally organized and maintained as a complex three-dimensional network of structures with different accessibility such as compartments, lamina associated domains, and membraneless bodies. Chromatin is epigenetically and transcriptionally regulated by an intricate and dynamic interplay of molecular processes to ensure genome stability. Phase separation, a process that involves the spontaneous organization of a solution into separate phases, has been proposed as a mechanism for the timely coordination of several cellular processes, including replication, transcription and DNA repair. Telomeres, the repetitive structures at the end of chromosomes, are epigenetically maintained in a repressed heterochromatic state that prevents their recognition as double-strand breaks (DSB), avoiding DNA damage repair and ensuring cell proliferation. In pluripotent embryonic stem cells, telomeres adopt a non-canonical, relaxed epigenetic state, which is characterized by a low density of histone methylation and expression of telomere non-coding transcripts (TERRA). Intriguingly, this telomere non-canonical conformation is usually associated with chromosome instability and aneuploidy in somatic cells, raising the question of how genome stability is maintained in a pluripotent background. In this review, we will explore how emerging technological and conceptual developments in 3D genome architecture can provide novel mechanistic perspectives for the pluripotent epigenetic paradox at telomeres. In particular, as RNA drives the formation of LLPS, we will consider how pluripotency-associated high levels of TERRA could drive and coordinate phase separation of several nuclear processes to ensure genome stability. These conceptual advances will provide a better understanding of telomere regulation and genome stability within the highly dynamic pluripotent background.
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Affiliation(s)
- Clara Lopes Novo
- The Francis Crick Institute, London, United Kingdom
- Imperial College London, London, United Kingdom
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19
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Liu Y, Chen P, Fei H, Li M, Li X, Li T. Natural killer cells contributed to recurrent miscarriage by SP1-CASP3-PARP1. Int Immunopharmacol 2021; 93:107424. [PMID: 33556666 DOI: 10.1016/j.intimp.2021.107424] [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: 10/24/2020] [Revised: 01/06/2021] [Accepted: 01/19/2021] [Indexed: 11/19/2022]
Abstract
Recurrent miscarriage (RM) is an early pregnancy complication. Natural Killer cells are an important part of the innate immune system of endometrial. In this study, weighted gene correlation network analysis was used to study the expression profile data of the endometrial tissue of patients with recurrent miscarriage and selected brown module as key module positively related to the numbers of miscarriages. With metascape tool, natural killer cells mediated cytotoxicity related genes, such as CASP3, were selected. DisNor database showed that CASP3 down-regulates PARP1. According to TRRUST database, CASP3 was regulated by SP1. Through comprehensive analysis of uNK cell related genes, we proposed that natural killer cells contribute to recurrent miscarriage by SP1-CASP3-PARP1.
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Affiliation(s)
- Yun Liu
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital, Sun Yat-sen University, China.
| | - Peigen Chen
- Reproductive Medicine Center, The Sixth Affiliated Hospital, Sun Yat-sen University, China.
| | - Hui Fei
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital, Sun Yat-sen University, China.
| | - Mengxiong Li
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital, Sun Yat-sen University, China.
| | - Xian Li
- Affiliated Hospital of Zunyi Medical University, China
| | - Tian Li
- Department of Obstetrics and Gynecology, The Seventh Affiliated Hospital, Sun Yat-sen University, China.
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20
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Blakemore D, Vilaplana-Lopera N, Almaghrabi R, Gonzalez E, Moya M, Ward C, Murphy G, Gambus A, Petermann E, Stewart GS, García P. MYBL2 and ATM suppress replication stress in pluripotent stem cells. EMBO Rep 2021; 22:e51120. [PMID: 33779025 PMCID: PMC8097389 DOI: 10.15252/embr.202051120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 02/10/2021] [Accepted: 02/19/2021] [Indexed: 12/30/2022] Open
Abstract
Replication stress, a major cause of genome instability in cycling cells, is mainly prevented by the ATR-dependent replication stress response pathway in somatic cells. However, the replication stress response pathway in embryonic stem cells (ESCs) may be different due to alterations in cell cycle phase length. The transcription factor MYBL2, which is implicated in cell cycle regulation, is expressed a hundred to a thousand-fold more in ESCs compared with somatic cells. Here we show that MYBL2 activates ATM and suppresses replication stress in ESCs. Consequently, loss of MYBL2 or inhibition of ATM or Mre11 in ESCs results in replication fork slowing, increased fork stalling and elevated origin firing. Additionally, we demonstrate that inhibition of CDC7 activity rescues replication stress induced by MYBL2 loss and ATM inhibition, suggesting that uncontrolled new origin firing may underlie the replication stress phenotype resulting from loss/inhibition of MYBL2 and ATM. Overall, our study proposes that in addition to ATR, a MYBL2-MRN-ATM replication stress response pathway functions in ESCs to control DNA replication initiation and prevent genome instability.
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Affiliation(s)
- Daniel Blakemore
- Institute of Cancer and Genomic Science, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nuria Vilaplana-Lopera
- Institute of Cancer and Genomic Science, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Ruba Almaghrabi
- Institute of Cancer and Genomic Science, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Elena Gonzalez
- Institute of Cancer and Genomic Science, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Miriam Moya
- Institute of Cancer and Genomic Science, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Carl Ward
- Laboratory of Integrative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences (CAS), Guangzhou, China.,Chinese Academy of Sciences (CAS), Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Guangzhou, China
| | - George Murphy
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Agnieszka Gambus
- Institute of Cancer and Genomic Science, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Eva Petermann
- Institute of Cancer and Genomic Science, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Science, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Paloma García
- Institute of Cancer and Genomic Science, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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21
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Li J, Shang Y, Wang L, Zhao B, Sun C, Li J, Liu S, Li C, Tang M, Meng FL, Zheng P. Genome integrity and neurogenesis of postnatal hippocampal neural stem/progenitor cells require a unique regulator Filia. SCIENCE ADVANCES 2020; 6:6/44/eaba0682. [PMID: 33115731 PMCID: PMC7608785 DOI: 10.1126/sciadv.aba0682] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 09/01/2020] [Indexed: 05/03/2023]
Abstract
Endogenous DNA double-strand breaks (DSBs) formation and repair in neural stem/progenitor cells (NSPCs) play fundamental roles in neurogenesis and neurodevelopmental disorders. NSPCs exhibit heterogeneity in terms of lineage fates and neurogenesis activity. Whether NSPCs also have heterogeneous regulations on DSB formation and repair to accommodate region-specific neurogenesis has not been explored. Here, we identified a regional regulator Filia, which is predominantly expressed in mouse hippocampal NSPCs after birth and regulates DNA DSB formation and repair. On one hand, Filia protects stalling replication forks and prevents the replication stress-associated DNA DSB formation. On the other hand, Filia facilitates the homologous recombination-mediated DNA DSB repair. Consequently, Filia-/- mice had impaired hippocampal NSPC proliferation and neurogenesis and were deficient in learning, memory, and mood regulations. Thus, our study provided the first proof of concept demonstrating the region-specific regulations of DSB formation and repair in subtypes of NSPCs.
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Affiliation(s)
- Jingzheng Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yafang Shang
- University of Chinese Academy of Sciences, Beijing 101408, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Bo Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Chunli Sun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Jiali Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650201, China
| | - Siling Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650201, China
| | - Cong Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Min Tang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650201, China
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22
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Yue L, Pei Y, Zhong L, Yang H, Wang Y, Zhang W, Chen N, Zhu Q, Gao J, Zhi M, Wen B, Zhang S, Xiang J, Wei Q, Liang H, Cao S, Lou H, Chen Z, Han J. Mthfd2 Modulates Mitochondrial Function and DNA Repair to Maintain the Pluripotency of Mouse Stem Cells. Stem Cell Reports 2020; 15:529-545. [PMID: 32679066 PMCID: PMC7419720 DOI: 10.1016/j.stemcr.2020.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 12/14/2022] Open
Abstract
The pluripotency of stem cells determines their developmental potential. While the pluripotency states of pluripotent stem cells are variable and interconvertible, the mechanisms underlying the acquisition and maintenance of pluripotency remain largely elusive. Here, we identified that methylenetetrahydrofolate dehydrogenase (NAD+-dependent), methenyltetrahydrofolate cyclohydrolase (Mthfd2) plays an essential role in maintaining embryonic stem cell pluripotency and promoting complete reprogramming of induced pluripotent stem cells. Mechanistically, in mitochondria, Mthfd2 maintains the integrity of the mitochondrial respiratory chain and prevents mitochondrial dysfunction. In the nucleus, Mthfd2 stabilizes the phosphorylation of EXO1 to support DNA end resection and promote homologous recombination repair. Our results revealed that Mthfd2 is a dual-function factor in determining the pluripotency of pluripotent stem cells through both mitochondrial and nuclear pathways, ultimately ensuring safe application of pluripotent stem cells.
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Affiliation(s)
- Liang Yue
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China
| | - Yangli Pei
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528231, China
| | - Liang Zhong
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Hebei Provincial Key Laboratory of Basic Medicine for Diabetes, The Shijiazhuang Second Hospital, Shijiazhuang, Hebei 050051, China
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Yanliang Wang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wei Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Naixin Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qianqian Zhu
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Gao
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Minglei Zhi
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Bingqiang Wen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaopeng Zhang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jinzhu Xiang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qingqing Wei
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hui Liang
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Suying Cao
- Animal Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Huiqiang Lou
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhongzhou Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianyong Han
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China; Advanced Innovation Center for Food Nutrition and Human Health, China Agricultural University, Beijing 100083, China.
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23
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Kafer GR, Cesare AJ. A Survey of Essential Genome Stability Genes Reveals That Replication Stress Mitigation Is Critical for Peri-Implantation Embryogenesis. Front Cell Dev Biol 2020; 8:416. [PMID: 32548123 PMCID: PMC7274024 DOI: 10.3389/fcell.2020.00416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
Murine development demands that pluripotent epiblast stem cells in the peri-implantation embryo increase from approximately 120 to 14,000 cells between embryonic days (E) 4.5 and E7.5. This is possible because epiblast stem cells can complete cell cycles in under 3 h in vivo. To ensure conceptus fitness, epiblast cells must undertake this proliferative feat while maintaining genome integrity. How epiblast cells maintain genome health under such an immense proliferation demand remains unclear. To illuminate the contribution of genome stability pathways to early mammalian development we systematically reviewed knockout mouse data from 347 DDR and repair associated genes. Cumulatively, the data indicate that while many DNA repair functions are dispensable in embryogenesis, genes encoding replication stress response and homology directed repair factors are essential specifically during the peri-implantation stage of early development. We discuss the significance of these findings in the context of the unique proliferative demands placed on pluripotent epiblast stem cells.
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Affiliation(s)
- Georgia R Kafer
- Genome Integrity Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Anthony J Cesare
- Genome Integrity Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
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24
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Elbracht M, Mackay D, Begemann M, Kagan KO, Eggermann T. Disturbed genomic imprinting and its relevance for human reproduction: causes and clinical consequences. Hum Reprod Update 2020; 26:197-213. [DOI: 10.1093/humupd/dmz045] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/07/2019] [Accepted: 11/15/2019] [Indexed: 12/19/2022] Open
Abstract
Abstract
BACKGROUND
Human reproductive issues affecting fetal and maternal health are caused by numerous exogenous and endogenous factors, of which the latter undoubtedly include genetic changes. Pathogenic variants in either maternal or offspring DNA are associated with effects on the offspring including clinical disorders and nonviable outcomes. Conversely, both fetal and maternal factors can affect maternal health during pregnancy. Recently, it has become evident that mammalian reproduction is influenced by genomic imprinting, an epigenetic phenomenon that regulates the expression of genes according to their parent from whom they are inherited. About 1% of human genes are normally expressed from only the maternally or paternally inherited gene copy. Since numerous imprinted genes are involved in (embryonic) growth and development, disturbance of their balanced expression can adversely affect these processes.
OBJECTIVE AND RATIONALE
This review summarises current our understanding of genomic imprinting in relation to human ontogenesis and pregnancy and its relevance for reproductive medicine.
SEARCH METHODS
Literature databases (Pubmed, Medline) were thoroughly searched for the role of imprinting in human reproductive failure. In particular, the terms ‘multilocus imprinting disturbances, SCMC, NLRP/NALP, imprinting and reproduction’ were used in various combinations.
OUTCOMES
A range of molecular changes to specific groups of imprinted genes are associated with imprinting disorders, i.e. syndromes with recognisable clinical features including distinctive prenatal features. Whereas the majority of affected individuals exhibit alterations at single imprinted loci, some have multi-locus imprinting disturbances (MLID) with less predictable clinical features. Imprinting disturbances are also seen in some nonviable pregnancy outcomes, such as (recurrent) hydatidiform moles, which can therefore be regarded as a severe form of imprinting disorders. There is growing evidence that MLID can be caused by variants in the maternal genome altering the imprinting status of the oocyte and the embryo, i.e. maternal effect mutations. Pregnancies of women carrying maternal affect mutations can have different courses, ranging from miscarriages to birth of children with clinical features of various imprinting disorders.
WIDER IMPLICATIONS
Increasing understanding of imprinting disturbances and their clinical consequences have significant impacts on diagnostics, counselling and management in the context of human reproduction. Defining criteria for identifying pregnancies complicated by imprinting disorders facilitates early diagnosis and personalised management of both the mother and offspring. Identifying the molecular lesions underlying imprinting disturbances (e.g. maternal effect mutations) allows targeted counselling of the family and focused medical care in further pregnancies.
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Affiliation(s)
- Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Deborah Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Matthias Begemann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Karl Oliver Kagan
- Obstetrics and Gynaecology, University Hospital of Tübingen, Tübingen, Germany
| | - Thomas Eggermann
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
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25
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Cops5 safeguards genomic stability of embryonic stem cells through regulating cellular metabolism and DNA repair. Proc Natl Acad Sci U S A 2020; 117:2519-2525. [PMID: 31964807 DOI: 10.1073/pnas.1915079117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The highly conserved COP9 signalosome (CSN), composed of 8 subunits (Cops1 to Cops8), has been implicated in pluripotency maintenance of human embryonic stem cells (ESCs). Yet, the mechanism for the CSN to regulate pluripotency remains elusive. We previously showed that Cops2, independent of the CSN, is essential for the pluripotency maintenance of mouse ESCs. In this study, we set out to investigate how Cops5 and Cops8 regulate ESC differentiation and tried to establish Cops5 and Cops8 knockout (KO) ESC lines by CRISPR/Cas9. To our surprise, no Cops5 KO ESC clones were identified out of 127 clones, while three Cops8 KO ESC lines were established out of 70 clones. We then constructed an inducible Cops5 KO ESC line. Cops5 KO leads to decreased expression of the pluripotency marker Nanog, proliferation defect, G2/M cell-cycle arrest, and apoptosis of ESCs. Further analysis revealed dual roles of Cops5 in maintaining genomic stability of ESCs. On one hand, Cops5 suppresses the autophagic degradation of Mtch2 to direct cellular metabolism toward glycolysis and minimize reactive oxygen species (ROS) production, thereby reducing endogenous DNA damage. On the other hand, Cops5 is required for high DNA damage repair (DDR) activities in ESCs. Without Cops5, elevated ROS and reduced DDR activities lead to DNA damage accumulation in ESCs. Subsequently, p53 is activated to trigger G2/M arrest and apoptosis. Altogether, our studies reveal an essential role of Cops5 in maintaining genome integrity and self-renewal of ESCs by regulating cellular metabolism and DDR pathways.
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27
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Zhang W, Chen Z, Zhang D, Zhao B, Liu L, Xie Z, Yao Y, Zheng P. KHDC3L mutation causes recurrent pregnancy loss by inducing genomic instability of human early embryonic cells. PLoS Biol 2019; 17:e3000468. [PMID: 31609975 PMCID: PMC6812846 DOI: 10.1371/journal.pbio.3000468] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 10/24/2019] [Accepted: 09/26/2019] [Indexed: 12/28/2022] Open
Abstract
Recurrent pregnancy loss (RPL) is an important complication in reproductive health. About 50% of RPL cases are unexplained, and understanding the genetic basis is essential for its diagnosis and prognosis. Herein, we report causal KH domain containing 3 like (KHDC3L) mutations in RPL. KHDC3L is expressed in human epiblast cells and ensures their genome stability and viability. Mechanistically, KHDC3L binds to poly(ADP-ribose) polymerase 1 (PARP1) to stimulate its activity. In response to DNA damage, KHDC3L also localizes to DNA damage sites and facilitates homologous recombination (HR)-mediated DNA repair. KHDC3L dysfunction causes PARP1 inhibition and HR repair deficiency, which is synthetically lethal. Notably, we identified two critical residues, Thr145 and Thr156, whose phosphorylation by Ataxia-telangiectasia mutated (ATM) is essential for KHDC3L’s functions. Importantly, two deletions of KHDC3L (p.E150_V160del and p.E150_V172del) were detected in female RPL patients, both of which harbor a common loss of Thr156 and are impaired in PARP1 activation and HR repair. In summary, our study reveals both KHDC3L as a new RPL risk gene and its critical function in DNA damage repair pathways. Recurrent pregnancy loss is an important complication in reproductive health, and about 50% of cases remain unexplained. This study shows that KHDC3L safeguards the genomic stability of human early embryonic cells, and damaging mutations in its gene cause recurrent pregnancy loss in humans.
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Affiliation(s)
- Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhongliang Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Dengfeng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
| | - Bo Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lu Liu
- Department of Obstetrics and Gynaecology, Yan An Hospital, Kunming Medical University, Kunming, China
| | - Zhengyuan Xie
- Yunnan Key Laboratory for Fertility Regulation and Birth Health of Minority Nationalities, Key Laboratory of Preconception Health in Western China, NHFPC, Population and Family Planning Institute of Yunnan Province, Kunming, China
| | - Yonggang Yao
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- * E-mail:
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TRIM66 reads unmodified H3R2K4 and H3K56ac to respond to DNA damage in embryonic stem cells. Nat Commun 2019; 10:4273. [PMID: 31537782 PMCID: PMC6753139 DOI: 10.1038/s41467-019-12126-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
Recognition of specific chromatin modifications by distinct structural domains within “reader” proteins plays a critical role in the maintenance of genomic stability. However, the specific mechanisms involved in this process remain unclear. Here we report that the PHD-Bromo tandem domain of tripartite motif-containing 66 (TRIM66) recognizes the unmodified H3R2-H3K4 and acetylated H3K56. The aberrant deletion of Trim66 results in severe DNA damage and genomic instability in embryonic stem cells (ESCs). Moreover, we find that the recognition of histone modification by TRIM66 is critical for DNA damage repair (DDR) in ESCs. TRIM66 recruits Sirt6 to deacetylate H3K56ac, negatively regulating the level of H3K56ac and facilitating the initiation of DDR. Importantly, Trim66-deficient blastocysts also exhibit higher levels of H3K56ac and DNA damage. Collectively, the present findings indicate the vital role of TRIM66 in DDR in ESCs, establishing the relationship between histone readers and maintenance of genomic stability. TRIM66 protein has an N-terminal tripartite motif and a C-terminal PHD Bromodomain. Here the authors show the specific histone modification recognition of TRIM66-PHD-Bromodomain through crystallography and biochemistry assay, and further reveal that TRIM66 recognition of certain histone modification is important for DNA damage repair in ESCs.
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29
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Chen ZZ, Niu YY. Stem cell therapy for Parkinson's disease using non-human primate models. Zool Res 2019; 40:349-357. [PMID: 31343853 PMCID: PMC6755115 DOI: 10.24272/j.issn.2095-8137.2019.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/26/2019] [Indexed: 12/23/2022] Open
Abstract
Stem cell therapy (SCT) for Parkinson's disease (PD) has received considerable attention in recent years. Non-human primate (NHP) models of PD have played an instrumental role in the safety and efficacy of emerging PD therapies and facilitated the translation of initiatives for human patients. NHP models of PD include primates with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced parkinsonism, who are responsive to dopamine replacement therapies, similar to human PD patients. Extensive research in SCT has been conducted to better treat the progressive dopaminergic neurodegeneration that underlies PD. For effective application of SCT in PD, however, a number of basic parameters still need to be tested and optimized in NHP models, including preparation and storage of cells for engraftment, methods of transplantation, choice of target sites, and timelines for recovery. In this review, we discuss the current status of NHP models of PD in stem cell research. We also analyze the advances and remaining challenges for successful clinical translation of SCT for this persistent disease.
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Affiliation(s)
- Zhen-Zhen Chen
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming Yunnan 650500, China
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming Yunnan 650500
| | - Yu-Yu Niu
- Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming Yunnan 650500, China; E-mail:
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30
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Petkova R, Zhelev N, Pankov R, Chakarov S. Individual capacity for repair of DNA damage and potential uses of stem cell lines for clinical applications: a matter of (genomic) integrity. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1520611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Rumena Petkova
- Faculty of Medicine, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
| | - Nikolai Zhelev
- CMCBR, School of Science, Engineering & Technology, Abertay University, Dundee, UK
| | - Roumen Pankov
- Department of Biochemistry, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
| | - Stoyan Chakarov
- Department of Biochemistry, Faculty of Biology, Sofia University ‘St. Kliment Ohridski’, Sofia, Bulgaria
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31
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Manic G, Sistigu A, Corradi F, Musella M, De Maria R, Vitale I. Replication stress response in cancer stem cells as a target for chemotherapy. Semin Cancer Biol 2018; 53:31-41. [PMID: 30081229 DOI: 10.1016/j.semcancer.2018.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/29/2018] [Accepted: 08/02/2018] [Indexed: 02/08/2023]
Abstract
Cancer stem cells (CSCs) are subpopulations of multipotent stem cells (SCs) responsible for the initiation, long-term clonal maintenance, growth and spreading of most human neoplasms. Reportedly, CSCs share a very robust DNA damage response (DDR) with embryonic and adult SCs, which allows them to survive endogenous and exogenous genotoxins. A range of experimental evidence indicates that CSCs have high but heterogeneous levels of replication stress (RS), arising from, and being boosted by, endogenous causes, such as specific genetic backgrounds (e.g., p53 deficiency) and/or aberrant karyotypes (e.g., supernumerary chromosomes). A multipronged RS response (RSR) is put in place by CSCs to limit and ensure tolerability to RS. The characteristics of such dedicated cascade have two opposite consequences, both relevant for cancer therapy. On the one hand, RSR efficiency often increases the reliance of CSCs on specific DDR components. On the other hand, the functional redundancy of pathways of the RSR can paradoxically promote the acquisition of resistance to RS- and/or DNA damage-inducing agents. Here, we provide an overview of the molecular mechanisms of the RSR in cancer cells and CSCs, focusing on the role of CHK1 and some emerging players, such as PARP1 and components of the homologous recombination repair, whose targeting can represent a long-term effective anti-CSC strategy.
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Affiliation(s)
- Gwenola Manic
- Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS - Regina Elena National Cancer Institute, Rome, Italy.
| | - Antonella Sistigu
- Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS - Regina Elena National Cancer Institute, Rome, Italy; Institute of General Pathology, Catholic University and Gemelli Polyclinic, Rome, Italy
| | - Francesca Corradi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Martina Musella
- Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS - Regina Elena National Cancer Institute, Rome, Italy; Department of Molecular Medicine, University "La Sapienza", Rome, Italy
| | - Ruggero De Maria
- Institute of General Pathology, Catholic University and Gemelli Polyclinic, Rome, Italy.
| | - Ilio Vitale
- Department of Research, Advanced Diagnostics and Technological Innovation, IRCCS - Regina Elena National Cancer Institute, Rome, Italy; Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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He DJ, Wang L, Zhang ZB, Guo K, Li JZ, He XC, Cui QH, Zheng P. Maternal gene Ooep may participate in homologous recombination-mediated DNA double-strand break repair in mouse oocytes. Zool Res 2018; 39:387-395. [PMID: 29955025 PMCID: PMC6085769 DOI: 10.24272/j.issn.2095-8137.2018.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
DNA damage in oocytes can cause infertility and birth defects. DNA double-strand breaks (DSBs) are highly deleterious and can substantially impair genome integrity. Homologous recombination (HR)-mediated DNA DSB repair plays dominant roles in safeguarding oocyte quantity and quality. However, little is known regarding the key players of the HR repair pathway in oocytes. Here, we identified oocyte-specific gene Ooep as a novel key component of the HR repair pathway in mouse oocytes. OOEP was required for efficient ataxia telangiectasia mutated (ATM) kinase activation and Rad51 recombinase (RAD51) focal accumulation at DNA DSBs. Ooep null oocytes were defective in DNA DSB repair and prone to apoptosis upon exogenous DNA damage insults. Moreover, Ooep null oocytes exhibited delayed meiotic maturation. Therefore, OOEP played roles in preserving oocyte quantity and quality by maintaining genome stability. Ooep expression decreased with the advance of maternal age, suggesting its involvement in maternal aging.
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Affiliation(s)
- Da-Jian He
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming Yunnan, 650204, China
| | - Lin Wang
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:
| | - Zhi-Bi Zhang
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming Yunnan 650091, China; E-mail:
| | - Kun Guo
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:
| | - Jing-Zheng Li
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:
| | - Xie-Chao He
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:
| | - Qing-Hua Cui
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming Yunnan 650091, China; E-mail:
| | - Ping Zheng
- Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming Yunnan 650223, China; E-mail:
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Zhao B, Zhang W, Cun Y, Li J, Liu Y, Gao J, Zhu H, Zhou H, Zhang R, Zheng P. Mouse embryonic stem cells have increased capacity for replication fork restart driven by the specific Filia-Floped protein complex. Cell Res 2017; 28:69-89. [PMID: 29125140 DOI: 10.1038/cr.2017.139] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 07/12/2017] [Accepted: 08/22/2017] [Indexed: 12/15/2022] Open
Abstract
Pluripotent stem cells (PSCs) harbor constitutive DNA replication stress during their rapid proliferation and the consequent genome instability hampers their applications in regenerative medicine. It is therefore important to understand the regulatory mechanisms of replication stress response in PSCs. Here, we report that mouse embryonic stem cells (ESCs) are superior to differentiated cells in resolving replication stress. Specifically, ESCs utilize a unique Filia-Floped protein complex-dependent mechanism to efficiently promote the restart of stalled replication forks, therefore maintaining genomic stability. The ESC-specific Filia-Floped complex resides on replication forks under normal conditions. Replication stress stimulates their recruitment to stalling forks and the serine 151 residue of Filia is phosphorylated in an ATR-dependent manner. This modification enables the Filia-Floped complex to act as a functional scaffold, which then promotes the stalling fork restart through a dual mechanism: both enhancing recruitment of the replication fork restart protein, Blm, and stimulating ATR kinase activation. In the Blm pathway, the scaffolds recruit the E3 ubiquitin ligase, Trim25, to the stalled replication forks, and in turn Trim25 tethers and concentrates Blm at stalled replication forks through ubiquitination. In differentiated cells, the recruitment of the Trim25-Blm complex to replication forks and the activation of ATR signaling are much less robust due to lack of the ESC-specific Filia-Floped scaffold. Thus, our study reveals that ESCs utilize an additional and unique regulatory layer to efficiently promote the stalled fork restart and maintain genomic stability.
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Affiliation(s)
- Bo Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Yixian Cun
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jingzheng Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Yan Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongwen Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute Cancer Center, The Wistar Institute, Philadelphia, PA 19104, USA
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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Mackay DJ, Temple IK. Human imprinting disorders: Principles, practice, problems and progress. Eur J Med Genet 2017; 60:618-626. [DOI: 10.1016/j.ejmg.2017.08.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/02/2017] [Accepted: 08/11/2017] [Indexed: 12/17/2022]
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Ohgushi M, Minaguchi M, Eiraku M, Sasai Y. A RHO Small GTPase Regulator ABR Secures Mitotic Fidelity in Human Embryonic Stem Cells. Stem Cell Reports 2017; 9:58-66. [PMID: 28579391 PMCID: PMC5511046 DOI: 10.1016/j.stemcr.2017.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 12/31/2022] Open
Abstract
Pluripotent stem cells can undergo repeated self-renewal while retaining genetic integrity, but they occasionally acquire aneuploidy during long-term culture, which is a practical obstacle for medical applications of human pluripotent stem cells. In this study, we explored the biological roles of ABR, a regulator of RHO family small GTPases, and found that it has pivotal roles during mitotic processes in human embryonic stem cells (hESCs). Although ABR has been shown to be involved in dissociation-induced hESC apoptosis, it does not appear to have direct effects on cell survival unless cell-cell contact is impaired. Instead, we found that it is important for faithful hESC division. Mechanistically, ABR depletion compromised centrosome dynamics and predisposed the cell to chromosome misalignment and missegregation, which raised the frequency of aneuploidy. These results provide insights into the mechanisms that support the genetic integrity of self-renewing hESCs. ABR depletion leads to G2/M accumulation in hESCs Centrosome dynamics and mitotic fidelity are compromised upon ABR depletion When mitosis progresses without ABR, hESCs show a high incidence of aneuploidy ABR safeguards faithful chromosome inheritance during hESC division
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Affiliation(s)
- Masatoshi Ohgushi
- Human Stem Cell Technology Unit, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan; Laboratory for Organogenesis and Neurogenesis, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan; Laboratory for in Vitro Histogenesis, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan.
| | - Maki Minaguchi
- Human Stem Cell Technology Unit, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan; Laboratory for Organogenesis and Neurogenesis, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
| | - Mototsugu Eiraku
- Laboratory for in Vitro Histogenesis, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan; Laboratory for Developmental Systems, Institute for Frontier Life and Medical Science, Kyoto University, Kyoto 606-8507, Japan
| | - Yoshiki Sasai
- Human Stem Cell Technology Unit, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan; Laboratory for Organogenesis and Neurogenesis, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
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Protein Kinases in Pluripotency—Beyond the Usual Suspects. J Mol Biol 2017; 429:1504-1520. [DOI: 10.1016/j.jmb.2017.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 12/14/2022]
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Vitale I, Manic G, De Maria R, Kroemer G, Galluzzi L. DNA Damage in Stem Cells. Mol Cell 2017; 66:306-319. [DOI: 10.1016/j.molcel.2017.04.006] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 03/23/2017] [Accepted: 04/05/2017] [Indexed: 01/03/2023]
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Li Y, Zhao Y, Zhou X, Ni W, Dai Z, Yang D, Hao J, Luo L, Liu Y, Luo X, Zhao X. Cytotoxic Indole Alkaloid 3α-Acetonyltabersonine Induces Glioblastoma Apoptosis via Inhibition of DNA Damage Repair. Toxins (Basel) 2017; 9:toxins9050150. [PMID: 28452946 PMCID: PMC5450698 DOI: 10.3390/toxins9050150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 04/16/2017] [Accepted: 04/19/2017] [Indexed: 01/17/2023] Open
Abstract
Cytotoxic indole alkaloids from Melodinus suaveolens, which belongs to the toxic plant family Apocynaceae, demonstrated impressive antitumor activities in many tumor types, but less application in glioblastoma, which is the lethal brain tumor. In the present study, we reported the anti-glioblastoma activity of an indole alkaloid, 3α-acetonyltabersonine, which was isolated from Melodinus suaveolens. 3α-acetonyltabersonine was cytotoxic to glioblastoma cell lines (U87 and T98G) and stem cells at low concentrations. We verified 3α-acetonyltabersonine could suppress tumor cell proliferation and cause apoptosis in glioblastoma stem cells (GSCs). Moreover, detailed investigation of transcriptome study and Western blotting analysis indicated the mitogen activated protein kinase (MAPK) pathway was activated by phosphorylation upon 3α-acetonyltabersonine treatment. Additionally, we found 3α-acetonyltabersonine inhibited DNA damage repair procedures, the accumulated DNA damage stimulated activation of MAPK pathway and, finally, induced apoptosis. Further evidence was consistently obtained from vivo experiments on glioblastoma mouse model: treatment of 3α-acetonyltabersonine could exert pro-apoptotic function and prolong the life span of tumor-bearing mice. These results in vitro and in vivo suggested that 3α-acetonyltabersonine could be a potential candidate antitumor agent.
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Affiliation(s)
- Yuan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 21 Qingsong Road, Kunming 650203, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Road, Kunming 650203, China.
- Graduate School, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China.
- Division of Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming 650500, China.
| | - Yunli Zhao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
| | - Xia Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 21 Qingsong Road, Kunming 650203, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Road, Kunming 650203, China.
- Graduate School, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China.
| | - Wei Ni
- Department of Neurosurgery, Tumor Hospital of Yunnan Province, 519 Kunzhou Road, Kunming 650000, China.
| | - Zhi Dai
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 21 Qingsong Road, Kunming 650203, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, 19 Qingsong Road, Kunming 650203, China.
- Graduate School, University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China.
| | - Dong Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 21 Qingsong Road, Kunming 650203, China.
| | - Junjun Hao
- State Key Lab of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 21 Qingsong Road, Kunming 650203, China.
| | - Lin Luo
- Department of Neurosurgery, Tumor Hospital of Yunnan Province, 519 Kunzhou Road, Kunming 650000, China.
| | - Yaping Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
| | - Xiaodong Luo
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, 132 Lanhei Road, Kunming 650201, China.
| | - Xudong Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, 21 Qingsong Road, Kunming 650203, China.
- Kunming Primate Research Center, Chinese Academy of Sciences, 32 East Jiaochang Road, Kunming 650223, China.
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Fu X, Cui K, Yi Q, Yu L, Xu Y. DNA repair mechanisms in embryonic stem cells. Cell Mol Life Sci 2017; 74:487-493. [PMID: 27614628 PMCID: PMC11107665 DOI: 10.1007/s00018-016-2358-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 08/28/2016] [Accepted: 09/05/2016] [Indexed: 10/21/2022]
Abstract
Embryonic stem cells (ESCs) can undergo unlimited self-renewal and retain the pluripotency to differentiate into all cell types in the body. Therefore, as a renewable source of various functional cells in the human body, ESCs hold great promise for human cell therapy. During the rapid proliferation of ESCs in culture, DNA damage, such as DNA double-stranded breaks, will occur in ESCs. Therefore, to realize the potential of ESCs in human cell therapy, it is critical to understand the mechanisms how ESCs activate DNA damage response and DNA repair to maintain genomic stability, which is a prerequisite for their use in human therapy. In this context, it has been shown that ESCs harbor much fewer spontaneous mutations than somatic cells. Consistent with the finding that ESCs are genetically more stable than somatic cells, recent studies have indicated that ESCs can mount more robust DNA damage responses and DNA repair than somatic cells to ensure their genomic integrity.
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Affiliation(s)
- Xuemei Fu
- Shenzhen Children's Hospital, 7019 Yitian Road, Shenzhen, 518026, China.
| | - Ke Cui
- Center for Regenerative and Translational Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Qiuxiang Yi
- Center for Regenerative and Translational Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China
| | - Lili Yu
- Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong, China
| | - Yang Xu
- Center for Regenerative and Translational Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China.
- Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Cancer Research Institute, Southern Medical University, Guangzhou, Guangdong, China.
- Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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Sankar A, Kooistra SM, Gonzalez JM, Ohlsson C, Poutanen M, Helin K. Maternal expression of the JMJD2A/KDM4A histone demethylase is critical for pre-implantation development. Development 2017; 144:3264-3277. [DOI: 10.1242/dev.155473] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 08/14/2017] [Indexed: 12/20/2022]
Abstract
Regulation of chromatin composition through post-translational modifications of histones contributes to transcriptional regulation and is essential for many cellular processes, including differentiation and development. JMJD2A/KDM4A is a lysine demethylase with specificity towards di- and tri-methylated lysine 9 and lysine 36 of histone H3 (H3K9me2/me3 and H3K36me2/me3). Here, we report that Kdm4a as a maternal factor plays a key role in embryo survival and is vital for female fertility. Kdm4a−/- female mice ovulate normally with comparable fertilization but poor implantation rates, and cannot support healthy transplanted embryos to term. This is due to a role for Kdm4a in uterine function, where its loss causes reduced expression of key genes involved in ion transport, nutrient supply and cytokine signalling, that impact embryo survival. In addition, a significant proportion of Kdm4a deficient oocytes displays a poor intrinsic ability to develop into blastocysts. These embryos cannot compete with healthy embryos for implantation in vivo, highlighting Kdm4a as a maternal effect gene. Thus, our study dissects an important dual role for maternal Kdm4a in determining faithful early embryonic development and the implantation process.
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Affiliation(s)
- Aditya Sankar
- Biotech Research and Innovation Centre, University of Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
- Present Address: Centre for Chromosome Stability, Institute of Cellular and Molecular Medicine, University of Copenhagen, Denmark
| | - Susanne Marije Kooistra
- Biotech Research and Innovation Centre, University of Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Denmark
- Present Address: Department of Neuroscience, University Medical Centre, Groningen, University of Groningen, Groningen, The Netherlands
| | - Javier Martin Gonzalez
- Core Facility for Transgenic Mice, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Claes Ohlsson
- Department of Physiology Turku Center for Disease Modeling (TCDM), Institute of Biomedicine, University of Turku, Turku, Finland
| | - Matti Poutanen
- Centre for Bone and Arthritis Research, Institute of Medicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Physiology Turku Center for Disease Modeling (TCDM), Institute of Biomedicine, University of Turku, Turku, Finland
| | - Kristian Helin
- Biotech Research and Innovation Centre, University of Copenhagen, Denmark
- Centre for Epigenetics, University of Copenhagen, Denmark
- The Danish Stem Cell Center (Danstem), Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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DNA Damage Response in Hematopoietic Stem Cell Ageing. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:147-154. [PMID: 27221660 PMCID: PMC4936660 DOI: 10.1016/j.gpb.2016.04.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/20/2016] [Accepted: 04/24/2016] [Indexed: 12/30/2022]
Abstract
Maintenance of tissue-specific stem cells is vital for organ homeostasis and organismal longevity. Hematopoietic stem cells (HSCs) are the most primitive cell type in the hematopoietic system. They divide asymmetrically and give rise to daughter cells with HSC identity (self-renewal) and progenitor progenies (differentiation), which further proliferate and differentiate into full hematopoietic lineages. Mammalian ageing process is accompanied with abnormalities in the HSC self-renewal and differentiation. Transcriptional changes and epigenetic modulations have been implicated as the key regulators in HSC ageing process. The DNA damage response (DDR) in the cells involves an orchestrated signaling pathway, consisting of cell cycle regulation, cell death and senescence, transcriptional regulation, as well as chromatin remodeling. Recent studies employing DNA repair-deficient mouse models indicate that DDR could intrinsically and extrinsically regulate HSC maintenance and play important roles in tissue homeostasis of the hematopoietic system. In this review, we summarize the current understanding of how the DDR determines the HSC fates and finally contributes to organismal ageing.
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Lu YQ, He XC, Zheng P. Decrease in expression of maternal effect gene Mater is associated with maternal ageing in mice. Mol Hum Reprod 2016; 22:252-60. [PMID: 26769260 DOI: 10.1093/molehr/gaw001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/08/2016] [Indexed: 12/29/2022] Open
Abstract
STUDY HYPOTHESIS What factors in mouse oocytes are involved in the ageing-related decline in oocyte quality? STUDY FINDING The maternal effect gene Mater is involved in ageing-related oocyte quality decline in mice. WHAT IS KNOWN ALREADY Premature loss of centromere cohesion is a hallmark of ageing-related oocyte quality decline; the maternal effect gene Mater (maternal antigen that embryos require, also known as Nlrp5) is required for preimplantation embryo development beyond the 2-cell stage, and mRNA expression of Mater decreases with maternal ageing. STUDY DESIGN, SAMPLES/MATERIALS, METHODS Mater protein expression level in mature oocytes from 7 young (5-8 weeks old) to 7 old mice (41-68 weeks old) was compared by immunoblotting analysis. Wild-type and Mater-null mice were used to examine whether Mater is necessary for maintaining normal centromere cohesion by means of cytogenetic karyotyping, time-lapse confocal microscopy and immunofluorescence staining. MAIN RESULTS AND THE ROLE OF CHANCE Mater protein is decreased in mature oocytes from old versus young mice (P = 0.0022). Depletion of Mater from oocytes leads to a reduction in centromere cohesion, manifested by precocious sister chromatid separation, enlargement of sister centromere distance and misalignment of chromosomes in the metaphase plate during meiosis I and II. LIMITATIONS, REASONS FOR CAUTION This study was conducted in mice. Whether or not the results are applicable to human remains further elucidation. In addition, we were unable to confirm if the strain of mice (C57BL/6XSv129) at the age of 41-68 weeks old has the 'cohesin-loss' phenotype. WIDER IMPLICATIONS OF THE FINDINGS Investigating Mater's functional mechanisms could provide fresh insights into understanding how the ageing-related oocyte quality decline occurs. LARGE SCALE DATA N/A. STUDY FUNDING AND COMPETING INTERESTS This work was supported by the research grant from Chinese NSFC to P.Z. (31071274). We have no conflict of interests to declare.
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Affiliation(s)
- Yong-qing Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Xie-chao He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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Abstract
Duchenne muscular dystrophy (DMD) is a severe genetic disorder caused by loss of function of the dystrophin gene on the X chromosome. Gene augmentation of dystrophin is challenging due to the large size of the dystrophin cDNA. Emerging genome editing technologies, such as TALEN and CRISPR-Cas9 systems, open a new erain the restoration of functional dystrophin and are a hallmark of bona fide gene therapy. In this review, we summarize current genome editing approaches, properties of target cell types for ex vivo gene therapy, and perspectives of in vivo gene therapy including genome editing in human zygotes. Although technical challenges, such as efficacy, accuracy, and delivery of the genome editing components, remain to be further improved, yet genome editing technologies offer a new avenue for the gene therapy of DMD.
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Affiliation(s)
- Akitsu Hotta
- Center for iPS Cell Research & Application (CiRA), Kyoto University, Japan.,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Japan
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