1
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Zhan T, Chen Y, Dong L, Wei T, Lu D, Wang Q, Wu Z, Xu J, Ge M. Nicotinamide phosphoribose transferase facilitates macrophage-mediated pulmonary fibrosis through the Sirt1-Smad7 pathway in mice. Eur J Pharmacol 2024; 967:176355. [PMID: 38280463 DOI: 10.1016/j.ejphar.2024.176355] [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: 09/10/2023] [Revised: 12/27/2023] [Accepted: 01/23/2024] [Indexed: 01/29/2024]
Abstract
Pulmonary fibrosis is a challenging lung disease characterized by a bleak prognosis. A pivotal element in the progression of this disease is the dysregulated recruitment of macrophages. Nicotinamide phosphoribose transferase (NAMPT), secreted by alveolar epithelial cells and inflammatory cells, has been previously identified to influence macrophage inflammation in acute lung injury through the nicotinamide adenine dinucleotide (NAD) rescue synthesis pathway. Nonetheless, the exact role of NAMPT in the regulation of lung fibrosis is yet to be elucidated. In our research, we employed bleomycin (BLM) to induce pulmonary fibrosis in Namptflox/flox;Cx3cr1CreER mice, using Namptflox/flox mice as controls. Our findings revealed an augmented expression of NAMPT concurrent with a marked increase in the secretion of NAD and inflammatory cytokines such as IL-6, TNF-α, and TGF-β1 post-BLM treatment. Furthermore, an upsurge in NAMPT-positive macrophages was observed in the lungs of BLM-treated Namptflox/flox mice. Notably, a conditional knockout of NAMPT (NAMPT cKO) in lung macrophages curtailed the BLM-induced inflammatory responses and significantly mitigated pulmonary fibrosis. This was associated with diminished phospho-Sirt1 (p-Sirt1) expression levels and a concomitant rise in mothers against decapentaplegic homolog 7 (Smad7) expression in BLM-treated mouse lungs and murine RAW 264.7 macrophage cells. Collectively, our data suggests that NAMPT exacerbates macrophage-driven inflammation and pulmonary fibrosis via the Sirt1-Smad7 pathway, positioning NAMPT as a promising therapeutic target for pulmonary fibrosis intervention.
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Affiliation(s)
- Tianwei Zhan
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), 158 Shang-Tang Road, 310014, Hangzhou, Zhejiang, People's Republic of China
| | - Yaling Chen
- Department of Pharmacology, Zhejiang University School of Medicine, 866 Yu-Hang-Tang Road, 310058, Hangzhou, Zhejiang, People's Republic of China
| | - Lingjun Dong
- Department of Thoracic Surgery, Shaoxing People's Hospital, 568-Zhongxing North Road, 312000, Shaoxing, Zhejiang, People's Republic of China
| | - Taofeng Wei
- Department of Pharmacology, Zhejiang University School of Medicine, 866 Yu-Hang-Tang Road, 310058, Hangzhou, Zhejiang, People's Republic of China
| | - Dongning Lu
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), 158 Shang-Tang Road, 310014, Hangzhou, Zhejiang, People's Republic of China
| | - Qi Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jie-Fang Road, 310009, Hangzhou, Zhejiang, People's Republic of China
| | - Zixiang Wu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, 88 Jie-Fang Road, 310009, Hangzhou, Zhejiang, People's Republic of China
| | - Jiajie Xu
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), 158 Shang-Tang Road, 310014, Hangzhou, Zhejiang, People's Republic of China.
| | - Minghua Ge
- Otolaryngology & Head and Neck Center, Cancer Center, Department of Head and Neck Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), 158 Shang-Tang Road, 310014, Hangzhou, Zhejiang, People's Republic of China.
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2
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Nam H, Xie K, Majumdar I, Yang S, Starzyk J, Lee D, Shan R, Li J, Wu H. Engineering Tripartite Gene Editing Machinery for Highly Efficient Non-Viral Targeted Genome Integration. RESEARCH SQUARE 2023:rs.3.rs-3365585. [PMID: 37961210 PMCID: PMC10635301 DOI: 10.21203/rs.3.rs-3365585/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Non-viral DNA donor template has been widely used for targeted genomic integration by homologous recombination (HR). This process has become more efficient with RNA guided endonuclease editor system such as CRISPR/Cas9. Circular single stranded DNA (cssDNA) has been harnessed previously as a genome engineering catalyst (GATALYST) for efficient and safe targeted gene knock-in. Here we developed enGager, a system with enhanced GATALYST associated genome editor, comprising a set of novel genome editors in which the integration efficiency of a circular single-stranded (css) donor DNA is elevated by directly tethering of the cssDNA to a nuclear-localized Cas9 fused with ssDNA binding peptides. Improvements in site-directed genomic integration and expression of a knocked-in DNA encoding GFP were observed at multiple genomic loci in multiple cell lines. The enhancement of integration efficiency, compared to unfused Cas9 editors, ranges from 1.5- to more than 6-fold, with the enhancement most pronounced for transgenes of > 4Kb in length in primary cells. enGager-enhanced genome integration prefers ssDNA donors which, unlike traditional dsDNA donors, are not concatemerized or rearranged prior to and during integration Using an enGager fused to an optimized cssDNA binding peptide, exceptionally efficient, targeted integration of the chimeric antigen receptor (CAR) transgene was achieved in 33% of primary human T cells. Enhanced anti-tumor function of these CAR-T primary cells demonstrated the functional competence of the transgenes. The 'tripartite editors with ssDNA optimized genome engineering' (TESOGENASE™) systems help address the efficacy needs for therapeutic gene modification while avoiding the safety and payload size limitations of viral vectors currently used for CAR-T engineering.
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Affiliation(s)
- Hangu Nam
- Department of Bioengineering, Northeastern University, Boston, MA 02115, United States
| | - Keqiang Xie
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Ishita Majumdar
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Shaobo Yang
- Department of Bioengineering, Northeastern University, Boston, MA 02115, United States
| | - Jakob Starzyk
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Danna Lee
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Richard Shan
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
| | - Jiahe Li
- Department of Biomedical Engineering, College of Engineering and School of Medicine, University of Michigan, Ann Arbor, MI 48109, United States
| | - Hao Wu
- Full Circles Therapeutics, INC. 625 Mount Auburn St., Ste. 105, Cambridge, MA 02138, United States
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Nam H, Xie K, Majumdar I, Yang S, Starzyk J, Lee D, Shan R, Li J, Wu H. TESOGENASE, An Engineered Nuclease Editor for Enhanced Targeted Genome Integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.28.553855. [PMID: 37693500 PMCID: PMC10491117 DOI: 10.1101/2023.08.28.553855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Non-viral DNA donor template has been widely used for targeted genomic integration by homologous recombination (HR). This process has become more efficient with RNA guided endonuclease editor system such as CRISPR/Cas9. Circular single stranded DNA (cssDNA) has been harnessed previously as a g enome engineering c atalyst (GATALYST) for efficient and safe targeted gene knock-in. However, the engineering efficiency is bottlenecked by the nucleoplasm trafficking and genomic tethering of cssDNA donor, especially for extra-large transgene integration. Here we developed enGager, en hanced G ATALYST a ssociated g enome e ditor system by fusion of nucleus localization signal (NLS) peptide tagged Cas9 with various single stranded DNA binding protein modules through a GFP reporter Knock-in screening. The enGager system assembles an integrative genome integration machinery by forming tripartite complex for engineered nuclease editors, sgRNA and ssDNA donors, thereby facilitate the nucleus trafficking of DNA donors and increase their active local concentration at the targeted genomic site. When applied for genome integration with cssDNA donor templates to diverse genomic loci in various cell types, these enGagers outperform unfused editors. The enhancement of integration efficiency ranges from 1.5- to more than 6-fold, with the effect being more prominent for > 4Kb transgene knock-in in primary cells. We further demonstrated that enGager mediated enhancement for genome integration is ssDNA, but less dsDNA dependent. Using one of the mini-enGagers, we demonstrated large chimeric antigen receptor (CAR) transgene integration in primary T cells with exceptional efficiency and anti-tumor function. These tripartite e ditors with s sDNA o ptimized g enome en gineering system (TESOGENASE TM ) add a set of novel endonuclease editors into the gene-editing toolbox for potential cell and gene therapeutic development based on ssDNA mediated non-viral genome engineering. Highlight A reporter Knock-in screening establishes enGager system to identify TESOGENASE editor to improving ssDNA mediated genome integrationMini-TESOGENASEs developed by fusing Cas9 nuclease with novel ssDNA binding motifsmRNA mini-TESOGENASEs enhance targeted genome integration via various non-viral delivery approachesEfficient functional CAR-T cell engineering by mini-TESOGENASE.
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4
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Liang P, Lister K, Yates L, Argunhan B, Zhang X. Phosphoregulation of DNA repair via the Rad51 auxiliary factor Swi5-Sfr1. J Biol Chem 2023; 299:104929. [PMID: 37330173 PMCID: PMC10366545 DOI: 10.1016/j.jbc.2023.104929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023] Open
Abstract
Homologous recombination (HR) is a major pathway for the repair of DNA double-strand breaks, the most severe form of DNA damage. The Rad51 protein is central to HR, but multiple auxiliary factors regulate its activity. The heterodimeric Swi5-Sfr1 complex is one such factor. It was previously shown that two sites within the intrinsically disordered domain of Sfr1 are critical for the interaction with Rad51. Here, we show that phosphorylation of five residues within this domain regulates the interaction of Swi5-Sfr1 with Rad51. Biochemical reconstitutions demonstrated that a phosphomimetic mutant version of Swi5-Sfr1 is defective in both the physical and functional interaction with Rad51. This translated to a defect in DNA repair, with the phosphomimetic mutant yeast strain phenocopying a previously established interaction mutant. Interestingly, a strain in which Sfr1 phosphorylation was blocked also displayed sensitivity to DNA damage. Taken together, we propose that controlled phosphorylation of Sfr1 is important for the role of Swi5-Sfr1 in promoting Rad51-dependent DNA repair.
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Affiliation(s)
- Pengtao Liang
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
| | - Katie Lister
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
| | - Luke Yates
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
| | - Bilge Argunhan
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK.
| | - Xiaodong Zhang
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK.
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5
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Multi-Level Control of the ATM/ATR-CHK1 Axis by the Transcription Factor E4F1 in Triple-Negative Breast Cancer. Int J Mol Sci 2022; 23:ijms23169217. [PMID: 36012478 PMCID: PMC9409040 DOI: 10.3390/ijms23169217] [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: 07/08/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/01/2022] Open
Abstract
E4F1 is essential for early embryonic mouse development and for controlling the balance between proliferation and survival of actively dividing cells. We previously reported that E4F1 is essential for the survival of murine p53-deficient cancer cells by controlling the expression of genes involved in mitochondria functions and metabolism, and in cell-cycle checkpoints, including CHEK1, a major component of the DNA damage and replication stress responses. Here, combining ChIP-Seq and RNA-Seq approaches, we identified the transcriptional program directly controlled by E4F1 in Human Triple-Negative Breast Cancer cells (TNBC). E4F1 binds and regulates a limited list of direct target genes (57 genes) in these cells, including the human CHEK1 gene and, surprisingly, also two other genes encoding post-transcriptional regulators of the ATM/ATR-CHK1 axis, namely, the TTT complex component TTI2 and the phosphatase PPP5C, that are essential for the folding and stability, and the signaling of ATM/ATR kinases, respectively. Importantly, E4F1 also binds the promoter of these genes in vivo in Primary Derived Xenograft (PDX) of human TNBC. Consequently, the protein levels and signaling of CHK1 but also of ATM/ATR kinases are strongly downregulated in E4F1-depleted TNBC cells resulting in a deficiency of the DNA damage and replicative stress response in these cells. The E4F1-depleted cells fail to arrest into S-phase upon treatment with the replication-stalling agent Gemcitabine, and are highly sensitized to this drug, as well as to other DNA-damaging agents, such as Cisplatin. Altogether, our data indicate that in breast cancer cells the ATM/ATR-CHK1 signaling pathway and DNA damage-stress response are tightly controlled at the transcriptional and post-transcriptional level by E4F1.
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6
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Liu L, Yu N, Leng W, Lu Y, Xia X, Yuan H. 6-Gingerol, a functional polyphenol of ginger, reduces pulmonary fibrosis by activating Sirtuin1. Allergol Immunopathol (Madr) 2022; 50:104-114. [PMID: 35257553 DOI: 10.15586/aei.v50i2.533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/07/2021] [Indexed: 11/18/2022]
Abstract
Pulmonary fibrosis in general is the final common outcome of various interstitial lung diseases. In recent years, the incidence of pulmonary fibrosis has been rising with poor prognosis. 6-gingerol is deemed as a functional polyphenol of ginger. The aim of the present study was to investigate the effect of 6-gingerol, on pulmonary fibrosis. Mice were randomly divided into four groups: control, bleomycin, bleomycin + 6-gingerol 100 mg/kg, bleomycin + 6-gingerol 250 mg/kg, and the survival rates of the groups were recorded. Pathological and fibrotic changes in the lungs were identified by H&E and Masson staining, respectively. The levels of hydroxyproline and protein deposited in lung tissues were then, respectively, determined by colorimetry and western blotting. Subsequently, the proportion of cells and inflammatory factors in the alveolar lavage fluid were estimated. Following the identification of the possibility of Sirtuin1 (SIRT1) in the pharmacological mechanism through molecular docking and western blotting, human embryonic lung fibroblasts MRC-5 were treated with TGF-β1 and SIRT1 inhibitor to study the role of SIRT1 in the regulatory effect of 6-gingerol. From the results, 6-gingerol was found to increase the survival rate of mice and reduce lung pathology and fibrosis in mice. And, it significantly reduced the levels of hydroxyproline and the proteins deposited in lung tissues. Moreover, the number of neutrophils, basophils, monocytes, and the levels of inflammatory factors in the alveolar lavage fluid were also reduced. SIRT1 inhibitor blocked the function of 6-gingerol to inhibit fibrosis. To sum up, 6-gingerol relieves pulmonary fibrosis via activating SIRT1. This finding expands the pharmacological effect of 6-gingerol, and it is expected to advance the development of treatments for pulmonary fibrosis.
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Affiliation(s)
- Li Liu
- The Affiliation Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Nan Yu
- The Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, China
| | - Wei Leng
- The Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, China
| | - Yun Lu
- The Affiliation Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xinxin Xia
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hui Yuan
- The Affiliated Hospital of Shaanxi University of Traditional Chinese Medicine, Xianyang, China;
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7
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Argunhan B, Iwasaki H, Tsubouchi H. Post-translational modification of factors involved in homologous recombination. DNA Repair (Amst) 2021; 104:103114. [PMID: 34111757 DOI: 10.1016/j.dnarep.2021.103114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 02/04/2023]
Abstract
DNA is the molecule that stores the chemical instructions necessary for life and its stability is therefore of the utmost importance. Despite this, DNA is damaged by both exogenous and endogenous factors at an alarming frequency. The most severe type of DNA damage is a double-strand break (DSB), in which a scission occurs in both strands of the double helix, effectively dividing a single normal chromosome into two pathological chromosomes. Homologous recombination (HR) is a universal DSB repair mechanism that solves this problem by identifying another region of the genome that shares high sequence similarity with the DSB site and using it as a template for repair. Rad51 possess the enzymatic activity that is essential for this repair but several auxiliary factors are required for Rad51 to fulfil its function. It is becoming increasingly clear that many HR factors are subjected to post-translational modification. Here, we review what is known about how these modifications affect HR. We first focus on cases where there is experimental evidence to support a function for the modification, then discuss speculative cases where a function can be inferred. Finally, we contemplate why such modifications might be necessary.
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Affiliation(s)
- Bilge Argunhan
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.
| | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Hideo Tsubouchi
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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8
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Afshar N, Argunhan B, Palihati M, Taniguchi G, Tsubouchi H, Iwasaki H. A novel motif of Rad51 serves as an interaction hub for recombination auxiliary factors. eLife 2021; 10:64131. [PMID: 33493431 PMCID: PMC7837696 DOI: 10.7554/elife.64131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/26/2020] [Indexed: 12/14/2022] Open
Abstract
Homologous recombination (HR) is essential for maintaining genome stability. Although Rad51 is the key protein that drives HR, multiple auxiliary factors interact with Rad51 to potentiate its activity. Here, we present an interdisciplinary characterization of the interactions between Rad51 and these factors. Through structural analysis, we identified an evolutionarily conserved acidic patch of Rad51. The neutralization of this patch completely abolished recombinational DNA repair due to defects in the recruitment of Rad51 to DNA damage sites. This acidic patch was found to be important for the interaction with Rad55-Rad57 and essential for the interaction with Rad52. Furthermore, biochemical reconstitutions demonstrated that neutralization of this acidic patch also impaired the interaction with Rad54, indicating that a single motif is important for the interaction with multiple auxiliary factors. We propose that this patch is a fundamental motif that facilitates interactions with auxiliary factors and is therefore essential for recombinational DNA repair.
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Affiliation(s)
- Negar Afshar
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Bilge Argunhan
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Maierdan Palihati
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Goki Taniguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Hideo Tsubouchi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Hiroshi Iwasaki
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
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9
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Argunhan B, Sakakura M, Afshar N, Kurihara M, Ito K, Maki T, Kanamaru S, Murayama Y, Tsubouchi H, Takahashi M, Takahashi H, Iwasaki H. Cooperative interactions facilitate stimulation of Rad51 by the Swi5-Sfr1 auxiliary factor complex. eLife 2020; 9:52566. [PMID: 32204793 PMCID: PMC7093153 DOI: 10.7554/elife.52566] [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: 10/08/2019] [Accepted: 02/13/2020] [Indexed: 01/26/2023] Open
Abstract
Although Rad51 is the key protein in homologous recombination (HR), a major DNA double-strand break repair pathway, several auxiliary factors interact with Rad51 to promote productive HR. We present an interdisciplinary characterization of the interaction between Rad51 and Swi5-Sfr1, a conserved auxiliary factor. Two distinct sites within the intrinsically disordered N-terminus of Sfr1 (Sfr1N) were found to cooperatively bind Rad51. Deletion of this domain impaired Rad51 stimulation in vitro and rendered cells sensitive to DNA damage. By contrast, amino acid-substitution mutants, which had comparable biochemical defects, could promote DNA repair, suggesting that Sfr1N has another role in addition to Rad51 binding. Unexpectedly, the DNA repair observed in these mutants was dependent on Rad55-Rad57, another auxiliary factor complex hitherto thought to function independently of Swi5-Sfr1. When combined with the finding that they form a higher-order complex, our results imply that Swi5-Sfr1 and Rad55-Rad57 can collaboratively stimulate Rad51 in Schizosaccharomyces pombe.
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Affiliation(s)
- Bilge Argunhan
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Masayoshi Sakakura
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Negar Afshar
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Misato Kurihara
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kentaro Ito
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Takahisa Maki
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Shuji Kanamaru
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Yasuto Murayama
- Center for Frontier Research, National Institute of Genetics, Shizuoka, Japan
| | - Hideo Tsubouchi
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Masayuki Takahashi
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Hideo Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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10
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Role of Rad51 and DNA repair in cancer: A molecular perspective. Pharmacol Ther 2020; 208:107492. [PMID: 32001312 DOI: 10.1016/j.pharmthera.2020.107492] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/13/2020] [Accepted: 01/22/2020] [Indexed: 12/24/2022]
Abstract
The maintenance of genome integrity is essential for any organism survival and for the inheritance of traits to offspring. To the purpose, cells have developed a complex DNA repair system to defend the genetic information against both endogenous and exogenous sources of damage. Accordingly, multiple repair pathways can be aroused from the diverse forms of DNA lesions, which can be effective per se or via crosstalk with others to complete the whole DNA repair process. Deficiencies in DNA healing resulting in faulty repair and/or prolonged DNA damage can lead to genes mutations, chromosome rearrangements, genomic instability, and finally carcinogenesis and/or cancer progression. Although it might seem paradoxical, at the same time such defects in DNA repair pathways may have therapeutic implications for potential clinical practice. Here we provide an overview of the main DNA repair pathways, with special focus on the role played by homologous repair and the RAD51 recombinase protein in the cellular DNA damage response. We next discuss the recombinase structure and function per se and in combination with all its principal mediators and regulators. Finally, we conclude with an analysis of the manifold roles that RAD51 plays in carcinogenesis, cancer progression and anticancer drug resistance, and conclude this work with a survey of the most promising therapeutic strategies aimed at targeting RAD51 in experimental oncology.
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11
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Klein HL, Ang KKH, Arkin MR, Beckwitt EC, Chang YH, Fan J, Kwon Y, Morten MJ, Mukherjee S, Pambos OJ, El Sayyed H, Thrall ES, Vieira-da-Rocha JP, Wang Q, Wang S, Yeh HY, Biteen JS, Chi P, Heyer WD, Kapanidis AN, Loparo JJ, Strick TR, Sung P, Van Houten B, Niu H, Rothenberg E. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. MICROBIAL CELL 2019; 6:65-101. [PMID: 30652106 PMCID: PMC6334232 DOI: 10.15698/mic2019.01.665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.
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Affiliation(s)
- Hannah L Klein
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Kenny K H Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Michelle R Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
| | - Emily C Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Yi-Hsuan Chang
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Michael J Morten
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
| | - Sucheta Mukherjee
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Oliver J Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Hafez El Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Elizabeth S Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - João P Vieira-da-Rocha
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA
| | - Quan Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Shuang Wang
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France
| | - Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Julie S Biteen
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.,Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.,Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Achillefs N Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Joseph J Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Terence R Strick
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.,Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France.,Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA
| | - Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Eli Rothenberg
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA
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Swi5-Sfr1 stimulates Rad51 recombinase filament assembly by modulating Rad51 dissociation. Proc Natl Acad Sci U S A 2018; 115:E10059-E10068. [PMID: 30297419 DOI: 10.1073/pnas.1812753115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eukaryotic Rad51 protein is essential for homologous-recombination repair of DNA double-strand breaks. Rad51 recombinases first assemble onto single-stranded DNA to form a nucleoprotein filament, required for function in homology pairing and strand exchange. This filament assembly is the first regulation step in homologous recombination. Rad51 nucleation is kinetically slow, and several accessory factors have been identified to regulate this step. Swi5-Sfr1 (S5S1) stimulates Rad51-mediated homologous recombination by stabilizing Rad51 nucleoprotein filaments, but the mechanism of stabilization is unclear. We used single-molecule tethered particle motion experiments to show that mouse S5S1 (mS5S1) efficiently stimulates mouse RAD51 (mRAD51) nucleus formation and inhibits mRAD51 dissociation from filaments. We also used single-molecule fluorescence resonance energy transfer experiments to show that mS5S1 promotes stable nucleus formation by specifically preventing mRAD51 dissociation. This leads to a reduction of nucleation size from three mRAD51 to two mRAD51 molecules in the presence of mS5S1. Compared with mRAD51, fission yeast Rad51 (SpRad51) exhibits fast nucleation but quickly dissociates from the filament. SpS5S1 specifically reduces SpRad51 disassembly to maintain a stable filament. These results clearly demonstrate the conserved function of S5S1 by primarily stabilizing Rad51 on DNA, allowing both the formation of the stable nucleus and the maintenance of filament length.
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Argunhan B, Murayama Y, Iwasaki H. The differentiated and conserved roles of Swi5-Sfr1 in homologous recombination. FEBS Lett 2017; 591:2035-2047. [PMID: 28423184 PMCID: PMC5573924 DOI: 10.1002/1873-3468.12656] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/10/2017] [Accepted: 04/12/2017] [Indexed: 11/13/2022]
Abstract
Homologous recombination (HR) is the process whereby two DNA molecules that share high sequence similarity are able to recombine to generate hybrid DNA molecules. Throughout evolution, the ability of HR to identify highly similar DNA sequences has been adopted for numerous biological phenomena including DNA repair, meiosis, telomere maintenance, ribosomal DNA amplification and immunological diversity. Although Rad51 and Dmc1 are the key proteins that promote HR in mitotic and meiotic cells, respectively, accessory proteins that allow Rad51 and Dmc1 to effectively fulfil their functions have been identified in all examined model systems. In this Review, we discuss the roles of the highly conserved Swi5‐Sfr1 accessory complex in yeast, mice and humans, and explore similarities and differences between these species.
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Affiliation(s)
- Bilge Argunhan
- Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Yasuto Murayama
- Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Hiroshi Iwasaki
- Institute of Innovative Research, Tokyo Institute of Technology, Japan
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