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Zhao H, Li J, You Z, Lindsay HD, Yan S. Distinct regulation of ATM signaling by DNA single-strand breaks and APE1. Nat Commun 2024; 15:6517. [PMID: 39112456 PMCID: PMC11306256 DOI: 10.1038/s41467-024-50836-6] [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: 07/06/2023] [Accepted: 07/21/2024] [Indexed: 08/10/2024] Open
Abstract
In response to DNA double-strand breaks or oxidative stress, ATM-dependent DNA damage response (DDR) is activated to maintain genome integrity. However, it remains elusive whether and how DNA single-strand breaks (SSBs) activate ATM. Here, we provide direct evidence in Xenopus egg extracts that ATM-mediated DDR is activated by a defined SSB structure. Our mechanistic studies reveal that APE1 promotes the SSB-induced ATM DDR through APE1 exonuclease activity and ATM recruitment to SSB sites. APE1 protein can form oligomers to activate the ATM DDR in Xenopus egg extracts in the absence of DNA and can directly stimulate ATM kinase activity in vitro. Our findings reveal distinct mechanisms of the ATM-dependent DDR activation by SSBs in eukaryotic systems and identify APE1 as a direct activator of ATM kinase.
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Affiliation(s)
- Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Howard D Lindsay
- Lancaster Medical School, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
- School of Data Science, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
- Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, USA.
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2
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Huang J, Jiang Z, Ruan Z, Sheng H, Liu S, Dong X, Su X, Feng L, Li Y, Xu H, Chen J, Xia H, Li T, Li J, Xu L, Lou J. Cr (VI)-induced ribosomal DNA copy number variation is associated with semen quality impairment: Evidence from human to animal study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116700. [PMID: 38981392 DOI: 10.1016/j.ecoenv.2024.116700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 06/27/2024] [Accepted: 07/05/2024] [Indexed: 07/11/2024]
Abstract
OBJECTIVES This study aimed to analyze the possible role of rDNA copy number variation in the association between hexavalent chromium [Cr (VI)] exposure and semen quality in semen donors and further confirm this association in mice. METHODS In this cross-sectional study, whole blood and semen samples were collected from 155 semen donors in the Zhejiang Human Sperm Bank from January 1st to April 31st, 2021. Adult C57BL/6 J male mice were treated with different doses of Cr (VI) (0, 10, or 15 mg/kg b.w./day). Semen quality, including semen volume, total spermatozoa count, sperm concentration, progressive motility, and total motility, were analyzed according to the WHO laboratory manual. Cr concentration was detected using inductively coupled plasma mass spectrometry. The rDNA copy number was measured using qPCR. RESULTS In semen donors, whole blood Cr concentration was negatively associated with semen concentration and total sperm counts. Semen 5 S and 45 S rDNA copy numbers were negatively associated with whole blood Cr concentration and whole blood 5.8 S rDNA copy number was negatively associated with semen Cr concentration. In mice, Cr (VI) damaged testicular tissue, decreased semen quality, and caused rDNA copy number variation. Semen quality was related to the rDNA copy number in whole blood, testicular tissue, and semen samples in mice. CONCLUSION Cr (VI) was associated with decreased semen quality in semen donors and mice. Our findings suggest an in-depth analysis of the role of the rDNA copy number variation in the Cr (VI)-induced impairment of semen quality.
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Affiliation(s)
- Jing Huang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Zhaoqiang Jiang
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Zheng Ruan
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Huiqiang Sheng
- Zhejiang Mater Child and Reproductive Health Center, Hangzhou, Zhejiang Province, China
| | - Shuang Liu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Xiaowen Dong
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Xin Su
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Yongxin Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Huadong Xu
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Junfei Chen
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Hailing Xia
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Tao Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Jiaping Li
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China
| | - Ling Xu
- Zhejiang Mater Child and Reproductive Health Center, Hangzhou, Zhejiang Province, China.
| | - Jianlin Lou
- School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang Province, China; School of Medicine, and The First Affiliated Hospital, Huzhou University, Huzhou, Zhejiang Province, China.
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3
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Shan L, Li P, Yu H, Chen LL. Emerging roles of nuclear bodies in genome spatial organization. Trends Cell Biol 2024; 34:595-605. [PMID: 37993310 DOI: 10.1016/j.tcb.2023.10.012] [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: 08/22/2023] [Revised: 10/09/2023] [Accepted: 10/26/2023] [Indexed: 11/24/2023]
Abstract
Nuclear bodies (NBs) are biomolecular condensates that participate in various cellular processes and respond to cellular stimuli in the nucleus. The assembly and function of these protein- and RNA-rich bodies, such as nucleoli, nuclear speckles, and promyelocytic leukemia (PML) NBs, contribute to the spatial organization of the nucleus, regulating chromatin activities locally and globally. Recent technological advancements, including spatial multiomics approaches, have revealed novel roles of nucleoli in modulating ribosomal DNA (rDNA) and adjacent non-rDNA chromatin activity, nuclear speckles in scaffolding active genome architecture, and PML NBs in maintaining genome stability during stress conditions. In this review, we summarize emerging functions of these important NBs in the spatial organization of the genome, aided by recently developed spatial multiomics approaches toward this direction.
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Affiliation(s)
- Lin Shan
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Pan Li
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; Department of Cardiology, Changhai Hospital, Shanghai 200433, China
| | - Hongtao Yu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; New Cornerstone Science Laboratory, Shenzhen, China.
| | - Ling-Ling Chen
- Key Laboratory of RNA Science and Engineering, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China; New Cornerstone Science Laboratory, Shenzhen, China.
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4
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Zhou Y, Li K, Adelson DL. An unmet need for pharmacology: Treatments for radiation-induced gastrointestinal mucositis. Biomed Pharmacother 2024; 175:116767. [PMID: 38781863 DOI: 10.1016/j.biopha.2024.116767] [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: 03/04/2024] [Revised: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024] Open
Abstract
Gastrointestinal mucositis (GIM) continues to be a significant issue in the management of abdominal cancer radiation treatments and chemotherapy, causing significant patient discomfort and therapy interruption or even cessation. This review will first focus on radiotherapy induced GIM, providing an understanding of its clinical landscape. Subsequently, the aetiology of GIM will be reviewed, highlighting diverse contributing factors. The cellular and tissue damage and associated molecular responses in GIM will be summarised in the context of the underlying complex biological processes. Finally, available drugs and pharmaceutical therapies will be evaluated, underscoring their insufficiency, and highlighting the need for further research and innovation. This review will emphasize the urgent need for improved pharmacologic therapeutics for GIM, which is a key research priority in oncology.
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Affiliation(s)
- Yan Zhou
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Zhendong Australia China Centre for Molecular Chinese Medicine, The University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Kun Li
- Beijing Zhendong Guangming Pharmaceutical Research Institute, Beijing 100120, China.
| | - David L Adelson
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; Zhendong Australia China Centre for Molecular Chinese Medicine, The University of Adelaide, Adelaide, South Australia 5005, Australia.
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5
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Trifault B, Mamontova V, Cossa G, Ganskih S, Wei Y, Hofstetter J, Bhandare P, Baluapuri A, Nieto B, Solvie D, Ade CP, Gallant P, Wolf E, Larsen DH, Munschauer M, Burger K. Nucleolar detention of NONO shields DNA double-strand breaks from aberrant transcripts. Nucleic Acids Res 2024; 52:3050-3068. [PMID: 38224452 PMCID: PMC11014278 DOI: 10.1093/nar/gkae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 12/11/2023] [Accepted: 01/04/2024] [Indexed: 01/16/2024] Open
Abstract
RNA-binding proteins emerge as effectors of the DNA damage response (DDR). The multifunctional non-POU domain-containing octamer-binding protein NONO/p54nrb marks nuclear paraspeckles in unperturbed cells, but also undergoes re-localization to the nucleolus upon induction of DNA double-strand breaks (DSBs). However, NONO nucleolar re-localization is poorly understood. Here we show that the topoisomerase II inhibitor etoposide stimulates the production of RNA polymerase II-dependent, DNA damage-inducible antisense intergenic non-coding RNA (asincRNA) in human cancer cells. Such transcripts originate from distinct nucleolar intergenic spacer regions and form DNA-RNA hybrids to tether NONO to the nucleolus in an RNA recognition motif 1 domain-dependent manner. NONO occupancy at protein-coding gene promoters is reduced by etoposide, which attenuates pre-mRNA synthesis, enhances NONO binding to pre-mRNA transcripts and is accompanied by nucleolar detention of a subset of such transcripts. The depletion or mutation of NONO interferes with detention and prolongs DSB signalling. Together, we describe a nucleolar DDR pathway that shields NONO and aberrant transcripts from DSBs to promote DNA repair.
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Affiliation(s)
- Barbara Trifault
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Victoria Mamontova
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Giacomo Cossa
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Yuanjie Wei
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Pranjali Bhandare
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Apoorva Baluapuri
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Blanca Nieto
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Daniel Solvie
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Carsten P Ade
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Peter Gallant
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Elmar Wolf
- Cancer Systems Biology Group, Theodor Boveri Institute, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Institute, Strandboulevarden 49, Copenhagen, Denmark
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
| | - Kaspar Burger
- Mildred Scheel Early Career Center for Cancer Research (Mildred-Scheel-Nachwuchszentrum, MSNZ) Würzburg, University Hospital Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany
- Department of Biochemistry and Molecular Biology, Biocenter of the University of Würzburg, Am Hubland, D-97074 Würzburg, Germany
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6
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Cai Z, Mei S, Zhou L, Ma X, Wuyun Q, Yan J, Ding H. Liquid-Liquid Phase Separation Sheds New Light upon Cardiovascular Diseases. Int J Mol Sci 2023; 24:15418. [PMID: 37895097 PMCID: PMC10607581 DOI: 10.3390/ijms242015418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/19/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
Liquid-liquid phase separation (LLPS) is a biophysical process that mediates the precise and complex spatiotemporal coordination of cellular processes. Proteins and nucleic acids are compartmentalized into micron-scale membrane-less droplets via LLPS. These droplets, termed biomolecular condensates, are highly dynamic, have concentrated components, and perform specific functions. Biomolecular condensates have been observed to organize diverse key biological processes, including gene transcription, signal transduction, DNA damage repair, chromatin organization, and autophagy. The dysregulation of these biological activities owing to aberrant LLPS is important in cardiovascular diseases. This review provides a detailed overview of the regulation and functions of biomolecular condensates, provides a comprehensive depiction of LLPS in several common cardiovascular diseases, and discusses the revolutionary therapeutic perspective of modulating LLPS in cardiovascular diseases and new treatment strategies relevant to LLPS.
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Affiliation(s)
- Ziyang Cai
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.C.); (S.M.); (L.Z.); (X.M.); (Q.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Shuai Mei
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.C.); (S.M.); (L.Z.); (X.M.); (Q.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Li Zhou
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.C.); (S.M.); (L.Z.); (X.M.); (Q.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Xiaozhu Ma
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.C.); (S.M.); (L.Z.); (X.M.); (Q.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Qidamugai Wuyun
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.C.); (S.M.); (L.Z.); (X.M.); (Q.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jiangtao Yan
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.C.); (S.M.); (L.Z.); (X.M.); (Q.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
- Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hu Ding
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (Z.C.); (S.M.); (L.Z.); (X.M.); (Q.W.)
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
- Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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7
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Lin Y, Li J, Zhao H, McMahon A, McGhee K, Yan S. APE1 recruits ATRIP to ssDNA in an RPA-dependent and -independent manner to promote the ATR DNA damage response. eLife 2023; 12:82324. [PMID: 37216274 DOI: 10.7554/elife.82324] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 05/08/2023] [Indexed: 05/24/2023] Open
Abstract
Cells have evolved the DNA damage response (DDR) pathways in response to DNA replication stress or DNA damage. In the ATR-Chk1 DDR pathway, it has been proposed that ATR is recruited to RPA-coated single-stranded DNA (ssDNA) by direct ATRIP-RPA interaction. However, it remains elusive how ATRIP is recruited to ssDNA in an RPA-independent manner. Here, we provide evidence that APE1 directly associates ssDNA to recruit ATRIP onto ssDNA in an RPA-independent fashion. The N-terminal motif within APE1 is required and sufficient for the APE1-ATRIP interaction in vitro and the distinct APE1-ATRIP interaction is required for ATRIP recruitment to ssDNA and the ATR-Chk1 DDR pathway activation in Xenopus egg extracts. In addition, APE1 directly associates with RPA70 and RPA32 via two distinct motifs. Taken together, our evidence suggests that APE1 recruits ATRIP onto ssDNA in an RPA-dependent and -independent manner in the ATR DDR pathway.
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Affiliation(s)
- Yunfeng Lin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Kelly McGhee
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, United States
- School of Data Science, University of North Carolina at Charlotte, Charlotte, United States
- Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, United States
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