1
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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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Zhan Z, Zhang J, Liang H, Wang C, Hong L, Liu W. KAT6A Condensates Impair PARP1 Trapping of PARP Inhibitors in Ovarian Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400140. [PMID: 38973255 DOI: 10.1002/advs.202400140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/04/2024] [Indexed: 07/09/2024]
Abstract
Most clinical PARP inhibitors (PARPis) trap PARP1 in a chromatin-bound state, leading to PARPi-mediated cytotoxicity. PARPi resistance impedes the treatment of ovarian cancer in clinical practice. However, the mechanism by which cancer cells overcome PARP1 trapping to develop PARPi resistance remains unclear. Here, it is shown that high levels of KAT6A promote PARPi resistance in ovarian cancer, regardless of its catalytic activity. Mechanistically, the liquid-liquid phase separation (LLPS) of KAT6A, facilitated by APEX1, inhibits the cytotoxic effects of PARP1 trapping during PARPi treatment. The stable KAT6A-PARP1-APEX1 complex reduces the amount of PARP1 trapped at the DNA break sites. In addition, inhibition of KAT6A LLPS, rather than its catalytic activity, impairs DNA damage repair and restores PARPi sensitivity in ovarian cancer both in vivo and in vitro. In conclusion, the findings demonstrate the role of KAT6A LLPS in fostering PARPi resistance and suggest that repressing KAT6A LLPS can be a potential therapeutic strategy for PARPi-resistant ovarian cancer.
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Affiliation(s)
- Zhiyan Zhan
- Department of Clinical Nutrition, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Clinical Research Center, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jiarong Zhang
- Department of Obstetrics and Gynecology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Huisheng Liang
- Department of Gynecology, Zhongshan Hospital, Fudan University (Xiamen Branch), Xiamen, 361000, China
| | - Chong Wang
- Department of Obstetrics and Gynecology, Shanghai General Hospital, School of Medicine, Shanghai Jiao Tong University, 85 Wujin Road, Shanghai, 200080, China
| | - Li Hong
- Department of Clinical Nutrition, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- Clinical Research Center, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Wenxue Liu
- Department of Obstetrics and Gynecology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
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3
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Zhang X, Yu D, Tang P, Chen F. Insights into the role of mitophagy in lung cancer: current evidence and perspectives. Front Pharmacol 2024; 15:1420643. [PMID: 38962310 PMCID: PMC11220236 DOI: 10.3389/fphar.2024.1420643] [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: 04/20/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024] Open
Abstract
Lung cancer, recognized globally as a leading cause of malignancy-associated morbidity and mortality, is marked by its high prevalence and lethality, garnering extensive attention within the medical community. Mitophagy is a critical cellular process that plays a crucial role in regulating metabolism and ensuring quality control within cells. Its relevance to lung cancer has garnered significant attention among researchers and scientists. Mitophagy's involvement in lung cancer encompasses its initiation, progression, metastatic dissemination and treatment. The regulatory landscape of mitophagy is complex, involving numerous signaling proteins and pathways that may exhibit aberrant alterations or mutations within the tumor environment. In the field of treatment, the regulation of mitophagy is considered key to determining cancer chemotherapy, radiation therapy, other treatment options, and drug resistance. Contemporary investigations are directed towards harnessing mitophagy modulators, both inhibitors and activators, in therapeutic strategies, with an emphasis on achieving specificity to minimize collateral damage to healthy cellular populations. Furthermore, molecular constituents and pathways affiliated with mitophagy, serving as potential biomarkers, offer promising avenues for enhancing diagnostic accuracy, prognostic assessment, and prediction of therapeutic responses in lung cancer. Future endeavors will also involve investigating the impact of mitophagy on the composition and function of immune cells within the tumor microenvironment, aiming to enhance our understanding of how mitophagy modulates the immune response to lung cancer. This review aims to comprehensively overview recent advancements about the role of mitophagy in the tumor genesis, progenesis and metastasis, and the impact of mitophagy on the treatment of lung cancer. We also discussed the future research direction of mitophagy in the field of lung cancer.
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Affiliation(s)
- Xin Zhang
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Dongzhi Yu
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Peng Tang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Fengshou Chen
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, Liaoning, China
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4
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Vemulapalli S, Hashemi M, Chen Y, Pramanik S, Bhakat KK, Lyubchenko YL. Nanoscale Interaction of Endonuclease APE1 with DNA. Int J Mol Sci 2024; 25:5145. [PMID: 38791183 PMCID: PMC11121393 DOI: 10.3390/ijms25105145] [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: 03/18/2024] [Revised: 04/17/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is involved in DNA repair and transcriptional regulation mechanisms. This multifunctional activity of APE1 should be supported by specific structural properties of APE1 that have not yet been elucidated. Herein, we applied atomic force microscopy (AFM) to characterize the interactions of APE1 with DNA containing two well-separated G-rich segments. Complexes of APE1 with DNA containing G-rich segments were visualized, and analysis of the complexes revealed the affinity of APE1 to G-rich DNA sequences, and their yield was as high as 53%. Furthermore, APE1 is capable of binding two DNA segments leading to the formation of loops in the DNA-APE1 complexes. The analysis of looped APE1-DNA complexes revealed that APE1 can bridge G-rich segments of DNA. The yield of loops bridging two G-rich DNA segments was 41%. Analysis of protein size in various complexes was performed, and these data showed that loops are formed by APE1 monomer, suggesting that APE1 has two DNA binding sites. The data led us to a model for the interaction of APE1 with DNA and the search for the specific sites. The implication of these new APE1 properties in organizing DNA, by bringing two distant sites together, for facilitating the scanning for damage and coordinating repair and transcription is discussed.
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Affiliation(s)
- Sridhar Vemulapalli
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA; (S.V.); (M.H.)
| | - Mohtadin Hashemi
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA; (S.V.); (M.H.)
- Department of Physics, Auburn University, Auburn, AL 36849-5318, USA
| | - Yingling Chen
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198-5805, USA; (Y.C.); (S.P.)
| | - Suravi Pramanik
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198-5805, USA; (Y.C.); (S.P.)
| | - Kishor K. Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198-5805, USA; (Y.C.); (S.P.)
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA; (S.V.); (M.H.)
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5
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Zhang YW, Wang SM, Li XQ, Kang B, Chen HY, Xu JJ. Endogenous AND Logic DNA Nanomachine for Highly Specific Cancer Cell Imaging. Anal Chem 2024; 96:7030-7037. [PMID: 38656919 DOI: 10.1021/acs.analchem.4c00211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Intracellular cancer-related biomarker imaging strategy has been used for specific identification of cancer cells, which was of great importance to accurate cancer clinical diagnosis and prognosis studies. Localized DNA circuits with improved sensitivity showed great potential for intracellular biomarkers imaging. However, the ability of localized DNA circuits to specifically image cancer cells is limited by off-site signal leakage associated with a single-biomarker sensing strategy. Herein, we integrated the endogenous enzyme-powered strategy with logic-responsive and localized signal amplifying capability to construct a self-assembled endogenously AND logic DNA nanomachine (EDN) for highly specific cancer cell imaging. When the EDN encountered a cancer cell, the overexpressed DNA repairing enzyme apurinic/apyrimidinic endonuclease 1 (APE1) and miR-21 could synergistically activate a DNA circuit via cascaded localized toehold-mediated strand displacement (TMSD) reactions, resulting in amplified fluorescence resonance energy transfer (FRET) signal. In this strategy, both endogenous APE1 and miR-21, served as two "keys" to activate the AND logic operation in cancer cells to reduce off-tumor signal leakage. Such a multiplied molecular recognition/activation nanomachine as a powerful toolbox realized specific capture and reliable imaging of biomolecules in living cancer cells.
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Affiliation(s)
- Yu-Wen Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shu-Min Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiao-Qiong Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Bin Kang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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6
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Du Y, Zhou Y, Yan X, Pan F, He L, Guo Z, Hu Z. APE1 inhibition enhances ferroptotic cell death and contributes to hepatocellular carcinoma therapy. Cell Death Differ 2024; 31:431-446. [PMID: 38418695 PMCID: PMC11043431 DOI: 10.1038/s41418-024-01270-0] [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: 08/03/2023] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 03/02/2024] Open
Abstract
Ferroptosis, a regulated form of cell death triggered by iron-dependent lipid peroxidation, has emerged as a promising therapeutic strategy for cancer treatment, particularly in hepatocellular carcinoma (HCC). However, the mechanisms underlying the regulation of ferroptosis in HCC remain to be unclear. In this study, we have identified a novel regulatory pathway of ferroptosis involving the inhibition of Apurinic/apyrimidinic endonuclease 1 (APE1), a key enzyme with dual functions in DNA repair and redox regulation. Our findings demonstrate that inhibition of APE1 leads to the accumulation of lipid peroxidation and enhances ferroptosis in HCC. At the molecular level, the inhibition of APE1 enhances ferroptosis which relies on the redox activity of APE1 through the regulation of the NRF2/SLC7A11/GPX4 axis. We have identified that both genetic and chemical inhibition of APE1 increases AKT oxidation, resulting in an impairment of AKT phosphorylation and activation, which leads to the dephosphorylation and activation of GSK3β, facilitating the subsequent ubiquitin-proteasome-dependent degradation of NRF2. Consequently, the downregulation of NRF2 suppresses SLC7A11 and GPX4 expression, triggering ferroptosis in HCC cells and providing a potential therapeutic approach for ferroptosis-based therapy in HCC. Overall, our study uncovers a novel role and mechanism of APE1 in the regulation of ferroptosis and highlights the potential of targeting APE1 as a promising therapeutic strategy for HCC and other cancers.
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Affiliation(s)
- Yu Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Yu Zhou
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Xinyu Yan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
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7
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Wu S, Chen Y, Chen Z, Wei F, Zhou Q, Li P, Gu Q. Reactive oxygen species and gastric carcinogenesis: The complex interaction between Helicobacter pylori and host. Helicobacter 2023; 28:e13024. [PMID: 37798959 DOI: 10.1111/hel.13024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/10/2023] [Accepted: 09/21/2023] [Indexed: 10/07/2023]
Abstract
Helicobacter pylori (H. pylori) is a highly successful human pathogen that colonizes stomach in around 50% of the global population. The colonization of bacterium induces an inflammatory response and a substantial rise in the production of reactive oxygen species (ROS) and reactive nitrogen species (RNS), mostly derived from host neutrophils and gastric epithelial cells, which play a crucial role in combating bacterial infections. However, H. pylori has developed various strategies to quench the deleterious effects of ROS, including the production of antioxidant enzymes, antioxidant proteins as well as blocking the generation of oxidants. The host's inability to eliminate H. pylori infection results in persistent ROS production. Notably, excessive ROS can disrupt the intracellular signal transduction and biological processes of the host, incurring chronic inflammation and cellular damage, such as DNA damage, lipid peroxidation, and protein oxidation. Markedly, the sustained inflammatory response and oxidative stress during H. pylori infection are major risk factor for gastric carcinogenesis. In this context, we summarize the literature on H. pylori infection-induced ROS production, the strategies used by H. pylori to counteract the host response, and subsequent host damage and gastric carcinogenesis.
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Affiliation(s)
- Shiying Wu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Yongqiang Chen
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Ziqi Chen
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Fangtong Wei
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Qingqing Zhou
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Ping Li
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Qing Gu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
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Das D, Duncton MAJ, Georgiadis TM, Pellicena P, Clark J, Sobol RW, Georgiadis MM, King-Underwood J, Jobes DV, Chang C, Gao Y, Deacon AM, Wilson DM. A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1. Int J Mol Sci 2023; 24:16637. [PMID: 38068959 PMCID: PMC10706420 DOI: 10.3390/ijms242316637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM ("SAR by X-ray Poses Quickly") platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or "undruggable" targets, allows for (i) hit generation; (ii) the mapping of protein-ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.
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Affiliation(s)
- Debanu Das
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | | | | | | | - Jennifer Clark
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
- Department of Pathology & Laboratory Medicine, Warrant Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Millie M. Georgiadis
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - David V. Jobes
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Mid-Atlantic BioTherapeutics, Inc., Doylestown, PA 18902, USA
| | - Caleb Chang
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Yang Gao
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Ashley M. Deacon
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | - David M. Wilson
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Biomedical Research Institute, Hasselt University, 3500 Diepenbeek, Belgium
- Belgium & Boost Scientific, 3550 Heusden-Zolder, Belgium
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9
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Zhou J, Wei Z, Yang C, Jia D, Pan B, Zeng Y, Sun D, Yu Y. APE1 promotes radiation resistance against radiation-induced pyroptosis by inhibiting the STING pathway in lung adenocarcinoma. Transl Oncol 2023; 36:101749. [PMID: 37544034 PMCID: PMC10424251 DOI: 10.1016/j.tranon.2023.101749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023] Open
Abstract
Mammalian apurinic/apyrimidinic endonuclease 1 (APE1, APEX1) is a multifunctional enzyme that maintains cellular homeostasis. It is involved in the base excision repair (BER) pathway and plays a key role in radiation-induced DNA damage response. However, the relationship between APE1-driven radiation resistance and pyroptosis in lung adenocarcinoma (LUAD) cells and the underlying molecular mechanisms remain unclear. We found that APE1 was significantly upregulated in LUAD tissues compared to para-carcinoma tissues and promoted the proliferation and invasion of LUAD cells in vitro and in vivo. Mechanistically, APE1 inhibited pyroptosis by inactivating the interferon gene stimulator (STING) pathway via direct interaction with AIM2 and DDX41, as detected by RNA-seq and co-immunoprecipitation. APE1 protects LUAD cells against radiation-induced damage and induces radio-resistance by targeting the STING pathway. It can induce pyroptosis and is negatively regulated by interactions with AIM2 and DDX41. Therefore, APE1 inhibitors should be considered to enhance the radiosensitivity of LUAD cells and improve patient prognosis and therapeutic outcomes. Thus, APE1 play a role in the tumor immune microenvironment and in tumor immunotherapy.
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Affiliation(s)
- Jing Zhou
- Department of Radiation Oncology, Harbin Medical University Cancer Hospital, Harbin 150040, China
| | - Zixin Wei
- Department of Medical Oncology, Sichuan Cancer Hospital, Chengdu 610042, China
| | - Chuan Yang
- Department of Gastroenterology, Heilongjiang Provincial Hospital, Harbin 150001, China
| | - Dexin Jia
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Nangang District, Harbin 150040, China
| | - Bo Pan
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Nangang District, Harbin 150040, China
| | - Yuan Zeng
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Nangang District, Harbin 150040, China
| | - Di Sun
- Department of Radiotherapy Technology Center, Harbin Medical University Cancer Hospital, Harbin 150040, China
| | - Yan Yu
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Nangang District, Harbin 150040, China.
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10
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Raungrut P, Tanyapattrapong S, Jirapongsak J, Geater SL, Thongsuksai P. Predictive and Prognostic Value of TUBB3, RRM1, APE1, and Survivin Expression in Chemotherapy-Receiving Patients with Advanced Non‑Small Cell Lung Cancer. Asian Pac J Cancer Prev 2023; 24:3003-3013. [PMID: 37774051 PMCID: PMC10762756 DOI: 10.31557/apjcp.2023.24.9.3003] [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: 02/02/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND This study aimed to evaluate the expression of class III β-tubulin (TUBB3), ribonucleoside-diphosphate reductase 1 (RRM1), apurinic/apyrimidinic endonuclease 1 (APE1), and survivin in patients with advanced non-small cell lung cancer (NSCLC) to predict response to chemotherapy. METHODS TUBB3, RRM1, APE1, and survivin expression levels were determined using immunohistochemistry. Protein expression was validated in Car/Pac-resistant human H1792 and A549 cells. This study included 86 patients, among whom 34 received cisplatin (Cis)/gemcitabine (Gem) and 52 received carboplatin (Car)/paclitaxel (Pac). RESULTS Patients with low TUBB3 expression and high RRM1 and survivin expression had higher response rates than those with low RRM1 and survivin expression and high TUBB3 expression in the Car/Pac regimen. The multivariate analysis indicated that TUBB3 and RRM1 were significant independent predictive biomarkers for the Car/Pac regimen; however, there was no association between any protein and overall response in patients treated with this regimen. In the Cis/Gem regimen, only high TUBB3 expression was associated with poor overall survival; however, it did not exhibit a prognostic ability. CONCLUSION The expression levels of TUBB3 and RRM1 in NSCLC cells are potential predictive biomarkers, but not prognostic factors, of response to chemotherapy in patients with NSCLC receiving the Car/Pac regimen.
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Affiliation(s)
- Pritsana Raungrut
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkhla University, Hat Yai, Songkhla, Thailand.
| | - Suchanan Tanyapattrapong
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkhla University, Hat Yai, Songkhla, Thailand.
| | - Jirapon Jirapongsak
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkhla University, Hat Yai, Songkhla, Thailand.
| | - Sarayut Lucien Geater
- Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand.
| | - Paramee Thongsuksai
- Department of Pathology, Faculty of Medicine, Prince of Songkhla University, Hat Yai, Songkhla, Thailand.
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11
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Hoitsma NM, Norris J, Khoang TH, Kaushik V, Chadda R, Antony E, Hedglin M, Freudenthal BD. Mechanistic insight into AP-endonuclease 1 cleavage of abasic sites at stalled replication fork mimics. Nucleic Acids Res 2023; 51:6738-6753. [PMID: 37264933 PMCID: PMC10359615 DOI: 10.1093/nar/gkad481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/13/2023] [Accepted: 05/31/2023] [Indexed: 06/03/2023] Open
Abstract
Many types of damage, including abasic sites, block replicative DNA polymerases causing replication fork uncoupling and generating ssDNA. AP-Endonuclease 1 (APE1) has been shown to cleave abasic sites in ssDNA. Importantly, APE1 cleavage of ssDNA at a replication fork has significant biological implications by generating double strand breaks that could collapse the replication fork. Despite this, the molecular basis and efficiency of APE1 processing abasic sites at replication forks remain elusive. Here, we investigate APE1 cleavage of abasic substrates that mimic APE1 interactions at stalled replication forks or gaps. We determine that APE1 has robust activity on these substrates, like dsDNA, and report rates for cleavage and product release. X-ray structures visualize the APE1 active site, highlighting an analogous mechanism is used to process ssDNA substrates as canonical APE1 activity on dsDNA. However, mutational analysis reveals R177 to be uniquely critical for the APE1 ssDNA cleavage mechanism. Additionally, we investigate the interplay between APE1 and Replication Protein A (RPA), the major ssDNA-binding protein at replication forks, revealing that APE1 can cleave an abasic site while RPA is still bound to the DNA. Together, this work provides molecular level insights into abasic ssDNA processing by APE1, including the presence of RPA.
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Affiliation(s)
- Nicole M Hoitsma
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jessica Norris
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Thu H Khoang
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Mark Hedglin
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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12
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Malfatti MC, Bellina A, Antoniali G, Tell G. Revisiting Two Decades of Research Focused on Targeting APE1 for Cancer Therapy: The Pros and Cons. Cells 2023; 12:1895. [PMID: 37508559 PMCID: PMC10378182 DOI: 10.3390/cells12141895] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
APE1 is an essential endodeoxyribonuclease of the base excision repair pathway that maintains genome stability. It was identified as a pivotal factor favoring tumor progression and chemoresistance through the control of gene expression by a redox-based mechanism. APE1 is overexpressed and serum-secreted in different cancers, representing a prognostic and predictive factor and a promising non-invasive biomarker. Strategies directly targeting APE1 functions led to the identification of inhibitors showing potential therapeutic value, some of which are currently in clinical trials. Interestingly, evidence indicates novel roles of APE1 in RNA metabolism that are still not fully understood, including its activity in processing damaged RNA in chemoresistant phenotypes, regulating onco-miRNA maturation, and oxidized RNA decay. Recent data point out a control role for APE1 in the expression and sorting of onco-miRNAs within secreted extracellular vesicles. This review is focused on giving a portrait of the pros and cons of the last two decades of research aiming at the identification of inhibitors of the redox or DNA-repair functions of APE1 for the definition of novel targeted therapies for cancer. We will discuss the new perspectives in cancer therapy emerging from the unexpected finding of the APE1 role in miRNA processing for personalized therapy.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Alessia Bellina
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
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13
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Muniyandi A, Hartman GD, Song Y, Mijit M, Kelley MR, Corson TW. Beyond VEGF: Targeting Inflammation and Other Pathways for Treatment of Retinal Disease. J Pharmacol Exp Ther 2023; 386:15-25. [PMID: 37142441 PMCID: PMC10289243 DOI: 10.1124/jpet.122.001563] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 03/17/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Neovascular eye diseases include conditions such as retinopathy of prematurity, proliferative diabetic retinopathy, and neovascular age-related macular degeneration. Together, they are a major cause of vision loss and blindness worldwide. The current therapeutic mainstay for these diseases is intravitreal injections of biologics targeting vascular endothelial growth factor (VEGF) signaling. Lack of universal response to these anti-VEGF agents coupled with the challenging delivery method underscore a need for new therapeutic targets and agents. In particular, proteins that mediate both inflammatory and proangiogenic signaling are appealing targets for new therapeutic development. Here, we review agents currently in clinical trials and highlight some promising targets in preclinical and early clinical development, focusing on the redox-regulatory transcriptional activator APE1/Ref-1, the bioactive lipid modulator soluble epoxide hydrolase, the transcription factor RUNX1, and others. Small molecules targeting each of these proteins show promise for blocking neovascularization and inflammation. The affected signaling pathways illustrate the potential of new antiangiogenic strategies for posterior ocular disease. SIGNIFICANCE STATEMENT: Discovery and therapeutic targeting of new angiogenesis mediators is necessary to improve treatment of blinding eye diseases like retinopathy of prematurity, diabetic retinopathy, and neovascular age-related macular degeneration. Novel targets undergoing evaluation and drug discovery work include proteins important for both angiogenesis and inflammation signaling, including APE1/Ref-1, soluble epoxide hydrolase, RUNX1, and others.
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Affiliation(s)
- Anbukkarasi Muniyandi
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Gabriella D Hartman
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Yang Song
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Mahmut Mijit
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Mark R Kelley
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Timothy W Corson
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute (A.M., G.D.H., Y.S., M.R.K., T.W.C.), Department of Pediatrics, Herman B Wells Center for Pediatric Research (M.M., M.R.K.), Stark Neurosciences Research Institute (G.D.H., T.W.C.), Departments of Pharmacology and Toxicology (M.R.K., T.W.C.) and Biochemistry and Molecular Biology (M.R.K., T.W.C.), and Melvin and Bren Simon Comprehensive Cancer Center (M.R.K., T.W.C.), Indiana University School of Medicine, Indianapolis, Indiana
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14
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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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15
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Wu Z, Liu Z, Sun Y, Yuan Y, Zou Q, Wen Y, Luo J, Liu R. APEX1 predicts poor prognosis of gallbladder cancer and affects biological properties of CD133 + GBC-SD cells via upregulating Jagged1. J Cancer 2023; 14:1443-1457. [PMID: 37283798 PMCID: PMC10240672 DOI: 10.7150/jca.83356] [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: 02/09/2023] [Accepted: 04/12/2023] [Indexed: 06/08/2023] Open
Abstract
Although APEX1 is associated with the tumorigenesis and progression of some human cancer types, the function of APEX1 in gallbladder cancer (GBC) is unclear. In this study, we found that APEX1 expression is up-regulated in GBC tissues, and APEX1 positive expression is related to aggressive clinicopathological features and poor prognosis of GBC. APEX1 was an independent risk factor of GBC prognosis, and presented some pathological diagnostic significance in GBC. Furthermore, APEX1 was overexpressed in CD133+ GBC-SD cells in comparison with GBC-SD cells. APEX1 knockdown increased the sensitivity of CD133+ GBC-SD cells to 5-Fluorouracil via facilitating cell necrosis and apoptosis. APEX1 knockdown in CD133+ GBC-SD cells dramatically inhibited cell proliferation, migration, and invasion, and promoted cell apoptosis in vitro. APEX1 knockdown in CD133+ GBC-SD cells accelerated tumor growth in the xenograft models. Mechanistically, APEX1 affected these malignant properties via upregulating Jagged1 in CD133+ GBC-SD cells. Thus, APEX1 is a promising prognostic biomarker, and a potential therapeutic target for GBC.
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Affiliation(s)
- Zhengchun Wu
- Department of Hepatobiliary and Intestinal Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan410013, China
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan410011, China
| | - Ziru Liu
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan410011, China
| | - Yi Sun
- Department of Pathology, Second Xiangya Hospital, Central South University, Changsha, Hunan410011, China
| | - Yuan Yuan
- Department of Pathology, Third Xiangya Hospital, Central South University, Changsha, Hunan410013, China
| | - Qiong Zou
- Department of Pathology, Third Xiangya Hospital, Central South University, Changsha, Hunan410013, China
| | - Yun Wen
- Department of General Surgery, Second Xiangya Hospital, Central South University, Changsha, Hunan410011, China
| | - Jia Luo
- Department of Hepatobiliary and Intestinal Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan410013, China
| | - Rushi Liu
- Laboratory of Medical Molecular and Immunological Diagnostics, School of medicine, Hunan Normal University, Changsha, Hunan 410013, China
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16
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Jaiswal AS, Kim HS, Schärer OD, Sharma N, Williamson E, Srinivasan G, Phillips L, Kong K, Arya S, Misra A, Dutta A, Gupta Y, Walter C, Burma S, Narayan S, Sung P, Nickoloff J, Hromas R. EEPD1 promotes repair of oxidatively-stressed replication forks. NAR Cancer 2023; 5:zcac044. [PMID: 36683914 PMCID: PMC9846428 DOI: 10.1093/narcan/zcac044] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/22/2022] [Accepted: 12/14/2022] [Indexed: 01/19/2023] Open
Abstract
Unrepaired oxidatively-stressed replication forks can lead to chromosomal instability and neoplastic transformation or cell death. To meet these challenges cells have evolved a robust mechanism to repair oxidative genomic DNA damage through the base excision repair (BER) pathway, but less is known about repair of oxidative damage at replication forks. We found that depletion or genetic deletion of EEPD1 decreases clonogenic cell survival after oxidative DNA damage. We demonstrate that EEPD1 is recruited to replication forks stressed by oxidative damage induced by H2O2 and that EEPD1 promotes replication fork repair and restart and decreases chromosomal abnormalities after such damage. EEPD1 binds to abasic DNA structures and promotes resolution of genomic abasic sites after oxidative stress. We further observed that restoration of expression of EEPD1 via expression vector transfection restores cell survival and suppresses chromosomal abnormalities induced by oxidative stress in EEPD1-depleted cells. Consistent with this, we found that EEPD1 preserves replication fork integrity by preventing oxidatively-stressed unrepaired fork fusion, thereby decreasing chromosome instability and mitotic abnormalities. Our results indicate a novel role for EEPD1 in replication fork preservation and maintenance of chromosomal stability during oxidative stress.
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Affiliation(s)
- Aruna S Jaiswal
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Hyun-Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Elizabeth A Williamson
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Gayathri Srinivasan
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Linda Phillips
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Kimi Kong
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Shailee Arya
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Anurag Misra
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Arijit Dutta
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Yogesh Gupta
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Christi A Walter
- Department of Cell Systems and Anatomy, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Sandeep Burma
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
- Department of Neurosurgery, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Satya Narayan
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, FL 32610, USA
| | - Patrick Sung
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Jac A Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX 78229, USA
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17
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Bakman AS, Kuznetsova AA, Yanshole LV, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. Fluorescently labeled human apurinic/apyrimidinic endonuclease APE1 reveals effects of DNA polymerase β on the APE1-DNA interaction. DNA Repair (Amst) 2023; 123:103450. [PMID: 36689867 DOI: 10.1016/j.dnarep.2023.103450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 12/26/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
The base excision repair (BER) pathway involves sequential action of DNA glycosylases and apurinic/apyrimidinic (AP) endonucleases to incise damaged DNA and prepare DNA termini for incorporation of a correct nucleotide by DNA polymerases. It has been suggested that the enzymatic steps in BER include recognition of a product-enzyme complex by the next enzyme in the pathway, resulting in the "passing-the-baton" model of transfer of DNA intermediates between enzymes. To verify this model, in this work, we aimed to create a suitable experimental system. We prepared APE1 site-specifically labeled with a fluorescent reporter that is sensitive to stages of APE1-DNA binding, of formation of the catalytic complex, and of subsequent dissociation of the enzyme-product complex. Interactions of the labeled APE1 with various model DNA substrates (containing an abasic site) of varied lengths revealed that the enzyme remains mostly in complex with the DNA product. By means of the fluorescently labeled APE1 in combination with a stopped-flow fluorescence assay, it was found that Polβ stimulates both i) APE1 binding to an abasic-site-containing DNA duplex with the formation of a catalytically competent complex and ii) the dissociation of APE1 from its product. These findings confirm DNA-mediated coordination of APE1 and Polβ activities and suggest that Polβ is the key trigger of the DNA transfer between the enzymes participating in initial steps of BER.
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Affiliation(s)
- Artemiy S Bakman
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Aleksandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Lyudmila V Yanshole
- International Tomography Center SB RAS, 3a Institutskaya Str., Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Group "Mechanisms of DNA Repair and Carcinogenesis", Gustave Roussy Cancer Campus, CNRS UMR9019, Université Paris-Saclay, 94805 Villejuif, France
| | - Murat Saparbaev
- Group "Mechanisms of DNA Repair and Carcinogenesis", Gustave Roussy Cancer Campus, CNRS UMR9019, Université Paris-Saclay, 94805 Villejuif, France; NCJSC "Al-Farabi Kazakh National University" Almaty, Kazakhstan
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia.
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18
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Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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19
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Tarpley M, Chen Y, Bhakat KK. Genome-Wide Binding Analysis of DNA Repair Protein APE1 in Tumor Cells by ChIP-Seq. Methods Mol Biol 2023; 2701:243-252. [PMID: 37574487 DOI: 10.1007/978-1-0716-3373-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The base excision repair (BER) is the primary damage repair pathway for repairing most of the endogenous DNA damage including oxidative base lesions, apurinic/apyrimidinic (AP) sites, and single-strand breaks (SSBs) in the genome. Repair of these damages in cells relies on sequential recruitment and coordinated actions of multiple DNA repair enzymes, which include DNA glycosylases (such as OGG1), AP-endonucleases (APE1), DNA polymerases, and DNA ligases. APE1 plays a key role in the BER pathway by repairing the AP sites and SSBs in the genome. Several methods have been developed to generate a map of endogenous AP sites or SSBs in the genome and the binding of DNA repair proteins. In this chapter, we describe detailed approaches to map genome-wide occupancy or enrichment of APE1 in human cells using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq). Further, we discuss standard bioinformatics approaches for analyzing ChIP-seq data to identify APE1 enrichment or binding peaks in the genome.
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Affiliation(s)
- Mason Tarpley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yingling Chen
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
- Fred and Pamela Buffett Cancer Center, Omaha, NE, USA.
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20
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Pidugu LS, Servius HW, Sevdalis SE, Cook ME, Varney KM, Pozharski E, Drohat AC. Characterizing inhibitors of human AP endonuclease 1. PLoS One 2023; 18:e0280526. [PMID: 36652434 PMCID: PMC9847973 DOI: 10.1371/journal.pone.0280526] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
AP endonuclease 1 (APE1) processes DNA lesions including apurinic/apyrimidinic sites and 3´-blocking groups, mediating base excision repair and single strand break repair. Much effort has focused on developing specific inhibitors of APE1, which could have important applications in basic research and potentially lead to clinical anticancer agents. We used structural, biophysical, and biochemical methods to characterize several reported inhibitors, including 7-nitroindole-2-carboxylic acid (CRT0044876), given its small size, reported potency, and widespread use for studying APE1. Intriguingly, NMR chemical shift perturbation (CSP) experiments show that CRT0044876 and three similar indole-2-carboxylic acids bind a pocket distal from the APE1 active site. A crystal structure confirms these findings and defines the pose for 5-nitroindole-2-carboxylic acid. However, dynamic light scattering experiments show the indole compounds form colloidal aggregates that could bind (sequester) APE1, causing nonspecific inhibition. Endonuclease assays show the compounds lack significant APE1 inhibition under conditions (detergent) that disrupt aggregation. Thus, binding of the indole-2-carboxylic acids at the remote pocket does not inhibit APE1 repair activity. Myricetin also forms aggregates and lacks APE1 inhibition under aggregate-disrupting conditions. Two other reported compounds (MLS000552981, MLS000419194) inhibit APE1 in vitro with low micromolar IC50 and do not appear to aggregate in this concentration range. However, NMR CSP experiments indicate the compounds do not bind specifically to apo- or Mg2+-bound APE1, pointing to a non-specific mode of inhibition, possibly DNA binding. Our results highlight methods for rigorous interrogation of putative APE1 inhibitors and should facilitate future efforts to discover compounds that specifically inhibit this important repair enzyme.
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Affiliation(s)
- Lakshmi S. Pidugu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hardler W. Servius
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Spiridon E. Sevdalis
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Mary E. Cook
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Kristen M. Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- * E-mail: (EP); (ACD)
| | - Alexander C. Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (EP); (ACD)
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21
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Laverde EE, Polyzos AA, Tsegay PP, Shaver M, Hutcheson JD, Balakrishnan L, McMurray CT, Liu Y. Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair. Genes (Basel) 2022; 14:genes14010098. [PMID: 36672839 PMCID: PMC9859040 DOI: 10.3390/genes14010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3'-5' exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity.
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Affiliation(s)
- Eduardo E. Laverde
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Aris A. Polyzos
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pawlos P. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Mohammad Shaver
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA
| | - Joshua D. Hutcheson
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana-Purdue University, Indianapolis, IN 46202, USA
| | - Cynthia T. McMurray
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Correspondence:
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22
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Moazamian A, Gharagozloo P, Aitken RJ, Drevet JR. OXIDATIVE STRESS AND REPRODUCTIVE FUNCTION: Sperm telomeres, oxidative stress, and infertility. Reproduction 2022; 164:F125-F133. [PMID: 35938805 DOI: 10.1530/rep-22-0189] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 08/05/2022] [Indexed: 11/08/2022]
Abstract
In brief Oxidative stress is recognized as an underlying driving factor of both telomere dysfunction and human subfertility/infertility. This review briefly reassesses telomere integrity as a fertility biomarker before proposing a novel, mechanistic rationale for the role of oxidative stress in the seemingly paradoxical lengthening of sperm telomeres with aging. Abstract The maintenance of redox balance in the male reproductive tract is critical to sperm health and function. Physiological levels of reactive oxygen species (ROS) promote sperm capacitation, while excess ROS exposure, or depleted antioxidant defenses, yields a state of oxidative stress which disrupts their fertilizing capacity and DNA structural integrity. The guanine moiety is the most readily oxidized of the four DNA bases and gets converted to the mutagenic lesion 8-hydroxy-deoxyguanosine (8-OHdG). Numerous studies have also confirmed oxidative stress as a driving factor behind accelerated telomere shortening and dysfunction. Although a clear consensus has not been reached, clinical studies also appear to associate telomere integrity with fertility outcomes in the assisted reproductive technology setting. Intriguingly, while sperm cellular and molecular characteristics make them more susceptible to oxidative insult than any other cell type, they are also the only cell type in which telomere lengthening accompanies aging. This article focuses on the oxidative stress response pathways to propose a mechanism for the explanation of this apparent paradox.
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Affiliation(s)
- Aron Moazamian
- CellOxess LLC, Ewing, New Jersey, USA.,Université Clermont Auvergne, GReD Institute, CNRS-INSERM, Clermont-Ferrand, France
| | | | - Robert J Aitken
- Priority Research Centre for Reproductive Science, University of Newcastle, Callaghan, New South Wales, Australia
| | - Joël R Drevet
- Université Clermont Auvergne, GReD Institute, CNRS-INSERM, Clermont-Ferrand, France
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23
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Li C, Xue Y, Ba X, Wang R. The Role of 8-oxoG Repair Systems in Tumorigenesis and Cancer Therapy. Cells 2022; 11:cells11233798. [PMID: 36497058 PMCID: PMC9735852 DOI: 10.3390/cells11233798] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/09/2022] [Accepted: 11/25/2022] [Indexed: 11/29/2022] Open
Abstract
Tumorigenesis is highly correlated with the accumulation of mutations. The abundant and extensive DNA oxidation product, 8-Oxoguanine (8-oxoG), can cause mutations if it is not repaired by 8-oxoG repair systems. Therefore, the accumulation of 8-oxoG plays an essential role in tumorigenesis. To avoid the accumulation of 8-oxoG in the genome, base excision repair (BER), initiated by 8-oxoguanine DNA glycosylase1 (OGG1), is responsible for the removal of genomic 8-oxoG. It has been proven that 8-oxoG levels are significantly elevated in cancer cells compared with cells of normal tissues, and the induction of DNA damage by some antitumor drugs involves direct or indirect interference with BER, especially through inducing the production and accumulation of reactive oxygen species (ROS), which can lead to tumor cell death. In addition, the absence of the core components of BER can result in embryonic or early post-natal lethality in mice. Therefore, targeting 8-oxoG repair systems with inhibitors is a promising avenue for tumor therapy. In this study, we summarize the impact of 8-oxoG accumulation on tumorigenesis and the current status of cancer therapy approaches exploiting 8-oxoG repair enzyme targeting, as well as possible synergistic lethality strategies involving exogenous ROS-inducing agents.
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Affiliation(s)
- Chunshuang Li
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China
- The Key Laboratory of Molecular Epigenetics of Education, School of Life Science, Northeast Normal University, Changchun 130024, China
| | - Yaoyao Xue
- The Key Laboratory of Molecular Epigenetics of Education, School of Life Science, Northeast Normal University, Changchun 130024, China
| | - Xueqing Ba
- The Key Laboratory of Molecular Epigenetics of Education, School of Life Science, Northeast Normal University, Changchun 130024, China
- Correspondence: (X.B.); (R.W.)
| | - Ruoxi Wang
- Center for Cell Structure and Function, Key Laboratory of Animal Resistance Biology of Shandong Province, College of Life Sciences, Shandong Normal University, Jinan 250014, China
- Correspondence: (X.B.); (R.W.)
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24
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Li J, Zhao H, McMahon A, Yan S. APE1 assembles biomolecular condensates to promote the ATR-Chk1 DNA damage response in nucleolus. Nucleic Acids Res 2022; 50:10503-10525. [PMID: 36200829 PMCID: PMC9561277 DOI: 10.1093/nar/gkac853] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/14/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Multifunctional protein APE1/APEX1/HAP1/Ref-1 (designated as APE1) plays important roles in nuclease-mediated DNA repair and redox regulation in transcription. However, it is unclear how APE1 regulates the DNA damage response (DDR) pathways. Here we show that siRNA-mediated APE1-knockdown or APE1 inhibitor treatment attenuates the ATR–Chk1 DDR under stress conditions in multiple immortalized cell lines. Congruently, APE1 overexpression (APE1-OE) activates the ATR DDR under unperturbed conditions, which is independent of APE1 nuclease and redox functions. Structural and functional analysis reveals a direct requirement of the extreme N-terminal motif within APE1 in the assembly of distinct biomolecular condensates in vitro and DNA/RNA-independent activation of the ATR DDR. Overexpressed APE1 co-localizes with nucleolar NPM1 and assembles biomolecular condensates in nucleoli in cancer but not non-malignant cells, which recruits ATR and activator molecules TopBP1 and ETAA1. APE1 protein can directly activate ATR to phosphorylate its substrate Chk1 in in vitro kinase assays. W119R mutant of APE1 is deficient in nucleolar condensation, and is incapable of activating nucleolar ATR DDR in cells and ATR kinase in vitro. APE1-OE-induced nucleolar ATR DDR activation leads to compromised ribosomal RNA transcription and reduced cell viability. Taken together, we propose distinct mechanisms by which APE1 regulates ATR DDR pathways.
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Affiliation(s)
- Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - 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, NC 28223, USA
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25
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Miner KM, Jamenis AS, Bhatia TN, Clark RN, Rajasundaram D, Sauvaigo S, Mason DM, Posimo JM, Abraham N, DeMarco BA, Hu X, Stetler RA, Chen J, Sanders LH, Luk KC, Leak RK. α-synucleinopathy exerts sex-dimorphic effects on the multipurpose DNA repair/redox protein APE1 in mice and humans. Prog Neurobiol 2022; 216:102307. [PMID: 35710046 PMCID: PMC9514220 DOI: 10.1016/j.pneurobio.2022.102307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 04/05/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022]
Abstract
Lewy body disorders are characterized by oxidative damage to DNA and inclusions rich in aggregated forms of α-synuclein. Among other roles, apurinic/apyrimidinic endonuclease 1 (APE1) repairs oxidative DNA damage, and APE1 polymorphisms have been linked to cases of Lewy body disorders. However, the link between APE1 and α-synuclein is unexplored. We report that knockdown or inhibition of APE1 amplified inclusion formation in primary hippocampal cultures challenged with preformed α-synuclein fibrils. Fibril infusions into the mouse olfactory bulb/anterior olfactory nucleus (OB/AON) elicited a modest decrease in APE1 expression in the brains of male mice but an increase in females. Similarly, men with Lewy body disorders displayed lower APE1 expression in the OB and amygdala compared to women. Preformed fibril infusions of the mouse OB/AON induced more robust base excision repair of DNA lesions in females than males. No fibril-mediated loss of APE1 expression was observed in male mice when the antioxidant N-acetylcysteine was added to their diet. These findings reveal a potential sex-biased link between α-synucleinopathy and APE1 in mice and humans. Further studies are warranted to determine how this multifunctional protein modifies α-synuclein inclusions and, conversely, how α-synucleinopathy and biological sex interact to modify APE1.
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Affiliation(s)
- Kristin M Miner
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Anuj S Jamenis
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Tarun N Bhatia
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Rachel N Clark
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Rangos Research Center, UPMC Children's Hospital of Pittsburgh, PA 15224, USA
| | | | - Daniel M Mason
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Jessica M Posimo
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Nevil Abraham
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Brett A DeMarco
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA
| | - Xiaoming Hu
- Department of Neurology, University of Pittsburgh, PA 15213, USA
| | - R Anne Stetler
- Department of Neurology, University of Pittsburgh, PA 15213, USA
| | - Jun Chen
- Department of Neurology, University of Pittsburgh, PA 15213, USA
| | - Laurie H Sanders
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kelvin C Luk
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19147, USA
| | - Rehana K Leak
- Graduate School of Pharmaceutical Sciences, Duquesne University, Pittsburgh, PA 15282, USA.
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26
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Tian C, Liang G, Wang C, He R, Ning K, Li Z, Liu R, Ma Y, Guan S, Deng J, Zhai J. Computer simulation and design of DNA-nanoprobe for fluorescence imaging DNA repair enzyme in living cells. Biosens Bioelectron 2022; 211:114360. [DOI: 10.1016/j.bios.2022.114360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/24/2022] [Accepted: 05/08/2022] [Indexed: 11/02/2022]
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27
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Hu Z, Ye W, Zhang Z, Xie T, Yuan W, Wu T. Sensitive detection of abasic sites in double-stranded DNA based on the selective reaction of enzymes. Anal Chim Acta 2022; 1223:340220. [DOI: 10.1016/j.aca.2022.340220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/28/2022]
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28
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Liu J, Liu Y, Zhang L, Fu S, Su X. Ultra-specific fluorescence detection of DNA modifying enzymes by dissipation system. Biosens Bioelectron 2022; 215:114561. [PMID: 35841766 DOI: 10.1016/j.bios.2022.114561] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 12/24/2022]
Abstract
Abnormal expression of DNA modifying enzymes (DMEs) is linked to a variety of diseases including cancers. It is desirable to develop accurate methods for DME detection. However, the substrate-based probe for target DMEs is disturbed by various non-target DMEs that have similar activity resulting in a loss of specificity. Here we utilized dissipative DNA networks to develop an ultra-specific fluorescence assay for DME, absolutely distinguishing between target and non-target enzymes. Unlike the conventional sensors in which the discrimination of target and non-target relies on signal intensity, in our system, target DMEs exhibit featured fluorescence oscillatory signals, while non-target DMEs show irreversible 'one-way' fluorescence increase. These dissipation-enabled probes (DEPs) exhibit excellent generality for various types of DMEs including DNA repair enzyme apurinic/apyrimidinic endonuclease 1 (APE1), polynucleotide kinase (T4 PNK), and methyltransferase (Dam). DEPs provide a novel quantification mode based on area under curve which is more robust than those intensity-based quantifications. The detection limits of APE1, T4 PNK, and Dam reach 0.025 U/mL, 0.44 U/mL, and 0.113 U/mL, respectively. DEPs can accurately identify their corresponding DMEs with excellent specificity in cell extracts. Fluorescence sensors based on DEPs herein represent a conceptually new class of methods for enzyme detection, which can be easily adapted to other sensing platforms such as electrochemical sensors.
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Affiliation(s)
- Jiajia Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yu Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Linghao Zhang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shengnan Fu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Xin Su
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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29
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Yu F, Shao Y, Chai X, Zhao Y, Li L. Spatially Selective Monitoring of Subcellular Enzyme Dynamics in Response to Mitochondria-Targeted Photodynamic Therapy. Angew Chem Int Ed Engl 2022; 61:e202203238. [PMID: 35412703 DOI: 10.1002/anie.202203238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Indexed: 11/10/2022]
Abstract
Tracking spatial and temporal dynamics of bioactive molecules such as enzymes responding to therapeutic treatment is highly important for understanding of the related functions. However, in situ molecular imaging at subcellular level during photodynamic therapy (PDT) has been hampered by the limitations of existing methods. Herein, we present a multifunctional nanoplatform (termed as UR-HAPT) that is able to simultaneously monitor subcellular dynamics of human apurinic/apyrimidinic endonuclease 1 (APE1) during the near-infrared (NIR) light-mediated PDT. UR-HAPT was constructed by the combination of an upconversion nanoparticle-based PDT design and a mitochondria-targeting strategy with an APE1-responsive DNA reporter. Benefiting from the gain-of-function approach, activatable mitochondrial accumulation of APE1 in response to the oxidative stress was observed during the NIR light-triggered, mitochondria-targeted PDT process. We envision that this nanoplatform can be applicable to screen and evaluate potential enzyme inhibitors to improve the PDT efficacy.
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Affiliation(s)
- Fangzhi Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yulei Shao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Xin Chai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China.,Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
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30
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Manils J, Marruecos L, Soler C. Exonucleases: Degrading DNA to Deal with Genome Damage, Cell Death, Inflammation and Cancer. Cells 2022; 11:cells11142157. [PMID: 35883600 PMCID: PMC9316158 DOI: 10.3390/cells11142157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 01/27/2023] Open
Abstract
Although DNA degradation might seem an unwanted event, it is essential in many cellular processes that are key to maintaining genomic stability and cell and organism homeostasis. The capacity to cut out nucleotides one at a time from the end of a DNA chain is present in enzymes called exonucleases. Exonuclease activity might come from enzymes with multiple other functions or specialized enzymes only dedicated to this function. Exonucleases are involved in central pathways of cell biology such as DNA replication, repair, and death, as well as tuning the immune response. Of note, malfunctioning of these enzymes is associated with immune disorders and cancer. In this review, we will dissect the impact of DNA degradation on the DNA damage response and its links with inflammation and cancer.
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Affiliation(s)
- Joan Manils
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, Feixa Llarga s/n, 08907 L’Hospitalet de Llobregat, Spain;
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
| | - Laura Marruecos
- Breast Cancer Laboratory, Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Concepció Soler
- Immunity, Inflammation and Cancer Group, Oncobell Program, Institut d’Investigació Biomèdica de Bellvitge—IDIBELL, 08907 L’Hospitalet de Llobregat, Spain
- Immunology Unit, Department of Pathology and Experimental Therapy, School of Medicine, Universitat de Barcelona, 08007 Barcelona, Spain
- Correspondence:
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31
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Bakman AS, Ishchenko AA, Saparbaev M, Fedorova OS, Kuznetsov NA. Pre-steady-state kinetic and mutational insights into mechanisms of endo- and exonuclease DNA processing by mutant forms of human AP endonuclease. Biochim Biophys Acta Gen Subj 2022; 1866:130198. [PMID: 35809816 DOI: 10.1016/j.bbagen.2022.130198] [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: 03/21/2022] [Revised: 06/09/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022]
Abstract
Human apurinic/apyrimidinic endonuclease APE1 catalyzes endonucleolytic hydrolysis of phosphodiester bonds on the 5' side of structurally unrelated damaged nucleotides in DNA or native nucleotides in RNA. APE1 additionally possesses 3'-5'-exonuclease, 3'-phosphodiesterase, and 3'-phosphatase activities. According to structural data, endo- and exonucleolytic cleavage of DNA is executed in different complexes when the excised residue is everted from the duplex or placed within the intrahelical DNA cavity without nucleotide flipping. In this study, we investigated the functions of residues Arg177, Arg181, Tyr171 and His309 in the APE1 endo- and exonucleolytic reactions. The interaction between residues Arg177 and Met270, which was hypothesized recently to be a switch for endo- and exonucleolytic catalytic mode regulation, was verified by pre-steady-state kinetic analysis of the R177A APE1 mutant. The function of another DNA-binding-site residue, Arg181, was analyzed too; it changed its conformation when enzyme-substrate and enzyme-product complexes were compared. Mutation R181A significantly facilitated the product dissociation stage and only weakly affected DNA-binding affinity. Moreover, R181A reduced the catalytic rate constant severalfold due to a loss of contact with a phosphate group. Finally, the protonation/deprotonation state of residues Tyr171 and His309 in the catalytic reaction was verified by their substitution. Mutations Y171F and H309A inhibited the chemical step of the AP endonucleolytic reaction by several orders of magnitude with retention of capacity for (2R,3S)-2-(hydroxymethyl)-3-hydroxytetrahydrofuran-containing-DNA binding and without changes in the pH dependence profile of AP endonuclease activity, indicating that deprotonation of these residues is likely not important for the catalytic reaction.
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Affiliation(s)
- Artemiy S Bakman
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Alexander A Ishchenko
- Group «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Murat Saparbaev
- Group «Mechanisms of DNA Repair and Carcinogenesis», CNRS UMR9019, Université Paris-Saclay, Gustave Roussy Cancer Campus, F-94805 Villejuif Cedex, France
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia.
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32
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Semlow DR, MacKrell VA, Walter JC. The HMCES DNA-protein cross-link functions as an intermediate in DNA interstrand cross-link repair. Nat Struct Mol Biol 2022; 29:451-462. [PMID: 35534579 PMCID: PMC9949344 DOI: 10.1038/s41594-022-00764-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/28/2022] [Indexed: 12/31/2022]
Abstract
The 5-hydroxymethylcytosine binding, embryonic stem-cell-specific (HMCES) protein forms a covalent DNA-protein cross-link (DPC) with abasic (AP) sites in single-stranded DNA, and the resulting HMCES-DPC is thought to suppress double-strand break formation in S phase. However, the dynamics of HMCES cross-linking and whether any DNA repair pathways normally include an HMCES-DPC intermediate remain unknown. Here, we use Xenopus egg extracts to show that an HMCES-DPC forms on the AP site generated during replication-coupled DNA interstrand cross-link repair. We show that HMCES cross-links form on DNA after the replicative CDC45-MCM2-7-GINS (CMG) helicase has passed over the AP site, and that HMCES is subsequently removed by the SPRTN protease. The HMCES-DPC suppresses double-strand break formation, slows translesion synthesis past the AP site and introduces a bias for insertion of deoxyguanosine opposite the AP site. These data demonstrate that HMCES-DPCs form as intermediates in replication-coupled repair, and they suggest a general model of how HMCES protects AP sites during DNA replication.
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Affiliation(s)
- Daniel R Semlow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Victoria A MacKrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, USA. .,Howard Hughes Medical Institute, Boston, MA, USA.
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33
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Yu F, Shao Y, Chai X, Zhao Y, Li L. Spatially Selective Monitoring of Subcellular Enzyme Dynamics in Response to Mitochondria‐Targeted Photodynamic Therapy. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Fangzhi Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of Sciences Beijing 100049 China
| | - Yulei Shao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Xin Chai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of Sciences Beijing 100049 China
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience National Center for Nanoscience and Technology Beijing 100190 China
- Center of Materials Science and Optoelectronics Engineering University of Chinese Academy of Sciences Beijing 100049 China
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Pramanik S, Chen Y, Song H, Khutsishvili I, Marky LA, Ray S, Natarajan A, Singh P, Bhakat K. The human AP-endonuclease 1 (APE1) is a DNA G-quadruplex structure binding protein and regulates KRAS expression in pancreatic ductal adenocarcinoma cells. Nucleic Acids Res 2022; 50:3394-3412. [PMID: 35286386 PMCID: PMC8990529 DOI: 10.1093/nar/gkac172] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/14/2022] [Accepted: 03/08/2022] [Indexed: 11/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), one of the most aggressive types of cancer, is characterized by aberrant activity of oncogenic KRAS. A nuclease-hypersensitive GC-rich region in KRAS promoter can fold into a four-stranded DNA secondary structure called G-quadruplex (G4), known to regulate KRAS expression. However, the factors that regulate stable G4 formation in the genome and KRAS expression in PDAC are largely unknown. Here, we show that APE1 (apurinic/apyrimidinic endonuclease 1), a multifunctional DNA repair enzyme, is a G4-binding protein, and loss of APE1 abrogates the formation of stable G4 structures in cells. Recombinant APE1 binds to KRAS promoter G4 structure with high affinity and promotes G4 folding in vitro. Knockdown of APE1 reduces MAZ transcription factor loading onto the KRAS promoter, thus reducing KRAS expression in PDAC cells. Moreover, downregulation of APE1 sensitizes PDAC cells to chemotherapeutic drugs in vitro and in vivo. We also demonstrate that PDAC patients' tissue samples have elevated levels of both APE1 and G4 DNA. Our findings unravel a critical role of APE1 in regulating stable G4 formation and KRAS expression in PDAC and highlight G4 structures as genomic features with potential application as a novel prognostic marker and therapeutic target in PDAC.
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Affiliation(s)
- Suravi Pramanik
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Yingling Chen
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Heyu Song
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Irine Khutsishvili
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Sutapa Ray
- Hematology/Oncology Division, Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Pankaj K Singh
- Eppley Institute for Research in Cancer and Allied Health, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Genome Integrity and Neurological Disease. Int J Mol Sci 2022; 23:ijms23084142. [PMID: 35456958 PMCID: PMC9025063 DOI: 10.3390/ijms23084142] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 02/06/2023] Open
Abstract
Neurological complications directly impact the lives of hundreds of millions of people worldwide. While the precise molecular mechanisms that underlie neuronal cell loss remain under debate, evidence indicates that the accumulation of genomic DNA damage and consequent cellular responses can promote apoptosis and neurodegenerative disease. This idea is supported by the fact that individuals who harbor pathogenic mutations in DNA damage response genes experience profound neuropathological manifestations. The review article here provides a general overview of the nervous system, the threats to DNA stability, and the mechanisms that protect genomic integrity while highlighting the connections of DNA repair defects to neurological disease. The information presented should serve as a prelude to the Special Issue “Genome Stability and Neurological Disease”, where experts discuss the role of DNA repair in preserving central nervous system function in greater depth.
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Label-free and highly sensitive APE1 detection based on rolling circle amplification combined with G-quadruplex. Talanta 2022; 244:123404. [PMID: 35349840 DOI: 10.1016/j.talanta.2022.123404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/12/2022] [Accepted: 03/22/2022] [Indexed: 12/13/2022]
Abstract
The highly sensitive detection of low-abundant apurinic/apyrimidinic endonuclease 1 (APE1) activity is of great significance for early diagnosis of disease and pathological research. Many methods for detecting APE1 based on isothermal nucleic acids amplification have been developed for improving its sensitivity. However, some of these methods have certain limitations, such as multiple reaction steps, narrow linear range, and complicated processes for fluorescent labeling. Herein, we develop a highly sensitive and label-free APE1 fluorescence detection method based on rolling circle amplification combined with G-quadruplex (RCA-G4). A hairpin probe (HP) labeled with the AP site can be recognized and cleaved by APE1, leading to the release of the primer sequence, which triggered RCA to produce long chain amplification products with a great amount of repeated sequences. The formed amplicon contains a series G-quadruplex structure, which can be combined with Thioflavin T (ThT) to produce fluorescence and achieve high sensitivity label-free detection of APE1. Benefit from the high amplification efficiency of RCA and the high fluorescence quantum yield of G-quadruplex/ThT, a detection limit as low as 1.52 × 10-6 U/mL and the linear range from 2 × 10-6 to 10 U/mL were obtained. The developed RCA-G4 method can be successfully used to detect APE1 in serum samples with a recovery from 96.3% to 105.7%. We believe that this approach is expected to play an important role in APE1-related disease research and drug development.
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Comparative Analysis of Exo- and Endonuclease Activities of APE1-like Enzymes. Int J Mol Sci 2022; 23:ijms23052869. [PMID: 35270011 PMCID: PMC8911113 DOI: 10.3390/ijms23052869] [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: 02/16/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/05/2022] Open
Abstract
Apurinic/apyrimidinic (AP)-endonucleases are multifunctional enzymes that are required for cell viability. AP-endonucleases incise DNA 5′ to an AP-site; can recognize and process some damaged nucleosides; and possess 3′-phosphodiesterase, 3′-phosphatase, and endoribonuclease activities. To elucidate the mechanism of substrate cleavage in detail, we analyzed the effect of mono- and divalent metal ions on the exo- and endonuclease activities of four homologous APE1-like endonucleases (from an insect (Rrp1), amphibian (xAPE1), fish (zAPE1), and from humans (hAPE1)). It was found that the enzymes had similar patterns of dependence on metal ions’ concentrations in terms of AP-endonuclease activity, suggesting that the main biological function (AP-site cleavage) was highly conserved among evolutionarily distant species. The efficiency of the 3′-5′ exonuclease activity was the highest in hAPE1 among these enzymes. In contrast, the endoribonuclease activity of the enzymes could be ranked as hAPE1 ≈ zAPE1 ≤ xAPE1 ≤ Rrp1. Taken together, the results revealed that the tested enzymes differed significantly in their capacity for substrate cleavage, even though the most important catalytic and substrate-binding amino acid residues were conserved. It can be concluded that substrate specificity and cleavage efficiency were controlled by factors external to the catalytic site, e.g., the N-terminal domain of these enzymes.
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Oliveira TT, Coutinho LG, de Oliveira LOA, Timoteo ARDS, Farias GC, Agnez-Lima LF. APE1/Ref-1 Role in Inflammation and Immune Response. Front Immunol 2022; 13:793096. [PMID: 35296074 PMCID: PMC8918667 DOI: 10.3389/fimmu.2022.793096] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/07/2022] [Indexed: 12/12/2022] Open
Abstract
Apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1) is a multifunctional enzyme that is essential for maintaining cellular homeostasis. APE1 is the major apurinic/apyrimidinic endonuclease in the base excision repair pathway and acts as a redox-dependent regulator of several transcription factors, including NF-κB, AP-1, HIF-1α, and STAT3. These functions render APE1 vital to regulating cell signaling, senescence, and inflammatory pathways. In addition to regulating cytokine and chemokine expression through activation of redox sensitive transcription factors, APE1 participates in other critical processes in the immune response, including production of reactive oxygen species and class switch recombination. Furthermore, through participation in active chromatin demethylation, the repair function of APE1 also regulates transcription of some genes, including cytokines such as TNFα. The multiple functions of APE1 make it an essential regulator of the pathogenesis of several diseases, including cancer and neurological disorders. Therefore, APE1 inhibitors have therapeutic potential. APE1 is highly expressed in the central nervous system (CNS) and participates in tissue homeostasis, and its roles in neurodegenerative and neuroinflammatory diseases have been elucidated. This review discusses known roles of APE1 in innate and adaptive immunity, especially in the CNS, recent evidence of a role in the extracellular environment, and the therapeutic potential of APE1 inhibitors in infectious/immune diseases.
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Affiliation(s)
- Thais Teixeira Oliveira
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
| | - Leonam Gomes Coutinho
- Instituto Federal de Educação, Ciência e Tecnologia do Rio Grande do Norte (IFRN), São Paulo do Potengi, Brazil
| | | | | | - Guilherme Cavalcanti Farias
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
| | - Lucymara Fassarella Agnez-Lima
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte (UFRN), Natal, Brazil
- *Correspondence: Lucymara Fassarella Agnez-Lima,
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SOX2 knockdown with siRNA reverses cisplatin resistance in NSCLC by regulating APE1 signaling. Med Oncol 2022; 39:36. [PMID: 35059870 PMCID: PMC8776672 DOI: 10.1007/s12032-021-01626-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 12/09/2021] [Indexed: 10/25/2022]
Abstract
AbstractSOX2 is related to drug resistance in many types of cancer, including lung cancer. Herein, we investigated the role of SOX2 and its regulatory signaling in cisplatin-treated non-small-cell lung cancer (NSCLC). The effects of SOX2 on cell viability, proliferation, and apoptosis were evaluated in vitro. Western blotting, real-time quantitative PCR, immunohistochemistry, and luciferase reporter assays were used to investigate the underlying mechanism. Kaplan–Meier survival analysis and the log-rank test were used to assess the relationship between SOX2 expression and patient survival. A549/CDDP cells had marked resistance to cisplatin and stronger colony formation ability than A549 cells. The expression of SOX2 protein or mRNA in A549/CDDP was higher than that in A549. Knockdown of SOX2 in A549/CDDP-induced apoptosis by inhibiting colony formation and decreasing viability, but overexpression of SOX2 reversed these effects. Interestingly, Genomatix software predicted that the APE1 promoter has some SOX2 binding sites, while the SOX2 promoter has no APE1 binding sites. Furthermore, luciferase reporter assays proved that SOX2 could bind the promoter of APE1 in 293T cells. We further verified that SOX2 expression was not affected by shAPE1 in A549/CDDP. As expected, colony formation was obviously inhibited and apoptosis was strongly enhanced in A549/CDDP treated with SOX2 siSOX2 alone or combined with CDDP compared with control cells. Meaningfully, patients with low expression of SOX2, and even including its regulating APE1, survived longer than those with high expression of SOX2, and APE1. siSOX2 overcomes cisplatin resistance by regulating APE1 signaling, providing a new target for overcoming cisplatin resistance in NSCLC.
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Sanchez-Roman I, Ferrando B, Holst CM, Mengel-From J, Rasmussen SH, Thinggaard M, Bohr VA, Christensen K, Stevnsner T. Molecular markers of DNA repair and brain metabolism correlate with cognition in centenarians. GeroScience 2021; 44:103-125. [PMID: 34966960 DOI: 10.1007/s11357-021-00502-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/14/2021] [Indexed: 11/26/2022] Open
Abstract
Oxidative stress is an important factor in age-associated neurodegeneration. Accordingly, mitochondrial dysfunction and genomic instability have been considered as key hallmarks of aging and have important roles in age-associated cognitive decline and neurodegenerative disorders. In order to evaluate whether maintenance of cognitive abilities at very old age is associated with key hallmarks of aging, we measured mitochondrial bioenergetics, mitochondrial DNA copy number and DNA repair capacity in peripheral blood mononuclear cells from centenarians in a Danish 1915 birth cohort (n = 120). Also, the circulating levels of brain-derived neurotrophic factor, NAD+ /NADH and carbonylated proteins were measured in plasma of the centenarians and correlated to cognitive capacity. Mitochondrial respiration was well preserved in the centenarian cohort when compared to young individuals (21-35 years of age, n = 33). When correlating cognitive performance of the centenarians with mitochondrial function such as basal respiration, ATP production, reserve capacity and maximal respiration, no overall correlations were observed, but when stratifying by sex, inverse associations were observed in the males (p < 0.05). Centenarians with the most severe cognitive impairment displayed the lowest activity of the central DNA repair enzyme, APE1 (p < 0.05). A positive correlation between cognitive capacity and levels of NAD+ /NADH was observed (p < 0.05), which may be because NAD+ /NADH consuming enzyme activities strive to reduce the oxidative DNA damage load. Also, circulating protein carbonylation was lowest in centenarians with highest cognitive capacity (p < 0.05). An opposite trend was observed for levels of brain-derived neurotrophic factor (p = 0.17). Our results suggest that maintenance of cognitive capacity at very old age may be associated with cellular mechanisms related to oxidative stress and DNA metabolism.
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Affiliation(s)
- Ines Sanchez-Roman
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish Aging Research Center, Aarhus, Denmark
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences (Animal Physiology Unit), School of Biology, Complutense University of Madrid, Madrid, Spain
| | - Beatriz Ferrando
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish Aging Research Center, Aarhus, Denmark
| | - Camilla Myrup Holst
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Danish Aging Research Center, Aarhus, Denmark
| | - Jonas Mengel-From
- Danish Aging Research Center, Aarhus, Denmark
- Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, Denmark
| | - Signe Høi Rasmussen
- Danish Aging Research Center, Aarhus, Denmark
- Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, Denmark
- Department of Geriatrics, Odense University Hospital, Svendborg, Denmark
| | - Mikael Thinggaard
- Danish Aging Research Center, Aarhus, Denmark
- Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, Denmark
| | - Vilhelm A Bohr
- Danish Aging Research Center, Aarhus, Denmark
- National Institute On Aging, NIH, Baltimore, MD, USA
| | - Kaare Christensen
- Danish Aging Research Center, Aarhus, Denmark
- Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, Denmark
| | - Tinna Stevnsner
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
- Danish Aging Research Center, Aarhus, Denmark.
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Alexeeva M, Moen MN, Xu XM, Rasmussen A, Leiros I, Kirpekar F, Klungland A, Alsøe L, Nilsen H, Bjelland S. Intrinsic Strand-Incision Activity of Human UNG: Implications for Nick Generation in Immunoglobulin Gene Diversification. Front Immunol 2021; 12:762032. [PMID: 35003074 PMCID: PMC8730318 DOI: 10.3389/fimmu.2021.762032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/17/2021] [Indexed: 12/05/2022] Open
Abstract
Uracil arises in cellular DNA by cytosine (C) deamination and erroneous replicative incorporation of deoxyuridine monophosphate opposite adenine. The former generates C → thymine transition mutations if uracil is not removed by uracil-DNA glycosylase (UDG) and replaced by C by the base excision repair (BER) pathway. The primary human UDG is hUNG. During immunoglobulin gene diversification in activated B cells, targeted cytosine deamination by activation-induced cytidine deaminase followed by uracil excision by hUNG is important for class switch recombination (CSR) and somatic hypermutation by providing the substrate for DNA double-strand breaks and mutagenesis, respectively. However, considerable uncertainty remains regarding the mechanisms leading to DNA incision following uracil excision: based on the general BER scheme, apurinic/apyrimidinic (AP) endonuclease (APE1 and/or APE2) is believed to generate the strand break by incising the AP site generated by hUNG. We report here that hUNG may incise the DNA backbone subsequent to uracil excision resulting in a 3´-α,β-unsaturated aldehyde designated uracil-DNA incision product (UIP), and a 5´-phosphate. The formation of UIP accords with an elimination (E2) reaction where deprotonation of C2´ occurs via the formation of a C1´ enolate intermediate. UIP is removed from the 3´-end by hAPE1. This shows that the first two steps in uracil BER can be performed by hUNG, which might explain the significant residual CSR activity in cells deficient in APE1 and APE2.
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Affiliation(s)
- Marina Alexeeva
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Marivi Nabong Moen
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Xiang Ming Xu
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
| | - Anette Rasmussen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Ingar Leiros
- Department of Chemistry, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Finn Kirpekar
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Lene Alsøe
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
- Section of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
- *Correspondence: Svein Bjelland, ; Hilde Nilsen,
| | - Svein Bjelland
- Department of Chemistry, Bioscience and Environmental Technology, University of Stavanger, Stavanger, Norway
- Section of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
- *Correspondence: Svein Bjelland, ; Hilde Nilsen,
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Vitexin inhibits APEX1 to counteract the flow-induced endothelial inflammation. Proc Natl Acad Sci U S A 2021; 118:2115158118. [PMID: 34810252 DOI: 10.1073/pnas.2115158118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 12/18/2022] Open
Abstract
Vascular endothelial cells are exposed to shear stresses with disturbed vs. laminar flow patterns, which lead to proinflammatory vs. antiinflammatory phenotypes, respectively. Effective treatment against endothelial inflammation and the consequent atherogenesis requires the identification of new therapeutic molecules and the development of drugs targeting these molecules. Using Connectivity Map, we have identified vitexin, a natural flavonoid, as a compound that evokes the gene-expression changes caused by pulsatile shear, which mimics laminar flow with a clear direction, vs. oscillatory shear (OS), which mimics disturbed flow without a clear direction. Treatment with vitexin suppressed the endothelial inflammation induced by OS or tumor necrosis factor-α. Administration of vitexin to mice subjected to carotid partial ligation blocked the disturbed flow-induced endothelial inflammation and neointimal formation. In hyperlipidemic mice, treatment with vitexin ameliorated atherosclerosis. Using SuperPred, we predicted that apurinic/apyrimidinic endonuclease1 (APEX1) may directly interact with vitexin, and we experimentally verified their physical interactions. OS induced APEX1 nuclear translocation, which was inhibited by vitexin. OS promoted the binding of acetyltransferase p300 to APEX1, leading to its acetylation and nuclear translocation. Functionally, knocking down APEX1 with siRNA reversed the OS-induced proinflammatory phenotype, suggesting that APEX1 promotes inflammation by orchestrating the NF-κB pathway. Animal experiments with the partial ligation model indicated that overexpression of APEX1 negated the action of vitexin against endothelial inflammation, and that endothelial-specific deletion of APEX1 ameliorated atherogenesis. We thus propose targeting APEX1 with vitexin as a potential therapeutic strategy to alleviate atherosclerosis.
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Hossain MA, Lin Y, Driscoll G, Li J, McMahon A, Matos J, Zhao H, Tsuchimoto D, Nakabeppu Y, Zhao J, Yan S. APE2 Is a General Regulator of the ATR-Chk1 DNA Damage Response Pathway to Maintain Genome Integrity in Pancreatic Cancer Cells. Front Cell Dev Biol 2021; 9:738502. [PMID: 34796173 PMCID: PMC8593216 DOI: 10.3389/fcell.2021.738502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/14/2021] [Indexed: 12/18/2022] Open
Abstract
The maintenance of genome integrity and fidelity is vital for the proper function and survival of all organisms. Recent studies have revealed that APE2 is required to activate an ATR-Chk1 DNA damage response (DDR) pathway in response to oxidative stress and a defined DNA single-strand break (SSB) in Xenopus laevis egg extracts. However, it remains unclear whether APE2 is a general regulator of the DDR pathway in mammalian cells. Here, we provide evidence using human pancreatic cancer cells that APE2 is essential for ATR DDR pathway activation in response to different stressful conditions including oxidative stress, DNA replication stress, and DNA double-strand breaks. Fluorescence microscopy analysis shows that APE2-knockdown (KD) leads to enhanced γH2AX foci and increased micronuclei formation. In addition, we identified a small molecule compound Celastrol as an APE2 inhibitor that specifically compromises the binding of APE2 but not RPA to ssDNA and 3′-5′ exonuclease activity of APE2 but not APE1. The impairment of ATR-Chk1 DDR pathway by Celastrol in Xenopus egg extracts and human pancreatic cancer cells highlights the physiological significance of Celastrol in the regulation of APE2 functionalities in genome integrity. Notably, cell viability assays demonstrate that APE2-KD or Celastrol sensitizes pancreatic cancer cells to chemotherapy drugs. Overall, we propose APE2 as a general regulator for the DDR pathway in genome integrity maintenance.
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Affiliation(s)
- Md Akram Hossain
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Yunfeng Lin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Garrett Driscoll
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Jia Li
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Joshua Matos
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
| | - Daisuke Tsuchimoto
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Jianjun Zhao
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States
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Liu J, Zheng J, Guo Y, Sheng X, Yin Y, Qian S, Xu B, Xiong W, Yin X. Association between APE1 rs1760944 and rs1130409 polymorphism with prostate cancer risk: A systematic review and meta-analysis. Medicine (Baltimore) 2021; 100:e27630. [PMID: 34797286 PMCID: PMC8601344 DOI: 10.1097/md.0000000000027630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 10/13/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Recently, some studies have suggested that the association of apurinic/apyrimidinic endonuclease 1 (APE1) gene polymorphism with prostate cancer (PCa) risk, but there are still some controversies. Hence, we elaborated the relationship between APE1 rs1760944 and rs1130409 gene and PCa risk through systematic literature review and meta-analysis. METHODS As of March 2020, EMBASE, PubMed, the Cochrane Library, Science Direct/Elsevier, MEDLINE and CNKI were used for systematic literature retrieval to investigate the correlation between APE1 rs1760944 and rs1130409 gene polymorphism with PCa risk. Meta-analysis was performed using Review Manager and Stata software. RESULTS Seven studies were distinguished, consists of 1769 cases of PCa patients and 2237 normal controls. Our results illustrated that there are significant correlation between the APE1 rs1760944 gene polymorphism and PCa in all genetic models (P < .05). The combined odds ratios and 95% confidence intervals were as follows: Additive model (ORs 0.62, 95%, CI [0.39, 0.97]); Codominant model (ORs 0.74, 95% CI [0.58, 0.95]); Dominant model (ORs 0.75, 95%, CI [0.59, 0.95]); Recessive model (ORs 0.63, 95% CI [0.41, 0.96]); Allele model (ORs 0.78, 95% CI [0.65, 0.94]). There also have significant associations between APE1 rs1130409 polymorphisms and PCa in all genetic models (P < .05). The combined odds ratios and 95% confidence intervals were as follows: Additive model (ORs 1.37, 95%, CI [1.01, 1.85]); Codominant model (ORs 1.21, 95% CI [1.01, 1.44]); Dominant model (ORs 1.33, 95%, CI [1.02, 1.73]); Recessive model (ORs 1.74, 95% CI [1.06, 2.85]); Allele model (ORs 1.14, 95% CI [1.00, 1.29]). CONCLUSION This study suggests that APE1 rs1760944 polymorphisms might be a protective factor of PCa, and APE1 rs1130409 is suggested to be a risk factor of PCa. APE1 rs1760944 and rs1130409 polymorphisms may be used in the risk assessment of PCa.
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Affiliation(s)
- Jinnian Liu
- Department of Urology, Second People's Hospital of Banan District, Chongqing, China
| | - Jian Zheng
- Department of Urology, Second People's Hospital of Banan District, Chongqing, China
| | - Yu Guo
- Department of Urology, Traditional Chinese Medicine Hospital, Chongqing, China
| | - Xia Sheng
- Department of Urology, Second People's Hospital of Banan District, Chongqing, China
| | - Yongjian Yin
- Department of Urology, Second People's Hospital of Banan District, Chongqing, China
| | - Shengqiang Qian
- Department of Urology, Traditional Chinese Medicine Hospital, Chongqing, China
| | - Bin Xu
- Department of Urology, Traditional Chinese Medicine Hospital, Chongqing, China
| | - Wei Xiong
- Department of Urology, Traditional Chinese Medicine Hospital, Chongqing, China
| | - Xiangrui Yin
- Department of Urology, Traditional Chinese Medicine Hospital, Chongqing, China
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Bhakat KK, Ray S. The FAcilitates Chromatin Transcription (FACT) complex: Its roles in DNA repair and implications for cancer therapy. DNA Repair (Amst) 2021; 109:103246. [PMID: 34847380 DOI: 10.1016/j.dnarep.2021.103246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/07/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022]
Abstract
Genomic DNA in the nucleus is wrapped around nucleosomes, a repeating unit of chromatin. The nucleosome, consisting of octamer of core histones, is a barrier for several cellular processes that require access to the naked DNA. The FAcilitates Chromatin Transcription (FACT), a histone chaperone complex, is involved in nucleosome remodeling via eviction or assembly of histones during transcription, replication, and DNA repair. Increasing evidence suggests that FACT plays an important role in multiple DNA repair pathways including transcription-coupled nucleotide excision repair (TC-NER) of UV-induced damage, DNA single- and double-strand breaks (DSBs) repair, and base excision repair (BER) of oxidized or alkylated damaged bases. Further, studies have shown overexpression of FACT in multiple types of cancer and its association with drug resistance and patients' poor prognosis. In this review, we discuss how FACT is accumulated at the damage site and what functions it performs. We describe the known mechanisms by which FACT facilitates repair of different types of DNA damage. Further, we highlight the recent advances in a class of FACT inhibitors, called curaxins, which show promise as a new adjuvant therapy to sensitize multiple types of cancer to chemotherapy and radiation.
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Affiliation(s)
- Kishor K Bhakat
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198.
| | - Sutapa Ray
- Department of Pediatric, Division of Hematology/oncology, University of Nebraska Medical Center, Omaha, NE, USA 68198; Fred and Pamela Buffet Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA 68198
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Chakraborty A, Tapryal N, Islam A, Mitra S, Hazra T. Transcription coupled base excision repair in mammalian cells: So little is known and so much to uncover. DNA Repair (Amst) 2021; 107:103204. [PMID: 34390916 DOI: 10.1016/j.dnarep.2021.103204] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 12/31/2022]
Abstract
Oxidized bases in the genome has been implicated in various human pathologies, including cancer, aging and neurological diseases. Their repair is initiated with excision by DNA glycosylases (DGs) in the base excision repair (BER) pathway. Among the five oxidized base-specific human DGs, OGG1 and NTH1 preferentially excise oxidized purines and pyrimidines, respectively, while NEILs remove both oxidized purines and pyrimidines. However, little is known about why cells possess multiple DGs with overlapping substrate specificities. Studies of the past decades revealed that some DGs are involved in repair of oxidized DNA base lesions in the actively transcribed regions. Preferential removal of lesions from the transcribed strands of active genes, called transcription-coupled repair (TCR), was discovered as a distinct sub-pathway of nucleotide excision repair; however, such repair of oxidized DNA bases had not been established until our recent demonstration of NEIL2's role in TC-BER of the nuclear genome. We have shown that NEIL2 forms a distinct transcriptionally active, repair proficient complex. More importantly, we for the first time reconstituted TC-BER using purified components. These studies are important for characterizing critical requirement for the process. However, because NEIL2 cannot remove all types of oxidized bases, it is unlikely to be the only DNA glycosylase involved in TC-BER. Hence, we postulate TC-BER process to be universally involved in maintaining the functional integrity of active genes, especially in post-mitotic, non-growing cells. We further postulate that abnormal bases (e.g., uracil), and alkylated and other small DNA base adducts are also repaired via TC-BER. In this review, we have provided an overview of the various aspects of TC-BER in mammalian cells with the hope of generating significant interest of many researchers in the field. Further studies aimed at better understanding the mechanistic aspects of TC-BER could help elucidate the linkage of TC-BER deficiency to various human pathologies.
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Affiliation(s)
- Anirban Chakraborty
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Nisha Tapryal
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Azharul Islam
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sankar Mitra
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Tapas Hazra
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
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Yu X, Zhang S, Guo W, Li B, Yang Y, Xie B, Li K, Zhang L. Recent Advances on Functional Nucleic-Acid Biosensors. SENSORS (BASEL, SWITZERLAND) 2021; 21:7109. [PMID: 34770415 PMCID: PMC8587875 DOI: 10.3390/s21217109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/17/2021] [Accepted: 10/23/2021] [Indexed: 02/07/2023]
Abstract
In the past few decades, biosensors have been gradually developed for the rapid detection and monitoring of human diseases. Recently, functional nucleic-acid (FNA) biosensors have attracted the attention of scholars due to a series of advantages such as high stability and strong specificity, as well as the significant progress they have made in terms of biomedical applications. However, there are few reports that systematically and comprehensively summarize its working principles, classification and application. In this review, we primarily introduce functional modes of biosensors that combine functional nucleic acids with different signal output modes. In addition, the mechanisms of action of several media of the FNA biosensor are introduced. Finally, the practical application and existing problems of FNA sensors are discussed, and the future development directions and application prospects of functional nucleic acid sensors are prospected.
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Affiliation(s)
| | | | | | | | | | | | | | - Li Zhang
- Department of Animal Nutrition and Feed Science, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (X.Y.); (S.Z.); (W.G.); (B.L.); (Y.Y.); (B.X.); (K.L.)
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Oliveira TT, Fontes-Dantas FL, de Medeiros Oliveira RK, Pinheiro DML, Coutinho LG, da Silva VL, de Souza SJ, Agnez-Lima LF. Chemical Inhibition of Apurinic-Apyrimidinic Endonuclease 1 Redox and DNA Repair Functions Affects the Inflammatory Response via Different but Overlapping Mechanisms. Front Cell Dev Biol 2021; 9:731588. [PMID: 34616737 PMCID: PMC8488223 DOI: 10.3389/fcell.2021.731588] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/27/2021] [Indexed: 01/21/2023] Open
Abstract
The presence of oxidized DNA lesions, such as 7,8-dihydro-8-oxoguanine (8-oxoG) and apurinic/apyrimidinic sites (AP sites), has been described as epigenetic signals that are involved in gene expression control. In mammals, Apurinic-apyrimidinic endonuclease 1/Redox factor-1 (APE1/Ref-1) is the main AP endonuclease of the base excision repair (BER) pathway and is involved in active demethylation processes. In addition, APE1/Ref-1, through its redox function, regulates several transcriptional factors. However, the transcriptional control targets of each APE1 function are not completely known. In this study, a transcriptomic approach was used to investigate the effects of chemical inhibition of APE1/Ref-1 redox or DNA repair functions by E3330 or methoxyamine (MX) in an inflammatory cellular model. Under lipopolysaccharide (LPS) stimulation, both E3330 and MX reduced the expression of some cytokines and chemokines. Interestingly, E3330 treatment reduced cell viability after 48 h of the treatment. Genes related to inflammatory response and mitochondrial processes were downregulated in both treatments. In the E3330 treatment, RNA processing and ribosome biogenesis genes were downregulated, while they were upregulated in the MX treatment. Furthermore, in the E3330 treatment, the cellular stress response was the main upregulated process, while the cellular macromolecule metabolic process was observed in MX-upregulated genes. Nuclear respiratory factor 1 (NRF1) was predicted to be a master regulator of the downregulated genes in both treatments, while the ETS transcription factor ELK1 (ELK1) was predicted to be a master regulator only for E3330 treatment. Decreased expression of ELK1 and its target genes and a reduced 28S/18S ratio were observed, suggesting impaired rRNA processing. In addition, both redox and repair functions can affect the expression of NRF1 and GABPA target genes. The master regulators predicted for upregulated genes were YY1 and FLI1 for the E3330 and MX treatments, respectively. In summary, the chemical inhibition of APE1/Ref-1 affects gene expression regulated mainly by transcriptional factors of the ETS family, showing partial overlap of APE1 redox and DNA repair functions, suggesting that these activities are not entirely independent. This work provides a new perspective on the interaction between APE1 redox and DNA repair activity in inflammatory response modulation and transcription.
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Affiliation(s)
- Thais Teixeira Oliveira
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | - Fabrícia Lima Fontes-Dantas
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil
| | | | | | - Leonam Gomes Coutinho
- Departamento de Biologia Celular e Genética, Universidade Federal do Rio Grande do Norte, UFRN, Natal, Brazil.,Instituto Federal de Educação Tecnológica do Rio Grande do Norte, IFRN, São Paulo do Potengi, Brazil
| | - Vandeclecio Lira da Silva
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), IMD, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Sandro José de Souza
- Instituto do Cérebro, Universidade Federal do Rio Grande do Norte, Natal, Brazil.,Bioinformatics Multidisciplinary Environment (BioME), IMD, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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A New Method for Exonuclease Activity Analysis of Apurinic/Apyrimidinic Endonuclease 1 and Application in Heavy-polluted Ramie. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2021. [DOI: 10.1016/s1872-2040(21)60117-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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