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Zhang M, Zhang Y, Wang Q, Liu K, Li L, Yu Z, Hou L, Zhang X, Zhao H, Cheng W, Zhang W. An APE1 gated signal amplified biosensor driven by catalytic hairpin assembly for the specific imaging of microRNA in situ. Int J Biol Macromol 2024; 262:129902. [PMID: 38307426 DOI: 10.1016/j.ijbiomac.2024.129902] [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: 11/27/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/04/2024]
Abstract
In situ imaging of microRNA (miRNA) content and distribution is valuable for monitoring tumor progression. However, tumor specific in situ imaging remains a challenge due to low miRNA abundance, lack of biological compatibility, and poor specificity. In this study, we designed a DNA tetrahedral framework complex with hairpins (DTF-HPAP) consisting of an apurinic/apyrimidinic site (AP site) that could be specifically recognized and cleaved by apurinic/apyrimidinic endonuclease 1 (APE1). Efficient and specific in situ imaging of miR-21 in tumors was thus achieved through catalytic hairpin assembly (CHA) reaction. In this study, DTF-HPAP was successfully constructed to trigger the cumulative amplification of fluorescence signal in situ. The specificity, sensitivity and serum stability of DTF-HPAP were verified in vitro, and DTF-HPAP could be easily taken up by cells, acting as a biosensor to detect tumors in mice. Furthermore, we verified the ability of DTF-HPAP to specifically image miR-21 in tumors, and demonstrated its capability for tumor-specific imaging in clinical samples.
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Affiliation(s)
- Mengxin Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Qionglin Wang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China; Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Kangbo Liu
- Henan Medical Equipment Inspection Institute, Zhengzhou 450018, China
| | - Lifeng Li
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Zhidan Yu
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Ligong Hou
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Xianwei Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Huan Zhao
- Department of oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450018, China
| | - Weyland Cheng
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China; Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China.
| | - Wancun Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China; Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China; Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China.
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2
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Parolini I, Degrassi M, Spadaro F, Caponnetto F, Fecchi K, Mastantuono S, Zhouyiyuan X, Demple B, Cesselli D, Tell G. Intraluminal vesicle trafficking is involved in the secretion of base excision repair protein APE1. FEBS J 2024. [PMID: 38401056 DOI: 10.1111/febs.17088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/24/2023] [Accepted: 01/31/2024] [Indexed: 02/26/2024]
Abstract
The apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) is an essential enzyme of the base excision repair pathway of non-distorting DNA lesions. In response to genotoxic treatments, APE1 is highly secreted (sAPE1) in association with small-extracellular vesicles (EVs). Interestingly, its presence in the serum of patients with hepatocellular or non-small-cell-lung cancers may represent a prognostic biomarker. The mechanism driving APE1 to associate with EVs is unknown, but is of paramount importance in better understanding the biological roles of sAPE1. Because APE1 lacks an endoplasmic reticulum-targeting signal peptide, it can be secreted through an unconventional protein secretion endoplasmic reticulum-Golgi-independent pathway, which includes an endosome-based secretion of intraluminal vesicles, mediated by multivesicular bodies (MVBs). Using HeLa and A549 cell lines, we investigated the role of endosomal sorting complex required for transport protein pathways (either-dependent or -independent) in the constitutive or trichostatin A-induced secretion of sAPE1, by means of manumycin A and GW 4869 treatments. Through an in-depth biochemical analysis of late-endosomes (LEs) and early-endosomes (EEs), we observed that the distribution of APE1 on density gradient corresponded to that of LE-CD63, LE-Rab7, EE-EEA1 and EE-Rab 5. Interestingly, the secretion of sAPE1, induced by cisplatin genotoxic stress, involved an autophagy-based unconventional secretion requiring MVBs. The present study enlightens the central role played by MVBs in the secretion of sAPE1 under various stimuli, and offers new perspectives in understanding the biological relevance of sAPE1 in cancer cells.
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Affiliation(s)
- Isabella Parolini
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Italy
| | - Monica Degrassi
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Italy
| | - Francesca Spadaro
- Core Facilities - Confocal Microscopy Unit, Istituto Superiore di Sanità, Rome, Italy
| | - Federica Caponnetto
- Department of Medicine, University of Udine, Italy
- Institute of Pathology, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Katia Fecchi
- Center for Gender-Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Serena Mastantuono
- Department of Medicine, University of Udine, Italy
- Institute of Pathology, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Xue Zhouyiyuan
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Daniela Cesselli
- Department of Medicine, University of Udine, Italy
- Institute of Pathology, Academic Hospital Santa Maria della Misericordia, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Italy
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3
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Mijit M, Kpenu E, Chowdhury NN, Gampala S, Wireman R, Liu S, Babb O, Georgiadis MM, Wan J, Fishel ML, Kelley MR. In vitro and In vivo evidence demonstrating chronic absence of Ref-1 Cysteine 65 impacts Ref-1 folding configuration, redox signaling, proliferation and metastasis in pancreatic cancer. Redox Biol 2024; 69:102977. [PMID: 38056311 PMCID: PMC10749280 DOI: 10.1016/j.redox.2023.102977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023] Open
Abstract
Ref-1/APE1 (Redox Effector/Apurinic Endonuclease 1) is a multifunctional enzyme that serves as a redox factor for several transcription factors (TFs), e.g., NF-kB, HIF-1α, which in an oxidized state fail to bind DNA. Conversion of these TFs to a reduced state serves to regulate various biological responses such as cell growth, inflammation, and cellular metabolism. The redox activity involves a thiol exchange reaction for which Cys65 (C65) serves as the nucleophile. Using CRISPR editing in human pancreatic ductal adenocarcinoma (PDAC) cells, we changed C65 to Ala (C65A) in Ref-1 to evaluate alteration of Ref-1 redox dynamics as well as chronic loss of Ref-1 redox activity on cell signaling pathways, specifically those regulated by NF-kB and HIF-1α. The redox activity of Ref-1 requires partial unfolding to expose C65, which is buried in the folded structure. Labeling of Ref-1 with polyethylene glycol-maleimide (PEGm) provides a readout of reduced Cys residues in Ref-1 and thereby an assessment of partial unfolding in Ref-1. In comparing Ref-1WT vs Ref-1C65A cell lines, we found an altered distribution of oxidized versus reduced states of Ref-1. Accordingly, activation of NF-kB and HIF-1α in Ref-1C65A lines was significantly lower compared to Ref-1WT lines. The bioinformatic data revealed significant downregulation of metabolic pathways including OXPHOS in Ref-1C65A expressing clones compared to Ref-1WT line. Ref-1C65A also demonstrated reduced cell proliferation and use of tricarboxylic acid (TCA) substrates compared to Ref-1WT lines. A subcutaneous as well as PDAC orthotopic in vivo model demonstrated a significant reduction in tumor size, weight, and growth in the Ref-1C65A lines compared to the Ref-1WT lines. Moreover, mice implanted with Ref-1C65A redox deficient cells demonstrate significantly reduced metastatic burden to liver and lung compared to mice implanted with Ref-1 redox proficient cells. These results from the current study provide direct evidence that the chronic absence of Cys65 in Ref-1 results in redox inactivity of the protein in human PDAC cells, and subsequent biological results confirm a critical involvement of Ref-1 redox signaling and tumorigenic phenotype.
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Affiliation(s)
- M Mijit
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - E Kpenu
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - N N Chowdhury
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - S Gampala
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - R Wireman
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - S Liu
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - O Babb
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - M M Georgiadis
- Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, Indianapolis, IN, USA
| | - J Wan
- Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - M L Fishel
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - M R Kelley
- Department of Pediatrics and Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA; Indiana University School of Medicine, Department of Biochemistry and Molecular Biology, Indianapolis, IN, USA; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
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4
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Moris VC, Bruneau L, Berthe J, Heuskin AC, Penninckx S, Ritter S, Weber U, Durante M, Danchin EGJ, Hespeels B, Doninck KV. Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga. BMC Biol 2024; 22:11. [PMID: 38273318 PMCID: PMC10809525 DOI: 10.1186/s12915-023-01807-8] [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: 08/18/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The remarkable resistance to ionizing radiation found in anhydrobiotic organisms, such as some bacteria, tardigrades, and bdelloid rotifers has been hypothesized to be incidental to their desiccation resistance. Both stresses produce reactive oxygen species and cause damage to DNA and other macromolecules. However, this hypothesis has only been investigated in a few species. RESULTS In this study, we analyzed the transcriptomic response of the bdelloid rotifer Adineta vaga to desiccation and to low- (X-rays) and high- (Fe) LET radiation to highlight the molecular and genetic mechanisms triggered by both stresses. We identified numerous genes encoding antioxidants, but also chaperones, that are constitutively highly expressed, which may contribute to the protection of proteins against oxidative stress during desiccation and ionizing radiation. We also detected a transcriptomic response common to desiccation and ionizing radiation with the over-expression of genes mainly involved in DNA repair and protein modifications but also genes with unknown functions that were bdelloid-specific. A distinct transcriptomic response specific to rehydration was also found, with the over-expression of genes mainly encoding Late Embryogenesis Abundant proteins, specific heat shock proteins, and glucose repressive proteins. CONCLUSIONS These results suggest that the extreme resistance of bdelloid rotifers to radiation might indeed be a consequence of their capacity to resist complete desiccation. This study paves the way to functional genetic experiments on A. vaga targeting promising candidate proteins playing central roles in radiation and desiccation resistance.
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Affiliation(s)
- Victoria C Moris
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium.
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium.
| | - Lucie Bruneau
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Jérémy Berthe
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Anne-Catherine Heuskin
- Namur Research Institute for Life Sciences (NARILIS), Laboratory of Analysis By Nuclear Reactions (LARN), University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Sébastien Penninckx
- Medical Physics Department, Institut Jules Bordet - Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070, Brussels, Belgium
| | - Sylvia Ritter
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Uli Weber
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
| | - Marco Durante
- Biophysics Department, GSI Helmholtzzentrum Für Schwerionenforschung, Darmstadt, Germany
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Etienne G J Danchin
- Institut Sophia Agrobiotech, INRAE, Université Côte d'Azur, CNRS, 06903, Sophia Antipolis, France
| | - Boris Hespeels
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
| | - Karine Van Doninck
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology - URBE, University of Namur, Rue de Bruxelles, 61, B-5000, Namur, Belgium
- Laboratory of Molecular Biology & Evolution (MBE), Department of Biology, Université Libre de Bruxelles, 1000, Brussels, Belgium
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5
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Zhou S, Li X, Shu X, Cai X, Wu H, Ding S, Yan Y. An all-in-one enzymatic DNA network based on catalytic hairpin assembly for label-free and highly sensitive detection of APE1. Anal Chim Acta 2023; 1278:341678. [PMID: 37709426 DOI: 10.1016/j.aca.2023.341678] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 09/16/2023]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1), identified as a prospective cancer biomarker, plays a vital role in the occurrence and progression of cancer cell lines and impacts on genome stability. However, conventional approaches typically rely on the interactions between the antigen and antibody, limiting their utility for qualitative assessments of APE1 expression. Herein, an all-in-one enzymatic DNA network (EDN) assay with catalytic hairpin assembly for label-free and ultrasensitive detection of APE1 has been developed. In this work, the blocking strand can inhibit the initiator by obstructing the complementary region, preventing the hairpin from hybridizing in the absence of APE1 targets. While the presence of targets can activate the unlocking of the initiator, which can trigger the catalytic hairpin reaction, and increase the fluorescent signal. Under optimal conditions, the developed sensing method can detect the target APE1 down to 4.78 × 10-6 U mL-1 with a wide linear range from 5 × 10-6 U mL-1 to 30 U mL-1. This strategy has also been successfully applied to the analysis of complicated biological samples compared to ELISA, demonstrating its potential applications in biochemical and molecular biology research as well as clinical diagnostics. Overall, benefiting from the high amplification efficiency, this strategy has successfully and simply detected low-abundance APE1 without additional enzyme isolation steps, presenting great potential for clinical detection applications.
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Affiliation(s)
- Shaoying Zhou
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China; Department of Clinical Laboratory, The People's Hospital of Yubei District of Chongqing City, Chongqing, 400120, China.
| | - Xingrong Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaojia Shu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaoying Cai
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Haiping Wu
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Yurong Yan
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China.
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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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Rai R, Dawodu OI, Johnson SM, Vilseck JZ, Kelley MR, Ziarek JJ, Georgiadis MM. Chemically induced partial unfolding of the multifunctional Apurinic/apyrimidinic endonuclease 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547112. [PMID: 37425839 PMCID: PMC10327033 DOI: 10.1101/2023.06.29.547112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Targeting of the multifunctional enzyme apurinic/apyrimidinic endonuclease I/redox factor 1 (APE1) has produced small molecule inhibitors of both its endonuclease and redox activities. While one of the small molecules, the redox inhibitor APX3330, completed a Phase I clinical trial for solid tumors and a Phase II clinical trial for Diabetic Retinopathy/Diabetic Macular Edema, the mechanism of action for this drug has yet to be fully understood. Here, we demonstrate through HSQC NMR studies that APX3330 induces chemical shift perturbations (CSPs) of both surface and internal residues in a concentration-dependent manner, with a cluster of surface residues defining a small pocket on the opposite face from the endonuclease active site of APE1. Furthermore, APX3330 induces partial unfolding of APE1 as evidenced by a time-dependent loss of chemical shifts for approximately 35% of the residues within APE1 in the HSQC NMR spectrum. Notably, regions that are partially unfolded include adjacent strands within one of two beta sheets that comprise the core of APE1. One of the strands comprises residues near the N-terminal region and a second strand is contributed by the C-terminal region of APE1, which serves as a mitochondrial targeting sequence. These terminal regions converge within the pocket defined by the CSPs. In the presence of a duplex DNA substrate mimic, removal of excess APX3330 resulted in refolding of APE1. Our results are consistent with a reversible mechanism of partial unfolding of APE1 induced by the small molecule inhibitor, APX3330, defining a novel mechanism of inhibition.
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8
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Siswanto FM, Okukawa K, Tamura A, Oguro A, Imaoka S. Hydrogen peroxide activates APE1/Ref-1 via NF-κB and Parkin: A role in liver cancer resistance to oxidative stress. Free Radic Res 2023:1-31. [PMID: 37364176 DOI: 10.1080/10715762.2023.2229509] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/09/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Cancer cells exhibit an altered redox balance and aberrant redox signaling due to genetic, metabolic, and microenvironment-associated reprogramming. Persistently elevated levels of reactive oxygen species (ROS) contribute to many aspects of tumor development and progression. Emerging studies demonstrated the vital role of apurinic/apyrimidinic endonuclease 1 or reduction/oxidation (redox) factor 1(APE1/Ref-1) in the oxidative stress response and survival of cancer cells. APE1/Ref-1 is a multifunctional enzyme involved in the DNA damage response and functions as a redox regulator of transcription factors. We herein demonstrated that basal hydrogen peroxide (H2O2) and APE1/Ref-1 expression levels were markedly higher in cancer cell lines than in non-cancerous cells. Elevated APE1/Ref-1 levels were associated with shorter survival in liver cancer patients. Mechanistically, we showed that H2O2 activated nuclear factor-κB (NF-κB). RelA/p65 inhibited the expression of the E3 ubiquitin ligase Parkin, possibly by interfering with ATF4 activity. Parkin was responsible for the ubiquitination and proteasomal degradation of APE1/Ref-1; therefore, the H2O2-induced suppression of Parkin expression increased APE1/Ref-1 levels. The probability of survival was lower in liver cancer patients with low Parkin and high RelA expression levels. Additionally, Parkin and RelA expression levels negatively and positively correlated with APE1/Ref-1 levels, respectively, in the TCGA liver cancer cohort. We concluded that increases in APE1/Ref-1 via the NF-κB and Parkin pathways are critical for cancer cell survival under oxidative stress. The present results show the potential of the NF-κB-Parkin-APE1/Ref-1 axis as a prognostic factor and therapeutic strategy to eradicate liver cancer.
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Affiliation(s)
- Ferbian Milas Siswanto
- Department of Biomedical Chemistry, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
- Department of Biochemistry, School of Medicine and Health Sciences, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Kenta Okukawa
- Department of Biomedical Chemistry, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Akiyoshi Tamura
- Department of Biomedical Chemistry, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
| | - Ami Oguro
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Susumu Imaoka
- Department of Biomedical Chemistry, School of Biological and Environmental Sciences, Kwansei Gakuin University, Sanda, Japan
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9
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Mijit M, Liu S, Sishtla K, Hartman GD, Wan J, Corson TW, Kelley MR. Identification of Novel Pathways Regulated by APE1/Ref-1 in Human Retinal Endothelial Cells. Int J Mol Sci 2023; 24:1101. [PMID: 36674619 PMCID: PMC9865623 DOI: 10.3390/ijms24021101] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
APE1/Ref-1 (apurinic/apyrimidinic endonuclease 1, APE1 or APEX1; redox factor-1, Ref-1) is a dual-functional enzyme with crucial roles in DNA repair, reduction/oxidation (redox) signaling, and RNA processing and metabolism. The redox function of Ref-1 regulates several transcription factors, such as NF-κB, STAT3, HIF-1α, and others, which have been implicated in multiple human diseases, including ocular angiogenesis, inflammation, and multiple cancers. To better understand how APE1 influences these disease processes, we investigated the effects of APEX1 knockdown (KD) on gene expression in human retinal endothelial cells. This abolishes both DNA repair and redox signaling functions, as well as RNA interactions. Using RNA-seq analysis, we identified the crucial signaling pathways affected following APEX1 KD, with subsequent validation by qRT-PCR. Gene expression data revealed that multiple genes involved in DNA base excision repair, other DNA repair pathways, purine or pyrimidine metabolism signaling, and histidine/one carbon metabolism pathways were downregulated by APEX1 KD. This is in contrast with the alteration of pathways by APEX1 KD in human cancer lines, such as pancreatic ductal adenocarcinoma, lung, HeLa, and malignant peripheral nerve sheath tumors. These results highlight the unique role of APE1/Ref-1 and the clinical therapeutic potential of targeting APE1 and pathways regulated by APE1 in the eye. These findings provide novel avenues for ocular neovascularization treatment.
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Affiliation(s)
- Mahmut Mijit
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sheng Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Kamakshi Sishtla
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Gabriella D. Hartman
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jun Wan
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Timothy W. Corson
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mark R. Kelley
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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10
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Malfatti MC, Antoniali G, Tell G. In Vitro Assay to Measure APE1 Enzymatic Activity on Ribose Monophosphate Abasic Site. Methods Mol Biol 2023; 2701:21-38. [PMID: 37574473 DOI: 10.1007/978-1-0716-3373-1_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
APE1 (apurinic/apyrimidinic endodeoxyribonuclease 1) is a central enzyme of the base excision repair (BER) pathway playing a pivotal role in protecting mammalian cells against genotoxins and in safeguarding genome stability. Recently, we demonstrated the APE1 ability to process abasic ribonucleotides embedded in DNA. Here, we provide a pipeline of protocols to quantify endodeoxyribonuclease activity by APE1 on these substrates, by using recombinant protein and whole-cell extracts. The repair capacity is measured by using fluorescent oligonucleotide substrates, which are then separated by polyacrylamide gel electrophoresis and detected by imaging scanning. The specificity of APE1 action is demonstrated using specific APE1 enzymatic inhibitors.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy.
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11
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Kaur R, Nikkel DJ, Aboelnga MM, Wetmore SD. The Impact of DFT Functional, Cluster Model Size, and Implicit Solvation on the Structural Description of Single-Metal-Mediated DNA Phosphodiester Bond Cleavage: The Case Study of APE1. J Phys Chem B 2022; 126:10672-10683. [PMID: 36485014 DOI: 10.1021/acs.jpcb.2c06756] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphodiester bond hydrolysis in nucleic acids is a ubiquitous reaction that can be facilitated by enzymes called nucleases, which often use metal ions to achieve catalytic function. While a two-metal-mediated pathway has been well established for many enzymes, there is growing support that some enzymes require only one metal for the catalytic step. Using human apurinic/apyrimidinic endonuclease (APE1) as a prototypical example and cluster models, this study clarifies the impact of DFT functional, cluster model size, and implicit solvation on single-metal-mediated phosphodiester bond cleavage and provides insight into how to efficiently model this chemistry. Initially, a model containing 69 atoms built from a high-resolution X-ray crystal structure is used to explore the reaction pathway mapped by a range of DFT functionals and basis sets, which provides support for the use of standard functionals (M06-2X and B3LYP-D3) to study this reaction. Subsequently, systematically increasing the model size to 185 atoms by including additional amino acids and altering residue truncation points highlights that small models containing only a few amino acids or β carbon truncation points introduce model strains and lead to incorrect metal coordination. Indeed, a model that contains all key residues (general base and acid, residues that stabilize the substrate, and amino acids that maintain the metal coordination) is required for an accurate structural depiction of the one-metal-mediated phosphodiester bond hydrolysis by APE1, which results in 185 atoms. The additional inclusion of the broader enzyme environment through continuum solvation models has negligible effects. The insights gained in the present work can be used to direct future computational studies of other one-metal-dependent nucleases to provide a greater understanding of how nature achieves this difficult chemistry.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada.,Chemistry Department, Faculty of Science, Damietta University, New Damietta 34517, Egypt
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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12
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Kaur R, Aboelnga MM, Nikkel DJ, Wetmore SD. The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme. Phys Chem Chem Phys 2022; 24:29130-29140. [PMID: 36444615 DOI: 10.1039/d2cp04338f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nucleases catalyze the cleavage of phosphodiester bonds in nucleic acids using a range of metal cofactors. Although it is well accepted that many nucleases rely on two metal ions, the one-metal mediated pathway is debated. Furthermore, one-metal mediated nucleases maintain activity in the presence of many different metals, but the underlying reasons for this broad metal specificity are unknown. The human apurinic/apyrimidinic endonuclease (APE1), which plays a key role in DNA repair, transcription regulation, and gene expression, is a prototypical example of a one-metal dependent nuclease. Although Mg2+ is the native metal cofactor, APE1 remains catalytically active in the presence of several metals, with the rate decreasing as Mg2+ > Mn2+ > Ni2+ > Zn2+, while Ca2+ completely abolished the activity. The present work uses quantum mechanics-molecular mechanics techniques to map APE1-facilitated phosphodiester bond hydrolysis in the presence of these metals. The structural differences in stationary points along the reaction pathway shed light on the interplay between several factors that allow APE1 to remain catalytically active for various metals, with the trend in the barrier heights correlating with the experimentally reported APE1 catalytic activity. In contrast, Ca2+ significantly changes the metal coordination and active site geometry, and thus completely inhibits catalysis. Our work thereby provides support for the controversial single-metal mediated phosphodiester bond cleavage and clarifies uncertainties regarding the role of the metal and metal identity in this important reaction. This information is key for future medicinal and biotechnological applications including disease diagnosis and treatment, and protein engineering.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Mohamed M Aboelnga
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Dylan J Nikkel
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada.
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13
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Post-Translational Modifications by Lipid Metabolites during the DNA Damage Response and Their Role in Cancer. Biomolecules 2022; 12:biom12111655. [DOI: 10.3390/biom12111655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Genomic DNA damage occurs as an inevitable consequence of exposure to harmful exogenous and endogenous agents. Therefore, the effective sensing and repair of DNA damage are essential for maintaining genomic stability and cellular homeostasis. Inappropriate responses to DNA damage can lead to genomic instability and, ultimately, cancer. Protein post-translational modifications (PTMs) are a key regulator of the DNA damage response (DDR), and recent progress in mass spectrometry analysis methods has revealed that a wide range of metabolites can serve as donors for PTMs. In this review, we will summarize how the DDR is regulated by lipid metabolite-associated PTMs, including acetylation, S-succinylation, N-myristoylation, palmitoylation, and crotonylation, and the implications for tumorigenesis. We will also discuss potential novel targets for anti-cancer drug development.
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14
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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: 0] [Impact Index Per Article: 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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15
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A simple and smart AND-gate DNA nanoprobe for correlated enzymes tracking and cell-selective imaging. Biosens Bioelectron 2022; 217:114724. [PMID: 36166888 DOI: 10.1016/j.bios.2022.114724] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/23/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022]
Abstract
Accurate cancer diagnosis and effective drug therapy entail sensitive and dynamic monitoring of intracellular key enzymes, since their expression level is closely related to disease progression. Simultaneous monitoring of correlated enzymes is promising to help unveiling mystery of cytobiological events during tumor progression and drug response, while is challenged by lacking of a robust and simple simultaneous detection strategy. In order to construct a simple and smart strategy which is complex design-avoided and doesn't need other auxiliary enzyme, here we develop an AND-gate strategy for simultaneously monitoring correlated enzymes which both are upregulated in cancer cells (telomerase and apurinic/apyrimidinic endonuclease 1). An innovative AND-gate DNA nanoprobe has been designed to avoid mutual interference and background noise, guaranteeing an enhanced fluorescent signal output upon catalyzation of dual enzymes. This AND-gate strategy achieves sensitive detection of two enzymes in an individual manner in test tube, through which the diagnostic potential of bladder cancer has been validated by telomerase detection in clinical urine sample. The AND-gate strategy enables specific intracellular imaging of dual enzymes in different cancer cell lines. Importantly, in contrast to traditional single-targeting strategies, AND-gate imaging of dual enzymes significantly improves cancer cell selectivity. Moreover, this strategy dynamically monitors enzymatic activity changes during chemoresistance induced by chemotherapeutic treatment. This simple and smart strategy has foreseeable prospect in the fields of disease diagnosis, drug prognosis evaluation, and precise fluorescence-guided surgery.
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16
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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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17
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Han R, Jiang J, Fang J, Contreras LM. PNPase and RhlB Interact and Reduce the Cellular Availability of Oxidized RNA in Deinococcus radiodurans. Microbiol Spectr 2022; 10:e0214022. [PMID: 35856907 PMCID: PMC9430589 DOI: 10.1128/spectrum.02140-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/30/2022] [Indexed: 01/01/2023] Open
Abstract
8-Oxo-7,8-dihydroguanine (8-oxoG) is a major RNA modification caused by oxidative stresses and has been implicated in carcinogenesis, neurodegeneration, and aging. Several RNA-binding proteins have been shown to have a binding preference for 8-oxoG-modified RNA in eukaryotes and protect cells from oxidative stress. To date, polynucleotide phosphorylase (PNPase) is one of the most well-characterized proteins in bacteria that recognize 8-oxoG-modified RNA, but how PNPase cooperates with other proteins to process oxidized RNA is still unclear. Here, we use RNA affinity chromatography and mass spectrometry to search for proteins that preferably bind 8-oxoG-modified RNA in Deinococcus radiodurans, an extremophilic bacterium with extraordinary resistance to oxidative stresses. We identified four proteins that preferably bind to oxidized RNA: PNPase (DR_2063), DEAD box RNA helicase (DR_0335/RhlB), ribosomal protein S1 (DR_1983/RpsA), and transcriptional termination factor (DR_1338/Rho). Among these proteins, PNPase and RhlB exhibit high-affinity binding to 8-oxoG-modified RNA in a dose-independent manner. Deletions of PNPase and RhlB caused increased sensitivity of D. radiodurans to oxidative stress. We further showed that PNPase and RhlB specifically reduce the cellular availability of 8-oxoG-modified RNA but have no effect on oxidized DNA. Importantly, PNPase directly interacts with RhlB in D. radiodurans; however, no additional phenotypic effect was observed for the double deletion of pnp and rhlB compared to the single deletions. Overall, our findings suggest the roles of PNPase and RhlB in targeting 8-oxoG-modified RNAs and thereby constitute an important component of D. radiodurans resistance to oxidative stress. IMPORTANCE Oxidative RNA damage can be caused by oxidative stress, such as hydrogen peroxide, ionizing radiation, and antibiotic treatment. 8-oxo-7,8-dihydroguanine (8-oxoG), a major type of oxidized RNA, is highly mutagenic and participates in a variety of disease occurrences and development. Although several proteins have been identified to recognize 8-oxoG-modified RNA, the knowledge of how RNA oxidative damage is controlled largely remains unclear, especially in nonmodel organisms. In this study, we identified four RNA binding proteins that show higher binding affinity to 8-oxoG-modified RNA compared to unmodified RNA in the extremophilic bacterium Deinococcus radiodurans, which can endure high levels of oxidative stress. Two of the proteins, polynucleotide phosphorylase (PNPase) and DEAD-box RNA helicase (RhlB), interact with each other and reduce the cellular availability of 8-oxoG-modified RNA under oxidative stress. As such, this work contributes to our understanding of how RNA oxidation is influenced by RNA binding proteins in bacteria.
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Affiliation(s)
- Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Jessie Jiang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Jaden Fang
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, USA
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18
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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: 17] [Impact Index Per Article: 8.5] [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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19
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Behrouzi A, Xia H, Thompson EL, Kelley MR, Fehrenbacher JC. Oxidative DNA Damage and Cisplatin Neurotoxicity Is Exacerbated by Inhibition of OGG1 Glycosylase Activity and APE1 Endonuclease Activity in Sensory Neurons. Int J Mol Sci 2022; 23:ijms23031909. [PMID: 35163831 PMCID: PMC8836551 DOI: 10.3390/ijms23031909] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 02/04/2023] Open
Abstract
Cisplatin can induce peripheral neuropathy, which is a common complication of anti-cancer treatment and negatively impacts cancer survivors during and after completion of treatment; therefore, the mechanisms by which cisplatin alters sensory neuronal function to elicit neuropathy are the subject of much investigation. Our previous work suggests that the DNA repair activity of APE1/Ref-1, the rate-limiting enzyme of the base excision repair (BER) pathway, is critical for neuroprotection against cisplatin. A specific role for 8-oxoguanine DNA glycosylase-1 (OGG1), the glycosylase that removes the most common oxidative DNA lesion, and putative coordination of OGG1 with APE1/Ref-1 in sensory neurons, has not been investigated. We investigated whether inhibiting OGG1 glycosylase activity with the small molecule inhibitor, TH5487, and/or APE1/Ref-1 endonuclease activity with APE Repair Inhibitor III would alter the neurotoxic effects of cisplatin in sensory neuronal cultures. Sensory neuron function was assessed by calcitonin gene-related peptide (CGRP) release, as a marker of sensitivity and by neurite outgrowth. Cisplatin altered neuropeptide release in an inverse U-shaped fashion, with low concentrations enhancing and higher concentrations diminishing CGRP release. Pretreatment with BER inhibitors exacerbated the functional effects of cisplatin and enhanced 8oxo-dG and adduct lesions in the presence of cisplatin. Our studies demonstrate that inhibition of OGG1 and APE1 endonuclease activity enhances oxidative DNA damage and exacerbates neurotoxicity, thus limiting oxidative DNA damage in sensory neurons that might alleviate cisplatin-induced neuropathy.
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Affiliation(s)
- Adib Behrouzi
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.B.); (H.X.); (E.L.T.); (M.R.K.)
| | - Hanyu Xia
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.B.); (H.X.); (E.L.T.); (M.R.K.)
| | - Eric L. Thompson
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.B.); (H.X.); (E.L.T.); (M.R.K.)
| | - Mark R. Kelley
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.B.); (H.X.); (E.L.T.); (M.R.K.)
- Department of Pediatrics, Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Jill C. Fehrenbacher
- Department of Pharmacology and Toxicology, Stark Neuroscience Research Institute, Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Correspondence: ; Tel.: +1-317-274-8360
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