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Quiñones JL, Tang M, Fang Q, Sobol RW, Demple B. C-terminal residues of DNA polymerase β and E3 ligase required for ubiquitin-linked proteolysis of oxidative DNA-protein crosslinks. DNA Repair (Amst) 2024; 143:103756. [PMID: 39243487 DOI: 10.1016/j.dnarep.2024.103756] [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: 07/01/2024] [Revised: 08/15/2024] [Accepted: 08/19/2024] [Indexed: 09/09/2024]
Abstract
Free radicals produce in DNA a large variety of base and deoxyribose lesions that are corrected by the base excision DNA repair (BER) system. However, the C1'-oxidized abasic residue 2-deoxyribonolactone (dL) traps DNA repair lyases in covalent DNA-protein crosslinks (DPC), including the core BER enzyme DNA polymerase beta (Polβ). Polβ-DPC are rapidly processed in mammalian cells by proteasome-dependent digestion. Blocking the proteasome causes oxidative Polβ-DPC to accumulate in a ubiquitylated form, and this accumulation is toxic to human cells. In the current study, we investigated the mechanism of Polβ-DPC processing in cells exposed to the dL-inducing oxidant 1,10-copper-ortho-phenanthroline. Alanine substitution of either or both of two Polβ C-terminal residues, lysine-206 and lysine-244, enhanced the accumulation of mutant Polβ-DPC relative to the wild-type protein, and removal of the mutant DPC was diminished. Substitution of the N-terminal lysines 41, 61, and 81 did not affect Polβ-DPC processing. For Polβ with the C-terminal lysine substitutions, the amount of ubiquitin in the stabilized DPC was lowered by ∼40 % relative to wild-type Polβ. Suppression of the HECT domain-containing E3 ubiquitin ligase TRIP12 augmented the formation of oxidative Polβ-DPC and prevented Polβ-DPC removal in oxidant-treated cells. Consistent with the toxicity of accumulated oxidative Polβ-DPC, TRIP12 knockdown increased oxidant-mediated cytotoxicity. Thus, ubiquitylation of lysine-206 and lysine-244 by TRIP12 is necessary for digestion of Polβ-DPC by the proteasome as the rapid first steps of DPC repair to prevent their cytotoxic accumulation. Understanding how DPC formed with Polβ or other AP lyases are repaired in vivo is an important step in revealing how cells cope with the toxic potential of such adducts.
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Affiliation(s)
- Jason L Quiñones
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Basic Science Tower 8-140, Stony Brook, New York 11794, USA
| | - Meiyi Tang
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Basic Science Tower 8-140, Stony Brook, New York 11794, USA
| | - Qingming Fang
- Mitchell Cancer Institute & Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
| | - Robert W Sobol
- Mitchell Cancer Institute & Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Stony Brook University School of Medicine, Basic Science Tower 8-140, Stony Brook, New York 11794, USA; Department of Radiation Oncology, Renaissance School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA.
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2
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Saville KM, Al-Rahahleh RQ, Siddiqui AH, Andrews ME, Roos WP, Koczor CA, Andrews JF, Hayat F, Migaud ME, Sobol RW. Oncometabolite 2-hydroxyglutarate suppresses basal protein levels of DNA polymerase beta that enhances alkylating agent and PARG inhibition induced cytotoxicity. DNA Repair (Amst) 2024; 140:103700. [PMID: 38897003 PMCID: PMC11239280 DOI: 10.1016/j.dnarep.2024.103700] [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: 03/10/2023] [Revised: 05/10/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024]
Abstract
Mutations in isocitrate dehydrogenase isoform 1 (IDH1) are primarily found in secondary glioblastoma (GBM) and low-grade glioma but are rare in primary GBM. The standard treatment for GBM includes radiation combined with temozolomide, an alkylating agent. Fortunately, IDH1 mutant gliomas are sensitive to this treatment, resulting in a more favorable prognosis. However, it's estimated that up to 75 % of IDH1 mutant gliomas will progress to WHO grade IV over time and develop resistance to alkylating agents. Therefore, understanding the mechanism(s) by which IDH1 mutant gliomas confer sensitivity to alkylating agents is crucial for developing targeted chemotherapeutic approaches. The base excision repair (BER) pathway is responsible for repairing most base damage induced by alkylating agents. Defects in this pathway can lead to hypersensitivity to these agents due to unresolved DNA damage. The coordinated assembly and disassembly of BER protein complexes are essential for cell survival and for maintaining genomic integrity following alkylating agent exposure. These complexes rely on poly-ADP-ribose formation, an NAD+-dependent post-translational modification synthesized by PARP1 and PARP2 during the BER process. At the lesion site, poly-ADP-ribose facilitates the recruitment of XRCC1. This scaffold protein helps assemble BER proteins like DNA polymerase beta (Polβ), a bifunctional DNA polymerase containing both DNA synthesis and 5'-deoxyribose-phosphate lyase (5'dRP lyase) activity. Here, we confirm that IDH1 mutant glioma cells have defective NAD+ metabolism, but still produce sufficient nuclear NAD+ for robust PARP1 activation and BER complex formation in response to DNA damage. However, the overproduction of 2-hydroxyglutarate, an oncometabolite produced by the IDH1 R132H mutant protein, suppresses BER capacity by reducing Polβ protein levels. This defines a novel mechanism by which the IDH1 mutation in gliomas confers cellular sensitivity to alkylating agents and to inhibitors of the poly-ADP-ribose glycohydrolase, PARG.
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Affiliation(s)
- Kate M Saville
- Department of Pharmacology & Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, United States
| | - Rasha Q Al-Rahahleh
- Department of Pharmacology & Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, United States; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, United States
| | - Aisha H Siddiqui
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, United States
| | - Morgan E Andrews
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, United States
| | - Wynand P Roos
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, United States
| | - Christopher A Koczor
- Department of Pharmacology & Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, United States
| | - Joel F Andrews
- Department Biochemistry and Molecular Biology & Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, United States
| | - Faisal Hayat
- Department of Pharmacology & Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, United States
| | - Marie E Migaud
- Department of Pharmacology & Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, United States
| | - Robert W Sobol
- Department of Pharmacology & Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, United States; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, United States.
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3
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Inanc B, Fang Q, Andrews JF, Zeng X, Clark J, Li J, Dey NB, Ibrahim M, Sykora P, Yu Z, Braganza A, Verheij M, Jonkers J, Yates NA, Vens C, Sobol RW. TRIP12 governs DNA Polymerase β involvement in DNA damage response and repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588474. [PMID: 38645048 PMCID: PMC11030427 DOI: 10.1101/2024.04.08.588474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The multitude of DNA lesion types, and the nuclear dynamic context in which they occur, present a challenge for genome integrity maintenance as this requires the engagement of different DNA repair pathways. Specific 'repair controllers' that facilitate DNA repair pathway crosstalk between double strand break (DSB) repair and base excision repair (BER), and regulate BER protein trafficking at lesion sites, have yet to be identified. We find that DNA polymerase β (Polβ), crucial for BER, is ubiquitylated in a BER complex-dependent manner by TRIP12, an E3 ligase that partners with UBR5 and restrains DSB repair signaling. Here we find that, TRIP12, but not UBR5, controls cellular levels and chromatin loading of Polβ. Required for Polβ foci formation, TRIP12 regulates Polβ involvement after DNA damage. Notably, excessive TRIP12-mediated shuttling of Polβ affects DSB formation and radiation sensitivity, underscoring its precedence for BER. We conclude that the herein discovered trafficking function at the nexus of DNA repair signaling pathways, towards Polβ-directed BER, optimizes DNA repair pathway choice at complex lesion sites.
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4
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Sobol RW. Mouse models to explore the biological and organismic role of DNA polymerase beta. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2024; 65 Suppl 1:57-71. [PMID: 38619421 PMCID: PMC11027944 DOI: 10.1002/em.22593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
Gene knock-out (KO) mouse models for DNA polymerase beta (Polβ) revealed that loss of Polβ leads to neonatal lethality, highlighting the critical organismic role for this DNA polymerase. While biochemical analysis and gene KO cell lines have confirmed its biochemical role in base excision repair and in TET-mediated demethylation, more long-lived mouse models continue to be developed to further define its organismic role. The Polb-KO mouse was the first of the Cre-mediated tissue-specific KO mouse models. This technology was exploited to investigate roles for Polβ in V(D)J recombination (variable-diversity-joining rearrangement), DNA demethylation, gene complementation, SPO11-induced DNA double-strand break repair, germ cell genome stability, as well as neuronal differentiation, susceptibility to genotoxin-induced DNA damage, and cancer onset. The revolution in knock-in (KI) mouse models was made possible by CRISPR/cas9-mediated gene editing directly in C57BL/6 zygotes. This technology has helped identify phenotypes associated with germline or somatic mutants of Polβ. Such KI mouse models have helped uncover the importance of key Polβ active site residues or specific Polβ enzyme activities, such as the PolbY265C mouse that develops lupus symptoms. More recently, we have used this KI technology to mutate the Polb gene with two codon changes, yielding the PolbL301R/V303R mouse. In this KI mouse model, the expressed Polβ protein cannot bind to its obligate heterodimer partner, Xrcc1. Although the expressed mutant Polβ protein is proteolytically unstable and defective in recruitment to sites of DNA damage, the homozygous PolbL301R/V303R mouse is viable and fertile, yet small in stature. We expect that this and additional targeted mouse models under development are poised to reveal new biological and organismic roles for Polβ.
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Affiliation(s)
- Robert W. Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912
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5
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Krishna Rao V, Paul S, Gulkis M, Shen Z, Nair H, Singh A, Li C, Sharma AK, Çağlayan M, Das C, Das B, Kundu CN, Narayan S, Guchhait SK. Molecular editing of NSC-666719 enabling discovery of benzodithiazinedioxide-guanidines as anticancer agents. RSC Med Chem 2024; 15:937-962. [PMID: 38516586 PMCID: PMC10953490 DOI: 10.1039/d3md00648d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/25/2024] [Indexed: 03/23/2024] Open
Abstract
DNA polymerase β (Polβ) is crucial for the base excision repair (BER) pathway of DNA damage repair and is an attractive target for suppressing tumorigenesis as well as chemotherapeutic intervention of cancer. In this study, a unique strategy of scaffold-hopping-based molecular editing of a bioactive agent NSC-666719 was investigated, which led to the development of new molecular motifs with Polβ inhibitory activity. NSC compound and its analogs (two series) were prepared, focusing on pharmacophore-based molecular diversity. Most compounds showed higher activities than the parent NSC-666719 and exhibited effects on apoptosis. The inhibitory activity of Polβ was evaluated in both in vitro reconstituted and in vivo intact cell systems. Compound 10e demonstrated significant Polβ interaction and inhibition characteristics, including direct, non-covalent, reversible, and comparable binding affinity. The investigated approach is useful, and the discovered novel analogs have a high potential for developing as anticancer therapeutics.
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Affiliation(s)
- Vajja Krishna Rao
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Sector 67, SAS Nagar Mohali Punjab 160062 India
| | - Subarno Paul
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Zhihang Shen
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Haritha Nair
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Amandeep Singh
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine 500 University Drive Hershey PA 17033 USA
| | - Chenglong Li
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida 1345 Center Drive Gainesville FL 32610 USA
| | - Arun K Sharma
- Department of Pharmacology, Penn State Cancer Institute, CH72, Penn State College of Medicine 500 University Drive Hershey PA 17033 USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Chinmay Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Biswajit Das
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Chanakya N Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University Campus-11, Patia Bhubaneswar-751024 Odisha India
| | - Satya Narayan
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida 1200 Newell Drive Gainesville FL 32610 USA
| | - Sankar K Guchhait
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Sector 67, SAS Nagar Mohali Punjab 160062 India
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6
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Almohdar D, Gulkis M, Ortiz A, Tang Q, Sobol RW, Çağlayan M. Impact of polβ/XRCC1 Interaction Variants on the Efficiency of Nick Sealing by DNA Ligase IIIα in the Base Excision Repair Pathway. J Mol Biol 2024; 436:168410. [PMID: 38135179 PMCID: PMC11090158 DOI: 10.1016/j.jmb.2023.168410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/17/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023]
Abstract
Base excision repair (BER) requires a coordination from gap filling by DNA polymerase (pol) β to subsequent nick sealing by DNA ligase (LIG) IIIα at downstream steps of the repair pathway. X-ray cross-complementing protein 1 (XRCC1), a non-enzymatic scaffolding protein, forms repair complexes with polβ and LIGIIIα. Yet, the impact of the polβ mutations that affect XRCC1 interaction and protein stability on the repair pathway coordination during nick sealing by LIGIIIα remains unknown. Our results show that the polβ colon cancer-associated variant T304 exhibits a reduced interaction with XRCC1 and the mutations in the interaction interface of V303 loop (L301R/V303R/V306R) and at the lysine residues (K206A/K244A) that prevent ubiquitin-mediated degradation of the protein exhibit a diminished repair protein complex formation with XRCC1. Furthermore, we demonstrate no significant effect on gap and nick DNA binding affinity of wild-type polβ by these mutations. Finally, our results reveal that XRCC1 leads to an efficient channeling of nick repair products after nucleotide incorporation by polβ variants to LIGIIIα, which is compromised by the L301R/V303R/V306R and K206A/K244A mutations. Overall, our findings provide insight into how the mutations in the polβ/XRCC1 interface and the regions affecting protein stability could dictate accurate BER pathway coordination at the downstream steps involving nick sealing by LIGIIIα.
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Affiliation(s)
- Danah Almohdar
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Mitchell Gulkis
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Abigail Ortiz
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Qun Tang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA
| | - Robert W Sobol
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
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7
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Zhang X, Wang L, Huang R, Wang J, Yan Q. Perfluoro-tert-butyl Group-Derived Capmatinib: Synthesis, Biological Evaluation and Its Application in 19 F Magnetic Resonance Imaging. Chembiochem 2023; 24:e202300354. [PMID: 37345408 DOI: 10.1002/cbic.202300354] [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: 05/11/2023] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 06/23/2023]
Abstract
Capmatinib is an FDA-approved drug to treat metastatic non-small cell lung cancer with MET-exon 14 skipping. Herein, the perfluoro-tert-butyl group, which possesses nine chemically identical fluorine atoms, was introduced on Capmatinib to afford a targeted 19 F magnetic resonance imaging (MRI) probe, perfluoro-tert-butyl group-derived Capmatinib (9F-CAP). The 19 F MRI concentration limit was found to be 25 mM in FLASH sequence. Molecular docking simulation, surface plasmon resonance (SPR) (with a Kd of 40.7 μM), half-inhibitory concentration (with a IC50 of 168 nM), Annexin V, and cytotoxicity assays jointly demonstrated that the 9F-CAP targeted cMET protein specifically. Therefore, the targeted imaging capability of 9F-CAP is of great significance for the preoperative diagnosis of specific cancers.
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Affiliation(s)
- Xinnan Zhang
- Key Laboratory for Advanced Materials and Feringa Nobel, Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd., Shanghai, 200237, China
| | - Luting Wang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd., Shanghai, 201203, China
| | - Ruimin Huang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd., Shanghai, 201203, China
| | - Jingbo Wang
- Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, 639 Zhizaoju Rd., Shanghai, 200025, China
| | - Qifan Yan
- Key Laboratory for Advanced Materials and Feringa Nobel, Prize Scientist Joint Research Center, School of Chemistry and Molecular Engineering, East China University of Science and Technology, 130 Meilong Rd., Shanghai, 200237, China
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8
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Li W, Zhang Z, Li J, Mu J, Sun M, Wu X, Niu X, Yang Y, Yan H, Xu X, Xue C, Qian L, Tian Y. Silibinin exerts neuroprotective effects against cerebral hypoxia/reoxygenation injury by activating the GAS6/Axl pathway. Toxicology 2023; 495:153598. [PMID: 37544575 DOI: 10.1016/j.tox.2023.153598] [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: 05/28/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
Abstract
Ischemic stroke is regarded one of the most common causes of brain vulnerability. Silibinin (SIL), extracted from the seeds of Silybinisus laborinum L., has been found to exhibit obvious therapeutic effects on neurodegenerative diseases. GAS6 has been proven to have significant neuroprotective effects; however, the role of SIL and GAS6 in ischemic stroke remains unclear. This study aimed to investigate the protective effects of SIL against cerebral ischemia-reperfusion injury in neuroblastoma N2a cells, as well as the mechanisms involved. Firstly, the toxicity of SIL was evaluated, and safe concentrations were chosen for subsequent experiments. Then, SIL exerts significant neuroprotection against hypoxia/reoxygenation (HR) injury in N2a cells, as manifested by increased cell viability, decreased apoptotic rate, LDH, and ROS generation. Additionally, SIL was found to inhibit HR-induced apoptosis, mitochondria dysfunction, and oxidative stress. However, silencing of GAS6 inhibited the neuroprotective effects of SIL. To sum up, these results suggest that SIL may be a promising therapeutic agent for the treatment of ischemic stroke.
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Affiliation(s)
- Weiping Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China
| | - Zhe Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China
| | - Jiawen Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China
| | - Jun Mu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China
| | - Meng Sun
- Department of Cardiology, The First Hospital of Shanxi Medical University, 85 Jiefang South Road, Taiyuan 030001, China
| | - Xue Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China
| | - Xiaochen Niu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China
| | - Huanle Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China
| | - Xiaoling Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China
| | - Chengxu Xue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China
| | - Lu Qian
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China.
| | - Ye Tian
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, 229 Taibai North Road, Xi'an 710069, China; Xi'an Key Laboratory of Cardiovascular and Cerebrovascular Diseases, Xi'an No.3 Hospital, Faculty of Life Sciences and Medicine, Northwest University, 10 Fengcheng Three Road, Xi'an 710021, China.
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9
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Kratz A, Kim M, Kelly MR, Zheng F, Koczor CA, Li J, Ono K, Qin Y, Churas C, Chen J, Pillich RT, Park J, Modak M, Collier R, Licon K, Pratt D, Sobol RW, Krogan NJ, Ideker T. A multi-scale map of protein assemblies in the DNA damage response. Cell Syst 2023; 14:447-463.e8. [PMID: 37220749 PMCID: PMC10330685 DOI: 10.1016/j.cels.2023.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/30/2023] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
The DNA damage response (DDR) ensures error-free DNA replication and transcription and is disrupted in numerous diseases. An ongoing challenge is to determine the proteins orchestrating DDR and their organization into complexes, including constitutive interactions and those responding to genomic insult. Here, we use multi-conditional network analysis to systematically map DDR assemblies at multiple scales. Affinity purifications of 21 DDR proteins, with/without genotoxin exposure, are combined with multi-omics data to reveal a hierarchical organization of 605 proteins into 109 assemblies. The map captures canonical repair mechanisms and proposes new DDR-associated proteins extending to stress, transport, and chromatin functions. We find that protein assemblies closely align with genetic dependencies in processing specific genotoxins and that proteins in multiple assemblies typically act in multiple genotoxin responses. Follow-up by DDR functional readouts newly implicates 12 assembly members in double-strand-break repair. The DNA damage response assemblies map is available for interactive visualization and query (ccmi.org/ddram/).
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Affiliation(s)
- Anton Kratz
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Minkyu Kim
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA; University of Texas Health Science Center San Antonio, Department of Biochemistry and Structural Biology, San Antonio, TX 78229, USA
| | - Marcus R Kelly
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Fan Zheng
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Christopher A Koczor
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Jianfeng Li
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA
| | - Keiichiro Ono
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Yue Qin
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Christopher Churas
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jing Chen
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Rudolf T Pillich
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Jisoo Park
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Maya Modak
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA
| | - Rachel Collier
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Kate Licon
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Dexter Pratt
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA
| | - Robert W Sobol
- University of South Alabama, Department of Pharmacology and Mitchell Cancer Institute, Mobile, AL 36604, USA; Brown University, Department of Pathology and Laboratory Medicine and Legorreta Cancer Center, Providence, RI 02903, USA.
| | - Nevan J Krogan
- University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA 94158, USA; The J. David Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
| | - Trey Ideker
- University of California San Diego, Department of Medicine, San Diego, CA 92093, USA; The Cancer Cell Map Initiative, San Francisco and La Jolla, CA, USA.
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10
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Hanson EK, Whelan RJ. Application of the Nicoya OpenSPR to Studies of Biomolecular Binding: A Review of the Literature from 2016 to 2022. SENSORS (BASEL, SWITZERLAND) 2023; 23:4831. [PMID: 37430747 DOI: 10.3390/s23104831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 07/12/2023]
Abstract
The Nicoya OpenSPR is a benchtop surface plasmon resonance (SPR) instrument. As with other optical biosensor instruments, it is suitable for the label-free interaction analysis of a diverse set of biomolecules, including proteins, peptides, antibodies, nucleic acids, lipids, viruses, and hormones/cytokines. Supported assays include affinity/kinetics characterization, concentration analysis, yes/no assessment of binding, competition studies, and epitope mapping. OpenSPR exploits localized SPR detection in a benchtop platform and can be connected with an autosampler (XT) to perform automated analysis over an extended time period. In this review article, we provide a comprehensive survey of the 200 peer-reviewed papers published between 2016 and 2022 that use the OpenSPR platform. We highlight the range of biomolecular analytes and interactions that have been investigated using the platform, provide an overview on the most common applications for the instrument, and point out some representative research that highlights the flexibility and utility of the instrument.
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Affiliation(s)
- Eliza K Hanson
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Rebecca J Whelan
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
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11
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Koczor CA, Thompson MK, Sharma N, Prakash A, Sobol RW. Polβ/XRCC1 heterodimerization dictates DNA damage recognition and basal Polβ protein levels without interfering with mouse viability or fertility. DNA Repair (Amst) 2023; 123:103452. [PMID: 36702010 PMCID: PMC9992099 DOI: 10.1016/j.dnarep.2023.103452] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/07/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
DNA Polymerase β (Polβ) performs two critical enzymatic steps during base excision repair (BER) - gap filling (nucleotidyl transferase activity) and gap tailoring (dRP lyase activity). X-ray repair cross complementing 1 (XRCC1) facilitates the recruitment of Polβ to sites of DNA damage through an evolutionarily conserved Polβ/XRCC1 interaction interface, the V303 loop. While previous work describes the importance of the Polβ/XRCC1 interaction for human Polβ protein stability and recruitment to sites of DNA damage, the impact of disrupting the Polβ/XRCC1 interface on animal viability, physiology, and fertility is unknown. Here, we characterized the effect of disrupting Polβ/XRCC1 heterodimerization in mice and mouse cells by complimentary approaches. First, we demonstrate, via laser micro-irradiation, that mouse Polβ amino acid residues L301 and V303 are critical to facilitating Polβ recruitment to sites of DNA damage. Next, we solved the crystal structures of mouse wild type Polβ and a mutant protein harboring alterations in residues L301 and V303 (L301R/V303R). Our structural analyses suggest that Polβ amino acid residue V303 plays a role in maintaining an interaction with the oxidized form of XRCC1. Finally, we created CRISPR/Cas9-modified Polb mice with homozygous L301R/V303R mutations (PolbL301R-V303R/L301R-V303R) that are fertile yet exhibit 15% reduced body weight at 17 weeks of age, as compared to heterozygous mice. Fibroblasts derived from PolbL301R-V303R/L301R-V303R mice demonstrate that mutation of mouse Polβ's XRCC1 interaction domain leads to an ∼85% decrease in Polβ protein levels. In all, these studies are consistent with a role for the oxidized form of XRCC1 in providing stability to the Polβ protein through Polβ/XRCC1 heterodimer formation.
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Affiliation(s)
- Christopher A Koczor
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Marlo K Thompson
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Nidhi Sharma
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA.
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; Department of Pathology and Laboratory Medicine, Warren Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA.
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12
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Koczor CA, Haider AJ, Saville KM, Li J, Andrews JF, Beiser AV, Sobol RW. Live Cell Detection of Poly(ADP-Ribose) for Use in Genetic and Genotoxic Compound Screens. Cancers (Basel) 2022; 14:3676. [PMID: 35954352 PMCID: PMC9367489 DOI: 10.3390/cancers14153676] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
Poly(ADP-ribose) (PAR) is a molecular scaffold that aids in the formation of DNA repair protein complexes. Tools to sensitively quantify PAR in live cells have been lacking. We recently described the LivePAR probe (EGFP fused to the RNF146-encoded WWE PAR binding domain) to measure PAR formation at sites of laser micro-irradiation in live cells. Here, we present two methods that expand on the use of LivePAR and its WWE domain. First, LivePAR enriches in the nucleus of cells following genotoxic challenge. Image quantitation can identify single-cell PAR formation following genotoxic stress at concentrations lower than PAR ELISA or PAR immunoblot, with greater sensitivity to genotoxic stress than CometChip. In a second approach, we used the RNF146-encoded WWE domain to develop a split luciferase probe for analysis in a 96-well plate assay. We then applied these PAR analysis tools to demonstrate their broad applicability. First, we show that both approaches can identify genetic modifications that alter PARylation levels, such as hyper-PARylation in BRCA2-deficient cancer cells. Second, we demonstrate the utility of the WWE split luciferase assay to characterize the cellular response of genotoxins, PARP inhibitors, and PARG inhibitors, thereby providing a screening method to identify PAR modulating compounds.
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Affiliation(s)
- Christopher A. Koczor
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Aaron J. Haider
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Kate M. Saville
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Jianfeng Li
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Joel F. Andrews
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Alison V. Beiser
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
| | - Robert W. Sobol
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL 36688, USA; (C.A.K.); (K.M.S.); (J.L.); (A.V.B.)
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA; (A.J.H.); (J.F.A.)
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13
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Targeting HIF-1α Function in Cancer through the Chaperone Action of NQO1: Implications of Genetic Diversity of NQO1. J Pers Med 2022; 12:jpm12050747. [PMID: 35629169 PMCID: PMC9146583 DOI: 10.3390/jpm12050747] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
HIF-1α is a master regulator of oxygen homeostasis involved in different stages of cancer development. Thus, HIF-1α inhibition represents an interesting target for anti-cancer therapy. It was recently shown that the HIF-1α interaction with NQO1 inhibits proteasomal degradation of the former, thus suggesting that targeting the stability and/or function of NQO1 could lead to the destabilization of HIF-1α as a therapeutic approach. Since the molecular interactions of NQO1 with HIF-1α are beginning to be unraveled, in this review we discuss: (1) Structure–function relationships of HIF-1α; (2) our current knowledge on the intracellular functions and stability of NQO1; (3) the pharmacological modulation of NQO1 by small ligands regarding function and stability; (4) the potential effects of genetic variability of NQO1 in HIF-1α levels and function; (5) the molecular determinants of NQO1 as a chaperone of many different proteins including cancer-associated factors such as HIF-1α, p53 and p73α. This knowledge is then further discussed in the context of potentially targeting the intracellular stability of HIF-1α by acting on its chaperone, NQO1. This could result in novel anti-cancer therapies, always considering that the substantial genetic variability in NQO1 would likely result in different phenotypic responses among individuals.
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14
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Li J, Garavaglia S, Ye Z, Moretti A, Belyaeva OV, Beiser A, Ibrahim M, Wilk A, McClellan S, Klyuyeva AV, Goggans KR, Kedishvili NY, Salter EA, Wierzbicki A, Migaud ME, Mullett SJ, Yates NA, Camacho CJ, Rizzi M, Sobol RW. A specific inhibitor of ALDH1A3 regulates retinoic acid biosynthesis in glioma stem cells. Commun Biol 2021; 4:1420. [PMID: 34934174 PMCID: PMC8692581 DOI: 10.1038/s42003-021-02949-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 12/07/2021] [Indexed: 01/31/2023] Open
Abstract
Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs may regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). Accordingly, potent, and selective inhibitors of key ALDH enzymes may represent a novel CSC-directed treatment paradigm for ALDH+ cancer types. Of the many ALDH isoforms, we and others have implicated the elevated expression of ALDH1A3 in mesenchymal glioma stem cells (MES GSCs) as a target for the development of novel therapeutics. To this end, our structure of human ALDH1A3 combined with in silico modeling identifies a selective, active-site inhibitor of ALDH1A3. The lead compound, MCI-INI-3, is a selective competitive inhibitor of human ALDH1A3 and shows poor inhibitory effect on the structurally related isoform ALDH1A1. Mass spectrometry-based cellular thermal shift analysis reveals that ALDH1A3 is the primary binding protein for MCI-INI-3 in MES GSC lysates. The inhibitory effect of MCI-INI-3 on retinoic acid biosynthesis is comparable with that of ALDH1A3 knockout, suggesting that effective inhibition of ALDH1A3 is achieved with MCI-INI-3. Further development is warranted to characterize the role of ALDH1A3 and retinoic acid biosynthesis in glioma stem cell growth and differentiation.
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Affiliation(s)
- Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Silvia Garavaglia
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Zhaofeng Ye
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Andrea Moretti
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Alison Beiser
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Md Ibrahim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Anna Wilk
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Steve McClellan
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Alla V Klyuyeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Kelli R Goggans
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - E Alan Salter
- Department of Chemistry, University of South Alabama, 6040 USA South Drive, Mobile, AL, 36688, USA
| | - Andrzej Wierzbicki
- Department of Chemistry, University of South Alabama, 6040 USA South Drive, Mobile, AL, 36688, USA
| | - Marie E Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Steven J Mullett
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nathan A Yates
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy.
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA.
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15
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Temporal dynamics of base excision/single-strand break repair protein complex assembly/disassembly are modulated by the PARP/NAD +/SIRT6 axis. Cell Rep 2021; 37:109917. [PMID: 34731617 PMCID: PMC8607749 DOI: 10.1016/j.celrep.2021.109917] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/03/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
Assembly and disassembly of DNA repair protein complexes at DNA damage sites are essential for maintaining genomic integrity. Investigating factors coordinating assembly of the base excision repair (BER) proteins DNA polymerase β (Polβ) and XRCC1 to DNA lesion sites identifies a role for Polβ in regulating XRCC1 disassembly from DNA repair complexes and, conversely, demonstrates Polβ’s dependence on XRCC1 for complex assembly. LivePAR, a genetically encoded probe for live-cell imaging of poly(ADP-ribose) (PAR), reveals that Polβ and XRCC1 require PAR for repair-complex assembly, with PARP1 and PARP2 playing unique roles in complex dynamics. Further, BER complex assembly is modulated by attenuation/augmentation of NAD+ biosynthesis. Finally, SIRT6 does not modulate PARP1 or PARP2 activation but does regulate XRCC1 recruitment, leading to diminished Polβ abundance at sites of DNA damage. These findings highlight coordinated yet independent roles for PARP1, PARP2, and SIRT6 and their regulation by NAD+ bioavailability to facilitate BER. Koczor et al. use quantitative confocal microscopy to characterize DNA-damage-induced poly(ADP-ribose) (PAR) formation and assembly/disassembly kinetics in human cells. These studies highlight the coordinated yet independent roles for XRCC1, POLΒ, PARP1, PARP2, and SIRT6 (and regulation by NAD+) to facilitate BER/SSBR protein complex dynamics.
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16
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Thompson MK, Sobol RW, Prakash A. Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair. BIOLOGY 2021; 10:530. [PMID: 34198612 PMCID: PMC8232306 DOI: 10.3390/biology10060530] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022]
Abstract
The earliest methods of genome editing, such as zinc-finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs), utilize customizable DNA-binding motifs to target the genome at specific loci. While these approaches provided sequence-specific gene-editing capacity, the laborious process of designing and synthesizing recombinant nucleases to recognize a specific target sequence, combined with limited target choices and poor editing efficiency, ultimately minimized the broad utility of these systems. The discovery of clustered regularly interspaced short palindromic repeat sequences (CRISPR) in Escherichia coli dates to 1987, yet it was another 20 years before CRISPR and the CRISPR-associated (Cas) proteins were identified as part of the microbial adaptive immune system, by targeting phage DNA, to fight bacteriophage reinfection. By 2013, CRISPR/Cas9 systems had been engineered to allow gene editing in mammalian cells. The ease of design, low cytotoxicity, and increased efficiency have made CRISPR/Cas9 and its related systems the designer nucleases of choice for many. In this review, we discuss the various CRISPR systems and their broad utility in genome manipulation. We will explore how CRISPR-controlled modifications have advanced our understanding of the mechanisms of genome stability, using the modulation of DNA repair genes as examples.
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Affiliation(s)
- Marlo K. Thompson
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Mitchell Cancer Institute, University of South Alabama Health, Mobile, AL 36604, USA; (M.K.T.); (R.W.S.)
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, AL 36688, USA
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17
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Ross D, Siegel D. The diverse functionality of NQO1 and its roles in redox control. Redox Biol 2021; 41:101950. [PMID: 33774477 PMCID: PMC8027776 DOI: 10.1016/j.redox.2021.101950] [Citation(s) in RCA: 204] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/20/2022] Open
Abstract
In this review, we summarize the multiple functions of NQO1, its established roles in redox processes and potential roles in redox control that are currently emerging. NQO1 has attracted interest due to its roles in cell defense and marked inducibility during cellular stress. Exogenous substrates for NQO1 include many xenobiotic quinones. Since NQO1 is highly expressed in many solid tumors, including via upregulation of Nrf2, the design of compounds activated by NQO1 and NQO1-targeted drug delivery have been active areas of research. Endogenous substrates have also been proposed and of relevance to redox stress are ubiquinone and vitamin E quinone, components of the plasma membrane redox system. Established roles for NQO1 include a superoxide reductase activity, NAD+ generation, interaction with proteins and their stabilization against proteasomal degradation, binding and regulation of mRNA translation and binding to microtubules including the mitotic spindles. We also summarize potential roles for NQO1 in regulation of glucose and insulin metabolism with relevance to diabetes and the metabolic syndrome, in Alzheimer's disease and in aging. The conformation and molecular interactions of NQO1 can be modulated by changes in the pyridine nucleotide redox balance suggesting that NQO1 may function as a redox-dependent molecular switch.
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Affiliation(s)
- David Ross
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - David Siegel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
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18
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Abstract
The enzymes of the base excision repair (BER) pathway form DNA lesion-dependent, transient complexes that vary in composition based on the type of DNA damage. These protein sub-complexes facilitate substrate/product handoff to ensure reaction completion so as to avoid accumulation of potentially toxic DNA repair intermediates. However, in the mammalian cell, additional signaling molecules are required to fine-tune the activity of the BER pathway enzymes and to facilitate chromatin/histone reorganization for access to the DNA lesion for repair. These signaling enzymes include nicotinamide adenine dinucleotide (NAD+) dependent poly(ADP-ribose) polymerases (PARP1, PARP2) and class III deacetylases (SIRT1, SIRT6) that comprise a key PARP-NAD-SIRT axis to facilitate the regulation and coordination of BER in the mammalian cell. Here, we briefly describe the key nodes in the BER pathway that are regulated by this axis and highlight the cellular and organismal variation in NAD+ bioavailability that can impact BER signaling potential. We discuss how cellular NAD+ is required for BER to maintain genome stability and to mount a robust cellular response to DNA damage. Finally, we consider the dependence of BER on the PARP-NAD-SIRT axis for BER protein complex assembly.
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19
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Insight into vaccine development for Alpha-coronaviruses based on structural and immunological analyses of spike proteins. J Virol 2021; 95:JVI.02284-20. [PMID: 33414160 PMCID: PMC8092709 DOI: 10.1128/jvi.02284-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Coronaviruses that infect humans belong to the Alpha-coronavirus (including HCoV-229E) and Beta-coronavirus (including SARS-CoV and SARS-CoV-2) genera. In particular, SARS-CoV-2 is currently a major threat to public health worldwide. The spike (S) homotrimers bind to their receptors via the receptor-binding domain (RBD), which is a major target to block viral entry. In this study, we selected Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) as models. Their RBDs exist two different conformational states (lying or standing) in the prefusion S-trimer structure. Then, the differences in the immune responses to RBDs from these coronaviruses were analyzed structurally and immunologically. Our results showed that more RBD-specific antibodies (antibody titers: 1.28×105; 2.75×105) were induced by the S-trimer with the RBD in the "standing" state (SARS-CoV and SARS-CoV-2) than the S-trimer with the RBD in the "lying" state (HCoV-229E, antibody titers: <500), and more S-trimer-specific antibodies were induced by the RBD in the SARS-CoV and SARS-CoV-2 (antibody titers: 6.72×105; 5×105) than HCoV-229E (antibody titers:1.125×103). Besides, we found that the ability of the HCoV-229E RBD to induce neutralizing antibodies was lower than S-trimer, and the intact and stable S1 subunit was essential for producing efficient neutralizing antibodies against HCoV-229E. Importantly, our results reveal different vaccine strategies for coronaviruses, and S-trimer is better than RBD as a target for vaccine development in Alpha-coronavirus Our findings will provide important implications for future development of coronavirus vaccines.Importance Outbreak of coronaviruses, especially SARS-CoV-2, poses a serious threat to global public health. Development of vaccines to prevent the coronaviruses that can infect humans has always been a top priority. Coronavirus spike (S) protein is considered as a major target for vaccine development. Currently, structural studies have shown that Alpha-coronavirus (HCoV-229E) and Beta-coronavirus (SARS-CoV and SARS-CoV-2) RBDs are in "lying" and "standing" states in the prefusion S-trimer structure. Here, we evaluated the ability of S-trimer and RBD to induce neutralizing antibodies among these coronaviruses. Our results showed that the S-trimer and RBD are both candidates for subunit vaccines in Beta-coronavirus (SARS-CoV and SARS-CoV-2) with a RBD "standing" state. However, for Alpha-coronavirus (HCoV-229E) with a RBD "lying" state, the S-trimer may be more suitable for subunit vaccines than the RBD. Our results will provide novel ideas for the development of vaccines targeting S protein in the future.
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20
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Song X, Shi Y, Ding W, Niu T, Sun L, Tan Y, Chen Y, Shi J, Xiong Q, Huang X, Xiao S, Zhu Y, Cheng C, Fu ZF, Liu ZJ, Peng G. Cryo-EM analysis of the HCoV-229E spike glycoprotein reveals dynamic prefusion conformational changes. Nat Commun 2021; 12:141. [PMID: 33420048 PMCID: PMC7794242 DOI: 10.1038/s41467-020-20401-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
Coronaviruses spike (S) glycoproteins mediate viral entry into host cells by binding to host receptors. However, how the S1 subunit undergoes conformational changes for receptor recognition has not been elucidated in Alphacoronavirus. Here, we report the cryo-EM structures of the HCoV-229E S trimer in prefusion state with two conformations. The activated conformation may pose the potential exposure of the S1-RBDs by decreasing of the interaction area between the S1-RBDs and the surrounding S1-NTDs and S1-RBDs compared to the closed conformation. Furthermore, structural comparison of our structures with the previously reported HCoV-229E S structure showed that the S trimers trended to open the S2 subunit from the closed conformation to open conformation, which could promote the transition from pre- to postfusion. Our results provide insights into the mechanisms involved in S glycoprotein-mediated Alphacoronavirus entry and have implications for vaccine and therapeutic antibody design.
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Affiliation(s)
- Xiyong Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuejun Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Wei Ding
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, P.O.Box 603, Beijing, China
| | - Tongxin Niu
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Limeng Sun
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yubei Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yong Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiale Shi
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Qiqi Xiong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Xiaojun Huang
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Yanping Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Chongyun Cheng
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zhen F Fu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.,Departments of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Zhi-Jie Liu
- Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, China. .,iHuman Institute, ShanghaiTech University, Shanghai, China.
| | - Guiqing Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. .,Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.
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