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Duan M, Leng S, Mao P. Cisplatin in the era of PARP inhibitors and immunotherapy. Pharmacol Ther 2024; 258:108642. [PMID: 38614254 DOI: 10.1016/j.pharmthera.2024.108642] [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: 01/02/2024] [Revised: 03/21/2024] [Accepted: 03/29/2024] [Indexed: 04/15/2024]
Abstract
Platinum compounds such as cisplatin, carboplatin and oxaliplatin are widely used in chemotherapy. Cisplatin induces cytotoxic DNA damage that blocks DNA replication and gene transcription, leading to arrest of cell proliferation. Although platinum therapy alone is effective against many tumors, cancer cells can adapt to the treatment and gain resistance. The mechanisms for cisplatin resistance are complex, including low DNA damage formation, high DNA repair capacity, changes in apoptosis signaling pathways, rewired cell metabolisms, and others. Drug resistance compromises the clinical efficacy and calls for new strategies by combining cisplatin with other therapies. Exciting progress in cancer treatment, particularly development of poly (ADP-ribose) polymerase (PARP) inhibitors and immune checkpoint inhibitors, opened a new chapter to combine cisplatin with these new cancer therapies. In this Review, we discuss how platinum synergizes with PARP inhibitors and immunotherapy to bring new hope to cancer patients.
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Affiliation(s)
- Mingrui Duan
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA
| | - Shuguang Leng
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA.
| | - Peng Mao
- Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA; University of New Mexico Comprehensive Cancer Center, Albuquerque, NM 87131, USA.
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2
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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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3
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Guo W, Wu W, Wen Y, Gao Y, Zhuang S, Meng C, Chen H, Zhao Z, Hu K, Wu B. Structural insights into the catalytic mechanism of the AP endonuclease AtARP. Structure 2024:S0969-2126(24)00053-4. [PMID: 38503293 DOI: 10.1016/j.str.2024.02.014] [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: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/21/2024] [Indexed: 03/21/2024]
Abstract
Base excision repair (BER) is a critical genome defense pathway that copes with a broad range of DNA lesions induced by endogenous or exogenous genotoxic agents. AP endonucleases in the BER pathway are responsible for removing the damaged bases and nicking the abasic sites. In plants, the BER pathway plays a critical role in the active demethylation of 5-methylcytosine (5mC) DNA modification. Here, we have determined the crystal structures of Arabidopsis AP endonuclease AtARP in complex with the double-stranded DNA containing tetrahydrofuran (THF) that mimics the abasic site. We identified the critical residues in AtARP for binding and removing the abasic site and the unique residues for interacting with the orphan base. Additionally, we investigated the differences among the three plant AP endonucleases and evaluated the general DNA repair capacity of AtARP in a mammalian cell line. Our studies provide further mechanistic insights into the BER pathway in plants.
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Affiliation(s)
- Wenting Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Weijun Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yan Wen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yuan Gao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Shuting Zhuang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Chunyan Meng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Haitao Chen
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Zhipeng Zhao
- Department of Basic Medical Sciences, Taizhou University, Taizhou, Zhejiang 318000, China.
| | - Kaishun Hu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
| | - Baixing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
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4
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Abugable AA, Antar S, El-Khamisy SF. Chromosomal single-strand break repair and neurological disease: Implications on transcription and emerging genomic tools. DNA Repair (Amst) 2024; 135:103629. [PMID: 38266593 DOI: 10.1016/j.dnarep.2024.103629] [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: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024]
Abstract
Cells are constantly exposed to various sources of DNA damage that pose a threat to their genomic integrity. One of the most common types of DNA breaks are single-strand breaks (SSBs). Mutations in the repair proteins that are important for repairing SSBs have been reported in several neurological disorders. While several tools have been utilised to investigate SSBs in cells, it was only through recent advances in genomics that we are now beginning to understand the architecture of the non-random distribution of SSBs and their impact on key cellular processes such as transcription and epigenetic remodelling. Here, we discuss our current understanding of the genome-wide distribution of SSBs, their link to neurological disorders and summarise recent technologies to investigate SSBs at the genomic level.
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Affiliation(s)
- Arwa A Abugable
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Sarah Antar
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Sherif F El-Khamisy
- School of Biosciences, Firth Court, University of Sheffield, Sheffield, UK; The healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK; Institute of Cancer Therapeutics, Faculty of Life Sciences, University of Bradford, Bradford, UK.
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5
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Su A, Luo D, Li S, Zhang Y, Wang H, Yang L, Yang W, Pang P. An electrochemical biosensor for T4 polynucleotide kinase activity assay based on host-guest recognition between phosphate pillar[5]arene@MWCNTs and thionine. Analyst 2024; 149:1271-1279. [PMID: 38226548 DOI: 10.1039/d3an01863f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
T4 polynucleotide kinase helps with DNA recombination and repair. In this study, an electrochemical biosensor was developed for a T4 polynucleotide kinase activity assay and inhibitor screening based on phosphate pillar[5]arene and multi-walled carbon nanotube nanocomposites. The water-soluble pillar[5]arene was employed as the host to complex thionine guest molecules. The substrate DNA with a 5'-hydroxyl group initially self-assembled on the gold electrode surface through chemical adsorption of the thiol group, which was phosphorylated in the presence of T4 polynucleotide kinase. Titanium dioxide nanoparticles served as a bridge to link phosphorylated DNA and phosphate pillar[5]arene and multi-walled carbon nanotube composite due to strong phosphate-Ti4+-phosphate chemistry. Through supramolecular host-guest recognition, thionine molecules were able to penetrate the pillar[5]arene cavity, resulting in an enhanced electrochemical response signal. The electrochemical signal is proportional to the T4 polynucleotide kinase concentration in the range of 10-5 to 15 U mL-1 with a detection limit of 5 × 10-6 U mL-1. It was also effective in measuring HeLa cell lysate-related T4 polynucleotide kinase activity and inhibitor screening. The proposed method offers a unique sensing platform for kinase activity measurement, holding great potential in nucleotide kinase-target drug development, clinical diagnostics, and inhibitor screening.
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Affiliation(s)
- Aiwen Su
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Dan Luo
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Shixuan Li
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Yanli Zhang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Hongbin Wang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Lijuan Yang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3217, Australia
| | - Pengfei Pang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
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Luo D, Liu Z, Su A, Zhang Y, Wang H, Yang L, Yang W, Pang P. An electrochemical biosensor for detection of T4 polynucleotide kinase activity based on host-guest recognition between phosphate pillar[5]arene and methylene blue. Talanta 2024; 266:124956. [PMID: 37499362 DOI: 10.1016/j.talanta.2023.124956] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/29/2023]
Abstract
T4 polynucleotide kinase (T4 PNK) is an important DNA repair-related enzyme that plays a crucial role in DNA recombination, replication and damage repair. Herein, an electrochemical biosensor was developed for detection of T4 PNK activity and inhibitor screening based on supramolecular host-guest recognition between phosphate pillar (Dumitrache and McKinnon, 2017) [5] arene (PP5) and methylene blue (MB). The water-soluble PP5 employed as the host for complexation of MB guest molecules. The substrate DNA with 5'-hydroxyl group was first self-assembled on the gold electrode surface through the chemical adsorption of the thiol group, which was phosphorylated in the presence of T4 PNK and adenosine triphosphate (ATP). TiO2 served as a bridge to link phosphorylated DNA and PP5 via the robust phosphate-Ti4+-phosphate chemistry. The immobilized PP5 captured the MB on electrode surface via the supramolecular host-guest recognition interaction, resulting in an enhanced electrochemical response signal. The electrochemical signal is proportional to the T4 PNK concentration in the range of 2 × 10-4 to 5 U mL-1 with a detection limit of 1 × 10-4 U mL-1. It was also successfully used for PNK inhibitor screening and PNK activity assay in HeLa cell lysates sample. The proposed strategy provides a novel sensing platform for kinase activity assay and inhibitor screening, holding a great potential in clinical diagnostics, inhibitor screening, and nucleotide kinase-target drug discovery.
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Affiliation(s)
- Dan Luo
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China
| | - Zaiqiong Liu
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China
| | - Aiwen Su
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China
| | - Yanli Zhang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China.
| | - Hongbin Wang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China
| | - Lijuan Yang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China.
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3217, Australia
| | - Pengfei Pang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China.
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7
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Zhang S, Shao H, Li KB, Shi W, Han DM. Nanofluidic sensing platform for PNK assay using nonlinear hybridization chain reaction and its application in DNA logic circuit. Biosens Bioelectron 2023; 240:115632. [PMID: 37647684 DOI: 10.1016/j.bios.2023.115632] [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: 05/07/2023] [Revised: 08/14/2023] [Accepted: 08/22/2023] [Indexed: 09/01/2023]
Abstract
In this study, a polyethyleneimine (PEI)/Zr4+-functionalized nanofluidic sensing platform based on nonlinear hybridization chain reaction (NHCR) was developed for PNK activity assay. With the existence of PNK, the hairpin HPNK was cleaved by λ exonuclease, liberating the initiator T-DNA. Then T-DNA triggered the nonlinear HCR in solution and the reaction products were absorbed onto the nanopore, which changed the surface charge of nanofluidic device and could be detected by current-voltage characteristic curves. Compared to traditional linear HCR, the nonlinear HCR exhibits a higher sensitivity and order of growth kinetics, making it a powerful signal amplifier in bioanalysis. Due to the powerful amplification efficiency of nonlinear HCR, high sensitivity of the nanopore and specific recognition site of PNK/λ-Exo, an ultrasensitive and selective PNK sensing approach had been developed and applied to precisely quantitate the PNK activity with a LOD of 0.0001 U/mL. Moreover, utilizing this nanofluidic system as a foundation, we constructed a logic circuit that utilized PNK, adenosine diphosphate (ADP), and (NH4)2SO4 as input elements. ADP and (NH4)2SO4 had a crucial function in facilitating the PNK to regulate the DNA logic gate. By modifying the target and inhibitors, the nanofluidic device could detect a variety of stimuli and execute more advanced logical operations.
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Affiliation(s)
- Siqi Zhang
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China
| | - Huahao Shao
- Zhijiang College of Zhejiang University of Technology, Shaoxing, Zhejiang, 312000, China
| | - Kai-Bin Li
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China.
| | - Wei Shi
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China
| | - De-Man Han
- School of Pharmaceutical and Chemical Engineering, Taizhou University, Jiaojiang, Zhejiang, 318000, China.
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8
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Gohil D, Sarker AH, Roy R. Base Excision Repair: Mechanisms and Impact in Biology, Disease, and Medicine. Int J Mol Sci 2023; 24:14186. [PMID: 37762489 PMCID: PMC10531636 DOI: 10.3390/ijms241814186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human disease, and using BER genes as potential inhibitory targets to develop therapeutics. Within its segregation of short nucleotide (SN-) and long patch (LP-), there are currently six known global mechanisms, with emerging work in transcription- and replication-associated BER. Knockouts (KOs) of BER genes in mouse models showed that single glycosylase knockout had minimal phenotypic impact, but the effects were clearly seen in double knockouts. However, KOs of downstream enzymes showed critical impact on the health and survival of mice. BER gene deficiency contributes to cancer, inflammation, aging, and neurodegenerative disorders. Medicinal targets are being developed for single or combinatorial therapies, but only PARP and APE1 have yet to reach the clinical stage.
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Affiliation(s)
- Dhara Gohil
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
| | - Altaf H. Sarker
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
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9
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Wu Y, Yi J, Su A, Zhang Y, Wang H, Yang L, Yang W, Pang P. An electrochemical biosensor for T4 polynucleotide kinase activity identification according to host-guest recognition among phosphate pillar[5]arene@palladium nanoparticles@reduced graphene oxide nanocomposite and toluidine blue. Mikrochim Acta 2023; 190:394. [PMID: 37715009 DOI: 10.1007/s00604-023-05983-w] [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: 06/11/2023] [Accepted: 09/02/2023] [Indexed: 09/17/2023]
Abstract
T4 polynucleotide kinase (T4 PNK) helps with DNA recombination and repair. In this work, a phosphate pillar[5]arene@palladium nanoparticles@reduced graphene oxide nanocomposite (PP5@PdNPs@rGO)-based electrochemical biosensor was created to identify T4 PNK activities. The PP5 used to complex toluidine blue (TB) guest molecules is water-soluble. With T4 PNK and ATP, the substrate DNA, which included a 5'-hydroxyl group, initially self-assembled over the gold electrode surface by chemical adsorption of the thiol units. Strong phosphate-Zr4+-phosphate chemistry allowed Zr4+ to act as a bridge between phosphorylated DNA and PP5@PdNPs@rGO. Through a supramolecular host-guest recognition connection, TB molecules were able to penetrate the PP5 cavity, where they produced a stronger electrochemical response. With a 5 × 10-7 U mL-1 detection limit, the electrochemical signal is linear in the 10-6 to 1 U mL-1 T4 PNK concentration range. It was also effective in measuring HeLa cell lysate-related PNK activities and screening PNK inhibitors. Nucleotide kinase-target drug development, clinical diagnostics, and screening for inhibitors all stand to benefit greatly from the suggested technology, which offers a unique sensing mechanism for kinase activity measurement.
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Affiliation(s)
- Yongju Wu
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Jinfei Yi
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Aiwen Su
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Yanli Zhang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China.
| | - Hongbin Wang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Lijuan Yang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3217, Australia
| | - Pengfei Pang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
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Herrmann GK, Yin YW. The Role of Poly(ADP-ribose) Polymerase 1 in Nuclear and Mitochondrial Base Excision Repair. Biomolecules 2023; 13:1195. [PMID: 37627260 PMCID: PMC10452840 DOI: 10.3390/biom13081195] [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: 04/15/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Poly(ADP-ribose) (PAR) Polymerase 1 (PARP-1), also known as ADP-ribosyl transferase with diphtheria toxin homology 1 (ARTD-1), is a critical player in DNA damage repair, during which it catalyzes the ADP ribosylation of self and target enzymes. While the nuclear localization of PARP-1 has been well established, recent studies also suggest its mitochondrial localization. In this review, we summarize the differences between mitochondrial and nuclear Base Excision Repair (BER) pathways, the involvement of PARP-1 in mitochondrial and nuclear BER, and its functional interplay with other BER enzymes.
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Affiliation(s)
- Geoffrey K. Herrmann
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA;
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Y. Whitney Yin
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA;
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
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11
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Islam A, Chakraborty A, Gambardella S, Campopiano R, Sarker AH, Boldogh I, Hazra T. Functional analysis of a conserved site mutation in the DNA processing enzyme PNKP leading to Ataxia with Oculomotor Apraxia type 4 (AOA4) in humans. J Biol Chem 2023; 299:104714. [PMID: 37061005 DOI: 10.1016/j.jbc.2023.104714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023] Open
Abstract
Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved Glutamine (Gln) in PNKP leads to late-onset Ataxia with Oculomotor Apraxia type 4 (AOA4) in humans, and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant vs. wild-type PNKP are comparable; however, cells expressing mutant PNKP as well as Peripheral Blood Mononuclear Cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break (DSB) accumulation and consequent activation of the DNA damage response (DDR). Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha, but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DDR due to persistent accumulation of DSBs in the mutant cells, triggering death of vulnerable brain cells-a potential cause of neurodegeneration in AOA4 patients.
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Affiliation(s)
- Azharul Islam
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Stefano Gambardella
- IRCCS Neuromed & Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Rosa Campopiano
- IRCCS Neuromed & Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Altaf H Sarker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tapas Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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12
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Liu XW, Liu WJ, Meng Y, Hu J, Zhang CY. Development of a tandem signal amplification strategy for label-free sensing polynucleotide kinase activity in cancer cells. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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13
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Ovejero-Sánchez M, González-Sarmiento R, Herrero AB. DNA Damage Response Alterations in Ovarian Cancer: From Molecular Mechanisms to Therapeutic Opportunities. Cancers (Basel) 2023; 15:448. [PMID: 36672401 PMCID: PMC9856346 DOI: 10.3390/cancers15020448] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
The DNA damage response (DDR), a set of signaling pathways for DNA damage detection and repair, maintains genomic stability when cells are exposed to endogenous or exogenous DNA-damaging agents. Alterations in these pathways are strongly associated with cancer development, including ovarian cancer (OC), the most lethal gynecologic malignancy. In OC, failures in the DDR have been related not only to the onset but also to progression and chemoresistance. It is known that approximately half of the most frequent subtype, high-grade serous carcinoma (HGSC), exhibit defects in DNA double-strand break (DSB) repair by homologous recombination (HR), and current evidence indicates that probably all HGSCs harbor a defect in at least one DDR pathway. These defects are not restricted to HGSCs; mutations in ARID1A, which are present in 30% of endometrioid OCs and 50% of clear cell (CC) carcinomas, have also been found to confer deficiencies in DNA repair. Moreover, DDR alterations have been described in a variable percentage of the different OC subtypes. Here, we overview the main DNA repair pathways involved in the maintenance of genome stability and their deregulation in OC. We also recapitulate the preclinical and clinical data supporting the potential of targeting the DDR to fight the disease.
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Affiliation(s)
- María Ovejero-Sánchez
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-Spanish National Research Council, 37007 Salamanca, Spain
| | - Rogelio González-Sarmiento
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-Spanish National Research Council, 37007 Salamanca, Spain
| | - Ana Belén Herrero
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
- Molecular Medicine Unit, Department of Medicine, University of Salamanca, 37007 Salamanca, Spain
- Institute of Molecular and Cellular Biology of Cancer (IBMCC), University of Salamanca-Spanish National Research Council, 37007 Salamanca, Spain
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14
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Chakraborty A, Hazra TK. Highly Sensitive Radioactivity-Based DNA 3'-Phosphatase Activity Assay for Polynucleotide Kinase 3'-Phosphatase. Methods Mol Biol 2023; 2701:39-54. [PMID: 37574474 DOI: 10.1007/978-1-0716-3373-1_3] [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] [Indexed: 08/15/2023]
Abstract
Endogenous and exogenous genotoxic agents can generate various types of non-ligatable DNA ends at the site of strand break in the mammalian genome. If not repaired, such lesions will impede transcription and replication and can lead to various cellular pathologies. Among various "dirty" DNA ends, 3'-phosphate is one of the most abundant lesions generated in the mammalian cells. Polynucleotide kinase 3'-phosphatase (PNKP) is the major DNA end-processing enzyme for resolving 3'-phosphate termini in the mammalian cells, and thus, it is involved in DNA base excision repair (BER), single-strand break repair, and classical nonhomologous end joining (C-NHEJ)-mediated DNA double-strand break (DSB) repair. The 3'-OH ends generated following PNKP-mediated processing of 3'-P are utilized by a DNA polymerase to fill in the gap, and subsequently, the nick is sealed by a DNA ligase to complete the repair process. Here we describe two novel assay systems to detect phosphate release by PNKP's 3'-phosphatase activity and PNKP-mediated in vitro single-strand break repair with minimal repair components (PNKP, DNA polymerase, and DNA ligase) using either purified proteins or cell-free nuclear extracts from mammalian cells/tissues. These assays are highly reproducible and sensitive, and the researchers would be able to detect any significant difference in PNKP's 3'-phosphatase activity as well as PNKP-mediated single-strand break repair activity in diseased mammalian cells/tissues vs normal healthy controls.
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Affiliation(s)
- Anirban Chakraborty
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Tapas K Hazra
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Texas Medical Branch, Galveston, TX, USA.
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15
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Construction of a simple, localized and homogeneous fluorescence detection platform for T4 PNK activity based on tetrahedral DNA nanostructure-mediated primer exchange reaction. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Zhang H, Gao H, Gu Y, John A, Wei L, Huang M, Yu J, Adeosun AA, Weinshilboum RM, Wang L. 3D CRISPR screen in prostate cancer cells reveals PARP inhibitor sensitization through TBL1XR1-SMC3 interaction. Front Oncol 2022; 12:999302. [PMID: 36523978 PMCID: PMC9746894 DOI: 10.3389/fonc.2022.999302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/14/2022] [Indexed: 08/24/2023] Open
Abstract
Poly(ADP-ribose) (PAR) polymerase inhibitors (PARPi) either have been approved or being tested in the clinic for the treatment of a variety of cancers with homologous recombination deficiency (HRD). However, cancer cells can develop resistance to PARPi drugs through various mechanisms, and new biomarkers and combination therapeutic strategies need to be developed to support personalized treatment. In this study, a genome-wide CRISPR screen was performed in a prostate cancer cell line with 3D culture condition which identified novel signals involved in DNA repair pathways. One of these genes, TBL1XR1, regulates sensitivity to PARPi in prostate cancer cells. Mechanistically, we show that TBL1XR1 interacts with and stabilizes SMC3 on chromatin and promotes γH2AX spreading along the chromatin of the cells under DNA replication stress. TBL1XR1-SMC3 double knockdown (knockout) cells have comparable sensitivity to PARPi compared to SMC3 knockdown or TBL1XR1 knockout cells, and more sensitivity than WT cells. Our findings provide new insights into mechanisms underlying response to PARPi or platin compounds in the treatment of malignancies.
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Affiliation(s)
- Huan Zhang
- School of Medicine, Nantong University, Nantong, China
| | - Huanyao Gao
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Yayun Gu
- School of Medicine, Nantong University, Nantong, China
| | - August John
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Lixuan Wei
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Minhong Huang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Jia Yu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Adeyemi A. Adeosun
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Richard M. Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
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17
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Thada V, Greenberg RA. Unpaved roads: How the DNA damage response navigates endogenous genotoxins. DNA Repair (Amst) 2022; 118:103383. [PMID: 35939975 PMCID: PMC9703833 DOI: 10.1016/j.dnarep.2022.103383] [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: 05/02/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 02/03/2023]
Abstract
Accurate DNA repair is essential for cellular and organismal homeostasis, and DNA repair defects result in genetic diseases and cancer predisposition. Several environmental factors, such as ultraviolet light, damage DNA, but many other molecules with DNA damaging potential are byproducts of normal cellular processes. In this review, we highlight some of the prominent sources of endogenous DNA damage as well as their mechanisms of repair, with a special focus on repair by the homologous recombination and Fanconi anemia pathways. We also discuss how modulating DNA damage caused by endogenous factors may augment current approaches used to treat BRCA-deficient cancers. Finally, we describe how synthetic lethal interactions may be exploited to exacerbate DNA repair deficiencies and cause selective toxicity in additional types of cancers.
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18
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Zhang Q, Zhang X, Ma F, Zhang CY. Advances in quantum dot-based biosensors for DNA-modifying enzymes assay. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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19
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Wei L, Kong X, Wang M, Zhang Y, Pan R, Cheng Y, Lv Z, Zhou J, Ming J. A label-free T4 polynucleotide kinase fluorescence sensor based on split dimeric G-quadruplex and ligation-induced dimeric G-quadruplex/thioflavin T conformation. Anal Bioanal Chem 2022; 414:7923-7933. [PMID: 36136111 DOI: 10.1007/s00216-022-04327-6] [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: 07/27/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/01/2022]
Abstract
The phosphorylation process of DNA by T4 polynucleotide kinase (T4 PNK) plays a crucial role in DNA recombination, DNA replication, and DNA repair. Traditional monomeric G-quadruplex (G4) systems are always activated by single cation such as K+ or Na+. The conformation transformation caused by the coexistence of multiple cations may interfere with the signal readout and limit their applications in physiological system. In view of the stability of dimeric G4 in multiple cation solution, we reported a label-free T4 PNK fluorescence sensor based on split dimeric G4 and ligation-induced dimeric G4/thioflavin T (ThT) conformation. The dimeric G4 was divided into two independent pieces of one normal monomeric G4 and the other monomeric G4 fragment phosphorylated by T4 PNK in order to decrease the background signal. With the introduction of template DNA, DNA ligase, and invasive DNA, the dimeric G4 could be generated and liberated to combine with ThT to show obvious fluorescence signal. Using our strategy, the linear range from 0.005 to 0.5 U mL-1, and the detection limit of 0.0021 U mL-1 could be achieved without the consideration of interference caused by the coexistence of multiple cations. Additionally, research in real sample determination and inhibition effect investigations indicated its further potential application value in biochemical process research and clinic diagnostics.
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Affiliation(s)
- Liuya Wei
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Xianglong Kong
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Mengran Wang
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Yixin Zhang
- School of Clinical Medicine, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Ruiyan Pan
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Yuanzheng Cheng
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China
| | - Zhihua Lv
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, People's Republic of China.
| | - Jin Zhou
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China.
| | - Jingjing Ming
- School of Pharmacy, Weifang Medical University, Weifang, 261053, People's Republic of China.
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20
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Ray S, Abugable AA, Parker J, Liversidge K, Palminha NM, Liao C, Acosta-Martin AE, Souza CDS, Jurga M, Sudbery I, El-Khamisy SF. A mechanism for oxidative damage repair at gene regulatory elements. Nature 2022; 609:1038-1047. [PMID: 36171374 DOI: 10.1038/s41586-022-05217-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 08/09/2022] [Indexed: 11/09/2022]
Abstract
Oxidative genome damage is an unavoidable consequence of cellular metabolism. It arises at gene regulatory elements by epigenetic demethylation during transcriptional activation1,2. Here we show that promoters are protected from oxidative damage via a process mediated by the nuclear mitotic apparatus protein NuMA (also known as NUMA1). NuMA exhibits genomic occupancy approximately 100 bp around transcription start sites. It binds the initiating form of RNA polymerase II, pause-release factors and single-strand break repair (SSBR) components such as TDP1. The binding is increased on chromatin following oxidative damage, and TDP1 enrichment at damaged chromatin is facilitated by NuMA. Depletion of NuMA increases oxidative damage at promoters. NuMA promotes transcription by limiting the polyADP-ribosylation of RNA polymerase II, increasing its availability and release from pausing at promoters. Metabolic labelling of nascent RNA identifies genes that depend on NuMA for transcription including immediate-early response genes. Complementation of NuMA-deficient cells with a mutant that mediates binding to SSBR, or a mitotic separation-of-function mutant, restores SSBR defects. These findings underscore the importance of oxidative DNA damage repair at gene regulatory elements and describe a process that fulfils this function.
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Affiliation(s)
- Swagat Ray
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK.,School of Life and Environmental Sciences, Department of Life Sciences, University of Lincoln, Lincoln, UK
| | - Arwa A Abugable
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Jacob Parker
- School of Biosciences, University of Sheffield, Sheffield, UK.,Center for Advanced Parkinson Research, Harvard Medical School, Boston, MA, USA
| | | | - Nelma M Palminha
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Chunyan Liao
- School of Biosciences, University of Sheffield, Sheffield, UK.,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK
| | - Adelina E Acosta-Martin
- biOMICS Facility, Faculty of Science Mass Spectrometry Centre, University of Sheffield, Sheffield, UK
| | - Cleide D S Souza
- School of Biosciences, University of Sheffield, Sheffield, UK.,Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Mateusz Jurga
- Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK
| | - Ian Sudbery
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - Sherif F El-Khamisy
- School of Biosciences, University of Sheffield, Sheffield, UK. .,The Healthy Lifespan and Neuroscience Institutes, University of Sheffield, Sheffield, UK. .,Institute of Cancer Therapeutics, School of Pharmacy and Medical Sciences, University of Bradford, Bradford, UK.
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21
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Li J, Beiser A, Dey NB, Takeda S, Saha L, Hirota K, Parker L, Carter M, Arrieta M, Sobol R. A high-throughput 384-well CometChip platform reveals a role for 3-methyladenine in the cellular response to etoposide-induced DNA damage. NAR Genom Bioinform 2022; 4:lqac065. [PMID: 36110898 PMCID: PMC9469923 DOI: 10.1093/nargab/lqac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 01/31/2023] Open
Abstract
The Comet or single-cell gel electrophoresis assay is a highly sensitive method to measure cellular, nuclear genome damage. However, low throughput can limit its application for large-scale studies. To overcome these limitations, a 96-well CometChip platform was recently developed that increases throughput and reduces variation due to simultaneous processing and automated analysis of 96 samples. To advance throughput further, we developed a 384-well CometChip platform that allows analysis of ∼100 cells per well. The 384-well CometChip extends the capacity by 4-fold as compared to the 96-well system, enhancing application for larger DNA damage analysis studies. The overall sensitivity of the 384-well CometChip is consistent with that of the 96-well system, sensitive to genotoxin exposure and to loss of DNA repair capacity. We then applied the 384-well platform to screen a library of protein kinase inhibitors to probe each as enhancers of etoposide induced DNA damage. Here, we found that 3-methyladenine significantly increased levels of etoposide-induced DNA damage. Our results suggest that a 384-well CometChip is useful for large-scale DNA damage analyses, which may have increased potential in the evaluation of chemotherapy efficacy, compound library screens, population-based analyses of genome damage and evaluating the impact of environmental genotoxins on genome integrity.
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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
| | - 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
| | - Nupur B Dey
- 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
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Liton Kumar Saha
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University Minamiosawa 1-1, Hachioji-shi, Tokyo, 192-0397, Japan
| | - L Lynette Parker
- Center for Healthy Communities, College of Medicine, University of South Alabama Mobile, AL 36604, USA
| | - Mariah Carter
- Center for Healthy Communities, College of Medicine, University of South Alabama Mobile, AL 36604, USA
| | - Martha I Arrieta
- Department of Internal Medicine, College of Medicine, University of South Alabama, Mobile, AL 36604, USA
- Center for Healthy Communities, College of Medicine, University of South Alabama Mobile, AL 36604, 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 36604, USA
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22
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Liao Z, Yi M, Li J, Zhang Y. DNA repair in lung cancer: a large-scale quantitative analysis for polymorphisms in DNA repairing pathway genes and lung cancer susceptibility. Expert Rev Respir Med 2022; 16:997-1010. [PMID: 35984915 DOI: 10.1080/17476348.2022.2115361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND The results of associations between single nucleotide polymorphisms (SNPs) of genes in DNA repairing pathway and lung cancer (LC) risk are inconsistent. METHODS We applied allele, dominant and recessive models to explore the risk of researched variants to LC in total LC and subgroups by ethnicity or LC subtypes with a cutoff point of p < 0.05. RESULTS A total of 76,935 cases and 88,649 controls from 192 articles were included. Among the analyzed 40 variants from 20 genes, we found 9 statistically significant variants in overall populations by allele model, including five SNPs (rs1760944, rs9344, rs13181, rs1001581, and rs915927) increasing LC risk (odd ratios [ORs] = 1.10-1.71) and four SNPs (rs1042522, rs3213245, rs11615, and rs238406) decreasing the risk (ORs = 0.75-0.94). We identified rs1042522 and rs13181 as significant variants for LC in three models. Additionally, we identified differential significant SNPs in ethnic and subtype's analysis with comparison to total population. CONCLUSIONS There are five SNPs in DNA repairing pathway associated with increased LC risk and four others decreased LC risk. Besides, the risky SNPs in different ethnicities and various LC subtypes were partly different, and the contribution of different genotypes to risk alleles were various as well.
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Affiliation(s)
- Zexi Liao
- Department of Respiratory Medicine, Central South University, Changsha, Hunan, China.,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Xiangya Medical School, Central South University, Changsha, Hunan, China
| | - Minhan Yi
- Department of Respiratory Medicine, Central South University, Changsha, Hunan, China.,School of Life Sciences, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiaxin Li
- Department of Respiratory Medicine, Central South University, Changsha, Hunan, China.,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Xiangya Medical School, Central South University, Changsha, Hunan, China
| | - Yuan Zhang
- Department of Respiratory Medicine, Central South University, Changsha, Hunan, China.,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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23
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Caldecott KW. DNA single-strand break repair and human genetic disease. Trends Cell Biol 2022; 32:733-745. [PMID: 35643889 DOI: 10.1016/j.tcb.2022.04.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 12/15/2022]
Abstract
DNA single-strand breaks (SSBs) are amongst the commonest DNA lesions arising in cells, with many tens of thousands induced in each cell each day. SSBs arise not only from exposure to intracellular and environmental genotoxins but also as intermediates of normal DNA metabolic processes, such as the removal of torsional stress in DNA by topoisomerase enzymes and the epigenetic regulation of gene expression by DNA base excision repair (BER). If not rapidly detected and repaired, SSBs can result in RNA polymerase stalling, DNA replication fork collapse, and hyperactivation of the SSB sensor protein poly(ADP-ribose) polymerase 1 (PARP1). The potential impact of unrepaired SSBs is illustrated by the existence of genetic diseases in which proteins involved in SSB repair (SSBR) are mutated, and which are typified by hereditary neurodevelopmental and/or neurodegenerative disease. Here, I review our current understanding of SSBR and its impact on human neurological disease, with a focus on recent developments and concepts.
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Affiliation(s)
- Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, Science Park Road, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
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24
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Wang Y, Chen Y, Wan Y, Hong C, Shang J, Li F, Liu X, Wang F. An Autocatalytic DNA Circuit Based on Hybridization Chain Assembly for Intracellular Imaging of Polynucleotide Kinase. ACS APPLIED MATERIALS & INTERFACES 2022; 14:31727-31736. [PMID: 35786848 DOI: 10.1021/acsami.2c08523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polynucleotide kinase (PNK) plays an essential role in various cellular events by regulating phosphorylation processes, and abnormal homeostasis of PNK could cause many human diseases. Herein, we proposed an autocatalytic hybridization system (AHS) through the elaborate integration of hybridization chain assembly (HCA) and catalytic DNA assembly (CDA) that enables a highly efficient positive feedback amplification. The PNK-targeting AHS biosensor is composed of three modules: a recognition module, an HCA amplification module, and a CDA autocatalytic module. In the presence of PNK, the recognition module could transform the PNK input into an exposed nucleic acid initiator (I). Then the initiator strand I could trigger the autonomous HCA process in the amplification module, and the resulted HCA products could reassemble the split CDA trigger strand T, subsequently inducing the CDA process in the autocatalytic module to form abundant DNA duplex products. Consequently, the embedded initiator strand I was liberated from the CDA duplex product to autonomously trigger the new rounds of HCA circuit. The rational integration and cooperative cross-activation between the HCA and CDA module could prominently accelerate the reaction and realize the exponential amplification efficiency by initiator regeneration. As a result, the self-sustainable AHS amplifier could implement the sensitive detection of PNK in vitro and in biological samples and further fulfill accurate monitoring of the intracellular PNK activity and the effective screening of PNK inhibitors. This work paves a way for exploiting highly efficient artificial DNA circuits to analyze low-abundance biomarkers, holding great potential in biochemical research and clinical diagnosis.
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Affiliation(s)
- Yushi Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yingying Chen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yeqing Wan
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Chen Hong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Jinhua Shang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fengzhe Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China
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25
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Jia D, Fan W, Ren W, Liu C. One-step detection of T4 polynucleotide kinase activity based on single particle-confined enzyme reaction and digital particle counting. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Xu R, Pan L, Zhou Y, Gao Z, Miao J, Yang Y, Li D. Reproductive toxicity induced by benzo[a]pyrene exposure: first exploration highlighting the multi-stage molecular mechanism in female scallop Chlamys farreri. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:48675-48693. [PMID: 35195870 DOI: 10.1007/s11356-022-19235-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Reproductive toxicity induced by benzo[a]pyrene (B[a]P) exposure has received great ecotoxicological concerns. However, huge gaps on the molecular mechanism still exist in bivalves. In this study, reproduction-related indicators were investigated in female scallops Chlamys farreri during life cycle of proliferative, growth, mature, and spawn stages, under gradient concentrations of B[a]P at 0, 0.04, 0.4, and 4 μg/L. Meanwhile, a multi-stage ovarian transcriptome analysis under 4 μg/L B[a]P exposure was also conducted to elucidate the potential molecular mechanisms. The results indicated that life-cycle exposure to 0.4 and 4 μg/L B[a]P significantly decreased GSI and sex steroid levels. Even 0.04 μg/L B[a]P could play the adverse role in DNA integrity at the mature and spawn stages. Ovarian histological sections showed that B[a]P inhibited the maturation and release of oocytes. Through the functional enrichment analysis of differentially expressed genes (DEGs) from transcriptome data, 18 genes involved in endocrine disruption effects, DNA damage and repair, and oogenesis were selected and further determined by qRT-PCR. The downregulation of genes involved in steroidogenic and estrogen signaling pathways indicated that B[a]P could cause endocrine disruption through both receptor-dependent and receptor-independent pathways. The variations of gene expressions involved in DNA single-strand break and repair implied the presence of toxic mechanisms similar with vertebrates. Additionally, the changes of gene expressions of cell cycle, apoptosis, and cell adhesion suggested that exposure to B[a]P possibly caused the reproductive toxicity effects by affecting oogenesis. Taken together, this study was a pioneer in combining genome-wide transcriptomic analysis with its corresponding reproductive indicators (GSI, sex steroid levels, DNA single-strand break, and histological sections) to explore the bivalves' toxic mechanisms under B[a]P exposure. Meanwhile, some genes involved in estrogen signaling pathway and DNA damage were firstly analyzed in bivalves, and the expression data might be useful in establishing new hypotheses and discovering new biomarkers for marine biomonitoring.
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Affiliation(s)
- Ruiyi Xu
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
| | - Luqing Pan
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China.
| | - Yueyao Zhou
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
| | - Zhongyuan Gao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
| | - Jingjing Miao
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
| | - Yingying Yang
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
| | - Dongyu Li
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Yushan Road 5, Qingdao, 266003, People's Republic of China
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27
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Insights into the Possible Molecular Mechanisms of Resistance to PARP Inhibitors. Cancers (Basel) 2022; 14:cancers14112804. [PMID: 35681784 PMCID: PMC9179506 DOI: 10.3390/cancers14112804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The increasingly wide use of PARP inhibitors in breast, ovarian, pancreatic, and prostate cancers harbouring a pathogenic variant in BRCA1 or BRCA2 has highlighted the problem of resistance to therapy. This review summarises the complex interactions between PARP1, cell cycle regulation, response to stress replication, homologous recombination, and other DNA damage repair pathways in the setting of BRCA1/2 mutated cancers that could explain the development of primary or secondary resistance to PARP inhibitors. Abstract PARP1 enzyme plays an important role in DNA damage recognition and signalling. PARP inhibitors are approved in breast, ovarian, pancreatic, and prostate cancers harbouring a pathogenic variant in BRCA1 or BRCA2, where PARP1 inhibition results mainly in synthetic lethality in cells with impaired homologous recombination. However, the increasingly wide use of PARP inhibitors in clinical practice has highlighted the problem of resistance to therapy. Several different mechanisms of resistance have been proposed, although only the acquisition of secondary mutations in BRCA1/2 has been clinically proved. The aim of this review is to outline the key molecular findings that could explain the development of primary or secondary resistance to PARP inhibitors, analysing the complex interactions between PARP1, cell cycle regulation, PI3K/AKT signalling, response to stress replication, homologous recombination, and other DNA damage repair pathways in the setting of BRCA1/2 mutated cancers.
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28
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Zhang T, Shen Y, Ge J, Wang W, Qu L, Li Z. A highly sensitive fluorescence method for the detection of T4 polynucleotide kinase phosphatase based on polydopamine nanotubes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120594. [PMID: 34776378 DOI: 10.1016/j.saa.2021.120594] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/19/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
T4 polynucleotide kinase phosphatase (T4 PNKP) plays a critical role in various cellular events, such as DNA damage repair, replication, and recombination. Here, we have described a novel biosensor to detect the activity of T4 PNKP based on polydopamine nanotubes (PDANTs) mediated fluorescence resonance energy transfer (FRET). A FAM-labelled (6-carboxyl-fluorescein) hairpin DNA probe with 3'-phosphoryl terminal was designed as the substrate for T4 PNKP. With the addition of PDANTs, the fluorescence of FAM-labelled hairpin DNA probe could be quenched because of the high adsorption of hairpin DNA on PDANTs. When T4 PNKP dephosphorylated the DNA probe, a double-stranded DNA (dsDNA) product was obtained by Klenow fragment polymerase (KF polymerase) on its 3'-hydroxyl terminal, which could retain most of the fluorescence due to the week adsorption of dsDNA on PDANTs. The developed method demonstrates the sensitivity for T4 PNKP assay in the range from 0.05 to 1.5 U mL-1 with the detection limit of 0.005 U mL-1, which endows the proposed strategy with high enough sensitivity for practical detection in cell lysates. With the advantages mentioned above, this novel sensitive strategy has the potential in the study of DNA damage repair mechanisms.
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Affiliation(s)
- Tuo Zhang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Yanmei Shen
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Jia Ge
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China.
| | - Weixia Wang
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
| | - Lingbo Qu
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China.
| | - Zhaohui Li
- College of Chemistry, Green Catalysis Center, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou Key Laboratory of Functional Nanomaterial and Medical Theranostic, Zhengzhou University, Zhengzhou 450001, China
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29
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Jiang X, Shen X, Talap J, Yang D, Zeng S, Liu H, Cai S. Phosphorothioated and phosphate-terminal dumbbell (PP-TD) probe-based rapid detection of polynucleotide kinase activity. Analyst 2022; 147:4986-4990. [DOI: 10.1039/d2an01431a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A primer-free, sensitive assay has been developed to detect polynucleotide kinase (PNK) activity. This proposed method provides a promising platform for PNK activity monitoring and inhibition screening for drug discovery and clinical treatment.
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Affiliation(s)
- Xianfeng Jiang
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310020, China
| | - Xudan Shen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jadera Talap
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dan Yang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Su Zeng
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310020, China
| | - Sheng Cai
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Science, Zhejiang University, Hangzhou, Zhejiang 310058, China
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30
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Ma F, Li CC, Zhang CY. Nucleic acid amplification-integrated single-molecule fluorescence imaging for in vitro and in vivo biosensing. Chem Commun (Camb) 2021; 57:13415-13428. [PMID: 34796887 DOI: 10.1039/d1cc04799j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single-molecule fluorescence imaging is among the most advanced analytical technologies and has been widely adopted for biosensing due to its distinct advantages of simplicity, rapidity, high sensitivity, low sample consumption, and visualization capability. Recently, a variety of nucleic acid amplification approaches have been developed to provide a straightforward and highly efficient way for amplifying low abundance target signals. The integration of single-molecule fluorescence imaging with nucleic acid amplification has greatly facilitated the construction of various fluorescent biosensors for in vitro and in vivo detection of DNAs, RNAs, enzymes, and live cells with high sensitivity and good selectivity. Herein, we review the advances in the development of fluorescent biosensors by integrating single-molecule fluorescence imaging with nucleic acid amplification based on enzyme (e.g., DNA polymerase, RNA polymerase, exonuclease, and endonuclease)-assisted and enzyme-free (e.g., catalytic hairpin assembly, entropy-driven DNA amplification, ligation chain reaction, and hybridization chain reaction) strategies, and summarize the principles, features, and in vitro and in vivo applications of the emerging biosensors. Moreover, we discuss the remaining challenges and future directions in this area. This review may inspire the development of new signal-amplified single-molecule biosensors and promote their practical applications in fundamental and clinical research.
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Affiliation(s)
- Fei Ma
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China. .,School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Chen-Chen Li
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China. .,Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chun-Yang Zhang
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.
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31
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Crewe M, Madabhushi R. Topoisomerase-Mediated DNA Damage in Neurological Disorders. Front Aging Neurosci 2021; 13:751742. [PMID: 34899270 PMCID: PMC8656403 DOI: 10.3389/fnagi.2021.751742] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/23/2021] [Indexed: 12/12/2022] Open
Abstract
The nervous system is vulnerable to genomic instability and mutations in DNA damage response factors lead to numerous developmental and progressive neurological disorders. Despite this, the sources and mechanisms of DNA damage that are most relevant to the development of neuronal dysfunction are poorly understood. The identification of primarily neurological abnormalities in patients with mutations in TDP1 and TDP2 suggest that topoisomerase-mediated DNA damage could be an important underlying source of neuronal dysfunction. Here we review the potential sources of topoisomerase-induced DNA damage in neurons, describe the cellular mechanisms that have evolved to repair such damage, and discuss the importance of these repair mechanisms for preventing neurological disorders.
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32
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Adamowicz M, Hailstone R, Demin AA, Komulainen E, Hanzlikova H, Brazina J, Gautam A, Wells SE, Caldecott KW. XRCC1 protects transcription from toxic PARP1 activity during DNA base excision repair. Nat Cell Biol 2021; 23:1287-1298. [PMID: 34811483 PMCID: PMC8683375 DOI: 10.1038/s41556-021-00792-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 10/11/2021] [Indexed: 11/22/2022]
Abstract
Genetic defects in the repair of DNA single-strand breaks (SSBs) can result in neurological disease triggered by toxic activity of the single-strand-break sensor protein PARP1. However, the mechanism(s) by which this toxic PARP1 activity triggers cellular dysfunction are unclear. Here we show that human cells lacking XRCC1 fail to rapidly recover transcription following DNA base damage, a phenotype also observed in patient-derived fibroblasts with XRCC1 mutations and Xrcc1−/− mouse neurons. This defect is caused by excessive/aberrant PARP1 activity during DNA base excision repair, resulting from the loss of PARP1 regulation by XRCC1. We show that aberrant PARP1 activity suppresses transcriptional recovery during base excision repair by promoting excessive recruitment and activity of the ubiquitin protease USP3, which as a result reduces the level of monoubiquitinated histones important for normal transcriptional regulation. Importantly, inhibition and/or deletion of PARP1 or USP3 restores transcriptional recovery in XRCC1−/− cells, highlighting PARP1 and USP3 as possible therapeutic targets in neurological disease. Adamowicz et al. report that toxic PARP1 activity, induced by ataxia-associated mutations in XRCC1, impairs the recovery of global transcription during DNA base excision repair by promoting aberrant recruitment and activity of the histone ubiquitin protease USP3.
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Affiliation(s)
- Marek Adamowicz
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Richard Hailstone
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Annie A Demin
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Emilia Komulainen
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Hana Hanzlikova
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK.,Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Science, Prague, Czech Republic
| | - Jan Brazina
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Amit Gautam
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Sophie E Wells
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre and Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Brighton, UK. .,Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Science, Prague, Czech Republic.
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33
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Park SH, Kim Y, Ra JS, Wie MW, Kang MS, Kang S, Myung K, Lee KY. Timely termination of repair DNA synthesis by ATAD5 is important in oxidative DNA damage-induced single-strand break repair. Nucleic Acids Res 2021; 49:11746-11764. [PMID: 34718749 PMCID: PMC8599757 DOI: 10.1093/nar/gkab999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) generate oxidized bases and single-strand breaks (SSBs), which are fixed by base excision repair (BER) and SSB repair (SSBR), respectively. Although excision and repair of damaged bases have been extensively studied, the function of the sliding clamp, proliferating cell nuclear antigen (PCNA), including loading/unloading, remains unclear. We report that, in addition to PCNA loading by replication factor complex C (RFC), timely PCNA unloading by the ATPase family AAA domain-containing protein 5 (ATAD5)-RFC-like complex is important for the repair of ROS-induced SSBs. We found that PCNA was loaded at hydrogen peroxide (H2O2)-generated direct SSBs after the 3'-terminus was converted to the hydroxyl moiety by end-processing enzymes. However, PCNA loading rarely occurred during BER of oxidized or alkylated bases. ATAD5-depleted cells were sensitive to acute H2O2 treatment but not methyl methanesulfonate treatment. Unexpectedly, when PCNA remained on DNA as a result of ATAD5 depletion, H2O2-induced repair DNA synthesis increased in cancerous and normal cells. Based on higher H2O2-induced DNA breakage and SSBR protein enrichment by ATAD5 depletion, we propose that extended repair DNA synthesis increases the likelihood of DNA polymerase stalling, shown by increased PCNA monoubiquitination, and consequently, harmful nick structures are more frequent.
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Affiliation(s)
- Su Hyung Park
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Youyoung Kim
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Min Woo Wie
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Mi-Sun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Sukhyun Kang
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea.,Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyoo-Young Lee
- Center for Genomic Integrity, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
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34
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Zhang L, Fan W, Jia D, Feng Q, Ren W, Liu C. Microchamber-Free Digital Flow Cytometric Analysis of T4 Polynucleotide Kinase Phosphatase Based on Single-Enzyme-to-Single-Bead Space-Confined Reaction. Anal Chem 2021; 93:14828-14836. [PMID: 34713697 DOI: 10.1021/acs.analchem.1c03724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Digital bioassays have attracted extensive attention in biomedical applications due to their ultrahigh sensitivity. However, traditional digital bioassays require numerous microchambers such as droplets or microwells, which restricts their application scope. Herein, we propose a microchamber-free flow cytometric method for the digital quantification of T4 polynucleotide kinase phosphatase (T4 PNKP) based on an unprecedented phenomenon that each T4 PNKP molecule-catalyzed reaction can be spatially self-confined on a single microbead, which ultimately enables the one-target-to-one-fluorescence-positive microbead digital signal transduction. The digital signal-readout mode can clearly detect T4 PNKP concentrations as low as 1.28 × 10-10 U/μL, making it most sensitive method to date. Significantly, T4 PNKP can be specifically distinguished from other phosphatases and nucleases in complex samples by digitally counting the fluorescence-positive microbeads, which cannot be realized by traditional bulk measurement-based methods. Taking advantage of the novel space-confined enzymatic feature of T4 PNKP, this digital mechanism can use T4 PNKP as the enzyme label to fabricate digital sensing systems toward various biomolecules such as digital enzyme-linked immunosorbent assay (ELISA). Therefore, this work not only enlarges the toolbox for high-sensitivity biomolecule detection but also opens new gates to fabricate next-generation digital assays.
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Affiliation(s)
- Lijun Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Dailu Jia
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Qinya Feng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
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35
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Zhang Y, Zhang X, Jin Z, Chen H, Zhang C, Wang W, Jing J, Pan W. Clinical Impact of X-Ray Repair Cross-Complementary 1 ( XRCC1) and the Immune Environment in Colorectal Adenoma-Carcinoma Pathway Progression. J Inflamm Res 2021; 14:5403-5417. [PMID: 34737598 PMCID: PMC8559027 DOI: 10.2147/jir.s331010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/08/2021] [Indexed: 12/03/2022] Open
Abstract
Purpose Colorectal cancer (CRC) can develop via a hypermutagenic pathway characterized by frequent somatic DNA base-pair mutations. Alternatively, the immunogenicity of tumor cells themselves may influence the anticancer activity of the immune effector cells. Impaired DNA repair mechanisms drive mutagenicity, which then increase the neoantigen load and immunogenicity. However, no studies have analyzed immune checkpoint protein expression, particularly programmed death-1 (PD-1)/programmed death-ligand 1 (PD-L1), in adenoma–carcinoma progression and its relationship with the emergence of other DNA repair gene mutation. Materials and Methods We investigated mutations of 10 genes involved in DNA repair function: XRCC1, TP53, MLH1, MSH, KRAS, GSTP, UMP, MTHF, DPYD, and ABCC2. We performed sequencing to determine mutations and immunohistochemistry of immune checkpoints in clinical samples and determined changes in XRCC1 expression during progression through the adenoma–carcinoma pathway. We further investigated the prognostic associations of gene XRCC1 according to the expression, mutational profile, and immune profile using The Cancer Genome Atlas-colon adenocarcinoma (TCGA-COAD) dataset. Results From clinical samples, XRCC1 mutation demonstrated the strongest association with adenomas with a mutation frequency of 56.2% in adenomas and 34% in CRCs (p =0.016). XRCC1 was abnormally expressed and altered by mutations contributing to adenoma carcinogenesis. High expression of XRCC1, CD4, FOXP3, and PD-1/PD-L1 showed an overall upward trend with increased lesion severity (all p < 0.01). PD-1/PD-L1 expression and CD4+ intraepithelial lymphocytes (IELs) correlated with cytological dysplasia progression, specifically in patients with wild-type XRCC1 (all p < 0.01), whereas FOXP3 expression was independently associated with adenoma–carcinoma progression. From TCGA-COAD analysis, XRCC1 expression was associated with patients survival, tumor-infiltrating lymphocytes and immune marker expression. Conclusion Increased IEL density and PD-1/PD-L1 expression correlate with cytological dysplasia progression and specifically with the XRCC1 mutation status in CRC. Our findings support a stepwise dysplasia-carcinoma sequence of adenoma carcinogenesis and an XRCC1 hypermutated phenotypic mechanism of lesions.
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Affiliation(s)
- Yu Zhang
- Department of Clinical Medicine, Medical College of Soochow University, Suzhou, 215006, People's Republic of China.,Department of Gastroenterology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Xin Zhang
- Department of Pathology, Laboratory Medicine Center, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Zhuoyi Jin
- Department of Gastroenterology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Huiyan Chen
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, People's Republic of China
| | - Chenjing Zhang
- Department of Gastroenterology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Wangyue Wang
- Department of Gastroenterology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Jiyong Jing
- Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Wensheng Pan
- Department of Clinical Medicine, Medical College of Soochow University, Suzhou, 215006, People's Republic of China.,Department of Gastroenterology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
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36
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Effects of Manganese on Genomic Integrity in the Multicellular Model Organism Caenorhabditis elegans. Int J Mol Sci 2021; 22:ijms222010905. [PMID: 34681565 PMCID: PMC8535284 DOI: 10.3390/ijms222010905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 12/30/2022] Open
Abstract
Although manganese (Mn) is an essential trace element, overexposure is associated with Mn-induced toxicity and neurological dysfunction. Even though Mn-induced oxidative stress is discussed extensively, neither the underlying mechanisms of the potential consequences of Mn-induced oxidative stress on DNA damage and DNA repair, nor the possibly resulting toxicity are characterized yet. In this study, we use the model organism Caenorhabditis elegans to investigate the mode of action of Mn toxicity, focusing on genomic integrity by means of DNA damage and DNA damage response. Experiments were conducted to analyze Mn bioavailability, lethality, and induction of DNA damage. Different deletion mutant strains were then used to investigate the role of base excision repair (BER) and dePARylation (DNA damage response) proteins in Mn-induced toxicity. The results indicate a dose- and time-dependent uptake of Mn, resulting in increased lethality. Excessive exposure to Mn decreases genomic integrity and activates BER. Altogether, this study characterizes the consequences of Mn exposure on genomic integrity and therefore broadens the molecular understanding of pathways underlying Mn-induced toxicity. Additionally, studying the basal poly(ADP-ribosylation) (PARylation) of worms lacking poly(ADP-ribose) glycohydrolase (PARG) parg-1 or parg-2 (two orthologue of PARG), indicates that parg-1 accounts for most of the glycohydrolase activity in worms.
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Abstract
Chemotherapy-induced peripheral neurotoxicity (CIPN) is a major dose-limiting side effect of many anti-cancer agents, including taxanes, platinums, vinca alkaloids, proteasome inhibitors, immunomodulatory drugs, and antibody-drug conjugates. The resultant symptoms often persist post treatment completion and continue to impact on long-term function and quality of life for cancer survivors. At present, dose reduction remains the only strategy to prevent severe neuropathy, often leading clinicians to the difficult decision of balancing maximal treatment exposure and minimal long-lasting side effects. This review examines the clinical presentations of CIPN with each class of neurotoxic treatment, describing signs, symptoms, and long-term outcomes. We provide an update on the proposed mechanisms of nerve damage and review current data on clinical and genetic risk factors contributing to CIPN development. We also examine recent areas of research in the treatment and prevention of CIPN, with specific focus on current clinical trials and consensus recommendations for CIPN management.
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Chakraborty A, Tapryal N, Islam A, Mitra S, Hazra T. Transcription coupled base excision repair in mammalian cells: So little is known and so much to uncover. DNA Repair (Amst) 2021; 107:103204. [PMID: 34390916 DOI: 10.1016/j.dnarep.2021.103204] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/06/2021] [Accepted: 08/03/2021] [Indexed: 12/31/2022]
Abstract
Oxidized bases in the genome has been implicated in various human pathologies, including cancer, aging and neurological diseases. Their repair is initiated with excision by DNA glycosylases (DGs) in the base excision repair (BER) pathway. Among the five oxidized base-specific human DGs, OGG1 and NTH1 preferentially excise oxidized purines and pyrimidines, respectively, while NEILs remove both oxidized purines and pyrimidines. However, little is known about why cells possess multiple DGs with overlapping substrate specificities. Studies of the past decades revealed that some DGs are involved in repair of oxidized DNA base lesions in the actively transcribed regions. Preferential removal of lesions from the transcribed strands of active genes, called transcription-coupled repair (TCR), was discovered as a distinct sub-pathway of nucleotide excision repair; however, such repair of oxidized DNA bases had not been established until our recent demonstration of NEIL2's role in TC-BER of the nuclear genome. We have shown that NEIL2 forms a distinct transcriptionally active, repair proficient complex. More importantly, we for the first time reconstituted TC-BER using purified components. These studies are important for characterizing critical requirement for the process. However, because NEIL2 cannot remove all types of oxidized bases, it is unlikely to be the only DNA glycosylase involved in TC-BER. Hence, we postulate TC-BER process to be universally involved in maintaining the functional integrity of active genes, especially in post-mitotic, non-growing cells. We further postulate that abnormal bases (e.g., uracil), and alkylated and other small DNA base adducts are also repaired via TC-BER. In this review, we have provided an overview of the various aspects of TC-BER in mammalian cells with the hope of generating significant interest of many researchers in the field. Further studies aimed at better understanding the mechanistic aspects of TC-BER could help elucidate the linkage of TC-BER deficiency to various human pathologies.
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Affiliation(s)
- Anirban Chakraborty
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Nisha Tapryal
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Azharul Islam
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Sankar Mitra
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Tapas Hazra
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA.
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Zhao Z, Gad H, Benitez-Buelga C, Sanjiv K, Xiangwei H, Kang H, Feng M, Zhao Z, Berglund UW, Xia Q, Helleday T. NEIL3 Prevents Senescence in Hepatocellular Carcinoma by Repairing Oxidative Lesions at Telomeres during Mitosis. Cancer Res 2021; 81:4079-4093. [PMID: 34045188 PMCID: PMC9398161 DOI: 10.1158/0008-5472.can-20-1028] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 01/06/2021] [Accepted: 05/25/2021] [Indexed: 01/07/2023]
Abstract
Patients with hepatocellular carcinoma (HCC) suffer from few treatment options and poor survival rates. Here we report that endonuclease VIII-like protein 3 (NEIL3) is overexpressed in HCC and correlates with poor survival. All six HCC cell lines investigated were dependent on NEIL3 catalytic activity for survival and prevention of senescence, while NEIL3 was dispensable for nontransformed cells. NEIL3-depleted HCC cell lines accumulated oxidative DNA lesions specifically at telomeres, resulting in telomere dysfunctional foci and 53BP1 foci formation. Following oxidative DNA damage during mitosis, NEIL3 relocated to telomeres and recruited apurinic endonuclease 1 (APE1), indicating activation of base excision repair. META-FISH revealed that NEIL3, but not NEIL1 or NEIL2, is required to initiate APE1 and polymerase beta (POLB)-dependent base excision repair at oxidized telomeres. Repeated exposure of NEIL3-depleted cells to oxidizing damage induced chromatin bridges and damaged telomeres. These results demonstrate a novel function for NEIL3 in repair of oxidative DNA damage at telomeres in mitosis, which is important to prevent senescence of HCC cells. Furthermore, these data suggest that NEIL3 could be a target for therapeutic intervention for HCC. SIGNIFICANCE: This study describes compartmentalization of base excision repair during mitosis that is dependent on NEIL3, APE1, and POLB to repair oxidative damage accumulating at telomeres in hepatocellular carcinoma.
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Affiliation(s)
- Zhenjun Zhao
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Helge Gad
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Carlos Benitez-Buelga
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Kumar Sanjiv
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Hua Xiangwei
- Organ Transplantation Center, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - He Kang
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Mingxuan Feng
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhicong Zhao
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Corresponding Authors: Thomas Helleday, Karolinska Institutet, Tomtebodavägen 23B, Stockholm S-171 65, Sweden. E-mail: ; and Xia Qiang, Renji Hospital, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200001, China. E-mail:
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom.,Corresponding Authors: Thomas Helleday, Karolinska Institutet, Tomtebodavägen 23B, Stockholm S-171 65, Sweden. E-mail: ; and Xia Qiang, Renji Hospital, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200001, China. E-mail:
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40
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Pillay N, Brady RM, Dey M, Morgan RD, Taylor SS. DNA replication stress and emerging prospects for PARG inhibitors in ovarian cancer therapy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:160-170. [PMID: 33524442 DOI: 10.1016/j.pbiomolbio.2021.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/13/2021] [Accepted: 01/19/2021] [Indexed: 02/07/2023]
Abstract
Poly (ADP-ribosyl)ation has central functions in maintaining genome stability, including facilitating DNA replication and repair. In cancer cells these processes are frequently disrupted, and thus interfering with poly (ADP-ribosyl)ation can exacerbate inherent genome instability and induce selective cytotoxicity. Indeed, inhibitors of poly (ADP-ribose) polymerase (PARP) are having a major clinical impact in treating women with BRCA-mutant ovarian cancer, based on a defect in homologous recombination. However, only around half of ovarian cancers harbour defects in homologous recombination, and most sensitive tumours eventually acquire PARP inhibitor resistance with treatment. Thus, there is a pressing need to develop alternative treatment strategies to target tumours with both inherent and acquired resistance to PARP inhibition. Several novel inhibitors of poly (ADP-ribose)glycohydrolase (PARG) have been described, with promising anti-cancer activity in vitro that is distinct from PARP inhibitors. Here we discuss, the role of poly (ADP-ribosyl)ation in genome stability, and the potential for PARG inhibitors as a complementary strategy to PARP inhibitors in the treatment of ovarian cancer.
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Affiliation(s)
- Nisha Pillay
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK; Divisions of Structural Biology & Cancer Biology, The Institute of Cancer Research (ICR), London, SW7 3RP, UK
| | - Rosie M Brady
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK
| | - Malini Dey
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK
| | - Robert D Morgan
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK; Department of Medical Oncology, The Christie NHS Foundation Trust, Wilmslow Rd, Manchester, M20 4BX, UK
| | - Stephen S Taylor
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Cancer Research Centre, Wilmslow Rd, Manchester, M20 4GJ, UK.
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41
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The scaffold protein XRCC1 stabilizes the formation of polβ/gap DNA and ligase IIIα/nick DNA complexes in base excision repair. J Biol Chem 2021; 297:101025. [PMID: 34339737 PMCID: PMC8405949 DOI: 10.1016/j.jbc.2021.101025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/22/2022] Open
Abstract
The base excision repair (BER) pathway involves gap filling by DNA polymerase (pol) β and subsequent nick sealing by ligase IIIα. X-ray cross-complementing protein 1 (XRCC1), a nonenzymatic scaffold protein, assembles multiprotein complexes, although the mechanism by which XRCC1 orchestrates the final steps of coordinated BER remains incompletely defined. Here, using a combination of biochemical and biophysical approaches, we revealed that the polβ/XRCC1 complex increases the processivity of BER reactions after correct nucleotide insertion into gaps in DNA and enhances the handoff of nicked repair products to the final ligation step. Moreover, the mutagenic ligation of nicked repair intermediate following polβ 8-oxodGTP insertion is enhanced in the presence of XRCC1. Our results demonstrated a stabilizing effect of XRCC1 on the formation of polβ/dNTP/gap DNA and ligase IIIα/ATP/nick DNA catalytic ternary complexes. Real-time monitoring of protein–protein interactions and DNA-binding kinetics showed stronger binding of XRCC1 to polβ than to ligase IIIα or aprataxin, and higher affinity for nick DNA with undamaged or damaged ends than for one nucleotide gap repair intermediate. Finally, we demonstrated slight differences in stable polβ/XRCC1 complex formation, polβ and ligase IIIα protein interaction kinetics, and handoff process as a result of cancer-associated (P161L, R194W, R280H, R399Q, Y576S) and cerebellar ataxia-related (K431N) XRCC1 variants. Overall, our findings provide novel insights into the coordinating role of XRCC1 and the effect of its disease-associated variants on substrate-product channeling in multiprotein/DNA complexes for efficient BER.
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42
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Shin W, Alpaugh W, Hallihan LJ, Sinha S, Crowther E, Martin GR, Scheidl-Yee T, Yang X, Yoon G, Goldsmith T, Berger ND, de Almeida LG, Dufour A, Dobrinski I, Weinfeld M, Jirik FR, Biernaskie J. PNKP is required for maintaining the integrity of progenitor cell populations in adult mice. Life Sci Alliance 2021; 4:4/9/e202000790. [PMID: 34226276 PMCID: PMC8321660 DOI: 10.26508/lsa.202000790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/24/2022] Open
Abstract
Knockout of Pnkp in adult mice impairs the growth of hair follicle, spermatogonial, and neural progenitor populations. DNA repair proteins are critical to the maintenance of genomic integrity. Specific types of genotoxic factors, including reactive oxygen species generated during normal cellular metabolism or as a result of exposure to exogenous oxidative agents, frequently leads to “ragged” single-strand DNA breaks. The latter exhibits abnormal free DNA ends containing either a 5′-hydroxyl or 3′-phosphate requiring correction by the dual function enzyme, polynucleotide kinase phosphatase (PNKP), before DNA polymerase and ligation reactions can occur to seal the break. Pnkp gene deletion during early murine development leads to lethality; in contrast, the role of PNKP in adult mice is unknown. To investigate the latter, we used an inducible conditional mutagenesis approach to cause global disruption of the Pnkp gene in adult mice. This resulted in a premature aging-like phenotype, characterized by impaired growth of hair follicles, seminiferous tubules, and neural progenitor cell populations. These results point to an important role for PNKP in maintaining the normal growth and survival of these murine progenitor populations.
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Affiliation(s)
- Wisoo Shin
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Whitney Alpaugh
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Laura J Hallihan
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Sarthak Sinha
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Emilie Crowther
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Gary R Martin
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | | | - Xiaoyan Yang
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Canada
| | - Grace Yoon
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Taylor Goldsmith
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Nelson D Berger
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Luiz Gn de Almeida
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Antoine Dufour
- McCaig Institute for Bone and Joint Health, Calgary, Canada.,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada.,Department of Physiology and Pharmacology, University of Calgary, Calgary, Canada
| | - Ina Dobrinski
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Canada
| | - Frank R Jirik
- McCaig Institute for Bone and Joint Health, Calgary, Canada .,Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada.,Alberta Children's Hospital Research Institute, Calgary, Canada
| | - Jeff Biernaskie
- Department of Comparative Biology and Experimental Medicine, University of Calgary, Calgary, Canada .,Department of Physiology and Pharmacology, University of Calgary, Calgary, Canada.,Department of Surgery, University of Calgary, Calgary, Canada.,Hotchkiss Brain Institute, Calgary, Canada
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43
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Rashid I, Hammel M, Sverzhinsky A, Tsai MS, Pascal JM, Tainer JA, Tomkinson AE. Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus. J Biol Chem 2021; 297:100921. [PMID: 34181949 PMCID: PMC8318918 DOI: 10.1016/j.jbc.2021.100921] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/10/2021] [Accepted: 06/23/2021] [Indexed: 02/07/2023] Open
Abstract
Tyrosyl DNA phosphodiesterase 1 (TDP1) and DNA Ligase IIIα (LigIIIα) are key enzymes in single-strand break (SSB) repair. TDP1 removes 3′-tyrosine residues remaining after degradation of DNA topoisomerase (TOP) 1 cleavage complexes trapped by either DNA lesions or TOP1 inhibitors. It is not known how TDP1 is linked to subsequent processing and LigIIIα-catalyzed joining of the SSB. Here we define a direct interaction between the TDP1 catalytic domain and the LigIII DNA-binding domain (DBD) regulated by conformational changes in the unstructured TDP1 N-terminal region induced by phosphorylation and/or alterations in amino acid sequence. Full-length and N-terminally truncated TDP1 are more effective at correcting SSB repair defects in TDP1 null cells compared with full-length TDP1 with amino acid substitutions of an N-terminal serine residue phosphorylated in response to DNA damage. TDP1 forms a stable complex with LigIII170–755, as well as full-length LigIIIα alone or in complex with the DNA repair scaffold protein XRCC1. Small-angle X-ray scattering and negative stain electron microscopy combined with mapping of the interacting regions identified a TDP1/LigIIIα compact dimer of heterodimers in which the two LigIII catalytic cores are positioned in the center, whereas the two TDP1 molecules are located at the edges of the core complex flanked by highly flexible regions that can interact with other repair proteins and SSBs. As TDP1and LigIIIα together repair adducts caused by TOP1 cancer chemotherapy inhibitors, the defined interaction architecture and regulation of this enzyme complex provide insights into a key repair pathway in nonmalignant and cancer cells.
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Affiliation(s)
- Ishtiaque Rashid
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA
| | - Michal Hammel
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Miaw-Sheue Tsai
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, USA.
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44
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XRCC1 prevents toxic PARP1 trapping during DNA base excision repair. Mol Cell 2021; 81:3018-3030.e5. [PMID: 34102106 PMCID: PMC8294329 DOI: 10.1016/j.molcel.2021.05.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/08/2021] [Accepted: 05/10/2021] [Indexed: 01/12/2023]
Abstract
Mammalian DNA base excision repair (BER) is accelerated by poly(ADP-ribose) polymerases (PARPs) and the scaffold protein XRCC1. PARPs are sensors that detect single-strand break intermediates, but the critical role of XRCC1 during BER is unknown. Here, we show that protein complexes containing DNA polymerase β and DNA ligase III that are assembled by XRCC1 prevent excessive engagement and activity of PARP1 during BER. As a result, PARP1 becomes "trapped" on BER intermediates in XRCC1-deficient cells in a manner similar to that induced by PARP inhibitors, including in patient fibroblasts from XRCC1-mutated disease. This excessive PARP1 engagement and trapping renders BER intermediates inaccessible to enzymes such as DNA polymerase β and impedes their repair. Consequently, PARP1 deletion rescues BER and resistance to base damage in XRCC1-/- cells. These data reveal excessive PARP1 engagement during BER as a threat to genome integrity and identify XRCC1 as an "anti-trapper" that prevents toxic PARP1 activity.
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45
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Wu W, Hill SE, Nathan WJ, Paiano J, Callen E, Wang D, Shinoda K, van Wietmarschen N, Colón-Mercado JM, Zong D, De Pace R, Shih HY, Coon S, Parsadanian M, Pavani R, Hanzlikova H, Park S, Jung SK, McHugh PJ, Canela A, Chen C, Casellas R, Caldecott KW, Ward ME, Nussenzweig A. Neuronal enhancers are hotspots for DNA single-strand break repair. Nature 2021; 593:440-444. [PMID: 33767446 PMCID: PMC9827709 DOI: 10.1038/s41586-021-03468-5] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/17/2021] [Indexed: 02/01/2023]
Abstract
Defects in DNA repair frequently lead to neurodevelopmental and neurodegenerative diseases, underscoring the particular importance of DNA repair in long-lived post-mitotic neurons1,2. The cellular genome is subjected to a constant barrage of endogenous DNA damage, but surprisingly little is known about the identity of the lesion(s) that accumulate in neurons and whether they accrue throughout the genome or at specific loci. Here we show that post-mitotic neurons accumulate unexpectedly high levels of DNA single-strand breaks (SSBs) at specific sites within the genome. Genome-wide mapping reveals that SSBs are located within enhancers at or near CpG dinucleotides and sites of DNA demethylation. These SSBs are repaired by PARP1 and XRCC1-dependent mechanisms. Notably, deficiencies in XRCC1-dependent short-patch repair increase DNA repair synthesis at neuronal enhancers, whereas defects in long-patch repair reduce synthesis. The high levels of SSB repair in neuronal enhancers are therefore likely to be sustained by both short-patch and long-patch processes. These data provide the first evidence of site- and cell-type-specific SSB repair, revealing unexpected levels of localized and continuous DNA breakage in neurons. In addition, they suggest an explanation for the neurodegenerative phenotypes that occur in patients with defective SSB repair.
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Affiliation(s)
- Wei Wu
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Sarah E Hill
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - William J Nathan
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.,Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jacob Paiano
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Elsa Callen
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Dongpeng Wang
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Kenta Shinoda
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | | | | | - Dali Zong
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Raffaella De Pace
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Han-Yu Shih
- National Eye Institute, NIH, Bethesda, MD, USA
| | - Steve Coon
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD, USA
| | - Maia Parsadanian
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA
| | - Raphael Pavani
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Hana Hanzlikova
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Solji Park
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Seol Kyoung Jung
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Andres Canela
- The Hakubi Center for Advanced Research and Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Chongyi Chen
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases and National Cancer Institute, NIH, Bethesda, MD, USA.,NIH Regulome Project, NIH, Bethesda, MD, USA
| | - Keith W Caldecott
- Department of Genome Dynamics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic. .,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK.
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, USA.
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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46
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Gu S, Bodai Z, Cowan QT, Komor AC. Base Editors: Expanding the Types of DNA Damage Products Harnessed for Genome Editing. ACTA ACUST UNITED AC 2021; 1. [PMID: 34368792 DOI: 10.1016/j.ggedit.2021.100005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Base editors are an innovative addition to the genome editing toolbox that introduced a new genome editing strategy to the field. Instead of using double-stranded DNA breaks, base editors use nucleobase modification chemistry to efficiently and precisely incorporate single nucleotide variants (SNVs) into the genome of living cells. Two classes of DNA base editors currently exist: deoxycytidine deamination-derived editors (CBEs, which facilitate C•G to T•A mutations) and deoxyadenosine deamination-derived base editors (ABEs, which facilitate A•T to G•C mutations). More recently, the development of mitochondrial base editors allowed the introduction of C•G to T•A mutations into mitochondrial DNA as well. Base editors show great potential as therapeutic agents and research tools, and extensive studies have been carried out to improve upon the original base editor constructs to aid researchers in a variety of disciplines. Despite their widespread use, there are few publications that focus on elucidating the biological pathways involved during the processing of base editor intermediates. Because base editors introduce unique types of DNA damage products (a U•G mismatch with a DNA backbone nick for CBEs, and an I•T mismatch with a DNA backbone nick for ABEs) to facilitate genome editing, a deep understanding of the DNA damage repair pathways that facilitate or impede base editing represents an important aspect for the further expansion and improvement of the technologies. Here, we first review canonical deoxyuridine, deoxyinosine, and single-stranded break repair. Then, we discuss how interactions among these different repair processes can lead to different base editing outcomes. Through this review, we hope to promote thoughtful discussions on the DNA repair mechanisms of base editing, as well as help researchers in the improvement of the current base editors and the development of new base editors.
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Affiliation(s)
- Sifeng Gu
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Zsolt Bodai
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
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Rapid Detection and Signaling of DNA Damage by PARP-1. Trends Biochem Sci 2021; 46:744-757. [PMID: 33674152 DOI: 10.1016/j.tibs.2021.01.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/14/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
Poly(ADP-ribosyl) polymerase-1 (PARP-1) is an abundant ADP-ribosyl transferase that regulates various biological processes. PARP-1 is widely recognized as a first-line responder molecule in DNA damage response (DDR). Here, we review the full cycle of detecting DNA damage by PARP-1, PARP-1 activation upon DNA binding, and PARP-1 release from a DNA break. We also discuss the allosteric consequence upon binding of PARP inhibitors (PARPi) and the opportunity to tune its release from a DNA break. It is now possible to harness this new understanding to design novel PARPi for treating diseases where cell toxicity caused by PARP-1 'trapping' on DNA is either the desired consequence or entirely counterproductive.
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Laytragoon Lewin N, Karlsson JE, Robinsson D, Fagerberg M, Kentsson M, Sayardoust S, Nilsson M, Shamoun L, Andersson BÅ, Löfgren S, Rutqvist LE, Lewin F. Influence of single nucleotide polymorphisms among cigarette smoking and non-smoking patients with coronary artery disease, urinary bladder cancer and lung cancer. PLoS One 2021; 16:e0243084. [PMID: 33507988 PMCID: PMC7842923 DOI: 10.1371/journal.pone.0243084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 11/13/2020] [Indexed: 11/21/2022] Open
Abstract
Introduction Cigarette smoke is suggested to be a risk factor for coronary artery disease (CAD), urinary bladder cancer (UBCa) or lung cancer (LCa). However, not all heavy smokers develop these diseases and elevated cancer risk among first-degree relatives suggests an important role of genetic factor. Methods Three hundred and ten healthy blood donors (controls), 98 CAD, 74 UBCa and 38 LCa patients were included in this pilot study. The influence of 92 single nucleotide polymorphisms (SNPs) and impact of cigarette smoking were analysed. Results Out of 92 SNPs tested, differences in distribution of 14 SNPs were detected between controls and patient groups. Only CTLA4 rs3087243 showed difference in both CAD and UBCa patient group compared to control group. Stratified by smoking status, the impact of smoking was associated to frequencies of 8, 3 and 4 SNPs in CAD, UBCa, LCa patients, respectively. None of these 92 SNPs showed a statistically significant difference to more than one type of disease among smoking patients. In non-smoking patients, 7, 3 and 6 SNPs were associated to CAD, UBCa, LCa, respectively. Out of these 92 SNPs, CTLA4 rs3087243 was associated to both non-smoking CAD and UBCa. The XRCC1 rs25487 was associated to both non-smoking UBCa and LCa. Conclusion SNPs might be important risk factors for CAD, UBCa and LCa. Distribution of the SNPs was specific for each patient group, not a random event. Impact of cigarette smoking on the disease was associated to the specific SNP sequences. Thus, smoking individuals with SNPs associated to risk of these serious diseases is an important target group for smoking cessation programs.
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Affiliation(s)
| | - Jan-Erik Karlsson
- Dept of Internal Medicine, Ryhov Hospital, Jönköping, Sweden
- Dept of Health Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | | | | | - Magnus Kentsson
- Dept of Internal Medicine, Ryhov Hospital, Jönköping, Sweden
| | | | - Mats Nilsson
- Futurum, Academy of Health and Care, Region Jönköping, Jönköping, Sweden
- Dept Medical and Health Sciences, Linköping University, Linköping, Sweden
| | - Levar Shamoun
- Dept Laboratory Medicine, Ryhov Hospital, Jönköping, Sweden
| | | | - Sture Löfgren
- Dept Laboratory Medicine, Ryhov Hospital, Jönköping, Sweden
| | | | - Freddi Lewin
- Dept Oncology, Ryhov Hospital, Jönköping, Sweden
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Hammel M, Rashid I, Sverzhinsky A, Pourfarjam Y, Tsai MS, Ellenberger T, Pascal JM, Kim IK, Tainer JA, Tomkinson AE. An atypical BRCT-BRCT interaction with the XRCC1 scaffold protein compacts human DNA Ligase IIIα within a flexible DNA repair complex. Nucleic Acids Res 2021; 49:306-321. [PMID: 33330937 PMCID: PMC7797052 DOI: 10.1093/nar/gkaa1188] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 11/21/2020] [Accepted: 12/13/2020] [Indexed: 01/08/2023] Open
Abstract
The XRCC1–DNA ligase IIIα complex (XL) is critical for DNA single-strand break repair, a key target for PARP inhibitors in cancer cells deficient in homologous recombination. Here, we combined biophysical approaches to gain insights into the shape and conformational flexibility of the XL as well as XRCC1 and DNA ligase IIIα (LigIIIα) alone. Structurally-guided mutational analyses based on the crystal structure of the human BRCT–BRCT heterodimer identified the network of salt bridges that together with the N-terminal extension of the XRCC1 C-terminal BRCT domain constitute the XL molecular interface. Coupling size exclusion chromatography with small angle X-ray scattering and multiangle light scattering (SEC-SAXS–MALS), we determined that the XL is more compact than either XRCC1 or LigIIIα, both of which form transient homodimers and are highly disordered. The reduced disorder and flexibility allowed us to build models of XL particles visualized by negative stain electron microscopy that predict close spatial organization between the LigIIIα catalytic core and both BRCT domains of XRCC1. Together our results identify an atypical BRCT–BRCT interaction as the stable nucleating core of the XL that links the flexible nick sensing and catalytic domains of LigIIIα to other protein partners of the flexible XRCC1 scaffold.
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Affiliation(s)
- Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ishtiaque Rashid
- Departments of Internal Medicine, Molecular Genetics & Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - Aleksandr Sverzhinsky
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Yasin Pourfarjam
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH 45221, USA
| | - Miaw-Sheue Tsai
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tom Ellenberger
- Department of Biochemistry, Washington University, St. Louis, MO, USA
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - In-Kwon Kim
- Department of Chemistry, University of Cincinnati, 301 Clifton Ct, Cincinnati, OH 45221, USA
| | - John A Tainer
- Departments of Cancer Biology and Molecular & Cellular Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics & Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
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Lipták N, Gál Z, Biró B, Hiripi L, Hoffmann OI. Rescuing lethal phenotypes induced by disruption of genes in mice: a review of novel strategies. Physiol Res 2021; 70:3-12. [PMID: 33453719 DOI: 10.33549/physiolres.934543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Approximately 35 % of the mouse genes are indispensable for life, thus, global knock-out (KO) of those genes may result in embryonic or early postnatal lethality due to developmental abnormalities. Several KO mouse lines are valuable human disease models, but viable homozygous mutant mice are frequently required to mirror most symptoms of a human disease. The site-specific gene editing systems, the transcription activator-like effector nucleases (TALENs), Zinc-finger nucleases (ZFNs) and the clustered regularly interspaced short palindrome repeat-associated Cas9 nuclease (CRISPR/Cas9) made the generation of KO mice more efficient than before, but the homozygous lethality is still an undesired side-effect in case of many genes. The literature search was conducted using PubMed and Web of Science databases until June 30th, 2020. The following terms were combined to find relevant studies: "lethality", "mice", "knock-out", "deficient", "embryonic", "perinatal", "rescue". Additional manual search was also performed to find the related human diseases in the Online Mendelian Inheritance in Man (OMIM) database and to check the citations of the selected studies for rescuing methods. In this review, the possible solutions for rescuing human disease-relevant homozygous KO mice lethal phenotypes were summarized.
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Affiliation(s)
- N Lipták
- NARIC-Agricultural Biotechnology Institute, Animal Biotechnology Department, Gödöllő, Hungary.
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