1
|
Noireterre A, Soudet J, Bagdiul I, Stutz F. The cullin Rtt101 promotes ubiquitin-dependent DNA-protein crosslink repair across the cell cycle. Nucleic Acids Res 2024; 52:9654-9670. [PMID: 39077933 PMCID: PMC11381328 DOI: 10.1093/nar/gkae658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 06/28/2024] [Accepted: 07/16/2024] [Indexed: 07/31/2024] Open
Abstract
DNA-protein crosslinks (DPCs) challenge faithful DNA replication and smooth passage of genomic information. Our study unveils the cullin E3 ubiquitin ligase Rtt101 as a DPC repair factor. Genetic analyses demonstrate that Rtt101 is essential for resistance to a wide range of DPC types including topoisomerase 1 crosslinks, in the same pathway as the ubiquitin-dependent aspartic protease Ddi1. Using an in vivo inducible Top1-mimicking DPC system, we reveal the significant impact of Rtt101 ubiquitination on DPC removal across different cell cycle phases. High-throughput methods coupled with next-generation sequencing specifically highlight the association of Rtt101 with replisomes as well as colocalization with DPCs. Our findings establish Rtt101 as a main contributor to DPC repair throughout the yeast cell cycle.
Collapse
Affiliation(s)
- Audrey Noireterre
- Department of Molecular and Cellular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Julien Soudet
- Department of Molecular and Cellular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Ivona Bagdiul
- Department of Molecular and Cellular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| | - Françoise Stutz
- Department of Molecular and Cellular Biology, University of Geneva, 1211 Geneva 4, Switzerland
| |
Collapse
|
2
|
Hurben AK, Zhang Q, Galligan JJ, Tretyakova N, Erber L. Endogenous Cellular Metabolite Methylglyoxal Induces DNA-Protein Cross-Links in Living Cells. ACS Chem Biol 2024; 19:1291-1302. [PMID: 38752800 PMCID: PMC11353540 DOI: 10.1021/acschembio.4c00100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Methylglyoxal (MGO) is an electrophilic α-oxoaldehyde generated endogenously through metabolism of carbohydrates and exogenously due to autoxidation of sugars, degradation of lipids, and fermentation during food and drink processing. MGO can react with nucleophilic sites within proteins and DNA to form covalent adducts. MGO-induced advanced glycation end-products such as protein and DNA adducts are thought to be involved in oxidative stress, inflammation, diabetes, cancer, renal failure, and neurodegenerative diseases. Additionally, MGO has been hypothesized to form toxic DNA-protein cross-links (DPC), but the identities of proteins participating in such cross-linking in cells have not been determined. In the present work, we quantified DPC formation in human cells exposed to MGO and identified proteins trapped on DNA upon MGO exposure using mass spectrometry-based proteomics. A total of 265 proteins were found to participate in MGO-derived DPC formation including gene products engaged in telomere organization, nucleosome assembly, and gene expression. In vitro experiments confirmed DPC formation between DNA and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), as well as histone proteins H3.1 and H4. Collectively, our study provides the first evidence for MGO-mediated DNA-protein cross-linking in living cells, prompting future studies regarding the relevance of these toxic lesions in cancer, diabetes, and other diseases linked to elevated MGO levels.
Collapse
Affiliation(s)
- Alexander K. Hurben
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States; Present Address: Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Qi Zhang
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - James J. Galligan
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, Arizona 85721, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States; Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Luke Erber
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
3
|
Torrecilla I, Ruggiano A, Kiianitsa K, Aljarbou F, Lascaux P, Hoslett G, Song W, Maizels N, Ramadan K. Isolation and detection of DNA-protein crosslinks in mammalian cells. Nucleic Acids Res 2024; 52:525-547. [PMID: 38084926 PMCID: PMC10810220 DOI: 10.1093/nar/gkad1178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 01/26/2024] Open
Abstract
DNA-protein crosslinks (DPCs) are toxic DNA lesions wherein a protein is covalently attached to DNA. If not rapidly repaired, DPCs create obstacles that disturb DNA replication, transcription and DNA damage repair, ultimately leading to genome instability. The persistence of DPCs is associated with premature ageing, cancer and neurodegeneration. In mammalian cells, the repair of DPCs mainly relies on the proteolytic activities of SPRTN and the 26S proteasome, complemented by other enzymes including TDP1/2 and the MRN complex, and many of the activities involved are essential, restricting genetic approaches. For many years, the study of DPC repair in mammalian cells was hindered by the lack of standardised assays, most notably assays that reliably quantified the proteins or proteolytic fragments covalently bound to DNA. Recent interest in the field has spurred the development of several biochemical methods for DPC analysis. Here, we critically analyse the latest techniques for DPC isolation and the benefits and drawbacks of each. We aim to assist researchers in selecting the most suitable isolation method for their experimental requirements and questions, and to facilitate the comparison of results across different laboratories using different approaches.
Collapse
Affiliation(s)
- Ignacio Torrecilla
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Annamaria Ruggiano
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Kostantin Kiianitsa
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
| | - Ftoon Aljarbou
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Pauline Lascaux
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Gwendoline Hoslett
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Wei Song
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Nancy Maizels
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7350, USA
| | - Kristijan Ramadan
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| |
Collapse
|
4
|
Essawy MM, Campbell C. Enzymatic Processing of DNA-Protein Crosslinks. Genes (Basel) 2024; 15:85. [PMID: 38254974 PMCID: PMC10815813 DOI: 10.3390/genes15010085] [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: 12/01/2023] [Revised: 12/30/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
DNA-protein crosslinks (DPCs) represent a unique and complex form of DNA damage formed by covalent attachment of proteins to DNA. DPCs are formed through a variety of mechanisms and can significantly impede essential cellular processes such as transcription and replication. For this reason, anti-cancer drugs that form DPCs have proven effective in cancer therapy. While cells rely on numerous different processes to remove DPCs, the molecular mechanisms responsible for orchestrating these processes remain obscure. Having this insight could potentially be harnessed therapeutically to improve clinical outcomes in the battle against cancer. In this review, we describe the ways cells enzymatically process DPCs. These processing events include direct reversal of the DPC via hydrolysis, nuclease digestion of the DNA backbone to delete the DPC and surrounding DNA, proteolytic processing of the crosslinked protein, as well as covalent modification of the DNA-crosslinked proteins with ubiquitin, SUMO, and Poly(ADP) Ribose (PAR).
Collapse
Affiliation(s)
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA;
| |
Collapse
|
5
|
Zhao T, Jiang T, Li X, Chang S, Sun Q, Kong F, Kong X, Wei F, He J, Hao J, Xie K. Nuclear GRP78 Promotes Metabolic Reprogramming and Therapeutic Resistance in Pancreatic Ductal Adenocarcinoma. Clin Cancer Res 2023; 29:5183-5195. [PMID: 37819952 DOI: 10.1158/1078-0432.ccr-23-1143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/04/2023] [Accepted: 10/06/2023] [Indexed: 10/13/2023]
Abstract
PURPOSE Stromal fibrosis limits nutritional supply and disarrays metabolism in pancreatic cancer (PDA, pancreatic ductal adenocarcinoma). Understanding of the molecular basis underlying metabolic cues would improve PDA management. The current study determined the interaction between glucose-regulated proteins 78 (GRP78) and hypoxia-inducible factor 1α (HIF-1α) and its mechanistic roles underlying PDA response to oxygen and glucose restrains. EXPERIMENTAL DESIGN Gene expression and its association with clinicopathologic characteristics of patients with PDA and mouse models were analyzed using IHC. Protein expression and their regulation were measured by Western blot and immunoprecipitation analyses. Protein interactions were determined using gain- and loss-of-function assays and molecular methods, including chromatin immunoprecipitation, co-immunoprecipitation, and dual luciferase reporter. RESULTS There was concomitant overexpression of both GRP78 and HIF-1α in human and mouse PDA tissues and cells. Glucose deprivation increased the expression of GRP78 and HIF-1α, particularly colocalization in nucleus. Induction of HIF-1α expression by glucose deprivation in PDA cells depended on the expression of and its own interaction with GRP78. Mechanistically, increased expression of both HIF-1α and LDHA under glucose deprivation was caused by the direct binding of GRP78 and HIF-1α protein complexes to the promoters of HIF-1α and LDHA genes and transactivation of their transcriptional activity. CONCLUSIONS Protein complex of GRP78 and HIF-1α directly binds to HIF-1α own promoter and LDHA promoter, enhances the transcription of both HIF-1α and LDHA, whereas glucose deprivation increases GRP78 expression and further enhances HIF-1α and LDHA transcription. Therefore, crosstalk and integration of hypoxia- and hypoglycemia-responsive signaling critically impact PDA metabolic reprogramming and therapeutic resistance.
Collapse
Affiliation(s)
- Tiansuo Zhao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Tingting Jiang
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, China
| | - Xiaojia Li
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, China
| | - Shaofei Chang
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Qihui Sun
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, China
| | - Fanyang Kong
- Department of Gastroenterology, Changhai Hospital, Shanghai, China
| | - Xiangyu Kong
- Department of Gastroenterology, Changhai Hospital, Shanghai, China
| | - Fang Wei
- Institute of Digestive Diseases, Guangzhou First People's Hospital and The Second Affiliated Hospital, The South China University of Technology School of Medicine, Guangzhou, China
| | - Jie He
- Institute of Digestive Diseases, Guangzhou First People's Hospital and The Second Affiliated Hospital, The South China University of Technology School of Medicine, Guangzhou, China
| | - Jihui Hao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Digestive Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Keping Xie
- Center for Pancreatic Cancer Research, The South China University of Technology School of Medicine, Guangzhou, China
- Institute of Digestive Diseases, Guangzhou First People's Hospital and The Second Affiliated Hospital, The South China University of Technology School of Medicine, Guangzhou, China
- The South China University of Technology Comprehensive Cancer Center, Guangzhou, China
| |
Collapse
|
6
|
Wen T, Kermarrec M, Dumont E, Gillet N, Greenberg MM. DNA-Histone Cross-Link Formation via Hole Trapping in Nucleosome Core Particles. J Am Chem Soc 2023; 145:23702-23714. [PMID: 37856159 PMCID: PMC10652223 DOI: 10.1021/jacs.3c08135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Radical cations (holes) produced in DNA by ionizing radiation and other oxidants yield DNA-protein cross-links (DPCs). Detailed studies of DPC formation in chromatin via this process are lacking. We describe here a comprehensive examination of DPC formation within nucleosome core particles (NCPs), which are the monomeric component of chromatin. DNA holes are introduced at defined sites within NCPs that are constructed from the bottom-up. DPCs form at DNA holes in yields comparable to those of alkali-labile DNA lesions that result from water trapping. DPC-forming efficiency and site preference within the NCP are dependent on translational and rotational positioning. Mass spectrometry and the use of mutant histones reveal that lysine residues in histone N-terminal tails and amino termini are responsible for the DPC formation. These studies are corroborated by computational simulation at the microsecond time scale, showing a wide range of interactions that can precede DPC formation. Three consecutive dGs, which are pervasive in the human genome, including G-quadruplex-forming sequences, are sufficient to produce DPCs that could impact gene expression.
Collapse
Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Maxime Kermarrec
- Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, ENS de Lyon, CNRS, F-69342 Lyon, France
| | - Elise Dumont
- Institut de Chimie de Nice UMR 7272, Université Côte d'Azur, CNRS, 06108 Nice, France
- Institut Universitaire de France, 5 Rue Descartes, 75005 Paris, France
| | - Natacha Gillet
- Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, ENS de Lyon, CNRS, F-69342 Lyon, France
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| |
Collapse
|
7
|
Impey S, Pelz C, Riparip LK, Tafessu A, Fareh F, Zuloaga DG, Marzulla T, Stewart B, Rosi S, Turker MS, Raber J. Postsynaptic density radiation signature following space irradiation. Front Physiol 2023; 14:1215535. [PMID: 37440997 PMCID: PMC10334289 DOI: 10.3389/fphys.2023.1215535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023] Open
Abstract
Introduction: The response of the brain to space radiation is an important concern for astronauts during space missions. Therefore, we assessed the response of the brain to 28Si ion irradiation (600 MeV/n), a heavy ion present in the space environment, on cognitive performance and whether the response is associated with altered DNA methylation in the hippocampus, a brain area important for cognitive performance. Methods: We determined the effects of 28Si ion irradiation on object recognition, 6-month-old mice irradiated with 28Si ions (600 MeV/n, 0.3, 0.6, and 0.9 Gy) and cognitively tested two weeks later. In addition, we determined if those effects were associated with alterations in hippocampal networks and/or hippocampal DNA methylation. Results: At 0.3 Gy, but not at 0.6 Gy or 0.9 Gy, 28Si ion irradiation impaired cognition that correlated with altered gene expression and 5 hmC profiles that mapped to specific gene ontology pathways. Comparing hippocampal DNA hydroxymethylation following proton, 56Fe ion, and 28Si ion irradiation revealed a general space radiation synaptic signature with 45 genes that are associated with profound phenotypes. The most significant categories were glutamatergic synapse and postsynaptic density. Discussion: The brain's response to space irradiation involves novel excitatory synapse and postsynaptic remodeling.
Collapse
Affiliation(s)
- Soren Impey
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR, United States
- Dow Neuroscience Laboratories, Department of Cell and Developmental Biology, Legacy Research Institute, Legacy Health Systems, Oregon Health and Science University, Portland, OR, United States
| | - Carl Pelz
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR, United States
| | - Lara-Kirstie Riparip
- Departments of Neurological Surgery and Physical Therapy and Rehabilitation Science, Brain and Spinal Injury Center, University of California, San Francisco, San Francisco, CA, United States
| | - Amanuel Tafessu
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR, United States
| | - Fatema Fareh
- Department of Pediatrics, Oregon Stem Cell Center, Oregon Health and Science University, Portland, OR, United States
| | - Damian G. Zuloaga
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
| | - Tessa Marzulla
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
| | - Blair Stewart
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
| | - Susanna Rosi
- Departments of Neurological Surgery and Physical Therapy and Rehabilitation Science, Brain and Spinal Injury Center, University of California, San Francisco, San Francisco, CA, United States
| | - Mitchell S. Turker
- Department of Molecular and Medical Genetics, Oregon Institute of Occupational Health Sciences, Oregon Health and Science University, Portland, OR, United States
| | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, United States
- Departments of Neurology and Radiation Medicine, Division of Neuroscience ONPRC, Oregon Health and Science University, Portland, OR, United States
| |
Collapse
|
8
|
Fahim TM, Mohamed MAELH, Abdelrahman SSM, Lotfy DM. Beneficial Effect of Rosuvastatin Therapy on Spleen Injury Induced by Gamma Irradiation in Rats: Targeting Nrf2/EPRE Pathway. Dose Response 2023; 21:15593258231179900. [PMID: 37255693 PMCID: PMC10226320 DOI: 10.1177/15593258231179900] [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] [Indexed: 06/01/2023] Open
Abstract
Purpose The present study investigates the new approach of rosuvastatin (RUV) administration as a drug for the management of spleen injury induced by gamma irradiation. Main Methods Forty rats were used and divided equally into 4 groups: control group, irradiated group, IRR + rosuvastatin group (10 mg/Kg b. wt), and IRR + rosuvastatin group (20 mg/kg b. wt) for 7 days orally. Results The possible curative effect can be illustrated via the improvement of hematopoietic cell count (Hb, RBCs, and WBCs) and oxidative stress markers (MDA and GST) in addition to biochemical parameters including [heme oxigenase-1 (HO-1), nuclear erythroid 2-related factor (Nrf2), NOD-, LRR- and pyrin domain- containing protein 3 (NLRP3) inflammasome] and immune assay of nuclear factor kappa beta (NF-kB P65) and inducible nitric oxide synthase (iNOS). Histological pictures emphasize the biochemical findings. Rosuvastatin treatments by using two different doses improve the tested parameters. High-dose administration of RUV (20 mg/kg p.o.) recorded better results than the low dose (10 mg/kg p.o.). Conclusion Our results suggested that rosuvastatin reversed the radiation-induced spleen-damaging effects. So, RUV can be introduced to the market as a new therapy for the management of spleen damages.
Collapse
Affiliation(s)
- Thanaa M. Fahim
- Drug Radiation Research Department, National Center for Radiation Research and
Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | - Marwa Abd EL-Hameed Mohamed
- Drug Radiation Research Department, National Center for Radiation Research and
Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| | | | - Dina M. Lotfy
- Drug Radiation Research Department, National Center for Radiation Research and
Technology (NCRRT), Egyptian Atomic Energy Authority (EAEA), Cairo, Egypt
| |
Collapse
|
9
|
Duarte GT, Volkova PY, Fiengo Perez F, Horemans N. Chronic Ionizing Radiation of Plants: An Evolutionary Factor from Direct Damage to Non-Target Effects. PLANTS (BASEL, SWITZERLAND) 2023; 12:1178. [PMID: 36904038 PMCID: PMC10005729 DOI: 10.3390/plants12051178] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
In present times, the levels of ionizing radiation (IR) on the surface of Earth are relatively low, posing no high challenges for the survival of contemporary life forms. IR derives from natural sources and naturally occurring radioactive materials (NORM), the nuclear industry, medical applications, and as a result of radiation disasters or nuclear tests. In the current review, we discuss modern sources of radioactivity, its direct and indirect effects on different plant species, and the scope of the radiation protection of plants. We present an overview of the molecular mechanisms of radiation responses in plants, which leads to a tempting conjecture of the evolutionary role of IR as a limiting factor for land colonization and plant diversification rates. The hypothesis-driven analysis of available plant genomic data suggests an overall DNA repair gene families' depletion in land plants compared to ancestral groups, which overlaps with a decrease in levels of radiation exposure on the surface of Earth millions of years ago. The potential contribution of chronic IR as an evolutionary factor in combination with other environmental factors is discussed.
Collapse
Affiliation(s)
| | | | | | - Nele Horemans
- Belgian Nuclear Research Centre—SCK CEN, 2400 Mol, Belgium
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| |
Collapse
|
10
|
Glucose-Regulated Protein 78 Is a Potential Serum and Imaging Marker for Early Detection of Ovarian Cancer. Cancers (Basel) 2023; 15:cancers15041140. [PMID: 36831486 PMCID: PMC9954741 DOI: 10.3390/cancers15041140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Understanding malignant transformation associated with ovarian cancer (OVCA) is important to establish early detection tests. This study examined whether expression of glucose-regulated protein 78 (GRP78, marker of cellular stress) increases during OVCA development, and whether GRP78 can be detected by targeted-transvaginal ultrasound (TVUS) imaging. METHODS Normal ovaries (n = 10), benign (n = 10) and malignant ovarian tumors at early (n = 8) and late stages (n = 16), hens with and without ovarian tumors at early and late stages (n = 10, each) were examined for GRP78 expression during OVCA development by immunohistochemistry, immunoblotting, gene expression and immunoassay. Feasibility of GRP78-targeted TVUS imaging in detecting early OVCA was examined. RESULTS Compared with normal ovaries and benign tumors, intensity of GRP78 expression was higher (p < 0.0001) in OVCA patients. Compared with normal (9007.76 ± 816.54 pg/mL), serum GRP78 levels were significantly higher (p < 0.05) in patients with early (12,730.59 ± 817.35 pg/mL) and late-stage OVCA (13,930.12 ± 202.35) (p < 0.01). Compared with normal (222.62 ± 181.69 pg/mL), serum GRP78 levels increased (p < 0.05) in hens with early (590.19 ± 198.18 pg/mL) and late-stage OVCA (1261.38 ± 372.85) (p < 0.01). Compared with non-targeted, GRP78-targeted imaging enhanced signal intensity of TVUS (p < 0.0001). CONCLUSIONS Tissue and serum levels of GRP78 increase in association with OVCA. GRP78 offers a potential serum and imaging marker for early OVCA detection.
Collapse
|
11
|
Direito I, Gomes D, Monteiro FL, Carneiro I, Lobo J, Henrique R, Jerónimo C, Helguero LA. The Clinicopathological Significance of BiP/GRP-78 in Breast Cancer: A Meta-Analysis of Public Datasets and Immunohistochemical Detection. Curr Oncol 2022; 29:9066-9087. [PMID: 36547124 PMCID: PMC9777260 DOI: 10.3390/curroncol29120710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 11/24/2022] Open
Abstract
The endoplasmic reticulum chaperone BiP (also known as GRP-78 or HSPA5) maintains protein folding to allow cell proliferation and survival and has been implicated in carcinogenesis, tumor progression, and therapy resistance. BiP's association with clinical factors and prognostic potential in breast cancer remains unclear. In this work, three types of analysis were conducted to improve the knowledge of BiP's clinicopathological potential: (1) analysis of publicly available RNA-seq and proteomics datasets stratified as high and low quartiles; (2) a systematic review and meta-analysis of immunohistochemical detection of BIP; (3) confirmation of findings by BiP immunohistochemical detection in two luminal-like breast cancer small cohorts of paired samples (pre- vs. post-endocrine therapy, and primary pre- vs. metastasis post-endocrine therapy). The TCGA PanCancer dataset and CPTAC showed groups with high BiP mRNA and protein associated with HER2, basal-like subtypes, and higher immune scores. The meta-analysis of BiP immunohistochemistry disclosed an association between higher BiP positivity and reduced relapse-free survival. BiP immunohistochemistry confirmed increased BiP expression in metastasis, an association of BiP positivity with HER2 expression, and nuclear BiP localization with higher a tumor stage and poor outcome. Therefore, three independent approaches showed that BiP protein is associated with worse outcomes and holds prognostic potential for breast cancer.
Collapse
Affiliation(s)
- Inês Direito
- iBiMED—Institute of Biomedicine, University of Aveiro, Agra do Crasto 30, 3810-193 Aveiro, Portugal
| | - Daniela Gomes
- iBiMED—Institute of Biomedicine, University of Aveiro, Agra do Crasto 30, 3810-193 Aveiro, Portugal
| | - Fátima Liliana Monteiro
- iBiMED—Institute of Biomedicine, University of Aveiro, Agra do Crasto 30, 3810-193 Aveiro, Portugal
| | - Isa Carneiro
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC) & RISE@CI-IPOP (Health Research Network), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - João Lobo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC) & RISE@CI-IPOP (Health Research Network), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Henrique
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC) & RISE@CI-IPOP (Health Research Network), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC) & RISE@CI-IPOP (Health Research Network), R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Luisa Alejandra Helguero
- iBiMED—Institute of Biomedicine, University of Aveiro, Agra do Crasto 30, 3810-193 Aveiro, Portugal
- Correspondence: ; Tel.: +35-1-234-247-240 (ext. 22112)
| |
Collapse
|
12
|
Leng X, Duxin JP. Targeting DNA-Protein Crosslinks via Post-Translational Modifications. Front Mol Biosci 2022; 9:944775. [PMID: 35860355 PMCID: PMC9289515 DOI: 10.3389/fmolb.2022.944775] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Covalent binding of proteins to DNA forms DNA-protein crosslinks (DPCs), which represent cytotoxic DNA lesions that interfere with essential processes such as DNA replication and transcription. Cells possess different enzymatic activities to counteract DPCs. These include enzymes that degrade the adducted proteins, resolve the crosslinks, or incise the DNA to remove the crosslinked proteins. An important question is how DPCs are sensed and targeted for removal via the most suited pathway. Recent advances have shown the inherent role of DNA replication in triggering DPC removal by proteolysis. However, DPCs are also efficiently sensed and removed in the absence of DNA replication. In either scenario, post-translational modifications (PTMs) on DPCs play essential and versatile roles in orchestrating the repair routes. In this review, we summarize the current knowledge of the mechanisms that trigger DPC removal via PTMs, focusing on ubiquitylation, small ubiquitin-related modifier (SUMO) conjugation (SUMOylation), and poly (ADP-ribosyl)ation (PARylation). We also briefly discuss the current knowledge gaps and emerging hypotheses in the field.
Collapse
|
13
|
Stalling of Eukaryotic Translesion DNA Polymerases at DNA-Protein Cross-Links. Genes (Basel) 2022; 13:genes13020166. [PMID: 35205211 PMCID: PMC8872012 DOI: 10.3390/genes13020166] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 02/05/2023] Open
Abstract
DNA-protein cross-links (DPCs) are extremely bulky adducts that interfere with replication. In human cells, they are processed by SPRTN, a protease activated by DNA polymerases stuck at DPCs. We have recently proposed the mechanism of the interaction of DNA polymerases with DPCs, involving a clash of protein surfaces followed by the distortion of the cross-linked protein. Here, we used a model DPC, located in the single-stranded template, the template strand of double-stranded DNA, or the displaced strand, to study the eukaryotic translesion DNA polymerases ζ (POLζ), ι (POLι) and η (POLη). POLι demonstrated poor synthesis on the DPC-containing substrates. POLζ and POLη paused at sites dictated by the footprints of the polymerase and the cross-linked protein. Beyond that, POLζ was able to elongate the primer to the cross-link site when a DPC was in the template. Surprisingly, POLη was not only able to reach the cross-link site but also incorporated 1–2 nucleotides past it, which makes POLη the most efficient DNA polymerase on DPC-containing substrates. However, a DPC in the displaced strand was an insurmountable obstacle for all polymerases, which stalled several nucleotides before the cross-link site. Overall, the behavior of translesion polymerases agrees with the model of protein clash and distortion described above.
Collapse
|
14
|
Ghodke PP, Guengerich FP. DNA polymerases η and κ bypass N 2-guanine-O 6-alkylguanine DNA alkyltransferase cross-linked DNA-peptides. J Biol Chem 2021; 297:101124. [PMID: 34461101 PMCID: PMC8463853 DOI: 10.1016/j.jbc.2021.101124] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/27/2022] Open
Abstract
DNA-protein cross-links are formed when proteins become covalently trapped with DNA in the presence of exogenous or endogenous alkylating agents. If left unrepaired, they inhibit transcription as well as DNA unwinding during replication and may result in genome instability or even cell death. The DNA repair protein O6-alkylguanine DNA-alkyltransferase (AGT) is known to form DNA cross-links in the presence of the carcinogen 1,2-dibromoethane, resulting in G:C to T:A transversions and other mutations in both bacterial and mammalian cells. We hypothesized that AGT-DNA cross-links would be processed by nuclear proteases to yield peptides small enough to be bypassed by translesion (TLS) polymerases. Here, a 15-mer and a 36-mer peptide from the active site of AGT were cross-linked to the N2 position of guanine via conjugate addition of a thiol containing a peptide dehydroalanine moiety. Bypass studies with DNA polymerases (pols) η and κ indicated that both can accurately bypass the cross-linked DNA peptides. The specificity constant (kcat/Km) for steady-state incorporation of the correct nucleotide dCTP increased by 6-fold with human (h) pol κ and 3-fold with hpol η, with hpol η preferentially inserting nucleotides in the order dC > dG > dA > dT. LC-MS/MS analysis of the extension product also revealed error-free bypass of the cross-linked 15-mer peptide by hpol η. We conclude that a bulky 15-mer AGT peptide cross-linked to the N2 position of guanine can retard polymerization, but that overall fidelity is not compromised because only correct bases are inserted and extended.
Collapse
Affiliation(s)
- Pratibha P Ghodke
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.
| |
Collapse
|
15
|
Gentry R, Thompson CM, Franzen A, Salley J, Albertini R, Lu K, Greene T. Using mechanistic information to support evidence integration and synthesis: a case study with inhaled formaldehyde and leukemia. Crit Rev Toxicol 2021; 50:885-918. [PMID: 33538218 DOI: 10.1080/10408444.2020.1854678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Formaldehyde is one of the most comprehensively studied chemicals, with over 30 years of research focused on understanding the development of cancer following inhalation. The causal conclusions regarding the potential for leukemia are largely based on the epidemiological literature, with little consideration of cancer bioassays, dosimetry studies, and mechanistic research, which challenge the biological plausibility of the disease. Recent reanalyzes of the epidemiological literature have also raised significant questions related to the purported associations between formaldehyde and leukemia. Because of this, considerable scientific debate and uncertainty remain on whether there is a causal association between formaldehyde inhalation exposure and leukemia. Further complexity in evaluating this association is related to the endogenous production of formaldehyde. Multiple modes of action (MOA) have been postulated for the development of leukemia following formaldehyde inhalation that includes unsupported hypotheses of direct or indirect toxicity to the target cell population. Herein, the available evidence relevant to evaluating the postulated MOAs for leukemia following formaldehyde inhalation exposure is organized in the IPCS MOA Framework. The integration of all the available evidence clearly highlights the limited amount of data that support any of the postulated MOAs and demonstrates a significant amount of research supporting the null hypothesis that there is no causal association between formaldehyde inhalation exposure and leukemia. These analyses result in a lack of confidence in any of the postulated MOAs, increasing confidence in the conclusion that there is a lack of biological plausibility for a causal association between formaldehyde inhalation exposure and leukemia.
Collapse
Affiliation(s)
| | | | | | | | - Richard Albertini
- Independent Consultant, Emeritus Professor, University of Vermont, Burlington, Vermont, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | |
Collapse
|
16
|
Hu Q, Klages-Mundt N, Wang R, Lynn E, Kuma Saha L, Zhang H, Srivastava M, Shen X, Tian Y, Kim H, Ye Y, Paull T, Takeda S, Chen J, Li L. The ARK Assay Is a Sensitive and Versatile Method for the Global Detection of DNA-Protein Crosslinks. Cell Rep 2020; 30:1235-1245.e4. [PMID: 31995761 PMCID: PMC7069250 DOI: 10.1016/j.celrep.2019.12.067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/28/2019] [Accepted: 12/17/2019] [Indexed: 11/03/2022] Open
Abstract
DNA-protein crosslinks (DPCs) are a frequent form of DNA lesion and are strongly inhibitive in diverse DNA transactions. Despite recent developments, the biochemical detection of DPCs remains a limiting factor for the in-depth mechanistic understanding of DPC repair. Here, we develop a sensitive and versatile assay, designated ARK, for the quantitative analysis of DPCs in cells. ARK uses sequential chaotropic and detergent-based isolation of DPCs and substantially enhances sample purity, resulting in a 5-fold increase in detection sensitivity and a 10-fold reduction in background reading. We validate the ARK assay with genetic mutants with established deficiencies in DPC repair and demonstrate its robustness by using common DPC-inducing reagents, including formaldehyde, camptothecin, and etoposide. In addition, we show that the Fanconi anemia pathway contributes to the repair of DPCs. Thus, ARK is expected to facilitate various studies aimed at understanding both fundamental biology and translational applications of DNA-protein crosslink repair. Hu et al. develop a protocol to analyze DNA-protein crosslinking (DPC) damage. Designated the ARK assay, this method outperforms widely used assays by allowing the detection of global DPCs with improved sensitivity and expanded readout. Defective DPC repair is detected in Fanconi anemia mutant cells by this protocol.
Collapse
Affiliation(s)
- Qianghua Hu
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Naeh Klages-Mundt
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Rui Wang
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Erica Lynn
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Liton Kuma Saha
- Department of Radiation Genetics, Kyoto University, Kyoto, Japan
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Xi Shen
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Yanyan Tian
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Hyeung Kim
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Yin Ye
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Tanya Paull
- Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Kyoto University, Kyoto, Japan
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| |
Collapse
|
17
|
Prasad R, Horton JK, Wilson SH. WITHDRAWN: Requirements for PARP-1 covalent crosslinking to DNA (PARP-1 DPC). DNA Repair (Amst) 2020; 89:102824. [PMID: 32151818 DOI: 10.1016/j.dnarep.2020.102824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 02/06/2023]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published in DNA Repair, 90C (2020) 102850, https://doi.org/10.1016/j.dnarep.2020.102850. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Collapse
Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, USA.
| |
Collapse
|
18
|
Prasad R, Horton JK, Wilson SH. Requirements for PARP-1 covalent crosslinking to DNA (PARP-1 DPC). DNA Repair (Amst) 2020; 90:102850. [PMID: 32438305 DOI: 10.1016/j.dnarep.2020.102850] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, North Carolina, 27709, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, North Carolina, 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, 111 T.W. Alexander Drive, Research Triangle Park, North Carolina, 27709, USA.
| |
Collapse
|
19
|
Ming X, Michaelson-Richie ED, Groehler AS, Villalta PW, Campbell C, Tretyakova NY. Cross-linking of the DNA repair protein O 6-alkylguanine DNA alkyltransferase to DNA in the presence of cisplatin. DNA Repair (Amst) 2020; 89:102840. [PMID: 32283495 DOI: 10.1016/j.dnarep.2020.102840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 12/23/2022]
Abstract
1,1,2,2-cis-diamminedichloroplatinum (II) (cisplatin) is a chemotherapeutic agent widely used in the clinic to treat various cancers. The antitumor activity of cisplatin is generally attributed to its ability to form intrastrand and interstrand DNA-DNA cross-links via sequential platination of two nucleophilic sites within the DNA duplex. However, cisplatin also induces DNA- protein lesions (DPCs) that may contribute to its biological effects due to their ability to block DNA replication and transcription. We previously reported that over 250 nuclear proteins including high mobility group proteins, histone proteins, and elongation factors formed DPCs in human HT1080 cells treated with cisplatin (Ming et al. Chem. Res. Toxicol. 2017, 30, 980-995). Interestingly, cisplatin-induced DNA-protein conjugates were reversed upon heating, by an unknown mechanism. In the present work, DNA repair protein O6-alkylguanine DNA alkyltransferase (AGT) was used as a model to investigate the molecular details of cisplatin-mediated DNA-protein cross-linking and to establish the mechanism of their reversal. We found that AGT is readily cross-linked to DNA in the presence of cisplatin. HPLC-ESI+-MS/MS sequencing of tryptic peptides originating from dG-Pt-AGT complexes revealed that the cross-linking occurred at six sites within this protein including Glu110, Lys125, Cys145, His146, Arg147, and Cys150. Cisplatin-induced Lys-Gua cross-links (1,1-cis-diammine-2-(5-amino-5-carboxypentyl)amino-2-(2'-deoxyguanosine-7-yl)-platinum(II) (dG-Pt-Lys) were detected by HPLC-ESI+-MS/MS of total digests of modified protein in comparison with the corresponding authentic standard. Upon heating, dG-Pt-AGT complexes were subject to platination migration from protein to DNA, forming cis-[Pt(NH3)2{d(GpG)}] cross-links which were detected by HPLC-ESI+-MS/MS. Our results provide a new insight into the mechanism of cisplatin-mediated DNA-protein cross-linking and their dynamic equilibrium with the corresponding DNA-DNA lesions.
Collapse
Affiliation(s)
- Xun Ming
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Erin D Michaelson-Richie
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Arnold S Groehler
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Peter W Villalta
- Mass Spectrometry Core at the Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota, Minneapolis, MN, 55455, USA.
| |
Collapse
|
20
|
Sayed AEDH, Saleh SMM, Mitani H. Comparative histology of wild-type and p53-deficient medaka (Oryzias latipes): nephrotoxic effect of ultraviolet A radiation. Photochem Photobiol Sci 2020; 19:261-273. [PMID: 31994581 DOI: 10.1039/c9pp00236g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ultraviolet radiation is an ecological factor that directly affects terrestrial organisms through suppression of immunity or damage to internal organs. The present study assessed the effects of ultraviolet A (UVA) radiation on the kidneys of both wild-type (WT) and p53-deficient medaka (Oryzias latipes) and evaluated which strain was more resistant to the effects of UVA. Fish were divided into four groups: control group 1 (Cwt and Cp53), kept for 3 days without UVA exposure; group 2 (1wt and 1p53), fish exposed daily to UVA for 1 h day-1 for 3 days; group 3 (2wt and 2p53), fish exposed daily to UVA for 2 h day-1 for 3 days; and group 4 (3wt and 3p53), fish exposed daily to UVA for 3 h day-1 for 3 days. Samples of tissues were obtained 24 h after UVA exposure. The most obvious histopathological changes induced by UVA radiation in kidney tissues of both strains of medaka (WT and p53-deficient) were high levels of vacuolation of tubular cells followed by necrosis. The tubular segments lost their normal shape which appeared like a network structure and their cells with clear cytoplasm. Necrosis of lymphoid tissues and spots of brown pigmentation (possibly melanomacrophages) were sporadically seen in interstitial lymphoid tissues, while shrinkage of glomeruli, diminution of periodic acid-Schiff staining, and increased amount of collagenous fibers were observed. Our results confirmed the harmful effects of UVA radiation on kidney tissues of both WT and p53-deficient medaka. However, WT medaka was affected more than p53-deficient medaka.
Collapse
Affiliation(s)
- Alaa El-Din H Sayed
- Zoology department, Faculty of Science, Assiut University, 71516 Assiut, Egypt.
| | | | | |
Collapse
|
21
|
Reinking HK, Hofmann K, Stingele J. Function and evolution of the DNA-protein crosslink proteases Wss1 and SPRTN. DNA Repair (Amst) 2020; 88:102822. [PMID: 32058279 DOI: 10.1016/j.dnarep.2020.102822] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 02/03/2020] [Accepted: 02/05/2020] [Indexed: 12/15/2022]
Abstract
Covalent DNA-protein crosslinks (DPCs) are highly toxic DNA adducts, which interfere with faithful DNA replication. The proteases Wss1 and SPRTN degrade DPCs and have emerged as crucially important DNA repair enzymes. Their protective role has been described in various model systems ranging from yeasts, plants, worms and flies to mice and humans. Loss of DPC proteases results in genome instability, cellular arrest, premature ageing and cancer predisposition. Here we discuss recent insights into the function and molecular mechanism of these enzymes. Furthermore, we present an in-depth phylogenetic analysis of the Wss1/SPRTN protease continuum. Remarkably flexible domain architectures and constantly changing protein-protein interaction motifs indicate ongoing evolutionary dynamics. Finally, we discuss recent data, which suggest that further partially-overlapping proteolytic systems targeting DPCs exist in eukaryotes. These new developments raise interesting questions regarding the division of labour between different DPC proteases and the mechanisms and principles of repair pathway choice.
Collapse
Affiliation(s)
- Hannah K Reinking
- Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany; Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Germany
| | - Julian Stingele
- Gene Center, Ludwig-Maximilians-University Munich, Munich, Germany; Department of Biochemistry, Ludwig-Maximilians-University Munich, Munich, Germany.
| |
Collapse
|
22
|
Nihei Y, Mori K, Werner G, Arzberger T, Zhou Q, Khosravi B, Japtok J, Hermann A, Sommacal A, Weber M, Kamp F, Nuscher B, Edbauer D, Haass C. Poly-glycine-alanine exacerbates C9orf72 repeat expansion-mediated DNA damage via sequestration of phosphorylated ATM and loss of nuclear hnRNPA3. Acta Neuropathol 2020; 139:99-118. [PMID: 31642962 PMCID: PMC6942035 DOI: 10.1007/s00401-019-02082-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/30/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022]
Abstract
Repeat expansion in C9orf72 causes amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Expanded sense and antisense repeat RNA transcripts in C9orf72 are translated into five dipeptide-repeat proteins (DPRs) in an AUG-independent manner. We previously identified the heterogeneous ribonucleoprotein (hnRNP) A3 as an interactor of the sense repeat RNA that reduces its translation into DPRs. Furthermore, we found that hnRNPA3 is depleted from the nucleus and partially mislocalized to cytoplasmic poly-GA inclusions in C9orf72 patients, suggesting that poly-GA sequesters hnRNPA3 within the cytoplasm. We now demonstrate that hnRNPA3 also binds to the antisense repeat RNA. Both DPR production and deposition from sense and antisense RNA repeats are increased upon hnRNPA3 reduction. All DPRs induced DNA double strand breaks (DSB), which was further enhanced upon reduction of hnRNPA3. Poly-glycine–arginine and poly-proline-arginine increased foci formed by phosphorylated Ataxia Telangiectasia Mutated (pATM), a major sensor of DSBs, whereas poly-glycine–alanine (poly-GA) evoked a reduction of pATM foci. In dentate gyri of C9orf72 patients, lower nuclear hnRNPA3 levels were associated with increased DNA damage. Moreover, enhanced poly-GA deposition correlated with reduced pATM foci. Since cytoplasmic pATM deposits partially colocalized with poly-GA deposits, these results suggest that poly-GA, the most frequent DPR observed in C9orf72 patients, differentially causes DNA damage and that poly-GA selectively sequesters pATM in the cytoplasm inhibiting its recruitment to sites of DNA damage. Thus, mislocalization of nuclear hnRNPA3 caused by poly-GA leads to increased poly-GA production, which partially depletes pATM, and consequently enhances DSB.
Collapse
|
23
|
Ji S, Thomforde J, Rogers C, Fu I, Broyde S, Tretyakova NY. Transcriptional Bypass of DNA-Protein and DNA-Peptide Conjugates by T7 RNA Polymerase. ACS Chem Biol 2019; 14:2564-2575. [PMID: 31573793 DOI: 10.1021/acschembio.9b00365] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
DNA-protein cross-links (DPCs) are unusually bulky DNA adducts that block the access of proteins to DNA and interfere with gene expression, replication, and repair. We previously described DPC formation at the N7-guanine position of DNA in human cells treated with antitumor nitrogen mustards and platinum compounds and have shown that DPCs can form endogenously at DNA epigenetic mark 5-formyl-dC. However, insufficient information is available about the effects of these structurally distinct DPCs on transcription. In the present work, we employ a combination of in vitro assays, mass spectrometry, and molecular dynamics simulations to examine the ability of phage T7 RNA polymerase to bypass DPCs conjugated to the C7 position of 7-deaza-dG and the C5 position of dC. These model adducts represent endogenous DPCs induced by exposure to antitumor drugs and formed at epigenetics DNA marks, respectively. Our results reveal that DPCs containing full-length proteins significantly inhibit in vitro transcription by T7 RNA polymerase, while short DNA-peptide cross-links (DpCs) are bypassed. DpCs conjugated to the C7 position of 7-deaza-dG are transcribed with high fidelity, while the same polypeptides attached to the C5 position of dC induce transcription errors. Molecular dynamics simulations of DpCs conjugated either to the C5 atom of dC or the C7 position of 7-deaza-dG on the template strand in T7 RNA polymerase explain how the conjugated peptide can be accommodated in the narrow major groove of the DNA-RNA hybrid and how the modified dC can form a stable mismatch with the incoming ATP in the polymerase active site, allowing for transcriptional mutagenesis.
Collapse
Affiliation(s)
| | | | | | - Iwen Fu
- Department of Biology New York University, New York, New York 10003, United States
| | - Suse Broyde
- Department of Biology New York University, New York, New York 10003, United States
| | | |
Collapse
|
24
|
Ji S, Fu I, Naldiga S, Shao H, Basu AK, Broyde S, Tretyakova NY. 5-Formylcytosine mediated DNA-protein cross-links block DNA replication and induce mutations in human cells. Nucleic Acids Res 2019; 46:6455-6469. [PMID: 29905846 PMCID: PMC6061883 DOI: 10.1093/nar/gky444] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/29/2018] [Indexed: 12/24/2022] Open
Abstract
5-Formylcytosine (5fC) is an epigenetic DNA modification introduced via TET protein-mediated oxidation of 5-methyl-dC. We recently reported that 5fC form reversible DNA–protein conjugates (DPCs) with histone proteins in living cells (Ji et al. (2017) Angew. Chem. Int. Ed., 56:14130–14134). We now examined the effects of 5fC mediated DPCs on DNA replication. Synthetic DNA duplexes containing site-specific DPCs between 5fC and lysine-containing proteins and peptides were subjected to primer extension experiments in the presence of human translesion synthesis DNA polymerases η and κ. We found that DPCs containing histones H2A or H4 completely inhibited DNA replication, but the replication block was removed when the proteins were subjected to proteolytic digestion. Cross-links to 11-mer or 31-mer peptides were bypassed by both polymerases in an error-prone manner, inducing targeted C→T transitions and –1 deletions. Similar types of mutations were observed when plasmids containing 5fC-peptide cross-links were replicated in human embryonic kidney (HEK) 293T cells. Molecular simulations of the 11-mer peptide-dC cross-links bound to human polymerases η and κ revealed that the peptide fits well on the DNA major groove side, and the modified dC forms a stable mismatch with incoming dATP via wobble base pairing in the polymerase active site.
Collapse
Affiliation(s)
- Shaofei Ji
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Iwen Fu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Spandana Naldiga
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Hongzhao Shao
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ashis K Basu
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
| | - Suse Broyde
- Department of Biology, New York University, New York, NY 10003, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.,Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| |
Collapse
|
25
|
Naldiga S, Ji S, Thomforde J, Nicolae CM, Lee M, Zhang Z, Moldovan GL, Tretyakova NY, Basu AK. Error-prone replication of a 5-formylcytosine-mediated DNA-peptide cross-link in human cells. J Biol Chem 2019; 294:10619-10627. [PMID: 31138652 DOI: 10.1074/jbc.ra119.008879] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/20/2019] [Indexed: 12/21/2022] Open
Abstract
DNA-protein cross-links can interfere with chromatin architecture, block DNA replication and transcription, and interfere with DNA repair. Here we synthesized a DNA 23-mer containing a site-specific DNA-peptide cross-link (DpC) by cross-linking an 11-mer peptide to the DNA epigenetic mark 5-formylcytosine in synthetic DNA and used it to generate a DpC-containing plasmid construct. Upon replication of the DpC-containing plasmid in HEK 293T cells, approximately 9% of progeny plasmids contained targeted mutations and 5% semitargeted mutations. Targeted mutations included C→T transitions and C deletions, whereas semitargeted mutations included several base substitutions and deletions near the DpC lesion. To identify DNA polymerases involved in DpC bypass, we comparatively studied translesion synthesis (TLS) efficiency and mutagenesis of the DpC in a series of cell lines with TLS polymerase knockouts or knockdowns. Knockdown of either hPol ι or hPol ζ reduced the mutation frequency by nearly 50%. However, the most significant reduction in mutation frequency (50%-70%) was observed upon simultaneous knockout of hPol η and hPol κ with knockdown of hPol ζ, suggesting that these TLS polymerases play a critical role in error-prone DpC bypass. Because TLS efficiency of the DpC construct was not significantly affected in TLS polymerase-deficient cells, we examined a possible role of replicative DNA polymerases in their bypass and determined that hPol δ and hPol ϵ can accurately bypass the DpC. We conclude that both replicative and TLS polymerases can bypass this DpC lesion in human cells but that mutations are induced mainly by TLS polymerases.
Collapse
Affiliation(s)
- Spandana Naldiga
- From the Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269
| | - Shaofei Ji
- the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jenna Thomforde
- the Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Claudia M Nicolae
- the Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033, and
| | - Marietta Lee
- the New York Medical College, Valhalla, New York 10595
| | | | | | - Natalia Y Tretyakova
- the Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Ashis K Basu
- From the Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269,
| |
Collapse
|
26
|
Türker H. Histological and ultrastructural analyses of mole rats lung cells exposed to ultraviolet radiation. JOURNAL OF RADIATION RESEARCH AND APPLIED SCIENCES 2019. [DOI: 10.1016/j.jrras.2014.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Hüseyin Türker
- Ankara University, Science Faculty, Department of Biology, Ankara, 06500, Turkey
| |
Collapse
|
27
|
Human Mesenchymal Stem Cell Secretome from Bone Marrow or Adipose-Derived Tissue Sources for Treatment of Hypoxia-Induced Pulmonary Epithelial Injury. Int J Mol Sci 2018; 19:ijms19102996. [PMID: 30274394 PMCID: PMC6212866 DOI: 10.3390/ijms19102996] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/20/2018] [Accepted: 09/27/2018] [Indexed: 02/07/2023] Open
Abstract
Alveolar epithelial dysfunction induced by hypoxic stress plays a significant role in the pathological process of lung ischemia-reperfusion injury (IRI). Mesenchymal stem cell (MSC) therapies have demonstrated efficacy in exerting protective immunomodulatory effects, thereby reducing airway inflammation in several pulmonary diseases. Aim: This study assesses the protective effects of MSC secretome from different cell sources, human bone marrow (BMSC) and adipose tissue (ADSC), in attenuating hypoxia-induced cellular stress and inflammation in pulmonary epithelial cells. Methods: Pulmonary epithelial cells, primary rat alveolar epithelial cells (AEC) and A549 cell line were pre-treated with BMSC, or ADSC conditioned medium (CM) and subjected to hypoxia for 24 h. Results: Both MSC-CM improved cell viability, reduced secretion of pro-inflammatory mediators and enhanced IL-10 anti-inflammatory cytokine production in hypoxic injured primary rat AECs. ADSC-CM reduced hypoxic cellular injury by mechanisms which include: inhibition of p38 MAPK phosphorylation and nuclear translocation of subunits in primary AECs. Both MSC-CM enhanced translocation of Bcl-2 to the nucleus, expression of cytoprotective glucose-regulated proteins (GRP) and restored matrix metalloproteinases (MMP) function, thereby promoting repair and cellular homeostasis, whereas inhibition of GRP chaperones was detrimental to cell survival. Conclusions: Elucidation of the protective mechanisms exerted by the MSC secretome is an essential step for maximizing the therapeutic effects, in addition to developing therapeutic targets-specific strategies for various pulmonary syndromes.
Collapse
|
28
|
Variable termination sites of DNA polymerases encountering a DNA-protein cross-link. PLoS One 2018; 13:e0198480. [PMID: 29856874 PMCID: PMC5983568 DOI: 10.1371/journal.pone.0198480] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/18/2018] [Indexed: 11/19/2022] Open
Abstract
DNA-protein cross-links (DPCs) are important DNA lesions induced by endogenous crosslinking agents such as formaldehyde or acetaldehyde, as well as ionizing radiation, cancer chemotherapeutic drugs, and abortive action of some enzymes. Due to their very bulky nature, they are expected to interfere with DNA and RNA synthesis and DNA repair. DPCs are highly genotoxic and the ability of cells to deal with them is relevant for many chemotherapeutic interventions. However, interactions of DNA polymerases with DPCs have been poorly studied due to the lack of a convenient experimental model. We have used NaBH4-induced trapping of E. coli formamidopyrimidine-DNA glycosylase with DNA to construct model DNA polymerase substrates containing a DPC in single-stranded template, or in the template strand of double-stranded DNA, or in the non-template (displaced) strand of double-stranded DNA. Nine DNA polymerases belonging to families A, B, X, and Y were studied with respect to their behavior upon encountering a DPC: Klenow fragment of E. coli DNA polymerase I, Thermus aquaticus DNA polymerase I, Pyrococcus furiosus DNA polymerase, Sulfolobus solfataricus DNA polymerase IV, human DNA polymerases β, κ and λ, and DNA polymerases from bacteriophages T4 and RB69. Although none were able to fully bypass DPCs in any context, Family B DNA polymerases (T4, RB69) and Family Y DNA polymerase IV were able to elongate the primer up to the site of the cross-link if a DPC was located in single-stranded template or in the displaced strand. In other cases, DNA synthesis stopped 4-5 nucleotides before the site of the cross-link in single-stranded template or in double-stranded DNA if the polymerases could displace the downstream strand. We suggest that termination of DNA polymerases on a DPC is mostly due to the unrelieved conformational strain experienced by the enzyme when pressing against the cross-linked protein molecule.
Collapse
|
29
|
Guo L, Zhao Y, Liu D, Liu Z, Chen C, Xu R, Tian M, Wang X, Chen H, Kong MG. Cold atmospheric-pressure plasma induces DNA-protein crosslinks through protein oxidation. Free Radic Res 2018; 52:783-798. [PMID: 29722278 DOI: 10.1080/10715762.2018.1471476] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Reactive oxygen and nitrogen species (ROS and RNS) generated by cold atmospheric-pressure plasma could damage genomic DNA, although the precise types of these DNA damage induced by plasma are poorly characterized. Understanding plasma-induced DNA damage will help to elucidate the biological effect of plasma and guide the application of plasma in ROS-based therapy. In this study, it was shown that ROS and RNS generated by physical plasma could efficiently induce DNA-protein crosslinks (DPCs) in bacteria, yeast, and human cells. An in vitro assay showed that plasma treatment resulted in the formation of covalent DPCs by activating proteins to crosslink with DNA. Mass spectrometry and hydroperoxide analysis detected oxidation products induced by plasma. DPC formation were alleviated by singlet oxygen scavenger, demonstrating the importance of singlet oxygen in this process. These results suggested the roles of DPC formation in DNA damage induced by plasma, which could improve the understanding of the biological effect of plasma and help to develop a new strategy in plasma-based therapy including infection and cancer therapy.
Collapse
Affiliation(s)
- Li Guo
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Yiming Zhao
- b School of Life Science and Technology , Xi'an Jiaotong University , Xi'an , PR China
| | - Dingxin Liu
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Zhichao Liu
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Chen Chen
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Ruobing Xu
- b School of Life Science and Technology , Xi'an Jiaotong University , Xi'an , PR China
| | - Miao Tian
- b School of Life Science and Technology , Xi'an Jiaotong University , Xi'an , PR China
| | - Xiaohua Wang
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Hailan Chen
- c Frank Reidy Center for Bioelectrics , Old Dominion University , Norfolk , VA , USA
| | - Michael G Kong
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China.,c Frank Reidy Center for Bioelectrics , Old Dominion University , Norfolk , VA , USA.,d Department of Electrical and Computer Engineering , Old Dominion University , Norfolk , VA , USA
| |
Collapse
|
30
|
Chesner LN, Campbell C. A Simple, Rapid, and Quantitative Assay to Measure Repair of DNA-protein Crosslinks on Plasmids Transfected into Mammalian Cells. J Vis Exp 2018. [PMID: 29553515 PMCID: PMC5898435 DOI: 10.3791/57413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The purpose of this method is to provide a flexible, rapid, and quantitative technique to examine the kinetics of DNA-protein crosslink (DPC) repair in mammalian cell lines. Rather than globally assaying removal of xenobiotic-induced or spontaneous chromosomal DPC removal, this assay examines the repair of a homogeneous, chemically defined lesion specifically introduced at one site within a plasmid DNA substrate. Importantly, this approach avoids the use of radioactive materials and is not dependent on expensive or highly-specialized technology. Instead, it relies on standard recombinant DNA procedures and widely available real-time, quantitative polymerase chain reaction (qPCR) instrumentation. Given the inherent flexibility of the strategy utilized, the size of the crosslinked protein, as well as the nature of the chemical linkage and the precise DNA sequence context of the attachment site can be varied to address the respective contributions of these parameters to the overall efficiency of DPC repair. Using this method, plasmids containing a site-specific DPC were transfected into cells and low molecular weight DNA recovered at various times post-transfection. Recovered DNA is then subjected to strand-specific primer extension (SSPE) using a primer complementary to the damaged strand of the plasmid. Since the DPC lesion blocks Taq DNA polymerase, the ratio of repaired to un-repaired DNA can be quantitatively assessed using qPCR. Cycle threshold (CT) values are used to calculate percent repair at various time points in the respective cell lines. This SSPE-qPCR method can also be used to quantitatively assess the repair kinetics of any DNA adduct that blocks Taq polymerase.
Collapse
|
31
|
Chesner LN, Campbell C. A quantitative PCR-based assay reveals that nucleotide excision repair plays a predominant role in the removal of DNA-protein crosslinks from plasmids transfected into mammalian cells. DNA Repair (Amst) 2018; 62:18-27. [PMID: 29413806 DOI: 10.1016/j.dnarep.2018.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/07/2018] [Accepted: 01/08/2018] [Indexed: 12/26/2022]
Abstract
DNA-protein crosslinks (DPCs) are complex DNA lesions that induce mutagenesis and cell death. DPCs are created by common antitumor drugs, reactive oxygen species, and endogenous aldehydes. Since these agents create other types of DNA damage in addition to DPCs, identification of the mechanisms of DPC repair is challenging. In this study, we created plasmid substrates containing site-specific DPC lesions, as well as plasmids harboring lesions that are selectively repaired by the base excision or nucleotide excision repair (NER) pathways. These substrates were transfected into mammalian cells and a quantitative real-time PCR assay employed to study their repair. This assay revealed that DPC lesions were rapidly repaired in wild-type human and Chinese hamster derived cells, as were plasmids harboring an oxoguanine residue (base excision repair substrate) or cholesterol lesion (NER substrate). Interestingly, the DPC substrate was repaired in human cells nearly three times as efficiently as in Chinese hamster cells (>75% vs ∼25% repair at 8 h post-transfection), while there was no significant species-specific difference in the efficiency with which the cholesterol lesion was repaired (∼60% repair). Experiments revealed that both human and hamster cells deficient in NER due to mutations in the xeroderma pigmentosum A or D genes were five to ten-fold less able to repair the cholesterol and DPC lesions than were wild-type control clones, and that both the global genome and transcription-coupled sub-pathways of NER were capable of repairing DPCs. In addition, analyses using this PCR-based assay revealed that a 4 kDa peptide DNA crosslink was repaired nearly twice as efficiently as was a ∼38 kDa DPC, suggesting that proteolytic degradation of crosslinked proteins occurs during DPC repair. These results highlight the utility of this PCR-based assay to study DNA repair and indicate that the NER machinery rapidly and efficiently repairs plasmid DPC lesions in mammalian cells.
Collapse
Affiliation(s)
- Lisa N Chesner
- Department of Pharmacology, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA.
| |
Collapse
|
32
|
König A, Zöller N, Kippenberger S, Bernd A, Kaufmann R, Layer PG, Heselich A. Non-thermal near-infrared exposure photobiomodulates cellular responses to ionizing radiation in human full thickness skin models. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 178:115-123. [DOI: 10.1016/j.jphotobiol.2017.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 10/18/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022]
|
33
|
Saberi H, Keshavarzi B, Shirpoor A, Gharalari FH, Rasmi Y. Rescue effects of ginger extract on dose dependent radiation-induced histological and biochemical changes in the kidneys of male Wistar rats. Biomed Pharmacother 2017; 94:569-576. [PMID: 28780473 DOI: 10.1016/j.biopha.2017.07.128] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/23/2017] [Accepted: 07/24/2017] [Indexed: 11/17/2022] Open
Abstract
Radiation is an essential modality in the management of cancer therapy, but its acute and chronic side effects on the normal organs limit the helpfulness of radiotherapy. The deleterious effects of radiation begin with oxidative stress and inflammatory reaction to radiolytic hydrolysis and formation of free radicals. The aim of the current study was to investigate the effect of dose dependent whole body radiation exposure on histological and biochemical alterations in rat kidney. It was also planned to find out whether ginger extract mitigated the deleterious effects of different doses of radiation in rat kidney. Male Wistar rats were exposed to three doses (2, 4, and 8Gy) of γ- ray with or without a 10day pretreatment with ginger extract. After 10days of whole body γ- ray exposure, the results revealed proliferation of glomerular and tubular cells, fibrosis in glomerular and peritubular and a significant increase in 8-OHdG, CRP, cystatin C (in 8Gy), plasma urea and creatinine levels, as well as a significant decrease in total antioxidant capacity of radiation groups compared to those of the control group. Ginger extract administration once daily for 10 consecutive days before exposure to 2-4-8Gy radiotherapy, which ameliorated histological and biochemical alterations in kidneys of the rats entirely or partially compared to those in the ethanol group rats. These findings indicate that whole body exposure to radiation induces kidney damage through oxidative DNA damage and inflammatory reactions, and that these effects can be alleviated using ginger pretreatment as an antioxidant and anti-inflammatory agent.
Collapse
Affiliation(s)
- Hassan Saberi
- Department of Medical Physics, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Behnaz Keshavarzi
- Department of Medical Physics, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Alireza Shirpoor
- Nephrology and Kidney Transplant Research Center, Urmia University of Medical Sciences, Urmia, Iran; Department of Physiology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
| | | | - Yousef Rasmi
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| |
Collapse
|
34
|
El-Hamoly T, El-Sharawy DM, El Refaye MS, Abd El-Rahman SS. L-thyroxine modifies nephrotoxicity by regulating the apoptotic pathway: The possible role of CD38/ADP-ribosyl cyclase-mediated calcium mobilization. PLoS One 2017; 12:e0184157. [PMID: 28892514 PMCID: PMC5593187 DOI: 10.1371/journal.pone.0184157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/18/2017] [Indexed: 11/18/2022] Open
Abstract
Thyroid hormones are well-established as a key regulator of many cellular metabolic pathways developed in various pathogeneses. Here, we dedicated the current work to investigate the role of thyroid hormone analogue (L-thyroxine, L-TH) in regulating the renal cytotoxicity using in vivo and in vitro models. Swiss mice were exposed to gamma radiation (IRR, 6Gy) or treated with cisplatin (CIS, 15 mg/kg, i.p.) for induction of nephrotoxicity. Remarkably, pretreatment with L-TH (1μg/kg) ameliorated the elevated kidney function biomarkers, oxidative stress and protected the renal tissue from the subsequent cellular damage. Likewise, L-TH inhibited the apoptotic cascade by down-regulating the extreme consumption of the cellular energy (ATP), the expression of caspase-3 and Bax, and the stimulation of cyclic ADP ribose (cADPR)/calcium mobilization. Moreover, incubation with L-TH (120nM/4h) significantly blocked the cytotoxicity of CIS on Vero cells and the depletion of NAD+ content as well as modified the ADP-ribose cyclase (CD38) enzymatic activity. High doses of L-TH (up to30 nM/4h) inversely increased the radiosensitivity of Vero cells towards IRR (up to 6Gy). On the other hand, L-TH did not interfere CIS-induced cytotoxicity of colorectal adenocarcinoma (Caco-2) cell line. In conclusion, pretreatment with L-TH could be a promising protective approach to the renal cellular damage induced during either CIS or IRR therapy by regulating the unbalanced oxidative status, the expression of pro-apoptotic biomarkers via modulation of cADPR mediated-calcium mobilization.
Collapse
Affiliation(s)
- Tarek El-Hamoly
- Drug Radiation Research Department, National Center for Radiation Research and Technology, Atomic Energy Authority, Cairo, Egypt
- Cyclotron Project, Center of Nuclear Researches, Atomic Energy Authority, Cairo, Egypt
| | - Dina M. El-Sharawy
- Cyclotron Project, Center of Nuclear Researches, Atomic Energy Authority, Cairo, Egypt
| | - Marwa S. El Refaye
- Cyclotron Project, Center of Nuclear Researches, Atomic Energy Authority, Cairo, Egypt
| | - Sahar S. Abd El-Rahman
- Department of Pathology, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
- * E-mail: ,
| |
Collapse
|
35
|
Nakano T, Xu X, Salem AMH, Shoulkamy MI, Ide H. Radiation-induced DNA-protein cross-links: Mechanisms and biological significance. Free Radic Biol Med 2017; 107:136-145. [PMID: 27894771 DOI: 10.1016/j.freeradbiomed.2016.11.041] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 12/20/2022]
Abstract
Ionizing radiation produces various DNA lesions such as base damage, DNA single-strand breaks (SSBs), DNA double-strand breaks (DSBs), and DNA-protein cross-links (DPCs). Of these, the biological significance of DPCs remains elusive. In this article, we focus on radiation-induced DPCs and review the current understanding of their induction, properties, repair, and biological consequences. When cells are irradiated, the formation of base damage, SSBs, and DSBs are promoted in the presence of oxygen. Conversely, that of DPCs is promoted in the absence of oxygen, suggesting their importance in hypoxic cells, such as those present in tumors. DNA and protein radicals generated by hydroxyl radicals (i.e., indirect effect) are responsible for DPC formation. In addition, DPCs can also be formed from guanine radical cations generated by the direct effect. Actin, histones, and other proteins have been identified as cross-linked proteins. Also, covalent linkages between DNA and protein constituents such as thymine-lysine and guanine-lysine have been identified and their structures are proposed. In irradiated cells and tissues, DPCs are repaired in a biphasic manner, consisting of fast and slow components. The half-time for the fast component is 20min-2h and that for the slow component is 2-70h. Notably, radiation-induced DPCs are repaired more slowly than DSBs. Homologous recombination plays a pivotal role in the repair of radiation-induced DPCs as well as DSBs. Recently, a novel mechanism of DPC repair mediated by a DPC protease was reported, wherein the resulting DNA-peptide cross-links were bypassed by translesion synthesis. The replication and transcription of DPC-bearing reporter plasmids are inhibited in cells, suggesting that DPCs are potentially lethal lesions. However, whether DPCs are mutagenic and induce gross chromosomal alterations remains to be determined.
Collapse
Affiliation(s)
- Toshiaki Nakano
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Xu Xu
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Amir M H Salem
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan; Department of Pathology, Medical Research Division, National Research Centre, El-Bohouth St., Dokki, Giza 12311, Egypt
| | - Mahmoud I Shoulkamy
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan; Department of Zoology, Biological Science Building, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Hiroshi Ide
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
| |
Collapse
|
36
|
Ming X, Groehler A, Michaelson-Richie ED, Villalta PW, Campbell C, Tretyakova NY. Mass Spectrometry Based Proteomics Study of Cisplatin-Induced DNA-Protein Cross-Linking in Human Fibrosarcoma (HT1080) Cells. Chem Res Toxicol 2017; 30:980-995. [PMID: 28282121 DOI: 10.1021/acs.chemrestox.6b00389] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Platinum-based antitumor drugs such as 1,1,2,2-cis-diamminedichloroplatinum(II) (cisplatin), carboplatin, and oxaliplatin are currently used to treat nearly 50% of all cancer cases, and novel platinum based agents are under development. The antitumor effects of cisplatin and other platinum compounds are attributed to their ability to induce interstrand DNA-DNA cross-links, which are thought to inhibit tumor cell growth by blocking DNA replication and/or preventing transcription. However, platinum agents also induce significant numbers of unusually bulky and helix-distorting DNA-protein cross-links (DPCs), which are poorly characterized because of their unusual complexity. We and others have previously shown that DPCs block DNA replication and transcription and causes toxicity in human cells, potentially contributing to the biological effects of platinum agents. In the present work, we have undertaken a system-wide investigation of cisplatin-mediated DNA-protein cross-linking in human fibrosarcoma (HT1080) cells using mass spectrometry-based proteomics. DPCs were isolated from cisplatin-treated cells using a modified phenol/chloroform DNA extraction in the presence of protease inhibitors. Proteins were released from DNA strands and identified by mass spectrometry-based proteomics and immunological detection. Over 250 nuclear proteins captured on chromosomal DNA following treatment with cisplatin were identified, including high mobility group (HMG) proteins, histone proteins, and elongation factors. To reveal the exact molecular structures of cisplatin-mediated DPCs, isotope dilution HPLC-ESI+-MS/MS was employed to detect 1,1-cis-diammine-2-(5-amino-5-carboxypentyl)amino-2-(2'-deoxyguanosine-7-yl)-platinum(II) (dG-Pt-Lys) conjugates between the N7 guanine of DNA and the ε-amino group of lysine. Our results demonstrate that therapeutic levels of cisplatin induce a wide range of DPC lesions, which likely contribute to both target and off target effects of this clinically important drug.
Collapse
Affiliation(s)
- Xun Ming
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Arnold Groehler
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Erin D Michaelson-Richie
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Peter W Villalta
- Mass Spectrometry Core at the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Colin Campbell
- Department of Pharmacology, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry and the Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| |
Collapse
|
37
|
Groehler A, Degner A, Tretyakova NY. Mass Spectrometry-Based Tools to Characterize DNA-Protein Cross-Linking by Bis-Electrophiles. Basic Clin Pharmacol Toxicol 2017; 121 Suppl 3:63-77. [PMID: 28032943 DOI: 10.1111/bcpt.12751] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/14/2016] [Indexed: 12/14/2022]
Abstract
DNA-protein cross-links (DPCs) are unusually bulky DNA adducts that form in cells as a result of exposure to endogenous and exogenous agents including reactive oxygen species, ultraviolet light, ionizing radiation, environmental agents (e.g. transition metals, formaldehyde, 1,2-dibromoethane, 1,3-butadiene) and common chemotherapeutic agents. Covalent DPCs are cytotoxic and mutagenic due to their ability to interfere with faithful DNA replication and to prevent accurate gene expression. Key to our understanding of the biological significance of DPC formation is identifying the proteins most susceptible to forming these unusually bulky and complex lesions and quantifying the extent of DNA-protein cross-linking in cells and tissues. Recent advances in bottom-up mass spectrometry-based proteomics have allowed for an unbiased assessment of the whole protein DPC adductome after in vitro and in vivo exposures to cross-linking agents. This MiniReview summarizes current and emerging methods for DPC isolation and analysis by mass spectrometry-based proteomics. We also highlight several examples of successful applications of these novel methodologies to studies of DPC lesions induced by bis-electrophiles such as formaldehyde, 1,2,3,4-diepoxybutane, nitrogen mustards and cisplatin.
Collapse
Affiliation(s)
- Arnold Groehler
- Department of Medicinal Chemistry, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Amanda Degner
- Department of Medicinal Chemistry, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
38
|
Salus K, Hoffmann M, Siodła T, Wyrzykiewicz B, Pluskota-Karwatka D. Synthesis, structural studies and stability of model cysteine containing DNA–protein cross-links. NEW J CHEM 2017. [DOI: 10.1039/c7nj00270j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the presence of Nα-acetyllysine, cross-links of aldehydic adenine nucleoside adducts with N-acetylcysteine lose an N-acetylcysteine moiety undergoing transformation into amino derivatives.
Collapse
Affiliation(s)
- Kinga Salus
- Adam Mickiewicz University in Poznań
- Faculty of Chemistry
- Umultowska 89b
- 61-614 Poznań
- Poland
| | - Marcin Hoffmann
- Adam Mickiewicz University in Poznań
- Faculty of Chemistry
- Umultowska 89b
- 61-614 Poznań
- Poland
| | - Tomasz Siodła
- Adam Mickiewicz University in Poznań
- Faculty of Chemistry
- Umultowska 89b
- 61-614 Poznań
- Poland
| | - Bożena Wyrzykiewicz
- Adam Mickiewicz University in Poznań
- Faculty of Chemistry
- Umultowska 89b
- 61-614 Poznań
- Poland
| | | |
Collapse
|
39
|
Villa M, Cassani C, Gobbini E, Bonetti D, Longhese MP. Coupling end resection with the checkpoint response at DNA double-strand breaks. Cell Mol Life Sci 2016; 73:3655-63. [PMID: 27141941 PMCID: PMC11108263 DOI: 10.1007/s00018-016-2262-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/08/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
Abstract
DNA double-strand breaks (DSBs) are a nasty form of damage that needs to be repaired to ensure genome stability. The DSB ends can undergo a strand-biased nucleolytic processing (resection) to generate 3'-ended single-stranded DNA (ssDNA) that channels DSB repair into homologous recombination. Generation of ssDNA also triggers the activation of the DNA damage checkpoint, which couples cell cycle progression with DSB repair. The checkpoint response is intimately linked to DSB resection, as some checkpoint proteins regulate the resection process. The present review will highlight recent works on the mechanism and regulation of DSB resection and its interplays with checkpoint activation/inactivation in budding yeast.
Collapse
Affiliation(s)
- Matteo Villa
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Diego Bonetti
- Institute of Molecular Biology gGmbH (IMB), 55128, Mainz, Germany
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy.
| |
Collapse
|
40
|
Wickramaratne S, Ji S, Mukherjee S, Su Y, Pence MG, Lior-Hoffmann L, Fu I, Broyde S, Guengerich FP, Distefano M, Schärer OD, Sham YY, Tretyakova N. Bypass of DNA-Protein Cross-links Conjugated to the 7-Deazaguanine Position of DNA by Translesion Synthesis Polymerases. J Biol Chem 2016; 291:23589-23603. [PMID: 27621316 DOI: 10.1074/jbc.m116.745257] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 12/22/2022] Open
Abstract
DNA-protein cross-links (DPCs) are bulky DNA lesions that form both endogenously and following exposure to bis-electrophiles such as common antitumor agents. The structural and biological consequences of DPCs have not been fully elucidated due to the complexity of these adducts. The most common site of DPC formation in DNA following treatment with bis-electrophiles such as nitrogen mustards and cisplatin is the N7 position of guanine, but the resulting conjugates are hydrolytically labile and thus are not suitable for structural and biological studies. In this report, hydrolytically stable structural mimics of N7-guanine-conjugated DPCs were generated by reductive amination reactions between the Lys and Arg side chains of proteins/peptides and aldehyde groups linked to 7-deazaguanine residues in DNA. These model DPCs were subjected to in vitro replication in the presence of human translesion synthesis DNA polymerases. DPCs containing full-length proteins (11-28 kDa) or a 23-mer peptide blocked human polymerases η and κ. DPC conjugates to a 10-mer peptide were bypassed with nucleotide insertion efficiency 50-100-fold lower than for native G. Both human polymerase (hPol) κ and hPol η inserted the correct base (C) opposite the 10-mer peptide cross-link, although small amounts of T were added by hPol η. Molecular dynamics simulation of an hPol κ ternary complex containing a template-primer DNA with dCTP opposite the 10-mer peptide DPC revealed that this bulky lesion can be accommodated in the polymerase active site by aligning with the major groove of the adducted DNA within the ternary complex of polymerase and dCTP.
Collapse
Affiliation(s)
| | - Shaofei Ji
- From the Masonic Cancer Center and.,the Departments of Chemistry
| | | | - Yan Su
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Matthew G Pence
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Lee Lior-Hoffmann
- Department of Biology, New York University, New York, New York 10003-6688, and
| | - Iwen Fu
- Department of Biology, New York University, New York, New York 10003-6688, and
| | - Suse Broyde
- Department of Biology, New York University, New York, New York 10003-6688, and
| | - F Peter Guengerich
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | | | - Orlando D Schärer
- Chemistry, Stony Brook University, Stony Brook, New York 11794.,Departments of Pharmacological Sciences and
| | | | - Natalia Tretyakova
- From the Masonic Cancer Center and .,Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| |
Collapse
|
41
|
Albertini RJ, Kaden DA. Do chromosome changes in blood cells implicate formaldehyde as a leukemogen? Crit Rev Toxicol 2016; 47:145-184. [DOI: 10.1080/10408444.2016.1211987] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
42
|
Gobbini E, Cassani C, Villa M, Bonetti D, Longhese MP. Functions and regulation of the MRX complex at DNA double-strand breaks. MICROBIAL CELL (GRAZ, AUSTRIA) 2016; 3:329-337. [PMID: 28357369 PMCID: PMC5349012 DOI: 10.15698/mic2016.08.517] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/03/2016] [Indexed: 12/22/2022]
Abstract
DNA double-strand breaks (DSBs) pose a serious threat to genome stability and cell survival. Cells possess mechanisms that recognize DSBs and promote their repair through either homologous recombination (HR) or non-homologous end joining (NHEJ). The evolutionarily conserved Mre11-Rad50-Xrs2 (MRX) complex plays a central role in the cellular response to DSBs, as it is implicated in controlling end resection and in maintaining the DSB ends tethered to each other. Furthermore, it is responsible for DSB signaling by activating the checkpoint kinase Tel1 that, in turn, supports MRX function in a positive feedback loop. The present review focuses mainly on recent works in the budding yeast Saccharomyces cerevisiae to highlight structure and regulation of MRX as well as its interplays with Tel1.
Collapse
Affiliation(s)
- Elisa Gobbini
- Dipartimento di Biotecnologie e Bioscienze, Università di
Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Corinne Cassani
- Dipartimento di Biotecnologie e Bioscienze, Università di
Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Matteo Villa
- Dipartimento di Biotecnologie e Bioscienze, Università di
Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Diego Bonetti
- Institute of Molecular Biology gGmbH (IMB), 55128 Mainz, Germany
| | - Maria P. Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di
Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| |
Collapse
|
43
|
Mu H, Liu Q, Niu H, Wang D, Tang J, Duan J. Autophagy promotes DNA-protein crosslink clearance. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2016; 797:21-5. [PMID: 26921017 DOI: 10.1016/j.mrgentox.2015.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/25/2015] [Accepted: 12/09/2015] [Indexed: 11/16/2022]
Abstract
Toxic DNA-protein crosslinks (DPCs) can result from exposure to radiation or chemotherapeutic agents. DPCs can also accumulate during aging or stress. However, the cellular mechanisms underlying clearance of DPCs remain largely unknown. Here, we have identified an important role of autophagy in the processing of DPCs induced by three representative agents: formaldehyde, a chemical used widely in industry; UV light; and camptothecin, a cytotoxic anticancer drug. Autophagy inhibitors, 3-methyladenine (3-MA) or chloroquine (CQ), promoted the accumulation of DPCs in damaged cells and injured organs. siRNA-mediated silencing of Atg5 or Atg7, two essential components for the formation of the autophagosome, gave similar results. In contrast, the autophagy inducer rapamycin (RAP) attenuated DPCs in vitro and in vivo. Our findings reveal the importance of autophagy in controlling the level of DPCs, and may open up a new avenue for understanding the formation and clearance of this detrimental DNA adduct.
Collapse
Affiliation(s)
- Haibo Mu
- College of Science, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Qianjin Liu
- College of Science, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hong Niu
- College of Science, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dongdong Wang
- College of Science, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiangjiang Tang
- College of Science, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Jinyou Duan
- College of Science, Northwest A&F University, Yangling 712100, Shaanxi, China.
| |
Collapse
|
44
|
Groehler A, Villalta PW, Campbell C, Tretyakova N. Covalent DNA-Protein Cross-Linking by Phosphoramide Mustard and Nornitrogen Mustard in Human Cells. Chem Res Toxicol 2016; 29:190-202. [PMID: 26692166 DOI: 10.1021/acs.chemrestox.5b00430] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
N,N-Bis-(2-chloroethyl)-phosphorodiamidic acid (phosphoramide mustard, PM) and N,N-bis-(2-chloroethyl)-amine (nornitrogen mustard, NOR) are the two biologically active metabolites of cyclophosphamide, a DNA alkylating drug commonly used to treat lymphomas, breast cancer, certain brain cancers, and autoimmune diseases. PM and NOR are reactive bis-electrophiles capable of cross-linking cellular biomolecules to form covalent DNA-DNA and DNA-protein cross-links (DPCs). In the present work, a mass spectrometry-based proteomics approach was employed to characterize PM- and NOR-mediated DNA-protein cross-linking in human cells. Following treatment of human fibrosarcoma cells (HT1080) with cytotoxic concentrations of PM, over 130 proteins were found to be covalently trapped to DNA, including those involved in transcriptional regulation, RNA splicing/processing, chromatin organization, and protein transport. HPLC-ESI(+)-MS/MS analysis of proteolytic digests of DPC-containing DNA from NOR-treated cells revealed a concentration-dependent formation of N-[2-[cysteinyl]ethyl]-N-[2-(guan-7-yl)ethyl]amine (Cys-NOR-N7G) conjugates, confirming that it cross-links cysteine thiols of proteins to the N7 position of guanines in DNA. Cys-NOR-N7G adduct numbers were higher in NER-deficient xeroderma pigmentosum cells (XPA) as compared with repair proficient cells. Furthermore, both XPA and FANCD2 deficient cells were sensitized to PM treatment as compared to that of wild type cells, suggesting that Fanconi anemia and nucleotide excision repair pathways are involved in the removal of cyclophosphamide-induced DNA damage.
Collapse
Affiliation(s)
- Arnold Groehler
- Department of Medicinal Chemistry, ‡Department of Pharmacology, and §Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Peter W Villalta
- Department of Medicinal Chemistry, ‡Department of Pharmacology, and §Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Colin Campbell
- Department of Medicinal Chemistry, ‡Department of Pharmacology, and §Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Natalia Tretyakova
- Department of Medicinal Chemistry, ‡Department of Pharmacology, and §Masonic Cancer Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| |
Collapse
|
45
|
Carrette LLG, Gyssels E, De Laet N, Madder A. Furan oxidation based cross-linking: a new approach for the study and targeting of nucleic acid and protein interactions. Chem Commun (Camb) 2016; 52:1539-54. [PMID: 26679922 DOI: 10.1039/c5cc08766j] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The coming of age story of furan oxidation cross-linking.
Collapse
Affiliation(s)
- L. L. G. Carrette
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| | - E. Gyssels
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| | - N. De Laet
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| | - A. Madder
- Organic and Biomimetic Chemistry Research Group
- Department of Organic and Macromolecular Chemistry
- Ghent University
- 9000 Gent
- Belgium
| |
Collapse
|
46
|
Ismail AF, Moawed FS, Mohamed MA. Protective mechanism of grape seed oil on carbon tetrachloride-induced brain damage in γ-irradiated rats. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 153:317-23. [DOI: 10.1016/j.jphotobiol.2015.10.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 09/12/2015] [Accepted: 10/13/2015] [Indexed: 12/31/2022]
|
47
|
Shimizu N, Ooka M, Takagi T, Takeda S, Hirota K. Distinct DNA Damage Spectra Induced by Ionizing Radiation in Normoxic and Hypoxic Cells. Radiat Res 2015; 184:442-8. [DOI: 10.1667/rr14117.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
48
|
Tretyakova NY, Groehler A, Ji S. DNA-Protein Cross-Links: Formation, Structural Identities, and Biological Outcomes. Acc Chem Res 2015; 48:1631-44. [PMID: 26032357 PMCID: PMC4704791 DOI: 10.1021/acs.accounts.5b00056] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Noncovalent DNA-protein interactions are at the heart of normal cell function. In eukaryotic cells, genomic DNA is wrapped around histone octamers to allow for chromosomal packaging in the nucleus. Binding of regulatory protein factors to DNA directs replication, controls transcription, and mediates cellular responses to DNA damage. Because of their fundamental significance in all cellular processes involving DNA, dynamic DNA-protein interactions are required for cell survival, and their disruption is likely to have serious biological consequences. DNA-protein cross-links (DPCs) form when cellular proteins become covalently trapped on DNA strands upon exposure to various endogenous, environmental and chemotherapeutic agents. DPCs progressively accumulate in the brain and heart tissues as a result of endogenous exposure to reactive oxygen species and lipid peroxidation products, as well as normal cellular metabolism. A range of structurally diverse DPCs are found following treatment with chemotherapeutic drugs, transition metal ions, and metabolically activated carcinogens. Because of their considerable size and their helix-distorting nature, DPCs interfere with the progression of replication and transcription machineries and hence hamper the faithful expression of genetic information, potentially contributing to mutagenesis and carcinogenesis. Mass spectrometry-based studies have identified hundreds of proteins that can become cross-linked to nuclear DNA in the presence of reactive oxygen species, carcinogen metabolites, and antitumor drugs. While many of these proteins including histones, transcription factors, and repair proteins are known DNA binding partners, other gene products with no documented affinity for DNA also participate in DPC formation. Furthermore, multiple sites within DNA can be targeted for cross-linking including the N7 of guanine, the C-5 methyl group of thymine, and the exocyclic amino groups of guanine, cytosine, and adenine. This structural complexity complicates structural and biological studies of DPC lesions. Two general strategies have been developed for creating DNA strands containing structurally defined, site-specific DPCs. Enzymatic methodologies that trap DNA modifying proteins on their DNA substrate are site specific and efficient, but do not allow for systematic studies of DPC lesion structure on their biological outcomes. Synthetic methodologies for DPC formation are based on solid phase synthesis of oligonucleotide strands containing protein-reactive unnatural DNA bases. The latter approach allows for a wider range of protein substrates to be conjugated to DNA and affords a greater flexibility for the attachment sites within DNA. In this Account, we outline the chemistry of DPC formation in cells, describe our recent efforts to identify the cross-linked proteins by mass spectrometry, and discuss various methodologies for preparing DNA strands containing structurally defined, site specific DPC lesions. Polymerase bypass experiments conducted with model DPCs indicate that the biological outcomes of these bulky lesions are strongly dependent on the peptide/protein size and the exact cross-linking site within DNA. Future studies are needed to elucidate the mechanisms of DPC repair and their biological outcomes in living cells.
Collapse
Affiliation(s)
- Natalia Y. Tretyakova
- Masonic Cancer Center and the Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455
| | - Arnold Groehler
- Masonic Cancer Center and the Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455
| | - Shaofei Ji
- Masonic Cancer Center and the Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455
| |
Collapse
|
49
|
Nicolas F, Wu C, Bukhari S, de Toledo SM, Li H, Shibata M, Azzam EI. S-Nitrosylation in Organs of Mice Exposed to Low or High Doses of γ-Rays: The Modulating Effect of Iodine Contrast Agent at a Low Radiation Dose. Proteomes 2015; 3:56-73. [PMID: 26317069 PMCID: PMC4548934 DOI: 10.3390/proteomes3020056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The covalent addition of nitric oxide (NO•) onto cysteine thiols, or S-nitrosylation, modulates the activity of key signaling proteins. The dysregulation of normal S-nitrosylation contributes to degenerative conditions and to cancer. To gain insight into the biochemical changes induced by low-dose ionizing radiation, we determined global S-nitrosylation by the “biotin switch” assay coupled with mass spectrometry analyses in organs of C57BL/6J mice exposed to acute 0.1 Gy of 137Cs γ-rays. The dose of radiation was delivered to the whole body in the presence or absence of iopamidol, an iodinated contrast agent used during radiological examinations. To investigate whether similar or distinct nitrosylation patterns are induced following high-dose irradiation, mice were exposed in parallel to acute 4 Gy of 137Cs γ rays. Analysis of modulated S-nitrosothiols (SNO-proteins) in freshly-harvested organs of animals sacrificed 13 days after irradiation revealed radiation dose- and contrast agent-dependent changes. The major results were as follows: (i) iopamidol alone had significant effects on S-nitrosylation in brain, lung and liver; (ii) relative to the control, exposure to 0.1 Gy without iopamidol resulted in statistically-significant SNO changes in proteins that differ in molecular weight in liver, lung, brain and blood plasma; (iii) iopamidol enhanced the decrease in S-nitrosylation induced by 0.1 Gy in brain; (iv) whereas a decrease in S-nitrosylation occurred at 0.1 Gy for proteins of ~50 kDa in brain and for proteins of ~37 kDa in liver, an increase was detected at 4 Gy in both organs; (v) mass spectrometry analyses of nitrosylated proteins in brain revealed differential modulation of SNO proteins (e.g., sodium/potassium-transporting ATPase subunit beta-1; beta tubulins; ADP-ribosylation factor 5) by low- and high-dose irradiation; and (vi) ingenuity pathway analysis identified major signaling networks to be modulated, in particular the neuronal nitric oxide synthase signaling pathway was differentially modulated by low- and high-dose γ-irradiation.
Collapse
Affiliation(s)
- Fadia Nicolas
- Department of Health Informatics, Rutgers School of Health Related Professions, Newark, NJ 07107, USA; E-Mail:
| | - Changgong Wu
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; E-Mail:
| | - Salwa Bukhari
- Department of Radiology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; E-Mail:
| | - Sonia M. de Toledo
- Department of Radiology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; E-Mail:
| | - Hong Li
- Department of Biochemistry and Molecular Biology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; E-Mail:
| | - Masayuki Shibata
- Department of Health Informatics, Rutgers School of Health Related Professions, Newark, NJ 07107, USA
- Authors to whom correspondence should be addressed; E-Mails: (M.S.); (E.I.A.); Tel.: +1-973-972-5323 (E.I.A.); Fax: +1-973-972-1865 (E.I.A.)
| | - Edouard I. Azzam
- Department of Radiology, RUTGERS New Jersey Medical School, Newark, NJ 07103, USA
- Authors to whom correspondence should be addressed; E-Mails: (M.S.); (E.I.A.); Tel.: +1-973-972-5323 (E.I.A.); Fax: +1-973-972-1865 (E.I.A.)
| |
Collapse
|
50
|
Jian Y, Lin G, Chomicz L, Li L. Reactivity of Damaged Pyrimidines: Formation of a Schiff Base Intermediate at the Glycosidic Bond of Saturated Dihydrouridine. J Am Chem Soc 2015; 137:3318-29. [DOI: 10.1021/ja512435j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yajun Jian
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
| | - Gengjie Lin
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
| | - Lidia Chomicz
- Department
of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
| | - Lei Li
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
- Department
of Biochemistry and Molecular Biology and Department of Dermatology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United States
| |
Collapse
|