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Rouleau-Turcotte É, Pascal JM. ADP-ribose contributions to genome stability and PARP enzyme trapping on sites of DNA damage; paradigm shifts for a coming-of-age modification. J Biol Chem 2023; 299:105397. [PMID: 37898399 PMCID: PMC10722394 DOI: 10.1016/j.jbc.2023.105397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023] Open
Abstract
ADP-ribose is a versatile modification that plays a critical role in diverse cellular processes. The addition of this modification is catalyzed by ADP-ribosyltransferases, among which notable poly(ADP-ribose) polymerase (PARP) enzymes are intimately involved in the maintenance of genome integrity. The role of ADP-ribose modifications during DNA damage repair is of significant interest for the proper development of PARP inhibitors targeted toward the treatment of diseases caused by genomic instability. More specifically, inhibitors promoting PARP persistence on DNA lesions, termed PARP "trapping," is considered a desirable characteristic. In this review, we discuss key classes of proteins involved in ADP-ribose signaling (writers, readers, and erasers) with a focus on those involved in the maintenance of genome integrity. An overview of factors that modulate PARP1 and PARP2 persistence at sites of DNA lesions is also discussed. Finally, we clarify aspects of the PARP trapping model in light of recent studies that characterize the kinetics of PARP1 and PARP2 recruitment at sites of lesions. These findings suggest that PARP trapping could be considered as the continuous recruitment of PARP molecules to sites of lesions, rather than the physical stalling of molecules. Recent studies and novel research tools have elevated the level of understanding of ADP-ribosylation, marking a coming-of-age for this interesting modification.
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Affiliation(s)
- Élise Rouleau-Turcotte
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - John M Pascal
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada.
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2
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Jokipii Krueger CC, Moran E, Tessier KM, Tretyakova NY. Isotope Labeling Mass Spectrometry to Quantify Endogenous and Exogenous DNA Adducts and Metabolites of 1,3-Butadiene In Vivo. Chem Res Toxicol 2023; 36:1409-1418. [PMID: 37477250 PMCID: PMC11009968 DOI: 10.1021/acs.chemrestox.3c00141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Human exposure to known carcinogen 1,3-butadiene (BD) is common due to its high concentrations in automobile exhaust, cigarette smoke, and forest fires, as well as its widespread use in the polymer industry. The adverse health effects of BD are mediated by epoxide metabolites such as 3,4-epoxy-1-butene (EB), which reacts with DNA to form 1-hydroxyl-3-buten-1-yl adducts on DNA nucleobases. EB-derived mercapturic acids (1- and 2-(N-acetyl-l-cysteine-S-yl)-1-hydroxybut-3-ene (MHBMA) and N-acetyl-S-(3,4-dihydroxybutyl)-l-cysteine (DHBMA)) and urinary N7-(1-hydroxyl-3-buten-1-yl) guanine DNA adducts (EB-GII) have been used as biomarkers of BD exposure and cancer risk in smokers and occupationally exposed workers. However, low but significant levels of MHBMA, DHBMA, and EB-GII have been reported in unexposed cultured cells, animals, and humans, suggesting that these metabolites and adducts may form endogenously and complicate risk assessment of butadiene exposure. In the present work, stable isotope labeling in combination with high-resolution mass spectrometry was employed to accurately quantify endogenous and exogenous butadiene metabolites and DNA adducts in vivo. Laboratory rats were exposed to 0.3, 0.5, or 3 ppm of BD-d6 by inhalation, and the amounts of endogenous (d0) and exogenous (d6) DNA adducts and metabolites were quantified in tissues and urine by isotope dilution capillary liquid chromatography/high resolution electrospray ionization tandem mass spectrometry (capLC-ESI-HRMS/MS). Our results reveal that EB-GII adducts and MHBMA originate exclusively from exogenous exposure to BD, while substantial amounts of DHBMA are formed endogenously. Urinary EB-GII concentrations were associated with genomic EB-GII levels in tissues of the same animals. Our findings confirm that EB-GII and MHBMA are specific biomarkers of exposure to BD, while endogenous DHBMA predominates at sub-ppm exposures to BD.
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Affiliation(s)
- Caitlin C. Jokipii Krueger
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Erik Moran
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Katelyn M. Tessier
- Masonic Cancer Center, Biostatistics Core, University of Minnesota, Minneapolis, Minnesota, 55455, USA
| | - Natalia Y. Tretyakova
- Masonic Cancer Center and Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, 55455, USA
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3
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Campbell JL, Clewell HJ, Van Landingham C, Gentry PR, Andersen ME. Using available in vitro metabolite identification and time course kinetics for β-chloroprene and its metabolite, (1-chloroethenyl) oxirane, to include reactive oxidative metabolites and glutathione depletion in a PBPK model for β-chloroprene. Front Pharmacol 2023; 14:1223808. [PMID: 37663267 PMCID: PMC10472072 DOI: 10.3389/fphar.2023.1223808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction: ß-chloroprene (2-chloro-1,3-butadiene; CP) causes lung tumors after inhalation exposures in rats and mice. Mice develop these tumors at lower exposures than rats. In rats CP exposures cause depletion of lung glutathione (GSH). Methods: PBPK models developed to relate the appearance of mouse lung tumors with rates of CP metabolism to reactive metabolites or total amounts metabolized during exposures have been expanded to include production of reactive metabolites from CP. The extended PBPK model describes both the unstable oxirane metabolite, 2-CEO, and metabolism of the more stable oxirane, 1-CEO, to reactive metabolites via microsomal oxidation to a diepoxide, and linked production of these metabolites to a PK model predicting GSH depletion with increasing CP exposure. Key information required to develop the model were available from literature studies identifying: 1) microsomal metabolites of CP, and 2) in vitro rates of clearance of CP and 1-CEO from active microsomal preparations from mice, rats, hamsters and humans. Results: Model simulation of concentration dependence of disproportionate increases in reactive metabolite concentrations as exposures increases and decreases in tissue GSH are consistent with the dose-dependence of tumor formation. At the middle bioassay concentrations with a lung tumor incidence, the predicted tissue GSH is less than 50% background. These simulations of reduction in GSH are also consistent with the gene expression results showing the most sensitive pathways are Nrf2-regulation of oxidative stress and GSH metabolism. Discussion: The PBPK model is used to correlate predicted tissue exposure to reactive metabolites with toxicity and carcinogenicity of CP.
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Affiliation(s)
| | | | | | - P. R. Gentry
- Ramboll US Corporation, Monroe, LA, United States
| | - M. E. Andersen
- Andersen ToxConsulting, LLC, Chapel Hill, NC, United States
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4
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Liu C, Le BH, Xu W, Yang CH, Chen YH, Zhao L. Dual chemical labeling enables nucleotide-resolution mapping of DNA abasic sites and common alkylation damage in human mitochondrial DNA. Nucleic Acids Res 2023; 51:e73. [PMID: 37293974 PMCID: PMC10359467 DOI: 10.1093/nar/gkad502] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/01/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA) modifications play an emerging role in innate immunity and inflammatory diseases. Nonetheless, relatively little is known regarding the locations of mtDNA modifications. Such information is critically important for deciphering their roles in mtDNA instability, mtDNA-mediated immune and inflammatory responses, and mitochondrial disorders. The affinity probe-based enrichment of lesion-containing DNA represents a key strategy for sequencing DNA modifications. Existing methods are limited in the enrichment specificity of abasic (AP) sites, a prevalent DNA modification and repair intermediate. Herein, we devise a novel approach, termed dual chemical labeling-assisted sequencing (DCL-seq), for mapping AP sites. DCL-seq features two designer compounds for enriching and mapping AP sites specifically at single-nucleotide resolution. For proof of principle, we mapped AP sites in mtDNA from HeLa cells under different biological conditions. The resulting AP site maps coincide with mtDNA regions with low TFAM (mitochondrial transcription factor A) coverage and with potential G-quadruplex-forming sequences. In addition, we demonstrated the broader applicability of the method in sequencing other DNA modifications in mtDNA, such as N7-methyl-2'-deoxyguanosine and N3-methyl-2'-deoxyadenosine, when coupled with a lesion-specific repair enzyme. Together, DCL-seq holds the promise to sequence multiple DNA modifications in various biological samples.
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Affiliation(s)
- Chaoxing Liu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Brandon H Le
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA
| | - Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Ching-Hsin Yang
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
| | - Yu Hsuan Chen
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
- Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, USA
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5
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Bokthier Rahman M, Hussain M, Probha Kabiraz M, Nordin N, Anusha Siddiqui S, Bhowmik S, Begum M. An update on formaldehyde adulteration in food: sources, detection, mechanisms, and risk assessment. Food Chem 2023; 427:136761. [PMID: 37406446 DOI: 10.1016/j.foodchem.2023.136761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/10/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
Formaldehyde is added illegally to food to extend its shelf life due to its antiseptic and preservation properties. Several research has been conducted to examine the consequences of adulteration with formaldehyde in food items. These findings suggest that adding formaldehyde to food is considered harmful as it accumulates in the body with long-term consumption. In this review includes study findings on food adulteration with formaldehyde and their assessment of food safety based on the analytical method applied to various geographical regions, food matrix types, and their sources in food items. Additionally, this review sought to assess the risk of formaldehyde-tainted food and the understanding of its development in food and its impacts on food safety in light of the widespread formaldehyde adulteration. Finally, the study would be useful as a manual for implementing adequate and successful risk assessment to increase food safety.
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Affiliation(s)
- Md Bokthier Rahman
- Department of Fisheries Technology, Patuakhali Science and Technology University, Dumki, Patuakhali-8602, Bangladesh
| | - Monayem Hussain
- Department of Fish Biology and Genetics, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Meera Probha Kabiraz
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Noordiana Nordin
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Shahida Anusha Siddiqui
- Technical University of Munich Campus Straubing for Biotechnology and Sustainability, Essigberg 3, 94315 Straubing, Germany; German Institute of Food Technologies (DIL e.V.), Prof.-von-Klitzing-Str. 7, 49610, Quakenbrück, Germany.
| | - Shuva Bhowmik
- Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin 9054, New Zealand; Department of Food Science, University of Otago, Dunedin 9054, New Zealand; Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali-3814, Bangladesh.
| | - Mohajira Begum
- BCSIR Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Rajshahi-6204, Bangladesh
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Rudge MVC, Alves FCB, Hallur RLS, Oliveira RG, Vega S, Reyes DRA, Floriano JF, Prudencio CB, Garcia GA, Reis FVDS, Emanueli C, Fuentes G, Cornejo M, Toledo F, Valenzuela-Hinrichsen A, Guerra C, Grismaldo A, Valero P, Barbosa AMP, Sobrevia L. Consequences of the exposome to gestational diabetes mellitus. Biochim Biophys Acta Gen Subj 2023; 1867:130282. [PMID: 36436753 DOI: 10.1016/j.bbagen.2022.130282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/14/2022] [Accepted: 11/16/2022] [Indexed: 11/26/2022]
Abstract
The exposome is the cumulative measure of environmental influences and associated biological responses throughout the lifespan, including those from the environment, diet, behaviour, and endogenous processes. The exposome concept and the 2030 Agenda for the Sustainable Development Goals (SDGs) from the United Nations are the basis for understanding the aetiology and consequences of non-communicable diseases, including gestational diabetes mellitus (GDM). Pregnancy may be developed in an environment with adverse factors part of the immediate internal medium for fetus development and the external medium to which the pregnant woman is exposed. The placenta is the interface between maternal and fetal compartments and acts as a protective barrier or easing agent to transfer exposome from mother to fetus. Under and over-nutrition in utero, exposure to adverse environmental pollutants such as heavy metals, endocrine-disrupting chemicals, pesticides, drugs, pharmaceuticals, lifestyle, air pollutants, and tobacco smoke plays a determinant role in the development of GDM. This phenomenon is worsened by metabolic stress postnatally, such as obesity which increases the risk of GDM and other diseases. Clinical risk factors for GDM development include its aetiology. It is proposed that knowledge-based interventions to change the potential interdependent ecto-exposome and endo-exposome could avoid the occurrence and consequences of GDM.
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Affiliation(s)
- Marilza V C Rudge
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil.
| | - Fernanda C B Alves
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil
| | - Raghavendra L S Hallur
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil; Centre for Biotechnology, Pravara Institute of Medical Sciences (DU), Loni-413736, Rahata Taluk, Ahmednagar District, Maharashtra, India
| | - Rafael G Oliveira
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil
| | - Sofia Vega
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil; Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrician, Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - David R A Reyes
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil
| | - Juliana F Floriano
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil
| | - Caroline B Prudencio
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil
| | - Gabriela A Garcia
- São Paulo State University (UNESP), School of Sciences, Postgraduate Program in Materials Science and Technology (POSMAT), 17033-360 Bauru, São Paulo, Brazil
| | - Fabiana V D S Reis
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
| | - Gonzalo Fuentes
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands; Faculty of Health Sciences, Universidad de Talca, Talca 3460000, Chile; Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrician, Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - Marcelo Cornejo
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands; Faculty of Health Sciences, Universidad de Talca, Talca 3460000, Chile; Faculty of Health Sciences, Universidad de Antofagasta, Antofagasta 02800, Chile; Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrician, Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - Fernando Toledo
- Faculty of Basic Sciences, Universidad del Bío-Bío, Chillán 3780000, Chile; Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrician, Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - Andrés Valenzuela-Hinrichsen
- Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrician, Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - Catalina Guerra
- Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrician, Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - Adriana Grismaldo
- Tecnologico de Monterrey, Eutra, The Institute for Obesity Research (IOR), School of Medicine and Health Sciences, Monterrey, Nuevo León 64710, Mexico; Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrician, Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - Paola Valero
- Faculty of Health Sciences, Universidad de Talca, Talca 3460000, Chile; Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrician, Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile
| | - Angelica M P Barbosa
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil; Department of Physiotherapy and Occupational Therapy, School of Philosophy and Sciences, São Paulo State University (UNESP), 17525-900 Marília, São Paulo, Brazil
| | - Luis Sobrevia
- Department of Gynaecology and Obstetrics, Botucatu Medical School, São Paulo State University (UNESP), 18618-687 Botucatu, São Paulo, Brazil; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713GZ Groningen, The Netherlands; Tecnologico de Monterrey, Eutra, The Institute for Obesity Research (IOR), School of Medicine and Health Sciences, Monterrey, Nuevo León 64710, Mexico; Department of Physiology, Faculty of Pharmacy, Universidad de Sevilla, Seville E-41012, Spain; University of Queensland Centre for Clinical Research (UQCCR), Faculty of Medicine and Biomedical Sciences, University of Queensland, Herston QLD 4029, Queensland, Australia; Cellular and Molecular Physiology Laboratory (CMPL), Department of Obstetrician, Division of Obstetrics and Gynaecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago 8330024, Chile.
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Conolly RP, Clewell HJ, Moore MM, Campbell JL, Cheng W, Gentry RR. PBPK modeling to evaluate maximum tolerated doses: A case study with 3-chloroallyl alcohol. Front Pharmacol 2023; 14:1088011. [PMID: 36909196 PMCID: PMC9992188 DOI: 10.3389/fphar.2023.1088011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction: A physiologically based pharmacokinetic (PBPK) model for 3-chloroallyl alcohol (3-CAA) was developed and used to evaluate the design of assays for the in vivo genotoxicity of 3-CAA. Methods: Model development was supported by read across from a published PBPK model for ethanol. Read across was motivated by the expectation that 3-CAA, which like ethanol is a primary alcohol, is metabolized largely by hepatic alcohol dehydrogenases. The PBPK model was used to evaluate how two metrics of tissue dosimetry, maximum blood concentration (Cmax; mg/L) and area under the curve (AUC; mg-hr/L) vary with dose of 3-CAA and with dose route (oral gavage, drinking water). Results: The model predicted that oral gavage results in a 6-fold higher Cmax than the same dose administered in drinking water, but in similar AUCs. Predicted Cmax provided the best correlation with severe toxicity (e.g., lethality) from 3-CAA, consistent with the production of a reactive metabolite. Therefore, drinking water administration can achieve higher sustained concentration without severe toxicity in vivo. Discussion: This evaluation is significant because cytotoxicity is a potential confounder of mutagenicity testing. The PBPK model can be used to ensure that studies meet OECD and USEPA test guidelines and that the highest dose used is not associated with severe toxicity. In addition, PBPK modeling provides assurance of target tissue (e.g., bone marrow) exposure even in the absence of laboratory data, by defining the relationship between applied dose and target tissue dose based on accepted principles of pharmacokinetics, relevant physiology and biochemistry of the dosed animals, and chemical-specific information.
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8
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Xu W, Tang J, Zhao L. DNA-protein cross-links between abasic DNA damage and mitochondrial transcription factor A (TFAM). Nucleic Acids Res 2022; 51:41-53. [PMID: 36583367 PMCID: PMC9841407 DOI: 10.1093/nar/gkac1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/25/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
In higher eukaryotic cells, mitochondria are essential organelles for energy production, metabolism, and signaling. Mitochondrial DNA (mtDNA) encodes 13 protein subunits for oxidative phosphorylation and a set of tRNAs and rRNAs. mtDNA damage, sourced from endogenous chemicals and environmental factors, contributes to mitochondrial genomic instability, which has been associated with various mitochondrial diseases. DNA-protein cross-links (DPCs) are deleterious DNA lesions that threaten genomic integrity. Although much has been learned about the formation and repair of DPCs in the nucleus, little is known about DPCs in mitochondria. Here, we present in vitro and in cellulo data to demonstrate the formation of DPCs between a prevalent abasic (AP) DNA lesion and a DNA-packaging protein, mitochondrial transcription factor A (TFAM). TFAM cleaves AP-DNA and forms DPCs and single-strand breaks (SSB). Lys residues of TFAM are critical for the formation of TFAM-DPC and a reactive 3'-phospho-α,β-unsaturated aldehyde (3'pUA) residue on SSB. The 3'pUA residue reacts with two Cys of TFAM and contributes to the stable TFAM-DPC formation. Glutathione reacts with 3'pUA and competes with TFAM-DPC formation, corroborating our cellular experiments showing the accumulation of TFAM-DPCs under limiting glutathione. Our data point to the involvement of TFAM in AP-DNA turnover and fill a knowledge gap regarding the protein factors in processing damaged mtDNA.
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Affiliation(s)
- Wenyan Xu
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Jin Tang
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Linlin Zhao
- To whom correspondence should be addressed. Tel: +1 951 827 9081;
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9
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Jinadasa B, Elliott C, Jayasinghe G. A review of the presence of formaldehyde in fish and seafood. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108882] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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10
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Avery CL, Howard AG, Ballou AF, Buchanan VL, Collins JM, Downie CG, Engel SM, Graff M, Highland HM, Lee MP, Lilly AG, Lu K, Rager JE, Staley BS, North KE, Gordon-Larsen P. Strengthening Causal Inference in Exposomics Research: Application of Genetic Data and Methods. ENVIRONMENTAL HEALTH PERSPECTIVES 2022; 130:55001. [PMID: 35533073 PMCID: PMC9084332 DOI: 10.1289/ehp9098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Advances in technologies to measure a broad set of exposures have led to a range of exposome research efforts. Yet, these efforts have insufficiently integrated methods that incorporate genetic data to strengthen causal inference, despite evidence that many exposome-associated phenotypes are heritable. Objective: We demonstrate how integration of methods and study designs that incorporate genetic data can strengthen causal inference in exposomics research by helping address six challenges: reverse causation and unmeasured confounding, comprehensive examination of phenotypic effects, low efficiency, replication, multilevel data integration, and characterization of tissue-specific effects. Examples are drawn from studies of biomarkers and health behaviors, exposure domains where the causal inference methods we describe are most often applied. Discussion: Technological, computational, and statistical advances in genotyping, imputation, and analysis, combined with broad data sharing and cross-study collaborations, offer multiple opportunities to strengthen causal inference in exposomics research. Full application of these opportunities will require an expanded understanding of genetic variants that predict exposome phenotypes as well as an appreciation that the utility of genetic variants for causal inference will vary by exposure and may depend on large sample sizes. However, several of these challenges can be addressed through international scientific collaborations that prioritize data sharing. Ultimately, we anticipate that efforts to better integrate methods that incorporate genetic data will extend the reach of exposomics research by helping address the challenges of comprehensively measuring the exposome and its health effects across studies, the life course, and in varied contexts and diverse populations. https://doi.org/10.1289/EHP9098.
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Affiliation(s)
- Christy L Avery
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Annie Green Howard
- Department of Biostatistics, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anna F Ballou
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Victoria L Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jason M Collins
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Carolina G Downie
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephanie M Engel
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Moa P Lee
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Adam G Lilly
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Sociology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Julia E Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Brooke S Staley
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Penny Gordon-Larsen
- Department of Nutrition, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Carolina Population Center, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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11
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The role of endogenous versus exogenous sources in the exposome of putative genotoxins and consequences for risk assessment. Arch Toxicol 2022; 96:1297-1352. [PMID: 35249149 PMCID: PMC9013691 DOI: 10.1007/s00204-022-03242-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/01/2022] [Indexed: 12/21/2022]
Abstract
AbstractThe “totality” of the human exposure is conceived to encompass life-associated endogenous and exogenous aggregate exposures. Process-related contaminants (PRCs) are not only formed in foods by heat processing, but also occur endogenously in the organism as physiological components of energy metabolism, potentially also generated by the human microbiome. To arrive at a comprehensive risk assessment, it is necessary to understand the contribution of in vivo background occurrence as compared to the ingestion from exogenous sources. Hence, this review provides an overview of the knowledge on the contribution of endogenous exposure to the overall exposure to putative genotoxic food contaminants, namely ethanol, acetaldehyde, formaldehyde, acrylamide, acrolein, α,β-unsaturated alkenals, glycation compounds, N-nitroso compounds, ethylene oxide, furans, 2- and 3-MCPD, and glycidyl esters. The evidence discussed herein allows to conclude that endogenous formation of some contaminants appears to contribute substantially to the exposome. This is of critical importance for risk assessment in the cases where endogenous exposure is suspected to outweigh the exogenous one (e.g. formaldehyde and acrolein).
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12
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Price EJ, Vitale CM, Miller GW, David A, Barouki R, Audouze K, Walker DI, Antignac JP, Coumoul X, Bessonneau V, Klánová J. Merging the exposome into an integrated framework for “omics” sciences. iScience 2022; 25:103976. [PMID: 35310334 PMCID: PMC8924626 DOI: 10.1016/j.isci.2022.103976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The exposome concept encourages holistic consideration of the non-genetic factors (environmental exposures including lifestyle) that influence an individual’s health over their life course. However, disconnect between the concept and practical application has promoted divergent interpretations of the exposome across disciplines and reinforced separation of the environmental (emphasizing exposures) and biological (emphasizing responses) research communities. In particular, while knowledge of biological responses can help to distinguish actual (i.e. experienced) from potential exposures, the inclusion of endogenous processes has generated confusion about the position of the exposome in a multi-omics systems biology context. We propose a reattribution of “exposome” to exclusively represent the totality of contact with external factors that a biological entity experiences, and introduce the term “functional exposomics” to denote the systematic study of exposure-phenotype interaction. This reoriented definition of the exposome allows a more readily integrable dataset for multi-omics and systems biology research. Reattribution of exposome concept to exclusively represent environmental exposures Generalized the exposome concept for all levels of biological organization Functional exposome presented as the totality of exposure-phenotype interaction
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13
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Felter SP, Bhat VS, Botham PA, Bussard DA, Casey W, Hayes AW, Hilton GM, Magurany KA, Sauer UG, Ohanian EV. Assessing chemical carcinogenicity: hazard identification, classification, and risk assessment. Insight from a Toxicology Forum state-of-the-science workshop. Crit Rev Toxicol 2022; 51:653-694. [DOI: 10.1080/10408444.2021.2003295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | | | - David A. Bussard
- U.S. Environmental Protection Agency, Office of the Science Advisor, Policy and Engagement, Washington, DC, USA
| | - Warren Casey
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - A. Wallace Hayes
- University of South Florida College of Public Health, Tampa, FL, USA
| | - Gina M. Hilton
- PETA Science Consortium International e.V., Stuttgart, Germany
| | | | | | - Edward V. Ohanian
- United States Environmental Protection Agency, Office of Water, Washington, DC, USA
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14
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Genome-wide mapping of genomic DNA damage: methods and implications. Cell Mol Life Sci 2021; 78:6745-6762. [PMID: 34463773 PMCID: PMC8558167 DOI: 10.1007/s00018-021-03923-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/02/2021] [Accepted: 08/11/2021] [Indexed: 12/19/2022]
Abstract
Exposures from the external and internal environments lead to the modification of genomic DNA, which is implicated in the cause of numerous diseases, including cancer, cardiovascular, pulmonary and neurodegenerative diseases, together with ageing. However, the precise mechanism(s) linking the presence of damage, to impact upon cellular function and pathogenesis, is far from clear. Genomic location of specific forms of damage is likely to be highly informative in understanding this process, as the impact of downstream events (e.g. mutation, microsatellite instability, altered methylation and gene expression) on cellular function will be positional—events at key locations will have the greatest impact. However, until recently, methods for assessing DNA damage determined the totality of damage in the genomic location, with no positional information. The technique of “mapping DNA adductomics” describes the molecular approaches that map a variety of forms of DNA damage, to specific locations across the nuclear and mitochondrial genomes. We propose that integrated comparison of this information with other genome-wide data, such as mutational hotspots for specific genotoxins, tumour-specific mutation patterns and chromatin organisation and transcriptional activity in non-cancerous lesions (such as nevi), pre-cancerous conditions (such as polyps) and tumours, will improve our understanding of how environmental toxins lead to cancer. Adopting an analogous approach for non-cancer diseases, including the development of genome-wide assays for other cellular outcomes of DNA damage, will improve our understanding of the role of DNA damage in pathogenesis more generally.
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15
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Chew K, Zhao L. Interactions of Mitochondrial Transcription Factor A with DNA Damage: Mechanistic Insights and Functional Implications. Genes (Basel) 2021; 12:genes12081246. [PMID: 34440420 PMCID: PMC8393399 DOI: 10.3390/genes12081246] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/17/2022] Open
Abstract
Mitochondria have a plethora of functions in eukaryotic cells, including cell signaling, programmed cell death, protein cofactor synthesis, and various aspects of metabolism. The organelles carry their own genomic DNA, which encodes transfer and ribosomal RNAs and crucial protein subunits in the oxidative phosphorylation system. Mitochondria are vital for cellular and organismal functions, and alterations of mitochondrial DNA (mtDNA) have been linked to mitochondrial disorders and common human diseases. As such, how the cell maintains the integrity of the mitochondrial genome is an important area of study. Interactions of mitochondrial proteins with mtDNA damage are critically important for repairing, regulating, and signaling mtDNA damage. Mitochondrial transcription factor A (TFAM) is a key player in mtDNA transcription, packaging, and maintenance. Due to the extensive contact of TFAM with mtDNA, it is likely to encounter many types of mtDNA damage and secondary structures. This review summarizes recent research on the interaction of human TFAM with different forms of non-canonical DNA structures and discusses the implications on mtDNA repair and packaging.
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16
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Evolutionary Origins of DNA Repair Pathways: Role of Oxygen Catastrophe in the Emergence of DNA Glycosylases. Cells 2021; 10:cells10071591. [PMID: 34202661 PMCID: PMC8307549 DOI: 10.3390/cells10071591] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/17/2021] [Accepted: 06/18/2021] [Indexed: 11/23/2022] Open
Abstract
It was proposed that the last universal common ancestor (LUCA) evolved under high temperatures in an oxygen-free environment, similar to those found in deep-sea vents and on volcanic slopes. Therefore, spontaneous DNA decay, such as base loss and cytosine deamination, was the major factor affecting LUCA’s genome integrity. Cosmic radiation due to Earth’s weak magnetic field and alkylating metabolic radicals added to these threats. Here, we propose that ancient forms of life had only two distinct repair mechanisms: versatile apurinic/apyrimidinic (AP) endonucleases to cope with both AP sites and deaminated residues, and enzymes catalyzing the direct reversal of UV and alkylation damage. The absence of uracil–DNA N-glycosylases in some Archaea, together with the presence of an AP endonuclease, which can cleave uracil-containing DNA, suggests that the AP endonuclease-initiated nucleotide incision repair (NIR) pathway evolved independently from DNA glycosylase-mediated base excision repair. NIR may be a relic that appeared in an early thermophilic ancestor to counteract spontaneous DNA damage. We hypothesize that a rise in the oxygen level in the Earth’s atmosphere ~2 Ga triggered the narrow specialization of AP endonucleases and DNA glycosylases to cope efficiently with a widened array of oxidative base damage and complex DNA lesions.
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17
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Geisen SM, Aloisi CMN, Huber SM, Sandell ES, Escher NA, Sturla SJ. Direct Alkylation of Deoxyguanosine by Azaserine Leads to O6-Carboxymethyldeoxyguanosine. Chem Res Toxicol 2021; 34:1518-1529. [PMID: 34061515 DOI: 10.1021/acs.chemrestox.0c00471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The O6-alkylguanosine adduct O6-carboxymethyldeoxyguanosine (O6-CMdG) has been detected at elevated levels in blood and tissue samples from colorectal cancer patients and from healthy volunteers after consuming red meat. The diazo compound l-azaserine leads to the formation of O6-CMdG as well as the corresponding methyl adduct O6-methyldeoxyguanosine (O6-MedG) in cells and is therefore in wide use as a chemical probe in cellular studies concerning DNA damage and mutation. However, there remain knowledge gaps concerning the chemical basis of DNA adduct formation by l-azaserine. To characterize O6-CMdG formation by l-azaserine, we carried out a combination of chemical and enzymatic stability and reactivity studies supported by liquid chromatography tandem mass spectrometry for the simultaneous quantification of O6-CMdG and O6-MedG. We found that l-azaserine is stable under physiological and alkaline conditions as well as in active biological matrices but undergoes acid-catalyzed hydrolysis. We show, for the first time, that l-azaserine reacts directly with guanosine (dG) and oligonucleotides to form an O6-serine-CMdG (O6-Ser-CMdG) adduct. Moreover, by characterizing the reaction of dG with l-azaserine, we demonstrate that O6-Ser-CMdG forms as an intermediate that spontaneously decomposes to form O6-CMdG. Finally, we quantified levels of O6-CMdG and O6-MedG in a human cell line exposed to l-azaserine and found maximal adduct levels after 48 h. The findings of this work elucidate the chemical basis of how l-azaserine reacts with deoxyguanosine and support its use as a chemical probe for N-nitroso compound exposure in carcinogenesis research, particularly concerning the identification of pathways and factors that promote adduct formation.
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Affiliation(s)
- Susanne M Geisen
- Department of Health Science and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Claudia M N Aloisi
- Department of Health Science and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Sabrina M Huber
- Department of Health Science and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Emma S Sandell
- Department of Health Science and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Nora A Escher
- Department of Health Science and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Shana J Sturla
- Department of Health Science and Technology, ETH Zurich, 8092 Zurich, Switzerland
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18
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Cordelli E, Bignami M, Pacchierotti F. Comet assay: a versatile but complex tool in genotoxicity testing. Toxicol Res (Camb) 2021; 10:68-78. [PMID: 33613974 DOI: 10.1093/toxres/tfaa093] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/26/2020] [Accepted: 11/12/2020] [Indexed: 12/11/2022] Open
Abstract
The comet assay is a versatile method for measuring DNA strand breaks in individual cells. It can also be applied to cells isolated from treated animals. In this review, we highlight advantages and limitations of this in vivo comet assay in a regulatory context. Modified versions of the standard protocol detect oxidized DNA bases and may be used to reveal sites of DNA base loss, DNA interstrand crosslinks, and the extent of DNA damage induced indirectly by reactive oxygen species elicited by chemical-induced oxidative stress. The assay is, however, at best semi-quantitative, and we discuss possible approaches to improving DNA damage quantitation and highlight the necessity of optimizing protocol standardization to enhance the comparability of results between laboratories. As a genotoxicity test in vivo, the in vivo comet assay has the advantage over the better established micronucleus erythrocyte test that it can be applied to any organ, including those that are specific targets of chemical carcinogens or those that are the first sites of contact of ingested or inhaled mutagens. We illustrate this by examples of its use in risk assessment for the food contaminants ochratoxin and furan. We suggest that improved quantitation is required to reveal the full potential of the comet assay and enhance its role in the battery of in vivo approaches to characterize the mechanisms of toxicity and carcinogenicity of chemicals and to aid the determination of safe human exposure limits.
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Affiliation(s)
- Eugenia Cordelli
- Territorial and Production Systems Sustainability Department, Health Protection Technology Division, ENEA, CR Casaccia, Via Anguillarese 301, Rome 00123, Italy
| | - Margherita Bignami
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, Rome 00161, Italy
| | - Francesca Pacchierotti
- Territorial and Production Systems Sustainability Department, Health Protection Technology Division, ENEA, CR Casaccia, Via Anguillarese 301, Rome 00123, Italy
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19
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Baillie TA. Approaches to mitigate the risk of serious adverse reactions in covalent drug design. Expert Opin Drug Discov 2020; 16:275-287. [PMID: 33006907 DOI: 10.1080/17460441.2021.1832079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Covalent inhibition of target proteins using high affinity ligands bearing weakly electrophilic warheads is being adopted increasingly as design strategy in the discovery of novel therapeutics, and several covalent drugs have now received regulatory approval for indications in oncology. Experience to date with targeted covalent inhibitors has led to a number of design principles that underlie the safety and efficacy of this increasingly important class of molecules. AREAS COVERED A review is provided of the current status of the covalent drug approach, emphasizing the unique benefits and attendant risks associated with reversible and irreversible binders. Areas of application beyond inhibition of tyrosine kinases are presented, and design considerations to de-risk covalent inhibitors with respect to undesirable off-target effects are discussed. EXPERT OPINION High selectivity for the intended protein target has emerged as a key consideration in mitigating safety risks associated with widespread proteome reactivity. Powerful chemical proteomics-based techniques are now available to assess selectivity in a drug discovery setting. Optimizing pharmacokinetics to capitalize on the intrinsically high potency of covalent drugs should lead to low daily doses and greater safety margins, while minimizing susceptibility to metabolic activation likewise will attenuate the risk of covalent drug toxicity.
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Affiliation(s)
- Thomas A Baillie
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington Seattle, Seattle, WA, USA
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20
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Kühbacher U, Duxin JP. How to fix DNA-protein crosslinks. DNA Repair (Amst) 2020; 94:102924. [PMID: 32683310 PMCID: PMC7511601 DOI: 10.1016/j.dnarep.2020.102924] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/18/2022]
Abstract
Proteins that act on DNA, or are in close proximity to it, can become inadvertently crosslinked to DNA and form highly toxic lesions, known as DNA-protein crosslinks (DPCs). DPCs are generated by different chemotherapeutics, environmental or endogenous sources of crosslinking agents, or by lesions on DNA that stall the catalytic cycle of certain DNA processing enzymes. These bulky adducts impair processes on DNA such as DNA replication or transcription, and therefore pose a serious threat to genome integrity. The large diversity of DPCs suggests that there is more than one canonical mechanism to repair them. Indeed, many different enzymes have been shown to act on DPCs by either processing the protein, the DNA or the crosslink itself. In addition, the cell cycle stage or cell type are likely to dictate pathway choice. In recent years, a detailed understanding of DPC repair during S phase has started to emerge. Here, we review the current knowledge on the mechanisms of replication-coupled DPC repair, and describe and also speculate on possible pathways that remove DPCs outside of S phase. Moreover, we highlight a recent paradigm shifting finding that indicates that DPCs are not always detrimental, but can also play a protective role, preserving the genome from more deleterious forms of DNA damage.
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Affiliation(s)
- Ulrike Kühbacher
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Julien P Duxin
- The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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21
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Interplay between Cellular Metabolism and the DNA Damage Response in Cancer. Cancers (Basel) 2020; 12:cancers12082051. [PMID: 32722390 PMCID: PMC7463900 DOI: 10.3390/cancers12082051] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/20/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022] Open
Abstract
Metabolism is a fundamental cellular process that can become harmful for cells by leading to DNA damage, for instance by an increase in oxidative stress or through the generation of toxic byproducts. To deal with such insults, cells have evolved sophisticated DNA damage response (DDR) pathways that allow for the maintenance of genome integrity. Recent years have seen remarkable progress in our understanding of the diverse DDR mechanisms, and, through such work, it has emerged that cellular metabolic regulation not only generates DNA damage but also impacts on DNA repair. Cancer cells show an alteration of the DDR coupled with modifications in cellular metabolism, further emphasizing links between these two fundamental processes. Taken together, these compelling findings indicate that metabolic enzymes and metabolites represent a key group of factors within the DDR. Here, we will compile the current knowledge on the dynamic interplay between metabolic factors and the DDR, with a specific focus on cancer. We will also discuss how recently developed high-throughput technologies allow for the identification of novel crosstalk between the DDR and metabolism, which is of crucial importance to better design efficient cancer treatments.
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22
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Participation of TDP1 in the repair of formaldehyde-induced DNA-protein cross-links in chicken DT40 cells. PLoS One 2020; 15:e0234859. [PMID: 32589683 PMCID: PMC7319324 DOI: 10.1371/journal.pone.0234859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 06/03/2020] [Indexed: 11/19/2022] Open
Abstract
Proteins are covalently trapped on DNA to form DNA-protein cross-links (DPCs) when cells are exposed to DNA-damaging agents. Aldehyde compounds produce common types of DPCs that contain proteins in an undisrupted DNA strand. Tyrosyl-DNA phosphodiesterase 1 (TDP1) repairs topoisomerase 1 (TOPO1) that is trapped at the 3’-end of DNA. In the present study, we examined the contribution of TDP1 to the repair of formaldehyde-induced DPCs using a reverse genetic strategy with chicken DT40 cells. The results obtained showed that cells deficient in TDP1 were sensitive to formaldehyde. The removal of formaldehyde-induced DPCs was slower in tdp1-deficient cells than in wild type cells. We also found that formaldehyde did not produce trapped TOPO1, indicating that trapped TOPO1 was not a primary cytotoxic DNA lesion that was generated by formaldehyde and repaired by TDP1. The formaldehyde treatment resulted in the accumulation of chromosomal breakages that were more prominent in tdp1-deficient cells than in wild type cells. Therefore, TDP1 plays a critical role in the repair of formaldehyde-induced DPCs that are distinct from trapped TOPO1.
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23
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A Comprehensive View of Translesion Synthesis in Escherichia coli. Microbiol Mol Biol Rev 2020; 84:84/3/e00002-20. [PMID: 32554755 DOI: 10.1128/mmbr.00002-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The lesion bypass pathway, translesion synthesis (TLS), exists in essentially all organisms and is considered a pathway for postreplicative gap repair and, at the same time, for lesion tolerance. As with the saying "a trip is not over until you get back home," studying TLS only at the site of the lesion is not enough to understand the whole process of TLS. Recently, a genetic study uncovered that polymerase V (Pol V), a poorly expressed Escherichia coli TLS polymerase, is not only involved in the TLS step per se but also participates in the gap-filling reaction over several hundred nucleotides. The same study revealed that in contrast, Pol IV, another highly expressed TLS polymerase, essentially stays away from the gap-filling reaction. These observations imply fundamentally different ways these polymerases are recruited to DNA in cells. While access of Pol IV appears to be governed by mass action, efficient recruitment of Pol V involves a chaperone-like action of the RecA filament. We present a model of Pol V activation: the 3' tip of the RecA filament initially stabilizes Pol V to allow stable complex formation with a sliding β-clamp, followed by the capture of the terminal RecA monomer by Pol V, thus forming a functional Pol V complex. This activation process likely determines higher accessibility of Pol V than of Pol IV to normal DNA. Finally, we discuss the biological significance of TLS polymerases during gap-filling reactions: error-prone gap-filling synthesis may contribute as a driving force for genetic diversity, adaptive mutation, and evolution.
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24
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Revisiting the evidence for genotoxicity of acrylamide (AA), key to risk assessment of dietary AA exposure. Arch Toxicol 2020; 94:2939-2950. [PMID: 32494932 PMCID: PMC7415744 DOI: 10.1007/s00204-020-02794-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 05/20/2020] [Indexed: 12/16/2022]
Abstract
The weight of evidence pro/contra classifying the process-related food contaminant (PRC) acrylamide (AA) as a genotoxic carcinogen is reviewed. Current dietary AA exposure estimates reflect margins of exposure (MOEs) < 500. Several arguments support the view that AA may not act as a genotoxic carcinogen, especially not at consumer-relevant exposure levels: Biotransformation of AA into genotoxic glycidamide (GA) in primary rat hepatocytes is markedly slower than detoxifying coupling to glutathione (GS). Repeated feeding of rats with AA containing foods, bringing about uptake of 100 µg/kg/day of AA, resulted in dose x time-related buildup of AA-hemoglobin (Hb) adducts, whereas GA-Hb adducts remained within the background. Since hepatic oxidative biotransformation of AA into GA was proven by simultaneous urinary mercapturic acid monitoring it can be concluded that at this nutritional intake level any GA formed in the liver from AA is quantitatively coupled to GS to be excreted as mercapturic acid in urine. In an oral single dose–response study in rats, AA induced DNA N7-GA-Gua adducts dose-dependently in the high dose range (> 100 µg/kg b w). At variance, in the dose range below 100 µg/kg b.w. down to levels of average consumers exposure, DNA N7 -Gua lesions were found only sporadically, without dose dependence, and at levels close to the lower bound of similar human background DNA N7-Gua lesions. No DNA damage was detected by the comet assay within this low dose range. GA is a very weak mutagen, known to predominantly induce DNA N7-GA-Gua adducts, especially in the lower dose range. There is consensus that DNA N7-GA-Gua adducts exhibit rather low mutagenic potency. The low mutagenic potential of GA has further been evidenced by comparison to preactivated forms of other process-related contaminants, such as N-Nitroso compounds or polycyclic aromatic hydrocarbons, potent food borne mutagens/carcinogens. Toxicogenomic studies provide no evidence supporting a genotoxic mode of action (MOA), rather indicate effects on calcium signalling and cytoskeletal functions in rodent target organs. Rodent carcinogenicity studies show induction of strain- and species-specific neoplasms, with MOAs not considered likely predictive for human cancer risk. In summary, the overall evidence clearly argues for a nongenotoxic/nonmutagenic MOA underlying the neoplastic effects of AA in rodents. In consequence, a tolerable intake level (TDI) may be defined, guided by mechanistic elucidation of key adverse effects and supported by biomarker-based dosimetry in experimental systems and humans.
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25
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Hartwig A, Arand M, Epe B, Guth S, Jahnke G, Lampen A, Martus HJ, Monien B, Rietjens IMCM, Schmitz-Spanke S, Schriever-Schwemmer G, Steinberg P, Eisenbrand G. Mode of action-based risk assessment of genotoxic carcinogens. Arch Toxicol 2020; 94:1787-1877. [PMID: 32542409 PMCID: PMC7303094 DOI: 10.1007/s00204-020-02733-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 03/31/2020] [Indexed: 12/16/2022]
Abstract
The risk assessment of chemical carcinogens is one major task in toxicology. Even though exposure has been mitigated effectively during the last decades, low levels of carcinogenic substances in food and at the workplace are still present and often not completely avoidable. The distinction between genotoxic and non-genotoxic carcinogens has traditionally been regarded as particularly relevant for risk assessment, with the assumption of the existence of no-effect concentrations (threshold levels) in case of the latter group. In contrast, genotoxic carcinogens, their metabolic precursors and DNA reactive metabolites are considered to represent risk factors at all concentrations since even one or a few DNA lesions may in principle result in mutations and, thus, increase tumour risk. Within the current document, an updated risk evaluation for genotoxic carcinogens is proposed, based on mechanistic knowledge regarding the substance (group) under investigation, and taking into account recent improvements in analytical techniques used to quantify DNA lesions and mutations as well as "omics" approaches. Furthermore, wherever possible and appropriate, special attention is given to the integration of background levels of the same or comparable DNA lesions. Within part A, fundamental considerations highlight the terms hazard and risk with respect to DNA reactivity of genotoxic agents, as compared to non-genotoxic agents. Also, current methodologies used in genetic toxicology as well as in dosimetry of exposure are described. Special focus is given on the elucidation of modes of action (MOA) and on the relation between DNA damage and cancer risk. Part B addresses specific examples of genotoxic carcinogens, including those humans are exposed to exogenously and endogenously, such as formaldehyde, acetaldehyde and the corresponding alcohols as well as some alkylating agents, ethylene oxide, and acrylamide, but also examples resulting from exogenous sources like aflatoxin B1, allylalkoxybenzenes, 2-amino-3,8-dimethylimidazo[4,5-f] quinoxaline (MeIQx), benzo[a]pyrene and pyrrolizidine alkaloids. Additionally, special attention is given to some carcinogenic metal compounds, which are considered indirect genotoxins, by accelerating mutagenicity via interactions with the cellular response to DNA damage even at low exposure conditions. Part C finally encompasses conclusions and perspectives, suggesting a refined strategy for the assessment of the carcinogenic risk associated with an exposure to genotoxic compounds and addressing research needs.
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Affiliation(s)
- Andrea Hartwig
- Department of Food Chemistry and Toxicology, Institute of Applied Biosciences (IAB), Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131, Karlsruhe, Germany.
| | - Michael Arand
- Institute of Pharmacology and Toxicology, University of Zurich, 8057, Zurich, Switzerland
| | - Bernd Epe
- Institute of Pharmacy and Biochemistry, University of Mainz, 55099, Mainz, Germany
| | - Sabine Guth
- Department of Toxicology, IfADo-Leibniz Research Centre for Working Environment and Human Factors, TU Dortmund, Ardeystr. 67, 44139, Dortmund, Germany
| | - Gunnar Jahnke
- Department of Food Chemistry and Toxicology, Institute of Applied Biosciences (IAB), Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131, Karlsruhe, Germany
| | - Alfonso Lampen
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Hans-Jörg Martus
- Novartis Institutes for BioMedical Research, 4002, Basel, Switzerland
| | - Bernhard Monien
- Department of Food Safety, German Federal Institute for Risk Assessment (BfR), 10589, Berlin, Germany
| | - Ivonne M C M Rietjens
- Division of Toxicology, Wageningen University, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Simone Schmitz-Spanke
- Institute and Outpatient Clinic of Occupational, Social and Environmental Medicine, University of Erlangen-Nuremberg, Henkestr. 9-11, 91054, Erlangen, Germany
| | - Gerlinde Schriever-Schwemmer
- Department of Food Chemistry and Toxicology, Institute of Applied Biosciences (IAB), Karlsruhe Institute of Technology (KIT), Adenauerring 20a, 76131, Karlsruhe, Germany
| | - Pablo Steinberg
- Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Haid-und-Neu-Str. 9, 76131, Karlsruhe, Germany
| | - Gerhard Eisenbrand
- Retired Senior Professor for Food Chemistry and Toxicology, Kühler Grund 48/1, 69126, Heidelberg, Germany.
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Prasad R, Horton JK, Wilson SH. Requirements for PARP-1 covalent crosslinking to DNA (PARP-1 DPC). DNA Repair (Amst) 2020; 89:102824. [DOI: 10.1016/j.dnarep.2020.102824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 02/06/2023]
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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.
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28
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Nakamura J, Nakamura M. DNA-protein crosslink formation by endogenous aldehydes and AP sites. DNA Repair (Amst) 2020; 88:102806. [PMID: 32070903 DOI: 10.1016/j.dnarep.2020.102806] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/19/2022]
Abstract
Covalent binding between proteins and a DNA strand produces DNA-protein crosslinks (DPC). DPC are one of the most deleterious types of DNA damage, leading to the blockage of DNA replication and transcription. Both DNA lesions and endogenous products with carbonyl functional groups can produce DPC in genomic DNA under normal physiological conditions. For example, formaldehyde, the most abundant endogenous human carcinogen, and apurinic/apyrimidinic (AP) sites, the most common type of endogenous DNA lesions, has been shown to crosslink proteins and/or DNA through their carbonyl functional groups. Unfortunately, compared to other types of DNA damage, DPC have been less studied and understood. However, a recent advancement has allowed researchers to determine accurate yields of various DNA lesions including formaldehyde-derived DPC with high sensitivity and specificity, paving the way for new developments in this field of research. Here, we review the current literature and remaining unanswered questions on DPC formation by endogenous formaldehyde and various aldehydic 2-deoxyribose lesions.
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Affiliation(s)
- Jun Nakamura
- Laboratory of Laboratory Animal Science, Graduate School of Life and Environmental Biosciences, Osaka Prefecture University, Izumisano, Osaka, Japan.
| | - Mai Nakamura
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Francés-Monerris A, Lineros-Rosa M, Miranda MA, Lhiaubet-Vallet V, Monari A. Photoinduced intersystem crossing in DNA oxidative lesions and epigenetic intermediates. Chem Commun (Camb) 2020; 56:4404-4407. [DOI: 10.1039/d0cc01132k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The propensity of 5-formyluracil and 5-formylcytosine, i.e. oxidative lesions and epigenetic intermediates, in acting as intrinsic DNA photosensitizers is unraveled by using a combination of molecular modeling, simulation and spectroscopy.
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Affiliation(s)
| | - Mauricio Lineros-Rosa
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Miguel Angel Miranda
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Virginie Lhiaubet-Vallet
- Instituto Universitario Mixto de Tecnologia Química UPV-CSIC
- Universitat Politècnica de València
- 46022 Valencia
- Spain
| | - Antonio Monari
- Université de Lorraine and CNRS
- LPCT UMR 7019
- F-54000 Nancy
- France
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30
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Heflich RH, Johnson GE, Zeller A, Marchetti F, Douglas GR, Witt KL, Gollapudi BB, White PA. Mutation as a Toxicological Endpoint for Regulatory Decision-Making. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:34-41. [PMID: 31600846 DOI: 10.1002/em.22338] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 09/09/2019] [Accepted: 09/14/2019] [Indexed: 05/23/2023]
Abstract
Mutations induced in somatic cells and germ cells are responsible for a variety of human diseases, and mutation per se has been considered an adverse health concern since the early part of the 20th Century. Although in vitro and in vivo somatic cell mutation data are most commonly used by regulatory agencies for hazard identification, that is, determining whether or not a substance is a potential mutagen and carcinogen, quantitative mutagenicity dose-response data are being used increasingly for risk assessments. Efforts are currently underway to both improve the measurement of mutations and to refine the computational methods used for evaluating mutation data. We recommend continuing the development of these approaches with the objective of establishing consensus regarding the value of including the quantitative analysis of mutation per se as a required endpoint for comprehensive assessments of toxicological risk. Environ. Mol. Mutagen. 61:34-41, 2020. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Robert H Heflich
- U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas
| | | | - Andreas Zeller
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - George R Douglas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
| | - Kristine L Witt
- National Institutes of Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | | | - Paul A White
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Canada
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31
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Land WG. Role of Damage-Associated Molecular Patterns in Light of Modern Environmental Research: A Tautological Approach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH 2020; 14:583-604. [PMID: 32837525 PMCID: PMC7415330 DOI: 10.1007/s41742-020-00276-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/30/2020] [Accepted: 08/01/2020] [Indexed: 05/06/2023]
Abstract
Two prominent models emerged as a result of intense interdisciplinary discussions on the environmental health paradigm, called the "exposome" concept and the "adverse outcome pathway" (AOP) concept that links a molecular initiating event to the adverse outcome via key events. Here, evidence is discussed, suggesting that environmental stress/injury-induced damage-associated molecular patterns (DAMPs) may operate as an essential integrating element of both environmental health research paradigms. DAMP-promoted controlled/uncontrolled innate/adaptive immune responses reflect the key events of the AOP concept. The whole process starting from exposure to a distinct environmental stress/injury-associated with the presence/emission of DAMPs-up to the manifestation of a disease may be regarded as an exposome. Clinical examples of such a scenario are briefly sketched, in particular, a model in relation to the emerging COVID-19 pandemic, where the interaction of noninfectious environmental factors (e.g., particulate matter) and infectious factors (SARS CoV-2) may promote SARS case fatality via superimposition of both exogenous and endogenous DAMPs.
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Affiliation(s)
- Walter Gottlieb Land
- German Academy for Transplantation Medicine, Munich, Germany
- Molecular ImmunoRheumatology, Laboratory of Excellence Transplantex, Faculty of Medicine, INSERM UMR_S1109, University of Strasbourg, Strasbourg, France
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Franco I, Helgadottir HT, Moggio A, Larsson M, Vrtačnik P, Johansson A, Norgren N, Lundin P, Mas-Ponte D, Nordström J, Lundgren T, Stenvinkel P, Wennberg L, Supek F, Eriksson M. Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type. Genome Biol 2019; 20:285. [PMID: 31849330 PMCID: PMC6918713 DOI: 10.1186/s13059-019-1892-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 11/18/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on specific processes active in different human tissues and their effect on the transition to cancer. RESULTS To analyze somatic mutation patterns, we compile a comprehensive genetic atlas of somatic mutations in healthy human cells. High-confidence variants are obtained from newly generated and publicly available whole genome DNA sequencing data from single non-cancer cells, clonally expanded in vitro. To enable a well-controlled comparison of different cell types, we obtain single genome data (92% mean coverage) from multi-organ biopsies from the same donors. These data show multiple cell types that are protected from mutagens and display a stereotyped mutation profile, despite their origin from different tissues. Conversely, the same tissue harbors cells with distinct mutation profiles associated to different differentiation states. Analyses of mutation rate in the coding and non-coding portions of the genome identify a cell type bearing a unique mutation pattern characterized by mutation enrichment in active chromatin, regulatory, and transcribed regions. CONCLUSIONS Our analysis of normal cells from healthy donors identifies a somatic mutation landscape that enhances the risk of tumor transformation in a specific cell population from the kidney proximal tubule. This unique pattern is characterized by high rate of mutation accumulation during adult life and specific targeting of expressed genes and regulatory regions.
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Affiliation(s)
- Irene Franco
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden.
| | - Hafdis T Helgadottir
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Aldo Moggio
- Department of Medicine Huddinge, Integrated Cardio Metabolic Center, Karolinska Institutet, Huddinge, Sweden
| | - Malin Larsson
- Science for Life Laboratory, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Peter Vrtačnik
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Anna Johansson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Nina Norgren
- Science for Life Laboratory, Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Pär Lundin
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics (DBB), Stockholm University, Stockholm, Sweden
| | - David Mas-Ponte
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
| | - Johan Nordström
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Division of Transplantation Surgery, Karolinska University Hospital, Huddinge, Sweden
| | - Torbjörn Lundgren
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Division of Transplantation Surgery, Karolinska University Hospital, Huddinge, Sweden
| | - Peter Stenvinkel
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Division of Renal Medicine, Karolinska University Hospital, Huddinge, Sweden
| | - Lars Wennberg
- Department of Clinical Sciences, Intervention and Technology, Karolinska Institutet, Division of Transplantation Surgery, Karolinska University Hospital, Huddinge, Sweden
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Maria Eriksson
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden.
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Terenzi A, Gattuso H, Spinello A, Keppler BK, Chipot C, Dehez F, Barone G, Monari A. Targeting G-quadruplexes with Organic Dyes: Chelerythrine-DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy. Antioxidants (Basel) 2019; 8:antiox8100472. [PMID: 31658666 PMCID: PMC6826623 DOI: 10.3390/antiox8100472] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/05/2019] [Accepted: 10/07/2019] [Indexed: 01/24/2023] Open
Abstract
The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences—representative of different topologies and possessing biological relevance, such as telomeric or regulatory sequences—have been considered. An original multiscale protocol, making use of molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations, allowed us to compare the theoretical and experimental circular dichroism spectra of the different DNA topologies, readily providing atomic-level details of the CHE–DNA binding modes. The binding selectivity towards G-quadruplexes is confirmed by both experimental and theoretical determination of the binding free energies. Overall, our mixed computational and experimental approach is able to shed light on the interaction of small molecules with different DNA conformations. In particular, CHE may be seen as the building block of promising drug candidates specifically targeting G-quadruplexes for both antitumoral and antiviral purposes.
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Affiliation(s)
- Alessio Terenzi
- Institute of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, A-1090 Vienna, Austria.
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 Donostia, Spain.
| | - Hugo Gattuso
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Angelo Spinello
- CNR-IOM DEMOCRITOS c/o International School for Advanced Studies (SISSA), 34136 Trieste, Italy.
| | - Bernhard K Keppler
- Institute of Inorganic Chemistry, University of Vienna, Währingerstrasse 42, A-1090 Vienna, Austria.
| | - Christophe Chipot
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA.
| | - François Dehez
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
- Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
| | - Giampaolo Barone
- Dipartimento di Scienze Biologiche, Chimiche e Farmaceutiche, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy.
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, F54000 Nancy, France.
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Fioranelli M, Sepehri A, Roccia MG, Linda C, Rossi C, Dawodo A, Vojvodic P, Lotti J, Barygina V, Vojvodic A, Wollina U, Tirant M, Van TN, Lotti T. Clinical Applications of System Regulation Medicine. Open Access Maced J Med Sci 2019; 7:3053-3060. [PMID: 31850122 PMCID: PMC6910802 DOI: 10.3889/oamjms.2019.775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 12/04/2022] Open
Abstract
Increasing incidence and poor outcome of chronic non-communicable diseases in western population would require a paradigm shift in the treatments. Guidelines-based medical approaches continue to be the standard rule in clinical practice, although only less than 15% of them are based on high-quality research. For each person who benefits from the 10 best-selling drugs in the USA, a number between 4 and 25 has no one beneficial effect. The reductionist linear medicine method does not offer solutions in the non-manifest preclinical stage of the disease when it would still be possible to reverse the pathological progression and the axiom “a drug, a target, a symptom” are still inconclusive. Needs additional tools to address these challenges. System Medicine considers the disease as a dysregulation of the biological networks that changes throughout the evolution of the pathological process and with the comorbidities development. The strength of the networks indicates their ability to withstand dysregulations during the perturbation phases, returning to the state of stability. The treatment of dysregulated networks before the symptomatological manifestation emerges offers the possibility of treating and preventing pathologies in the preclinical phase and potentially reversing the pathological process, stopping it or preventing comorbidities. Furthermore, treating shared networks instead of individual phenotypic symptoms can reduce drug use, offering a solution to the problem of ineffective drug use.
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Affiliation(s)
- Massimo Fioranelli
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Alireza Sepehri
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Maria Grazia Roccia
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Cota Linda
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Chiara Rossi
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Amos Dawodo
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Petar Vojvodic
- Clinic for Psychiatric Disorders "Dr. Laza Lazarevic", Belgrade, Serbia
| | - Jacopo Lotti
- Department of Nuclear Physics, Sub-nuclear and Radiation, G. Marconi University, Rome, Italy
| | - Victoria Barygina
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Aleksandra Vojvodic
- Department of Dermatology and Venereology, Military Medical Academy, Belgrade, Serbia
| | - Uwe Wollina
- Department of Dermatology and Allergology, Städtisches Klinikum Dresden, Dresden, Germany
| | | | - Thuong Nguyen Van
- Vietnam National Hospital of Dermatology and Venereology, Hanoi, Vietnam
| | - Torello Lotti
- Department of Dermatology, University of G. Marconi, Rome, Italy
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35
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Detection of DNA Double-Strand Breaks Using Pulsed-Field Gel Electrophoresis. Methods Mol Biol 2019. [PMID: 31473967 DOI: 10.1007/978-1-4939-9646-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
DNA is one of the most biologically important targets of exogenous and endogenous toxicants as well as carcinogens. Damage to DNA can be of different types (e.g., DNA adducts, DNA protein cross-links, single-strand breaks, oxidized bases, abasic sites, and double-strand breaks (DSBs)). DSBs are considered the most lethal form of DNA damage for eukaryotic cells, and if left unrepaired or misrepaired, can cause cell death, chromosome instability, and cancer. DSBs can arise in the cells through different sources and can be distinguished as endogenous or exogenous DSBs. Exogenous sources can be chemotherapeutic drugs, irradiation, and environmental chemicals. The endogenous causes of DNA DSBs in the cells are mainly reactive oxygen species and faulty repair of oxidative clustered DNA lesions. Qualitative and quantitative analysis of DNA DSBs is of utmost importance to understand physiologically relevant cellular processes as well as to investigate the genotoxic or clastogenic effects of toxicants. Pulsed-field gel electrophoresis (PFGE) is a widely used method for direct quantification of DNA DSBs. In this method, the cells exposed to DSB-inducing agents are embedded in the agarose blocks and lysed. These agarose blocks containing DNA are then run under multiple electric fields which are at 120° angle, to aid in the movement of large DNA strands. It gives a direct and specific measure of DSBs unlike the foci-based assays. This chapter provides a brief overview of the various commonly used approaches to analyze DNA DSBs and describes the theory, advantages and method of PFGE, for use in cells exposed to DNA DSB inducing agents.
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36
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Hognon C, Gebus A, Barone G, Monari A. Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes. Antioxidants (Basel) 2019; 8:antiox8090337. [PMID: 31443537 PMCID: PMC6770428 DOI: 10.3390/antiox8090337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 01/23/2023] Open
Abstract
By using all atom molecular dynamics simulations, we studied the behavior of human DNA telomere sequences in guanine quadruplex (G4) conformation and in the presence of oxidative lesions, namely abasic sites. In particular, we evidenced that while removing one guanine base induces a significant alteration and destabilization of the involved leaflet, human telomere oligomers tend, in most cases, to maintain at least a partial quadruplex structure, eventually by replacing the empty site with undamaged guanines of different leaflets. This study shows that (i) the disruption of the quadruplex leaflets induces the release of at least one of the potassium cations embedded in the quadruplex channel and that (ii) the electrostatic interactions of the DNA sequence with the aforementioned cations are fundamental to the maintenance of the global quadruplex structure.
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Affiliation(s)
- Cecilia Hognon
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Adrien Gebus
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France
| | - Giampaolo Barone
- Department of Biological, Chenical and Pharmaceutical Sciences and Technologies, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
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37
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Mitochondrial transcription factor A promotes DNA strand cleavage at abasic sites. Proc Natl Acad Sci U S A 2019; 116:17792-17799. [PMID: 31413200 DOI: 10.1073/pnas.1911252116] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In higher eukaryotic cells, mitochondria are essential subcellular organelles for energy production, cell signaling, and the biosynthesis of biomolecules. The mitochondrial DNA (mtDNA) genome is indispensable for mitochondrial function because it encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. MtDNA degradation has emerged as an essential quality control measure to maintain mtDNA and to cope with mtDNA damage resulting from endogenous and environmental factors. Among all types of DNA damage known, abasic (AP) sites, sourced from base excision repair and spontaneous base loss, are the most abundant endogenous DNA lesions in cells. In mitochondria, AP sites trigger rapid DNA loss; however, the mechanism and molecular factors involved in the process remain elusive. Herein, we demonstrate that the stability of AP sites is reduced dramatically upon binding to a major mtDNA packaging protein, mitochondrial transcription factor A (TFAM). The half-life of AP lesions within TFAM-DNA complexes is 2 to 3 orders of magnitude shorter than that in free DNA, depending on their position. The TFAM-catalyzed AP-DNA destabilization occurs with nonspecific DNA or mitochondrial light-strand promoter sequence, yielding DNA single-strand breaks and DNA-TFAM cross-links. TFAM-DNA cross-link intermediates prior to the strand scission were also observed upon treating AP-DNA with mitochondrial extracts of human cells. In situ trapping of the reaction intermediates (DNA-TFAM cross-links) revealed that the reaction proceeds via Schiff base chemistry facilitated by lysine residues. Collectively, our data suggest a novel role of TFAM in facilitating the turnover of abasic DNA.
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38
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Moore MM, Pottenger LH, House‐Knight T. Critical review of styrene genotoxicity focused on the mutagenicity/clastogenicity literature and using current organization of economic cooperation and development guidance. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:624-663. [PMID: 30786062 PMCID: PMC6767453 DOI: 10.1002/em.22278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 02/08/2019] [Accepted: 02/18/2019] [Indexed: 05/06/2023]
Abstract
Styrene is an important high production volume chemical used to manufacture polymeric products. In 2018, International Agency for Research on Cancer classified styrene as probably carcinogenic to humans; National Toxicology Program lists styrene as reasonably anticipated to be a human carcinogen. The genotoxicity literature for styrene and its primary metabolite, styrene 7,8-oxide (SO), begins in the 1970s. Organization of Economic Cooperation and Development (OECD) recently updated most genotoxicity test guidelines, making substantial new recommendations for assay conduct and data evaluation for the standard mutagenicity/clastogenicity assays. Thus, a critical review of the in vitro and in vivo rodent mutagenicity/clastogenicity studies for styrene and SO, based on the latest OECD recommendations, is timely. This critical review considered whether a study was optimally designed, conducted, and interpreted and provides a critical assessment of the evidence for the mutagenicity/clastogenicity of styrene/SO. Information on the ability of styrene/SO to induce other types of genotoxicity endpoints is summarized but not critically reviewed. We conclude that when styrene is metabolized to SO, it can form DNA adducts, and positive in vitro mutagenicity/clastogenicity results can be obtained. SO is mutagenic in bacteria and the in vitro mouse lymphoma gene mutation assay. No rodent in vivo mutation studies were identified. SO is clastogenic in cultured mammalian cells. Although the in vitro assays gave positive responses, styrene/SO is not clastogenic/aneugenic in vivo in rodents. In addition to providing updated information for styrene, this review demonstrates the application of the new OECD guidelines for chemicals with large genetic toxicology databases where published results may or may not be reliable. Environ. Mol. Mutagen. 2019. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Martha M. Moore
- Ramboll124 West Capitol Avenue, Suite 1605, Little RockArkansas
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Pottenger LH, Boysen G, Brown K, Cadet J, Fuchs RP, Johnson GE, Swenberg JA. Understanding the importance of low-molecular weight (ethylene oxide- and propylene oxide-induced) DNA adducts and mutations in risk assessment: Insights from 15 years of research and collaborative discussions. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:100-121. [PMID: 30536466 PMCID: PMC6590209 DOI: 10.1002/em.22248] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 08/10/2018] [Accepted: 08/23/2018] [Indexed: 05/11/2023]
Abstract
The interpretation and significance of DNA adduct data, their causal relationship to mutations, and their role in risk assessment have been debated for many years. An extended effort to identify key questions and collect relevant data to address them was focused on the ubiquitous low MW N7-alkyl/hydroxyalkylguanine adducts. Several academic, governmental, and industrial laboratories collaborated to gather new data aimed at better understanding the role and potential impact of these adducts in quantifiable genotoxic events (gene mutations/micronucleus). This review summarizes and evaluates the status of dose-response data for DNA adducts and mutations from recent experimental work with standard mutagenic agents and ethylene oxide and propylene oxide, and the importance for risk assessment. This body of evidence demonstrates that small N7-alkyl/hydroxyalkylguanine adducts are not pro-mutagenic and, therefore, adduct formation alone is not adequate evidence to support a mutagenic mode of action. Quantitative methods for dose-response analysis and derivation of thresholds, benchmark dose (BMD), or other points-of-departure (POD) for genotoxic events are now available. Integration of such analyses of genetox data is necessary to properly assess any role for DNA adducts in risk assessment. Regulatory acceptance and application of these insights remain key challenges that only the regulatory community can address by applying the many learnings from recent research. The necessary tools, such as BMDs and PODs, and the example datasets, are now available and sufficiently mature for use by the regulatory community. Environ. Mol. Mutagen. 60: 100-121, 2019. © 2018 The Authors. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- L. H. Pottenger
- Olin Corporation/Blue Cube Operations, LLC, retired, LHP TOX CONSULT, LLCMidlandMIUSA
| | - G. Boysen
- Department of Environmental and Occupational Health and The Winthrop P Rockefeller Cancer Institute University of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - K. Brown
- Leicester Cancer Research CentreUniversity of LeicesterLeicesterUnited Kingdom
| | - J. Cadet
- Institut Nanosciences et Cryogénie, CEA‐GrenobleGrenobleFrance
- Université de SherbrookeSherbrookeCanada
| | - R. P. Fuchs
- Centre de Recherche en Cancérologie de Marseille (CRCM), Inserm, U1068Marseille, 13009France
- CNRS, UMR7258Marseille, 13009France
- Institut Paoli‐CalmettesMarseille, 13009France
- Aix‐Marseille UniversityUM 105, 13284, MarseilleFrance
| | - G. E. Johnson
- Swansea University, Institute of Life SciencesSwanseaUnited Kingdom
| | - J. A. Swenberg
- University of North CarolinaChapel HillNorth CarolinaUSA
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Olympio KPK, Salles FJ, Ferreira APSDS, Pereira EC, Oliveira ASD, Leroux IN, Vieira FBA. The human exposome unraveling the impact of environment on health: promise or reality? Rev Saude Publica 2019; 53:6. [PMID: 30726487 PMCID: PMC6390641 DOI: 10.11606/s1518-8787.2019053000649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/21/2018] [Indexed: 11/13/2022] Open
Abstract
Considering the innovative nature of the approach to human exposome, we present the state of the art of studies on exposome, and discuss current challenges and perspectives in this area. Several reading and discussion activities were conducted by the Expossoma e Saúde do Trabalhador (eXsat – Group Exposome and Worker's Health), with systematization of the literature in the area published between January 2005 and January 2017, available in the databases PubMed and Web of Science. This comment brings a thematic analysis to encourage the dissemination of the exposome approach for studies in the Public Health area.
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Affiliation(s)
- Kelly Polido Kaneshiro Olympio
- Universidade de São Paulo. Faculdade de Saúde Pública. Departamento de Saúde Ambiental. São Paulo, SP, Brasil.,Universidade de São Paulo. Faculdade de Saúde Pública. Departamento de Saúde Ambiental. Grupo de Pesquisa eXsat. Expossoma e Saúde do Trabalhador. The Human Exposome Research Group. São Paulo, SP, Brasil
| | - Fernanda Junqueira Salles
- Universidade de São Paulo. Faculdade de Saúde Pública. Departamento de Saúde Ambiental. Grupo de Pesquisa eXsat. Expossoma e Saúde do Trabalhador. The Human Exposome Research Group. São Paulo, SP, Brasil
| | - Ana Paula Sacone da Silva Ferreira
- Universidade de São Paulo. Faculdade de Saúde Pública. Departamento de Saúde Ambiental. Grupo de Pesquisa eXsat. Expossoma e Saúde do Trabalhador. The Human Exposome Research Group. São Paulo, SP, Brasil
| | - Elizeu Chiodi Pereira
- Universidade de São Paulo. Faculdade de Saúde Pública. Departamento de Saúde Ambiental. Grupo de Pesquisa eXsat. Expossoma e Saúde do Trabalhador. The Human Exposome Research Group. São Paulo, SP, Brasil
| | - Allan Santos de Oliveira
- Universidade de São Paulo. Faculdade de Saúde Pública. Departamento de Saúde Ambiental. Grupo de Pesquisa eXsat. Expossoma e Saúde do Trabalhador. The Human Exposome Research Group. São Paulo, SP, Brasil
| | - Isabelle Nogueira Leroux
- Universidade de São Paulo. Faculdade de Saúde Pública. Departamento de Saúde Ambiental. Grupo de Pesquisa eXsat. Expossoma e Saúde do Trabalhador. The Human Exposome Research Group. São Paulo, SP, Brasil
| | - Flávia Bosquê Alves Vieira
- Universidade de São Paulo. Faculdade de Saúde Pública. Departamento de Saúde Ambiental. Grupo de Pesquisa eXsat. Expossoma e Saúde do Trabalhador. The Human Exposome Research Group. São Paulo, SP, Brasil
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Improving risk assessment approaches for chemicals with both endogenous and exogenous exposures. Regul Toxicol Pharmacol 2019; 103:210-215. [PMID: 30703408 DOI: 10.1016/j.yrtph.2019.01.029] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/17/2019] [Accepted: 01/20/2019] [Indexed: 02/02/2023]
Abstract
To conduct risk assessments of exogenous chemicals for which there are also endogenous exposures, knowledge of the chemistry and biology of both types of exposures needs to be integrated into problem formulation and carried through to risk characterization. This issue is framed in a risk assessment context, highlighting the importance of quantifying increments of dose from all sources of the same or similar chemicals interacting with biological targets; understanding the influence of endogenous chemical concentrations on disease risk; and assessing total dose to targets in evaluating risk from incremental environmental exposures. Examples of recent assessments illustrate the importance of addressing this issue. Evaluations of data on blood or organ concentrations of ammonia, methanol, formaldehyde, acetaldehyde, and three gaseous signaling molecules (hydrogen sulfide, carbon monoxide, and nitric oxide) provide examples where current data are already informing perspectives on relative exposures at the portal of entry and systemically. To facilitate quality risk assessments of exogenous chemicals with endogenous exposures, a series of specific questions are presented that need to be addressed in systematic review to enhance problem formulation, improve the development of holistic conceptual models, and to facilitate the identification of priority data needs for improving risk assessments.
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Zhao L. Mitochondrial DNA degradation: A quality control measure for mitochondrial genome maintenance and stress response. Enzymes 2019; 45:311-341. [PMID: 31627882 DOI: 10.1016/bs.enz.2019.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Mitochondria play a central role in bioenergetics, and fulfill a plethora of functions in cell signaling, programmed cell death, and biosynthesis of key protein cofactors. Mitochondria harbor their own genomic DNA, which encodes protein subunits of the electron transport chain and a full set of transfer and ribosomal RNAs. Mitochondrial DNA (mtDNA) is essential for cellular and organismal functions, and defects in mitochondrial genome maintenance have been implicated in common human diseases and mitochondrial disorders. mtDNA repair and degradation are known pathways to cope with mtDNA damage; however, molecular factors involved in this process have remained unclear. Such knowledge is fundamental to the understanding of mitochondrial genomic maintenance and pathology, because mtDNA degradation may contribute to the etiology of mtDNA depletion syndromes and to the activation of the innate immune response by fragmented mtDNA. This article reviews the current literature regarding the importance of mitochondrial DNA degradation in mtDNA maintenance and stress response, and the recent progress in uncovering molecular factors involved in mtDNA degradation. These factors include key components of the mtDNA replication machinery, such as DNA polymerase γ, helicase Twinkle, and exonuclease MGME1, as well as a major DNA-packaging protein, mitochondrial transcription factor A (TFAM).
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Affiliation(s)
- Linlin Zhao
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States.
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Delplancke TDJ, Wu Y, Han TL, Joncer LR, Qi H, Tong C, Baker PN. Metabolomics of Pregnancy Complications: Emerging Application of Maternal Hair. BIOMED RESEARCH INTERNATIONAL 2018; 2018:2815439. [PMID: 30662903 PMCID: PMC6312607 DOI: 10.1155/2018/2815439] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/18/2018] [Indexed: 02/01/2023]
Abstract
In recent years, the study of metabolomics has begun to receive increasing international attention, especially as it pertains to medical research. This is due in part to the potential for discovery of new biomarkers in the metabolome and to a new understanding of the "exposome", which refers to the endogenous and exogenous compounds that reflect external exposures. Consequently, metabolomics research into pregnancy-related issues has increased. Biomarkers discovered through metabolomics may shed some light on the etiology of certain pregnancy-related complications and their adverse effects on future maternal health and infant development and improve current clinical management. The discoveries and methods used in these studies will be compiled and summarized within the following paper. A further focus of this paper is the use of hair as a biological sample, which is gaining increasing attention across diverse fields due to its noninvasive sampling method and the metabolome stability. Its significance in exposome studies will be considered in this review, as well as the potential to associate exposures with adverse pregnancy outcomes. Currently, hair has been used in only two metabolomics studies relating to fetal growth restriction (FGR) and gestational diabetes mellitus (GDM).
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Affiliation(s)
- Thibaut D. J. Delplancke
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing 400016, China
- International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing 400016, China
| | - Yue Wu
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing 400016, China
- International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing 400016, China
| | - Ting-Li Han
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing 400016, China
- International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing 400016, China
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Lingga R. Joncer
- International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing 400016, China
| | - Hongbo Qi
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing 400016, China
- International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing 400016, China
| | - Chao Tong
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- State Key Laboratory of Maternal and Fetal Medicine of Chongqing Municipality, Chongqing Medical University, Chongqing 400016, China
- International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing 400016, China
| | - Philip N. Baker
- International Collaborative Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, Chongqing 400016, China
- Liggins Institute, University of Auckland, Auckland, New Zealand
- College of Medicine, University of Leicester, Leicester LE1 7RH, UK
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Cooke MS, Hu CW, Chang YJ, Chao MR. Urinary DNA adductomics - A novel approach for exposomics. ENVIRONMENT INTERNATIONAL 2018; 121:1033-1038. [PMID: 30392940 PMCID: PMC6279464 DOI: 10.1016/j.envint.2018.10.041] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/01/2018] [Accepted: 10/20/2018] [Indexed: 05/07/2023]
Abstract
The exposome is a concept that encompasses the totality of internal and external environmental exposures, from conception onwards. Evaluation of the exposome, across the lifecourse represents a significant challenge, e.g., methods/technology may simply not exist to comprehensively assess all exposures, or they may not be applicable to human populations, or may have insufficient sensitivity. Cellular DNA adductomics aims to determine the totality of DNA adducts in the cellular genome. However, application to human populations requires the necessarily invasive sampling of tissue, to obtain sufficient DNA for sensitive analysis, which can represent a logistical and IRB challenge, particularly when investigating vulnerable populations. To circumvent this, we recently applied DNA adductomics to urine, detecting a range of expected and unexpected 2'-deoxyribonucleoside DNA adducts. However, base excision repair, the main DNA repair pathway for non-bulky DNA adducts, and processes such as spontaneous depurination, generate nucleobase adducts. Herein we propose a strategy to simultaneously assess 2'-deoxyribonucleoside and nucleobase adducts, using a widely used mass spectrometic platform (i.e., triple quadrupole tandem mass spectrometry). This will provide a much needed DNA adductomic approach for non-invasively, biomonitoring environmental exposures, through assessing the totality of DNA adducts; contributing to the evaluation of the exposome, across the life-course.
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Affiliation(s)
- Marcus S Cooke
- Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA; Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA.
| | - Chiung-Wen Hu
- Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA; Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Mu-Rong Chao
- Oxidative Stress Group, Department of Environmental Health Sciences, Florida International University, Miami, FL 33199, USA; Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan; Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan.
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45
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Prasad R, Horton JK, Dai DP, Wilson SH. Repair pathway for PARP-1 DNA-protein crosslinks. DNA Repair (Amst) 2018; 73:71-77. [PMID: 30466837 DOI: 10.1016/j.dnarep.2018.11.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/03/2018] [Accepted: 11/09/2018] [Indexed: 02/06/2023]
Abstract
Poly(ADP-ribose) polymerase-1 (PARP-1) is a regulatory enzyme involved in many different processes of DNA and RNA metabolism, including DNA repair. Previously, PARP-1 was found capable of forming a covalent DNA-protein crosslink (DPC) at the apurinic/apyrimidinic (AP) site in double-stranded DNA. The C1´ atom of the AP site participates in Schiff base formation with a lysine side chain in PARP-1, and a covalent bond is formed upon reduction of the Schiff base. The PARP-1 DPC is formed in vivo where DPC formation correlates with AP site induction by a monofunctional alkylating agent. Here, we examined repair of PARP-1 DPCs in mouse fibroblasts and found that a proteasome inhibitor, MG-132, reduces repair resulting in accumulation of PARP-1 DPCs and increased alkylating agent cytotoxicity. Using a model DNA substrate mimicking the PARP-1 DPC after proteasomal degradation, we found that repair is completed by a sub-pathway of base excision repair (BER). Tyrosyl-DNA phosphodiesterase 1 was proficient in removing the ring-open AP site sugar at the phosphodiester linkage, leaving an intermediate for processing by other BER enzymes. The results reveal proteasomal degradation of the PARP-1 DPC is active in mouse fibroblasts and that a model repair intermediate is processed by the BER machinery.
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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
| | - Da-Peng Dai
- 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.
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Sobus JR, Wambaugh JF, Isaacs KK, Williams AJ, McEachran AD, Richard AM, Grulke CM, Ulrich EM, Rager JE, Strynar MJ, Newton SR. Integrating tools for non-targeted analysis research and chemical safety evaluations at the US EPA. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2018; 28:411-426. [PMID: 29288256 PMCID: PMC6661898 DOI: 10.1038/s41370-017-0012-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Revised: 08/04/2017] [Accepted: 08/25/2017] [Indexed: 05/18/2023]
Abstract
Tens-of-thousands of chemicals are registered in the U.S. for use in countless processes and products. Recent evidence suggests that many of these chemicals are measureable in environmental and/or biological systems, indicating the potential for widespread exposures. Traditional public health research tools, including in vivo studies and targeted analytical chemistry methods, have been unable to meet the needs of screening programs designed to evaluate chemical safety. As such, new tools have been developed to enable rapid assessment of potentially harmful chemical exposures and their attendant biological responses. One group of tools, known as "non-targeted analysis" (NTA) methods, allows the rapid characterization of thousands of never-before-studied compounds in a wide variety of environmental, residential, and biological media. This article discusses current applications of NTA methods, challenges to their effective use in chemical screening studies, and ways in which shared resources (e.g., chemical standards, databases, model predictions, and media measurements) can advance their use in risk-based chemical prioritization. A brief review is provided of resources and projects within EPA's Office of Research and Development (ORD) that provide benefit to, and receive benefits from, NTA research endeavors. A summary of EPA's Non-Targeted Analysis Collaborative Trial (ENTACT) is also given, which makes direct use of ORD resources to benefit the global NTA research community. Finally, a research framework is described that shows how NTA methods will bridge chemical prioritization efforts within ORD. This framework exists as a guide for institutions seeking to understand the complexity of chemical exposures, and the impact of these exposures on living systems.
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Affiliation(s)
- Jon R Sobus
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA.
| | - John F Wambaugh
- U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Kristin K Isaacs
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Antony J Williams
- U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Andrew D McEachran
- Oak Ridge Institute for Science and Education (ORISE) Participant, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Ann M Richard
- U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Christopher M Grulke
- U.S. Environmental Protection Agency, Office of Research and Development, National Center for Computational Toxicology, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Elin M Ulrich
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Julia E Rager
- Oak Ridge Institute for Science and Education (ORISE) Participant, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
- ToxStrategies, Inc., 9390 Research Blvd., Suite 100, Austin, TX, 78759, USA
| | - Mark J Strynar
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Seth R Newton
- U.S. Environmental Protection Agency, Office of Research and Development, National Exposure Research Laboratory, 109 T.W. Alexander Drive, Research Triangle Park, NC, 27709, USA
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Sharma V, Collins LB, Chen TH, Herr N, Takeda S, Sun W, Swenberg JA, Nakamura J. Oxidative stress at low levels can induce clustered DNA lesions leading to NHEJ mediated mutations. Oncotarget 2018; 7:25377-90. [PMID: 27015367 PMCID: PMC5041911 DOI: 10.18632/oncotarget.8298] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 03/13/2016] [Indexed: 12/12/2022] Open
Abstract
DNA damage and mutations induced by oxidative stress are associated with various different human pathologies including cancer. The facts that most human tumors are characterized by large genome rearrangements and glutathione depletion in mice results in deletions in DNA suggest that reactive oxygen species (ROS) may cause gene and chromosome mutations through DNA double strand breaks (DSBs). However, the generation of DSBs at low levels of ROS is still controversial. In the present study, we show that H2O2 at biologically-relevant levels causes a marked increase in oxidative clustered DNA lesions (OCDLs) with a significant elevation of replication-independent DSBs. Although it is frequently reported that OCDLs are fingerprint of high-energy IR, our results indicate for the first time that H2O2, even at low levels, can also cause OCDLs leading to DSBs specifically in G1 cells. Furthermore, a reverse genetic approach revealed a significant contribution of the non-homologous end joining (NHEJ) pathway in H2O2-induced DNA repair & mutagenesis. This genomic instability induced by low levels of ROS may be involved in spontaneous mutagenesis and the etiology of a wide variety of human diseases like chronic inflammation-related disorders, carcinogenesis, neuro-degeneration and aging.
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Affiliation(s)
- Vyom Sharma
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Leonard B Collins
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Ting-Huei Chen
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie Herr
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Wei Sun
- Department of Genetics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James A Swenberg
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
| | - Jun Nakamura
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, Chapel Hill, NC 27599, USA
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Parsons BL, McKim KL, Myers MB. Variation in organ-specific PIK3CA and KRAS mutant levels in normal human tissues correlates with mutation prevalence in corresponding carcinomas. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:466-476. [PMID: 28755461 PMCID: PMC5601221 DOI: 10.1002/em.22110] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 05/27/2023]
Abstract
Large-scale sequencing efforts have described the mutational complexity of individual cancers and identified mutations prevalent in different cancers. As a complementary approach, allele-specific competitive blocker PCR (ACB-PCR) is being used to quantify levels of hotspot cancer driver mutations (CDMs) with high sensitivity, to elucidate the tissue-specific properties of CDMs, their occurrence as tumor cell subpopulations, and their occurrence in normal tissues. Here we report measurements of PIK3CA H1047R mutant fraction (MF) in normal colonic mucosa, normal lung, colonic adenomas, colonic adenocarcinomas, and lung adenocarcinomas. We report PIK3CA E545K MF measurements in those tissues, as well as in normal breast, normal thyroid, mammary ductal carcinomas, and papillary thyroid carcinomas. We report KRAS G12D and G12V MF measurements in normal colon. These MF measurements were integrated with previously published ACB-PCR data on KRAS G12D, KRAS G12V, and PIK3CA H1047R. Analysis of these data revealed a correlation between the degree of interindividual variability in these mutations (as log10 MF standard deviation) in normal tissues and the frequencies with which the mutations are detected in carcinomas of the corresponding organs in the COSMIC database. This novel observation has important implications. It suggests that interindividual variability in mutation levels of normal tissues may be used as a metric to identify mutations with critical early roles in tissue-specific carcinogenesis. Additionally, it raises the possibility that personalized cancer therapeutics, developed to target specifically activated oncogenic products, might be repurposed as prophylactic therapies to reduce the accumulation of cells carrying CDMs and, thereby, reduce future cancer risk. Environ. Mol. Mutagen. 58:466-476, 2017. © 2017 This article is a U.S. Government work and is in the public domain in the USA. Environmental and Molecular Mutagenesis published by Wiley Periodicals, Inc. on behalf of Environmental Mutagen Society.
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Affiliation(s)
- Barbara L. Parsons
- Division of Genetic and Molecular ToxicologyU.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansas
| | - Karen L. McKim
- Division of Genetic and Molecular ToxicologyU.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansas
| | - Meagan B. Myers
- Division of Genetic and Molecular ToxicologyU.S. Food and Drug Administration, National Center for Toxicological ResearchJeffersonArkansas
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Olivieri F, Capri M, Bonafè M, Morsiani C, Jung HJ, Spazzafumo L, Viña J, Suh Y. Circulating miRNAs and miRNA shuttles as biomarkers: Perspective trajectories of healthy and unhealthy aging. Mech Ageing Dev 2017; 165:162-170. [PMID: 27986629 PMCID: PMC5481482 DOI: 10.1016/j.mad.2016.12.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/06/2016] [Accepted: 12/12/2016] [Indexed: 12/22/2022]
Abstract
Human aging is a lifelong process characterized by a continuous trade-off between pro-and anti-inflammatory responses, where the best-adapted and/or remodeled genetic/epigenetic profile may develop a longevity phenotype. Centenarians and their offspring represent such a phenotype and their comparison to patients with age-related diseases (ARDs) is expected to maximize the chance to unravel the genetic makeup that better associates with healthy aging trajectories. Seemingly, such comparison is expected to allow the discovery of new biomarkers of longevity together with risk factor for the most common ARDs. MicroRNAs (miRNAs) and their shuttles (extracellular vesicles in particular) are currently conceived as those endowed with the strongest ability to provide information about the trajectories of healthy and unhealthy aging. We review the available data on miRNAs in aging and underpin the evidence suggesting that circulating miRNAs (and cognate shuttles), especially those involved in the regulation of inflammation (inflamma-miRs) may constitute biomarkers capable of reliably depicting healthy and unhealthy aging trajectories.
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Affiliation(s)
- Fabiola Olivieri
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/A, Ancona, Italy; Center of Clinical Pathology and Innovative Therapy, Italian National Research Center on Aging, INRCA-IRCCS, Ancona, Italy
| | - Miriam Capri
- DIMES- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Via S. Giacomo, 12, Bologna, Italy; CIG, Interdepartmental Center "L. Galvani", Alma Mater Studiorum, Pzza Porta S. Donato, 1, Bologna, Italy.
| | - Massimiliano Bonafè
- DIMES- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Via S. Giacomo, 12, Bologna, Italy
| | - Cristina Morsiani
- DIMES- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, Via S. Giacomo, 12, Bologna, Italy; CIG, Interdepartmental Center "L. Galvani", Alma Mater Studiorum, Pzza Porta S. Donato, 1, Bologna, Italy
| | - Hwa Jin Jung
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Liana Spazzafumo
- Center of Clinical Pathology and Innovative Therapy, Italian National Research Center on Aging, INRCA-IRCCS, Ancona, Italy
| | - Jose Viña
- Department of Physiology, Faculty of Medicine, University of Valencia. INCLIVA Avda, Blasco Ibañez 15, 46010 Valencia, Spain
| | - Yousin Suh
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
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Andra SS, Austin C, Patel D, Dolios G, Awawda M, Arora M. Trends in the application of high-resolution mass spectrometry for human biomonitoring: An analytical primer to studying the environmental chemical space of the human exposome. ENVIRONMENT INTERNATIONAL 2017; 100:32-61. [PMID: 28062070 PMCID: PMC5322482 DOI: 10.1016/j.envint.2016.11.026] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 11/23/2016] [Accepted: 11/27/2016] [Indexed: 05/05/2023]
Abstract
Global profiling of xenobiotics in human matrices in an untargeted mode is gaining attention for studying the environmental chemical space of the human exposome. Defined as the study of a comprehensive inclusion of environmental influences and associated biological responses, human exposome science is currently evolving out of the metabolomics science. In analogy to the latter, the development and applications of high resolution mass spectrometry (HRMS) has shown potential and promise to greatly expand our ability to capture the broad spectrum of environmental chemicals in exposome studies. HRMS can perform both untargeted and targeted analysis because of its capability of full- and/or tandem-mass spectrum acquisition at high mass accuracy with good sensitivity. The collected data from target, suspect and non-target screening can be used not only for the identification of environmental chemical contaminants in human matrices prospectively but also retrospectively. This review covers recent trends and advances in this field. We focus on advances and applications of HRMS in human biomonitoring studies, and data acquisition and mining. The acquired insights provide stepping stones to improve understanding of the human exposome by applying HRMS, and the challenges and prospects for future research.
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Affiliation(s)
- Syam S Andra
- Exposure Biology, Senator Frank R. Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Christine Austin
- Exposure Biology, Senator Frank R. Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dhavalkumar Patel
- Exposure Biology, Senator Frank R. Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georgia Dolios
- Exposure Biology, Senator Frank R. Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mahmoud Awawda
- Exposure Biology, Senator Frank R. Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Manish Arora
- Exposure Biology, Senator Frank R. Lautenberg Environmental Health Sciences Laboratory, Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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