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Havlickova L, He Z, Berger M, Wang L, Sandmann G, Chew YP, Yoshikawa GV, Lu G, Hu Q, Banga SS, Beaudoin F, Bancroft I. Genomics of predictive radiation mutagenesis in oilseed rape: modifying seed oil composition. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:738-750. [PMID: 37921406 PMCID: PMC10893948 DOI: 10.1111/pbi.14220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Rapeseed is a crop of global importance but there is a need to broaden the genetic diversity available to address breeding objectives. Radiation mutagenesis, supported by genomics, has the potential to supersede genome editing for both gene knockout and copy number increase, but detailed knowledge of the molecular outcomes of radiation treatment is lacking. To address this, we produced a genome re-sequenced panel of 1133 M2 generation rapeseed plants and analysed large-scale deletions, single nucleotide variants and small insertion-deletion variants affecting gene open reading frames. We show that high radiation doses (2000 Gy) are tolerated, gamma radiation and fast neutron radiation have similar impacts and that segments deleted from the genomes of some plants are inherited as additional copies by their siblings, enabling gene dosage decrease. Of relevance for species with larger genomes, we showed that these large-scale impacts can also be detected using transcriptome re-sequencing. To test the utility of the approach for predictive alteration of oil fatty acid composition, we produced lines with both decreased and increased copy numbers of Bna.FAE1 and confirmed the anticipated impacts on erucic acid content. We detected and tested a 21-base deletion expected to abolish function of Bna.FAD2.A5, for which we confirmed the predicted reduction in seed oil polyunsaturated fatty acid content. Our improved understanding of the molecular effects of radiation mutagenesis will underpin genomics-led approaches to more efficient introduction of novel genetic variation into the breeding of this crop and provides an exemplar for the predictive improvement of other crops.
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Affiliation(s)
| | - Zhesi He
- Department of BiologyUniversity of YorkYorkUK
| | | | - Lihong Wang
- Department of BiologyUniversity of YorkYorkUK
| | | | | | - Guilherme V. Yoshikawa
- Department of BiologyUniversity of YorkYorkUK
- Present address:
School of Agriculture, Food and Wine, Waite Research InstituteUniversity of AdelaideGlen OsmondSAAustralia
| | - Guangyuan Lu
- Department of Rapeseed Genetics and Breeding, Oil Crops Research InstituteCAASWuhanChina
- College of Biology and Food EngineeringGuangdong University of Petrochemical TechnologyMaomingChina
| | - Qiong Hu
- Department of Rapeseed Genetics and Breeding, Oil Crops Research InstituteCAASWuhanChina
| | - Surinder S. Banga
- Department of Plant Breeding and GeneticsPunjab Agricultural UniversityLudhianaIndia
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2
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Benedetti F, Silvestri G, Saadat S, Denaro F, Latinovic OS, Davis H, Williams S, Bryant J, Ippodrino R, Rathinam CV, Gallo RC, Zella D. Mycoplasma DnaK increases DNA copy number variants in vivo. Proc Natl Acad Sci U S A 2023; 120:e2219897120. [PMID: 37459550 PMCID: PMC10372619 DOI: 10.1073/pnas.2219897120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/14/2023] [Indexed: 07/20/2023] Open
Abstract
The human microbiota affects critical cellular functions, although the responsible mechanism(s) is still poorly understood. In this regard, we previously showed that Mycoplasma fermentans DnaK, an HSP70 chaperone protein, hampers the activity of important cellular proteins responsible for DNA integrity. Here, we describe a novel DnaK knock-in mouse model generated in our laboratory to study the effect of M. fermentans DnaK expression in vivo. By using an array-based comparative genomic hybridization assay, we demonstrate that exposure to DnaK was associated with a higher number of DNA copy number variants (CNVs) indicative of unbalanced chromosomal alterations, together with reduced fertility and a high rate of fetal abnormalities. Consistent with their implication in genetic disorders, one of these CNVs caused a homozygous Grid2 deletion, resulting in an aberrant ataxic phenotype that recapitulates the extensive biallelic deletion in the Grid2 gene classified in humans as autosomal recessive spinocerebellar ataxia 18. Our data highlight a connection between components of the human urogenital tract microbiota, namely Mycoplasmas, and genetic abnormalities in the form of DNA CNVs, with obvious relevant medical, diagnostic, and therapeutic implications.
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Affiliation(s)
- Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD21201
| | - Giovannino Silvestri
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Saman Saadat
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Frank Denaro
- Department of Biology, Morgan State University, Baltimore, MD21251
| | - Olga S. Latinovic
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD21201
| | - Harry Davis
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Sumiko Williams
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | - Joseph Bryant
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
| | | | - Chozha V. Rathinam
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Robert C. Gallo
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Medicine, School of Medicine, University of Maryland School of Medicine, Baltimore, MD21201
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, MD21201
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD21201
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3
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Shakyawar SK, Mishra NK, Vellichirammal NN, Cary L, Helikar T, Powers R, Oberley-Deegan RE, Berkowitz DB, Bayles KW, Singh VK, Guda C. A Review of Radiation-Induced Alterations of Multi-Omic Profiles, Radiation Injury Biomarkers, and Countermeasures. Radiat Res 2023; 199:89-111. [PMID: 36368026 PMCID: PMC10279411 DOI: 10.1667/rade-21-00187.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/24/2022] [Indexed: 11/13/2022]
Abstract
Increasing utilization of nuclear power enhances the risks associated with industrial accidents, occupational hazards, and the threat of nuclear terrorism. Exposure to ionizing radiation interferes with genomic stability and gene expression resulting in the disruption of normal metabolic processes in cells and organs by inducing complex biological responses. Exposure to high-dose radiation causes acute radiation syndrome, which leads to hematopoietic, gastrointestinal, cerebrovascular, and many other organ-specific injuries. Altered genomic variations, gene expression, metabolite concentrations, and microbiota profiles in blood plasma or tissue samples reflect the whole-body radiation injuries. Hence, multi-omic profiles obtained from high-resolution omics platforms offer a holistic approach for identifying reliable biomarkers to predict the radiation injury of organs and tissues resulting from radiation exposures. In this review, we performed a literature search to systematically catalog the radiation-induced alterations from multi-omic studies and radiation countermeasures. We covered radiation-induced changes in the genomic, transcriptomic, proteomic, metabolomic, lipidomic, and microbiome profiles. Furthermore, we have covered promising multi-omic biomarkers, FDA-approved countermeasure drugs, and other radiation countermeasures that include radioprotectors and radiomitigators. This review presents an overview of radiation-induced alterations of multi-omics profiles and biomarkers, and associated radiation countermeasures.
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Affiliation(s)
- Sushil K Shakyawar
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nitish K Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Neetha N Vellichirammal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Lynnette Cary
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln NE 65888, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 65888, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln NE 68588, USA
| | - Rebecca E Oberley-Deegan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln NE 65888, USA
| | - Kenneth W Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vijay K Singh
- Division of Radioprotectants, Department of Pharmacology and Molecular Therapeutics, F. Edward Hébert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Center for Biomedical Informatics Research and Innovation, University of Nebraska Medical Center, Omaha, NE 68198, USA
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4
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Li K, Gong J, Zheng Q, Yang L, Mei X, Chen J, Liao G, Liang Y. Preliminary study on the molecular features of mutation in multiple primary oral cancer by whole exome sequencing. Front Oncol 2022; 12:971546. [PMID: 36338765 PMCID: PMC9632273 DOI: 10.3389/fonc.2022.971546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/16/2022] [Indexed: 11/26/2022] Open
Abstract
Multiple primary cancers (MPCs) refer to cancers that occur simultaneously or metachronously in the same individual. The incidence of MPC has increased recently, as the survival time of malignant tumor patients has been greatly prolonged. It is difficult to differentiate MPC from primary cancers (PCs) in the same anatomical region from the clinical manifestation alone. However, their biological behaviors appear to be distinct. In this study, we show that the prognosis of multiple primary oral cancers (MP-OCs) is worse than primary oral cancers (P-OCs). To better understand the molecular mechanisms of MP-OC, we used whole exome sequencing (WES) to analyze samples from 9 patients with MP-OC and 21 patients with P-OC. We found more somatic mutations in MP-OC than in P-OC. MP-OC had more complicated mutation signatures, which were associated with age-related and Apolipoprotein B mRNA Editing Catalytic Polypeptide-like (APOBEC) activity-related signatures. Tumor mutational burden (TMB) and mutant-allele tumor heterogeneity (MATH) of MP-OC trended higher compared to P-OC. KEGG and GO analysis showed the differential pathways of MP-OC versus P-OC. In addition, MP-OC took amplification, not loss, as the main pattern of copy number variation (CNV), while P-OC took both. Lastly, we did not find significantly different mutant germline genes, but MSH-6 mutation may be a potential MP-OC driver. In short, our preliminary results show that MP-OC and P-OC have different molecular characteristics.
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Affiliation(s)
- Kan Li
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jianbin Gong
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Qiuhan Zheng
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Le Yang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Xueying Mei
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jianghai Chen
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Guiqing Liao
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Yujie Liang
- Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, China
- Guanghua School of Stomatology, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yujie Liang,
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5
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Park SH, Bennett-Baker P, Ahmed S, Arlt MF, Ljungman M, Glover TW, Wilson TE. Locus-specific transcription silencing at the FHIT gene suppresses replication stress-induced copy number variant formation and associated replication delay. Nucleic Acids Res 2021; 49:7507-7524. [PMID: 34181717 PMCID: PMC8287918 DOI: 10.1093/nar/gkab559] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 12/11/2022] Open
Abstract
Impaired replication progression leads to de novo copy number variant (CNV) formation at common fragile sites (CFSs). We previously showed that these hotspots for genome instability reside in late-replicating domains associated with large transcribed genes and provided indirect evidence that transcription is a factor in their instability. Here, we compared aphidicolin (APH)-induced CNV and CFS frequency between wild-type and isogenic cells in which FHIT gene transcription was ablated by promoter deletion. Two promoter-deletion cell lines showed reduced or absent CNV formation and CFS expression at FHIT despite continued instability at the NLGN1 control locus. APH treatment led to critical replication delays that remained unresolved in G2/M in the body of many, but not all, large transcribed genes, an effect that was reversed at FHIT by the promoter deletion. Altering RNase H1 expression did not change CNV induction frequency and DRIP-seq showed a paucity of R-loop formation in the central regions of large genes, suggesting that R-loops are not the primary mediator of the transcription effect. These results demonstrate that large gene transcription is a determining factor in replication stress-induced genomic instability and support models that CNV hotspots mainly result from the transcription-dependent passage of unreplicated DNA into mitosis.
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Affiliation(s)
- So Hae Park
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Samreen Ahmed
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas W Glover
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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6
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Copy number variation: Characteristics, evolutionary and pathological aspects. Biomed J 2021; 44:548-559. [PMID: 34649833 PMCID: PMC8640565 DOI: 10.1016/j.bj.2021.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Copy number variants (CNVs) were the subject of extensive research in the past years. They are common features of the human genome that play an important role in evolution, contribute to population diversity, development of certain diseases, and influence host–microbiome interactions. CNVs have found application in the molecular diagnosis of many diseases and in non-invasive prenatal care, but their full potential is only emerging. CNVs are expected to have a tremendous impact on screening, diagnosis, prognosis, and monitoring of several disorders, including cancer and cardiovascular disease. Here, we comprehensively review basic definitions of the term CNV, outline mechanisms and factors involved in CNV formation, and discuss their evolutionary and pathological aspects. We suggest a need for better defined distinguishing criteria and boundaries between known types of CNVs.
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7
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Basile A, De Pascale F, Bianca F, Rossi A, Frizzarin M, De Bernardini N, Bosaro M, Baldisseri A, Antoniali P, Lopreiato R, Treu L, Campanaro S. Large-scale sequencing and comparative analysis of oenological Saccharomyces cerevisiae strains supported by nanopore refinement of key genomes. Food Microbiol 2021; 97:103753. [PMID: 33653526 DOI: 10.1016/j.fm.2021.103753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/09/2020] [Accepted: 01/27/2021] [Indexed: 12/30/2022]
Abstract
Saccharomyces cerevisiae has long been part of human activities related to the production of food and wine. The industrial demand for fermented beverages with well-defined and stable characteristics boosted the isolation and selection of strains conferring a distinctive aroma profile to the final product. To uncover variants characterizing oenological strains, the sequencing of 65 new S. cerevisiae isolates, and the comparison with other 503 publicly available genomes were performed. A hybrid approach based on short Illumina and long Oxford Nanopore reads allowed the in-depth investigation of eleven genomes and the identification of putative laterally transferred regions and structural variants. A comparative analysis between clusters of strains belonging to different datasets allowed the identification of novel relevant genetic features including single nucleotide polymorphisms, insertions and structural variants. Detection of oenological single nucleotide variants shed light on the existence of different levels of modulation for the mevalonate pathway relevant for the biosynthesis of aromatic compounds.
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Affiliation(s)
- Arianna Basile
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Fabio De Pascale
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Federico Bianca
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Alessandro Rossi
- Department of Biology, University of Padua, 35131, Padova, Italy
| | - Martina Frizzarin
- Department of Biomedical Sciences, University of Padua, 35131, Padova, Italy; Italiana Biotecnologie, Via Vigazzolo 112, 36054, Montebello Vicentino, Italy
| | | | - Matteo Bosaro
- Italiana Biotecnologie, Via Vigazzolo 112, 36054, Montebello Vicentino, Italy
| | - Anna Baldisseri
- Department of Biomedical Sciences, University of Padua, 35131, Padova, Italy
| | - Paolo Antoniali
- Italiana Biotecnologie, Via Vigazzolo 112, 36054, Montebello Vicentino, Italy
| | - Raffaele Lopreiato
- Department of Biomedical Sciences, University of Padua, 35131, Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padua, 35131, Padova, Italy.
| | - Stefano Campanaro
- Department of Biology, University of Padua, 35131, Padova, Italy; CRIBI Biotechnology Center, University of Padua, 35121, Padova, Italy
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8
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Stainforth R, Schuemann J, McNamara AL, Wilkins RC, Chauhan V. Challenges in the quantification approach to a radiation relevant adverse outcome pathway for lung cancer. Int J Radiat Biol 2020; 97:85-101. [PMID: 32909875 DOI: 10.1080/09553002.2020.1820096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE Adverse outcome pathways (AOPs) provide a modular framework for describing sequences of biological key events (KEs) and key event relationships (KERs) across levels of biological organization. Empirical evidence across KERs can support construction of quantified AOPs (qAOPs). Using an example AOP of energy deposition from ionizing radiation onto DNA leading to lung cancer incidence, we investigate the feasibility of quantifying data from KERs supported by all types of stressors. The merits and challenges of this process in the context of AOP construction are discussed. MATERIALS AND METHODS Empirical evidence across studies of dose-response from four KERs of the AOP were compiled independently for quantification. Three upstream KERs comprised of evidence from various radiation types in line with AOP guidelines. For these three KERs, a focused analysis of data from alpha-particle studies was undertaken to better characterize the process to the adverse outcome (AO) for a radon gas stressor. Numerical information was extracted from tables and graphs to plot and tabulate the response of KEs. To complement areas of the AOP quantification process, Monte Carlo (MC) simulations in TOPAS-nBio were performed to model exposure conditions relevant to the AO for an example bronchial compartment of the lung with secretory cell nuclei targets. RESULTS Quantification of AOP KERs highlighted the relevance of radiation types under the stressor-agnostic intent of AOP design, motivating a focus on specific types. For a given type, significant differences of KE response indicate meaningful data to derive linkages from the MIE to the AO is lacking and that better response-response focused studies are required. The MC study estimates the linear energy transfer (LET) of alpha-particles emitted by radon-222 and its progeny in the secretory cell nuclei of the example lung compartment to range from 94 - 5 + 5 to 192 - 18 + 15 keV/µm. CONCLUSION Quantifying AOP components provides a means to assemble empirical evidence across different studies. This highlights challenges in the context of studies examining similar endpoints using different radiation types. Data linking KERs to a MIE of 'deposition of energy' is shown to be non-compatible with the stressor-agnostic principles of AOP design. Limiting data to that describing response-response relationships between adjacent KERs may better delineate studies relevant to the damage that drives a pathway to the next KE and still support an 'all hazards' approach. Such data remains limited and future investigations in the radiation field may consider this approach when designing experiments and reporting their results and outcomes.
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Affiliation(s)
| | - Jan Schuemann
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Aimee L McNamara
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Ruth C Wilkins
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Canada
| | - Vinita Chauhan
- Consumer and Clinical Radiation Protection Bureau, Health Canada, Ottawa, Canada
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9
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Alkhalil A, Clifford JL, Ball R, Day A, Chan R, Carney BC, Miller SA, Campbell R, Kumar R, Gautam A, Hammamieh R, Moffatt LT, Shupp JW. Blood RNA Integrity is a Direct and Simple Reporter of Radiation Exposure and Prognosis: A Pilot Study. Radiat Res 2020; 193:543-551. [PMID: 32282289 DOI: 10.1667/rr15527.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/09/2020] [Indexed: 11/03/2022]
Abstract
In the event of a mass casualty radiation scenario, rapid assessment of patients' health and triage is required for optimal resource utilization. Identifying the level and extent of exposure as well as prioritization of care is extremely challenging under such disaster conditions. Blood-based biomarkers, such as RNA integrity numbers (RIN), could help healthcare personnel quickly and efficiently determine the extent and effect of multiple injuries on patients' health. Evaluation of the effect of different radiation doses, alone or in combination with burn injury, on total RNA integrity over multiple time points was performed. Total RNA integrity was tallied in blood samples for potential application as a marker of radiation exposure and survival. Groups of aged mice (3-6 mice/group, 13-18 months old) received 0.5, 1, 5, 10 or 20 Gy ionizing radiation. Two additional mouse groups received low-dose irradiation (0.5 or 1 Gy) with a 15% total body surface area (TBSA) burn injury. Animals were euthanized at 2 or 12 h and at day 1, 2, 3, 7 or 14 postirradiation, or when injury-mediated mortality occurred. Total RNA was isolated from blood. The quality of RNA was evaluated and RNA RIN were obtained. Analysis of RIN indicated that blood showed the clearest radiation effect. There was a time- and radiation-dose-dependent reduction in RIN that was first detectable at 12 h postirradiation for all doses in animals receiving irradiation alone. This effect was reversible in lower-dose groups (i.e., 0.5, 1 and 5 Gy) that survived to the end of the study (14 days). In contrast, the effect persisted for 10 and 20 Gy groups, which showed suppression of RIN values <4.5 with high mortalities. Radiation doses of 20 Gy were lethal and required euthanasia by day 6. A low RIN (<2.5) at any time point was associated with 100% mortality. Combined radiation-burn injury produced significantly increased mortality such that no dually-injured animals survived beyond day 3, and no radiation dose >1 Gy resulted in survival past day 1. More modest suppression of RIN was observed in the surviving dually challenged mice, and no statistically significant changes were identified in RIN values of burn-only mice at any time point. In this study of an animal model, a proof of concept is presented for a simple and accurate method of assessing radiation dose exposure in blood which potentially predicts lethality. RIN assessment of blood-derived RNA could form the basis for a clinical decision-support tool to guide healthcare providers under the strenuous conditions of a radiation-based mass casualty event.
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Affiliation(s)
- Abdulnaser Alkhalil
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, DC 20010
| | - John L Clifford
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, Maryland 21702
| | - Robert Ball
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, DC 20010.,The Burn Center, MedStar Washington Hospital Center, Washington, DC 20010
| | - Anna Day
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, DC 20010
| | - Rosanna Chan
- Department of Radiology, MedStar Washington Hospital Center, Washington, DC 20010
| | - Bonnie C Carney
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, DC 20010.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University School of Medicine, Washington, DC 20010
| | - Stacy Ann Miller
- Integrative Systems Biology, The Oak Ridge Institute for Science and Education, Fort Detrick, Maryland 21702-5000
| | - Ross Campbell
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, Maryland 21702.,Advanced Biomedical Computational Science, Frederick National Lab for Cancer Research/Advanced Biomedical Computational, Frederick, Maryland, 21702
| | - Raina Kumar
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, Maryland 21702.,Advanced Biomedical Computational Science, Frederick National Lab for Cancer Research/Advanced Biomedical Computational, Frederick, Maryland, 21702
| | - Aarti Gautam
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, Maryland 21702
| | - Rasha Hammamieh
- Integrative Systems Biology Program, U.S. Army Center for Environmental Health Research, Fort Detrick, Maryland 21702
| | - Lauren T Moffatt
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, DC 20010.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University School of Medicine, Washington, DC 20010.,Department of Surgery, Georgetown University School of Medicine, Washington, DC 20010
| | - Jeffrey W Shupp
- Firefighters' Burn and Surgical Research Laboratory, MedStar Health Research Institute, Washington, DC 20010.,The Burn Center, MedStar Washington Hospital Center, Washington, DC 20010.,Department of Biochemistry and Molecular and Cellular Biology, Georgetown University School of Medicine, Washington, DC 20010.,Department of Surgery, Georgetown University School of Medicine, Washington, DC 20010
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10
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Khalyuzova MV, Litviakov NV, Takhauov RM, Isubakova DS, Usova TV, Bronikovskaya EV, Takhauova LR, Karpov AB. Delayed Changes in the Frequency of Unstable Chromosomal Aberrations and the CNA-Genetic Landscape of Blood Leukocytes in People Exposed to Long-Term Occupational Irradiation. BIOL BULL+ 2020. [DOI: 10.1134/s1062359019110049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Chauhan V, Sherman S, Said Z, Yauk CL, Stainforth R. A case example of a radiation-relevant adverse outcome pathway to lung cancer. Int J Radiat Biol 2020; 97:68-84. [PMID: 31846388 DOI: 10.1080/09553002.2019.1704913] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
BACKGROUND Adverse outcome pathways (AOPs) describe how a measurable sequence of key events, beginning from a molecular initiator, can lead to an adverse outcome of relevance to risk assessment. An AOP is modular by design, comprised of four main components: (1) a Molecular Initiating Event (MIE), (2) Key Events (KEs), (3) Key Event Relationships (KERs) and (4) an Adverse Outcome (AO). PURPOSE Here, we illustrate the utility of the AOP concept through a case example in the field of ionizing radiation, using the Organisation for Economic Cooperation and Development (OECD) Users' Handbook. This AOP defines a classic targeted response to a radiation insult with an AO of lung cancer that is relevant to radon gas exposure. MATERIALS AND METHODS To build this AOP, over 500 papers were reviewed and categorized based on the modified Bradford-Hill Criteria. Data-rich key events from the MIE, to several measurable KEs and KERs related to DNA damage response/repair were identified. RESULTS The components for this AOP begin with direct deposition of energy as the MIE. Energy deposited into a cell can lead to multiple ionization events to targets such as DNA. This energy can damage DNA leading to double-strand breaks (DSBs) (KE1), this will initiate repair activation (KE2) in higher eukaryotes through mechanisms that are quick and efficient, but error-prone. If DSBs occur in regions of the DNA transcribing critical genes, then mutations (KE3) generated through faulty repair may alter the function of these genes or may cause chromosomal aberrations (KE4). This can impact cellular pathways such as cell growth, cell cycling and then cellular proliferation (KE5). This will form hyperplasia in lung cells, leading eventually to lung cancer (AO) induction and metastasis. The weight of evidence for the KERs was built using biological plausibility, incidence concordance, dose-response, time-response and essentiality studies. The uncertainties and inconsistencies surrounding this AOP are centered on dose-response relationships associated with dose, dose-rates and radiation quality. CONCLUSION Overall, the AOP framework provided an effective means to organize the scientific knowledge surrounding the KERs and identify those with strong dose-response relationships and those with inconsistencies. This case study is an example of how the AOP methodology can be applied to sources of radiation to help support areas of risk assessment.
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Affiliation(s)
- Vinita Chauhan
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Samantha Sherman
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Zakaria Said
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Carole L Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
| | - Robert Stainforth
- Consumer and Clinical Radiation Protection Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Canada
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12
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Hovhannisyan G, Harutyunyan T, Aroutiounian R, Liehr T. DNA Copy Number Variations as Markers of Mutagenic Impact. Int J Mol Sci 2019; 20:ijms20194723. [PMID: 31554154 PMCID: PMC6801639 DOI: 10.3390/ijms20194723] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 12/26/2022] Open
Abstract
DNA copy number variation (CNV) occurs due to deletion or duplication of DNA segments resulting in a different number of copies of a specific DNA-stretch on homologous chromosomes. Implications of CNVs in evolution and development of different diseases have been demonstrated although contribution of environmental factors, such as mutagens, in the origin of CNVs, is poorly understood. In this review, we summarize current knowledge about mutagen-induced CNVs in human, animal and plant cells. Differences in CNV frequencies induced by radiation and chemical mutagens, distribution of CNVs in the genome, as well as adaptive effects in plants, are discussed. Currently available information concerning impact of mutagens in induction of CNVs in germ cells is presented. Moreover, the potential of CNVs as a new endpoint in mutagenicity test-systems is discussed.
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Affiliation(s)
- Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, Alex Manoogian 1, 0025 Yerevan, Armenia.
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Am Klinikum 1, D-07747 Jena, Germany.
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13
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Beal MA, Meier MJ, Williams A, Rowan-Carroll A, Gagné R, Lindsay SJ, Fitzgerald T, Hurles ME, Marchetti F, Yauk CL. Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring. Commun Biol 2019; 2:228. [PMID: 31240266 PMCID: PMC6586636 DOI: 10.1038/s42003-019-0476-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/23/2019] [Indexed: 01/14/2023] Open
Abstract
Understanding the effects of environmental exposures on germline mutation rates has been a decades-long pursuit in genetics. We used next-generation sequencing and comparative genomic hybridization arrays to investigate genome-wide mutations in the offspring of male mice exposed to benzo(a)pyrene (BaP), a common environmental pollutant. We demonstrate that offspring developing from sperm exposed during the mitotic or post-mitotic phases of spermatogenesis have significantly more de novo single nucleotide variants (1.8-fold; P < 0.01) than controls. Both phases of spermatogenesis are susceptible to the induction of heritable mutations, although mutations arising from post-fertilization events are more common after post-mitotic exposure. In addition, the mutation spectra in sperm and offspring of BaP-exposed males are consistent. Finally, we report a significant increase in transmitted copy number duplications (P = 0.001) in BaP-exposed sires. Our study demonstrates that germ cell mutagen exposures induce genome-wide mutations in the offspring that may be associated with adverse health outcomes.
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Affiliation(s)
- Marc A. Beal
- Carleton University, Ottawa, Ontario K1S 5B6 Canada
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Matthew J. Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Rémi Gagné
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Sarah J. Lindsay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Tomas Fitzgerald
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
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14
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Harutyunyan T, Hovhannisyan G, Sargsyan A, Grigoryan B, Al-Rikabi AH, Weise A, Liehr T, Aroutiounian R. Analysis of copy number variations induced by ultrashort electron beam radiation in human leukocytes in vitro. Mol Cytogenet 2019; 12:18. [PMID: 31131024 PMCID: PMC6524226 DOI: 10.1186/s13039-019-0433-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 05/01/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Environmental risk factors have been shown to alter DNA copy number variations (CNVs). Recently, CNVs have been described to arise after low-dose ionizing radiation in vitro and in vivo. Development of cost- and size-effective laser-driven electron accelerators (LDEAs), capable to deliver high energy beams in pico- or femtosecond durations requires examination of their biological effects. Here we studied in vitro impact of LDEAs radiation on known CNV hotspots in human peripheral blood lymphocytes on single cell level. RESULTS Here CNVs in chromosomal regions 1p31.1, 7q11.22, 9q21.3, 10q21.1 and 16q23.1 earlier reported to be sensitive to ionizing radiation were analyzed using molecular cytogenetics. Irradiation of cells with 0.5, 1.5 and 3.0 Gy significantly increased signal intensities in all analyzed chromosomal regions compared to controls. The latter is suggested to be due to radiation-induced duplication or amplification of CNV stretches. As significantly lower gains in mean fluorescence intensities were observed only for chromosomal locus 1p31.1 (after irradiation with 3.0 Gy variant sensitivites of different loci to LDEA is suggested. Negative correlation was found between fluorescence intensities and chromosome size (r = - 0.783, p < 0.001) in cells exposed to 3.0 Gy irradiation and between fluorescence intensities and gene density (r = - 0.475, p < 0.05) in cells exposed to 0.5 Gy irradiation. CONCLUSIONS In this study we demonstrated that irradiation with laser-driven electron bunches can induce molecular-cytogenetically visible CNVs in human blood leukocytes in vitro. These CNVs occur most likely due to duplications or amplification and tend to inversely correlate with chromosome size and gene density. CNVs can last in cell population as stable chromosomal changes for several days after radiation exposure; therefore this endpoint can be used for characterization of genetic effects of accelerated electrons. These findings should be complemented with other studies and implementation of more sophisticated approaches for CNVs analysis.
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Affiliation(s)
- Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia
| | - Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia
| | - Anzhela Sargsyan
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia
| | - Bagrat Grigoryan
- CANDLE Synchrotron Research Institute, Acharyan 31, 0040 Yerevan, Armenia
| | - Ahmed H. Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07740 Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07740 Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, D-07740 Jena, Germany
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia
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15
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Lauer S, Gresham D. An evolving view of copy number variants. Curr Genet 2019; 65:1287-1295. [PMID: 31076843 DOI: 10.1007/s00294-019-00980-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 01/08/2023]
Abstract
Copy number variants (CNVs) are regions of the genome that vary in integer copy number. CNVs, which comprise both amplifications and deletions of DNA sequence, have been identified across all domains of life, from bacteria and archaea to plants and animals. CNVs are an important source of genetic diversity, and can drive rapid adaptive evolution and progression of heritable and somatic human diseases, such as cancer. However, despite their evolutionary importance and clinical relevance, CNVs remain understudied compared to single-nucleotide variants (SNVs). This is a consequence of the inherent difficulties in detecting CNVs at low-to-intermediate frequencies in heterogeneous populations of cells. Here, we discuss molecular methods used to detect CNVs, the limitations associated with using these techniques, and the application of new and emerging technologies that present solutions to these challenges. The goal of this short review and perspective is to highlight aspects of CNV biology that are understudied and define avenues for further research that address specific gaps in our knowledge of these complex alleles. We describe our recently developed method for CNV detection in which a fluorescent gene functions as a single-cell CNV reporter and present key findings from our evolution experiments in Saccharomyces cerevisiae. Using a CNV reporter, we found that CNVs are generated at a high rate and undergo selection with predictable dynamics across independently evolving replicate populations. Many CNVs appear to be generated through DNA replication-based processes that are mediated by the presence of short, interrupted, inverted-repeat sequences. Our results have important implications for the role of CNVs in evolutionary processes and the molecular mechanisms that underlie CNV formation. We discuss the possible extension of our method to other applications, including tracking the dynamics of CNVs in models of human tumors.
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Affiliation(s)
- Stephanie Lauer
- Institute for Systems Genetics, New York University Langone Health, New York, NY, USA
| | - David Gresham
- Center for Genomics and System Biology, Department of Biology, New York University, New York, NY, USA.
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16
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Walen KH. Genomic Instability in Cancer II: 4N-Skewed (90°) Reductive Division via Fragile Sites to Fitness Increase for Solid and Hematological Cancer Beginnings. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/jct.2019.107045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Palumbo E, Russo A. Common fragile site instability in normal cells: Lessons and perspectives. Genes Chromosomes Cancer 2018; 58:260-269. [PMID: 30387295 DOI: 10.1002/gcc.22705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/26/2022] Open
Abstract
Mechanisms and events related to common fragile site (CFS) instability are well known in cancer cells. Here, we argue that normal cells remain an important experimental model to address questions related to CFS instability in the absence of alterations in cell cycle and DNA damage repair pathways, which are common features acquired in cancer. Furthermore, a major gap of knowledge concerns the stability of CFSs during gametogenesis. CFS instability in meiotic or postmeiotic stages of the germ cell line could generate chromosome deletions or large rearrangements. This in turn can lead to the functional loss of the several CFS-associated genes with tumor suppressor function. Our hypothesis is that such mutations can potentially result in genetic predisposition to develop cancer. Indirect evidence for CFS instability in human germ cells has been provided by genomic investigations in family pedigrees associated with genetic disease. The issue of CFS instability in the germ cell line should represent one of the future efforts, and may take advantage of the existence of sequence and functional conservation of CFSs between rodents and humans.
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Affiliation(s)
- Elisa Palumbo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
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18
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Arlt MF, Rajendran S, Holmes SN, Wang K, Bergin IL, Ahmed S, Wilson TE, Glover TW. Effects of hydroxyurea on CNV induction in the mouse germline. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:698-714. [PMID: 30218578 PMCID: PMC7275641 DOI: 10.1002/em.22233] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/19/2018] [Accepted: 07/27/2018] [Indexed: 06/08/2023]
Abstract
Copy number variants (CNVs) are important in genome variation and genetic disease, with new mutations arising frequently in the germline and somatic cells. Replication stress caused by aphidicolin and hydroxyurea (HU) is a potent inducer of de novo CNVs in cultured mammalian cells. HU is used extensively for long-term management of sickle cell disease. Here, we examined the effects of HU treatment on germline CNVs in vivo in male mice to explore whether replication stress can act as a CNV mutagen in germline mitotic divisions as in cultured cells and whether this would support a concern for increased CNV mutations in offspring of men treated with HU. Several trials of HU administration were performed by oral gavage and subcutaneous pump, with CNVs characterized in C57BL/6 x C3H/HeJ hybrid mouse offspring by microarray and mate-pair sequencing. HU had a short half-life of ~14 min and a narrow dose window over which studies could be performed while maintaining fertility. Tissue histopathology and reticulocyte micronucleus assays verified that doses had a substantial tissue and genetic toxicity. CNVs were readily detected in offspring that originated in both paternal and maternal mouse strains, as de novo and inherited events. However, HU did not increase CNV formation above baseline levels. These results reveal a high rate of CNV mutagenesis in the mouse germline but do not support the hypothesis that HU would increase CNV formation during mammalian spermatogenesis, perhaps due to highly toxic effects on sperm development or experimental variables related to HU pharmacology in mice. Environ. Mol. Mutagen. 59:698-714, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Martin F. Arlt
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sountharia Rajendran
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sandra N. Holmes
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kathleen Wang
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ingrid L. Bergin
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Samreen Ahmed
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas E. Wilson
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Thomas W. Glover
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
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19
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Flunkert J, Maierhofer A, Dittrich M, Müller T, Horvath S, Nanda I, Haaf T. Genetic and epigenetic changes in clonal descendants of irradiated human fibroblasts. Exp Cell Res 2018; 370:322-332. [PMID: 29964050 DOI: 10.1016/j.yexcr.2018.06.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/12/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
To study delayed genetic and epigenetic radiation effects, which may trigger radiation-induced carcinogenesis, we have established single-cell clones from irradiated and non-irradiated primary human fibroblasts. Stable clones were endowed with the same karyotype in all analyzed metaphases after 20 population doublings (PDs), whereas unstable clones displayed mosaics of normal and abnormal karyotypes. To account for variation in radiation sensitivity, all experiments were performed with two different fibroblast strains. After a single X-ray dose of 2 Gy more than half of the irradiated clones exhibited radiation-induced genome instability (RIGI). Irradiated clones displayed an increased rate of loss of chromosome Y (LOY) and copy number variations (CNVs), compared to controls. CNV breakpoints clustered in specific chromosome regions, in particular 3p14.2 and 7q11.21, coinciding with common fragile sites. CNVs affecting the FHIT gene in FRA3B were observed in independent unstable clones and may drive RIGI. Bisulfite pyrosequencing of control clones and the respective primary culture revealed global hypomethylation of ALU, LINE-1, and alpha-satellite repeats as well as rDNA hypermethylation during in vitro ageing. Irradiated clones showed further reduced ALU and alpha-satellite methylation and increased rDNA methylation, compared to controls. Methylation arrays identified several hundred differentially methylated genes and several enriched pathways associated with in vitro ageing. Methylation changes in 259 genes and the MAP kinase signaling pathway were associated with delayed radiation effects (after 20 PDs). Collectively, our results suggest that both genetic (LOY and CNVs) and epigenetic changes occur in the progeny of exposed cells that were not damaged directly by irradiation, likely contributing to radiation-induced carcinogenesis. We did not observe epigenetic differences between stable and unstable irradiated clones. The fact that the DNA methylation (DNAm) age of clones derived from the same primary culture varied greatly suggests that DNAm age of a single cell (represented by a clone) can be quite different from the DNAm age of a tissue. We propose that DNAm age reflects the emergent property of a large number of individual cells whose respective DNAm ages can be highly variable.
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Affiliation(s)
- Julia Flunkert
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Anna Maierhofer
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany.
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20
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Small de novo CNVs as biomarkers of parental exposure to low doses of ionizing radiation of caesium-137. Sci Rep 2018; 8:5914. [PMID: 29651024 PMCID: PMC5897394 DOI: 10.1038/s41598-018-23813-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 03/20/2018] [Indexed: 12/21/2022] Open
Abstract
The radiological accident in Goiania in 1987 caused a trail of human contamination, animal, plant and environmental by a radionuclide. Exposure to ionizing radiation results in different types of DNA lesions. The mutagenic effects of ionizing radiation on the germline are special concern because they can endures for several generations, leading to an increase in the rate of mutations in children of irradiated parents. Thus, to evaluate the biological mechanisms of ionizing radiation in somatic and germline cells, with consequent determination of the rate mutations, is extremely important for the estimation of genetic risks. Recently it was established that Chromosomal Microarray Analysis is an important tool for detecting wide spectra of gains or losses in the human genome. Here we present the results of the effect of accidental exposure to low doses of ionizing radiation on the formation of CNVs in the progeny of a human population accidentally exposed to Caesium-137 during the radiological accident in Goiânia, Brazil.
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21
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Steenwyk JL, Rokas A. Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation. Front Microbiol 2018; 9:288. [PMID: 29520259 PMCID: PMC5826948 DOI: 10.3389/fmicb.2018.00288] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 02/07/2018] [Indexed: 11/13/2022] Open
Abstract
In recent years, copy number (CN) variation has emerged as a new and significant source of genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants are defined as genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population. CN variants range in size from 50 base pairs to whole chromosomes, can influence gene activity, and are associated with a wide range of phenotypes in diverse organisms, including the budding yeast Saccharomyces cerevisiae. In this review, we introduce CN variation, discuss the genetic and molecular mechanisms implicated in its generation, how they can contribute to genetic and phenotypic diversity in fungal populations, and consider how CN variants may influence wine yeast adaptation in fermentation-related processes. In particular, we focus on reviewing recent work investigating the contribution of changes in CN of fermentation-related genes in yeast wine strains and offer notable illustrations of such changes, including the high levels of CN variation among the CUP genes, which confer resistance to copper, a metal with fungicidal properties, and the preferential deletion and duplication of the MAL1 and MAL3 loci, respectively, which are responsible for metabolizing maltose and sucrose. Based on the available data, we propose that CN variation is a substantial dimension of yeast genetic diversity that occurs largely independent of single nucleotide polymorphisms. As such, CN variation harbors considerable potential for understanding and manipulating yeast strains in the wine fermentation environment and beyond.
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Affiliation(s)
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
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22
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Abstract
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics; the Department of Pathology; and the Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics; and the Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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23
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Galloway SM. International regulatory requirements for genotoxicity testing for pharmaceuticals used in human medicine, and their impurities and metabolites. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:296-324. [PMID: 28299826 DOI: 10.1002/em.22077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/05/2017] [Indexed: 06/06/2023]
Abstract
The process of developing international (ICH) guidelines is described, and the main guidelines reviewed are the ICH S2(R1) guideline that includes the genotoxicity test battery for human pharmaceuticals, and the ICH M7 guideline for assessing and limiting potentially mutagenic impurities and degradation products in drugs. Key aspects of the guidelines are reviewed in the context of drug development, for example the incorporation of genotoxicity assessment into non-clinical toxicity studies, and ways to develop and assess weight of evidence. In both guidelines, the existence of "thresholds" or non-linear dose responses for genotoxicity plays a part in the strategies. Differences in ICH S2(R1) protocol recommendations from OECD guidelines are highlighted and rationales explained. The use of genotoxicity data during clinical development and in assessment of carcinogenic potential is also described. There are no international guidelines on assessment of potentially genotoxic metabolites, but some approaches to safety assessment are discussed for these. Environ. Mol. Mutagen. 58:296-324, 2017. © 2017 Wiley Periodicals, Inc.
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Steenwyk J, Rokas A. Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains. G3 (BETHESDA, MD.) 2017; 7:1475-1485. [PMID: 28292787 PMCID: PMC5427499 DOI: 10.1534/g3.117.040105] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/08/2017] [Indexed: 01/30/2023]
Abstract
Due to the importance of Saccharomyces cerevisiae in wine-making, the genomic variation of wine yeast strains has been extensively studied. One of the major insights stemming from these studies is that wine yeast strains harbor low levels of genetic diversity in the form of single nucleotide polymorphisms (SNPs). Genomic structural variants, such as copy number (CN) variants, are another major type of variation segregating in natural populations. To test whether genetic diversity in CN variation is also low across wine yeast strains, we examined genome-wide levels of CN variation in 132 whole-genome sequences of S. cerevisiae wine strains. We found an average of 97.8 CN variable regions (CNVRs) affecting ∼4% of the genome per strain. Using two different measures of CN diversity, we found that gene families involved in fermentation-related processes such as copper resistance (CUP), flocculation (FLO), and glucose metabolism (HXT), as well as the SNO gene family whose members are expressed before or during the diauxic shift, showed substantial CN diversity across the 132 strains examined. Importantly, these same gene families have been shown, through comparative transcriptomic and functional assays, to be associated with adaptation to the wine fermentation environment. Our results suggest that CN variation is a substantial contributor to the genomic diversity of wine yeast strains, and identify several candidate loci whose levels of CN variation may affect the adaptation and performance of wine yeast strains during fermentation.
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Affiliation(s)
- Jacob Steenwyk
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235
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Kodaira M, Asakawa JI, Nakamura N. Radiation-Induced Deletions in Mouse Spermatogonia are Usually Large (over 200 kb) and Contain Little Sequence Similarity at the Junctions. Radiat Res 2017; 187:722-731. [DOI: 10.1667/rr14660.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Mieko Kodaira
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima 732-0815, Japan
| | - Jun-ichi Asakawa
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima 732-0815, Japan
| | - Nori Nakamura
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima 732-0815, Japan
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26
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Wirbisky SE, Freeman JL. Atrazine exposure elicits copy number alterations in the zebrafish genome. Comp Biochem Physiol C Toxicol Pharmacol 2017; 194:1-8. [PMID: 28111253 PMCID: PMC5325771 DOI: 10.1016/j.cbpc.2017.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/13/2017] [Accepted: 01/17/2017] [Indexed: 12/30/2022]
Abstract
Atrazine is an agricultural herbicide used throughout the Midwestern United States that frequently contaminates potable water supplies resulting in human exposure. Using the zebrafish model system, an embryonic atrazine exposure was previously reported to decrease spawning rates with an increase in progesterone and ovarian follicular atresia in adult females. In addition, alterations in genes associated with distinct molecular pathways of the endocrine system were observed in brain and gonad tissue of the adult females and males. Current hypotheses for mechanistic changes in the developmental origins of health and disease include genetic (e.g., copy number alterations) or epigenetic (e.g., DNA methylation) mechanisms. As such, in the current study we investigated whether an atrazine exposure would generate copy number alterations (CNAs) in the zebrafish genome. A zebrafish fibroblast cell line was used to limit detection to CNAs caused by the chemical exposure. First, cells were exposed to a range of atrazine concentrations and a crystal violet assay was completed, showing confluency decreased by ~60% at 46.3μM. Cells were then exposed to 0, 0.463, 4.63, or 46.3μM atrazine and array comparative genomic hybridization completed. Results showed 34, 21, and 44 CNAs in the 0.463, 4.63, and 46.3μM treatments, respectively. Furthermore, CNAs were associated with previously reported gene expression alterations in adult male and female zebrafish. This study demonstrates that atrazine exposure can generate CNAs that are linked to gene expression alterations observed in adult zebrafish exposed to atrazine during embryogenesis providing a mechanism of the developmental origins of atrazine endocrine disruption.
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Affiliation(s)
- Sara E Wirbisky
- School of Health Sciences, Purdue University, West Lafayette, IN, 47909, United States.
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN, 47909, United States.
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Borczuk AC, Pei J, Taub RN, Levy B, Nahum O, Chen J, Chen K, Testa JR. Genome-wide analysis of abdominal and pleural malignant mesothelioma with DNA arrays reveals both common and distinct regions of copy number alteration. Cancer Biol Ther 2016; 17:328-35. [PMID: 26853494 DOI: 10.1080/15384047.2016.1145850] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Malignant mesothelioma (MM) is an aggressive tumor arising from mesothelial linings of the serosal cavities. Pleural space is the most common site, accounting for about 80% of cases, while peritoneum makes up the majority of the remaining 20%. While histologically similar, tumors from these sites are epidemiologically and clinically distinct and their attribution to asbestos exposure differs. We compared DNA array-based findings from 48 epithelioid peritoneal MMs and 41 epithelioid pleural MMs to identify similarities and differences in copy number alterations (CNAs). Losses in 3p (BAP1 gene), 9p (CDKN2A) and 22q (NF2) were seen in tumors from both tumor sites, although CDKN2A and NF2 losses were seen at a higher rate in pleural disease (p<0.01). Overall, regions of copy number gain were more common in peritoneal MM, whereas losses were more common in pleural MM, with regions of loss containing known tumor suppressor genes and regions of gain encompassing genes encoding receptor tyrosine kinase pathway members. Cases with known asbestos causation (n = 32 ) were compared with those linked to radiation exposure (n = 9 ). Deletions in 6q, 14q, 17p and 22q, and gain of 17q were seen in asbestos-associated but not radiation-related cases. As reported in post-radiation sarcoma, gains outnumbered losses in radiation-associated MM. The patterns of genomic imbalances suggest overlapping and distinct molecular pathways in MM of the pleura and peritoneum, and that differences in causation (i.e., asbestos vs. radiation) may account for some of these site-dependent differences.
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Affiliation(s)
- Alain C Borczuk
- a Department of Pathology and Medicine , Weill Cornell Medicine , New York , USA
| | - Jianming Pei
- b Cancer Biology Program and Genomics Facility, Fox Chase Cancer Center , Philadelphia , USA
| | - Robert N Taub
- c Department of Medicine , Division of Hematology and Oncology
| | - Brynn Levy
- d Department of Pathology and Cell Biology , Columbia University Medical Center , New York , USA
| | - Odelia Nahum
- d Department of Pathology and Cell Biology , Columbia University Medical Center , New York , USA
| | - Jinli Chen
- d Department of Pathology and Cell Biology , Columbia University Medical Center , New York , USA
| | - Katherine Chen
- a Department of Pathology and Medicine , Weill Cornell Medicine , New York , USA
| | - Joseph R Testa
- b Cancer Biology Program and Genomics Facility, Fox Chase Cancer Center , Philadelphia , USA
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28
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Conover HN, Argueso JL. Contrasting mechanisms of de novo copy number mutagenesis suggest the existence of different classes of environmental copy number mutagens. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:3-9. [PMID: 26247157 DOI: 10.1002/em.21967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/05/2015] [Accepted: 07/07/2015] [Indexed: 05/23/2023]
Abstract
While gene copy number variations (CNVs) are abundant in the human genome, and often are associated with disease consequences, the mutagenic pathways and environmental exposures that cause these large structural mutations are understudied relative to conventional nucleotide substitutions in DNA. The members of the environmental mutagenesis community are currently seeking to remedy this deficiency, and there is a renewed interest in the development of mutagenicity assays to identify and characterize compounds that may induce de novo CNVs in humans. To achieve this goal, it is critically important to acknowledge that CNVs exist in two very distinct classes: nonrecurrent and recurrent CNVs. The goal of this commentary is to emphasize the deep contrasts that exist between the proposed pathways that lead to these two mutation classes. Nonrecurrent de novo CNVs originate primarily in mitotic cells through replication-dependent DNA repair pathways that involve microhomologies (<10 bp), and are detected at higher frequency in children of older fathers. In contrast, recurrent de novo CNVs are most often formed in meiotic cells through homologous recombination between nonallelic large low-copy repeats (>10,000 bp), without an associated paternal age effect. Given the biological differences between the two CNV classes, it is our belief that nonrecurrent and recurrent CN mutagens will probably differ substantially in their modes of action. Therefore, each CNV class may require their own uniquely designed assays, so that we as a field may succeed in uncovering the broadest possible spectrum of environmental CN mutagens.
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Affiliation(s)
- Hailey N Conover
- Department of Environmental and Radiological Health Sciences, Cell and Molecular Biology Graduate Program, Institute for Genome Architecture and Function, Colorado State University, Fort Collins, Colorado
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Cell and Molecular Biology Graduate Program, Institute for Genome Architecture and Function, Colorado State University, Fort Collins, Colorado
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29
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Zotina T, Medvedeva M, Trofimova E, Alexandrova Y, Dementyev D, Bolsunovsky A. Chromosomal abnormalities in roots of aquatic plant Elodea canadensis as a tool for testing genotoxicity of bottom sediments. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2015; 122:384-391. [PMID: 26342689 DOI: 10.1016/j.ecoenv.2015.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 06/05/2023]
Abstract
Submersed freshwater macrophytes are considered as relevant indicators for use in bulk bottom sediment contact tests. The purpose of this study was to estimate the validity of endpoints of aquatic plant Elodea canadensis for laboratory genotoxicity testing of natural bottom sediments. The inherent level of chromosome abnormalities (on artificial sediments) in roots of E. canadensis under laboratory conditions was lower than the percentage of abnormal cells in bulk sediments from the Yenisei River. The percentage of abnormal cells in roots of E. canadensis was more sensitive to the presence of genotoxic agents in laboratory contact tests than in the natural population of the plant. The spectra of chromosomal abnormalities that occur in roots of E. canadensis under natural conditions in the Yenisei River and in laboratory contact tests on the bulk bottom sediments from the Yenisei River were similar. Hence, chromosome abnormalities in roots of E. canadensis can be used as a relevant and sensitive genotoxicity endpoint in bottom sediment-contact tests.
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Affiliation(s)
- Tatiana Zotina
- Institute of Biophysics SB RAS, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia.
| | - Marina Medvedeva
- Institute of Biophysics SB RAS, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia.
| | - Elena Trofimova
- Institute of Biophysics SB RAS, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia.
| | - Yuliyana Alexandrova
- Institute of Biophysics SB RAS, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia.
| | - Dmitry Dementyev
- Institute of Biophysics SB RAS, 50/50 Akademgorodok, Krasnoyarsk 660036, Russia.
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30
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Russo A, Pacchierotti F, Cimini D, Ganem NJ, Genescà A, Natarajan AT, Pavanello S, Valle G, Degrassi F. Genomic instability: Crossing pathways at the origin of structural and numerical chromosome changes. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:563-580. [PMID: 25784636 DOI: 10.1002/em.21945] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/02/2015] [Accepted: 02/19/2015] [Indexed: 06/04/2023]
Abstract
Genomic instability leads to a wide spectrum of genetic changes, including single nucleotide mutations, structural chromosome alterations, and numerical chromosome changes. The accepted view on how these events are generated predicts that separate cellular mechanisms and genetic events explain the occurrence of these types of genetic variation. Recently, new findings have shed light on the complexity of the mechanisms leading to structural and numerical chromosome aberrations, their intertwining pathways, and their dynamic evolution, in somatic as well as in germ cells. In this review, we present a critical analysis of these recent discoveries in this area, with the aim to contribute to a deeper knowledge of the molecular networks leading to adverse outcomes in humans following exposure to environmental factors. The review illustrates how several technological advances, including DNA sequencing methods, bioinformatics, and live-cell imaging approaches, have contributed to produce a renewed concept of the mechanisms causing genomic instability. Special attention is also given to the specific pathways causing genomic instability in mammalian germ cells. Remarkably, the same scenario emerged from some pioneering studies published in the 1980s to 1990s, when the evolution of polyploidy, the chromosomal effects of spindle poisons, the fate of micronuclei, were intuitively proposed to share mechanisms and pathways. Thus, an old working hypothesis has eventually found proper validation.
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Affiliation(s)
| | - Francesca Pacchierotti
- Laboratory of Toxicology, Unit of Radiation Biology and Human Health, ENEA CR Casaccia, Rome, Italy
| | - Daniela Cimini
- Department of Biological Sciences and Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia
| | - Neil J Ganem
- Department of Pharmacology, Division of Hematology and Oncology, Boston University School of Medicine, Boston, Massachusetts
| | - Anna Genescà
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | - Sofia Pavanello
- Department of Cardiac, Thoracic and Vascular Sciences, Unit of Occupational Medicine, University of Padova, Italy
| | - Giorgio Valle
- Department of Biology, University of Padova, Padova, Italy
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31
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Rothkamm K, Barnard S, Moquet J, Ellender M, Rana Z, Burdak-Rothkamm S. DNA damage foci: Meaning and significance. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:491-504. [PMID: 25773265 DOI: 10.1002/em.21944] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 02/13/2015] [Indexed: 06/04/2023]
Abstract
The discovery of DNA damage response proteins such as γH2AX, ATM, 53BP1, RAD51, and the MRE11/RAD50/NBS1 complex, that accumulate and/or are modified in the vicinity of a chromosomal DNA double-strand break to form microscopically visible, subnuclear foci, has revolutionized the detection of these lesions and has enabled studies of the cellular machinery that contributes to their repair. Double-strand breaks are induced directly by a number of physical and chemical agents, including ionizing radiation and radiomimetic drugs, but can also arise as secondary lesions during replication and DNA repair following exposure to a wide range of genotoxins. Here we aim to review the biological meaning and significance of DNA damage foci, looking specifically at a range of different settings in which such markers of DNA damage and repair are being studied and interpreted.
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Affiliation(s)
- Kai Rothkamm
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
- Department of Radiotherapy, Laboratory of Radiation Biology and Experimental Radiation Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen Barnard
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
| | - Jayne Moquet
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
| | - Michele Ellender
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
| | - Zohaib Rana
- Public Health England, Centre for Radiation, Chemical and Environmental Hazards, Chilton, United Kingdom
| | - Susanne Burdak-Rothkamm
- Department of Cellular Pathology, Oxford University Hospitals, Headley Way, Headington, Oxford, United Kingdom
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32
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Macheret M, Halazonetis TD. DNA replication stress as a hallmark of cancer. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2015; 10:425-48. [PMID: 25621662 DOI: 10.1146/annurev-pathol-012414-040424] [Citation(s) in RCA: 511] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human cancers share properties referred to as hallmarks, among which sustained proliferation, escape from apoptosis, and genomic instability are the most pervasive. The sustained proliferation hallmark can be explained by mutations in oncogenes and tumor suppressors that regulate cell growth, whereas the escape from apoptosis hallmark can be explained by mutations in the TP53, ATM, or MDM2 genes. A model to explain the presence of the three hallmarks listed above, as well as the patterns of genomic instability observed in human cancers, proposes that the genes driving cell proliferation induce DNA replication stress, which, in turn, generates genomic instability and selects for escape from apoptosis. Here, we review the data that support this model, as well as the mechanisms by which oncogenes induce replication stress. Further, we argue that DNA replication stress should be considered as a hallmark of cancer because it likely drives cancer development and is very prevalent.
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Affiliation(s)
- Morgane Macheret
- Department of Molecular Biology, University of Geneva, 1205 Geneva, Switzerland;
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33
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Lupski JR. Structural variation mutagenesis of the human genome: Impact on disease and evolution. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:419-36. [PMID: 25892534 PMCID: PMC4609214 DOI: 10.1002/em.21943] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/01/2015] [Indexed: 05/19/2023]
Abstract
Watson-Crick base-pair changes, or single-nucleotide variants (SNV), have long been known as a source of mutations. However, the extent to which DNA structural variation, including duplication and deletion copy number variants (CNV) and copy number neutral inversions and translocations, contribute to human genome variation and disease has been appreciated only recently. Moreover, the potential complexity of structural variants (SV) was not envisioned; thus, the frequency of complex genomic rearrangements and how such events form remained a mystery. The concept of genomic disorders, diseases due to genomic rearrangements and not sequence-based changes for which genomic architecture incite genomic instability, delineated a new category of conditions distinct from chromosomal syndromes and single-gene Mendelian diseases. Nevertheless, it is the mechanistic understanding of CNV/SV formation that has promoted further understanding of human biology and disease and provided insights into human genome and gene evolution. Environ. Mol. Mutagen. 56:419-436, 2015. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza Room 604B, Houston, Texas
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Harutyunyan T, Hovhannisyan G, Babayan N, Othman MA, Liehr T, Aroutiounian R. Influence of aflatoxin B1 on copy number variants in human leukocytes in vitro. Mol Cytogenet 2015; 8:25. [PMID: 25901182 PMCID: PMC4404608 DOI: 10.1186/s13039-015-0131-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/25/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Aflatoxin B1 (AFB1) is a mycotoxin produced by Aspergillus spec. The latter are worldwide contaminants of food with mutagenic and carcinogenic activities in animals and humans. AFB1 was shown to have deleterious effects on metabolism of eukaryotes in many model systems, including the ability to inhibit DNA replication. An agent that disturbs DNA replication may also have the potential to induce de novo DNA copy number variations (CNVs). RESULTS Blood samples of three clinically healthy carriers were treated in vitro with AFB1 and chromosome preparations were subjected to parental origin determination fluorescence in situ hybridization (pod-FISH). Probes able to visualize CNVs in 8p21.2 and 15q11.2 were applied. In this setting here for the first time an influence of AFB1 on molecular-cytogenetically detectable CNVs could be shown. CONCLUSIONS The obtained results indicate that: (i) pod-FISH is a single cell directed, sensitive and suitable method for the analysis of mutagen induced CNVs, (ii) AFB1 has the potential to induce in vitro instability of known CNVs in human leukocytes.
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Affiliation(s)
- Tigran Harutyunyan
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia
| | - Galina Hovhannisyan
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia
| | - Nelly Babayan
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia ; Institute of Molecular Biology, National Academy of Sciences, 7 Hasratyan, 0014 Yerevan, Armenia
| | - Moneeb Ak Othman
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena, D-07743 Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena, D-07743 Germany
| | - Rouben Aroutiounian
- Department of Genetics and Cytology, Yerevan State University, 1 Alex Manoogian, 0025 Yerevan, Armenia
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Yauk CL, Aardema MJ, Benthem JV, Bishop JB, Dearfield KL, DeMarini DM, Dubrova YE, Honma M, Lupski JR, Marchetti F, Meistrich ML, Pacchierotti F, Stewart J, Waters MD, Douglas GR. Approaches for identifying germ cell mutagens: Report of the 2013 IWGT workshop on germ cell assays(☆). MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 783:36-54. [PMID: 25953399 DOI: 10.1016/j.mrgentox.2015.01.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 01/06/2023]
Abstract
This workshop reviewed the current science to inform and recommend the best evidence-based approaches on the use of germ cell genotoxicity tests. The workshop questions and key outcomes were as follows. (1) Do genotoxicity and mutagenicity assays in somatic cells predict germ cell effects? Limited data suggest that somatic cell tests detect most germ cell mutagens, but there are strong concerns that dictate caution in drawing conclusions. (2) Should germ cell tests be done, and when? If there is evidence that a chemical or its metabolite(s) will not reach target germ cells or gonadal tissue, it is not necessary to conduct germ cell tests, notwithstanding somatic outcomes. However, it was recommended that negative somatic cell mutagens with clear evidence for gonadal exposure and evidence of toxicity in germ cells could be considered for germ cell mutagenicity testing. For somatic mutagens that are known to reach the gonadal compartments and expose germ cells, the chemical could be assumed to be a germ cell mutagen without further testing. Nevertheless, germ cell mutagenicity testing would be needed for quantitative risk assessment. (3) What new assays should be implemented and how? There is an immediate need for research on the application of whole genome sequencing in heritable mutation analysis in humans and animals, and integration of germ cell assays with somatic cell genotoxicity tests. Focus should be on environmental exposures that can cause de novo mutations, particularly newly recognized types of genomic changes. Mutational events, which may occur by exposure of germ cells during embryonic development, should also be investigated. Finally, where there are indications of germ cell toxicity in repeat dose or reproductive toxicology tests, consideration should be given to leveraging those studies to inform of possible germ cell genotoxicity.
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Affiliation(s)
- Carole L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
| | | | - Jan van Benthem
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Jack B Bishop
- National Institute of Environmental Health Sciences, NC, USA
| | | | | | | | | | - James R Lupski
- Department of Molecular and Human Genetics, and Department of Pediatrics, Baylor College of Medicine, USA
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | | | - Francesca Pacchierotti
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Italy
| | | | | | - George R Douglas
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada.
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36
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Abstract
DNA copy number variation is long associated with highly penetrant genomic disorders, but it was not until recently that the widespread occurrence of copy number variation among phenotypically normal individuals was realized as a considerable source of genetic variation. It is also now appreciated that copy number variants (CNVs) play a role in the onset of complex diseases. Many of the complex diseases in which CNVs are associated are reported to be influenced by yet to be identified environmental factors. It is hypothesized that exposure to environmental chemicals generates CNVs and influences disease onset and pathogenesis. In this study a proof of principle experiment was completed with ethyl methanesulfonate (EMS) and cytosine arabinoside (Ara-C) to investigate the generation of CNVs using array comparative genomic hybridization (CGH) and the zebrafish vertebrate model system. Exposure to both chemicals resulted in CNVs. CNVs were detected in similar genomic regions among multiple exposure concentrations with EMS and five CNVs were common among both chemicals. Furthermore, CNVs were correlated to altered gene expression. This study suggests that chemical exposure generates CNVs with impacts on gene expression warranting further investigation of this phenomenon with environmental chemicals.
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37
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Wilson TE, Arlt MF, Park SH, Rajendran S, Paulsen M, Ljungman M, Glover TW. Large transcription units unify copy number variants and common fragile sites arising under replication stress. Genome Res 2014; 25:189-200. [PMID: 25373142 PMCID: PMC4315293 DOI: 10.1101/gr.177121.114] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Copy number variants (CNVs) resulting from genomic deletions and duplications and common fragile sites (CFSs) seen as breaks on metaphase chromosomes are distinct forms of structural chromosome instability precipitated by replication inhibition. Although they share a common induction mechanism, it is not known how CNVs and CFSs are related or why some genomic loci are much more prone to their occurrence. Here we compare large sets of de novo CNVs and CFSs in several experimental cell systems to each other and to overlapping genomic features. We first show that CNV hotpots and CFSs occurred at the same human loci within a given cultured cell line. Bru-seq nascent RNA sequencing further demonstrated that although genomic regions with low CNV frequencies were enriched in transcribed genes, the CNV hotpots that matched CFSs specifically corresponded to the largest active transcription units in both human and mouse cells. Consistently, active transcription units >1 Mb were robust cell-type-specific predictors of induced CNV hotspots and CFS loci. Unlike most transcribed genes, these very large transcription units replicated late and organized deletion and duplication CNVs into their transcribed and flanking regions, respectively, supporting a role for transcription in replication-dependent lesion formation. These results indicate that active large transcription units drive extreme locus- and cell-type-specific genomic instability under replication stress, resulting in both CNVs and CFSs as different manifestations of perturbed replication dynamics.
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Affiliation(s)
| | | | | | | | - Michelle Paulsen
- Department of Radiation Oncology and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Mats Ljungman
- Department of Radiation Oncology and Translational Oncology Program, University of Michigan, Ann Arbor, Michigan 48109, USA
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