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Gifford DR, Bhattacharyya A, Geim A, Marshall E, Krašovec R, Knight CG. Environmental and genetic influence on the rate and spectrum of spontaneous mutations in Escherichia coli. Microbiology (Reading) 2024; 170:001452. [PMID: 38687010 PMCID: PMC11084559 DOI: 10.1099/mic.0.001452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024]
Abstract
Spontaneous mutations are the ultimate source of novel genetic variation on which evolution operates. Although mutation rate is often discussed as a single parameter in evolution, it comprises multiple distinct types of changes at the level of DNA. Moreover, the rates of these distinct changes can be independently influenced by genomic background and environmental conditions. Using fluctuation tests, we characterized the spectrum of spontaneous mutations in Escherichia coli grown in low and high glucose environments. These conditions are known to affect the rate of spontaneous mutation in wild-type MG1655, but not in a ΔluxS deletant strain - a gene with roles in both quorum sensing and the recycling of methylation products used in E. coli's DNA repair process. We find an increase in AT>GC transitions in the low glucose environment, suggesting that processes relating to the production or repair of this mutation could drive the response of overall mutation rate to glucose concentration. Interestingly, this increase in AT>GC transitions is maintained by the glucose non-responsive ΔluxS deletant. Instead, an elevated rate of GC>TA transversions, more common in a high glucose environment, leads to a net non-responsiveness of overall mutation rate for this strain. Our results show how relatively subtle changes, such as the concentration of a carbon substrate or loss of a regulatory gene, can substantially influence the amount and nature of genetic variation available to selection.
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Affiliation(s)
- Danna R. Gifford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Anish Bhattacharyya
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Alexandra Geim
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Pembroke College, University of Cambridge, Cambridge, UK
| | - Eleanor Marshall
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Rok Krašovec
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Christopher G. Knight
- Department of Earth and Environmental Sciences, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, Manchester, UK
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2
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Baldo MS, Nogueira C, Pereira C, Janeiro P, Ferreira S, Lourenço CM, Bandeira A, Martins E, Magalhães M, Rodrigues E, Santos H, Ferreira AC, Vilarinho L. Leigh Syndrome Spectrum: A Portuguese Population Cohort in an Evolutionary Genetic Era. Genes (Basel) 2023; 14:1536. [PMID: 37628588 PMCID: PMC10454233 DOI: 10.3390/genes14081536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial diseases are the most common inherited inborn error of metabolism resulting in deficient ATP generation, due to failure in homeostasis and proper bioenergetics. The most frequent mitochondrial disease manifestation in children is Leigh syndrome (LS), encompassing clinical, neuroradiological, biochemical, and molecular features. It typically affects infants but occurs anytime in life. Considering recent updates, LS clinical presentation has been stretched, and is now named LS spectrum (LSS), including classical LS and Leigh-like presentations. Apart from clinical diagnosis challenges, the molecular characterization also progressed from Sanger techniques to NGS (next-generation sequencing), encompassing analysis of nuclear (nDNA) and mitochondrial DNA (mtDNA). This upgrade resumed steps and favored diagnosis. Hereby, our paper presents molecular and clinical data on a Portuguese cohort of 40 positive cases of LSS. A total of 28 patients presented mutation in mtDNA and 12 in nDNA, with novel mutations identified in a heterogeneous group of genes. The present results contribute to the better knowledge of the molecular basis of LS and expand the clinical spectrum associated with this syndrome.
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Affiliation(s)
- Manuela Schubert Baldo
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.S.B.)
| | - Célia Nogueira
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.S.B.)
- Neonatal Screening, Metabolism and Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal
| | - Cristina Pereira
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.S.B.)
- Neonatal Screening, Metabolism and Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal
| | - Patrícia Janeiro
- Inherited Metabolic Disease Reference Center, Lisbon North University Hospital Center (CHULN), EPE, 1649-028 Lisbon, Portugal
| | - Sara Ferreira
- Inherited Metabolic Disease Reference Center, Pediatric Hospital, Hospital and University Center of Coimbra, 3004-561 Coimbra, Portugal
| | - Charles M. Lourenço
- Neurogenetics Department, Faculdade de Medicina de São Jose do Rio Preto, São Jose do Rio Preto 15090-000, Brazil
| | - Anabela Bandeira
- Oporto Hospital Centre, University of Porto, 4099-001 Porto, Portugal
| | - Esmeralda Martins
- Oporto Hospital Centre, University of Porto, 4099-001 Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Instituto de Ciências Biomédicas Abel Salazar, Porto University, 4050-313 Porto, Portugal
| | - Marina Magalhães
- Department of Neurology Porto Hospital and University Centre, EPE, 4050-011 Porto, Portugal
| | - Esmeralda Rodrigues
- Reference Center for Inherited Metabolic Disorders, University Hospital Centre S. João, 4200-319 Porto, Portugal
| | - Helena Santos
- Department of Pediatrics, Hospital Centre, EPE, 4434-502 Vila Nova de Gaia, Portugal
| | | | - Laura Vilarinho
- Research and Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal; (M.S.B.)
- Neonatal Screening, Metabolism and Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, 4000-055 Porto, Portugal
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3
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Cherry JL. T Residues Preceded by Runs of G are Hotspots of T→G Mutation in Bacteria. Genome Biol Evol 2023:7175262. [PMID: 37216188 DOI: 10.1093/gbe/evad087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/11/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023] Open
Abstract
The rate of mutation varies among positions in a genome. Local sequence context can affect the rate, and has different effects on different types of mutation. Here I report an effect of local context that operates to some extent in all bacteria examined: the rate of T→G mutation is greatly increased by preceding runs of three or more G residues. The strength of the effect increases with the length of the run. In Salmonella, in which the effect is strongest, a G run of length three increases the rate by a factor of ∼26, a run of length four increases it by almost a factor of 100, and runs of length five or more increase it by a factor of more than 400 on average. The effect is much stronger when the T is on the leading rather than the lagging strand of DNA replication. Several observations eliminate the possibility that this effect is an artifact of sequencing error.
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Affiliation(s)
- Joshua L Cherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
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4
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Ruis C, Peacock TP, Polo LM, Masone D, Alvarez MS, Hinrichs AS, Turakhia Y, Cheng Y, McBroome J, Corbett-Detig R, Parkhill J, Floto RA. A lung-specific mutational signature enables inference of viral and bacterial respiratory niche. Microb Genom 2023; 9. [PMID: 37185044 DOI: 10.1099/mgen.0.001018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Exposure to different mutagens leaves distinct mutational patterns that can allow inference of pathogen replication niches. We therefore investigated whether SARS-CoV-2 mutational spectra might show lineage-specific differences, dependent on the dominant site(s) of replication and onwards transmission, and could therefore rapidly infer virulence of emergent variants of concern (VOCs). Through mutational spectrum analysis, we found a significant reduction in G>T mutations in the Omicron variant, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both the URT and lower respiratory tract (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalizable association of high G>T mutations with replication within the LRT. Monitoring G>T mutation rates over time, we found early separation of Omicron from Beta, Gamma and Delta, while mutational patterns in Alpha varied consistent with changes in transmission source as social restrictions were lifted. Mutational spectra may be a powerful tool to infer niches of established and emergent pathogens.
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Affiliation(s)
- Christopher Ruis
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Thomas P Peacock
- Department of Infectious Disease, Imperial College London, London, UK
| | - Luis M Polo
- Instituto de Histología y Embriología de Mendoza - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Maria Soledad Alvarez
- Instituto de Medicina y Biología Experimental de Cuyo (IMBECU), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), Mendoza, Argentina
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
| | - Ye Cheng
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
| | - Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - R Andres Floto
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
- Cambridge Centre for Lung Infection, Papworth Hospital, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
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5
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Bloom JD, Beichman AC, Neher RA, Harris K. Evolution of the SARS-CoV-2 Mutational Spectrum. Mol Biol Evol 2023; 40:msad085. [PMID: 37039557 PMCID: PMC10124870 DOI: 10.1093/molbev/msad085] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/07/2023] [Accepted: 04/06/2023] [Indexed: 04/12/2023] Open
Abstract
SARS-CoV-2 evolves rapidly in part because of its high mutation rate. Here, we examine whether this mutational process itself has changed during viral evolution. To do this, we quantify the relative rates of different types of single-nucleotide mutations at 4-fold degenerate sites in the viral genome across millions of human SARS-CoV-2 sequences. We find clear shifts in the relative rates of several types of mutations during SARS-CoV-2 evolution. The most striking trend is a roughly 2-fold decrease in the relative rate of G→T mutations in Omicron versus early clades, as was recently noted by Ruis et al. (2022. Mutational spectra distinguish SARS-CoV-2 replication niches. bioRxiv, doi:10.1101/2022.09.27.509649). There is also a decrease in the relative rate of C→T mutations in Delta, and other subtle changes in the mutation spectrum along the phylogeny. We speculate that these changes in the mutation spectrum could arise from viral mutations that affect genome replication, packaging, and antagonization of host innate-immune factors, although environmental factors could also play a role. Interestingly, the mutation spectrum of Omicron is more similar than that of earlier SARS-CoV-2 clades to the spectrum that shaped the long-term evolution of sarbecoviruses. Overall, our work shows that the mutation process is itself a dynamic variable during SARS-CoV-2 evolution and suggests that human SARS-CoV-2 may be trending toward a mutation spectrum more similar to that of other animal sarbecoviruses.
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Affiliation(s)
- Jesse D Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Howard Hughes Medical Institute, Seattle, WA
| | | | - Richard A Neher
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Kelley Harris
- Department of Genome Sciences, University of Washington, Seattle, WA
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6
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Zeng B, Lu Q, Chen S, Guan H, Xu X, Zou Y, Wang F, Huang S, Liu Y, Yang B. Screening and mutation analysis of phenylalanine hydroxylase deficiency in newborns from Jiangxi province. Front Genet 2023; 14:1049816. [PMID: 36845377 PMCID: PMC9946975 DOI: 10.3389/fgene.2023.1049816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Background: Phenylalanine hydroxylase deficiency (PAHD) is an autosomal recessive disorder of amino acid metabolism and caused by mutations in the phenylalanine hydroxylase (PAH) gene. Without timely and appropriate dietary management, the disturbance of amino acid metabolism may impair cognitive development and neurophysiological function. Newborn screening (NBS) can aid the early diagnosis of PAHD, which can give accurate therapy to PAHD patients in time. In China, the PAHD incidence and PAH mutation spectrum vary enormously across the provinces. A total of 5,541,627 newborns from Jiangxi province were screened by NBS between 1997 and 2021. Method: One seventy one newborns from Jiangxi province were diagnosed with PAHD. By Sanger sequencing and the multiplex ligation-dependent probe amplification (MLPA) analysis, mutation analysis was performed in 123 PAHD patients. Using an arbitrary values (AV)-based model, we compared the observed phenotype with the predicted phenotype based on the genotype. Results: In this study, we speculated the PAHD incidence of Jiangxi province was about 30.9 per 1,000,000 live births (171/5,541,627). We summarized the PAH mutation spectrum in Jiangxi province for the first time. Two novel variants (c.433G > C, c.706 + 2T > A) were found. The most prevalent variant was c.728G > A (14.1%). The overall prediction rate of the genotype-phenotype was 77.4%. Conclusion: This mutation spectrum is very meaningful to improve the diagnostic rate of PAHD and to increase the accuracy genetic counseling. This study offers data for the genotype-phenotype prediction suitable for Chinese population.
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Affiliation(s)
- Baitao Zeng
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China,Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Qing Lu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China,Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Shaohong Chen
- Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Huizhen Guan
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China,Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Xiaolan Xu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China,Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yongyi Zou
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China,Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Feng Wang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China,Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Shuhui Huang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China,Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China
| | - Yanqiu Liu
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China,Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China,*Correspondence: Yanqiu Liu, ; Bicheng Yang,
| | - Bicheng Yang
- Department of Medical Genetics, Jiangxi Maternal and Child Health Hospital, Nanchang, China,Jiangxi Provincial Key Laboratory of Birth Defect for Prevention and Control, Jiangxi Maternal and Child Health Hospital, Nanchang, China,*Correspondence: Yanqiu Liu, ; Bicheng Yang,
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7
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Zhao L, Hall M, de Cesare M, MacIntyre-Cockett G, Lythgoe K, Fraser C, Bonsall D, Golubchik T, Ferretti L. The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA. Proc Biol Sci 2022; 289:20221747. [PMID: 36382519 PMCID: PMC9667359 DOI: 10.1098/rspb.2022.1747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The raw material for viral evolution is provided by intra-host mutations occurring during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense 'antigenomes' acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the mutational spectrum of SARS-CoV-2 (sub)genomic and anti(sub)genomic RNA. We use a high-quality deep sequencing dataset produced using a quantitative strand-aware sequencing method, controlled for artefacts and sequencing errors, and scrutinized for accurate detection of within-host diversity. The nucleotide differences between negative- and positive-sense strand consensus vary between patients and do not show dependence on age or sex. Similarities and differences in mutational patterns between within-host minor variants on the two RNA strands suggested strand-specific mutations or editing by host deaminases and oxidative damage. We observe generally neutral and slight negative selection on the negative strand, contrasting with purifying selection in ORF1a, ORF1b and S genes of the positive strand of the genome.
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Affiliation(s)
- Lele Zhao
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Matthew Hall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | | | | | - Katrina Lythgoe
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - Christophe Fraser
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
| | - David Bonsall
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK,Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Tanya Golubchik
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK,Sydney Infectious Diseases Institute (Sydney ID), Faculty of Medicine and Health, University of Sydney, Sydney NSW 2006, Australia
| | | | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, UK
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8
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Korry BJ, Lee SYE, Chakrabarti AK, Choi AH, Ganser C, Machan JT, Belenky P. Genotoxic Agents Produce Stressor-Specific Spectra of Spectinomycin Resistance Mutations Based on Mechanism of Action and Selection in Bacillus subtilis. Antimicrob Agents Chemother 2021; 65:e0089121. [PMID: 34339280 PMCID: PMC8448107 DOI: 10.1128/aac.00891-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
Mutagenesis is integral for bacterial evolution and the development of antibiotic resistance. Environmental toxins and stressors are known to elevate the rate of mutagenesis through direct DNA toxicity, known as stress-associated mutagenesis, or via a more general stress-induced process that relies on intrinsic bacterial pathways. Here, we characterize the spectra of mutations induced by an array of different stressors using high-throughput sequencing to profile thousands of spectinomycin-resistant colonies of Bacillus subtilis. We found 69 unique mutations in the rpsE and rpsB genes, and that each stressor leads to a unique and specific spectrum of antibiotic-resistance mutations. While some mutations clearly reflected the DNA damage mechanism of the stress, others were likely the result of a more general stress-induced mechanism. To determine the relative fitness of these mutants under a range of antibiotic selection pressures, we used multistrain competitive fitness experiments and found an additional landscape of fitness and resistance. The data presented here support the idea that the environment in which the selection is applied (mutagenic stressors that are present), as well as changes in local drug concentration, can significantly alter the path to spectinomycin resistance in B. subtilis.
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Affiliation(s)
- Benjamin J. Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Stella Ye Eun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Amit K. Chakrabarti
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Ashley H. Choi
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Collin Ganser
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Jason T. Machan
- Department of Orthopedics, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Surgery, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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9
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Tonkin-Hill G, Martincorena I, Amato R, Lawson ARJ, Gerstung M, Johnston I, Jackson DK, Park N, Lensing SV, Quail MA, Gonçalves S, Ariani C, Spencer Chapman M, Hamilton WL, Meredith LW, Hall G, Jahun AS, Chaudhry Y, Hosmillo M, Pinckert ML, Georgana I, Yakovleva A, Caller LG, Caddy SL, Feltwell T, Khokhar FA, Houldcroft CJ, Curran MD, Parmar S, Alderton A, Nelson R, Harrison EM, Sillitoe J, Bentley SD, Barrett JC, Torok ME, Goodfellow IG, Langford C, Kwiatkowski D. Patterns of within-host genetic diversity in SARS-CoV-2. eLife 2021; 10:e66857. [PMID: 34387545 PMCID: PMC8363274 DOI: 10.7554/elife.66857] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 07/22/2021] [Indexed: 12/15/2022] Open
Abstract
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95.1% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within- and between-host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.
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Affiliation(s)
| | | | | | | | | | | | | | - Naomi Park
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | | | | | | | | | | | - Luke W Meredith
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Grant Hall
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Aminu S Jahun
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Yasmin Chaudhry
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Myra Hosmillo
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Malte L Pinckert
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Iliana Georgana
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Anna Yakovleva
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Laura G Caller
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Sarah L Caddy
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Theresa Feltwell
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | - Fahad A Khokhar
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of CambridgeCambridgeUnited Kingdom
| | | | | | | | | | | | | | - Ewan M Harrison
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- European Bioinformatics InstituteHinxtonUnited Kingdom
| | | | | | | | - M Estee Torok
- Department of Medicine, University of CambridgeCambridgeUnited Kingdom
| | - Ian G Goodfellow
- Department of Pathology, University of CambridgeCambridgeUnited Kingdom
| | | | - Dominic Kwiatkowski
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
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10
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Lin X, Li S, Zhang Z, Yue H. Clinical and Genetic Characteristics of 153 Chinese Patients With X-Linked Hypophosphatemia. Front Cell Dev Biol 2021; 9:617738. [PMID: 34141703 PMCID: PMC8204109 DOI: 10.3389/fcell.2021.617738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/16/2021] [Indexed: 11/27/2022] Open
Abstract
X-linked hypophosphatemia (XLH) is caused by inactivating mutations in the phosphate-regulating endopeptidase homolog, X-linked (PHEX) gene, resulting in an excess of circulating intact fibroblast growth factor-23 (iFGF-23) and a waste of renal phosphate. In the present study, we retrospectively reviewed the clinical and molecular features of 153 Chinese patients, representing 87 familial and 66 sporadic cases with XLH. A total of 153 patients with XLH presented with signs or symptoms at a median age of 18.0 months (range, 9.0 months–26.0 years). Lower-limb deformity was the most frequent clinical manifestation, accounting for 79.1% (121/153). Biochemical screening showed increased serum levels of iFGF23 in patients with XLH, with a wide variation ranging from 14.39 to 730.70 pg/ml. Median values of serum iFGF23 in pediatric and adult patients were 94.87 pg/ml (interquartile range: 74.27–151.86 pg/ml) and 72.82 pg/ml (interquartile range: 39.42–136.00 pg/ml), respectively. Although no difference in circulating iFGF23 levels between these two groups was observed (P = 0.062), the proportion of patients with high levels of circulating iFGF23 (>42.2 pg/ml) was greater in the pediatric group than in the adult group (P = 0.026). Eighty-eight different mutations in 153 patients were identified, with 27 (30.7%) being novel. iFGF23 levels and severity of the disease did not correlate significantly with truncating and non-truncating mutations or N-terminal and C-terminal PHEX mutations. This study provides a comprehensive description of the clinical profiles, circulating levels of iFGF23 and gene mutation features of patients with XLH, further enriching the genotypic spectrum of the diseases. The findings show no evident correlation of circulating iFGF23 levels with the age or disease severity in patients with XLH.
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Affiliation(s)
- Xiaoyun Lin
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Shanshan Li
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Zhenlin Zhang
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
| | - Hua Yue
- Shanghai Clinical Research Center of Bone Diseases, Department of Osteoporosis and Bone Diseases, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University, Shanghai, China
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11
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Wu RH, Tang WT, Qiu KY, Li XJ, Tang DX, Meng Z, He ZW. Identification of novel CSNK2A1 variants and the genotype-phenotype relationship in patients with Okur-Chung neurodevelopmental syndrome: a case report and systematic literature review. J Int Med Res 2021; 49:3000605211017063. [PMID: 34038195 PMCID: PMC8161887 DOI: 10.1177/03000605211017063] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
De novo germline variants of the casein kinase 2α subunit (CK2α) gene (CSNK2A1) have been reported in individuals with the congenital neuropsychiatric disorder Okur-Chung neurodevelopmental syndrome (OCNS). Here, we report on two unrelated children with OCNS and review the literature to explore the genotype-phenotype relationship in OCNS. Both children showed facial dysmorphism, growth retardation, and neuropsychiatric disorders. Using whole-exome sequencing, we identified two novel de novo CSNK2A1 variants: c.479A>G p.(H160R) and c.238C>T p.(R80C). A search of the literature identified 12 studies that provided information on 35 CSNK2A1 variants in various protein-coding regions of CK2α. By quantitatively analyzing data related to these CSNK2A1 variants and their corresponding phenotypes, we showed for the first time that mutations in protein-coding CK2α regions appear to influence the phenotypic spectrum of OCNS. Mutations altering the ATP/GTP-binding loop were more likely to cause the widest range of phenotypes. Therefore, any assessment of clinical spectra for this disorder should be extremely thorough. This study not only expands the mutational spectrum of OCNS, but also provides a comprehensive overview to improve our understanding of the genotype-phenotype relationship in OCNS.
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Affiliation(s)
- Ruo-Hao Wu
- Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University Guangzhou, P. R. China.,Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong High Education Institutes, Sun Yat-sen University Guangzhou, P. R. China
| | - Wen-Ting Tang
- Department of Research and Molecular Diagnostics, Sun Yat-sen Cancer Center, Sun Yat-sen University Guangzhou, P. R. China.,State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, 71067Sun Yat-sen University Cancer Center Guangzhou, P. R. China
| | - Kun-Yin Qiu
- Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University Guangzhou, P. R. China.,Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong High Education Institutes, Sun Yat-sen University Guangzhou, P. R. China
| | - Xiao-Juan Li
- Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong High Education Institutes, Sun Yat-sen University Guangzhou, P. R. China.,Department of Research and Molecular Diagnostics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University Guangzhou, P. R. China
| | - Dan-Xia Tang
- Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University Guangzhou, P. R. China.,Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong High Education Institutes, Sun Yat-sen University Guangzhou, P. R. China
| | - Zhe Meng
- Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University Guangzhou, P. R. China.,Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong High Education Institutes, Sun Yat-sen University Guangzhou, P. R. China
| | - Zhan-Wen He
- Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University Guangzhou, P. R. China.,Key Laboratory of Malignant Tumor Gene Regulation and Target Therapy of Guangdong High Education Institutes, Sun Yat-sen University Guangzhou, P. R. China
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12
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Nguyen DT, Wu B, Long H, Zhang N, Patterson C, Simpson S, Morris K, Thomas WK, Lynch M, Hao W. Variable Spontaneous Mutation and Loss of Heterozygosity among Heterozygous Genomes in Yeast. Mol Biol Evol 2021; 37:3118-3130. [PMID: 33219379 DOI: 10.1093/molbev/msaa150] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mutation and recombination are the primary sources of genetic variation. To better understand the evolution of genetic variation, it is crucial to comprehensively investigate the processes involving mutation accumulation and recombination. In this study, we performed mutation accumulation experiments on four heterozygous diploid yeast species in the Saccharomycodaceae family to determine spontaneous mutation rates, mutation spectra, and losses of heterozygosity (LOH). We observed substantial variation in mutation rates and mutation spectra. We also observed high LOH rates (1.65-11.07×10-6 events per heterozygous site per cell division). Biases in spontaneous mutation and LOH together with selection ultimately shape the variable genome-wide nucleotide landscape in yeast species.
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Affiliation(s)
- Duong T Nguyen
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | - Baojun Wu
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | - Hongan Long
- Institute of Evolution and Marine Biodiversity, KLMME, Ocean University of China, Qingdao, Shandong Province, China
| | - Nan Zhang
- Department of Biological Sciences, Wayne State University, Detroit, MI
| | | | | | | | | | - Michael Lynch
- Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ
| | - Weilong Hao
- Department of Biological Sciences, Wayne State University, Detroit, MI
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13
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Hernando B, Dietzen M, Parra G, Gil-Barrachina M, Pitarch G, Mahiques L, Valcuende-Cavero F, McGranahan N, Martinez-Cadenas C. The effect of age on the acquisition and selection of cancer driver mutations in sun-exposed normal skin. Ann Oncol 2021; 32:412-421. [PMID: 33307203 PMCID: PMC7614988 DOI: 10.1016/j.annonc.2020.11.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/18/2020] [Accepted: 11/29/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The accumulation of somatic mutations contributes to ageing and cancer. Sunlight is the principal aetiological factor associated with skin cancer development. However, genetic and phenotypic factors also contribute to skin cancer risk. This study aimed at exploring the role of photoaging, as well as other well-known epidemiological risk factors, in the accumulation of somatic mutations in cancer-free human epidermis. MATERIAL AND METHODS We deeply sequenced 46 genes in normal skin biopsies from 123 healthy donors, from which phenotypic data (including age, pigmentation-related genotype and phenotype) and sun exposure habits were collected. We determined the somatic mutational burden, mutational signatures, clonal selection and frequency of driver mutations in all samples. RESULTS Our results reveal an exponential accumulation of UV-related somatic mutations with age, matching skin cancer incidence. The increase of mutational burden is in turn modified by an individual's skin phototype. Somatic mutations preferentially accumulated in cutaneous squamous cell carcinoma cancer genes and clonally expanded with age, with distinct mutational processes underpinning different age groups. Our results suggest a loss of fidelity in transcription-coupled repair later in life. CONCLUSION Our findings reveal that ageing is not only associated with an exponential increase in the number of somatic mutations accumulated in normal epidermis, but also with selection and expansion of cancer-associated mutations. Aged, sun-exposed normal skin is thus an extended mosaic of multiple clones with driver mutations, poised for the acquisition of transforming events.
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Affiliation(s)
- B Hernando
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | - M Dietzen
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, UK
| | - G Parra
- Centre Nacional d'Anàlisi Genòmica-Centre de Regulació Genòmica (CNAG-CRG), Barcelona, Spain
| | - M Gil-Barrachina
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain
| | - G Pitarch
- Department of Dermatology, Castellon University General Hospital, Castellon, Spain
| | - L Mahiques
- Department of Dermatology, Castellon University General Hospital, Castellon, Spain
| | - F Valcuende-Cavero
- Department of Dermatology, La Plana University Hospital, Villarreal, Spain
| | - N McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, UK.
| | - C Martinez-Cadenas
- Department of Medicine, Jaume I University of Castellon, Castellon, Spain.
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14
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Saclier N, Chardon P, Malard F, Konecny-Dupré L, Eme D, Bellec A, Breton V, Duret L, Lefebure T, Douady CJ. Bedrock radioactivity influences the rate and spectrum of mutation. eLife 2020; 9:56830. [PMID: 33252037 PMCID: PMC7723406 DOI: 10.7554/elife.56830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 11/30/2020] [Indexed: 12/24/2022] Open
Abstract
All organisms on Earth are exposed to low doses of natural radioactivity but some habitats are more radioactive than others. Yet, documenting the influence of natural radioactivity on the evolution of biodiversity is challenging. Here, we addressed whether organisms living in naturally more radioactive habitats accumulate more mutations across generations using 14 species of waterlice living in subterranean habitats with contrasted levels of radioactivity. We found that the mitochondrial and nuclear mutation rates across a waterlouse species’ genome increased on average by 60% and 30%, respectively, when radioactivity increased by a factor of three. We also found a positive correlation between the level of radioactivity and the probability of G to T (and complementary C to A) mutations, a hallmark of oxidative stress. We conclude that even low doses of natural bedrock radioactivity influence the mutation rate possibly through the accumulation of oxidative damage, in particular in the mitochondrial genome.
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Affiliation(s)
- Nathanaëlle Saclier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Patrick Chardon
- LPC, Université Clermont Auvergne, CNRS/IN2P3 UMR6533, Clermont-Ferrand, France
| | - Florian Malard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Lara Konecny-Dupré
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - David Eme
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Arnaud Bellec
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France.,Univ Lyon, Université Jean Moulin Lyon 3, CNRS UMR 5600 Environnement Ville Société, Lyon, France
| | - Vincent Breton
- LPC, Université Clermont Auvergne, CNRS/IN2P3 UMR6533, Clermont-Ferrand, France
| | - Laurent Duret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Tristan Lefebure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Christophe J Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France.,Institut Universitaire de France, Paris, France
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15
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Brennenstuhl H, Didiasova M, Assmann B, Bertoldi M, Molla G, Jung-Klawitter S, Kuseyri Hübschmann O, Schröter J, Opladen T, Tikkanen R. Succinic Semialdehyde Dehydrogenase Deficiency: In Vitro and In Silico Characterization of a Novel Pathogenic Missense Variant and Analysis of the Mutational Spectrum of ALDH5A1. Int J Mol Sci 2020; 21:E8578. [PMID: 33203024 DOI: 10.3390/ijms21228578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/09/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022] Open
Abstract
Succinic semialdehyde dehydrogenase deficiency (SSADHD) is a rare, monogenic disorder affecting the degradation of the main inhibitory neurotransmitter γ-amino butyric acid (GABA). Pathogenic variants in the ALDH5A1 gene that cause an enzymatic dysfunction of succinic semialdehyde dehydrogenase (SSADH) lead to an accumulation of potentially toxic metabolites, including γ-hydroxybutyrate (GHB). Here, we present a patient with a severe phenotype of SSADHD caused by a novel genetic variant c.728T > C that leads to an exchange of leucine to proline at residue 243, located within the highly conserved nicotinamide adenine dinucleotide (NAD)+ binding domain of SSADH. Proline harbors a pyrrolidine within its side chain known for its conformational rigidity and disruption of protein secondary structures. We investigate the effect of this novel variant in vivo, in vitro, and in silico. We furthermore examine the mutational spectrum of all previously described disease-causing variants and computationally assess all biologically possible missense variants of ALDH5A1 to identify mutational hotspots.
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16
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Jiang B, Xiao F, Li X, Xiao Y, Wang Y, Zhang T. Case Report: Pediatric Recurrent Acute Liver Failure Caused by Neuroblastoma Amplified Sequence ( NBAS) Gene Mutations. Front Pediatr 2020; 8:607005. [PMID: 33520894 PMCID: PMC7838493 DOI: 10.3389/fped.2020.607005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022] Open
Abstract
Acute liver failure (ALF) in childhood is a rapidly progressive, potentially life-threatening condition that occurs in previously healthy children of all ages. However, the etiology of ~50% of cases with pediatric ALF remains unknown. We herein report a 4-year-old Chinese girl with recurrent ALF (RALF) due to a mutation in the neuroblastoma amplified sequence (NBAS) gene. The patient had suffered from multiple episodes of fever-related ALF since early childhood. She had also suffered from acute kidney injury, hypertension, mild pulmonary hypertension, pleural effusion, and hypothyroidism. A novel compound heterozygote mutation, c.3596G> A (p.C1199Y)/ex.9del (p.216-248del), in the NBAS gene was identified by whole-exome sequencing (WES). The missense mutation c.3596G> A (p. C1199Y) was inherited from her father, and ex.9del (p.216-248del) was inherited from her mother. The patient was managed with intensive treatments, such as renal replacement therapy (CRRT), intravenous antibiotics, and glucose infusion, and was discharged after full recovery. We identified a novel compound heterozygote mutation in the NBAS gene that caused fever-related RALF in a Chinese child, which further expands the mutational spectrum of NBAS.
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Affiliation(s)
- Bingxin Jiang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Fangfei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaolu Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yongmei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Pediatric Infection, Immunity and Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Institute of Pediatric Infection, Immunity and Critical Care Medicine, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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17
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Ponard D, Gaboriaud C, Charignon D, Ghannam A, Wagenaar-Bos IGA, Roem D, López-Lera A, López-Trascasa M, Tosi M, Drouet C. SERPING1 mutation update: Mutation spectrum and C1 Inhibitor phenotypes. Hum Mutat 2019; 41:38-57. [PMID: 31517426 DOI: 10.1002/humu.23917] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022]
Abstract
C1 inhibitor (C1Inh) deficiency is responsible for hereditary angioedema (C1-INH-HAE) and caused by variants of the SERPING1/C1INH/C1NH gene. C1Inh is the major control of kallikrein-kinin system. C1Inh deficiency leads to its uncontrolled activation, with subsequent generation of the vasoactive peptide bradykinin. This update documents 748 different SERPING1 variants, including published variants and additional 120 unpublished ones. They were identified as heterozygous variants (n = 729), as homozygous variants in 10 probands and as compound heterozygous variants (nine combinations). Six probands with heterozygous variants exhibited gonadal mosaicism. Probands with heterozygous (n = 72) and homozygous (n = 1) variants were identified as de novo cases. Overall, 58 variants were found at positions showing high residue conservation among serpins, and have been referred to as a mousetrap function of C1Inh: reactive center loop, gate, shutter, breach, and hinge. C1Inh phenotype analysis identified dysfunctional serpin variants with failed serpin-protease association and a residual 105-kDa species after incubation with target protease. Regarding this characteristic, in conditions with low antigenic C1Inh, 74 C1-INH-HAE probands presented with an additional so-called intermediate C1-INH-HAE phenotype. The present update addresses a comprehensive SERPING1 variant spectrum that facilitates genotype-phenotype correlations, highlighting residues of strategic importance for serpin function and for identification of C1Inh deficiency as serpinopathy.
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Affiliation(s)
- Denise Ponard
- Centre de Référence des Angioedèmes (CREAK), Filière MaRIH, CHU Grenoble, Grenoble, France.,Laboratoire d'Immunologie, CHU Grenoble Alpes, Grenoble, France
| | | | - Delphine Charignon
- GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,KininX SAS, Grenoble, France
| | - Arije Ghannam
- GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,KininX SAS, Grenoble, France
| | | | - Dorina Roem
- Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands
| | - Alberto López-Lera
- Biomedical Research Network on Rare Diseases (CIBERER)-U754, Instituto de Investigación Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | | | - Mario Tosi
- Inserm U1245, University of Rouen, Rouen, France
| | - Christian Drouet
- Centre de Référence des Angioedèmes (CREAK), Filière MaRIH, CHU Grenoble, Grenoble, France.,GREPI EA7408, Université Grenoble Alpes and EFS Rhône-Alpes, Grenoble, France.,Inserm U1016, CNRS UMR8104, Institut Cochin, Université Paris-Descartes, France
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18
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Nicolson NG, Healy JM, Korah R, Carling T. Whole-Exome Sequencing of Syndromic Adrenocortical Carcinoma Reveals Distinct Mutational Profile From Sporadic ACC. J Endocr Soc 2019; 3:1819-1824. [PMID: 31555752 PMCID: PMC6749842 DOI: 10.1210/js.2019-00176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/25/2019] [Indexed: 11/19/2022] Open
Abstract
Next-generation sequencing has provided genetic profiles of a large number of sporadic adrenocortical carcinomas (ACCs), but the applicability of these results to ACC cases associated with tumor predisposition syndromes is unclear. Although the germline features of these syndromes have been well described, the somatic mutational landscape of the tumors they give rise to is less clear. Our group obtained germline and tumor tissue from a pediatric patient who developed ACC during her first year of life, which was treated successfully. She was subsequently diagnosed with additional tumors later in childhood. Whole exome sequencing analysis was performed followed by in silico protein function prediction, revealing a probably deleterious germline TP53 L265P mutation. The somatic mutational burden was comparable between the index case and a previously published cohort of 40 sporadic cases, but the mutational spectrum was distinct in terms of raw base-change frequency as well as in a trinucleotide context-specific analysis. No canonical somatic genetic drivers of ACC were identified in the reported case, suggesting that syndromic adrenocortical tumors may represent a genetically distinct entity from sporadic tumors.
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Affiliation(s)
- Norman G Nicolson
- Yale Endocrine Neoplasia Laboratory, Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - James M Healy
- Yale Endocrine Neoplasia Laboratory, Department of Surgery, Yale School of Medicine, New Haven, Connecticut.,Connecticut Children's Medical Center, Hartford, Connecticut
| | - Reju Korah
- Yale Endocrine Neoplasia Laboratory, Department of Surgery, Yale School of Medicine, New Haven, Connecticut
| | - Tobias Carling
- Yale Endocrine Neoplasia Laboratory, Department of Surgery, Yale School of Medicine, New Haven, Connecticut
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19
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Cui L, Cheng Z, Hu K, Pang Y, Liu Y, Qian T, Quan L, Dai Y, Pang Y, Ye X, Shi J, Fu L. Prognostic value of the PDLIM family in acute myeloid leukemia. Am J Transl Res 2019; 11:6124-6131. [PMID: 31632581 PMCID: PMC6789254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
Acute myeloid leukemia (AML) is a genetically complex, highly aggressive hematological malignancy. Prognosis is usually with grim. PDZ and LIM domain proteins (PDLIM) are involved in the regulation of a variety of biological processes, including cytoskeletal organization, cell differentiation, organ development, neural signaling or tumorigenesis. The clinical and prognostic value of the PDLIM family in AML is unclear. To understand the role of PDLIM expression in AML, The Cancer Genome Atlas (TCGA) database was screened and 155 de novo AML patients with complete clinical information and the expression data of the PDLIM family were included in the study. The clinical and molecular characteristics associated with the expression of different members of the PDLIM family were summarized using various statistical methods. In 84 patients who only received chemotherapy, univariate analysis indicated that high expression of PDLIM2 or PDLIM7 was associated with shorter EFS and OS (both P<0.05 for PDLIM2, and both P<0.01 for PDLIM7). Multivariate analysis suggested that high expression of PDLIM7 was an independent risk factor for EFS and OS (both P<0.05). In the other 71 patients who underwent allogeneic hematopoietic stem cell transplantation (allo-HSCT), survival was unaffected by PDLIM expressions. In summary, high expression of PDLIM2 and PDLIM7, especially the latter, could serve as adverse prognostic factors for AML, but their prognostic effects could be reversed by allo-HSCT.
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Affiliation(s)
- Longzhen Cui
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
- Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
- Translational Medicine Center, Huaihe Hospital of Henan UniversityKaifeng 475000, Henan, China
- Department of Hematology, Huaihe Hospital of Henan UniversityKaifeng 475000, Henan, China
| | - Zhiheng Cheng
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of GroningenGroningen, Netherlands
| | - Kai Hu
- Department of Hematology and Lymphoma Research Center, Peking University, Third HospitalBeijing 100191, China
| | - Yifan Pang
- Department of Medicine, William Beaumont HospitalRoyal Oak, MI 48073, USA
| | - Yan Liu
- Translational Medicine Center, Huaihe Hospital of Henan UniversityKaifeng 475000, Henan, China
| | - Tingting Qian
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
- Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
| | - Liang Quan
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
- Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
| | - Yifeng Dai
- Immunoendocrinology, Division of Medical Biology, Department of Pathology and Medical Biology, University Medical Center Groningen, University of GroningenGroningen, Netherlands
| | - Ying Pang
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
| | - Xu Ye
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
| | - Jinlong Shi
- Department of Medical Big Data, Chinese PLA General HospitalBeijing 100853, China
| | - Lin Fu
- Department of Hematology, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
- Translational Medicine Center, The Second Affiliated Hospital of Guangzhou Medical UniversityGuangzhou 510260, Guangdong, China
- Department of Hematology, Huaihe Hospital of Henan UniversityKaifeng 475000, Henan, China
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Bian K, Delaney JC, Zhou X, Li D. Biological Evaluation of DNA Biomarkers in a Chemically Defined and Site-Specific Manner. Toxics 2019; 7:E36. [PMID: 31242562 DOI: 10.3390/toxics7020036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 06/13/2019] [Accepted: 06/14/2019] [Indexed: 02/06/2023]
Abstract
As described elsewhere in this Special Issue on biomarkers, much progress has been made in the detection of modified DNA within organisms at endogenous and exogenous levels of exposure to chemical species, including putative carcinogens and chemotherapeutic agents. Advances in the detection of damaged or unnatural bases have been able to provide correlations to support or refute hypotheses between the level of exposure to oxidative, alkylative, and other stresses, and the resulting DNA damage (lesion formation). However, such stresses can form a plethora of modified nucleobases, and it is therefore difficult to determine the individual contribution of a particular modification to alter a cell's genetic fate, as measured in the form of toxicity by stalled replication past the damage, by subsequent mutation, and by lesion repair. Chemical incorporation of a modification at a specific site within a vector (site-specific mutagenesis) has been a useful tool to deconvolute what types of damage quantified in biologically relevant systems may lead to toxicity and/or mutagenicity, thereby allowing researchers to focus on the most relevant biomarkers that may impact human health. Here, we will review a sampling of the DNA modifications that have been studied by shuttle vector techniques.
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Paraboschi EM, Menegatti M, Peyvandi F, Duga S, Asselta R. Understanding the Impact of Aberrant Splicing in Coagulation Factor V Deficiency. Int J Mol Sci 2019; 20:E910. [PMID: 30791524 DOI: 10.3390/ijms20040910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 11/23/2022] Open
Abstract
Rare inherited coagulation disorders (RICDs) are congenital deficiencies of the plasma proteins that are involved in blood coagulation, which generally lead to lifelong bleeding manifestations. These diseases are generally qualitative and/or quantitative defects that are associated with monoallelic or biallelic mutations in the relevant gene. Among RICDs, factor V (FV) deficiency is one of the least characterized at the molecular level. Here, we investigated four unrelated patients with reduced plasma FV levels (three severe, one mild), which were associated with a moderately severe bleeding tendency. Sequence analysis of the FV gene identified seven different variants, five hitherto unknown (p.D1669G, c.5789-11C>A, c.5789-12C>A, c.5789-5T>G, and c.6528G>C), and two previously reported (c.158+1G>A and c.5789G>A). The possible pathogenic role of the newly identified missense variant was studied by in silico approaches. The remaining six genetic defects (all putative splicing mutations) were investigated for their possible effects on pre-mRNA splicing by transient transfection experiments in HeLa cells with plasmids expressing appropriate hybrid minigenes. The preparation of minigene constructs was instrumental to demonstrate that the two adjacent variants c.5789-11C>A and c.5789-12C>A are indeed present in cis in the analyzed FV-deficient patient (thus leading to the c.5789-11_12CC>AA mutation). Ex vivo experiments demonstrated that each variant causes either a skipping of the relevant exon or the activation of cryptic splice sites (exonic or intronic), eventually leading to the introduction of a premature termination codon.
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22
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Zhang Z, Gao JJ, Feng Y, Zhu LL, Yan H, Shi XF, Chang AM, Shi Y, Wang P. Mutational spectrum of the phenylalanine hydroxylase gene in patients with phenylketonuria in the central region of China. Scand J Clin Lab Invest 2018; 78:211-218. [PMID: 29390883 DOI: 10.1080/00365513.2018.1434898] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/23/2018] [Accepted: 01/28/2018] [Indexed: 01/15/2023]
Abstract
Phenylketonuria (PKU, OMIM 261600) caused by phenylalanine hydroxylase (PAH) deficiency is an autosomal recessive disease that is characterized by abnormalities of phenylalanine metabolism. In this study, a total of 77 patients, originating from the central region of China and who were diagnosed with PAH deficiency at the third affiliated hospital of Zhengzhou University, were enrolled in this study. The 13 exons and 12 flanking introns of the PAH gene were analyzed by Sanger sequencing and next generation sequencing. The sequencing data were aligned to the hg19, PAHvdb and HGMD databases to characterize the genotypes of PKU patients, and genotype-phenotype correlations and BH4 responsiveness predictions were performed using BIOPKUdb. In total, 149 alleles were characterized among the 154 PKU alleles. These mutations were located in exons 2-13, and intron 12 of the PAH gene, with a relative frequency of ≥5%, for EX6-96A>G, p.R241C, p.R243Q, p.V399V and p.R53H. Additionally, a novel variant, p.D84G, was identified. The genotype correlated with clinical symptoms in 33.3-100% of the cases, depending on the disease severity, and BH4 responsiveness predictions show that only five patients with MHP-PKU and one patient with Mild-PKU were predicted to be BH4 responsive. In conclusion, we have characterized the mutational spectrum of PAH in the central region of China and have identified a novel mutation. The hotspot mutation information might be useful for screening, diagnosis and treatment of PKU.
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Affiliation(s)
- Zhan Zhang
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
- b Shangqiu Medical College , Shangqiu , China
| | - Jun-Jun Gao
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Yang Feng
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Lin-Lin Zhu
- c School of Laboratory Medicine , Xinxiang Medical University , Xinxiang , China
| | - Huan Yan
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Xu-Feng Shi
- d Department of Obstetrics , Henan Province People's Hospital , Zhengzhou , China
| | - Ai-Min Chang
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Ying Shi
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Ping Wang
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
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23
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Abstract
Life is maintained through alternating phases of cell division and quiescence. The causes and consequences of spontaneous mutations have been extensively explored in proliferating cells, and the major sources include errors of DNA replication and DNA repair. The foremost consequences are genetic variations within a cell population that can lead to heritable diseases and drive evolution. While most of our knowledge on DNA damage response and repair has been gained through cells actively dividing, it remains essential to also understand how DNA damage is metabolized in cells which are not dividing. In this review, we summarize the current knowledge concerning the type of lesions that arise in non-dividing budding and fission yeast cells, as well as the pathways used to repair them. We discuss the contribution of these models to our current understanding of age-related pathologies.
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Xu Y, Li Y, Xu Q, Chen Y, Lv N, Jing Y, Dou L, Bo J, Hou G, Guo J, Wang X, Wang L, Li Y, Chen C, Yu L. Implications of mutational spectrum in myelodysplastic syndromes based on targeted next-generation sequencing. Oncotarget 2017; 8:82475-82490. [PMID: 29137279 PMCID: PMC5669905 DOI: 10.18632/oncotarget.19628] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 06/30/2017] [Indexed: 02/01/2023] Open
Abstract
Myelodysplastic syndromes (MDS) are a group of myeloid hematological malignancies, with a high risk of progression to acute myeloid leukemia (AML). To explore the role of acquired mutations in MDS, 111 MDS-associated genes were screened using next-generation sequencing (NGS), in 125 patients. One or more mutations were detected in 84% of the patients. Some gene mutations are specific for MDS and were associated with disease subtypes, and the patterns of mutational pathways could be associated with progressive MDS. The patterns, frequencies and functional pathways of gene mutations are different, but somehow related, between MDS and AML. Multivariate analysis suggested that patients with ≥ 2 mutations had poor progression-free survival, while GATA1/GATA2, DNMT3A and KRAS/NRAS mutations were associated with poor overall survival. Based on a novel system combining IPSS-R and molecular markers, these MDS patients were further divided into 3 more accurate prognostic subgroups. A panel of 11 target genes was proposed for genetic profiling of MDS. The study offers new insights into the molecular signatures of MDS and the genetic consistency between MDS and AML. Furthermore, results indicate that MDS could be classified by mutation combinations to guide the administration of individualized therapeutic interventions.
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Affiliation(s)
- Yuanyuan Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, Hainan Province, China
| | - Yan Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, Hainan Branch of Chinese PLA General Hospital, Sanya 572013, Hainan Province, China
| | - Qingyu Xu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Medical school of Nankai University, Tianjin 300071, China
| | - Yuelong Chen
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Na Lv
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yu Jing
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Liping Dou
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Jian Bo
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Guangyuan Hou
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Jing Guo
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Xiuli Wang
- Annoroad Gene Technology Co. Ltd, Beijing 100176, China
| | - Lili Wang
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yonghui Li
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China
| | | | - Li Yu
- Department of Hematology and BMT center, Chinese PLA General Hospital, Beijing 100853, China.,Department of Hematology, General Hospital of Shenzhen University, Shenzhen 518060, China
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Abstract
Background: A mechanism of innate antiviral immunity operating against viruses infecting mammalian cells has been described during the last decade. Host cytidine deaminases (
e.g., APOBEC3 proteins) edit viral genomes, giving rise to hypermutated nonfunctional viruses; consequently, viral fitness is reduced through lethal mutagenesis. By contrast, sub-lethal hypermutagenesis may contribute to virus evolvability by increasing population diversity. To prevent genome editing, some viruses have evolved proteins that mediate APOBEC3 degradation. The model plant
Arabidopsis thaliana genome encodes nine cytidine deaminases (
AtCDAs), raising the question of whether deamination is an antiviral mechanism in plants as well. Methods: Here we tested the effects of expression of
AtCDAs on the pararetrovirus Cauliflower mosaic virus (CaMV). Two different experiments were carried out. First, we transiently overexpressed each one of the nine
A. thalianaAtCDA genes in
Nicotianabigelovii plants infected with CaMV, and characterized the resulting mutational spectra, comparing them with those generated under normal conditions. Secondly, we created
A. thaliana transgenic plants expressing an artificial microRNA designed to knock-out the expression of up to six
AtCDA genes. This and control plants were then infected with CaMV. Virus accumulation and mutational spectra where characterized in both types of plants. Results: We have shown that the
A. thalianaAtCDA1 gene product exerts a mutagenic activity, significantly increasing the number of G to A mutations
in vivo, with a concomitant reduction in the amount of CaMV genomes accumulated. Furthermore, the magnitude of this mutagenic effect on CaMV accumulation is positively correlated with the level of
AtCDA1 mRNA expression in the plant. Conclusions: Our results suggest that deamination of viral genomes may also work as an antiviral mechanism in plants.
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Affiliation(s)
- Susana Martín
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de València, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de València, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain.,Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| | - Ana Grande-Pérez
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", CSIC-Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain.,Área de Genética, Universidad de Málaga, Campus de Teatinos, 29071 Málaga, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universidad Politécnica de València, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain.,Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Científic UV, Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain.,The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
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Rizo-de-la-Torre LC, Ibarra B, Sánchez-López JY, Magaña-Torres MT, Rentería-López VM, Perea-Díaz FJ. Three novel HBB mutations, c.-140C>G (-90 C>G), c.237_256delGGACAACCTCAAGGGCACCT (FS Cd 78/85 -20 bp), and c.315+2T>G (IVS2:2 T>G). Update of the mutational spectrum of β-Thalassemia in Mexican mestizo patients. Int J Lab Hematol 2017; 39:539-545. [PMID: 28603845 DOI: 10.1111/ijlh.12692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 03/24/2017] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Beta-thalassemia (β-thal) is frequent in Mexican patients with microcytosis and hypochromia. We report three novel mutations and analyze the actual mutational spectrum in Mexican population. METHODS One hundred and forty-nine β-thal Mexican mestizo patients were studied (154 alleles). ARMS-PCR was performed to identify Cd39C>T, IVS1:1G>A, IVS1:110G>A, -28A>C, initiation codonA>G and IVS1:5G>A mutations, and gap-PCR for δβ-thal Spanish type. DNA sequencing of HBB gene was carried out in negative samples for the initial screening. RESULTS Fifteen different HBB gene mutations were observed in 148 alleles; three of them are novel: -90C>G, 20 bp deletion (at codons 78/85), and IVS2:2T>G; the mutation IVS1:6T>C that was observed for first time in our population; and eleven previously described mutations. Six alleles showed normal HBB sequence. To date, a total of 21 different mutations have been observed in Mexican patients; the four most frequent mutations are of Mediterranean origin: Cd39C>T (37.2%), IVS1:1G>A (17.3%), IVS1:110G>A (13.9%), and δβ-thal Spanish type (9.0%), which represent 77.4% of the total studied alleles. CONCLUSION Considering the novel mutations -90C>G, -20 bp Cd78/85, IVS2:2T>G and the first observation of IVS1:6T>C, the molecular spectrum of β-thal in Mexicans comprises 21 different mutations, confirming the high allelic heterogeneity in Mexicans.
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Affiliation(s)
- L C Rizo-de-la-Torre
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, México.,División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - B Ibarra
- Doctorado en Genética Humana, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, México
| | - J Y Sánchez-López
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - M T Magaña-Torres
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - V M Rentería-López
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
| | - F J Perea-Díaz
- División de Genética, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara, Jalisco, México
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Farra C, Badra R, Fares F, Muwakkit S, Dbaibo G, Dabbous I, Ashkar H, Mounsef C, Abboud MR. Alpha thalassemia allelic frequency in Lebanon. Pediatr Blood Cancer 2015; 62:120-2. [PMID: 25284125 DOI: 10.1002/pbc.25242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 08/12/2014] [Indexed: 11/06/2022]
Abstract
BACKGROUND Hemoglobinopathies are the most common reported monogenic disorders worldwide. It is well established that Mediterranean and Arab countries are high risk areas for thalassemia in general, and for alpha thalassemia in particular. Reports of alpha thalassemia gene mutations from the Lebanese population are limited. PROCEDURE We investigated the spectrum of alpha thalassemia mutations in a sample of 70 unrelated Lebanese families. Six different mutations of alpha thalassemia gene were identified. RESULTS The most prevalent mutations were the single gene deletion -α(3.7) (43%) and the non-gene deletion α2 IVS1 [-5nt] (37%). The double deletional determinant -(MED) was detected only in 14% of thalassemic chromosomes. CONCLUSION We determined the mutational spectrum of alpha thalassemia which might be used in the future for molecular investigations of the disease in susceptible patients in our population.
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Affiliation(s)
- Chantal Farra
- Department of Pathology & Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon; Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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28
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Abstract
Angiosperm mitochondrial genomes exhibit many unusual properties, including heterogeneous nucleotide composition and exceptionally large and variable genome sizes. Determining the role of nonadaptive mechanisms such as mutation bias in shaping the molecular evolution of these unique genomes has proven challenging because their dynamic structures generally prevent identification of homologous intergenic sequences for comparative analyses. Here, we report an analysis of angiosperm mitochondrial DNA sequences that are derived from inserted plastid DNA (mtpts). The availability of numerous completely sequenced plastid genomes allows us to infer the evolutionary history of these insertions, including the specific nucleotide substitutions and indels that have occurred because their incorporation into the mitochondrial genome. Our analysis confirmed that many mtpts have a complex history, including frequent gene conversion and multiple examples of horizontal transfer between divergent angiosperm lineages. Nevertheless, it is clear that the majority of extant mtpt sequence in angiosperms is the product of recent transfer (or gene conversion) and is subject to rapid loss/deterioration, suggesting that most mtpts are evolving relatively free from functional constraint. The evolution of mtpt sequences reveals a pattern of biased mutational input in angiosperm mitochondrial genomes, including an excess of small deletions over insertions and a skew toward nucleotide substitutions that increase AT content. However, these mutation biases are far weaker than have been observed in many other cellular genomes, providing insight into some of the notable features of angiosperm mitochondrial architecture, including the retention of large intergenic regions and the relatively neutral GC content found in these regions.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins
| | - Zhiqiang Wu
- Department of Biology, Colorado State University, Fort Collins
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29
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Abstract
Evolutionary innovations are dependent on mutations. Mutation rates are increased by adverse conditions in the laboratory, but there is no evidence that stressful environments that do not directly impact on DNA leave a mutational imprint on extant genomes. Mutational spectra in the laboratory are normally determined with unstressed cells but are unavailable with stressed bacteria. To by-pass problems with viability, selection effects, and growth rate differences due to stressful environments, in this study we used a set of genetically engineered strains to identify the mutational spectrum associated with nutritional stress. The strain set members each had a fixed level of the master regulator protein, RpoS, which controls the general stress response of Escherichia coli. By assessing mutations in cycA gene from 485 cycloserine resistant mutants collected from as many independent cultures with three distinct perceived stress (RpoS) levels, we were able establish a dose-dependent relationship between stress and mutational spectra. The altered mutational patterns included base pair substitutions, single base pair indels, longer indels, and transpositions of different insertion sequences. The mutational spectrum of low-RpoS cells closely matches the genome-wide spectrum previously generated in laboratory environments, while the spectra of high RpoS, high perceived stress cells more closely matches spectra found in comparisons of extant genomes. Our results offer an explanation of the uneven mutational profiles such as the transition-transversion biases observed in extant genomes and provide a framework for assessing the contribution of stress-induced mutagenesis to evolutionary transitions and the mutational emergence of antibiotic resistance and disease states.
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Affiliation(s)
- Ram Maharjan
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
| | - Thomas Ferenci
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, Australia
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30
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Ivády G, Koczok K, Madar L, Gombos E, Toth I, Gyori K, Balogh I. Molecular Analysis of Cystic Fibrosis Patients in Hungary - An Update to the Mutational Spectrum. J Med Biochem 2015; 34:46-51. [PMID: 28356823 DOI: 10.2478/jomb-2014-0055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 05/25/2014] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND In this study the authors present an update to the CFTR mutation profile in Hungary, utilizing data from a selected cohort of 45 cystic fibrosis (CF) patients from different regions of the country. METHODS Depending on the preceding analysis, four different mutation detection methods were used. A commercial assay targeting the most common CF-causing mutations was performed as the first test followed by an allele specific PCR for CFTRdele2,3(21kb), Sanger sequencing and MLPA analysis of the coding region of the CFTR gene. RESULTS In our recent study 27 different mutations were detected, including 2 novel ones (c.1037_1038insA and c.1394C>T). Besides F508del (c.1521_1523delCTT), the following mutations were found at a frequency of ≥ 4.0%: W1282X (c.3846G>A), N1303K (c.3909C>G), CFTRdele2,3(21kb) (c.54-5940_273+10250del21kb) and 2184insA (c.2052_2053insA). In addition, four mutations (G542X, Y1092X, 621+1G>T, and 2143delT) were found in more than one allele. CONCLUSIONS The updated database of Hungarian mutations not only enables to increase the efficiency of the existing diagnostic approach, but also provides a further refined basis for the introduction of the molecular newborn screening (NBS) program in Hungary.
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31
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Kohan R, Noelia Carabelos M, Xin W, Sims K, Guelbert N, Adriana Cismondi I, Pons P, Alonso GI, Troncoso M, Witting S, Pearce DA, de Kremer RD, Oller-Ramírez AM, de Halac IN. Neuronal ceroid lipofuscinosis type CLN2: a new rationale for the construction of phenotypic subgroups based on a survey of 25 cases in South America. Gene 2013; 516:114-21. [PMID: 23266810 PMCID: PMC3855401 DOI: 10.1016/j.gene.2012.12.058] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/03/2012] [Indexed: 11/18/2022]
Abstract
Tripeptidyl-peptidase 1 (TPP1) null or residual activity occurs in neuronal ceroid lipofuscinosis (NCL) with underlying TPP1/CLN2 mutations. A survey of 25 South American CLN2 affected individuals enabled the differentiation of two phenotypes: classical late-infantile and variant juvenile, each in approximately 50% of patients, with residual TPP1 activity occurring in approximately 32%. Each individual was assigned to one of three subgroups: (I) n=11, null TPP1 activity in leukocytes; (II) n=8, residual TPP1 activity of 0.60-15.85 nmol/h/mg (nr 110-476); (III) n=6, activity not measured in leukocytes. Curvilinear bodies (CB) appeared in almost all studied CLN2 subjects; the only exceptions occurred in cases of subgroup II: two individuals had combined CBs/fingerprints (FPs), and one case had pure FPs. There were 15 mutations (4 first published in this paper, 3 previously observed in South America by our group, and 8 previously observed by others). In subgroup I, mutations were either missense or nonsense; in subgroups II and III, mutations prevailed at the non-conserved intronic site, c.887-10A>G (intron 7), and to a lesser extent at c.89+5G>C (intron 2), in heterozygous combinations. Grouping phenotypically and genetically known individuals on the basis of TPP1 activity supported the concept that residual enzyme activity underlies a protracted disease course. The prevalence of intronic mutations at non-conserved sites in subgroup II individuals indicates that some alternative splicing might allow some residual TPP1 activity.
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Affiliation(s)
- Romina Kohan
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
- Facultad de Odontología, Universidad Nacional de Córdoba. Haya de la Torre s/n, (5000) Córdoba, Argentina
- Secretaría de Ciencia y Tecnología (SECyT), Universidad Nacional de Córdoba. Juan Filloy s/n, (5000) Córdoba, Argentina
| | - María Noelia Carabelos
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Winnie Xin
- Massachussets General Hospital, Neurogenetics DNA Diagnostic Laboratory, Simches Research Building, 5 300, 185 Cambridge St., Boston, Massachussets 02114, USA
| | - Katherine Sims
- Massachussets General Hospital, Neurogenetics DNA Diagnostic Laboratory, Simches Research Building, 5 300, 185 Cambridge St., Boston, Massachussets 02114, USA
| | - Norberto Guelbert
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Inés Adriana Cismondi
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
- Massachussets General Hospital, Neurogenetics DNA Diagnostic Laboratory, Simches Research Building, 5 300, 185 Cambridge St., Boston, Massachussets 02114, USA
| | - Patricia Pons
- Centro de Microscopía Electrónica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba, Haya de la Torre esq. Enrique Barros, 1° piso, (5000) Córdoba, Argentina
| | - Graciela Irene Alonso
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Mónica Troncoso
- Servicio de Neuropsiquiatría Infantil. Hospital Clínico San Borja Arriarán, Avenida Santa Rosa 1234, Santiago, Chile
| | - Scarlet Witting
- Servicio de Neuropsiquiatría Infantil. Hospital Clínico San Borja Arriarán, Avenida Santa Rosa 1234, Santiago, Chile
| | - David A. Pearce
- Sanford Childrens Health Research Center, Sanford Research/USD, Sioux Falls, South Dakota, USA
| | - Raquel Dodelson de Kremer
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Ana María Oller-Ramírez
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
| | - Inés Noher de Halac
- Centro de Estudio de las Metabolopatías Congénitas (CEMECO), Cátedra de Clínica Pediátrica, Facultad de Ciencias Médicas, Universidad Nacional de Córdoba. Ferroviarios 1250, (5014) Córdoba, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Av. Rivadavia 1917, C1033AAJ CABA, Argentina
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32
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Abstract
Although mutation provides the fuel for phenotypic evolution, it also imposes a substantial burden on fitness through the production of predominantly deleterious alleles, a matter of concern from a human-health perspective. Here, recently established databases on de novo mutations for monogenic disorders are used to estimate the rate and molecular spectrum of spontaneously arising mutations and to derive a number of inferences with respect to eukaryotic genome evolution. Although the human per-generation mutation rate is exceptionally high, on a per-cell division basis, the human germline mutation rate is lower than that recorded for any other species. Comparison with data from other species demonstrates a universal mutational bias toward A/T composition, and leads to the hypothesis that genome-wide nucleotide composition generally evolves to the point at which the power of selection in favor of G/C is approximately balanced by the power of random genetic drift, such that variation in equilibrium genome-wide nucleotide composition is largely defined by variation in mutation biases. Quantification of the hazards associated with introns reveals that mutations at key splice-site residues are a major source of human mortality. Finally, a consideration of the long-term consequences of current human behavior for deleterious-mutation accumulation leads to the conclusion that a substantial reduction in human fitness can be expected over the next few centuries in industrialized societies unless novel means of genetic intervention are developed.
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Affiliation(s)
- Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
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