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Ren P, Zhang J, Vijg J. Somatic mutations in aging and disease. GeroScience 2024; 46:5171-5189. [PMID: 38488948 PMCID: PMC11336144 DOI: 10.1007/s11357-024-01113-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Time always leaves its mark, and our genome is no exception. Mutations in the genome of somatic cells were first hypothesized to be the cause of aging in the 1950s, shortly after the molecular structure of DNA had been described. Somatic mutation theories of aging are based on the fact that mutations in DNA as the ultimate template for all cellular functions are irreversible. However, it took until the 1990s to develop the methods to test if DNA mutations accumulate with age in different organs and tissues and estimate the severity of the problem. By now, numerous studies have documented the accumulation of somatic mutations with age in normal cells and tissues of mice, humans, and other animals, showing clock-like mutational signatures that provide information on the underlying causes of the mutations. In this review, we will first briefly discuss the recent advances in next-generation sequencing that now allow quantitative analysis of somatic mutations. Second, we will provide evidence that the mutation rate differs between cell types, with a focus on differences between germline and somatic mutation rate. Third, we will discuss somatic mutational signatures as measures of aging, environmental exposure, and activities of DNA repair processes. Fourth, we will explain the concept of clonally amplified somatic mutations, with a focus on clonal hematopoiesis. Fifth, we will briefly discuss somatic mutations in the transcriptome and in our other genome, i.e., the genome of mitochondria. We will end with a brief discussion of a possible causal contribution of somatic mutations to the aging process.
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Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jie Zhang
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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2
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Heid J, Cutler R, Lee M, Vijg J, Maslov AY. Concurrent analysis of genome and transcriptome in one single cell. BMC Res Notes 2024; 17:267. [PMID: 39285281 PMCID: PMC11403997 DOI: 10.1186/s13104-024-06927-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 08/29/2024] [Indexed: 09/22/2024] Open
Abstract
Thus far, multiple techniques for single cell analysis have been developed, yet we lack a relatively simple tool to assess DNA and RNA from the same cell at whole-transcriptome and whole-genome depths. Here we present an updated method for physical separation of cytoplasmic RNA from the nuclei, which allows for simultaneous studies of DNA and RNA from the same single cell. The method consists of three steps-(1) immobilization of a single cell on solid substrate, (2) hypotonic lysis of immobilized single cell, and (3) separation of cytosol containing aqueous phase and immobilized nucleus. We found that DNA and RNA extracted from single cell using our approach is suitable for downstream sequencing-based applications. We demonstrated that the coverage of transcriptome and genome sequencing data obtained after DNA/RNA separation is similar to that observed without separation. We also showed that the separation procedure does not create any noticeable bias in observed mutational load or mutation spectra. Thus, our method can serve as a tool for simultaneous complex analysis of the genome and transcriptome, providing necessary information on the relationship between somatic mutations and the regulation of gene expression.
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Affiliation(s)
- Johanna Heid
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Perlmutter Cancer Center, NYU Langone, New York, USA.
| | - Ronald Cutler
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
- Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technology, Voronezh, 394000, Russia.
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3
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Heid J, Cutler R, Sun S, Lee M, Maslov AY, Dong X, Sidoli S, Vijg J. Negative selection allows human primary fibroblasts to tolerate high somatic mutation loads induced by N-ethyl-N-nitrosourea. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588286. [PMID: 38617356 PMCID: PMC11014556 DOI: 10.1101/2024.04.07.588286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Single-cell sequencing has shown that thousands of mutations accumulate with age in most human tissues. While there is ample evidence that some mutations can clonally amplify and lead to disease, the total burden of mutations a cell tolerates without functional decline remains unknown. Here we addressed this question by exposing human primary fibroblasts to multiple, low doses of N-ethyl-N-nitrosourea (ENU) and analyzed somatic mutation burden using single-cell whole genome sequencing. The results indicate that individual cells can sustain ∼60,000 single-nucleotide variants (SNVs) with only a slight adverse effect on growth rate. We provide evidence that such high levels of mutations are only tolerated through negative selection against variants in gene coding regions, and in sequences associated with genetic pathways for maintaining basic cellular function and growth. Since most tissues in adults are non-dividing, these results suggest that somatic mutations in the absence of negative selection may have functionally adverse effects.
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4
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Pfeifer GP, Jin SG. Methods and applications of genome-wide profiling of DNA damage and rare mutations. Nat Rev Genet 2024:10.1038/s41576-024-00748-4. [PMID: 38918545 DOI: 10.1038/s41576-024-00748-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
DNA damage is a threat to genome integrity and can be a cause of many human diseases, owing to either changes in the chemical structure of DNA or conversion of the damage into a mutation, that is, a permanent change in DNA sequence. Determining the exact positions of DNA damage and ensuing mutations in the genome are important for identifying mechanisms of disease aetiology when characteristic mutations are prevalent and probably causative in a particular disease. However, this approach is challenging particularly when levels of DNA damage are low, for example, as a result of chronic exposure to environmental agents or certain endogenous processes, such as the generation of reactive oxygen species. Over the past few years, a comprehensive toolbox of genome-wide methods has been developed for the detection of DNA damage and rare mutations at single-nucleotide resolution in mammalian cells. Here, we review and compare these methods, describe their current applications and discuss future research questions that can now be addressed.
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Affiliation(s)
- Gerd P Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA.
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
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5
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Zhang L, Lee M, Maslov AY, Montagna C, Vijg J, Dong X. Analyzing somatic mutations by single-cell whole-genome sequencing. Nat Protoc 2024; 19:487-516. [PMID: 37996541 PMCID: PMC11406548 DOI: 10.1038/s41596-023-00914-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/18/2023] [Indexed: 11/25/2023]
Abstract
Somatic mutations are the cause of cancer and have been implicated in other, noncancerous diseases and aging. While clonally expanded mutations can be studied by deep sequencing of bulk DNA, very few somatic mutations expand clonally, and most are unique to each cell. We describe a detailed protocol for single-cell whole-genome sequencing to discover and analyze somatic mutations in tissues and organs. The protocol comprises single-cell multiple displacement amplification (SCMDA), which ensures efficiency and high fidelity in amplification, and the SCcaller software tool to call single-nucleotide variations and small insertions and deletions from the sequencing data by filtering out amplification artifacts. With SCMDA and SCcaller at its core, this protocol describes a complete procedure for the comprehensive analysis of somatic mutations in a single cell, covering (1) single-cell or nucleus isolation, (2) single-cell or nucleus whole-genome amplification, (3) library preparation and sequencing, and (4) computational analyses, including alignment, variant calling, and mutation burden estimation. Methods are also provided for mutation annotation, hotspot discovery and signature analysis. The protocol takes 12-15 h from single-cell isolation to library preparation and 3-7 d of data processing. Compared with other single-cell amplification methods or single-molecular sequencing, it provides high genomic coverage, high accuracy in single-nucleotide variation and small insertions and deletion calling from the same single-cell genome, and fewer processing steps. SCMDA and SCcaller require basic experience in molecular biology and bioinformatics. The protocol can be utilized for studying mutagenesis and genome mosaicism in normal and diseased human and animal tissues under various conditions.
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Affiliation(s)
- Lei Zhang
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA.
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technology, Voronezh, Russia
| | - Cristina Montagna
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Dong
- Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, USA.
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA.
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6
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Maslov AY, Vijg J. Somatic mutation burden in relation to aging and functional life span: implications for cellular reprogramming and rejuvenation. Curr Opin Genet Dev 2023; 83:102132. [PMID: 37931583 PMCID: PMC10841402 DOI: 10.1016/j.gde.2023.102132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/02/2023] [Accepted: 10/07/2023] [Indexed: 11/08/2023]
Abstract
The accrual of somatic mutations has been implicated as causal factors in aging since the 1950s. However, the quantitative analysis of somatic mutations has posed a major challenge due to the random nature of de novo mutations in normal tissues, which has limited analysis to tumors and other clonal lineages. Advances in single-cell and single-molecule next-generation sequencing now allow to obtain, for the first time, detailed insights into the landscape of somatic mutations in different human tissues and cell types as a function of age under various conditions. Here, we will briefly recapitulate progress in somatic mutation analysis and discuss the possible relationship between somatic mutation burden with functional life span, with a focus on differences between germ cells, stem cells, and differentiated cells.
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Affiliation(s)
- Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technologies, Voronezh, Russia.
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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7
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Heid J, Cutler R, Lee M, Vijg J, Maslov AY. Concurrent analysis of genome and transcriptome in one single cell. RESEARCH SQUARE 2023:rs.3.rs-3186428. [PMID: 37577506 PMCID: PMC10418558 DOI: 10.21203/rs.3.rs-3186428/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Thus far, multiple techniques for single cell analysis have been developed, yet we lack a relatively simple tool to assess DNA and RNA from the same cell at whole-transcriptome and whole-genome depths. Here we present an updated method for physical separation of cytoplasmic RNA from the nuclei, which allows for simultaneous studies of DNA and RNA from the same single cell. The method consists of three steps - 1) immobilization of a single cell on solid substrate, 2) hypotonic lysis of immobilized single cell, and 3) separation of cytosol containing aqueous phase and immobilized nucleus. We found that DNA and RNA extracted from single cell using our approach is suitable for downstream sequencing-based applications. We demonstrated that the coverage of transcriptome and genome sequencing data obtained after DNA/RNA separation is similar to that observed without separation. We also showed that the separation procedure does not create any noticeable bias in observed mutational load or mutation spectra. Thus, our method can serve as a tool for simultaneous complex analysis of the genome and transcriptome, providing necessary information on the relationship between somatic mutations and the regulation of gene expression.
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Affiliation(s)
| | | | | | - Jan Vijg
- Albert Einstein College of Medicine
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8
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Schneider BK, Sun S, Lee M, Li W, Skvir N, Neretti N, Vijg J, Secombe J. Expression of retrotransposons contributes to aging in Drosophila. Genetics 2023; 224:iyad073. [PMID: 37084379 PMCID: PMC10213499 DOI: 10.1093/genetics/iyad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/12/2022] [Accepted: 04/11/2023] [Indexed: 04/23/2023] Open
Abstract
Retrotransposons are a class of transposable elements capable of self-replication and insertion into new genomic locations. Across species, the mobilization of retrotransposons in somatic cells has been suggested to contribute to the cell and tissue functional decline that occurs during aging. Retrotransposons are broadly expressed across cell types, and de novo insertions have been observed to correlate with tumorigenesis. However, the extent to which new retrotransposon insertions occur during normal aging and their effect on cellular and animal function remains understudied. Here, we use a single nucleus whole genome sequencing approach in Drosophila to directly test whether transposon insertions increase with age in somatic cells. Analyses of nuclei from thoraces and indirect flight muscles using a newly developed pipeline, Retrofind, revealed no significant increase in the number of transposon insertions with age. Despite this, reducing the expression of two different retrotransposons, 412 and Roo, extended lifespan, but did not alter indicators of health such as stress resistance. This suggests a key role for transposon expression and not insertion in regulating longevity. Transcriptomic analyses revealed similar changes to gene expression in 412 and Roo knockdown flies and highlighted changes to genes involved in proteolysis and immune function as potential contributors to the observed changes in longevity. Combined, our data show a clear link between retrotransposon expression and aging.
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Affiliation(s)
- Blair K Schneider
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Ullmann 809 Bronx, NY 10461, USA
| | - Shixiang Sun
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Price 468 Bronx, NY 10461, USA
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Price 468 Bronx, NY 10461, USA
| | - Wenge Li
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Ullmann 909 Bronx, NY 10461, USA
| | - Nicholas Skvir
- Department of Molecular biology, Cell biology and Biochemistry, Brown University, 70 Ship St., Providence 02903, USA
| | - Nicola Neretti
- Department of Molecular biology, Cell biology and Biochemistry, Brown University, 70 Ship St., Providence 02903, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Price 468 Bronx, NY 10461, USA
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Ullmann 809 Bronx, NY 10461, USA
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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9
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Ren P, Dong X, Vijg J. Age-related somatic mutation burden in human tissues. FRONTIERS IN AGING 2022; 3:1018119. [PMID: 36213345 PMCID: PMC9534562 DOI: 10.3389/fragi.2022.1018119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
The genome of multicellular organisms carries the hereditary information necessary for the development of all organs and tissues and to maintain function in adulthood. To ensure the genetic stability of the species, genomes are protected against changes in sequence information. However, genomes are not static. De novo mutations in germline cells are passed on to offspring and generate the variation needed in evolution. Moreover, postzygotic mutations occur in all somatic cells during development and aging. These somatic mutations remain limited to the individual, generating tissues that are genome mosaics. Insight into such mutations and their consequences has been limited due to their extremely low abundance, with most mutations unique for each cell. Recent advances in sequencing, including whole genome sequencing at the single-cell level, have now led to the first insights into somatic mutation burdens in human tissues. Here, we will first briefly describe the latest methodology for somatic mutation analysis, then review our current knowledge of somatic mutation burden in human tissues and, finally, briefly discuss the possible functional impact of somatic mutations on the aging process and age-related diseases, including cancer and diseases other than cancer.
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Affiliation(s)
- Peijun Ren
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
| | - Xiao Dong
- Department of Genetics, Cell Biology and Development, Institute on the Biology of Aging and Metabolism, University of Minnesota, Minneapolis, MN, United States,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
| | - Jan Vijg
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Department of Genetics, Albert Einstein College of Medicine, New York City, NY, United States,*Correspondence: Peijun Ren, ; Xiao Dong, ; Jan Vijg, ,
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Huang AY, Lee EA. Identification of Somatic Mutations From Bulk and Single-Cell Sequencing Data. FRONTIERS IN AGING 2022; 2:800380. [PMID: 35822012 PMCID: PMC9261417 DOI: 10.3389/fragi.2021.800380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
Abstract
Somatic mutations are DNA variants that occur after the fertilization of zygotes and accumulate during the developmental and aging processes in the human lifespan. Somatic mutations have long been known to cause cancer, and more recently have been implicated in a variety of non-cancer diseases. The patterns of somatic mutations, or mutational signatures, also shed light on the underlying mechanisms of the mutational process. Advances in next-generation sequencing over the decades have enabled genome-wide profiling of DNA variants in a high-throughput manner; however, unlike germline mutations, somatic mutations are carried only by a subset of the cell population. Thus, sensitive bioinformatic methods are required to distinguish mutant alleles from sequencing and base calling errors in bulk tissue samples. An alternative way to study somatic mutations, especially those present in an extremely small number of cells or even in a single cell, is to sequence single-cell genomes after whole-genome amplification (WGA); however, it is critical and technically challenging to exclude numerous technical artifacts arising during error-prone and uneven genome amplification in current WGA methods. To address these challenges, multiple bioinformatic tools have been developed. In this review, we summarize the latest progress in methods for identification of somatic mutations and the challenges that remain to be addressed in the future.
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Affiliation(s)
- August Yue Huang
- Division of Genetics and Genomics, Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, United States, Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Manton Center for Orphan Diseases, Boston Children's Hospital, Boston, MA, United States, Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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11
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Maslov AY, Makhortov S, Sun S, Heid J, Dong X, Lee M, Vijg J. Single-molecule, quantitative detection of low-abundance somatic mutations by high-throughput sequencing. SCIENCE ADVANCES 2022; 8:eabm3259. [PMID: 35394831 PMCID: PMC8993124 DOI: 10.1126/sciadv.abm3259] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
Postzygotic somatic mutations have been found associated with human disease, including diseases other than cancer. Most information on somatic mutations has come from studying clonally amplified mutant cells, based on a growth advantage or genetic drift. However, almost all somatic mutations are unique for each cell, and the quantitative analysis of these low-abundance mutations in normal tissues remains a major challenge in biology. Here, we introduce single-molecule mutation sequencing (SMM-seq), a novel approach for quantitative identification of point mutations in normal cells and tissues.
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Affiliation(s)
- Alexander Y. Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technologies, Voronezh, Russia
| | - Sergey Makhortov
- Department of Programming and Information Technology, Voronezh State University, Voronezh, Russia
| | - Shixiang Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Johanna Heid
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Institute on the Biology of Aging and Metabolism and Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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12
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Vijg J. From DNA damage to mutations: All roads lead to aging. Ageing Res Rev 2021; 68:101316. [PMID: 33711511 PMCID: PMC10018438 DOI: 10.1016/j.arr.2021.101316] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/20/2022]
Abstract
Damage to the repository of genetic information in cells has plagued life since its very beginning 3-4 billion years ago. Initially, in the absence of an ozone layer, especially damage from solar UV radiation must have been frequent, with other sources, most notably endogenous sources related to cell metabolism, gaining in importance over time. To cope with this high frequency of damage to the increasingly long DNA molecules that came to encode the growing complexity of cellular functions in cells, DNA repair evolved as one of the earliest genetic traits. Then as now, errors during the repair of DNA damage generated mutations, which provide the substrate for evolution by natural selection. With the emergence of multicellular organisms also the soma became a target of DNA damage and mutations. In somatic cells selection against the adverse effects of DNA damage is greatly diminished, especially in postmitotic cells after the age of first reproduction. Based on an abundance of evidence, DNA damage is now considered as the single most important driver of the degenerative processes that collectively cause aging. Here I will first briefly review the evidence for DNA damage as a cause of aging since the beginning of life. Then, after discussing the possible direct adverse effects of DNA damage and its cellular responses, I will provide an overview of the considerable progress that has recently been made in analyzing a major consequence of DNA damage in humans and other complex organisms: somatic mutations and the resulting genome mosaicism. Recent advances in studying somatic mutagenesis and genome mosaicism in different human and animal tissues will be discussed with a focus on the possible mechanisms through which loss of DNA sequence integrity could cause age-related functional decline and disease.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA; Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
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13
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Jivanji S, Harland C, Cole S, Brophy B, Garrick D, Snell R, Littlejohn M, Laible G. The genomes of precision edited cloned calves show no evidence for off-target events or increased de novo mutagenesis. BMC Genomics 2021; 22:457. [PMID: 34139989 PMCID: PMC8212539 DOI: 10.1186/s12864-021-07804-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/31/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Animal health and welfare are at the forefront of public concern and the agricultural sector is responding by prioritising the selection of welfare-relevant traits in their breeding schemes. In some cases, welfare-enhancing traits such as horn-status (i.e., polled) or diluted coat colour, which could enhance heat tolerance, may not segregate in breeds of primary interest, highlighting gene-editing tools such as the CRISPR-Cas9 technology as an approach to rapidly introduce variation into these populations. A major limitation preventing the acceptance of CRISPR-Cas9 mediated gene-editing, however, is the potential for off-target mutagenesis, which has raised concerns about the safety and ultimate applicability of this technology. Here, we present a clone-based study design that has allowed a detailed investigation of off-target and de novo mutagenesis in a cattle line bearing edits in the PMEL gene for diluted coat-colour. RESULTS No off-target events were detected from high depth whole genome sequencing performed in precursor cell-lines and resultant calves cloned from those edited and non-edited cell lines. Long molecule sequencing at the edited site and plasmid-specific PCRs did not reveal structural variations and/or plasmid integration events in edited samples. Furthermore, an in-depth analysis of de novo mutations across the edited and non-edited cloned calves revealed that the mutation frequency and spectra were unaffected by editing status. Cells in culture, however, appeared to have a distinct mutation signature where de novo mutations were predominantly C > A mutations, and in cloned calves they were predominantly T > G mutations, deviating from the expected excess of C > T mutations. CONCLUSIONS We found no detectable CRISPR-Cas9 associated off-target mutations in the gene-edited cells or calves derived from the gene-edited cell line. Comparison of de novo mutation in two gene-edited calves and three non-edited control calves did not reveal a higher mutation load in any one group, gene-edited or control, beyond those anticipated from spontaneous mutagenesis. Cell culture and somatic cell nuclear transfer cloning processes contributed the major source of contrast in mutational profile between samples.
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Affiliation(s)
- Swati Jivanji
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand.
| | - Chad Harland
- Livestock Improvement Corporation, Newstead, New Zealand
| | - Sally Cole
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand
| | - Brigid Brophy
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand
| | - Dorian Garrick
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Russell Snell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Mathew Littlejohn
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
- Livestock Improvement Corporation, Newstead, New Zealand
| | - Götz Laible
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand
- School of Medical Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
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14
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Accurate genomic variant detection in single cells with primary template-directed amplification. Proc Natl Acad Sci U S A 2021; 118:2024176118. [PMID: 34099548 PMCID: PMC8214697 DOI: 10.1073/pnas.2024176118] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Improvements in whole genome amplification (WGA) would enable new types of basic and applied biomedical research, including studies of intratissue genetic diversity that require more accurate single-cell genotyping. Here, we present primary template-directed amplification (PTA), an isothermal WGA method that reproducibly captures >95% of the genomes of single cells in a more uniform and accurate manner than existing approaches, resulting in significantly improved variant calling sensitivity and precision. To illustrate the types of studies that are enabled by PTA, we developed direct measurement of environmental mutagenicity (DMEM), a tool for mapping genome-wide interactions of mutagens with single living human cells at base-pair resolution. In addition, we utilized PTA for genome-wide off-target indel and structural variant detection in cells that had undergone CRISPR-mediated genome editing, establishing the feasibility for performing single-cell evaluations of biopsies from edited tissues. The improved precision and accuracy of variant detection with PTA overcomes the current limitations of accurate WGA, which is the major obstacle to studying genetic diversity and evolution at cellular resolution.
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15
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Pan B, Kaldhone PR, Alund AW, Du H, Guo X, Yan J, Chen Y, Zhou T, Robison TW, Chen T. Mutagenicity of silver nanoparticles evaluated using whole-genome sequencing in mouse lymphoma cells. Nanotoxicology 2021; 15:418-432. [PMID: 33710943 DOI: 10.1080/17435390.2021.1894614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The increasing medical and food applications of silver nanoparticles (AgNPs) raise concerns about their safety, including the potential health consequences of human exposure. Previous studies found that AgNPs were negative in the Ames test due to both their microbicidal activity and the inability of nanoparticles to penetrate bacterial cell walls. Thus, the mutagenicity of AgNPs is still not completely clear, though they do induce chromosome damage, as suggested by many previous genotoxicity studies. In this study, whole-genome sequencing (WGS) was used to analyze the mutagenicity of AgNPs in mouse lymphoma cells expanded from single-cell clones. The cells were treated with AgNPs, 4-nitroquinolone-1-oxide (4-NQO) as the positive control, and vehicle controls. Both AgNPs and 4-NQO significantly increased mutation frequencies over their concurrent controls by 1.12-fold and 4.89-fold with mutation rates at 4-fold and 130-fold, respectively. AgNP-induced mutations mainly occurred at G:C sites with G:C > T:A transversions, G:C > A:T transitions, and deletions as the most commonly observed mutations. AgNPs also induced higher fold changes in tandem mutations. The results suggest that the WGS mutation assay conducted here can detect the low-level mutagenicity of AgNPs, providing substantial support for the use of the WGS method as a possible alternative assay with respect to the mutagenic assessment of nanomaterials.
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Affiliation(s)
- Bohu Pan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Pravin R Kaldhone
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Alexander W Alund
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Hua Du
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Xiaoqing Guo
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Ying Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
| | - Tong Zhou
- Center for Veterinary Medicine, Food and Drug Administration, Rockville, MD, USA
| | - Timothy W Robison
- Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
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16
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Principles of the Molecular and Cellular Mechanisms of Aging. J Invest Dermatol 2021; 141:951-960. [PMID: 33518357 DOI: 10.1016/j.jid.2020.11.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022]
Abstract
Aging can be defined as a state of progressive functional decline accompanied by an increase in mortality. Time-dependent accumulation of cellular damage, namely lesions and mutations in the DNA and misfolded proteins, impair organellar and cellular function. Ensuing cell fate alterations lead to the accumulation of dysfunctional cells and hamper homeostatic processes, thus limiting regenerative potential; trigger low-grade inflammation; and alter intercellular and intertissue communication. The accumulation of molecular damage together with modifications in the epigenetic landscape, dysregulation of gene expression, and altered endocrine communication, drive the aging process and establish age as the main risk factor for age-associated diseases and multimorbidity.
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17
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Dong X, Zhang L, Hao X, Wang T, Vijg J. SCCNV: A Software Tool for Identifying Copy Number Variation From Single-Cell Whole-Genome Sequencing. Front Genet 2020; 11:505441. [PMID: 33304377 PMCID: PMC7701142 DOI: 10.3389/fgene.2020.505441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 10/28/2020] [Indexed: 01/07/2023] Open
Abstract
Identification of de novo copy number variations (CNVs) across the genome in single cells requires single-cell whole-genome amplification (WGA) and sequencing. Although many experimental protocols of amplification methods have been developed, all suffer from uneven distribution of read depth across the genome after sequencing of DNA amplicons, which constrains the usage of conventional CNV calling methodologies. Here, we present SCCNV, a software tool for detecting CNVs from whole genome-amplified single cells. SCCNV is a read-depth based approach with adjustment for the WGA bias. We demonstrate its performance by analyzing data obtained with most of the single-cell amplification methods that have been employed for CNV analysis, including DOP-PCR, MDA, MALBAC, and LIANTI. SCCNV is freely available at https://github.com/biosinodx/SCCNV.
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Affiliation(s)
- Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Xiaoxiao Hao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, United States
- Center for Single-Cell Omics in Aging and Disease, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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18
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Albertini RJ, Kaden DA. Mutagenicity monitoring in humans: Global versus specific origin of mutations. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 786:108341. [PMID: 33339577 DOI: 10.1016/j.mrrev.2020.108341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 10/08/2020] [Accepted: 10/14/2020] [Indexed: 01/19/2023]
Abstract
An underappreciated aspect of human mutagenicity biomonitoring is tissue specificity reflected in different assays, especially those that measure events that can only occur in developing bone marrow (BM) cells. Reviewed here are 9 currently-employed human mutagenicity biomonitoring assays. Several assays measure chromosome-level events in circulating T-lymphocytes (T-cells), i.e., traditional analyses of aberrations, translocation studies involving chromosome painting and fluorescence in situ hybridization (FISH) and determinations of micronuclei (MN). Other T-cell assays measure gene mutations. i.e., hypoxanthine-guanine phosphoriboslytransferase (HPRT) and phosphoribosylinositol glycan class A (PIGA). In addition to the T-cell assays, also reviewed are those assays that measure events in peripheral blood cells that necessarily arose in BM cells, i.e., MN in reticulocytes; glycophorin A (GPA) gene mutations in red blood cells (RBCs), and PIGA gene mutations in RBC or granulocytes. This review considers only cell culture- or cytometry-based assays to describe endpoints measured, methods, optimal sampling times, and sample summaries of typical quantitative and qualitative results. However, to achieve its intended focus on the target cells where events occur, kinetics of the cells of peripheral blood that derive at some point from precursor cells are reviewed to identify body sites and tissues where the genotoxic events originate. Kinetics indicate that in normal adults, measured events in T-cells afford global assessments of in vivo mutagenicity but are not specific for BM effects. Therefore, an agent's capacity for inducing mutations in BM cells cannot be reliably inferred from T-cell assays as the magnitude of effect in BM, if any, is unknown. By contrast, chromosome or gene level mutations measured in RBCs/reticulocytes or granulocytes must originate in BM cells, i.e. in RBC or granulocyte precursors, thereby making them specific indicators for effects in BM. Assays of mutations arising directly in BM cells may quantitatively reflect the mutagenicity of potential leukemogenic agents.
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Affiliation(s)
- Richard J Albertini
- University of Vermont, 111 Colchester Avenue, Burlington, VT 05401, United States
| | - Debra A Kaden
- Ramboll US Consulting, Inc., 101 Federal Street, Suite 1900, Boston, MA 02110, United States.
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19
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He X, Memczak S, Qu J, Belmonte JCI, Liu GH. Single-cell omics in ageing: a young and growing field. Nat Metab 2020; 2:293-302. [PMID: 32694606 DOI: 10.1038/s42255-020-0196-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 03/17/2020] [Indexed: 12/28/2022]
Abstract
Organismal ageing results from interlinked molecular changes in multiple organs over time. The study of ageing at the molecular level is complicated by varying decay characteristics and kinetics-both between and within organs-driven by intrinsic and extracellular factors. Emerging single-cell omics methods allow for molecular and spatial profiling of cells, and probing of regulatory states and cell-fate determination, thus providing promising tools for unravelling the heterogeneous process of ageing and making it amenable to intervention. These new strategies are enabled by advances in genomic, epigenomic and transcriptomic technologies. Combined with methods for proteome and metabolome analysis, single-cell techniques provide multidimensional, integrated data with unprecedented detail and throughput. Here, we provide an overview of the current state, and perspectives on the future, of this emerging field. We discuss how single-cell approaches can advance understanding of mechanisms underlying organismal ageing and aid in the development of interventions for ageing and ageing-associated diseases.
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Affiliation(s)
- Xiaojuan He
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Sebastian Memczak
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | | | - Guang-Hui Liu
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing, China.
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing, China.
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20
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Brazhnik K, Sun S, Alani O, Kinkhabwala M, Wolkoff AW, Maslov AY, Dong X, Vijg J. Single-cell analysis reveals different age-related somatic mutation profiles between stem and differentiated cells in human liver. SCIENCE ADVANCES 2020; 6:eaax2659. [PMID: 32064334 PMCID: PMC6994209 DOI: 10.1126/sciadv.aax2659] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 11/22/2019] [Indexed: 06/10/2023]
Abstract
Accumulating somatic mutations have been implicated in age-related cellular degeneration and death. Because of their random nature and low abundance, somatic mutations are difficult to detect except in single cells or clonal cell lineages. Here, we show that in single hepatocytes from human liver, an organ exposed to high levels of genotoxic stress, somatic mutation frequencies are high and increase substantially with age. Considerably lower mutation frequencies were observed in liver stem cells (LSCs) and organoids derived from them. Mutational spectra in hepatocytes showed signatures of oxidative stress that were different in old age and in LSCs. A considerable number of mutations were found in functional parts of the liver genome, suggesting that somatic mutagenesis could causally contribute to the age-related functional decline and increased incidence of disease of human liver. These results underscore the importance of stem cells in maintaining genome sequence integrity in aging somatic tissues.
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Affiliation(s)
- K. Brazhnik
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - S. Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - O. Alani
- Division of Transplant Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - M. Kinkhabwala
- Division of Transplant Surgery, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - A. W. Wolkoff
- Marion Bessin Liver Research Center, Division of Hepatology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, NY, USA
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - A. Y. Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - X. Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - J. Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
- Center for Single-Cell Omics in Aging and Disease, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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21
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Saini N, Gordenin DA. Somatic mutation load and spectra: A record of DNA damage and repair in healthy human cells. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:672-686. [PMID: 30152078 PMCID: PMC6188803 DOI: 10.1002/em.22215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/07/2018] [Accepted: 06/11/2018] [Indexed: 05/31/2023]
Abstract
Somatic genome instability is a hallmark of cancer genomes and has been linked to aging and a variety of other pathologies. Large-scale cancer genome and exome sequencing have revealed that mutation load and spectra in cancers can be influenced by environmental exposures, the anatomical site of exposures, and tissue type. There is now an abundance of data favoring the hypothesis that a substantial portion of the mutations in cancers originate prior to carcinogenesis in stem cells of the healthy individual. Rapid advances in sequencing of noncancer cells from healthy humans have shown that their mutation loads and spectra resemble cancer data. Similar to cancer genomes, mutation profiles of healthy cells show marked intra-individual variation, thus providing a metric of the various factors-environmental and endogenous-involved in mutagenesis in these individuals. This review focuses on the current methodologies to measure mutation loads and to determine mutation signatures for evaluating the environmental and endogenous sources of DNA damage in human somatic cells. We anticipate that in future, such large-scale studies aimed at exploring the landscapes of somatic mutations across different cell types in healthy people would provide a valuable resource for designing personalized preventative strategies against diseases associated with somatic genome instability. Environ. Mol. Mutagen. 59:672-686, 2018. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA
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22
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Accelerated aging in schizophrenia and related disorders: Future research. Schizophr Res 2018; 196:4-8. [PMID: 28689755 DOI: 10.1016/j.schres.2017.06.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 06/15/2017] [Accepted: 06/19/2017] [Indexed: 01/17/2023]
Abstract
Several lines of evidence suggest schizophrenia is a segmental progeria, that is, some but not all aspects of accelerated aging may be present. However, the evidence has not been consistent. Problems with matching and confounding may account for some of these discrepancies. Given the etiopathophysiological heterogeneity of schizophrenia, it is possible that only a specific pathophysiological group within schizophrenia is associated with progeroid features, while others are not, or that one group is associated with a particular segment of aging features, while other progeroid features are found in another pathophysiological subgroup. In the aging research field, significant progress has been made in identifying the molecular pathways that confer aging: epigenetic changes, inflammation, proteostasis, adult stem cell function, metabolic changes, and adaptation to stress, and macromolecular damage. In addition to replication and clarification of existing kinds of evidence, examining these aging pathways would improve our understanding of progeria in schizophrenia.
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23
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Tian X, Seluanov A, Gorbunova V. Molecular Mechanisms Determining Lifespan in Short- and Long-Lived Species. Trends Endocrinol Metab 2017; 28:722-734. [PMID: 28888702 PMCID: PMC5679293 DOI: 10.1016/j.tem.2017.07.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/16/2017] [Accepted: 07/25/2017] [Indexed: 12/20/2022]
Abstract
Aging is a global decline of physiological functions, leading to an increased susceptibility to diseases and ultimately death. Maximum lifespans differ up to 200-fold between mammalian species. Although considerable progress has been achieved in identifying conserved pathways that regulate individual lifespan within model organisms, whether the same pathways are responsible for the interspecies differences in longevity remains to be determined. Recent cross-species studies have begun to identify pathways responsible for interspecies differences in lifespan. Here, we review the evidence supporting the role of anticancer mechanisms, DNA repair machinery, insulin/insulin-like growth factor 1 signaling, and proteostasis in defining species lifespans. Understanding the mechanisms responsible for the dramatic differences in lifespan between species will have a transformative effect on developing interventions to improve human health and longevity.
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Affiliation(s)
- Xiao Tian
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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24
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Abstract
A central challenge in sequencing single-cell genomes is the accurate determination of point mutations, phasing of these mutations, and identifying copy number variations with few assumptions. Ideally, this is accomplished under as low sequencing coverage as possible. Here we report our attempt to meet these goals with a novel library construction and library amplification methodology. In our approach, single-cell genomic DNA is first fragmented with saturated transposition to make a primary library that uniformly covers the whole genome by short fragments. The library is then amplified by a carefully optimized PCR protocol in a uniform and synchronized fashion for next-generation sequencing. Each step of the protocol can be quantitatively characterized. Our shallow sequencing data show that the library is tightly distributed and is useful for the determination of copy number variations.
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25
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Du H, Pan B, Chen T. Evaluation of chemical mutagenicity using next generation sequencing: A review. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2017; 35:140-158. [PMID: 28506110 DOI: 10.1080/10590501.2017.1328831] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Mutations are heritable changes in the nucleotide sequence of DNA that can lead to many adverse effects. Genotoxicity assays have been used to identify chemical mutagenicity. Recently, next generation sequencing (NGS) has been used for this purpose. In this review, we present the progress in NGS application for assessing mutagenicity of chemicals, including the methods used for detecting the induced mutations, bioinformatics tools for analyzing the sequencing data, and chemicals whose mutagenicity has been evaluated using NGS. Available information suggests that NGS technology has unparalleled advantages for evaluating mutagenicity of chemicals can be applied for the next generation of mutagenicity tests.
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Affiliation(s)
- Hua Du
- a Division of Genetic and Molecular Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Bohu Pan
- a Division of Genetic and Molecular Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
| | - Tao Chen
- a Division of Genetic and Molecular Toxicology, National Center for Toxicological Research , U.S. Food and Drug Administration , Jefferson , Arkansas , USA
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26
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Sha Y, Sha Y, Ji Z, Ding L, Zhang Q, Ouyang H, Lin S, Wang X, Shao L, Shi C, Li P, Song Y. Comprehensive Genome Profiling of Single Sperm Cells by Multiple Annealing and Looping-Based Amplification Cycles and Next-Generation Sequencing from Carriers of Robertsonian Translocation. Ann Hum Genet 2017; 81:91-97. [PMID: 28205220 DOI: 10.1111/ahg.12187] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 01/23/2017] [Indexed: 01/06/2023]
Abstract
Robertsonian translocation (RT) is a common cause for male infertility, recurrent pregnancy loss, and birth defects. Studying meiotic recombination in RT-carrier patients helps decipher the mechanism and improve the clinical management of infertility and birth defects caused by RT. Here we present a new method to study spermatogenesis on a single-gamete basis from two RT carriers. By using a combined single-cell whole-genome amplification and sequencing protocol, we comprehensively profiled the chromosomal copy number of 88 single sperms from two RT-carrier patients. With the profiled information, chromosomal aberrations were identified on a whole-genome, per-sperm basis. We found that the previously reported interchromosomal effect might not exist with RT carriers. It is suggested that single-cell genome sequencing enables comprehensive chromosomal aneuploidy screening and provides a powerful tool for studying gamete generation from patients carrying chromosomal diseases.
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Affiliation(s)
- Yanwei Sha
- Center of Reproductive Medicine, Xiamen Maternity and Child Health Hospital, Xiamen, Fujian Province, China
| | - Yankun Sha
- Liaoning Medical University, Jinzhou City, Liaoning Province, China
| | - Zhiyong Ji
- Center of Reproductive Medicine, Xiamen Maternity and Child Health Hospital, Xiamen, Fujian Province, China
| | - Lu Ding
- Center of Reproductive Medicine, Xiamen Maternity and Child Health Hospital, Xiamen, Fujian Province, China
| | - Qing Zhang
- Center of Reproductive Medicine, Xiamen Maternity and Child Health Hospital, Xiamen, Fujian Province, China
| | - Honggen Ouyang
- Center of Reproductive Medicine, Xiamen Maternity and Child Health Hospital, Xiamen, Fujian Province, China
| | - Shaobin Lin
- Center of Reproductive Medicine, Xiamen Maternity and Child Health Hospital, Xiamen, Fujian Province, China
| | - Xu Wang
- Center of Reproductive Medicine, Xiamen Maternity and Child Health Hospital, Xiamen, Fujian Province, China
| | - Lin Shao
- Yikon Genomics, Caohejing Development Zone, Shanghai, China
| | - Chong Shi
- Yikon Genomics, Caohejing Development Zone, Shanghai, China
| | - Ping Li
- Center of Reproductive Medicine, Xiamen Maternity and Child Health Hospital, Xiamen, Fujian Province, China
| | - Yueqiang Song
- Center of Reproductive Medicine, Xiamen Maternity and Child Health Hospital, Xiamen, Fujian Province, China
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27
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Differences between germline and somatic mutation rates in humans and mice. Nat Commun 2017; 8:15183. [PMID: 28485371 PMCID: PMC5436103 DOI: 10.1038/ncomms15183] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 03/08/2017] [Indexed: 12/22/2022] Open
Abstract
The germline mutation rate has been extensively studied and has been found to vary greatly between species, but much less is known about the somatic mutation rate in multicellular organisms, which remains very difficult to determine. Here, we present data on somatic mutation rates in mice and humans, obtained by sequencing single cells and clones derived from primary fibroblasts, which allows us to make the first direct comparison with germline mutation rates in these two species. The results indicate that the somatic mutation rate is almost two orders of magnitude higher than the germline mutation rate and that both mutation rates are significantly higher in mice than in humans. Our findings demonstrate both the privileged status of germline genome integrity and species-specific differences in genome maintenance. Germline mutation rates are known to vary between species but somatic mutation rates are less well understood. Here the authors compare mice and humans, observing that somatic mutation rates were nearly two orders of magnitude higher in both species, with both mutation rates significantly higher in mice.
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28
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Dutta AK, Hewett DR, Fink JL, Grady JP, Zannettino ACW. Cutting edge genomics reveal new insights into tumour development, disease progression and therapeutic impacts in multiple myeloma. Br J Haematol 2017; 178:196-208. [PMID: 28466550 DOI: 10.1111/bjh.14649] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/03/2017] [Accepted: 01/06/2017] [Indexed: 12/19/2022]
Abstract
Multiple Myeloma (MM) is a haematological malignancy characterised by the clonal expansion of plasma cells (PCs) within the bone marrow. Despite advances in therapy, MM remains a largely incurable disease with a median survival of 6 years. In almost all cases, the development of MM is preceded by the benign PC condition Monoclonal Gammopathy of Undetermined Significance (MGUS). Recent studies show that the transformation of MGUS to MM is associated with complex genetic changes. Understanding how these changes contribute to evolution will present targets for clinical intervention. We discuss three models of MM evolution; the linear, the expansionist and the intraclonal heterogeneity models. Of particular interest is the intraclonal heterogeneity model. Here, distinct populations of MM PCs carry differing combinations of genetic mutations. Acquisition of additional mutations can contribute to subclonal lineages where "driver" mutations may influence selective pressure and dominance, and "passenger" mutations are neutral in their effects. Furthermore, studies show that clinical intervention introduces additional selective pressure on tumour cells and can influence subclone survival, leading to therapy resistance. This review discusses how Next Generation Sequencing approaches are revealing critical insights into the genetics of MM development, disease progression and treatment. MM disease progression will illuminate possible mechanisms underlying the tumour.
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Affiliation(s)
- Ankit K Dutta
- School of Medicine Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.,Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - Duncan R Hewett
- School of Medicine Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.,Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
| | - J Lynn Fink
- The University of Queensland, Diamantina Institute, Woolloongabba, QLD, Australia
| | - John P Grady
- The University of Queensland, Diamantina Institute, Woolloongabba, QLD, Australia
| | - Andrew C W Zannettino
- School of Medicine Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia.,Cancer Theme, South Australian Health & Medical Research Institute, Adelaide, SA, Australia
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29
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Dong X, Zhang L, Milholland B, Lee M, Maslov AY, Wang T, Vijg J. Accurate identification of single-nucleotide variants in whole-genome-amplified single cells. Nat Methods 2017; 14:491-493. [PMID: 28319112 PMCID: PMC5408311 DOI: 10.1038/nmeth.4227] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/22/2017] [Indexed: 01/22/2023]
Abstract
Mutation analysis in single-cell genomes is prone to artifacts associated with cell lysis and whole-genome amplification. Here we addressed these issues by developing single-cell multiple displacement amplification (SCMDA) and a general-purpose single-cell-variant caller, SCcaller (https://github.com/biosinodx/SCcaller/). By comparing SCMDA-amplified single cells with unamplified clones from the same population, we validated the procedure as a firm foundation for standardized somatic-mutation analysis in single-cell genomics.
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Affiliation(s)
- Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Lei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Brandon Milholland
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Alexander Y. Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
- Department of Ophthalmology & Visual Sciences, Albert Einstein College of Medicine, Bronx, New York 10461, U.S.A
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30
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Andriani GA, Vijg J, Montagna C. Mechanisms and consequences of aneuploidy and chromosome instability in the aging brain. Mech Ageing Dev 2017; 161:19-36. [PMID: 27013377 PMCID: PMC5490080 DOI: 10.1016/j.mad.2016.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/17/2016] [Accepted: 03/19/2016] [Indexed: 01/31/2023]
Abstract
Aneuploidy and polyploidy are a form of Genomic Instability (GIN) known as Chromosomal Instability (CIN) characterized by sporadic abnormalities in chromosome copy numbers. Aneuploidy is commonly linked to pathological states. It is a hallmark of spontaneous abortions and birth defects and it is observed virtually in every human tumor, therefore being generally regarded as detrimental for the development or the maturation of tissues under physiological conditions. Polyploidy however, occurs as part of normal physiological processes during maturation and differentiation of some mammalian cell types. Surprisingly, high levels of aneuploidy are present in the brain, and their frequency increases with age suggesting that the brain is able to maintain its functionality in the presence of high levels of mosaic aneuploidy. Because somatic aneuploidy with age can reach exceptionally high levels, it is likely to have long-term adverse effects in this organ. We describe the mechanisms accountable for an abnormal DNA content with a particular emphasis on the CNS where cell division is limited. Next, we briefly summarize the types of GIN known to date and discuss how they interconnect with CIN. Lastly we highlight how several forms of CIN may contribute to genetic variation, tissue degeneration and disease in the CNS.
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Affiliation(s)
- Grasiella A Andriani
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department Ophthalmology and Visual Science, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Pathology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA.
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31
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Taylor PH, Cinquin A, Cinquin O. Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq. Genome Res 2016; 26:1600-1611. [PMID: 27803194 PMCID: PMC5088601 DOI: 10.1101/gr.200501.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 09/13/2016] [Indexed: 01/04/2023]
Abstract
Assaying in vivo accrual of DNA damage and DNA mutations by stem cells and pinpointing sources of damage and mutations would further our understanding of aging and carcinogenesis. Two main hurdles must be overcome. First, in vivo mutation rates are orders of magnitude lower than raw sequencing error rates. Second, stem cells are vastly outnumbered by differentiated cells, which have a higher mutation rate—quantification of stem cell DNA damage and DNA mutations is thus best performed from small, well-defined cell populations. Here we report a mutation detection technique, based on the “duplex sequencing” principle, with an error rate below ∼10−10 and that can start from as little as 50 pg DNA. We validate this technique, which we call SIP-HAVA-seq, by characterizing Caenorhabditis elegans germline stem cell mutation accrual and asking how mating affects that accrual. We find that a moderate mating-induced increase in cell cycling correlates with a dramatic increase in accrual of mutations. Intriguingly, these mutations consist chiefly of deletions in nonexpressed genes. This contrasts with results derived from mutation accumulation lines and suggests that mutation spectrum and genome distribution change with replicative age, chronological age, cell differentiation state, and/or overall worm physiological state. We also identify single-stranded gaps as plausible deletion precursors, providing a starting point to identify the molecular mechanisms of mutagenesis that are most active. SIP-HAVA-seq provides the first direct, genome-wide measurements of in vivo mutation accrual in stem cells and will enable further characterization of underlying mechanisms and their dependence on age and cell state.
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Affiliation(s)
- Pete H Taylor
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA.,Center for Complex Biological Systems, University of California, Irvine, Irvine, California 92697, USA
| | - Amanda Cinquin
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA.,Center for Complex Biological Systems, University of California, Irvine, Irvine, California 92697, USA
| | - Olivier Cinquin
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California 92697, USA.,Center for Complex Biological Systems, University of California, Irvine, Irvine, California 92697, USA
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32
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Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq. Nat Protoc 2016; 11:2081-103. [DOI: 10.1038/nprot.2016.138] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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Milholland B, Auton A, Suh Y, Vijg J. Age-related somatic mutations in the cancer genome. Oncotarget 2016; 6:24627-35. [PMID: 26384365 PMCID: PMC4694783 DOI: 10.18632/oncotarget.5685] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 09/15/2015] [Indexed: 11/25/2022] Open
Abstract
Aging is associated with an increased risk of cancer, possibly in part because of an age-related increase in mutations in normal tissues. Due to their extremely low abundance, somatic mutations in normal tissues frequently escape detection. Tumors, as clonal expansions of single cells, can provide information about the somatic mutations present in these cells prior to tumorigenesis. Here, we used data from The Cancer Genome Atlas (TCGA), to systematically study the frequency and spectrum of somatic mutations in a total of 6,969 patients and 34 different tumor types as a function of the age of the patient. After using linear modeling to control for the age structure of different tumor types, we found that the number of identified somatic mutations increases exponentially with age. Using additional data from the literature, we found that accumulation of somatic mutations is associated with cell division rate, cancer risk and cigarette smoking, with the latter also associated with a distinct spectrum of mutations. Our results confirm that aging is associated with the accumulation of somatic mutations, and strongly suggest that the level of genome instability of normal cells, modified by both endogenous and environmental factors, is the main risk factor for cancer.
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Affiliation(s)
| | - Adam Auton
- Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yousin Suh
- Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jan Vijg
- Albert Einstein College of Medicine, Bronx, NY, USA
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34
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Quispe-Tintaya W, Gorbacheva T, Lee M, Makhortov S, Popov VN, Vijg J, Maslov AY. Quantitative detection of low-abundance somatic structural variants in normal cells by high-throughput sequencing. Nat Methods 2016; 13:584-6. [PMID: 27271197 PMCID: PMC4927357 DOI: 10.1038/nmeth.3893] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/19/2016] [Indexed: 12/31/2022]
Abstract
The detection and quantification of low-abundance somatic DNA mutations by high throughput sequencing is challenging because of the difficulty in distinguishing errors from true mutations. While there are several approaches available for analyzing somatic point mutations and small indels, an accurate genome-wide assessment of somatic structural variants (somSVs) in bulk DNA is still not possible. Here we present Structural Variant Search (SVS), a method to accurately detect rare somSVs by low-coverage sequencing. We demonstrate direct quantitative assessment of elevated somSV frequencies induced by known clastogenic compounds in human primary cells.
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Affiliation(s)
| | - Tatyana Gorbacheva
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.,Department of Genetics, Cytology, and Bioengineering, Voronezh State University, Voronezh, Russia
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sergei Makhortov
- Department of Applied and System Software, Voronezh State University, Voronezh, Russia
| | - Vasily N Popov
- Department of Genetics, Cytology, and Bioengineering, Voronezh State University, Voronezh, Russia
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
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35
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Gregory MT, Bertout JA, Ericson NG, Taylor SD, Mukherjee R, Robins HS, Drescher CW, Bielas JH. Targeted single molecule mutation detection with massively parallel sequencing. Nucleic Acids Res 2015; 44:e22. [PMID: 26384417 PMCID: PMC4756847 DOI: 10.1093/nar/gkv915] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 09/02/2015] [Indexed: 11/14/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have transformed genomic research and have the potential to revolutionize clinical medicine. However, the background error rates of sequencing instruments and limitations in targeted read coverage have precluded the detection of rare DNA sequence variants by NGS. Here we describe a method, termed CypherSeq, which combines double-stranded barcoding error correction and rolling circle amplification (RCA)-based target enrichment to vastly improve NGS-based rare variant detection. The CypherSeq methodology involves the ligation of sample DNA into circular vectors, which contain double-stranded barcodes for computational error correction and adapters for library preparation and sequencing. CypherSeq is capable of detecting rare mutations genome-wide as well as those within specific target genes via RCA-based enrichment. We demonstrate that CypherSeq is capable of correcting errors incurred during library preparation and sequencing to reproducibly detect mutations down to a frequency of 2.4 × 10−7 per base pair, and report the frequency and spectra of spontaneous and ethyl methanesulfonate-induced mutations across the Saccharomycescerevisiae genome.
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Affiliation(s)
- Mark T Gregory
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jessica A Bertout
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sean D Taylor
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Rithun Mukherjee
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Harlan S Robins
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Charles W Drescher
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Department of Pathology, University of Washington, Seattle, WA 98195, USA
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36
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Garvin T, Aboukhalil R, Kendall J, Baslan T, Atwal GS, Hicks J, Wigler M, Schatz MC. Interactive analysis and assessment of single-cell copy-number variations. Nat Methods 2015; 12:1058-60. [PMID: 26344043 PMCID: PMC4775251 DOI: 10.1038/nmeth.3578] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 07/07/2015] [Indexed: 01/19/2023]
Abstract
We present Ginkgo (http://qb.cshl.edu/ginkgo), a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs). Ginkgo automatically constructs copy-number profiles of cells from mapped reads and constructs phylogenetic trees of related cells. We validated Ginkgo by reproducing the results of five major studies. After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis.
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Affiliation(s)
- Tyler Garvin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | | | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Timour Baslan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York, USA
| | - Gurinder S Atwal
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - James Hicks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
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37
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Noyes HA, Daly D, Goodhead I, Kay S, Kemp SJ, Kenny J, Saccheri I, Schnabel RD, Taylor JF, Hall N. A simple procedure for directly obtaining haplotype sequences of diploid genomes. BMC Genomics 2015; 16:642. [PMID: 26311067 PMCID: PMC4551521 DOI: 10.1186/s12864-015-1818-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/05/2015] [Indexed: 11/24/2022] Open
Abstract
Background Almost all genome sequencing projects neglect the fact that diploid organisms contain two genome copies and consequently what is published is a composite of the two. This means that the relationship between alternate alleles at two or more linked loci is lost. We have developed a simplified method of directly obtaining the haploid sequences of each genome copy from an individual organism. Results The diploid sequences of three groups of cattle samples were obtained using a simple sample preparation procedure requiring only a microscope and a haemocytometer. Samples were: 1) lymphocytes from a single Angus steer; 2) sperm cells from an Angus bull; 3) lymphocytes from East African Zebu (EAZ) cattle collected and processed in a field laboratory in Eastern Kenya. Haploid sequence from a fosmid library prepared from lymphocytes of an EAZ cow was used for comparison. Cells were serially diluted to a concentration of one cell per microlitre by counting with a haemocytometer at each dilution. One microlitre samples, each potentially containing a single cell, were lysed and divided into six aliquots (except for the sperm samples which were not divided into aliquots). Each aliquot was amplified with phi29 polymerase and sequenced. Contigs were obtained by mapping to the bovine UMD3.1 reference genome assembly and scaffolds were assembled by joining adjacent contigs that were within a threshold distance of each other. Scaffolds that appeared to contain artefacts of CNV or repeats were filtered out leaving scaffolds with an N50 length of 27–133 kb and a 88–98 % genome coverage. SNP haplotypes were assembled with the Single Individual Haplotyper program to generate an N50 size of 97–201 kb but only ~27–68 % genome coverage. This method can be used in any laboratory with no special equipment at only slightly higher costs than conventional diploid genome sequencing. A substantial body of software for analysis and workflow management was written and is available as supplementary data. Conclusions We have developed a set of laboratory protocols and software tools that will enable any laboratory to obtain haplotype sequences at only modestly greater cost than traditional mixed diploid sequences.
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Affiliation(s)
- Harry A Noyes
- Centre for Genome Research, Institute of Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK.
| | - Derek Daly
- Centre for Genome Research, Institute of Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK.
| | - Ian Goodhead
- Centre for Genome Research, Institute of Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK.
| | - Suzanne Kay
- Centre for Genome Research, Institute of Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK.
| | - Steven J Kemp
- Centre for Genome Research, Institute of Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK.
| | - John Kenny
- Centre for Genome Research, Institute of Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK.
| | - Ilik Saccheri
- Centre for Genome Research, Institute of Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK.
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA.
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA.
| | - Neil Hall
- Centre for Genome Research, Institute of Integrative Biology, University of Liverpool, Crown St., Liverpool, L69 7ZB, UK.
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38
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Li W, Calder RB, Mar JC, Vijg J. Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles. Mutat Res 2015; 772:55-62. [PMID: 25733965 DOI: 10.1016/j.mrfmmm.2015.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recently, great progress has been made in single cell genomics and transcriptomics. Here, we present an integrative method, termed single-cell transcriptogenomics (SCTG), in which whole exome sequencing and RNA-seq is performed concurrently on single cells. This methodology enables one to track germline and somatic variants directly from the genome to the transcriptome in individual cells. Mouse embryonic fibroblasts were treated with the powerful mutagen ethylnitrosourea (ENU) and subjected to SCTG. Interestingly, while germline variants were found to be transcribed in an allelically balanced fashion, a significantly different pattern of allelic exclusion was observed for ENU-mutant variants. These results suggest that the adverse effects of induced mutations, in contrast to germline variants, may be mitigated by allelically biased transcription. They also illustrate how SCTG can be instrumental in the direct assessment of phenotypic consequences of genomic variants.
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39
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Maslov AY, Quispe-Tintaya W, Gorbacheva T, White RR, Vijg J. High-throughput sequencing in mutation detection: A new generation of genotoxicity tests? Mutat Res 2015; 776:136-43. [PMID: 25934519 DOI: 10.1016/j.mrfmmm.2015.03.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 03/07/2015] [Accepted: 03/27/2015] [Indexed: 10/23/2022]
Abstract
The advent of next generation sequencing (NGS) technology has provided the means to directly analyze the genetic material in primary cells or tissues of any species in a high throughput manner for mutagenic effects of potential genotoxic agents. In principle, direct, genome-wide sequencing of human primary cells and/or tissue biopsies would open up opportunities to identify individuals possibly exposed to mutagenic agents, thereby replacing current risk assessment procedures based on surrogate markers and extrapolations from animal studies. NGS-based tests can also precisely characterize the mutation spectra induced by genotoxic agents, improving our knowledge of their mechanism of action. Thus far, NGS has not been widely employed in genetic toxicology due to the difficulties in measuring low-abundant somatic mutations. Here, we review different strategies to employ NGS for the detection of somatic mutations in a cost-effective manner and discuss the potential applicability of these methods in testing the mutagenicity of genotoxic agents.
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Affiliation(s)
- Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA.
| | - Wilber Quispe-Tintaya
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
| | - Tatyana Gorbacheva
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
| | - Ryan R White
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA.
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40
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Gravina S, Ganapathi S, Vijg J. Single-cell, locus-specific bisulfite sequencing (SLBS) for direct detection of epimutations in DNA methylation patterns. Nucleic Acids Res 2015; 43:e93. [PMID: 25897117 PMCID: PMC4538804 DOI: 10.1093/nar/gkv366] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/07/2015] [Indexed: 12/14/2022] Open
Abstract
Stochastic epigenetic changes drive biological processes, such as development, aging and disease. Yet, epigenetic information is typically collected from millions of cells, thereby precluding a more precise understanding of cell-to-cell variability and the pathogenic history of epimutations. Here we present a novel procedure for directly detecting epimutations in DNA methylation patterns using single-cell, locus-specific bisulfite sequencing (SLBS). We show that within gene promoter regions of mouse hepatocytes the epimutation rate is two orders of magnitude higher than the mutation rate.
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Affiliation(s)
- Silvia Gravina
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Shireen Ganapathi
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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41
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Somatic mosaicism in the human genome. Genes (Basel) 2014; 5:1064-94. [PMID: 25513881 PMCID: PMC4276927 DOI: 10.3390/genes5041064] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/26/2014] [Accepted: 11/28/2014] [Indexed: 12/17/2022] Open
Abstract
Somatic mosaicism refers to the occurrence of two genetically distinct populations of cells within an individual, derived from a postzygotic mutation. In contrast to inherited mutations, somatic mosaic mutations may affect only a portion of the body and are not transmitted to progeny. These mutations affect varying genomic sizes ranging from single nucleotides to entire chromosomes and have been implicated in disease, most prominently cancer. The phenotypic consequences of somatic mosaicism are dependent upon many factors including the developmental time at which the mutation occurs, the areas of the body that are affected, and the pathophysiological effect(s) of the mutation. The advent of second-generation sequencing technologies has augmented existing array-based and cytogenetic approaches for the identification of somatic mutations. We outline the strengths and weaknesses of these techniques and highlight recent insights into the role of somatic mosaicism in causing cancer, neurodegenerative, monogenic, and complex disease.
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42
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Chen M, Song P, Zou D, Hu X, Zhao S, Gao S, Ling F. Comparison of multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC) in single-cell sequencing. PLoS One 2014; 9:e114520. [PMID: 25485707 PMCID: PMC4259343 DOI: 10.1371/journal.pone.0114520] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 11/09/2014] [Indexed: 01/01/2023] Open
Abstract
Single-cell sequencing promotes our understanding of the heterogeneity of cellular populations, including the haplotypes and genomic variability among different generation of cells. Whole-genome amplification is crucial to generate sufficient DNA fragments for single-cell sequencing projects. Using sequencing data from single sperms, we quantitatively compare two prevailing amplification methods that extensively applied in single-cell sequencing, multiple displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Our results show that MALBAC, as a combination of modified MDA and tweaked PCR, has a higher level of uniformity, specificity and reproducibility.
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Affiliation(s)
- Minfeng Chen
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Pengfei Song
- The fourth people's hospital of Shenzhen (Futian hospital), Shenzhen, 518033, China
| | - Dan Zou
- School of Computer, National University of Defense Technology, Changsha, 410073, China
| | | | - Shancen Zhao
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- * E-mail: (FL); (SG); (SZ)
| | - Shengjie Gao
- BGI-Shenzhen, Shenzhen, 518083, China
- State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- * E-mail: (FL); (SG); (SZ)
| | - Fei Ling
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, 510006, China
- * E-mail: (FL); (SG); (SZ)
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43
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Somatic mutations, genome mosaicism, cancer and aging. Curr Opin Genet Dev 2014; 26:141-9. [PMID: 25282114 DOI: 10.1016/j.gde.2014.04.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 04/04/2014] [Accepted: 04/11/2014] [Indexed: 01/11/2023]
Abstract
Genomes are inherently unstable due to the need for DNA sequence variation in the germ line to fuel evolution through natural selection. In somatic tissues mutations accumulate during development and aging, generating genome mosaics. There is little information about the possible causal role of increased somatic mutation loads in late-life disease and aging, with the exception of cancer. Characterizing somatic mutations and their functional consequences in normal tissues remains a formidable challenge due to their low, individual abundance. Here, I will briefly review our current knowledge of somatic mutations in animals and humans in relation to aging, how they arise and lead to genome mosaicism, the technology to study somatic mutations and how they possibly could cause non-clonal disease.
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44
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Furgason JM, Li W, Milholland B, Cross E, Li Y, McPherson CM, Warnick RE, Rixe O, Stambrook PJ, Vijg J, Bahassi EM. Whole genome sequencing of glioblastoma multiforme identifies multiple structural variations involved in EGFR activation. Mutagenesis 2014; 29:341-50. [PMID: 25103728 DOI: 10.1093/mutage/geu026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Next generation sequencing has become a powerful tool in dissecting and identifying mutations and genomic structural variants that accompany tumourigenesis. Sequence analysis of glioblastoma multiforme (GBM) illustrates the ability to rapidly identify mutations that may affect phenotype. Approximately 50% of human GBMs overexpress epidermal growth factor receptor (EGFR) which renders the EGFR protein a compelling therapeutic target. In brain tumours, attempts to target EGFR as a cancer therapeutic, however, have achieved little or no benefit. The mechanisms that drive therapeutic resistance to EGFR inhibitors in brain tumours are not well defined, and drug resistance contributes to the deadly and aggressive nature of the disease. Whole genome sequencing of four primary GBMs revealed multiple pathways by which EGFR protein abundance becomes deregulated in these tumours and will guide the development of new strategies for treating EGFR overexpressing tumours. Each of the four tumours displayed a different mechanism leading to increased EGFR protein levels. One mechanism is mediated by gene amplification and tandem duplication of the kinase domain. A second involves an intragenic deletion that generates a constitutively active form of the protein. A third combines the loss of a gene which encodes a protein that regulates EGFR abundance as well as an miRNA that modulates EGFR expression. A fourth mechanism entails loss of an ubiquitin ligase docking site in the C-terminal part of the protein whose absence inhibits turnover of the receptor.
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Affiliation(s)
- John M Furgason
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati College of Medicine, 231, Albert Sabin Way, Cincinnati, OH, USA
| | - Wenge Li
- Albert Einstein Medical Center, 1301 Morris Park Avenue, New York, NY, USA
| | - Brandon Milholland
- Albert Einstein Medical Center, 1301 Morris Park Avenue, New York, NY, USA
| | - Emily Cross
- Department of Molecular Genetics, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH, USA
| | - Yaqin Li
- Department of Molecular Genetics, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH, USA
| | - Christopher M McPherson
- Department of Neurosurgery and UC Brain Tumor Center, University of Cincinnati, 234 Goodman Street, Cincinnati, OH, USA
| | - Ronald E Warnick
- Department of Neurosurgery and UC Brain Tumor Center, University of Cincinnati, 234 Goodman Street, Cincinnati, OH, USA
| | - Olivier Rixe
- GRU Cancer Center, 1411 Laney Walker Boulevard Augusta, GA, USA
| | - Peter J Stambrook
- Department of Molecular Genetics, University of Cincinnati, 231 Albert Sabin Way, Cincinnati, OH, USA
| | - Jan Vijg
- Albert Einstein Medical Center, 1301 Morris Park Avenue, New York, NY, USA
| | - El Mustapha Bahassi
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati College of Medicine, 231, Albert Sabin Way, Cincinnati, OH, USA, UC Brain Tumor Center, University of Cincinnati, 234 Goodman Street, Cincinnati, OH, USA,
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45
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Abstract
High-throughput DNA sequencing has revolutionized the study of cancer genomics with numerous discoveries that are relevant to cancer diagnosis and treatment. The latest sequencing and analysis methods have successfully identified somatic alterations, including single-nucleotide variants, insertions and deletions, copy-number aberrations, structural variants and gene fusions. Additional computational techniques have proved useful for defining the mutations, genes and molecular networks that drive diverse cancer phenotypes and that determine clonal architectures in tumour samples. Collectively, these tools have advanced the study of genomic, transcriptomic and epigenomic alterations in cancer, and their association to clinical properties. Here, we review cancer genomics software and the insights that have been gained from their application.
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46
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Comparative genetics of longevity and cancer: insights from long-lived rodents. Nat Rev Genet 2014; 15:531-40. [PMID: 24981598 DOI: 10.1038/nrg3728] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mammals have evolved a remarkable diversity of ageing rates. Within the single order of Rodentia, maximum lifespans range from 4 years in mice to 32 years in naked mole rats. Cancer rates also differ substantially between cancer-prone mice and almost cancer-proof naked mole rats and blind mole rats. Recent progress in rodent comparative biology, together with the emergence of whole-genome sequence information, has opened opportunities for the discovery of genetic factors that control longevity and cancer susceptibility.
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47
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Derks KWJ, Hoeijmakers JHJ, Pothof J. The DNA damage response: the omics era and its impact. DNA Repair (Amst) 2014; 19:214-20. [PMID: 24794401 DOI: 10.1016/j.dnarep.2014.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The emergence of high density technologies monitoring the genome, transcriptome and proteome in relation to genotoxic stress have tremendously enhanced our knowledge on global responses and dynamics in the DNA damage response, including its relation with cancer and aging. Moreover, '-omics' technologies identified many novel factors, their post-translational modifications, pathways and global responses in the cellular response to DNA damage. Based on omics, it is currently estimated that thousands of gene(product)s participate in the DNA damage response, recognizing complex networks that determine cell fate after damage to the most precious cellular molecule, DNA. The development of next generation sequencing technology and associated specialized protocols can quantitatively monitor RNA and DNA at unprecedented single nucleotide resolution. In this review we will discuss the contribution of omics technologies and in particular next generation sequencing to our understanding of the DNA damage response and the future prospective of next generation sequencing, its single cell application and omics dataset integration in unraveling intricate DNA damage signaling networks.
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Affiliation(s)
- Kasper W J Derks
- Department of Genetics, Netherlands Toxicogenomics Center, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Jan H J Hoeijmakers
- Department of Genetics, Netherlands Toxicogenomics Center, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Joris Pothof
- Department of Genetics, Netherlands Toxicogenomics Center, Erasmus University Medical Center, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands.
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48
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Blainey PC, Quake SR. Dissecting genomic diversity, one cell at a time. Nat Methods 2014; 11:19-21. [PMID: 24524132 DOI: 10.1038/nmeth.2783] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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49
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Single cell analysis of cancer genomes. Curr Opin Genet Dev 2014; 24:82-91. [PMID: 24531336 DOI: 10.1016/j.gde.2013.12.004] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 12/15/2013] [Indexed: 12/19/2022]
Abstract
Genomic studies have provided key insights into how cancers develop, evolve, metastasize and respond to treatment. Cancers result from an interplay between mutation, selection and clonal expansions. In solid tumours, this Darwinian competition between subclones is also influenced by topological factors. Recent advances have made it possible to study cancers at the single cell level. These methods represent important tools to dissect cancer evolution and provide the potential to considerably change both cancer research and clinical practice. Here we discuss state-of-the-art methods for the isolation of a single cell, whole-genome and whole-transcriptome amplification of the cell's nucleic acids, as well as microarray and massively parallel sequencing analysis of such amplification products. We discuss the strengths and the limitations of the techniques, and explore single-cell methodologies for future cancer research, as well as diagnosis and treatment of the disease.
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50
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Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 2014; 56:61-4, 66, 68, passim. [PMID: 24502796 DOI: 10.2144/000114133] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/21/2014] [Indexed: 01/03/2023] Open
Abstract
High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of sequencing applications increasing exponentially. Here, we examine the critical role of sequencing library quality and consider important challenges when preparing NGS libraries from DNA and RNA sources. Factors such as the quantity and physical characteristics of the RNA or DNA source material as well as the desired application (i.e., genome sequencing, targeted sequencing, RNA-seq, ChIP-seq, RIP-seq, and methylation) are addressed in the context of preparing high quality sequencing libraries. In addition, the current methods for preparing NGS libraries from single cells are also discussed.
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Affiliation(s)
- Steven R Head
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA
| | - H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Thomas Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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