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Derényi I, Demeter MC, Pérez-Jiménez M, Grajzel D, Szöllősi GJ. How mutation accumulation depends on the structure of the cell lineage tree. Phys Rev E 2024; 109:044407. [PMID: 38755817 DOI: 10.1103/physreve.109.044407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/08/2024] [Indexed: 05/18/2024]
Abstract
All the cells of a multicellular organism are the product of cell divisions that trace out a single binary tree, the so-called cell lineage tree. Because cell divisions are accompanied by replication errors, the shape of the cell lineage tree is a key determinant of how somatic evolution, which can potentially lead to cancer, proceeds. Carcinogenesis requires the accumulation of a certain number of driver mutations. By mapping the accumulation of mutations into a graph theoretical problem, we present an exact numerical method to calculate the probability of collecting a given number of mutations and show that for low mutation rates it can be approximated with a simple analytical formula, which depends only on the distribution of the lineage lengths, and is dominated by the longest lineages. Our results are crucial in understanding how natural selection can shape the cell lineage trees of multicellular organisms and curtail somatic evolution.
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Affiliation(s)
- Imre Derényi
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary and MTA-ELTE Statistical and Biological Physics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary
| | - Márton C Demeter
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary and MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary
| | - Mario Pérez-Jiménez
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary and MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary
| | - Dániel Grajzel
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary and MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary
| | - Gergely J Szöllősi
- ELTE Eötvös University, Department of Biological Physics, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary; MTA-ELTE "Lendület" Evolutionary Genomics Research Group, Pázmány Péter Sétány 1A, H-1117 Budapest, Hungary; HUN-REN Centre for Ecological Research, Institute of Evolution, H-1113 Budapest, Hungary; and Model-Based Evolutionary Genomics Unit, Okinawa Institute of Science and Technology Graduate University, 904-0412 Okinawa, Japan
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Balogun EJ, Ness RW. The Effects of De Novo Mutation on Gene Expression and the Consequences for Fitness in Chlamydomonas reinhardtii. Mol Biol Evol 2024; 41:msae035. [PMID: 38366781 PMCID: PMC10910851 DOI: 10.1093/molbev/msae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/01/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Mutation is the ultimate source of genetic variation, the bedrock of evolution. Yet, predicting the consequences of new mutations remains a challenge in biology. Gene expression provides a potential link between a genotype and its phenotype. But the variation in gene expression created by de novo mutation and the fitness consequences of mutational changes to expression remain relatively unexplored. Here, we investigate the effects of >2,600 de novo mutations on gene expression across the transcriptome of 28 mutation accumulation lines derived from 2 independent wild-type genotypes of the green algae Chlamydomonas reinhardtii. We observed that the amount of genetic variance in gene expression created by mutation (Vm) was similar to the variance that mutation generates in typical polygenic phenotypic traits and approximately 15-fold the variance seen in the limited species where Vm in gene expression has been estimated. Despite the clear effect of mutation on expression, we did not observe a simple additive effect of mutation on expression change, with no linear correlation between the total expression change and mutation count of individual MA lines. We therefore inferred the distribution of expression effects of new mutations to connect the number of mutations to the number of differentially expressed genes (DEGs). Our inferred DEE is highly L-shaped with 95% of mutations causing 0-1 DEG while the remaining 5% are spread over a long tail of large effect mutations that cause multiple genes to change expression. The distribution is consistent with many cis-acting mutation targets that affect the expression of only 1 gene and a large target of trans-acting targets that have the potential to affect tens or hundreds of genes. Further evidence for cis-acting mutations can be seen in the overabundance of mutations in or near differentially expressed genes. Supporting evidence for trans-acting mutations comes from a 15:1 ratio of DEGs to mutations and the clusters of DEGs in the co-expression network, indicative of shared regulatory architecture. Lastly, we show that there is a negative correlation with the extent of expression divergence from the ancestor and fitness, providing direct evidence of the deleterious effects of perturbing gene expression.
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Affiliation(s)
- Eniolaye J Balogun
- Department of Biology, William G. Davis Building, University of Toronto, Mississauga L5L-1C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto M5S-3B2, Canada
| | - Rob W Ness
- Department of Biology, William G. Davis Building, University of Toronto, Mississauga L5L-1C6, Canada
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3
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Lemaître JF, Moorad J, Gaillard JM, Maklakov AA, Nussey DH. A unified framework for evolutionary genetic and physiological theories of aging. PLoS Biol 2024; 22:e3002513. [PMID: 38412150 PMCID: PMC10898761 DOI: 10.1371/journal.pbio.3002513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Why and how we age are 2 intertwined questions that have fascinated scientists for many decades. However, attempts to answer these questions remain compartmentalized, preventing a comprehensive understanding of the aging process. We argue that the current lack of knowledge about the evolution of aging mechanisms is due to a lack of clarity regarding evolutionary theories of aging that explicitly involve physiological processes: the disposable soma theory (DST) and the developmental theory of aging (DTA). In this Essay, we propose a new hierarchical model linking genes to vital rates, enabling us to critically reevaluate the DST and DTA in terms of their relationship to evolutionary genetic theories of aging (mutation accumulation (MA) and antagonistic pleiotropy (AP)). We also demonstrate how these 2 theories can be incorporated in a unified hierarchical framework. The new framework will help to generate testable hypotheses of how the hallmarks of aging are shaped by natural selection.
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Affiliation(s)
- Jean-François Lemaître
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France
| | - Jacob Moorad
- Institute of Ecology & Evolution, School of Biological Science, University of Edinburgh, Edinburgh, United Kingdom
| | - Jean-Michel Gaillard
- Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR 5558, Villeurbanne, France
| | - Alexei A. Maklakov
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Daniel H. Nussey
- Institute of Ecology & Evolution, School of Biological Science, University of Edinburgh, Edinburgh, United Kingdom
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4
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Sandell L, König SG, Otto SP. Schrödinger's yeast: the challenge of using transformation to compare fitness among Saccharomyces cerevisiae that differ in ploidy or zygosity. PeerJ 2023; 11:e16547. [PMID: 38077443 PMCID: PMC10704993 DOI: 10.7717/peerj.16547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023] Open
Abstract
How the number of genome copies modifies the effect of random mutations remains poorly known. In yeast, researchers have investigated these effects for knock-out or other large-effect mutations, but have not accounted for differences at the mating-type locus. We set out to compare fitness differences among strains that differ in ploidy and/or zygosity using a panel of spontaneously arising mutations acquired in haploid yeast from a previous study. To ensure no genetic differences, even at the mating-type locus, we embarked on a series of transformations, which first sterilized and then temporarily introduced plasmid-borne mating types. Despite these attempts to equalize the haplotypes, fitness variation introduced during transformation swamped the differences among the original mutation-accumulation lines. While colony size looked normal, we observed a bi-modality in the maximum growth rate of our transformed yeast and determined that many of the slow growing lines were respiratory deficient ("petite"). Not previously reported, we found that yeast that were TID1/RDH54 knockouts were less likely to become petite. Even for lines with the same petite status, however, we found no correlation in fitness between the two replicate transformations performed. These results pose a challenge for any study using transformation to measure the fitness effect of genetic differences among strains. By attempting to hold haplotypes constant, we introduced more mutations that overwhelmed our ability to measure fitness differences between the genetic states. In this study, we transformed over one hundred different lines of yeast, using two independent transformations, and found that this common laboratory procedure can cause large changes to the microbe studied. Our study provides a cautionary tale of the need to use multiple transformants in fitness assays.
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Affiliation(s)
- Linnea Sandell
- Department of Zoology and Biodiversity Research Center, University of British Columbia, Vancouver, Canada
| | - Stephan G. König
- Department of Zoology and Biodiversity Research Center, University of British Columbia, Vancouver, Canada
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sarah P. Otto
- Department of Zoology and Biodiversity Research Center, University of British Columbia, Vancouver, Canada
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5
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Sharp NP, Smith DR, Driscoll G, Sun K, Vickerman CM, Martin SCT. Contribution of Spontaneous Mutations to Quantitative and Molecular Variation at the Highly Repetitive rDNA Locus in Yeast. Genome Biol Evol 2023; 15:evad179. [PMID: 37847861 PMCID: PMC10581546 DOI: 10.1093/gbe/evad179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2023] [Indexed: 10/19/2023] Open
Abstract
The ribosomal DNA array in Saccharomyces cerevisiae consists of many tandem repeats whose copy number is believed to be functionally important but highly labile. Regulatory mechanisms have evolved to maintain copy number by directed mutation, but how spontaneous variation at this locus is generated and selected has not been well characterized. We applied a mutation accumulation approach to quantify the impacts of mutation and selection on this unique genomic feature across hundreds of mutant strains. We find that mutational variance for this trait is relatively high, and that unselected mutations elsewhere in the genome can disrupt copy number maintenance. In consequence, copy number generally declines gradually, consistent with a previously proposed model of rDNA maintenance where a downward mutational bias is normally compensated by mechanisms that increase copy number when it is low. This pattern holds across ploidy levels and strains in the standard lab environment but differs under some stressful conditions. We identify several alleles, gene categories, and genomic features that likely affect copy number, including aneuploidy for chromosome XII. Copy number change is associated with reduced growth in diploids, consistent with stabilizing selection. Levels of standing variation in copy number are well predicted by a balance between mutation and stabilizing selection, suggesting this trait is not subject to strong diversifying selection in the wild. The rate and spectrum of point mutations within the rDNA locus itself are distinct from the rest of the genome and predictive of polymorphism locations. Our findings help differentiate the roles of mutation and selection and indicate that spontaneous mutation patterns shape several aspects of ribosomal DNA evolution.
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Affiliation(s)
- Nathaniel P Sharp
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Denise R Smith
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gregory Driscoll
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kexin Sun
- Present address: Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Sterling C T Martin
- Present address: Department of Biology, Washington University, St. Louis, Missouri, USA
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6
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Avila P, Lehmann L. Life history and deleterious mutation rate coevolution. J Theor Biol 2023; 573:111598. [PMID: 37598761 DOI: 10.1016/j.jtbi.2023.111598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
The cost of germline maintenance gives rise to a trade-off between lowering the deleterious mutation rate and investing in life history functions. Therefore, life history and the mutation rate coevolve, but this coevolution is not well understood. We develop a mathematical model to analyse the evolution of resource allocation traits, which simultaneously affect life history and the deleterious mutation rate. First, we show that the invasion fitness of such resource allocation traits can be approximated by the basic reproductive number of the least-loaded class; the expected lifetime production of offspring without deleterious mutations born to individuals without deleterious mutations. Second, we apply the model to investigate (i) the coevolution of reproductive effort and germline maintenance and (ii) the coevolution of age-at-maturity and germline maintenance. This analysis provides two resource allocation predictions when exposure to environmental mutagens is higher. First, selection favours higher allocation to germline maintenance, even if it comes at the expense of life history functions, and leads to a shift in allocation towards reproduction rather than survival. Second, life histories tend to be faster, characterised by individuals with shorter lifespans and smaller body sizes at maturity. Our results suggest that mutation accumulation via the cost of germline maintenance can be a major force shaping life-history traits.
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Affiliation(s)
- Piret Avila
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland.
| | - Laurent Lehmann
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland
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Yokogawa T, Nagano K, Fujita M, Miyakawa H, Iijima M. Characterization of a Treponema denticola ATCC 35405 mutant strain with mutation accumulation, including a lack of phage-derived genes. PLoS One 2022; 17:e0270198. [PMID: 35749516 PMCID: PMC9231711 DOI: 10.1371/journal.pone.0270198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/06/2022] [Indexed: 11/18/2022] Open
Abstract
Trepoenema denticola, a spirochetal bacterium, is associated with periodontal diseases. The type strain of the bacterium, ATCC 35405, is commonly used in a basic research. Here, we report that our stock strain derived from ATCC 35405 had a mutation on the chromosome and expressed differential characteristics from the original strain. Genome sequencing analysis revealed the lack of a phage-derived region, and over 200 mutations in the mutant strain. The mutant grew to a higher density in broth culture as compared with the origin. In addition, the mutant formed a colony on the surface of the agar medium, whereas the origin could not. On contrary, the mutant showed decreased motility and adhesion to gingival epithelial cells. There were no differences in the bacterial cell length and a chymotrypsin-like protease activity between the two strains. RNA and genome sequencing analysis could not identify the genes that introduced the phenotypic differences between the strains. This mutant is potentially useful for examining the genetic background responsible for the physiological and pathogenic characteristics of T. denticola.
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Affiliation(s)
- Tadaharu Yokogawa
- Division of Orthodontics and Dentofacial Orthopedics, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Keiji Nagano
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, Japan
- * E-mail:
| | - Mari Fujita
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Hiroshi Miyakawa
- Division of Microbiology, Department of Oral Biology, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, Japan
| | - Masahiro Iijima
- Division of Orthodontics and Dentofacial Orthopedics, Department of Oral Growth and Development, School of Dentistry, Health Sciences University of Hokkaido, Hokkaido, Japan
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8
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Abstract
Predicting fitness in natural populations is a major challenge in biology. It may be possible to leverage fast-accumulating genomic data sets to infer the fitness effects of mutant alleles, allowing evolutionary questions to be addressed in any organism. In this paper, we investigate the utility of one such tool, called PROVEAN. This program compares a query sequence with existing data to provide an alignment-based score for any protein variant, with scores categorized as neutral or deleterious based on a pre-set threshold. PROVEAN has been used widely in evolutionary studies, for example, to estimate mutation load in natural populations, but has not been formally tested as a predictor of aggregate mutational effects on fitness. Using three large published data sets on the genome sequences of laboratory mutation accumulation lines, we assessed how well PROVEAN predicted the actual fitness patterns observed, relative to other metrics. In most cases, we find that a simple count of the total number of mutant proteins is a better predictor of fitness than the number of proteins with variants scored as deleterious by PROVEAN. We also find that the sum of all mutant protein scores explains variation in fitness better than the number of mutant proteins in one of the data sets. We discuss the implications of these results for studies of populations in the wild.
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Affiliation(s)
- Linnea Sandell
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- Systematic Biology, Department of Organismal Biology, Uppsala University, Sweden
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9
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Abstract
Mutation is the source of genetic variation and the fundament of evolution. Temperature has long been suggested to have a direct impact on realized spontaneous mutation rates. If mutation rates vary in response to environmental conditions, such as the variation of the ambient temperature through space and time, they should no longer be described as species-specific constants. By combining mutation accumulation with whole-genome sequencing in a multicellular organism, we provide empirical support to reject the null hypothesis of a constant, temperature-independent mutation rate. Instead, mutation rates depended on temperature in a U-shaped manner with increasing rates toward both temperature extremes. This relation has important implications for mutation-dependent processes in molecular evolution, processes shaping the evolution of mutation rates, and even the evolution of biodiversity as such.
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Affiliation(s)
- Ann-Marie Waldvogel
- Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
- Institute of Zoology, University of Cologne, 50674 Cologne, Germany
| | - Markus Pfenninger
- Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, 60325 Frankfurt am Main, Germany
- Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, 55128 Mainz, Germany
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López-Cortegano E, Craig RJ, Chebib J, Samuels T, Morgan AD, Kraemer SA, Böndel KB, Ness RW, Colegrave N, Keightley PD. De Novo Mutation Rate Variation and Its Determinants in Chlamydomonas. Mol Biol Evol 2021; 38:3709-3723. [PMID: 33950243 PMCID: PMC8383909 DOI: 10.1093/molbev/msab140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
De novo mutations are central for evolution, since they provide the raw material for natural selection by regenerating genetic variation. However, studying de novo mutations is challenging and is generally restricted to model species, so we have a limited understanding of the evolution of the mutation rate and spectrum between closely related species. Here, we present a mutation accumulation (MA) experiment to study de novo mutation in the unicellular green alga Chlamydomonas incerta and perform comparative analyses with its closest known relative, Chlamydomonas reinhardtii. Using whole-genome sequencing data, we estimate that the median single nucleotide mutation (SNM) rate in C. incerta is μ = 7.6 × 10-10, and is highly variable between MA lines, ranging from μ = 0.35 × 10-10 to μ = 131.7 × 10-10. The SNM rate is strongly positively correlated with the mutation rate for insertions and deletions between lines (r > 0.97). We infer that the genomic factors associated with variation in the mutation rate are similar to those in C. reinhardtii, allowing for cross-prediction between species. Among these genomic factors, sequence context and complexity are more important than GC content. With the exception of a remarkably high C→T bias, the SNM spectrum differs markedly between the two Chlamydomonas species. Our results suggest that similar genomic and biological characteristics may result in a similar mutation rate in the two species, whereas the SNM spectrum has more freedom to diverge.
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Affiliation(s)
- Eugenio López-Cortegano
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rory J Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jobran Chebib
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Toby Samuels
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew D Morgan
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Katharina B Böndel
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Nick Colegrave
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter D Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Sipos EH, Léty-Stefanska A, Denby Wilkes C, Soutourina J, Malloggi F. Microfluidic platform for monitoring Saccharomyces cerevisiae mutation accumulation. Lab Chip 2021; 21:2407-2416. [PMID: 33960358 DOI: 10.1039/d1lc00086a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Mutations in DNA have large-ranging consequences, from evolution to disease. Many mechanisms contribute to mutational processes such as dysfunctions in DNA repair pathways and exogenous or endogenous mutagen exposures. Model organisms and mutation accumulation (MA) experiments are indispensable to study mutagenesis. Classical MA is, however, time consuming and laborious. To fill the need for more efficient approaches to characterize mutational profiles, we have developed an innovative microfluidic-based system that automatizes MA culturing over many generations in budding yeast. This unique experimental tool, coupled with high-throughput sequencing, reduces by one order of magnitude the time required for genome-wide measurements of mutational profiles, while also parallelizing and simplifying the cell culture. To validate our approach, we performed microfluidic MA experiments on two different genetic backgrounds, a wild-type strain and a base-excision DNA repair ung1 mutant characterized by a well-defined mutational profile. We show that the microfluidic device allows for mutation accumulation comparable to the traditional method on plate. Our approach thus paves the way to massively-parallel MA experiments with minimal human intervention that can be used to investigate mutational processes at the origin of human diseases and to identify mutagenic compounds relevant for medical and environmental research.
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Affiliation(s)
- Eliet H Sipos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | | | - Cyril Denby Wilkes
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Julie Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Florent Malloggi
- Université Paris-Saclay, CEA, CNRS, NIMBE, 91191 Gif-sur-Yvette Cedex, France.
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12
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Araujo DV, Wang A, Torti D, Leon A, Marsh K, McCarthy A, Berman H, Spreafico A, Hansen AR, Razak AA, Bedard PL, Wang L, Plackmann E, Chow H, Bao H, Wu X, Pugh TJ, Siu LL. Applications of Circulating Tumor DNA in a Cohort of Phase I Solid Tumor Patients Treated With Immunotherapy. JNCI Cancer Spectr 2021; 5:pkaa122. [PMID: 34056539 PMCID: PMC8152803 DOI: 10.1093/jncics/pkaa122] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/25/2020] [Accepted: 11/13/2020] [Indexed: 12/18/2022] Open
Abstract
Background The correlation between blood-based tumor mutation burden (bTMB) and tissue-based tumor mutation burden(tTMB) has not been broadly tested in a multicancer cohort. Here, we assess the correlation between bTMB with tTMB in phase I trial patients treated with immunotherapy. As an exploratory analysis, we evaluated circulating tumor DNA (ctDNA) dynamics in responders. Methods Patients treated with immunotherapy at the Princess Margaret phase I trials unit were enrolled. Pretreatment plasma ctDNA and matched normal blood controls were collected. Available archival tissue formalin-fixed paraffin-embedded (FFPE) samples were analyzed. A 425-gene panel was used to sequence both ctDNA and FFPE samples. Samples with TMB within the highest tertile were considered as high TMB. Results Thirty-eight patients were accrued from 25 different trials, 86.8% of which involved an anti-PD-1/PD-L1 agent. Thirty patients (78.9%) had detectable mutations in ctDNA, of which the median (range) bTMB was 5 (1-53) mutations per megabase (mut/Mb). Of the 22 patients with available FFPE samples, mutations were detected in 21 (95.4%); the median (range) tTMB was 6 (2-124) mut/Mb. Among the 16 patients with detectable mutations in both FFPE and ctDNA, a statistically significant correlation between bTMB and tTMB was observed (ρ = 0.71; P = .002). High TMB was not associated with better survival. All 3 responders had a decrease in the variant allele frequency of mutations detected in ctDNA at a second timepoint relative to baseline, indicating a potential early marker of response. Conclusions In this small series, bTMB correlated with tTMB. An on-treatment decrease in VAF of mutations detected in ctDNA at baseline was observed in responders. Larger studies to verify our findings are warranted.
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Affiliation(s)
- Daniel V Araujo
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ao Wang
- Geneseeq Technology Inc, Toronto, Ontario, Canada
| | - Dax Torti
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Alberto Leon
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Kayla Marsh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Aoife McCarthy
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Hal Berman
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron R Hansen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Albiruni-Abdul Razak
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Philippe L Bedard
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lisa Wang
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Eric Plackmann
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Helen Chow
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Hua Bao
- Geneseeq Technology Inc, Toronto, Ontario, Canada
| | - Xue Wu
- Geneseeq Technology Inc, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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13
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Gu X, Li X, Xu J, Yang J, Li H, Wu Q, Qian J. Accumulated genetic mutations leading to accelerated initiation and progression of colorectal cancer in a patient with Gardner syndrome: A case report. Medicine (Baltimore) 2021; 100:e25247. [PMID: 33787608 PMCID: PMC8021328 DOI: 10.1097/md.0000000000025247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/04/2021] [Indexed: 01/04/2023] Open
Abstract
RATIONALE Gardner syndrome is a rare autosomal dominant disorder with a high degree of penetrance, which is characterized by intestinal polyposis, osteomas, and dental abnormalities. Majority of patients with Gardner syndrome will develop colorectal cancer by the age of 40 to 50 years. Mutations in the adenomatous polyposis coli gene are supposed to be responsible for the initiation of Gardner syndrome. PATIENT CONCERNS A 22-year-old Chinese female was admitted to our hospital due to abdominal pain and bloody stool. DIAGNOSIS The patient presented with multiple intestinal polyposis, desmoid tumors, and dental abnormalities was diagnosed as Gardner syndrome and further examination revealed a colon tumor. INTERVENTIONS AND OUTCOMES Patients were implanted with stents to alleviate bowel obstruction, and were treated with oxaliplatin combined with 5-Fu for 4 cycles, but the efficacy was not good. We performed next generation sequencing of 390 genes for the tumor specimens. We detected adenomatous polyposis coli E1538Ifs∗5, KRAS G12D, NF1 R652C, loss of SMAD4, TP53 R175H, IRF2 p.R82S, TCF7L2 p.A418Tfs∗14, and SMAD4 p.L43F in this patient. LESSONS We reported serial mutations in key genes responsible for initiation and progression of colorectal cancer from a patient with Gardner syndrome.
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Valesano AL, Rumfelt KE, Dimcheff DE, Blair CN, Fitzsimmons WJ, Petrie JG, Martin ET, Lauring AS. Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts. PLoS Pathog 2021; 17:e1009499. [PMID: 33826681 PMCID: PMC8055005 DOI: 10.1371/journal.ppat.1009499] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/19/2021] [Accepted: 03/24/2021] [Indexed: 01/12/2023] Open
Abstract
Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified viral load as a critical factor in variant identification. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.
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Affiliation(s)
- Andrew L. Valesano
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kalee E. Rumfelt
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Derek E. Dimcheff
- Division of Hospital Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Christopher N. Blair
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - William J. Fitzsimmons
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Joshua G. Petrie
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Emily T. Martin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Adam S. Lauring
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America
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15
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Osum SH, Watson AL, Largaespada DA. Spontaneous and Engineered Large Animal Models of Neurofibromatosis Type 1. Int J Mol Sci 2021; 22:1954. [PMID: 33669386 PMCID: PMC7920315 DOI: 10.3390/ijms22041954] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/13/2022] Open
Abstract
Animal models are crucial to understanding human disease biology and developing new therapies. By far the most common animal used to investigate prevailing questions about human disease is the mouse. Mouse models are powerful tools for research as their small size, limited lifespan, and defined genetic background allow researchers to easily manipulate their genome and maintain large numbers of animals in general laboratory spaces. However, it is precisely these attributes that make them so different from humans and explains, in part, why these models do not accurately predict drug responses in human patients. This is particularly true of the neurofibromatoses (NFs), a group of genetic diseases that predispose individuals to tumors of the nervous system, the most common of which is Neurofibromatosis type 1 (NF1). Despite years of research, there are still many unanswered questions and few effective treatments for NF1. Genetically engineered mice have drastically improved our understanding of many aspects of NF1, but they do not exemplify the overall complexity of the disease and some findings do not translate well to humans due to differences in body size and physiology. Moreover, NF1 mouse models are heavily reliant on the Cre-Lox system, which does not accurately reflect the molecular mechanism of spontaneous loss of heterozygosity that accompanies human tumor development. Spontaneous and genetically engineered large animal models may provide a valuable supplement to rodent studies for NF1. Naturally occurring comparative models of disease are an attractive prospect because they occur on heterogeneous genetic backgrounds and are due to spontaneous rather than engineered mutations. The use of animals with naturally occurring disease has been effective for studying osteosarcoma, lymphoma, and diabetes. Spontaneous NF-like symptoms including neurofibromas and malignant peripheral nerve sheath tumors (MPNST) have been documented in several large animal species and share biological and clinical similarities with human NF1. These animals could provide additional insight into the complex biology of NF1 and potentially provide a platform for pre-clinical trials. Additionally, genetically engineered porcine models of NF1 have recently been developed and display a variety of clinical features similar to those seen in NF1 patients. Their large size and relatively long lifespan allow for longitudinal imaging studies and evaluation of innovative surgical techniques using human equipment. Greater genetic, anatomic, and physiologic similarities to humans enable the engineering of precise disease alleles found in human patients and make them ideal for preclinical pharmacokinetic and pharmacodynamic studies of small molecule, cellular, and gene therapies prior to clinical trials in patients. Comparative genomic studies between humans and animals with naturally occurring disease, as well as preclinical studies in large animal disease models, may help identify new targets for therapeutic intervention and expedite the translation of new therapies. In this review, we discuss new genetically engineered large animal models of NF1 and cases of spontaneous NF-like manifestations in large animals, with a special emphasis on how these comparative models could act as a crucial translational intermediary between specialized murine models and NF1 patients.
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Affiliation(s)
- Sara H. Osum
- Masonic Cancer Center, Department of Pediatrics, Division of Hematology and Oncology, University of Minnesota, Minneapolis, MN 55455, USA;
| | | | - David A. Largaespada
- Masonic Cancer Center, Department of Pediatrics, Division of Hematology and Oncology, University of Minnesota, Minneapolis, MN 55455, USA;
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16
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Roy C, Mandal SM, Mondal SK, Mukherjee S, Mapder T, Ghosh W, Chakraborty R. Trends of mutation accumulation across global SARS-CoV-2 genomes: Implications for the evolution of the novel coronavirus. Genomics 2020; 112:5331-5342. [PMID: 33161087 PMCID: PMC7644180 DOI: 10.1016/j.ygeno.2020.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/22/2022]
Abstract
To understand SARS-CoV-2 microevolution, this study explored the genome-wide frequency, gene-wise distribution, and molecular nature of all point-mutations detected across its 71,703 RNA-genomes deposited in GISAID till 21 August 2020. Globally, nsp1/nsp2 and orf7a/orf3a were the most mutation-ridden non-structural and structural genes respectively. Phylogeny of 4618 spatiotemporally-representative genomes revealed that entities belonging to the early lineages are mostly spread over Asian countries, including India, whereas the recently-derived lineages are more globally distributed. Of the total 20,163 instances of polymorphism detected across global genomes, 12,594 and 7569 involved transitions and transversions, predominated by cytidine-to-uridine and guanosine-to-uridine conversions, respectively. Positive selection of nonsynonymous mutations (dN/dS >1) in most of the structural, but not the non-structural, genes indicated that SARS-CoV-2 has already harmonized its replication/transcription machineries with the host metabolism, while it is still redefining virulence/transmissibility strategies at the molecular level. Mechanistic bases and evolutionary/pathogenicity-related implications are discussed for the predominant mutation-types.
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Affiliation(s)
- Chayan Roy
- College of Veterinary Medicine, Western University of Health Sciences, 309 East Second Street, Pomona, CA 91766, USA
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Suresh K Mondal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Shriparna Mukherjee
- Department of Botany, Prasannadeb Women's College, Jalpaiguri, West Bengal, India
| | - Tarunendu Mapder
- Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Wriddhiman Ghosh
- Department of Microbiology, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, West Bengal, India.
| | - Ranadhir Chakraborty
- Department of Biotechnology, University of North Bengal, Raja Rammohanpur, Darjeeling 734013, West Bengal, India.
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17
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Wang HC, Yeh TJ, Chan LP, Hsu CM, Cho SF. Exploration of Feasible Immune Biomarkers for Immune Checkpoint Inhibitors in Head and Neck Squamous Cell Carcinoma Treatment in Real World Clinical Practice. Int J Mol Sci 2020; 21:E7621. [PMID: 33076306 PMCID: PMC7589088 DOI: 10.3390/ijms21207621] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 02/06/2023] Open
Abstract
Recurrent locally advanced or metastatic head and neck squamous cell carcinoma (HNSCC) is associated with dismal prognosis because of its highly invasive behavior and resistance to conventional intensive chemotherapy. The combination of targeted therapy and conventional chemotherapy has significantly improved clinical outcomes. In recent years, the development of immunotherapies, such as immune checkpoint inhibitors (ICIs), has further increased treatment responses and prolonged survival. However, the limited response rate, risk of immunotherapy-related adverse effects and high cost of immunotherapy make the identification of predictive markers to optimize treatment efficacy a critical issue. Biomarkers are biological molecules that have been widely utilized to predict treatment response to certain treatments and clinical outcomes or to detect disease. An ideal biomarker should exhibit good predictive ability, which can guide healthcare professionals to achieve optimal treatment goals and bring clinical benefit to patients. In this review, we summarized the results of recent and important studies focused on HNSCC ICI immunotherapy and discussed potential biomarkers including their strengths and limitations, aiming to gain more insight into HNSCC immunotherapy in real world clinical practice.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (T.-J.Y.); (L.-P.C.)
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Tsung-Jang Yeh
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (T.-J.Y.); (L.-P.C.)
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Leong-Perng Chan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (T.-J.Y.); (L.-P.C.)
- Department of Otolaryngology-Head and Neck Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chin-Mu Hsu
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shih-Feng Cho
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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18
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Willemsen D, Cui R, Reichard M, Valenzano DR. Intra-species differences in population size shape life history and genome evolution. eLife 2020; 9:e55794. [PMID: 32869739 PMCID: PMC7462614 DOI: 10.7554/elife.55794] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 08/14/2020] [Indexed: 12/16/2022] Open
Abstract
The evolutionary forces shaping life history divergence within species are largely unknown. Turquoise killifish display differences in lifespan among wild populations, representing an ideal natural experiment in evolution and diversification of life history. By combining genome sequencing and population genetics, we investigate the evolutionary forces shaping lifespan among wild turquoise killifish populations. We generate an improved reference genome assembly and identify genes under positive and purifying selection, as well as those evolving neutrally. Short-lived populations from the outer margin of the species range have small population size and accumulate deleterious mutations in genes significantly enriched in the WNT signaling pathway, neurodegeneration, cancer and the mTOR pathway. We propose that limited population size due to habitat fragmentation and repeated population bottlenecks, by increasing the genome-wide mutation load, exacerbates the effects of mutation accumulation and cumulatively contribute to the short adult lifespan.
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Affiliation(s)
| | - Rongfeng Cui
- Max Planck Institute for Biology of AgeingCologneGermany
| | - Martin Reichard
- Czech Academy of Sciences, Institute of Vertebrate BiologyBrnoCzech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk UniversityBrnoCzech Republic
| | - Dario Riccardo Valenzano
- Max Planck Institute for Biology of AgeingCologneGermany
- CECAD, University of CologneCologneGermany
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19
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Harvey EF, Cristescu ME, Dale J, Hunter H, Randall C, Crease TJ. Metal exposure causes rDNA copy number to fluctuate in mutation accumulation lines of Daphnia pulex. Aquat Toxicol 2020; 226:105556. [PMID: 32652413 DOI: 10.1016/j.aquatox.2020.105556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 05/29/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Ribosomal (r)DNA is a highly dynamic, conserved, multigene family whose sequence homogeneity is thought to be maintained by intra- and interchromosomal recombination, which are capable of changing rDNA copy number. It is generally not known how environmental stress such as sublethal exposure to environmentally relevant concentrations of metals impacts rDNA copy number. To determine how chronic metal exposure affects rDNA, we measured copy number of the 18S rRNA gene in 355 copper and nickel-exposed samples and 132 metal-free samples derived from 325 mutation accumulation (MA) lines of two genetically distinct Daphnia pulex lineages. The MA lines were sampled at four time points over 100+ generations of clonal propagation. The copy number of rDNA was also measured in 15 individuals sampled from a metal-free non-MA control population established from the same progenitor as one of the MA lineages. We found that mean rDNA copy number fluctuated across lines exposed to metals with a tendency to decrease over time. In contrast, mean rDNA copy number in the metal-free control lines and the non-MA population remained stable over time. It is generally accepted that extreme rDNA loss results in the loss of organism fitness. Thus, fluctuations in rDNA copy number, including losses, could affect the long-term viability of natural populations of Daphnia in metal-contaminated habitats.
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Affiliation(s)
- Eleanor F Harvey
- Department of Integrative Biology, University of Guelph, 50 Stone Road West, Guelph, ON, N1G 2W1, Canada
| | - Melania E Cristescu
- Biology Department, McGill University, Stewart Biology Building, 1205 Dr Penfield Ave, Montreal, QC, H3A 1B1, Canada
| | - Jenna Dale
- Department of Integrative Biology, University of Guelph, 50 Stone Road West, Guelph, ON, N1G 2W1, Canada
| | - Hailey Hunter
- Department of Integrative Biology, University of Guelph, 50 Stone Road West, Guelph, ON, N1G 2W1, Canada
| | - Connor Randall
- Department of Integrative Biology, University of Guelph, 50 Stone Road West, Guelph, ON, N1G 2W1, Canada
| | - Teresa J Crease
- Department of Integrative Biology, University of Guelph, 50 Stone Road West, Guelph, ON, N1G 2W1, Canada.
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20
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Rougemont Q, Moore JS, Leroy T, Normandeau E, Rondeau EB, Withler RE, Van Doornik DM, Crane PA, Naish KA, Garza JC, Beacham TD, Koop BF, Bernatchez L. Demographic history shaped geographical patterns of deleterious mutation load in a broadly distributed Pacific Salmon. PLoS Genet 2020; 16:e1008348. [PMID: 32845885 PMCID: PMC7478589 DOI: 10.1371/journal.pgen.1008348] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/08/2020] [Accepted: 06/24/2020] [Indexed: 12/24/2022] Open
Abstract
A thorough reconstruction of historical processes is essential for a comprehensive understanding of the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded recently, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored. Reconstruction of a species’ past demographic history from genetic data can highlight historical factors that have shaped the distribution of genetic diversity along its genome and its geographic range. Here, we combine genotyping-by-sequencing with demographic modelling to address these issues in the Coho salmon, a Pacific salmon of conservation concern in some parts of its range, notably in the south. Our demographic reconstructions reveal a linear decrease in genetic diversity toward the north of the species range, supporting the hypothesis of a northern route of postglacial recolonization from a single major southern refugium. As predicted by theory, we also observed a higher proportion of deleterious mutations in the most distant populations from this refugium. Beyond this general pattern, among-site variation in the proportion of deleterious mutations is consistent with different local trends in effective population sizes. Our results highlight the potential importance of understanding historical factors that have shaped geographic patterns of the distribution of deleterious mutations in order to implement effective management programs for the conservation of wild populations. Such fundamental knowledge of human historical demography is now having major impacts on health sciences, and we argue it is time to integrate such approaches in conservation science as well.
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Affiliation(s)
- Quentin Rougemont
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
- * E-mail:
| | - Jean-Sébastien Moore
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Thibault Leroy
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Department of Botany & Biodiversity Research, University of Vienna, Vienna, Austria
| | - Eric Normandeau
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Eric B. Rondeau
- Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Ruth E. Withler
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Donald M. Van Doornik
- National Oceanic and Atmospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, Manchester Research Station, Port Orchard, Washington, United States of America
| | - Penelope A. Crane
- Conservation Genetics Laboratory, U.S. Fish and Wildlife Service, Anchorage, Alaska, United States of America
| | - Kerry A. Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States of America
| | - John Carlos Garza
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service and Institute of Marine Sciences, University of California–Santa Cruz, Santa Cruz, California, United States of America
| | - Terry D. Beacham
- Department of Fisheries and Ocean, Pacific Biological Station, Nanaimo, British Columbia, Canada
| | - Ben F. Koop
- Centre for Biomedical Research, University of Victoria, Victoria, BC, Canada
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Louis Bernatchez
- Département de Biologie, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
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21
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Hepple RT. mtDNA Mutation Accumulation in Muscle Is Not a Major Cause of Fiber Loss. Reply to "Comment on: Mitochondrial Mechanisms of Neuromuscular Junction Degeneration with Aging. Cells 2020, 9, 197". Cells 2020; 9:cells9081821. [PMID: 32752189 PMCID: PMC7465963 DOI: 10.3390/cells9081821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Affiliation(s)
- Russell T Hepple
- Department of Physical Therapy, University of Florida, Gainesville, FL 32610, USA
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22
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Hasaart KAL, Manders F, van der Hoorn ML, Verheul M, Poplonski T, Kuijk E, de Sousa Lopes SMC, van Boxtel R. Mutation accumulation and developmental lineages in normal and Down syndrome human fetal haematopoiesis. Sci Rep 2020; 10:12991. [PMID: 32737409 PMCID: PMC7395765 DOI: 10.1038/s41598-020-69822-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/17/2020] [Indexed: 11/30/2022] Open
Abstract
Children show a higher incidence of leukemia compared to young adolescents, yet their cells have less age-related (oncogenic) somatic mutations. Newborns with Down syndrome have an even higher risk of developing leukemia, which is thought to be driven by mutations that accumulate during fetal development. To characterize mutation accumulation in individual stem and progenitor cells of Down syndrome and karyotypically normal fetuses, we clonally expanded single cells and performed whole-genome sequencing. We found a higher mutation rate in haematopoietic stem and progenitor cells during fetal development compared to the post-infant rate. In fetal trisomy 21 cells the number of somatic mutations is even further increased, which was already apparent during the first cell divisions of embryogenesis before gastrulation. The number and types of mutations in fetal trisomy 21 haematopoietic stem and progenitor cells were similar to those in Down syndrome-associated myeloid preleukemia and could be attributed to mutational processes that were active during normal fetal haematopoiesis. Finally, we found that the contribution of early embryonic cells to human fetal tissues can vary considerably between individuals. The increased mutation rates found in this study, may contribute to the increased risk of leukemia early during life and the higher incidence of leukemia in Down syndrome.
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Affiliation(s)
- Karlijn A L Hasaart
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | - Freek Manders
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | | | - Mark Verheul
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | - Tomasz Poplonski
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine, University Medical Center Utrecht and Oncode Institute, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | | | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Heidelberglaan 25, 3584CS, Utrecht, The Netherlands.
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23
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Wood MA, Weeder BR, David JK, Nellore A, Thompson RF. Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival. Genome Med 2020; 12:33. [PMID: 32228719 PMCID: PMC7106909 DOI: 10.1186/s13073-020-00729-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/10/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Tumor mutational burden (TMB; the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as a result. However, TMB harbors intrinsic variability across cancer types, and its assessment and interpretation are poorly standardized. METHODS Using a standardized approach, we quantify the robustness of TMB as a metric and its potential as a predictor of immunotherapy response and survival among a diverse cohort of cancer patients. We also explore the additive predictive potential of RNA-derived variants and neoepitope burden, incorporating several novel metrics of immunogenic potential. RESULTS We find that TMB is a partial predictor of immunotherapy response in melanoma and non-small cell lung cancer, but not renal cell carcinoma. We find that TMB is predictive of overall survival in melanoma patients receiving immunotherapy, but not in an immunotherapy-naive population. We also find that it is an unstable metric with potentially problematic repercussions for clinical cohort classification. We finally note minimal additional predictive benefit to assessing neoepitope burden or its bulk derivatives, including RNA-derived sources of neoepitopes. CONCLUSIONS We find sufficient cause to suggest that the predictive clinical value of TMB should not be overstated or oversimplified. While it is readily quantified, TMB is at best a limited surrogate biomarker of immunotherapy response. The data do not support isolated use of TMB in renal cell carcinoma.
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Affiliation(s)
- Mary A Wood
- Computational Biology Program, Oregon Health & Science University, Portland, USA
- Portland VA Research Foundation, Portland, USA
| | - Benjamin R Weeder
- Computational Biology Program, Oregon Health & Science University, Portland, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA
| | - Julianne K David
- Computational Biology Program, Oregon Health & Science University, Portland, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, USA
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA
- Department of Surgery, Oregon Health & Science University, Portland, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, USA.
- Portland VA Research Foundation, Portland, USA.
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, USA.
- Department of Radiation Medicine, Oregon Health & Science University, Portland, USA.
- Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University, Portland, USA.
- VA Portland Healthcare System, Division of Hospital and Specialty Medicine, Portland, USA.
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24
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Werner B, Case J, Williams MJ, Chkhaidze K, Temko D, Fernández-Mateos J, Cresswell GD, Nichol D, Cross W, Spiteri I, Huang W, Tomlinson IPM, Barnes CP, Graham TA, Sottoriva A. Measuring single cell divisions in human tissues from multi-region sequencing data. Nat Commun 2020; 11:1035. [PMID: 32098957 PMCID: PMC7042311 DOI: 10.1038/s41467-020-14844-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/29/2020] [Indexed: 01/06/2023] Open
Abstract
Both normal tissue development and cancer growth are driven by a branching process of cell division and mutation accumulation that leads to intra-tissue genetic heterogeneity. However, quantifying somatic evolution in humans remains challenging. Here, we show that multi-sample genomic data from a single time point of normal and cancer tissues contains information on single-cell divisions. We present a new theoretical framework that, applied to whole-genome sequencing data of healthy tissue and cancer, allows inferring the mutation rate and the cell survival/death rate per division. On average, we found that cells accumulate 1.14 mutations per cell division in healthy haematopoiesis and 1.37 mutations per division in brain development. In both tissues, cell survival was maximal during early development. Analysis of 131 biopsies from 16 tumours showed 4 to 100 times increased mutation rates compared to healthy development and substantial inter-patient variation of cell survival/death rates.
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Affiliation(s)
- Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Evolutionary Dynamics Group, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
| | - Jack Case
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- University of Cambridge, Cambridge, UK
| | - Marc J Williams
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK
- Department of Cell and Developmental Biology, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Ketevan Chkhaidze
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Temko
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Javier Fernández-Mateos
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - William Cross
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Weini Huang
- Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, 510060, Guangzhou, China
- School of Mathematical Sciences, Queen Mary University London, London, UK
| | - Ian P M Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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25
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Harrison MC, Mallon EB, Twell D, Hammond RL. Deleterious Mutation Accumulation in Arabidopsis thaliana Pollen Genes: A Role for a Recent Relaxation of Selection. Genome Biol Evol 2020; 11:1939-1951. [PMID: 31209485 PMCID: PMC6640295 DOI: 10.1093/gbe/evz127] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2019] [Indexed: 12/19/2022] Open
Abstract
In many studies, sex-related genes have been found to evolve rapidly. We therefore expect plant pollen genes to evolve faster than sporophytic genes. In addition, pollen genes are expressed as haploids which can itself facilitate rapid evolution because recessive advantageous and deleterious alleles are not masked by dominant alleles. However, this mechanism is less straightforward to apply in the model plant species Arabidopsis thaliana. For 1 Myr, A. thaliana has been self-compatible, a life history switch that has caused: a reduction in pollen competition, increased homozygosity, and a dilution of masking in diploid expressed, sporophytic genes. In this study, we have investigated the relative strength of selection on pollen genes compared with sporophytic genes in A. thaliana. We present two major findings: 1) before becoming self-compatible, positive selection was stronger on pollen genes than sporophytic genes for A. thaliana and 2) current polymorphism data indicate that selection is weaker on pollen genes compared with sporophytic genes. This weaker selection on pollen genes can in part be explained by their higher tissue specificity, which in outbreeding plants can be outweighed by the effects of haploid expression and pollen competition. These results indicate that since A. thaliana has become self-compatible, selection on pollen genes has become more relaxed. This has led to higher polymorphism levels and a higher build-up of deleterious mutations in pollen genes compared with sporophytic genes.
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Abstract
Microsatellite loci (tandem repeats of short nucleotide motifs) are highly abundant in eukaryotic genomes and often used as genetic markers because they can exhibit variation both within and between populations. Although widely recognized for their mutability and utility, the mutation rates of microsatellites have only been empirically estimated in a few species, and have rarely been compared across genotypes and populations within a species. Here, we investigate the dynamics of microsatellite mutation over long- and short-time periods by quantifying the starting abundance and mutation rates for microsatellites for six different genotypes of Daphnia magna, an aquatic microcrustacean, collected from three populations (Finland, Germany, and Israel). Using whole-genome sequences of these six starting genotypes, descendent mutation accumulation (MA) lines, and large population controls (non-MA lines), we find each genotype exhibits a distinctive initial microsatellite profile which clusters according to the population-of-origin. During the period of MA, we observe motif-specific, highly variable, and rapid microsatellite mutation rates across genotypes of D. magna, the average of which is order of magnitude greater than the recently reported rate observed in a single genotype of the congener, Daphnia pulex. In our experiment, genotypes with more microsatellites starting out exhibit greater losses and those with fewer microsatellites starting out exhibit greater gains—a context-dependent mutation bias that has not been reported previously. We discuss how genotype-specific mutation rates and spectra, in conjunction with evolutionary forces, can shape both the differential accumulation of repeat content in the genome and the evolution of mutation rates.
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Affiliation(s)
- Eddie K H Ho
- Department of Biology, Reed College, Portland, OR
| | | | - Leigh C Latta
- Department of Biology, Reed College, Portland, OR
- Division of Natural Sciences and Mathematics, Lewis-Clark State College, Lewiston, ID
| | | | - Cheng Sun
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Sarah Schaack
- Department of Biology, Reed College, Portland, OR
- Corresponding author: E-mail:
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27
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Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, Jorde LB, Quinlan AR. Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. eLife 2019; 8:e46922. [PMID: 31549960 PMCID: PMC6759356 DOI: 10.7554/elife.46922] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 08/13/2019] [Indexed: 12/27/2022] Open
Abstract
The number of de novo mutations (DNMs) found in an offspring's genome increases with both paternal and maternal age. But does the rate of mutation accumulation in human gametes differ across families? Using sequencing data from 33 large, three-generation CEPH families, we observed significant variability in parental age effects on DNM counts across families, ranging from 0.19 to 3.24 DNMs per year. Additionally, we found that ~3% of DNMs originated following primordial germ cell specification in a parent, and differed from non-mosaic germline DNMs in their mutational spectra. We also discovered that nearly 10% of candidate DNMs in the second generation were post-zygotic, and present in both somatic and germ cells; these gonosomal mutations occurred at equivalent frequencies on both parental haplotypes. Our results demonstrate that rates of germline mutation accumulation vary among families with similar ancestry, and confirm that post-zygotic mosaicism is a substantial source of human DNM.
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Affiliation(s)
- Thomas A Sasani
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Brent S Pedersen
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Ziyue Gao
- Howard Hughes Medical Institute and Department of GeneticsStanford UniversityStanfordUnited States
| | - Lisa Baird
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Molly Przeworski
- Department of Biological SciencesColumbia UniversityNew York CityUnited States
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
| | - Lynn B Jorde
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
- USTAR Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUnited States
| | - Aaron R Quinlan
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
- USTAR Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUnited States
- Department of Biomedical InformaticsUniversity of UtahSalt Lake CityUnited States
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28
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Dugo M, Devecchi A, De Cecco L, Cecchin E, Mezzanzanica D, Sensi M, Bagnoli M. Focal Recurrent Copy Number Alterations Characterize Disease Relapse in High Grade Serous Ovarian Cancer Patients with Good Clinical Prognosis: A Pilot Study. Genes (Basel) 2019; 10:genes10090678. [PMID: 31491988 PMCID: PMC6770978 DOI: 10.3390/genes10090678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 02/01/2023] Open
Abstract
High grade serous ovarian cancer (HGSOC) retains high molecular heterogeneity and genomic instability, which currently limit the treatment opportunities. HGSOC patients receiving complete cytoreduction (R0) at primary surgery and platinum-based therapy may unevenly experience early disease relapse, in spite of their clinically favorable prognosis. To identify distinctive traits of the genomic landscape guiding tumor progression, we focused on the R0 patients of The Cancer Genome Atlas (TCGA) ovarian serous cystadenocarcinoma (TCGA-OV) dataset and classified them according to their time to relapse (TTR) from surgery. We included in the study two groups of R0-TCGA patients experiencing substantially different outcome: Resistant (R; TTR ≤ 12 months; n = 11) and frankly Sensitive (fS; TTR ≥ 24 months; n = 16). We performed an integrated clinical, RNA-Sequencing, exome and somatic copy number alteration (sCNA) data analysis. No significant differences in mutational landscape were detected, although the lack of BRCA-related mutational signature characterized the R group. Focal sCNA analysis showed a higher frequency of amplification in R group and deletions in fS group respectively, involving cytobands not commonly detected by recurrent sCNA analysis. Functional analysis of focal sCNA with a concordantly altered gene expression identified in R group a gain in Notch, and interferon signaling and fatty acid metabolism. We are aware of the constraints related to the low number of OC cases analyzed. It is worth noting, however, that the sCNA identified in this exploratory analysis and characterizing Pt-resistance are novel, deserving validation in a wider cohort of patients achieving complete surgical debulking.
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Affiliation(s)
- Matteo Dugo
- Platform of Integrated Biology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Andrea Devecchi
- Platform of Integrated Biology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Loris De Cecco
- Platform of Integrated Biology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico, IRCCS National Cancer Institute, 33081 Aviano, Pordenone, Italy.
| | - Delia Mezzanzanica
- Molecular Therapy Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Marialuisa Sensi
- Platform of Integrated Biology, Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
| | - Marina Bagnoli
- Molecular Therapy Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy.
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29
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Konrad A, Brady MJ, Bergthorsson U, Katju V. Mutational Landscape of Spontaneous Base Substitutions and Small Indels in Experimental Caenorhabditis elegans Populations of Differing Size. Genetics 2019; 212:837-854. [PMID: 31110155 PMCID: PMC6614903 DOI: 10.1534/genetics.119.302054] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/16/2019] [Indexed: 02/08/2023] Open
Abstract
Experimental investigations into the rates and fitness effects of spontaneous mutations are fundamental to our understanding of the evolutionary process. To gain insights into the molecular and fitness consequences of spontaneous mutations, we conducted a mutation accumulation (MA) experiment at varying population sizes in the nematode Caenorhabditis elegans, evolving 35 lines in parallel for 409 generations at three population sizes (N = 1, 10, and 100 individuals). Here, we focus on nuclear SNPs and small insertion/deletions (indels) under minimal influence of selection, as well as their accrual rates in larger populations under greater selection efficacy. The spontaneous rates of base substitutions and small indels are 1.84 (95% C.I. ± 0.14) × 10-9 substitutions and 6.84 (95% C.I. ± 0.97) × 10-10 changes/site/generation, respectively. Small indels exhibit a deletion bias with deletions exceeding insertions by threefold. Notably, there was no correlation between the frequency of base substitutions, nonsynonymous substitutions, or small indels with population size. These results contrast with our previous analysis of mitochondrial DNA mutations and nuclear copy-number changes in these MA lines, and suggest that nuclear base substitutions and small indels are under less stringent purifying selection compared to the former mutational classes. A transition bias was observed in exons as was a near universal base substitution bias toward A/T. Strongly context-dependent base substitutions, where 5'-Ts and 3'-As increase the frequency of A/T → T/A transversions, especially at the boundaries of A or T homopolymeric runs, manifest as higher mutation rates in (i) introns and intergenic regions relative to exons, (ii) chromosomal cores vs. arms and tips, and (iii) germline-expressed genes.
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Affiliation(s)
- Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845
| | - Meghan J Brady
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845
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30
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Abstract
Mutation is the ultimate genetic source of evolution and biodiversity, but to what extent the environment impacts mutation rate and spectrum is poorly understood. Past studies discovered mutagenesis induced by antibiotic treatment or starvation, but its relevance and importance to long-term evolution is unclear because these severe stressors typically halt cell growth and/or cause substantial cell deaths. Here, we quantify the mutation rate and spectrum in Saccharomyces cerevisiae by whole-genome sequencing following mutation accumulation in each of seven environments with relatively rapid cell growths and minimal cell deaths. We find the point mutation rate per generation to differ by 3.6-fold among the seven environments, generally increasing in environments with slower cell growths. This trend renders the mutation rate per year more constant than that per generation across environments, which has implications for neutral evolution and the molecular clock. Additionally, we find substantial among-environment variations in mutation spectrum, such as the transition to transversion ratio and AT mutational bias. Other main mutation types, including small insertion or deletion, segmental duplication or deletion, and chromosome gain or loss also tend to occur more frequently in environments where yeast grows more slowly. In contrast to these findings from the nuclear genome, the yeast mitochondrial mutation rate rises with the growth rate, consistent with the metabolic rate hypothesis. Together, these observations indicate that environmental changes, which are ubiquitous in nature, influence not only natural selection, but also the amount and type of mutations available to selection, and suggest that ignoring the latter impact, as is currently practiced, may mislead evolutionary inferences.
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Affiliation(s)
- Haoxuan Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jianzhi Zhang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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31
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Wang L, Ji Y, Hu Y, Hu H, Jia X, Jiang M, Zhang X, Zhao L, Zhang Y, Jia Y, Qin C, Yu L, Huang J, Yang S, Hurst LD, Tian D. The architecture of intra-organism mutation rate variation in plants. PLoS Biol 2019; 17:e3000191. [PMID: 30964866 PMCID: PMC6456163 DOI: 10.1371/journal.pbio.3000191] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 03/06/2019] [Indexed: 12/30/2022] Open
Abstract
Given the disposability of somatic tissue, selection can favor a higher mutation rate in the early segregating soma than in germline, as seen in some animals. Although in plants intra-organismic mutation rate heterogeneity is poorly resolved, the same selectionist logic can predict a lower rate in shoot than in root and in longer-lived terminal tissues (e.g., leaves) than in ontogenetically similar short-lived ones (e.g., petals), and that mutation rate heterogeneity should be deterministic with no significant differences between biological replicates. To address these expectations, we sequenced 754 genomes from various tissues of eight plant species. Consistent with a selectionist model, the rate of mutation accumulation per unit time in shoot apical meristem is lower than that in root apical tissues in perennials, in which a high proportion of mutations in shoots are themselves transmissible, but not in annuals, in which somatic mutations tend not to be transmissible. Similarly, the number of mutations accumulated in leaves is commonly lower than that within a petal of the same plant, and there is no more heterogeneity in accumulation rates between replicate branches than expected by chance. High mutation accumulation in runners of strawberry is, we argue, the exception that proves the rule, as mutation transmission patterns indicate that runner has a restricted germline. However, we also find that in vitro callus tissue has a higher mutation rate (per unit time) than the wild-grown comparator, suggesting nonadaptive mutational "fragility". As mutational fragility does not obviously explain why the shoot-root difference varies with plant longevity, we conclude that some mutation rate variation between tissues is consistent with selectionist theory but that a mechanistic null of mutational fragility should be considered.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yilun Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yingwen Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Huaying Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xianqin Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Lina Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yanchun Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yanxiao Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Chao Qin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Luyao Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Laurence D. Hurst
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
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32
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Singh S, Singh V, Salas-Perez RA, Bagavathiannan MV, Lawton-Rauh A, Roma-Burgos N. Target-site mutation accumulation among ALS inhibitor-resistant Palmer amaranth. Pest Manag Sci 2019; 75:1131-1139. [PMID: 30298618 DOI: 10.1002/ps.5232] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/03/2018] [Accepted: 10/04/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Palmer amaranth (Amaranthus palmeri S. Wats) is one of the most common and troublesome weeds in the USA. Palmer amaranth resistance to acetolactate synthase (ALS) inhibitors is widespread in the USA, as in Arkansas. The cross-resistance patterns and mechanism of resistance are not known. Experiments were conducted to determine cross-resistance to ALS inhibitors and identify target-site mutations in 20 Palmer amaranth localities from 13 counties in Arkansas. RESULTS All Palmer amaranth localities tested had plants cross-resistant to imazethapyr, flumetsulam, primisulfuron, pyrithiobac and trifloxysulfuron. The dose of trifloxysulfuron that caused 50% control was 21-56-fold greater for resistant accessions than for susceptible ones. All but three resistant plants analyzed had one or two relative copies of ALS; one plant had seven relative copies. All resistant plants tested (18 localities) carried the Trp574Leu mutation, which is known to confer broad resistance to ALS inhibitors, supporting the cross-resistance pattern observed. Besides the Trp574Leu mutation, 30% of localities had individuals with one additional resistance-conferring mutation including Ala122Thr, Pro197Ala or Ser653Asn. CONCLUSION The Trp574Leu mutation in ALS is the primary mechanism of resistance to ALS inhibitors in Palmer amaranth from Arkansas, USA. In some localities, multiple mutations have accumulated in one plant. All localities tested contained plants with resistance to five families of ALS inhibitors. Localities with extremely high resistance to ALS inhibitors, and those outside the subset we studied, may harbor non-target site resistance mechanisms. ALS inhibitors are generally no longer effective on Palmer amaranth in these localities from the US mid-south. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Shilpa Singh
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Vijay Singh
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | | | - Amy Lawton-Rauh
- University of Arkansas Cooperative Extension Service, Lonoke, AR, USA
| | - Nilda Roma-Burgos
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
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33
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Katju V, Bergthorsson U. Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches. Genome Biol Evol 2019; 11:136-165. [PMID: 30476040 PMCID: PMC6330053 DOI: 10.1093/gbe/evy252] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Abstract
Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mutations for four decades. In the pregenomic era, phenotypic measurements of fitness-related traits in MA lines were used to indirectly estimate key mutational parameters, such as the genomic mutation rate, new mutational variance per generation, and the average fitness effect of mutations. Rapidly emerging next-generating sequencing technology has supplanted this phenotype-dependent approach, enabling direct empirical estimates of the mutation rate and a more nuanced understanding of the relative contributions of different classes of mutations to the standing genetic variation. Whole-genome sequencing of MA lines bears immense potential to provide a unified account of the evolutionary process at multiple levels-the genetic basis of variation, and the evolutionary dynamics of mutations under the forces of selection and drift. In this review, we have attempted to synthesize key insights into the spontaneous mutation process that are rapidly emerging from the partnering of classical MA experiments with high-throughput sequencing, with particular emphasis on the spontaneous rates and molecular properties of different mutational classes in nuclear and mitochondrial genomes of diverse taxa, the contribution of mutations to the evolution of gene expression, and the rate and stability of transgenerational epigenetic modifications. Future advances in sequencing technologies will enable greater species representation to further refine our understanding of mutational parameters and their functional consequences.
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Affiliation(s)
- Vaishali Katju
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
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Abstract
How mutation and selection determine the fitness landscape of tumors and hence clinical outcome is an open fundamental question in cancer biology, crucial for the assessment of therapeutic strategies and resistance to treatment. Here we explore the mutation-selection phase diagram of 6,721 tumors representing 23 cancer types by quantifying the overall somatic point mutation load (ML) and selection (dN/dS) in the entire proteome of each tumor. We show that ML strongly correlates with patient survival, revealing two opposing regimes around a critical point. In low-ML cancers, a high number of mutations indicates poor prognosis, whereas high-ML cancers show the opposite trend, presumably due to mutational meltdown. Although the majority of cancers evolve near neutrality, deviations are observed at extreme MLs. Melanoma, with the highest ML, evolves under purifying selection, whereas in low-ML cancers, signatures of positive selection are observed, demonstrating how selection affects tumor fitness. Moreover, different cancers occupy specific positions on the ML-dN/dS plane, revealing a diversity of evolutionary trajectories. These results support and expand the theory of tumor evolution and its nonlinear effects on survival.
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Affiliation(s)
- Erez Persi
- Center for Bioinformatics and Computational Biology, Institute of Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742;
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Mark D M Leiserson
- Center for Bioinformatics and Computational Biology, Institute of Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894;
| | - Eytan Ruppin
- Center for Bioinformatics and Computational Biology, Institute of Advanced Computer Studies, Department of Computer Science, University of Maryland, College Park, MD 20742;
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD 20894
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Sanders MA, Chew E, Flensburg C, Zeilemaker A, Miller SE, Al Hinai AS, Bajel A, Luiken B, Rijken M, Mclennan T, Hoogenboezem RM, Kavelaars FG, Fröhling S, Blewitt ME, Bindels EM, Alexander WS, Löwenberg B, Roberts AW, Valk PJM, Majewski IJ. MBD4 guards against methylation damage and germ line deficiency predisposes to clonal hematopoiesis and early-onset AML. Blood 2018; 132:1526-1534. [PMID: 30049810 PMCID: PMC6172562 DOI: 10.1182/blood-2018-05-852566] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/18/2018] [Indexed: 02/07/2023] Open
Abstract
The tendency of 5-methylcytosine (5mC) to undergo spontaneous deamination has had a major role in shaping the human genome, and this methylation damage remains the primary source of somatic mutations that accumulate with age. How 5mC deamination contributes to cancer risk in different tissues remains unclear. Genomic profiling of 3 early-onset acute myeloid leukemias (AMLs) identified germ line loss of MBD4 as an initiator of 5mC-dependent hypermutation. MBD4-deficient AMLs display a 33-fold higher mutation burden than AML generally, with >95% being C>T in the context of a CG dinucleotide. This distinctive signature was also observed in sporadic cancers that acquired biallelic mutations in MBD4 and in Mbd4 knockout mice. Sequential sampling of germ line cases demonstrated repeated expansion of blood cell progenitors with pathogenic mutations in DNMT3A, a key driver gene for both clonal hematopoiesis and AML. Our findings reveal genetic and epigenetic factors that shape the mutagenic influence of 5mC. Within blood cells, this links methylation damage to the driver landscape of clonal hematopoiesis and reveals a conserved path to leukemia. Germ line MBD4 deficiency enhances cancer susceptibility and predisposes to AML.
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Affiliation(s)
- Mathijs A Sanders
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Edward Chew
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Clinical Hematology, Peter MacCallum Cancer Center, Royal Melbourne Hospital, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Christoffer Flensburg
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Annelieke Zeilemaker
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sarah E Miller
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Adil S Al Hinai
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
- National Genetic Center, Royal Hospital, Ministry of Health, Muscat, Sultanate of Oman
| | - Ashish Bajel
- Clinical Hematology, Peter MacCallum Cancer Center, Royal Melbourne Hospital, Parkville, VIC, Australia
- Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Bram Luiken
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Melissa Rijken
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tamara Mclennan
- Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Remco M Hoogenboezem
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - François G Kavelaars
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Stefan Fröhling
- Division of Translational Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany; and
- Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marnie E Blewitt
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Division of Molecular Medicine, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Eric M Bindels
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Warren S Alexander
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
| | - Bob Löwenberg
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrew W Roberts
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Clinical Hematology, Peter MacCallum Cancer Center, Royal Melbourne Hospital, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
- Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ian J Majewski
- Division of Cancer and Haematology, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, Australia
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Everman ER, Morgan TJ. Antagonistic pleiotropy and mutation accumulation contribute to age-related decline in stress response. Evolution 2018; 72:303-317. [PMID: 29214647 DOI: 10.1111/evo.13408] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 01/17/2023]
Abstract
As organisms age, the effectiveness of natural selection weakens, leading to age-related decline in fitness-related traits. The evolution of age-related changes associated with senescence is likely influenced by mutation accumulation (MA) and antagonistic pleiotropy (AP). MA predicts that age-related decline in fitness components is driven by age-specific sets of alleles, nonnegative genetic correlations within trait across age, and an increase in the coefficient of genetic variance. AP predicts that age-related decline in a trait is driven by alleles with positive effects on fitness in young individuals and negative effects in old individuals, and is expected to lead to negative genetic correlations within traits across age. We build on these predictions using an association mapping approach to investigate the change in additive effects of SNPs across age and among traits for multiple stress-response fitness-related traits, including cold stress with and without acclimation and starvation resistance. We found support for both MA and AP theories of aging in the age-related decline in stress tolerance. Our study demonstrates that the evolution of age-related decline in stress tolerance is driven by a combination of alleles that have age-specific additive effects, consistent with MA, as well as nonindependent and antagonistic genetic architectures characteristic of AP.
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Affiliation(s)
- Elizabeth R Everman
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045
| | - Theodore J Morgan
- Division of Biology, Kansas State University, Manhattan, Kansas 66506
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Abstract
In many organisms, local deviations from Chargaff's second parity rule are observed around replication and transcription start sites and within intron sequences. Here, we use expression data as well as a whole-genome data set of nearly 200 haplotypes to investigate such compositional skews in Drosophila melanogaster genes. We find a positive correlation between compositional skew and gene expression, comparable in strength to similar correlations between expression levels and genome-wide sequence features. This correlation is relatively stronger for germline, compared with somatic expression, consistent with the process of transcription-associated mutation bias. We also inferred mutation rates from alleles segregating at low frequencies in short introns, and show that, whereas the overall GC content of short introns does not conform to the equilibrium expectation, the level of the observed deviation from the second parity rule is generally consistent with the inferred rates.
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Affiliation(s)
- Juraj Bergman
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Wien, Austria
| | - Andrea J Betancourt
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
- Present address: Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Claus Vogl
- Institut für Tierzucht und Genetik, Vetmeduni Vienna, Wien, Austria
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38
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Jiang T, Li X, Wang J, Su C, Han W, Zhao C, Wu F, Gao G, Li W, Chen X, Li J, Zhou F, Zhao J, Cai W, Zhang H, Du B, Zhang J, Ren S, Zhou C, Yu H, Hirsch FR. Mutational Landscape of cfDNA Identifies Distinct Molecular Features Associated With Therapeutic Response to First-Line Platinum-Based Doublet Chemotherapy in Patients with Advanced NSCLC. Theranostics 2017; 7:4753-4762. [PMID: 29187901 PMCID: PMC5706097 DOI: 10.7150/thno.21687] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/13/2017] [Indexed: 01/15/2023] Open
Abstract
Rationale To investigate whether the mutational landscape of circulating cell-free DNA (cfDNA) could predict and dynamically monitor the response to first-line platinum-based chemotherapy in patients with advanced non-small-cell lung cancer (NSCLC). Methods Eligible patients were included and blood samples were collected from a phase III trial. Both cfDNA fragments and fragmented genomic DNA were extracted for enrichment in a 1.15M size panel covering exon regions of 1,086 genes. Molecular mutational burden (MMB) was calculated to investigate the relationship between molecular features of cfDNA and response to chemotherapy. Results In total, 52 eligible cases were enrolled and their blood samples were prospectively collected at baseline, every cycle of chemotherapy and time of disease progression. At baseline, alterations of 17 genes were found. Patients with partial response (PR) had significantly lower baseline MMB of these genes than those patients with either stable disease (SD) (P = 0.0006) or progression disease (PD) (P = 0.0074). Further analysis revealed that the mutational landscape of cfDNA from pretreatment blood samples were distinctly different among patients with PR vs. SD/PD. For patients with baseline TP53 mutation, those with PR experienced a significant reduction in MMB whereas patients with SD or PD experienced an increase after two, three or four cycles of chemotherapy. Furthermore, patients with low MMB had superior response rate and significantly longer progression-free survival than those with high MMB. Conclusion This study indicated that the mutational landscape of cfDNA has potential clinical value to predict the therapeutic response to first-line platinum-based doublet chemotherapy in NSCLC patients. At the single gene level, dynamic change of molecular mutational burden of TP53 is valuable to monitor efficacy (and, therefore, might aid in early recognition of resistance and relapse) in patients harboring this mutation at baseline.
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Affiliation(s)
- Tao Jiang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Xuefei Li
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Jianfei Wang
- Beijing Genecast Biotechnology Co., Beijing, P.R. China
| | - Chunxia Su
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Wenbo Han
- Beijing Genecast Biotechnology Co., Beijing, P.R. China
| | - Chao Zhao
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, P.R. China
| | - Fengying Wu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Guanghui Gao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Wei Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Xiaoxia Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Jiayu Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Fei Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Jing Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Weijing Cai
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Henghui Zhang
- Beijing Genecast Biotechnology Co., Beijing, P.R. China
| | - Bo Du
- Beijing Genecast Biotechnology Co., Beijing, P.R. China
| | - Jun Zhang
- Division of Hematology, Oncology and Blood & Marrow Transplantation, Department of Internal Medicine, Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Thoracic Cancer Institute, Tongji University School of Medicine, Shanghai, P.R. China
| | - Hui Yu
- Department of Medicine, Division of Medical Oncology, University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, USA
| | - Fred R. Hirsch
- Department of Medicine, Division of Medical Oncology, University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO, USA
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Brammeld JS, Petljak M, Martincorena I, Williams SP, Alonso LG, Dalmases A, Bellosillo B, Robles-Espinoza CD, Price S, Barthorpe S, Tarpey P, Alifrangis C, Bignell G, Vidal J, Young J, Stebbings L, Beal K, Stratton MR, Saez-Rodriguez J, Garnett M, Montagut C, Iorio F, McDermott U. Genome-wide chemical mutagenesis screens allow unbiased saturation of the cancer genome and identification of drug resistance mutations. Genome Res 2017; 27:613-625. [PMID: 28179366 PMCID: PMC5378179 DOI: 10.1101/gr.213546.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 02/07/2017] [Indexed: 01/26/2023]
Abstract
Drug resistance is an almost inevitable consequence of cancer therapy and ultimately proves fatal for the majority of patients. In many cases, this is the consequence of specific gene mutations that have the potential to be targeted to resensitize the tumor. The ability to uniformly saturate the genome with point mutations without chromosome or nucleotide sequence context bias would open the door to identify all putative drug resistance mutations in cancer models. Here, we describe such a method for elucidating drug resistance mechanisms using genome-wide chemical mutagenesis allied to next-generation sequencing. We show that chemically mutagenizing the genome of cancer cells dramatically increases the number of drug-resistant clones and allows the detection of both known and novel drug resistance mutations. We used an efficient computational process that allows for the rapid identification of involved pathways and druggable targets. Such a priori knowledge would greatly empower serial monitoring strategies for drug resistance in the clinic as well as the development of trials for drug-resistant patients.
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Affiliation(s)
| | - Mia Petljak
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | | | | | - Luz Garcia Alonso
- European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge CB10 1SA, United Kingdom
| | - Alba Dalmases
- Pathology Department, Hospital del Mar, 08003 Barcelona, Spain
| | | | - Carla Daniela Robles-Espinoza
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Santiago de Querétaro 76230, Mexico
| | - Stacey Price
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Syd Barthorpe
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Patrick Tarpey
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | | | - Graham Bignell
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Joana Vidal
- Cancer Research Program, FIMIM and Medical Oncology Department, Hospital del Mar, 08003 Barcelona, Spain
| | - Jamie Young
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Lucy Stebbings
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Kathryn Beal
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | | | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge CB10 1SA, United Kingdom
- RWTH Aachen University Hospital, 52062 Aachen, Germany
| | - Mathew Garnett
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Clara Montagut
- Cancer Research Program, FIMIM and Medical Oncology Department, Hospital del Mar, 08003 Barcelona, Spain
| | - Francesco Iorio
- European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge CB10 1SA, United Kingdom
| | - Ultan McDermott
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom
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40
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Santiago E, Caballero A. Joint Prediction of the Effective Population Size and the Rate of Fixation of Deleterious Mutations. Genetics 2016; 204:1267-1279. [PMID: 27672094 PMCID: PMC5105856 DOI: 10.1534/genetics.116.188250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 09/20/2016] [Indexed: 11/18/2022] Open
Abstract
Mutation, genetic drift, and selection are considered the main factors shaping genetic variation in nature. There is a lack, however, of general predictions accounting for the mutual interrelation between these factors. In the context of the background selection model, we provide a set of equations for the joint prediction of the effective population size and the rate of fixation of deleterious mutations, which are applicable both to sexual and asexual species. For a population of N haploid individuals and a model of deleterious mutations with effect s appearing with rate U in a genome L Morgans long, the asymptotic effective population size (Ne) and the average number of generations (T) between consecutive fixations can be approximated by [Formula: see text] and [Formula: see text] The solution is applicable to Muller's ratchet, providing satisfactory approximations to the rate of accumulation of mutations for a wide range of parameters. We also obtain predictions of the effective size accounting for the expected nucleotide diversity. Predictions for sexual populations allow for outlining the general conditions where mutational meltdown occurs. The equations can be extended to any distribution of mutational effects and the consideration of hotspots of recombination, showing that Ne is rather insensitive and not proportional to changes in N for many combinations of parameters. This could contribute to explain the observed small differences in levels of polymorphism between species with very different census sizes.
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Affiliation(s)
- Enrique Santiago
- Departamento de Biología Funcional, Facultad de Biología, Universidad de Oviedo, 33071 Oviedo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain
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Blokzijl F, de Ligt J, Jager M, Sasselli V, Roerink S, Sasaki N, Huch M, Boymans S, Kuijk E, Prins P, Nijman IJ, Martincorena I, Mokry M, Wiegerinck CL, Middendorp S, Sato T, Schwank G, Nieuwenhuis EES, Verstegen MMA, van der Laan LJW, de Jonge J, IJzermans JNM, Vries RG, van de Wetering M, Stratton MR, Clevers H, Cuppen E, van Boxtel R. Tissue-specific mutation accumulation in human adult stem cells during life. Nature 2016; 538:260-264. [PMID: 27698416 PMCID: PMC5536223 DOI: 10.1038/nature19768] [Citation(s) in RCA: 605] [Impact Index Per Article: 75.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 08/16/2016] [Indexed: 12/20/2022]
Abstract
The gradual accumulation of genetic mutations in human adult stem cells (ASCs) during life is associated with various age-related diseases, including cancer. Extreme variation in cancer risk across tissues was recently proposed to depend on the lifetime number of ASC divisions, owing to unavoidable random mutations that arise during DNA replication. However, the rates and patterns of mutations in normal ASCs remain unknown. Here we determine genome-wide mutation patterns in ASCs of the small intestine, colon and liver of human donors with ages ranging from 3 to 87 years by sequencing clonal organoid cultures derived from primary multipotent cells. Our results show that mutations accumulate steadily over time in all of the assessed tissue types, at a rate of approximately 40 novel mutations per year, despite the large variation in cancer incidence among these tissues. Liver ASCs, however, have different mutation spectra compared to those of the colon and small intestine. Mutational signature analysis reveals that this difference can be attributed to spontaneous deamination of methylated cytosine residues in the colon and small intestine, probably reflecting their high ASC division rate. In liver, a signature with an as-yet-unknown underlying mechanism is predominant. Mutation spectra of driver genes in cancer show high similarity to the tissue-specific ASC mutation spectra, suggesting that intrinsic mutational processes in ASCs can initiate tumorigenesis. Notably, the inter-individual variation in mutation rate and spectra are low, suggesting tissue-specific activity of common mutational processes throughout life.
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Affiliation(s)
- Francis Blokzijl
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Joep de Ligt
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Myrthe Jager
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Valentina Sasselli
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Sophie Roerink
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Nobuo Sasaki
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Meritxell Huch
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Pjotr Prins
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Isaac J Nijman
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Inigo Martincorena
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michal Mokry
- Department of Pediatrics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Caroline L Wiegerinck
- Department of Pediatrics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Sabine Middendorp
- Department of Pediatrics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Toshiro Sato
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Gerald Schwank
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Edward E S Nieuwenhuis
- Department of Pediatrics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands
| | - Monique M A Verstegen
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Jeroen de Jonge
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Jan N M IJzermans
- Department of Surgery, Erasmus MC-University Medical Center, Postbus 2040, 3000 CA Rotterdam, The Netherlands
| | - Robert G Vries
- Foundation Hubrecht Organoid Technology (HUB), Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Marc van de Wetering
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
| | - Ruben van Boxtel
- Center for Molecular Medicine, Cancer Genomics Netherlands, Department of Genetics, University Medical Center Utrecht, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Hubrecht Institute for Developmental Biology and Stem Cell Research, KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands
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Davies SK, Leroi A, Burt A, Bundy JG, Baer CF. The mutational structure of metabolism in Caenorhabditis elegans. Evolution 2016; 70:2239-2246. [PMID: 27465022 PMCID: PMC5050113 DOI: 10.1111/evo.13020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 06/27/2016] [Accepted: 07/10/2016] [Indexed: 12/14/2022]
Abstract
A properly functioning organism must maintain metabolic homeostasis. Deleterious mutations degrade organismal function, presumably at least in part via effects on metabolic function. Here we present an initial investigation into the mutational structure of the Caenorhabditis elegans metabolome by means of a mutation accumulation experiment. We find that pool sizes of 29 metabolites vary greatly in their vulnerability to mutation, both in terms of the rate of accumulation of genetic variance (the mutational variance, VM) and the rate of change of the trait mean (the mutational bias, ΔM). Strikingly, some metabolites are much more vulnerable to mutation than any other trait previously studied in the same way. Although we cannot statistically assess the strength of mutational correlations between individual metabolites, principal component analysis provides strong evidence that some metabolite pools are genetically correlated, but also that there is substantial scope for independent evolution of different groups of metabolites. Averaged over mutation accumulation lines, PC3 is positively correlated with relative fitness, but a model in which metabolites are uncorrelated with fitness is nearly as good by Akaike's Information Criterion.
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Affiliation(s)
- Sarah K Davies
- Department of Life Sciences, Imperial College London, United Kingdom
- Department of Surgery and Cancer, Imperial College London, United Kingdom
| | - Armand Leroi
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Austin Burt
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Jacob G Bundy
- Department of Surgery and Cancer, Imperial College London, United Kingdom
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, Florida.
- Genetics Institute, University of Florida, Gainesville, Florida.
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43
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Robles-Espinoza CD, Roberts ND, Chen S, Leacy FP, Alexandrov LB, Pornputtapong N, Halaban R, Krauthammer M, Cui R, Timothy Bishop D, Adams DJ. Germline MC1R status influences somatic mutation burden in melanoma. Nat Commun 2016; 7:12064. [PMID: 27403562 PMCID: PMC4945874 DOI: 10.1038/ncomms12064] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 05/27/2016] [Indexed: 01/07/2023] Open
Abstract
The major genetic determinants of cutaneous melanoma risk in the general population are disruptive variants (R alleles) in the melanocortin 1 receptor (MC1R) gene. These alleles are also linked to red hair, freckling, and sun sensitivity, all of which are known melanoma phenotypic risk factors. Here we report that in melanomas and for somatic C>T mutations, a signature linked to sun exposure, the expected single-nucleotide variant count associated with the presence of an R allele is estimated to be 42% (95% CI, 15-76%) higher than that among persons without an R allele. This figure is comparable to the expected mutational burden associated with an additional 21 years of age. We also find significant and similar enrichment of non-C>T mutation classes supporting a role for additional mutagenic processes in melanoma development in individuals carrying R alleles.
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Affiliation(s)
- Carla Daniela Robles-Espinoza
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Santiago de Querétaro 76230, Mexico
| | - Nicola D. Roberts
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- The Cancer Genome Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Shuyang Chen
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine. Boston, Massachusetts 02118, USA
| | - Finbarr P. Leacy
- MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
- Division of Population Health Sciences, Royal College of Surgeons in Ireland, Lower Mercer Street, Dublin 2, Ireland
| | - Ludmil B. Alexandrov
- The Cancer Genome Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Natapol Pornputtapong
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Michael Krauthammer
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06519, USA
- Program in Computational Biology and Bioinformatics, Yale University School of Medicine, New Haven, Connecticut 06519, USA
| | - Rutao Cui
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine. Boston, Massachusetts 02118, USA
| | - D. Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, LS9 7TF, UK
| | - David J. Adams
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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Takahashi M. [Genetic Mutation Accumulation and Clinical Outcome of Immune Checkpoint Blockade Therapy]. Gan To Kagaku Ryoho 2016; 43:678-682. [PMID: 27306805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Immune checkpoint blockade therapy has recently attracted great attention in the area of oncology. In Japan, since 2014, an anti-PD-1 antibody nivolumab and anti-CTLA-4 antibody ipilimumab have been available for the treatment of patients with malignant melanoma, and nivolumab has been available for patients with non-small cell lung cancer. Clinical trials using these drugs and other immune checkpoint inhibitors are currently in progress worldwide. The immune checkpoint blockade therapy is a promising new cancer therapy; however, not all patients with cancer can benefit from this therapy. Recent evidence shows that markers reflecting the extent of genetic mutation accumulation, including mutation burden, non-synonymous mutation that produces neoantigen, and microsatellite instability, possibly serve as promising marker to predict who can benefit from the immune checkpoint blockade therapy. Here, I introduce the recent evidence and discuss the correlation between genetic mutation accumulation and clinical outcome of immune checkpoint blockade therapy.
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45
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Martin SD, Brown SD, Wick DA, Nielsen JS, Kroeger DR, Twumasi-Boateng K, Holt RA, Nelson BH. Low Mutation Burden in Ovarian Cancer May Limit the Utility of Neoantigen-Targeted Vaccines. PLoS One 2016; 11:e0155189. [PMID: 27192170 PMCID: PMC4871527 DOI: 10.1371/journal.pone.0155189] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/25/2016] [Indexed: 01/07/2023] Open
Abstract
Due to advances in sequencing technology, somatically mutated cancer antigens, or neoantigens, are now readily identifiable and have become compelling targets for immunotherapy. In particular, neoantigen-targeted vaccines have shown promise in several pre-clinical and clinical studies. However, to date, neoantigen-targeted vaccine studies have involved tumors with exceptionally high mutation burdens. It remains unclear whether neoantigen-targeted vaccines will be broadly applicable to cancers with intermediate to low mutation burdens, such as ovarian cancer. To address this, we assessed whether a derivative of the murine ovarian tumor model ID8 could be targeted with neoantigen vaccines. We performed whole exome and transcriptome sequencing on ID8-G7 cells. We identified 92 somatic mutations, 39 of which were transcribed, missense mutations. For the 17 top predicted MHC class I binding mutations, we immunized mice subcutaneously with synthetic long peptide vaccines encoding the relevant mutation. Seven of 17 vaccines induced robust mutation-specific CD4 and/or CD8 T cell responses. However, none of the vaccines prolonged survival of tumor-bearing mice in either the prophylactic or therapeutic setting. Moreover, none of the neoantigen-specific T cell lines recognized ID8-G7 tumor cells in vitro, indicating that the corresponding mutations did not give rise to bonafide MHC-presented epitopes. Additionally, bioinformatic analysis of The Cancer Genome Atlas data revealed that only 12% (26/220) of HGSC cases had a ≥90% likelihood of harboring at least one authentic, naturally processed and presented neoantigen versus 51% (80/158) of lung cancers. Our findings highlight the limitations of applying neoantigen-targeted vaccines to tumor types with intermediate/low mutation burdens.
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Affiliation(s)
- Spencer D. Martin
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
- Interdisciplinary Oncology Program, University of British Columbia, Vancouver, Canada
- Michael Smith’s Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Scott D. Brown
- Michael Smith’s Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
| | - Darin A. Wick
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
| | - Julie S. Nielsen
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
| | - David R. Kroeger
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
| | - Kwame Twumasi-Boateng
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
| | - Robert A. Holt
- Michael Smith’s Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
- Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Brad H. Nelson
- Trev and Joyce Deeley Research Centre, British Columbia Cancer Agency, Victoria, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Biochemistry, University of Victoria, Victoria, Canada
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46
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Stoyanov S, Aleksandrova E, Ivanova K, Ignatova M, Gulubova M. [MICROSATELLITE INSTABILITY IN ENDOMETRIAL CANCER]. Akush Ginekol (Sofiia) 2015; 54:31-35. [PMID: 27025106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Microsatellite instability (MSI) is involved in the pathogenesis of about 30% of endometrial cancer cases. In accumulating data from the past few years MSI is shown to have both clinical and prognostic value. In the present work we are discussing the components and molecular mechanisms of functioning of the mismatch repair system (MMR). MSI is a hallmark of endometrial tumors with DNA MMR deficiency. We summarized the main pathways for accumulating mutations in coding and non-coding DNA sequences, which is a result of errors during replication of microsatellite tandem repeats. A few studies rising valuable conclusions about the correlation between MSI and endometrial cancer are revised.
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