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Synergistic epistasis among cancer drivers can rescue early tumors from the accumulation of deleterious passengers. PLoS Comput Biol 2024; 20:e1012081. [PMID: 38687804 PMCID: PMC11087069 DOI: 10.1371/journal.pcbi.1012081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 05/10/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024] Open
Abstract
Epistasis among driver mutations is pervasive and explains relevant features of cancer, such as differential therapy response and convergence towards well-characterized molecular subtypes. Furthermore, a growing body of evidence suggests that tumor development could be hampered by the accumulation of slightly deleterious passenger mutations. In this work, we combined empirical epistasis networks, computer simulations, and mathematical models to explore how synergistic interactions among driver mutations affect cancer progression under the burden of slightly deleterious passengers. We found that epistasis plays a crucial role in tumor development by promoting the transformation of precancerous clones into rapidly growing tumors through a process that is analogous to evolutionary rescue. The triggering of epistasis-driven rescue is strongly dependent on the intensity of epistasis and could be a key rate-limiting step in many tumors, contributing to their unpredictability. As a result, central genes in cancer epistasis networks appear as key intervention targets for cancer therapy.
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Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses. Genome Biol 2023; 24:250. [PMID: 37904249 PMCID: PMC10614367 DOI: 10.1186/s13059-023-03089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 10/16/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes. RESULTS Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables. CONCLUSIONS Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.
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53P Real-world outcomes of first-line pembrolizumab (Pem) for metastatic non-small cell lung cancer (mNSCLC) with ≥50% expression of programmed cell death-ligand 1 (PD-L1): A multicentre retrospective study. J Thorac Oncol 2023. [DOI: 10.1016/s1556-0864(23)00307-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Protocol for comparing gene-level selection on coding mutations between two groups of samples with Coselens. STAR Protoc 2023; 4:102117. [PMID: 36853661 PMCID: PMC9958080 DOI: 10.1016/j.xpro.2023.102117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/12/2023] [Accepted: 01/26/2023] [Indexed: 02/16/2023] Open
Abstract
The study of genes that evolve under conditional selection can shed light on the genomic underpinnings of adaptation, revealing epistasis and phenotypic plasticity. This protocol describes how to use the Coselens package to compare gene-level selection between two groups of samples. After installing Coselens and preparing the datasets, a typical run on a laptop takes less than 10 min. Coselens is best suited to analyze somatic mutations and data from experimental evolution, for which independently evolved samples are available. For complete details on the use and execution of this protocol, please refer to Iranzo et al. (2022).1.
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Pervasive conditional selection of driver mutations and modular epistasis networks in cancer. Cell Rep 2022; 40:111272. [PMID: 36001960 DOI: 10.1016/j.celrep.2022.111272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/18/2022] [Accepted: 08/05/2022] [Indexed: 11/19/2022] Open
Abstract
Cancer driver mutations often display mutual exclusion or co-occurrence, underscoring the key role of epistasis in carcinogenesis. However, estimating the magnitude of epistasis and quantifying its effect on tumor evolution remains a challenge. We develop a method (Coselens) to quantify conditional selection on the excess of nonsynonymous substitutions in cancer genes. Coselens infers the number of drivers per gene in different partitions of a cancer genomics dataset using covariance-based mutation models and determines whether coding mutations in a gene affect selection for drivers in any other gene. Using Coselens, we identify 296 conditionally selected gene pairs across 16 cancer types in the TCGA dataset. Conditional selection affects 25%-50% of driver substitutions in tumors with >2 drivers. Conditionally co-selected genes form modular networks, whose structures challenge the traditional interpretation of within-pathway mutual exclusivity and across-pathway synergy, suggesting a more complex scenario where gene-specific across-pathway epistasis shapes differentiated cancer subtypes.
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UG/Abi: a highly diverse family of prokaryotic reverse transcriptases associated with defense functions. Nucleic Acids Res 2022; 50:6084-6101. [PMID: 35648479 PMCID: PMC9226505 DOI: 10.1093/nar/gkac467] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 04/11/2022] [Accepted: 05/17/2022] [Indexed: 11/20/2022] Open
Abstract
Reverse transcriptases (RTs) are enzymes capable of synthesizing DNA using RNA as a template. Within the last few years, a burst of research has led to the discovery of novel prokaryotic RTs with diverse antiviral properties, such as DRTs (Defense-associated RTs), which belong to the so-called group of unknown RTs (UG) and are closely related to the Abortive Infection system (Abi) RTs. In this work, we performed a systematic analysis of UG and Abi RTs, increasing the number of UG/Abi members up to 42 highly diverse groups, most of which are predicted to be functionally associated with other gene(s) or domain(s). Based on this information, we classified these systems into three major classes. In addition, we reveal that most of these groups are associated with defense functions and/or mobile genetic elements, and demonstrate the antiphage role of four novel groups. Besides, we highlight the presence of one of these systems in novel families of human gut viruses infecting members of the Bacteroidetes and Firmicutes phyla. This work lays the foundation for a comprehensive and unified understanding of these highly diverse RTs with enormous biotechnological potential.
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High density of unrepaired genomic ribonucleotides leads to Topoisomerase 1-mediated severe growth defects in absence of ribonucleotide reductase. Nucleic Acids Res 2020; 48:4274-4297. [PMID: 32187369 PMCID: PMC7192613 DOI: 10.1093/nar/gkaa103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/12/2022] Open
Abstract
Cellular levels of ribonucleoside triphosphates (rNTPs) are much higher than those of deoxyribonucleoside triphosphates (dNTPs), thereby influencing the frequency of incorporation of ribonucleoside monophosphates (rNMPs) by DNA polymerases (Pol) into DNA. RNase H2-initiated ribonucleotide excision repair (RER) efficiently removes single rNMPs in genomic DNA. However, processing of rNMPs by Topoisomerase 1 (Top1) in absence of RER induces mutations and genome instability. Here, we greatly increased the abundance of genomic rNMPs in Saccharomyces cerevisiae by depleting Rnr1, the major subunit of ribonucleotide reductase, which converts ribonucleotides to deoxyribonucleotides. We found that in strains that are depleted of Rnr1, RER-deficient, and harbor an rNTP-permissive replicative Pol mutant, excessive accumulation of single genomic rNMPs severely compromised growth, but this was reversed in absence of Top1. Thus, under Rnr1 depletion, limited dNTP pools slow DNA synthesis by replicative Pols and provoke the incorporation of high levels of rNMPs in genomic DNA. If a threshold of single genomic rNMPs is exceeded in absence of RER and presence of limited dNTP pools, Top1-mediated genome instability leads to severe growth defects. Finally, we provide evidence showing that accumulation of RNA/DNA hybrids in absence of RNase H1 and RNase H2 leads to cell lethality under Rnr1 depletion.
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Game-Theoretical Modeling of Interviral Conflicts Mediated by Mini-CRISPR Arrays. Front Microbiol 2020; 11:381. [PMID: 32265856 PMCID: PMC7099407 DOI: 10.3389/fmicb.2020.00381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/20/2020] [Indexed: 12/30/2022] Open
Abstract
All cellular organisms coevolve with multiple viruses, so that both virus-host and intervirus conflicts are major factors of evolution. Accordingly, hosts evolve multiple, elaborate defense systems and viruses respond by evolving means of antidefense. Although less thoroughly characterized, several dedicated mechanisms of intervirus competition have been described as well. Recently, the genomes of some bacterial and archaeal viruses have been shown to harbor CRISPR mini-arrays that typically contain a single spacer targeting a closely related virus. The involvement of mini-arrays in an intervirus conflict has been experimentally demonstrated for a pair of archaeal viruses. We model the evolution of virus-encoded CRISPR mini-arrays using a game theoretical approach. Analysis of the model reveals multiple equilibria that include mutual targeting, unidirectional targeting, no targeting, cyclic polymorphism, and bistability. The choice between these evolutionary regimes depends on the model parameters including the coinfection frequency, differential productivity of the conflicting viruses, and the fitness cost of mini-arrays. At high coinfection frequencies, the model becomes a version of the Prisoner’s dilemma in which defection, i.e., mutual targeting between the competing viruses, is the winning strategy.
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Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 2019; 18:67-83. [DOI: 10.1038/s41579-019-0299-x] [Citation(s) in RCA: 797] [Impact Index Per Article: 159.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2019] [Indexed: 12/16/2022]
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11
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Two RNase H2 Mutants with Differential rNMP Processing Activity Reveal a Threshold of Ribonucleotide Tolerance for Embryonic Development. Cell Rep 2019; 25:1135-1145.e5. [PMID: 30380406 PMCID: PMC6309994 DOI: 10.1016/j.celrep.2018.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/18/2018] [Accepted: 10/03/2018] [Indexed: 11/30/2022] Open
Abstract
RNase H2 has two distinct functions: initiation of the ribonucleotide excision repair (RER) pathway by cleaving ribonucleotides (rNMPs) incorporated during DNA replication and processing the RNA portion of an R-loop formed during transcription. An RNase H2 mutant lacking RER activity but supporting R-loop removal revealed that rNMPs in DNA initiate p53-dependent DNA damage response and early embryonic arrest in mouse. However, an RNase H2 AGS-related mutant with residual RER activity develops to birth. Estimations of the number of rNMPs in DNA in these two mutants define a ribonucleotide threshold above which p53 induces apoptosis. Below the threshold, rNMPs in DNA trigger an innate immune response. Compound heterozygous cells, containing both defective enzymes, retain rNMPs above the threshold, indicative of competition for RER substrates between active and inactive enzymes, suggesting that patients with compound heterozygous mutations in RNASEH2 genes may not reflect the properties of recombinantly expressed proteins. Uehara et al. use RNase H2 mice with differing activity levels for removal of rNMPs embedded in DNA. Moderate levels of rNMPs lead to perinatal lethality activating the cGAS-Sting DNA sensing innate immune response. Exceeding a threshold, high abundance of rNMPs activates p53-dependent DNA damage, causing early embryonic lethality.
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Gene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence. Nat Commun 2019; 10:5376. [PMID: 31772262 PMCID: PMC6879757 DOI: 10.1038/s41467-019-13429-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/07/2019] [Indexed: 02/05/2023] Open
Abstract
Bacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic trees of prokaryotes can be constructed both by traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we show here that terminal branches of gene trees are systematically compressed compared to those of genome trees. Thus, sequence evolution is delayed compared to genome evolution by gene gain and loss. The extent of this delay differs widely among bacteria and archaea. Mathematical modeling shows that the divergence delay can result from sequence homogenization by homologous recombination. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Once evolving genomes become isolated by barriers impeding homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation. A significant proportion of the molecular evolution of bacteria and archaea occurs through gene gain and loss. Here Iranzo et al. develop a mathematical model that explains observed differential patterns of sequence evolution vs. gene content evolution as a consequence of homologous recombination.
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Abstract
Cancer genomics has produced extensive information on cancer-associated genes, but the number and specificity of cancer-driver mutations remains a matter of debate. We constructed a bipartite network in which 7,665 tumors from 30 cancer types are connected via shared mutations in 198 previously identified cancer genes. We show that about 27% of the tumors can be assigned to statistically supported modules, most of which encompass one or two cancer types. The rest of the tumors belong to a diffuse network component suggesting lower gene specificity of driver mutations. Linear regression of the mutational loads in cancer genes was used to estimate the number of drivers required for the onset of different cancers. The mean number of drivers in known cancer genes is approximately two, with a range of one to five. Cancers that are associated with modules had more drivers than those from the diffuse network component, suggesting that unidentified and/or interchangeable drivers exist in the latter.
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Viruses of archaea: Structural, functional, environmental and evolutionary genomics. Virus Res 2017; 244:181-193. [PMID: 29175107 DOI: 10.1016/j.virusres.2017.11.025] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 11/18/2022]
Abstract
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.
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A network perspective on the virus world. Commun Integr Biol 2017; 10:e1296614. [PMID: 28451057 PMCID: PMC5398231 DOI: 10.1080/19420889.2017.1296614] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/10/2017] [Accepted: 02/13/2017] [Indexed: 11/15/2022] Open
Abstract
Viral evolution is characterized by high rates of horizontal gene transfer and fast sequence divergence. Furthermore, there are no universal genes shared by all viruses. As a result, distant relationships among viruses are better represented by a network than by a tree. Here we discuss 3 network representations of the virus world with decreasing levels of complexity, from a multilayer network that integrates sequence conservation and patterns of gene sharing to a classic genome similarity network. As new tools for network analysis are developed, we expect that novel insights into virus evolution will result from the study of more complex representations of the virus world.
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Competition among networks highlights the power of the weak. Nat Commun 2016; 7:13273. [PMID: 27841258 PMCID: PMC5114531 DOI: 10.1038/ncomms13273] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/16/2016] [Indexed: 11/08/2022] Open
Abstract
The unpreventable connections between real networked systems have recently called for an examination of percolation, diffusion or synchronization phenomena in multilayer networks. Here we use network science and game theory to explore interactions in networks-of-networks and model these as a game for gaining importance. We propose a viewpoint where networks choose the connection strategies, in contrast with classical approaches where nodes are the active players. Specifically, we investigate how creating paths between networks leads to different Nash equilibria that determine their structural and dynamical properties. In a wide variety of cases, selecting adequate connections leads to a cooperative solution that allows weak networks to overcome the strongest opponent. Counterintuitively, each weak network can induce a global transition to such cooperative configuration regardless of the actions of the strongest network. This power of the weak reveals a critical dominance of the underdogs in the fate of networks-of-networks.
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Abstract
Almost all cellular life forms are hosts to diverse genetic parasites with various levels of autonomy including plasmids, transposons and viruses. Theoretical modeling of the evolution of primordial replicators indicates that parasites (cheaters) necessarily evolve in such systems and can be kept at bay primarily via compartmentalization. Given the (near) ubiquity, abundance and diversity of genetic parasites, the question becomes pertinent: are such parasites intrinsic to life? At least in prokaryotes, the persistence of parasites is linked to the rate of horizontal gene transfer (HGT). We mathematically derive the threshold value of the minimal transfer rate required for selfish element persistence, depending on the element duplication and loss rates as well as the cost to the host. Estimation of the characteristic gene duplication, loss and transfer rates for transposons, plasmids and virus-related elements in multiple groups of diverse bacteria and archaea indicates that most of these rates are compatible with the long term persistence of parasites. Notably, a small but non-zero rate of HGT is also required for the persistence of non-parasitic genes. We hypothesize that cells cannot tune their horizontal transfer rates to be below the threshold required for parasite persistence without experiencing highly detrimental side-effects. As a lower boundary to the minimum DNA transfer rate that a cell can withstand, we consider the process of genome degradation and mutational meltdown of populations through Muller's ratchet. A numerical assessment of this hypothesis suggests that microbial populations cannot purge parasites while escaping Muller's ratchet. Thus, genetic parasites appear to be virtually inevitable in cellular organisms.
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Abstract
Unicellular eukaryotes and most prokaryotes possess distinct mechanisms of programmed cell death (PCD). How an “altruistic” trait, such as PCD, could evolve in unicellular organisms? To address this question, we developed a mathematical model of the virus-host co-evolution that involves interaction between immunity, PCD and cellular aggregation. Analysis of the parameter space of this model shows that under high virus load and imperfect immunity, joint evolution of cell aggregation and PCD is the optimal evolutionary strategy. Given the abundance of viruses in diverse habitats and the wide spread of PCD in most organisms, these findings imply that multiple instances of the emergence of multicellularity and its essential attribute, PCD, could have been driven, at least in part, by the virus-host arms race.
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Immunity, suicide or both? Ecological determinants for the combined evolution of anti-pathogen defense systems. BMC Evol Biol 2015; 15:43. [PMID: 25881094 PMCID: PMC4372072 DOI: 10.1186/s12862-015-0324-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/24/2015] [Indexed: 01/09/2023] Open
Abstract
Background Parasite-host arms race is one of the key factors in the evolution of life. Most cellular life forms, in particular prokaryotes, possess diverse forms of defense against pathogens including innate immunity, adaptive immunity and programmed cell death (altruistic suicide). Coevolution of these different but interacting defense strategies yields complex evolutionary regimes. Results We develop and extensively analyze a computational model of coevolution of different defense strategies to show that suicide as a defense mechanism can evolve only in structured populations and when the attainable degree of immunity against pathogens is limited. The general principle of defense evolution seems to be that hosts do not evolve two costly defense mechanisms when one is sufficient. Thus, the evolutionary interplay of innate immunity, adaptive immunity and suicide, leads to an equilibrium state where the combination of all three defense strategies is limited to a distinct, small region of the parameter space. The three strategies can stably coexist only if none of them are highly effective. Coupled adaptive immunity-suicide systems, the existence of which is implied by the colocalization of genes for the two types of defense in prokaryotic genomes, can evolve either when immunity-associated suicide is more efficacious than other suicide systems or when adaptive immunity functionally depends on the associated suicide system. Conclusions Computational modeling reveals a broad range of outcomes of coevolution of anti-pathogen defense strategies depending on the relative efficacy of different mechanisms and population structure. Some of the predictions of the model appear compatible with recent experimental evolution results and call for additional experiments.
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Autoimmunity and tumor immunology: two facets of a probabilistic immune system. BMC SYSTEMS BIOLOGY 2014; 8:120. [PMID: 25385554 PMCID: PMC4236429 DOI: 10.1186/s12918-014-0120-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/13/2014] [Indexed: 12/17/2022]
Abstract
Background The immune system of vertebrates has evolved the ability to mount highly elaborate responses to a broad range of pathogen-driven threats. Accordingly, it is quite a challenge to understand how a primitive adaptive immune system that probably lacked much of its present complexity could provide its bearers with significant evolutionary advantage, and therefore, continue to be selected for. Results We have developed a very simple model of the immune system that captures the probabilistic communication between its innate and adaptive components. Probabilistic communication arises specifically from the fact that antigen presenting cells collect and present a range of antigens from which the adaptive immune system must (probabilistically) identify its target. Our results show that although some degree of self-reactivity in the immune repertoire is unavoidable, the system is generally able to correctly target pathogens rather than self-antigens. Particular circumstances that impair correct targeting and that may lead to infection-induced autoimmunity can be predicted within this framework. Notably, the probabilistic immune system exhibits the remarkable ability to detect sudden increases in the abundance of rare self-antigens, which represents a first step towards developing anti-tumoral responses. Conclusion A simple probabilistic model of the communication between the innate and adaptive immune system provides a robust immune response, including targeting tumors, but at the price of being at risk of developing autoimmunity.
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Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes. PLoS Comput Biol 2014; 10:e1003680. [PMID: 24967627 PMCID: PMC4072520 DOI: 10.1371/journal.pcbi.1003680] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 05/08/2014] [Indexed: 11/18/2022] Open
Abstract
Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events—punctuations—during which the state of coexistence of IS and host becomes perturbated. Insertion sequences (IS) are mobile genetic elements found in most prokaryotic genomes. They are able to autonomously change position and proliferate in chromosomes. The nature of the coevolutionary dynamics of IS with the genome that hosts them is a matter of debate: Do IS proliferate to the point of causing the extinction of the host? Is it possible that IS and hosts stably coexist? Can environmental perturbations cause IS expansions? What is the role of selection in controlling IS copy number? In this study, we have analysed abundance patterns of IS families to test two different evolutionary hypotheses: in the first one IS evolve neutrally, while in the second case they are affected by selection. Our results indicate that, most of the time, IS and their hosts coexist stably in a neutral scenario where the proliferation of IS through duplications and lateral gene transfer is balanced by regular deletions. Occasionally, though, this balance may be disrupted, causing temporary explosions of IS abundance.
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Evolutionary dynamics of genome segmentation in multipartite viruses. Proc Biol Sci 2012; 279:3812-9. [PMID: 22764164 PMCID: PMC3415918 DOI: 10.1098/rspb.2012.1086] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 06/08/2012] [Indexed: 12/19/2022] Open
Abstract
Multipartite viruses are formed by a variable number of genomic fragments packed in independent viral capsids. This fact poses stringent conditions on their transmission mode, demanding, in particular, a high multiplicity of infection (MOI) for successful propagation. The actual advantages of the multipartite viral strategy are as yet unclear. The origin of multipartite viruses represents an evolutionary puzzle. While classical theories suggested that a faster replication rate or higher replication fidelity would favour shorter segments, recent experimental results seem to point to an increased stability of virions with incomplete genomes as a factor able to compensate for the disadvantage of mandatory complementation. Using as main parameters differential stability as a function of genome length and MOI, we calculate the conditions under which a set of complementary segments of a viral genome would outcompete the non-segmented variant. Further, we examine the likeliness that multipartite viral forms could be the evolutionary outcome of the competition among the defective genomes of different lengths that spontaneously arise under replication of a complete, wild-type genome. We conclude that only multipartite viruses with a small number of segments could be produced in our scenario, and discuss alternative hypotheses for the origin of multipartite viruses with more than four segments.
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The impact of quasispecies dynamics on the use of therapeutics. Trends Microbiol 2012; 20:595-603. [PMID: 22989762 DOI: 10.1016/j.tim.2012.08.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 08/13/2012] [Accepted: 08/20/2012] [Indexed: 01/31/2023]
Abstract
The application of quasispecies theory to viral populations has boosted our understanding of how endogenous and exogenous features condition their adaptation. Mounting empirical evidence demonstrates that internal interactions within mutant spectra may cause unexpected responses to antiviral treatments. In this scenario, increased mutagenesis could be efficient at low mutagen doses due to the lethal action of defective genomes, whereas sequential administration of antiviral drugs might be superior to combination therapies. Our ability to predict the outcome of a particular therapy takes advantage of the complementary use of in vivo observations, in vitro experiments, and mathematical models.
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The spatial Ultimatum game revisited. J Theor Biol 2011; 278:1-10. [PMID: 21371480 DOI: 10.1016/j.jtbi.2011.02.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 02/19/2011] [Accepted: 02/23/2011] [Indexed: 10/18/2022]
Abstract
We revisit the issue of the emergence of fair behavior in the framework of the spatial Ultimatum game, adding many important results and insights to the pioneering work by Page et al. [2000. The spatial Ultimatum game. Proc. R. Soc. London B 267, 2177], who showed in a specific example that on a two-dimensional setup evolution may lead to strategies with some degree of fairness. Within this spatial framework, we carry out a thorough simulation study and show that the emergence of altruism is a very generic phenomenon whose details depend on the dynamics considered. A very frequent feature is the spontaneous emergence and fixation of quasiempathetic individuals, whose offers are very close to their acceptance thresholds. We present analytical arguments that allow an understanding of our results and give insights on the manner in which local effects in evolution may lead to such non-rational or apparently maladaptive behaviors.
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