From antagonism to synergism: Extreme differences in stressor interactions in one species.
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ABSTRACT:
SUBMITTER: Straub L
PROVIDER: S-EPMC7069998 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Antagonistic interactions in biological systems, which occur when one perturbation blunts the effect of another, are typically interpreted as evidence that the two perturbations impact the same cellular pathway or function. Yet, this interpretation ignores extreme antagonistic interactions wherein an otherwise deleterious perturbation compensates for the function lost because of a prior perturbation. Here, we report on gene-environment interactions involving genetic mutations that are deleterious in a permissive environment but beneficial in a specific environment that restricts growth. These extreme antagonistic interactions constitute gene-environment analogs of synthetic rescues previously observed for gene-gene interactions. Our approach uses two independent adaptive evolution steps to address the lack of experimental methods to systematically identify such extreme interactions. We apply the approach to Escherichia coli by successively adapting it to defined glucose media without and with the antibiotic rifampicin. The approach identified multiple mutations that are beneficial in the presence of rifampicin and deleterious in its absence. The analysis of transcription shows that the antagonistic adaptive mutations repress a stringent response-like transcriptional program, whereas nonantagonistic mutations have an opposite transcriptional profile. Our approach represents a step toward the systematic characterization of extreme antagonistic gene-drug interactions, which can be used to identify targets to select against antibiotic resistance.
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Project description:We compared RNA-seq expression patterns in liver, an organ with high oxidative metabolism and abundant spontaneous DNA damage, from humans, naked mole rats, and mice, differing in maximum lifespan over a range of ~100, 30, and 3 years, respectively, for 130 genes involved in DNA repair. The results show that the longer-lived species, human and naked mole rat, share higher expression of these DNA repair genes, including core genes in several DNA repair pathways. A more systematic approach of signaling pathway analysis (SPA) indicates statistically significant upregulation of several DNA repair signaling pathways in human and naked mole rat compared with mouse.
2015-12-03 | GSE75606 | GEO
Project description:BackgroundEvidence bearing on the role of statins in the prevention and treatment of cancer is confounded by the diversity of statins, chemotherapeutic agents and cancer types included in the numerous published studies; consequently, the adjunctive value of statins with chemotherapy remains uncertain.MethodsWe assayed lovastatin in combination with each of ten commonly prescribed chemotherapy drugs in highly reproducible in vitro assays, using a neutral cellular substrate, Saccharomyces cerevisiae. Cell density (OD600) data were analyzed for synergism and antagonism using the Loewe additivity model implemented with the Combenefit software.ResultsFour of the ten chemotherapy drugs - tamoxifen, doxorubicin, methotrexate and rapamycin - exhibited net synergism with lovastatin. The remaining six agents (5-fluorouracil, gemcitabine, epothilone, cisplatin, cyclophosphamide and etoposide) compiled neutral or antagonistic scores. Distinctive patterns of synergism and antagonism, often coexisting within the same concentration space, were documented with the various combinations, including those with net synergism scores. Two drug pairs, lovastatin combined with tamoxifen or cisplatin, were also assayed in human cell lines as proof of principle.ConclusionsThe synergistic interactions of tamoxifen, doxorubicin, methotrexate and rapamycin with lovastatin - because they suggest the possibility of clinical utility - merit further exploration and validation in cell lines and animal models. No less importantly, strong antagonistic interactions between certain agents and lovastatin argue for a cautious, data-driven approach before adding a statin to any chemotherapeutic regimen. We also urge awareness of adventitious statin usage by patients entering cancer treatment protocols.
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Project description:The potential for complex synergistic or antagonistic interactions between multiple stressors presents one of the largest uncertainties when predicting ecological change but, despite common use of the terms in the scientific literature, a consensus on their operational definition is still lacking. The identification of synergism or antagonism is generally straightforward when stressors operate in the same direction, but if individual stressor effects oppose each other, the definition of synergism is paradoxical because what is synergistic to one stressor's effect direction is antagonistic to the others. In their highly cited meta-analysis, Crain et al. (Ecology Letters, 11, 2008: 1304) assumed in situations with opposing individual effects that synergy only occurs when the cumulative effect is more negative than the additive sum of the opposing individual effects. We argue against this and propose a new systematic classification based on an additive effects model that combines the magnitude and response direction of the cumulative effect and the interaction effect. A new class of "mitigating synergism" is identified, where cumulative effects are reversed and enhanced. We applied our directional classification to the dataset compiled by Crain et al. (Ecology Letters, 11, 2008: 1304) to determine the prevalence of synergistic, antagonistic, and additive interactions. Compared to their original analysis, we report differences in the representation of interaction classes by interaction type and we document examples of mitigating synergism, highlighting the importance of incorporating individual stressor effect directions in the determination of synergisms and antagonisms. This is particularly pertinent given a general bias in ecology toward investigating and reporting adverse multiple stressor effects (double negative). We emphasize the need for reconsideration by the ecological community of the interpretation of synergism and antagonism in situations where individual stressor effects oppose each other or where cumulative effects are reversed and enhanced.
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Project description:Differences in DNA repair capacity have been hypothesized to underlie the great range of maximum lifespans among mammals. However, measurements of individual DNA repair activities in cells and animals have not substantiated such a relationship because utilization of repair pathways among animals--depending on habitats, anatomical characteristics, and life styles--varies greatly between mammalian species. Recent advances in high-throughput genomics, in combination with increased knowledge of the genetic pathways involved in genome maintenance, now enable a comprehensive comparison of DNA repair transcriptomes in animal species with extreme lifespan differences. Here we compare transcriptomes of liver, an organ with high oxidative metabolism and abundant spontaneous DNA damage, from humans, naked mole rats, and mice, with maximum lifespans of ~120, 30, and 3 years, respectively, with a focus on genes involved in DNA repair. The results show that the longer-lived species, human and naked mole rat, share higher expression of DNA repair genes, including core genes in several DNA repair pathways. A more systematic approach of signaling pathway analysis indicates statistically significant upregulation of several DNA repair signaling pathways in human and naked mole rat compared with mouse. The results of this present work indicate, for the first time, that DNA repair is upregulated in a major metabolic organ in long-lived humans and naked mole rats compared with short-lived mice. These results strongly suggest that DNA repair can be considered a genuine longevity assurance system.
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Project description:DNA repair in species with extreme lifespan differences
| PRJNA304727 | ENA
Project description:Bacterial Vaginosis (BV) involves the presence of a multi-species biofilm adhered to vaginal epithelial cells, but its in-depth study has been limited due to the complexity of the bacterial community, which makes the design of in vitro models challenging. Perhaps the most common experimental technique to quantify biofilms is the crystal violet (CV) staining method. Despite its widespread utilization, the CV method is not without flaws. While biofilm CV quantification within the same strain in different conditions is normally accepted, assessing multi-species biofilms formation by CV staining might provide significant bias. For BV research, determining possible synergism or antagonism between species is a fundamental step for assessing the roles of individual species in BV development. Herein, we provide our perspective on how CV fails to properly quantify an in vitro triple-species biofilm composed of Gardnerella vaginalis, Fannyhessea (Atopobium) vaginae, and Prevotella bivia, three common BV-associated bacteria thought to play key roles in incident BV pathogenesis. We compared the CV method with total colony forming units (CFU) and fluorescence microscopy cell count methods. Not surprisingly, when comparing single-species biofilms, the relationship between biofilm biomass, total number of cells, and total cultivable cells was very different between each tested method, and also varied with the time of incubation. Thus, despite its wide utilization for single-species biofilm quantification, the CV method should not be considered for accurate quantification of multi-species biofilms in BV pathogenesis research.
| S-EPMC8766793 | biostudies-literature
Project description:The cell dose in umbilical cord blood units is a major determinant for the outcome of hematopoietic cell transplantation. Prostaglandin analogs and dipeptidylpeptidase-4 (DPP4/CD26)-inhibitors enhance the ability of hematopoietic stem cells (HSCs) to reconstitute hematopoiesis. Here we explored the synergism between treprostinil, a stable prostaglandin agonist, and the DPP4/CD26-inhibitor vildagliptin. The combination of treprostinil and forskolin caused a modest but statistically significant increase in the surface levels of DPP4/CD26 on hematopoietic stem and progenitor cells (HSPCs) derived from murine bone and human cord blood. Their migration towards stromal cell-derived factor-1 (SDF-1/CXCL12) was enhanced, if they were pretreated with treprostinil and forskolin, and further augmented by vildagliptin. Administration of vildagliptin rescued 25% of lethally irradiated recipient mice injected with a limiting number of untreated HSPCs, but 90 to 100% of recipients injected with HSPCs preincubated with treprostinil and forskolin. The efficacy of vildagliptin surpassed that of treprostinil (60% rescue). Surprisingly, concomitant administration of vildagliptin and treprostinil resulted in poor survival of recipients indicating mutual antagonism, which was recapitulated when homing of and colony formation by HSPCs were assessed. These observations of regimen-dependent synergism and antagonism of treprostinil and vildagliptin are of translational relevance for the design of clinical trials. KEY MESSAGES: Pretreatment with treprostinil increases surface levels of DPP4/CD26 in HSPCs. Vildagliptin enhances in vitro migration of pretreated HSPCs. Vildagliptin enhances in vivo homing and engraftment of pretreated HSPCs. Unexpected mutual antagonism in vivo by concomitant administration of vildagliptin and treprostinil.
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Project description:BACKGROUND: Safer and more effective mixtures of anticancer drugs are needed, and modeling can assist in this endeavor. This paper describes classification models that were constructed to predict which fixed-ratio mixtures created from a pool of 10 drugs would show a high degree of in-vitro synergism against H460 human lung cancer cells. One of the tested drugs was doxorubicin and the others were natural compounds including quercetin, curcumin, and EGCG. Explanatory variables were based on virtual docking profiles. Docking profiles for the 10 drugs were obtained for 1087 proteins using commercial docking software. The cytotoxicity of all 10 drugs and of 45 of the 1,013 possible mixtures was tested in the laboratory and synergism indices were generated using the MixLow method. Model accuracy was assessed using cross validation, as well as using predictions on a new set of 10 tested mixtures. Results were compared to models where explanatory variables were constructed using the pseudomolecule approach of Sheridan. RESULTS: On this data set, the pseudomolecule and docking data approach produce models of similar accuracy. Leave-one-out precision for the negative (highly synergistic) class and the positive (low- or non-synergistic) class was 0.73 and 0.80, respectively. Precision for a nonstandard leave-many-out cross validation procedure was 0.60 and 0.77 for the negative and positive classes, respectively. CONCLUSION: Useful classification models can be constructed to predict drug synergism, even in those situations where a limited subset of component drugs can be tested. Compared to the pseudomolecule approach, the virtual docking approach has the advantage of greater potential for biologic interpretation. This distinction may become important as virtual docking software becomes more accurate and docking results more closely resemble actual binding affinities. This is the first published report of a model designed to predict the degree of in-vitro synergism based on the pseudomolecule or docking data approach.
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Project description:Gap disturbance is assumed to maintain species diversity by creating environmental heterogeneity. However, little is known about how interactions with neighbours, such as competition and facilitation, alter the emerging gap patterns after extreme events. Using a spatially explicit community model we demonstrate that negative interactions, especially intraspecific competition, greatly promote both average gap size and gap-size diversity relative to positive interspecific interaction. This suggests that competition would promote diversity maintenance but also increase community invasibility, as large gaps with a wide size variety provide more diverse niches for both local and exotic species. Under interspecific competition, both gap metrics interestingly increased with species richness, while they were reduced under intraspecific competition. Having a wider range of species interaction strengths led to a smaller average gap size only under intraspecific competition. Increasing conspecific clumping induced larger gaps with more variable sizes under intraspecific competition, in contrast to interspecific competition. Given the range of intraspecific clumping in real communities, models or experiments based on randomly synthesized communities may yield biased estimates of the opportunities for potential colonizers to fill gaps. Overall, our "static" model on gap formation offers perspectives to better predict recolonization opportunity and thus community secondary succession under extreme event regimes.
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