RESUMEN
An inverse correlation between stature and risk of coronary artery disease (CAD) has been observed in several epidemiologic studies, and recent Mendelian randomization (MR) experiments have suggested causal association. However, the extent to which the effect estimated by MR can be explained by cardiovascular, anthropometric, lung function, and lifestyle-related risk factors is unclear, with a recent report suggesting that lung function traits could fully explain the height-CAD effect. To clarify this relationship, we utilized a well-powered set of genetic instruments for human stature, comprising >1,800 genetic variants for height and CAD. In univariable analysis, we confirmed that a one standard deviation decrease in height (~6.5 cm) was associated with a 12.0% increase in the risk of CAD, consistent with previous reports. In multivariable analysis accounting for effects from up to 12 established risk factors, we observed a >3-fold attenuation in the causal effect of height on CAD susceptibility (3.7%, p = 0.02). However, multivariable analyses demonstrated independent effects of height on other cardiovascular traits beyond CAD, consistent with epidemiologic associations and univariable MR experiments. In contrast with published reports, we observed minimal effects of lung function traits on CAD risk in our analyses, indicating that these traits are unlikely to explain the residual association between height and CAD risk. In sum, these results suggest the impact of height on CAD risk beyond previously established cardiovascular risk factors is minimal and not explained by lung function measures.
Asunto(s)
Estatura , Enfermedad de la Arteria Coronaria , Análisis de la Aleatorización Mendeliana , Humanos , Estatura/genética , Enfermedad de la Arteria Coronaria/genética , Enfermedad de la Arteria Coronaria/epidemiología , Enfermedades Cardiovasculares/genética , Enfermedades Cardiovasculares/epidemiología , Factores de Riesgo , Masculino , Predisposición Genética a la Enfermedad , Polimorfismo de Nucleótido Simple , FemeninoRESUMEN
As climatic variation re-shapes global biodiversity, understanding eco-evolutionary feedbacks during species range shifts is of increasing importance. Theory on range expansions distinguishes between two different forms: "pulled" and "pushed" waves. Pulled waves occur when the source of the expansion comes from low-density peripheral populations, while pushed waves occur when recruitment to the expanding edge is supplied by high-density populations closer to the species' core. How extreme events shape pushed/pulled wave expansion events, as well as trailing-edge declines/contractions, remains largely unexplored. We examined eco-evolutionary responses of a marine invertebrate (the owl limpet, Lottia gigantea) that increased in abundance during the 2014-2016 marine heatwaves near the poleward edge of its geographic range in the northeastern Pacific. We used whole-genome sequencing from 19 populations across >11 degrees of latitude to characterize genomic variation, gene flow, and demographic histories across the species' range. We estimated present-day dispersal potential and past climatic stability to identify how contemporary and historical seascape features shape genomic characteristics. Consistent with expectations of a pushed wave, we found little genomic differentiation between core and leading-edge populations, and higher genomic diversity at range edges. A large and well-mixed population in the northern edge of the species' range is likely a result of ocean current anomalies increasing larval settlement and high-dispersal potential across biogeographic boundaries. Trailing-edge populations have higher differentiation from core populations, possibly driven by local selection and limited gene flow, as well as high genomic diversity likely as a result of climatic stability during the Last Glacial Maximum. Our findings suggest that extreme events can drive poleward range expansions that carry the adaptive potential of core populations, while also cautioning that trailing-edge extirpations may threaten unique evolutionary variation. This work highlights the importance of understanding how both trailing and leading edges respond to global change and extreme events.
Asunto(s)
Evolución Biológica , Cambio Climático , Animales , Flujo Génico , Dinámica Poblacional , Distribución Animal , Variación GenéticaRESUMEN
The diversity of nemerteans along the Pacific coast of the United States is regarded as well characterized, but there remain many cryptic, undescribed, and "orphan" species (those known only in their larval form). Recent sampling of nemerteans in Oregon and Washington has begun to fill in these taxonomic gaps, but nemertean diversity in California has received relatively little attention over the past 60 years. During the summers of 2019 and 2020, nemertean specimens were collected from 20 locations in the Bodega Bay region of northern California, USA, including rocky intertidal shores, sandy beaches, mudflats, and other habitats. Based on morphological assessment and DNA sequence analysis (partial Cytochrome Oxidase I and 16S rRNA genes), our surveys identified 34 nemertean species. Only 13 of these (38%) can be confidently assigned to described species. Another 11 represent species that are new to science, including members of the genera Riserius, Nipponnemertes, Poseidonemertes, Zygonemertes, Nemertellina, Oerstedia, and three species of uncertain affiliation. The remaining ten species include undescribed or cryptic species of uncertain status that have been found previously along the Pacific Coast of North America. Our surveys also document extensions of known geographic ranges for multiple species, including the first records in California of Antarctonemertesphyllospadicola, Cephalothrixhermaphroditica, and Maculauraoregonensis. This is the first report of the genus Nemertellina in the northeast Pacific and Riserius in California. Overall, our findings highlight how much remains to be learned about the diversity and distribution of nemerteans in the northeast Pacific.
RESUMEN
An inverse correlation between stature and risk of coronary artery disease (CAD) has been observed in several epidemiologic studies, and recent Mendelian randomization (MR) experiments have suggested causal association. However, the extent to which the effect estimated by MR can be explained by established cardiovascular risk factors is unclear, with a recent report suggesting that lung function traits could fully explain the height-CAD effect. To clarify this relationship, we utilized a well-powered set of genetic instruments for human stature, comprising >1,800 genetic variants for height and CAD. In univariable analysis, we confirmed that a one standard deviation decrease in height (~6.5 cm) was associated with a 12.0% increase in the risk of CAD, consistent with previous reports. In multivariable analysis accounting for effects from up to 12 established risk factors, we observed a >3-fold attenuation in the causal effect of height on CAD susceptibility (3.7%, p = 0.02). However, multivariable analyses demonstrated independent effects of height on other cardiovascular traits beyond CAD, consistent with epidemiologic associations and univariable MR experiments. In contrast with published reports, we observed minimal effects of lung function traits on CAD risk in our analyses, indicating that these traits are unlikely to explain the residual association between height and CAD risk. In sum, these results suggest the impact of height on CAD risk beyond previously established cardiovascular risk factors is minimal and not explained by lung function measures.
RESUMEN
A major goal in the field of transcriptional regulation is the mapping of changes in the binding of transcription factors to the resultant changes in gene expression. Recently, methods for measuring chromatin accessibility have enabled us to measure changes in accessibility across the genome, which are thought to correspond to transcription factor-binding events. In concert with RNA-sequencing, these data in principle enable such mappings; however, few studies have looked at their concordance over short-duration treatments with specific perturbations. Here, we used tandem, bulk ATAC-seq, and RNA-seq measurements from MCF-7 breast carcinoma cells to systematically evaluate the concordance between changes in accessibility and changes in expression in response to retinoic acid and TGF-ß. We found two classes of genes whose expression showed a significant change: those that showed some changes in the accessibility of nearby chromatin, and those that showed virtually no change despite strong changes in expression. The peaks associated with genes in the former group had lower baseline accessibility prior to exposure to signal. Focusing the analysis specifically on peaks with motifs for transcription factors associated with retinoic acid and TGF-ß signaling did not reduce the lack of correspondence. Analysis of paired chromatin accessibility and gene expression data from distinct paths along the hematopoietic differentiation trajectory showed a much stronger correspondence, suggesting that the multifactorial biological processes associated with differentiation may lead to changes in chromatin accessibility that reflect rather than driving altered transcriptional status. Together, these results show many gene expression changes can happen independently of changes in the accessibility of local chromatin in the context of a single-factor perturbation.
Asunto(s)
Secuenciación de Inmunoprecipitación de Cromatina , Cromatina , Cromatina/genética , Factores de Transcripción/genética , Factores de Transcripción/metabolismo , Factor de Crecimiento Transformador beta/genética , Tretinoina/farmacologíaRESUMEN
Inducible prey defences occur when organisms undergo plastic changes in phenotype to reduce predation risk. When predation pressure varies persistently over space or time, such as when predator and prey co-occur over only part of their biogeographic ranges, prey populations can become locally adapted in their inducible defences. In California estuaries, native Olympia oyster (Ostrea lurida) populations have evolved disparate phenotypic responses to an invasive predator, the Atlantic oyster drill (Urosalpinx cinerea). In this study, oysters from an estuary with drills, and oysters from an estuary without drills, were reared for two generations in a laboratory common garden, and subsequently exposed to cues from Atlantic drills. Comparative proteomics was then used to investigate molecular mechanisms underlying conserved and divergent aspects of their inducible defences. Both populations developed smaller, thicker, and harder shells after drill exposure, and these changes in shell phenotype were associated with upregulation of calcium transport proteins that could influence biomineralization. Inducible defences evolve in part because defended phenotypes incur fitness costs when predation risk is low. Immune proteins were downregulated by both oyster populations after exposure to drills, implying a trade-off between biomineralization and immune function. Following drill exposure, oysters from the population that co-occurs with drills grew smaller shells than oysters inhabiting the estuary not yet invaded by the predator. Variation in the response to drills between populations was associated with isoform-specific protein expression. This trend suggests that a stronger inducible defence response evolved in oysters that co-occur with drills through modification of an existing mechanism.
Asunto(s)
Gastrópodos , Ostrea , Adaptación Fisiológica , Animales , Conducta Predatoria , ProteómicaRESUMEN
Marine ecosystems are increasingly impacted by global environmental changes, including warming temperatures, deoxygenation, and ocean acidification. Marine scientists recognize intuitively that these environmental changes are translated into community changes via organismal physiology. However, physiology remains a black box in many ecological studies, and coexisting species in a community are often assumed to respond similarly to environmental stressors. Here, we emphasize how greater attention to physiology can improve our ability to predict the emergent effects of ocean change. In particular, understanding shifts in the intensity and outcome of species interactions such as competition and predation requires a sharpened focus on physiological variation among community members and the energetic demands and trophic mismatches generated by environmental changes. Our review also highlights how key species interactions that are sensitive to environmental change can operate as ecological leverage points through which small changes in abiotic conditions are amplified into large changes in marine ecosystems.
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Cambio Climático , Ecosistema , Concentración de Iones de Hidrógeno , Océanos y Mares , Agua de MarRESUMEN
Quantifying the strength of non-trophic interactions exerted by foundation species is critical to understanding how natural communities respond to environmental stress. In the case of ocean acidification (OA), submerged marine macrophytes, such as seagrasses, may create local areas of elevated pH due to their capacity to sequester dissolved inorganic carbon through photosynthesis. However, although seagrasses may increase seawater pH during the day, they can also decrease pH at night due to respiration. Therefore, it remains unclear how consequences of such diel fluctuations may unfold for organisms vulnerable to OA. We established mesocosms containing different levels of seagrass biomass (Zostera marina) to create a gradient of carbonate chemistry conditions and explored consequences for growth of juvenile and adult oysters (Crassostrea gigas), a non-native species widely used in aquaculture that can co-occur, and is often grown, in proximity to seagrass beds. In particular, we investigated whether increased diel fluctuations in pH due to seagrass metabolism affected oyster growth. Seagrasses increased daytime pH up to 0.4 units but had little effect on nighttime pH (reductions less than 0.02 units). Thus, both the average pH and the amplitude of diel pH fluctuations increased with greater seagrass biomass. The highest seagrass biomass increased oyster shell growth rate (mm day-1) up to 40%. Oyster somatic tissue weight and oyster condition index exhibited a different pattern, peaking at intermediate levels of seagrass biomass. This work demonstrates the ability of seagrasses to facilitate oyster calcification and illustrates how non-trophic metabolic interactions can modulate effects of environmental change.
Asunto(s)
Crassostrea , Zosteraceae , Animales , Dióxido de Carbono , Carbonatos , Concentración de Iones de Hidrógeno , Agua de MarRESUMEN
Global-scale ocean acidification has spurred interest in the capacity of seagrass ecosystems to increase seawater pH within crucial shoreline habitats through photosynthetic activity. However, the dynamic variability of the coastal carbonate system has impeded generalization into whether seagrass aerobic metabolism ameliorates low pH on physiologically and ecologically relevant timescales. Here we present results of the most extensive study to date of pH modulation by seagrasses, spanning seven meadows (Zostera marina) and 1000 km of U.S. west coast over 6 years. Amelioration by seagrass ecosystems compared to non-vegetated areas occurred 65% of the time (mean increase 0.07 ± 0.008 SE). Events of continuous elevation in pH within seagrass ecosystems, indicating amelioration of low pH, were longer and of greater magnitude than opposing cases of reduced pH or exacerbation. Sustained elevations in pH of >0.1, comparable to a 30% decrease in [H+ ], were not restricted only to daylight hours but instead persisted for up to 21 days. Maximal pH elevations occurred in spring and summer during the seagrass growth season, with a tendency for stronger effects in higher latitude meadows. These results indicate that seagrass meadows can locally alleviate low pH conditions for extended periods of time with important implications for the conservation and management of coastal ecosystems.
Asunto(s)
Ecosistema , Zosteraceae , Carbono , Concentración de Iones de Hidrógeno , Agua de MarRESUMEN
Two different cell signals often affect transcription of the same gene. In such cases, it is natural to ask how the combined transcriptional response compares to the individual responses. The most commonly used mechanistic models predict additive or multiplicative combined responses, but a systematic genome-wide evaluation of these predictions is not available. Here, we analyzed the transcriptional response of human MCF-7 cells to retinoic acid and TGF-ß, applied individually and in combination. The combined transcriptional responses of induced genes exhibited a range of behaviors, but clearly favored both additive and multiplicative outcomes. We performed paired chromatin accessibility measurements and found that increases in accessibility were largely additive. There was some association between super-additivity of accessibility and multiplicative or super-multiplicative combined transcriptional responses, while sub-additivity of accessibility associated with additive transcriptional responses. Our findings suggest that mechanistic models of combined transcriptional regulation must be able to reproduce a range of behaviors.
Asunto(s)
Regulación de la Expresión Génica , Cromatina/efectos de los fármacos , Cromatina/metabolismo , Regulación de la Expresión Génica/efectos de los fármacos , Genes/efectos de los fármacos , Humanos , Células MCF-7/metabolismo , Proteínas Smad/efectos de los fármacos , Proteínas Smad/metabolismo , Transcripción Genética/efectos de los fármacos , Factor de Crecimiento Transformador beta/farmacología , Tretinoina/farmacología , Regulación hacia ArribaRESUMEN
Ocean acidification (OA) poses a major threat to marine ecosystems and shellfish aquaculture. A promising mitigation strategy is the identification and breeding of shellfish varieties exhibiting resilience to acidification stress. We experimentally compared the effects of OA on two populations of red abalone (Haliotis rufescens), a marine mollusc important to fisheries and global aquaculture. Results from our experiments simulating captive aquaculture conditions demonstrated that abalone sourced from a strong upwelling region were tolerant of ongoing OA, whereas a captive-raised population sourced from a region of weaker upwelling exhibited significant mortality and vulnerability to OA. This difference was linked to population-specific variation in the maternal provisioning of lipids to offspring, with a positive correlation between lipid concentrations and survival under OA. This relationship also persisted in experiments on second-generation animals, and larval lipid consumption rates varied among paternal crosses, which is consistent with the presence of genetic variation for physiological traits relevant for OA survival. Across experimental trials, growth rates differed among family lineages, and the highest mortality under OA occurred in the fastest growing crosses. Identifying traits that convey resilience to OA is critical to the continued success of abalone and other shellfish production, and these mitigation efforts should be incorporated into breeding programs for commercial and restoration aquaculture.
Asunto(s)
Acuicultura/métodos , Gastrópodos/crecimiento & desarrollo , Gastrópodos/metabolismo , Animales , Fenómenos Biológicos , Ecosistema , Metabolismo Energético , Explotaciones Pesqueras , Gastrópodos/fisiología , Concentración de Iones de Hidrógeno , Larva , Moluscos/metabolismo , Alimentos Marinos , Agua de Mar/química , MariscosRESUMEN
Ocean acidification (OA) represents a serious challenge to marine ecosystems. Laboratory studies addressing OA indicate broadly negative effects for marine organisms, particularly those relying on calcification processes. Growing evidence also suggests OA combined with other environmental stressors may be even more deleterious. Scaling these laboratory studies to ecological performance in the field, where environmental heterogeneity may mediate responses, is a critical next step toward understanding OA impacts on natural communities. We leveraged an upwelling-driven pH mosaic along the California Current System to deconstruct the relative influences of pH, ocean temperature, and food availability on seasonal growth, condition and shell thickness of the ecologically dominant intertidal mussel Mytilus californianus. In 2011 and 2012, ecological performance of adult mussels from local and commonly sourced populations was measured at 8 rocky intertidal sites between central Oregon and southern California. Sites coincided with a large-scale network of intertidal pH sensors, allowing comparisons among pH and other environmental stressors. Adult California mussel growth and size varied latitudinally among sites and inter-annually, and mean shell thickness index and shell weight growth were reduced with low pH. Surprisingly, shell length growth and the ratio of tissue to shell weight were enhanced, not diminished as expected, by low pH. In contrast, and as expected, shell weight growth and shell thickness were both diminished by low pH, consistent with the idea that OA exposure can compromise shell-dependent defenses against predators or wave forces. We also found that adult mussel shell weight growth and relative tissue mass were negatively associated with increased pH variability. Including local pH conditions with previously documented influences of ocean temperature, food availability, aerial exposure, and origin site enhanced the explanatory power of models describing observed performance differences. Responses of local mussel populations differed from those of a common source population suggesting mussel performance partially depended on genetic or persistent phenotypic differences. In light of prior research showing deleterious effects of low pH on larval mussels, our results suggest a life history transition leading to greater resilience in at least some performance metrics to ocean acidification by adult California mussels. Our data also demonstrate "hot" (more extreme) and "cold" (less extreme) spots in both mussel responses and environmental conditions, a pattern that may enable mitigation approaches in response to future changes in climate.
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Carbonatos/metabolismo , Cambio Climático , Mytilus/crecimiento & desarrollo , Océanos y Mares , Agua de Mar/química , Adaptación Fisiológica , Exoesqueleto/química , Animales , Océano Atlántico , Carbonato de Calcio/análisis , Ecosistema , Concentración de Iones de Hidrógeno , Mytilus/metabolismo , Nutrientes , Tamaño de los Órganos , Fitoplancton , Temperatura , Olas de MareaRESUMEN
Non-genetic transcriptional variability is a potential mechanism for therapy resistance in melanoma. Specifically, rare subpopulations of cells occupy a transient pre-resistant state characterized by coordinated high expression of several genes and survive therapy. How might these rare states arise and disappear within the population? It is unclear whether the canonical models of probabilistic transcriptional pulsing can explain this behavior, or if it requires special, hitherto unidentified mechanisms. We show that a minimal model of transcriptional bursting and gene interactions can give rise to rare coordinated high expression states. These states occur more frequently in networks with low connectivity and depend on three parameters. While entry into these states is initiated by a long transcriptional burst that also triggers entry of other genes, the exit occurs through independent inactivation of individual genes. Together, we demonstrate that established principles of gene regulation are sufficient to describe this behavior and argue for its more general existence. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Resistencia a Antineoplásicos/genética , Redes Reguladoras de Genes/genética , Melanoma/genética , Expresión Génica/genética , Regulación Neoplásica de la Expresión Génica/genética , Humanos , Modelos Genéticos , Modelos Teóricos , Neoplasias/genética , Factores de Transcripción/genética , Transcripción Genética/genéticaRESUMEN
An organism's ability to cope with thermal stress is an important predictor of survival in a changing climate. One way in which organisms may acclimatize to thermal stress in the short-term is through induced thermotolerance, whereby exposure to a sublethal heat shock enables the organism to subsequently survive what might otherwise be a lethal event. Whether induced thermotolerance is related to basal thermotolerance is not well understood for marine organisms. Furthermore, whether populations often differ in their capacity for induced thermotolerance is also unclear. Here, we tested for differences in basal thermotolerance and induced thermotolerance among six populations of Olympia oysters (Ostrea lurida) from three California estuaries. Oysters were raised under common-garden laboratory conditions for a generation and then exposed to two treatments (control or sublethal heat shock) followed by a spectrum of temperatures that bound the upper critical temperature in order to determine LT50 (temperature at which 50% of the population dies). All populations exhibited induced thermotolerance by increasing their LT50 to a similar maximum temperature when extreme thermal stress was preceded by a sublethal heat shock. However, populations differed in their basal thermotolerance and their plasticity in thermotolerance. Populations with the highest basal thermotolerance were least able to modify upper critical temperature, while the population with the lowest basal thermotolerance exhibited the greatest plasticity in the upper critical temperature. Our results highlight that populations with high basal thermotolerance may be most vulnerable to climate warming because they lack the plasticity required to adjust their upper thermal limits.
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Ostreidae/fisiología , Aclimatación , Animales , Cambio Climático , Respuesta al Choque Térmico , Calor , TermotoleranciaRESUMEN
Microsatellite instability (MSI) is an important biomarker for predicting response to immune checkpoint inhibitor therapy, as emphasized by the recent checkpoint inhibitor approval for MSI-high (MSI-H) solid tumors. Herein, we describe and validate a novel method for determining MSI status from a next-generation sequencing comprehensive genomic profiling assay using formalin-fixed, paraffin-embedded samples. This method is 97% (65/67) concordant with current standards, PCR and immunohistochemistry. We further apply this method to >67,000 patient tumor samples to identify genes and pathways that are enriched in MSI-stable or MSI-H tumor groups. Data show that although rare in tumors other than colorectal and endometrial carcinomas, MSI-H samples are present in many tumor types. Furthermore, the large sample set revealed that MSI-H tumors selectively share alterations in genes across multiple common pathways, including WNT, phosphatidylinositol 3-kinase, and NOTCH. Last, MSI is sufficient, but not necessary, for a tumor to have elevated tumor mutation burden. Therefore, MSI can be determined from comprehensive genomic profiling with high accuracy, allowing for efficient MSI-H detection across all tumor types, especially those in which routine use of immunohistochemistry or PCR-based assays would be impractical because of a rare incidence of MSI. MSI-H tumors are enriched in alterations in specific signaling pathways, providing a rationale for investigating directed immune checkpoint inhibitor therapies in combination with pathway-targeted therapies.
Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Inestabilidad de Microsatélites , Neoplasias/genética , Algoritmos , Femenino , Frecuencia de los Genes , Secuenciación de Nucleótidos de Alto Rendimiento/estadística & datos numéricos , Humanos , Masculino , Mutación , Análisis de Componente PrincipalRESUMEN
During 2014-2016, severe marine heatwaves in the northeast Pacific triggered well-documented disturbances including mass mortalities, harmful algal blooms, and declines in subtidal kelp beds. However, less attention has been directed towards understanding how changes in sea surface temperature (SST) and alongshore currents during this period influenced the geographic distribution of coastal taxa. Here, we examine these effects in northern California, USA, with a focus on the region between Point Reyes and Point Arena. This region represents an important biogeographic transition zone that lies <150 km north of Monterey Bay, California, where numerous southern species have historically reached their northern (poleward) range limits. We report substantial changes in geographic distributions and/or abundances across a diverse suite of 67 southern species, including an unprecedented number of poleward range extensions (37) and striking increases in the recruitment of owl limpets (Lottia gigantea) and volcano barnacles (Tetraclita rubescens). These ecological responses likely arose through the combined effects of extreme SST, periods of anomalous poleward flow, and the unusually long duration of heatwave events. Prolonged marine heatwaves and enhanced poleward dispersal may play an important role in longer-term shifts in the composition of coastal communities in northern California and other biogeographic transition zones.
Asunto(s)
Bahías , Biota/fisiología , Crustáceos/fisiología , Gastrópodos/fisiología , Animales , CaliforniaRESUMEN
The Olympia oyster (Ostrea lurida) is a foundation species inhabiting estuaries along the North American west coast. In California estuaries, O. lurida is adapted to local salinity regimes and populations differ in low salinity tolerance. In this study, oysters from three California populations were reared for two generations in a laboratory common garden and subsequently exposed to low salinity seawater. Comparative transcriptomics was then used to understand species-level responses to hyposmotic stress and population-level mechanisms underlying divergent salinity tolerances. Gene expression patterns indicate Olympia oysters are sensitive to hyposmotic stress: All populations respond to low salinity by up-regulating transcripts indicative of protein unfolding, DNA damage and cell cycle arrest after sub-lethal exposure. Among O. lurida populations, transcriptomic profiles differed constitutively and in response to low salinity. Despite two generations in common-garden conditions, transcripts encoding apoptosis modulators were constitutively expressed at significantly different levels in the most tolerant population. Expression of cell death regulators may facilitate cell fate decisions when salinity declines. Following low salinity exposure, oysters from the more tolerant population expressed a small number of mRNAs at significantly higher levels than less tolerant populations. Proteins encoded by these transcripts regulate ciliary activity within the mantle cavity and may function to prolong valve closure and reduce mortality in low salinity seawater. Collectively, gene expression patterns suggest sub-lethal impacts of hyposmotic stress in Olympia oysters are considerable and that even oysters with greater low salinity tolerance may be vulnerable to future freshwater flooding events.
Asunto(s)
Genética de Población , Ostrea/genética , Tolerancia a la Sal/genética , Transcriptoma , Adaptación Fisiológica/genética , Animales , California , Estuarios , SalinidadRESUMEN
A key constraint in genomic testing in oncology is that matched normal specimens are not commonly obtained in clinical practice. Thus, while well-characterized genomic alterations do not require normal tissue for interpretation, a significant number of alterations will be unknown in whether they are germline or somatic, in the absence of a matched normal control. We introduce SGZ (somatic-germline-zygosity), a computational method for predicting somatic vs. germline origin and homozygous vs. heterozygous or sub-clonal state of variants identified from deep massively parallel sequencing (MPS) of cancer specimens. The method does not require a patient matched normal control, enabling broad application in clinical research. SGZ predicts the somatic vs. germline status of each alteration identified by modeling the alteration's allele frequency (AF), taking into account the tumor content, tumor ploidy, and the local copy number. Accuracy of the prediction depends on the depth of sequencing and copy number model fit, which are achieved in our clinical assay by sequencing to high depth (>500x) using MPS, covering 394 cancer-related genes and over 3,500 genome-wide single nucleotide polymorphisms (SNPs). Calls are made using a statistic based on read depth and local variability of SNP AF. To validate the method, we first evaluated performance on samples from 30 lung and colon cancer patients, where we sequenced tumors and matched normal tissue. We examined predictions for 17 somatic hotspot mutations and 20 common germline SNPs in 20,182 clinical cancer specimens. To assess the impact of stromal admixture, we examined three cell lines, which were titrated with their matched normal to six levels (10-75%). Overall, predictions were made in 85% of cases, with 95-99% of variants predicted correctly, a significantly superior performance compared to a basic approach based on AF alone. We then applied the SGZ method to the COSMIC database of known somatic variants in cancer and found >50 that are in fact more likely to be germline.
Asunto(s)
Biología Computacional , Mutación de Línea Germinal , Secuenciación de Nucleótidos de Alto Rendimiento , Neoplasias/genética , Algoritmos , Alelos , Neoplasias de la Mama/genética , Carcinoma de Pulmón de Células no Pequeñas/genética , Neoplasias del Colon/genética , Simulación por Computador , Variaciones en el Número de Copia de ADN , Bases de Datos Genéticas , Exoma , Exones , Femenino , Frecuencia de los Genes , Genoma Humano , Genómica , Heterocigoto , Homocigoto , Humanos , Neoplasias Pulmonares/genética , Mutación , Ploidias , Polimorfismo de Nucleótido Simple , Probabilidad , Reproducibilidad de los Resultados , Análisis de Secuencia de ADN/métodosRESUMEN
Successful antibody discovery relies on diversified libraries, where two aspects are implied, namely the absolute number of unique clones and the percentage of functional clones. Instead of pursuing the absolute quantity thresholded by current display technology, we have sought to maximize the effective diversity by improving functional clone percentage. With the combined effort of bioinformatics, structural biology, molecular immunology and phage display technology, we devised a bioinformatic pipeline to construct and validate libraries via combinatorial assembly of sequences from a database of experimentally validated antibodies. Furthermore, we showed that the libraries constructed as such yielded a significantly increased success rate against different antigen types and generated over 20-fold more unique hits per targets compared with libraries based on traditional degenerate nucleotide methods. Our study indicated that predefined CDR sequences with optimized CDR-framework compatibility could be a productive direction of functional library construction for in vitro antibody development.