Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences.

The dichotomous model of "drivers" and "passengers" in cancer posits that only a few mutations in a tumor strongly affect its progression, with the remaining ones being inconsequential. Here, we leveraged the comprehensive variant dataset from the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) project to demonstrate that-in addition to the dichotomy of high- and low-impact variants-there is a third group of medium-impact putative passengers. Moreover, we also found that molecular impact correlates with subclonal architecture (i.e., early versus late mutations), and different signatures encode for mutations with divergent impact. Furthermore, we adapted an additive-effects model from complex-trait studies to show that the aggregated effect of putative passengers, including undetected weak drivers, provides significant additional power (∼12% additive variance) for predicting cancerous phenotypes, beyond PCAWG-identified driver mutations. Finally, this framework allowed us to estimate the frequency of potential weak-driver mutations in PCAWG samples lacking any well-characterized driver alterations.

Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns.

Genomics has provided a detailed structural description of the cancer genome. Identifying oncogenic drivers that work primarily through dosage changes is a current challenge. Unrestrained proliferation is a critical hallmark of cancer. We constructed modular, barcoded libraries of human open reading frames (ORFs) and performed screens for proliferation regulators in multiple cell types. Approximately 10% of genes regulate proliferation, with most performing in an unexpectedly highly tissue-specific manner. Proliferation drivers in a given cell type showed specific enrichment in somatic copy number changes (SCNAs) from cognate tumors and helped predict aneuploidy patterns in those tumors, implying that tissue-type-specific genetic network architectures underlie SCNA and driver selection in different cancers. In vivo screening confirmed these results. We report a substantial contribution to the catalog of SCNA-associated cancer drivers, identifying 147 amplified and 107 deleted genes as potential drivers, and derive insights about the genetic network architecture of aneuploidy in tumors.

Global variation in diversification rate and species richness are unlinked in plants.

Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world's most important engineers of terrestrial ecosystems, we investigated the role of diversification rate as a link between the environment and global species richness patterns. Applying structural equation modeling to a comprehensive distribution dataset and phylogenetic tree covering all circa 332,000 seed plant species and 99.9% of the world's terrestrial surface (excluding Antarctica), we test five broad hypotheses postulating that diversification serves as a mechanistic link between species richness and climate, climatic stability, seasonality, environmental heterogeneity, or the distribution of biomes. Our results show that the global patterns of species richness and diversification rate are entirely independent. Diversification rates were not highest in warm and wet climates, running counter to the Metabolic Theory of Ecology, one of the dominant explanations for global gradients in species richness. Instead, diversification rates were highest in edaphically diverse, dry areas that have experienced climate change during the Neogene. Meanwhile, we confirmed climate and environmental heterogeneity as the main drivers of species richness, but these effects did not involve diversification rates as a mechanistic link, calling for alternative explanations. We conclude that high species richness is likely driven by the antiquity of wet tropical areas (supporting the "tropical conservatism hypothesis") or the high ecological carrying capacity of warm, wet, and/or environmentally heterogeneous environments.

Net effect of environmental fluctuations in multiple global-change drivers across the tree of life.

Jensen's inequality predicts that the response of any given system to average constant conditions is different from its average response to varying ones. Environmental fluctuations in abiotic conditions are pervasive on Earth; yet until recently, most ecological research has addressed the effects of multiple environmental drivers by assuming constant conditions. One could thus expect to find significant deviations in the magnitude of their effects on ecosystems when environmental fluctuations are considered. Drawing on experimental studies published during the last 30 years reporting more than 950 response ratios (n = 5,700), we present a comprehensive analysis of the role that environmental fluctuations play across the tree of life. In contrast to the predominance of interactive effects of global-change drivers reported in the literature, our results show that their cumulative effects were additive (58%), synergistic (26%), and antagonistic (16%) when environmental fluctuations were present. However, the dominant type of interaction varied by trophic level (autotrophs: interactive; heterotrophs: additive) and phylogenetic group (additive in Animalia; additive and positive antagonism in Chromista; negative antagonism and synergism in Plantae). In addition, we identify the need to tackle how complex communities respond to fluctuating environments, widening the phylogenetic and biogeographic ranges considered, and to consider other drivers beyond warming and acidification as well as longer timescales. Environmental fluctuations must be taken into account in experimental and modeling studies as well as conservation plans to better predict the nature, magnitude, and direction of the impacts of global change on organisms and ecosystems.

Pandemic origins and a One Health approach to preparedness and prevention: Solutions based on SARS-CoV-2 and other RNA viruses.

COVID-19 is the latest zoonotic RNA virus epidemic of concern. Learning how it began and spread will help to determine how to reduce the risk of future events. We review major RNA virus outbreaks since 1967 to identify common features and opportunities to prevent emergence, including ancestral viral origins in birds, bats, and other mammals; animal reservoirs and intermediate hosts; and pathways for zoonotic spillover and community spread, leading to local, regional, or international outbreaks. The increasing scientific evidence concerning the origins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is most consistent with a zoonotic origin and a spillover pathway from wildlife to people via wildlife farming and the wildlife trade. We apply what we know about these outbreaks to identify relevant, feasible, and implementable interventions. We identify three primary targets for pandemic prevention and preparedness: first, smart surveillance coupled with epidemiological risk assessment across wildlife-livestock-human (One Health) spillover interfaces; second, research to enhance pandemic preparedness and expedite development of vaccines and therapeutics; and third, strategies to reduce underlying drivers of spillover risk and spread and reduce the influence of misinformation. For all three, continued efforts to improve and integrate biosafety and biosecurity with the implementation of a One Health approach are essential. We discuss new models to address the challenges of creating an inclusive and effective governance structure, with the necessary stable funding for cross-disciplinary collaborative research. Finally, we offer recommendations for feasible actions to close the knowledge gaps across the One Health continuum and improve preparedness and response in the future.

A genetic interaction analysis identifies cancer drivers that modify EGFR dependency.

A large number of cancer drivers have been identified through tumor sequencing efforts, but how they interact and the degree to which they can substitute for each other have not been systematically explored. To comprehensively investigate how cancer drivers genetically interact, we searched for modifiers of epidermal growth factor receptor (EGFR) dependency by performing CRISPR, shRNA, and expression screens in a non-small cell lung cancer (NSCLC) model. We elucidated a broad spectrum of tumor suppressor genes (TSGs) and oncogenes (OGs) that can genetically modify proliferation and survival of cancer cells when EGFR signaling is altered. These include genes already known to mediate EGFR inhibitor resistance as well as many TSGs not previously connected to EGFR and whose biological functions in tumorigenesis are not well understood. We show that mutation of PBRM1, a subunit of the SWI/SNF complex, attenuates the effects of EGFR inhibition in part by sustaining AKT signaling. We also show that mutation of Capicua (CIC), a transcriptional repressor, suppresses the effects of EGFR inhibition by partially restoring the EGFR-promoted gene expression program, including the sustained expression of Ets transcription factors such as ETV1 Together, our data provide strong support for the hypothesis that many cancer drivers can substitute for each other in certain contexts and broaden our understanding of EGFR regulation.

The anthropocene biogeography of alien birds on islands: Drivers of their functional and phylogenetic diversities.

A branch of island biogeography has emerged to explain alien species diversity in the light of the biogeographic and anthropogenic context, yet overlooking the functional and phylogenetic facets. Evaluating alien and native birds of 407 oceanic islands worldwide, we built structural equation models to assess the direct and indirect influence of biotic, geographic, and anthropogenic contexts on alien functional diversity (FD) and phylogenetic diversity (PD). We found that alien taxonomic richness was the main predictor of both diversities. Anthropogenic factors, including colonization pressure, associated with classic biogeographical variables also strongly influenced alien FD and PD. Specifically, habitat modification and human connectivity markedly drove alien FD, especially when controlled by taxonomic richness, whereas the human population size, gross domestic product, and native PD were crucial at explaining alien PD. Our findings suggest that humans not only shape taxonomic richness but also other facets of alien diversity in a complex way.

Reading tea leaves worldwide: Decoupled drivers of initial litter decomposition mass-loss rate and stabilization.

The breakdown of plant material fuels soil functioning and biodiversity. Currently, process understanding of global decomposition patterns and the drivers of such patterns are hampered by the lack of coherent large-scale datasets. We buried 36,000 individual litterbags (tea bags) worldwide and found an overall negative correlation between initial mass-loss rates and stabilization factors of plant-derived carbon, using the Tea Bag Index (TBI). The stabilization factor quantifies the degree to which easy-to-degrade components accumulate during early-stage decomposition (e.g. by environmental limitations). However, agriculture and an interaction between moisture and temperature led to a decoupling between initial mass-loss rates and stabilization, notably in colder locations. Using TBI improved mass-loss estimates of natural litter compared to models that ignored stabilization. Ignoring the transformation of dead plant material to more recalcitrant substances during early-stage decomposition, and the environmental control of this transformation, could overestimate carbon losses during early decomposition in carbon cycle models.

Cumulative adversity and survival in the wild.

Protecting populations contending with co-occurring stressors requires a better understanding of how multiple early-life stressors affect the fitness of natural systems. However, the complexity of such research has limited its advancement and prevented us from answering new questions. In human studies, cumulative risk models predict adult health risk based on early adversity exposure. We apply a similar framework in wild yellow-bellied marmots (Marmota flaviventer). We tested cumulative adversity indices (CAIs) across different adversity types and time windows. All CAIs were associated with decreased pup survival and were well supported. Moderate and acute, but not standardized CAIs were associated with decreased lifespan, supporting the cumulative stress hypothesis and the endurance of early adversity. Multivariate models showed that differences in lifespan were driven by weaning date, precipitation, and maternal loss, but they performed poorly compared with CAI models. We highlight the development, utility, and insights of CAI approaches for ecology and conservation.

Nonlinear life table response experiment analysis: Decomposing nonlinear and nonadditive population growth responses to changes in environmental drivers.

Life table response experiments (LTREs) decompose differences in population growth rate between environments into separate contributions from each underlying demographic rate. However, most LTRE analyses make the unrealistic assumption that the relationships between demographic rates and environmental drivers are linear and independent, which may result in diminished accuracy when these assumptions are violated. We extend regression LTREs to incorporate nonlinear (second-order) terms and compare the accuracy of both approaches for three previously published demographic datasets. We show that the second-order approach equals or outperforms the linear approach for all three case studies, even when all of the underlying vital rate functions are linear. Nonlinear vital rate responses to driver changes contributed most to population growth rate responses, but life history changes also made substantial contributions. Our results suggest that moving from linear to second-order LTRE analyses could improve our understanding of population responses to changing environments.

Potential New Inflammatory Markers in Bronchiectasis: A Literature Review.

Specific molecular and inflammatory endotypes have been identified for chronic respiratory disorders, including asthma and COPD (chronic obstructive pulmonary disease). These endotypes correspond with clinical aspects of disease, enabling targeted medicines to address certain pathophysiologic pathways, often referred to as "precision medicine". With respect to bronchiectasis, many comorbidities and underlying causes have been identified. Inflammatory endotypes have also been widely studied and reported. Additionally, several genes have been shown to affect disease progression. However, the lack of a clear classification has also hampered our understanding of the disease's natural course. The aim of this review is, thus, to summarize the current knowledge on biomarkers and actionable targets of this complex pathologic condition and to point out unmet needs, which are required in the design of effective diagnostic and therapeutic trials.

Identifying the drivers of overall rating of cancer care: Insights from the second wave of the Swiss Cancer Patient Experiences study.

BACKGROUND: Patient experience surveys gather information on various aspects of care via numerous survey items. Identifying the most critical areas of patient experience to prioritize for quality care improvement can be challenging. The objective of this study was to determine which care experience items are the drivers influencing patients' overall rating of cancer care. METHODS: Data from 2750 adult patients with cancer from the second wave of the Swiss Cancer Patient Experiences study were analyzed. This cross-sectional survey was conducted in eight Swiss hospitals from September 2021 to February 2022. Stepwise logistic regression examined the relationship between overall care rating and 29 patient experience items covering different patient-centered care dimensions while adjusting for sociodemographic and health variables. RESULTS: Overall, patients rated their cancer care experience at 8.9 out of 10. Stepwise regression identified seven drivers contributing to overall care rating. The strongest drivers were "professionals worked well together" (odds ratio [OR], 4.81) and "tests were not repeated" (OR, 2.09) from the coordination and integration dimension, "offered support for symptoms during treatment" (OR, 2.11) from the physical comfort dimension, followed by "hospital staff ensured available home support" (OR, 1.99), "offered to see health professional for concerns" (OR, 1.91), "treatment options were explained" (OR, 1.75), and "involved in treatment decisions as desired" (OR, 1.68). CONCLUSIONS: This study evaluated the care experiences of patients with cancer with a comprehensive tool that identified seven key factors independently associated with overall care rating. By concentrating on these areas, hospitals can not only improve the patient care experience but also efficiently allocate resources to quality improvement initiatives.

The Evolutionary Landscape of Colorectal Tumorigenesis: Recent Paradigms, Models, and Hypotheses.

Using colorectal cancer as a model, we review some of the insights into cancer evolution afforded by cancer sequencing. These include nonlinear and neutral evolution; polyclonality of driver mutations and parallel evolution in adenomas, although these are rare in carcinomas; the ability of mutational processes to shape evolution against the force of selection; the presence of rare driver genes that function in the same signaling pathways as the longstanding canonical drivers; and the existence of selective windows that constrain the functional effects of cancer driver mutations within limits. Many of these nascent evolutionary paradigms are potentially important for treating colorectal cancers as well as understanding their development.

Cool-edge populations of the kelp Ecklonia radiata under global ocean change scenarios: strong sensitivity to ocean warming but little effect of ocean acidification.

Kelp forests are threatened by ocean warming, yet effects of co-occurring drivers such as CO2 are rarely considered when predicting their performance in the future. In Australia, the kelp Ecklonia radiata forms extensive forests across seawater temperatures of approximately 7-26°C. Cool-edge populations are typically considered more thermally tolerant than their warm-edge counterparts but this ignores the possibility of local adaptation. Moreover, it is unknown whether elevated CO2 can mitigate negative effects of warming. To identify whether elevated CO2 could improve thermal performance of a cool-edge population of E. radiata, we constructed thermal performance curves for growth and photosynthesis, under both current and elevated CO2 (approx. 400 and 1000 µatm). We then modelled annual performance under warming scenarios to highlight thermal susceptibility. Elevated CO2 had minimal effect on growth but increased photosynthesis around the thermal optimum. Thermal optima were approximately 16°C for growth and approximately 18°C for photosynthesis, and modelled performance indicated cool-edge populations may be vulnerable in the future. Our findings demonstrate that elevated CO2 is unlikely to offset negative effects of ocean warming on the kelp E. radiata and highlight the potential susceptibility of cool-edge populations to ocean warming.

Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis.

Numerous cancer types have shown to present hypermethylation of CpG islands, also known as a CpG island methylator phenotype (CIMP), often associated with survival variation. Despite extensive research on CIMP, the etiology of this variability remains elusive, possibly due to lack of consistency in defining CIMP. In this work, we utilize a pan-cancer approach to further explore CIMP, focusing on 26 cancer types profiled in the Cancer Genome Atlas (TCGA). We defined CIMP systematically and agnostically, discarding any effects associated with age, gender or tumor purity. We then clustered samples based on their most variable DNA methylation values and analyzed resulting patient groups. Our results confirmed the existence of CIMP in 19 cancers, including gliomas and colorectal cancer. We further showed that CIMP was associated with survival differences in eight cancer types and, in five, represented a prognostic biomarker independent of clinical factors. By analyzing genetic and transcriptomic data, we further uncovered potential drivers of CIMP and classified them in four categories: mutations in genes directly involved in DNA demethylation; mutations in histone methyltransferases; mutations in genes not involved in methylation turnover, such as KRAS and BRAF; and microsatellite instability. Among the 19 CIMP-positive cancers, very few shared potential driver events, and those drivers were only IDH1 and SETD2 mutations. Finally, we found that CIMP was strongly correlated with tumor microenvironment characteristics, such as lymphocyte infiltration. Overall, our results indicate that CIMP does not exhibit a pan-cancer manifestation; rather, general dysregulation of CpG DNA methylation is caused by heterogeneous mechanisms.

Readmission After Neonatal Intensive Care Unit Discharge: The Importance of Social Drivers of Health.

OBJECTIVE: To determine associations between sociodemographic and medical factors and odds of readmission after discharge from the neonatal intensive care unit for infants with very low birth weight (<1500g). STUDY DESIGN: Cohort study using linked data from the California Perinatal Quality Care Collaborative, California Vital Statistics, and the Child Opportunity Index (COI) 2.0. Infants with very low birth weight born from 2009 through 2018 in California were considered. Odds ratios of readmission within 30 days of discharge adjusting for infant medical factors, maternal sociodemographic factors, and birth hospital were calculated via multivariable logistic regression and fixed-effect logistic regression models. RESULTS: A total of 42 411 infants met inclusion criteria. Also, 8.5% of all infants were readmitted within 30 days of discharge. In addition to traditional medical risk factors, two sociodemographic factors were significantly associated with increased odds of readmission in adjusted models: payor other than private insurance for delivery [aOR = 1.25 (95% CI 1.14-1.36)] and maternal education of less than high school degree [aOR = 1.19 (95% CI 1.06-1.33)]. Neighborhood Child Opportunity Index was not associated with odds of readmission. CONCLUSIONS: Sociodemographic factors, including lack of private insurance and lower maternal educational attainment, are significantly and independently associated with increased odds of readmission after neonatal intensive care unit discharge, in addition to traditional medical risk factors. Socioeconomic deprivation and health literacy may contribute to risk of readmission. Targeted discharge interventions focused on addressing social drivers of health warrant exploration.

Reliable focal and rotational activations in CARTOFINDER mapping using the OctaRay catheter.

INTRODUCTION: The aim of the current study was to elucidated the reliable atrial fibrillation (AF) drivers identified by CARTOFINDER using OctaRay catheter. METHODS AND RESULTS: The reliability of focal and rotational activations identified by CARTOFINDER using OctaRay catheter was assessed by the sequential recordings in each site of both atrium before and after pulmonary vein isolation (PVI) in 10 persistent AF patients. The outcome measures were the reproducibility rate during the sequential recordings and the stability rate between pre- and post-PVI as reliable focal and rotational activations. The study results were compared with those under use of PentaRay catheter (N = 18). Total 68928 points of 360 sites in OctaRay group and 24 177 points of 311 sites in PentaRay were assessed. More focal activation sites were identified in OctaRay group than PentaRay group (7.9% vs. 5.7%, p < .001), although the reproducibility rate and the stability rate were significantly lower in OctaRay group (45.3% vs. 58.9%, p < .001; 11.2% vs. 28.4%, p < .001). Meanwhile, the prevalence of reproducible focal activation sites among overall points was comparable (3.6% vs. 3.3%, p = .08). Regarding rotational activation, more rotational activation sites were identified in OctaRay group (5.1% vs. 0.2%, p < .001), and the reproducibility rate and the stability rate were significantly higher in OctaRay group (45.2% and 12.5% vs. 0.0%, p < .001). Both reliable focal and rotational activation sites were characterized by significantly shorter AF-cycle length (CL) and higher repetition of focal and rotational activations during the recordings compared with the sites of non or unreliable focal and rotational activations. CONCLUSION: In CARTOFINDER, OctaRay catheter could identify reliable focal activation with high resolution and reliable rotational activation compared with PentaRay catheter. The repetitive focal and rotational activations with short AF-CL could be the potential target during ablation.

Global increase of lianas in tropical forests.

Lianas profoundly affect tropical forests dynamics, reducing productivity and carbon storage, which underscores the importance of monitoring change in their abundance in projecting the future of the global terrestrial carbon store. While increasing liana populations are documented within the Neotropics, the global consistency of these patterns is questioned, and remains to be determined. To evaluate pantropical trends in liana abundance comprehensively and quantitatively, we conducted a systematic literature review and meta-analysis. This approach allowed us to synthesize data from published longitudinal studies examining liana trends across the tropics. We calculated standardized effect sizes and standard errors, and applied a Bayesian hierarchical meta-analytic model to adjust for publication bias. Our analysis reveals an overall pan-tropical increase in lianas abundance, occurring at an average rate of 1.7 ± 0.7 SE% per year (~10% to 24% per decade). This upward trend, confirmed to be robust against publication bias, extends beyond Neotropical regions, indicating a widespread phenomenon. Although a global trend of increasing liana abundance is evident, significant local variation exist, attributable to differences in life cycle stages, abundance metrics, forest successional stages, and biogeographical realms. Notably, increases in stem density of saplings and biomass of canopy lianas, especially in old-growth forests, point to global climatic drivers and heightened turnover rates in tropical forests as factors promoting sustained liana growth in the canopy and clonal colonization in the understory. These trends suggest that the rise in liana abundance may not only persist but could also intensify under climate change. Considering both previous and current research on lianas, our findings confirm growing concerns about lianas' expanding impact on pan-tropical carbon storage, highlighting their significant potential effect on global carbon dynamics.

Cell and gene therapy investment: evolution and future outlook on investor perspectives.

BACKGROUND AIMS: To better understand the attitudes and behaviors of investors involved in funding cell and gene therapy (CGT) businesses, the Business Development and Finance) subcommittee of International Society for Cell and Gene Therapy, in collaboration with Truist Securities, conducted a broad survey of the investment community in late 2021. METHODS: This survey follows a similar study that this group executed in 2018, and the longitudinal comparisons between the two time periods provide insights into how investor behavior in the CGT field has evolved. RESULTS: The vast majority of investor respondents are specialist biotech investors who are primarily active in deploying capital in North America and Europe. There was a notable increase in the proportion of investors actively deploying capital in China and Japan between 2018 and 2021. The percentage of respondents' portfolios dedicated to CGT companies has also increased in this period, reflecting a noteworthy trend in the therapeutic landscape. CONCLUSIONS: Clinically significant data remain the dominant force behind investment decisions, whereas competition from other drug modalities has now emerged as the most-cited barrier to making a CGT investment, eclipsing safety concerns as the most significant barrier to investment in 2018. Concerns around manufacturing and scale-up have also increased in prominence amongst the investment community. Gene-editing technologies are attracting investors as the most compelling new CGT technology. This survey also revealed that most investors expect to increase their level of investment in allogeneic technologies relative to autologous products in the coming years.

Drivers of breast cancer and cervical cancer screening among women of reproductive age: insights from the Ghana Demographic and Health Survey.

BACKGROUND: The two major causes of cancer-related deaths among women in Ghana are breast cancer (BC) and cervical cancer (CC). These types of cancers typically do not show any symptoms until they have progressed. Therefore, it is important to screen for early detection. This research aimed to investigate the rate of breast cancer and cervical cancer screening, as well as the factors associated with it, among women of reproductive age in Ghana. METHODS: This study analysed data from the 2022 Ghana Demographic and Health Survey. A total of 15,014 women aged 15 to 49 years were included in the analysis. Descriptive statistics and binary logistic regression were employed to analyse the data with the aid of STATA/SE, version 17. RESULTS: It was found that 18.4% and 5.0% of the women had screened for BC and CC, respectively. Women aged 45-49 years were about three times more likely (aOR = 2.83, 95% CI: 1.88-4.24) to screen for BC compared to those aged 15-19 years. Women who had tested for HIV had increased odds (aOR = 1.88, 95% CI: 1.56-2.25) of screening for BC compared to their counterparts. Women within the richest wealth index (aOR = 1.95, 95% CI: 1.40-2.72) had increased odds of screening for BC compared to those in the poorest wealth index. Regarding CC screening, women with higher education (aOR = 2.56, 95% CI: 1.53-4.29) were two times more likely to screen for CC compared to those with no formal education. Women who did not use tobacco (aOR = 0.45, 95% CI: 0.21-0.96) had decreased odds of CC screening compared to their counterparts. CONCLUSIONS: This study showed that the uptake of BC and CC screening services among women in Ghana was very low. The drivers of BC and CC screening included enabling, predisposing, and need factors. Stakeholders can leverage the mass media to raise awareness and educate women in reproductive age about the importance of BC and CC screening. This study provides relevant information that can inform BC and CC policies and programmes in Ghana.