Genomic and epigenomic analysis of plasma cell-free DNA identifies stemness features associated with worse survival in AR -altered lethal prostate cancer.

Metastatic castration-resistant prostate cancer (mCRPC) resistant to androgen receptor (AR)-targeted agents is often lethal. Unfortunately, biomarkers for this deadly disease remain under investigation, and underpinning mechanisms are ill-understood. Here, we applied deep sequencing to ∼100 mCRPC patients prior to the initiation of first-line AR-targeted therapy, which detected AR /enhancer alterations in over a third of patients, which correlated with lethality. To delve into the mechanism underlying why these patients with cell-free AR /enhancer alterations developed more lethal prostate cancer, we next performed genome-wide cell-free DNA epigenomics. Strikingly, we found that binding sites for transcription factors associated with developmental stemness were nucleosomally more accessible. These results were corroborated using cell-free DNA methylation data, as well as tumor RNA sequencing from a held-out cohort of mCRPC patients. Thus, we validated the importance of AR /enhancer alterations as a prognostic biomarker in lethal mCRPC, and showed that the underlying mechanism for lethality involves reprogramming developmental states toward increased stemness.

Call combination patterns in Icelandic killer whales (Orcinus orca).

Acoustic sequences have been described in a range of species and in varying complexity. Cetaceans are known to produce complex song displays but these are generally limited to mysticetes; little is known about call combinations in odontocetes. Here we investigate call combinations produced by killer whales (Orcinus orca), a highly social and vocal species. Using acoustic recordings from 22 multisensor tags, we use a first order Markov model to show that transitions between call types or subtypes were significantly different from random, with repetitions and specific call combinations occurring more often than expected by chance. The mixed call combinations were composed of two or three calls and were part of three call combination clusters. Call combinations were recorded over several years, from different individuals, and several social clusters. The most common call combination cluster consisted of six call (sub-)types. Although different combinations were generated, there were clear rules regarding which were the first and last call types produced, and combinations were highly stereotyped. Two of the three call combination clusters were produced outside of feeding contexts, but their function remains unclear and further research is required to determine possible functions and whether these combinations could be behaviour- or group-specific.

Don't mind if I do: Arctic humpback whales respond to winter foraging opportunities before migration.

Migration patterns are fundamentally linked to the spatio-temporal distributions of prey. How migrating animals can respond to changes in their prey's distribution and abundance remains largely unclear. During the last decade, humpback whales (Megaptera novaeangliae) used specific winter foraging sites in fjords of northern Norway, outside of their main summer foraging season, to feed on herring that started overwintering in the area. We used photographic matching to show that whales sighted during summer in the Barents Sea foraged in northern Norway from late October to February, staying up to three months and showing high inter-annual return rates (up to 82%). The number of identified whales in northern Norway totalled 866 individuals by 2019. Genetic sexing and hormone profiling in both areas demonstrate a female bias in northern Norway and suggest higher proportions of pregnancy in northern Norway. This may indicate that the fjord-based winter feeding is important for pregnant females before migration. Our results suggest that humpback whales can respond to foraging opportunities along their migration pathways, in some cases by continuing their feeding season well into winter. This provides an important reminder to implement dynamic ecosystem management that can account for changes in the spatio-temporal distribution of migrating marine mammals.

Predictive model of sperm whale prey capture attempts from time-depth data.

BACKGROUND: High-resolution sound and movement recording tags offer unprecedented insights into the fine-scale foraging behaviour of cetaceans, especially echolocating odontocetes, enabling the estimation of a series of foraging metrics. However, these tags are expensive, making them inaccessible to most researchers. Time-Depth Recorders (TDRs), which have been widely used to study diving and foraging behaviour of marine mammals, offer a more affordable alternative. Unfortunately, data collected by TDRs are bi-dimensional (time and depth only), so quantifying foraging effort from those data is challenging. METHODS: A predictive model of the foraging effort of sperm whales (Physeter macrocephalus) was developed to identify prey capture attempts (PCAs) from time-depth data. Data from high-resolution acoustic and movement recording tags deployed on 12 sperm whales were downsampled to 1 Hz to match the typical TDR sampling resolution and used to predict the number of buzzes (i.e., rapid series of echolocation clicks indicative of PCAs). Generalized linear mixed models were built for dive segments of different durations (30, 60, 180 and 300 s) using multiple dive metrics as potential predictors of PCAs. RESULTS: Average depth, variance of depth and variance of vertical velocity were the best predictors of the number of buzzes. Sensitivity analysis showed that models with segments of 180 s had the best overall predictive performance, with a good area under the curve value (0.78 ± 0.05), high sensitivity (0.93 ± 0.06) and high specificity (0.64 ± 0.14). Models using 180 s segments had a small difference between observed and predicted number of buzzes per dive, with a median of 4 buzzes, representing a difference in predicted buzzes of 30%. CONCLUSIONS: These results demonstrate that it is possible to obtain a fine-scale, accurate index of sperm whale PCAs from time-depth data alone. This work helps leveraging the potential of time-depth data for studying the foraging ecology of sperm whales and the possibility of applying this approach to a wide range of echolocating cetaceans. The development of accurate foraging indices from low-cost, easily accessible TDR data would contribute to democratize this type of research, promote long-term studies of various species in several locations, and enable analyses of historical datasets to investigate changes in cetacean foraging activity.

Comparison of circulating tumor DNA between African American and Caucasian patients with metastatic castrate-resistant prostate cancer post-abiraterone and/or enzalutamide.

BACKGROUND: African American men are much more likely than Caucasian men to be diagnosed with and to die of prostate cancer. Genetic differences likely play a role. The cBioPortal database reveals that African American men with prostate cancer have higher rates of CDK12 somatic mutations compared to Caucasian men. However, this does not account for prior prostate cancer treatments, which are particularly important in the castrate-resistant setting. We aimed to compare somatic mutations based on circulating tumor DNA (ctDNA) in metastatic castration-resistant prostate cancer (mCRPC) between African American and Caucasian men after exposure to abiraterone and/or enzalutamide. METHODS: This single-institution retrospective study characterizes the somatic mutations detected on ctDNA for African American and Caucasian men with mCRPC who had progressed after abiraterone and/or enzalutamide from 2015 through 2022. We evaluated the gene mutations and types of mutations in this mCRPC cohort. RESULTS: There were 50 African American and 200 Caucasian men with CRPC with available ctDNA data. African American men were younger at the time of diagnosis (p = 0.008) and development of castration resistance (p = 0.006). African American men were more likely than Caucasian men to have pathogenic/likely pathogenic (P/LP) mutations in CDK12 (12% vs. 1.5%; p = 0.003) and copy number amplifications and P/LP mutations in KIT (8.0% vs. 1.5%; p = 0.031). African American men were also significantly more likely to have frameshift mutations (28% vs. 14%; p = 0.035). CONCLUSIONS: Compared to Caucasian men, African American men with mCRPC after exposure to abiraterone and/or enzalutamide had a higher incidence of somatic CDK12 P/LP mutations and KIT amplifications and P/LP mutations based on ctDNA. African American men also had more frameshift mutations. We hypothesize that these findings have potential implications for tumor immunogenicity.

Modelling the impact of condition-dependent responses and lipid-store availability on the consequences of disturbance in a cetacean.

Lipid-store body condition is fundamental to how animals cope with environmental fluctuations, including anthropogenic change. As it provides an energetic buffer, body condition is expected to influence risk-taking strategies, with both positive and negative relationships between body condition and risk-taking posited in the literature. Individuals in good condition may take more risks due to state-dependent safety ('ability-based' explanation), or alternatively fewer risks due to asset protection and reduced need to undertake risky foraging ('needs-based' explanation). Such state-dependent responses could drive non-linear impacts of anthropogenic activities through feedback between body condition and behavioural disturbance. Here, we present a simple bioenergetic model that explicitly incorporates hypothetical body condition-dependent response strategies for a cetacean, the sperm whale. The model considered the consequences of state-dependent foraging cessation and availability of wax ester (WE) lipids for calf provisioning and female survival. We found strikingly different consequences of disturbance depending on strategy and WE availability scenarios. Compared with the null strategy, where responses to disturbance were independent of body condition, the needs-based strategy mitigated predicted reductions in provisioning by 10%-13%, while the ability-based strategy exaggerated reductions by 63%-113%. Lower WE availability resulted in more extreme outcomes because energy stores were smaller relative to the daily energy balance. In the 0% availability scenario, while the needs-based strategy reduced deaths by 100%, the ability-based strategy increased them by 335% relative to null and by 56% relative to the same strategy under the 5%-6.7% WE availability scenario. These results highlight that state-dependent disturbance responses and energy store availability could substantially impact the population consequences of disturbance. Our ability to set appropriate precautionary disturbance thresholds therefore requires empirical tests of ability- vs needs-based response modification as a function of body condition and a clearer understanding of energy store availability.

Managing the effects of multiple stressors on wildlife populations in their ecosystems: developing a cumulative risk approach.

Assessing cumulative effects of human activities on ecosystems is required by many jurisdictions, but current science cannot meet regulatory demands. Regulations define them as effect(s) of one human action combined with other actions. Here we argue for an approach that evaluates the cumulative risk of multiple stressors for protected wildlife populations within their ecosystems. Monitoring effects of each stressor is necessary but not sufficient to estimate how multiple stressors interact to affect wildlife populations. Examining the mechanistic pathways, from cellular to ecological, by which stressors affect individuals can help prioritize stressors and interpret how they interact. Our approach uses health indicators to accumulate the effects of stressors on individuals and to estimate changes in vital rates, driving population status. We advocate using methods well-established in human health and integrating them into ecosystem-based management to protect the health of commercially and culturally important wildlife populations and to protect against risk of extinction for threatened species. Our approach will improve abilities to conserve and manage ecosystems but will also demand significant increases in research and monitoring effort. We advocate for increased investment proportional to the economic scale of human activities in the Anthropocene and their pervasive effects on ecology and biodiversity.

Genomics reveal population structure, evolutionary history, and signatures of selection in the northern bottlenose whale, Hyperoodon ampullatus.

Information on wildlife population structure, demographic history, and adaptations are fundamental to understanding species evolution and informing conservation strategies. To study this ecological context for a cetacean of conservation concern, we conducted the first genomic assessment of the northern bottlenose whale, Hyperoodon ampullatus, using whole-genome resequencing data (n = 37) from five regions across the North Atlantic Ocean. We found a range-wide pattern of isolation-by-distance with a genetic subdivision distinguishing three subgroups: the Scotian Shelf, western North Atlantic, and Jan Mayen regions. Signals of elevated levels of inbreeding in the Endangered Scotian Shelf population indicate this population may be more vulnerable than the other two subgroups. In addition to signatures of inbreeding, evidence of local adaptation in the Scotian Shelf was detected across the genome. We found a long-term decline in effective population size for the species, which poses risks to their genetic diversity and may be exacerbated by the isolating effects of population subdivision. Protecting important habitat and migratory corridors should be prioritized to rebuild population sizes that were diminished by commercial whaling, strengthen gene flow, and ensure animals can move across regions in response to environmental changes.

Behavioral responses to predatory sounds predict sensitivity of cetaceans to anthropogenic noise within a soundscape of fear.

SignificanceAcoustic signals travel efficiently in the marine environment, allowing soniferous predators and prey to eavesdrop on each other. Our results with four cetacean species indicate that they use acoustic information to assess predation risk and have evolved mechanisms to reduce predation risk by ceasing foraging. Species that more readily gave up foraging in response to predatory sounds of killer whales also decreased foraging more during 1- to 4-kHz sonar exposures, indicating that species exhibiting costly antipredator responses also have stronger behavioral reactions to anthropogenic noise. This advance in our understanding of the drivers of disturbance helps us to predict what species and habitats are likely to be most severely impacted by underwater noise pollution in oceans undergoing increasing anthropogenic activities.

Understanding the combined effects of multiple stressors: A new perspective on a longstanding challenge.

Wildlife populations and their habitats are exposed to an expanding diversity and intensity of stressors caused by human activities, within the broader context of natural processes and increasing pressure from climate change. Estimating how these multiple stressors affect individuals, populations, and ecosystems is thus of growing importance. However, their combined effects often cannot be predicted reliably from the individual effects of each stressor, and we lack the mechanistic understanding and analytical tools to predict their joint outcomes. We review the science of multiple stressors and present a conceptual framework that captures and reconciles the variety of existing approaches for assessing combined effects. Specifically, we show that all approaches lie along a spectrum, reflecting increasing assumptions about the mechanisms that regulate the action of single stressors and their combined effects. An emphasis on mechanisms improves analytical precision and predictive power but could introduce bias if the underlying assumptions are incorrect. A purely empirical approach has less risk of bias but requires adequate data on the effects of the full range of anticipated combinations of stressor types and magnitudes. We illustrate how this spectrum can be formalised into specific analytical methods, using an example of North Atlantic right whales feeding on limited prey resources while simultaneously being affected by entanglement in fishing gear. In practice, case-specific management needs and data availability will guide the exploration of the stressor combinations of interest and the selection of a suitable trade-off between precision and bias. We argue that the primary goal for adaptive management should be to identify the most practical and effective ways to remove or reduce specific combinations of stressors, bringing the risk of adverse impacts on populations and ecosystems below acceptable thresholds.

Beaked whales and state-dependent decision-making: how does body condition affect the trade-off between foraging and predator avoidance?

Body condition is central to how animals balance foraging with predator avoidance-a trade-off that fundamentally affects animal fitness. Animals in poor condition may accept greater predation risk to satisfy current foraging 'needs', while those in good condition may be more risk averse to protect future 'assets'. These state-dependent behavioural predictions can help interpret responses to human activities, but are little explored in marine animals. This study investigates the influence of body condition on how beaked whales trade-off foraging and predator avoidance. Body density (indicating lipid-energy stores) was estimated for 15 foraging northern bottlenose whales tagged near Jan Mayen, Norway. Composite indices of foraging (diving and echolocation clicks) and anti-predation (long ascents, non-foraging dives and silent periods reducing predator eavesdropping) were negatively related. Experimental sonar exposures led to decreased foraging and increased risk aversion, confirming a foraging/perceived safety trade-off. However, lower lipid stores were not related to a decrease in predator avoidance versus foraging, i.e. worse condition animals did not prioritize foraging. Individual differences (personalities) or reproductive context could offer alternative explanations for the observed state-behaviour relationships. This study provides evidence of foraging/predator-avoidance trade-offs in a marine top predator and demonstrates that animals in worse condition might not always take more risks.

Aerial photogrammetry and tag-derived tissue density reveal patterns of lipid-store body condition of humpback whales on their feeding grounds.

Monitoring the body condition of free-ranging marine mammals at different life-history stages is essential to understand their ecology as they must accumulate sufficient energy reserves for survival and reproduction. However, assessing body condition in free-ranging marine mammals is challenging. We cross-validated two independent approaches to estimate the body condition of humpback whales (Megaptera novaeangliae) at two feeding grounds in Canada and Norway: animal-borne tags (n = 59) and aerial photogrammetry (n = 55). Whales that had a large length-standardized projected area in overhead images (i.e. whales looked fatter) had lower estimated tissue body density (TBD) (greater lipid stores) from tag data. Linking both measurements in a Bayesian hierarchical model to estimate the true underlying (hidden) tissue body density (uTBD), we found uTBD was lower (-3.5 kg m-3) in pregnant females compared to adult males and resting females, while in lactating females it was higher (+6.0 kg m-3). Whales were more negatively buoyant (+5.0 kg m-3) in Norway than Canada during the early feeding season, possibly owing to a longer migration from breeding areas. While uTBD decreased over the feeding season across life-history traits, whale tissues remained negatively buoyant (1035.3 ± 3.8 kg m-3) in the late feeding season. This study adds confidence to the effectiveness of these independent methods to estimate the body condition of free-ranging whales.

Declining reproductive success in the Gulf of St. Lawrence's humpback whales (Megaptera novaeangliae) reflects ecosystem shifts on their feeding grounds.

Climate change has resulted in physical and biological changes in the world's oceans. How the effects of these changes are buffered by top predator populations, and therefore how much plasticity lies at the highest trophic levels, are largely unknown. Here endocrine profiling, longitudinal observations of known individuals over 15 years between 2004 and 2018, and environmental data are combined to examine how the reproductive success of a top marine predator is being affected by ecosystem change. The Gulf of St. Lawrence, Canada, is a major summer feeding ground for humpback whales (Megaptera novaeangliae) in the North Atlantic. Blubber biopsy samples (n = 185) of female humpback whales were used to investigate variation in pregnancy rates through the quantification of progesterone. Annual pregnancy rates showed considerable variability, with no overall change detected over the study. However, a total of 457 photo-identified adult female sightings records with/without calves were collated, and showed that annual calving rates declined significantly. The probability of observing cow-calf pairs was related to favourable environmental conditions in the previous year; measured by herring spawning stock biomass, Calanus spp. abundance, overall copepod abundance and phytoplankton bloom magnitude. Approximately 39% of identified pregnancies were unsuccessful over the 15 years, and the average annual pregnancy rate was higher than the average annual calving rate at ~37% and ~23% respectively. Together, these data suggest that the declines in reproductive success could be, at least in part, the result of females being unable to accumulate the energy reserves necessary to maintain pregnancy and/or meet the energetic demands of lactation in years of poorer prey availability rather than solely an inability to become pregnant. The decline in calving rates over a period of major environmental variability may suggest that this population has limited resilience to such ecosystem change.

Diving apart together: call propagation in diving long-finned pilot whales.

Group-living animals must communicate to stay in contact. In long-finned pilot whales, there is a trade-off between the benefits of foraging individually at depth and the formation of tight social groups at the surface. Using theoretical modelling and empirical data of tagged pairs within a group, we examined the potential of pilot whale social calls to reach dispersed group members during foraging periods. Both theoretical predictions and empirical data of tag pairs showed a potential for communication between diving and non-diving group members over separation distances up to 385 m (empirical) and 1800 m (theoretical). These distances match or exceed pilot whale dive depths recorded across populations. Call characteristics and environmental characteristics were analysed to investigate determinants of call detectability. Longer calls with a higher sound pressure level (SPL) that were received in a quieter environment were more often detected than their shorter, lower SPL counterparts within a noisier environment. In a noisier environment, calls were louder and had a lower peak frequency, indicating mechanisms for coping with varying conditions. However, the vulnerability of pilot whales to anthropogenic noise is still of concern as the ability to cope with increasing background noise may be limited. Our study shows that combining propagation modelling and actual tag recordings provides new insights into the communicative potential for social calls in orientation and reunion with group members for deep-diving pilot whales.

When the noise goes on: received sound energy predicts sperm whale responses to both intermittent and continuous navy sonar.

Anthropogenic noise sources range from intermittent to continuous, with seismic and navy sonar technology moving towards near-continuous transmissions. Continuous active sonar (CAS) may be used at a lower amplitude than traditional pulsed active sonar (PAS), but potentially with greater cumulative sound energy. We conducted at-sea experiments to contrast the effects of navy PAS versus CAS on sperm whale behaviour using animal-attached sound- and movement-recording tags (n=16 individuals) in Norway. Changes in foraging effort and proxies for foraging success and cost during sonar and control exposures were assessed while accounting for baseline variation [individual effects, time of day, bathymetry and blackfish (pilot/killer whale) presence] in generalized additive mixed models (GAMMs). We found no reduction in time spent foraging during exposures to medium-level PAS (MPAS) transmitted at the same peak amplitude as CAS. In contrast, we found similar reductions in foraging during CAS (d.f.=1, F=8.0, P=0.005) and higher amplitude PAS (d.f.=1, F=20.8, P<0.001) when received at similar energy levels integrated over signal duration. These results provide clear support for sound energy over amplitude as the response driver. We discuss the importance of exposure context and the need to measure cumulative sound energy to account for intermittent versus more continuous sources in noise impact assessments.

Evidence for discrimination between feeding sounds of familiar fish and unfamiliar mammal-eating killer whale ecotypes by long-finned pilot whales.

Killer whales (KW) may be predators or competitors of other cetaceans. Since their foraging behavior and acoustics differ among populations ('ecotypes'), we hypothesized that other cetaceans can eavesdrop on KW sounds and adjust their behavior according to the KW ecotype. We performed playback experiments on long-finned pilot whales (Globicephala melas) in Norway using familiar fish-eating KW sounds (fKW) simulating a sympatric population that might compete for foraging areas, unfamiliar mammal-eating KW sounds (mKW) simulating a potential predator threat, and two control sounds. We assessed behavioral responses using animal-borne multi-sensor tags and surface visual observations. Pilot whales barely changed behavior to a broadband noise (CTRL-), whereas they were attracted and exhibited spyhops to fKW, mKW, and to a repeated-tonal upsweep signal (CTRL+). Whales never stopped nor started feeding in response to fKW, whereas they reduced or stopped foraging to mKW and CTRL+. Moreover, pilot whales joined other subgroups in response to fKW and CTRL+, whereas they tightened individual spacing within group and reduced time at surface in response to mKW. Typical active intimidation behavior displayed to fKW might be an antipredator strategy to a known low-risk ecotype or alternatively a way of securing the habitat exploited by a heterospecific sympatric population. Cessation of feeding and more cohesive approach to mKW playbacks might reflect an antipredator behavior towards an unknown KW ecotype of potentially higher risk. We conclude that pilot whales are able to acoustically discriminate between familiar and unfamiliar KW ecotypes, enabling them to adjust their behavior according to the perceived disturbance type.

Pre-Operative Cardiovascular Testing and Post-Renal Transplant Clinical Outcomes.

BACKGROUND: Cardiovascular disease, a major contributor to morbidity and mortality in chronic kidney disease and kidney transplant patients, is closely evaluated before kidney transplant. We aimed to characterize pre-transplant cardiac testing practices and post-transplant cardiac outcomes at a single academic center. METHODS: This was a retrospective, single-center analysis of consecutive adults receiving first renal transplant from 1/1/2016 to 6/31/2017. Data included demographics, medical history, and medications. Pre-transplant workup included echocardiograms, cardiac stress testing, coronary computed tomography, left heart catheterization (LHC), and any revascularization. Outcomes included all-cause mortality, cardiac mortality, myocardial infarction (MI), and myocardial injury. RESULTS: Our analysis included 235 patients with mean follow-up of 1.6 ±â€¯0.53 years. Of these, 219 (93%) patients had non-invasive functional testing before transplant, with 198 normal and 21 abnormal. The most common modalities were dobutamine stress echocardiogram (88) and pharmacological myocardial perfusion imaging (60). Twenty-four (10%) patients had an LHC, including 14 abnormal studies, and 10 who subsequently underwent successful revascularization. There were 3 deaths, 2 that were cardiac-specific. There were no ST-elevation MIs and 1 Type I non-ST-elevation MI (NSTEMI), occurring 2 days after transplant. Of those patients with a 30-day post-operative troponin, 30 (13%) patients had an elevation due to a type II NSTEMI or myocardial injury. CONCLUSIONS: Non-invasive functional testing is common prior to renal transplantation, with most being normal. Few patients are revascularized before transplantation. Perioperative death and acute coronary syndrome are rare, but troponin elevations due to type II NSTEMI and myocardial injury are common.

Northern bottlenose whales in a pristine environment respond strongly to close and distant navy sonar signals.

Impact assessments for sonar operations typically use received sound levels to predict behavioural disturbance in marine mammals. However, there are indications that cetaceans may learn to associate exposures from distant sound sources with lower perceived risk. To investigate the roles of source distance and received level in an area without frequent sonar activity, we conducted multi-scale controlled exposure experiments ( n = 3) with 12 northern bottlenose whales near Jan Mayen, Norway. Animals were tagged with high-resolution archival tags ( n = 1 per experiment) or medium-resolution satellite tags ( n = 9 in total) and subsequently exposed to sonar. We also deployed bottom-moored recorders to acoustically monitor for whales in the exposed area. Tagged whales initiated avoidance of the sound source over a wide range of distances (0.8-28 km), with responses characteristic of beaked whales. Both onset and intensity of response were better predicted by received sound pressure level (SPL) than by source distance. Avoidance threshold SPLs estimated for each whale ranged from 117-126 dB re 1 µPa, comparable to those of other tagged beaked whales. In this pristine underwater acoustic environment, we found no indication that the source distances tested in our experiments modulated the behavioural effects of sonar, as has been suggested for locations where whales are frequently exposed to sonar.