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Abstract Glioblastoma multiforme (GBM) encompasses brain malignancies marked by phenotypic and transcriptional heterogeneity thought to render these tumors aggressive, resistant to therapy, and inevitably recurrent. However, little is known about how the spatial organization of GBM genomes underlies this heterogeneity and its effects. Here, we compile a cohort of 28 patient-derived glioblastoma stem cell-like lines (GSCs) known to reflect the properties of their tumor-of-origin; six of these were primary-relapse tumor pairs from the same patient. We generate and analyze 5 kbp-resolution chromosome conformation capture (Hi-C) data from all GSCs to systematically map thousands of standalone and complex structural variants (SVs) and the multitude of neoloops arising as a result. By combining Hi-C, histone modification, and gene expression data with chromatin folding simulations, we explain how the pervasive, uneven, and idiosyncratic occurrence of neoloops sustains tumor-specific transcriptional programs via the formation of new enhancer-promoter contacts. We also show how even moderately recurrent neoloops can relate to patient-specific vulnerabilities. Together, our data provide a resource for dissecting GBM biology and heterogeneity, as well as for informing therapeutic approaches.

Abstract Drowsiness while driving negatively impacts road safety, especially in truck drivers. The present study investigated the feasibility and alerting effects of a daylight-supplementing in-truck lighting system (DS) providing short-wavelength enriched light before, during, and after driving. In a within-participants design, eight truck drivers drove a fully-loaded truck under wintry Scandinavian conditions (low daylight levels) with a DS or placebo system for five days. Subjective and objective measures of alertness were recorded several times daily, and evening melatonin levels were recorded three times per study condition. DS significantly increased daytime light exposure without causing negative side effects while driving. In addition, no negative carry-over effects were observed on evening melatonin and sleepiness levels or on nighttime sleep quality. Moreover, objective alertness (i.e., psychomotor vigilance) before and after driving was significantly improved by bright light exposure. This effect was accompanied by improved subjective alertness in the morning. This field study demonstrated that DS was able to increase daytime light exposure in low-daylight conditions and to improve alertness in truck drivers before and after driving (e.g., during driving rest periods). Further studies are warranted to investigate the effects of daylight-supplementing in-cabin lighting on driving performance and road safety measures.

Abstract Background Lung cancer is the leading cause of cancer-related death in the world. In contrast to many other cancers, a direct connection to modifiable lifestyle risk in the form of tobacco smoke has long been established. More than 50% of all smoking-related lung cancers occur in former smokers, 40% of which occur more than 15 years after smoking cessation. Despite extensive research, the molecular processes for persistent lung cancer risk remain unclear. We thus set out to examine whether risk stratification in the clinic and in the general population can be improved upon by the addition of genetic data and to explore the mechanisms of the persisting risk in former smokers. Methods We analysed transcriptomic data from accessible airway tissues of 487 subjects, including healthy volunteers and clinic patients of different smoking statuses. We developed a computational model to assess smoking-associated gene expression changes and their reversibility after smoking is stopped, comparing healthy subjects to clinic patients with and without lung cancer. Results We find persistent smoking-associated immune alterations to be a hallmark of the clinic patients. Integrating previous GWAS data using a transcriptional network approach, we demonstrate that the same immune- and interferon-related pathways are strongly enriched for genes linked to known genetic risk factors, demonstrating a causal relationship between immune alteration and lung cancer risk. Finally, we used accessible airway transcriptomic data to derive a non-invasive lung cancer risk classifier. Conclusions Our results provide initial evidence for germline-mediated personalized smoke injury response and risk in the general population, with potential implications for managing long-term lung cancer incidence and mortality.

Summary: Neuroblastoma exhibits significant inter- and intra-tumor genetic heterogeneity and varying clinical outcomes. Extrachromosomal DNAs (ecDNAs) may drive this heterogeneity by independently segregating during cell division, leading to rapid oncogene amplification. While ecDNA-mediated oncogene amplification is linked to poor prognosis in various cancers, the effects of ecDNA copy-number heterogeneity on intermediate phenotypes are poorly understood. Here, we leverage DNA and RNA sequencing from the same single cells in cell lines and neuroblastoma patients to investigate these effects. By analyzing ecDNA amplicon structures, we reveal extensive intercellular ecDNA copy-number heterogeneity. We also provide direct evidence of how this heterogeneity influences the expression of cargo genes, including MYCN and its downstream targets, and the overall transcriptional state of neuroblastoma cells. Our findings highlight the role of ecDNA copy number in promoting rapid adaptability of cellular states within tumors, underscoring the need for ecDNA-specific treatment strategies to address tumor formation and adaptation.

The fitness effects of new mutations determine key properties of evolutionary processes. Beneficial mutations drive evolution, yet selection is also shaped by the frequency of small-effect deleterious mutations, whose combined effect can burden otherwise adaptive lineages and alter evolutionary trajectories and outcomes in clonally evolving organisms such as viruses, microbes, and tumors. The small effect sizes of these important mutations have made accurate measurements of their rates difficult. In microbes, assessing the effect of mutations on growth can be especially instructive, as this complex phenotype is closely linked to fitness in clonally evolving organisms. Here, we perform high-throughput time-lapse microscopy on cells from mutation-accumulation strains to precisely infer the distribution of mutational effects on growth rate in the budding yeast, Saccharomyces cerevisiae. We show that mutational effects on growth rate are overwhelmingly negative, highly skewed towards very small effect sizes, and frequent enough to suggest that deleterious hitchhikers may impose a significant burden on evolving lineages. By using lines that accumulated mutations in either wild-type or slippage repair-defective backgrounds, we further disentangle the effects of 2 common types of mutations, single-nucleotide substitutions and simple sequence repeat indels, and show that they have distinct effects on yeast growth rate. Although the average effect of a simple sequence repeat mutation is very small (approximately 0.3%), many do alter growth rate, implying that this class of frequent mutations has an important evolutionary impact.

Abstract Background Distributed healthcare settings such as district hospitals, primary care, and public health facilities are becoming the real-life settings for workplace-based learning required to educate the future healthcare workforce. Therefore, a major focus should be on designing and developing workplace-based learning in these learning environments. Healthcare professionals and educational policymakers play a significant role in these settings as role models in workplace-based learning, and as leaders in integrating learning into their work environments. It is relevant to explore their beliefs, attitudes, and behaviors towards workplace-based learning in their own settings, in order to provide context-relevant recommendations that can assist in shaping workplace-based learning environments. Methods We used individual interviews to understand professionals’ experiences with workplace-based learning in distributed healthcare settings. We - three clinicians, an educationalist, and a philosopher - thematically analyzed transcripts of 13 interviews with healthcare professionals and educational policymakers from different healthcare settings who were involved in the clinical phase of undergraduate medical education. Results Clustering and categorizing of the data led to the construction of five overarching themes: Identification with and attitude towards medical education, Sense of ownership, Perceived time and space, Mutual preconceptions and relations, and Curriculum for a changing profession. Conclusions These themes accentuate aspects relevant to the development of workplace-based learning in distributed healthcare settings on the individual, team, or organizational level. We highlight the significance of individual professionals in the development of workplace-based learning and emphasize the need for recognition and support for those occupying the ‘broker’ role at the intersection of education and practice. For future research and educational practice, we recommend prioritizing initiatives that build on good-practices in workplace-based learning and involve dedicated individuals in distributed healthcare settings.

Background: Donor lungs are often discarded, with gastric aspiration accounting for ~9% of lungs unsuitable for transplantation. To increase the donor pool, it is important to understand the pathophysiology of aspiration-induced lung damage (AILD) and to assess its treatment. Methods: Precision-cut lung slices (PCLS) were prepared from murine lungs and exposed to acid—pH 1.5 to 5.5—for 15 min. We also investigated whether acid-exposed slices (pH 3.5) could affect unexposed slices. In addition, we investigated whether dexamethasone (0.5 or 1 μM) could mitigate and treat the damage in each group. In each experiment (n = 3), we analyzed cell viability (ATP/protein content) and markers of inflammation (IL-1β, IL-6, TNF-𝛼, TRAIL). Results: PCLS subjected to pH 1.5–3.5 had a significantly reduced amount of ATP, albeit no increase in inflammation markers. There was no interaction of secretions from acid-exposed slices on unexposed slices. Dexamethasone had no beneficial effects in either group. Conclusion: Direct exposure to acid in the PCLS leads to a decrease in cell viability. Acid-exposed slices had no effect on the cell viability of unexposed slices. Treatment with dexamethasone offered no mitigation. More studies have to be performed to elucidate the pathophysiology of AILD and the possible treatment of aspiration-induced injury.

IntroductionAlthough checkpoint inhibitors (CPIs) have improved outcomes for patients with metastatic melanoma, those progressing on CPIs have limited therapeutic options. To address this unmet need and overcome CPI resistance mechanisms, novel immunotherapies, such as T-cell engaging agents, are being developed. The use of these agents has sometimes been limited by the immune response mounted against them in the form of anti-drug antibodies (ADAs), which is challenging to predict preclinically and can lead to neutralization of the drug and loss of efficacy.MethodsTYRP1-TCB (RO7293583; RG6232) is a T-cell engaging bispecific (TCB) antibody that targets tyrosinase-related protein 1 (TYRP1), which is expressed in many melanomas, thereby directing T cells to kill TYRP1-expressing tumor cells. Preclinical studies show TYRP1-TCB to have potent anti-tumor activity. This first-in-human (FIH) phase 1 dose-escalation study characterized the safety, tolerability, maximum tolerated dose/optimal biological dose, and pharmacokinetics (PK) of TYRP1-TCB in patients with metastatic melanoma (NCT04551352).ResultsTwenty participants with cutaneous, uveal, or mucosal TYRP1-positive melanoma received TYRP1-TCB in escalating doses (0.045 to 0.4 mg). All participants experienced ≥1 treatment-related adverse event (TRAE); two participants experienced grade 3 TRAEs. The most common toxicities were grade 1–2 cytokine release syndrome (CRS) and rash. Fractionated dosing mitigated CRS and was associated with lower levels of interleukin-6 and tumor necrosis factor-alpha. Measurement of active drug (dual TYPR1- and CD3-binding) PK rapidly identified loss of active drug exposure in all participants treated with 0.4 mg in a flat dosing schedule for ≥3 cycles. Loss of exposure was associated with development of ADAs towards both the TYRP1 and CD3 domains. A total drug PK assay, measuring free and ADA-bound forms, demonstrated that TYRP1-TCB-ADA immune complexes were present in participant samples, but showed no drug activity in vitro.DiscussionThis study provides important insights into how the use of active drug PK assays, coupled with mechanistic follow-up, can inform and enable ongoing benefit/risk assessment for individuals participating in FIH dose-escalation trials. Translational studies that lead to a better understanding of the underlying biology of cognate T- and B-cell interactions, ultimately resulting in ADA development to novel biotherapeutics, are needed.

Background. Normothermic machine perfusion (NMP) is used to preserve and test donor livers before transplantation. During NMP, the liver is metabolically active and produces waste products, which are released into the perfusate. In this study, we describe our simplified and inexpensive setup that integrates continuous renal replacement therapy (CRRT) with NMP for up to 7 d. We also investigated if the ultrafiltrate could be used for monitoring perfusate concentrations of small molecules such as glucose and lactate. Methods. Perfusate composition (urea, osmolarity, sodium, potassium, chloride, calcium, magnesium, phosphate, glucose, and lactate) was analyzed from 56 human NMP procedures without CRRT. Next, in 6 discarded human donor livers, CRRT was performed during NMP by integrating a small dialysis filter (0.2 m2) into the circuit to achieve continuous ultrafiltration combined with continuous fluid substitution for up to 7 d. Results. Within a few hours of NMP without CRRT, a linear increase in osmolarity and concentrations of urea and phosphate to supraphysiological levels was observed. After integration of CRRT into the NMP circuit, the composition of the perfusate was corrected to physiological values within 12 h, and this homeostasis was maintained during NMP for up to 7 d. Glucose and lactate levels, as measured in the CRRT ultrafiltrate, were strongly correlated with perfusate levels (r = 0.997, P

Summary: Discovery of genomic safe harbor sites (SHSs) is fundamental for multiple transgene integrations, such as reporter genes, chimeric antigen receptors (CARs), and safety switches, which are required for safe cell products for regenerative cell therapies and immunotherapies. Here we identified and characterized potential SHS in human cells. Using the CRISPR-MAD7 system, we integrated transgenes at these sites in induced pluripotent stem cells (iPSCs), primary T and natural killer (NK) cells, and Jurkat cell line, and demonstrated efficient and stable expression at these loci. Subsequently, we validated the differentiation potential of engineered iPSC toward CD34+ hematopoietic stem and progenitor cells (HSPCs), lymphoid progenitor cells (LPCs), and NK cells and showed that transgene expression was perpetuated in these lineages. Finally, we demonstrated that engineered iPSC-derived NK cells retained expression of a non-virally integrated anti-CD19 CAR, suggesting that several of the investigated SHSs can be used to engineer cells for adoptive immunotherapies.

Objective To outline current knowledge regarding workplace-based learning about health promotion in individual patient care.Design Scoping review.Data sources PubMed, ERIC, CINAHL and Web of Science from January 2000 to August 2023.Eligibility criteria We included articles about learning (activities) for healthcare professionals (in training), about health promotion in individual patient care and in the context of workplace-based learning.Data extraction and synthesis The studies were evaluated using a charting template and were analysed thematically using a template based on Designable Elements of Learning Environments model.Results From 7159 studies, we included 31 that described evaluations of workplace-based learning about health promotion, around a variety of health promotion topics, for different health professions. In the articles, health promotion was operationalised as knowledge, skills or attitudes related to specific lifestyle factors or more broadly, with concepts such as health literacy, advocacy and social determinants of health. We assembled an overview of spatial and instrumental, social, epistemic and temporal elements of learning environments in which health promotion is learnt.Conclusions The studies included in our analysis varied greatly in their approach to health promotion topics and the evaluation of learning outcomes. Our findings suggest the importance of providing opportunities for health profession learners to engage in authentic practice situations and address potential challenges they may experience translating related theory into practice. Additionally, our results highlight the need for conscious and articulated integration of health promotion in curricula and assessment structures. We recommend the exploration of opportunities for health profession students, professionals and patients to learn about health promotion together. Additionally, we see potential in using participatory research methods to study future health promotion learning.Study registration Open Science Framework, https://doi.org/10.17605/OSF.IO/6QPTV.

Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.

Summary: Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.

Abstract The Popeye domain containing (POPDC) genes encode sarcolemma-localized cAMP effector proteins. Mutations in blood vessel epicardial substance (BVES) also known as POPDC1 and POPDC2 have been associated with limb-girdle muscular dystrophy and cardiac arrhythmia. Muscle biopsies of affected patients display impaired membrane trafficking of both POPDC isoforms. Biopsy material of patients carrying mutations in BVES were immunostained with POPDC antibodies. The interaction of POPDC proteins was investigated by co-precipitation, proximity ligation, bioluminescence resonance energy transfer and bimolecular fluorescence complementation. Site-directed mutagenesis was utilised to map the domains involved in protein–protein interaction. Patients carrying a novel homozygous variant, BVES (c.547G > T, p.V183F) displayed only a skeletal muscle pathology and a mild impairment of membrane trafficking of both POPDC isoforms. In contrast, variants such as BVES p.Q153X or POPDC2 p.W188X were associated with a greater impairment of membrane trafficking. Co-transfection analysis in HEK293 cells revealed that POPDC proteins interact with each other through a helix-helix interface located at the C-terminus of the Popeye domain. Site-directed mutagenesis of an array of ultra-conserved hydrophobic residues demonstrated that some of them are required for membrane trafficking of the POPDC1–POPDC2 complex. Mutations in POPDC proteins that cause an impairment in membrane localization affect POPDC complex formation while mutations which leave protein–protein interaction intact likely affect some other essential function of POPDC proteins.

Abstract Aneuploidy, chromosomal instability, somatic copy-number alterations, and whole-genome doubling (WGD) play key roles in cancer evolution and provide information for the complex task of phylogenetic inference. We present MEDICC2, a method for inferring evolutionary trees and WGD using haplotype-specific somatic copy-number alterations from single-cell or bulk data. MEDICC2 eschews simplifications such as the infinite sites assumption, allowing multiple mutations and parallel evolution, and does not treat adjacent loci as independent, allowing overlapping copy-number events. Using simulations and multiple data types from 2780 tumors, we use MEDICC2 to demonstrate accurate inference of phylogenies, clonal and subclonal WGD, and ancestral copy-number states.

Objectives To compare the rates and injury sites among competitors in European and Swiss karate tournaments and to identify differences in these incidence rates by sex and age.Methods This prospective cohort study collected data from two European and four national tournaments in Switzerland between 2011 and 2019. The on-site medical staff completed an anonymised report sheet with demographic data and injury characteristics in all injuries requiring medical treatment. The incidence rates per 1000 exposed athletes (AoE) and 1000 min of exposition (MoE) were analysed. Furthermore, the relative risk of injury related to sex and age was calculated and compared.Results In total, 228 injuries were observed in 2404 fights, for an incidence rate of 47.4 per 1000 AoE (95% CI 41.5 to 54.0) or 22.5 injuries per 1000 MoE (95% CI 19.7 to 25.6), respectively. The oldest age group (senior) of both sexes had a 3.6-fold (95% CI 2.7 to 4.8) significantly higher relative risk of injury than younger participants. Furthermore, there was a 2.9-fold (95% CI 1.6 to 5.6) statistically higher risk of injury for males in the senior age group compared with senior females. The most injured body part was the head, followed by the lower extremity, trunk and upper extremity.Conclusion Senior athletes, especially senior males, had significantly more injuries compared with younger and female senior competitors. Medical staff should be aware of the increased propensity for injury among this age and sex group to facilitate injury prevention and intervention.

Acute radiation syndrome (ARS) develops after exposure to high doses of ionizing radiation and features immune suppression and organ failure. Currently, there are no diagnostics to identify the occurrence or severity of exposure and there are limited treatments and preventative strategies to mitigate ARS. Extracellular vesicles (EVs) are mediators of intercellular communication that contribute to immune dysfunction across many diseases. We investigated if EV cargo can identify whole body irradiation (WBIR) exposure and if EVs promote ARS immune dysfunction. We hypothesized that beneficial EVs derived from mesenchymal stem cells (MSC-EVs) would blunt ARS immune dysfunction and might serve as prophylactic radioprotectants. Mice received WBIR (2 or 9 Gy) with assessment of EVs at 3 and 7 days after exposure. LC-MS/MS proteomic analysis of WBIR-EVs found dose-related changes as well as candidate proteins that were increased with both doses and timepoints (34 total) such as Thromboxane-A Synthase and lymphocyte cytosolic protein 2. Suprabasin and Sarcalumenin were increased only after 9 Gy suggesting these proteins may indicate high dose/lethal exposure. Analysis of EV miRNAs identified miR-376 and miR-136, which were increased up to 200- and 60-fold respectively by both doses of WBIR and select miRNAs such as miR-1839 and miR-664 were increased only with 9 Gy. WBIR-EVs (9 Gy) were biologically active and blunted immune responses to LPS in RAW264.7 macrophages, inhibiting canonical signaling pathways associated with wound healing and phagosome formation. When given 3 days after exposure, MSC-EVs slightly modified immune gene expression changes in the spleens of mice in response to WBIR and in a combined radiation plus burn injury exposure (RCI). MSC-EVs normalized the expression of certain key immune genes such as NFκBia and Cxcr4 (WBIR), Map4k1, Ccr9 and Cxcl12 (RCI) and lowered plasma TNFα cytokine levels after RCI. When given prophylactically (24 and 3 hours before exposure), MSC-EVs prolonged survival to the 9 Gy lethal exposure. Thus, EVs are important participants in ARS. EV cargo might be used to diagnose WBIR exposure, and MSC-EVs might serve as radioprotectants to blunt the impact of toxic radiation exposure.

The need to educate medical professionals in changing medical organizations has led to a revision of the Radboudumc's undergraduate medical curriculum. Entrustable professional activities (EPAs) were used as a learning tool to support participation and encourage feedback-seeking behavior, in order to offer students the best opportunities for growth. This paper describes the development of the Radboudumc's EPA-based Master's curriculum and how EPAs can facilitate continuity in learning in the clerkships. Four guiding principles were used to create a curriculum that offers possibilities for the students’ development: (1) working with EPAs, (2) establishing entrustment, (3) providing continuity in learning, and (4) organizing smooth transitions. The new curriculum was designed with the implementation of EPAs and an e-portfolio, based on these 4 principles. The authors found that the revised curriculum corresponds to daily practice in clerkships. Students used their e-portfolios throughout all clerkships, which stimulates feedback-seeking behavior. Moreover, EPAs promote continuity in learning while rotating clerkships every 1 to 2 months. This might encourage curriculum developers to use EPAs when aiming for greater continuity in the development of students. Future research needs to focus on the effect of EPAs on transitions across clerkships in order to further improve the undergraduate medical curriculum.

The aquatic environment has been recognized as a source of antibiotic resistance (AR) that factors into the One Health approach to combat AR. To provide much needed data on AR in the environment, a comprehensive survey of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic residues was conducted in a mixed-use watershed and wastewater treatment plants (WWTPs) within the watershed to evaluate these contaminants in surface water. A culture-based approach was used to determine prevalence and diversity of ARB in surface water. Low levels of AR Salmonella (9.6%) and Escherichia coli (6.5%) were detected, while all Enterococcus were resistant to at least one tested antibiotic. Fewer than 20% of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae (17.3%) and carbapenem-resistant Enterobacteriaceae (CRE) (7.7%) were recovered. Six ARGs were detected using qPCR, primarily the erythromycin-resistance gene, ermB. Of the 26 antibiotics measured, almost all water samples (98.7%) had detectable levels of antibiotics. Analysis of wastewater samples from three WWTPs showed that WWTPs did not completely remove AR contaminants. ARGs and antibiotics were detected in all the WWTP effluent discharges, indicating that WWTPs are the source of AR contaminants in receiving water. However, no significant difference in ARGs and antibiotics between the upstream and downstream water suggests that there are other sources of AR contamination. The widespread occurrence and abundance of medically important antibiotics, bacteria resistant to antibiotics used for human and veterinary purposes, and the genes associated with resistance to these antibiotics, may potentially pose risks to the local populations exposed to these water sources.

Abstract Background Entrustable professional activities (EPAs) are widely used in medical education, and they might be an important incentive to stimulate professional identity formation (PIF) of medical students, by actively encouraging participation in the workplace. The goal of this study was to explore the effects of an EPA-based curriculum on the PIF of medical students in undergraduate curricula. Methods In this study at the Radboud University Medical Center in Nijmegen, the Netherlands, the authors interviewed twenty-one medical students in three focus group interviews (November 2019), and conducted a thematic analysis based on both the synthesizing concepts PIF, communities of practice and EPAs, and newly defined themes. Results Four central themes proved crucial for understanding the influence of EPAs on PIF: creating learning opportunities, managing feedback, dealing with supervision in context and developing confidence. EPAs helped students to create learning opportunities and to choose activities purposefully, and the use of EPAs stimulated their feedback-seeking behavior. The context and way of supervision had a great impact on their development, where some contexts offer better learning opportunities than others. EPAs helped them develop trust and self-confidence, but trust from supervisors hardly appears to result from using EPAs. Conclusions An EPA-based curriculum does stimulate PIF in the complex context of working and learning by supporting participation in the workplace and by encouraging feedback-seeking behavior. Striking the right balance between participation, feedback-seeking behavior and choosing learning activities is essential. Trial registration This study was approved by the ethics committee of the Netherlands Association of Medical Education (NVMO, case number 2019.5.12).

Neuroblastoma is a devastating tumour in children. Here, the authors analyse multi-region patient samples using genomics and transcriptomics, revealing temporal and spatial heterogeneity and questioning the reliability of single-biopsy based diagnostics.

AbstractMutations in simple sequence repeat loci underlie many inherited disorders in humans, and are increasingly recognized as important determinants of natural phenotypic variation. In eukaryotes, mutations in these sequences are primarily repaired by the MutSβ mismatch repair complex. To better understand the role of this complex in mismatch repair and the determinants of simple sequence repeat mutation predisposition, we performed mutation accumulation in yeast strains with abrogated MutSβ function. We demonstrate that mutations in simple sequence repeat loci in the absence of mismatch repair are primarily deletions. We also show that mutations accumulate at drastically different rates in short (

Abstract In colorectal cancer, oncogenic mutations transform a hierarchically organized and homeostatic epithelium into invasive cancer tissue lacking visible organization. We sought to define transcriptional states of colorectal cancer cells and signals controlling their development by performing single‐cell transcriptome analysis of tumors and matched non‐cancerous tissues of twelve colorectal cancer patients. We defined patient‐overarching colorectal cancer cell clusters characterized by differential activities of oncogenic signaling pathways such as mitogen‐activated protein kinase and oncogenic traits such as replication stress. RNA metabolic labeling and assessment of RNA velocity in patient‐derived organoids revealed developmental trajectories of colorectal cancer cells organized along a mitogen‐activated protein kinase activity gradient. This was in contrast to normal colon organoid cells developing along graded Wnt activity. Experimental targeting of EGFR‐BRAF‐MEK in cancer organoids affected signaling and gene expression contingent on predictive KRAS/BRAF mutations and induced cell plasticity overriding default developmental trajectories. Our results highlight directional cancer cell development as a driver of non‐genetic cancer cell heterogeneity and re‐routing of trajectories as a response to targeted therapy.

Abstract The forage maturation hypothesis (FMH) assumes that herbivores cope with the trade‐off between digestibility and biomass in forage by selecting vegetation at intermediate growth. The green wave hypothesis (GWH) extends the FMH to suggest how spatiotemporal heterogeneity in plant quality shapes migratory movements of herbivores. Growing empirical support for these hypotheses mainly comes from studies in vast landscapes with large‐scale habitat heterogeneity. It is unclear, however, to what extent ungulates surf green waves in human‐altered landscapes with small‐scale heterogeneity in terms of land use and topography. We used plant phenological proxies derived from Sentinel 2 satellite data to analyze the habitat selection of 93 collared red deer (Cervus elaphus) in montane and alpine habitats. Using a step selection analysis, we investigated how plant phenology, that is, the instantaneous rate of green‐up (IRG) and normalized difference vegetation index (NDVI), and a set of variables describing topography and human presence influenced red deer resource selection in open habitats. We learned that red deer selected areas with high biomass at green‐up and avoided habitats with possible exposure to human activity. Additionally, landscape structure and topography strongly influenced spatial behavior of red deer. We further compared cumulative access to high‐quality forage across migrant strategies and found migrants gained better access than residents. Many migratory individuals surfed the green wave, and their surfing behavior, however, became less pronounced with decreasing distance to settlements. Within the constraints of topography and human land use, red deer track spring green‐up on a fine spatiotemporal scale and follow the green wave across landscapes in migration movements. Thus, they benefit from high‐quality forage even in human‐dominated landscapes with small‐scale heterogeneity and vegetation emerging in a heterogenic, dynamic mosaic.

Abstract Background Popeye domain-containing proteins 1 and 2 (POPDC1 and POPDC2) are transmembrane proteins involved in cyclic AMP-mediated signalling processes and are required for normal cardiac pacemaking and conduction. In order to identify novel protein interaction partners, POPDC1 and 2 proteins were attached to beads and compared by proteomic analysis with control beads in the pull-down of proteins from cultured human skeletal myotubes. Results There were highly-significant interactions of both POPDC1 and POPDC2 with XIRP1 (Xin actin binding repeat-containing protein 1), actin and, to a lesser degree, annexin A5. In adult human skeletal muscle, both XIRP1 and POPDC1/2 were present at the sarcolemma and in T-tubules. The interaction of POPDC1 with XIRP1 was confirmed in adult rat heart extracts. Using new monoclonal antibodies specific for POPDC1 and POPDC2, both proteins, together with XIRP1, were found mainly at intercalated discs but also at T-tubules in adult rat and human heart. Conclusions Mutations in human POPDC1, POPDC2 and in human XIRP1, all cause pathological cardiac arrhythmias, suggesting a possible role for POPDC1/2 and XIRP1 interaction in normal cardiac conduction.

Abstract Objective The biological interpretation of gene expression measurements is a challenging task. While ordination methods are routinely used to identify clusters of samples or co-expressed genes, these methods do not take sample or gene annotations into account. We aim to provide a tool that allows users of all backgrounds to assess and visualize the intrinsic correlation structure of complex annotated gene expression data and discover the covariates that jointly affect expression patterns. Results The Bioconductor package covRNA provides a convenient and fast interface for testing and visualizing complex relationships between sample and gene covariates mediated by gene expression data in an entirely unsupervised setting. The relationships between sample and gene covariates are tested by statistical permutation tests and visualized by ordination. The methods are inspired by the fourthcorner and RLQ analyses used in ecological research for the analysis of species abundance data, that we modified to make them suitable for the distributional characteristics of both, RNA-Seq read counts and microarray intensities, and to provide a high-performance parallelized implementation for the analysis of large-scale gene expression data on multi-core computational systems. CovRNA provides additional modules for unsupervised gene filtering and plotting functions to ensure a smooth and coherent analysis workflow.

Abstract Background Sex and gender influence health and disease outcomes, therefore, doctors should be able to deliver gender-sensitive care. To train gender-sensitive doctors, relevant sex and gender differences have to be included in medical education. In order to develop appealing, relevant, and effective education for undergraduate medical students, education should be tailored to students’ level and anticipated on their ideas and assumptions. Therefore, we wanted to answer the following research questions: 1. What do aspiring medical students want to learn about gender medicine?; 2. How would they like to learn about gender medicine?; and 3. What are their ideas and assumptions about sex and gender differences in health and disease? Methods We performed an explorative thematic document analysis of educational assignments made by successful applicants (n = 50) during the selection procedure of their entry into medical school. To test aspirants’ capacity for self-directed learning, students were asked to formulate their own study plan after they watched a video that resembled a future practical experience (a consultation with a patient). As the content of this video was gender-sensitive, the assignments of the successful applicants gave us the unique opportunity to examine aspiring medical students’ views about gender medicine. Results Aspiring medical students were eager to start their training to become gender-sensitive doctors. They believed in better care for all patients and thought doctors should obtain gender competences during their medical training. Students preferred to start with acquiring basic biomedical knowledge about differences between men and women and continue their training by developing gender-sensitive communication skills in (simulated) practical settings. Students differed in their interpretation of the gender-sensitive video, some generalized potential differences to all men and all women. Teachers were considered as important role models in learning about gender medicine. Conclusions We advise medical schools to teach gender medicine from the beginning of medical school, by focusing on sex differences first and adding gender related themes later on in the curriculum. As students may interpret gender-sensitive information differently, structurally embedding reflection on gender medicine with gender competent teachers is necessary.

The occurrence of an immune response against therapeutic proteins poses a major risk for the development of biologics and for successful treatment of patients. Generation of anti-drug antibodies (ADAs) can lead to formation of immune complexes (ICs), consisting of drug and ADAs, with potential impact on safety, efficacy and exposure. Here, we focus on the effects of IC formation, i.e., specific IC sizes, ADA and drug properties, on drug pharmacokinetics. Pre-formed IC preparations of an IgG1 drug (with wild type or with an ablated effector function at the Fc domain) and different ADA surrogates (directed against the complementarity-determining regions or Fc domain of the drug) were administered to rats and collected serum was analyzed to determine the total drug concentration. A combination of size-exclusion chromatography and ELISA enabled a size-specific evaluation of IC profiles in serum and their changes over time. Within five minutes, total drug concentration decreased by ~20–60% when the drug was complexed. Independent of the ADA surrogate and drug variant used, increasing IC size led to increased clearance. Comparing ICs formed with the same ADA surrogate but different IgG1 variants, we observed that complexed drug with a wildtype Fc domain showed faster clearance compared to immune effector function modified drug. Data generated in this study indicated that clearance of drug due to ADA generation is driven by size and structure of the formed ICs, but also by the immune effector functions of the Fc domains of IgGs.Abbreviations Ab: antibody, ADA: anti-drug antibody, AUC: area under the curve, Bi: biotin, CDR: complementary-determining region, cmax: maximal concentration, Dig: digoxigenin, ELISA: enzyme-linked immunosorbent assay, Fc: fragment crystallizable, FcRn: neonatal Fc receptor, HMW: high molecular weight, IC: immune complex, IC-QC: immune complex quality control, IgG: immunoglobulin G, mAb: monoclonal antibody, mADA: monoclonal ADA, pAb: polyclonal antibody, pADA: polyclonal ADA, PD: pharmacodynamics; PK: pharmacokinetic, QC: quality control, SEC: size-exclusion chromatography, WT: wildtype

Background: Early-life risk factors, including maternal hyperglycaemia and birthweight, are thought to contribute to the high burden of cardiometabolic disease experienced by Indigenous populations. We examined rates of pre-existing diabetes in pregnancy, gestational diabetes mellitus (GDM) and extremes of birthweight over three decades in the Northern Territory (NT) of Australia. Methods: We performed a retrospective cohort analysis of the NT Perinatal Data Collection from 1987 to 2016, including all births >20 weeks gestation, stratified by maternal Aboriginal identification. Key outcomes were annual rates of pre-existing diabetes, GDM, small-for-gestational-age, large-for-gestational-age, low birthweight (4000 g). Logistic regression was used to assess trends and interactions. Findings: 109 349 babies were born to 64 877 mothers, 36% of whom identified as Aboriginal ethnicity. Among Aboriginal women, rates of GDM and pre-existing diabetes, respectively, were 3 · 4% and 0 · 6% in 1987 and rose to 13% and 5 · 7% in 2016 (both trends p

The inhibitory activity of the essential oils (EO) of mint and thyme on Candida albicans are well known, however, their valorization in a dosage form for the management of cutaneous candidiasis has been little explored. This study aimed to formulate innovative and cost-effective dermatological topicals based on mint and thyme essential oils for the treatment of cutaneous candidiasis. Thyme essential oil was obtained commercially, while that of mint was obtained by hydrodistillation. In order to determine their antifungal activity, both essentials oils were tested alone and in combination against a reference strain of Candida albicans (strain MHMR) and clinical strains of Candida albicans and Candida tropicalis. Three creams were formulated using natural (shea butter, palm oil) and chemical (cetomacrogol) excipients. The efficacies of these creams were assessed in vivo using Wistar rats infected with Candida albicans MHMR. The in vitro antimicrobial study showed that C. albicans MHMR was more sensitive to thyme essential oil with a MIC of 310 μgmL−1, which was higher than the reference fluconazole used for the in vitro study (32 μgmL−1). The antimicrobial synergy study of both essential oils using checkerboard test demonstrated an additive effect of mint and thyme essential oils on C. albicans MHMR. GC/FID and GC/MS analyses led to the identification of thymol and menthol respectively as the main components of thyme and mint essential oils. A shea butter cream base and a shea butter and palm oil cream both containing 5% of EO (mint and thyme) exhibited the best in vivo antimicrobial activities, inducing optimal wound healing in infected rats compared with ketoconazole commercial cream used for the in vivo study. These results provide a solid basis at least in part, for the use of essential oil in creams formulated with natural excipients for the management of cutaneous candidiasis.

mtDNA variations often result in bioenergetic dysfunction inducing a metabolic switch toward glycolysis resulting in an unbalanced pH homeostasis. In hypoxic cells, expression of the tumor-associated carbonic anhydrase IX (CAIX) is enhanced to maintain cellular pH homeostasis. We hypothesized that cells with a dysfunctional oxidative phosphorylation machinery display elevated CAIX expression levels. Increased glycolysis was observed for cytoplasmic 143B mutant hybrid (m.3243A>G, >94.5%) cells (p < 0.05) and 143B mitochondrial DNA (mtDNA) depleted cells (p < 0.05). Upon hypoxia (0.2%, 16 h), genetic or pharmacological oxidative phosphorylation (OXPHOS) inhibition resulted in decreased CAIX (p < 0.05), vascular endothelial growth factor (VEGF) and hypoxia-inducible factor 1-alpha (HIF-1α) expression levels. Reactive oxygen species (ROS) and prolyl-hydroxylase 2 (PHD2) levels could not explain these observations. In vivo, tumor take (>500 mm3) took longer for mutant hybrid xenografts, but growth rates were comparable with control tumors upon establishment. Previously, it has been shown that HIF-1α is responsible for tumor establishment. In agreement, we found that HIF-1α expression levels and the pimonidazole-positive hypoxic fraction were reduced for the mutant hybrid xenografts. Our results demonstrate that OXPHOS dysfunction leads to a decreased HIF-1α stabilization and subsequently to a reduced expression of its downstream targets and hypoxic fraction in vivo. In contrast, hypoxia-inducible factor 2-alpha (HIF-2α) expression levels in these xenografts were enhanced. Inhibition of mitochondrial function is therefore an interesting approach to increase therapeutic efficacy in hypoxic tumors.

Inflammasomes activate the protease caspase-1, which cleaves interleukin-1β and interleukin-18 to generate the mature cytokines and controls their secretion and a form of inflammatory cell death called pyroptosis. By generating mice expressing enzymatically inactive caspase-1C284A, we provide genetic evidence that caspase-1 protease activity is required for canonical IL-1 secretion, pyroptosis, and inflammasome-mediated immunity. In caspase-1-deficient cells, caspase-8 can be activated at the inflammasome. Using mice either lacking the pyroptosis effector gasdermin D (GSDMD) or expressing caspase-1C284A, we found that GSDMD-dependent pyroptosis prevented caspase-8 activation at the inflammasome. In the absence of GSDMD-dependent pyroptosis, the inflammasome engaged a delayed, alternative form of lytic cell death that was accompanied by the release of large amounts of mature IL-1 and contributed to host protection. Features of this cell death modality distinguished it from apoptosis, suggesting it may represent a distinct form of pro-inflammatory regulated necrosis.

Abstract Background Diabetes-related end stage renal disease (DM-ESRD) is a devastating consequence of the type 2 diabetes epidemic, both of which disproportionately affect Indigenous peoples. Projecting case numbers and costs into future decades would help to predict resource requirements, and simulating hypothetical interventions could guide the choice of best practices to mitigate current trends. Methods An agent based model (ABM) was built to forecast First Nations and non-First Nations cases of DM-ESRD in Saskatchewan from 1980 to 2025 and to simulate two hypothetical interventions. The model was parameterized with data from the Canadian Institute for Health Information, Saskatchewan Health Administrative Databases, the Canadian Organ Replacement Register, published studies and expert judgement. Input parameters without data sources were estimated through model calibration. The model incorporated key patient characteristics, stages of diabetes and chronic kidney disease, renal replacement therapies, the kidney transplant assessment and waiting list processes, costs associated with treatment options, and death. We used this model to simulate two interventions: 1) No new cases of diabetes after 2005 and 2) Pre-emptive renal transplants carried out on all diabetic persons with new ESRD. Results There was a close match between empirical data and model output. Going forward, both incidence and prevalence cases of DM-ESRD approximately doubled from 2010 to 2025, with 250–300 new cases per year and almost 1300 people requiring RRT by 2025. Prevalent cases of First Nations people with DM-ESRD increased from 19% to 27% of total DM-ESRD numbers from 1990 to 2025. The trend in yearly costs paralleled the prevalent DM-ESRD case count. For Scenario 1, despite eliminating diabetes incident cases after 2005, prevalent cases of DM-ESRD continued to rise until 2019 before slowly declining. When all DM-ESRD incident cases received a pre-emptive renal transplant (scenario 2), a substantial increase in DM-ESRD prevalence occurred reflecting higher survival, but total costs decreased reflecting the economic advantage of renal transplantation. Conclusions This ABM can forecast numbers and costs of DM-ESRD in Saskatchewan and be modified for application in other jurisdictions. This can aid in resource planning and be used by policy makers to evaluate different interventions in a safe and economical manner.

The pathogenicity ofFrancisellaspecies largely depends on their escape from phagosomes in macrophages, mediated by a type VI secretion system (T6SS). Here, the authors show dynamics of T6SS assembly and disassembly and identify the genes essential for phagosome escape and pathogenicity in mice.

Background: First Nations people are experiencing increasing rates of obesity and type 2 diabetes but no anthropometric information exists from before the 1950s to provide context to these epidemics. Objective: To compare anthropometric indices of First Nations children and youth on first entering residential schools with historical and contemporary reference groups. Methods: This observational cross-sectional study used archival records from the Department of Indian Affairs to calculate body mass index (BMI), height for age (HA) and weight for age (WA) of all known children and youth undergoing physical examinations on first entering residential schools in Saskatchewan and Manitoba from 1919 to 1953. Proportions of children and youth in each BMI category were determined by age, sex, time period and residential school. Z-scores for HA and WA were determined by age group and sex. Finally, median heights and weights were compared with a non-Indigenous cohort from the 1953 Canadian survey. Results: On admission to residential schools, 1,767 First Nations children and youth (847 boys, 920 girls) were more likely to have normal BMIs (79.8%) than Canadian children and youth today (66.5%), but lower rates of overweight/obesity (10.9% vs. 32.0%) and higher rates of underweight (9.3% vs. −2, age-specific median heights tended to be higher than Canadian children and youth in 1953. Under 3% of children and youth had WA Z-scores of >−2. Conclusions: A large majority of First Nations children and youth exhibited normal anthropometric indices on first entering residential schools in Manitoba and Saskatchewan from 1919 to 1953. These historical findings provide an important context to the current epidemics of obesity and type 2 diabetes and suggest that the nutritional conditions in these First Nations children's communities were satisfactory during the residential school era.

Outdoor recreational activities are increasing worldwide and occur at high frequency especially close to cities. Forests are a natural environment often used for such activities as jogging, hiking, dog walking, mountain biking, or horse riding. The mere presence of people in forests can disturb wildlife, which may perceive humans as potential predators. Many of these activities rely on trails, which intersect an otherwise contiguous habitat and hence impact wildlife habitat. The aim of this study was to separate the effect of the change in vegetation and habitat structure through trails, from the effect of human presence using these trails, on forest bird communities. Therefore we compared the effects of recreational trails on birds in two forests frequently used by recreationists with that in two rarely visited forests. In each forest, we conducted paired point counts to investigate the differences between the avian community close (50 m) and far (120 m) from trails, while accounting for possible habitat differences, and, for imperfect detection, by applying a multi-species N-mixture model. We found that in the disturbed (i.e., high-recreation-level forests) the density of birds and species richness were both reduced at points close to trails when compared to points further away (−13 and −4% respectively), whereas such an effect was not statistically discernible in the forests with a low-recreation-level. Additionally we found indications that the effects of human presence varied depending on the traits of the species. These findings imply that the mere presence of humans can negatively affect the forest bird community along trails. Visitor guidance is an effective conservation measure to reduce the negative impacts of recreationists. In addition, prevention of trail construction in undeveloped natural habitats would reduce human access, and thus disturbance, most efficiently.

Background. Obesity history may provide a better understanding of the contribution of obesity to T2DM risk. Methods. 17,634 participants from the 1958 National Child Development Study were followed from birth to 50 years. Cumulative obesity dose, a measure of obesity history, was calculated by subtracting the upper cut-off of the normal BMI from the actual BMI at each follow-up and summing the areas under the obesity dose curve. Hazard ratios (HRs) for diabetes were calculated using Cox regression analysis. Three separate models compared the predictive ability of cumulative obesity dose on diabetes risk with the time-varying BMI and last BMI. Results. In final models, 341 of 15,043 (2.27%) participants developed diabetes; male sex and low birth weight were significant confounding variables. Adjusted HRs were 1.080 (95% CI: 1.071, 1.088) per 10-unit cumulative obesity dose, 1.098 (95% CI: 1.080, 1.117) per unit of the time-varying BMI, and 1.146 (95% CI: 1.084, 1.212) per unit of the last BMI. Cumulative obesity dose provided the best predictive ability for diabetes. Conclusions. Cumulative obesity dose is an improved method for evaluating the impact of obesity history on diabetes risk. The link between low birth weight and T2DM is strengthened by adjusting for cumulative obesity dose.

Several clinically used drugs are mitotoxic causing mitochondrial DNA (mtDNA) variations, and thereby influence cancer treatment response. We hypothesized that radiation responsiveness will be enhanced in cellular models with decreased mtDNA content, attributed to altered reactive oxygen species (ROS) production and antioxidant capacity. For this purpose BEAS-2B, A549, and 143B cell lines were depleted from their mtDNA (ρ0). Overall survival after irradiation was increased (p

Depression is a leading cause of HIV/AIDS disease burden; it worsens health outcomes and quality of life. Addressing this problem requires accurate quantification of the extra burden of depression to HIV/AIDS in a given population, and knowledge of the baseline depression prevalence in the general population. There has been no previous study of depression in the general Cameroonian population. The current study attempts to address that important need. We used the Beck Depression Inventory-II to assess the prevalence and severity of depressive symptoms in 270 HIV-infected and seronegative Cameroonians. Univariate analyses showed a trend toward higher depressive symptoms among cases, compared to controls (p = 0.055), and among older subjects (>40 years), compared to younger subjects (≤40 years) (p = 0.059). Analysis of depression severity showed that 33.73% of cases had moderate-to-severe depressive symptoms, compared to 19.8% of controls (p

3'-5'-cyclic adenosine monophosphate (cAMP) is a second messenger, which plays an important role in the heart. It is generated in response to activation of G-protein-coupled receptors (GPCRs). Initially, it was thought that protein kinase A (PKA) exclusively mediates cAMP-induced cellular responses such as an increase in cardiac contractility, relaxation, and heart rate. With the identification of the exchange factor directly activated by cAMP (EPAC) and hyperpolarizing cyclic nucleotide-gated (HCN) channels as cAMP effector proteins it became clear that a protein network is involved in cAMP signaling. The Popeye domain containing (Popdc) genes encode yet another family of cAMP-binding proteins, which are prominently expressed in the heart. Loss-of-function mutations in mice are associated with cardiac arrhythmia and impaired skeletal muscle regeneration. Interestingly, the cardiac phenotype, which is present in both, Popdc1 and Popdc2 null mutants, is characterized by a stress-induced sinus bradycardia, suggesting that Popdc proteins participate in cAMP signaling in the sinuatrial node. The identification of the two-pore channel TREK-1 and Caveolin 3 as Popdc-interacting proteins represents a first step into understanding the mechanisms of heart rate modulation triggered by Popdc proteins.

Locomotion is driven by shape changes coordinated by the nervous system through time; thus, enumerating an animal's complete repertoire of shape transitions would provide a basis for a comprehensive understanding of locomotor behaviour. Here we introduce a discrete representation of behaviour in the nematode C. elegans. At each point in time, the worm's posture is approximated by its closest matching template from a set of 90 postures and locomotion is represented as sequences of postures. The frequency distribution of postural sequences is heavy-tailed with a core of frequent behaviours and a much larger set of rarely used behaviours. Responses to optogenetic and environmental stimuli can be quantified as changes in postural syntax: worms show different preferences for different sequences of postures drawn from the same set of templates. A discrete representation of behaviour will enable the use of methods developed for other kinds of discrete data in bioinformatics and language processing to be harnessed for the study of behaviour.

BackgroundThe major clinical challenge in the treatment of high-grade serous ovarian cancer (HGSOC) is the development of progressive resistance to platinum-based chemotherapy. The objective of this study was to determine whether intra-tumour genetic heterogeneity resulting from clonal evolution and the emergence of subclonal tumour populations in HGSOC was associated with the development of resistant disease.Methods and findingsEvolutionary inference and phylogenetic quantification of heterogeneity was performed using the MEDICC algorithm on high-resolution whole genome copy number profiles and selected genome-wide sequencing of 135 spatially and temporally separated samples from 14 patients with HGSOC who received platinum-based chemotherapy. Samples were obtained from the clinical CTCR-OV03/04 studies, and patients were enrolled between 20 July 2007 and 22 October 2009. Median follow-up of the cohort was 31 mo (interquartile range 22-46 mo), censored after 26 October 2013. Outcome measures were overall survival (OS) and progression-free survival (PFS). There were marked differences in the degree of clonal expansion (CE) between patients (median 0.74, interquartile range 0.66-1.15), and dichotimization by median CE showed worse survival in CE-high cases (PFS 12.7 versus 10.1 mo, p = 0.009; OS 42.6 versus 23.5 mo, p = 0.003). Bootstrap analysis with resampling showed that the 95% confidence intervals for the hazard ratios for PFS and OS in the CE-high group were greater than 1.0. These data support a relationship between heterogeneity and survival but do not precisely determine its effect size. Relapsed tissue was available for two patients in the CE-high group, and phylogenetic analysis showed that the prevalent clonal population at clinical recurrence arose from early divergence events. A subclonal population marked by a NF1 deletion showed a progressive increase in tumour allele fraction during chemotherapy.ConclusionsThis study demonstrates that quantitative measures of intra-tumour heterogeneity may have predictive value for survival after chemotherapy treatment in HGSOC. Subclonal tumour populations are present in pre-treatment biopsies in HGSOC and can undergo expansion during chemotherapy, causing clinical relapse.