Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse.

Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide. In doing so, we identify pre-existing and treatment-persistent cell subpopulations that possess regenerative potential when subjected to treatment. We find distinct chromatin landscapes associated with enzalutamide treatment and resistance that are linked to alternative transcriptional programs. Transcriptional profiles characteristic of persistent cells are able to stratify the treatment response of patients. Ultimately, we show that defining changes in chromatin and gene expression in single-cell populations from pre-clinical models can reveal as yet unrecognized molecular predictors of treatment response. This suggests that the application of single-cell methods with high analytical resolution in pre-clinical models may powerfully inform clinical decision-making.

Multi-isotope analysis reveals that feasts in the Stonehenge environs and across Wessex drew people and animals from throughout Britain.

The great henge complexes of southern Britain are iconic monuments of the third millennium BCE, representing great feats of engineering and labor mobilization that hosted feasting events on a previously unparalleled scale. The scale of movement and the catchments that the complexes served, however, have thus far eluded understanding. Presenting the largest five-isotope system archeological dataset (87Sr/86Sr, δ34S, δ18O, δ13C, and δ15N) yet fully published, we analyze 131 pigs, the prime feasting animals, from four Late Neolithic (approximately 2800 to 2400 BCE) complexes to explore the networks that the feasts served. Because archeological evidence excludes continental contact, sources are considered only in the context of the British Isles. This analysis reveals wide-ranging origins across Britain, with few pigs raised locally. This finding demonstrates great investment of effort in transporting pigs raised elsewhere over vast distances to supply feasts and evidences the very first phase of pan-British connectivity.

An analysis of the cosmetic surgery experience acquired through UK plastic surgery training.

AIMS: Cosmetic surgery is an essential component of Plastic Surgery training. Our study demonstrates the average cosmetic surgery experience of UK Plastic Surgery registrars over their 6-year training scheme. Comparison is made with the operative requirements for the Certificate of Completion of Training (CCT) and the Royal College of Surgeons (RCS) Cosmetic Certification scheme. METHODS: By using the web-based eLogbook, we analysed all the cosmetic surgery operations recorded by Plastic Surgery registrars during their specialist training. The weighted mean average number of procedures was calculated for different areas of cosmetic surgery practice, according to the level of supervision. The number of RCS cosmetic credits acquired for eight domains of cosmetic surgery was calculated, thus enabling comparison with the operative requirements for certification. RESULTS: eLogbook data were collated for 454 registrars from 2010 to 2016 inclusive. Trainees participated in a mean of 122 cosmetic operations during their training (50% as an assistant), which satisfies the requirement of 100 procedures for CCT. The majority of trainee involvement (66%) was with cosmetic breast and body contouring cases. Comparison with the criteria for cosmetic certification reveals that on average, trainees could certify in cosmetic breast and body contouring surgery but would be unable to accredit in other areas of practice. CONCLUSIONS: Current UK training affords sufficient cosmetic surgery exposure for CCT but offers a limited breadth of exposure. Trainees who wish to certify in cosmetic surgery of the head and neck region will likely be required to seek additional experience outside their deanery training programme.

A portable magneto-optical trap with prospects for atom interferometry in civil engineering.

The high precision and scalable technology offered by atom interferometry has the opportunity to profoundly affect gravity surveys, enabling the detection of features of either smaller size or greater depth. While such systems are already starting to enter into the commercial market, significant reductions are required in order to reach the size, weight and power of conventional devices. In this article, the potential for atom interferometry based gravimetry is assessed, suggesting that the key opportunity resides within the development of gravity gradiometry sensors to enable drastic improvements in measurement time. To push forward in realizing more compact systems, techniques have been pursued to realize a highly portable magneto-optical trap system, which represents the core package of an atom interferometry system. This can create clouds of 107 atoms within a system package of 20 l and 10 kg, consuming 80 W of power.This article is part of the themed issue 'Quantum technology for the 21st century'.

Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study.

BACKGROUND: Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome. METHODS: In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone. FINDINGS: We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions. INTERPRETATION: For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

Protease activated receptor-1 mediates cytotoxicity during ischemia using in vivo and in vitro models.

Protease activated receptors (PARs) populate neurons and astrocytes in the brain. The serine protease thrombin, which activates PAR-1 during the first hours after stroke, appears to be associated with the cytotoxicity. Thrombin antagonists and PAR-1 inhibitors have been correlated with reduced cell death and behavioral protection after stroke, but no data yet support a mechanistic link between PAR-1 action and benefit. We sought to establish the essential role of PAR-1 in mediating ischemic damage. Using a short hairpin mRNA packaged with green fluorescent protein in a lentivirus vector, we knocked downPAR-1 in the medial caudate nucleus prior to rat middle cerebral artery occlusion (MCAo) and in rat neurons prior to oxygen-glucose deprivation. We also compared aged PAR-1 knockout mice with aged PAR-3, PAR-4 mice and young wild-type mice in a standard MCAo model. Silencing PAR-1 significantly reduced neurological deficits, reduced endothelial barrier leakage, and decreased neuronal degeneration in vivo during MCAo. PAR-1 knock-down in the ischemic medial caudate allowed cells to survive the ischemic injury; infected cells were negative for terminal deoxynucleotidyl transferase mediated dUTP Nick End Labeling (TUNEL) and c-Fos injury markers. Primary cultured neurons infected with PAR-1 short hairpin ribonucleic acid (shRNA) showed increased neuroprotection during hypoxic/aglycemic conditions with or without added thrombin. The aged PAR-1 knockout mice showed decreased infarction and vascular disruption compared to aged controls or young wild types. We demonstrated an essential role for PAR-1 during ischemia. Silencing or removing PAR-1 significantly protected neurons and astrocytes. Further development of agents that act at PAR-1 or its downstream pathways could yield powerful stroke therapy.

Elevated levels of FOXA1 facilitate androgen receptor chromatin binding resulting in a CRPC-like phenotype.

Castration-resistant prostate cancer (CRPC) continues to pose a significant clinical challenge with new generation second-line hormonal therapies affording limited improvement in disease outcome. As the androgen receptor (AR) remains a critical driver in CRPC, understanding the determinants of its transcriptional activity is important for developing new AR-targeted therapies. FOXA1 is a key component of the AR transcriptional complex yet its role in prostate cancer progression and the relationship between AR and FOXA1 are not completely resolved. It is well established that FOXA1 levels are elevated in advanced prostate cancer and metastases. We mimicked these conditions by overexpressing FOXA1 in the androgen-responsive LNCaP prostate cancer cell line and observed a significant increase in AR genomic binding at novel regions that possess increased chromatin accessibility. High levels of FOXA1 resulted in increased proliferation at both sub-optimal and high 5α-dihydrotestosterone (DHT) concentrations. Immunohistochemical staining for FOXA1 in a clinical prostate cancer cohort revealed that high FOXA1 expression is associated with shorter time to biochemical recurrence after radical prostatectomy (hazard ratio (HR) 5.0, 95% confidence interval (CI) 1.2-21.1, P=0.028), positive surgical margins and higher stage disease at diagnosis. The gene expression program that results from FOXA1 overexpression is enriched for PTEN, Wnt and other pathways typically represented in CRPC gene signatures. Together, these results suggest that in an androgen-depleted state, elevated levels of FOXA1 enhance AR binding at genomic regions not normally occupied by AR, which in turn facilitates prostate cancer cell growth.

Highly efficient methane biocatalysis revealed in a methanotrophic bacterium.

Methane is an essential component of the global carbon cycle and one of the most powerful greenhouse gases, yet it is also a promising alternative source of carbon for the biological production of value-added chemicals. Aerobic methane-consuming bacteria (methanotrophs) represent a potential biological platform for methane-based biocatalysis. Here we use a multi-pronged systems-level approach to reassess the metabolic functions for methane utilization in a promising bacterial biocatalyst. We demonstrate that methane assimilation is coupled with a highly efficient pyrophosphate-mediated glycolytic pathway, which under oxygen limitation participates in a novel form of fermentation-based methanotrophy. This surprising discovery suggests a novel mode of methane utilization in oxygen-limited environments, and opens new opportunities for a modular approach towards producing a variety of excreted chemical products using methane as a feedstock.

Mathematical modelling of toxicity associated with intracellular chromium reduction.

Chromium is a known allergen and carcinogen, but the mechanisms by which damage is caused are not clearly understood. Based on experimental literature, we devise a conceptual model examining the intracellular reduction of chromium through reductants such as glutathione and ascorbic acid. From this, we build a mathematical model describing these events in detail and we use this to clarify the key steps in the process of chromium reduction within cells.In particular, we consider the free radicals which are generated as a result of chromium reduction and that are likely to cause most harm to the cell. To explore the practical implications of the model predication, we investigate what the effects of a single eight hours of exposure and multiple eight hour exposures over the course of 3 days with increasing extracellular chromium concentration are. The dependence on initial chromium concentration is of particular significance with the proportions of the various chromium states changing as well as free radical generation increasing with greater chromium exposure.

Evaluation of maxillary arterial blood flow in anesthetized cats with the mouth closed and open.

The mouth-gag is a common tool used in veterinary medicine during oral and transoral procedures in cats but its use has recently been associated with the development of blindness. The goal of this study was to investigate whether maximal opening of the mouth affects maxillary artery blood flow in six anesthetized cats. To assess blood flow, the electroretinogram (ERG), brainstem auditory evoked response (BAER) and magnetic resonance angiography (MRA) were evaluated qualitatively with the mouth closed and open. During dynamic computer tomography (CT) examinations, detection of contrast medium in the maxillary artery was quantified by measuring the Hounsfield units (HUs). The peak HU, time to peak and mean HU were determined. Changes ⩾10% of these parameters were considered indicative of altered blood flow. ERG and BAER were normal with the mouth closed in all cats, but was abnormal with the mouth opened maximally in two cats and one cat, respectively. During MRA, blood flow was undetected in either maxillary artery in one cat and reduced in the right maxillary artery in two cats, when the mouth was open. During CT, the peak HU decreased ⩾10% in three cats, the time to peak was ⩾10% longer in two cats, and the mean HU was ⩾10% lower in one cat when the mouth was open. No cat developed apparent blindness or deafness. Maximal opening of the mouth caused alterations in several indicators of blood flow in some individual cats.

Helicobacter pylori CagA targets gastric tumor suppressor RUNX3 for proteasome-mediated degradation.

Chronic infection with cagA-positive Helicobacter pylori is the strongest risk factor for the development of gastric adenocarcinoma. The cagA gene product CagA is injected into gastric epithelial cells and disturbs cellular functions by physically interacting with and deregulating a variety of cellular signaling molecules. RUNX3 is a tumor suppressor in many tissues, and it is frequently inactivated in gastric cancer. In this study, we show that H. pylori infection inactivates the gastric tumor suppressor RUNX3 in a CagA-dependent manner. CagA directly associates with RUNX3 through a specific recognition of the PY motif of RUNX3 by a WW domain of CagA. Deletion of the WW domains of CagA or mutation of the PY motif in RUNX3 abolishes the ability of CagA to induce the ubiquitination and degradation of RUNX3, thereby extinguishing its ability to inhibit the transcriptional activation of RUNX3. Our studies identify RUNX3 as a novel cellular target of H. pylori CagA and also reveal a mechanism by which CagA functions as an oncoprotein by blocking the activity of gastric tumor suppressor RUNX3.

Clinical and molecular characterization of individuals with recurrent genomic disorder at 10q22.3q23.2.

The identification of genomic imbalances in young patients can affect medical management by allowing early intervention for developmental delay and by identifying patients at risk for unexpected medical complications. Using a 105K-feature oligonucleotide array, we identified a 7.25 Mb deletion at 10q22.3q23.2 in six unrelated patients. Deletions of this region have been described in individuals with cognitive and behavioral abnormalities, including autistic features, and may represent a recurring genetic syndrome. All four patients in this study for whom clinical information was available had mild dysmorphic features and three had developmental delay. Of note is the emerging clinical phenotype in these individuals with similar dysmorphic features such as macrocephaly, hypertelorism, and arachnodactyly, and neurodevelopmental delay that includes failure to thrive, hypotonia, and feeding difficulties in the neonatal period, and receptive and expressive language delay with global neurodevelopmental delay after the neonatal period. However, there is no pattern of abnormalities, craniofacial, behavioral, or otherwise, that would have aroused clinical suspicion of a specific syndrome. Finally, the patients' deletions encompass BMPR1A but not PTEN, and these patients may be at risk for colon cancer and should be referred for appropriate prophylactic care and surveillance. Of the two patients in this study who had colonoscopy following the array results, neither had polyps. Therefore, the magnitude of the increased risk for colon cancer is currently unknown.

Refinement of the Region for Split Hand/Foot Malformation 5 on 2q31.1.

Background: Deletions that encompass 2q31.1 have been proposed as a microdeletion syndrome with common clinical features, including intellectual disability/developmental delay, microcephaly, cleft palate, growth delay, and hand/foot anomalies. In addition, several genes within this region have been proposed as candidates for split hand-foot malformation 5 (SHFM5). Methods: To delineate the genotype-phenotype correlation between deletions of this region, we identified 14 individuals with deletions at 2q31.1 detected by microarray analysis for physical and developmental disabilities. Results: All subjects for whom detailed clinical records were available had neurological deficits of varying degree. Seven subjects with deletions encompassing the HOXD cluster had hand/foot anomalies of varying severity, including syndactyly, brachydactyly, and ectrodactyly. Of 7 subjects with deletions proximal to the HOXD cluster, 5 of which encompassed DLX1/DLX2, none had clinically significant hand/foot anomalies. In contrast to previous reports, the individuals in our study did not display a characteristic gestalt of dysmorphic facial features. Conclusion: The absence of hand/foot anomalies in any of the individuals with deletions of DLX1/DLX2 but not the HOXD cluster supports the hypothesis that haploinsufficiency of the HOXD cluster, rather than DLX1/DLX2, accounts for the skeletal abnormalities in subjects with 2q31.1 microdeletions.

Orthopaedic training experience in the UK and Ireland: an analysis using the eLogbook.

The eLogbook is used to collect and collate the operative experience of every orthopaedic trainee in the UK and Ireland. We describe the project and discuss the national data now emerging on elective and trauma training.

Plain radiography still is required in the planning of treatment for urolithiasis.

INTRODUCTION: Nonenhanced computed tomography (NCT) is recognised as the most sensitive tool in diagnosis of renal tract calculi. However, its role as the sole imaging investigation, for decisions regarding management is less clear. OBJECTIVE: To determine the proportion of new stone patient referrals in which management is altered by interpretation of a plain abdominal kidneys, ureters and bladder (KUB) radiograph in addition to NCT. METHODS: One hundred consecutive new referrals to a national lithotripsy centre were considered prospectively for treatment of renal tract calculi. RESULTS: A significant change in management was undertaken in 17 patients on the basis of KUB findings. Eleven patients had radio-lucent ureteric stones, for which Extracorporeal Shockwave Lithotripsy (ESWL) was consequently not possible and who required endoscopic management. There were six inaccuracies in measurement of size or positioning on NCT. In a further 43 patients it was not possible to confirm management until the KUB was reviewed, although in these cases ESWL or expectant management was still pursued. Thus additional imaging with a KUB was required in order to confirm optimum management in 60 patients. CONCLUSION: Additional plain radiography confers a significant advantage in the planning of treatment for urolithiasis once the diagnosis has been established by NCT because of information it provides regarding radio-opacity as well as stone size and visibility. This information cannot be delivered by NCT alone. We therefore recommend that KUB imaging is performed on all new stone patients referred for treatment.