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The Scholarship is available to UK/EU students only. To work with a named Principal Investigator in NDS in the field of Neurosurgery. Open to new students who begin their programme of study in October 2014
Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole-genome sequencing with histopathological features.
BACKGROUND: Extension of prostate cancer beyond the primary site by local invasion or nodal metastasis is associated with poor prognosis. Despite significant research on tumour evolution in prostate cancer metastasis, the emergence and evolution of cancer clones at this early stage of expansion and spread are poorly understood. We aimed to delineate the routes of evolution and cancer spread within the prostate and to seminal vesicles and lymph nodes, linking these to histological features that are used in diagnostic risk stratification. METHODS: We performed whole-genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and lymph nodes of five treatment-naive patients with locally advanced disease. We spatially mapped the clonal composition of cancer across the prostate and the routes of spread of cancer cells within the prostate and to seminal vesicles and lymph nodes in each individual by analysing a total of > 19,000 copy number corrected single nucleotide variants. RESULTS: In each patient, we identified sample locations corresponding to the earliest part of the malignancy. In patient 10, we mapped the spread of cancer from the apex of the prostate to the seminal vesicles and identified specific genomic changes associated with the transformation of adenocarcinoma to amphicrine morphology during this spread. Furthermore, we show that the lymph node metastases in this patient arose from specific cancer clones found at the base of the prostate and the seminal vesicles. In patient 15, we observed increased mutational burden, altered mutational signatures and histological changes associated with whole genome duplication. In all patients in whom histological heterogeneity was observed (4/5), we found that the distinct morphologies were located on separate branches of their respective evolutionary trees. CONCLUSIONS: Our results link histological transformation with specific genomic alterations and phylogenetic branching. These findings have implications for diagnosis and risk stratification, in addition to providing a rationale for further studies to characterise the genetic changes causally linked to morphological transformation. Our study demonstrates the value of integrating multi-region sequencing with histopathological data to understand tumour evolution and identify mechanisms of prostate cancer spread.
Data integration in eHealth: a domain/disease specific roadmap.
The paper documents a series of data integration workshops held in 2006 at the UK National e-Science Centre, summarizing a range of the problem/solution scenarios in multi-site and multi-scale data integration with six HealthGrid projects using schizophrenia as a domain-specific test case. It outlines emerging strategies, recommendations and objectives for collaboration on shared ontology-building and harmonization of data for multi-site trials in this domain.
Multiarterial vs Single-Arterial Coronary Surgery: 10-Year Follow-up of 1 Million Patients.
BACKGROUND: Although many options exist for multivessel coronary revascularization, controversy persists over whether multiarterial grafting (MAG) confers a survival advantage over single-arterial grafting (SAG) with saphenous vein in coronary artery bypass grafting (CABG). This study sought to compare longitudinal survival between patients undergoing MAG and those undergoing SAG. METHODS: All patients undergoing isolated CABG with ≥2 bypass grafts in The Society of Thoracic Surgeons Adult Cardiac Surgery Database (2008-2019) were linked to the National Death Index. Risk adjustment was performed using inverse probability weighting and multivariable modeling. The primary end point was longitudinal survival. Subpopulation analyses were performed and volume thresholds were analyzed to determine optimal benefit. RESULTS: A total of 1,021,632 patients underwent isolated CABG at 1108 programs (100,419 MAG [9.83%]; 920,943 SAG [90.17%]). Median follow-up was 5.30 years (range, 0-12 years). After risk adjustment, all characteristics were well balanced. At 10 years, MAG was associated with improved unadjusted (hazard ratio, 0.59; 95% CI 0.58-0.61) and adjusted (hazard ratio, 0.86; 95% CI, 0.85-0.88) 10-year survival. Center volume of ≥10 MAG cases/year was associated with benefit. MAG was associated with an overall survival advantage over SAG in all subgroups, including stable coronary disease, acute coronary syndrome, and acute infarction. Survival was equivalent to that with SAG for patients age ≥80 years and those with severe heart failure, renal failure, peripheral vascular disease, or obesity. Only patients with a body mass index ≥40 kg/m2 had superior survival with SAG. CONCLUSIONS: Multiarterial CABG is associated with superior long-term survival and should be the surgical multivessel revascularization strategy of choice for patients with a body mass index of less than 40 kg/m2.
Artificial Intelligence-Based Quality Assessment of Histopathology Whole-Slide Images within a Clinical Workflow: Assessment of 'PathProfiler' in a Diagnostic Pathology Setting.
Digital pathology continues to gain momentum, with the promise of artificial intelligence to aid diagnosis and for assessment of features which may impact prognosis and clinical management. Successful adoption of these technologies depends upon the quality of digitised whole-slide images (WSI); however, current quality control largely depends upon manual assessment, which is inefficient and subjective. We previously developed PathProfiler, an automated image quality assessment tool, and in this feasibility study we investigate its potential for incorporation into a diagnostic clinical pathology setting in real-time. A total of 1254 genitourinary WSI were analysed by PathProfiler. PathProfiler was developed and trained on prostate tissue and, of the prostate biopsy WSI, representing 46% of the WSI analysed, 4.5% were flagged as potentially being of suboptimal quality for diagnosis. All had concordant subjective issues, mainly focus-related, 54% severe enough to warrant remedial action which resulted in improved image quality. PathProfiler was less reliable in assessment of non-prostate surgical resection-type cases, on which it had not been trained. PathProfiler shows potential for incorporation into a digitised clinical pathology workflow, with opportunity for image quality improvement. Whilst its reliability in the current form appears greatest for assessment of prostate specimens, other specimen types, particularly biopsies, also showed benefit.
Stratification of acute myocardial and endothelial cell injury, salvage index and final infarct size by systematic microRNA profiling in acute ST-elevation myocardial infarction.
AIM: Acute injury and subsequent remodelling responses to ST-segment elevation myocardial infarction (STEMI) are major determinants of clinical outcome. Current imaging and plasma biomarkers provide delayed readouts of myocardial injury and recovery. Here, we sought to systematically characterize all microRNAs (miRs) released during the acute phase of STEMI and relate miR release to magnetic resonance imaging (MRI) findings to predict acute and late responses to STEMI, from a single early blood sample. METHODS AND RESULTS: miRs were quantified in blood samples obtained from patients after primary PCI (PPCI) for STEMI. Cardiac MRI (cMRI) was performed to quantify myocardial edema, infarct size and salvage index. Regression models were constructed to predict these outcomes measures, which were then tested with a validation cohort. Transcoronary miR release was quantified from paired measurements of coronary artery and coronary sinus samples. A cell culture model was used to identify endothelial cell-derived miRs.A total of 72 patients undergoing PPCI for acute STEMI underwent miR analysis and cMRI. About >200 miRs were detectable in plasma after STEMI, from which 128 miRs were selected for quantification in all patients. Known myocardial miRs demonstrated a linear correlation with troponin release, and these increased across the transcoronary gradient. We identified novel miRs associated with microvascular injury and myocardial salvage. Regression models were constructed using a training cohort, then tested in a validation cohort, and predicted myocardial oedema, infarct size and salvage index. CONCLUSION: Analysis of miR release after STEMI identifies biomarkers that predict both acute and late outcomes after STEMI. A novel miR-based biomarker score enables the estimation of area at risk, late infarct size and salvage index from a single blood sample 6 hours after PPCI, providing a simple and rapid alternative to serial cMRI characterization of STEMI outcome.
Spatiotemporal signal space separation for regions of interest: Application for extracting neuromagnetic responses evoked by deep brain stimulation.
Magnetoencephalography (MEG) recordings are often contaminated by interference that can exceed the amplitude of physiological brain activity by several orders of magnitude. Furthermore, the activity of interference sources may spatially extend (known as source leakage) into the activity of brain signals of interest, resulting in source estimation inaccuracies. This problem is particularly apparent when using MEG to interrogate the effects of brain stimulation on large-scale cortical networks. In this technical report, we develop a novel denoising approach for suppressing the leakage of interference source activity into the activity representing a brain region of interest. This approach leverages spatial and temporal domain projectors for signal arising from prespecified anatomical regions of interest. We apply this denoising approach to reconstruct simulated evoked response topographies to deep brain stimulation (DBS) in a phantom recording. We highlight the advantages of our approach compared to the benchmark-spatiotemporal signal space separation-and show that it can more accurately reveal brain stimulation-evoked response topographies. Finally, we apply our method to MEG recordings from a single patient with Parkinson's disease, to reveal early cortical-evoked responses to DBS of the subthalamic nucleus.
Moving forward on tumor pathology research reporting: a guide for pathologists from the WHO Classification of Tumors EVI MAP Group.
Evidence-based medicine (EBM) can be unfamiliar territory for those working in tumor pathology research and there is a great deal of uncertainty about how to undertake an EBM approach to planning and reporting histopathology-based studies. In this article, endorsed by the WHO International Agency for Research on Cancer's (IARC) International Collaboration for Cancer Classification and Research (IC3R), we aim to help pathologists and researchers to understand the basics of planning an evidence-based tumor pathology research study, as well as our recommendations on how to report the findings from these. We introduce some basic EBM concepts, the PICO model, thoughts on study design, and emphasize the concept of reporting standards. There are many study-specific reporting guidelines available, and we provide an overview of these. However, existing reporting guidelines perhaps do not always fit tumor pathology research papers, and so here we collate the key reporting dataset together into one generic checklist that we think will simplify the task for pathologists. The article aims to complement our recent Hierarchy of Evidence for Tumor Pathology and Glossary of Evidence (study) Types in tumor pathology. Together, these articles should help any researcher get to grips with the basics of EBM for planning and publishing research in tumor pathology, as well as encourage an improved standard of the reports available to us all in the literature.
Continuous drain irrigation as a risk mitigation strategy for postoperative pancreatic fistula: a meta-analysis
Background: Postoperative pancreatic fistula serves as the principle cause for the morbidity and mortality observed after pancreatectomy. Continuous drain irrigation as a treatment strategy for infected pancreatic necrosis has previously been described; however, its role adter pancreatectomy has yet to be determined. The aim of this study was to determine whether continuous drain irrigation reduces postoperative pancreatic fistula. Methods: A meta-analysis of the pre-existing literature was performed. The primary end point was whether continuous drain irrigation reduced postoperative pancreatic fistula after pancreatectomy. The secondary end point evaluated its impact on postoperative morbidity, mortality, and length of stay. Results: Nine articles involving 782 patients were included. Continuous drain irrigation use was associated with a statistically significant reduction in postoperative pancreatic fistula rates (odds ratio [95% confidence interval] 0.40 [0.19–0.82], P = .01). Upon subgroup analysis, a significant reduction in clinically relevant postoperative pancreatic fistula was also noted (odds ratio 0.37 [0.20–0.66], P = .0008). A reduction in postoperative complications was also observed—delayed gastric emptying (0.45 [0.24–0.84], P = .01) and the need for re-operation (0.33 [0.11–0.96], P = .04). This reduction in postoperative complications translated into a reduced length of stay (mean difference −2.62 [−4.97 to −0.26], P = .03). Conclusion: Continuous drain irrigation after pancreatectomy is a novel treatment strategy with a limited body of published evidence. After acknowledging the limitations of the data, initial analysis would suggest that it may serve as an effective risk mitigation strategy against postoperative pancreatic fistula. Further research in a prospective context utilizing patient risk stratification for fistula development is, however, required to define its role within clinical practice.
A feasibility study using motivational interviewing and a smartphone application to promote physical activity (+Stay-Active) for women with gestational diabetes.
BACKGROUND: Physical activity (PA) interventions have an encouraging role in gestational diabetes mellitus (GDM) management. Digital technologies can potentially be used at scale to support PA. The aim of this study was to assess the feasibility and acceptability of + Stay-Active: a complex intervention which combines motivational interviewing with a smartphone application to promote PA levels in women with GDM. METHODS: This non-randomised feasibility study used a mixed methods approach. Participants were recruited from the GDM antenatal clinic at Oxford University Hospitals. Following baseline assessments (visit 1) including self-reported and device determined PA measurements (wrist worn accelerometer), women participated in an online motivational interview, and then downloaded (visit 2) and used the Stay-Active app (Android or iOS). Women had access to Stay-Active until 36 weeks' gestation, when acceptability and PA levels were reassessed (visit 3). The primary outcome measures were recruitment and retention rates, participant engagement, and acceptability and fidelity of the intervention. Secondary outcome measures included PA levels, app usage, blood glucose and perinatal outcomes. Descriptive statistics were performed for assessments at study visits. Statistics software package Stata 14 and R were used. RESULTS: Over the recruitment period (46 weeks), 114 of 285 women met inclusion criteria and 67 (58%) enrolled in the study. Mean recruitment rate of 1.5 participants/clinic with 2.5 women/clinic meeting inclusion criteria. Fifty-six (83%) received the intervention at visit 2 and 53 (79%) completed the study. Compliance to accelerometer measurement protocols were sufficient in 78% of participants (52/67); wearing the device for more than 10 h on 5 or more days at baseline and 61% (41/67) at 36 weeks. There was high engagement with Stay-Active; 82% (55/67) of participants set goals on Stay-Active. Sustained engagement was evident, participants regularly accessed and logged multiples activities on Stay-Active. The intervention was deemed acceptable; 85% of women rated their care was satisfactory or above, supported by written feedback. CONCLUSIONS: This combined intervention was feasible and accepted. Recruitment rates were lower than expected. However, retention rates remained satisfactory and participant compliance with PA measurements and engagement was a high. Future work will explore the intervention's efficacy to increase PA and impact on clinical outcomes. TRIAL REGISTRATION: The study has received a favourable opinion from South Central-Hampshire B Research Ethics Committee; REC reference: 20/SC/0342. ISRCTN11366562.
The role of flavin mononucleotide (FMN) as a potentially clinically relevant biomarker to predict the quality of kidney grafts during hypothermic (oxygenated) machine perfusion.
Hypothermic machine perfusion (HMP) provides preservation superior to cold storage and may allow for organ assessment prior to transplantation. Since flavin mononucleotide (FMN) in perfusate has been proposed as a biomarker of organ quality during HMP of donor livers, the aim of this study was to validate FMN as a biomarker for organ quality in the context of HMP preserved kidneys. Perfusate samples (n = 422) from the paired randomised controlled COPE-COMPARE-trial, comparing HMP with oxygenation (HMPO2) versus standard HMP in kidneys, were used. Fluorescence intensity (FI) was assessed using fluorescence spectroscopy (excitation 450nm; emission 500-600nm) and validated by fluorospectrophotometer and targeted liquid chromatography mass spectrometry (LC-MS/MS). Fluorescence intensity (FI)(ex450;em500-600) increased over time during machine perfusion in both groups (p<0.0001). This increase was similar for both groups (p = 0.83). No correlation, however, was found between FI(ex450;em500-600) and post-transplant outcomes, including day 5 or 7 serum creatinine (p = 0.11; p = 0.16), immediate graft function (p = 0.91), creatinine clearance and biopsy-proven rejection at one year (p = 0.14; p = 0.59). LC-MS/MS validation experiments of samples detected FMN in only one perfusate sample, whilst the majority of samples with the highest fluorescence (n = 37/38, 97.4%) remained negative. In the context of clinical kidney HMP, fluorescence spectroscopy unfortunately appears to be not specific and probably unsuitable for FMN. This study shows that FMN does not classify as a clinically relevant predictive biomarker of kidney graft function after transplantation.
Doppler ultrasound surveillance of recently formed haemodialysis arteriovenous fistula: the SONAR observational cohort study.
BACKGROUND: Arteriovenous fistulas are considered the best option for haemodialysis provision, but as many as 30% fail to mature or suffer early failure. OBJECTIVE: To assess the feasibility of performing a randomised controlled trial that examines whether, by informing early and effective salvage intervention of fistulas that would otherwise fail, Doppler ultrasound surveillance of developing arteriovenous fistulas improves longer-term arteriovenous fistula patency. DESIGN: A prospective multicentre observational cohort study (the 'SONAR' study). SETTING: Seventeen haemodialysis centres in the UK. PARTICIPANTS: Consenting adults with end-stage renal disease who were scheduled to have an arteriovenous fistula created. INTERVENTION: Participants underwent Doppler ultrasound surveillance of their arteriovenous fistulas at 2, 4, 6 and 10 weeks after creation, with clinical teams blinded to the ultrasound surveillance findings. MAIN OUTCOME MEASURES: Fistula maturation at week 10 defined according to ultrasound surveillance parameters of representative venous diameter and blood flow (wrist arteriovenous fistulas: ≥ 4 mm and > 400 ml/minute; elbow arteriovenous fistulas: ≥ 5 mm and > 500 ml/minute). Mixed multivariable logistic regression modelling of the early ultrasound scan data was used to predict arteriovenous fistula non-maturation by 10 weeks and fistula failure at 6 months. RESULTS: A total of 333 arteriovenous fistulas were created during the study window (47.7% wrist, 52.3% elbow). By 2 weeks, 37 (11.1%) arteriovenous fistulas had failed (thrombosed), but by 10 weeks, 219 of 333 (65.8%) of created arteriovenous fistulas had reached maturity (60.4% wrist, 67.2% elbow). Persistently lower flow rates and venous diameters were observed in those fistulas that did not mature. Models for arteriovenous fistulas' non-maturation could be optimally constructed using the week 4 scan data, with fistula venous diameter and flow rate the most significant variables in explaining wrist fistula maturity failure (positive predictive value 60.6%, 95% confidence interval 43.9% to 77.3%), whereas resistance index and flow rate were most significant for elbow arteriovenous fistulas (positive predictive value 66.7%, 95% confidence interval 48.9% to 84.4%). In contrast to non-maturation, both models predicted fistula maturation much more reliably [negative predictive values of 95.4% (95% confidence interval 91.0% to 99.8%) and 95.6% (95% confidence interval 91.8% to 99.4%) for wrist and elbow, respectively]. Additional follow-up and modelling on a subset (n = 192) of the original SONAR cohort (the SONAR-12M study) revealed the rates of primary, assisted primary and secondary patency arteriovenous fistulas at 6 months were 76.5, 80.7 and 83.3, respectively. Fistula vein size, flow rate and resistance index could identify primary patency failure at 6 months, with similar predictive power as for 10-week arteriovenous fistula maturity failure, but with wide confidence intervals for wrist (positive predictive value 72.7%, 95% confidence interval 46.4% to 99.0%) and elbow (positive predictive value 57.1%, 95% confidence interval 20.5% to 93.8%). These models, moreover, performed poorly at identifying assisted primary and secondary patency failure, likely because a subset of those arteriovenous fistulas identified on ultrasound surveillance as at risk underwent subsequent successful salvage intervention without recourse to early ultrasound data. CONCLUSIONS: Although early ultrasound can predict fistula maturation and longer-term patency very effectively, it was only moderately good at identifying those fistulas likely to remain immature or to fail within 6 months. Allied to the better- than-expected fistula patency rates achieved (that are further improved by successful salvage), we estimate that a randomised controlled trial comparing early ultrasound-guided intervention against standard care would require at least 1300 fistulas and would achieve only minimal patient benefit. TRIAL REGISTRATION: This trial is registered as ISRCTN36033877 and ISRCTN17399438. FUNDING: This award was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme (NIHR award ref: NIHR135572) and is published in full in Health Technology Assessment; Vol. 28, No. 24. See the NIHR Funding and Awards website for further award information.
Comparison of in-gel and in-solution proteolysis in the proteome profiling of organ perfusion solutions.
PURPOSE: The organ perfusion solution (perfusate), collected at clinically and temporally significant stages of the organ preservation and transplantation process, provides a valuable insight into the biological status of an organ over time and prior to reperfusion (transplantation) in the recipient. The objective of this study was to assess two bottom-up proteomics workflows for the extraction of tryptic peptides from the perfusate. EXPERIMENTAL DESIGN: Two different kinds of perfusate samples from kidney and liver trials were profiled using liquid chromatography-mass spectrometry (LC-MS/MS). The preparation of clean peptide mixtures for downstream analysis was performed considering different aspects of sample preparation; protein estimation, enrichment, in-gel and urea-based in-solution digestion. RESULTS: In-solution digestion of perfusate allowed identification of the highest number of peptides and proteins with greater sequence coverage and higher confidence data in kidney and liver perfusate. Key pathways identified by gene ontology analysis included complement, coagulation and antioxidant pathways, and a number of biomarkers previously linked to ischemia-reperfusion injury were also observed in perfusate. CONCLUSIONS: This study showed that in-solution digestion is a more efficient method for LC-MS/MS analysis of kidney and liver organ perfusion solutions. This method is also quicker and easier than in-gel digestion, allowing for greater sample throughput, with fewer opportunities for experimental error or peptide loss.
Patient-derived podocyte spheroids reveal new insights into the etiopathogenesis of Alport syndrome.
Alport syndrome (AS) is a rare disease characterized by defective glomerular basement membranes, caused by mutations in COL4A3, COL4A4, and COL4A5, which synthesize collagen type IV. Patients present with progressive proteinuria, hematuria and podocyte loss. There is currently no cure for Alport syndrome, and this is mainly due to its complex and variable pathogenesis, as well as the lack of models that can faithfully mimic the human phenotype. Here we have developed a novel human culture model of Alport syndrome and used it to study the effects of different mutations on podocyte development and biology. First, we established a differentiation protocol that allowed us to generate podocyte spheroids from patient-derived human induced pluripotent stem cells (hiPSCs). We have then carried out discovery proteomics and demonstrated that a total of 178 proteins were differentially expressed between Alport (AS1 and AS3) and control (LT) podocytes. GO analysis indicated alterations in several metabolic pathways, such as oxidative phosphorylation, RNA maturation, chromatin condensation, and proliferation. Although functional assays showed no changes in lactate production and mitochondrial potential compared to healthy controls, immunofluorescence and electron microscopy analysis showed key morphological changes related to the phenotypical maturation of Alport podocytes. Moreover, the studied mutations led to persistent proliferation, increased reactive oxygen species (ROS) production and the concomitant expression of peroxisome proliferator-activated receptors α and γ (PPARα and PPARγ) in podocytes. These data on patient-derived podocytes provide evidence that collagen mutations, in addition to playing a central role in the defective development of the glomerular filtration barrier, cause significant alterations in podocyte development and metabolism very early in development, even before the formation of the filtering apparatus. In conclusion, our study provides a new methodological platform for the differentiation of podocytes and to study human podocytopathies in a personalized manner, and reveals new insights into the etiopathogenesis and pathobiology of Alport syndrome.