Diagnostic and interventional neuroradiology training in the UK: a national trainee survey

AIM

Training structure in neuroradiology can be variable, nationally and internationally. Globally, there is a trend towards standardised training pathways, curricula and targeted competencies. Currently, there is limited understanding of the structure of neuroradiology training in the UK. This survey aims to: [1] identify different contemporary models of neuroradiology training in the UK, [2] compare UK trainees' commitments against national and international standards, and [3] understand whether career expectations match the predicted future demands of neuroradiologists.

MATERIALS AND METHODS

A survey was developed after consultation with BSNR and UKNG representatives. The eligibility criteria included current neuroradiology trainees in the UK with at least 3 months of experience or had recently completed neuroradiology training, but less than 18 months had elapsed since achieving a certificate of completion of training.

RESULTS

A total of 50 trainees responded to the survey; 26 (52%) diagnostic neuroradiologists (DNRs) and 24 (48%) interventional neuroradiologists (INRs) with an overall mean age of 33 years. The mean duration of training at the time of survey was 18 months. The survey details trainee demographics, experience at work, research and teaching commitments and future goals.

CONCLUSION

Most respondents are satisfied with their training and 90% want to remain in the UK after completion of training. There is room for improvement but the future of training and working in neuroradiology seems promising internationally, with ever-evolving techniques and developments.

ADVANCES IN KNOWLEDGE

Advances in knowledge: This study evaluates neuroradiology training in the UK to enhance the training of future neuroradiologists, and safeguard the future of the speciality.

MLX plays a key role in lipid and glucose metabolism in humans: Evidence from in vitro and in vivo studies

BACKGROUND AND AIM

Enhanced hepatic de novo lipogenesis (DNL) has been proposed as an underlying mechanism for the development of NAFLD and insulin resistance. Max-like protein factor X (MLX) acts as a heterodimer binding partner for glucose sensing transcription factors and inhibition of MLX or downstream targets has been shown to alleviate intrahepatic triglyceride (IHTG) accumulation in mice. However, its effect on insulin sensitivity remains unclear. As human data is lacking, the aim of the present work was to investigate the role of MLX in regulating lipid and glucose metabolism in primary human hepatocytes (PHH) and in healthy participants with and without MLX polymorphisms.

METHODS

PHH were transfected with non-targeting or MLX siRNA to assess the effect of MLX knockdown on lipid and glucose metabolism, insulin signalling and the hepatocellular transcriptome. A targeted association analysis on imputed genotype data for MLX on healthy individuals was undertaken to assess associations between specific MLX SNPs (rs665268, rs632758 and rs1474040), plasma biochemistry, IHTG content, DNL and gluconeogenesis.

RESULTS

MLX knockdown in PHH altered lipid metabolism (decreased DNL (p < 0.05), increased fatty acid oxidation and ketogenesis (p < 0.05), and reduced lipid accumulation (p < 0.001)). Additionally, MLX knockdown increased glycolysis, lactate secretion and glucose production (p < 0.001) and insulin-stimulated pAKT levels (p < 0.01) as assessed by transcriptomic, steady-state and dynamic measurements. Consistent with the in vitro data, individuals with the rs1474040-A and rs632758-C variants had lower fasting plasma insulin (p < 0.05 and p < 0.01, respectively) and TG (p < 0.05 and p < 0.01, respectively). Although there was no difference in IHTG or gluconeogenesis, individuals with rs632758 SNP had notably lower hepatic DNL (p < 0.01).

CONCLUSION

We have demonstrated using human in vitro and in vivo models that MLX inhibition favored lipid catabolism over anabolism and increased glucose production, despite increased glycolysis and phosphorylation of Akt, suggesting a metabolic mechanism that involves futile cycling.

Central androgen action reverses hypothalamic astrogliosis and atherogenic risk factors induced by orchiectomy and high-fat diet feeding in male mice

Hypogonadism in males confers elevated cardiovascular disease (CVD) risk by unknown mechanisms. Recent radiological evidence suggests that low testosterone (T) is associated with mediobasal hypothalamic (MBH) gliosis, a central nervous system (CNS) cellular response linked to metabolic dysfunction. To address mechanisms linking CNS androgen action to CVD risk, we generated a hypogonadal, hyperlipidemic mouse model with orchiectomy (ORX) combined with hepatic PCSK9 overexpression. After 4 wk of high-fat, high-sucrose diet (HFHS) consumption, despite equal body weights and glucose tolerance, androgen-deficient ORX mice had a more atherogenic lipid profile and increased liver and leukocyte inflammatory signaling compared with sham-operated control mice. Along with these early CVD risk indicators, ORX markedly amplified HFHS-induced astrogliosis in the MBH. Transcriptomic analysis further revealed that ORX and high-fat diet feeding induced upregulation of inflammatory pathways and downregulation of metabolic pathways in hypothalamic astrocytes. To interrogate the role of sex steroid signaling in the CNS in cardiometabolic risk and MBH inflammation, central infusion of T and dihydrotestosterone (DHT) was performed on ORX mice. Central DHT prevented MBH astrogliosis and reduced the liver inflammatory signaling and monocytosis induced by HFHS and ORX; T had a partial protective effect. Finally, a cross-sectional study in 41 adult men demonstrated a positive correlation between radiological evidence of MBH gliosis and plasma lipids. These findings demonstrate that T deficiency in combination with a Western-style diet promotes hypothalamic gliosis concomitant with increased atherogenic risk factors and provide supportive evidence for regulation of lipid metabolism and cardiometabolic risk determinants by the CNS action of sex steroids.NEW & NOTEWORTHY This study provides evidence that hypothalamic gliosis is a key early event through which androgen deficiency in combination with a Western-style diet might lead to cardiometabolic dysregulation in males. Furthermore, this work provides the first evidence in humans of a positive association between hypothalamic gliosis and LDL-cholesterol, advancing our knowledge of CNS influences on CVD risk progression.

Hepatocyte mARC1 promotes fatty liver disease

Background & Aims

Non-alcoholic fatty liver disease (NAFLD) has a prevalence of ∼25% worldwide, with significant public health consequences yet few effective treatments. Human genetics can help elucidate novel biology and identify targets for new therapeutics. Genetic variants in mitochondrial amidoxime-reducing component 1 (MTARC1) have been associated with NAFLD and liver-related mortality; however, its pathophysiological role and the cell type(s) mediating these effects remain unclear. We aimed to investigate how MTARC1 exerts its effects on NAFLD by integrating human genetics with in vitro and in vivo studies of mARC1 knockdown.

Methods

Analyses including multi-trait colocalisation and Mendelian randomisation were used to assess the genetic associations of MTARC1. In addition, we established an in vitro long-term primary human hepatocyte model with metabolic readouts and used the Gubra Amylin NASH (GAN)-diet non-alcoholic steatohepatitis mouse model treated with hepatocyte-specific N-acetylgalactosamine (GalNAc)-siRNA to understand the in vivo impacts of MTARC1.

Results

We showed that genetic variants within the MTARC1 locus are associated with liver enzymes, liver fat, plasma lipids, and body composition, and these associations are attributable to the same causal variant (p.A165T, rs2642438 G>A), suggesting a shared mechanism. We demonstrated that increased MTARC1 mRNA had an adverse effect on these traits using Mendelian randomisation, implying therapeutic inhibition of mARC1 could be beneficial. In vitro mARC1 knockdown decreased lipid accumulation and increased triglyceride secretion, and in vivo GalNAc-siRNA-mediated knockdown of mARC1 lowered hepatic but increased plasma triglycerides. We found alterations in pathways regulating lipid metabolism and decreased secretion of 3-hydroxybutyrate upon mARC1 knockdown in vitro and in vivo.

Conclusions

Collectively, our findings from human genetics, and in vitro and in vivo hepatocyte-specific mARC1 knockdown support the potential efficacy of hepatocyte-specific targeting of mARC1 for treatment of NAFLD.

Impact and implications

We report that genetically predicted increases in MTARC1 mRNA associate with poor liver health. Furthermore, knockdown of mARC1 reduces hepatic steatosis in primary human hepatocytes and a murine NASH model. Together, these findings further underscore the therapeutic potential of targeting hepatocyte MTARC1 for NAFLD.

RNA G-quadruplex organizes stress granule assembly through DNAPTP6 in neurons

Consecutive guanine RNA sequences can adopt quadruple-stranded structures, termed RNA G-quadruplexes (rG4s). Although rG4-forming sequences are abundant in transcriptomes, the physiological roles of rG4s in the central nervous system remain poorly understood. In the present study, proteomics analysis of the mouse forebrain identified DNAPTP6 as an RNA binding protein with high affinity and selectivity for rG4s. We found that DNAPTP6 coordinates the assembly of stress granules (SGs), cellular phase-separated compartments, in an rG4-dependent manner. In neurons, the knockdown of DNAPTP6 diminishes the SG formation under oxidative stress, leading to synaptic dysfunction and neuronal cell death. rG4s recruit their mRNAs into SGs through DNAPTP6, promoting RNA self-assembly and DNAPTP6 phase separation. Together, we propose that the rG4-dependent phase separation of DNAPTP6 plays a critical role in neuronal function through SG assembly.

Decitabine increases neoantigen and cancer testis antigen expression to enhance T-cell-mediated toxicity against glioblastoma

BACKGROUND

Glioblastoma (GBM) is the most common and malignant primary brain tumor in adults. Despite maximal treatment, median survival remains dismal at 14-24 months. Immunotherapies, such as checkpoint inhibition, have revolutionized management of some cancers but have little benefit for GBM patients. This is, in part, due to the low mutational and neoantigen burden in this immunogenically "cold" tumor.

METHODS

U87MG and patient-derived cell lines were treated with 5-aza-2'-deoxycytidine (DAC) and underwent whole-exome and transcriptome sequencing. Cell lines were then subjected to cellular assays with neoantigen and cancer testis antigen (CTA) specific T cells.

RESULTS

We demonstrate that DAC increases neoantigen and CTA mRNA expression through DNA hypomethylation. This results in increased neoantigen presentation by MHC class I in tumor cells, leading to increased neoantigen- and CTA-specific T-cell activation and killing of DAC-treated cancer cells. In addition, we show that patients have endogenous cancer-specific T cells in both tumor and blood, which show increased tumor-specific activation in the presence of DAC-treated cells.

CONCLUSIONS

Our work shows that DAC increases GBM immunogenicity and consequent susceptibility to T-cell responses in vitro. Our results support a potential use of DAC as a sensitizing agent for immunotherapy.

NMDA Receptor Antagonists Increase the Release of GLP-1 From Gut Endocrine Cells

Type 2 diabetes mellitus (T2DM) remains one of the most pressing health issues facing modern society. Several antidiabetic drugs are currently in clinical use to treat hyperglycaemia, but there is a need for new treatments that effectively restore pancreatic islet function in patients. Recent studies reported that both murine and human pancreatic islets exhibit enhanced insulin release and β-cell viability in response to N-methyl-D-aspartate (NMDA) receptor antagonists. Furthermore, oral administration of dextromethorphan, an over-the-counter NMDA receptor antagonist, to diabetic patients in a small clinical trial showed improved glucose tolerance and increased insulin release. However, the effects of NMDA receptor antagonists on the secretion of the incretin hormone GLP-1 was not tested, and nothing is known regarding how NMDA receptor antagonists may alter the secretion of gut hormones. This study demonstrates for the first time that, similar to β-cells, the NMDA receptor antagonist MK-801 increases the release of GLP-1 from a murine L-cell enteroendocrine model cell line, GLUTag cells. Furthermore, we report the 3′ mRNA expression profiling of GLUTag cells, with a specific focus on glutamate-activated receptors. We conclude that if NMDA receptor antagonists are to be pursued as an alternative, orally administered treatment for T2DM, it is essential that the effects of these drugs on the release of gut hormones, and specifically the incretin hormones, are fully investigated.

Endonuclease enrichment TAPS for cost-effective genome-wide base-resolution DNA methylation detection

Whole genome base-resolution methylome sequencing allows for the most comprehensive analysis of DNA methylation, however, the considerable sequencing cost often limits its applications. While reduced representation sequencing can be an affordable alternative, over 80% of CpGs in the genome are not covered. Building on our recently developed TET-assisted pyridine borane sequencing (TAPS) method, we here described endonuclease enrichment TAPS (eeTAPS), which utilizes dihydrouracil (DHU)-cleaving endonuclease digestion of TAPS-converted DNA to enrich methylated CpG sites (mCpGs). eeTAPS can accurately detect 87% of mCpGs in the mouse genome with a sequencing depth equivalent to 4× whole genome sequencing. In comparison, reduced representation TAPS (rrTAPS) detected less than 4% of mCpGs with 2.5× sequencing depth. Our results demonstrate eeTAPS to be a new strategy for cost-effective genome-wide methylation analysis at single-CpG resolution that can fill the gap between whole-genome and reduced representation sequencing.

Half-Integer Quantized Topological Response in Quasiperiodically Driven Quantum Systems

A spin strongly driven by two harmonic incommensurate drives can pump energy from one drive to the other at a quantized average rate, in close analogy with the quantum Hall effect. The pumping rate is a nonzero integer in the topological regime, while the trivial regime does not pump. The dynamical transition between the regimes is sharp in the zero-frequency limit and is characterized by a Dirac point in a synthetic band structure. We show that the pumping rate is half-integer quantized at the transition and present universal Kibble-Zurek scaling functions for energy transfer processes. Our results adapt ideas from quantum phase transitions, quantum information, and topological band theory to nonequilibrium dynamics, and identify qubit experiments to observe the universal linear and nonlinear response of a Dirac point in synthetic dimensions.

Universal Entanglement of Typical States in Constrained Systems

Constraints play an important role in the entanglement dynamics of many quantum systems. We develop a diagrammatic formalism to exactly evaluate the entanglement spectrum of random pure states in large constrained Hilbert spaces. The resulting spectra may be classified into universal "phases" depending on their singularities. The simplest class of local constraints reveals a nontrivial phase diagram with a Marchenko-Pastur phase which terminates in a critical point with new singularities. We propose a certain quantum defect chain as a microscopic realization of the critical point. The much studied Rydberg-blockaded or Fibonacci chain lies in the Marchenko-Pastur phase with a modified Page correction to the entanglement entropy. Our results predict the entanglement of infinite temperature eigenstates in thermalizing constrained Floquet spin chains, as we confirm numerically.

P113 Efficacy, safety and long-term durability of endovascular treatment of MCA aneuryms: a review of 161 treated aneurysms

Objectives

The aim of this study was to assess the long-term outcomes of endovascular treatment of MCA aneurysms and identify factors associated with recurrence.

Subjects

161 aneurysms in 147 patients treated between January 2008 and August 2011.

Methods

A retrospective case note review was performed. Aneurysm occlusion was assessed using the Raymond-Roy classification. Clinical outcome was graded using the mRS.

Results

The minimum period of follow up was 65 months, with a maximum follow up period of 120 months. 49% of aneurysms were ruptured at the time of treatment. Morbidity was observed in 15% of the unruptured aneurysms (6% permanent neurological deficit), and in 33% of ruptured aneurysms (15% permanent neurological deficit). 84% of aneurysms were fully occluded following first treatment. Of these, 34% demonstrated angiographic recurrence and 10% required re-intervention. 25% of aneurysms≤7 mm in maximal diameter demonstrated angiographic recurrence, as compared with 50% of aneurysms>7 mm. Aneurysm size >7 mm was associated with a significantly shorter time to recurrence (log rank=9.655, p=0.002).

Conclusions

This is a large series of MCA aneurysms with a long period of follow up. Our results demonstrate that endovascular treatment of MCA aneurysms is associated with a low morbidity and mortality. Given the increasing use of adjunctive devices (stents, web devices) full occlusion of ruptured aneurysms in the acute phase is not necessary, and deliberate staged treatment a reasonable strategy.

Quasiperiodic Quantum Ising Transitions in 1D

Unlike random potentials, quasiperiodic modulation can induce localization-delocalization transitions in one dimension. In this Letter, we analyze the implications of this for symmetry breaking in the quasiperiodically modulated quantum Ising chain. Although weak modulation is irrelevant, strong modulation induces new ferromagnetic and paramagnetic phases which are fully localized and gapless. The quasiperiodic potential and localized excitations lead to quantum criticality that is intermediate to that of the clean and randomly disordered models with exponents of ν=1^{+} (exact) and z≈1.9, Δ_{σ}≈0.16, and Δ_{γ}≈0.63 (up to logarithmic corrections). Technically, the clean Ising transition is destabilized by logarithmic wandering of the local reduced couplings. We conjecture that the wandering coefficient w controls the universality class of the quasiperiodic transition and show its stability to smooth perturbations that preserve the quasiperiodic structure of the model.

Thermal inclusions: how one spin can destroy a many-body localized phase

Many-body localized (MBL) systems lie outside the framework of statistical mechanics, as they fail to equilibrate under their own quantum dynamics. Even basic features of MBL systems, such as their stability to thermal inclusions and the nature of the dynamical transition to thermalizing behaviour, remain poorly understood. We study a simple central spin model to address these questions: a two-level system interacting with strength J with N≫1 localized bits subject to random fields. On increasing J, the system transitions from an MBL to a delocalized phase on the vanishing scale Jc(N)∼1/N, up to logarithmic corrections. In the transition region, the single-site eigenstate entanglement entropies exhibit bimodal distributions, so that localized bits are either 'on' (strongly entangled) or 'off' (weakly entangled) in eigenstates. The clusters of 'on' bits vary significantly between eigenstates of the same sample, which provides evidence for a heterogeneous discontinuous transition out of the localized phase in single-site observables. We obtain these results by perturbative mapping to bond percolation on the hypercube at small J and by numerical exact diagonalization of the full many-body system. Our results support the arguments that the MBL phase is unstable in systems with short-range interactions and quenched randomness in dimensions d that are high but finite.This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'.

Clinical characteristics, treatment and 2-year outcomes in Malaysian and Bruneian patients with stable coronary artery within the worldwide CLARIFY registry

INTRODUCTION

The on-going, international, prospective, observational, longitudinal CLARIFY registry is investigating the demographics, clinical profiles, management and outcomes of patients with stable coronary artery disease (CAD). This paper assesses baseline characteristics, treatment, and clinical outcomes at two years' follow-up of Malaysian/Bruneian patients compared with the overall registry population.

METHOD

Between November 2009 and July 2010, outpatients from 45 countries who met the criteria for stable CAD were recruited into the registry. Baseline characteristics were documented at enrolment, and patients were reassessed during their annual visits over a five-year follow-up period. Key outcomes measured were sudden death and cardiovascular (CV) death, non-CV death and CV morbidity.

RESULTS

At baseline, 33,283 patients were available for analysis within the registry; 380 and 27 were Malaysians and Bruneians, respectively. The mean ages of Malaysian/Bruneian patients and the rest of the world (RoW) were 57.83 ±9.98 years and 64.23 ± 10.46 years, respectively (p<0.001). The median body mass index values were 26.6 (24.4-29.6) kg/m² and 27.3 (24.8-30.3) kg/m², respectively (p=0.014). Malaysian/Bruneian patients had lower rates of myocardial infarction (54.55% versus 59.76%, p=0.033) and higher rates of diabetes (43.24% versus 28.99%, p<0.001) and dyslipidaemia (90.42% versus 74.66%, p<0.001) compared with the RoW. Measured clinical outcomes in Malaysian and Bruneian patients at 2-years follow-up were low and generally comparable to the RoW.

CONCLUSION

Malaysian/Bruneian patients with stable CAD tend to be younger with poorer diabetic control compared with the RoW. However, they had similar outcomes as the main registry following two years of treatment.

Acute Retropharyngeal Abscess Masquerading as Meningitis

Retropharyngeal abscess is a potentially serious deep neck space infection occurring more frequently in children than in adults. The clinical picture of RPA is highly variable with paucity of physical findings. Prompt diagnosis of RPA especially in infants is mandatory to prevent potential fatal complications including airway obstruction. The diagnosis of RPA should be based on high index of clinical suspicion with supportive imaging studies like lateral X-ray of neck and CT. We present a case of acute retropharyngeal abscess which was initially misdiagnosed as meningitis and led to airway obstruction. This case is reported to create awareness among emergency physicians, paediatricians and otolaryngologists to have high index of suspicion in diagnosing RPA especially in infants.

Continued Sex-Differences in the Rate and Severity of Knee Injuries among Collegiate Soccer Players: The NCAA Injury Surveillance System, 2004-2009

We extend previous analyses and examined sex-differences in the rate and severity of knee injuries among collegiate soccer players between 2004 and 2009. Data from the National Collegiate Athletic Association Injury Surveillance System (NCAA ISS) were used to calculate injury incidence density (ID) per 1 000 athletic exposures (AE). Multivariable regression modeling then tested the relation between sex and knee injury incidence and severity among all injured soccer players, while controlling for contact, setting, and division level, as well as for the interactions among these variables. The rate of knee injuries was 1.19 per 1 000 AEs in women and 0.91 per 1 000 AEs in men (RR=1.31, 95% Wald CI=[1.16, 1.47]). In the multivariable modeling, women continued to experience significantly higher odds of knee injury compared with men (aOR=1.44, 95% CI=[1.27,1.63]). Also, the adjusted odds of a knee injury that resulted in surgery remained higher in women compared with men (aOR=1.61 (1.00, 2.58), as well as the amount of time lost from participation (beta=0.129; p=0.05). Given the prominence of soccer play in the United States, continued efforts to evaluate and improve knee injury prevention practices and policies may be especially important for female players.

Radiation Dose Reduction in 4D Cerebral CT Angiography by Individualized Estimation of Cerebral Circulation Time

BACKGROUND AND PURPOSE

The novel technique of 4D CTA for dynamic assessment of the intracranial vessels has a greater radiation burden than conventional CTA. Previous descriptions of the technique used a fixed-duration exposure protocol. This study examines the potential for dose reduction by individualizing exposure time to patient physiology by the use of time-enhancement curve techniques as previously applied in CT angiography and venography.

MATERIALS AND METHODS

4D-CTA examinations performed at our institution were retrospectively reviewed. Scan protocols used a test-bolus scan with either a subjective estimate of the main acquisition timing (estimated-duration method) or a quantitative measure (measured-duration method). The estimated-duration method used peak arterial enhancement to determine the start of exposure, with the duration chosen at the radiologist's discretion. The measured-duration method used arterial and venous time-enhancement curves to determine exposure start and duration. Exposure duration, study adequacy, quality score, and maximum venous enhancement were compared among groups.

RESULTS

One hundred fifty-one examinations used the estimated-duration method, and 53 used measured-duration. The measured-duration method used a shorter exposure time (10 versus 15.8 seconds; P < .001). There was no statistically significant difference in the study adequacy rate, subjective quality score, or maximum venous enhancement. The radiation dose was reduced by 51% in the measured-duration method (3021 mGy × cm, 6.9 mSv, versus 1473 mGy × cm, 3.4 mSv). Both methods showed good agreement with DSA (κ = 0.88 for estimated-duration, κ = 1.0 for measured duration).

CONCLUSIONS

Exposure time in 4D-CTA can be reduced with dual time-enhancement curves to match exposure to physiology without degrading study adequacy or quality.

Sequence-specific DNA binding by long hairpin pyrrole-imidazole polyamides containing an 8-amino-3,6-dioxaoctanoic acid unit

With the aim of improving aqueous solubility, we designed and synthesized five N-methylpyrrole (Py)-N-methylimidazole (Im) polyamides capable of recognizing 9-bp sequences. Their DNA-binding affinities and sequence specificities were evaluated by SPR and Bind-n-Seq analyses. The design of polyamide 1 was based on a conventional model, with three consecutive Py or Im rings separated by a β-alanine to match the curvature and twist of long DNA helices. Polyamides 2 and 3 contained an 8-amino-3,6-dioxaoctanoic acid (AO) unit, which has previously only been used as a linker within linear Py-Im polyamides or between Py-Im hairpin motifs for tandem hairpin. It is demonstrated herein that AO also functions as a linker element that can extend to 2-bp in hairpin motifs. Notably, although the AO-containing unit can fail to bind the expected sequence, polyamide 4, which has two AO units facing each other in a hairpin form, successfully showed the expected motif and a KD value of 16nM was recorded. Polyamide 5, containing a β-alanine-β-alanine unit instead of the AO of polyamide 2, was synthesized for comparison. The aqueous solubilities and nuclear localization of three of the polyamides were also examined. The results suggest the possibility of applying the AO unit in the core of Py-Im polyamide compounds.

Deciphering the genomic targets of alkylating polyamide conjugates using high-throughput sequencing

Chemically engineered small molecules targeting specific genomic sequences play an important role in drug development research. Pyrrole-imidazole polyamides (PIPs) are a group of molecules that can bind to the DNA minor-groove and can be engineered to target specific sequences. Their biological effects rely primarily on their selective DNA binding. However, the binding mechanism of PIPs at the chromatinized genome level is poorly understood. Herein, we report a method using high-throughput sequencing to identify the DNA-alkylating sites of PIP-indole-seco-CBI conjugates. High-throughput sequencing analysis of conjugate 2: showed highly similar DNA-alkylating sites on synthetic oligos (histone-free DNA) and on human genomes (chromatinized DNA context). To our knowledge, this is the first report identifying alkylation sites across genomic DNA by alkylating PIP conjugates using high-throughput sequencing.

Identification of Sequence Specificity of 5-Methylcytosine Oxidation by Tet1 Protein with High-Throughput Sequencing

Tet (ten-eleven translocation) family proteins have the ability to oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC). However, the oxidation reaction of Tet is not understood completely. Evaluation of genomic-level epigenetic changes by Tet protein requires unbiased identification of the highly selective oxidation sites. In this study, we used high-throughput sequencing to investigate the sequence specificity of mC oxidation by Tet1. A 6.6×10(4) -member mC-containing random DNA-sequence library was constructed. The library was subjected to Tet-reactive pulldown followed by high-throughput sequencing. Analysis of the obtained sequence data identified the Tet1-reactive sequences. We identified mCpG as a highly reactive sequence of Tet1 protein.

Investigation on the temporal variation and source tracking of faecal bacteria in a forest dominated watershed (Comox Lake), British Columbia, Canada

AIMS

The aims of this study were to investigate the temporal variation in Escherichia coli density and its sources at the drinking water intake of Comox Lake for a period of 3 years (2011-2013).

METHODS AND RESULTS

Density of E. coli was assessed by standard membrane filtration method. Source tracking of E. coli were done by using BOX-A1R-based rep-PCR DNA fingerprinting method. Over the years, the mean E. coli density ranged from nondetectable to 9·8 CFU 100 ml(-1) . The density of E. coli in each of the years did not show any significant difference (P > 0·05); however, a comparatively higher density was observed during the fall. Wildlife was (64·28%, 153/238) identified as the major contributing source of E. coli, followed by human (18·06%, 43/238) and unknown sources (17·64%, 42/238). Although the sources were varied by year and season, over all, the predominant contributing sources were black bear, human, unknown, elk, horse and gull.

CONCLUSIONS

The findings of this investigation identified the multiple animal sources contributing faecal bacteria into the drinking water intake of Comox Lake and their varying temporal occurrence.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results of this study can reliably inform the authorities about the most vulnerable period (season) of faecal bacterial loading and their potential sources in the lake for improving risk assessment and pollution mitigation.

A Synthetic DNA-Binding Domain Guides Distinct Chromatin-Modifying Small Molecules to Activate an Identical Gene Network

Synthetic dual-function ligands targeting specific DNA sequences and histone-modifying enzymes were applied to achieve regulatory control over multi-gene networks in living cells. Unlike the broad array of targeting small molecules for histone deacetylases (HDACs), few modulators are known for histone acetyltransferases (HATs), which play a central role in transcriptional control. As a novel chemical approach to induce selective HAT-regulated genes, we conjugated a DNA-binding domain (DBD) "I" to N-(4-chloro-3-trifluoromethyl-phenyl)-2-ethoxy-benzamide (CTB), an artificial HAT activator. In vitro enzyme activity assays and microarray studies were used to demonstrate that distinct functional small molecules could be transformed to have identical bioactivity when conjugated with a targeting DBD. This proof-of-concept synthetic strategy validates the switchable functions of HDACs and HATs in gene regulation and provides a molecular basis for developing versatile bioactive ligands.

Glucocorticoid usage in giant cell arteritis over six decades (1950 to 2009)

OBJECTIVES

To evaluate the trends in glucocorticoid (GC) therapy in patients with giant cell arteritis (GCA).

METHODS

Using a population-based inception cohort, GC therapy details were collected for all patients with GCA diagnosed between 1950-2009. GC usage for patients diagnosed with GCA between 1980-2009 was compared to those diagnosed between 1950-1979.

RESULTS

The mean starting dose was similar in both time-periods but the mean cumulative dosages at different time points were significantly higher for patients diagnosed between 1980-2009 than in 1950-1979 (at 1-year: 6.3 vs. 4.1g; and at 5 years 10.7 vs. 7.6g, respectively, p<0.001). The median time to permanent discontinuation of GC was 2.6 years for 1980-2009 vs. 1.5 years for 1950-1979 (p=0.004). The risk for GC-associated adverse events was similar in both time periods (p=0.52).

CONCLUSIONS

GCA patients diagnosed in the last three decades were treated with higher cumulative GC doses and were less likely to achieve GC discontinuation. However, their risks for GC-related complications were not significantly higher than their earlier counterparts.

Targeted suppression of EVI1 oncogene expression by sequence-specific pyrrole-imidazole polyamide

Human ectopic viral integration site 1 (EVI1) is an oncogenic transcription factor known to play a critical role in many aggressive forms of cancer. Its selective modulation is thought to alter the cancer-specific gene regulatory networks. Pyrrole-imidazole polyamides (PIPs) are a class of small DNA binders that can be designed to target any destined DNA sequence. Herein, we report a sequence-specific pyrrole-imidazole polyamide, PIP1, which can target specific base pairs of the REL/ELK1 binding site in the EVI1 minimal promoter. The designed PIP1 significantly inhibited EVI1 in MDA-MB-231 cells. Whole-transcriptome analysis confirmed that PIP1 affected a fraction of EVI1-mediated gene regulation. In vitro assays suggested that this polyamide can also effectively inhibit breast cancer cell migration. Taken together, these results suggest that EVI1-targeted PIP1 is an effective transcriptional regulator in cancer cells.