Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA

Circulating tumour DNA (ctDNA) can be used to detect and profile residual tumour cells persisting after curative intent therapy1. The study of large patient cohorts incorporating longitudinal plasma sampling and extended follow-up is required to determine the role of ctDNA as a phylogenetic biomarker of relapse in early-stage non-small-cell lung cancer (NSCLC). Here we developed ctDNA methods tracking a median of 200 mutations identified in resected NSCLC tissue across 1,069 plasma samples collected from 197 patients enrolled in the TRACERx study2. A lack of preoperative ctDNA detection distinguished biologically indolent lung adenocarcinoma with good clinical outcome. Postoperative plasma analyses were interpreted within the context of standard-of-care radiological surveillance and administration of cytotoxic adjuvant therapy. Landmark analyses of plasma samples collected within 120 days after surgery revealed ctDNA detection in 25% of patients, including 49% of all patients who experienced clinical relapse; 3 to 6 monthly ctDNA surveillance identified impending disease relapse in an additional 20% of landmark-negative patients. We developed a bioinformatic tool (ECLIPSE) for non-invasive tracking of subclonal architecture at low ctDNA levels. ECLIPSE identified patients with polyclonal metastatic dissemination, which was associated with a poor clinical outcome. By measuring subclone cancer cell fractions in preoperative plasma, we found that subclones seeding future metastases were significantly more expanded compared with non-metastatic subclones. Our findings will support (neo)adjuvant trial advances and provide insights into the process of metastatic dissemination using low-ctDNA-level liquid biopsy.

The impact of apraxia and neglect on early rehabilitation outcome after stroke

Background

This study aims to characterize the impact of apraxia and visuospatial neglect on stroke patients’ cognitive and functional outcomes during early rehabilitation. Prior work implies an unfavorable effect of visuospatial neglect on rehabilitation; however, previous findings remain ambiguous and primarily considered long-term effects. Even less is known about the impact of apraxia on rehabilitation outcomes. Although clinicians agree on the significance of the first few weeks after stroke for the course of rehabilitation, studies exploring the impact of neglect and apraxia in this early rehabilitation period remain scarce.

Methods

Based on a screening of 515 hospitalized stroke patients from an early rehabilitation ward, 150 stroke patients (75 left-hemispheric strokes, 75 right hemispheric strokes) fulfilled the inclusion criteria and were enrolled in this observational, longitudinal study. The patients’ cognitive and functional statuses were documented at admission to the early rehabilitation ward and discharge. Also, detailed apraxia and neglect assessments were performed at midterm. The predictive values of age and apraxia and neglect severity (as reflected in two components from a principal component analysis of the neglect and apraxia assessments) for cognitive and functional outcomes at discharge were evaluated by multiple regression analyses.

Results

Besides the expected influence of the respective variables at admission, we observed a significant effect of apraxia severity on the cognitive outcome at discharge. Moreover, neglect severity predicted the Early Rehabilitation Barthel Index (Frühreha-Barthel-Index) at discharge. Supplementary moderator analysis revealed a differential effect of neglect severity on the cognitive outcome depending on the affected hemisphere.

Conclusion

Data indicate a strong association between apraxia and visuospatial neglect and early rehabilitation outcomes after stroke.

Abstract 2144: Holistic sampling of clonal dynamics using cfDNA in lung TRACERx

Background: Minimal residual disease (MRD) detection using liquid biopsy has the potential to improve patient outcomes in non-small cell lung cancer (NSCLC). Liquid biopsy may also provide representative clonal sampling through the disease course, but current clonal deconvolution methods are ineffective in plasma samples with <1% tumor content, common in the localised or MRD setting.

Methods: We analysed 1071 plasma samples from 198 TNM I-III NSCLC patients in TRACERx who underwent multiregion exome sequencing of primary tumor and relapse tissue, with 416 standard of care surveillance scans. Seventy-four patients suffered a relapse. We targeted a median of 200 tumor-specific mutations per patient consisting of clonal and subclonal variants and sequenced cell-free DNA (cfDNA) using anchored multiplex PCR to a median unique depth of 2230X with 5 supporting duplicates. We used library-specific trinucleotide background models to call MRD. We developed ECLIPSE (Extraction of CLonality from LIquid bioPSiEs), to perform formal clonal deconvolution in <1% purity plasma samples by leveraging copy number and mutation clone identities from tumor tissue.

Results: Median MRD lead time was 119 days (range 0-1137) in patients with pre-operative circulating tumor DNA (ctDNA) detection. In the 13% of relapse patients lacking pre-operative ctDNA detection the median MRD lead time was 0 days (range 0-589). MRD lead times positively correlated with clonal ctDNA fraction doubling times (DTs). Cancer cell fractions (CCFs) of subclones estimated in plasma with ECLIPSE and tissue collected concurrently were proportional (P < 0.001, R2 = 0.6). Subclonal mutations that would appear clonal in single biopsies could be separated from true clonal mutations using their CCF in plasma (P < 0.001, OR = 0.44), distinguishing clonal from subclonal mutations, where the latter are unlikely to represent effective therapeutic targets. Where cfDNA and tissue was available at relapse we detected 28/29 metastatic tissue subclones in cfDNA with an additional 8 cfDNA-unique subclones. These subclones were more frequently estimated as present in only a subset of metastatic cells using cfDNA (P = 0.008, OR = 5.5) consistent with localisation to unsampled metastatic sites. Metastatic competent subclones had higher CCFs in pre-operative plasma (P < 0.001, OR = 4.5). Shifts in clonal dynamics were concurrent with treatment. Finally, patients with cfDNA-detected polyphyletic metastatic seeding had shorter disease-free survival than those with monophyletic seeding (HR = 2.89, 95% CIs 1.46-5.73).

Conclusions: Tumor-informed anchored multiplex PCR most commonly detected MRD before clinical relapse and allowed determination of clonal ctDNA DT. Using ECLIPSE, plasma samples of <1% purity allow formal measurements of clonal dynamics from diagnosis to relapse, which impacts patient outcome and has the potential to guide personalised medicine.

Citation Format: Alexander Mark Frankell, Christopher Abbosh, Aaron Garnett, Judit Kisistok, Thomas Harrison, Morgan Weichert, Abel Licon, Selvaraju Veeriah, Bob Daber, Mike Moreau, Aamir Shahpurwalla, Aaron Odell, Adrian Chesh, Kevin Litchfield, Emilia Lim, Daniel E. Cook, Clare Puttick, Maise Al-Bakir, Fabio Gomes, Akshay Patel, Lizi Manzano, Paula Roberts, Ariana Huebner, Nicolas Carey, Joan Riley, Todd Druley, Jacqui A. Shaw, Nicholas McGranahan, Mariam Jamal-Hanjani, Josh Stahl, Nicolai Birkbak, the Lung TRACERx consortium, Charles Swanton. Holistic sampling of clonal dynamics using cfDNA in lung TRACERx [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2144.

Abstract CT023: Phylogenetic tracking and minimal residual disease detection using ctDNA in early-stage NSCLC: A lung TRACERx study

Introduction Minimal residual disease (MRD) detection in solid tumors describes isolation of circulating tumor DNA (ctDNA) molecules in plasma following definitive treatment of a cancer. Detection of MRD following surgical tumor excision categorizes patients as high risk for disease recurrence. Establishing an MRD approach to treating early-stage NSCLC will facilitate escalation of standard of care (SoC) treatment only in patients destined to relapse from their cancer and overcome challenges associated with conventional adjuvant drug-trial design. Here, we present data from the lung TRACERx study where patients with early-stage NSCLC underwent phylogenetic ctDNA profiling following resection. Methods Patient specific anchored-multiplex PCR (AMP) enrichment panels were generated for 78 lung TRACERx patients who underwent surgery for stage I-III NSCLC; 608 plasma samples were analyzed. Extensive patient-specific cfDNA enrichment panels targeted a median of 196 (range 72 to 482) clonal and subclonal variants detected in primary tumor tissue by multi-region exome sequencing. A novel MRD-caller controlled and estimated background sequencing error to maximize ctDNA detection at low mutant allele frequencies (MAFs). Analytical validation experiments benchmarked assay performance. Results Analytical validation of a 50-variant AMP-MRD assay demonstrated a sensitivity of 89% for mutant DNA at a MAF of 0.008% (with 25ng of DNA input into the assay), specificity was 100% experimentally and 99.9% (95% CI: 99.67 to 99.99%) modelled in-silico. 45 patients suffered relapse of their primary NSCLC; ctDNA was detected at or before clinical relapse in 37 of 45 patients. In these 37 patients the median ctDNA lead-time (time from ctDNA detection to clinical relapse) was 151 days (range 0 to 984 days) and the median time to relapse from surgery was 413 days (range 41 to 1242 days). In 10 of 10 patients who developed second primary cancers during follow-up no ctDNA was detected, reflecting specificity of the MRD assay toward the primary tumor. In 23 patients who remained relapse-free during a median of 1184 days of study follow-up, ctDNA was detected in 1 of 199 time-points analyzed. Analysis of SoC adjuvant surveillance imaging (CT, PET-CT or MRI, 220 encounters) revealed examples of MRD positive patients where SoC radiological surveillance was negative for impending relapse. Through application of large cfDNA enrichment panels targeting up to 483 variants per patient we observed dynamic changes in clonal composition and copy-number status prior to NSCLC relapse, categorized relapse as monoclonal or polyclonal and identified distinct subclonal dynamics during systemic intervention for disease recurrence. Conclusions ctDNA is an adjuvant biomarker capable of both detecting MRD following surgery and defining the clonality of relapsing disease. These data pave the way for clinical trials predicated on escalation of adjuvant standard of care in NSCLC patients who exhibit MRD positive status following surgery.

Citation Format: Chris Abbosh, Alexander Frankell, Aaron Garnett, Thomas Harrison, Morgan Weichert, Abel Licon, Selvaraju Veeriah, Bob Daber, Mike Moreau, Adrian Chesh, Kevin Litchfield, Emilia Lim, Daniel Cooke, Clare Puttick, Maise Al Bakir, Fabio Gomes, Akshay Patel, Lizi Manzano, Ariana Huebner, Nicolas Carey, Joan Riley, Paula Roberts, Todd Druley, Jacqui A. Shaw, Nicholas McGranahan, Mariam Jamal-Hanjani, Nicolai Birkbak, Josh Stahl, Charles Swanton, Lung TRACERx consortium. Phylogenetic tracking and minimal residual disease detection using ctDNA in early-stage NSCLC: A lung TRACERx study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT023.

Extended Magnetic Dome Induced by Low Pressures in Superconducting FeSe_{1-x}S_{x}

We report muon spin rotation and magnetization measurements under pressure on Fe_{1+δ}Se_{1-x}S_{x} with x≈0.11. Above p≈0.6  GPa we find a microscopic coexistence of superconductivity with an extended dome of long range magnetic order that spans a pressure range between previously reported separated magnetic phases. The magnetism initially competes on an atomic scale with the coexisting superconductivity leading to a local maximum and minimum of the superconducting T_{c}(p). The maximum of T_{c} corresponds to the onset of magnetism while the minimum coincides with the pressure of strongest competition. A shift of the maximum of T_{c}(p) for a series of single crystals with x up to 0.14 roughly extrapolates to a putative magnetic and superconducting state at ambient pressure for x≥0.2.

Systematic dimensional reduction of the layered β-FeSe structure by solvothermal synthesis

Dimensional reduction of superconducting anti PbO-type iron selenide has been achieved by terminating the tetragonal square layers of FeSe_4/4 tetrahedra by ethylenediamine (en) ligands. We obtained three new structures in the Fe-Se-en system. Fe₃Se₄(en)₃ contains FeSe₂ single chains bridged via Fe(en)₃ complexes. Fe₁₀Se₁₂(en)₇ has Fe₂Se₃ double strands separated by Fe(en)₃ complexes and free en molecules. Fe_0.85Se(en)_0.3 conserves the tetragonal layers of bulk FeSe which are now widely separated by en molecules. Through systematic dilution of the solvent we were able to introduce an additional parameter in solvothermal synthesis and thus have control over the connectivity of the tetrahedra. Additionally, a phase diagram of the Fe-Se-en system is generated by variation of the reaction temperature. The magnetic properties of the FeSe derivatives range from superconductivity and antiferromagnetism to paramagnetism.

Abstract 762: A concordance study of the ArcherDX RevealTM ctDNA 28 NGS panel and Biocept’s Target SelectorTM mutation assay using ctDNA collected in Biocept CEE-sureTM blood collection tubes

Biocept’s Target Selector technology is a targeted hotspot mutation panel designed to enrich for mutant targets in a large excess of WT DNA. The test is specific to small regions of interest, is highly sensitive, validated down to 7 mutant copies in a background of 14,000 WT at >98% sensitivity. The ArcherDX Reveal ctDNA test is a 28 gene NGS panel that targets key oncogene activating mutations, drug resistance mutations, in addition to full coverage of TP53. The Reveal ctDNA assay utilizes Anchored Multiplex PCR to enrich, tag, and efficiently capture short ctDNA fragments. Both technologies are designed specifically for use with plasma associated ctDNA. We undertook to evaluate the feasibility of using the ArcherDX Reveal ctDNA 28 NGS panel with the DNA extracted from plasma collected with Biocept’s patented blood collection tube which has been validated at room temperature for 4 days for circulating tumor cells and 8 days for ctDNA. The ability to build complex, targeted libraries, free of chemically induced mutations is of major importance for the detection of the vanishingly rare mutations that can be present in the plasma of cancer patients. We found that high quality NGS libraries were produced from plasma collected and stored in the Biocept blood tube, indicating that little damage occurred to the DNA during preservation. In addition, the two methods were found to be highly concordant and complementary when using both mutation positive and negative patient samples. The Target-Selector assay was the more sensitive, however, the ArcherDX panel revealed several additional mutations not targeted by the Biocept Target Selector assay.

Citation Format: Jason C. Poole, Brian Kudlow, Jill Stefanelli, Skyler Mishkin, Anh Pham, Jeff Chen, Veena M. Singh, Josh Stahl, Lyle J. Arnold. A concordance study of the ArcherDX RevealTM ctDNA 28 NGS panel and Biocept’s Target SelectorTM mutation assay using ctDNA collected in Biocept CEE-sureTM blood collection tubes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 762. doi:10.1158/1538-7445.AM2017-762

Efficacy and safety of cold snare resection in preventive screening colonoscopy

BACKGROUND AND AIM

 Removal of polyps during colonoscopy effectively prevents the development of colorectal cancer. So far, snare resection with high frequency current with or without prior submucosal saline injection is the method of choice. The aim of this study was to evaluate the feasibility, safety, and outcome of cold snare resection during routine endoscopy.

METHODS

 In this prospective study, 522 patients undergoing outpatient colonoscopy were included. Cold snare resection for diminutive (< 6 mm), small (6 - 9 mm), and larger polyps (> 9 - 15 mm) was performed using a dedicated cold snare device (Exacto ^® ) without prior submucosal injection. Outcome parameters included bleeding rate, perforation rate, procedure time, histologic evaluation of polyp margins, and success rates. The data were compared to a group of patients undergoing hot snare resection.

RESULTS

 Overall, 1233 polyps were removed using cold snare resection with an overall success rate of 99.4 %. All failures of cold snare resection occurred in the cecum (8/82, failure rate 9.8 %). In the remaining colon, the success rate was 100 %. Immediate post-polypectomy bleeding occurred in 0.49 % of all patients and was most frequently seen in polyps larger than 9 mm. The procedure time was significantly shorter using cold snare resection compared with hot snare resection (27.6 min vs. 35.7 min, P  < 0.01).

CONCLUSION

 Cold snare resection can be performed safely in outpatients for removal of small polyps in screening colonoscopy. It does not require prior saline injection and reduces procedure time without an increased risk of bleeding.

Widespread Usutu virus outbreak in birds in the Netherlands, 2016

We report a widespread Usutu virus outbreak in birds in the Netherlands. Viral presence had been detected through targeted surveillance as early as April 2016 and increased mortality in common blackbirds and captive great grey owls was noticed from August 2016 onwards. Usutu virus infection was confirmed by post-mortem examination and RT-PCR. Extensive Usutu virus activity in the Netherlands in 2016 underlines the need to monitor mosquito activity and mosquito-borne infections in 2017 and beyond.

Amelogenin Exon4 Forms a Novel miRNA That Directs Ameloblast and Osteoblast Differentiation

Amelogenins constitute the major portion of secretory enamel matrix proteins and are known to be highly alternative spliced. Of all the alternatively spliced forms of amelogenins, exon4 is most commonly spliced out. Our analyses of the exon4 sequence led us to hypothesize that when spliced out, exon4 may generate a novel mature miRNA. To explore this possibility, we used in vivo mouse models (wild-type and Amel knockout mice) and in vitro cell culture to investigate the presence and function of a mature miRNA derived from exon4 (miR-exon4). When ameloblast-like cells (LS8) were transfected with an amelogenin minigene to increase amelogenin synthesis, the transfected cells synthesized miR-exon4. Introduction of a mutation in the conserved CNNC sequence required for primary miRNA recognition, downstream of the mature miR-exon4 sequence, resulted in a significantly reduced production of miR-exon4 in the transfected cells. In vivo, miR-exon4 was most highly amplified from wild-type mouse enamel organs at the secretory stage. In Amel knockout mice, an in vivo model for reduced amelogenin synthesis, we found reduced miR-exon4, with no changes in expression of enamel matrix-related genes. However, expression of Runx2 and its downstream genes Odam and Amtn were significantly downregulated. Transfection of miR-exon4 mimic to the LS8 cells also significantly upregulated Runx2. The mature miR-exon4 as well as Runx2 was also present in mouse osteoblasts with no apparent change in expression level between wild-type and Amel knockout mice. However, transfecting miR-exon4 inhibitor to the MC3T3-E1 osteoblastic cells resulted in a significant downregulation of Runx2 expression. These data indicate that when exon4 is spliced out, as occurs most of the time during alternative splicing of amelogenin pre-mRNA, a novel mature miRNA is generated from exon4. This miR-exon4 may contribute to the differentiation of ameloblasts and osteoblasts through regulation of Runx2 expression.

Exon4 amelogenin transcripts in enamel biomineralization

Amelogenins are proteins formed by alternative splicing of the amelogenin gene, and are essential for tooth enamel formation. However, the unique functions of various alternatively spliced amelogenins in enamel formation are not well understood. In this study, we determined the spatiotemporal location of amelogenins derived from transcripts containing exon4 (AMG+4) in the enamel matrix, and the relative binding of recombinant AMG+4 to hydroxyapatite (HAP). Immunohistochemistry and mass spectrometry analyses showed that AMG+4 proteins were secreted into the enamel matrix at the early maturation stage. A stage-specific increase in the synthesis of AMG+4 was further supported by our observation that in mice overexpressing leucine-rich amelogenin peptide (TgLRAP), in which ameloblasts differentiate earlier, AMG+4 transcripts were also upregulated earlier. In vitro binding studies, supported by in silico modeling of protein binding to calcium and phosphate, showed that more recombinant AMG+4 bound to hydroxyapatite (HAP) as compared with recombinant AMG-4. The temporal and spatial localization of amelogenins containing exon4 peptide, and their functional differences in HAP binding, suggests that the unique properties of amelogenins containing exon4 cause a specific enhancement of biomineralization related to stabilization of early-formed HAP at the maturation stage.

Biodegradation of metallic magnesium elicits an inflammatory response in primary nasal epithelial cells

Resorbable magnesium-based implants hold great promise for various biomedical applications, such as osteosynthesis and coronary stenting. They also offer a new therapeutic option for the treatment of chronic rhinosinusitis, but little data is yet available regarding the use of magnesium in the nasal cavity. To model this field of application, primary porcine nasal epithelial cells were used to test the biocompatibility of degrading pure magnesium and investigate whether the degradation products may also affect cellular metabolism. Magnesium specimens did not induce apoptosis and we found no major influence on enzyme activities or protein synthesis, but cell viability was reduced and elevated interleukin 8 secretion indicated proinflammatory reactions. Necrotic damage was most likely due to osmotic stress, and our results suggest that magnesium ion build-up is also involved in the interleukin 8 release. Furthermore, the latter seems to be mediated, at least in part, by the p38 signaling pathway. These effects probably depended on the accumulation of very high concentrations of magnesium ions in the in vitro set-up, which might not be achieved in vivo, although we cannot exclude that further, as yet unknown, factors played a role in the inflammatory response during the degradation process. In conclusion, the biocompatibility of pure magnesium with cells in the immediate vicinity appears less ideal than is often supposed, and this needs to be considered in the evaluation of magnesium materials containing additional alloying elements.

Characterization of MgNd2 alloy for potential applications in bioresorbable implantable devices

The aim of this study is to investigate and demonstrate the mechanical and corrosive characteristics of the neodymium-containing magnesium alloy MgNd2 (Nd2), which can be used as a resorbable implant material, especially in the field of stenting applications. To determine the mechanical characteristics of Nd2, tensile and compression tests were initially carried out in the hot extruded state. Here a unique elongation ratio (~30%) of the alloy could be observed. Subsequent T5 and T6 heat treatments were arranged to reveal their effect on the alloy's strengths and elongation values. The general degradation behaviour of Nd2 in a 0.9% NaCl solution was investigated by means of polarization curves and hydrogen evolution. In addition to this, by using various in vivo parameters, a corrosion environment was established to determine the alloy's degradation in vitro. Here, the mass loss per day in (MgF(2) and Bioglass)-coated and uncoated states and the corresponding maximum forces resulting from subsequent three-point bending tests revealed slow and steady corrosion behaviour. The cell viability and proliferation tests carried out on L-929 and MSC-P5 cells also showed good results. The mechanical and corrosive characteristics determined, as well as the in vitro test results obtained within the scope of this study, led to the development and successful in vivo testing of an MgF(2)-coated Nd2 mucosa stent which was introduced as an appropriate resorbable application.

The isolated perfused equine distal limb as an ex vivo model for pharmacokinetic studies

Even though intra-articular injections play an important role in the treatment of joint-related lameness in horses, little is known about pharmacokinetic properties of substances used. Therefore, an ex vivo model for pharmacokinetic studies was developed using distal forelimbs of slaughtered horses. The extremity was perfused with gassed Tyrode solution for up to 8 h. Tissue viability was confirmed by measurements of glucose consumption, lactate production, and lactate dehydrogenase activity in the perfusate. Standard criteria for tissue viability had been determined in preliminary experiments (n = 11), which also included histological examinations of the joint capsule. As the model's first implementation, the articular efflux rate of betamethasone (BM), administered as BM disodium phosphate intra-articularly to the fetlock joint (4 mg BM/joint), was investigated. The concentration of BM in the venous perfusate of the radial vein was measured by means of high-performance liquid chromatography. The average BM efflux rate per minute was calculated to be 5.1 μg/min with values ranging from 9 μg/min to 2.9 μg/min. 7.5 h after i.a. application, 2.3 mg BM had left the joint via the radial vein. Using this inexpensive setup, the presented model allows studying a variety of pharmacological topics without the ethical limitations of animal studies.

Exploring optimal current stimuli that provide membrane voltage tracking in a neuron model

Studying neurons from an energy efficiency perspective has produced results in the research literature. This paper presents a method that enables computation of low energy input current stimuli that are able to drive a reduced Hodgkin-Huxley neuron model to approximate a prescribed time-varying reference membrane voltage. An optimal control technique is used to discover an input current that optimally minimizes a user selected balance between the square of the input stimulus current (input current 'energy') and the difference between the reference voltage and the membrane voltage (tracking error) over a stimulation period. Selecting reference signals to be membrane voltages produced by the neuron model in response to common types of input currents i(t) enables a comparison between i(t) and the determined optimal current stimulus i*(t). The intent is not to modify neuron dynamics, but through comparison of i(t) and i*(t) provide insight into neuron dynamics. Simulation results for four different bifurcation types demonstrate that this method consistently finds lower energy stimulus currents i*(t) that are able to approximate membrane voltages as produced by higher energy input currents i(t) in this neuron model.

[Protein S3 fragments neighboring mRNA during elongation and translation termination on the human ribosome]

Protein S3 fragments were determined that crosslink to modified mRNA analogues in positions +5 to +12 relative to the first nucleotide in the P-site binding codon in model complexes mimicking states of ribosomes at the elongation and translation termination steps. The mRNA analogues contained a Phe codon UUU/UUC at the 5'-termini that could predetermine the position of the tRNA(Phe) on the ribosome by the location of P-site binding and perfluorophenylazidobenzoyl group at a nucleotide in various positions 3' of the UUU/UUC codon. The crosslinked S3 protein was isolated from 80S ribosomal complexes irradiated with mild UV light and subjected to cyanogen bromide-induced cleavage at methionine residues with subsequent identification of the crosslinked oligopeptides. An analysis of the positions of modified oligopeptides resulting from the cleavage showed that, in dependence on the positions of modified nucleotides in the mRNA analogue, the crosslinking sites were found in the N-terminal half of the protein (fragment 2-127) and/or in the C-terminal fragment 190-236; the latter reflects a new peculiarity in the structure of the mRNA binding center in the ribosome, unknown to date. The results of crosslinking did not depend on the type of A-site codon or on the presence of translation termination factor eRF1.

Associates of change in liver fat content in the morbidly obese after laparoscopic gastric banding surgery

AIM

Hepatic steatosis affects up to 30% of the population. After weight loss, monitoring of the change in hepatic steatosis is not routinely performed. This study aimed to define the closest associates of change in liver fat content in a population of obese females following laparoscopic gastric banding surgery.

METHODS

Before and 3 months after surgery, proton magnetic resonance spectroscopy and magnetic resonance imaging were used to estimate the amount of lipid contained within the liver and abdominal subcutaneous and visceral compartments of 29 obese [mean body mass index (BMI) 39 +/- 5 kg/m(2)], non-diabetic women aged between 20 and 62 years. Liver enzymes, fasting plasma glucose and insulin were also measured as well as body weight, BMI and waist circumference. Insulin sensitivity was estimated using homeostasis model assessment insulin resistance index.

RESULTS

Significant reductions occurred in body weight (p < 0.001), abdominal fat volumes (p < 0.001) and liver fat (p = 0.037) 3 months after surgery. Change in liver fat content more closely associated with change in serum gamma-glutamyl transferase (GGT; r = 0.71, p < 0.001) than with changes in weight (r = 0.10, p = 0.612) and waist circumference (r = 0.15, p = 0.468).

CONCLUSIONS

Our findings suggest that obese non-diabetic female patients who have undergone significant weight loss over 3 months can be better assessed for the regression of excess liver fat content by monitoring changes in serum GGT levels rather than changes in simple anthropometry.

Renal prothrombin mRNA is significantly decreased in a hyperoxaluric rat model of nephrolithiasis

Although urinary prothrombin fragment 1 (UPTF1) possesses several hallmarks expected of a regulatory protein in urolithiasis, its precise role remains unknown. To determine the relationship between renal prothrombin (PT), the parent molecule of UPTF1, and lithogenesis, this study quantified and compared levels of renal PT mRNA in healthy rats (n = 10) and rats rendered lithogenic (n = 10) by ingestion of 0.75% ethylene glycol for 8 weeks. Studies included morphological and histological examination of the kidneys with scanning electron microscopy of the urinary filtrates of control and experimental animals. Haematuria and calcium oxalate (CaOx) crystals occurred in the urine of all experimental rats, but not in those of controls. Histological examination showed birefringent nephroliths and associated damage in kidneys of lithogenic rats, which were not seen in the control group. The amounts of total RNA extracted from both groups of rats were similar, but the median ratio of PT to beta-actin transcript of 11.14 x 10(-4) (10.65 x 10(-4) +/- 2.24 x 10(-4)) in the control rats was significantly (p < or = 0.001) reduced to 6.47 x 10(-4) (6.57 x 10(-4) +/- 2.72 x 10(-4)) in the lithogenic group. These results demonstrate that renal PT mRNA is reduced by approximately 42% in lithogenic rats and confirm the existence of a direct association between renal PT synthesis and calculogenesis. Attempts to compare renal PT and urinary levels of PTF1 were unsuccessful because of interference from hepatic PT circulating in the blood, haematuria, and the presence of urinary CaOx crystals. This is the first report of a significant reduction in the renal expression of a urinary protein well documented to inhibit CaOx crystal growth and aggregation in undiluted human urine in vitro.

Apolipoprotein-D: a novel cellular marker for HGPIN and prostate cancer

BACKGROUND

High grade prostatic intraepithelial neoplasia (HGPIN) is a putative pre-malignant lesion of the prostate. While apolipoprotein-D (Apo-D), an androgen-regulated hydrophobic transporter protein, is expressed in prostate tumors, its expression in HGPIN is unknown.

METHODS

Immunoreactivity for Apo-D and another androgen-regulated protein, prostate specific antigen (PSA), was investigated in 64 radical prostatectomy tissues by video image analysis.

RESULTS

Eighty two percent of prostatectomy specimens demonstrated moderate to strong Apo-D immunoreactivity in areas of HGPIN. In comparison, weak Apo-D immunoreactivity was observed in non-malignant areas in only 24% of specimens. The median (range) percentage cellular area of HGPIN immunopositive for Apo-D (9.7%, 0-42.9), and the cellular concentration of Apo-D (MIOD 3.1, 0-13.3), were intermediate between that of normal (area 0%, 0-53.5%, MIOD 0, 0-12.6) and early stage prostate cancer tissues (area 29.2%, 0-90.8%, MIOD 6.7, 0-28.1). This increase in Apo-D expression from non-malignant, through HGPIN to prostate cancer was statistically significant (P < 0.001), and contrasted with the decrease observed in PSA staining between adjacent areas of normal glands, HGPIN, and cancer (P = 0.026).

CONCLUSIONS

The presence of high levels of immunoreactive Apo-D in HGPIN and prostate cancer, but not in non-malignant epithelial cells, is consistent with HGPIN being an intermediate lesion in the transition to prostate cancer, and suggests that cellular Apo-D expression is a marker of malignant transformation of the prostate.

CAT administration of language placement examinations

This article describes the development of a computerized adaptive test for Cegep de Jonquiere, a community college located in Quebec, Canada. Computerized language proficiency testing allows the simultaneous presentation of sound stimuli as the question is being presented to the test-taker. With a properly calibrated bank of items, the language proficiency test can be offered in an adaptive framework. By adapting the test to the test-taker's level of ability, an assessment can be made with significantly fewer items. We also describe our initial attempt to detect instances in which "cheating low" is occurring. In the "cheating low" situation, test-takers deliberately answer questions incorrectly, questions that they are fully capable of answering correctly had they been taking the test honestly.

[Telemedicine in pediatric oncology]

The telemedicine project of the Competence Net Pediatric Oncology of the German/Austrian Gesellschaft für Pädiatrische Onkologie und Hämatologie (GPOH) has as an initial step of its work-programme sent out a questionnaire to the 54 largest pediatric hematology/oncology units in Germany. Institutions were asked for their experience, motivation, existing infrastructure, and anticipated benefits and obstacles regarding the implementation of telemedicine in patient care and research. Of the 54 largest German Pediatric Oncology institutions asked, 46 completed the questionnaire (85 %).

RESULTS

1. The need for further detailed information on implementation and for help in technical realization of telemedicine applications was expressed by all participants. 2. The majority expected practical advantages from telemedicine communication and anticipated that telemedicine will increase quality in treating children with cancer. 3. Expert consultation (study chairman, reference radiologists) is stated as to be most important. 4. Thirty-three of 46 physicians (72 %) believe that telemedicine will reduce costs in medical care within the next years. 5. It is anticipated that the introduction of telemedicine is time consuming. 6. The lack of available medical informatics competence and manpower was regarded as the most important obstacle. 7. Data security and standardization, transfer speed and transmission quality are considered most important. 8. Most of the institutions (91 %) use computers in the management of patients. Fourty-four (96 %) are connected to the Internet. 9. Thirty-seven of 46 institutions were prepared to invest in the implementation of telemedicine. This analysis demonstrates that the use of telemedicine is expected to become standard in pediatric oncology, while the existing infrastructure and status of information regarding this subject at present are insufficient. The most pressing practical need for telemedicine applications is seen in the field of electronic expert consultation. Hence, the Telemedicine-Project of the GPOH Competence Net will focus on this aspect first.

Evaluation of a waterless, scrubless chlorhexidine gluconate/ethanol surgical scrub for antimicrobial efficacy

A new waterless surgical hand preparation containing 1% chlorhexidine gluconate (CHG) and 61% ethyl alcohol was evaluated for antimicrobial efficacy in comparison with a standard 4% CHG surgical scrub and a 61% ethyl alcohol control. Clinical studies were based on the Tentative Final Monograph for Health-Care Antiseptic Drug Products (TFM) (proposed rule) and the Standard Test Method for Evaluation of Surgical Hand Scrub Formulations (ASTM E1115-91). Two randomized, blinded, well-controlled clinical studies involving 137 healthy subjects were conducted to evaluate the antimicrobial effectiveness of the CHG/ethanol hand preparation in producing an immediate and persistent reduction in the normal bacterial flora of the hands. The CHG/ethanol hand preparation was applied without scrubbing or the use of water, and a standard 4% CHG reference product was applied with a scrub brush in 2 traditional 3-minute surgical scrubs. In 1 study, a 61% ethanol vehicle control treatment was applied without scrubbing or use of water. During a 5-day period, each study subject performed a series of 11 surgical scrubs with 1 of the test treatments. After the first treatment on days 1, 2, and 5, surgical gloves were worn for 3 or 6 hours. Bacterial samples were taken with the glove-juice technique at 1 minute, 3 hours, and 6 hours after treatment. The immediate bactericidal effect of the CHG/ethanol hand preparation after a single application resulted in a 2.5-log reduction in normal flora. This bactericidal effect persisted throughout the studies and eventually increased to a 3.6-log reduction after the 11th scrub on day 5. The log reductions of the CHG/ethanol hand preparation proved to be significantly better (P <.05) than that of the 4% CHG product at each sampling interval on days 1 and 2 and the sampling at 6 hours on day 5 and significantly better than the 61% ethanol vehicle at all times. The combination of 1% CHG and 61% ethanol had significantly greater microbial reduction than either the 4% CHG (without ethanol) or the 61% ethanol vehicle (without CHG).

Apoptosis in neonatal murine lung exposed to hyperoxia

Exposure to high concentrations of oxygen in the neonatal period may impair lung growth and is a major contributing factor to the development of bronchopulmonary dysplasia. Cell death from hyperoxic injury may occur through either an apoptotic or nonapoptotic pathway, and we were interested in determining the type of cell death that occurs in the lung of neonatal mice exposed to hyperoxia. We found increased levels of Bax messenger RNA, a gene associated with apoptosis, in the lungs of neonatal mice born and raised in 92% hyperoxia. We next determined the extent of apoptosis taking place in the lungs of neonatal mice exposed to hyperoxia using terminal deoxyribonucleotidyl transferase-mediated deoxyuridine triphosphate-biotin nick-end labeling in 3.5-, 4.5-, and 5.5-d-old neonatal lung. The number of apoptotic cells in peripheral lung was significantly higher in the 3.5-, 4.5-, and 5.5-d-old mice treated with oxygen compared with that in the room-air control mice. Further, the number of apoptotic cells in the lung increased with longer exposure duration. In murine lung bronchus cells exposed to hyperoxia, growth arrest occurred after 48 h of oxygen exposure. Using annexin V binding, necrotic cell death was found to be the major form of cell death in these cells after 72 h of hyperoxic exposure. We conclude that 92% hyperoxia causes significant lung injury in neonatal mice exposed to hyperoxia, and that the number of apoptotic cells in the lung increases the longer the duration of exposure. The increase in apoptosis from hyperoxic exposure during a critical period of lung development may be an important factor in the impaired lung growth and remodeling that occur in animals exposed to high oxygen concentrations. Finally, it appears that hyperoxic injured cells in neonatal lung undergo both apoptotic and nonapoptotic cell death.

Signal transducer gp130: biochemical characterization of the three membrane-proximal extracellular domains and evaluation of their oligomerization potential

Glycoprotein 130 (gp130) is a type I transmembrane protein and serves as the common signal-transducing receptor subunit of the interleukin-6-type cytokines. Whereas the membrane-distal half of the gp130 extracellular part confers ligand binding and has been subject to intense investigation, the structural and functional features of its membrane-proximal half are poorly understood. On the basis of predictions of tertiary structure, the membrane-proximal part consists of three fibronectin-type-III-like domains D4, D5 and D6. Here we describe the bacterial expression of the polypeptides predicted to comprise each of these three domains. The recombinant proteins were refolded from solubilized inclusion bodies in vitro, purified to homogeneity and characterized by means of size-exclusion chromatography and CD spectroscopy. For the first time the prediction of three individual membrane-proximal protein domains for gp130 has been verified experimentally. The three domains do not show intermediate-affinity or high-affinity interactions between each other. Mapping of a neutralizing gp130 monoclonal antibody against D4 suggested a particular functional role of this domain for gp130 activation, because above that an intrinsic tendency for low-affinity oligomerization was demonstrated for D4.

Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus

Translational initiation of hepatitis C virus (HCV) genome RNA occurs via its highly structured 5' noncoding region called the internal ribosome entry site (IRES). Recent studies indicate that HCV IRES and 40 S ribosomal subunit form a stable binary complex that is believed to be important for the subsequent assembly of the 48 S initiation complex. Ribosomal protein (rp) S9 has been suggested as the prime candidate protein for binding of the HCV IRES to the 40 S subunit. RpS9 has a molecular mass of approximately 25 kDa in UV cross-linking experiments. In the present study, we examined the approximately 25-kDa proteins of the 40 S ribosome that form complexes with the HCV IRES upon UV cross-linking. Immunoprecipitation with specific antibodies against two 25-kDa 40 S proteins, rpS5 and rpS9, clearly identified rpS5 as the protein bound to the IRES. Thus, our results support rpS5 as the critical element in positioning the HCV RNA on the 40 S ribosomal subunit during translation initiation.