Vitamin E: Not only a single stereoisomer

The recent publication by Azzi and colleagues puts forth the argument that only RRR-α-tocopherol should be considered as vitamin E from a physiological point of view. They base their argument primarily on the assertion that only this form has been used to treat stark vitamin E deficiency in humans (known as AVED, or Ataxia with Vitamin E Deficiency). Azzi et al. also argue that other chemically similar molecules, such as tocopherols other than α-tocopherol and tocotrienols do not provide vitamin E activity. Azzi and colleagues are correct on this second point. An investigation into the biological activities of vitamin E, and the mechanisms behind these activities, confirms that physiological vitamin E activity is limited to certain α-tocopherol forms. However, it is also clear that these activities are not restricted only to the RRR-form but include other 2R-forms as well. Indeed, the α-tocopherol transfer protein (α-TTP), which is critical to mediate vitamin E trafficking and biological activity, and genetic defects of which lead to vitamin E deficiency, binds well to all 2R-forms of α-tocopherol. Furthermore, both RRR-α-tocopherol and the other 2R-forms are maintained in human plasma and distributed to tissues and organs, whereas the 2S-stereoisomers are excreted quickly. As such, in recent years the definition of vitamin E including both 2R- and RRR-α-tocopherol has gained both broad scientific and regulatory acceptance. Consistent with this understanding, we provide evidence that AVED has indeed been treated successfully with forms in addition to RRR-α-tocopherol, again arguing against the restriction of the definition to RRR-α-tocopherol only. Finally, we provide evidence against any safety concerns utilizing the currently accepted definition of vitamin E.

Vaporized nicotine use among patients in HIV care who smoke tobacco: perceived health effects and effectiveness as a smoking cessation tool

Evidence suggests adverse health effects from vaporized nicotine (VN) use, such as electronic "e" cigarettes, and limited efficacy to aid tobacco cessation. People with HIV (PWH) smoke tobacco at higher rates than the general population, with greater morbidity, highlighting the necessity of effective tobacco cessation tools. PWH may be more vulnerable to adverse effects of VN. Using semi-structured 1:1 interviews, we examined health beliefs regarding VN, patterns of use, and perceived effectiveness for tobacco cessation among PWH in HIV care at three geographically diverse U.S. sites. PWH (n = 24) had limited understanding of VN product content or health effects, presuming VN less harmful than tobacco cigarettes (TC). VN failed to adequately replicate the psychoactive effects or desired ritual of smoking TC. Concurrent TC use, and continuous VN use throughout the day, was common. Satiety using VN was elusive, and consumption quantity was difficult to track. VN had limited desirability and durability as a TC cessation tool among the interviewed PWH.

Search for Gamma-Ray Spectral Lines from Dark Matter Annihilation up to 100 TeV toward the Galactic Center with MAGIC

Linelike features in TeV γ rays constitute a "smoking gun" for TeV-scale particle dark matter and new physics. Probing the Galactic Center region with ground-based Cherenkov telescopes enables the search for TeV spectral features in immediate association with a dense dark matter reservoir at a sensitivity out of reach for satellite γ-ray detectors, and direct detection and collider experiments. We report on 223 hours of observations of the Galactic Center region with the MAGIC stereoscopic telescope system reaching γ-ray energies up to 100 TeV. We improved the sensitivity to spectral lines at high energies using large-zenith-angle observations and a novel background modeling method within a maximum-likelihood analysis in the energy domain. No linelike spectral feature is found in our analysis. Therefore, we constrain the cross section for dark matter annihilation into two photons to ⟨σv⟩≲5×10^{-28}  cm^{3} s^{-1} at 1 TeV and ⟨σv⟩≲1×10^{-25}  cm^{3} s^{-1} at 100 TeV, achieving the best limits to date for a dark matter mass above 20 TeV and a cuspy dark matter profile at the Galactic Center. Finally, we use the derived limits for both cuspy and cored dark matter profiles to constrain supersymmetric wino models.

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.

P 7 SARS-CoV2 infection causes a worsening of the modified ranking scale (mRS) in patients with neuromuscular diseases – first results of the German covid19-nme registry

Background: Patients with neuromuscular diseases (NMD) are classified as risk groups for a potentially severe course of a SARS-CoV-2 infection. An online registry (www.covid19-nme.com) was developed to gather information about the severity of COVID19, a potential progression of NMD through the SARS-CoV-2 infection and the possible influence of medication on the course of the infection.

Methods: Since February 2021, patients of all ages (children, adolescents and adults) with NMD and an infection with SARS-CoV-2 have been included in this register. In addition to demographic data, pre-existing diseases and therapies, information about the NMD, the course of the SARS-CoV-2 infection as well as the clinical findings before and after the infection are recorded.

Results: So far 94 patients (37% female, age: median 60 years (1-94 years)) from Germany and Austria have been recorded. The diagnoses represent the entire spectrum of NMD: different forms of polyneuropathies (PN) including CIDP and hereditary PN, ICUAW, myasthenic syndromes, motor neuron diseases (SMA and ALS) as well as various muscle diseases such as dystrophinopathies and myotonic syndromes. The collected mRS (measure for description of neurological impairment) depicts a significant worsening after the SARS-CoV2 infection (p = 0.02; Wilcoxon), whereby the patients with ICUAW were excluded from the analysis. The duration of symptoms showed a positive correlation with age (r = 0.343; p = 0.005) and weight (r = 0.291; p = 0.030), but not with the type of NMD. In total, 13 patients deceased due to the SARS-CoV2 infection. The probability of a fatal outcome of COVID19 correlates with increasing age (r = 0.313; p = 0.004) but not the type of NMD. The ventilation situation did not change in NMD patients due to the infection with SARS-CoV2.

Summary: The first results of the evaluation of the covid-19.nme registry indicate that the clinical symptoms of NMD progress due to an infection with SARS-CoV2. The underlying cause for this remains unclear. Autoimmunological processes and a possible neurotropy can be considered as pathophysiological mechanisms.

Prioritisation of colonoscopy services in colorectal cancer screening programmes to minimise impact of COVID-19 pandemic on predicted cancer burden: A comparative modelling study

Objectives

Colorectal cancer (CRC) screening with a faecal immunochemical test (FIT) has been disrupted in many countries during the COVID-19 pandemic. Performing catch-up of missed screens while maintaining regular screening services requires additional colonoscopy capacity that may not be available. This study aimed to compare strategies that clear the screening backlog using limited colonoscopy resources.

Methods

A range of strategies were simulated using four country-specific CRC natural-history models: Adenoma and Serrated pathway to Colorectal CAncer (ASCCA) and MIcrosimulation SCreening ANalysis for CRC (MISCAN-Colon) (both in the Netherlands), Policy1-Bowel (Australia) and OncoSim (Canada). Strategies assumed a 3-month screening disruption with varying recovery period lengths (6, 12, and 24 months) and varying FIT thresholds for diagnostic colonoscopy. Increasing the FIT threshold reduces the number of referrals to diagnostic colonoscopy. Outcomes for each strategy were colonoscopy demand and excess CRC-related deaths due to the disruption.

Results

Performing catch-up using the regular FIT threshold in 6, 12 and 24 months could prevent most excess CRC-related deaths, but required 50%, 25% and 12.5% additional colonoscopy demand, respectively. Without exceeding usual colonoscopy demand, up to 60% of excess CRC-related deaths can be prevented by increasing the FIT threshold for 12 or 24 months. Large increases in FIT threshold could lead to additional deaths rather than preventing them.

Conclusions

Clearing the screening backlog in 24 months could avert most excess CRC-related deaths due to a 3-month disruption but would require a small increase in colonoscopy demand. Increasing the FIT threshold slightly over 24 months could ease the pressure on colonoscopy resources.

Is fruit intake associated with common carotid intima-media thickness?

Background

Common carotid intima-media thickness (ccIMT) is an established risk marker for cardiovascular events, including myocardial infarction and stroke, which are of high public health relevance. While a higher fruit intake is generally considered beneficial for cardiovascular health, recent studies have shown that a fruit intake of > 2 portions per day may be harmful. Therefore, we tested if there is an association between categories of fruit intake and mean ccIMT.

Methods

We conducted an exploratory, non-prespecified, cross-sectional analysis of baseline values of 167 mostly middle-aged participants of a controlled lifestyle intervention, recruited from the general population in rural northwest Germany (male: n = 58; female: n = 109). Fruit intake was classified into low (<1 portion of fruit/day), intermediate (1-2 portions of fruit/day), and high (>2 portions of fruit/day). Mean ccIMT was measured in accordance with the Mannheim consensus. Between-group differences in mean ccIMT were assessed with analysis of covariance.

Results

Mean age was 57.3 ± 0.7 years (mean ± SEM). Mean fruit intake was 1.6 ± 0.1 portions/day. Average mean ccIMT was 0.679 ± 0.010 mm. There was a significant difference in mean ccIMT between subjects with low (0.676 ± 0.020 mm; n = 50), intermediate (0.653 ± 0.014 mm; n = 72), and high fruit intake (0.724 ± 0.019 mm; n = 45; p = 0.016). But this difference was attenuated when adjusting for age, sex, and homocysteine (p = 0.418).

Conclusions

We found only a non-significant association between consuming >2 portions of fruit per day and ccIMT. Thus, our study could not confirm a negative effect of fruit intake on ccIMT. Age, sex, and homocysteine may confound this association.

Key messages

Current recommendations of 2 portions of fruit per day seem adequate and do not negatively influence carotid intima-media thickness. Future studies should address confounding of the association between fruit intake and cardiovascular risk markers.

Neuroplastic effects of a selective serotonin reuptake inhibitor in relearning and retrieval

Animal studies using selective serotonin reuptake inhibitors (SSRIs) and learning paradigms have demonstrated that serotonin is important for flexibility in executive functions and learning. SSRIs might facilitate relearning through neuroplastic processes and thus exert their clinical effects in psychiatric diseases where cognitive functioning is affected. However, translation of these mechanisms to humans is missing. In this randomized placebo-controlled trial, we assessed functional brain activation during learning and memory retrieval in healthy volunteers performing associative learning tasks aiming to translate facilitated relearning by SSRIs.

To this extent, seventy-six participants underwent three MRI scanning sessions: (1) at baseline, (2) after three weeks of daily associative learning and subsequent retrieval (face-matching or Chinese character–noun matching) and (3) after three weeks of relearning under escitalopram (10 mg/day) or placebo. Associative learning and retrieval tasks were performed during each functional MRI (fMRI) session. Statistical modeling was done using a repeated-measures ANOVA, to test for content-by-treatment-by-time interaction effects.

During the learning task, a significant substance-by-time interaction was found in the right insula showing a greater deactivation in the SSRI cohort after 21 days of relearning compared to the learning phase. In the retrieval task, there was a significant content-by-time interaction in the left angular gyrus (AG) with an increased activation in face-matching compared to Chinese-character matching for both learning and relearning phases. A further substance-by-time interaction was found in task performance after 21 days of relearning, indicating a greater decrease of performance in the placebo group.

Our findings that escitalopram modulate insula activation demonstrates successful translation of relearning as a mechanism of SSRIs in human. Furthermore, we show that the left AG is an active component of correct memory retrieval, which coincides with previous literature. We extend the function of this region by demonstrating its activation is not only stimulus dependent but also time constrained. Finally, we were able to show that escitalopram aids in relearning, irrespective of content.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

The Influence of Acute SSRI Administration on White Matter Microstructure in Patients Suffering From Major Depressive Disorder and Healthy Controls

BACKGROUND

Selective serotonin reuptake inhibitors (SSRIs) are predominantly prescribed for people suffering from major depressive disorder. These antidepressants exert their effects by blocking the serotonin transporter (SERT), leading to increased levels of serotonin in the synaptic cleft and subsequently to an attenuation of depressive symptoms and elevation in mood. Although long-term studies investigating white matter (WM) alterations after exposure to antidepressant treatment exist, results on the acute effects on the brain's WM microstructure are lacking.

METHODS

In this interventional longitudinal study, 81 participants were included (33 patients and 48 healthy controls). All participants underwent diffusion weighted imaging on 2 separate days, receiving either citalopram or placebo using a randomized, double-blind, cross-over design. Fractional anisotropy, mean diffusivity, axial diffusivity, and radial diffusivity were calculated within the FMRIB software library and analyzed using tract-based spatial statistics.

RESULTS

The repeated-measures ANOVA model revealed significant decreases after SSRI administration in mean diffusivity, axial diffusivity, and radial diffusivity regardless of the group (P < .05, family-wise error [FWE] corrected). Results were predominantly evident in frontal WM regions comprising the anterior corona radiata, corpus callosum, and external capsule and in distinct areas of the frontal blade. No increases in diffusivity were found, and no changes in fractional anisotropy were present.

CONCLUSIONS

Our investigation provides the first evidence, to our knowledge, that fast WM microstructure adaptations within 1 hour after i.v. SSRI administration precede elevations in mood due to SSRI treatment. These results add a new facet to the complex mode of action of antidepressant therapy. This study was registered at clinicaltrials.gov with the identifier NCT02711215.

Effect of a 6-Month Controlled Lifestyle Intervention on Common Carotid Intima-Media Thickness

OBJECTIVES

The intima-media thickness of the common carotid artery (ccIMT) is an established risk marker for cardiovascular disease (CVD). However, it is unclear whether lifestyle interventions can easily demonstrate an improvement in ccIMT. The objective was to test if our intervention would beneficially affect ccIMT (among other CVD markers).

DESIGN

Non-randomized controlled trial.

SETTING

Rural northwest Germany.

PARTICIPANTS

Middle-aged and elderly participants from the general population (intervention: n = 114; control: n = 87).

INTERVENTION

A community-based, 6-month controlled lifestyle intervention focusing on four areas of lifestyle change: a plant-based diet, physical activity, stress management, and an improved social life. A strong emphasis was on dietary change.

MEASUREMENTS

We tested whether ccIMT change from baseline to 6 months was different between groups.

RESULTS

With all participants included, no significant difference in mean ccIMT change between groups was observed (p = 0.708). However, in a subgroup analysis with participants with high baseline mean ccIMT (≥0.800 mm) a significant difference in mean ccIMT change between intervention (-0.023 [95% CI -0.052, 0.007] mm; n = 22; baseline mean ccIMT: 0.884 ± 0.015 mm) and control (0.041 [95% CI 0.009, 0.073] mm; n = 13; baseline mean ccIMT: 0.881 ± 0.022 mm) was observed (p = 0.004). Adjusting for potential confounders did not substantially alter the results.

CONCLUSION

The results indicate that healthy lifestyle changes can beneficially affect ccIMT within 6 months and that such a beneficial effect may be more easily demonstrated if participants with high baseline ccIMT are recruited. The observed effect is of relevance for the prevention of CVD events, including myocardial infarction and stroke.

Bounds on Lorentz Invariance Violation from MAGIC Observation of GRB 190114C

On January 14, 2019, the Major Atmospheric Gamma Imaging Cherenkov telescopes detected GRB 190114C above 0.2 TeV, recording the most energetic photons ever observed from a gamma-ray burst. We use this unique observation to probe an energy dependence of the speed of light in vacuo for photons as predicted by several quantum gravity models. Based on a set of assumptions on the possible intrinsic spectral and temporal evolution, we obtain competitive lower limits on the quadratic leading order of speed of light modification.

Gait Characteristics of Transtibial Amputees on Level Ground in a Cohort of 53 Amputees - Comparison of Kinetics and Kinematics With Non-amputees

STUDY DESIGN

Retrospective analysis.

BACKGROUND

The gait characteristics of transtibial amputees (TTs) have been described many times. In general, the literature reported nearly consistent results for the kinematic and kinetic parameters of the prosthetic side. However, the literature revealed inconsistent findings on kinetic parameters for determining the risk of developing knee osteoarthritis, such as the peak knee adduction moment, knee flexion moment and vertical ground reaction forces.

OBJECTIVES

The objective of our study was to describe the sagittal kinetic and kinematic gait characteristics of the ankle and residual knee joint of the prosthetic limb and the knee loading parameters of the sound side of unilateral TTs. This specific consideration may contribute to resolving the controversy of these parameters in the literature.

METHODS

We analysed our database containing gait analyses from 53 unilateral TTs and compared data to a control group (CG), also taken from our database. The sagittal kinetic and kinematic gait characteristics of the ankle and residual knee joint of the prosthetic limb, and selected knee loading parameters of the sound side (the peak knee adduction moment, knee flexion moment and vertical ground reaction forces) were evaluated. Beside these parameters we reported typical spatiotemporal gait parameters as gait velocity, step length, step length asymmetry, stance phase duration and asymmetry of stance phase duration.

RESULTS

The TTs walked slower and more asymmetrically than the CG. The kinematic pattern of the prosthetic ankle differed from that found in the CG. The largest difference was observed for the range of motion of the plantarflexion at push-off, which was significantly reduced for the prosthetic foot. The residual knee joint was generally affected with respect to decreased moments and reduced knee flexion during stance phase. The peaks of the vertical ground reaction forces and knee adduction moments showed no differences between the sound side of amputees and the CG. The peak knee flexion moment at midstance was significantly reduced for the sound side of amputees in comparison with the CG.

CONCLUSION

The biomechanical data measured for the prosthetic side in a cohort of 53 unilateral TT amputees conformed with the literature. The parameters determining the risk of developing knee osteoarthritis investigated in our retrospective analysis were not increased on the sound side in comparison with non-amputees. We deem it reasonable to assume that an appropriate prosthesis will reduce the likelihood of overloading the knee on the sound side during normal walking.

Simultaneous Determination of Multiple Tetracycline Residues in Milk by Metal Chelate Affinity Chromatography: Collaborative Study

To meet federal and state regulatory needs, a liquid chromatographic (LC) method with ultraviolet (UV) detection was developed for determination of 7 tetracyclines at 30 ng/mL in milk. Raw milk samples are defatted, acidified, and centrifuged to remove proteins, and tetracyclines are specifically absorbed from the milk by chelation with metal ions bound to small Chelating Sepharose Fast Flow columns. Tetracyclines are removed from these columns with EDTA-containing buffer, and extracts are further cleaned by ultrafiltration. Finally, extracts are concentrated and analyzed simultane ously by using on-line concentration. This method was validated in a collaborative study that involved 11 laboratories, including the authors’ laboratory. Each laboratory was asked to prepare and analyze known control and fortified milk samples, as well as 18 coded blind samples. Eight laboratories completed all analyses. Average interlaboratory recoveries for the known fortified samples ranged from 59% (methacycline at 15 ng/mL) to 78% (oxytetracy cline at 60 ng/mL). Average recovery for each of 7 residues at 30 ng/mL were between 60 and 110%, meeting single-residue guidelines for accuracy set by the U.S. Food and Drug Administration. Reproducibility relative standard deviation (RSDR) for the known fortified samples varied from 11 to 39%, with 6 of 7 residues at the 30 ng/mL level having RSDR values at or below 20%. Seven of 8 laboratories correctly identified blind control milk samples and all 28 residues present in blind samples. The metal chelate affinity—LC method for determination of multiple tetracycline residues in milk has been adopted first action by AOAC INTERNATIONAL.

An integrative correlation of myopathology, phenotype and genotype in late onset Pompe disease

AIMS

Pompe disease is caused by pathogenic mutations in the alpha 1,4-glucosidase (GAA) gene and in patients with late onset Pome disease (LOPD), genotype-phenotype correlations are unpredictable. Skeletal muscle pathology includes glycogen accumulation and altered autophagy of various degrees. A correlation of the muscle morphology with clinical features and the genetic background in GAA may contribute to the understanding of the phenotypic variability.

METHODS

Muscle biopsies taken before enzyme replacement therapy were analysed from 53 patients with LOPD. On resin sections, glycogen accumulation, fibrosis, autophagic vacuoles and the degree of muscle damage (morphology-score) were analysed and the results were compared with clinical findings. Additional autophagy markers microtubule-associated protein 1A/1B-light chain 3, p62 and Bcl2-associated athanogene 3 were analysed on cryosections from 22 LOPD biopsies.

RESULTS

The myopathology showed a high variability with, in most patients, a moderate glycogen accumulation and a low morphology-score. High morphology-scores were associated with increased fibrosis and autophagy highlighting the role of autophagy in severe stages of skeletal muscle damage. The morphology-score did not correlate with the patient's age at biopsy, disease duration, nor with the residual GAA enzyme activity or creatine-kinase levels. In 37 patients with LOPD, genetic analysis identified the most frequent mutation, c.-32-13T>G, in 95%, most commonly in combination with c.525delT (19%). No significant correlation was found between the different GAA genotypes and muscle morphology type.

CONCLUSIONS

Muscle morphology in LOPD patients shows a high variability with, in most cases, moderate pathology. Increased pathology is associated with more fibrosis and autophagy.

Active site rearrangement and structural divergence in prokaryotic respiratory oxidases

Cytochrome bd–type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of theEscherichia colicytochrome bd-I oxidase by single-particle cryo–electron microscopy to a resolution of 2.7 angstroms. Our structure contains a previously unknown accessory subunit CydH, the L-subfamily–specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway. Comparison with another cytochrome bd oxidase reveals structural divergence in the family, including rearrangement of high-spin hemes and conformational adaption of a transmembrane helix to generate a distinct oxygen-binding site.

Clinical and genetic spectrum of SCN2A-associated episodic ataxia

BACKGROUND

Pathogenic variants in SCN2A are associated with various neurological disorders including epilepsy, autism spectrum disorder and intellectual disability. Few reports have recently described SCN2A-associated episodic ataxia (EA). Our study identifies its broader clinical and genetic spectrum, and describes pharmacological approaches.

RESULTS

We report 21 patients with SCN2A-associated EA, of which 9 are unpublished cases. The large majority of patients present with epileptic seizures (18/21, 86%), often starting within the first three months of life (12/18, 67%). In contrast, onset of episodic ataxia ranged from 10 months to 14 years of age. The frequency of EA episodes ranged from brief, daily events up to 1-2 episodes per year each lasting several weeks. Potential triggers include minor head traumas and sleep deprivation. Cognitive outcome is favorable in most patients with normal or mildly impaired cognitive development in 17/21 patients (81%). No clear genotype-phenotype correlations were identified in this cohort. However, two mutational hotspots were identified, i.e. 7/21 patients (33%) harbor the identical pathogenic variant p.A263V, whereas 5/21 (24%) carry pathogenic variants that affect the S4 segment and its cytoplasmic loop within the domain IV. In addition, we identified six novel pathogenic variants in SCN2A. While acetazolamide was previously reported as beneficial in SCN2A-associated EA in one case, our data show a conflicting response in 8 additional patients treated with acetazolamide: three of them profited from acetazolamide treatment, while 5/8 did not.

CONCLUSIONS

Our study describes the heterogeneous clinical spectrum of SCN2A-associated EA, identifies two mutational hotspots and shows positive effects of acetazolamide in about 50%.

Abstract P6-21-11: Final results from IMPROVE: A randomized, controlled, open-label, cross-over phase IV study to determine the patients' preference for either combined endocrine therapy (exemestane plus everolimus) or immunochemotherapy (capecitabine plus bevacizumab) as first line treatment for advanced HR+/HER2- breast cancer

For patients (pts) with advanced HR+/HER2- breast cancer various treatment options exist. Endocrine therapy or chemotherapy are the recommended 1st-line treatment options according to international guidelines. With comparable efficacy, it is of utmost importance to identify the treatment that has the least negative impact on the pts' quality of life (QoL). Randomized studies to determine the pts' preference (pref) for equi-effective treatment concepts, are lacking. IMPROVE compared both therapeutic concepts by assessing the pts' pref for either a combined antihormonal approach (everolimus /exemestane (E/E)) or chemotherapy (capecitabine /bevacizumab (C/B)).

In total, 77 pts were recruited from 10/14 until 04/17 at 26 sites in GER. Upon diagnosis of locally advanced, inoperable or metastatic disease, pts were randomized to receive 1st-line C/B until disease progression followed by 2nd-line E/E (Arm A) or vice versa (Arm B). Primary objective was the patient-reported pref for either treatment protocol 12 weeks after switching therapy. Key secondary endpoints include PFS, OS, safety and QoL. Descriptive statistics were used to to analyse data, PFS and OS were calculated by using the Kaplan-Meier method.

Baseline characteristics were well balanced with a slightly shorter disease-free interval after primary diagnosis and more prior treatments in Arm B.In Arm A [95% CI], 39% [13.9-68.4] vs 23% [5.0-53.8] of pts preferred E/E compared to C/B, 23% [5.0-53.8] were undecided. In Arm B, 56% [30.8-78.5] vs 11% [1.4-34.7] preferred C/B, 22% [6.4-47.6] undecided. Overall, 42% [24.5-60.9] vs 23% [9.6-41.1] of pts preferred C/B, 23% [9.6-41.1] were undecided.

Physicians' pref had a tendency for C/B treatment (Arm A, 62% [31.6-86.1] vs 39% [13.9-68.4] for C/B. Arm B, 56% [30.8-78.5] vs 28% [9.7-53.5] for C/B, no pref 17% [3.6-41.4]).

Median 1st-line PFS [months, 95% CI] was 11.1 [7.8-18.0] for C/B (Arm A) vs 3.5 [2.7-5.5] for E/E (Arm B). Median 2nd-line PFS was 3.7 [2.4-7.8] for E/E (Arm A) vs 3.6 [2.3-5.5] for C/B (Arm B). Median OS [months, 95% CI] was 28.8 [19.7-NA] (Arm A) and 24.7 [13.9-28.8] (Arm B). 73.0% and 52.6% (1st and 2nd line, C/B) vs 54.1% and 52.9% (1st and 2nd line, E/E) of pts developed grade 3/4 AEs. Most common grade 3/4 AEs (%) were hand-foot syndrome (18.9), fatigue (17.6), hypertension (13.5) for C/B and anaemia (23.5), fatigue, dyspnoea, cough (each 17.6) for E/E (either line). No treatment-related deaths occurred. Patient-reported QoL (EORTC-QLQC30) and treatment satisfaction were not significantly different between arms in either treatment phase.

In the IMPROVE study, pts had no pref for either endocrine therapy or immunochemotherapy. Overall, there was a tendency in favour of the chemotherapeutic approach (C/B), which was in line with the therapy pref reported by the physicians. C/B was found to have slightly better efficacy results but at the cost of a higher frequency of grade 3/4 AEs, bearing in mind the difference in duration of therapy between the two regimens. Patient-reported QoL, however, was similar in both arms.

Citation Format: Kurbacher CM, Söling U, Hahn A, Chiabudini M, Maintz C, Rieger L, Falkenstein J, Runkel E, Potthoff K, Decker T. Final results from IMPROVE: A randomized, controlled, open-label, cross-over phase IV study to determine the patients' preference for either combined endocrine therapy (exemestane plus everolimus) or immunochemotherapy (capecitabine plus bevacizumab) as first line treatment for advanced HR+/HER2- breast cancer [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-21-11.

Pathogenic Germline Variants in 10,389 Adult Cancers

We conducted the largest investigation of predisposition variants in cancer to date, discovering 853 pathogenic or likely pathogenic variants in 8% of 10,389 cases from 33 cancer types. Twenty-one genes showed single or cross-cancer associations, including novel associations of SDHA in melanoma and PALB2 in stomach adenocarcinoma. The 659 predisposition variants and 18 additional large deletions in tumor suppressors, including ATM, BRCA1, and NF1, showed low gene expression and frequent (43%) loss of heterozygosity or biallelic two-hit events. We also discovered 33 such variants in oncogenes, including missenses in MET, RET, and PTPN11 associated with high gene expression. We nominated 47 additional predisposition variants from prioritized VUSs supported by multiple evidences involving case-control frequency, loss of heterozygosity, expression effect, and co-localization with mutations and modified residues. Our integrative approach links rare predisposition variants to functional consequences, informing future guidelines of variant classification and germline genetic testing in cancer.

Diffusion effects in myelin sheath free induction decay

Myelin sheath microstructure and composition produce MR signal decay characteristics that can be used to evaluate status and outcome of demyelinating disease. We extend a recently proposed model of neuronal magnetic susceptibility, that accounts for both the structural and inherent anisotropy of the myelin sheath, by including the whole dynamic range of diffusion effects. The respective Bloch-Torrey equation for local spin dephasing is solved with a uniformly convergent perturbation expansion method, and the resulting magnetization decay is validated with a numerical solution based on a finite difference method. We show that a variation of diffusion strengths can lead to substantially different MR signal decay curves. Our results may be used to adjust or control simulations for water diffusion in neuronal structures.

PCR-based rapid diagnostic tests as a strategy for preventing infections with sexually transmitted diseases-a 'diagnostics-as-prevention' modelling approach

The potential was modelled of molecular rapid diagnostic tests (RDTs) that target agents of sexually transmitted diseases (STDs) to contribute to a reduction in the exposure risk for sexually active populations who prefer condom-free high-risk contacts. The biostatistical approach is exemplified by considering the use of a PCR-based RDT for Chlamydia trachomatis and Neisseria gonorrhoeae in a population of German men having sex with men. We modelled the exposure risk as risk of sexual contact with individuals infected by a STD in spite of multiple RDTs having been conducted to identify STDs that could lead to avoidance of an infectious sexual contact. The risk for a given specific disease is influenced by the diagnostic accuracy of all diagnostic tests conducted. The simulation showed a reduction in exposure risk through conducting the selected PCR-based RDT as a strategy to prevent infections with C. trachomatis and N. gonorrhoeae in comparison with unprotected sexual contact of >97% for C. trachomatis and ≥96% for N. gonorrhoeae. Reliable knowledge of the performance characteristics of the diagnostic tests applied is essential for a thorough risk assessment based on such diagnostic approaches.

SIGNIFICANCE AND IMPACT OF THE STUDY

A low-threshold use of molecular rapid diagnostic tests in settings where risky sexual activity is undertaken with deliberate non-use of condoms is modelled. Such an approach might contribute to a considerable reduction in the exposure risk if positively tested individuals are excluded from unprotected sexual intercourse. Protective effects are influenced by the prevalence of the disease and the performance characteristics of the applied tests. Precise knowledge of the performance characteristics of the test assays employed are prerequisites of a reliable risk assessment. The modelling approach is of particular use for preventive health experts.

Recurrent tumor-specific regulation of alternative polyadenylation of cancer-related genes

Background

Alternative polyadenylation (APA) results in messenger RNA molecules with different 3′ untranslated regions (3’ UTRs), affecting the molecules’ stability, localization, and translation. APA is pervasive and implicated in cancer. Earlier reports on APA focused on 3’ UTR length modifications and commonly characterized APA events as 3’ UTR shortening or lengthening. However, such characterization oversimplifies the processing of 3′ ends of transcripts and fails to adequately describe the various scenarios we observe.

Results

We built a cloud-based targeted de novo transcript assembly and analysis pipeline that incorporates our previously developed cleavage site prediction tool, KLEAT. We applied this pipeline to elucidate the APA profiles of 114 genes in 9939 tumor and 729 tissue normal samples from The Cancer Genome Atlas (TCGA). The full set of 10,668 RNA-Seq samples from 33 cancer types has not been utilized by previous APA studies. By comparing the frequencies of predicted cleavage sites between normal and tumor sample groups, we identified 77 events (i.e. gene-cancer type pairs) of tumor-specific APA regulation in 13 cancer types; for 15 genes, such regulation is recurrent across multiple cancers. Our results also support a previous report showing the 3’ UTR shortening of FGF2 in multiple cancers. However, over half of the events we identified display complex changes to 3’ UTR length that resist simple classification like shortening or lengthening.

Conclusions

Recurrent tumor-specific regulation of APA is widespread in cancer. However, the regulation pattern that we observed in TCGA RNA-seq data cannot be described as straightforward 3’ UTR shortening or lengthening. Continued investigation into this complex, nuanced regulatory landscape will provide further insight into its role in tumor formation and development.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4903-7) contains supplementary material, which is available to authorized users.

HIV prevention strategies and risk of infection: a model-based analysis

Risk populations for HIV infections tend to neglect condom use, making alternative preventive approaches necessary. Accordingly, we modelled the risk of sexual HIV transmission for condom use vs. use of rapid diagnostic test (RDT) systems with subsequent exclusion of potential sexual partners with a correctly or falsely positive test from unprotected sex with and without the use of HIV pre-exposure prophylaxis (PrEP) in a bio-statistical approach. We combined a previously described model of transmission risk for HIV-exposed individuals with a newly suggested model of risk of HIV exposure for sexually active HIV-negative individuals. The model was adapted for several stages of infection and different strategies of HIV infection prevention.HIV prevention with RDTs can reduce the transmission risk by up to 97% compared with having sex without any prevention and up to 80% compared with condom use. Nevertheless, RDT-based prevention strategies demonstrate a lack of protection in several stages of infection; in particular, RNA-based RDT systems may fail under treatment. RDT-based pre-screening of potential sex partners prior to unprotected sexual contacts substantially reduces HIV transmission risk. Combination of different prevention strategies is advisable for high-risk groups.

Dysregulated autophagy in restrictive cardiomyopathy due to Pro209Leu mutation in BAG3

Myofibrillary myopathies (MFM) are hereditary myopathies histologically characterized by degeneration of myofibrils and aggregation of proteins in striated muscle. Cardiomyopathy is common in MFM but the pathophysiological mechanisms are not well understood. The BAG3-Pro209Leu mutation is associated with early onset MFM and severe restrictive cardiomyopathy (RCM), often necessitating heart transplantation during childhood. We report on a young male patient with a BAG3-Pro209Leu mutation who underwent heart transplantation at eight years of age. Detailed morphological analyses of the explanted heart tissue showed intracytoplasmic inclusions, aggregation of BAG3 and desmin, disintegration of myofibers and Z-disk alterations. The presence of undegraded autophagosomes, seen by electron microscopy, as well as increased levels of p62, LC3-I and WIPI1, detected by immunohistochemistry and western blot analyses, indicated a dysregulation of autophagy. Parkin and PINK1, proteins involved in mitophagy, were slightly increased whereas mitochondrial OXPHOS activities were not altered. These findings indicate that altered autophagy plays a role in the pathogenesis and rapid progression of RCM in MFM caused by the BAG3-Pro209Leu mutation, which could have implications for future therapeutic strategies.

Association of Protein Distribution and Gene Expression Revealed by PET and Post-Mortem Quantification in the Serotonergic System of the Human Brain

Regional differences in posttranscriptional mechanisms may influence in vivo protein densities. The association of positron emission tomography (PET) imaging data from 112 healthy controls and gene expression values from the Allen Human Brain Atlas, based on post-mortem brains, was investigated for key serotonergic proteins. PET binding values and gene expression intensities were correlated for the main inhibitory (5-HT1A) and excitatory (5-HT2A) serotonin receptor, the serotonin transporter (SERT) as well as monoamine oxidase-A (MAO-A), using Spearman's correlation coefficients (rs) in a voxel-wise and region-wise analysis. Correlations indicated a strong linear relationship between gene and protein expression for both the 5-HT1A (voxel-wise rs = 0.71; region-wise rs = 0.93) and the 5-HT2A receptor (rs = 0.66; 0.75), but only a weak association for MAO-A (rs = 0.26; 0.66) and no clear correlation for SERT (rs = 0.17; 0.29). Additionally, region-wise correlations were performed using mRNA expression from the HBT, yielding comparable results (5-HT1Ars = 0.82; 5-HT2Ars = 0.88; MAO-A rs = 0.50; SERT rs = -0.01). The SERT and MAO-A appear to be regulated in a region-specific manner across the whole brain. In contrast, the serotonin-1A and -2A receptors are presumably targeted by common posttranscriptional processes similar in all brain areas suggesting the applicability of mRNA expression as surrogate parameter for density of these proteins.

The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research

The ISB Cancer Genomics Cloud (ISB-CGC) is one of three pilot projects funded by the National Cancer Institute to explore new approaches to computing on large cancer datasets in a cloud environment. With a focus on Data as a Service, the ISB-CGC offers multiple avenues for accessing and analyzing The Cancer Genome Atlas, TARGET, and other important references such as GENCODE and COSMIC using the Google Cloud Platform. The open approach allows researchers to choose approaches best suited to the task at hand: from analyzing terabytes of data using complex workflows to developing new analysis methods in common languages such as Python, R, and SQL; to using an interactive web application to create synthetic patient cohorts and to explore the wealth of available genomic data. Links to resources and documentation can be found at www.isb-cgc.org Cancer Res; 77(21); e7-10. ©2017 AACR.

Comparing a single-day swabbing regimen with an established 3-day protocol for MRSA decolonization control

OBJECTIVES

Success of methicillin-resistant Staphylococcus aureus (MRSA) decolonization procedures is usually verified by control swabs of the colonized body region. This prospective controlled study compared a single-day regimen with a well-established 3-day scheme for noninferiority and adherence to the testing scheme.

METHODS

Two sampling schemes for screening MRSA patients of a single study cohort at a German tertiary-care hospital 2 days after decolonization were compared regarding their ability to identify MRSA colonization in throat or nose. In each patient, three nose and three throat swabs were taken at 3- to 4-hour intervals during screening day 1, and in the same patients once daily on days 1, 2 and 3. Swabs were analysed using chromogenic agar and broth enrichment. The study aimed to investigate whether the single-day swabbing scheme is not inferior to the 3-day scheme with a 15% noninferiority margin.

RESULTS

One hundred sixty patients were included, comprising 105 and 101 patients with results on all three swabs for decolonization screening of the nose and throat, respectively. Noninferiority of the single-day swabbing scheme was confirmed for both pharyngeal and nasal swabs, with 91.8% and 89% agreement, respectively. The absolute difference of positivity rates between the swabbing regimens was 0.025 (-0.082, 0.131) for the nose and 0.006 (-0.102, 0.114) (95% confidence interval) for the pharynx as calculated with McNemar's test for matched or paired data. Compliance with the single-day scheme was better, with 12% lacking second-day swabs and 27% lacking third-day swabs from the nostrils.

CONCLUSIONS

The better adherence to the single-day screening scheme with noninferiority suggests its implementation as the new gold standard.

Emergence of dalbavancin non-susceptible, vancomycin-intermediate Staphylococcus aureus (VISA) after treatment of MRSA central line-associated bloodstream infection with a dalbavancin- and vancomycin-containing regimen

OBJECTIVES

Dalbavancin is a long-acting lipoglycopeptide with activity against gram-positives, including methicillin-resistant Staphylococcus aureus (MRSA). The potential for lipoglycopeptides, with half-lives greater than 1 week, to select for resistance is unknown. Here we explore a case of MRSA central line-associated bloodstream infection in which dalbavancin and vancomycin non-susceptibility emerged in a urine isolate collected after the patient was treated with vancomycin and dalbavancin sequentially.

METHODS

Isolates from blood and urine underwent susceptibility testing, and whole genome sequencing (WGS). The blood isolate was subjected to successive passage in vitro in the presence of escalating dalbavancin concentrations and the emergent isolate was subjected to repeat susceptibility testing and WGS.

RESULTS

The blood isolate was fully susceptible to vancomycin; however, MICs of the urine isolate to dalbavancin, vancomycin, telavancin, and daptomycin were at least fourfold higher than the blood-derived strain. Both strains were indistinguishable by spa and variable number tandem repeat (VNTR) typing, and WGS revealed only seven variants, indicating clonality. Four variants affected genes, including a 3bp in-frame deletion in yvqF, a gene which has been implicated in glycopeptide resistance. Vancomycin and dalbavancin non-susceptibility emerged in the blood isolate after successive passage in vitro in the presence of dalbavancin, and WGS identified a single non-synonymous variant in yvqF.

CONCLUSIONS

This is the first case in which VISA has emerged in the context of a dalbavancin-containing regimen. The selection for cross-resistance to vancomycin in vitro by dalbavancin exposure alone is troubling. Clinicians should be aware of the possibility for emergence of dalbavancin non-susceptibility and glycopeptide cross-resistance arising following therapy.