Reliability of panel-based mutational signatures for immune-checkpoint-inhibition efficacy prediction in non-small cell lung cancer

OBJECTIVES: Mutational signatures (MS) are gaining traction for deriving therapeutic insights for immune checkpoint inhibition (ICI). We asked if MS attributions from comprehensive targeted sequencing assays are reliable enough for predicting ICI efficacy in non-small cell lung cancer (NSCLC).METHODS: Somatic mutations of m = 126 patients were assayed using panel-based sequencing of 523 cancer-related genes. In silico simulations of MS attributions for various panels were performed on a separate dataset of m = 101 whole genome sequenced patients. Non-synonymous mutations were deconvoluted using COSMIC v3.3 signatures and used to test a previously published machine learning classifier.RESULTS: The ICI efficacy predictor performed poorly with an accuracy of 0.51 -0.09 +0.09, average precision of 0.52 -0.11 +0.11, and an area under the receiver operating characteristic curve of 0.50 -0.09 +0.10. Theoretical arguments, experimental data, and in silico simulations pointed to false negative rates (FNR) related to panel size. A secondary effect was observed, where deconvolution of small ensembles of point mutations lead to reconstruction errors and misattributions. CONCLUSION: MS attributions from current targeted panel sequencing are not reliable enough to predict ICI efficacy. We suggest that, for downstream classification tasks in NSCLC, signature attributions be based on whole exome or genome sequencing instead.</p

Evidence for tidal interaction and a supergiant HI shell in the Local Group dwarf galaxy NGC 6822

We present a wide-field, high spatial and velocity resolution map of the entire extended HI distribution of the Local Group dwarf galaxy NGC 6822. The observations were obtained with the Australia Telescope Compact Array in mosaicing mode. The interstellar medium of NGC 6822 is shaped by the presence of numerous H{\sc i} holes and shells, including a supergiant shell, and the effects of tidal interaction, in the form of a tidal arm and an infalling or interacting HI complex. The HI shell is situated outside the optical galaxy and occupies roughly a quarter of the area of the main HI disk. It measures 2.0 times 1.4 kpc, making it one of the largest supergiant HI shells ever found. The giant hole shows no signs of expansion and no obvious creation mechanism is evident from our data. If star formation was the cause, an energy equivalent of \~100 supernovae (10^53 erg) is needed to create the hole. We derive an upper limit for the age of order 100 Myr. The presence of a possible tidal arm indicates that NGC 6822 may recently have undergone some interaction. An HI complex located in the north-west of the galaxy may be the interaction partner. We argue that it is likely that these features were created about 100 Myr ago in an event that also enhanced the star formation rateComment: Accepted for publication in Astrophysical Journal Letters (needs emulateapj5.sty, included

Rotation Curves of Spiral Galaxies

Rotation curves of spiral galaxies are the major tool for determining the distribution of mass in spiral galaxies. They provide fundamental information for understanding the dynamics, evolution and formation of spiral galaxies. We describe various methods to derive rotation curves, and review the results obtained. We discuss the basic characteristics of observed rotation curves in relation to various galaxy properties, such as Hubble type, structure, activity, and environment.Comment: 40 pages, 6 gif figures; Ann. Rev. Astron. Astrophys. Vol. 39, p.137, 200

The Netherlands Arrhythmogenic Cardiomyopathy Registry:design and status update

BACKGROUND: Clinical research on arrhythmogenic cardiomyopathy (ACM) is typically limited by small patient numbers, retrospective study designs, and inconsistent definitions. AIM: To create a large national ACM patient cohort with a vast amount of uniformly collected high-quality data that is readily available for future research. METHODS: This is a multicentre, longitudinal, observational cohort study that includes (1) patients with a definite ACM diagnosis, (2) at-risk relatives of ACM patients, and (3) ACM-associated mutation carriers. At baseline and every follow-up visit, a medical history as well information regarding (non-)invasive tests is collected (e. g. electrocardiograms, Holter recordings, imaging and electrophysiological studies, pathology reports, etc.). Outcome data include (non-)sustained ventricular and atrial arrhythmias, heart failure, and (cardiac) death. Data are collected on a research electronic data capture (REDCap) platform in which every participating centre has its own restricted data access group, thus empowering local studies while facilitating data sharing. DISCUSSION: The Netherlands ACM Registry is a national observational cohort study of ACM patients and relatives. Prospective and retrospective data are obtained at multiple time points, enabling both cross-sectional and longitudinal research in a hypothesis-generating approach that extends beyond one specific research question. In so doing, this registry aims to (1) increase the scientific knowledge base on disease mechanisms, genetics, and novel diagnostic and treatment strategies of ACM; and (2) provide education for physicians and patients concerning ACM, e. g. through our website ( www.acmregistry.nl ) and patient conferences

INSPIRE: A European training network to foster research and training in cardiovascular safety pharmacology

Safety pharmacology is an essential part of drug development aiming to identify, evaluate and investigate undesirable pharmacodynamic properties of a drug primarily prior to clinical trials. In particular, cardiovascular adverse drug reactions (ADR) have halted many drug development programs. Safety pharmacology has successfully implemented a screening strategy to detect cardiovascular liabilities, but there is room for further refinement. In this setting, we present the INSPIRE project, a European Training Network in safety pharmacology for Early Stage Researchers (ESRs), funded by the European Commission's H2020-MSCA-ITN programme. INSPIRE has recruited 15 ESR fellows that will conduct an individual PhD-research project for a period of 36 months. INSPIRE aims to be complementary to ongoing research initiatives. With this as a goal, an inventory of collaborative research initiatives in safety pharmacology was created and the ESR projects have been designed to be complementary to this roadmap. Overall, INSPIRE aims to improve cardiovascular safety evaluation, either by investigating technological innovations or by adding mechanistic insight in emerging safety concerns, as observed in the field of cardio-oncology. Finally, in addition to its hands-on research pillar, INSPIRE will organize a number of summer schools and workshops that will be open to the wider community as well. In summary, INSPIRE aims to foster both research and training in safety pharmacology and hopes to inspire the future generation of safety scientists

Diclofenac Prolongs Repolarization in Ventricular Muscle with Impaired Repolarization Reserve

Background: The aim of the present work was to characterize the electrophysiological effects of the non-steroidal anti- inflammatory drug diclofenac and to study the possible proarrhythmic potency of the drug in ventricular muscle. Methods: Ion currents were recorded using voltage clamp technique in canine single ventricular cells and action potentials were obtained from canine ventricular preparations using microelectrodes. The proarrhythmic potency of the drug was investigated in an anaesthetized rabbit proarrhythmia model. Results: Action potentials were slightly lengthened in ventricular muscle but were shortened in Purkinje fibers by diclofenac (20 mM). The maximum upstroke velocity was decreased in both preparations. Larger repolarization prolongation was observed when repolarization reserve was impaired by previous BaCl 2 application. Diclofenac (3 mg/kg) did not prolong while dofetilide (25 mg/kg) significantly lengthened the QT c interval in anaesthetized rabbits. The addition of diclofenac following reduction of repolarization reserve by dofetilide further prolonged QT c . Diclofenac alone did not induce Torsades de Pointes ventricular tachycardia (TdP) while TdP incidence following dofetilide was 20%. However, the combination of diclofenac and dofetilide significantly increased TdP incidence (62%). In single ventricular cells diclofenac (30 mM) decreased the amplitude of rapid (I Kr ) and slow (I Ks ) delayed rectifier currents thereby attenuating repolarization reserve. L-type calcium current (I Ca ) was slightly diminished, but the transient outward (I to ) and inward rectifier (I K1 ) potassium currents were not influenced. Conclusions: Diclofenac at therapeutic concentrations and even at high dose does not prolong repolarization markedly and does not increase the risk of arrhythmia in normal heart. However, high dose diclofenac treatment may lengthen repolarization and enhance proarrhythmic risk in hearts with reduced repolarization reserve

Galaxy Populations and Evolution in Clusters IV: Deep HI Observations of Dwarf Ellipticals in the Virgo Cluster

We present in this paper the deepest Arecibo HI observations of Virgo cluster dwarf ellipticals (dEs) taken to date. Based on this data we argue that a significant fraction of Virgo cluster dEs recently underwent evolution. Our new observations consist of HI 21-cm line observations for 22 classified dE galaxies with optical radial velocities consistent with membership in the Virgo cluster. Cluster members VCC 390 and VCC 1713 are detected with HI masses M(HI) = 6*10^7 M_solar and 8*10^7 M_solar, respectively, while M(HI) in the remaining 20 dE galaxies have upper limits as low as 5*10^5 M_solar. We combine our results with those for 27 other Virgo cluster dEs with HI observations in the literature, 7 of which have HI detection claims. New optical images from the WIYN telescope of 5 of these HI-detected dEs, along with archival data, suggest that seven of the claimed detections are real, yielding a ~ 15% detection rate. These HI-detected classified dEs are preferentially located near the periphery of the Virgo cluster. Three Virgo dEs have observed HI velocity widths > 200 km/s, possibly indicating the presence of a large dark matter content, or transient extended HI. We discuss the possible origins of these objects and argue that they originate from field galaxies accreted onto high angular momentum orbits by Virgo in the last few Gyr. As a result these galaxies are slowly transformed within the cluster by gradual gas stripping processes, associated truncation of star formation, and passive fading of stellar populations. Low-mass early-type cluster galaxies are therefore currently being produced as the product of cluster environmental effects. We utilize our results to estimate the recent (past 1-3 Gyr) average mass accretion rate into the Virgo cluster, finding dM/dt ~ 50 M_solar/year.Comment: Accepted to ApJ, 21 page

HI in the Outskirts of Nearby Galaxies

The HI in disk galaxies frequently extends beyond the optical image, and can trace the dark matter there. I briefly highlight the history of high spatial resolution HI imaging, the contribution it made to the dark matter problem, and the current tension between several dynamical methods to break the disk-halo degeneracy. I then turn to the flaring problem, which could in principle probe the shape of the dark halo. Instead, however, a lot of attention is now devoted to understanding the role of gas accretion via galactic fountains. The current $\rm \Lambda$ cold dark matter theory has problems on galactic scales, such as the core-cusp problem, which can be addressed with HI observations of dwarf galaxies. For a similar range in rotation velocities, galaxies of type Sd have thin disks, while those of type Im are much thicker. After a few comments on modified Newtonian dynamics and on irregular galaxies, I close with statistics on the HI extent of galaxies.Comment: 38 pages, 17 figures, invited review, book chapter in "Outskirts of Galaxies", Eds. J. H. Knapen, J. C. Lee and A. Gil de Paz, Astrophysics and Space Science Library, Springer, in pres

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world’s largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org