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Significant association of cutaneous adverse events with hydroxyurea: Results from a prospective non-interventional study inBCR-ABL1-negative myeloproliferative neoplasms (MPN)-on behalf of the German Study Group-MPN.
No full textRequirement for LIM kinases in acute myeloid leukemia.
No full textAcute myeloid leukemia (AML) is an aggressive disease for which only few targeted therapies are available. Using high-throughput RNA interference (RNAi) screening in AML cell lines, we identified LIM kinase 1 (LIMK1) as a potential novel target for AML treatment. HighLIMK1expression was significantly correlated with shorter survival of AML patients and coincided withFLT3mutations,KMT2Arearrangements, and elevatedHOXgene expression. RNAi- and CRISPR-Cas9-mediated suppression as well as pharmacologic inhibition of LIMK1 and its close homolog LIMK2 reduced colony formation and decreased proliferation due to slowed cell-cycle progression ofKMT2A-rearranged AML cell lines and patient-derived xenograft (PDX) samples. This was accompanied by morphologic changes indicative of myeloid differentiation. Transcriptome analysis showed upregulation of several tumor suppressor genes as well as downregulation of HOXA9 targets and mitosis-associated genes in response to LIMK1 suppression, providing a potential mechanistic basis for the anti-leukemic phenotype. Finally, we observed a reciprocal regulation between LIM kinases (LIMK) and CDK6, a kinase known to be involved in the differentiation block ofKMT2A-rearranged AML, and addition of the CDK6 inhibitor palbociclib further enhanced the anti-proliferative effect of LIMK inhibition. Together, these data suggest that LIMK are promising targets for AML therapy
High-resolution spatiotemporal modeling of daily near-surface air temperature in Germany over the period 2000–2020.
No full textThe commonly used weather stations cannot fully capture the spatiotemporal variability of near-surface air temperature (Tair), leading to exposure misclassification and biased health effect estimates. We aimed to improve the spatiotemporal coverage of Tair data in Germany by using multi-stage modeling to estimate daily 1 × 1 km minimum (Tmin), mean (Tmean), maximum (Tmax) Tair and diurnal Tair range during 2000–2020. We used weather station Tair observations, satellite-based land surface temperature (LST), elevation, vegetation and various land use predictors. In the first stage, we built a linear mixed model with daily random intercepts and slopes for LST adjusted for several spatial predictors to estimate Tair from cells with both Tair and LST available. In the second stage, we used this model to predict Tair for cells with only LST available. In the third stage, we regressed the second stage predictions against interpolated Tair values to obtain Tair countrywide. All models achieved high accuracy (0.91 ≤ R2 ≤ 0.98) and low errors (1.03 °C ≤ Root Mean Square Error (RMSE) ≤ 2.02 °C). Validation with external data confirmed the good performance, locally, i.e., in Augsburg for all models (0.74 ≤ R2 ≤ 0.99, 0.87 °C ≤ RMSE ≤ 2.05 °C) and countrywide, for the Tmean model (0.71 ≤ R2 ≤ 0.99, 0.79 °C ≤ RMSE ≤ 1.19 °C). Annual Tmean averages ranged from 8.56 °C to 10.42 °C with the years beyond 2016 being constantly hotter than the 21-year average. The spatial variability within Germany exceeded 15 °C annually on average following patterns including mountains, rivers and urbanization. Using a case study, we showed that modeling leads to broader Tair variability representation for exposure assessment of participants in health cohorts. Our results indicate the proposed models as suitable for estimating nationwide Tair at high resolution. Our product is critical for temperature-based epidemiological studies and is also available for other research purposes
Clinical presentation and differential splicing of SRSF2, U2AF1 and SF3B1 mutations in patients with acute myeloid leukemia.
No full textPrevious studies demonstrated that splicing factor mutations are recurrent events in hematopoietic malignancies with both clinical and functional implications. However, their aberrant splicing patterns in acute myeloid leukemia remain largely unexplored. In this study, we characterized mutations in SRSF2, U2AF1, and SF3B1, the most commonly mutated splicing factors. In our clinical analysis of 2678 patients, splicing factor mutations showed inferior relapse-free and overall survival, however, these mutations did not represent independent prognostic markers. RNA-sequencing of 246 and independent validation in 177 patients revealed an isoform expression profile which is highly characteristic for each individual mutation, with several isoforms showing a strong dysregulation. By establishing a custom differential splice junction usage pipeline, we accurately detected aberrant splicing in splicing factor mutated samples. A large proportion of differentially used junctions were novel, including several junctions in leukemia-associated genes. In SRSF2(P95H) mutants, we further explored the possibility of a cascading effect through the dysregulation of the splicing pathway. Furthermore, we observed a validated impact on overall survival for two junctions overused in SRSF2(P95H) mutants. We conclude that splicing factor mutations do not represent independent prognostic markers. However, they do have genome-wide consequences on gene splicing leading to dysregulated isoform expression of several genes
Isolation of nuclei from flash-frozen liver tissue for single-cell multiomics.
No full textThe liver is a complex and heterogenous tissue responsible for carrying out many critical physiological functions, such as the maintenance of energy homeostasis and the metabolism of xenobiotics, among others. These tasks are performed through tight coordination between hepatic parenchymal and non-parenchymal cells. Additionally, various metabolic activities are confined to specific areas of the hepatic lobule-a phenomenon called liver zonation. Recent advances in single-cell sequencing technologies have empowered researchers to investigate tissue heterogeneity at a single-cell resolution. In many complex tissues, including the liver, harsh enzymatic and/or mechanical dissociation protocols can negatively affect the viability or the quality of the single-cell suspensions needed to comprehensively characterize this organ in health and disease. This paper describes a robust and reproducible protocol for isolating nuclei from frozen, archived liver tissues. This method yields high-quality nuclei that are compatible with downstream, single-cell omics approaches, including single-nucleus RNA-seq, assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), as well as multimodal omics (joint RNA-seq and ATAC-seq). This method has been successfully used for the isolation of nuclei from healthy and diseased human, mouse, and non-human primate frozen liver samples. This approach allows the unbiased isolation of all the major cell types in the liver and, therefore, offers a robust methodology for studying the liver at the single-cell resolution
Condensed tannins as antioxidants that protect poplar against oxidative stress from drought and UV-B.
No full textCondensed tannins (CTs, proanthocyanidins) are widespread polymeric flavan-3-ols known for their ability to bind proteins. In poplar (Populus spp.), leaf condensed tannins are induced by both biotic and abiotic stresses, suggesting diverse biological functions. Here we demonstrate the ability of CTs to function as physiological antioxidants, preventing oxidative and cellular damage in response to drought and UV-B irradiation. Chlorophyll fluorescence was used to monitor photosystem II performance, and both hydrogen peroxide and malondialdehyde content was assayed as a measure of oxidative damage. Transgenic MYB-overexpressing poplar (Populus tremula x tremuloides) with high CT content showed reduced photosystem damage and lower hydrogen peroxide and malondialdehyde content after drought and UV-B stress. This antioxidant effect of CT was observed using two different poplar MYB CT regulators, in multiple independent lines and different genetic backgrounds. Additionally, low-CT MYB134-RNAi transgenic poplars showed enhanced susceptibility to drought-induced oxidative stress. UV-B radiation had different impacts than drought on chlorophyll fluorescence, but all high-CT poplar lines displayed reduced sensitivity to both stresses. Our data indicate that CTs are significant defenses against oxidative stress. The broad distribution of CTs in forest systems which are exposed to diverse abiotic stresses suggests that these compounds have wider functional roles than previously realized. This article is protected by copyright. All rights reserved
Comprehensive assessment of dissolved organic matter processing in the Amazon River and its major tributaries revealed by positive and negative electrospray mass spectrometry and NMR spectroscopy.
No full textRivers are natural biogeochemical systems shaping the fates of dissolved organic matter (DOM) from leaving soils to reaching the oceans. This study focuses on Amazon basin DOM processing employing negative and positive electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI[±] FT-ICR MS) and nuclear magnetic resonance spectroscopy (NMR) to reveal effects of major processes on the compositional space and structural characteristics of black, white and clear water systems. These include non-conservative mixing at the confluences of (1) Solimões and the Negro River, (2) the Amazon River and the Madeira River, and (3) in-stream processing of Amazon River DOM between the Madeira River and the Tapajós River. The Negro River (black water) supplies more highly oxygenated and high molecular weight compounds, whereas the Solimões and Madeira Rivers (white water) contribute more CHNO and CHOS molecules to the Amazon River main stem. Aliphatic CHO and abundant CHNO compounds prevail in Tapajos River DOM (clear water), likely originating from primary production. Sorption onto particles and heterotrophic microbial degradation are probably the principal mechanisms for the observed changes in DOM composition in the Amazon River and its tributaries
Clinical validation of saliency maps for understanding deep neural networks in ophthalmology.
No full textDeep neural networks (DNNs) have achieved physician-level accuracy on many imaging-based medical diagnostic tasks, for example classification of retinal images in ophthalmology. However, their decision mechanisms are often considered impenetrable leading to a lack of trust by clinicians and patients. To alleviate this issue, a range of explanation methods have been proposed to expose the inner workings of DNNs leading to their decisions. For imaging-based tasks, this is often achieved via saliency maps. The quality of these maps are typically evaluated via perturbation analysis without experts involved. To facilitate the adoption and success of such automated systems, however, it is crucial to validate saliency maps against clinicians. In this study, we used three different network architectures and developed ensembles of DNNs to detect diabetic retinopathy and neovascular age-related macular degeneration from retinal fundus images and optical coherence tomography scans, respectively. We used a variety of explanation methods and obtained a comprehensive set of saliency maps for explaining the ensemble-based diagnostic decisions. Then, we systematically validated saliency maps against clinicians through two main analyses — a direct comparison of saliency maps with the expert annotations of disease-specific pathologies and perturbation analyses using also expert annotations as saliency maps. We found the choice of DNN architecture and explanation method to significantly influence the quality of saliency maps. Guided Backprop showed consistently good performance across disease scenarios and DNN architectures, suggesting that it provides a suitable starting point for explaining the decisions of DNNs on retinal images
Utility of outdoor central site monitoring in assessing exposure of school children to ultrafine particles.
No full textEpidemiological studies investigating the association between daily particle exposure and health effects are frequently based on a single monitoring site located in an urban background. Using a central site in epidemiological time-series studies has been established based on the premises of low spatial variability of particles within the areas of interest and hence the adequacy of the central sites to monitor the exposure. This is true to a large extent in relation to larger particles (PM2.5, PM10) that are typically monitored and regulated. However, the distribution of ultrafine particles (UFP), which in cities predominantly originate from traffic, is heterogeneous. With increasing pressure to improve the epidemiology of UFP, an important question to ask is, whether central site monitoring is representative of community exposure to this size fraction of particulate matter; addressing this question is the aim of this paper. To achieve this aim, we measured personal exposure to UFP, expressed as particle number concentration (PNC), using Philips Aerasense Nanotracers (NT) carried by the participants of the study, and condensation particle counters (CPC) or scanning mobility particle sizers (SMPS) at central fixed-site monitoring stations. The measurements were conducted at three locations in Brisbane (Australia), Cassino (Italy) and Accra (Ghana). We then used paired t-tests to compare the average personal and average fixed-site PNC measured over the same 24-h, and hourly, periods. We found that, at all three locations, the 24-h average fixed-site PNC was no different to the personal PNC, when averaged over the study period and all the participants. However, the corresponding hourly averages were significantly different at certain times of the day. These were generally times spent commuting and during cooking and eating at home. Our analysis of the data obtained in Brisbane, showed that maximum personal exposure occurred in the home microenvironment during morning breakfast and evening dinner time. The main source of PNC for personal exposure was from the home-microenvironment. We conclude that the 24-h average PNC from the central-site can be used to estimate the 24-h average personal exposure for a community. However, the hourly average PNC from the central site cannot consistently be used to estimate hourly average personal exposure, mainly because they are affected by very different sources
JMJD1C-mediated metabolic dysregulation contributes to HOXA9-dependent leukemogenesis.
No full textAbnormal metabolism is a fundamental hallmark of cancer and represents a therapeutic opportunity, yet its regulation by oncogenes remains poorly understood. Here, we uncover that JMJD1C, a jumonji C (JmjC)-containing H3K9 demethylase, is a critical regulator of aberrant metabolic processes in homeobox A9 (HOXA9)-dependent acute myeloid leukemia (AML). JMJD1C overexpression increases in vivo cell proliferation and tumorigenicity through demethylase-independent upregulation of a glycolytic and oxidative program, which sustains leukemic cell bioenergetics and contributes to an aggressive AML phenotype in vivo. Targeting JMJD1C-mediated metabolism via pharmacologic inhibition of glycolysis and oxidative phosphorylation led to ATP depletion, induced necrosis/apoptosis and decreased tumor growth in vivo in leukemias co-expressing JMJD1C and HOXA9. The anti-metabolic therapy effectively diminished AML stem/progenitor cells and reduced tumor burden in a primary AML patient-derived xenograft. Our data establish a direct link between drug responses and endogenous expression of JMJD1C and HOXA9 in human AML cell line-and patient-derived xenografts. These findings demonstrate a previously unappreciated role for JMJD1C in counteracting adverse metabolic changes and retaining the metabolic integrity during tumorigenesis, which can be exploited therapeutically