Publications by authors named "Andreas Keller"

331 Publications

Sex Differences in Cardiovascular Research: A Scientometric Analysis.

J Am Heart Assoc 2021 Oct 11:e021522. Epub 2021 Oct 11.

Department of Internal Medicine III, Cardiology, Angiology, Intensive Care Medicine Saarland University Hospital Homburg Saar Germany.

Background We sought to investigate sex-specific differences in authorship of cardiovascular research over the past decade. Methods and Results All 387 463 cardiovascular publications between 2010 and 2019 were retrieved from Web of Science. Articles increased from 19 960 to 29 604 articles per year (>0.001). The number of articles written by female first authors increased by 76.3% (6434-11 343 articles) and by 35.0% for male first authors (13 526-18 261) (<0.001). The first author was more likely to be a female author in articles with female last authors. The median impact factor (IF) for articles by female first authors was lower (2.46 [interquartile range, 7 1.11-4.03] versus 2.51 [interquartile range, 1.17-4.10]; <0.001). Female authorship articles reached the highest IF in North America (average IF, 3.7), with the lowest in Africa (average IF, 1.8). Conclusions Publications in cardiovascular research have increased over the past decade, particularly by female authors. Female researchers are cited less often compared with their male peers. The IF remains lower for articles by female researchers.
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http://dx.doi.org/10.1161/JAHA.121.021522DOI Listing
October 2021

GeneTrail: A Framework for the Analysis of High-Throughput Profiles.

Front Mol Biosci 2021 16;8:716544. Epub 2021 Sep 16.

Center for Bioinformatics, Saarland Informatics Campus, Saarbrücken, Germany.

Experimental high-throughput techniques, like next-generation sequencing or microarrays, are nowadays routinely applied to create detailed molecular profiles of cells. In general, these platforms generate high-dimensional and noisy data sets. For their analysis, powerful bioinformatics tools are required to gain novel insights into the biological processes under investigation. Here, we present an overview of the GeneTrail tool suite that offers rich functionality for the analysis and visualization of (epi-)genomic, transcriptomic, miRNomic, and proteomic profiles. Our framework enables the analysis of standard bulk, time-series, and single-cell measurements and includes various state-of-the-art methods to identify potentially deregulated biological processes and to detect driving factors within those deregulated processes. We highlight the capabilities of our web service with an analysis of a single-cell COVID-19 data set that demonstrates its potential for uncovering complex molecular mechanisms. GeneTrail can be accessed freely and without login requirements at http://genetrail.bioinf.uni-sb.de.
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http://dx.doi.org/10.3389/fmolb.2021.716544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8481803PMC
September 2021

Hemoglobin Absorption Spectral Imaging (H.A.S.I.): a novel optical staining technique for microlaryngoscopy.

Eur Arch Otorhinolaryngol 2021 Sep 28. Epub 2021 Sep 28.

ATMOS MedizinTechnik GmbH and Co. KG, 79853, Lenzkirch, Germany.

Purpose: Optical image enhancement techniques are widely used in endoscopy to improve the visualization of blood vessels for diagnostic and therapeutic purposes. These techniques are monitor-based and therefore not available for direct microscopy. In this study, a novel optical microscope filter, Hemoglobin absorption spectral imaging (H.A.S.I.) was tested for use in microlaryngoscopy.

Methods: A novel dichroic filter was designed to improve contrast in small blood vessels by highlighting transmission in the spectrum range of hemoglobin absorption maxima. A surgical microscope equipped with the novel H.A.S.I. filter was installed in one operating room in our institution. 68 consecutive patients referred to our ENT department for endoscopy were examined using white light and the novel H.A.S.I. filter during microlaryngoscopy. Surgeons described the blood vessels of the vocal cords using a classification chart and assessed for suspected malignancy using both white light and H.A.S.I.

Results: 77 consecutive microlaryngoscopies were performed on 68 patients. 142 vocal cords were visualized in microlaryngoscopy and the blood vessels classified according to the chart. With white light, 152 blood vessel characteristics were documented and 157 with H.A.S.I. Notably, pathologies like benign horizontal blood vessel changes, leukoplakia, and vertical blood vessel changes like dots and loops were seen more frequently with H.A.S.I. Finally, seven lesions were treated by transoral laser microsurgery (TLM) with H.A.S.I. to test the practicability of the method for microlaryngoscopic laser surgery.

Conclusion: This is the first study describing H.A.S.I. as an optical staining method for microlaryngoscopy. In our experience, the method was practical and improved the evaluation of vocal cord blood vessels. In some cases, the use of H.A.S.I. led to a change in diagnosis and treatment. Also, H.A.S.I. was found to be helpful in microlaryngeal laser surgery for demarcating resection margins. This is, to our knowledge, the first optical staining method integrated into a surgical microscope and can be conveniently used during microlaryngeal laser surgery and does not require further equipment.
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http://dx.doi.org/10.1007/s00405-021-07090-zDOI Listing
September 2021

miRNATissueAtlas2: an update to the human miRNA tissue atlas.

Nucleic Acids Res 2021 Sep 27. Epub 2021 Sep 27.

Center for Human and Molecular Biology, Junior Research Group Human Genetics, Saarland University, 66421 Homburg, Germany.

Small non-coding RNAs (sncRNAs) are pervasive regulators of physiological and pathological processes. We previously developed the human miRNA Tissue Atlas, detailing the expression of miRNAs across organs in the human body. Here, we present an updated resource containing sequencing data of 188 tissue samples comprising 21 organ types retrieved from six humans. Sampling the organs from the same bodies minimizes intra-individual variability and facilitates the making of a precise high-resolution body map of the non-coding transcriptome. The data allow shedding light on the organ- and organ system-specificity of piwi-interacting RNAs (piRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs) and other non-coding RNAs. As use case of our resource, we describe the identification of highly specific ncRNAs in different organs. The update also contains 58 samples from six tissues of the Tabula Muris collection, allowing to check if the tissue specificity is evolutionary conserved between Homo sapiens and Mus musculus. The updated resource of 87 252 non-coding RNAs from nine non-coding RNA classes for all organs and organ systems is available online without any restrictions (https://www.ccb.uni-saarland.de/tissueatlas2).
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http://dx.doi.org/10.1093/nar/gkab808DOI Listing
September 2021

Distinct Patterns of Blood Cytokines Beyond a Cytokine Storm Predict Mortality in COVID-19.

J Inflamm Res 2021 15;14:4651-4667. Epub 2021 Sep 15.

Department of Internal Medicine and Pulmonology, SHG-Hospital Völklingen, Saarbrücken, 66333, Germany.

Background: COVID-19 comprises several severity stages ranging from oligosymptomatic disease to multi-organ failure and fatal outcomes. The mechanisms why COVID-19 is a mild disease in some patients and progresses to a severe multi-organ and often fatal disease with respiratory failure are not known. Biomarkers that predict the course of disease are urgently needed. The aim of this study was to evaluate a large spectrum of established laboratory measurements.

Patients And Methods: Patients from the prospective PULMPOHOM and CORSAAR studies were recruited and comprised 35 patients with COVID-19, 23 with conventional pneumonia, and 28 control patients undergoing elective non-pulmonary surgery. Venous blood was used to measure the serum concentrations of 79 proteins by Luminex multiplex immunoassay technology. Distribution of biomarkers between groups and association with disease severity and outcomes were analyzed.

Results: The biomarker profiles between the three groups differed significantly with elevation of specific proteins specific for the respective conditions. Several biomarkers correlated significantly with disease severity and death. Uniform manifold approximation and projection (UMAP) analysis revealed a significant separation of the three disease groups and separated between survivors and deceased patients. Different models were developed to predict mortality based on the baseline measurements of several protein markers. A score combining IL-1ra, IL-8, IL-10, MCP-1, SCF and CA-9 was associated with significantly higher mortality (AUC 0.929).

Discussion: Several newly identified blood markers were significantly increased in patients with severe COVID-19 (AAT, EN-RAGE, myoglobin, SAP, TIMP-1, vWF, decorin) or in patients that died (IL-1ra, IL-8, IL-10, MCP-1, SCF, CA-9). The use of established assay technologies allows for rapid translation into clinical practice.
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http://dx.doi.org/10.2147/JIR.S320685DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8451220PMC
September 2021

Disrupting biological sensors of force promotes tissue regeneration in large organisms.

Nat Commun 2021 09 6;12(1):5256. Epub 2021 Sep 6.

Department of Surgery, Division of Plastic and Reconstructive Surgery, Stanford University School of Medicine, Stanford, CA, USA.

Tissue repair and healing remain among the most complicated processes that occur during postnatal life. Humans and other large organisms heal by forming fibrotic scar tissue with diminished function, while smaller organisms respond with scarless tissue regeneration and functional restoration. Well-established scaling principles reveal that organism size exponentially correlates with peak tissue forces during movement, and evolutionary responses have compensated by strengthening organ-level mechanical properties. How these adaptations may affect tissue injury has not been previously examined in large animals and humans. Here, we show that blocking mechanotransduction signaling through the focal adhesion kinase pathway in large animals significantly accelerates wound healing and enhances regeneration of skin with secondary structures such as hair follicles. In human cells, we demonstrate that mechanical forces shift fibroblasts toward pro-fibrotic phenotypes driven by ERK-YAP activation, leading to myofibroblast differentiation and excessive collagen production. Disruption of mechanical signaling specifically abrogates these responses and instead promotes regenerative fibroblast clusters characterized by AKT-EGR1.
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http://dx.doi.org/10.1038/s41467-021-25410-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8421385PMC
September 2021

Towards the sustainable discovery and development of new antibiotics.

Nat Rev Chem 2021 Aug 19:1-24. Epub 2021 Aug 19.

Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University Campus E8.1, Saarbrücken, Germany.

An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.
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http://dx.doi.org/10.1038/s41570-021-00313-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8374425PMC
August 2021

Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells.

Nat Commun 2021 07 14;12(1):4316. Epub 2021 Jul 14.

Division of Personalized Tumor Therapy, Fraunhofer-Institute for Toxicology and Experimental Medicine, Regensburg, Germany.

Molecular single cell analyses provide insights into physiological and pathological processes. Here, in a stepwise approach, we first evaluate 19 protocols for single cell small RNA sequencing on MCF7 cells spiked with 1 pg of 1,006 miRNAs. Second, we analyze MCF7 single cell equivalents of the eight best protocols. Third, we sequence single cells from eight different cell lines and 67 circulating tumor cells (CTCs) from seven SCLC patients. Altogether, we analyze 244 different samples. We observe high reproducibility within protocols and reads covered a broad spectrum of RNAs. For the 67 CTCs, we detect a median of 68 miRNAs, with 10 miRNAs being expressed in 90% of tested cells. Enrichment analysis suggested the lung as the most likely organ of origin and enrichment of cancer-related categories. Even the identification of non-annotated candidate miRNAs was feasible, underlining the potential of single cell small RNA sequencing.
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http://dx.doi.org/10.1038/s41467-021-24611-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8280203PMC
July 2021

Differential degradation of RNA species by autophagy related pathways in Arabidopsis.

J Exp Bot 2021 Jul 9. Epub 2021 Jul 9.

Department of Biology, Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany.

The plant vacuole recycles proteins and RNA delivered to it by autophagy. Here, we provide a comprehensive characterization of the plant vacuolar RNAome by isolating intact vacuoles from Arabidopsis plants, subsequent RNA purification and deep sequencing. In the vacuolar RNAomes, we detected ribosomal RNAs, and transfer RNAs, including those of chloroplast origin and small RNA types in addition. As autophagy is a main mechanism for the transport of RNA to the vacuole, atg5-1 mutants deficient in autophagy were included in our analysis. We observed severely reduced amounts of most chloroplast-derived RNA species in these mutants. By comparison with the cellular RNA composition, indications for the upregulation of alternative RNA breakdown pathways were obtained. By contrast, vacuolar RNA processing and composition in plants lacking vacuolar ribonuclease 2, involved in cellular RNA homeostasis, only showed minor alterations, possibly because of the presence of further so far unknown vacuolar RNase species. Among the small RNA types, we detected mature miRNAs in all vacuolar preparations but at much lower frequency in atg5-1, raising the possibility of a biological role for vacuolar miRNAs.
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http://dx.doi.org/10.1093/jxb/erab321DOI Listing
July 2021

Characterization of micro-RNA in women with different ovarian reserve.

Sci Rep 2021 06 25;11(1):13351. Epub 2021 Jun 25.

Institute of Human Genetics, Saarland University, 66421, Homburg, Saar, Germany.

Women undergoing infertility treatment are routinely subjected to one or more tests of ovarian reserve. Therefore, an adequate assessment of the ovarian reserve is necessary for the treatment. In this study, we aimed to characterize the potential role of microRNAs (miRNAs) as biomarkers for women with different ovarian reserves. A total of 159 women were recruited in the study and classified according to their anti-Müllerian hormone (AMH) level into three groups: (1) low ovarian reserve (LAMH, n = 39), (2) normal ovarian reserve (NAMH, n = 80), and (3) high ovarian reserve (HAMH, n = 40). SurePrint Human miRNA array screening and reverse transcription-quantitative PCR (RT-qPCR) were respectively employed to screen and validate the miRNA abundance level in the three tested groups. Compared with NAMH, the abundance level of 34 and 98 miRNAs was found to be significantly altered in LAMH and HAMH, respectively. The abundance level of miRNAs was further validated by RT-qPCR in both, the screening samples as well as in an independent set of validation samples. The abundance levels of the validated miRNAs were significantly correlated with the AMH level. The best AUC value for the prediction of the increase and decrease in the AMH level was obtained for the miR-100-5p and miR-21-5p, respectively. The level of miRNAs abundance correlates with the level of AMH, which may serve as a tool for identifying women with a different ovarian reserve and may help to lay the ground for the development of novel diagnostic approaches.
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http://dx.doi.org/10.1038/s41598-021-92901-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8233349PMC
June 2021

hsa-miR-374b-5p regulates expression of the gene U2AF homology motif (UHM) kinase 1.

J Periodontal Res 2021 Jun 23. Epub 2021 Jun 23.

Charité - University Medicine Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.

Objective: We aimed to identify a microRNA (miRNA) that is significantly upregulated in blood and in cells of the oral mucosa upon exposure to the periodontitis main risk factors oral inflammation and tobacco smoke, to subsequently identify its target gene and to describe the molecular mechanism of gene regulation.

Background: miRNAs are associated with many disorders. Array-based miRNA expression studies indicated a number of differentially expressed miRNAs in the pathology of oral diseases. However, these miRNAs mostly lacked replication, and their target genes have remained unknown.

Methods: 863 miRNAs were analyzed in blood from 18 PD cases and 70 controls (Geniom Biochip). Selected miRNAs were analyzed for upregulation in the inflamed oral mucosa of PD patients using published miRNA expression profiling studies from gingival cells. hsa-miR-374b-5p mimic was overexpressed in primary gingival fibroblasts (pGFs) from 3 donors, and genome-wide mRNA expression was quantified (Clarion Array). Gene-specific regulation was validated by qRT-PCR and Luciferase activity in HeLa cells.

Results: hsa-miR-374b-5p showed >twofold change (FC) in 3 independent studies performed in blood, gingival tissues, and cells. After hsa-miR-374b-5p overexpression, genome-wide expression analysis showed UHMK1 as top 1 downregulated gene in pGFs (p = 2.5 × 10 , fold change = -1.8). Reporter genes demonstrated that hsa-miR-374b-5p downregulates mRNA levels (p = .02; FC = -1.5), leading to reduction in protein activity (p = .013, FC = -1.3).

Conclusions: hsa-miR-374b-5p is upregulated in blood and ginvial cells exposed to oral inflammation and tobacco smoke and regulates UHMK1, which has a role in osteoclast differentiation.
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http://dx.doi.org/10.1111/jre.12913DOI Listing
June 2021

Dysregulation of brain and choroid plexus cell types in severe COVID-19.

Nature 2021 07 21;595(7868):565-571. Epub 2021 Jun 21.

ChEM-H, Stanford University, Stanford, CA, USA.

Although SARS-CoV-2 primarily targets the respiratory system, patients with and survivors of COVID-19 can suffer neurological symptoms. However, an unbiased understanding of the cellular and molecular processes that are affected in the brains of patients with COVID-19 is missing. Here we profile 65,309 single-nucleus transcriptomes from 30 frontal cortex and choroid plexus samples across 14 control individuals (including 1 patient with terminal influenza) and 8 patients with COVID-19. Although our systematic analysis yields no molecular traces of SARS-CoV-2 in the brain, we observe broad cellular perturbations indicating that barrier cells of the choroid plexus sense and relay peripheral inflammation into the brain and show that peripheral T cells infiltrate the parenchyma. We discover microglia and astrocyte subpopulations associated with COVID-19 that share features with pathological cell states that have previously been reported in human neurodegenerative disease. Synaptic signalling of upper-layer excitatory neurons-which are evolutionarily expanded in humans and linked to cognitive function-is preferentially affected in COVID-19. Across cell types, perturbations associated with COVID-19 overlap with those found in chronic brain disorders and reside in genetic variants associated with cognition, schizophrenia and depression. Our findings and public dataset provide a molecular framework to understand current observations of COVID-19-related neurological disease, and any such disease that may emerge at a later date.
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http://dx.doi.org/10.1038/s41586-021-03710-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8400927PMC
July 2021

Deep learning-based detection of eosinophilic esophagitis.

Endoscopy 2021 May 31. Epub 2021 May 31.

Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany.

Background:  For eosinophilic esophagitis (EoE), a substantial diagnostic delay is still a clinically relevant phenomenon. Deep learning-based algorithms have demonstrated potential in medical image analysis. Here we establish a convolutional neuronal network (CNN)-based approach that can distinguish the appearance of EoE from normal findings and candida esophagitis.

Methods:  We trained and tested a CNN using 484 real-world endoscopic images from 134 subjects consisting of three classes (normal, EoE, and candidiasis). Images were split into two completely independent datasets. The proposed approach was evaluated against three trainee endoscopists using the test set. Model-explainability was enhanced by deep Taylor decomposition.

Results:  Global accuracy (0.915 [95 % confidence interval (CI) 0.880-0.940]), sensitivity (0.871 [95 %CI 0.819-0.910]), and specificity (0.936 [95 %CI 0.910-0.955]) were significantly higher than for the endoscopists on the test set. Global area under the receiver operating characteristic curve was 0.966 [95 %CI 0.954-0.975]. Results were highly reproducible. Explainability analysis found that the algorithm identified the characteristic signs also used by endoscopists.

Conclusions:  Complex endoscopic classification tasks including more than two classes can be solved by CNN-based algorithms. Therefore, our algorithm may assist clinicians in making the diagnosis of EoE.
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http://dx.doi.org/10.1055/a-1520-8116DOI Listing
May 2021

Swarm Learning for decentralized and confidential clinical machine learning.

Nature 2021 06 26;594(7862):265-270. Epub 2021 May 26.

Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Bonn, Germany.

Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine. Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation. Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning-a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine.
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http://dx.doi.org/10.1038/s41586-021-03583-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8189907PMC
June 2021

Aviator: a web service for monitoring the availability of web services.

Nucleic Acids Res 2021 07;49(W1):W46-W51

Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.

With Aviator, we present a web service and repository that facilitates surveillance of online tools. Aviator consists of a user-friendly website and two modules, a literature-mining based general and a manually curated module. The general module currently checks 9417 websites twice a day with respect to their availability and stores many features (frontend and backend response time, required RAM and size of the web page, security certificates, analytic tools and trackers embedded in the webpage and others) in a data warehouse. Aviator is also equipped with an analysis functionality, for example authors can check and evaluate the availability of their own tools or those of their peers. Likewise, users can check the availability of a certain tool they intend to use in research or teaching to avoid including unstable tools. The curated section of Aviator offers additional services. We provide API snippets for common programming languages (Perl, PHP, Python, JavaScript) as well as an OpenAPI documentation for embedding in the backend of own web services for an automatic test of their function. We query the respective APIs twice a day and send automated notifications in case of an unexpected result. Naturally, the same analysis functionality as for the literature-based module is available for the curated section. Aviator can freely be used at https://www.ccb.uni-saarland.de/aviator.
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http://dx.doi.org/10.1093/nar/gkab396DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262725PMC
July 2021

miRTargetLink 2.0-interactive miRNA target gene and target pathway networks.

Nucleic Acids Res 2021 07;49(W1):W409-W416

Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.

Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.
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http://dx.doi.org/10.1093/nar/gkab297DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262750PMC
July 2021

The Impact of Focus and Context Visualization Techniques on Depth Perception in Optical See-Through Head-Mounted Displays.

IEEE Trans Vis Comput Graph 2021 May 12;PP. Epub 2021 May 12.

Estimating the depth of virtual content has proven to be a challenging task in Augmented Reality (AR) applications. Existing studies have shown that the visual system uses multiple depth cues to infer the distance of objects, occlusion being one of the most important ones. Generating appropriate occlusions becomes particularly important for AR applications that require the visualization of augmented objects placed below a real surface. Examples of these applications are medical scenarios in which anatomical information needs to be observed within the patients body. In this regard, existing works have proposed several focus and context (F+C) approaches to aid users in visualizing this content using Video See-Through (VST) Head-Mounted Displays (HMDs). However, the implementation of these approaches in Optical See-Through (OST) HMDs remains an open question due to the additive characteristics of the display technology. In this paper, we, for the first time, design and conduct a user study that compares depth estimation between VST and OST HMDs using existing in-situ visualization methods. Our results show that these visualizations cannot be directly transferred to OST displays without increasing error in depth perception tasks. To tackle this gap, we perform a structured decomposition of the visual properties of AR F+C methods to find best-performing combinations. We propose the use of chromatic shadows and hatching approaches transferred from computer graphics. In a second study, we perform a factorized analysis of these combinations, showing that varying the shading type and using colored shadows can lead to better depth estimation when using OST HMDs.
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http://dx.doi.org/10.1109/TVCG.2021.3079849DOI Listing
May 2021

miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale.

Nucleic Acids Res 2021 07;49(W1):W397-W408

Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.

Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.
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http://dx.doi.org/10.1093/nar/gkab268DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8262700PMC
July 2021

MicroRNA-targeting in spermatogenesis: Over-expressions of microRNA-23a/b-3p and its affected targeting of the genes ODF2 and UBQLN3 in spermatozoa of patients with oligoasthenozoospermia.

Andrology 2021 07 30;9(4):1137-1144. Epub 2021 Mar 30.

Institute of Human Genetics, Saarland University, Homburg, Germany.

Background: Male infertility is a multifactorial syndrome with diverse phenotypic representations. MicroRNAs (miRNAs) are small, non-coding RNAs that are involved in the post-transcriptional regulation of gene expression. Altered abundance levels of ODF2 and UBQLN3 have been reported in patients with different spermatogenic impairments. However, the transcriptional regulation of these two genes by miR-23a/b-3p is still unclear.

Objectives: To investigate experimentally whether miR-23a/b-3p targets the genes ODF2 and UBQLN3 and whether this targeting impacts abundance levels of ODF2 and UBQLN3 in patients with oligoasthenozoospermia.

Materials And Methods: A total of 92 men attending a fertility clinic were included in the study, including 46 oligoasthenozoospermic men and 46 age-matched normozoospermic volunteers who served as controls. Reverse transcription-quantitative PCR (RT-qPCR), Western blot, and dual-luciferase (Firefly-Renilla) assays were used to validate the miRNAs and their target genes.

Results: RT-qPCR revealed that miR-23a/b-3p was more abundant and ODF2 and UBQLN3 targets were less abundant in men with impaired spermatogenesis. Besides, Western blot shows that ODF2 and UBQLN3 protein levels were reduced in men with impaired spermatogenesis. In silico prediction and dual-luciferase assays revealed that potential links exist between the higher abundance level of miR-23a/b-3p and the lower abundance level of ODF2 and UBQLN3 targets. Mutations in the miR-23a/b-3p-binding site within the 3'UTRs (3'untranslated regions) of ODF2 and UBQLN3 genes resulted in abrogated responsiveness to miR-23a/b-3p. Correlation analysis showed that sperm count, motility, and morphology were negatively correlated with miR-23a/b-3p and positively correlated with the lower abundance level of UBQLN3, while ODF lower abundance level was positively correlated with sperm motility.

Conclusion: Findings indicate that the higher abundance level of miR-23a/b-3p and the lower abundance level of ODF2 and UBQLN3 targets are associated with oligoasthenozoospermia and male subfertility.
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http://dx.doi.org/10.1111/andr.13004DOI Listing
July 2021

Energy Metabolites as Biomarkers in Ischemic and Dilated Cardiomyopathy.

Int J Mol Sci 2021 Feb 18;22(4). Epub 2021 Feb 18.

Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany.

With more than 25 million people affected, heart failure (HF) is a global threat. As energy production pathways are known to play a pivotal role in HF, we sought here to identify key metabolic changes in ischemic- and non-ischemic HF by using a multi-OMICS approach. Serum metabolites and mRNAseq and epigenetic DNA methylation profiles were analyzed from blood and left ventricular heart biopsy specimens of the same individuals. In total we collected serum from = 82 patients with Dilated Cardiomyopathy (DCM) and = 51 controls in the screening stage. We identified several metabolites involved in glycolysis and citric acid cycle to be elevated up to 5.7-fold in DCM ( = 1.7 × 10). Interestingly, cardiac mRNA and epigenetic changes of genes encoding rate-limiting enzymes of these pathways could also be found and validated in our second stage of metabolite assessment in = 52 DCM, = 39 ischemic HF and = 57 controls. In conclusion, we identified a new set of metabolomic biomarkers for HF. We were able to identify underlying biological cascades that potentially represent suitable intervention targets.
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http://dx.doi.org/10.3390/ijms22041999DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7923201PMC
February 2021

MicroRNA-29b/c-3p Indicate Advanced Liver Fibrosis/Cirrhosis in Univentricular Heart Patients With and Without Fontan Palliation.

Front Cardiovasc Med 2020 8;7:619083. Epub 2021 Jan 8.

Department of Pediatric Cardiology, Saarland University Medical Center, Homburg, Germany.

The present study aims to identify those microRNAs (miRNAs) in patients with univentricular heart (UVH) disease with and without Fontan palliation that may be associated with advanced liver fibrosis/cirrhosis. SurePrint™ 8 × 60K Human v21 miRNA arrays were used to determine the miRNA abundance profiles in the blood of 48 UVH patients with and without Fontan palliation and 32 matched healthy controls. The abundance levels of selected miRNAs have been validated by quantitative reverse transcription-polymerase chain reaction (RT-qPCR). According to microarray analysis, 50 miRNAs were found to be significantly abundant in UVH patients of which miR-29b-3p and miR-29c-3p were significantly related to the model of end-stage liver disease (MELD)-Albumin and albumin-bilirubin (ALBI) score representing advanced liver fibrosis/cirrhosis. Relative expression levels of both miRNAs were significantly higher in patients with a higher collapsibility index representing venous hepatic congestion, a higher MELD-Albumin or ALBI score and incomplete or no Fontan palliation. In the logistic regression analysis, a MELD-Albumin score ≥ 11 or ALBI score > -2.6 were best predicted by total bilirubin (OR 6.630, = 0.016), albumin (OR 0.424, = 0.026), and miR-29c-3p (OR 33.060, = 0.047). After adjustment to the status of Fontan palliation, however, no statistical significance of these parameters was found thus underlining the importance of palliation status on progression of liver fibrosis/ cirrhosis in UVH patients. In UVH patients with and without Fontan palliation, miR-29b-3p and miR-29c-3p seem to be markers of advanced liver fibrosis/cirrhosis and thus may be used in the risk assessment of these patients.
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http://dx.doi.org/10.3389/fcvm.2020.619083DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820747PMC
January 2021

Encyclopedia of tools for the analysis of miRNA isoforms.

Brief Bioinform 2021 07;22(4)

Saarland Center for Bioinformatics and Chair for Clinical Bioinformatics, Saarland University Building E2.1, 66123 Saarbrücken, Germany.

RNA sequencing data sets rapidly increase in quantity. For microRNAs (miRNAs), frequently dozens to hundreds of billion reads are generated per study. The quantification of annotated miRNAs and the prediction of new miRNAs are leading computational tasks. Now, the increased depth of coverage allows to gain deeper insights into the variability of miRNAs. The analysis of isoforms of miRNAs (isomiRs) is a trending topic, and a range of computational tools for the analysis of isomiRs has been developed. We provide an overview on 27 available computational solutions for the analysis of isomiRs. These include both stand-alone programs (17 tools) and web-based solutions (10 tools) and span a publication time range from 2010 to 2020. Seven of the tools were published in 2019 and 2020, confirming the rising importance of the topic. While most of the analyzed tools work for a broad range of organisms or are completely independent of a reference organism, several tools have been tailored for the analysis of human miRNA data or for plants. While 14 of the tools are general analysis tools of miRNAs, and isomiR analysis is one of their features, the remaining 13 tools have specifically been developed for isomiR analysis. A direct comparison on 20 deep sequencing data sets for selected tools provides insights into the heterogeneity of results. With our work, we provide users a comprehensive overview on the landscape of isomiR analysis tools and in that support the selection of the most appropriate tool for their respective research task.
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http://dx.doi.org/10.1093/bib/bbaa346DOI Listing
July 2021

A multivariable miRNA signature delineates the systemic hemodynamic impact of arteriovenous shunt placement in a pilot study.

Sci Rep 2020 12 11;10(1):21809. Epub 2020 Dec 11.

BG Trauma Center Ludwigshafen, Heidelberg University, Ludwigshafen, Germany.

Arteriovenous (AV) fistulas for hemodialysis can lead to cardiac volume loading and increased serum brain natriuretic peptide (BNP) levels. Whether short-term AV loop placement in patients undergoing microsurgery has an impact on cardiac biomarkers and circulating microRNAs (miRNAs), potentially indicating an increased hemodynamic risk, remains elusive. Fifteen patients underwent AV loop placement with delayed free flap anastomosis for microsurgical reconstructions of lower extremity soft-tissue defects. N-terminal pro-BNP (NT-proBNP), copeptin (CT-proAVP), and miRNA expression profiles were determined in the peripheral blood before and after AV loop placement. MiRNA expression in the blood was correlated with miRNA expression from AV loop vascular tissue. Serum NT-proBNP and copeptin levels exceeded the upper reference limit after AV loop placement, with an especially strong NT-proBNP increase in patients with preexistent cardiac diseases. A miRNA signature of 4 up-regulated (miR-3198, miR-3127-5p, miR-1305, miR-1288-3p) and 2 down-regulated miRNAs (miR30a-5p, miR-145-5p) which are related to cardiovascular physiology, showed a significant systemic deregulation in blood and venous tissue after AV loop placement. AV loop placement causes serum elevations of NT-proBNP, copeptin as well as specific circulating miRNAs, indicating a potentially increased hemodynamic risk for patients with cardiovascular comorbidities, if free flap anastomosis is delayed.
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http://dx.doi.org/10.1038/s41598-020-78905-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7733519PMC
December 2020

Validation of human microRNA target pathways enables evaluation of target prediction tools.

Nucleic Acids Res 2021 01;49(1):127-144

Institute of Human Genetics, Saarland University, 66421 Homburg, Germany.

MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9% of the target genes for miR-34a-5p and 46.7% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.
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http://dx.doi.org/10.1093/nar/gkaa1161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7797041PMC
January 2021

A Disinhibitory Circuit for Contextual Modulation in Primary Visual Cortex.

Neuron 2020 12 9;108(6):1181-1193.e8. Epub 2020 Dec 9.

Department of Physiology, University of California, San Francisco, San Francisco, CA 94158-0444, USA; Center for Neural Circuits and Behavior, Neurobiology Section and Department of Neuroscience, University of California, San Diego, La Jolla, CA 92093-0634, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, USA. Electronic address:

Context guides perception by influencing stimulus saliency. Accordingly, in visual cortex, responses to a stimulus are modulated by context, the visual scene surrounding the stimulus. Responses are suppressed when stimulus and surround are similar but not when they differ. The underlying mechanisms remain unclear. Here, we use optical recordings, manipulations, and computational modeling to show that disinhibitory circuits consisting of vasoactive intestinal peptide (VIP)-expressing and somatostatin (SOM)-expressing inhibitory neurons modulate responses in mouse visual cortex depending on similarity between stimulus and surround, primarily by modulating recurrent excitation. When stimulus and surround are similar, VIP neurons are inactive, and activity of SOM neurons leads to suppression of excitatory neurons. However, when stimulus and surround differ, VIP neurons are active, inhibiting SOM neurons, which leads to relief of excitatory neurons from suppression. We have identified a canonical cortical disinhibitory circuit that contributes to contextual modulation and may regulate perceptual saliency.
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http://dx.doi.org/10.1016/j.neuron.2020.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7850578PMC
December 2020

CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing.

Nucleic Acids Res 2021 01;49(2):e10

Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.

Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.
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http://dx.doi.org/10.1093/nar/gkaa1122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826284PMC
January 2021

On the lifetime of bioinformatics web services.

Nucleic Acids Res 2020 12;48(22):12523-12533

Chair for Clinical Bioinformatics, Saarland University, Saarbrücken 66123, Germany.

Web services are used through all disciplines in life sciences and the online landscape is growing by hundreds of novel servers annually. However, availability varies, and maintenance practices are largely inconsistent. We screened the availability of 2396 web tools published during the past 10 years. All servers were accessed over 133 days and 318 668 index files were stored in a local database. The number of accessible tools almost linearly increases in time with highest availability for 2019 and 2020 (∼90%) and lowest for tools published in 2010 (∼50%). In a 133-day test frame, 31% of tools were always working, 48.4% occasionally and 20.6% never. Consecutive downtimes were typically below 5 days with a median of 1 day, and unevenly distributed over the weekdays. A rescue experiment on 47 tools that were published from 2019 onwards but never accessible showed that 51.1% of the tools could be restored in due time. We found a positive association between the number of citations and the probability of a web server being reachable. We then determined common challenges and formulated categorical recommendations for researchers planning to develop web-based resources. As implication of our study, we propose to develop a repository for automatic API testing and sustainability indexing.
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http://dx.doi.org/10.1093/nar/gkaa1125DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736811PMC
December 2020

CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method.

Nucleic Acids Res 2021 01;49(2):e11

Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.

Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.
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http://dx.doi.org/10.1093/nar/gkaa1127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826285PMC
January 2021
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