Biology subjects

Dirnagl, U.

Publications and source records attributed to Dirnagl, U..

10 recordsLinked to original sources

bioRxiv2024

Ide copy number variant does not influence lesion size and mortality in two C57BL/6J mouse models of cerebrovascular ischemia nor in human cerebrovascular disease. An exploratory study

Contrary to the common belief, the most commonly used laboratory mouse inbred strains are shaped by a distinctive genetic and phenotypic diversity. In the past 10 years next generation sequencing unveiled a wide spectrum of genetic variants in different mouse inbred strains and the meticulous observation of researchers pointed to a variegate intra-and inter-strain phenotypic diversity. Although a genotype-phenotype correlation has been described for some traits, the relationship between several endophenotypes and causative genetic variability remains still unknown. Recently, we characterized the brain collateral plasticity in two brain ischemia C57BL/6J mouse models (i.e bilateral common carotid artery stenosis [BCCAS] and 60-min transient unilateral middle cerebral artery occlusion [MCAO]) and observed a Mendelian-like fashion of inheritance of the posterior communicating artery (PcomA) plasticity. Interestingly, a copy number variant (CNV) spanning Ide locus was reported to segregate in an analogous Mendelian-like pattern in the C57BL/6J colonies of the Jackson Laboratory. Given the critical role of Ide in vascular plasticity, Ide CNV was an excellent candidate to explain PcomA variability in C57BL/6J inbred mice. To investigate this hypothesis, we applied a combination of complementary techniques (i.e T2-weighted magnetic resonance imaging [MRI], time of flight [TOF] angiography [MRA], cerebral blood flow [CBF] imaging and histology) to characterize the collaterome in C57BL/6J BCCAS and MCAO mice and performed on these Taqman genotyping, exome sequencing, and RNA sequencing. We report an Ide CNV in a BCCAS mouse with 2 patent PcomAs. We then investigated the hypothesis that IDE gain and loss of function mutations may have influenced the vascular phenotype in a cohort of 438,250 cases and controls (UK Biobank) and 15,790 neurological patients (Genomics England), respectively. We identified four IDE CNVs resulting in a loss of function (LoF) in one patient with hereditary ataxia, a patient with hereditary congenital heart disease and two healthy individuals. In addition, we report four IDE LoF point mutations (p.Leu5X, p.Met394ValfsX29, p.Pro14SerfsX26, p.Leu889X) present in controls or inherited from healthy parents. Ide CNV and LoF variants do not crucially influence PcomA variability in C57BL/6J inbred mice and do not cause a vascular phenotype in humans.

genetics↗

bioRxiv2024

A randomized, controlled, two-center preclinical trial assessing the efficacy of a new benzodiazepine-dihydropyridine hybrid molecule (JM-20) in rodent models of ischemic stroke

JM-20 is a novel multifunctional benzodiazepine molecule with potent neuroprotective effects in rat focal cerebral ischemia. To confirm previous results obtained in single laboratories with small sample sizes, and to provide a robust preclinical evidence base for potential clinical development in stroke, we have performed a two-center preclinical trial with sufficiently large group sizes to detect relevant effects, minimizing biases in experimental design as much as possible (randomization, blinding, predefined in- and exclusion criteria) and increasing external and construct validities by performing experimental focal cerebral ischemia by different surgeons in two different laboratories on two continents, including two species (480 mice and 55 rats), different suppliers, young, young adult, and mature adult animals (range 2 -16 months) as well as comorbid animals (diabetes). While JM-20 improved functional outcomes after middle cerebral artery occlusion in young adult mice at day 7 and appeared to reduce mortality (not statistically significant), it had no effect in mature adult or comorbid (STZ-induced diabetes) mice. Effect sizes, where statistically significant, were modest, and much lower than those reported in the previous studies. Meta-analysis of all individual mouse data did not reveal statistically significant different functional outcomes or mortalities between vehicle- and JM-20-treated animals, although neuroscores and survival were slightly better in JM-20-treated animals. In the less severe model of permanent cortical focal cerebral ischemia in rats, JM-20 significantly reduced brain infarction. We conclude that we were able to confirm the neuroprotective potential of JM-20. However, effect sizes were substantially lower as previously described in small, monocentric trials. Further study is needed to determine whether JM-20 could be effective in less severe cases of focal cerebral ischemia or when used in combination with thrombolysis.

pharmacology and toxicology↗

bioRxiv2023

Refined movement analysis in the Staircase test reveals differential motor deficits in mouse models of stroke

Accurate assessment of post-stroke deficits is vital in translational research. Recent advances in machine learning provide unprecedented precision in quantifying rodent motor behavior post-stroke. However, the extent to which these tools can detect lesion-specific upper extremity deficits remains unclear. Using proximal middle cerebral artery occlusion (MCAO) and cortical photothrombosis (PT), we assessed post-stroke impairments in mice through the Staircase test. Lesion locations were identified using 7T-MRI. Machine learning was applied to reconstruct kinematic trajectories using MouseReach, a data-processing toolbox. This yielded 30 refined outcome parameters effectively capturing motor deficits. Lesion reconstructions located ischemic centers in the striatum (MCAO) and sensorimotor cortex (PT). Pellet retrieval was altered in both cases but did not correlate with stroke volume or ischemia extent. Instead, cortical ischemia was characterized by increased hand slips and modified reaching success. Striatal ischemia led to progressively prolonged reach durations, mirroring delayed symptom onset in basal ganglia strokes. In summary, refined machine learning-based movement analysis revealed specific deficits in mice after cortical and striatal ischemia. These findings emphasize the importance of thorough behavioral profiling in preclinical stroke research to increase translational validity of behavioral assessments.

neuroscience↗

bioRxiv2022

Prediction of Stroke Outcome in Mice Based on Non-Invasive MRI and Behavioral Testing

BackgroundPrediction of post-stroke outcome using the degree of subacute deficit or magnetic resonance imaging is well studied in humans. While mice are frequently used animals in preclinical stroke research, systematic analysis of outcome predictors is lacking. MethodsWe introduced heterogeneity into our study to broaden the applicability of our prediction tools. We analyzed the effect of 30, 45 and 60 minutes of arterial occlusion on the variance of stroke volumes. Next, we built a heterogeneous cohort of 215 mice using data from 15 studies that included 45 minutes of middle cerebral artery occlusion and various genotypes. Motor function was measured using the staircase test of skilled reaching. Phases of subacute and residual deficit were defined. Magnetic resonance images of stroke lesions were co-registered on the Allen Mouse Brain Atlas to characterize stroke topology. Different random forest prediction models that either used motor-functional deficit or imaging parameters were generated for the subacute and residual deficits. ResultsVariance of stroke volumes was increased by 45 minutes of arterial occlusion compared to 60 minutes and including various genotypes. We detected both a subacute and residual motor-functional deficit after stroke and different recovery trajectories. In mice with small cortical lesions, lesion volume was the best predictor of the subacute deficit. The residual deficit was most accurately predicted by the degree of the subacute deficit. When using imaging parameters for the prediction of the residual deficit, including information about the lesion topology increased prediction accuracy. A subset of anatomical regions within the ischemic lesion had particular impact on the prediction of long-term outcome. ConclusionsWe developed and validated a robust tool for the prediction of functional outcome after stroke in mice using a large heterogeneous cohort. Study design and imaging limitations are discussed. In the future, using outcome prediction can improve the design of preclinical studies and guide intervention decisions.

neuroscience↗

bioRxiv2022

Increasing discovery rates in preclinical research through optimised statistical decision criteria

The success of scientific discovery in preclinical research is based on the different roles of exploration and confirmation. Exploration involves identifying potential effects (high sensitivity), which are then tested more rigorously during confirmation (high specificity). Here, we examine different experimental strategies and their ability to balance sensitivity and specificity to identify relevant effects. In simulations based on empirical data, we specifically compare a conventional p-value based approach with a method based on an a priori determined smallest effect size of interest (SESOI). Using a SESOI increases transition rates from exploration to confirmation and leads to higher detection rates across the trajectory. In particular, specificity in the SESOI trajectory increases if number of true effects are low. We conclude that employing a SESOI is superior to a p-value based approach in many contexts. Based on our findings, we propose a reconsideration of planning and conducting preclinical experiments, especially when the prior probability of true hypotheses is low.

scientific communication and education↗

bioRxiv2020

Vascular cognitive impairment in the mouse reshapes visual, spatial network functional connectivity.

Connectome analysis of neuroimaging data is a rapidly expanding field to identify disease specific biomarkers. Structural diffusion MRI connectivity has been useful in individuals with radiological features of small vessel disease, such as white matter hyperintensities. Global efficiency, a network metric calculated from the structural connectome, is an excellent predictor of cognitive decline. To dissect the biological underpinning of these changes, animal models are required. We tested whether the structural connectome is altered in a mouse model of vascular cognitive impairment. White matter damage was more pronounced by 6 compared to 3 months. Global efficiency remained intact, but the visual association cortex exhibited increased structural connectivity with other brain regions. Exploratory resting state functional MRI connectivity analysis revealed diminished default mode network activity in the model compared to shams. Further perturbations were observed in a primarily cortical hub and the retrosplenial and visual cortices, and the hippocampus were the most affected nodes. Behavioural deficits were observed in the cued water maze, supporting the suggestion that the visual and spatial memory networks are affected. We demonstrate specific circuitry is rendered vulnerable to vascular stress in the mouse, and the model will be useful to examine pathophysiological mechanisms of small vessel disease. Graphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

neuroscience↗

bioRxiv2019

The ARRIVE guidelines 2019: updated guidelines for reporting animal research

Reproducible science requires transparent reporting. The ARRIVE guidelines were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and reproduce the methods and results. Despite considerable levels of endorsement by funders and journals over the years, adherence to the guidelines has been inconsistent, and the anticipated improvements in the quality of reporting in animal research publications have not been achieved.\n\nHere we introduce ARRIVE 2019. The guidelines have been updated and information reorganised to facilitate their use in practice. We used a Delphi exercise to prioritise the items and split the guidelines into two sets, the ARRIVE Essential 10, which constitute the minimum requirement, and the Recommended Set, which describes the research context. This division facilitates improved reporting of animal research by supporting a stepwise approach to implementation. This helps journal editors and reviewers to verify that the most important items are being reported in manuscripts. We have also developed the accompanying Explanation and Elaboration document that serves 1) to explain the rationale behind each item in the guidelines, 2) to clarify key concepts and 3) to provide illustrative examples. We aim through these changes to help ensure that researchers, reviewers and journal editors are better equipped to improve the rigour and transparency of the scientific process and thus reproducibility.

scientific communication and education↗

bioRxiv2019

Reporting animal research: Explanation and Elaboration for the ARRIVE guidelines 2019

Improving the reproducibility of biomedical research is a major challenge. Transparent and accurate reporting are vital to this process; it allows readers to assess the reliability of the findings, and repeat or build upon the work of other researchers. The NC3Rs developed the ARRIVE guidelines in 2010 to help authors and journals identify the minimum information necessary to report in publications describing in vivo experiments.\n\nDespite widespread endorsement by the scientific community, the impact of the ARRIVE guidelines on the transparency of reporting in animal research publications has been limited. We have revised the ARRIVE guidelines to update them and facilitate their use in practice. The revised guidelines are published alongside this paper. This Explanation and Elaboration document was developed as part of the revision. It provides further information about each of the 21 items in ARRIVE 2019, including the rationale and supporting evidence for their inclusion in the guidelines, elaboration of details to report, and examples of good reporting from the published literature.

scientific communication and education↗

bioRxiv2018

Benchmarking university medical centres for responsible metrics. A cross sectional study on timely results dissemination across 36 German centres

ObjectiveTimely and comprehensive reporting of clinical trial results build the backbone of evidence-based medicine and responsible research. The proportion of timely disseminated trial results can inform alternative national and international benchmarking of university medical centers (UMCs).\n\nStudy Design and SettingFor all German UMCs we tracked all registered trials completed between 2009 and 2013. The results and an interactive website benchmark German UMCs regarding their performance in results dissemination.\n\nResultsWe identified and tracked 2,132 clinical trials. For 1,509 trials, one of the German UMCs took the academic lead. Of these 1,509 \"lead trials\", 39% published their results (mostly via journal publications) in a timely manner (<24 months after completion). More than six years after study completion, 26% of all eligible lead trials still had not disseminated results.\n\nConclusionDespite substantial attention from many stakeholders to the topic, there is still a strong delay or even absence of results dissemination for many trials. German UMCs have several opportunities to improve this situation. Further research should evaluate whether and how a transparent benchmarking of UMC performance in results dissemination helps to increase value and reduce waste in medical research.

scientific communication and education↗

bioRxiv2017

Pebbles as Dry Ice Replacement for Snap Freezing of Rodents Brains

Dry ice is commonly used as a cooling agent in the preclinical research environment. It permits rapid freezing of tissues and organs through liquid media. Laboratories depend on a constant supply of dry ice because it disintegrates in a matter of days. Here we tested whether commercially available pebble gravel could be used as dry ice replacement for snap freezing mouse brains in 2-methylbutane. We monitored 2-methylbutane temperature for one hour and tested different setups with the focus on creating a practical solution that can be used in every research laboratory. While gravel pebbles cannot replace dry ice in the laboratory entirely, they present a useful addition as readily available and reusable cooling agent.

neuroscience↗