A5061261005- MicroRNA in disease regulation
- Cancer-related molecular mechanisms research
- Extracellular vesicles in disease
- Circular RNAs in diseases
- RNA modifications and cancer
- Electrospun Nanofibers in Biomedical Applications
- Single-cell and spatial transcriptomics
- Advanced biosensing and bioanalysis techniques
- RNA Research and Splicing
- Wound Healing and Treatments
- Radioactivity and Radon Measurements
- Advanced Neural Network Applications
- Metabolomics and Mass Spectrometry Studies
- Gut microbiota and health
- RNA regulation and disease
- Mesenchymal stem cell research
- Genomics and Phylogenetic Studies
- AI in cancer detection
- RNA Interference and Gene Delivery
Saarland University
2022-2025
Helmholtz Institute for Pharmaceutical Research Saarland
2024
German Research Centre for Artificial Intelligence
2021
Abstract Molecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map noncoding RNA (ncRNA) expression in (16 organs at ten timepoints from 1 to 27 months) rejuvenated mice. We found molecular trajectories are largely tissue-specific except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence circulating plasma extracellular vesicles (EVs) whereas ncRNAs were less present. For...
Neurodegenerative diseases and infections can produce lasting effects on brain function, yet the spatial molecular mechanisms underlying these changes remain poorly understood. Here, we present high-resolution transcriptomics of 40 postmortem samples from patients with Parkinson's disease, frontotemporal dementia, dementia Lewy bodies, severe COVID-19. Analyzing over 1.5 million spatially resolved cells across dorsolateral prefrontal cortex anterior cingulate revealed disease-specific...
An in-depth understanding of the molecular processes composing aging is crucial to develop therapeutic approaches that decrease as a key risk factor for cognitive decline. Herein, we present spatio-temporal brain atlas (15 different regions) microRNA (miRNA) expression across mouse lifespan (7 time points) and two interventions composed 1009 samples. MiRNAs are promising targets, they silence genes by complementary base-pair binding messenger RNAs known mediate speed. We first established...
Abstract The identification of targetomes remains a challenge given the pleiotropic effect miRNAs, limited effects miRNAs on individual targets, and sheer number estimated miRNA–target gene interactions (MTIs), which is around 44,571,700. Currently, targetome for single relies computational evidence functional studies covering smaller numbers targets. To ensure that analysis could be experimentally verified by assays, we employed systematic approach explored four (miR-129-5p, miR-129-1-3p,...
A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients' samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected annotated isomiR information available databases remains limited. We thus developed isomiRdb, comprehensive resource that compiles expression data at...
Previous work on murine models and humans demonstrated global as well tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane mediating the horizontal transfer genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across lifespan from 2–18 months: (1) sncRNAs that free-circulating (fc-RNA) (2) bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit...
Single-cell RNA sequencing (RNA-seq) has revolutionized our understanding of cell biology, developmental and pathophysiological molecular processes, paving the way toward novel diagnostic therapeutic approaches. However, most gene regulatory processes on single-cell level are still unknown, including post-transcriptional control conferred by microRNAs (miRNAs). Like established expression analysis, advanced computational expertise is required to comprehensively process newly emerging...
Obtaining high-quality omics data at the single-cell level from archived human tissue samples is crucial for gaining insights into cellular heterogeneity and pushing field of personalized medicine forward. In this technical brief we present a comprehensive methodological framework efficient enzyme-free preparation tissue-derived single cell suspensions their conversion miRNA sequencing libraries. The resulting study have potential to deepen our understanding expression its relevance in...
For cancers and other pathologies, early diagnosis remains the most promising path to survival. Profiling of longitudinal cohorts facilitates insights into trajectories biomarkers. We measured microRNA expression in 240 serum samples from patients with colon, lung, breast cancer cancer-free controls. Each patient provided at least two samples, one prior following diagnosis. The median time interval between was 11.6 years. Using computational models, we evaluated circulating profiles 21...
Quantifying microbiome species and composition from metagenomic assays is often challenging due to its time-consuming nature computational complexity. In Bioinformatics, k-mer-based approaches were long established expedite the analysis of large sequencing data are now widely used annotate data. We make use k-mer counting techniques for efficient accurate compositional microbiota whole metagenome sequencing. Mibianto solves this problem by operating directly on read files, without manual...
Non-thermal plasma, a partially ionized gas, holds significant potential for clinical applications, including wound-healing support, oral therapies, and anti-tumour treatments. While its applications showed promising outcomes, the underlying molecular mechanisms remain incompletely understood. We thus apply non-thermal plasma to mouse auricular skin conducted non-coding RNA sequencing, as well single-cell blood sequencing. In time-series analysis (five timepoints spanning 2 hours), we...
Previous work on murine models and human demonstrated global as well tissue-specific molecular aging trajectories in solid tissues body fluids 1–8 . Extracellular vesicles like exosomes play a crucial role communication information exchange between such systemic factors 9,10 We sequenced freely circulating vesicle-bound small regulatory RNAs mice at five time points across the average life span from 2 to 18 months. Intriguingly, each RNA class exhibits unique patterns, which showed...
For decades, in diffusion cloud chambers, different types of subatomic particle tracks from radioactive sources or cosmic radiation had to be identified with the naked eye which limited amount data that could processed. In order allow these classical detectors enter digital era, we successfully developed a neuro-explicit artificial intelligence model that, given an image chamber, automatically annotates most visible according type process created it. To achieve this goal, combined attention...