Biology subjects

Weinert, M.

Publications and source records attributed to Weinert, M..

6 recordsLinked to original sources

bioRxiv2026

A roadmap for enriching rare cell populations from human post-mortem brain, demonstrated by 100% microglial purity.

Understanding brain disease requires studying the specific cell types that drive each condition: microglia in Alzheimers, dopaminergic neurons in Parkinsons, motor neurons in ALS, and many others. For most of these rare populations, protocols to isolate them from human post-mortem brain at the required purity have never been developed. The shared hurdles are reliable nuclear markers, compatible fluorescent dyes, antibody host-species cross-reactivity, and achieving pure rather than merely enriched populations. Here we present a generalisable roadmap for developing fluorescence-activated nuclear sorting (FANS) protocols for rare cell populations in human brain. We demonstrate it on microglia, reaching 100% purity in cortex and 98% in cerebellum, with the cortex sort simultaneously yielding astrocytes at 93% purity. The roadmap tackles each hurdle including an on-bench antibody labelling step that expands fluorescence channels without cross-reactivity problem and an affordable single-nucleus RNA-seq validation workflow, giving labs a pathway for enriching any rare cell type reliably.

neuroscience↗

bioRxiv2025

MotifPeeker: R package for benchmarking epigenomic profiling methods using motif enrichment as a key metric

MotifPeeker benchmarks epigenomic profiling methods targeting transcription factors (TFs) where no "gold standard" reference exists, using motif enrichment as a key metric. With minimal input, users can analyse their data in a single function and receive an intuitive HTML report. Availability and ImplementationMotifPeeker is available on Bioconductor ([≥] v3.21) at https://bioconductor.org/packages/MotifPeeker. The complete source code is available on GitHub at https://github.com/neurogenomics/MotifPeeker, with full documentation provided at https://neurogenomics.github.io/MotifPeeker. Additionally, the MotifPeeker Docker image is hosted on GitHub at https://github.com/neurogenomics/MotifPeeker/pkgs/container/motifpeeker.

bioinformatics↗

bioRxiv2024

Rational design of peak calling parameters for TIP-seq based on pA-Tn5 insertion patterns improves predictive power

Epigenomic profiling provides insights into the regulatory mechanisms that govern gene expression. At a fundamental level, these mechanisms are determined by proteins that bind the DNA or modify the chromatin. Techniques such as ChIP-seq and CUT&Tag have been instrumental in mapping the binding sites of such proteins across the genome. Recent advances have led to the development of TIP-seq, a highly sensitive method devised to increase the number of unique reads per sample. Its design results in novel library features, which have not yet been explored with comparative analytics. Through the extensive assessment of bioinformatics tools and parameters we have developed an analysis pipeline that is ideally suited for TIP-seq data, including linear deduplication, read prioritisation and read shifting. Using transcription factor binding profiles (TFs), we show that our optimised pipeline greatly reduces the width of peaks to below 50% and more precisely aligns the peak summit with known motifs. A tutorial of the optimised peak calling is available on GitHub at https://github.com/neurogenomics/peak_calling_tutorial.git. Our methodological advancement substantially improves TIP-seq data quality, and the thoughtful design of analysis parameters is widely applicable to all pA-Tn5 based profiling assays.

bioinformatics↗

bioRxiv2023

Lipid signatures and inter-cellular heterogeneity of naive and lipopolysaccharide-stimulated human microglia-like cells

Microglia are non-neuronal cells, which are residing in the central nervous system and are known to play an important role in health and disease. We investigated lipidomic phenotypes of human naive and stimulated microglia-like cells by atmospheric-pressure scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging (AP-SMALDI MSI). With lateral resolutions between 5 m and 1.5 m, we were able to chart lipid compositions of individual cells, enabling to differentiate cell lines and stimulation conditions. This allowed us to reveal local lipid heterogeneities in naive and lipopolysaccharide (LPS)-stimulated cells. We were able to identify individual cells with elevated triglyceride (TG) levels and could show that the number of these TG-enriched cells increased with LPS stimulation as a hallmark for a proinflammatory phenotype. Additionally, observed local abundance alterations of specific phosphatidylinositols (PIs) indicate a cell specific regulation of the PI metabolism.

biochemistry↗

bioRxiv2022

Translocator protein is a marker of activated microglia in rodent models but not human neurodegenerative diseases

Microglial activation plays central roles in neuro-inflammatory and neurodegenerative diseases. Positron emission tomography (PET) targeting 18kDa Translocator Protein (TSPO) is widely used for localising inflammation in vivo, but its quantitative interpretation remains uncertain. We show that TSPO expression increases in activated microglia in mouse brain disease models but does not change in a non-human primate disease model or in common neurodegenerative and neuroinflammatory human diseases. We describe genetic divergence in the TSPO gene promoter, consistent with the hypothesis that the increase in TSPO expression in activated myeloid cells is unique to a subset of species within the Muroidea superfamily of rodents. We show that TSPO is mechanistically linked to classical pro-inflammatory myeloid cell function in rodents but not humans. These data emphasise that TSPO expression in human myeloid cells is related to different phenomena than in mice, and that TSPO PET reflects density of inflammatory cells rather than activation state.

neuroscience↗

bioRxiv2021

Diverse human astrocyte and microglial transcriptional responses to Alzheimer's pathology

To better define roles that astrocytes and microglia play in Alzheimers disease (AD), we used single-nuclei RNA sequencing to comprehensively characterize transcriptomes in astrocyte and microglia nuclei isolated post mortem from neuropathologically-defined AD and control brains with a range of amyloid-beta and phospho-tau (pTau) pathology. Significant differences in glial gene expression (including AD risk genes expressed in astrocytes [CLU, MEF2C, IQCK] and microglia [APOE, MS4A6A, PILRA]) were correlated with tissue amyloid and pTau expression. Astrocytes were enriched for proteostatic, inflammatory and metal ion homeostasis pathways. Pathways for phagocytosis, proteostasis and autophagy were highly enriched in microglia and perivascular macrophages. Gene co-expression analyses revealed potential functional associations of soluble biomarkers of AD in astrocytes (CLU) and microglia (GPNMB). Our work highlights responses of both astrocytes and microglia for pathological protein clearance and inflammation, as well as glial transcriptional diversity in AD.

neuroscience↗