Biology subjects

Richter, M. L.

Publications and source records attributed to Richter, M. L..

8 recordsLinked to original sources

bioRxiv2026

Antagonizing niche signals regulate the emergence of postnatal neural stem cells and allow enlargement of their pool

Adult neural stem cells (aNSCs) of the lateral ventricular sub-ventricular zone (V-SVZ) are set aside during embryogenesis from a pool of slowly dividing neural stem/progenitor cells (NSPCs) residing in the lateral ganglionic eminence (LGE). The time of aNSCs specification coincides with the peak of embryonic neurogenesis, raising the question of which mechanisms allow only a subpopulation of NSPCs to retain stem cell identity while others proceed to divide and differentiate into neurons. To address this, we isolated rapidly and slowly dividing NSPCs from the mouse LGE at mid-neurogenesis, when aNSCs are specified, and profiled the transcriptome at the single cell level. We find that slowly dividing NSPCs constitute a heterogeneous population encompassing both radial glia cells (RGCs) and intermediate progenitors (IPs) and characterized by different gene signatures. Focusing on RGCs, we show that slowly and rapidly dividing RGCs differentially express genes involved in the formation - such as Lamb2 - or degradation - such as Mmp15 - of the extracellular matrix (ECM), pointing to opposite niche-remodelling strategies as a potential mechanism of fate determination. In vivo perturbation of Lamb2 and Mmp15 affects the seeding and maintenance of NSCs in an opposing manner, with knockdown of Mmp15 increasing the NSC pool as also shown by single-cell RNA-sequencing. These findings suggest that opposite ECM remodelling by slowly and rapidly dividing RGCs constitutes a novel cross-regulatory niche-level mechanism regulating aNSCs emergence, opening new avenues for regulating their numbers and thereby long-term maintenance of the brains regenerative potential.

developmental biology↗

bioRxiv2026

Comprehensive single cell profiling of ageing glial cells reveals impaired Wnt signalling and Jun transcription factors regulating cortical astrocytes

Understanding age-related cellular dysfunction in the brain is essential for developing strategies to promote healthy ageing. Towards this aim, we took advantage of a previously established mild dissociation method to profile cells in the cerebral cortex grey matter of adult and aged mice. This revealed glial cells with largely up-regulated and other glia and neurons with largely down-regulated gene expression upon ageing. Astrocytes were involved in increased interactions with microglia and decreased interaction with neurons, high-lighting potent age-induced changes in their regulatory roles. Single cell RNA-seq and single nuclei multiome analysis of astrocytes uncovered down-regulation of Wnt-signalling with increased expression of its inhibitors and reduced RNA and protein levels of its effectors JunB/D, acting downstream of Wnt signalling in ageing. This was confirmed by RNA-scope and immunostainings, as well as in human data. Notably, injection of JunD-expressing viral vectors in astrocytes increased their proliferation and HMGB1 levels in the aged brain, indicative of a more youthful astrocyte state. Main pointsO_LITranscriptomic analysis uncovers cell type-specific impact of ageing in the cortical grey matter, including altered intercellular communication networks. C_LIO_LIMultiomic profiling identifies dysregulated Wnt signalling in ageing cortical astrocytes. C_LIO_LIAgeing astrocytes exhibit upregulation of the Wnt signalling regulators Maml2 and Daam2, accompanied by downregulation of the AP-1 transcriptional complex component JunD. C_LIO_LIOverexpression of JunD increases proliferation after mild injury in aged astrocytes. C_LI

neuroscience↗

bioRxiv2026

Cilia beating of ependymal cells regulates adult neural stem cell quiescence via mechanical forces mediated by PKD1/2-TRPM3

In many tissues stem cells are located lining a fluid-filled volume and their neighboring niche cells include cells with beating cilia. However, the role of mechanical forces created by cilia beating on stem cells remains elusive. We developed an approach to transiently inhibit the cilia beating of ependymal cells (EC) lining the forebrain ventricle by injecting magnetic beads-coupled antibodies targeting EC cilia and then applying a magnetic field. We show that EC cilia beating enforces neural stem cells (NSCs) quiescence through mechano-sensitive PKD1/2- and TRPM3-mediated Ca2+ transients. Only a few hours of EC cilia beating inhibition triggered NSC activation in vivo. CRISPR-Cas9-mediated deletion of TRPM3 or PKD1/2 in NSCs phenocopied the effect of EC cilia beating inhibition, while TRPM3 pharmacological activation rescued NSC quiescence in the absence of cilia beating. Our data reveal a novel regulator of stem cells exposed to fluids via the mechanical forces mediated by cilia beating.

neuroscience↗

bioRxiv2025

TGIF2 is a major regulator of neural stem cell fate and neurogenic priming

During brain development, neural stem cells (NSCs) must balance self-renewal with differentiation and ensure lineage progression. To identify novel regulators of NSCs during neurogenesis, we isolated NSCs by FACS from the mouse cerebral cortex and ganglionic eminence at mid-neurogenesis, and at birth, when gliogenesis starts in both, but neurogenesis only continues in the latter region. RNA-seq and ATAC-seq revealed major transcriptional and chromatin changes between these stages and identified TGFB-Induced Homeobox Factor 2 (TGIF2) as a key candidate factor in neurogenic NSCs. In vitro and in vivo experiments demonstrated a potent role of TGIF2 controlling NSC fate maintenance mediated by its interaction with the SIN3A/HDAC repressor complex suppressing neuronal differentiation genes. Multiomic comparison of NSC and neuron gene expression allowed the comprehensive analysis of neurogenic priming in cortical NSCs, identifying TGIF2 as its major regulator by restraining neuronal differentiation gene activation in NSCs.

neuroscience↗

bioRxiv2024

Benchmarking scRNA-seq copy number variation callers

Copy number variations (CNVs), the gain or loss of genomic regions, are associated with different diseases and cancer types, where they are related to tumor progression and treatment outcome. Single cell technologies offer new possibilities to measure CNVs in individual cells, allowing to assess population heterogeneity and to delineate subclonal structures. Single cell whole-genome sequencing is considered the gold-standard for the quantification of CNVs in single cells. However, the majority of existing single cell datasets interrogate gene expression, using scRNA-seq. Consequently, several computational approaches have been developed to identify CNVs from that data modality. Nevertheless, an independent benchmarking of these methods is lacking. We used 15 scRNA-seq datasets and evaluated six popular computational methods in their ability to recover the ground truth CNVs using a large set of performance metrics. Additionally, we explored whether they could correctly identify euploid cells, especially also in fully diploid samples, and subclonal structures in heterogeneous tumor samples. We discovered several dataset-specific factors that influence the performance of the methods, such as the dataset size and the number and type of CNVs in the analyzed sample. We found that the choice of the reference dataset can have a large impact on the performance. Methods which included additional allelic information from the scRNA-seq reads performed more robustly across scenarios, but at the cost of higher runtime. Furthermore, the methods differed substantially in their additional functionalities and resource requirements. We offer a benchmarking pipeline to help identify the optimal CNV calling method for newly generated scRNA-seq datasets, and to benchmark and improve new methods performance.

bioinformatics↗

bioRxiv2024

Cross-species analyses reveal RORγt-expressing dendritic cells are a lineage of antigen presenting cells conserved across tissues

Conventional dendritic cells (cDCs) are potent antigen presenting cells (APCs) that exhibit tissue and age-specific diversity allowing them to direct situation-adapted immunity. Thereby they harbor great potential for being targeted in vaccination and cancer. Here, we resolve conflicting data about expression of retinoic acid receptor-related orphan receptor-{gamma}t (ROR{psi}t) in cDCs. We show that ROR{psi}t+ DCs exist in murine lymphoid and non-lymphoid tissues across age. Fate mapping, functional assays and single cell multiomic profiling reveal these cells as ontogenetically and transcriptionally distinct from other well characterized cDC subtypes, as well as from ROR{psi}t+ type 3 innate lymphocytes (ILC3s). We show that ROR{psi}t+ DCs can migrate to lymph nodes and activate naive CD4+ T cells in response to inflammatory triggers. Comparative and cross-species transcriptomics revealed homologous populations in human spleen, lymph nodes and intestines. Further, integrated meta-analyses aligned ROR{psi}t+ DCs identified here with other emerging populations of ROR{psi}t+APCs, including R-DC-like cells, Janus cells/extrathymic Aire expressing cells (eTACs) and subtypes of Thetis cells. While ROR{psi}t+APCs have primarily been linked to T cell tolerance, our work establishes ROR{psi}t+ DCs as unique lineage of immune sentinel cells conserved across tissues and species that expands the functional repertoire of ROR{psi}t+ APCs beyond promoting tolerance. One sentence summaryROR{gamma}t+ DC exhibit versatile APC functions and are a distinct immune lineage conserved across age, tissues and species that entails Thetis cells, Janus cells/ROR{gamma}t+ eTACs and R-DC-like cells.

immunology↗

bioRxiv2022

Single-cell metabolic profiling reveals subgroups of primary human hepatocytes showing heterogeneous responses to drug challenge.

Xenobiotics are primarily metabolized by hepatocytes in the liver, and primary human hepatocytes (PHHs) are the gold standard model for the assessment of drug efficacy, safety and toxicity in the early phases of drug development. Recent advances in single-cell genomics have shown liver zonation and ploidy as main drivers of cellular heterogeneity. However, little is known about the impact of hepatocyte specialization on liver function upon metabolic challenge, including hepatic metabolism, detoxification, and protein synthesis. Here, we investigate the metabolic capacity of individual human hepatocytes in vitro, and assess how chronic accumulation of lipids enhances cellular heterogeneity and impairs the metabolisms of drugs. A phenotyping five-probe cocktail was used to identify four functional subgroups of hepatocytes that respond differently to drug challenge and fatty acid accumulation. These four subgroups display differential gene expression profiles upon cocktail treatment and xenobiotic metabolism-related specialization. Notably, intracellular fat accumulation leads to increased transcriptional variability and diminished the drug-related metabolic capacity of hepatocytes. Our results demonstrate that, upon a metabolic challenge such as exposure to drugs or intracellular fat accumulation, hepatocyte subgroups lead to different and heterogeneous transcriptional responses.

cell biology↗

bioRxiv2019

epiScanpy: integrated single-cell epigenomic analysis

Epigenetic single-cell measurements reveal a layer of regulatory information not accessible to single-cell transcriptomics, however single-cell-omics analysis tools mainly focus on gene expression data. To address this issue, we present epiScanpy, a computational framework for the analysis of single-cell DNA methylation and single-cell ATAC-seq data. EpiScanpy makes the many existing RNA-seq workflows from scanpy available to large-scale single-cell data from other -omics modalities. We introduce and compare multiple feature space constructions for epigenetic data and show the feasibility of common clustering, dimension reduction and trajectory learning techniques. We benchmark epiScanpy by interrogating different single-cell brain mouse atlases of DNA methylation, ATAC-seq and transcriptomics. We find that differentially methylated and differentially open markers between cell clusters enrich transcriptome-based cell type labels by orthogonal epigenetic information.

bioinformatics↗