Biology subjects

Wahle, P.

Publications and source records attributed to Wahle, P..

8 recordsLinked to original sources

bioRxiv2026

SALL1 and neural microenvironmental contextspecify identity of stem cell derived humanmicroglia-like cells

Microglia, the immune cells of the brain parenchyma, play a pivotal role in neurodevelopment and neuroprotection. Human stem cell-derived microglia-like cells (MGL) offer a valuable, human-relevant system to study microglia in vitro. However, their cell states and intercellular interactions within complex 3-dimensional (3D) tissue contexts in vitro remain underexplored. Here, we analyze the gene expression profiles of MGL generated by two differentiation protocols in conventional 2D cultures. We show that co-culture with neural organoids promotes a more mature, in vivo-like MGL phenotype but this signature is lost during long-term co-culture. By varying media compositions, we modulate 2D MGL states toward more active or more homeostatic identities, which may enhance the similarity to primary microglia identities upon subsequent co-culture. Moreover, forced expression of the microglial lineage regulator SALL1 shifts MGL away from a general myeloid state toward a more defined pre-microglial fate. SALL1 overexpression within a 3D neural organoid environment further amplifies the shift toward a homeostatic developmental microglia population. Collectively, our transcriptomic analysis delineates human MGL states in 2D and 3D contexts, refines existing differentiation protocols toward more authentic MGL, and establishes a framework to investigate the intricate microglia-neural tissue interplay.

developmental biology↗

bioRxiv2024

Vascular development of fetal and postnatal neocortex of the pig, the European wild boar Sus scrofa.

The development of the brains vascular system is a predominantly prenatal process in mammalian species and required for neurogenesis and further brain development. Our recent work on fetal pig has revealed that many neurodevelopmental processes start well before birth and proceed rapidly reaching near-mature status already around birth. Here, we analyzed the development of neocortical vasculature from embryonic day (E) 45 onwards (gestation in pig lasts 114 days) using qualitative and quantitative image analyses and protein blots. In all cortical layers, vessel volume from total brain volume at E100 resembled that of a postnatal day (P) 30 piglet. Endothelial cells expressed the tight junction protein claudin-5 from E45 onwards. GFAP+ and AQP4+ astrocytes, PDGFR{beta}+ pericytes and -SMA+ smooth muscle cells are detectable near vessels at E60 suggesting an early assembly of blood-brain barrier components. The vascular system in the visual cortex is advanced before birth with an almost mature pattern at E100. Findings were confirmed by blots which showed a steady increase of expression of tight junction and angiogenesis-related proteins (claudin-5, occludin, VE-cadherin, PECAM-1/CD31) from E65 onwards until P90. The expression profile was similar in visual and somatosensory cortex. Together, we report a rapid maturation of the vascular system in pig cortex. Regarding activity-dependent aspects, the data suggest that angiogenesis might be influenced by spontaneous rather than sensory-evoked activity. Author contributionConceptualization and methodology: ES and PW; investigation and analysis: ES, KC; provided resources: CB, CB, MM, DU; visualization: ES, MM, DU; writing--original draft: ES, PW; writing--review and editing: ES, GM, PW; supervision and project administration: PW. All authors approved the manuscript. Summary statementVascular impairment is associated with neurodegenerative disorders. As a groundwork for future studies, we quantitatively analyzed development of cortical vasculature in the emerging translational model, the pig. ETHICAL APPROVALAll applicable international, national, and/or institutional guidelines for the care and use of animals were followed. All procedures were in accordance with the ethical standards or practice of the institution at which the studies were conducted.

developmental biology↗

bioRxiv2023

Axons of cortical basket cells originating from dendrites develop higher local complexity than axons emerging from basket cell somata

Neuronal differentiation is regulated by neuronal activity. Here, we analyzed dendritic and axonal growth of Basket cells and non-Basket cells using sparse transfection of channelrhodopsin-YFP and repetitive optogenetic stimulation in slice cultures of rat visual cortex. Neocortical interneurons often display axon-carrying dendrites (AcDs). We found that the AcDs of Basket cells and non-Basket cells were on average their most complex dendrite. Further, the AcD configuration had an influence on Basket cell axonal development. Axons originating from an AcD formed denser arborizations with more terminal endings within the dendritic field of the parent cell. Intriguingly, this occurred already in unstimulated Basket cells, and complexity was not increased further by optogenetic stimulation. However, optogenetic stimulation exerted a growth-promoting effect on axons emerging from Basket cell somata. The axons of non-Basket cells neither responded to the AcD configuration nor to the optogenetic stimulation. The results suggest that the formation of locally dense Basket cell plexuses is regulated by spontaneous activity. Moreover, in the AcD configuration, the AcD and the axon it carries mutually support each others growth. TeaserTextbooks usually draw cortical neurons with axons emerging from the cell body. Axons emerging from dendrites have been considered a caprice of nature until recent work demonstrated that axon-carrying dendrites are neither a rare nor a random phenomenon. Rather, this morphological configuration awards specific functional properties. Here, we discovered a morphogenetic role of the AcD configuration in developing Basket neurons which deliver axo-somatic inhibition to pyramidal neurons. Driven by spontaneous activity, AcD and the axon mutually promote each others growth such that the axon rapidly forms a denser presynaptic terminal field. Basket cells with axons from the cell body achieve the same complexity with technical assistance via an optogenetic stimulation. This way, a dendritic origin accelerates Basket cell axonal development.

neuroscience↗

bioRxiv2022

Multimodal spatiotemporal phenotyping of human organoid development

Organoids generated from human pluripotent stem cells (PSCs) provide experimental systems to study development and disease. However, we lack quantitative spatiotemporal descriptions of organoid development that incorporate measurements across different molecular modalities. Here we focus on the retina and use a single-cell multimodal approach to reconstruct human retinal organoid development. We establish an experimental and computational pipeline to generate multiplexed spatial protein maps over a retinal organoid time course and primary adult human retina, registering protein expression features at the population, cellular, and subcellular levels. We develop an analytical toolkit to segment nuclei, identify local and global tissue units, infer morphology trajectories, and analyze cell neighborhoods from multiplexed imaging data. We use this toolkit to visualize progenitor and neuron location, the spatial arrangements of extracellular and subcellular components, and global patterning in each organoid and primary tissue. In addition, we generate a single-cell transcriptome and chromatin accessibility time course dataset and infer a gene regulatory network underlying organoid development. We then integrate genomic data with spatially segmented nuclei into a multi-modal atlas enabling virtual exploration of retinal organoid development. We visualize molecular, cellular, and regulatory dynamics during organoid lamination, and identify regulons associated with neuronal differentiation and maintenance. We use the integrated atlas to explore retinal ganglion cell (RGC) spatial neighborhoods, highlighting pathways involved in RGC cell death. Finally, we show that mosaic CRISPR/Cas genetic perturbations in retinal organoids provide insight into cell fate regulation. Altogether, our work is a major advance toward a virtual human retinal organoid, and provides new directions for how to approach disorders of the visual system. More broadly, our approaches can be adapted to many organoid systems.

systems biology↗

bioRxiv2022

Functional assessment of the ionotropic receptors IR25a and IR93a in predator perception in the freshwater crustacean Daphnia using RNA interference

Acquiring environmental information is vital for organisms as it informs about the location of resources, mating partners, and predators. The freshwater crustacean Daphnia detects predator specific chemical cues released by its predators and subsequently develops defensive morphological features that reduce the predation risk. The detection of such chemical information is generally processed via distinct chemoreceptors that are located on chemoreceptor cells. Lately an ancestral type of ionotropic receptors (IRs) has been identified in crustaceans. IRs and the putative co-receptors IR25a and IR93a are postulated to be involved in chemoreception However, functional roles have not been assessed. Here, using three Daphnia species as model, we report that the two co-receptors are expressed within the chemosensory antennules and gene expression is increased with predator perception. Importantly, RNA interference mediated knock-down of the two IRs impedes species-specific defense expression in the three Daphnia species. Our results suggest that (albeit not testing the enigmatic receptor protein directly), the reduction of two associated proteins has impaired the functional aggregation of the postulated chemoreceptor complex. This in turn has hampered the perception of environmentally relevant chemical cues resulting in a substantial reduction of defensive morphological features.

ecology↗

bioRxiv2021

Neocortical pyramidal neurons with axons emerging from dendrites are frequent in non-primates, but rare in monkey and human

The canonical view of neuronal function is that inputs are received by dendrites and somata, become integrated in the somatodendritic compartment and upon reaching a sufficient threshold, generate axonal output with axons emerging from the cell body. The latter is not necessarily the case. Instead, axons may originate from dendrites. The terms "axon carrying dendrite" (AcD) and "AcD neurons" have been coined to describe this feature. Here, we report on the diversity of axon origins in neocortical pyramidal cells. We found that in non-primates (rodent, cat, ferret, pig), 10-21% of pyramidal cells of layers II-VI had an AcD. In marked contrast, in macaque and human, this proportion was lower, and it was particularly low for supragranular neurons. Unexpectedly, pyramidal cells in the white matter of postnatal cat and aged human cortex exhibit AcDs to much higher percentages. In rodent hippocampus, AcD cells are functionally privileged, since inputs here can circumvent somatic integration and lead to immediate action potential initiation in the axon. Our findings expand the current knowledge regarding the distribution and proportion of AcD cells in neocortial regions of non-primate taxa, which strikingly differs from primates where these cells are mainly found in deeper layers and white matter.

neuroscience↗

bioRxiv2018

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.

Cell type specification during early nervous system development in Drosophila melanogaster requires precise regulation of gene expression in time and space. Resolving the programs driving neurogenesis has been a major challenge owing to the complexity and rapidity with which distinct cell populations arise. To resolve the cell type-specific gene expression dynamics in early nervous system development, we have sequenced the transcriptomes of purified neurogenic cell types across consecutive time points covering critical events in neurogenesis. The resulting gene expression atlas comprises a detailed resource of global transcriptome dynamics that permits systematic analysis of how cells in the nervous system acquire distinct fates. We resolve known gene expression dynamics and uncover novel expression signatures for hundreds of genes among diverse neurogenic cell types, most of which remain unstudied. We also identified a set of conserved and processed long-noncoding RNAs (lncRNAs) that exhibit spatiotemporal expression during neurogenesis with exquisite specificity. LncRNA expression is highly dynamic and demarcates specific subpopulations within neurogenic cell types. Our spatiotemporal transcriptome atlas provides a comprehensive resource to investigate the function of coding genes and noncoding RNAs during critical stages of early neurogenesis.\n\nSummary statementWe present a spatiotemporal transcriptome during early Drosophila embryonic nervous system development, revealing a complex cell type-specific network of mRNAs and IncRNAs.

developmental biology↗

bioRxiv2017

The Drosophila Embryo at Single Cell Transcriptome Resolution

Drosophila is a premier model system for understanding the molecular mechanisms of development. By the onset of morphogenesis, ~6000 cells express distinct gene combinations according to embryonic position. Despite extensive mRNA in situ screens, combinatorial gene expression within individual cells is largely unknown. Therefore, it is difficult to comprehensively identify the coding and non-coding transcripts that drive patterning and to decipher the molecular basis of cellular identity. Here, we single-cell sequence precisely staged embryos, measuring >3100 genes per cell. We produce a transcriptomic blueprint of development - a virtual embryo where 3D locations of sequenced cells are confidently identified. Our \"Drosophila-Virtual-Expression-eXplorer\" performs virtual in situ hybridizations and computes expression gradients. Using DVEX, we predict spatial expression and discover patterned lncRNAs. DEVX is sensitive enough to detect subtle evolutionary changes in expression patterns between Drosophila species. We believe DVEX is a prototype for powerful single cell studies in complex tissues.

genomics↗