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O'Carroll, D.

Publications and source records attributed to O'Carroll, D..

6 recordsLinked to original sources

Large-Scale Control of Neuronal Networks In Vitro Using Perforated Microfluidic Devices

Neurons in the brain are organized and connected into complex networks in which electrochemical signaling forms the basis for all brain function. Cortical neuronal net-works are arranged in distinct modular, layered, and hierarchical structures, underlying its diverse functions such as learning, memory, or vision. Modern biotechnology has enabled an array of techniques to culture human neural cells, ranging from discreet co-cultures to complex developmental organoids, but all of which almost exclusively form unstructured and hypersynchronous networks. Overcoming this and capturing the functional and anatomical properties of the brain in vitro has proven to be a great challenge. Current techniques for guiding neuronal connectivity in vitro is often limited to a small fraction of the total population of neural cells, leaving most of the culture effectively unguided. To provide large-scale guidance of neurons in culture, we developed a microtunnel device which allows large-scale cell entry through an array of perforations, and guides neuronal network formation through a series of tunnels. Human neural stem cells capable of forming extensive neuronal projections were used to investigate several different microtunnel designs. One particularity noteworthy design which produced predominantly unidirectional growth was used to successfully validate its effect on propagation of neural activity on microelectrode arrays. Serendipitously, we found that our microtunnels had an extraordinary effect on signal-to-noise ratio and the quality of electrophysiological recordings with regards to number of active channels and detected spikes. Since we often found the neuronal growth surprising, we developed a simple computer model which could reproduce neuronal growth in the various tunnels, allowing computer aided design (CAD) of future projects.

neuroscience↗

A new double reporter strategy reveals a subset of non-migratory hematopoietic stem cells localized in a dynamic bone marrow niche.

Interactions of hematopoietic stem cells (HSCs) with the bone marrow microenvironment are critical to regulate stem cell function in homeostasis, emergency hematopoiesis and ageing. The dynamic behavior of endogenous HSCs in their niches has been challenging to study due to the complexity of markers required to define pure HSCs. Multiple recently developed reporter strategies advanced our capacity to identify HSCs in situ. Yet, they provide different levels of HSC enrichment and are frequently not stable in situations of perturbed hematopoiesis, leading to contradictory observations of HSC migratory behavior. Here we employed a new double reporter strategy by combining the Hoxb5-mKO2 and Vwf-GFP reporters, that are stably expressed in homeostasis, stress and ageing. Hoxb5+Vwf+ cells represent a subset of highly pure and potent long-term HSCs with a platelet-biased pattern of differentiation, that are included in the populations identified by other reporter strategies. Intravital microscopy revealed Hoxb5+Vwf+ cells to be non-migratory in homeostasis, following platelet depletion when these cells are actively proliferating, and during ageing. This non-migratory behavior of HSCs in homeostasis and stress indicates that their activation does not inherently depend on relocation to alternative niches eliciting proliferation, as previously proposed. We found Hoxb5+Vwf+ HSCs in direct contact with vasculature and LepR+ perivascular cells but not preferentially closer to megakaryocytes. Nevertheless, increased megakaryopoiesis following platelet depletion brings megakaryocytes into close proximity of Hoxb5+Vwf+ HSCs, revealing previously unrecognized niche dynamics in HSC regulation during regeneration. DATA SHARING STATEMENTOriginal data will be made available upon reasonable request. The RNA sequencing data used in this study has been published before35 and is available from GEO (GSE81682). The code used for analysis is available from https://github.com/loversaber/Secchi_Paper_RNAseq_Analysis.git. KEY POINTSO_LICombined expression of Hoxb5-mKO2 and Vwf-GFP reporters defines a population of highly enriched long-term HSCs in situ and in vivo. C_LIO_LIHoxb5+Vwf+ HSCs are non-migratory in homeostasis, stress hematopoiesis and ageing, while their niche is highly dynamic. C_LI

cell biology↗

PROSER1 Modulates DNA Demethylation through Dual Mechanisms to Prevent Syndromic Developmental Malformations

The link between DNA methylation and neurodevelopmental disorders is well established. However, how DNA methylation is fine-tuned - ensuring precise gene expression and developmental fidelity - remains poorly understood. PROSER1, a known TET2 interactor, was recently linked to a severe neurodevelopmental disorder. Here, we demonstrate that PROSER1 interacts with all TET enzymes and stabilizes chromatin-bound TET-OGT-PROSER1-DBHS (TOPD) complexes, which regulate DNA demethylation and developmental gene expression. Surprisingly, we find that PROSER1 also sequesters TET enzymes, preventing widespread demethylation and transposable element de-repression. Our findings identify PROSER1 as a key factor which both positively and negatively regulates DNA demethylation essential for mammalian neurodevelopment.

developmental biology↗

A time and single-cell resolved model of hematopoiesis

The paradigmatic tree model of hematopoiesis is increasingly recognized to be limited as it is based on heterogeneous populations and largely inferred from non-homeostatic cell fate assays. Here, we combine persistent labeling with time-series single-cell RNA-Seq to build the first real- time, quantitative model of in vivo tissue dynamics for any mammalian organ. We couple cascading single-cell expression patterns with dynamic changes in differentiation and growth speeds. The resulting explicit linkage between single cell molecular states and cellular behavior reveals widely varying self-renewal and differentiation properties across distinct lineages. Transplanted stem cells show strong acceleration of neutrophil differentiation, illustrating how the new model can quantify the impact of perturbations. Our reconstruction of dynamic behavior from snapshot measurements is akin to how a Kinetoscope allows sequential images to merge into a movie. We posit that this approach is broadly applicable to empower single cell genomics to reveal important tissue scale dynamics information. HighlightsO_LICell flux analysis reveals high-resolution kinetics of native bone marrow hematopoiesis C_LIO_LIQuantitative model simulates cell behavior in real-time and connects it with gene expression patterns C_LIO_LIDistinct lineage-affiliated progenitors have unique self-renewal and differentiation properties C_LIO_LITransplanted HSCs display accelerated stage- and lineage-specific differentiation C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/506735v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@244ad6org.highwire.dtl.DTLVardef@ad632borg.highwire.dtl.DTLVardef@149daf9org.highwire.dtl.DTLVardef@1c7183f_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Molecular basis of indispensable accuracy of mammalian miRNA biogenesis

Mammalian Dicer is the gatekeeper into the essential gene-regulating miRNA pathway. What is committing mammalian Dicer to the miRNA pathway remains unknown. We report that Dicers highly conserved DExD/H helicase domain is the key structural element supporting accurate miRNA biogenesis. While ATPase activity of the domain is non-essential, its loss is lethal in mice. It is required during canonical miRNA biogenesis for efficient recognition, high-fidelity cleavage, and strand selection. Structure of Dicer-miRNA precursor complexes showed that the DExD/H domain acquired helicase-unrelated function defining Dicer conformations, which affect substrate loading and facilitate pre-selection of miRNA precursors. Dicer lacking the DExD/H domain favors conformations enabling reduced substrate selectivity and supporting RNA interference, a different small RNA pathway. Therefore, Dicers DExD/H domain ensures indispensable high-fidelity precursor processing of mammalian miRNAs, which constitutes a structural "mold" for adaptive miRNA evolution.

molecular biology↗

Terminal uridylyltransferases target RNA viruses as part of the innate immune system in animals

RNA viruses are a major threat to animals and plants. RNA interference (RNAi) and the interferon response provide innate antiviral defense against RNA viruses. Here we performed a large-scale screen using C. elegans and its natural pathogen, the Orsay virus (OrV), and identified cde-1 as important for antiviral defense. CDE-1 is a homologue of the mammalian TUT4/7 terminal uridylyltransferases; its catalytic activity is required for its antiviral function. CDE-1 uridylates the 3' end of the OrV RNA genome and promotes its degradation, independently of the RNAi pathway. Likewise, TUT4/7 uridylate influenza A virus (IAV) mRNAs in mammalian cells. Deletion of TUT4/7 leads to increased IAV mRNA and protein levels. We have defined 3' terminal uridylation of viral RNAs as a conserved antiviral defense mechanism.

immunology↗