De Spiegelaere, W. | bioRxiv Science

bioRxiv2024

Newly discovered base barrier cells provide compartmentalization of choroid plexus, brain and CSF

The choroid plexus (ChP) is a highly understudied structure of the central nervous system (CNS). The structure hangs in the brain ventricles, is composed of an epithelial cell layer, which produces the cerebrospinal fluid (CSF) and forms the blood-CSF barrier. It encapsulates a stromal mix of fenestrated capillaries, fibroblasts and a broad range of immune cells. Here, we report that the ChP base region harbors unique fibroblasts that cluster together, are connected by tight junctions and seal the ChP stroma from brain and CSF, thereby forming ChP base barrier cells (ChP BBCs). ChP BBCs are derived from meningeal mesenchymal precursors, arrive early during embryonic development, are maintained throughout life and are conserved across species. Moreover, we provide transcriptional profiles and key markers to label ChP BBCs and observe a striking transcriptional similarity with meningeal arachnoid barrier cells (ABCs). Finally, we provide evidence that this fibroblast cluster functions as a barrier to control communication between CSF and the ChP stroma and between the latter and the brain parenchyma. Moreover, loss of barrier function was observed during an inflammatory insult. Altogether, we have identified a novel barrier that provides functional compartmentalization of ChP, brain and CSF. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/601696v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@181e787org.highwire.dtl.DTLVardef@1875f33org.highwire.dtl.DTLVardef@7b2bcdorg.highwire.dtl.DTLVardef@78baa6_HPS_FORMAT_FIGEXP M_FIG Newly discovered base barrier cells provide compartmentalization of choroid plexus, brain and CSF The choroid plexus (ChP) hangs in the brain ventricles and is composed of an epithelial cell layer which produces the cerebrospinal fluid (CSF) and forms the blood-CSF barrier. The ChP epithelial cells are continuous with the ependymal cells lining the ventricle wall. At this base region, we identified and characterized a novel subtype of fibroblasts coined the ChP base barrier cells (BBCs). ChP BBCs express tight junctions (TJs), cluster together and seal the ChP stroma from CSF and brain parenchyma. The subarachnoid space (SAS) CSF penetrates deep into choroid plexus invaginations where it is halted by ChP BBCs. Abbreviations: E9-16.5 (embryonic day 9-16.5); P1-4 (postnatal day 1-4). C_FIG

neuroscience↗

bioRxiv2023

Flexible Methods for Standard Error Calculation in digital PCR Experiments

Digital PCR (dPCR) is a highly accurate and precise technique for the quantification of target nucleic acid(s) in a biological sample. This digital quantification relies on the binomial or Poisson distribution to estimate the amount of target molecules based on positive and negative partitions. However, the implementation of these distributions require adherence to underlying assumptions that are often neglected, leading to a suboptimal (too optimistic) variance estimation of the target concentration, especially when considering the multiple sources of variation in experimental dPCR setups. Moreover, these parametric methods cannot be easily used for downstream statistical inference when more advanced analysis are required, such as for copy number variation. We evaluated the performance of three new statistical methods (BootsVar, NonPVar, BinomVar) in both simulations and real-life datasets for target and variance estimation in dPCR setups while taking into account a combination of commonly observed sources of experimental variability that can interfere with the underlying assumptions of the current parametric methods. The results demonstrate the capability of the new methods for variance estimation and present a more accurate reflection of the true variability over the classical binomial approach. In addition, these statistical methods are flexible and generic in the way that they work well for the variance estimation of non-linear statistics that work with ratios (e.g. CNV) and for multiplex dPCR setups. In this study, we provide guidelines when to use the binomial-assumption based methods and when the non-parametric one is better to achieve more accurate variance estimates.

bioinformatics↗