Biology subjects

Nakaki, F.

Publications and source records attributed to Nakaki, F..

5 recordsLinked to original sources

bioRxiv2025

Innate immune responses to Plasmodium falciparum disrupt the blood-brain barrier

Plasmodium falciparum accumulation at the blood-brain barrier (BBB) is a hallmark of cerebral malaria, a life-threatening complication. Conversely, the contribution of the immune response to vascular injury has long been debated. Here, we studied the role of innate immune cells as potential effectors of vascular damage using a human in vitro 3D-BBB model. Parasite-stimulated immune cells from malaria-naive donors increased adhesion to microvessels, at least partly through LFA-1. This caused barrier disruption and inflammatory activation of BBB cells. Secretion of TNF-, IFN-{gamma}, and granzyme B by monocytes, NK and {gamma}{delta} T cells correlated with vascular injury, and accumulation of immune cells was required for local barrier damage. Our computational analysis disentangled pathogenic mechanisms driven specifically by either P. falciparum parasite or immune cells, as well as shared pathways. These findings demonstrate how vascular-immune interactions may contribute to vascular injury in cerebral malaria and point towards the potential of immunomodulatory therapeutics.

immunology↗

bioRxiv2025

Axial patterning of gastruloids via diverse cell type compositions

The formation of the germ layers and antero-posterior (AP) axial patterning are interlinked milestones of embryogenesis. Gastruloids, in vitro models from aggregated embryonic stem cells (ESCs), permit the study and deconstruction of these events. Gastruloids are successfully generated from ESCs of variable pluripotent states, but it remains unknown how the initial conditions influence cell type composition and to what degree resulting variations in spatial patterning can converge onto an elongated body axis. To address this, we comparatively study aggregates from varying proportions of primed and naive ESCs. Despite differences in AP symmetry-breaking dynamics and distinct trajectories toward either anterior mesodermal or neuro-ectodermal fates, all conditions produce elongated gastruloids. Furthermore, timed modulation of Activin/Nodal signaling in aggregates equalizes AP polarization modes and mixing of initial ESC pluripotent states generates gastruloids with enhanced tissue type diversity. This work therefore uncovers a previously unappreciated developmental flexibility underlying mammalian AP axial patterning.

developmental biology↗

bioRxiv2024

Pathogenic mechanisms of Plasmodium falciparum egress unveiled by a microvascular 3D blood-brain barrier model

Cerebral malaria is a severe neurovascular complication of Plasmodium falciparum infection, with high mortality rates even after treatment with effective antimalarials. Limitations in current experimental models have hindered our knowledge of the disease. We developed a 3D blood-brain barrier (BBB) model with enhanced barrier properties using primary brain endothelial cells, astrocytes and pericytes. Exposure to parasite egress products increased microvascular permeability, likely due to transcriptional downregulation of junctional and vascular development genes in endothelial cells. In addition, it increased the expression of ferroptosis markers, antigen presentation and type I interferon genes and upregulated the JAK-STAT pathway across all BBB cell types. Incubation with cytoadherent schizont-stage P. falciparum-infected erythrocytes induced a similar, but highly localized transcriptional shift, along with inter-endothelial gaps at sites of parasite egress, significantly increasing permeability. The co-administration of egress products with the JAK-STAT inhibitor Ruxolitinib prevented junctional disruption and BBB breakdown. These findings provide key insights into the parasite-mediated mechanisms driving brain microvascular pathogenesis in cerebral malaria and suggest potential avenues for adjunctive therapies.

microbiology↗

bioRxiv2023

Probability of stealth multiplets in sample-multiplexing for droplet-based single-cell analysis

BackgroundRecent advances in sample-multiplexing droplet-based single-cell RNA sequencing (mx-scRNA-seq) enable us to evaluate large numbers of different samples or experiments simultaneously by reducing the occurrence of undetectable multiplets, that is, the droplets that capture multiple cells. However, the probability of potential multiplets in mx-scRNA-seq is yet to be quantitatively examined. ResultsWe developed a simple theoretical model to predict four classes of possible multiplets in mx-scRNA-seq: Homogeneous stealth, partial stealth, multilabelled, and unlabelled. We estimated the probability of each class and have found that the partial tsealth multiplet, which has been overlooked, may sub-stantially affect the whole data when the labelling process is suboptimal. Next, we illustrated their presence in actual mx-scRNA-seq datasets when the sample labelling was suboptimal. In addition, we found that choosing a suitable sample-demultiplexing algorithm was critical to circumvent the partial stealth multiplets. ConclusionOur results show the necessity of optimising the labelling procedure and offer a theoretical basis to estimate the probability of each type of multiplets to ensure the integrity of mx-scRNA-seq.

molecular biology↗

bioRxiv2021

Dynamics of anteroposterior axis establishment in a mammalian embryo-like system

1.In the mammalian embryo, specification of the anteroposterior (AP) axis demarcates one of the first steps of body plan formation. While this process requires interactions with extra-embryonic tissues in the native embryo, minimal in vitro systems from embryonic stem cells (ESCs) undergo initial AP polarization in the absence of any localized, external cues. This self-organizing potential of stem cells remains not well understood. Here, we study such an initial symmetry breaking event in gastruloids, an established in vitro model for mammalian body plan formation, using the mesodermal marker gene Brachyury or T (Bra/T) to denote the onset of AP axis specification and concomitant germ layer formation. Through aggregate fusion experiments and manipulation of initial culture conditions as well as key developmental signalling pathways, we probe the dynamics of Bra/T polarization. We further conduct single-cell (sc) RNA sequencing of gastruloids at early stages to identify incipient molecular signatures of germ layer commitment and differences between Bra/T+ and Bra/T- populations during as well as after symmetry breaking. Moreover, we transcriptionally compare early development of gastruloids to the mouse embryo and conclude that gastruloids reproducibly undergo AP axis and germ layer specification in a parallel, but distinct manner: While their primed pluripotent cell populations adopt a more mesenchymal state in lieu of an epithelial epiblast-like transcriptome, the emerging mesendodermal lineages in vitro are nevertheless similar to their in vivo equivalents. Altogether, this study provides a comprehensive analysis of self-organized body plan establishment in a minimal in vitro system of early mammalian patterning and highlights the regulative capacity of mESCs, thereby shedding light on underlying principles of axial polarity formation.

developmental biology↗