Biology subjects

Spassky, N.

Publications and source records attributed to Spassky, N..

11 recordsLinked to original sources

bioRxiv2026

Static2Dynamic: Reconstructing videos of unobservable cellular, developmental, and disease processes

A fundamental limitation in biology is that many of its most important processes unfold as visual dynamics that cannot be directly observed. Development, tissue remodeling, and disease progression often occur deep in living organisms, over extended timescales, and at cellular resolution beyond the reach of current live imaging technologies. As a result, much of biology remains accessible only through static snapshots, while the underlying phenotypic trajectories and visual transformations remain hidden. Here, we introduce Static2Dynamic, a general framework to reconstruct unseen biological dynamics from sets of cross-sectional image data. Starting from time-unpaired static samples, Static2Dynamic first recovers a continuous pseudotime for individual images in a time-discriminative deep representation space, then learns a generative model of images conditionally to the underlying process, and finally reconstructs temporally coherent videos initialized from real samples. This makes it possible to infer past and future visual states of a static image and to simulate complete trajectories of cellular, developmental, and disease processes that were never directly recorded. We quantitatively validate Static2Dynamic on two large-scale experimental microscopy video datasets generated specifically for benchmarking, enabling direct comparison of inferred pseudotime trajectories and reconstructed videos against ground-truth biological dynamics. We further show that the framework generalizes across biological scales, organisms, and imaging modalities, including processes inaccessible to continuous live observation. More broadly, Static2Dynamic establishes the foundations of pseudotime microscopy, a new paradigm for reconstructing the visual and temporal dynamics of biological processes directly from static imaging data, thereby expanding the observable space of living systems beyond current experimental limits.

bioinformatics↗

bioRxiv2025

tRNA thiolation defects disrupt cellular proteostasis and tissue homeostasis in mammals

Sulfur modification of tRNA wobble uridines is an evolutionarily conserved mechanism that ensures efficient protein synthesis. In humans, loss of this anticodon modification due to mutations in CTU2 (cytosolic thiouridylase 2) causes DREAM-PL syndrome, a severe congenital disorder often leading to early postnatal death. However, the mechanisms by which loss of tRNA thiolation drives pathology remain unclear. Here, we show that loss of CTU2 triggers significant cellular proteostasis defects in patient cells and model cell lines. Structural and biochemical analyses reveal that the pathogenic CTU2L63P mutation destabilizes the CTU1/CTU2 complex and abolishes tRNA binding and thiolation. Acute loss of CTU2 caused codon-specific ribosome pausing at A-ending codons decoded by thiolated tRNAs, and decreased ribosome occupancy of A-rich transcripts in a dosage-dependent manner. Codon-biased mRNAs transcribed from genes critical for ciliogenesis are predicted to be most affected, linking their reduced translation to DREAM-PL etiology in humans. Surprisingly, Ctu2L63P mice display severe thiolation defects, but develop normally, are viable and fertile. Our findings highlight the importance of functional tRNA thiolation for organismal health in humans and identify species-specific vulnerabilities during embryonic development in mammals.

cell biology↗

bioRxiv2025

GPR161 mechanosensitivity at the primary cilium drives neuronal saltatory migration

The saltatory migration of neurons is essential for brain formation. Whether mechanical stimuli regulate this process is unknown. Here we show that the primary cilium acts as a mechanical sensor through GPR161. Using an ex vivo neuronal migration model and microfluidic assays, we demonstrate that fluid shear stress induces migration via the mechanoreceptor GPR161 at the primary cilium, with its mechanosensitive Helix 8 being essential. We demonstrate that GPR161 activates a recently discovered cAMP/PKA signaling pathway leading to the phosphorylation of NDE1, a dynein complex regulator, and microtubule organization to regulate migration. These findings unveil a dynamic primary cilium-based pathway sensing mechanical stimulus to drive cyclic saltatory neuronal migration during brain development.

neuroscience↗

bioRxiv2025

Chemical inhibition of Exon Junction Complex assembly impairs mRNA localization and neural stem cells ciliogenesis

The Exon Junction Complex (EJC) is formed by the essential eIF4A3, MAGOH and Y14 core proteins. It is universally deposited during splicing at exon-exon junctions. The EJC is known to impact almost every post-transcriptional regulatory step throughout the life of mRNAs including their modifications, splicing, decay and trafficking. Its dysregulation leads to neurodevelopmental pathologies. Here we show that EJC-i, a compound known to block the ATPase activity of eIF4A3, inhibits de novo EJC assembly. EJC-i and targeted knockdown of either eIF4A3 or Y14 core EJC subunits lead to very similar phenotypes by impacting the destiny of mRNAs due to alterations in alternative splicing, nonsense-mediated mRNA decay, genome-wide m6A methylation and proper intracellular addressing of specific transcripts, in particular to the centrosome. Both EJC impairment methods disrupt the centrosome function that might be responsible for mitotic arrest at prometaphase. As a small molecule that readily diffuses into cells, EJC-i is a particularly attractive easy to use and versatile tool to investigate EJC functions in live cells or whole organism that are not prone to genetic manipulation. Indeed, this property was used to disrupt ciliogenesis in primary neural stem cells.

molecular biology↗

bioRxiv2024

Differential contribution of P73+ Cajal-Retzius cells and Reelin to cortical morphogenesis

Cajal-Retzius cells (CRs) are a peculiar neuronal type within the developing mammalian cerebral cortex. One of their best documented feature is the robust secretion of Reln, a glycoprotein essential for the establishment of cortical layers through the control of radial migration of glutamatergic neurons. We previously identified Gmnc as a critical fate determinant for P73+ CRs subtypes from the hem, septum and thalamic eminence. In Gmnc-/- mutants, P73+ CRs are initially produced, cover the telencephalic vesicle but undergo massive apoptosis resulting in their complete depletion at mid-corticogenesis. Here we investigated the consequence of such a CRs depletion on dorsal cortex lamination and hippocampal morphogenesis. We found preplate splitting occurs normally in Gmnc-/- mutants but is followed by defective radial migration arrest in the dorsal cortex, altered cellular organization in the lateral cortex, aberrant hippocampal progenitor proliferation resulting in abnormal CA1 folding and lack of vasculature development in the hippocampal fissure. We then performed conditional Reln deletion in P73+ CRs to evaluate its relative contribution and found that only radial migration defects were recapitulated. We concluded that at mid-corticogenesis, CRs-derived Reln is required for radial migration arrest and additionally identified Reln-independent functions for CRs in the control of hippocampal progenitor proliferation and vessel remodelling.

neuroscience↗

bioRxiv2024

Identification of a new cell cycle variant during multiciliated cell differentiation

2A complex and conserved regulatory network drives the cell cycle. Individual components of this network are sometimes used in differentiated cells, i.e. to control organelle destruction in mammalian lens cells or light response in land plants. Some differentiated cells co-opt cell-cycle regulators more largely, to increase their ploidy using a cell cycle variant named endoreplication. Using single-cell RNA-seq profiling and functional assays in differentiating multiciliated cells, we identified a novel type of cell cycle variant that supports cytoplasmic organelle, rather than nuclear content amplification. This variant operates in post-mitotic, centriole-amplifying differentiating multiciliated cells and is characterized by (i) a circular trajectory of the transcriptome, (ii) sequential expression of more than 70% of the genes involved in S, G2 and M-like progression along this trajectory, and (iii) successive waves of cyclins. This cell cycle variant is tailored by the expression of the non-canonical cyclins O and A1 - which replace the transcriptionally silent cyclins E2 and A2 - and by the silencing of the APC/C inhibitor Emi1, two switches also detected in male meiosis, another variant of the canonical cell cycle where centriole and DNA replications are uncoupled. Re-expressing Cyclin E2, cyclin A2 or Emi1 is sufficient to induce partial replication and mitosis, suggesting that change in the regulation of expression of a few cell cycle key players drives a qualitative and quantitative tuning of Cdk activity, allowing the diversion of the cell cycle in the multiciliation variant. We also propose that this new cell cycle variant relies on the existence of a cytoplasmic - or centriolar - Cdk threshold, lower than the S-phase threshold, which affects only the cytoplasmic reorganization. One-Sentence SummaryMCC progenitors undergo a final, tailored iteration of the cell cycle during differentiation, to drive centriole amplification without DNA replication or mitosis.

cell biology↗

bioRxiv2024

Cyclin O controls entry into the cell-cycle variant required for multiciliated cell differentiation

Multiciliated cells (MCC) ensure proper fluid circulation in various organs in metazoans. Their differentiation is marked by the massive ampliication of cilia-nucleating centrioles and is known to be controlled by various cell cycle components. Tn a companion study, we show that the differentiation of MCC is driven by a genuine cell-cycle variant characterized by sequential and wave-like expression of canonical and non-canonical cyclins such as Cyclin O (CCNO). Patients with CCNO mutations exhibit a subtype of Primary Ciliary Dyskinesia (PCD) designated as Reduced Generation of Multiple Motile Cilia (RGMC), yet the role of CCNO during MCC differentiation remains unclear. Here, using mice and human cellular models, single cell transcriptomics and functional studies, we show that Cena is activated during a strategic temporal window at the crossroads between the onset of MCC differentiation, the entry into the MCC cell cycle variant, and the activation of the centriole biogenesis program. We ind that the absence of Cena leads to a block of MCC progenitor differentiation at the G1/S-like transition, just before the beginning of centriole formation. This leads to a complete lack of centrioles and cilia in mouse brain and human airway MCC. Altogether, our study identifies CCNO as a core regulator of entry into the MCC cell cycle variant and shows that the coupling of centriole biogenesis to an S-like phase, maintained in MCC, is dependent on CCNO. One sentence summaryCyclin O is necessary for multiciliated cells to enter their differentiation cell cycle variant and allows the massive amplification of centrioles, which serve as basal bodies for cilia nucleation.

cell biology↗

bioRxiv2024

Microtubule-dependent orchestration of centriole amplification in brain multiciliated cells

Multiciliated cell (MCC) differentiation is a calibrated version of the canonical cell cycle. The MCC cell cycle variant sustains amplification of centrioles for the nucleation of dozens of motile cilia, while avoiding cell division. In this study, we show that the MCC cell cycle variant is an accelerated version of the canonical cell cycle, which superposes two cycles of centriole biogenesis, in order to obtain multiple mature centrioles within a single -instead of double- cell cycle iteration. We further show that the precocious maturation of amplified procentrioles is even determinant for their spatial self-organization, disengagement and apical migration for cilia nucleation. Our findings collectively suggest that the decomposition of centriole biogenesis over two cycle iterations in dividing cells may have been adopted to ensure the growth of a solitary primary cilium, and exemplify how minimal deviations of the canonical cell cycle allow MCC progenitors to both amplify, and accelerate, centriole biogenesis for vital motile ciliogenesis.

cell biology↗

bioRxiv2023

Actin-based deformations of the nucleus control multiciliated ependymal cell differentiation.

Ependymal cells (ECs) are multi-ciliated cells in the brain that contribute to cerebrospinal fluid flow. ECs are specified at embryonic stages but differentiate later in development. Differentiation depends on genes such as GEMC1 and MCIDAS with E2F4/5, but also on cell cycle related factors. In the mouse brain, we observe that nuclear deformation accompanies EC differentiation. Tampering with these deformations either by decreasing F-actin levels or by severing the link between the nucleus and the actin cytoskeleton blocks differentiation. Conversely, increasing F-actin by knocking out the Arp2/3 complex inhibitor Arpin or artificially deforming the nucleus activates differentiation. These data are consistent with actin polymerization triggering nuclear deformation and jump-starting the signaling that produces ECs. A player in this process is the retinoblastoma1 (RB1) protein whose phosphorylation prompts MCIDAS activation. Overall, this study reveals an important role for actin-based mechanical inputs to the nucleus as controlling factors in cell differentiation.

developmental biology↗

bioRxiv2019

Synchronization of mammalian motile cilia in the brain with hydrodynamic forces

Motile cilia are widespread across the animal and plant kingdoms, displaying complex collective dynamics central to their physiology. Their coordination mechanism is not generally understood, with pre-vious work mainly focusing on algae and protists. We study here the synchronization of cilia beat in multiciliated cells from brain ven-tricles. The response to controlled oscillatory external flows shows that strong flows at a similar frequency to the actively beating cilia can entrain cilia oscillations. We find that the hydrodynamic forces required for this entrainment strongly depend on the number of cilia per cell. Cells with few cilia (up to five) can be entrained at flows comparable to the cilia-driven flows reported in vivo. Simulations of a minimal model of cilia interacting hydrodynamically show the same trends observed in cilia. Our results suggest that hydrody-namic forces between cilia are sufficient to be the mechanism behind the synchronization of mammalian brain cilia dynamics.\n\nSignificance StatementIt is shown experimentally, and also reproducing key qualitative results in a minimal mechanistic model simulated numerically, that in the motile cilia of the brain hydrodynamic forces of the magnitude that cilia themselves can generate are sufficient to establish the coordination of dynamics which is so crucial phys-iologically. This is the first experiment of its kind on multicilated cells, the key result is the unexpected importance of cilia num-ber per cell, with cells with fewer cilia much more susceptible to external flows. This finding changes the way in which we think about the question of collective cilia beating - it is not correct to simply examine isolated cilia and draw conclusions about the behaviour of cilia assemblies in multiciliated cells.

biophysics↗

bioRxiv2018

Dynamics of centriole amplification in centrosome-depleted brain multiciliated progenitors

Centrioles are essential microtubule-based organelles organizing cilia and centrosomes. Their mode of biogenesis is semi-conservative: each pre-existing centriole scaffolds the formation of a new one, a process coordinated with the cell cycle. By contrast, multiciliated progenitors with two centrosomal centrioles massively amplify centrioles to support the nucleation of hundred of motile cilia and transport vital fluids. This occurs through cell type-specific organelles called deuterosomes, composed of centrosome-related elements, and is regulated by the cell cycle machinery. Deuterosome-dependent centriole amplification was proposed for decades to occur de novo, i.e. independently from pre-existing centrioles. Challenging this hypothesis, we recently reported an accumulation of procentriole and deuterosome precursors at the centrosomal daughter centriole during centriole amplification in brain multiciliated cells. Here we further investigate the relationship between the centrosome and the dynamic of centriole amplification by (i) characterizing the centrosome behavior during the centriole amplification dynamics and (ii) assessing the dynamics of amplification in centrosome-depleted cells. Surprisingly, although our data strengthen the centrosomal origin of amplified centrioles, we show limited consequences in deuterosome/centriole number when we deplete centrosomal centrioles. Interestingly, in absence of centrosomal centrioles, procentrioles are still amplified sequentially from a single focal region, characterized by microtubule convergence and pericentriolar material (PCM) self-assembly. The relevance of deuterosome association with the daughter centriole as well as the role of the PCM in the focal and sequential genesis of centrioles in absence of centrosomal centrioles are discussed.

cell biology↗