Biology subjects

Imoto, Y.

Publications and source records attributed to Imoto, Y..

13 recordsLinked to original sources

bioRxiv2026

CycloCross: Adversarial single-cell RNA-seq data translation across species

Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cellular heterogeneity, yet most datasets are limited to a handful of model organisms, leaving critical gaps in cross-species biology. Existing computational methods for integrating multi-species scRNA-seq data often rely on one-to-one ortholog mapping, which fails to account for gene duplications, losses, or functional divergences. To address these challenges, we introduce CycloCross, an adversarial method based on the CycleGAN architecture, designed to translate scRNA-seq data between species without requiring a priori gene correspondences. Unlike generative models that synthesize data from noise, CycloCross leverages real data from a source species, enabling more realistic and data-efficient translations. We demonstrate its effectiveness in germ cell development, translating data between mouse, macaque, and human with conserved yet divergent transcriptional programs. CycloCross not only preserves temporal dynamics but also enables interpolation and extrapolation of gene expression at missing time points, offering predictions for experimentally inaccessible states. Furthermore, CycloCross generates biologically plausible samples even with limited data, outperforming traditional generative models.

bioinformatics↗

bioRxiv2026

Microglia extract neuronal proteolytic organelles via skoupocytosis

Neurons face unique challenges in maintaining protein homeostasis due to their tortuous morphology and extended processes. Proteolytic organelles are typically transported retrogradely towards their soma for degradation where lysosomes are enriched, but some organelles are larger than these neuronal processes, questioning how these organelles are degraded. Here we show that microglia, the resident immune cells of the brain, extract proteolytic organelles from neurons both in vitro and in vivo. Microglia make transient contact with neuronal membranes where proteolytic organelles are stationed beneath. At these sites of interaction, microglia pinch off a small portion of the neuronal process containing the organelle, leaving the rest of the process intact. We term this process skoupocytosis after the Greek word for garbage. Phosphatidylserine (PS) lipase ABHD16a accumulates near these proteolytic organelles and converts PS into lyso-PS to initiate microglial skoupocytosis. Skoupocytosis bypasses the need for retrograde organelle transport, providing homeostatic advantages for neurons that must maintain function in processes that extend extraordinarily long distances from the cell soma.

neuroscience↗

bioRxiv2025

Geometric inference of cross-species transcriptome correspondence using Gromov-Wasserstein optimal transport

Sequence homology reveals evolutionary gene correspondences, but identifying functionally corresponding genes within specific cell types or during cell fate specification remains non-trivial. Here, frameworks that translate insights from model organisms into other species would accelerate wet-lab studies, so we develop Species-OT, a cross-species transcriptome analysis framework using Gromov-Wasserstein optimal transport, which quantitatively compares the geometry of transcriptome distributions. Given a pair of bulk or single-cell RNA-sequencing datasets, Species-OT returns a gene-to-gene correspondence capturing probabilistic alignments of regulatory roles, and a transcriptomic distance quantifying overall divergence. Applied pairwise, Species-OT yields a transcriptomic discrepancy array and a hierarchical clustering tree analogous to a phylogenetic tree. We validate Species-OT using bulk RNA-seq data for cell fate specification from pluripotent stem cells in mice, monkeys, and humans and scRNA-seq data from pluripotent stem cells of six mammalian species. Species-OT identifies gene correspondences within cell fate specification, while transcriptomic discrepancies recapitulate expected species relationships.

bioinformatics↗

bioRxiv2025

Accurate highly variable gene selection using RECODE in scRNA-seq data analysis

Recent transcriptomics technologies enable gene-expression profiling at single-cell or micrometer-scale spatial resolution, but capture only a small fraction of true RNA molecules, introducing substantial technical noise driven by random sampling. These noise effects distort the earliest analytical steps, dimensionality reduction or highly variable gene (HVG) selection, and their consequences propagate into downstream analyses. The central aim of this study is to address this issue fundamentally by appropriately removing technical noise at its source. Here, I demonstrate that HVG selection based on RECODE, a de-noising method grounded in high-dimensional statistical theory, outperforms widely used approaches for both scRNA-seq and spatial transcriptomics data. RECODE-based HVG selection achieves higher accuracy and robustness, avoids missing values, improves down-stream performance, and provides the fastest runtime and best scalability among noise-reduction methods. These findings show that theory-driven noise removal is essential for recovering true biological signals and establish RECODE as a practical and reliable preprocessing strategy for single-cell analysis.

bioinformatics↗

bioRxiv2024

Ultrastructural membrane dynamics of mouse and human cortical synapses

Live human brain tissues provide unique opportunities for understanding synaptic transmission. Investigations have been limited to anatomy, electrophysiology, and protein localization--while crucial parameters such as synaptic vesicle dynamics were not visualized. Here we utilize zap-and-freeze time-resolved electron microscopy to overcome this hurdle. First, we validate the approach with acute mouse brain slices to demonstrate that slices can be stimulated to produce calcium signaling. Next, we show that synaptic vesicle endocytosis is induced in both mouse and human brain slices. Crucially, clathrin-free endocytic pits appear immediately next to the active zone, where ultrafast endocytosis normally occurs, and can be trapped at this location by a dynamin inhibitor. In both species a protein essential for ultrafast endocytosis, Dynamin 1xA, localizes to the region peripheral to the active zone, the putative endocytic zone, indicating a possible conserved mechanism between mouse and human. This approach has the potential to reveal dynamic, high-resolution information about synaptic membrane trafficking in intact human brain slices.

neuroscience↗

bioRxiv2024

Comprehensive Noise Reduction in Single-Cell Data with the RECODE Platform

AO_SCPLOWBSTRACTC_SCPLOWSingle-cell sequencing generates vast amounts of genomic and epigenomic data from thousands of individual cells and can reveal insights into biological principles at the single-cell resolution. However, challenges such as technical noise (dropout) and batch effects hinder obtaining high-resolution structures that are essential for tasks such as the identification of rare cell types and dataset comparison across different cultures. Here, I introduce integrative RECODE (iRECODE), a comprehensive method for noise reduction that is based on the RECODE platform, which targets the technical noise in single-cell RNA-sequencing data using high-dimensional statistics. I show iRECODE effectively mitigates both technical and batch noise with high accuracy and low computational cost. Additionally, the application of RECODE extended to other single-cell sequencing data types including single-cell Hi-C and spatial transcriptomics data and the recent enhancements in RECODE have markedly improved its accuracy and computational efficiency. Thus, the RECODE platform presents a robust solution for mitigating noise in single-cell sequencing, offering promise for advancing our understanding of biological phenomena beyond transcriptomics, encompassing epigenomic and spatial transcriptomic domains.

bioinformatics↗

bioRxiv2023

Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis

Dynamin 1 (Dyn1) has two major splice variants, xA and xB, with unique C-terminal extensions of 20 and 7 amino acids, respectively. Of these, only Dyn1xA is enriched at endocytic zones and accelerates vesicle fission during ultrafast endocytosis. Here, we report that the long tail variant, Dyn1xA, achieves this localization by preferentially binding to Endophilin A through a newly defined Class II binding site overlapping with its extension, at a site spanning the splice boundary. Endophilin binds this site at higher affinity than the previously reported site, and this affinity is determined by amino acids outside the binding sites acting as long distance elements within the xA tail. Their interaction is regulated by the phosphorylation state of two serine residues specific to the xA variant. Dyn1xA and Endophilin colocalize in patches near the active zone of synapses. Mutations selectively disrupting Endophilin binding to the long extension cause Dyn1xA mislocalization along axons. In these mutants, endocytic pits are stalled on the plasma membrane during ultrafast endocytosis. These data suggest that the specificity for ultrafast endocytosis is defined by the phospho-regulated interaction of Endophilin A through a newly identified site of Dyn1xAs long tail.

cell biology↗

bioRxiv2023

scEGOT: Single-cell trajectory inference framework based on entropic Gaussian mixture optimal transport

Time-series scRNA-seq data have opened a door to elucidate cell differentiation, and in this context, the optimal transport theory has been attracting much attention. However, there remain critical issues in interpretability and computational cost. We present scEGOT, a comprehensive framework for single-cell trajectory inference, as a generative model with high interpretability and low computational cost. Applied to the human primordial germ cell-like cell (PGCLC) induction system, scEGOT identified the PGCLC progenitor population and bifurcation time of segregation. Our analysis shows TFAP2A is insufficient for identifying PGCLC progenitors, requiring NKX1-2. Additionally, MESP1 and GATA6 are also crucial for PGCLC/somatic cell segregation. These findings shed light on the mechanism that segregates PGCLC from somatic lineages. Notably, not limited to scRNA-seq, scEGOTs versatility can extend to general single-cell data like scATAC-seq, and hence has the potential to revolutionize our understanding of such datasets and, thereby also, developmental biology.

bioinformatics↗

bioRxiv2022

Membrane compression by synaptic vesicle exocytosis triggers ultrafast endocytosis

Compensatory endocytosis keeps the surface area of secretory cells constant following exocytosis. At chemical synapses, clathrin-independent ultrafast endocytosis maintains such homeostasis. This endocytic pathway is temporally and spatially coupled to exocytosis, initiating within 50 ms at the region immediately next to where vesicles fuse: the active zone. How synaptic vesicle exocytosis induces ultrafast endocytosis is unknown. Here, we demonstrate that actin filaments are enriched in the region surrounding active zone at mouse hippocampal synapses and that the membrane area conservation due to this actin corral is necessary for exo-endocytic coupling. Simulations suggest that flattening of fused vesicles exerts lateral membrane pressure in the plasma membrane against the actin corral, resulting in rapid formation of endocytic pits at the border between the active zone and the surrounding actin-enriched region. Consistent with our simulations, ultrafast endocytosis does not initiate when actin organization is disrupted, either pharmacologically or by ablation of the actin-binding protein Epsin1. These data suggest that endocytosis is mechanically coupled to exocytosis at synapses.

cell biology↗

bioRxiv2022

Dynamin forms liquid-like condensates at synapses to support ultrafast endocytosis

Endocytosis at synapses is accelerated by the pre-accumulation of Dynamin 1xA at the endocytic zone by Syndapin 1. However, it is unclear how these proteins support the ultrafast kinetics of endocytosis. Here we report that these proteins phase separate at the presynaptic endocytic zone where ultrafast endocytosis takes place. Specifically, the proline-rich motif of Dynamin 1xA interacts with the Src-Homology 3 domain of Syndapin 1 and forms liquid-like condensates. Single-particle tracking of Dynamin 1xA molecules at synapses shows that their diffusion slows down substantially when they are in the condensates, indicating the presence of molecular crowding and intermolecular interaction. When Dynamin 1xA is mutated to disrupt its interaction with Syndapin 1 the condensates do not form. Thus, the liquid-like assembly of these endocytic proteins provides a catalytic platform for ultrafast endocytosis.

neuroscience↗

bioRxiv2022

Resolution of the curse of dimensionality in single-cell RNA sequencing data analysis

Single-cell RNA sequencing (scRNA-seq) can determine gene expression in numerous individual cells simultaneously, promoting progress in the biomedical sciences. However, scRNA-seq data are high-dimensional with substantial technical noise, including dropouts. During analysis of scRNA-seq data, such noise engenders a statistical problem known as the curse of dimensionality (COD). Based on high-dimensional statistics, we herein formulate a noise reduction method, RECODE (resolution of the curse of dimensionality), for high-dimensional data with random sampling noise. We show that RECODE consistently eliminates COD in relevant scRNA-seq data with unique molecular identifiers. RECODE does not involve dimension reduction and recovers expression values for all genes, including lowly expressed genes, realizing precise delineation of cell-fate transitions and identification of rare cells with all gene information. Compared to other representative imputation methods, RECODE employs different principles and exhibits superior overall performance in cell-clustering and single-cell level analysis. The RECODE algorithm is parameter-free, data-driven, deterministic, and high-speed, and notably, its applicability can be predicted based on the variance normalization performance. We propose RECODE as a general strategy for preprocessing noisy high-dimensional data.

bioinformatics↗

bioRxiv2021

Dynamin is primed at endocytic sites for ultrafast endocytosis

Dynamin mediates fission of vesicles from the plasma membrane during endocytosis. Typically, dynamin is recruited from the cytosol to endocytic sites, requiring seconds to tens of seconds. However, ultrafast endocytosis in neurons internalizes vesicles as quickly as 50 ms during synaptic vesicle recycling. Here we demonstrate that Dynamin 1 is pre-recruited to endocytic sites for ultrafast endocytosis. Specifically, Dynamin 1xA, a splice variant of Dynamin 1, interacts with Syndapin 1 to form molecular condensates on the plasma membrane when the proline-rich domain of this variant is dephosphorylated. When this domain is mutated to include phosphomimetic residues or Syndapin 1s dynamin-interacting domain is mutated, Dynamin 1xA becomes diffuse, and consequently, ultrafast endocytosis slows down by [~]100-fold. Mechanistically, Syndapin 1 acts as an adaptor by binding the plasma membrane and stores Dynamin 1xA at endocytic sites. This cache bypasses the recruitment step and accelerates endocytosis at synapses.

neuroscience↗

bioRxiv2020

KIF13A mediates the activity-dependent transport of ESCRT-0 proteins in axons

Turnover of synaptic vesicle (SV) proteins is vital for the maintenance of healthy and functional synapses. SV protein turnover is driven by neuronal activity in an ESCRT (endosomal sorting complex required for transport)-dependent manner. Here, we characterize a critical step in this process: axonal transport of ESCRT-0 component Hrs, necessary for sorting proteins into the ESCRT pathway and recruiting downstream ESCRT machinery to catalyze multivesicular body (MVB) formation. We find that neuronal activity stimulates the formation of presynaptic endosomes and MVBs, as well as the motility of Hrs+ vesicles in axons and their delivery to SV pools. Hrs+ vesicles co-transport ESCRT-0 component STAM1 and comprise a subset of Rab5+ vesicles, likely representing pro-degradative early endosomes. Furthermore, we identify kinesin motor protein KIF13A as essential for the activity-dependent transport of Hrs to SV pools and the degradation of SV membrane proteins. Together, these data demonstrate a novel activity- and KIF13A-dependent mechanism for mobilizing axonal transport of ESCRT machinery to facilitate the degradation of SV membrane proteins.

neuroscience↗