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Results for “cell biology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 451 records · Page 25Linked to original sources

bioRxiv2025

Identification of stem cell marker-positive subpopulations in the vocal fold of the larynx through transcriptomic analyses

Information on the maintenance of tissue homeostasis is important for the development of effective therapeutic methods, however, reports on the cellular composition and tissue stem cells of the larynx were scarce. Therefore, we analyzed mouse laryngeal mucosa using scRNA-seq, and spatial transcriptomics by photo-isolation chemistry, and performed the generation of laryngeal organoid used as an in vitro model from mouse laryngeal mucosa. As a result, we found a SOX9-positive basal cell subpopulation and a Lgr5-positive fibroblast subpopulation in the mouse vocal fold, and obtained three types of epithelial organoids from laryngeal epithelium. We also confirmed the differences in pseudostratified ciliated columnar epithelium composition between the supraglottis and subglottis of the mouse larynx. These findings provide novel insights and valuable tools for future research in laryngology and stem cell biology.

cell biology↗

bioRxiv2026

A nematode-trapping fungus orchestrates polarity cues, septins, and NOX signaling for trap formation

The ability to reprogram cell morphogenesis in response to environmental cues is fundamental to microbial adaptation and survival. The nematode-trapping fungus Arthrobotrys oligospora exemplifies this plasticity by developing adhesive traps to capture nematodes. This morphological transition involves spatial reorientation of cell polarity, cytoskeletal remodeling, and cell fusion. However, the molecular mechanisms that coordinate these processes remain unclear. Using live-cell imaging, genetics, and functional assays, we demonstrated that cell polarity proteins localize to hyphal tips to direct growth, while actin and septins assemble at the curving inner rim to shape trap architecture. Conserved NADPH oxidases are induced by the presence of nematodes and are required for the recruitment of cell polarity proteins and cytoskeletal factors to promote trap cell fusion. Together, these findings reveal that polarity cues, cytoskeletal organization, and reactive oxygen species signaling are integrated to orchestrate nematode-induced trap development, establishing nematode-trapping fungi as a versatile model to study fungal cell biology.

cell biology↗

bioRxiv2022

In situ structural analysis reveals membrane shape transitions during autophagosome formation

Autophagosomes are unique organelles which form de novo as double-membrane vesicles engulfing cytosolic material for destruction. Their biogenesis involves a series of membrane transformations with distinctly shaped intermediates whose ultrastructure is poorly understood. Here, we combine cell biology, correlative cryo-electron tomography (ET) and novel data analysis to reveal the step-by-step structural progression of autophagosome biogenesis at high resolution directly within yeast cells. By mapping individual structures onto a timeline based on geometric features, we uncover dynamic changes in membrane shape and curvature. Moreover, we reveal the organelle interactome of growing autophagosomes, highlighting a polar organization of contact sites between the phagophore and organelles such as the vacuole and the ER. Collectively, these findings have important implications for the contribution of different membrane sources during autophagy and for the forces shaping and driving phagophores towards closure without a templating cargo.

cell biology↗

bioRxiv2023

Polychaetoid/ZO-1 strengthens cell junctions under tension while localizing differently than core adherens junction proteins

During embryonic development dramatic cell shape changes and movements re-shape the embryonic body plan. These require robust but dynamic linkage between the cell-cell adherens junctions and the force-generating actomyosin cytoskeleton. Our view of this linkage has evolved, and we now realize linkage is mediated by a mechanosensitive multiprotein complex assembled via multivalent connections. Here we combine genetic, cell biological and modeling approaches to define the mechanism of action and functions of an important player, Drosophila Polychaetoid, homolog of mammalian ZO-1. Our data reveal that Pyd reinforces cell junctions under elevated tension, and facilitates cell rearrangements. Pyd is important to maintain junctional contractility and in its absence cell rearrangements stall. We next use structured illumination microscopy to define the molecular architecture of cell-cell junctions during these events. The cadherin-catenin complex and Cno both localize to puncta along the junctional membrane, but are differentially enriched in different puncta. Pyd, in contrast, exhibits a distinct localization to strands that extend out from the region occupied by core junction proteins. We then discuss the implications for the protein network at the junction-cytoskeletal interface, suggesting different proteins localize and function in distinct ways but combine to produce robust connections.

cell biology↗

bioRxiv2019

Microtubule bundling by MAP65-1 protects against severing by inhibiting the binding of katanin

The microtubule-severing enzyme katanin regulates the organization and turnover of microtubule arrays by the localized breakdown of microtubule polymers. In land plants, katanin (KTN1) activity is essential for the formation of linearly organized cortical microtubule arrays which determine the axis of cell expansion. Cell biological studies have shown that even though KTN1 binds to the sidewalls of single and bundled microtubules, severing activity is restricted to microtubule crossover and nucleation sites, indicating that cells contain protective mechanisms to prevent indiscriminate microtubule severing. Here, we show that the microtubule bundling protein MAP65-1 inhibits KTN1-mediated microtubule severing in vitro. Severing is inhibited at bundled microtubule segments and the severing rate of non-bundled microtubules is reduced by MAP65-1 in a concentration-dependent manner. Using various MAP65-1 mutant proteins, we demonstrate that efficient crosslinking of microtubules is crucial for this protective effect and that microtubule binding alone is not sufficient. Reduced severing due to microtubule bundling by MAP65-1 correlated to decreased binding of KTN1 to these microtubules. Taken together, our work reveals that crosslinking of microtubules by MAP65-1 confers resistance to severing by inhibiting the binding of katanin and identifies the structural features of MAP65-1 that are important for this activity.\n\nHighlight SummaryCortical microtubule bundles resist severing in vivo. Here, we show that crosslinking of microtubules by MAP65-1 inhibits severing in a dose-dependent manner by preventing katanin from binding to these microtubules.

cell biology↗

bioRxiv2017

Single cell transcriptional profiling reveals cellular diversity, communication, and sexual dimorphism in the mouse heart

INTRODUCTORY PARAGRAPHCharacterization of the cardiac cellulome--the network of cells that form the heart--is essential for understanding cardiac development and normal organ function, and for formulating precise therapeutic strategies to combat heart disease. Recent studies have challenged assumptions about both the cellular composition1 and functional significance of the cardiac non-myocyte cell pool, with unexpected roles identified for resident fibroblasts2 and immune cell populations3,4. In this study, we characterized single-cell transcriptional profiles of the murine non-myocyte cardiac cellular landscape using single-cell RNA sequencing (scRNA-Seq). Detailed molecular analyses revealed the diversity of the cardiac cellulome and facilitated the development of novel techniques to isolate understudied cardiac cell populations such as mural cells and glia. Our analyses also revealed networks of intercellular communication as well as extensive sexual dimorphism in gene expression in the heart, most notably demonstrated by the upregulation of immune-sensing and pro-inflammatory genes in male cardiac macrophages. This study offers new insights into the structure and function of the mammalian cardiac cellulome and provides an important resource that will stimulate new studies in cardiac cell biology.

cell biology↗

bioRxiv2023

Global organelle profiling reveals subcellular localization and remodeling at proteome scale

Defining the subcellular distribution of all human proteins and its remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immuno-capture coupled to mass spectrometry. We apply this proteomics workflow to a cell-wide collection of membranous and membrane-less compartments. A graph-based representation of our data reveals the subcellular localization of over 7,600 proteins, defines spatial protein networks, and uncovers interconnections between cellular compartments. We demonstrate that our approach can be deployed to comprehensively profile proteome remodeling during cellular perturbation. By characterizing the cellular landscape following hCoV-OC43 viral infection, we discover that many proteins are regulated by changes in their spatial distribution rather than by changes in their total abundance. Our results establish that proteome-wide analysis of subcellular remodeling provides essential insights for the elucidation of cellular responses. Our dataset can be explored at organelles.czbiohub.org.

cell biology↗

bioRxiv2024

SwinCell: a transformer-based framework for dense 3D cellular segmentation

Segmentation of three-dimensional (3D) cellular images is fundamental for studying and understanding cell structure and function. However, 3D cellular segmentation is challenging, particularly for dense cells and tissues. This challenge arises mainly from the complex contextual information within 3D images, anisotropic properties, and the sensitivity to internal cellular structures, which often lead to miss-segmentation. In this work, we introduce SwinCell, a 3D transformer-based framework that leverages Swin-transformer for flow prediction and effectively distinguishes individual cell instances in 3D. We demonstrate the broad utility of the SwinCell in the segmentation of nuclei, colon tissue cells, and dense cultured cells. SwinCell strikes a balance between maintaining detailed local feature recognition and understanding broader contextual information. Tested extensively with both public and in-house 3D cell imaging datasets, SwinCell shows superior performance in segmenting dense cells in 3D, making it a powerful 3D segmentation tool for cellular analysis that could expedite research in cell biology and tissue engineering.

cell biology↗

bioRxiv2024

3D nanoscale architecture of the respiratory epithelium reveals motile cilia-rootlets-mitochondria axis of communication

A major frontier in single cell biology is decoding how transcriptional states result in cellular-level architectural changes, ultimately driving function. A remarkable example of this cellular remodelling program is the differentiation of airway stem cells into the human respiratory multiciliated epithelium, a tissue barrier protecting against bacteria, viruses and particulate matter. Here, we present the first isotropic three-dimensional map of the airway epithelium at the nanometre scale unveiling the coordinated changes in cellular organisation, organelle topology and contacts, occurring during multiciliogenesis. This analysis led us to discover a cellular mechanism of communication whereby motile cilia relay mechanical information to mitochondria through striated cytoskeletal fibres, the rootlets, to promote effective ciliary motility and ATP generation. Altogether, this study integrates nanometre-scale structural, functional and dynamic insights to elucidate fundamental mechanisms responsible for airway defence.

cell biology↗

bioRxiv2026

Human iPSCs and iPSC-Derived Endothelial Cells from PAD Patients and Healthy Donors Exhibit Comparable Characteristics and Potency: Implications for Autologous Cell Therapy in Peripheral Artery Disease

BACKGROUND: Peripheral artery disease (PAD) can lead to amputation in advanced cases, making cell therapy using human induced pluripotent stem cells (hiPSCs) a promising therapeutic option. hiPSC-derived endothelial cells (hiPSC-ECs) have shown favorable effects in treating experimental ischemic cardiovascular disease. An autologous approach for PAD patients is preferable to avoid immunological reactions. However, it is yet unknown whether hiPSCs and hiPSC-ECs derived from PAD patients have similar characteristics and potency compared to those derived from non-PAD donors. Therefore, we explored whether there are significant differences in the characteristics and potency of hiPSCs and hiPSC-ECs between non-PAD donors and PAD patients. METHODS: We generated hiPSCs from the blood of non-PAD donors and patients with PAD. We determined the pluripotency of hiPSCs using qRT-PCR, flow cytometry, immunostaining, RNA-seq, and teratoma formation assay. The genetic stability of hiPSCs was confirmed by G-banding karyotyping. We then differentiated hiPSCs into endothelial cells (ECs) in a clinically compatible manner. We compared the characteristics and therapeutic potency of hiPSC-ECs derived from non-PAD and PAD groups using qRT-PCR, flow cytometry, immunostaining, and RNA-seq. In vitro endothelial functions were determined by nitric oxide (NO) production and capillary network formation. Therapeutic potency and incorporation of engrafted hiPSC-ECs were evaluated in a hindlimb ischemia model. RESULTS: We successfully generated hiPSCs from the blood of seven non-PAD donors and eight PAD patients. Both non-PAD and PAD-derived hiPSCs exhibited similar expression levels of pluripotency markers. All hiPSCs, regardless of the group, formed teratomas and showed normal karyotypes. RNA-seq analyses revealed similar gene expression profiles between the groups. hiPSC-ECs derived from both non-PAD and PAD donors exhibited similar expression levels of EC markers at both the gene and protein levels. RNA-seq analyses showed no significant overall differences in gene expression profiles between the groups. Functional analyses demonstrated similar endothelial characteristics and function in hiPSC-ECs from both groups. Both groups showed similar perfusion recovery, limb salvage, and vessel-forming capacity. Engrafted hiPSC-ECs from both groups also exhibited similar angiogenic and vessel-forming capabilities. CONCLUSIONS: Our study demonstrated no significant differences in hiPSCs and hiPSC-ECs derived from non-PAD donors and PAD patients in terms of molecular and cell biological characteristics, therapeutic effects, and vessel-forming capability. Our study indicates that hiPSCs and hiPSC-ECs derived from PAD patients can serve as a novel platform for autologous cell therapy.

cell biology↗

bioRxiv2019

Photoswitchable microtubule inhibitors enabling robust, GFP-orthogonal optical control over the tubulin cytoskeleton

Here we present GFP-orthogonal optically controlled reagents for reliable and repetitive in cellulo modulation of microtubule dynamics and its dependent processes. Optically controlled reagents (\"photopharmaceuticals\") have developed into powerful tools for high-spatiotemporal-precision control of endogenous biology, with numerous applications in neuroscience, embryology, and cytoskeleton research. However, the restricted chemical domain of photopharmaceutical scaffolds has constrained their properties and range of applications. Styrylbenzothiazoles are an as-yet unexplored scaffold for photopharmaceuticals, which we now rationally design to feature potent photocontrol, switching microtubule cytoskeleton function off and on according to illumination conditions. We show more broadly that this scaffold is exceptionally chemically and biochemically robust as well as substituent-tolerant, and offers particular advantages for intracellular biology through a range of desirable photopharmaceutical and drug-like properties not accessible to the current classes of photoswitches. We expect that these reagents will find powerful applications enabling robust, high precision, optically controlled cell biological experimentation in cytoskeleton research and beyond.

cell biology↗

bioRxiv2025

Unfolded protein response signaling promotes myeloid cell production and cooperates with oncogenic mutation

Unfolded protein response (UPR) promotes protein homeostasis under endoplasmic reticulum stress. UPR signaling has numerous functions in metabolism, cancer, immunology, and neurodegenerative diseases. Recent studies also showed that UPR signaling has important roles in hematopoietic stem and progenitor cell biology. However, whether UPR signaling regulates hematopoietic lineage fate decision remains elusive. Here, we found that Fc{gamma}R- MPP3 generates erythroid lineage and Jak2V617F mutation leads to overproduction of erythroid cells by expanding Fc{gamma}R- MPP3. We showed that UPR signaling increases myeloid cell production through promoting Fc{gamma}R- MPP3 transition to granulocyte/macrophage progenitor producing Fc{gamma}R+ MPP3 at the expense of erythroid lineage via the XBP1 pathway. Under a disease condition, UPR signaling cooperates with Jak2V617F mutation and exacerbates disease phenotype in a mouse model of polycythemia vera (PV) through the ATF4 pathway. Activation of UPR signaling also increased myeloid output in healthy donor bone marrow MPP cells while skewing the output towards erythroid lineage in PV patient bone marrow MPP cells. Together, our results identify a novel function of UPR signaling in hematopoietic lineage specification and provide critical insights into targeting UPR signaling in hematological malignancies. Key pointsO_LIUPR signaling promotes myeloid cell production at the expense of erythroid lineage in steady state. C_LIO_LIUPR signaling collaborates with Jak2V617F mutation and increases red blood cell production. C_LI

cell biology↗

bioRxiv2025

An Asgard archaeon with internal membrane compartments

The emergence of eukaryotes from a merger between an archaeon and a bacterial cell [~]two billion years ago involved a profound change in cellular organisation. While the order in which different features of the eukaryotic cell arose remains a matter of controversy1-3, close archaeal relatives of eukaryotes have recently been identified that possess homologues of eukaryotic trafficking machinery4,5 and a complex cell architecture6,7. The members of this phylum, the Asgard archaea (syn. Prometheoarchaeota) described so far, however, lack internal membrane-bound compartments, and therefore have shed little light on origins of the hallmark eukaryotic endomembrane system. Here we report the cell biological analysis of a member of the Heimdallarchaeia, Candidatus Y. umbracryptum in enriched mixed microbial communities. Possessing a small genome encoding few homologues of eukaryotic membrane remodelling machinery8, Ca. Y. umbracryptum cells in late-stage cultures resemble previously described Asgard archaea with extensive cellular protrusions. Surprisingly, during early stages of culture growth Ca. Y. umbracryptum cells have fewer protrusions but possess numerous intracellular vesicles, most of which have a luminal surface that morphologically resembles the outer coat of the plasma membrane. These data alter our view of eukaryogenesis by identifying a close archaeal relative of eukaryotes with an endomembrane system, whose appearance changes with cell state.

cell biology↗

bioRxiv2021

Low-dose fluvoxamine modulates endocytic trafficking of SARS-CoV-2 spike protein: a potential mechanism for anti-COVID-19 protection by antidepressants

Commonly prescribed antidepressants may be associated with protection against severe COVID-19, with one drug (fluvoxamine) currently undergoing a Phase 3 clinical trial. The mechanism of their action, however, remains unknown. Here, I investigated the effect of fluvoxamine on membrane trafficking of the SARS-CoV-2 spike protein and its cell host receptor ACE2 in HEK293T cells. A sub-therapeutic concentration (80 nM) of fluvoxamine rapidly upregulated fluid-phase endocytosis, resulting in enhanced accumulation of the spike-ACE2 complex in enlarged early endosomes. Diversion of endosomal trafficking may provide a simple cell biological mechanism consistent with the protective effect of antidepressants against COVID-19, highlighting their therapeutic and prophylactic potential.

cell biology↗

bioRxiv2024

Single-cell analysis reveals multi-faceted features of B cell development together with age-associated B cell subpopulations

The development and maturation of B lymphocytes involve intricate orchestrated processes, where dedicated gene regulations (GR) take place within specific microenvironments shaped by both extracellular matrix and neighboring cells. Despite extensive investigations aimed at deepening our comprehension of these mechanisms, there remains a dearth of high-dimensional and integrated analysis concerning B cell heterogeneity, gene regulation, and external factors implicated in B cell development. In this study, we scrutinized single-cell transcriptomic data and B cell receptor (BCR) sequencing data obtained from B cells and their surrounding counterparts in the bone marrow, tonsil, and peripheral blood. A full picture of the GR dynamics, the heterogeneity of conventional B cells and cell-cell interactions (CCIs) along B cell development axis was depicted. We found immature B cells represent the most quiescent stage characterized by the least number of expressed genes and low RNA velocity. The homeostatic proliferation and activation of naive B cells is niche-confined and individualized, respectively. Two development models for memory B cell subpopulations seem not mutually exclusive and warrant in-depth investigation. Moreover, CCI analysis reveals a pivotal role of myeloid cells and two dominant and stage-dependent CCI categories, TNF and adhesion signaling, in B cell development. Besides, we unexpectedly identified two age-associated B cell subpopulations that respectively express S100A8/S100A9 and C1q and experimentally confirmed the secretion of S100A8/A9 from human B cells in vitro, suggesting a senescence-associated secretion phenotype. Our integrated analysis provides valuable insights into GR dynamics, the evolution of B cells, and potential intercellular communication networks involved in B cell development and revealed novel phenotypes of age-associated B cell aberrance. This study serves as a valuable resource for in-depth exploration of the intricacies of B cell biology.

cell biology↗

bioRxiv2024

Ciliary length regulation by intraflagellar transport in zebrafish

How cells regulate the size of their organelles remains a fundamental question in cell biology. Cilia, with their simple structure and surface localization, provide an ideal model for investigating organelle size control. However, most studies on cilia length regulation are primarily performed on several single-celled organisms. In contrast, the mechanism of length regulation in cilia across diverse cell types within multicellular organisms remains a mystery. Similar to humans, zebrafish contain diverse types of cilia with variable lengths. Taking advantage of the transparency of zebrafish embryos, we conducted a comprehensive investigation into intraflagellar transport (IFT), an essential process for ciliogenesis. By generating a transgenic line carrying Ift88-GFP transgene, we observed IFT in multiple types of cilia with varying lengths. Remarkably, cilia exhibited variable IFT speeds in different cell types, with longer cilia exhibiting faster IFT speeds. This increased IFT speed in longer cilia is likely not due to changes in common factors that regulate IFT, such as motor selection, BBSome proteins, or tubulin modification. Interestingly, longer cilia in the ear cristae tend to form larger IFT compared to shorter spinal cord cilia. Reducing the size of IFT particles by knocking down Ift88 slowed IFT speed and resulted in the formation of shorter cilia. Our study proposes an intriguing model of cilia length regulation via controlling IFT speed through the modulation of the size of the IFT complex. This discovery may provide further insights into our understanding of how organelle size is regulated in higher vertebrates.

cell biology↗

bioRxiv2021

Zoom in on Ca2+ pattern and ion flux dynamics to decode spatial and temporal regulation of cotton fiber growth

Cotton fibers are single-celled trichomes initiated from ovule epidermis prior to anthesis. Thereafter, the fibers undergo rapid elongation for 20 d before switching to intensive cell wall cellulose synthesis. The final length attained determines fiber yield and quality. As such, cotton fiber represents an excellent single cell model to study regulation of cell growth and differentiation, with significant agronomical implications. One major unresolved question is whether fiber elongation follows a diffusive or a tip growth pattern. We addressed this issue by using cell biology and electrophysiological approaches. Confocal imaging of Ca2+ binding dye, fluo-3 acetoxymethyl (Fluo-3), and in situ microelectrode ion flux measurement revealed that cytosolic Ca2+ was evenly distributed along the elongating fiber cells with Ca2+ and H+ fluxes oscillating from apical to basal regions of the elongating fibers. These findings demonstrate that, contrary to growing pollen tubes or root hairs, cotton fiber growth follows a diffusive, but not the tip growth, pattern. Further analyses showed that the elongating fibers exhibited substantial net H+ efflux, indicating a strong activity of the plasma membrane H+-ATPase required for energy dependent solute uptake. Interestingly, the growing cotton fibers were responding to H2O2 treatment, know to promote fiber elongation, by a massive increase in the net Ca2+ and H+ efflux in both tip and basal zones, while non-growing cells lacked this ability. These observations suggest that desensitization of the cell and a loss of its ability to respond to H2O2 may be causally related to the termination of the cotton fiber elongation. One sentence summaryConfocal imaging of Ca2+ patterning and in situ microelectrode ion flux measurements demonstrate that, contrary to growing pollen tubes or root hairs, cotton fiber growth follows a diffusive, but not the tip growth, pattern.

cell biology↗

bioRxiv2023

A proximity-dependent biotinylation map of cytosol-facing organelle outer membrane proteome in living Arabidopsis cells

The cytosol-facing outer membrane (OM) of organelles communicates with other cellular compartments to exchange proteins, metabolites and signaling molecules. Cellular surveillance systems also target OM-resident proteins to control organellar homeostasis and ensure cell survival under stress. Using traditional approaches to discover OM proteins and identify their dynamically interacting partners remains challenging. In this study, we developed an OM proximity labeling (OMPL) system using biotin ligase-mediated proximity biotinylation to map the proximity proteome of the OMs of mitochondria, chloroplasts, and peroxisomes in living Arabidopsis (Arabidopsis thaliana) cells. We demonstrate the power of this system with the discovery of cytosolic factors and OM receptor candidates involved in local protein translation and translocation, membrane contact sites, and organelle quality control. This system also performed admirably for the rapid isolation of intact mitochondria and peroxisomes. Our data support the notion that TOM20-3 is a candidate for both a mitochondrial and a chloroplast receptor, and that PEX11D is a candidate for a peroxisome receptor for the coupling of protein translation and import. OMPL-generated OM proximity proteomes are valuable sources of candidates for functional validation and suggest directions for further investigation of important questions in cell biology.

cell biology↗