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<title>bioRxiv Subject Collection: Cell Biology</title>
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This feed contains articles for bioRxiv Subject Collection "Cell Biology"
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<title>bioRxiv</title>
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<link>https://www.biorxiv.org</link>
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.23.720483v1?rss=1">
<title>
<![CDATA[
Culture of preimplantation embryos in media containing L-proline increases intracellular GSH concentration throughout development 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.23.720483v1?rss=1
</link>
<description><![CDATA[
Careful balance of the redox status of the embryo and reduction of oxidative stress is crucial in early development. Here we show that the culture of preimplantation mouse embryos in the conditionally non-essential amino acid L-proline (Pro) increases the intracellular concentration of the potent antioxidant glutathione as shown by staining of 2-cell, 4-cell and 8-cell embryos with tetrafluoroterephthalonitrile (4F-2CN). Further, liquid-chromatography/mass spectrometry showed increased GSH levels in all Pro-treated preimplantation stages of development compared to controls. The GSH:GSSG ratio also showed a Pro-dependent increase. Overall, our results indicate that the beneficial effect of Pro in preimplantation embryo culture is due to the reduction in oxidative stress mediated through an increase in cellular GSH concentration.
]]></description>
<dc:creator><![CDATA[ Hardy, M. L., Morris, M. B., Day, M. L. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.23.720483</dc:identifier>
<dc:title><![CDATA[Culture of preimplantation embryos in media containing L-proline increases intracellular GSH concentration throughout development]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.22.720139v1?rss=1">
<title>
<![CDATA[
Genome-Wide CRISPRi Screening Identifies XPO5 as a Regulator of B Cell Mutation and Fitness 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.22.720139v1?rss=1
</link>
<description><![CDATA[
The B cell receptor (BCR) is the defining factor of B lymphocyte identity and function, allowing for a robust adaptive immune response through antigen recognition. Strict regulation of BCR surface density dictates proper B cell signaling, immune regulation, and the prevention of malignancy, yet the factors regulating this density remain undefined. Here, we performed a genome-wide CRISPR interference (CRISPRi) screen in Ramos B cells, which undergo constitutive somatic hypermutation (SHM) and identified Exportin-5 (XPO5) as a central regulator of BCR surface expression. XPO5 depleted cells exhibited an accelerated loss of surface BCR with no change in transcript levels, suggesting a potential post-transcriptional regulatory mechanism. Further analysis revealed XPO5 depletion led to an accumulation of non-functional BCR light chain sequences driven by an increase in AID signature mutations, implicating XPO5 in balancing mutagenesis and repair during somatic hypermutation (SHM). Transcriptomic and small RNA sequencing revealed a global reduction in miRNA levels and enrichment of target gene sets indicative of cell cycle arrest and increased DNA damage response. These data suggest that XPO5 plays a multi-faceted regulatory role in B cells via a miRNA-mediated control, supporting both proliferation and regulating DNA repair thresholds to maintain B cell receptor expression and functionality.
]]></description>
<dc:creator><![CDATA[ Kirch, T. G., Miller, Z. D., Dearborn, J. S., Dowell, W. G., Languon, S., Paculova, H., Cleary, J. H., Frietze, S., Freeman, K., MAJUMDAR, D. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.22.720139</dc:identifier>
<dc:title><![CDATA[Genome-Wide CRISPRi Screening Identifies XPO5 as a Regulator of B Cell Mutation and Fitness]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.23.719722v1?rss=1">
<title>
<![CDATA[
A Müller glia-retinal pigment epithelium apical network surrounding cone outer segments in fish and mouse 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.23.719722v1?rss=1
</link>
<description><![CDATA[
Homeostasis of the vertebrate retina is supported by two non-neuronal cell types, Muller glia and the retinal pigment epithelium (RPE). Their apical domains delineate the subretinal space, where photoreceptor outer segments reside. While the individual interactions between the supporting cells and photoreceptors are well studied, Muller glia and RPE are presumed to remain physically separate in a healthy retina. Here, we describe a revised model of the subretinal space architecture based on detailed FIB-SEM and confocal microscopy imaging of the zebrafish and mouse outer retina. Long apical processes extend from both Muller glia and the RPE, interacting with one another while also encircling cone outer segments. These contact regions, at the interface of the three cell types are highly elaborated in fish and, although sparser, are still present in mouse. The growth and overlap of Muller glial and RPE apical processes occurs subsequent to the emergence of the outer segment in both species, and coincides with the onset of visual function in mouse. Although enriched at cone sites, this specialized interaction does not appear to depend solely on cone localization in either species, pointing to a general hallmark of the vertebrate subretinal space. Together, our work provides major insights into the architecture of the subretinal space and the interactions between Muller glia, RPE and photoreceptors, while demonstrating conservation across species.
]]></description>
<dc:creator><![CDATA[ Sharkova, M., Housset, M., Boudreau, S., Amidian, S., Cayouette, M., Hocking, J. C. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.23.719722</dc:identifier>
<dc:title><![CDATA[A Müller glia-retinal pigment epithelium apical network surrounding cone outer segments in fish and mouse]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.22.720057v1?rss=1">
<title>
<![CDATA[
Retrograde signalling mediates cellular adaptation to mitochondrial DNA copy number alterations 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.22.720057v1?rss=1
</link>
<description><![CDATA[
Eukaryotic cells maintain multiple copies of the mitochondrial genome, which is essential for cellular metabolism. Accordingly, alterations in the mitochondrial DNA (mtDNA) copy number are associated with severe human diseases and ageing. However, the mechanisms through which cells regulate mtDNA copy number and the cellular consequences of altered copy number remain poorly understood. Here, using budding yeast as a model, we show that mtDNA copy number is determined by the amount of three limiting factors, Mip1, Abf2, and Rim1. By synthetically tuning the concentrations of only these three proteins, we can modulate mtDNA dosage inside the cell. This revealed that cells are surprisingly robust to mtDNA copy number alterations, with increased copy numbers even accelerating cell growth. Our findings suggest that this robustness is due to protein dosage compensation and independent regulation of mitochondrial morphology. Mechanistically, we identified a critical role of the retrograde signalling pathway for this adaptation. We show that signalling from mitochondria to the nucleus is upregulated in cells with higher mtDNA copy number, and disruption of this regulation diminishes their faster growth. Taken together, our work reveals regulatory principles that enable cells to adapt to mtDNA copy number alterations.
]]></description>
<dc:creator><![CDATA[ Benedikt, A., Job, K., Li, X., Sarkar, S., Hernandez Goetz, L., Kukhtevich, I. V., Padovani, F., Chadha, Y., Paukstyte, J., Saarikangas, J., Skotheim, J. M., Schneider, R., Swaffer, M. P., Scialdone, A., Lanz, M. C., Kohler, A., Schmoller, K. M. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.22.720057</dc:identifier>
<dc:title><![CDATA[Retrograde signalling mediates cellular adaptation to mitochondrial DNA copy number alterations]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719984v1?rss=1">
<title>
<![CDATA[
Selective conservation of symbiont cell-surface glycans across generations in a vertically transmitting coral 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719984v1?rss=1
</link>
<description><![CDATA[
Coral resilience under climate change depends on the stability of coral-Symbiodiniaceae symbioses. While vertically transmitting corals inherit symbionts directly from parental colonies, the extent to which symbiont cellular traits are conserved across life stages remains unclear. Here, we examined cell-surface glycan profiles of Symbiodiniaceae in parental colonies and eggs of the coral Montipora capitata. Glycan signatures were structured by symbiont genus and differed between life stages, with mannose/glucose- and galactose-containing glycoproteins as primary drivers of variation. Despite life-stage differences, parent-offspring comparisons revealed significant conservation of glycan profiles, indicating intergenerational transmission of symbiont cellular traits that differed between Cladocopium and Durusdinium and were driven by distinct glycan classes. These results suggest that vertical transmission preserves key recognition-relevant glycans while allowing flexibility in other symbionts' surface traits, providing a mechanistic basis for symbiosis stability.
]]></description>
<dc:creator><![CDATA[ Tortorelli, G., Fisher, N., Varela, A., Rosset, S., Ashley, I., Majerova, E., Smith, K., Hughes, K., Drury, C. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719984</dc:identifier>
<dc:title><![CDATA[Selective conservation of symbiont cell-surface glycans across generations in a vertically transmitting coral]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.23.720310v1?rss=1">
<title>
<![CDATA[
Mechanosensation Promotes Local Cell Wall Repair 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.23.720310v1?rss=1
</link>
<description><![CDATA[
Walled cells, such as those of fungi, plants and bacteria, must continuously survey the integrity of their protective cell wall (CW), as they grow, divide, or face mechanical challenges from their high internal turgor and environment. To date, however, how cells detect defects in their CW to activate local reinforcement or repair machineries remains unclear. We implemented a laser irradiation assay to locally wound the CW of model rod-shaped fission yeast cells. We found that laser irradiation causes a near instantaneous local thinning of the CW accompanied by the formation of a local bulge, a drop in turgor and growth arrest, followed by a progressive recovery of CW thickness over tens of minutes with cells eventually resuming growth. Remarkably, wounding the CW away from cell tips, caused the re-localization of canonical polarity regulators including the Rho GTPases Cdc42 and Rho1, that recruited actin assembly and vesicular trafficking of CW synthases to repair the CW. A candidate screen approach suggests that the transmembrane surface mechanosensors Wsc1 and Mlt2 detect local CW defects and promote the recruitment of the Rho GEFs Gef1 and Rgf1 that activate Cdc42 and Rho1. Therefore, these findings delineate a mechanochemical pathway, coupling surface mechanosensing to polarity regulation and CW synthesis, that defines how walled cells may detect and repair local defects in their CWs to safeguard surface integrity.
]]></description>
<dc:creator><![CDATA[ Reignier, Y., Amiri-Czajkowski, D., Le Borgne, R., MINC, N. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.23.720310</dc:identifier>
<dc:title><![CDATA[Mechanosensation Promotes Local Cell Wall Repair]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.22.720116v1?rss=1">
<title>
<![CDATA[
Comparative proteomics reveals a conserved core of tegumental proteins in parasitic flatworms. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.22.720116v1?rss=1
</link>
<description><![CDATA[
Parasitic flatworms, including cestodes and trematodes, are covered by a specialized syncytial tegument that mediates nutrient uptake and host-parasite interactions. While the tegument of trematodes has been extensively characterized, its molecular composition in cestodes remains largely unknown. In this work, we performed a comparative proteomic analysis of the tegument of three cestode species, including larval and adult stages: Hymenolepis microstoma, Mesocestoides corti (syn. M. vogae) and Echinococcus multilocularis. Using stringent enrichment criteria relative to whole-worm extracts, we identified hundreds of tegument-enriched proteins in each species. Comparative analyses revealed a conserved core of tegumental proteins shared among all three species, including members of the Tegument Allergen-Like (TAL) family, vesicular trafficking components and calcium-sensing proteins, and identified candidates for nutrient uptake activities such as glucose and nucleoside transporters. Further comparative analyses revealed a set of shared tegumental proteins with the trematode Schistosoma mansoni, including conserved proteins that are specific to parasitic flatworms, supporting the existence of a conserved ancestral tegumental proteome. Finally, we confirmed tegumental expression of several candidate genes in H. microstoma and E. multilocularis, and demonstrated regionally restricted gene expression among tegumental cytons, suggesting functional specialization within the syncytial tegument. Altogether, these results reveal an evolutionarily conserved composition of the tegument of parasitic flatworms, providing a foundation for future work targeting this critical host-parasite interface.
]]></description>
<dc:creator><![CDATA[ Guarnaschelli, I., Lima, A., Velazco, R., Bergmann, M., Preza, M., Calvelo, J., Cucher, M., Rosenzvit, M. C., Brehm, K., Iriarte, A., Koziol, U. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.22.720116</dc:identifier>
<dc:title><![CDATA[Comparative proteomics reveals a conserved core of tegumental proteins in parasitic flatworms.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719966v1?rss=1">
<title>
<![CDATA[
XIST Is a Key Modulator Associated with the Adhesome Network 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719966v1?rss=1
</link>
<description><![CDATA[
A long non-coding RNA (lncRNA) known as the X-inactivation specific transcript (XIST) plays a central role in X chromosome inactivation: a transcriptional process that silences one of the two X chromosomes in females to ensure dosage compensation between males and females. Much research has been conducted on how XIST regulates X chromosome transcription critical to embryonic development, but recent studies suggest a non-canonical role for XIST in regulating cancer stem cells and cellular plasticity. As cell adhesion and adhesome genes are integral to the regulation of cancer stemness, we explored the previously unrecognized link between XIST and the adhesome network. By performing gene expression and gene ontology analysis on XIST-knockdown ovarian cancer cells, our study showed that XIST loss altered adhesome gene expression and downstream adhesion pathways. Using Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) datasets, we identified distinct correlations between XIST lncRNA and adhesome genes across normal and cancer tissue samples, which are associated with cell stemness. Furthermore, network analysis suggests that XIST may interact with specific adhesome genes within the cell nucleus. This interaction may have significant functional implications, as demonstrated by the hazard ratio analysis of XIST and adhesome gene expression in relation to clinical outcomes. Overall, our results show that among well-annotated functional lncRNAs, XIST appears to be a modulator strongly associated with the adhesome network and cell stemness. Our findings thus support a novel link between lncRNA-mediated epigenetic regulation of cell adhesion genes, highlighting XIST as a key regulator contributing to the adhesome network.
]]></description>
<dc:creator><![CDATA[ Chen, D., Origer, N., Sun, S., Downing, T. L. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719966</dc:identifier>
<dc:title><![CDATA[XIST Is a Key Modulator Associated with the Adhesome Network]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.22.720102v1?rss=1">
<title>
<![CDATA[
Epithelial density controls cell migration through an adhesion-nucleus mechanotransduction pathway 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.22.720102v1?rss=1
</link>
<description><![CDATA[
Cell density is thought to regulate tissue growth, homeostasis, and regeneration, yet how cells sense and respond to density remains poorly understood. To investigate density-dependent mechanotransduction, we combined genetically encoded biosensors with quantitative fluorescence microscopy in epithelial cells subjected to genetic, pharmacological, and mechanical perturbations. We found that low epithelial density promotes focal adhesion growth, causing mechanical relaxation of vinculin and release of its competitive binding with FAK and ERK. This enables FAK to bind and activate ERK in the cytoplasm. Cytoskeletal tension transmitted through LINC complexes drives their nuclear translocation, where low density induces ERKdependent chromatin decondensation and increased nuclear envelope tension. This recruits and activates cPLA2, leading to arachidonic acid production and enhanced cell migration. Together, these findings identify a mechanochemical pathway linking cell density to epithelial migration via ERK, cPLA2, and mechanically regulated signaling from adhesions to the nucleus.
]]></description>
<dc:creator><![CDATA[ Laurent, L., Germier, T., Auduge, N., Canever, H., Schelle, J., Lachuer, H., Girard, P. P., Manneville, J.-B., Sipieter, F., Borghi, N. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.22.720102</dc:identifier>
<dc:title><![CDATA[Epithelial density controls cell migration through an adhesion-nucleus mechanotransduction pathway]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.23.720437v1?rss=1">
<title>
<![CDATA[
ER-associated control of axonal vesicle trafficking during neuronal development 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.23.720437v1?rss=1
</link>
<description><![CDATA[
Axonal vesicle trafficking is essential for presynaptic assembly, yet the intracellular structures that spatially and temporally regulate vesicle transport during neuronal development remain unclear. Here we identify previously uncharacterized membrane contact sites (MCSs) between the endoplasmic reticulum (ER) and both synaptic vesicle precursors (SVPs) and dense-core vesicles (DCVs). Using super-resolution and cryo-electron microscopy, we reveal that vesicle transport undergoes a transient developmental slowdown in the axons of rat hippocampal neurons associated with increased vesicle tethering to the ER. Using proximity biotinylation, we identify the ER protein PRG1 as a developmentally regulated factor enriched at these sites that modulates vesicle mobility. Notably, a disease-associated PRG1 mutant fails to regulate vesicle trafficking. Finally, we demonstrate that PRG1 modulation of vesicle trafficking serves as a developmental checkpoint by delaying synapse formation and preventing premature network activity. Together, our findings establish ER-vesicle contact sites as a previously unrecognized layer of control of axonal trafficking and link intracellular organization to the timing of synapse assembly.
]]></description>
<dc:creator><![CDATA[ Subra, M., Meehl, J. B., Abrisch, R. G., Voeltz, G. K. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.23.720437</dc:identifier>
<dc:title><![CDATA[ER-associated control of axonal vesicle trafficking during neuronal development]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.22.720067v1?rss=1">
<title>
<![CDATA[
hnRNPA2B1 Modulates Early TIA1 Recruitment into Stress Granules through an RNA-Dependent Assembly Mechanism 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.22.720067v1?rss=1
</link>
<description><![CDATA[
Stress granules (SGs) are dynamic, membrane-less assemblies that form in the cytoplasm in response to cellular stress. The ordered recruitment of proteins into SGs is fundamental to condensate composition and function, yet the molecular determinants of this ordered client recruitment remain incompletely understood. Using proximity photo-crosslinking proteomics, we identified heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) as a TIA1-proximal protein preferentially enriched in SGs under arsenite stress. Knockdown of hnRNPA2B1 preferentially delayed TIA1 enrichment in G3BP1-marked SGs at 20 min without affecting G3BP1 or the overall SG-positive cell fraction, and this phenotype showed directional rescue upon re-expression. In vitro droplet reconstitution assays with purified proteins revealed that hnRNPA2B1 and RNA cooperatively increased TIA1 incorporation capacity into G3BP1 condensates, an effect not attributable to changes in droplet size. Kinetic fitting identified hnRNPA2B1 + RNA as uniquely increasing the plateau amplitude of TIA1 recruitment (Cohen's d = 1.62 versus RNA-alone condition). Coarse-grained simulations support an inside-out assembly model in which hnRNPA2B1 stabilizes the condensate core through homotypic interactions while RNA-bound TIA1 accumulates at the periphery. Together, these findings identify hnRNPA2B1 as a capacity-determining modulator of early TIA1 recruitment and provide a framework for understanding ordered protein assembly within stress granules.
]]></description>
<dc:creator><![CDATA[ Teshirogi, Y., Mihara, R., Saito, Y., Rhee, H.-W., Terada, T., Tate, S.-i., Kyota, Y. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.22.720067</dc:identifier>
<dc:title><![CDATA[hnRNPA2B1 Modulates Early TIA1 Recruitment into Stress Granules through an RNA-Dependent Assembly Mechanism]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.22.720193v1?rss=1">
<title>
<![CDATA[
Rewiring Mitochondrial Phosphatidylethanolamine Metabolism Identifies New and Unaccounted Trafficking Steps 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.22.720193v1?rss=1
</link>
<description><![CDATA[
The distinct compositions of the two mitochondrial membranes are generated through a combination of phospholipids that mitochondria can make and those they take; both processes depend on a series of distinct lipid trafficking steps. Mitochondria make phosphatidylethanolamine (PE) through the action of the phosphatidylserine decarboxylase Psd1, an intermembrane space (IMS)-facing integral inner membrane (IM) protein. Psd1 has been proposed to act on its endoplasmic reticulum-derived substrate, phosphatidylserine (PS), after its transport to the mitochondrial outer membrane (OM) and either following its Ups2/Mdm35-mediated transport across the IMS to the IM or instead, on the IMS-side of the OM in a process enabled by the mitochondrial contact site and cristae organizing system (MICOS). Here, we implement a two-pronged Psd1 rewiring-based strategy predicted to either 1) circumvent the need for Ups2/Mdm35 and/or MICOS; or 2) selectively ablate the ability of Psd1 to work in trans. Our results with yeast harboring Psd1 targeted to the OM demonstrate that, with respect to mitochondrial PE production, Ups2/Mdm35 and MICOS indeed function within the IMS. Using yeast expressing a topologically inverted Psd1 chimera that faces the matrix, we identify previously unappreciated transbilayer lipid trafficking steps within the IM and show that Psd1 does not operate via a MICOS-organized in trans mechanism. Further, retained flux through inverted Psd1 when both Ups2/Mdm35 and MICOS are absent strongly implicates the existence of a major, yet presently unknown, mediator(s) of lipid movement across the IMS. Collectively, these data suggest a new model of how mitochondrial membrane diversity is established and maintained.
]]></description>
<dc:creator><![CDATA[ Prem, R., Avery, E., Marquez, J. M., Xie, C., Claypool, S. M. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.22.720193</dc:identifier>
<dc:title><![CDATA[Rewiring Mitochondrial Phosphatidylethanolamine Metabolism Identifies New and Unaccounted Trafficking Steps]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.22.719970v1?rss=1">
<title>
<![CDATA[
Multiscale volume electron microscopy of the human liver maps vascular-cellular architecture, organelle dynamics and inter-organelle communication 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.22.719970v1?rss=1
</link>
<description><![CDATA[
The human liver depends on multiscale structural organization from vasculature to cells to organelles to perform its diverse metabolic functions. A unified three-dimensional view linking these hierarchical scales in intact human tissue would be useful for better understanding these levels and how they relate to each other. We present a high-resolution volume electron microscopy reconstruction of human periportal liver tissue acquired by serial block-face scanning electron microscopy. Using a multiscale deep learning approach, we performed automated segmentation across the entire volume, enabling comprehensive annotation of vasculature, cells, and organelles. Quantitative analysis of bile duct architecture revealed coordinated scaling between lumen geometry and cholangiocyte number and size. Sinusoidal capillary branches exhibited distinct structural profiles with differential endothelial coverage. Analysis of 35,790 complete mitochondria identified substantial morphological heterogeneity, with elongated mitochondria displaying preferential endoplasmic reticulum (ER) contacts at narrowing sites, a pattern consistent with ER-mediated fission or fusion. This multiscale reconstruction establishes an ultrastructural reference for the healthy human liver and provides a quantitative framework for investigating hepatic physiology and disease.
]]></description>
<dc:creator><![CDATA[ Xing, C., Xie, R., Mulcahy, B., Darbandi, A., Thoeni, C., Chandok, I., Lee, Y., Ma, J., Ali, F., McGilvray, I., MacParland, S., Zhen, M., Bader, G. ]]></dc:creator>
<dc:date>2026-04-24</dc:date>
<dc:identifier>doi:10.64898/2026.04.22.719970</dc:identifier>
<dc:title><![CDATA[Multiscale volume electron microscopy of the human liver maps vascular-cellular architecture, organelle dynamics and inter-organelle communication]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-24</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719846v1?rss=1">
<title>
<![CDATA[
Loss of catalytic activity and impaired proteostasis in guanosine nucleotide-depleted LRRK2 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719846v1?rss=1
</link>
<description><![CDATA[
Coding mutations in the Leucine-rich repeat kinase 2 (LRRK2) gene represent the most common cause of familial Parkinson's disease (PD), and are frequently observed in idiopathic PD. In addition, variation around the LRRK2 locus has been shown to alter PD risk by genome-wide association studies. Disease-causing mutations cluster within the catalytic core of LRRK2 - composed of GTPase (ROC) and serine-threonine kinase domains - and lead to an increase in kinase activity, resulting in hyperphosphorylation of a subset of RAB GTPases and consequent cellular toxicity. However, the interplay between LRRK2s GTPase and kinase, and with the surrounding scaffold regions has remained underexplored, with implications for the prediction of on- and off-target effects associated with kinase inhibition. To address this gap, here we dissected the contributions of kinase, GTPase and scaffold domains to LRRK2 function in murine macrophages and tissues expressing endogenous levels of GTP/GDP-binding deficient Lrrk2 T1348N. Nucleotide-free Lrrk2 is devoid of both catalytic activities but maintains the scaffold shell, leading to significant reshaping of Lrrk2 interactome and engagement in novel interactions. This altered functional state leads to impaired autophagy and accumulation of enlarged lysosomes and autophagic cargo in macrophages and kidneys. Since pharmacological inhibition of LRRK2 is under clinical evaluation, our results reveal novel gain of scaffold functions upon loss of catalytic activity that warrant careful consideration.
]]></description>
<dc:creator><![CDATA[ Favetta, G., Herbst, S., Tombesi, G., Iannotta, L., Masato, A., Battisti, I., Tomkins, J. E., Trabzuni, D., Plotegher, N., Gutierrez, M., Arrigoni, G., Manzoni, C., Lewis, P. A., Greggio, E., Cogo, S. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719846</dc:identifier>
<dc:title><![CDATA[Loss of catalytic activity and impaired proteostasis in guanosine nucleotide-depleted LRRK2]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719842v1?rss=1">
<title>
<![CDATA[
Nuclear Pct1 couples phosphatidylcholine synthesis with membrane biogenesis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719842v1?rss=1
</link>
<description><![CDATA[
Phosphatidylcholine (PC) is the major eukaryotic phospholipid and its synthesis must be homeostatically controlled to prevent excess membrane and organelle growth. Here we investigate how PC synthesis by the Kennedy pathway is coordinated with membrane biogenesis. In budding yeast, the rate-limiting enzyme Pct1 is nuclear and reversibly associates with the inner nuclear membrane (INM) in response to lipid packing defects caused by low PC. We show that the enzymes acting after Pct1 to generate PC remain at the endoplasmic reticulum (ER) during pathway activation. Relocating the final PC synthesis step to different endomembrane sites does not alter the kinetics of Pct1 release from the INM, indicating that newly made PC equilibrates with the INM rapidly. In contrast, elevated phosphatidic acid locks Pct1 at the INM, prevents pathway inactivation and drives nuclear/ER membrane proliferation. These results support a model in which nuclear Pct1 senses lipid imbalance while ER-localized enzymes supply PC; disrupting this homeostasis leads to uncontrolled membrane biogenesis.
]]></description>
<dc:creator><![CDATA[ Lysyganicz, P. K., Toprakcioglu, Z., Guo, J., Barbosa, A. D., Jenkins, B. J., Lim, K., Koulman, A., Knowles, T. P. J., Dymond, M. K., Savage, D. B., Siniossoglou, S. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719842</dc:identifier>
<dc:title><![CDATA[Nuclear Pct1 couples phosphatidylcholine synthesis with membrane biogenesis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719635v1?rss=1">
<title>
<![CDATA[
Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double-strand breaks reveals specific gene expression programs 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719635v1?rss=1
</link>
<description><![CDATA[
Chromatin structure is extensively modified and remodeled to allow for efficient signaling and repair of DNA double-strand breaks (DSBs), a process which is influenced by the nature and properties of the damaged locus or the repair pathway involved. However, the extent of cell-to-cell variability in these DSB-induced chromatin modifications remains poorly characterized. Here, we report how chromatin accessibility is reshuffled at the damaged locus at high resolution. Notably, we identify a long-range increase in chromatin accessibility which is dependent on functional resection. We report that resection-dependent chromatin remodeling events at individual damaged loci display significant heterogeneity in single cells which are only partly explained by the cell cycle, and can frequently be detected as asymmetric and unidirectional. Moreover, we identify strong transcriptional phenotypes upon sustained DNA damage as well as subpopulations of S and G2/M cells for which similar resection-dependent chromatin accessibility patterns occur simultaneously at multiple DSBs. These coordinated chromatin accessibility patterns at multiple DSBs are associated with specific gene expression programs, including DNA damage checkpoint signaling, inflammation and apoptosis. Altogether, our results highlight the heterogeneity in chromatin remodeling during DSB repair and suggest unexpected links between DNA end resection and specific gene expression programs mounted in response to genotoxic stress.
]]></description>
<dc:creator><![CDATA[ Collins, S., Finoux, A.-L., Arnould, C., Carette, R., Rocher, V., Legube, G., Clouaire, T. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719635</dc:identifier>
<dc:title><![CDATA[Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double-strand breaks reveals specific gene expression programs]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719776v1?rss=1">
<title>
<![CDATA[
Cardiac-Detargeted MyoAAV Enables Systemic Nrl-Mediated Fast Myofiber Remodeling and Hypertrophy Across Multiple Skeletal Muscles 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719776v1?rss=1
</link>
<description><![CDATA[
Inducing fast myofiber programs offers therapeutic potential for skeletal muscle disorders such as sarcopenia, where fast myofibers are preferentially lost. Engineered muscle-specific AAV (MyoAAV) vectors enable efficient transduction of skeletal muscles after systemic administration; however, cardiac transgene expression limits applications requiring skeletal muscle-selective delivery. We generated modified MyoAAV vectors by incorporating cardiac-specific miR-208a target sequences into the transgene 3'UTR. This design markedly suppressed cardiac expression while preserving skeletal muscle output, with target-site variation enabling tunable trade-offs between cardiac detargeting and skeletal muscle expression levels. We validated this platform using neural retina leucine zipper (Nrl), a large Maf transcription factor regulating type IIb myofiber identity. Systemic delivery of conventional MyoAAV-Nrl caused severe cardiac hypertrophy and uniform lethality within one month. Conversely, incorporating miR-208a target sequences prevented detectable hypertrophy and eliminated mortality during the experimental observation period. This modification significantly reduced cardiac Nrl expression while maintaining skeletal muscle levels, successfully promoting type IIb myofiber formation and hypertrophy across multiple skeletal muscles. These findings demonstrate that miR-208a-mediated cardiac detargeting combined with MyoAAV-Nrl enables safe systemic induction of fast myofiber remodeling and hypertrophy, establishing a platform for gene therapies targeting skeletal muscle disorders associated with fast myofiber loss.
]]></description>
<dc:creator><![CDATA[ Hitachi, K., Sadaki, S., Watanabe, M., Tsuji, R., Kubo, A., Yamasaki, Y., Kiyofuji, Y., Inui, M., Kudo, T., Suzuki, T., Takahashi, S., Tsuchida, K., Fujita, R. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719776</dc:identifier>
<dc:title><![CDATA[Cardiac-Detargeted MyoAAV Enables Systemic Nrl-Mediated Fast Myofiber Remodeling and Hypertrophy Across Multiple Skeletal Muscles]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719739v1?rss=1">
<title>
<![CDATA[
Cellular senescence dysregulates antiviral interferon responses in idiopathic pulmonary fibrosis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719739v1?rss=1
</link>
<description><![CDATA[
Patients with idiopathic pulmonary fibrosis (IPF) are highly vulnerable to respiratory virus infections, but the cellular mechanisms linking fibrotic remodeling to impaired local antiviral defense remain unclear. Here, we investigated how cellular senescence shapes the response of patient-derived healthy and IPF primary lung fibroblasts to influenza A virus (IAV) infection. Transcriptomic profiling identified infection as the driver of gene expression in both DNA damage-induced senescent healthy and IPF fibroblasts and revealed induction of canonical antiviral pathways in both cell states. However, senescent IPF fibroblasts adopted a distinct antiviral response state characterized by a broader set of uniquely induced genes and differential coordination of antiviral transcriptional networks. Functionally, senescence increased viral titers in healthy and IPF fibroblasts, while senescent IPF fibroblasts displayed an altered inflammatory response. Network analysis linked viral response- and cell cycle-associated modules specifically to the senescent healthy infected state, whereas these programs were weaker in senescent IPF fibroblasts. Transcription factor inference identified IRF3 and STAT1 as candidate regulators of this altered antiviral state in both senescent healthy and IPF fibroblasts. Consistent with the network and transcription factor analyses, siRNA-mediated depletion of IRF3 or STAT1 significantly reduced IFN-{beta} secretion in senescent healthy fibroblasts, whereas IPF fibroblasts showed only milder effects, indicating a disease-specific dependence on these pathways for antiviral control. Together, these findings show that the combination of cellular senescence and fibrotic fibroblast identity creates a dysfunctional antiviral state that may help explain the high susceptibility of IPF patients to virus-associated acute exacerbations and disease worsening.
]]></description>
<dc:creator><![CDATA[ Hughes, J.-W. B., Reisser, Y., Hornung, F., Hilsabeck, T. A. U., Senchyna, F., Coelho, A. L., Ho, T.-C., Schneider, K., Furman, D., Hogaboam, C. M., Le Saux, C. J., Desprez, P.-Y., Deinhardt-Emmer, S. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719739</dc:identifier>
<dc:title><![CDATA[Cellular senescence dysregulates antiviral interferon responses in idiopathic pulmonary fibrosis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.22.720215v1?rss=1">
<title>
<![CDATA[
Computational and Proteomic Analyses Reveal Cardiac Dysfunction and Heart Failure-Associated Biomarker Secretion from Venezuelan Equine Encephalitis Virus TC83-infected human IPSC-derived Cardiomyocytes 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.22.720215v1?rss=1
</link>
<description><![CDATA[
Arthropod-borne pathogens, many of which are neurotropic, can disseminate beyond the central nervous system to infect peripheral organs. In recent years, an increasing number of cardiac dysfunctions have been reported following arthropod-borne viral infections; however, the mechanism underlying these cardiac manifestations remains poorly understood. In this study, we investigated the impact of Venezuelan Equine Encephalitis Virus (VEEV) TC-83 infection on cardiac function and immune-response of human induced-pluripotent stem cell (hIPSC)-derived cardiomyocytes (hIPSC-CMs). We first confirmed the successful differentiation of hIPSCs into spontaneously beating hIPSC-CMs. We then demonstrated that these cells are highly susceptible to VEEV TC-83 infection, which induced pronounced arrhythmias and complete cessation of beating within 24 hours post-infection. To quantify these functional changes, we developed a segmentation-free computational pipeline that converts frame-to-frame motion in brightfield time-lapse movies into a one-dimensional signal reflecting contractile activity and extracts beat timing, beat rate, and rhythm-regularity features in the time and frequency domains. This analysis revealed progressive disruption of beating dynamics following VEEV TC-83 infection, with early rhythm instability and complete loss of coordinated beating by 24 hours post-infection. Furthermore, mass spectrometry analysis of VEEV TC-83-infected hIPSC-CMs supernatants revealed the presence of biomarkers typically associated with heart failure in patients, underscoring a virus-induced cardiac functional impairment. Together, these findings provide new insight into cardiac complications associated with arthropod-borne viral infections and may support advances in preventive medicine.
]]></description>
<dc:creator><![CDATA[ Trefry, S. V., Wahdan, L., DiGangi, T., Andberg, C., Konadu, M., Opoku, L., Walls, S. D., Galarza, M. F., Zhou, W., Alem, F., Narayanan, A., Wei, Q., Ronzier, E. ]]></dc:creator>
<dc:date>2026-04-23</dc:date>
<dc:identifier>doi:10.64898/2026.04.22.720215</dc:identifier>
<dc:title><![CDATA[Computational and Proteomic Analyses Reveal Cardiac Dysfunction and Heart Failure-Associated Biomarker Secretion from Venezuelan Equine Encephalitis Virus TC83-infected human IPSC-derived Cardiomyocytes]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-23</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719674v1?rss=1">
<title>
<![CDATA[
Pathogenic human huntingtin expression causes prolific intramuscular aggregation, leading to nuclear, metabolic, and physiological dysregulation in striated muscle. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719674v1?rss=1
</link>
<description><![CDATA[
Huntington disease is caused by expansion of a CAG repeat in the human HTT gene, producing a mutant huntingtin protein that misfolds and forms intracellular aggregates. Although Huntington disease is primarily characterized as a neurodegenerative disorder, mutant huntingtin is ubiquitously expressed, and peripheral tissues such as skeletal muscle exhibit pathological abnormalities. To define the muscle-intrinsic consequences of pathogenic huntingtin expression, we expressed caspase-6 truncated pathogenic human huntingtin in body wall muscle of Drosophila melanogaster larvae and performed quantitative structural and functional analyses. Aggregate analysis revealed that fluorescence intensity increased with aggregate size while aggregate morphology became more irregular. Delaying transgene expression until later stages of larval development dramatically reduced aggregate number, demonstrating a strong temporal dependence of aggregate formation. Myonuclei were enlarged, misshapen, and exhibited significantly reduced fluorescence intensity, consistent with altered chromatin organization. Notably, huntingtin aggregates were observed within the nucleus, indicating that nuclear proteostasis is directly perturbed by pathogenic huntingtin in muscle cells. Despite these intracellular defects, muscle fiber shape and sarcomere organization were preserved, suggesting that contractile apparatus assembly is not overtly disrupted. In contrast, mitochondrial organization was severely affected, with extensive mitochondrial aggregation throughout muscle fibers, consistent with altered organelle homeostasis. Functional analyses demonstrated that pathogenic huntingtin expression significantly impaired neuromuscular performance. Larvae exhibited reduced excitatory junctional potentials and diminished muscle contractile force, indicating compromised synaptic transmission and muscle function. Together, these findings demonstrate that pathogenic human huntingtin expression in skeletal muscle is sufficient to drive widespread protein aggregation, nuclear and mitochondrial abnormalities, and functional deficits despite the absence of overt structural changes. Our results highlight the importance of muscle-intrinsic pathogenic mechanisms and provide a quantitative framework for understanding how mutant huntingtin disrupts cellular organization and physiology outside the nervous system.
]]></description>
<dc:creator><![CDATA[ Hana, T. A., Ormerod, K. G. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719674</dc:identifier>
<dc:title><![CDATA[Pathogenic human huntingtin expression causes prolific intramuscular aggregation, leading to nuclear, metabolic, and physiological dysregulation in striated muscle.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719546v1?rss=1">
<title>
<![CDATA[
A Rapid 10-Minute Silver Nitrate Staining Method for Visualizing the Osteocyte Lacuno-Canalicular System 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719546v1?rss=1
</link>
<description><![CDATA[
The Ploton silver method employs a 50% silver nitrate solution (w/v; 2.943 mol/L) for staining and quantitative analysis of the osteocyte lacuno-canalicular system (LCS). We previously demonstrated that lower silver nitrate concentrations (0.5-1 mol/L) stain the LCS more effectively, revealing a greater number of LCS than the Ploton silver method. However, the staining duration of our initial modified method (60 minutes) remained comparable to that of the Ploton silver method (55 minutes), limiting its broader adoption. Here, we developed a rapid silver nitrate staining method by systematically evaluating the effects of temperature on staining efficacy. We found that incubation at 50-70 degrees Celsius for 10 minutes with a 1 mol/L silver nitrate solution produced optimal results. This rapid high-temperature method achieved excellent LCS visualization in bone samples from multiple animal species and in mouse pathological models. Moreover, high-temperature staining mitigated the LCS damage and insufficient staining associated with the 50% silver nitrate solution used in the Ploton silver method. This rapid 10-minute silver staining technique, designated the Wu-Wang silver method, provides a more accurate and efficient approach for LCS staining and quantitative analysis. Its adoption will facilitate systematic characterization of LCS morphological variations across vertebrate species, thereby advancing our understanding of osteocyte morphogenesis and the pathogenic mechanisms underlying bone and joint diseases.
]]></description>
<dc:creator><![CDATA[ Wu, J., Wang, L. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719546</dc:identifier>
<dc:title><![CDATA[A Rapid 10-Minute Silver Nitrate Staining Method for Visualizing the Osteocyte Lacuno-Canalicular System]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719762v1?rss=1">
<title>
<![CDATA[
E-cadherin clustering as a regulator of morphogenesis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719762v1?rss=1
</link>
<description><![CDATA[
Cell adhesion enables animal multicellular development. E-cadherin and the cadherin-catenin adhesion complex at adherens junctions are engaged in dynamic interactions with actomyosin generated contractile forces to drive epithelial morphogenesis. However, our understanding of how adhesion is regulated and how the tuning of adhesion contributes to morphogenesis remains incomplete. One key determinant of E-cadherin adhesion strength is clustering of the cadherin-catenin adhesion complex, a property studied extensively in vitro. Here, we use optogenetics to enhance E-cadherin cluster formation in the Drosophila embryo. Enlarged clusters were associated with increased E-cadherin surface abundance, assembled a normal cadherin-catenin complex, and showed reduced membrane mobility and turnover consistent with an increase in cell adhesion strength. Drosophila embryos with enhanced E-cadherin clustering displayed a severe reduction in cell intercalation and convergent extension of the anterior-posterior axis. To account for these observations, we modified existing vertex models to include junction-specific viscous forces representing E-cadherin-mediated friction between cells. This dissipative adhesion model predicts that enhanced adhesion increases resistance to cell rearrangements, thereby reducing cell neighbor exchanges and impairing convergent extension. To test model predictions, we analyzed two types of morphogenetic movements in embryos with enhanced E-cadherin clustering. Neuroblast ingression, which requires both apical constriction and cell rearrangement, was severely slowed. In contrast, mesoderm invagination, which requires apical constriction without neighbor exchanges, proceeded normally. Our findings suggest that optogenetic clustering, in contrast to overexpression of E-cadherin, is a valuable tool to examine the consequences of enhancing adhesion strength in tissue morphogenesis. Moreover, we propose that regulating E-cadherin clustering is essential for movements that require cell-cell contact changes.
]]></description>
<dc:creator><![CDATA[ Lerchbaumer, G., Simoes, S., Etemadi, E., Zidan, F., Erdemci-Tandogan, G., Tepass, U. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719762</dc:identifier>
<dc:title><![CDATA[E-cadherin clustering as a regulator of morphogenesis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719911v1?rss=1">
<title>
<![CDATA[
Nuclear Factor I genes drive chondrogenic cell-fate commitment 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719911v1?rss=1
</link>
<description><![CDATA[
Human induced pluripotent stem cells (hiPSCs) offer a powerful platform to model chondrogenesis and enable regenerative strategies, yet regulation of cell-fate commitment remains elusive. Here, we systematically mapped cell-fate trajectories from 7 time points during a 49-day chondrogenic hiPSC differentiation protocol using single-nucleus multimodal transcriptomic and chromatin accessibility profiling (scRNA-seq and scATAC-seq). Integrative analysis of dynamics revealed branching differentiation trajectories with clear bifurcation points and distinct cell-fates. Notably, the chondrogenic trajectory originated at day 6 as a neurogenic development and branched off at day 21 to a chondrogenic cell-fate. Through transcription factor activity analysis (TFAA) and cis-co-accessibility networks, we found that NFIA and NFIB drove chondrogenic distinction, exhibited in both modalities as directly targeting chondrogenic genes such as COMP, FIBIN, VIM. This was then confirmed by experimental validation as modulation of NFIA expression at this point further enhanced chondrocyte formation. Together, our study provides a high-resolution multimodal atlas of chondrogenic differentiation and identified critical transcriptional regulators that can now be leveraged to implement regenerative cartilage therapies from hiPSCs.
]]></description>
<dc:creator><![CDATA[ Meulenbelt, I., Mulders, R., Nickel-Maunu, M., van Hoolwerff, M., Mazzini, G., Klomp, L., Meijer, H., Post, J., Ramos, Y. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719911</dc:identifier>
<dc:title><![CDATA[Nuclear Factor I genes drive chondrogenic cell-fate commitment]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.20.719627v1?rss=1">
<title>
<![CDATA[
Lack of effect of physiological oxidative stress on N-terminal cysteine dependent proteolysis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.20.719627v1?rss=1
</link>
<description><![CDATA[
Oxidative post-translational modifications on the sulfhydryl group of cysteines can occur spontaneously or enzymatically. The dioxygenation of N-terminal cysteines has emerged as a new oxygen sensing paradigm, catalysed by 2-aminoethanethiol dioxygenase (ADO) in mammals. Conflicting evidence has been reported in recent years on whether this reaction can occur in the absence of ADO. Here we sought to address definitively whether physiological oxidative stress can interfere with ADO-catalysed N-terminal dioxygenation. Using a system to produce titratable intracellular levels of H2O2, we demonstrate that the stability of RGS5 is not affected by oxidative stress, whether ADO is present or not. However, cytotoxic levels of oxidative stress did induce an increase in RGS4/5 protein levels that occurred independently of the Cys N-degron pathway. This effect of tBHP was reduced by Fe2+ chelation and perturbations of lysosomal function, suggesting the possible involvement of ferroptosis. We conclude that N-terminal cysteine dependent proteolysis of RGS4/5 is not sensitive to physiological oxidative stress, but these proteins can be stabilised during the process of oxidative stress-induced cell death through an N-terminal cysteine independent mechanism.
]]></description>
<dc:creator><![CDATA[ Tian, Y.-M., Kim, H., Ratcliffe, P., Keeley, T. P. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.20.719627</dc:identifier>
<dc:title><![CDATA[Lack of effect of physiological oxidative stress on N-terminal cysteine dependent proteolysis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.19.719232v1?rss=1">
<title>
<![CDATA[
Therapeutic Potential of Hypoxia-Preconditioned hiPSC-Epicardial Cell-Derived Exosomes in Mice with Myocardial Infarction 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.19.719232v1?rss=1
</link>
<description><![CDATA[
Background: It has been demonstrated that stem cell transplantation promotes healing of the infarcted heart through paracrine effects. However, the therapeutic potential of exosomes secreted by hiPSC-derived epicardial cells (hEP-Exos) for treating infarcted hearts remains unclear. Myocardial infarction (MI) can trigger EP activation, increasing EP paracrine function. Therefore, this study aims to determine and compare the cardioprotective effects of exosomes secreted by hEPs under normoxic (Exo-N) and hypoxic (Exo-H) conditions in MI mice and to explore the underlying mechanisms. Methods: Two types of exosomes were collected by ultracentrifugation and delivered via intramyocardial injection in a murine MI model. The protective effects of Exo-N and Exo-H on the infarcted heart were assessed using echocardiography, histological examination, and immunofluorescence analysis. Additionally, microRNA sequencing, luciferase activity assays, and miRNA gain- and loss-of-function experiments were performed to identify enriched miRNAs and investigate their roles in different exosome populations. Results: In vitro, both Exo-N and Exo-H enhanced the migration and tube-formation capacities in human umbilical vein endothelial cells (HUVECs) and reduced the apoptosis in hiPSC-derived cardiomyocytes (hCMs) under oxygen-glucose deprivation (OGD), with Exo-H exhibiting a stronger effect. In vivo, both Exo-N and Exo-H significantly improved contractile function, reduced infarct size, and mitigated adverse remodeling in mouse hearts with MI, accompanied by increased cardiomyocyte survival and angiogenesis, with Exo-H showing superior efficacy. Mechanistically, miRNA sequencing revealed distinct cargo profiles between Exo-N and Exo-H. miR-214-3p was identified as a key mediator of the enhanced therapeutic potency of Exo-H. miR-214-3p promoted EC angiogenesis by suppressing vasohibin-1 and attenuated cardiomyocyte mitochondrial fission and apoptosis by suppressing mitochondrial elongation factor 2 (MIEF2). Conclusions: This study demonstrates that administration of hEP-Exos, particularly Exo-H, provides robust cardioprotection by enhancing cardiomyocyte survival and angiogenesis, potentially mediated by miR-214-3p. These findings suggest that conditioned hEP-Exos could be a promising and effective acellular therapeutic option for treating MI.
]]></description>
<dc:creator><![CDATA[ gao, l., Qiu, Z., Jiang, Y., Zhang, P., Li, H., Yu, Y., Gong, Y. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.19.719232</dc:identifier>
<dc:title><![CDATA[Therapeutic Potential of Hypoxia-Preconditioned hiPSC-Epicardial Cell-Derived Exosomes in Mice with Myocardial Infarction]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.18.719303v1?rss=1">
<title>
<![CDATA[
The nail mesenchyme creates a regeneration-specific ligand environment that orchestrates mammalian regeneration versus fibrotic wound healing 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.18.719303v1?rss=1
</link>
<description><![CDATA[
The adult digit tip is one of a few privileged mammalian tissues that regenerate. Here, we asked why this is so. Using single cell spatial transcriptomics and genetic mouse models we show regeneration requires the nail organ and associated nail mesenchyme, and that in their absence fibrotic wound-healing occurs. We show the nail organ/mesenchyme orchestrates a highly-organized regenerative response that includes reprogramming of tissue-resident mesenchymal cells to a blastema state. It does this by creating a regeneration-specific ligand environment that includes multiple BMPs. Loss of the resultant downstream BMP signaling by genetic deletion of Smad4 in all mesenchymal cells or specifically in the nail mesenchyme inhibits multiple aspects of the regenerative response, including expression of regeneration-specific ligands. Thus, the nail mesenchyme creates a BMP-rich local ligand environment that reprograms mesenchymal cells and orchestrate tissues regeneration versus fibrotic wound-healing, findings with implications for tissue repair and anti-fibrosis strategies.
]]></description>
<dc:creator><![CDATA[ Purushothaman, S., Saxena, S., Eisner, C., Karamboulas, K., Kaplan, D. R., Rossi, F. M. V., Miller, F. D. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.18.719303</dc:identifier>
<dc:title><![CDATA[The nail mesenchyme creates a regeneration-specific ligand environment that orchestrates mammalian regeneration versus fibrotic wound healing]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719629v1?rss=1">
<title>
<![CDATA[
Keratin 7 protein presence in stool is indicative of active pediatric-onset inflammatory bowel disease 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719629v1?rss=1
</link>
<description><![CDATA[
Background Inflammatory bowel disease (IBD) is associated with early structural changes in intestinal epithelial cells; however, the associated molecular alterations remain incompletely understood. The cytoskeletal protein keratin (K) 7 was recently found to be focally expressed in the colonic epithelium in IBD, while absent in the healthy colon. Here, we investigated the applicability of K7 as a noninvasive stool biomarker for pediatric IBD. Methods In this case-control study including adolescent patients with IBD (n=27) and healthy controls (n=15), stool lysates were analyzed by proteomics, immunoassay and qPCR to determine K7 protein and mRNA content, respectively. Additionally, stool mRNA levels of the simple epithelial keratins, K8, K18, K19 and K20, were measured. Results Stool proteomic analysis identified focal K7 and K19 in IBD samples. Additionally, 23 differentially abundant proteins, of which 18 were higher in IBD, were identified and Gene Ontology enrichment analysis highlighted immune and inflammatory pathways. K7 specific immunoassay detected fecal K7 protein in all patients with active IBD, including both ulcerative colitis and Crohn's disease, while K7 was near or below the detection limit in controls and IBD patients in remission (area under ROC curve=0.88, p<0.0001). While KRT7 mRNA levels were below the detection limit, KRT8 and KRT18 transcripts were elevated in IBD samples compared to controls (p<0.05). Conclusions K7 protein is elevated in IBD patient stool, reflecting intestinal de novo expression and increased epithelial cell exfoliation. Fecal K7 may provide a novel, noninvasive marker for IBD diagnosis and monitoring.
]]></description>
<dc:creator><![CDATA[ Ilomäki, M. A., Kotharkar, E., Rovapalo, J., Lehtonen, N., Nikkonen, A., Ventin-Holmberg, R., Merilahti, J., Kauko, O., Kolho, K.-L., Polari, L., Toivola, D. M. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719629</dc:identifier>
<dc:title><![CDATA[Keratin 7 protein presence in stool is indicative of active pediatric-onset inflammatory bowel disease]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719727v1?rss=1">
<title>
<![CDATA[
View Tomo: Context-aware targeting and analysis in electron cryo-tomography 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719727v1?rss=1
</link>
<description><![CDATA[
Electron cryo-tomography (cryoET) resolves cellular structure in three dimensions, yet region selection is still typically based on two-dimensional projection images. Here, we introduce View Tomo, a workflow for rapid acquisition of low-magnification tomograms that enables screening, targeting and analysis in 3D. View Tomo tilt series are acquired in minutes at low dose (~3 e-[A]-2), producing high-contrast tomograms that remain compatible with subsequent high-resolution structural determination. We implemented View Tomo using an automated acquisition and reconstruction pipeline for rapid alignment. Across multiple viral and cellular systems, view tomograms revealed membrane remodelling events, assembly intermediates and cellular organisation that are difficult to identify in projection images. These data enabled targeted high-resolution imaging and quantitative analysis of spatial relationships within cells. View Tomo therefore extends cryoET workflows by improving target selection, enabling analysis of mesoscale organisation, and facilitating integration with correlative imaging approaches.
]]></description>
<dc:creator><![CDATA[ Gebauer, R., Machala, E. A., Mironova, Y., Jönsson, M.-R., Mazur, J., Feldmann, C. A., Zimmeck, M. A., Silvester, E., Caragliano, E., Falckenhayn, J., Yuen, E. L. H., Ibrahim, T., Hellert, J., Bozkurt, T. O., Kaufmann, R., Quemin, E. R. J., Grünewald, K., Prazak, V. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719727</dc:identifier>
<dc:title><![CDATA[View Tomo: Context-aware targeting and analysis in electron cryo-tomography]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.21.719969v1?rss=1">
<title>
<![CDATA[
An Interpretable 3D Bag-Of-Visual-Words Pipeline for Volumetric Microscopy Classification 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.21.719969v1?rss=1
</link>
<description><![CDATA[
Fluorescence microscopy increasingly produces complex volumetric datasets whose biologically meaningful differences are difficult to capture with hand-crafted measurements, especially when signal is distributed across three-dimensional space. Here, we present an interpretable 3D Bag-of-Visual-Words (BoVW) pipeline for classification and analysis of volumetric microscopy data. The framework detects multiscale local keypoints, computes rotationally robust 3D gradient-based descriptors, and aggregates them into image-level visual-word representations. These features are then used for low-dimensional visualization and logistic regression classification, while model weights are mapped back to the original volumes to generate attention maps that localize discriminative structures. We applied the pipeline to two cerebellar granule neuron datasets spanning both ideal and non-ideal imaging conditions. In a near-isotropic lattice light-sheet dataset of chromatin organization, the method separated control and NIPBL loss-of-function nuclei and supported accurate classification, with strongest performance in the facultative heterochromatin and H3.3 channels. Attention mapping and downstream connected-component and Haralick analyses revealed that loss-of-function nuclei contained more fragmented high-attention regions and smoother, more homogeneous chromatin-associated textures than controls. We then evaluated the same framework on an anisotropic confocal timelapse dataset of receptor clustering in dense neuronal cultures, where single-cell segmentation was impractical. Despite these challenges, the representation captured the expected ligand-driven clustering response and resolved subtler differences associated with a polarity protein overexpression. Together, these results establish a simple, interpretable, and broadly applicable framework for extracting biologically meaningful structure from volumetric microscopy datasets while preserving native 3D context.
]]></description>
<dc:creator><![CDATA[ Pittman, A. E., Campbell, K. R., Laumonnerie, C., Solecki, D. J. ]]></dc:creator>
<dc:date>2026-04-22</dc:date>
<dc:identifier>doi:10.64898/2026.04.21.719969</dc:identifier>
<dc:title><![CDATA[An Interpretable 3D Bag-Of-Visual-Words Pipeline for Volumetric Microscopy Classification]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-22</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.18.719364v1?rss=1">
<title>
<![CDATA[
Physics-Guided Deep Neural Networks: Correcting Physical Distortions in Protein Phase Separation Prediction 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.18.719364v1?rss=1
</link>
<description><![CDATA[
BackgroundIn computational biology, embedding known physical laws into deep learning models to construct "Physics-Informed Neural Networks" (PINNs) is a mainstream paradigm for enhancing model interpretability and extrapolation capability. However, in complex multi-physics coupling problems, there is a risk of competitive imbalance between the physical term and the flexible artificial intelligence (AI) residual term, causing the model to degenerate into a "black-box" fit and lose the original purpose of being physics-driven.

MethodsIn this study, targeting the problem of predicting protein liquid-liquid phase separation (LLPS) behavior in response to environmental factors (temperature, salt concentration), we identified physical distortions, gradient vanishing, and numerical instability in the initial physics-AI hybrid model. Three core correction strategies were proposed: (1) Weight Allocation Logic Reconstruction: Force the physical trunk weight to 1.0 at the output layer, suppressing the AI residual term to the perturbation level of 0.05~0.1, ensuring physics dominance; (2) Robust Physics Formula Construction: Abandon the unstable power function and introduce a combination of Softplus and logarithmic functions to stably simulate the nonlinear effects of charge shielding; (3) Gain Compensation Alignment: Apply gain compensation to the weak signal branch (temperature) to ensure its effective participation in optimization.

ResultsThe optimized model maintained a fitting accuracy of R2{approx}0.62 on the test set, while physical consistency was significantly enhanced. The model successfully restored the monotonic increase in solubility with temperature characteristic of UCST-type phase diagrams and correctly captured the nonlinear charge shielding features in the salt concentration response. The weights of key physical parameters (e.g., hydrophobic contribution w_h, net charge contribution w_ncpr) increased from <10-3 to the 10-2 magnitude, demonstrating the reactivation of the physical branch.

ConclusionsThe weight control, formula stabilization, and signal gain alignment strategies proposed in this study effectively address the classic problem of "AI hijacking" physics in physics-AI hybrid models. This work provides a universal solution for constructing biophysical predictive models that combine high fitting accuracy with strong physical interpretability.
]]></description>
<dc:creator><![CDATA[ Wang, M., Lu, T., Song, Y.-h., Li, y. ]]></dc:creator>
<dc:date>2026-04-21</dc:date>
<dc:identifier>doi:10.64898/2026.04.18.719364</dc:identifier>
<dc:title><![CDATA[Physics-Guided Deep Neural Networks: Correcting Physical Distortions in Protein Phase Separation Prediction]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-21</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
