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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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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750046v1?rss=1">
<title>
<![CDATA[
Interconnections with and within the trypanosomal respiratory chain revealed by complexome profiling 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750046v1?rss=1
</link>
<description><![CDATA[
Proteins are frequently integrated into multicomponent complexes that execute the elaborate processes supporting life. Thus, a protein's function can only be defined by the company it keeps within a complex. Proteomes provide informative protein inventories but lack information about protein quaternary structures. Complexome profiling (CP) has been transformative in capturing the comprehensive population structure of complexes at a given moment within a cell. We have employed CP to chart the multiprotein complex landscape of two life cycle stages of Trypanosoma brucei. These data have allowed the observation of previously hidden interactions with and within the mitochondrial respiratory chain. We have found (1) an exceptional case of a SLC25 solute transporter that interacts with NADH dehydrogenase, (2) two ATP synthase subunit g paralogs that are intriguingly excluded from the enzyme's dimers, and (3) refined the known composition of ubiquinol:cytochrome c oxidoreductase by addition of missing subunits and removing an incorrectly assigned subunit, which more likely acts to insert the iron-sulfur co-factor into the complex. Further investigation into ubiquinol:cytochrome c oxidoreductase assembly revealed crosstalk between incorporation of its nuclear subunits with mitochondrial translation, possibly facilitating a hitherto unknown quality control mechanism. These discoveries demonstrate the power of our CP data for generation and testing of hypotheses about the mitochondrial and other organellar multiprotein complexes of T. brucei, a protist of medical and evolutionary importance.
]]></description>
<dc:creator><![CDATA[ Benz, C., Khan, R. T., Hammond, M., Gahura, O., Koblar, U., Cadena, L. R., Skodova-Sverakova, I., Butterill, P. T., Vrbacky, M., Hashimi, H. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750046</dc:identifier>
<dc:title><![CDATA[Interconnections with and within the trypanosomal respiratory chain revealed by complexome profiling]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749889v1?rss=1">
<title>
<![CDATA[
Adjunctive nebulization of Idursulfase to intravenous treatment enhances cardiac proteome adaptations in IDS-KO mice 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749889v1?rss=1
</link>
<description><![CDATA[
Mucopolysaccharidosis Type II (MPS-II) is a rare X-linked lysosomal storage disorder, characterized by deficiency of the lysosomal hydrolase iduronate 2-sulphatase (IDS). Cardiac impairments contribute to mortality in patients. Enzyme replacement therapy (ERT) with Idursulfase is a promising treatment for the cardiac dysfunction. We compared the proteome changes following intravenous (IV) with and without adjunct nebulized ERT in IDS-KO mice. Male mice were assigned to 4 groups: 1) WT IV + nebulized saline (WT; n=8); 2) IDS-KO IV + nebulized saline (KO; n=5); 3) IDS-KO IV Idursulfase (1 mg/kg; KO-IV, n=5); 4) IDS-KO IV (1 mg/kg) + nebulized Idursulfase (0.33 mg/mouse; KO-NEB, n=5). Treatments were administered once a week starting at 8 weeks of age and the heart was harvested 12 weeks post-ERT. Mouse heart samples were prepared for global proteomics measurements with Nano-liquid chromatography tandem mass spectrometry (n=3/group; Nano-LC/MS/MS). Global limma moderated F-test analysis identified 928 differently abundant proteins across the four groups. Pairwise Euclidean distances from the IDS-KO were significantly greater for the KO-NEB vs KO-IV group (47.5, 3.7 vs 40.8, 1.1; p < 0.001), showing that adjunct nebulization elicited a more profound proteomic shift than IV alone. The mean z-score compartment analysis revealed that the subcellular compartment protein profile of KO-NEB shifted towards the WT profile, whereas this pattern was less evident in KO-IV. The cluster analysis also revealed treatment-specific and rescue-like protein modules. Overall, our results suggest that adjunctive nebulized Idursulfase ERT enhances the cardiac proteomic changes caused by IV treatment in IDS-KO mice. Proteomics data are available via ProteomeXchange with identifier PXD083242.
]]></description>
<dc:creator><![CDATA[ Mariani, V. M., Labilloy, A., Cade, W. T., Ferreira, P. R., Ferreira, L. F. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749889</dc:identifier>
<dc:title><![CDATA[Adjunctive nebulization of Idursulfase to intravenous treatment enhances cardiac proteome adaptations in IDS-KO mice]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750032v1?rss=1">
<title>
<![CDATA[
Molecular mechanisms behind the functional (non)redundancy of CK1 paralogs in the Wnt pathway 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750032v1?rss=1
</link>
<description><![CDATA[
The casein kinase 1 (CK1) family of serine/threonine protein kinases consists of seven isoforms in humans. CK1 family members are important regulators of the Wnt/{beta}-catenin signaling pathway. Using a comprehensive panel of CRISPR/Cas9-generated knockout cell lines, we demonstrated the opposing roles of endogenous CK1 (negative, via phosphorylation of {beta}-catenin in the destruction complex) and CK1{delta}/{epsilon} (positive, via phosphorylation of DVL in the signalosome), while no phenotype was observed for CK1{gamma}1/2/3 triple knockout cells. Using in vitro kinase assays and TurboID-based interactomics, we revealed that this functional divergence between CK1 and CK1{epsilon} is not due to the intrinsically different capacity to phosphorylate {beta}-catenin or DVL but rather due to different affinities for the destruction complex and signalosome in the cellular environment. Through functional analysis of CK1-CK1{epsilon} chimeras containing both N-terminal and C-terminal domain swaps, we identified the N-terminal lobe of CK1 and the C-terminus of CK1{epsilon} as determinants mediating increased affinity towards the degradasome and signalosome, respectively. We further show that the CK1 N-lobe not only drives cellular activity toward {beta}-catenin but also underlies the CK1-specific interaction with the scaffolding protein SACK1G (also known as FAM83G and PAWS1). Additionally, despite clearly distinct physiological roles of CK1 and CK1{delta}/{epsilon}, we provide evidence that, in the absence of CK1, CK1{delta} and CK1{epsilon} can physically and functionally substitute for CK1 in the {beta}-catenin destruction complex. This rewires CK1{delta} and CK1{epsilon} as negative regulators acting via phosphorylation of {beta}-catenin in the destruction complex. These findings resolve prior contradictions by (i) clarifying context-dependent CK1 roles, (ii) identifying mechanistic determinants navigating CK1 and CK1{epsilon} to different substrates, and (iii) defining the limitations of these affinity-based subcellular distributions that become apparent especially in the physical absence of the physiological, high-affinity kinase. An important implication of our findings is the identification of a mechanism that changes the ultimate outcome of CK1{delta}/{epsilon} inhibitor treatment from Wnt/{beta}-catenin pathway inhibition to its robust activation.
]]></description>
<dc:creator><![CDATA[ Gybel, T., Gömöryova, K., Coufalova, J., Cihalova, T., Bologna, S., Micka, M., Ganji, R. S., Potesil, D., Sedo, O., Radaszkiewicz, T. W., Zdrahal, Z., Tripsianes, K., Sapkota, G. P., Bryja, V. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750032</dc:identifier>
<dc:title><![CDATA[Molecular mechanisms behind the functional (non)redundancy of CK1 paralogs in the Wnt pathway]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749865v1?rss=1">
<title>
<![CDATA[
Investigating the Role of Different Co-receptors on T-cell Activation Through IFN-γ Secretion Using Spatially Controlled Cell Monitoring Platform 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749865v1?rss=1
</link>
<description><![CDATA[
Conventional methods for studying T-cell activation typically assess receptor engagement and downstream functional outputs in separate experimental formats, thereby obscuring the spatial correlation between initial receptor arrangement and localized functional outputs. This makes it difficult to examine the individual and combined effects of receptors and co-receptors engagement within the immunological synapse within the same controlled cellular microenvironment. Building upon the recently published CellStudio platform, previously validated for monitoring growth factor interactions in adherent cell models like mesenchymal stem cells and HeLa cells, we adapted this modular system to investigate non-adherent immune cells. This platform integrates Printing and Vacuum Lithography (PnVlitho) with bead-based immunoassays to generate defined activation patterns surrounded by cytokine capture antibodies, establishing a "present-and-measure" framework for localized biosensing. Jurkat T-cells were patterned on fibronectin alone or in combination with anti-CD3 and/or anti-CD4 antibodies, enabling precise engagement and activation of the co-receptors. Cell capture, basal contact morphology, and IFN-{gamma} secretion were evaluated for each condition. While CD4 engagement alone had a minimal effect, presenting anti-CD3 and anti-CD4 together caused the cells to spread into wide, circular contact zones and trigger the strongest local IFN-{gamma} signals. These findings show that first adaptation of CellStudio for suspension cells enables the standardized comparison of receptor-dependent differences in Jurkat-cell capture, contact morphology, and local cytokine-associated signals within a spatially defined assay, emerging as a powerful tool for understanding co-receptor cooperation in T-cell function and immunotherapy.
]]></description>
<dc:creator><![CDATA[ Lartitegui-Meneses, N., Azuaje-Hualde, E. A., Merino, A., Lopez-de-Lacalle, S., Benito-Lopez, F., Colom, A., BASABE-DESMONTS, L. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749865</dc:identifier>
<dc:title><![CDATA[Investigating the Role of Different Co-receptors on T-cell Activation Through IFN-γ Secretion Using Spatially Controlled Cell Monitoring Platform]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.05.749603v1?rss=1">
<title>
<![CDATA[
Transcriptomic Characterization of Terminal Complement Complex-bound Cells in Human Choroid Using Single-Cell RNA Sequencing 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.05.749603v1?rss=1
</link>
<description><![CDATA[
Age-related macular degeneration (AMD) is among the leading causes of blindness worldwide. Early AMD is characterized by dysfunction in the choroid, including early dropout of endothelial cells and increased deposition of the complement cascade's membrane attack complex (MAC) in the choriocapillaris. In this study, we used a single-cell RNA sequencing-based approach with barcoded antibodies to measure abundance of the MAC and other surface proteins at single cell resolution on RPE/choroid samples from four aged human donor eyes. We included antibodies to detect the MAC, CD34, CD45, and complement regulators CD55 and CD59, in addition to control antibodies. Our analysis of these data revealed cell clusters with expected gene expression profiles and antibody-based detection of CD34 and CD45 congruent with transcriptome-based cell identity. We also detected surface complement regulators CD55 and CD59 across a wide variety of cell types. Across endothelial cells, surface CD55 and CD59 appeared more abundant on venous clusters, and abundance of each was correlated with expression of a third complement regulator, clusterin (CLU). The MAC was detected on a variety of cell types, but was most abundant on the surface of cells in the macrophage family, smooth muscle cells, and pericytes. We confirmed these findings by identifying MAC deposition on choriocapillaris pericytes using immunohistochemistry for MAC, endothelial, and pericyte markers. Ultimately, these data showcase a valuable new approach to analyze gene expression and surface complement in human donor eyes, and provide novel insight into patterns of MAC deposition and complement protection in the aging human choroid.
]]></description>
<dc:creator><![CDATA[ Jensen, R. D., Mullin, N. K., Mulfaul, K., Miller, J. E. B., Navratil, E., Voigt, A. P., Scheetz, T., Wiley, L. A., Stone, E., Tucker, B., Mullins, R. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.05.749603</dc:identifier>
<dc:title><![CDATA[Transcriptomic Characterization of Terminal Complement Complex-bound Cells in Human Choroid Using Single-Cell RNA Sequencing]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750074v1?rss=1">
<title>
<![CDATA[
iPSC-Derived Chondroprogenitors as a Promising Cell Source for Cartilage Engineering: A Comparison with MSCs in Unmodified and Peptide-Functionalized Alginate Hydrogels 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750074v1?rss=1
</link>
<description><![CDATA[
Articular cartilage degeneration is a hallmark of degenerative joint diseases, yet its limited regenerative capacity poses significant challenges for tissue engineering. While mesenchymal stem cells (MSCs) are the most commonly employed cell type in cartilage tissue engineering, they exhibit donor variability, restricted expansion capacity, and tendencies toward fibrocartilage formation and hypertrophic differentiation. Human induced pluripotent stem cell-derived chondroprogenitors (iCPs) represent a promising alternative, offering scalable production of developmentally relevant cells with intrinsic chondrogenic commitment. However, their performance within three-dimensional biomaterial scaffolds remains largely unexplored. Here, we compared chondrogenic differentiation of iCPs and MSCs within alginate hydrogels of varying stiffness (0.37 - 4.55 kPa) exhibiting physiologically relevant stress relaxation properties. Intermediate stiffness (2% alginate, ~2.17 kPa) optimally supported chondrogenesis for both cell types. While MSCs differentiated as single cells, iCPs spontaneously self-organized into cartilaginous aggregates without requiring a separate pellet pre-culture step, showing significantly higher hyaline indices and reduced COL10 expression, despite initial low viability in hydrogels. To further enhance chondrogenesis, we functionalized 2% alginate gels with RGD and HAVDI peptides mimicking integrin- and cadherin-mediated signaling. HAVDI/RGD functionalization significantly enhanced hyaline cartilage marker expression in both cell types, with iCPs exhibiting superior matrix composition characterized by elevated aggrecan and SOX9 expression and reduced COL10 and MMP13 compared to MSCs. These findings establish iCPs as a promising cell source for cartilage tissue engineering and disease modeling, particularly within biomaterials integrating mechanical and bioactive cues that recapitulate the native cartilage microenvironment.
]]></description>
<dc:creator><![CDATA[ Vieri, M. L., Thomson, A. R., Dalby, M. J., Kolundzic, N., Ansalone, C., Dietrich, B., Tsimbouri, P. M., Shaw, T., Huesa, C., Adams, D. J., Goodyear, C. S. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750074</dc:identifier>
<dc:title><![CDATA[iPSC-Derived Chondroprogenitors as a Promising Cell Source for Cartilage Engineering: A Comparison with MSCs in Unmodified and Peptide-Functionalized Alginate Hydrogels]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750209v1?rss=1">
<title>
<![CDATA[
The life cycle of an archaeon with multiple membranes 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750209v1?rss=1
</link>
<description><![CDATA[
Many prokaryotes are diderms. They divide using an FtsZ division ring to simultaneously constrict physically coupled inner and outer membranes to form daughter cells with two membranes. Currently, only one archaeon, Ignicoccus hospitalis, is known to have an outer and inner membrane. Here, in exploring Ignicoccus cell division, we show by expansion microscopy that I. hospitalis uses a contractile CdvA-ESCRT-III ring to repeatedly constrict and cut its inner membrane in a way that yields clusters containing multiple cytoplasms within a shared periplasm. The outer bounding membrane then bursts to release the progeny cells, which regain their parental cell architecture via a membrane duplication process. Furthermore, this life cycle appears conserved across Ignicoccus strains, even though the precise timing of events changes. Taken together, these data show that Ignicoccus cells propagate by undergoing dynamic changes in their architecture as they transit between single and multi-cellular states.
]]></description>
<dc:creator><![CDATA[ Mayer, F., von Kugelgen, A., Stockl, R., Seitz, V., Parham, J., Wang, Z., Reichelt, R., Bharat, T. A. M., Huber, H., Spang, A., Grohmann, D., Baum, B. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750209</dc:identifier>
<dc:title><![CDATA[The life cycle of an archaeon with multiple membranes]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750183v1?rss=1">
<title>
<![CDATA[
Cardiac Extracellular Matrix derived from younger animals stabilizes macrophage inflammatory polarization through modulation of the interferon signaling pathway 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750183v1?rss=1
</link>
<description><![CDATA[
Neonatal mammals exhibit a remarkable capacity for cardiac repair that declines rapidly after birth and continues to diminish with age. This loss of regenerative potential is accompanied by age-dependent changes in macrophage behavior, shifting from pro-regenerative to pro-fibrotic responses following injury. We investigated whether extracellular matrix (ECM)-derived matrikines from different developmental ages regulate macrophage polarization. Cardiac ECM was isolated from neonatal (P2), adolescent (6-week), and adult (16-20-week) rat hearts through decellularization and pepsin digestion. ECM peptides were adsorbed onto tissue culture surfaces, and murine RAW 264.7 macrophages were cultured on ECM-coated or uncoated controls. After 24 hours, macrophage phenotype and gene expression were assessed using marker analysis and RNA sequencing. Macrophages cultured on neonatal cardiac ECM displayed reduced inflammatory activation and maintained expression of pro-reparative markers, even in the presence of inflammatory stimuli. Transcriptomic analysis revealed a distinct ECM-driven phenotype that differed from canonical M1 and M2 polarization states. Gene ontology analysis demonstrated significant downregulation of pathways associated with antiviral responses, immune activation, and interferon signaling in macrophages exposed to neonatal ECM. These effects were not observed with adolescent or adult ECM. Collectively, these findings suggest that neonatal ECM matrikines suppress interferon-mediated inflammatory signaling, potentially contributing to the reduced inflammation and enhanced repair observed following myocardial injury in neonatal hearts.
]]></description>
<dc:creator><![CDATA[ Nugnes, K., Costello, G., McCarey, N., Canas, E., Black, L. D. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750183</dc:identifier>
<dc:title><![CDATA[Cardiac Extracellular Matrix derived from younger animals stabilizes macrophage inflammatory polarization through modulation of the interferon signaling pathway]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749722v1?rss=1">
<title>
<![CDATA[
ULK1 and ULK2 Restrain Skeletal Myofiber Growth by Balancing Protein Synthesis and Degradation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749722v1?rss=1
</link>
<description><![CDATA[
Background Skeletal muscle is vital for mobility and metabolic regulation, impacting independence and overall health. Increases in skeletal muscle mass and contractile function during development, and their maintenance during adulthood and aging, rely on an intricate coordination between protein synthesis and degradation processes that remains incompletely understood. Here, we investigated a potential role for the autophagy-initiating kinases ULK1 and ULK2 in broadly modulating protein metabolism in skeletal muscle. Methods Studies were conducted in young (4-6 wk-old) and adult (7-10 mo.-old) mice with skeletal muscle-specific knockout of Ulk1 and Ulk2 (i.e., Ulk1/2skmDKO) and wild-type littermates (WT). Short-term deficiency of these proteins was achieved via electroporation of plasmids (encoding specific microRNAs targeting Ulk1 and Ulk2) into muscles of 4 mo.-old wild-type mice. Protein metabolism was assessed via deuterium oxide (D2O) labeling, whereas anabolic signaling was investigated under insulin and leucine administration. Results Lifelong Ulk1/2 deficiency markedly impaired autophagy flux (i.e., LC3-II accumulated with colchicine treatment only in wild-type mice, P<0.001), compromised muscle quality, as evidenced by an increase in centrally nucleated fibers (from 0.1% to 4.5% in females, and from 0.8% to 22.7% in males (P<0.001), primarily involving MyHC type 2b fibers) and impaired force of dorsiflexors and plantar flexors in males (20%, P<0.01), and plantar flexors in females (24%, P<0.01). Despite these deficits, Ulk1/2 deficiency promoted robust muscle hypertrophy, evidenced by increased diameters of all major MyHC fiber types in the tibialis anterior and soleus muscles (i.e., by 10-15% in males, and 14-20% in females, P<0.05). Short-term deficiency (up to 4 weeks) of Ulk1/2 in adult skeletal muscle, however, led to myofiber hypertrophy (13%, P<0.05) without impairments in force or changes in central nucleation of fibers, pointing to an initial period of muscle quality preservation. Mechanistically, Ulk1/2 deficiency led to elevated myofibrillar protein synthesis (23% higher Ksyn, P<0.05) and decreased mitochondrial and sarcoplasmic protein degradation (16% and 14% lower Kdeg, P=0.09 and P<0.05, respectively). Further mechanistic studies revealed that hypertrophy was accompanied by enhanced mTORC1 activity independent of AKT in Ulk1/2-deficient muscle. Conclusions These results indicate that ULK1 and ULK2 jointly sustain autophagy and limit mTORC1-driven protein synthesis to govern skeletal muscle protein metabolism, with lifelong deficiency increasing muscle size at the expense of quality and function, while short-term deficiency permits hypertrophy without impairment. These findings identify ULK1/2 as a novel node coordinating protein turnover in skeletal muscle, warranting investigation as a therapeutic strategy for atrophy and weakness.
]]></description>
<dc:creator><![CDATA[ Son, W., Fuqua, J., Harris, M. P., Allen, R. J., Kronemberger, A., Hughes, J., de Sousa, L. G. O., Zingman, L., Bodine, S. C., Miller, B. F., Lira, V. A. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749722</dc:identifier>
<dc:title><![CDATA[ULK1 and ULK2 Restrain Skeletal Myofiber Growth by Balancing Protein Synthesis and Degradation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750178v1?rss=1">
<title>
<![CDATA[
MUC5B and MUC5AC function in combination to regulate mucociliary transport on human airway epithelium 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750178v1?rss=1
</link>
<description><![CDATA[
Muco-obstructive lung diseases are characterized by impaired airway clearance and altered mucin composition. MUC5B and MUC5AC are the primary gel-forming mucins in airway mucus, yet how their relative abundance influences the physical and functional properties of mucus remains poorly understood. Here, we investigated how compositional variations in MUC5B and MUC5AC within mucus impact mucociliary transport. Mucus enriched in either MUC5B or MUC5AC was generated using human airway epithelial models depleted for each mucin via CRISPR/Cas9-targeted knockout. Defined mixtures of these mucins were generated at physiologically relevant ratios, for assessment of their microrheological properties and mucociliary transport behavior in differentiated primary human airway epithelial tissue cultures. We found that increasing MUC5AC content reduced network pore size and increased microviscosity, concomitant with reduced mucociliary transport, demonstrating that mucin composition alters the biophysical and functional properties of the mucus barrier. In normal airway tissue cultures with MUC5B-predominant mucus, overlay of MUC5AC on the apical surface impaired mucociliary transport, whereas MUC5B had minimal effect. Conversely, MUC5B supplementation uniquely improved mucociliary transport in IL-13 stimulated cultures exhibiting mucostasis, whereas additional MUC5AC did not alter transport. Together, these findings demonstrate that the ratio of MUC5B to MUC5AC can shape mucus organization at the microscale, which in turn governs mucociliary transport at the tissue scale.
]]></description>
<dc:creator><![CDATA[ Kumar, S., Boboltz, A., Duncan, G. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750178</dc:identifier>
<dc:title><![CDATA[MUC5B and MUC5AC function in combination to regulate mucociliary transport on human airway epithelium]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750279v1?rss=1">
<title>
<![CDATA[
A SUN1-ApoD feedback loop promotes cellular aging via microtubule-nuclear mechanotransduction 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750279v1?rss=1
</link>
<description><![CDATA[
Alterations in nuclear envelope proteins such as SUN1 and prelamin A are known hallmarks of cellular aging, but how they cause aging phenotypes beyond the expressing cells is unknown. With a tissue culture version of parabiosis, we found that aged fibroblasts secrete an activity that induces aging-related polarity defects in young fibroblasts. Secretomics identified the factor as apolipoprotein D (ApoD), a circulating protein whose levels are known to rise with age. ApoD increased SUN1 levels and disrupted polarity in fibroblasts via SUN1-promoted coupling of microtubules to the nucleus. In turn, elevated SUN1 enhanced ApoD expression and secretion, forming a feedback loop that promotes acquisition of aged phenotypes. In mice, ApoD induced aging-related phenotypes in muscle. Elevated ApoD expression required coupling between SUN1, its outer nuclear membrane binding partner nesprin-2, and microtubules. Broader analysis revealed that this pathway regulates hundreds of genes. These findings define microtubule-nuclear coupling as a direct mechanotransduction pathway controlling gene expression and promoting aging-associated phenotypes.
]]></description>
<dc:creator><![CDATA[ Chen, M., Wilson, P. C., Yang, W., Ma, Y., Li, Y., Wang, X., Bennett, R. L., Licht, J. D., Gundersen, G. G., Chang, W. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750279</dc:identifier>
<dc:title><![CDATA[A SUN1-ApoD feedback loop promotes cellular aging via microtubule-nuclear mechanotransduction]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.749861v1?rss=1">
<title>
<![CDATA[
Cfap410a and Cby work together with tissue-specific requirements to build Drosophila ciliary transition zones 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.749861v1?rss=1
</link>
<description><![CDATA[
Cilia and flagella perform essential physiological functions in eukaryotes, and defects in these organelles cause several human diseases, including cancer and ciliopathies. The architecture of cilia is highly organized. The ciliary compartment is separated from the cytoplasm by the transition zone (TZ). The severity of ciliopathies linked to TZ assembly defects highlights the TZ's critical role. Although several core conserved complexes are involved in TZ assembly, variations in TZ composition are associated with structurally and functionally diverse cilia. Here, we identify Cfap410a as a novel component of the ciliary TZ in the two Drosophila ciliated tissues, male germ cells and sensory neurons. Cfap410a is one of the two Drosophila paralogs (Cfap410a and Cfap410b) of human CFAP410, whose mutations are associated with axial spondylo-metaphyseal dysplasia, retinitis pigmentosa and amyotrophic lateral sclerosis. We show here that Cfap410a is a proximity partner of Cby and that they act cooperatively in the hierarchy of the TZ assembly program by bridging the CEP290 and MKS transition zone modules. Simultaneous loss of Cfap410a and Cby halts ciliary growth by disrupting TZ formation in multiple types of Drosophila ciliated cells, each of which exhibiting varying dependence on these two proteins. Interestingly, the function of Cfap410a and Cfap410b are not functionally redundant, indicating that the two proteins have evolved towards specific functions. In summary, our results propose a novel role for CFAP410a at the TZ and provide an explanation for how deregulation of conserved TZ components could lead to tissue-specific ciliopathies.
]]></description>
<dc:creator><![CDATA[ Billon, A., Vieillard, J., Priya, P., Desai, M., Fontaine, E., De Freitas, S., Lapart, J.-A., Mange, A., Dar, H. A., Morel, V., Thomas, J., Jana, S. C., Durand, B. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.749861</dc:identifier>
<dc:title><![CDATA[Cfap410a and Cby work together with tissue-specific requirements to build Drosophila ciliary transition zones]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.05.749613v1?rss=1">
<title>
<![CDATA[
Functional diversification across yeast lineages of the nucleus-vacuole junction forming protein Nvj1 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.05.749613v1?rss=1
</link>
<description><![CDATA[
Nucleus-vacuole junctions (NVJs) in Saccharomyces cerevisiae serve as an inter-organellar hub for multiple cell processes, including lipid transport and biosynthesis, an intra-nuclear quality control mechanism, and piecemeal microautophagy of the nucleus. NVJs are formed by complexes between Vac8 in the vacuole membrane and Nvj1 in the nuclear envelope. Nvj1 also links the inner and outer nuclear membranes across the perinuclear lumen. Orthologs of Nvj1 had previously only been found in yeasts of the order Saccharomycetales, raising the possibility that NVJs are restricted to this clade. Using homology and synteny, we discovered scores of novel Nvj1 orthologs across 200 million years of evolution within the subphylum Saccharomycotina. Not all orthologs mediate NVJ formation when expressed in S. cerevisiae, and some lack a sequence motif necessary for this function. Furthermore, the sequence motif required for binding the oxysterol binding protein Osh1 and an associated novel sequence motif, both found only in the order Saccharomycetales, were independently lost in three different lineages. This collection suggests specific opportunities to explore evolutionary and functional adaptations of Nvj1s in ecologically and physiologically diverse yeasts.
]]></description>
<dc:creator><![CDATA[ Kramer, F., Millen, J., Goldfarb, A. M., Farre, J.-C., Wolters, J. F., Rokas, A., Hittinger, C. T., Subramani, S., Fay, J. C., Thumm, M., Goldfarb, D. S. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.05.749613</dc:identifier>
<dc:title><![CDATA[Functional diversification across yeast lineages of the nucleus-vacuole junction forming protein Nvj1]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.05.749615v1?rss=1">
<title>
<![CDATA[
An in vitro System for Studying Osteochondrogenic Differentiation of Smooth Muscle Cells and Modeling Intimal Vascular Calcification 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.05.749615v1?rss=1
</link>
<description><![CDATA[
Objective: Smooth muscle cells (SMCs) undergo phenotypic transitions during atherosclerosis, including towards a chondromyocyte (CMC) state associated with intimal calcification. Although standard in vitro calcification assays robustly reproduce mineral deposition, it remains unclear how well they recapitulate these disease-associated SMC states. We sought to define the CMC transcriptional phenotype in atherosclerosis and develop an in vitro system that faithfully reproduces it. Approach and Results: We firstly identified a CMC transcriptional signature in murine and human atherosclerotic plaque through single-cell RNA-sequencing, and spatial transcriptomics. CMCs showed a conserved osteochondrogenic program which localized within plaques and adjacent to calcified regions. We then developed an osteochondrogenic differentiation (OCD) assay by combining well-established calcification components with a high-density SMC micromass culture and TGF-{beta}1 supplementation and benchmarked it against a standard calcification (SC) assay using calcium quantification and bulk RNA-sequencing. Despite comparable calcification, OCD and SC resulted in distinct transcriptional states, with OCD showing preferential upregulation of osteochondrogenic programs, and a higher CMC signature score. Additionally, OCD upregulated genes with a stronger enrichment near coronary artery disease (CAD)-associated loci. These responses were reproducible across several primary human SMC lines. Timecourse analysis also showed that chondrogenic programs preceded calcification and showed directional concordance with the inferred in vivo SMC-to-CMC trajectory. To interrogate regulatory pathways controlling this process, we overexpressed the chondrogenic regulator SOX9, which enhanced cartilage and extracellular matrix programs while repressing inflammatory pathways. Finally, we examined 552 CAD-associated genes nominated across five genome-wide association studies. Of these, 240 were differentially expressed by day 12, and included established SMC regulators as well as a number of candidates not previously characterized in osteochondrogenic SMC transition. Conclusions: The OCD assay results in a strong calcification phenotype together with a disease-associated CMC-like transcriptional state, providing a reliable in vitro model for mechanistic investigation of SMC phenotypic transition and prioritization of candidate regulators.
]]></description>
<dc:creator><![CDATA[ Monteiro, J. P., Worssam, M. D., Gu, W., Li, D. Y., Zhao, Q., Karius, A. K., Ramste, M., Qin, G. T., Damiani, I., Zheng, S., Nguyen, T., Palmisano, B. T., Weldy, C. S., Kim, J. B., Kaikkonen, M. U., Cheng, P., Quertermous, T. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.05.749615</dc:identifier>
<dc:title><![CDATA[An in vitro System for Studying Osteochondrogenic Differentiation of Smooth Muscle Cells and Modeling Intimal Vascular Calcification]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749987v1?rss=1">
<title>
<![CDATA[
A Full Spectrum Fibroblast Profiling Panel Reveals Phenotypic and Metabolic Heterogeneity of Cancer-Associated Fibroblasts at the Single-Cell Level 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749987v1?rss=1
</link>
<description><![CDATA[
Cancer-associated fibroblasts (CAFs) exhibit extensive transcriptional and phenotypic heterogeneity and are highly plastic. Routine approaches to resolving CAF heterogeneity at the single-cell and protein levels are lacking, making it difficult to assess changes in CAF state in response to perturbations. Here, we present an optimized 28-marker spectral flow cytometry panel that uses unsupervised clustering to resolve CAF states across in vivo and in vitro models. Using this new fibroblast profiling panel (FPP), we show that LRRC15+ CAFs in murine pancreatic ductal adenocarcinoma are phenotypically distinct from canonical SMA+ myofibroblasts, rather than representing a subset of this population. We find that marker expression is graded rather than discrete across clusters, indicating that CAF identity spans a continuum rather than fixed states. Metabolic profiling further shows that hypoxic CAFs were enriched for glucose uptake and an inflammatory phenotype. Using in vitro models, we further demonstrate how the FPP can resolve plasticity outcomes. In a 3D organoid co-culture model, direct contact between tumor cells and fibroblasts, but not organoid-derived factors alone, induces a stem-like CAF state also observed in vivo. In 2D, TGF{beta} and inflammatory/hypoxic stimuli each enrich distinct, pre-existing CAF states rather than generating new ones. These findings establish our FPP as a practical method for resolving fibroblast heterogeneity at the protein level in cancer and beyond.
]]></description>
<dc:creator><![CDATA[ Munoz Forti, K., Storl-Desmond, M., Isaac, S. E., Martinez, D., Nizio, M., Lin, S., Solanki, A., Schwörer, S. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749987</dc:identifier>
<dc:title><![CDATA[A Full Spectrum Fibroblast Profiling Panel Reveals Phenotypic and Metabolic Heterogeneity of Cancer-Associated Fibroblasts at the Single-Cell Level]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750128v1?rss=1">
<title>
<![CDATA[
Concanavalin A as a pan-eukaryotic nuclear envelope marker for expansion microscopy 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750128v1?rss=1
</link>
<description><![CDATA[
Across eukaryotes, the nuclear envelope exhibits distinct remodelling strategies during mitosis: complete breakdown (open mitosis), partial disruption (intermediate), or full retention (closed). However, both light and electron microscopy of the nuclear envelope, at sufficient resolution to determine integrity and mode of remodelling, have proven technically challenging. Here, Concanavalin A (ConA), a glycan-binding plant lectin, provides discernible nuclear envelope/endoplasmic reticulum (NE/ER) labelling in Ultrastructure Expansion Microscopy (U-ExM). Applied post-expansion, ConA circumvents antibody optimisation and labels the NE across mammalian cells and diverse microbial eukaryotes. By imaging four opisthokont and amoebozoan species with established mitotic strategies, C. perkinsii, D. discoideum, S. pombe, and S. arctica, we distinguished the full spectrum of NE remodelling. Applied to species with poorly characterised mitotic strategies, ConA revealed intermediate mitosis with polar fenestrae in the multinucleate stramenopile A. limacinum and a life cycle-coupled switch between open and closed mitosis in the amoebozoan P. polycephalum. These observations support the hypothesis that multinucleated life cycles favour closed or intermediate mitosis, protecting chromosomes from capture by neighbouring spindles during synchronous divisions. Together, these results establish ConA in combination with expansion microscopy as a broadly applicable tool for uncovering the diversity and evolution of NE remodelling across eukaryotes.
]]></description>
<dc:creator><![CDATA[ Hoogenberg, B., Mikus, F., Parihar, P. S., Verbanac, I., Beltrame, D., Olivetta, M., Richards, T. A., Dey, G., Dudin, O. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750128</dc:identifier>
<dc:title><![CDATA[Concanavalin A as a pan-eukaryotic nuclear envelope marker for expansion microscopy]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.04.749547v1?rss=1">
<title>
<![CDATA[
Native in situ architecture of the human inactive X chromosome revealed by correlative light and electron microscopy 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.04.749547v1?rss=1
</link>
<description><![CDATA[
Knowledge of the nuclear organization of specific chromatin domains at the ultrastructural level remains limited. To address this, we employed correlative light and electron microscopy (CLEM) approaches to investigate the inactive X chromosome (Xi) in female human RPE1cells. Tandem fusion of macroH2A (mH2A), a histone variant enriched on the Xi, to eGFP and APEX2 enabled direct labeling and identification of the Xi by light microscopy, transmission electron microscopy, and electron tomography using conventional CLEM. The eGFP tag further allowed us to visualize the Xi at single nucleosome resolution under close-to-native conditions using cryo-CLEM. We found that, although heterochromatin domains of the Xi are substantially larger than those of autosomal regions, their chromatin density was not significantly different. Furthermore, our data reveal the organization of the interchromatin compartment (IC) within the Xi, characterized by a network of larger lacunae and smaller channels. Overall, we provide an ultrastructural characterization of a specific heterochromatin domain at unprecedented resolution, advancing our understanding of 3D chromatin organization and nuclear architecture in situ.
]]></description>
<dc:creator><![CDATA[ Ludwig, A., Huebner, B., Sandin, S., Wee, M. L., Chan, H. Y. S. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.04.749547</dc:identifier>
<dc:title><![CDATA[Native in situ architecture of the human inactive X chromosome revealed by correlative light and electron microscopy]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749720v1?rss=1">
<title>
<![CDATA[
A TFIIB paralog drives cyclic transcription to orchestrate the archaeal cell cycle 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749720v1?rss=1
</link>
<description><![CDATA[
Cyclic transcription is a hallmark of the cell cycle. While transcriptional waves in eukaryotes are driven by oscillations in cyclin-dependent kinase (CDK) activity, many archaea have an ordered cell cycle despite lacking CDKs. Here in exploring how cyclic transcription is achieved in Sulfolobus acidocaldarius, we show that TFB2, a paralog of eukaryotic TFIIB, is cyclically expressed, associated with the promoters of division genes (including tfb2 itself), contains a cyclin-box and is degraded as cells exit division. Furthermore, a dominant-negative TFB2 mutant interferes with division gene expression and cytokinesis. These data identify TFB2 as a central player in the circuitry orchestrating the orderly cell cycle in Sulfolobus and, despite the absence of CDKs, reveal parallels between the regulatory logic of archaeal cell division and eukaryotic mitosis.
]]></description>
<dc:creator><![CDATA[ Kuo, Y.-W., Blombach, F., Schult, F., Siebers, B., Werner, F., Baum, B. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749720</dc:identifier>
<dc:title><![CDATA[A TFIIB paralog drives cyclic transcription to orchestrate the archaeal cell cycle]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749962v1?rss=1">
<title>
<![CDATA[
Nuclear envelope buffering of cytoskeletal force stabilizes chromosome interactions in C. elegans meiosis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749962v1?rss=1
</link>
<description><![CDATA[
Meiosis requires coordination between chromosome and nuclear envelope (NE) dynamics. Cytoskeletal forces transmitted through the NE via linker of nucleoskeleton and cytoskeleton (LINC) complexes drive chromosome movement but can also compromise nuclear integrity if not properly balanced. Here, we identify the conserved inner nuclear membrane protein NEMP-1 as a key regulator that contributes to buffering of excessive force at the meiotic NE in Caenorhabditis elegans. NEMP-1 localizes to the NE throughout meiotic prophase and becomes enriched at the NE in nuclei with a weakened nuclear lamina. Simultaneous depletion of NEMP-1 and the lamin protein LMN-1 results in premature nuclear collapse and defects in chromosome synapsis and homolog pairing. These phenotypes depend on excessive dynein-mediated forces acting on a compromised NE. Furthermore, analysis of homolog pairing in the absence of synapsis revealed that NEMP-1 and LMN-1 contribute to the stabilization of synapsis-independent homolog interactions at the NE. Together, our findings reveal that excessive force at the NE can destabilize homolog interactions, and support a model in which NEMP-1 and LMN-1 cooperatively buffer cytoskeletal forces to maintain nuclear integrity while stabilizing chromosome interactions during meiosis.
]]></description>
<dc:creator><![CDATA[ Nenstiel, R., Liu, C. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749962</dc:identifier>
<dc:title><![CDATA[Nuclear envelope buffering of cytoskeletal force stabilizes chromosome interactions in C. elegans meiosis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749677v1?rss=1">
<title>
<![CDATA[
Accurate chromosome segregation is more dependent on kinetochore-bound Stu2 in meiosis than mitosis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749677v1?rss=1
</link>
<description><![CDATA[
Accurate chromosome segregation requires bipolar kinetochore-microtubule attachments. Error correction mechanisms promote cycles of kinetochore-microtubule release and reattachment until bipolar attachments are established. Although conserved error correction pathways operate in mitosis and meiosis, whether they have distinct requirements during meiosis remains unclear. Here, we investigate the role of Stu2/XMAP215/chTOG in kinetochore-microtubule error correction and compare its function with that of Ipl1/Aurora B during budding yeast mitosis and meiosis. Reducing kinetochore-bound Stu2 causes substantially more chromosome missegregation during meiosis than mitosis, revealing a heightened requirement for Stu2-mediated error correction. Whereas Ipl1-depleted cells fail to release initial improper kinetochore-microtubule attachments, kinetochore-defective stu2 mutants undergo repeated error correction attempts yet missegregate chromosomes. Our findings reveal distinct but complementary functions for Ipl1 and Stu2. Ipl1 releases initial improper attachments, while kinetochore-bound Stu2 promotes the formation and stabilization of productive attachments and enables error correction attempts to establish biorientation. We propose that features of meiotic chromosome segregation increase the requirement for multiple error correction pathways.
]]></description>
<dc:creator><![CDATA[ Robow, B., Lacefield, S. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749677</dc:identifier>
<dc:title><![CDATA[Accurate chromosome segregation is more dependent on kinetochore-bound Stu2 in meiosis than mitosis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749635v1?rss=1">
<title>
<![CDATA[
GSDMD transcript levels are higher in endothelial than cardiomyocyte compartments across three human heart cohorts 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749635v1?rss=1
</link>
<description><![CDATA[
Cardiac GSDMD research has largely centred on cardiomyocytes. We quantified donor-level endothelial-minus-cardiomyocyte differences in two single-nucleus cohorts and one GeoMx spatial cohort, retaining assay-specific scales. GSDMD was higher in endothelial compartments in 42/42, 38/38 and 27/32 donors and ranked, post hoc, at the 94.9th, 95.1st and 97.4th percentiles of the corresponding within-cohort signed-contrast distributions. Although positive direction and complete donor concordance were not unique transcriptome-wide, this hypothesis-led target retained high rank across markedly different reference backgrounds and assay modalities. A fixed eight-transcript panel included both endothelial- and cardiomyocyte-shifted members, arguing against a uniform panel-wide directional shift or simple detection failure. GeoMx provided the most discriminating transcriptome background but remained composition-sensitive. GSDMD transcripts are therefore recurrently higher in endothelial than cardiomyocyte compartments across human-heart cohorts, showing that a cardiomyocyte-only interpretation of human-heart GSDMD transcript signals is incomplete.
]]></description>
<dc:creator><![CDATA[ Oryoji, D., Doi, G., Fujimoto, S., Nishimura, N., Otsuka, K., Kuwahara, A., Ayano, M., Kimoto, Y., Akashi, K., Niiro, H., Mitoma, H. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749635</dc:identifier>
<dc:title><![CDATA[GSDMD transcript levels are higher in endothelial than cardiomyocyte compartments across three human heart cohorts]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749697v1?rss=1">
<title>
<![CDATA[
phyB photobodies display molecular memory, regulating light signaling transcriptional states through phase separation. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749697v1?rss=1
</link>
<description><![CDATA[
Phytochrome B is a crucial red and far-red light sensor, which controls plant development and environmental responses to light and temperature. In the nucleus, phyB forms phase separated condensates, also called photobodies, consisting of various transcriptional regulators and transcription factors. phyB photobodies can form or disperse depending on the amount of light, the light quality, or ambient temperature. However, the biological relevance for forming photobodies is still unclear. In recent years the study of condensates has given rise to the idea that condensates can act as molecular memory, either due to long equilibration timescales arising from strong interactions can kinetically trap a mixture in a phase-separated state beyond the equilibrium coexistence line, or from phase-separation dependent modification processes or transcriptional regulation. Here, we hypothesize that the formation of phyB photobodies and the associated sequestration of signaling molecules allows for the formation of cell-type specific memory about light conditions. To address this hypothesis, we first developed a live imaging setup of phyB photobodies which shows that they do not follow classic liquid-liquid phase separation dynamics, but instead have a restriction on their size, intensity and minimum number. Fluorescence recovery after photobleaching (FRAP) then showed that photobodies between cell types have different levels of mobilities and diffusivities, suggesting that they are more stable in darkness or high red light, versus low red light. These differences in phyB photobody stability between cell types were also confirmed through whole-mount confocal imaging and single-nucleus transcriptomics in the same light-perturbation series. Through sci-Seq single nucleus spatial transcriptomics of the cotyledon in this light perturbation series, we identify a photobody-associated transcriptional cluster of nuclei that regulates photosynthesis, circadian rhythm, and RNA processing; the phyB photobody likely promotes its own stability by regulating TZP and PCH1 expression. The correlation between photobodies and transcriptional regulation shows how phyB condensates can provide cell-type specific light responses and exhibit signaling memory in changing environmental conditions.
]]></description>
<dc:creator><![CDATA[ Igiebor, F., Wuerthner, L., Stamm, F., Haque, S., Havlicek, O., Schmidt, J., Cetiner, M., Zubcic, I., Heliel, O., Saunders, L. M., Graf, I. R., van Gelderen, K. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749697</dc:identifier>
<dc:title><![CDATA[phyB photobodies display molecular memory, regulating light signaling transcriptional states through phase separation.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749571v1?rss=1">
<title>
<![CDATA[
Ultrastructural dynamics of basal bodies during microgamete formation and fertilisation in Plasmodium 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749571v1?rss=1
</link>
<description><![CDATA[
Cilia and flagella are microtubule-based organelles found in a wide range of eukaryotic organisms that form cilia and flagella are assembled from basal bodies. In the malaria parasite, eight flagellated microgametes are assembled from 8 basal bodies that form de novo as a single group (not next to a parent basal body) in the cytoplasm of microgametocytes extremely rapidly, in as little 8 minutes but is not synchronised. The flagellated microgametes exit from a microgametocyte, each consisting of an axoneme and a haploid nucleus. Fertilisation occurs via a HAP2-mediated fusion with the macrogamete. Despite the essential role of microgametes in malaria transmission and being the only flagellated stage, little is known about the process of basal body formation, biogenesis at the ultrastructure level and their role in fertilisation. We used dual axis serial section electron tomography (ssET) to reveal the unusual single microtubule structure of the basal body and discovered an associated electron dense basal body granule. Using whole cell reconstructions of microgametocytes, free microgametes and macrogametes by serial block face scanning electron microscopy (SBF-SEM), we discovered a deuterosome-like structure only present during the initial formation of 8 basal bodies that could be a nucleating platform for de novo basal body formation. Finally, we reveal that entry of the microgamete into the macrogamete occurs via directed event at a single point of entry with the basal body and granule leading entry. These discoveries highlight the essential functions of basal bodies from initial microgamete assembly to male-female gamete fertilisation.
]]></description>
<dc:creator><![CDATA[ Hair, M., Yanase, R., Ferguson, D. J. P., Brady, D., Wheeler, R. J., Tewari, R., Vaughan, S. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749571</dc:identifier>
<dc:title><![CDATA[Ultrastructural dynamics of basal bodies during microgamete formation and fertilisation in Plasmodium]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.05.749077v1?rss=1">
<title>
<![CDATA[
Febrile temperatures influence the transmission competence of mature Plasmodium falciparum gametocytes 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.05.749077v1?rss=1
</link>
<description><![CDATA[
Malaria transmission depends on the survival and mosquito infectivity of mature Plasmodium falciparum gametocytes. Despite malaria febrile episodes reaching 39 to 41.5{degrees}C in infected humans, the impact of febrile temperatures of varying durations on gametocyte viability and transmissibility remains undefined. Here we quantify the effects of exposing mature stage V gametocytes in vitro to febrile temperatures (39{degrees}C, 40{degrees}C, and 41.5{degrees}C) for varying durations (3 to 12 hours). To assess gametocyte morphology, functionality, and mosquito infectivity, we used light microscopy of Giemsa-stained thin blood smears, exflagellation assays, and standard membrane feeding assays (SMFAs). Following exposure to 39{degrees}C, gametocytes retained normal morphology, exflagellation capacity, and mosquito infectivity across all exposure durations. At 40{degrees}C, gametocytes remained morphologically intact and capable of exflagellation but exhibited a time-dependent reduction in mosquito infection, both in prevalence and oocyst intensity, following prolonged exposure. In contrast, exposure of mature gametocytes to 41.5{degrees}C, even for the minimum duration tested of 3 hours, resulted in complete loss of normal morphology, exflagellation capacity and ability to infect mosquitoes. These findings reveal that mosquito infectivity of mature gametocytes is affected both by the magnitude of the febrile temperature and the duration of exposure. This provides insight into how host fever dynamics may influence parasite transmission.
]]></description>
<dc:creator><![CDATA[ Ubiaru, P. C., Nyirongo, J., Pallikara, A., Ranford-Cartwright, L. C., Janha, O. ]]></dc:creator>
<dc:date>2026-09-09</dc:date>
<dc:identifier>doi:10.64898/2026.09.05.749077</dc:identifier>
<dc:title><![CDATA[Febrile temperatures influence the transmission competence of mature Plasmodium falciparum gametocytes]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-09</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.04.749496v1?rss=1">
<title>
<![CDATA[
Mechanistic Insights into MYO1C-Mediated Rhodopsin Trafficking and Rod Photoreceptor Homeostasis. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.04.749496v1?rss=1
</link>
<description><![CDATA[
Rhodopsin trafficking from the photoreceptor inner segment to the outer segment is essential for photoreceptor function, yet the molecular mechanism(s) regulating this process remain incompletely understood. MYO1C is an actin-based motor protein implicated in intracellular cargo trafficking. Here, we investigated its role in rhodopsin trafficking and photoreceptor cell homeostasis. In-silico docking identified a putative interaction between the MYO1C C-terminal region and the C-terminal region of rhodopsin containing the conserved VxPx ciliary trafficking motif. Biochemical studies confirmed that full-length MYO1C interacts with rhodopsin, whereas deletion of the MYO1C C-terminal domain abolished this interaction. Live-cell imaging, ciliary localization, and fluorescence recovery after photobleaching in hTERT-RPE1 cells demonstrated that the MYO1C C-terminal region is required for efficient rhodopsin trafficking, membrane localization, and ciliary targeting. In native murine rod photoreceptors MYO1C localized to both inner and outer segments. Global Myo1c deficiency in mice caused age-dependent rhodopsin mislocalization, apo-opsin accumulation and progressive retinal dysfunction, characterized primarily by reduced scotopic ERG responses and delayed a-wave recovery, beginning at 6-months, while photopic responses were relatively preserved. Rod-specific Myo1c deletion similarly caused progressive scotopic dysfunction and reduced a-wave recovery following light stimulation. In contrast, cone-specific Myo1c deletion preserved photopic function and a-wave recovery. Together, these findings identify MYO1C as an important regulator of rhodopsin trafficking and demonstrate a preferential, cell-autonomous requirement for MYO1C in maintaining rod photoreceptor homeostasis and phototransduction recovery. These findings establish a mechanistic link between MYO1C-dependent rhodopsin trafficking and age-dependent rod photoreceptor cell dysfunction.
]]></description>
<dc:creator><![CDATA[ Radhakrishnan, R., Norton, V., Roehrich, H., Cureoglu, S., Kondkar, A. A., Monsanto, R. d. C., Kuijk, F. J. v., Lobo, G. P. ]]></dc:creator>
<dc:date>2026-09-09</dc:date>
<dc:identifier>doi:10.64898/2026.09.04.749496</dc:identifier>
<dc:title><![CDATA[Mechanistic Insights into MYO1C-Mediated Rhodopsin Trafficking and Rod Photoreceptor Homeostasis.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-09</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.04.749506v1?rss=1">
<title>
<![CDATA[
Methyl-substituted 1,10-phenanthroline derivatives in copper(II) complexes enhance antitumor activity and inhibit NHE1 in MDA-MB-231 breast cancer cells 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.04.749506v1?rss=1
</link>
<description><![CDATA[
Three copper(II) complexes containing 1,10-phenanthroline derivatives, [CuCl2(phen)].0.5H2O (1), [CuCl2(neo)].0.75H2O (2), and [CuCl2(tmp)].H2O (3), were evaluated for their antitumor activity in MDA-MB-231 breast cancer cells. All complexes markedly reduced cell viability, exhibiting significantly lower IC values and higher selectivity indices than the corresponding free ligands, CuCl2, and cisplatin, highlighting the therapeutic advantage of metal complexation. Among them, only 1 induced DNA damage at sub-IC concentrations. Cytotoxicity in all complexes was associated with intracellular ROS generation and apoptosis, although 2 and 3 produced a stronger oxidative response. Complex 3 additionally promoted necrosis. Cell proliferation was inhibited in a concentration-dependent manner, accompanied by increased intracellular copper accumulation. Moreover, 2 and 3 significantly inhibited Na/H exchanger 1 (NHE1) activity, reducing cell migration and MMP-9 activity. Western blot analysis further demonstrated that all three complexes modulated the expression of NHE1, G protein-coupled estrogen receptor (GPER), and apoptosis-related proteins. Overall, our findings show that ligand methylation enhances the antitumor activity of copper(II) complexes and shifts their mechanism of action from DNA damage-driven cytotoxicity toward ROS-mediated apoptosis, while also improving inhibition of NHE1-dependent migratory pathways. These results identify NHE1 as a key molecular target underlying the enhanced antitumor activity of methylated phenanthroline copper(II) complexes.
]]></description>
<dc:creator><![CDATA[ Munoz Garzon, K. S., De Giusti, V., Yanez Fernandez, C., Facchin, G., Martinez, V., Di Virgilio, A. L. ]]></dc:creator>
<dc:date>2026-09-09</dc:date>
<dc:identifier>doi:10.64898/2026.09.04.749506</dc:identifier>
<dc:title><![CDATA[Methyl-substituted 1,10-phenanthroline derivatives in copper(II) complexes enhance antitumor activity and inhibit NHE1 in MDA-MB-231 breast cancer cells]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-09</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749928v1?rss=1">
<title>
<![CDATA[
Derivation of primary fetal epithelial organoids from cryopreserved human amniotic fluid cells. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749928v1?rss=1
</link>
<description><![CDATA[
Primary fetal human epithelial organoids are canonically derived from tissue samples obtained after termination of pregnancy. Recently, we have demonstrated that these organoids can be consistently generated from amniotic fluid cells isolated prenatally during diagnostic and interventional procedures. Amniotic Fluid-derived Organoids (AFOs) are promising fetal epithelial lung, kidney and small intestine tissue models that bypass some of the ethical and legal constraints associated with obtaining primary fetal tissue. Despite this, the widespread adoption of this technology is limited by the lack of standardised and accessible pipelines for the biobanking, culturing and distribution of organoid-forming amniotic fluid cells. To enable broader AFO use for research and clinical purposes, this work investigates two cryopreservation strategies to optimise AF cell recovery for organoid derivation. In Strategy 1, viable AF cells were sorted before freezing, while in Strategy 2 unsorted AF was frozen, and viable AF cells were sorted for viability after thawing. We present here a comprehensive evaluation of 5 commercially available GMP-compliant freezing media (FM1-5) alongside a standard lab-grade control (FM CT). AFOs were assessed for formation efficiency, morphological characteristics, proliferation capacity, epithelial identity, and tissue type. Our results demonstrate that organoid-forming AF cells can be successfully cryopreserved both pre- and post-sorting. Strategy 1 yielded higher organoid formation efficiency, with AFOs derived from cryopreserved and fresh cells exhibiting comparable expansion potential. Finally, FM4 provided minimal to no decline in survival rate, making it the most effective GMP-grade freezing medium tested. In conclusion, we present two viable cryopreservation strategies adaptable to different laboratory settings and identify optimal GMP-compliant freezing media, to support safe distribution and centralised processing, thereby facilitating scalability and collaborative work on the AFO technology.
]]></description>
<dc:creator><![CDATA[ D'Ariano, G., Zhang, G. J., Cala, G., Carrino, G. M., Agarwal, A., Mariani, A., Marinaro, M., Matias de Sousa, R., Cenedese, G., Camilli, C., David, A. L., Eaton, S., Pellegata, A. F., Pellegrini, M., De Coppi, P., Gerli, M. F. M. ]]></dc:creator>
<dc:date>2026-09-09</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749928</dc:identifier>
<dc:title><![CDATA[Derivation of primary fetal epithelial organoids from cryopreserved human amniotic fluid cells.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-09</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.02.749027v1?rss=1">
<title>
<![CDATA[
Evaluation of the Translational Readiness of Pluripotent Stem Cell-Derived Vascular Cell Therapy for Limb Ischemia: A Systematic Review and Meta-analysis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.02.749027v1?rss=1
</link>
<description><![CDATA[
Background: For the first time, pluripotent stem cell (PSC)-derived endothelial cells were administered to a human for peripheral artery disease (PAD), in August 2026. This translation is based on a large preclinical literature claiming that donor cells build blood vessels in animal models of limb ischemia, but whether it supports that claim has not been assessed systematically. Methods: In this systematic review and meta-analysis, we searched MEDLINE, Web of Science, Europe PMC, and Embase to August 2026 for studies of PSC-derived vascular cells in animal models of limb ischemia with an acellular control. Limb perfusion at each experiment's primary timepoint was pooled as Hedges' g in a three-level random-effects model with cluster-robust variance. Donor-cell fate and a seven-level ordinal of vascular contribution were graded for every study. This meta-analysis was registered on PROSPERO (CRD420261465308). Results: Sixty-eight studies in 69 reports met the criteria; 51 contributed 114 comparisons at primary timepoints. Cell therapy increased perfusion (Hedges' g 2.26, 95% CI 1.72-2.79; P=4.1x10-11; I2=87.5%; 95% prediction interval -1.47 to 5.98). No prespecified moderator survived Holm-Bonferroni adjustment, including the donor-cell fate grade (P=0.30). A donor cell was resolved in a vessel wall in 35 studies, and flow through such a vessel in 7. Small-study effects were strong (Egger t=6.25, P=9x10-8) but were not reproduced by a sample-size-based test (P=0.80); trim-and-fill moved the estimate to 1.15. On the natural scale, treated limbs recovered about twice the control perfusion (ratio of means 1.96, 95% CI 1.66-2.33). Limb preservation favored cell therapy in 11 studies with countable events (risk ratio 4.88, 95% CI 2.28-10.45), but 43 of 68 studies reported no functional outcome, and only 22 comparisons from 8 studies were both randomized and blindly assessed. In a post hoc analysis that did not survive multiplicity adjustment, effects were largest in studies whose images could not resolve their incorporation claims (g 3.23) versus those that resolved incorporation (g 2.33). Conclusions: PSC-derived vascular cell therapy improved limb perfusion in animal models, consistently across every sensitivity analysis, although the magnitude is uncertain given heterogeneity and small-study effects. Benefit was not associated with the degree of donor-cell incorporation across studies and was largest where incorporation was least resolvable, a pattern more consistent with reporting and measurement bias than with a true mechanistic effect. The first rigorous, blinded test of that benefit may come not from animals but from the patients now receiving these cells.
]]></description>
<dc:creator><![CDATA[ Shin, M., Choi, H., Kim, T., Jeon, J. P., Jung, S., Cho, K. ]]></dc:creator>
<dc:date>2026-09-09</dc:date>
<dc:identifier>doi:10.64898/2026.09.02.749027</dc:identifier>
<dc:title><![CDATA[Evaluation of the Translational Readiness of Pluripotent Stem Cell-Derived Vascular Cell Therapy for Limb Ischemia: A Systematic Review and Meta-analysis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-09</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.04.749305v1?rss=1">
<title>
<![CDATA[
Characterization of tri-culture alveolar-like organoids to study fibrotic lung diseases 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.04.749305v1?rss=1
</link>
<description><![CDATA[
Rationale: Fibrotic interstitial lung diseases are progressive disorders characterized by lung scarring and declining respiratory function. Repeated injury and dysregulated epithelial-mesenchymal crosstalk are implicated in disease pathogenesis but remain incompletely understood. Three-dimensional (3D) organoids incorporating epithelial-mesenchymal crosstalk provide a physiologically relevant platform for investigating these mechanisms. Here, we present a 3D tri-co-culture alveolar organoid model and evaluate its responses to two profibrotic stimuli, TGF-{beta} and bleomycin. Methods: CI-huArlo, NCI-H441, and MRC-5 cells were co-cultured for 14 days to generate alveolar-like organoids. Cell marker expression was assessed by immunofluorescence (IF). To test injury response, organoids were exposed to TGF-{beta} (50 ng/mL) or bleomycin (20 g/mL) for 48 hours and characterized. Supernatants were collected to assess interleukin 8 (IL-8) and procollagen I by ELISA. qPCR assessed expression of CDKN1A and COL1A1 following treatments. Bulk RNA sequencing (RNA-seq) evaluated the transcriptomic responses to fibrotic stimulus. Results: Cellular marker expression was confirmed using IF for aquaporin-5 (alveolar type I cell marker) and TE-7 (fibroblast marker). Bleomycin exposure reduced viability and significantly increased IL-8 (126.3 {+/-} 16.86 vs. 48.88 {+/-} 4.470 pg/mL; p = 0.0002; N=6), with no change in secreted procollagen I compared to control. TGF-{beta} stimulation significantly increased secreted procollagen I (149.6 {+/-} 27.07 vs. 53.38 {+/-} 5.672 pg/mL; p <0.0001; N=6) without affecting viability or IL-8 release. qPCR resulted in no change in CDKN1A expression, while COL1A1 expression was increased with TGF-{beta} treatment compared with control and bleomycin. RNA sequencing demonstrated distinct and reproducible transcriptional responses to TGF-{beta} and bleomycin. TGF-{beta} induced 750 significantly upregulated and 641 downregulated genes, including increased COL1A1, COL4A1, FN1, and TGFB1, with enrichment of epithelial-mesenchymal transition and TGF-{beta} signalling programs. In contrast, bleomycin induced 953 significantly upregulated and 552 downregulated genes relative to untreated controls and was characterized by p53 signalling, DNA-damage responses, and reduced cell-cycle progression. Reference-state analysis further indicated reduced normal alveolar epithelial signatures following both treatments, with TGF-{beta} producing the strongest aberrant basaloid and myofibroblast-associated signatures. Conclusions: Tri-culture alveolar-like organoids exhibited stimulus-specific responses in a 3D multicellular system, supporting their use for mechanistic studies of epithelial-mesenchymal crosstalk, environmental exposures, and therapeutic responses.
]]></description>
<dc:creator><![CDATA[ Guo, T. J. F., Meng, Y., Kim, S., Machiri, T., Miscampbell, A., Lau, K. S. K., Gibbons, C., Penton, M. R., Lee, C. P. S., Li, I. T. S., Goobie, G. C., Halayko, A. J., Ryerson, C. J., Carlsten, C., Ryu, M. H., Osei, E. T. ]]></dc:creator>
<dc:date>2026-09-09</dc:date>
<dc:identifier>doi:10.64898/2026.09.04.749305</dc:identifier>
<dc:title><![CDATA[Characterization of tri-culture alveolar-like organoids to study fibrotic lung diseases]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-09</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.03.749104v1?rss=1">
<title>
<![CDATA[
The microtubule-associated proteins CKAP2 and its paralog CKAP2-Like control ciliogenesis in human cells 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.03.749104v1?rss=1
</link>
<description><![CDATA[
Ciliogenesis is an evolutionarily conserved process that leads to the assembly of cilia. This process relies on microtubule-associated proteins (MAPs) to regulate axonemal microtubule dynamics. Misregulation of MAPs often leads to changes in ciliary homeostasis, contributing to numerous ciliopathies. Although CKAP2 and CKAP2-Like are best known for regulating microtubule dynamics during cell division, they are also components of ciliary organelles. Notably, CKAP2 overexpression promotes chromosomal instability and cancer, whereas CKAP2-Like deficiency causes Filippi syndrome, a developmental disorder with clinical features overlapping those of ciliopathies. How both MAPs operate at primary cilia remains poorly understood. Here, we identify both MAPs as axonemal components of motile and primary cilia in human cells. We find that CKAP2-positive cilia are linked to cell cycle progression and that the conserved intrinsically disordered microtubule-binding domain of CKAP2, which is essential for microtubule polymerization and stabilization, is required for its ciliary localization. Unexpectedly, CRISPR-mediated loss of either paralog results in elongated cilia without affecting ciliogenesis, accompanied by increased ciliary enrichment of the remaining paralog and impaired Gli2 accumulation at the ciliary tip. In contrast, simultaneous deletion of both MAPs suppresses ciliogenesis and has minimal effect on the ciliary length as compared to wild-type levels. These findings uncover that CKAP2 and CKAP2-Like are axonemal MAPs that contribute to ciliogenesis, partially compensating for each other in human cells.
]]></description>
<dc:creator><![CDATA[ Bechstedt, S., Da Silva, L. E., Campolina-Silva, G., Afani, J., Belleannee, C. ]]></dc:creator>
<dc:date>2026-09-08</dc:date>
<dc:identifier>doi:10.64898/2026.09.03.749104</dc:identifier>
<dc:title><![CDATA[The microtubule-associated proteins CKAP2 and its paralog CKAP2-Like control ciliogenesis in human cells]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-08</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
