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Preprint

Preprint: explore 500 source-linked works published from 2026 to 2026, with original documents and citations.

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Includes records with this source-supplied label or an explicit phrase match in their metadata. Matches indicate a mention, not proof that a paper uses a method or tests a material. Source versions are consolidated by DOI.

Sources: biorxiv. Collection updated 2026-09-15. Counts describe this index, not the complete source archives.

Profiling Siglec-7 and Siglec-9 ligands across the LuCaP PDX series: Implications for glyco-immune checkpoint inhibition in advanced prostate cancer

Advanced prostate cancer exhibits profound cellular and molecular heterogeneity, frequently becoming resistant to androgen receptor (AR) targeting through lineage plasticity and neuroendocrine differentiation. Immunotherapies have shown limited efficacy in prostate cancer, largely due to its immunosuppressive tumour microenvironment. Hypersialylation contributes to immune evasion by engaging sialic acid-binding immunoglobulin-like lectins (Siglecs) on immune cells, forming glyco-immune checkpoints. Although this pathway represents a promising therapeutic target, the distribution of Siglec ligands across diverse prostate cancer phenotypes and their response to standard-of-care hormone therapy remain poorly understood. Here, we utilised high-affinity engineered sialoglycan-binding reagents (HYDRA) to perform comprehensive immunohistochemical profiling of Siglec-7 and Siglec-9 ligands across a panel of 40 Washington Carcinoma of the Prostate (LuCaP) patient-derived xenograft (PDX) models. Ligand expression was evaluated in relation to AR status and neuroendocrine phenotype. To determine the impact of androgen deprivation on the tumour glycome, ligand expression was compared between matched PDX lines grown in intact and castrated mice. Our findings reveal widespread but heterogeneous expression of Siglec-7 and Siglec-9 ligands across the LuCaP cohort. Expression levels were comparable between AR-positive adenocarcinoma models and AR-negative neuroendocrine variants, demonstrating that this glyco-immune checkpoint is maintained across distinct prostate cancer lineages. Under castration conditions, glycan remodelling occurred in a model-dependent manner. A subset of PDX models exhibited reduced Siglec ligand expression following castration, suggesting partial AR dependence. In contrast, other models displayed increased ligand expression, consistent with adaptive immune evasion in response to therapeutic stress, while a third group remained largely unchanged. Collectively, our study demonstrates that the Siglec-7/9 glyco-immune checkpoint axis is broadly maintained across the spectrum of prostate cancer lineage plasticity but is dynamically remodelled by androgen deprivation in a patient-specific manner. These findings support the sialoglycan-Siglec axis as a lineage-independent immunotherapeutic target and suggest that strategies aimed at disrupting Siglec-mediated immune suppression, such as tumour desialylation, may be most effective when combined with androgen deprivation therapy to enhance anti-tumour immunity.

cancer biology

Geometric causes of species rarity

Understanding the limits of species distributions is a central objective of biogeography and macroecology and has become increasingly important as climate change drives rapid shifts in geographic ranges. Species range sizes follow a highly skewed frequency distribution, with most species occupying ranges orders of magnitude smaller than those of the most widespread species. Range sizes also exhibit pronounced geographic patterns, with small-ranged species concentrated near continental margins and other geographic boundaries. No universally accepted explanation has been proposed for these patterns. Here we present a simple geometric model showing that species range size patterns emerge from the random placement of dispersal barriers within continental domains. The model predicts both the observed frequency distribution and the spatial distribution of range sizes across amphibians, birds, and mammals. It therefore provides a first-order explanation for global patterns of species rarity and can be refined by incorporating elevational barriers and spatial variation in species richness. Our findings suggest that species range size is constrained by the geometry of dispersal barriers and the geographic domain, with proximity to domain boundaries acting as a primary determinant of species rarity. These results have important implications for understanding species' evolutionary potential and vulnerability to extinction.

ecology

Membrane voltage and connexin expression work together to enhance tumor growth and metastasis in cancer

There is strong evidence of tumors manipulating their resting membrane potential (Vmem). While most fully-differentiated cells have a Vmem of roughly -70mV, tumor cells are generally depolarized, with Vmem {approx}-30mV, which more closely resembles the Vmem of stem cells. This is often believed to serve the purpose of accelerating the cell cycle and hence advantaging tumor proliferation. But when the tumor becomes invasive, its cells sometimes revert to a hyperpolarized Vmem with no obvious reason why. Separately, it is well accepted that solid tumors that are not yet invasive greatly underexpress connexins relative to healthy tissue; connexins, for our purpose, form gap junctions (GJs), small connecting tubes between nearby cells. Tumors that are invasive, by contrast, overexpress connexins. There is very little explanation for the paradox that connexins are first underexpressed and then overexpressed. However, it has long been known that Vmem electrically gates GJs; specifically, that homotypic GJs conduct best when the two cells they connect have a similar Vmem. Our in-silico model results explain this phenomenon, showing that when considered together, tumors' electrical and connexin-expression behaviors form a unified and effective strategy to control communication between the tumor and its healthy neighbor cells. This has implications for the emerging field of cancer bioelectrics, potentially leading to more precisely-targeted therapies.

cancer biology

Systems-level proteomic reprogramming reveals mitochondrial restoration and inhibition of Rho GTPase-mediated cytoskeletal and inflammatory signaling in CKD

Chronic kidney disease (CKD) is a progressive disorder characterized by metabolic dysfunction, mitochondrial impairment, oxidative stress, and chronic inflammation, ultimately leading to irreversible renal damage. Despite advances in understanding CKD pathophysiology, effective therapies targeting these interconnected molecular processes remain limited. In this study, we performed a comprehensive data-independent acquisition (DIA)-based proteomic analysis to investigate the molecular alterations associated with CKD and to evaluate the therapeutic impact of DVA treatment. Using a CKD model with three treatment conditions (DVA, KY, and DVA+KY) alongside disease and healthy controls, we quantified global proteomic changes and applied statistical filtering (fold change [≥]2, p [≤]0.05) followed by K-means clustering (k=10). Distinct protein clusters revealed bidirectional modulation upon DVA treatment. Notably, Cluster 1 comprised proteins downregulated in CKD but significantly restored following DVA administration, while Cluster 2 included proteins elevated in CKD that were suppressed by DVA. Pathway enrichment and network analyses demonstrated that Cluster 1 proteins were predominantly associated with mitochondrial function, oxidative phosphorylation, and metabolic processes, whereas Cluster 2 proteins were enriched in immune signaling, oxidative stress, cytoskeletal remodeling, and proteostasis pathways. At the molecular level, DVA treatment restored key mitochondrial and metabolic regulators, including components of the electron transport chain (e.g., COX5A, NDUFS5, SDHB) and redox homeostasis proteins, indicating recovery of cellular bioenergetics. Concurrently, DVA suppressed inflammatory mediators (STAT2, IFI47, GBP2), oxidative stress-related proteins (CYBB, PRDX5), and cytoskeletal regulators linked to renal injury (ARHGEF12, FMNL2). Network and Reactome analyses further confirmed coordinated modulation of interconnected biological systems rather than isolated protein changes. Collectively, our findings demonstrate that DVA exerts a dual therapeutic effect by restoring essential mitochondrial and metabolic pathways while simultaneously suppressing inflammation, oxidative stress, and cytoskeletal dysregulation in CKD. This systems-level proteomic reprogramming highlights DVA as a promising candidate for CKD intervention and provides mechanistic insights into disease progression and therapeutic targeting.

systems biology

Shared neurogenesis onset is sufficient to explain bilateral matching in the vertebrate retina

Bilateral symmetry is a hallmark of many paired organs and often essential for optimal functionality. The vertebrate eyes are a prominent example of this, as the matched development of the two retinas is required for accurate visual processing. While macroscopic aspects of symmetry emergence across systems have been investigated, how bilateral matching is maintained once cells start to differentiate remains less understood. Here we address this question using the zebrafish retina as a model to follow neurogenic programs in vivo at single-cell resolution. We perform quantitative 3D live imaging of both retinas simultaneously and directly compare neurogenesis onset and propagation within and across embryos. We find that neurogenic waves initiate at the retinal poles and progress towards the mid-retina in a conserved spatiotemporal pattern. Within embryos, the two eyes exhibit highly similar neurogenesis dynamics when it comes to timing of neurogenesis onset, cell number increase, and spatial wave progression. Across embryos, however, variability is larger. While these observations hint at active inter-retinal coordination, a stochastic model predicts that a shared onset of neurogenesis can be sufficient to explain bilateral matching. Targeted genetic perturbation experiments support this prediction. We find that altering wave propagation affects patterning but not bilateral similarity. Disrupting neurogenesis onset timing, however, reduces bilateral symmetry between eyes. Thus, the combination of experiment and theory identifies synchronized neurogenesis onset as a key determinant of bilateral symmetry, revealing a minimal principle for how reproducible development of paired organs can emerge from stochastic processes.

developmental biology

Living multicellular systems induce decodable spatial patterns in bacterial collectives

Living systems continuously modify their environments through chemical, mechanical, metabolic and bioelectrical activity. Whether a presence of a multicellular system can be encoded into the emergent spatial organization of another living collective in a distributed and decodable way is unknown. Here we show that motile Bacillus subtilis populations reorganize their spatial and ionic collective states in response to nearby Xenopus embryos and Xenobots. The bacteria in a liquid culture formed autonomous motility-dependent patterns that were redirected by living targets into attraction halos, which tracked target position at a distance. Extracellular levels of potassium amplified attraction, altered local potassium dynamics, and coupled target presence to global pattern complexity. Self-supervised machine learning further identified distributed bacterial spatial signatures predictive of Xenopus embryo vs. Xenobot presence at a distance from the target. Together, these findings suggest that bacterial collectives can encode information about the state of other biota in their environment, revealing a previously unrecognized form of inter-kingdom interaction between living morphogenetic systems.

systems biology

SARAF represses the mild hypothermia response through the regulation of JUN

The mild hypothermia response (MHR) is a conserved mammalian cytoprotective program activated upon exposure to mild hypothermia (32 degrees C) that contributes to the neuroprotective effects of therapeutic hypothermia following hypoxic injury. Although rapid changes in intracellular calcium occur upon cooling, the mechanisms linking calcium dynamics to the activation of core MHR factors such as SP1 and RBM3 remain incompletely defined. In this study, we used siRNA-mediated knockdown (KD) of candidate regulators in conjunction with novel mild hypothermia indicator (MHI) reporters to identify upstream modulators of MHR-associated transcription. We identify SARAF, a negative regulator of store-operated calcium entry (SOCE), as a repressor of both SP1 and RBM3 under normothermic conditions. SARAF depletion is associated with increased intracellular calcium release and enhanced SP1- and RBM3-linked transcriptional outputs. We identify JUN as an important downstream factor mediating SARAF depletion-dependent de-repression of the MHR and demonstrate that it undergoes activation rapidly upon cooling. Finally, SARAF depletion conferred significant cytoprotection against hypoxia-induced early apoptosis. Collectively, these findings establish SARAF as an upstream regulator of MHR-associated transcription and provide a functional link between cold-induced intracellular calcium dynamics and the induction of core MHR effectors.

molecular biology

Clonal memory in human embryonic stem cells biases fate potential during endoderm differentiation

Cell fate decisions during development are shaped not only by extrinsic signals but also by heritable intrinsic states passed on across cell division. The extent to which this phenomenon, termed clonal memory, can explain the persistent heterogeneity observed from directed differentiation of human embryonic stem cells is unclear. Here, we combine lineage tracing with single-cell transcriptomics and chromatin accessibility profiling to track clonal behaviour across human embryonic stem cell differentiation towards definitive endoderm. Using a lentiviral barcoding system coupled with a split-well sampling strategy, we find that clonally related cells exhibit reproducible, probabilistic fate outcomes that cannot be explained by signalling environment alone. Fate-biased clones are transcriptionally indistinguishable at the pluripotent stage yet display distinct chromatin accessibility landscapes at lineage-specific cis-regulatory elements. Pre-existing accessibility at these lineage-specific regulatory regions distinguish clones that undergo successful endoderm differentiation from those that generate off-target mesoderm derivatives. Together, these findings provide an explanation for how off-target populations arise during directed differentiation, identifying heritable chromatin states within pluripotent cultures as a source of variability relevant to stem cell-derived in vitro models and cell therapies.

developmental biology

High-dimensional HIV-1 quasispecies modeling guides escape-proof antibody design

Rapidly evolving viruses form diverse quasispecies that enable escape from immune responses and treatments. For example, HIV-1 can rebound within weeks of broadly neutralizing antibody (bNAb) treatment through the outgrowth of high-fitness escape mutants in the quasispecies or the evolution of new escape variants. Most existing models of viral dynamics consider only a small number of viral variants and either assume arbitrary mutant fitness distributions or require extensive fitting to sparse clinical data. Here, we develop a high-dimensional HIV-1 quasispecies model that captures the dynamics of millions of viral strains and parameterize this using in silico binding affinity predictions. Without fitting to experimental data, the model qualitatively reproduces viral rebound following bNAb treatment. Lower-dimensional model projections recover these dynamics only when informed by features derived from the high-dimensional model. Finally, we use the model to develop a quasispecies-based framework for antibody optimization and identify antibodies predicted to effectively suppress viremia. Together, our results demonstrate that integrating mechanistic genotype-phenotype maps with high-dimensional quasispecies models provides unprecedented insights into viral evolution.

systems biology

A novel target associated with senescence and inflammatory signaling in human intervertebral disc degeneration

Background Intervertebral disc degeneration (IDD) is a leading cause of chronic low back pain and disability worldwide, affecting most individuals over 50 years of age. Despite its prevalence, no disease-modifying therapies exist, and current interventions are limited to reducing pain. Cellular senescence and the associated secretory phenotype (SASP) have been increasingly recognized as major drivers of disc matrix degradation and inflammation. However, the upstream molecular mechanisms that lead to IDD degeneration are still unknown. Connexin 43 (Cx43), a gap junction protein implicated in progression of age-related diseases, has emerged as a key regulator of cellular senescence and inflammatory signalling in musculoskeletal tissues. Methods Human primary cells were isolated from intervertebral disc samples obtained from patients classified into clinically meaningful groups: healthy controls, chronic/mechanical degeneration (DDD, ADJ, ASD), and acute/inflammatory event (herniated nucleus pulposus, HNP). Cx43 expression was assessed by qPCR and Western blotting. Cellular senescence was evaluated through SA-{beta}-gal staining and analysis of p53/p21 expression. SASP factors and EMT-related markers were measured by qPCR. Protein expression was quantified by immunoblotting across different age groups and degeneration grades. Results In this current study Cx43, was identified as the most abundant connexin isoform in human intervertebral discs, showing a progressive increase in expression with age and disc degeneration. Also, high Cx43 expression correlated with increased expression of the senescent markers p53 and p21 and increased SA-{beta}-gal activity. Besides, increased expression of EMT-related and differentiation markers has been correlated with high Cx43 levels in human IDD samples, consistent with fibrotic remodeling processes. Conclusions These findings identify aberrant upregulation of Cx43 signaling as a potential mechanistic link between intervertebral disc cellular senescence and extracellular matrix degradation, with the ensuing inflammatory response, representing a novel potential therapeutic target to modulate senescence-driven pathogenesis and modulate IDD progression.

molecular biology

Cholesterol and p53 promote senescence and systemic fibrosis in metabolic dysfunction-associated steatohepatitis

Background & aims: TP53 (p53) coordinates diverse cellular stress response programmes including pro-survival activities, senescence, and cell death. During tissue damage, p53 can shape both the local cellular response to injury, including the fibrotic response, and influence distal organ biology. Fibrosis in the liver is a major driver of hepatocellular carcinoma (HCC) risk within metabolic dysfunction-associated steatohepatitis (MASH). It is also an important determinant of dysfunction in multiple distal tissues including the kidneys, lungs, and heart. Despite significant clinical burden, our understanding of the molecular determinants of fibrotic MASH and its relationship to multiorgan fibrosis remain incomplete. Here, we investigate local and systemic effects of hepatocellular p53 activity and cholesterol during MASH development, with implications for disease prevention. Methods: This study utilised a genetic model of stabilised p53, diet-induced MASH models with varying cholesterol compositions, and an in vitro obesogenic system to investigate p53 activity during liver disease development. Non-invasive imaging and histopathological analyses were employed to monitor p53 activity, MASH, and multiorgan fibrosis in vivo. Complementary approaches, including in vitro human multicomponent liver spheroids, cytokine arrays, and analyses of human MASH transcriptomic and proteomic datasets, were used to examine molecular drivers and patient relevance. Results: Using an inducible mouse model of MDM2 E3 ubiquitin ligase deficiency to stabilise p53, we report that hepatocellular MDM2 E3 loss results in progressive fibrotic damage, robust hepatocellular expression of the p53 target gene CDKN1A/p21 (p21),and induces p21 and fibrosis in the kidneys of male mice in a sex-specific manner. In diet-induced MASH, we observe cholesterol and p53-dependent development of liver fibrosis, high expression of hepatocellular p21, and induction of p21 and fibrosis in the kidneys of male mice-reminiscent of features observed in MDM2 E3-deficient mice. We also observe fibrosis in the lungs and heart of male MASH mice. Both a cholesterol-free obesogenic diet and liver-specific loss of p53 mitigate hepatic fibrosis and systemic induction of p21 and fibrosis. Mechanistically, p53 induces hepatic expression of senescence-associated secretory phenotype (SASP) factors, including GDF15, in vivo. A human multicomponent LiverACE spheroid model showed a concordant trend towards increased GDF15 protein abundance under steatotic stress, while in humans, elevated circulating GDF15 levels in advanced MASH correlate with increased TNFRSF1A and EPHA2, circulating markers linked to kidney injury. Conclusions: Our work identifies undue p53 activity within the liver as a driver of multiorgan fibrosis in a sex-specific manner, affecting male but not female mice. We implicate cholesterol in promoting this pro-fibrotic environment in vivo and highlight circulating factors that could identify at-risk patients for multiorgan fibrosis in MASH.

cancer biology

Vitamin D counters bone invasion by mammary cancer through inhibition of inflammation and epithelial-to-mesenchymal transition

Vitamin D deficiency is associated with poor outcome in several cancers in humans, and administration of vitamin D or analogs has been shown to decrease tumor progression and metastasis in animal mammary cancer models. We previously demonstrated significant acceleration of carcinogenesis in vitamin D-deficient mouse mammary tumor virus-polyoma middle T (MMTV-PyMT) mammary cancer model as well as of its spontaneous metastasis to lungs. While vitamin D also plays a role in skeletal metastasis, detailed mechanisms of its promotion of bone invasion and metastatic events are not completely elucidated. In the present study we used tibially-injected MMTV-PyMT mammary tumor cells to analyse how dietary-induced vitamin D deficiency in non-immunodeficient FVB mice accelerates bone invasion. Mechanistically, we observed vitamin D deficiency to increase pro-inflammation cytokines and nestin expression in internal bone surface and marrow, and to increase epithelial-to-mesenchymal transition (EMT) through Zeb1 transcription factor. In vitro, treatment of MMTV-PyMT tumor cells with CXCL12 was observed to stimulate Zeb1 expression, and this effect was efficiently countered by 1,25(OH)2D treatment. Analysis of cytokines in MMTV-PyMT mammary tumor cells in vitro showed significant reduction in several pro-inflammatory cytokines with 1,25(OH)2D treatment (GM-CSF, ICAM-1, IL-1ra, IP-10, JE, MCP-5, MIP-1, MIP-1{beta}, MIP-2, RANTES and CXCL12), a crucial observation in view of the current evidence that inflammation is one of the hallmarks of cancer. Furthermore, vitamin D repleteness is associated with very high expression of Socs1 (suppressor of cytokine signalling 1), an inhibitor of JAK/STAT pathway which prevents excessive inflammatory responses and has a tumor-suppressive role. These findings provide a strong link between vitamin D deficiency and acceleration of inflammation-driven bone invasion, and nestin and EMT. The evidence suggests that vitamin D-repleteness in breast cancer patients could enhance the efficacy of co-administered therapies in preventing invasion of skeletal sites.

cancer biology

Patterned alginate hydrogel spatially guides collagen fibrillogenesis, viscoelasticity and endothelial cell invasion

Angiogenesis following injury has been shown to be driven by fibrillar proteins of the extracellular matrix (ECM), such as collagen. However, the use of protein-based biomaterials presents some challenges, such as uncontrolled degradation and limited tuneability. We demonstrate how to create patterned interpenetrating networks (IPNs) based on covalently crosslinked alginate and physically crosslinked collagen that provide suitable mechanical properties to support migration of endothelial cells (ECs) in a spatially controlled manner. Low molecular weight alginate is functionalized with norbornene (N) or tetrazine (T), which enables two independent covalent crosslinking methods: UV-mediated and degradable crosslinks with matrix metalloproteinase (MMP) sensitive peptides (Deg) and slower spontaneous N:T non-degradable crosslinks (noDeg). Using photolithography, patterns in degradation, collagen fibrillogenesis, microarchitecture and matrix viscoelasticity are created. The potential of such 3D patterned alginate-collagen (Alg-Col) IPNs to spatially guide EC invasion and proliferation was tested in a microfluidics platform resembling an early healing setting. Only regions combining collagen fibrillogenesis, alginate degradability and viscoelasticity demonstrated EC cell invasion similar to the ones found in vivo following injury. The 3D patterned Alg-Col IPNs are compatible with microfluidics, offer an strategy to widen the applications of protein-based hydrogels and present a versatile platform for tissue engineering and disease modeling.

bioengineering

SOX2 can associate with chromatin directly by binding to DNA or indirectly via association with other chromatin-bound proteins

It is widely assumed that SOX2 regulates gene expression and facilitates the opening of chromatin by binding directly at SOX motifs. To test this assumption, we created a SOX2 DNA binding mutant to determine whether other regions of SOX2 contribute to gene target specificity. When exogenously expressed in cells, this SOX2 mutant [SOX2(G76P)], like elevated unmodified SOX2, dramatically alters the transcriptome, but it does so by regulating vastly different gene sets and gene networks than SOX2. Consistent with their differential effects on the transcriptome, ChIP-seq analysis demonstrates that SOX2 and SOX2(G76P) associate primarily with different genomic loci, and motif analysis indicates that SOX2 binds primarily at SOX motifs, whereas SOX2(G76P) associates with chromatin at non-SOX motifs, including AP-1 motifs. Additionally, ATAC-seq analysis indicates that SOX2 substantially increases chromatin accessibility, but SOX2(G76P) does not. The findings presented lead to the conclusion that SOX2(G76P) associates with chromatin indirectly by a "piggyback" mechanism through its association with other chromatin-associated proteins, including AP-1 complexes. Remarkably, we also show that SOX2 and SOX2(G76P) each associate with a subset of the same gene loci that contain several different DNA motifs, including AP-1 motifs, but no high confidence SOX motifs. Overall, our findings provide new perspectives on SOX2 and lead to two important conclusions: 1) selection of gene targets by SOX2 is not solely determined by its DNA binding domain, and 2) SOX2 not only associates with chromatin directly by binding to SOX motifs but can also associate with a subset of gene loci indirectly through its association with other chromatin-associated proteins.

molecular biology

An ecological model of masting reproduction matches empirical dynamics

Masting, characterized by highly variable, synchronized, and intermittent seed or fruit production, represents a common reproductive strategy among perennial plants and has profound ecological consequences. Resource provisioning and pollen limitation have long been viewed as central physiological mechanisms underlying this strategy, recent empirical evidence also highlights the role of weather cues in initiating and synchronizing reproductive effort. Drawing on mechanisms that drive periodicity in disease dynamics, this study proposes an alternative proximate mechanism for masting. We develop and analyze a stage-structured population growth model in which developmental delays create population-level cycles, and demographic stochasticity adds individual-level variation; together, yielding masting-like patterns. We compare the behaviour of this novel model with that of the widely used resource budget model and empirically observed patterns of masting in perennial plants. To quantify and compare model outputs and empirical observations, we employ three continuous metrics of masting that capture volatility, synchrony, and periodicity. Our study provides an alternative proximate mechanism for masting. Comparison of this novel mechanism and the established resource-budget model to empirical time-series reveals that both represent realistic yet distinct forms of masting reproduction. Together, these models provide a foundation for further exploration of the conditions under which this reproductive strategy can evolve. Beyond masting, our results highlight the general importance of life-history timing and demographic stochasticity in shaping population ecology.

ecology

Multiscale spatial analysis implicates chromosomal metaloops in gene patterning across the Drosophila brain

Scores of chromosome-scale loops, or metaloops, arise in the Drosophila brain, but their spatial organization and relationship to neural gene expression patterns remain unclear. Here, we used multiplexed Optical Reconstruction of Chromatin Architecture (ORCA) to examine the multiscale spatial organization of metaloops in cross-sections of 100s of larval and adult Drosophila brains. We find metaloops form preferentially in the central regions of the brain, where they nucleate the formation of metadomains, characterized by the intermingling of distal topologically associating domains (TADs). At the sub-cellular scale, metaloops tend to arise towards the nuclear center, and multiple metaloops in the same cell have a preference to form hubs (3 or more contacts). Each brain nucleus generally harbors only a few loops or hubs. An in-depth analysis of the hub centered on DIP-epsilon, a synaptic wiring gene, identified a three-way metadomain that brings together the DIP-epsilon TAD; a distal TAD carrying a paralog of DIP-epsilon, DIP-zeta; and a putative regulatory TAD, across 3 Mb. This metadomain adopts distinct conformations depending on gene expression; cells expressing DIP-epsilon or DIP-zeta show preferential interactions between the TAD carrying the corresponding gene and the putative regulatory TAD. We posit that the neuron-specific formation of different subsets of metadomains might coordinate the expression of diverse combinations of synaptic wiring genes underlying complex brain architecture.

molecular biology

Stomatal and xylem plasticity, not growth rate, determines white spruce resilience to warmer and drier climates

In a warmer and drier climate, forest productivity will depend on trees' ability to maintain carbon uptake and hydraulic function. Whether fast-growing genotypes of boreal conifers are more vulnerable to combined climatic stress remains uncertain. Using a full-factorial field experiment, we investigated how progressive soil drying combined with extended warming affects growth, xylem development, and photosynthesis in two Picea glauca families with contrasting growth strategies. Rainout structures first reduced soil moisture from 25% to 18%, followed by a +5{degrees}C warming treatment applied using infrared heaters. During the warmest and driest period in August, air temperature reached 34.5{degrees}C in the warmed plots, while soil moisture declined to a low of 15% in the combined rainout and warming treatment. Contrary to expectations, both fast- and slow-growing white spruce families exhibited similar resilience to concurrent warming and soil drying. This finding challenges the prevailing theory that faster growth increases vulnerability to climatic stress. Despite an approximately 50% reduction in rainfall, pre-dawn water potential remained above -0.5 MPa across treatments, reflecting that seedlings were able to avoid hydraulic stress. Although the fast-growing family maintained greater height and diameter growth compared to the slow-growing family, both exhibited similar physiological and anatomical responses to warming. Warming decreased stomatal conductance, which increased intrinsic water-use efficiency. Latewood xylem traits related to hydraulic efficiency were also reduced under warming. Together, these coordinated stomatal and xylem adjustments decreased water loss and protected hydraulic function, enabling both families to maintain high photosynthesis and growth under simulated climate conditions. Overall, white spruce exhibits strong phenotypic plasticity, supporting intraspecific resilience to moderate warming and soil drying representative of projected 21st-century summer conditions for central and eastern Canada.

plant biology

Functional Contribution of Multienzyme Glucosome Condensates to Cellular Redox Homeostasis in Cancer Cells

Glucosomes are liquid-liquid phase-separated condensates observed in human cells, formed by phosphofructokinase and other rate-determining enzymes in glycolysis and gluconeogenesis. While glucosomes are spatially formed into small-, medium-, and large-sized assemblies in cancer cells, medium-sized glucosomes are functionally characterized to shunt glucose flux to the pentose phosphate pathway (PPP). As the PPP is the primary pathway responsible for maintaining cytosolic NADPH levels during oxidative stress, we hypothesize that medium-sized glucosomes regulate cellular redox homeostasis through the promotion of the PPP. In this work, we started treating Hs578T cells with hydrogen peroxide (H2O2) to evaluate how glucosomes respond to redox perturbation. High-content imaging demonstrated that H2O2 significantly promotes medium-sized glucosomes at both single-cell and population levels. The extracellular acidification rate by Seahorse extracellular flux analysis then corroborated that H2O2 effectively diverts glycolytic flux to the PPP through the upregulation of medium-sized glucosomes. We then investigated the glutathione redox cycle as a potential mechanistic link between medium-sized glucosomes and H2O2 detoxification. Treatment with oxidized glutathione (GSSG), but not reduced glutathione (GSH), markedly increased the population of cells showing medium-sized glucosomes. Moreover, shRNA-mediated knockdown of glutathione reductase, which converts GSSG to GSH at the expense of NADPH, attenuated H2O2-induced glucosome formation in Hs578T cells. Collectively, we demonstrate that glucosome-mediated metabolic reprogramming couples glucose metabolism to the glutathione redox cycle to facilitate H2O2 detoxification, thereby establishing the functional role of glucosomes in cellular redox homeostasis.

cell biology
Compare source metadata on this page
WorkPublishedSource identifierSource
Profiling Siglec-7 and Siglec-9 ligands across the LuCaP PDX series: Implications for glyco-immune checkpoint inhibition in advanced prostate cancer2026-09-0310.64898/2026.09.02.748828v1biorxiv
Geometric causes of species rarity2026-09-0310.64898/2026.09.02.748835v1biorxiv
Membrane voltage and connexin expression work together to enhance tumor growth and metastasis in cancer2026-09-0310.64898/2026.09.02.748840v1biorxiv
Systems-level proteomic reprogramming reveals mitochondrial restoration and inhibition of Rho GTPase-mediated cytoskeletal and inflammatory signaling in CKD2026-09-0310.64898/2026.09.02.748845v1biorxiv
Shared neurogenesis onset is sufficient to explain bilateral matching in the vertebrate retina2026-09-0310.64898/2026.09.02.748850v1biorxiv
Living multicellular systems induce decodable spatial patterns in bacterial collectives2026-09-0310.64898/2026.09.02.748853v1biorxiv
SARAF represses the mild hypothermia response through the regulation of JUN2026-09-0310.64898/2026.09.02.748854v1biorxiv
Clonal memory in human embryonic stem cells biases fate potential during endoderm differentiation2026-09-0310.64898/2026.09.02.748863v1biorxiv
High-dimensional HIV-1 quasispecies modeling guides escape-proof antibody design2026-09-0310.64898/2026.09.02.748882v1biorxiv
A novel target associated with senescence and inflammatory signaling in human intervertebral disc degeneration2026-09-0310.64898/2026.09.02.748888v1biorxiv
Cholesterol and p53 promote senescence and systemic fibrosis in metabolic dysfunction-associated steatohepatitis2026-09-0310.64898/2026.09.02.748892v1biorxiv
Vitamin D counters bone invasion by mammary cancer through inhibition of inflammation and epithelial-to-mesenchymal transition2026-09-0310.64898/2026.09.02.748895v1biorxiv
Patterned alginate hydrogel spatially guides collagen fibrillogenesis, viscoelasticity and endothelial cell invasion2026-09-0310.64898/2026.09.02.748900v1biorxiv
SOX2 can associate with chromatin directly by binding to DNA or indirectly via association with other chromatin-bound proteins2026-09-0310.64898/2026.09.02.748901v1biorxiv
An ecological model of masting reproduction matches empirical dynamics2026-09-0310.64898/2026.09.02.748907v1biorxiv
Multiscale spatial analysis implicates chromosomal metaloops in gene patterning across the Drosophila brain2026-09-0310.64898/2026.09.02.748911v1biorxiv
Stomatal and xylem plasticity, not growth rate, determines white spruce resilience to warmer and drier climates2026-09-0310.64898/2026.09.02.748918v1biorxiv
Functional Contribution of Multienzyme Glucosome Condensates to Cellular Redox Homeostasis in Cancer Cells2026-09-0310.64898/2026.09.02.748920v1biorxiv

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