Biology subjects

Zhang, S.

Publications and source records attributed to Zhang, S..

At least 343 records · Page 19Linked to original sources

bioRxiv2025

Effects of C3aR activated mast cells in eosinophilic esophagitis

BackgroundEosinophilic esophagitis is a chronic food induced allergic inflammatory disease of the esophagus. Eosinophil-depleting antibodies have not shown significant improvement in clinical symptoms, which has turned attention to mast cells. These cells also accumulate in the esophagus of EoE at levels that correlate with symptoms, demonstrate extensive activation including degranulation, correlate and remain elevated and poised for reactivation even in EoE patients in remission as defined by reduced eosinophil levels. Herein, we examine a mechanism of mast cell activation in EoE. MethodsEsophageal mast cell degranulation was quantitated by CD63 expression by flow cytometry. Mast cell degranulation activity of esophageal biopsies was examined employing a bioassay with human CD34 progenitor cell derived primary human mast cells. Bulk and single cell RNA sequencing data of the esophagus were analyzed for complement dysregulation and mast cell properties as a function of disease state. Human esophageal biopsies were stained for C3 and analyzed for C3a and C3 protein content. Primary human mast cells and fibroblasts were further interrogated by flow cytometry, immunostaining, and RNA sequencing. ResultsEsophageal mast cells demonstrated increased CD63 expression, a measure of degranulation, in subjects with active compared with remission EoE. Esophageal biopsy lysates induced mast cell degranulation. Analysis of esophageal bulk RNA sequencing data demonstrated that the mast cell marker CPA3 strongly correlated with C3AR1. Accordingly, the level of C3a receptor on esophageal mast cells was proportional with CD63 expression. C3AR1 expression was increased in the fibrostenotic endoscopic phenotype compared to normal appearing active EoE patients. Esophageal biopsies were notably enriched in the expression of multiple complement genes (including C3AR1, C3, CFB, C1QA, C1QB, and C1QC) some of which were increased in active vs remission EoE (C3AR1, CFB, C1QA, C1QB, and C1QC). Single cell RNA (scRNA) sequencing data revealed enrichment of C3 in fibroblasts at levels higher in EoE compared with non-EoE controls. The ratio of C3a/C3 protein levels in the esophagus was increased in EoE compared to control. Mast cells and fibroblasts have increased proximity in EoE compared with non-EoE control subjects. Additionally, C3a stimulated mast cells to express increased CD117 and release multiple EoE-relevant cytokines including fibroblast active mediators including granzyme B, which is enriched in esophageal mast cells. ConclusionTaken together, our findings present evidence for the interplay of mast cells and fibroblasts via C3a in the pathogenesis of EoE.

immunology↗

bioRxiv2025

A First-in-Class Therapy Targeting Transcription-Replication Conflicts Drives Synthetic Lethality in Homologous Recombination Deficient Cancers

Hidden beneath the layer of tumor malignancy lies unchecked proliferation driven by hyperactive transcription, which fosters the formation of RNA:DNA hybrids. These structural intermediates precipitate collisions between the transcription and replication machineries. Central to mitigating this genomic threat is interleukin enhancer-binding factor 2 (ILF2), which orchestrates the recruitment of RNA:DNA helicases to resolve R-loops and, in doing so, reveals cancer cells dependency on stress-mitigating mechanisms to avert genome catastrophe. Our discovery of Molephantin and its lead derivative, NYH0002 is the outcome of delineating ILF2s function. NYH002 exerts direct binding to the ILF2 complex and disrupts RNA:DNA helicase activity to elicit genome-wide DNA breakages. Tumors with elevated cyclin E and E2F1 expression are sensitive to NYH002, while those deficient in homologous recombination repair exhibit lethality. Collectively, these findings position ILF2 as a key regulator of R-loop homeostasis and reveal a therapeutic vulnerability that NYH002 exploits to suppress tumor malignancy.

cancer biology↗

bioRxiv2025

CNVPipe: An enhanced pipeline for accurate analysis of copy number variation from whole-genome sequencing

Copy number variations (CNVs) are critical contributors to the genetic architecture of complex diseases, yet many existing pipelines for whole-genome sequencing (WGS) data exhibit persistently high false discovery rates (FDR). Here, we introduce CNVPipe, an enhanced workflow that integrates widely used CNV-calling tools with a novel machine-learning framework to achieve lower FDR and higher sensitivity. CNVPipe also provides a specialised module for single-cell CNV analysis, featuring a new model that accurately estimates the ploidy of single cells to get integer copy number profile. Benchmark evaluations demonstrate that CNVPipe outperforms current pipelines in various genomic contexts. In addition to detecting recurrent CNVs in paediatric developmental disorders, CNVPipe enables large-scale functional genomics applications involving stem cell technologies. Moreover, its application to sparse single-cell DNA sequencing data provides a new aspect of research in cancer evolution. Collectively, these findings underscore the versatility and reliability of CNVPipe as a comprehensive solution for CNV detection in WGS-based research.

systems biology↗

bioRxiv2025

Energy trade-offs under fluctuating light govern bioenergetics and growth in Chlamydomonas reinhardtii

Rapidly changing light intensity is a natural challenge that photosynthetic organisms can tolerate. Regulatory mechanisms of light harvesting and alternative electron pathways are critical in dissipating and distributing energy under fluctuating light intensities (FL), but less is known about downstream metabolic regulations. Here, we compared the cellular responses of Chlamydomonas reinhardtii grown under FL to cells acclimated to constant high (HL) or low light (LL), either under high (2 %) or low (0.04 %) CO2. Under low CO2, the physiology of FL cells resembled HL cells and proteomics revealed an induction of the ATP consuming carbon-concentrating mechanism, and photorespiration particularly under FL. High CO2 promoted growth under FL, albeit by a lesser extent than under HL and led to higher ATP contents than under low CO2. To fuel ATP production under low CO2, cells upregulated mitochondrial respiration under FL, while enhanced cyclic electron flow and redox shuttling between intracellular compartments was most evident under FL and LL. Chloroplastic carbon metabolism rapidly responded to light changes, independent of CO2 availability, whereas metabolites associated with mitochondrial bioenergetics responded slower, and remained abundant under high CO2. The accumulation of enzymes involved in starch synthesis and breakdown under FL, together with the transient accumulation of hexoses and hexose phosphates, indicated that cells relied on sugars as a transient carbon pool to meet changing metabolic demands under FL. We conclude that the interplay between light intensity and CO2 availability drives critical energy trade-offs, balancing photoprotection, repair, and carbon allocation, that regulate growth under FL.

plant biology↗

bioRxiv2025

Cis-regulatory divergence and mate recognition in behaviourally isolated cricket species.

Cis-regulatory evolution has been implicated in morphological and physiological reproductive isolation, but its role in divergence of mate recognition behaviours is unknown. The latter are often the first, most powerful mating barriers to evolve during speciation, but understanding their genetics is hampered by the context-dependence of mate choice. We circumvented this challenge by using allele-specific expression analyses in F1 hybrids of sexually isolated cricket species, Teleogryllus oceanicus and T. commodus. Female crickets choose mating partners based on species-specific male advertisement songs, and we found extensive cis-regulatory divergence in neural tissues exposed to conspecific, heterospecific, or mixed-species songs. Genes with divergent expression were implicated in learning, memory and transcriptional regulation, and they showed elevated population genetic differentiation in allopatry but not sympatry. This implies that genes recruited during evolutionary divergence of mate recognition systems may be homogenised by gene flow. Regulatory divergence was asymmetrical between the two species; divergent selection on genes associated with female perception of male song was more prominent in T. oceanicus than in T. commodus. Evolved differences in gene regulation are strongly associated with sexual signal perception in closely related species, supporting the idea that rapid cis-regulatory evolution of mate recognition can accelerate speciation.

evolutionary biology↗

bioRxiv2025

The cryo-EM structure of mouse radial spoke 3 reveals a unique metabolic and regulatory hub in cilia

Cilia are complex, microtubule-based organelles that protrude from many eukaryotic cells and have important roles in sensing, signaling, and motility. Recent studies have revealed the atomic structures of many multi-component ciliary complexes, providing new insights into their mechanisms of action that are vital for cilias biological functions. However, little is known about the structure, proteome, and function of full-length radial spoke 3 (RS3), which is distinct from the structurally well-characterized RS1 and RS2. Radial spokes are conserved megadalton complexes that transmit mechanochemical signals from the central pair of microtubules to the dynein motors, thereby coordinating ciliary motility. Here, we combined cryo-electron microscopic single-particle reconstruction, cryo-electron tomography (cryo-ET), proteomic analysis, and computational modeling to determine the 3D structure and atomic model of RS3 from mouse respiratory cilia. Our structure reveals all protein components of RS3, including regulatory and metabolic enzymes, such as a protein kinase A subunit, adenylate kinases and malate dehydrogenases. We have confirmed the important role of adenylate kinase 7 in RS3 by cryo-ET analyses of respiratory cilia in AK7-deficient mice, which display primary ciliary dyskinesia. Our findings suggest that RS3 is an important regulatory hub and cluster of metabolic proteins that helps to maintain ATP at the levels required for sustained dynein motor activity and ciliary beating. This work advances our understanding of the structure and function of RS3 in ciliary motility and provides insights into the etiology of ciliopathies.

biophysics↗

bioRxiv2025

Spatial control of secretory vesicle targeting by the Ync13-Rga7-Rng10 complex during cytokinesis

Cytokinesis requires precise coordination of contractile-ring constriction, vesicle trafficking and fusion to the plasma membrane, and extracellular matrix assembly/remodeling at the cleavage furrow to ensure faithful cell division and maintain cell integrity. These processes and proteins involved are broadly conserved across eukaryotes, yet molecular mechanisms controlling the spatiotemporal pathways of membrane trafficking remain poorly understood. Here, using fission yeast genetics, microscopy, and in vitro binding assays, we identify a conserved module including the Munc13 protein Ync13, F-BAR protein Rga7, and coiled-coil protein Rng10 to be critical for precise and selective vesicle targeting during cytokinesis. The module specifically recruit the TRAPP-II but not exocyst complex to tether vesicles containing the glucan synthases Bgs4 and Ags1 along the cleavage furrow. Ync13 subsequently interacts with the SM protein Sec1 for vesicle fusion. Mutations in this pathway disrupt septum integrity and lead to cell lysis. Our work provides key insights into how membrane trafficking is tightly controlled to maintain cell integrity during cytokinesis.

cell biology↗

bioRxiv2025

Roles of the MO25 protein Pmo25 in contractile-ring stability and localization of the NDR kinase Sid2 during cytokinesis

Mouse protein-25 (MO25) family proteins are crucial in development and morphogenesis from plants to humans. The fission yeast MO25 protein Pmo25 is essential for cell polarity and division. However, how Pmo25 regulates cytokinesis remains largely unknown. Here we found that the actomyosin contractile ring and septum formation were defective during cytokinesis in pmo25 mutants. Pmo25 physically and genetically interacted with the myosin-II light chain Cdc4, which is essential for the contractile-ring assembly and function. Additionally, pmo25 mutations had synthetic genetic interactions with all other tested mutations in contractile-ring proteins. Moreover, Pmo25 colocalized with the NDR kinase Sid2 and participated in its recruitment to the division plane. Furthermore, Pmo25 directly bound the Munc13/UNC-13 protein Ync13 and modulated the secretion of glucanase Eng1 to the division site for daughter-cell separation. Our data provide insight into how Pmo25 regulates cytokinesis and suggest that the conserved MO25 proteins can link various steps of cytokinesis.

cell biology↗

bioRxiv2025

miR-486-3p ameliorates aging-related impaired angiogenesis in adult moyamoya disease by targeting Forkhead Box O4

ObjectiveInvestigate miR-486-3ps role in alleviating age-related angiogenic decline in Moyamoya disease (MMD) by regulating senescent endothelial cells. MethodsClinical analysis of 151 MMD patients correlated age with postoperative angiogenesis (DSA grading). Senescent HUVECs (SA-{beta}-gal>80%) exhibited elevated SASP factors (IL-6/IL-8/MCP-1). Functional assays (EdU/Transwell/Matrigel) and bioinformatics identified miR-486-3p targets, validated via luciferase/Western blot. ResultsPatients [≥]35 years had 3.67-fold higher risk of poor angiogenesis (OR=3.67). Senescent HUVECs showed 10-16-fold higher SASP secretion (p<0.01). miR-486-3p overexpression increased proliferation (EdU+25%), migration (1.7-fold), and tube formation (+40% branches) in senescent cells (p<0.01) and enhanced angiogenesis in vivo (p<0.001). miR-486-3p directly targeted FOXO4, reducing its luciferase activity (-35%) and protein levels (-37%) (p<0.01), suppressing SASP. ConclusionmiR-486-3p enhances post-revascularization angiogenesis in MMD by inhibiting FOXO4-mediated SASP, offering a therapeutic target and predictive biomarker.

molecular biology↗

bioRxiv2025

Spatially Organized IGF1 mTOR Signaling Controls Human Forebrain Progenitor Fate Through Coordinated Transcriptional and Translational Programs

The specification and maintenance of human forebrain neural progenitor cells (NPCs) depend on both intrinsic gene networks and spatially localized niche signals, but the interplay between these cues remains incompletely understood. Here, we identify a spatially organized, paracrine IGF1 signaling architecture that regulates human FOXG1 NPCs through multilayered transcriptional and translational control. Using a pluripotent stem cell-derived forebrain model, we show that FOXG1 NPCs express IGF1 receptors but lack endogenous IGF1, instead depending on neighboring epithelial-like domains that secrete IGF1. IGF1 promotes progenitor proliferation, clonal expansion, and vertical tissue growth by activating PI3K-AKT-mTOR and MEK-ERK pathways. Ribosome profiling and 5'UTR reporter assays reveal that mTOR signaling selectively enhances translation of neurodevelopmental and biosynthetic transcripts-- including GSX1, a ventral fate determinant implicated in interneuron specification and autism. These findings uncover a human-specific regulatory mechanism in which spatially restricted IGF1-mTOR signaling integrates niche signals with translational output to support progenitor identity, biosynthetic capacity, and developmental resilience.

neuroscience↗

bioRxiv2025

APOE genotype confers context dependent neurovascular vulnerability in immune-vascularized human forebrain organoids

The APOE gene is a major genetic determinant of neurovascular and immune function, yet the mechanisms by which its isoforms modulate brain vulnerability to pathogenic stress remain incompletely understood. Here, we employ isogenic human iPSC-derived immune-vascularized--Forebrain Organoid-based Multicellular Assembled Cerebral Organoids (FORMA-COs)--to dissect isoform-specific responses to a clinically relevant viral challenge. We find that APOE2/2 and APOE4/4 FORMA-COs exhibit heightened viral RNA burden and distinct neuroinflammatory profiles compared to APOE3/3. Specifically, APOE4/4 promotes IL-1 and VEGFA induction, whereas APOE2/2 leads to elevated TNF-{beta} and VEGFA protein accumulation, indicating divergent pathways of injury. Integrated transcriptomic analyses, combined with known and predicted APOE protein-protein interaction networks, reveal genotype-dependent enrichment of cytokine signaling, angiogenic remodeling, and immune dysregulation. In vivo validation using humanized mouse models corroborates APOE genotype- specific vascular remodeling, microglial activation, and oligodendrocyte perturbation. These findings demonstrate that APOE genotype confers context-specific susceptibility to neuroimmune and vascular injury, providing insight into genetic risk mechanisms underlying infection-related and neurodegenerative brain disorders.

neuroscience↗

bioRxiv2025

Engineering Artificial 5' Regulatory Sequences for Thermostable Protein Expression in the Extremophile Thermus thermophilus

The utilisation of biocatalysts in biotechnological applications often necessitates their heterologous expression in suitable host organisms. However, the range of standardised microbial hosts for recombinant protein production remains limited, with most being mesophilic and suboptimal for certain protein types. Although the thermophilic bacterium Thermus thermophilus has long been established as a valuable extremophile host, thanks to its high-temperature tolerance, robust growth, and extensively characterised proteome, its genetic toolkit has predominantly depended on a limited set of native promoters. To overcome this bottleneck, we have expanded the available regulatory repertoire in T. thermophilus by developing novel artificial 5' regulatory sequences. In this study, we applied our Gene Expression Engineering platform to engineer 53 artificial 5' regulatory sequences (ARES) in T. thermophilus. These ARES, which comprise both promoter and 5' untranslated regions (UTRs), were functionally characterised in both T. thermophilus and Escherichia coli, revealing distinct host-specific expression patterns. Furthermore, we demonstrated the utility of these ARES by demonstrating high-level expression of thermostable proteins, including {beta}-galactosidase, a superfolder citrine fluorescent protein, and phytoene synthase. A bioinformatic analysis of the novel sequences has also being carried out indicating that the ARES possess markedly lower GC content compared to native promoters. This study contributes to expanding the genetic toolkit for recombinant protein production by providing a set of functionally validated ARES, enhancing the versatility of T. thermophilus as a synthetic biology chassis for thermostable protein expression.

synthetic biology↗

bioRxiv2025

Ancient DNA Reveals Hominoid Evolution: Intermediate DNA Sequences and Advances in Molecular Paleontology

AbstractFossils and ancient crude pottery vessels function as physical "DNA containers," preserving oriDNA (original, in situ DNA) and accumulating eDNA (environmental DNA) over time. Ancient DNA (aDNA) serves as molecular fossils, chronicling evolutionaryhistory. Using "nano-affinitybead technology", we extracted and sequenced DNAfrom Lycoptera fossils in the Jehol region and a "round-bellied jar (Jar)" from the Erlitou period in Guangwu Town, yielding 236,545 primate sequences from the fossils and 86,908 from the pottery. We observed that the AFF value of DNA sequences negatively corre lates with species divergence time1, offering a quantitative measure of DNA preservation and host divergence. Some fragments distinct from modern genomic sequences, termed "intermediate DNAsequences" (IDS), have been identified. Many IDS exhibit an upper age limit, preserving characteristics of the last common ancestor (LCA) of the Hominidae and offering molecular insights into "Darwins puzzle". Among IDS, the SRRA subtype (Sequence Reversal and Rearrangement), identified in mRNA-coding exonic sequences, arises from the incorporation of a complementary antisense strand upstream of the sense strand, either adjacent to it or separated bya sequence interval. This introduces a novel post-transcriptional regulatory mechanism at the mRNA level, driven by SRRA, which presets hairpin structures and Indels in the UTR or CDS of exonic sequences, modulating gene variation. We propose: "SRRAs played a critical trial-and-error role in early Hominidae evolution, facilitating adaptive genomic changes, with some SRRA sequences later excised from exons", positioning SRRAas an evolutionary "genetic switch". Additionally, seven species -specific fragments (SSFs) of non-human primates (NHPs) linked to Asian Homo erectus were identified in the fossils, and pottery DNA reveale d sequences from tropical species (e.g., zebrass, oil palms), providing evidence of climate-driven local extinction and supporting paleo-ecological and paleo-environmental reconstruction. This method of analyzing aDNA from non-skeletal materials opens new avenues in paleontology, archaeology, and geology, guiding the tracing of ancient migration patterns and fossil searches. DNAfragments preserved within "DNA containers " exhibit an "old-few, new-many" turnover pattern, with many aDNA fragments displaying non-deamination. This evidence challenges prevailing perspectives, the authenticity criteria for aDNA, and the capabilities and scope of the traditional research method, necessitating a thorough reevaluation of the relevant knowledge framework. Furthermore, this study opens new opportunities for frontier research.

paleontology↗

bioRxiv2025

Deep Learning-Based 3D Leukocyte Differentiation Using Label-Free Higher Harmonic Generation Microscopy

Both in clinical practice and translational research, cell differentiation of leukocytes provides important information used for diagnostics or insights into pathophysiological mechanisms. The current gold-standard method for bronchoalveolar lavage fluid (BALF) analysis involves histochemical staining of cytospins, followed by manual morphological quantification. However, this approach is labor-intensive, time-consuming, and highly operator-dependent, limiting its efficiency and throughput. This study proposes a deep learning framework for rapid, automated 3D leukocyte differentiation using label-free higher harmonic generation microscopy (HHGM). 3D leukocyte characterization was performed with label-free HHGM. Two deep learning models, ResNet 3D-50 and Vision Transformer (ViT) 3D, were trained, validated and tested for leucocyte differentiation on both BALF and blood fraction samples from 14 interstitial lung disease (ILDs) and 12 acute respiratory distress syndrome (ARDS) patients. Deep-learning model-prediction and cytospin analysis were performed by separate investigators. Results were compared using Bland-Altman analysis. The deep learning algorithm achieved >96% accuracy in quantifying neutrophils, eosinophils, lymphocytes, and macrophages/monocytes. Bland-Altman analysis showed mean differences of less than 3% between cytospin analysis and the deep learning based approach across all cell types. By integrating the label-free imaging capabilities of HHGM with deep learning, this study established a fast, accurate and high-throughput leukocyte differentiation in fresh BALF and blood samples. By significantly improving efficiency and reproducibility, this technology has the potential to transform clinical workflows and advance precision medicine.

biophysics↗

bioRxiv2025

Capacity for compensatory cyclin D2 response confers trametinib resistance in canine mucosal melanoma

Background/objectiveMucosal melanoma (MM) is a poorly responsive, rare and aggressive subtype with paucity of targetable recurrent driver mutations, although Ras/MAPK and PI3K/AKT/mTOR signaling pathway activations are common. Eventual tumor evasion of targeted therapy continues to limit treatment success. Adequate models are necessary to address therapeutic resistance. The relatively greater incidence of naturally occurring MM in dogs, as well as its comparable clinical and pathological characteristics to human MM, represents a promising opportunity for predictive patient modeling. Resistance-promoting crosstalk between Ras/MAPK and PI3K/AKT/mTOR signaling under trametinib inhibition of MEK was studied in a canine MM model. Emphasis was placed on the suppressive effect of trametinib on cell cycle entry and its potential role in drug resistance. MethodsD-type cyclins were investigated using five MM cell lines exhibiting differential sensitivities to trametinib. Drug-treated cells were analyzed for signaling pathway activation, proliferation, survival, cell death, and cell cycle in the context of D-type cyclin expression. Cyclin D2 expression was manipulated using siRNA knock down or inducible recombinant overexpression. ResultsWith diminished cyclin D1 under trametinib treatment, relatively trametinib-resistant MM cells exhibited capacity to upregulate cyclin D2, which promoted proliferation, whereas sensitive cells did not similarly respond. Inhibition of the compensatory cyclin D2 response restored sensitivity to resistant cells. Induced cyclin D2 overexpression promoted survival to otherwise trametinib-sensitive MM cells that did not exhibit capacity to upregulate endogenous cyclin D2. PI3K/AKT/mTOR signaling upregulation under trametinib was suppressed by mTORC1/2 inhibition, which similarly diminished cyclin D2 response. ConclusionThe compensatory switch from preferential reliance on cyclin D1 to D2 appears to play a role in MM resistance to MEK inhibition.

cancer biology↗

bioRxiv2025

RIP2 inhibits DOCK8-mediated platelet dense granule release and alleviates experimental myocardial infarction

ObjectiveReceptor-interacting protein 2 (RIP2) is an essential mediator of inflammation and innate immunity downstream of pattern recognition receptors (PRRs). Platelets express RIP2, while its role in platelet activation, thrombosis, and myocardial infarction (MI) is unknown. Approach and ResultsHere we show that RIP2 deficiency enhances platelet dense granule secretion in response to GPIb and GPVI activation; platelet aggregation in whole blood and adhesion under arterial shear are also increased. Consistently, RIP2 inhibitor WEHI-345 potentiates human platelet dense granule secretion and inhibits RIP2 phosphorylation induced by thrombin and collagen. These phenotypes are translated into shorter bleeding time, accelerated FeCl3-induced arterial thrombosis. Importantly, platelets from patients with coronary artery disease and mice with atherosclerosis express lower RIP2, and RIP2 deficiency deteriorates MI and cardiac function in a mouse ischemia/reperfusion model. Mechanistically, we found that platelets express dedicator of cytogenesis protein 8 (DOCK8), which is sequestered by phosphorylated RIP2 (p-RIP2), causing inhibition of Cdc42 activation and subsequent dense granule release. ConclusionsIn conclusion, RIP2 inhibits platelet activation, thrombosis, and ameliorates MI. Our results also suggest that a novel PRR-independent pathway, p-RIP2-DOCK8-Cdc42, negatively regulates platelet activation downstream of GPIb and GPVI. Platelet RIP2 pathway may be promising for therapeutic intervention of atherothrombotic diseases from early atherosclerosis stage to arterial thrombosis and MI. HighlightsO_LIRIP2 inhibits platelet dense granule release NOD2-independenly via pRIP2-DOCK8-Cdc42. C_LIO_LIThe negative regulation of RIP2 on platelet activation is translated into enhanced thrombosis, exacerbated myocardial infarction (MI). C_LIO_LIRIP2 pathway booster may be an approach for therapeutic intervention of atherothrombotic diseases. C_LI

molecular biology↗

bioRxiv2025

Oncogene Silencing via ecDNA Micronucleation

Extrachromosomal DNA (ecDNA) contributes to cancer genome instability by enabling high-copy oncogene amplification, intratumoural heterogeneity and rapid genetic change. Micronuclei (MN) are frequently observed in chromosomally unstable cancers, yet their origins and relevance in ecDNA-driven tumours remain incompletely understood. Here, we investigate the relationship between ecDNA segregation errors and MN formation. We find that ecDNA frequently localizes to MN and represents a prominent source of MN content in ecDNA-positive cancer cells. Mitotic clustering of oncogene-bearing ecDNAs is associated with asymmetric inheritance and mis-segregation into MN. Transfer of oncogenes from ecDNA into MN is accompanied by reduced transcriptional output. Single-MN sequencing shows that individual MN are enriched for ecDNA to a degree that exceeds expectations from stochastic mis-segregation and that in MN oncogenes originating from multiple distinct ecDNAs coalesce. Using live-cell imaging, we observe that cells inheriting ecDNA-positive MN show limited proliferative capacity and an increased likelihood of cell death. In neuroblastoma patients with MYCN-amplified ecDNA, higher frequencies of ecDNA-positive MN at diagnosis are associated with improved event-free and overall survival. Together, these findings link ecDNA mis-segregation to MN formation and reduced cellular fitness, suggesting that ecDNA-positive MN may reflect a state of impaired oncogenic ecDNA function with potential relevance for clinical outcome.

cancer biology↗

bioRxiv2025

Scaling Large Language Models for Next-Generation Single-Cell Analysis

AO_SCPLOWBSTRACTC_SCPLOWSingle-cell RNA sequencing has transformed our understanding of cellular diversity, yet current single-cell foundation models (scFMs) remain limited in their scalability, flexibility across diverse tasks, and ability to natively integrate textual information. In this work, we build upon the Cell2Sentence (C2S) framework, which represents scRNA-seq profiles as textual "cell sentences," to train Large Language Models (LLMs) on a corpus comprising over one billion tokens of transcriptomic data, biological text, and metadata. Scaling the model to 27 billion parameters yields consistent improvements in predictive and generative capabilities and supports advanced downstream tasks that require synthesis of information across multi-cellular contexts. Targeted fine-tuning with modern reinforcement learning techniques produces strong performance in perturbation response prediction, natural language interpretation, and complex biological reasoning. This predictive strength enabled a dual-context virtual screen that nominated the kinase inhibitor silmitasertib (CX-4945) as a candidate for context-selective upregulation of antigen presentation. Experimental assessment in human cell models unseen during training supported this prediction, demonstrating that C2S-Scale can effectively guide the discovery of context-conditioned biology. C2S-Scale unifies transcriptomic and textual data at unprecedented scales, surpassing both specialized single-cell models and general-purpose LLMs to provide a platform for next-generation single-cell analysis and the development of "virtual cells."

bioinformatics↗