Biology subjects

Zhang, S.

Publications and source records attributed to Zhang, S..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

An inherent T cell-activating mRNA delivery platform for in vivo CAR T generation

The clinical success of CAR T cell therapy has underscored the need for scalable, non-invasive strategies for in vivo T cell engineering. Although mRNA delivery offers a promising alternative, current lipid-based vectors lack intrinsic T cell tropism and often rely on antibody conjugation, complicating manufacturing and raising safety concerns. Here we present an inherent T cell-activating polymer-lipid nanoparticle (ERTLNPs) that enable ligand-free, efficient mRNA transfection and activation of T cells in vivo. ERTLNPs, composed of p-toluenesulfonyl arginine (RT)-functionalized polyethylenimine (denoted as PEI-RT) and helper lipids, preferentially accumulate in the spleen following systemic administration. Without exogenous stimulation, ERTLNPs intrinsically activate T cells, triggering robust mRNA expression and proliferation. Mechanistically, ERTLNPs engage the PI3K/AKT/mTOR signaling axis to reprogram T cell metabolism, promoting expansion while restraining exhaustion. Systemic delivery of mRNA encoding fibroblast activation protein chimeric antigen receptor (mFAP CAR) via ERTLNPs leads to in situ generation of functional CAR T cells, which efficiently eliminate pathological fibroblasts in models of cancer and fibrosis, with minimal off-target effects. This ligand-free, metabolically reprogramming mRNA delivery platform provides a clinically translatable approach for in vivo CAR T cell generation and broadens the landscape of non-viral immunotherapeutic engineering.

bioengineering↗

bioRxiv2025

Epithelial FOXP3 Drives Pancreatic Fibrosis through O-glycosylated IL-6

BACKGROUND & AIMSThe transcription factor FOXP3, known for specifying regulatory T cell fate, is unexpectedly expressed in the epithelium of precancerous pancreatic lesions. Here we investigate its non-immune role in initiating pancreatic fibrosis, a process driving therapeutic resistance and organ failure in pancreatic ductal adenocarcinoma (PDAC) with unknown origins in early neoplasia. METHODSUsing human tissues and genetically engineered mouse models, we analysed FOXP3 expression in premalignant lesions. We employed epithelial-specific FOXP3 knockout and knock-in strategies to determine its functional impact on fibrogenesis and neoplasia progression. Mechanistic studies included chromatin immunoprecipitation, glycomic analyses, and signalling assays. RESULTSFOXP3 was consistently expressed in the epithelial compartment of human and murine precancerous pancreas. Epithelial-specific deletion of FOXP3 attenuated pancreatic fibrosis and delayed neoplasia, whereas its knock-in induced spontaneous stromal activation and accelerated PanIN progression. Mechanistically, epithelial FOXP3 directly transactivated the glycosyltransferase GALNT1. GALNT1, in turn, mediated O-glycosylation of interleukin (IL)-6, which was essential for its rapid secretion. CONCLUSIONSOur study establishes epithelial-derived FOXP3 as a master regulator of early pancreatic fibrocarcinogenesis. It drives a glycosylation-dependent amplification loop for IL-6 signalling, orchestrating sustained stromal activation. This pathway represents a promising target for intercepting pancreatic fibrosis and carcinogenesis at its origin.

cancer biology↗

bioRxiv2025

SpaTranslator: A deep generative framework for universal spatial multi-omics cross-modality translation

Recent advances in spatial omics technologies have enabled the simultaneous analysis of multiple molecular patterns in tissue sections, offering unprecedented insights into cellular microenvironments. However, the high cost of measurements and the sparsity of data restrict the availability of paired spatial multi-omics datasets. Here, we present SpaTranslator, a deep generative framework that integrates graph neural networks with an adversarial variational generative model to fully capture spatial characteristics and enable effective cross-modality translation of spatial omics data, enabling simulation of paired spatial multi-omics data from single-omics measurements. Extensive experiments demonstrate that SpaTranslator consistently outperforms baseline methods in both clustering accuracy and biological coherence across various real-world scenarios, including spatial transcriptomics-epigenomics and spatial transcriptomics-proteomics translation tasks. Furthermore, SpaTranslator provides biologically meaningful insights through marker genes and proteins recovery, motif enrichment analysis, and gene regulation inference. Our work offers an effective and adaptable solution for spatial multi-omics cross-modality translation, supporting a broad range of biological and biomedical research.

bioinformatics↗

bioRxiv2025

YAP1 Depletion Enhances TAZ and its Complexation with TEAD4 and AP-1 Heterodimer C-JUN/FOSB to Promote Gastric Cancer Progression and Metastases

BackgroundDysregulation of the Hippo signaling pathway, characterized by aberrant activation of the transcriptional coactivators YAP1 and TAZ, drives tumour progression, immunosuppression and metastasis. Hippo pathway components are emerging therapeutic targets in several solid tumours, however, the expression profiles of Hippo coactivators YAP1, TAZ and their transcriptional factors TEAD1-4 in gastric cancer peritoneal metastases (GCPMs) and their therapeutic value are unknown. ObjectiveTo determine expression status of YAP1, TAZ and TEAD1-4 in GCPMs; and to evaluate whether dual targeting of YAP1 and TAZ provides superior antitumour activity compared with inhibition of either coactivator alone. DesignExpression of YAP1, TAZ and TEAD1-4 was examined in GCPMs by single-cell RNA sequencing and co-immunofluorescent staining. Functional studies using genetic knockout and antisense oligonucleotide (ASO) inhibition of YAP1 or TAZ were performed to assess antineoplastic effects in vitro and in vivo. Co-immunoprecipitation and luciferase reporter assays were used to characterize YAP1/TAZ interactions with TEADs and AP-1 components (JUN and FOSB) and to quantify transcriptional activity. Antitumour efficacy was validated in patient-derived xenograft (PDX) and KP-Luc2 syngeneic models. ResultsYAP1, TAZ, and TEADs1- 4 were highly coexpressed in GCPMs and correlated with poor survival. YAP1 inhibition alone elicited compensatory upregulation of TAZ, while combined inhibition of both coactivators maximally repressed cell proliferation and invasion in vitro, and tumor growth in vivo. Increased TAZ complexation with TEAD4 and AP-1 (c-JUN and FOSB) heterodimer was observed following YAP1 knockdown or pharmacological ASO inhibition. Dual inhibition of YAP1 and TAZ was required to maximally suppress YAP1/TAZ expression and reduce their nuclear accumulation, transactivation of TEAD, and activation of downstream genes. ConclusionsThese findings show that combined YAP1 and TAZ inhibition holds promise for the treatment of GCPMs, a highly lethal disease with an urgent need for novel treatment options. WHAT IS ALREADY KNOWN ON THIS TOPICO_LIGastric cancer with peritoneal metastasis (GCPM), occurring in > 45% of gastric cancer (GC) patients, is a highly lethal malignancy with limited therapeutic options. C_LIO_LIThe Hippo pathway mediator Yes-associated protein 1 (YAP1) is intimately involved in chemoresistance, cancer stemness properties, and the epithelial-to-mesenchymal transition in gastric and other cancers. C_LIO_LIWhile YAP1 represents a promising therapeutic target, clinical trial of YAP1 antisense oligonucleotides has been disappointing. C_LI WHAT THIS STUDY ADDSO_LIHippo coactivators YAP1, TAZ and their main transcription factors TEAD1-4 are markedly upregulated in GCPMs and associated with poor prognosis. C_LIO_LIAntisense targeting of YAP1 results in compensatory upregulation of its paralog TAZ. C_LIO_LIUpon YAP1 depletion, TAZ forms transcriptional complexes with TEAD4 and the AP-1 heterodimer (JUN and FOSB). C_LIO_LIDual targeting of YAP1 and TAZ, by oligonucleotides, achieves maximal suppression of tumour growth in vitro and in vivo. C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYO_LIThese findings provide a strong mechanistic rationale for co-targeting YAP1 and TAZ as a therapeutic approach in metastatic gastric cancer. C_LIO_LIDual Hippo coactivator inhibition could inform the design of future clinical trials aimed at improving outcomes for patients with GCPMs. C_LI

cancer biology↗

bioRxiv2025

MitoEM 2.0 - A Benchmark for Challenging 3D MitochondriaInstance Segmentation from EM Images

We present MitoEM 2.0, a curated data resource for training and evaluating three-dimensional (3D) mitochondria instance segmentation in volume electron microscopy. The collection assembles multiscale vEM datasets (FIB-SEM, SBF-SEM, ssSEM) spanning diverse tissues and species, with expert-verified instance labels emphasizing biologically difficult scenarios, including dense mitochondrial packing, hyperfused networks, and thin filamentous connections with ambiguous boundaries. All releases include native-resolution volumes and standardized processed versions, per-volume metadata (voxel size, modality, tissue, splits), and official train/validation/test partitions to enable reproducible benchmarking. Annotations follow a consistent protocol with quality checks and instance reindexing. Data are provided in NIfTI with nnU-Net-compatible layout, alongside machine-readable split files and checksums. Baseline scripts support common training pipelines and size-stratified evaluation. By consolidating challenging volumes and harmonized labels, MitoEM 2.0 facilitates robust model development and fair comparison across methods while supporting reuse in bioimage analysis, algorithm benchmarking, and teaching.

neuroscience↗

bioRxiv2025

Tumor cell-specific loss of GPX4 reprograms triacylglycerol metabolism to escape ferroptosis and impair antitumor immunity in NSCLC

Glutathione peroxidase 4 (GPX4) is a master regulator of ferroptosis, a process that has been proposed as a potential therapeutic strategy for cancer. Here we have unexpectedly found that inducible knockout of GPX4 in tumor cells significantly promotes non-small cell lung cancer (NSCLC) progression in the autochthonous KrasLSL-G12D/+Lkb1fl/fl (KL) and KrasLSL-G12D/+Tp53fl/fl (KP) mouse models, whereas inducible overexpression of GPX4 in tumor cells exerts the opposite effect. GPX4-deficient tumor cells evade ferroptosis by upregulating the expression of DGAT1/2 to promote the synthesis of triacylglycerol (TAG) and oxidized TAG (oxTAG) and the formation of lipid droplets in cells. In addition, GPX4-deficient tumor cells secrete TAG and oxTAG into the extracellular space to induce dysfunction of antitumor CD8+ T cells, thereby coordinating an immunoinhibitory tumor microenvironment (TME). Consistently, treatment with DGAT1/2 inhibitors or inducible overexpression of GPX4 in tumor cells significantly resensitizes tumor cells to ferroptosis and ignites the activation of T cells in the TME to inhibit NSCLC progression. These findings highlight a previously uncharacterized role of tumor cell-specific GPX4 in NSCLC progression and provide potential therapeutic strategies for NSCLC.

cell biology↗

bioRxiv2025

Key molecular and cellular events of table olive fruit abscission zone formation during natural maturation and after ethephon treatment

Abscission zones are specialized cell layers that enable organ detachment, yet their morphology and regulation vary among species. Olive (Olea europaea), a non-climacteric fruit, requires high concentrations of ethylene-releasing compounds to reduce fruit removal force (FRF) for mechanical harvest. To elucidate mechanisms of fruit abscission zone (FAZ) development in olive, we integrated physiological, transcriptomic, and cellular analyses during natural maturation and after ethephon treatment. Olive fruits emitted low ethylene at color transition, coinciding with declining FRF, and application of 1500 ppm ethephon reduced FRF after one week. Transcriptome analyses of FAZ tissues, using a mesocarp-subtraction strategy to isolate FAZ-specific responses, identified 733 FAZ-specific genes shared between natural maturation and ethephon treatments, including genes of {beta}-1,3-glucanases, pectate lyases, and the phenylpropanoid pathway. Microscopy revealed lignification and alkalization of FAZ, accompanied by reduced low-methylesterified homogalacturonan and non-fucosylated xyloglucan. Increased glucanase activity and reduction in plasmodesmata callose likely facilitate cellular communication during abscission. Further, this study provides the first evidence of FAZ alkalization and implicates transporter upregulation in pH regulation preceding abscission. Our findings advance understanding of abscission biology in non-climacteric fruits and delineate conserved features of FAZ development. Summary StatementIntegrated physiological, transcriptomic, and cellular analyses reveal that fruit abscission zone development in olive involves lignification, alkalization, and coordinated cell wall remodeling, identifying {beta}-1,3-glucanases, pH-regulating transporters, and pectate lyases that facilitate cell separation in a non-climacteric fruit.

plant biology↗

bioRxiv2025

Scalable spike sorting across thousands of neurons by modeling neural dynamics with NeuroSort

Neural circuit research requires resolving the functional coding mechanisms at the single-neuron scale. However, neural signals captured from extracellular recordings are inherently complex, shaped both by electrode properties and the spatially distributed neural population activity across recording sites. These factors introduce strong signal mixing and waveform variation, making it diffcult for existing spike sorting methods to reliably isolate individual neurons from large-scale recodings. To address this, we develop NeuroSort, which fuses spatiotemporal information through a contrastive learning strategy to adaptively model neural dynamics. NeuroSort is a GPU-enabled, highly efficient spike sorting framework, enabling the isolating of up to thousands of neurons. We validated NeuroSort on in vivo extracellular recordings, including Utah array data from rhesus macaques performing motor tasks and Neuropixels 1.0 probe data from a rat during rest. Moreover, in a recording collected by the 1,024-channel Neuroscroll probe, NeuroSort sorted the largest number of well-isolated neurons from different brain areas while achieving a 2-8 times speedup over other methods. Taken together, NeuroSort generalizes across recording conditions, providing an interpretable and scalable paradigm for whole-brain dynamic analysis.

neuroscience↗

bioRxiv2025

Microcompartments in Hodarchaeales: a bioenergetic engine that could have fuelled eukaryogenesis

Eukaryotic intracellular compartmentalization is a key innovation in the evolution of complex cellular life. While microcompartments enable metabolic specialization in many bacteria, to our knowledge, no analogous systems have been identified in Archaea. Here, we report the discovery of archaeal microcompartments (AMCs) in Hodarchaeales, an order within the phylum Promethearchaeati (Asgard archaea) that includes the closest known archaeal relatives of eukaryotes. Phylogenetic and structural analyses indicate that these catabolic AMCs, which are specialized for sugar-phosphate metabolism, were acquired by horizontal gene transfer from deep-rooted bacteria of the phylum Myxococcota. The shell pentamers of AMCs are fused to lysine/arginine-rich intrinsically disordered regions that capture cytosolic DNA, facilitating nutrient scavenging. Reaction-diffusion modelling predicts that enzyme colocalization and substrate channelling within AMCs can increase the NADH flux approximately 100-fold. Thus, the AMCs substantially boost energy production in the cell and might have primed the archaeal host for eukaryogenesis.

microbiology↗

bioRxiv2025

Blood originates in hypoblasts during embryonic development

Blood is essential for oxygen supply throughout life. The emergence of blood in the human embryo remains poorly understood. Our study leverages multiple stem cell embryo models and advanced lineage barcoding to unveil that hypoblast, originally regarded as forming the yolk sac wall, is heterogeneous and contributes to CDX2+ extraembryonic mesoderm, followed by hemoglobin+ cells as the first blood cells. CDX2 marks the hypoblast-to-hemoglobin+ cell trajectory that functionally sustains oxygen levels in embryo models. These hemoglobin+ cells molecularly and functionally resemble phagocytes. We show that the erythro-core regulatory network is poised in hypoblasts, and its boost endows erythropoiesis to both hypoblasts and phagocytes. Hypoblasts are the origin of the first blood in humans and non-human primates, providing a conceptual framework that earlier blood generation than expected fills the gap in the establishment of circulation. Further, the hypoblast is a place where primates may repurpose the phagocyte program to carry oxygen throughout embryos. HighlightsO_LIBarcode-traced hypoblast fate in human embryo models; C_LIO_LIThe first blood comes from the hypoblast that contributes to hemoglobin+ phagocyte-like cells; C_LIO_LICDX2 marks hypoblast blood that sustains oxygen supply in embryos before heart formation; C_LIO_LIErythro-core regulatory network endows erythropoiesis to human hypoblasts and phagocytes. C_LI

developmental biology↗

bioRxiv2025

Quantitative Calibration of a Spatial QSP Model Identifies Fibroblast Impact on HCC Immunotherapy

AbstractComputational models are increasingly used to predict treatment response and optimize cancer therapy strategies. Among these, quantitative systems pharmacology (QSP) models mechanistically simulate tumor progression and pharmacological interventions, enabling virtual clinical trials, model-informed drug development, and biomarker identification. Coupling QSP with an agent-based model yields a spatial QSP (spQSP) platform that captures tissue-level spatial organization of the tumor microenvironment (TME). However, parameterizing such models to represent tumor biology remains an open problem. In this study, we developed a calibration framework using the Approximate Bayesian Computation - Sequential Monte Carlo (ABC-SMC) approach to calibrate the spQSP model with a combination of clinical and spatial molecular data, reflecting the TME characteristics of human tumors. This calibration framework matches tumor architectures between spQSP model predictions and patient spatial molecular data by fitting statistical summaries of cellular neighborhoods. We demonstrate that model calibration using CODEX data from untreated HCC patients enables prediction of TME spatial molecular states in an independent cohort receiving immune-checkpoint inhibitor (ICI) and tyrosine kinase inhibitor (TKI) combination therapy. Finally, we identify spatial and non-spatial pretreatment biomarkers and assess their predictive power for therapeutic response. This workflow demonstrates how integrating spatial-omics with multiscale mechanistic models enables quantitative calibration, biological insight, and in silico biomarker discovery, providing a framework for personalized cancer therapy across tumor types. SignificanceDigital twins and computational models are increasingly used to simulate disease and guide therapy, but they often struggle to capture the immense complexity driving the spatiotemporal evolution of the TME. The challenge is compounded by clinical sample limitations, which typically provide measurements from only static snapshots of the TME for parameter estimation. We demonstrate how mechanistic modeling frameworks can overcome this limitation by enabling inference of spatiotemporal model parameters from static spatial data - an intractable task for purely data-driven approaches. Ultimately, our work presents a workflow that integrates spatial-omics with multiscale mechanistic models, enabling quantitative calibration, deeper biological insight, and in silico biomarker discovery.

bioinformatics↗

bioRxiv2025

Bio-synthesis of 15N-Labeled G-Quadruplexes to Investigate the Structure and Interactions in the Cell Lysate using Nuclear Magnetic Resonance

G-quadruplexes (G4) play key roles in biology, making it critical to understand their structure and ligand-binding behavior in cellular environments for advancing G4-targeted therapeutics. While in-cell nuclear magnetic resonance (NMR) is a powerful technique for studying G4 in situ, its application is limited by the challenge of producing isotope-labeled single-stranded DNA (ssDNA). Here, we introduce Restriction Endonuclease Digestion (RED), a simple and cost-effective method to generate 15N-labeled ssDNA. This approach combines molecular cloning and enzymatic design processing by propagating plasmids in E. coli cultured with 15NH4Cl, followed by double restriction digestion and isolation target 15N-ssDNA. Using RED, we produced milligram-scale quantities of 96%-enriched 15N-labeled human telomeric G4 ssDNA (wtTel23c, CTAGGG(TTAGGG)3), ideal for NMR analysis. The NMR spectra revealed that wtTel23c adopts G4 topology and undergoes multiple conformations of wtTel23c in potassium-containing solutions and in Xenopus laevis cell lysate. Interaction studies with the ligand TMPyP4 showed distinct binding profiles in cellular and dilute environments. In dilute solution, TMPyP4 binds to the top tetrad of wtTel23c, while it binds to the loop in cellular environments. The RED method offers an efficient strategy for producing stable isotope-labeled ssDNA, opening new avenues for studying G4 structures and their ligand interactions in complex biological contexts.

biochemistry↗

bioRxiv2025

A chromosome-level assembly and functional genomic resources for the model annelid Capitella teleta

BackgroundThe polychaete Capitella teleta is a commonly used annelid for studies in evolutionary developmental biology, comparative genomics, conservation, and ecotoxicology. Over a decade ago, it was the first polychaete to have its genome sequenced and assembled, contributing to pioneering studies that transformed our understanding of animal genomes and their evolution. However, this early resource is now outdated compared to current genome sequencing standards, limiting the use of modern functional genomic tools that could further our understanding of numerous biological processes. ResultsWe combine long-read and short-read sequencing with Hi-C chromatin conformation capture data to assemble the chromosome-level nuclear and mitochondrial genomes of the laboratory strain of C. teleta. This reference assembly more accurately reflects the expected genome size for this polychaete ([~]243.6 Mb) and contains a highly complete, evolutionarily conserved gene repertoire. Notably, the nuclear and mitochondrial genomes are heavily rearranged, indicating a decoupling between gene family repertoire and chromosomal evolution. The analyses of multi-omic datasets available for C. teleta, including developmental time courses of bulk and single-cell RNA-seq, ATAC-seq, and EM-seq, using the new reference assembly, resulted in a significant quality improvement, allowing us to identify new cell-type-specific gene markers and gain additional insights of biological relevance. Finally, we generated a publicly available genome browser that ensures all these resources are easily findable, accessible, interoperable, and reusable. ConclusionsOur study provides state-of-the-art genomic resources for the polychaete model C. teleta, addressing a pressing community need that will open new research opportunities in animal and genome evolution.

genomics↗

bioRxiv2025

Blind Prediction of Complex Water and Ion Ensembles Around RNA in CASP16

Biomolecules rely on water and ions for stable folding, but these interactions are often transient, dynamic, or disordered and thus hidden from experiments and evaluation challenges that represent biomolecules as single, ordered structures. Here, we compare blindly predicted ensembles of water and ion structure to the cryo-EM densities observed around the Tetrahymena ribozyme at 2.2-2.3 [A] resolution, collected through target R1260 in the CASP16 competition. 26 groups participated in this solvation cryo-ensemble prediction challenge, submitting over 350 million atoms in total, offering the first opportunity to compare blind predictions of dynamic solvent shell ensembles to cryo-EM density. Predicted atomic ensembles were converted to density through local alignment and these densities were compared to the cryo-EM densities using Pearson correlation, Spearman correlation, mutual information, and precision-recall curves. These predictions show that an ensemble representation is able to capture information of transient or dynamic water and ions better than traditional atomic models, but there remains a large accuracy gap to the performance ceiling set by experimental uncertainty. Overall, molecular dynamics approaches best matched the cryo-EM density, with blind predictions from bussilab_plain_md, SoutheRNA, bussilab_replex, coogs2, and coogs3 outperforming the baseline molecular dynamics prediction. This study indicates that simulations of water and ions can be quantitatively evaluated with cryo-EM maps. We propose that further community-wide blind challenges can drive and evaluate progress in modeling water, ions and other previously hidden components of biomolecular systems.

biophysics↗

bioRxiv2025

Development of an efficient PEG-Mediated protoplast transformation system for the medicinal fungus Ophiocordyceps xuefengensis

Ophiocordyceps xuefengensis is a newly identified medicinal fungus with significant pharmacological and economic value, but its genetic manipulation has been impeded by the lack of an efficient transformation system. Here, we established the first stable and highly efficient polyethylene glycol (PEG)-mediated protoplast transformation platform for O. xuefengensis using hygromycin B as a selectable marker. Through systematic optimization of critical parameters such as enzyme composition, enzyme concentration, mycelial age, and digestion conditions, we developed an optimized protocol for protoplast preparation. A high protoplast yield of 9.42x107 CFU/mL was achieved using 4-day-old mycelia with 1.5% lywallzyme 1 and 1.5% snailase digested at 34{whitebullet}C with shaking at 130 rpm for 3.5 h. PY medium containing 0.6 M mannitol significantly enhanced protoplast regeneration. Stable plasmid integration and robust hygR gene expression were confirmed through PCR detection and sustained antibiotic resistance over four successive generations. Furthermore, a controllable expression system was established by using the endogenous promoter that drove the stable expression of the glycoside hydrolase gene cbhI. The result of enzymatic assay confirmed the functional production of CBHI enzyme, demonstrating the credibility of this system. This work provides a reliable genetic toolbox for functional genomics studies, targeted gene manipulation, and strain engineering in O. xuefengensis, facilitating fundamental research and sustainable utilization of this valuable medicinal species. IMPORTANCEThe conservation and sustainable utilization of medicinal fungi represents a critical challenge in biotechnology and natural product research. Ophiocordyceps xuefengensis, a newly identified species with significant pharmacological potential, exemplifies this challenge: its wild resources are diminishing while artificial cultivation remains restricted by limited understanding of its fundamental biology. The lack of genetic tools has impeded progress in elucidating its biosynthetic pathways, regulating fruiting body development, and enhancing metabolite production. We established a highly efficient PEG-mediated transformation system that directly addresses this technological gap. In addition, we demonstrated that this transformation system can support heterologous gene expression using endogenous promoters. This platform enables reliable genetic manipulation in O. xuefengensis, permitting functional genomics studies and targeted bioactive compounds synthesis.

microbiology↗

bioRxiv2025

Glycolytic ATP production enables rapid mammalian cell growth

Cells use ATP to fuel growth and maintenance. Surprisingly, much of the ATP in rapidly growing cells is produced through glycolytic fermentation rather than the more efficient process of respiration, a puzzling phenomenon known as the Warburg Effect. One proposed explanation is that glycolysis produces ATP faster than respiration, thereby enabling faster growth rates. But whether this explains the Warburg Effect is uncertain, as the ATP costs of mammalian cell growth have not been rigorously estimated. Here, we perform over 7500 measurements to estimate the ATP costs of growth and maintenance in mammalian cells across a range of growth rates and under perturbations to ATP production and demand. We find that respiration alone cannot meet the ATP demands of cells doubling faster than every 30 hours, roughly one-third of the maximal mammalian cell growth rate, demonstrating that the Warburg Effect is required to sustain the ATP demands of rapid cell growth.

systems biology↗

bioRxiv2025

CRISPR-mediated transcriptional activation as a mutation-independent therapeutic strategy for SYNGAP1-related intellectual disability

Synaptic Ras GTPase-activating protein (SynGAP) regulates synaptic strength and neuronal signaling, with essential roles in cortical development and synaptic plasticity. Heterozygous loss-of-function variants in SYNGAP1 cause SYNGAP1-related intellectual disability (SRID), a severe neurodevelopmental disorder characterized by epilepsy, developmental delay, and autism. SYNGAP1 mutations often result in haploinsufficiency, providing a strong rationale for gene-targeted therapies. However, no treatment currently addresses the underlying genetic cause of SRID. Here, we developed a CRISPR-mediated transcriptional activation (CRISPRa) approach to upregulate the functional Syngap1 allele in a SRID mouse model. CRISPRa activated Syngap1, normalized SynGAP protein expression and downstream signaling, and rescued working memory deficits. We validated the translational potential of this strategy in human induced pluripotent stem cell (hiPSC)-derived excitatory cortical neurons. CRISPRa rescued SYNGAP1 in two distinct loss-of-function variant lines. Together, these findings demonstrate the feasibility of mutation-independent transcriptional activation as a therapeutic approach for SRID and its broader applicability to haploinsufficiency disorders.

neuroscience↗

bioRxiv2025

Proinflammatory circulating extracellular vesicles from type 1 diabetes patients contribute to beta cell cytotoxicity and disease pathogenicity

In Type 1 diabetes (T1D), {beta}-cell loss and autoimmunity initiate years before disease diagnosis. However, the mechanisms remain unknown. Here, we investigated the role and mechanisms of circulating extracellular vesicles (cEVs) on T1D pathogenesis and {beta}-cell cytotoxicity. We used cEVs isolated from healthy donors (HD), T1D, multiple autoantibody-positive (AAb+), pre- and post-islet transplantation T1D subjects, NOD-T1D mice, and T1D PBMCs. Patient T1D-cEVs significantly induced apoptosis in vitro in human {beta}-cells but not -cells compared to HD-cEVs. cEVs from AAb+ subjects and pre-diabetic mice were cytotoxic, demonstrating that cEV-induced {beta}-cell cytotoxicity precedes T1D onset and diagnosis. cEV reduction in prediabetic NOD-T1D mice improved {beta}-cell health implying cEV contribution to T1D development. Proteomic analysis of patient T1D-cEVs found several proinflammatory proteins, including interferon gamma, which induced {beta}-cell cytotoxicity. Our data using cEVs from pre- and post-islet transplant and PBMC-EVs from T1D patients implicated immune cells as a potential cellular source of cytotoxic cEVs in T1D. Collectively, our data using T1D patient samples coupled with studies in mice demonstrate that cEVs contribute to {beta}-cell cytotoxicity and to the progression of T1D pathogenicity. Our study is one of the first to demonstrate a functional role of the proinflammatory cEV protein cargo on glucose homeostasis, {beta}-cell health, and insulitis. Our studies on T1D-cEVs may lead to discovery of novel biomarkers and therapeutic targets for T1D.

cell biology↗