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Xu, S.

Publications and source records attributed to Xu, S..

At least 73 records · Page 4Linked to original sources

In vivo-compatible spatial multi-omics via hydrogen peroxide-independent APEX2 labeling

Proximity labeling (PL) technologies like APEX2 have transformed spatial multi-omics in live cells, but their long-standing dependence on hydrogen peroxide (H2O2) disrupts redox signaling and prevents use in live animals. Here we introduce H2O2-independent APEX2 (Hi-APEX), which uses a clickable tetrazine-phenol probe, requiring no enzyme engineering. We show that APEX2 directly catalyzes TP radical formation without H2O2 via a mechanism requiring the probes tetrazine group and a key histidine residue. We benchmarked Hi-APEX-based spatial multi-omics by mapping the mitochondrial matrix and dynamic secretomes. Hi-APEX significantly outperforms traditional APEX in capturing redox-sensitive processes such as stress response and ferroptosis, enabling discovering authentic stress granule components and protein interaction networks for mitochondria-localized GPx4. One mGPx4 interactor TRMT61B--known to regulate mitochondrial m{superscript 1}A modifications--promotes ferroptosis. Crucially, Hi-APEX achieves full in vivo compatibility, enabling direct PL in tumor xenografts and hippocampal neurons, thereby expanding PL-based spatial multi-omics from cellular systems to living organisms.

biochemistry↗

Cellular transcriptomics reveals evolutionary adaptation and rumination of vertebrate stomachs

Stomach, an essential digestive organ in vertebrates, has undergone significant changes in its morphology, chamber numbers, and physiology, in response to dietary diversity. However, its cellular and molecular basis underlying evolutionary adaptation remains largely uncharacterized. Here we report a single-cell and spatial transcriptomic atlas of stomachs from 23 vertebrate species with diverse feeding habits (e.g., omnivores, carnivores, and herbivores) and gastric architectures, including monogastric (e.g., primates), two- (e.g., aves), three- (e.g., camel) and four-chambered stomachs (e.g., sheep). We reveal conservation and divergence in cell-type composition, developmental trajectory, evolutionary origins and forces, spatial distribution, gene regulatory network and effect, metabolic signature and disease susceptibility associated with the feeding habits and stomach chamber. The diversification of plant based diets, particularly the expansion of coarse fibrous plants that required enhanced mechanical processing, driving the rapid evolution of specific cells and associated genes. Ruminants have evolved chamber-specific cell types with enhanced expressions of relevant functional genes (e.g., KRT6A in spinous cells of forestomach, LUC7L in SMCs of abomasum, and TSPYL4 in abomasal enteroendocrine cells), which were validated by fluorescence in situ hybridization and spatial transcriptomic profiling. The three cell-specific expressed genes showed significant effects on cell proliferation and migration by RNA interference to knock down their expressions. In particular, the knockdown of LUC7L in SMCs promotes a transition from a contractile to a synthetic phenotype, and Luc7l knock-out in mice delays gastric emptying and impairs gastric motility, demonstrating that this gene is essential for the coordinated multi-chambered gastric motility that underlies rumination in ruminants. These findings elucidate the cellular and molecular adaptations underlying the evolution of stomach coupled with the emergence of diet land plants. Our results provide potential cellular and gene targets for engineering monogastric animals to acquire functional rumination digestive capabilities as well as for medication of gastric mobility.

evolutionary biology↗

CEACAM5/6+ Tumor Cells and IL-1β+ Macrophages Drive Resistance to Chemo-immunotherapy in Gastric Cancer

Chemo-immunotherapy is a first-line treatment for advanced gastric cancer, yet response rates remain limited and resistance mechanisms are poorly defined. Here we generate a single-cell atlas of 542,121 cells from 35 patients treated with anti-PD-1 plus chemotherapy, profiling pre- and post-treatment tumors linked to clinical response. Integrating spatial transcriptomics, immunohistochemistry, and bulk RNA sequencing, we identify two temporally distinct resistance programs. Intrinsic resistance in pre-treatment non-responders is marked by enrichment of CEACAM5/6 tumor cells that form immune-excluded spatial niches characterized by macrophage recruitment and CD8 T-cell exhaustion. Acquired resistance in post-treatment non-responders is driven by expansion of IL-1{beta} macrophages, which induces coordinated NF-{kappa}B activation across tumor and stromal compartments, promoting PD-L1 upregulation, epithelial-mesenchymal transition, and chronic inflammation. These findings delineate an evolutionary trajectory of resistance and nominate CEACAM5/6 and IL-1{beta} as predictive biomarkers and therapeutic targets to improve anti-PD-1-based combination strategies.

cancer biology↗

AI-2 Production in Fusobacterium nucleatum Is Subspecies-Specific and Uncoupled from Quorum Sensing

Autoinducer-2 (AI-2) is a LuxS-dependent product of the activated methyl cycle (AMC) that functions as a quorum-sensing signal in diverse bacteria. Fusobacterium nucleatum is a genetically heterogeneous oral anaerobe comprising four subspecies: nucleatum (FNN), vincentii (FNV), polymorphum (FNP), and animalis (FNA). Previous studies have reported that FNN and FNP strains produce AI-2 and have proposed that AI-2-mediated quorum sensing contributes to biofilm formation and virulence. However, the distribution and functional relevance of AI-2 across all subspecies have not been systematically examined. Here, we show that AI-2 production is restricted to FNA strains. Genomic analysis revealed that FNN and FNV lack luxS, whereas FNP carries a disrupted luxS homolog. Consistent with these findings, AI-2 bioassays using the Vibrio harveyi BB170 reporter detected AI-2 exclusively in FNA strains. Deletion of luxS in FNA abolished AI-2 production but resulted in minimal transcriptional changes, and exogenous AI-2 failed to elicit global gene expression responses in non-producing subspecies. These results demonstrate that AI-2 production in F. nucleatum is subspecies-specific and uncoupled from quorum sensing. Our findings revise current assumptions regarding AI-2-mediated communication in F. nucleatum and reveal previously unrecognized metabolic divergence within the species complex. IMPORTANCEPeriodontitis affects nearly half of adults in the United States and remains a leading cause of tooth loss worldwide. Fusobacterium nucleatum is a central member of oral biofilms and has also been linked to adverse pregnancy outcomes and colorectal cancer. Although AI-2-mediated quorum sensing has been proposed to contribute to its biofilm formation and virulence, our study demonstrates that AI-2 production is confined to subsp. animalis and is absent in other subspecies. Moreover, AI-2 does not function as a conserved quorum-sensing regulator in this species. These findings fundamentally revise prevailing assumptions about AI-2 signaling in F. nucleatum and suggest that subspecies-specific metabolic traits, rather than universal quorum sensing, may underlie ecological adaptation and host association.

microbiology↗

Xylulose 5-Phosphate/Phosphate Translocator Mediates Carbon Allocation for Anabolic Metabolism in the Chlamydomonas Chloroplast

Metabolite movement into chloroplasts is essential for sustaining chloroplast anabolic metabolism and cellular growth, and yet how the specific factors/transporters that enable import and support metabolism under heterotrophic conditions (in the dark in the presence of fixed carbon) remain poorly understood. Here, we identify CreTPT10, a chloroplast envelope-localized transporter in the unicellular green alga Chlamydomonas reinhardtii (Chlamydomonas throughout) that, of the substrates tested, has the highest specificity for xylulose 5-phosphate (X5P). We also demonstrated that the loss of CreTPT10 caused a pronounced reduction in growth and respiratory activity in the dark, whereas no growth defects were observed in the tpt10 mutants when they were maintained in the light or under nutrient-limiting conditions. Furthermore, dark-grown tpt10 mutants exhibited markedly reduced levels of lipids, nucleotides, isoprenoids, and aromatic secondary metabolites, accompanied by coordinated repression of genes encoding enzymes associated with chloroplast-localized biosynthetic pathways. This metabolic suppression extended beyond the chloroplast, as genes associated with the mitochondrial respiratory chain and cell cycle progression were markedly downregulated in darkness. Together, these findings indicate that X5P import via CreTPT10 is critical for sustaining chloroplast anabolic metabolism and functionally coordinates chloroplast and mitochondrial energy metabolism to support heterotrophic growth.

plant biology↗

T2T Genome and Population Resequencing Reveal OfCCD4 Alleles Orchestrate Petal Color and Scent in Osmanthus fragrans

Osmanthus fragrans is prized for its floral color and fragrance, both key targets for genetic improvement. However, the lack of a complete genome assembly and comprehensive population structure hinders gene dissection and marker development for breeding. To investigate the genetic basis of color-scent interaction, a telomere-to-telomere (T2T) genome assembly is generated, and whole-genome resequencing of 100 cultivars is performed. Integrative population and metabolomic analyses reveal a trade-off: orange-red ( Aurantiacus) cultivars accumulate high /{beta}-carotene but low aromatic apocarotenoids (/{beta}-ionone), while yellow-white cultivars show the opposite pattern. Divergence mapping identifies OfCCD4 as the major underlying locus. Three alleles are characterized--functional (A), partially functional (aDel), and a frameshift null (aStop)--with aStop strictly co-segregating with the Aurantiacus phenotype. Transient and stable transformations confirm that A and aDel cleave /{beta}-carotene into /{beta}-ionone, while aStop abolishes this activity. A co-dominant PCR marker is developed based on allele-specific polymorphisms. OfCCD4 is thus established as the key regulator of the color-scent trade-off in osmanthus. The identified alleles and molecular marker enable rapid, low-cost genotyping at the seedling stage--offering particular value for marker-assisted selection in ornamental breeding, where extended juvenility makes phenotypic selection highly time- and resource-intensive.

plant biology↗

Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

Histone modifications underpin the cell-type-specific gene regulatory programs that drive the remarkable cellular diversity of the mammalian brain. Here, we jointly profiled four histone modifications and the transcriptome in 2.5 million nuclei from the adult mouse brain. By integrating these data with chromatin accessibility, DNA methylation, and three-dimensional genome organization, we constructed a unified epigenomic atlas spanning over 100 brain cell subclasses, and assigned active, primed, and repressive chromatin states across 81% of the genome. Active chromatin states marked by combinatorial histone modifications better nominate candidate enhancers with functional support than chromatin accessibility alone, while H3K27me3- and H3K9me3-marked chromatin states delineate distinct modes of cell-type-specific gene repression. Finally, this multimodal resource enables deep learning models that predict cell-type-specific epigenomic features and gene expression from DNA sequence, providing a comprehensive framework for annotating the brain regulatory genome and interpreting non-coding disease risk variants. HIGHLIGHTS- A single-cell epigenome atlas of transcription and four histone modifications across 2.5M mouse brain cells - Multimodal integration maps chromatin states across [~]81% of the adult mouse brain genome - Cell-type-resolved chromatin landscapes reveal regulatory programs mediated by enhancers, Polycomb and H3K9me3 - Deep learning models predict cell-type-specific epigenomic features and gene expression from DNA sequence

genomics↗

Computational modeling of head direction cells in three-dimensional space: directional encoding and visual cue manipulation

Head direction (HD) cells can fire selectively as a function of the animals head azimuth direction and form an internal compass for navigation. They were found in the mammalian limbic system including the dorsal presubiculum and entorhinal cortex. The underlying network updates its directional estimate in a self-organized fashion and can be recalibrated by external sensory cues. Although ring-attractor models were proposed to account for azimuth coding on horizontal planes, they cannot explain conjunctive azimuth-and-pitch tuning observed in HD cells of the presubiculum of flying bats navigating in three-dimensional (3-D) space. Based on the 3-D electrophysiological recordings, we developed a toroidal continuous attractor network that jointly encodes horizontal azimuth and vertical pitch angle of head direction. The model can reproduce the experimentally recorded tuning curves of individual HD cells, and accurately encode the 3-D dynamic head direction of bat by HD cell population. The model also simulate the influence of horizontal visual cue manipulation on the HD system in 3-D space and predicts how horizontal landmark rotation induces a sustained azimuthal offset that persists after the cue is removed, which is comparable to two-dimensional experimental findings. This research clarifies how conjunctive 3-D direction codes are generated and modified by vestibular input, visual information and recurrent connectivity. It also uncovers the computational principles and properties of the brains navigation functions in realistic 3-D environments and offers new theoretical reference for future studies. Author summaryA central function of the brains navigation system is to track head direction, which in terrestrial mammals is largely confined to a horizontal plane. However, for animals like bats that navigate freely in three-dimensional (3-D) space, the neural code for head direction has been found to be high-dimensional. While ring attractor network models elegantly explain horizontal azimuth coding, how the 3-D head direction code is formed and affected by sensory information remains unknown. Here, we develop a toroidal continuous attractor network model with vestibular and visual modules that explains the jointly encoding of azimuth and pitch angles, and the effect of visual cue. We introduce the toroidal topology to the continuous attractor network, and the high-dimensional angular velocity signal from vestibular system and visual input are used to update the population dynamics of the network. Our model is constrained by and reproduces 3-D electrophysiological data from flying bats, captures the unique tuning curves of individual head direction cells, and further achieves the accurate encoding of dynamic 3-D head movements by population activity. Evidences in the rodent have suggested visual cue manipulation recalibrates head direction coding horizontally. Our model further successfully simulates the influence of visual cue rotation in 3-D space, predicting a persistent, global offset in the azimuth encoding--an effect that endures after cue removal and aligns with 2-D rodent experimental phenomena. This work provides a mechanistic, network-level explanation for 3-D head direction encoding and reveals how multimodal cues are integrated to form the internal compass in a volumetric world.

neuroscience↗

Getting over ANOVA: Estimation graphics for multi-group comparisons

Data analysis in experimental science mainly relies on null-hypothesis significance testing, despite its well-known limitations. A powerful alternative is estimation statistics, which focuses on effect-size quantification. However, current estimation tools struggle with the complex, multi-group comparisons common in biological research. Here we introduce DABEST 2.0, an estimation framework for complex experimental designs, including shared-control, repeated-measures, two-way factorial experiments, and meta-analysis of replicates.

bioinformatics↗

CRISPR-Cas9-induced genetic mosaicism in three species of the microcrustacean Daphnia

Genetic mosaicism can arise from in vivo CRISPR-Cas9 gene editing, especially in the embryos. This study evaluates the extent of genetic mosaicism resulted from CRISPR-Cas9-mediated knockout for 11 genes in the freshwater microcrustacean Daphnia magna, D. pulex, and D. sinensis. Based on extensive genotyping data of the asexually produced progenies of successfully edited females, we find strong evidence of mosaicism in 9 of these genes. The genotyping data also suggest the gene editing activity can take place as early as the one-cell embryo stage and extends into the 32-cell and later stages. This study establishes genetic mosaicism as an important feature of Cas9-mediated gene editing in Daphnia.

genomics↗

Epigenetic Programming of Macrophage Phenotypes by STING-IRF3 Drives Inflammation in Ascending Thoracic Aortic Dissection

BackgroundAscending thoracic aortic dissection (ATAD) is characterized by extensive macrophage (M{Phi}) accumulation and profound inflammation; however, the mechanisms sustaining pro-inflammatory M{Phi} activation remain incompletely defined. Emerging evidence indicates that epigenetically generated immune memory drives innate immune cells toward persistent inflammatory states. In this study, we investigated whether epigenetic reprogramming governs M{Phi} phenotypic fate and contributes to ATAD pathogenesis. MethodsWe performed single-cell RNA sequencing of human ascending aortic tissues from controls, patients with ascending thoracic aortic aneurysm (ATAA), and patients with acute ascending thoracic aortic dissection (ATAD). We also performed integrated single-cell RNA sequencing, single-cell ATAC sequencing, and spatial transcriptomics in an angiotensin II (Ang II)-infused mouse model. The role of the STING-IRF3 signaling axis in M{Phi} epigenetic programming was examined using M{Phi}-Sting -/- and M{Phi}-Irf3-/- mice. ResultsIn human and mouse aortic tissues, we identified multiple functional M{Phi} populations including pro-inflammatory, phagocytic/anti-inflammatory, proliferative, and reparative/healing M{Phi}s. Aortic M{Phi}s in both sporadic ATAD patients and Ang II-induced ATAD mice exhibited a pronounced pro-inflammatory bias with enhanced differentiation toward pro-inflammatory M{Phi}s and impaired differentiation toward phagocytic/anti-inflammatory states. Pro-inflammatory M{Phi}s were particularly abundant in dissection sites, whereas phagocytic M{Phi}s were enriched in discrete adventitial niches. Origin analyses revealed a substantial increase in CCR2 recruited M{Phi}s within the aortic wall, which preferentially differentiated into pro-inflammatory M{Phi}s. In contrast, LYVE1 resident M{Phi}s-- predominantly biased toward phagocytic phenotypes--were markedly depleted in ATAD. Single-cell ATAC sequencing identified coordinated chromatin remodeling with increased accessibility at pro-inflammatory gene loci and decreased accessibility at phagocytic gene loci. Among candidate transcriptional regulators identified, IRF family TFs, including IRF3 emerged as unique factors capable of simultaneously promoting pro-inflammatory gene programs while suppressing phagocytic gene expression. Mechanistically, STING-IRF3 signaling orchestrates this biased transcriptional state, likely through coordinated BRG1-dependent chromatin opening at pro-inflammatory gene loci and chromatin closing at phagocytic/anti-inflammatory gene loci. M{Phi} specific Sting -/- and Irf3-/- mice exhibited attenuated inflammatory reprogramming and reduced aortic destruction and dissection. ConclusionsThese findings identify STING-IRF3-mediated epigenetic programming of M{Phi}s as a fundamental mechanism driving aortic inflammation and ATAD development. Targeting M{Phi} epigenetic programming may represent a promising therapeutic strategy to prevent aortic dissection. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/701198v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@c97bcdorg.highwire.dtl.DTLVardef@1df0ca8org.highwire.dtl.DTLVardef@b7fd04org.highwire.dtl.DTLVardef@1443e16_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

BRD8 Disruption Unlocks Retrotransposon-Driven Tumor-Intrinsic Immunogenicity via Redistribution of Histone Acetylation in Liver Cancer

Overall response rate for immune checkpoint blockade (ICB) therapy remains limited in advanced hepatocellular carcinoma (HCC). Epigenetic perturbation has been shown to enhance tumor-intrinsic immunogenicity and thus reverse resistance to immunotherapy in multiple cancer types. Here, through domain-focused CRISPR/Cas9 genetic screens targeting chromatin regulators, we identified the bromodomain-containing protein 8 (BRD8) as a novel epigenetic factor that functions to suppress tumor-intrinsic immunity through BRD8/EP400 chromatin remodeling complex in HCC. Depletion of BRD8 potently induces anti-tumor immune responses and sensitizes tumors to ICB therapy in mouse tumor models. Mechanistically, BRD8 knockout leads to partial redistribution of H3K27ac to repetitive elements, activating double-stranded RNA (dsRNA) accumulation and subsequent type I interferon (IFN) response, leading to tumor rejection via remodeling the tumor microenvironment. The first-in-class selective chemical probe DN02 targeting the bromodomain of BRD8 also exhibits immunomodulatory and anti-tumor effects. In line with these findings, low BRD8 expression correlated with enriched interferon signatures, elevated immune cell infiltration, and prolonged survival in HCC patients. Together, this study reveals BRD8 as a selective epigenetic vulnerability for promoting tumor immunogenicity, and its bromodomain as a druggable target to overcome immunotherapy resistance in liver cancer patients. SignificanceThe induction of viral mimicry by epigenetic interference could trigger tumor-intrinsic immune response and enhance immunotherapy efficacy. Here, through domain-focused CRISPR/Cas9 screening, we identify BRD8 complex as a regulator involved in the suppression of repetitive elements by controlling H3K27ac distribution and propose BRD8 as a novel target to enhance anti-tumor immunity.

cancer biology↗

Integrated Multi-omics Analysis Identifies Molecular Signatures of Regular Physical Activity in Human Peripheral Blood

Regular physical activity is well established to protect against metabolic disorders and bolster immunity; yet, the underlying molecular and cellular mechanisms remain incompletely understood. We integrated plasma metabolomics and lipidomics with single-cell transcriptomic and chromatin accessibility profiles to decode the systemic impact of physical activity on human immunity and metabolism. Our data reveal that regular physical activity is linked to a coordinated metabolic signature marked by enhanced fatty acid oxidation and antioxidant defense. In circulating immune cells, regularly active individuals exhibited synchronous enhancement at both the chromatin accessibility and transcriptional levels for antigen presentation-related genes in antigen-presenting cells (APCs), particularly in classical monocytes, naive B cells, and switched memory B cells. Meanwhile, cytotoxic programs in CD8+ cytotoxic T and mature NK cells showed epigenetic pre-activation of effector function regulators. Intercellular communication analysis further revealed that regular exercise enhanced MHC-I/II signaling between APCs and T cells and suppressed inflammatory signaling networks. Together, these findings elucidate molecular mechanisms underlying the health benefits of regular exercise and offer a theoretical basis for enhancing public health and preventing chronic diseases.

bioinformatics↗

Proton-Activated Chloride Channel 1 (PACC1) is essential for innate host defense against bacterial sepsis

Bacterial sepsis remains a devastating clinical problem. Here, we describe a protective role for the recently discovered acid-sensitive, proton-activated chloride channel, PACC1 (PAC/ASOR/TMEM206), during sepsis. Initially, we found PACC1 was enriched in healthy human and mouse mononuclear phagocytes, particularly macrophages, and differentially regulated by inflammatory stimuli, suggesting PACC1 involvement in innate immunity. To further investigate, we generated de novo Pacc1 knockout (-/-) mice, which presented without major immunologic abnormalities at baseline. Compared to wildtype (WT), Pacc1-/- myeloid cells showed normal phagocytic uptake of acid-insensitive Escherichia coli BioParticles, but impaired development of the acidifying phagolysosome using acid-sensitive E. coli BioParticles. Transcriptomic profiling of Pacc1-/- macrophages revealed dysregulated phagolysosomal and cytokine networks (e.g., interferons). Because phagolysosomal bacterial clearance is essential to resolve infection, we challenged Pacc1-/- mice with intraperitoneal gram-negative E. coli sepsis. Pacc1-/- mice displayed increased bacterial burden, immune cell infiltration, inflammation, and lethality. In contrast, phagocytosis-independent E. coli lipopolysaccharide (LPS)-induced endotoxemia yielded comparable WT and Pacc1-/- survival, as well as similar inflammatory responses. Finally, we engineered Pacc1-floxed (fl/fl) mice crossed with a myeloid lineage Cre-deleter strain to interrogate myeloid cell-intrinsic PACC1 in vivo. Consistent with a predominate role for PACC1 during phagocytosis and bacterial clearance in these cells, LysM-Cre/Pacc1fl/fl mice exhibited impaired E. coli sepsis survival but indifferent endotoxemia phenotypes. In conclusion, PACC1 links sterilizing phagolysosomal activity with immune networks in sepsis pathobiology. Significance StatementBacterial sepsis remains a major global health burden. Here, we report an essential role for the recently discovered acid-sensitive chloride channel, PACC1 (PAC/ASOR/TMEM206), in protective host defense during bacterial infection and sepsis. PACC1 is highly expressed in human and mouse phagocytic myeloid cells, particularly macrophages, where it regulates phagocytic bacterial clearance and inflammatory responses. Using de novo generated mice, we show that global or myeloid cell-targeted deletion of PACC1 impairs development of phagolysosomal acidification, confers susceptibility to bacterial infection and excessive inflammation, and undermines host defense. These findings warrant further investigation of PACC1 in sepsis pathobiology.

immunology↗

Focused ultrasound programmed characteristic NIR-IIb lanthanide mechanoluminescence for high sensitivity bioimaging in vivo

Optical imaging techniques for biodetection are hindered by limited sensitivity and resolution in deep tissues, arising primarily from photon scattering and endogenous autofluorescence. Herein, we report a focused ultrasound (FUS) programmable NIR-IIb emissive mechanoluminescent nanoparticle for in vivo bioimaging. Specifically, CaZnOS nanoparticles co-doped with Mn2+ and Er3+ were engineered to exhibit mechanoluminescence (ML) emission peaked at 1550 nm. FUS stimulation elicits ML without the need for optical excitation, thereby enabling deep-tissue imaging devoid of background interference from excitation light. By modulating the excitation frequency of FUS, ML can be programmed as a characteristic signal. Integrated with a Fourier frequency-transform identification reconstruction (FFIR) algorithm, the specific ML signals can be detected with high sensitivity, reaching sub-millimeter spatial resolution and markedly enhanced signal-to-background ratios compared to conventional photoluminescence-based approaches. By macrophage internalization of the ML nanoparticles to yield functional macrophage-nanoparticle (FMNs), a ultralow detection limit of 10 cells can be achieved. In murine tumor models, the FMNs facilitated real-time monitoring of early-stage tumor progression, underscoring their biocompatibility and translational promise for high-precision diagnostics in deep-seated neoplasms.

bioengineering↗

Developing High-Yield and Safe Therapeutic EVs by Ablating Tissue Factor-Mediated Toxicity

The clinical translation of extracellular vesicles (EVs) as next-generation drug delivery vehicles is currently stalled by two interrelated challenges: the difficulty of manufacturing EVs at an industrial scale ("the yield problem") and the risks of toxicity associated with systemic administration of high doses ("the safety ceiling"). In this comprehensive study, we present a two-pronged genetic engineering strategy to overcome these limitations. First, we discovered that overexpression of glycosylphosphatidylinositol (GPI)-anchored proteins, such as CD55 and CD59, significantly enhances EV production in HEK293T and Expi293F cells. By engineering a truncated CD55 variant (TR3) that retains the GPI-anchor but lacks functional domains, we developed the ExoBoost cell line, which boosts EVs yield by approximately 50-fold without altering vesicle morphology. Second, we observed acute toxicity in mice following intravenous administration of high-dose ExoBoost EVs, with symptoms resembling venous thromboembolism. Through comparative analysis of EVs derived from other cell types, including keratinocyte stem cells (KSCs) and mesenchymal stem cells (MSCs), we identified Tissue Factor (TF/F3) as the critical causative agent of this lethal response. Moreover, we completely abolished this toxicity by generating a F3-knockout cell line (ExoBoost2.0) using CRISPR/Cas9, thereby raising the safe dose to as high as 1.5E12 particles per mouse, as quantified by nano flow-cytometry (nFCM). Finally, using a novel CD46-nanoluciferase reporter system, we demonstrated that high-dose administration of these safe EVs saturates hepatic and splenic clearance pathways, leading to a dramatic increase of systemic EVs accumulation, particularly in hard-to-target tissues such as the brain ([~]10,000-fold) and muscle ([~]1,000-fold). Additionally, repeated high-dose administration of ExoBoost2.0 EVs did not upregulate inflammatory cytokines or production of IgG and IgM. In summary, these findings establish a scalable, safe, and highly biocompatible EVs platform, potentially revolutionizing the drug delivery system in clinical application.

bioengineering↗

Genome assembly and population genomic analysis of Aegilops caudata uncover a rich source for disease and insect pest resistance for wheat improvement

Aegilops caudata L. is a rich source of resistance genes to major wheat pathogens and pests, yet its complex genome structure and lack of a reference sequence have hindered genetic analysis, gene discovery, and introgression. Here, we report a high-quality genome sequence assembly of Ae. caudata accession S740-69, integrated with optical mapping to precisely delineate introgressed segments from structurally altered genomic regions in wheat-Ae. caudata translocation lines carrying a novel stem rust resistance gene. Resequencing and phenotyping of 95 diverse accessions, coupled with k-mer-based association mapping, enabled population-level identification of several novel loci for resistance to wheat pests and diseases, such as greenbug and stem rust. Virus-induced gene silencing confirmed Aecau6C01G127270 (SrAect1) as the first functionally characterized stem rust resistance gene from Ae. caudata. This new genomic framework provides a foundation for systematic mining of resistance genes in this species and their efficient introgression into wheat.

genomics↗

DINOcell: Learning Generalizable Perturbation Effects through Self-Distillation

AO_SCPLOWBSTRACTC_SCPLOWPredicting cellular responses to therapeutics is a promising approach for novel target discovery. However, state-of-the-art computational models designed to predict perturbation effects struggle to generalize and outperform simple baselines. We present DINOcell, a weakly supervised framework that adapts self-distillation to single-cell transcriptomics for predicting perturbation effects. We demonstrate that DINOcell outperforms baselines in predicting the effects of single gene perturbations. Furthermore, DINOcell accurately predicts non-additive effects of combination perturbations, indicating its capacity to model complex genetic interactions. Finally, we show that DINOcell learns representations that capture biological signals and is a promising, generalizable approach for in silico perturbation modeling, providing a valuable tool for accelerating therapeutic target discovery.

bioinformatics↗