Biology subjects

Zhu, F.

Publications and source records attributed to Zhu, F..

At least 19 recordsLinked to original sources

bioRxiv2026

Simultaneous multi-area recordings in macaque frontoparietal cortex during a manual object-interaction task

Dexterous hand control is essential for daily activities and a top restoration priority for people with tetraplegia, yet neurophysiological datasets suitable for studying and decoding naturalistic hand behavior remain scarce. Most available recordings constrain movements to a small number of degrees of freedom or cover only a single stereotypical grasp-and-hold structure. Moreover, previous brain-computer interface (BCI) studies have largely relied on signals from a single cortical area, even though dexterous hand control is distributed across an interconnected frontoparietal network. To address these limitations, we designed a paradigm that elicits rich hand movements across 40 distinct hand-object interaction conditions. We recorded simultaneous frontoparietal activity with hand kinematics from a rhesus macaque performing them. Neural activity was recorded from the primary motor cortex, anterior intraparietal area, and ventral premotor cortex using microelectrode arrays spanning 1,920 channels, while a multi-camera markerless motion-capture system acquired video from which kinematics were extracted offline. The dataset comprises data from 20 sessions, including processed neural features, synchronized 3D coordinates of hand and elbow keypoints, and trial-level metadata including task conditions and event timing. We further provide technical validation, including a neural decoding benchmark with multiple algorithms for continuous keypoint coordination reconstruction. We found that cross-day and cross-task decoding performance varied among algorithms. Variation in channel availability leads to different performance degradation curves in different algorithms. This task-rich dataset offers a valuable resource for investigating the neural mechanisms of dexterous hand control and for advancing the performance of motor BCIs.

neuroscience↗

bioRxiv2026

Spatiotemporal atlas resolves the mesenchymal-epithelial stem cell axis governing human hair follicle aging and pathology

How adult stem cell populations coordinate tissue regeneration across physiological and pathological states remains unclear. Hair follicles contain epithelial and mesenchymal stem cells that codetermine hair regeneration. Here, we integrate a multimodal spatiotemporal atlas with functional validation to define the mesenchymal-epithelial stem cell dynamics governing human hair follicle homeostasis, aging, and androgenetic alopecia. Aging is characterized by passive depletion of hDSC-derived regenerative cues, whereas AGA involves a shift of hDSC toward an inhibitory signaling hub that promotes HFSC dysfunction. We further pinpoint hDSC-secreted PTN as a key regenerative factor that promotes hair growth and counteracts androgen-induced growth suppression. This study provides a holistic framework of adult stem cell crosstalk across physiological and pathological states, offering a mechanistic roadmap to reinstate tissue regeneration.

cell biology↗

bioRxiv2026

An AI System for Autonomous Algorithm Evolution in Drug Development

Artificial intelligence (AI) is increasingly permeating the drug development pipeline. Numerous algorithms for accelerating this multi-stage and multi-task process have been constructed, which depends heavily on expert design and labor-intensive task-specific optimization. Given that AI-driven acceleration of drug development is recognized as a cumulative, often synergistic, effect across multiple stages, the autonomous evolution of existing algorithms across the entire pipeline is demanded to achieve a holistic advancement. Here, we present DrugEvolve, a multi-role large language model system for systematic and autonomous algorithm evolution in drug development. DrugEvolve realizes a closed-loop evolution process by incorporating Researcher, Engineer, and Analyst domains, and enables an iterative design, implementation, evaluation, and refinement of algorithm by leveraging scientific knowledge and accumulated evolutionary experience. Across eleven representative tasks spanning target identification, drug discovery, preclinical study, and clinical trial, DrugEvolve autonomously evolved the corresponding task-specific algorithms and achieved substantial performance enhancement on 120 benchmark test sets. Moreover, it showed robust generalizabilities across heterogeneous data modalities (ranging from biological sequence and graph to molecular topology and textual language), and realized gains in both predictive and generative tasks. Collectively, this AI system can serve not only as an algorithmic infrastructure for drug development, but also as a transferable paradigm for broader scientific domains.

pharmacology and toxicology↗

bioRxiv2026

Desert hedgehog enhances endothelial resilience and prevents atherosclerosis by mitigating PAI-1 signaling

BACKGROUNDAtherosclerotic cardiovascular disease remains the leading cause of death worldwide. Most current pharmacotherapies target conventional risk factors that promote atherosclerosis (e.g., hyperlipidemia) rather than intrinsic resilience factors that protect against atherosclerosis in the face of risk factors. Here, we investigated the role of desert hedgehog (DHH), a canonical ligand of the hedgehog signaling pathway, as a novel resilience factor that restrains endothelial mesenchymal transition (EndoMT) and protects against atherosclerosis. METHODSSingle-cell RNA sequencing (scRNA-seq) was performed on atheroprone and atheroprotective regions of the ApoE knockout mouse aorta to identify mechanoresponsive genes associated with atherosclerosis. Endothelial cell-specific Dhh knockout mice were subjected to partial carotid ligation and hypercholesterolemic conditions to investigate the role of endothelial Dhh in atherosclerosis progression. scRNA-seq, bulk RNA sequencing, endothelial lineage tracing, immunoprecipitation-coupled mass spectrometry, and surface plasmon resonance were used to in-vestigate the role and mechanism of DHH in EndoMT. Pharmacological interventions and recombinant DHH administration were performed in vivo to evaluate therapeutic potential of DHH targeting. DHH expression was also examined in human atherosclerotic arteries and serum samples from patients with coronary artery disease. RESULTSDHH protein expression was enriched in arterial endothelium from mice, porcine, and humans. However, DHH expression was significantly reduced in atherosclerotic arteries and serum from patients with coronary artery disease. scRNA-seq of atheroprone and atheroresistant region of mouse aorta identified Dhh as a novel mechanoresponsive gene enriched in aortic regions exposed to unidirectional laminar flow. Endothelial cell-specific Dhh knockout (DhhecKO) mice exhibited increased atherosclerotic lesion area, large necrotic cores, and reduced collagen content following partial carotid ligation. Similarly, under hypercholesterolemic conditions, both male and female DhhecKO mice showed aggravated atherosclerosis progression. scRNA-seq of DhhecKO mouse aortas revealed an increased proportion of endothelial cells undergoing mesenchymal transition, indicating enhanced EndoMT. These findings were corroborated by bulk RNA-sequencing of DHH depleted HUVECs and endothelial lineage tracing in inducible DhhecKO mice. Mechanistically, DHH directly interacted with plasminogen activator inhibitor type 1 (PAI-1) and suppressed PAI-1-induced EndoMT. PAI-1 promoted EndoMT in ECs through activation of canonical TGF-{beta} signaling (SMAD2/3) and noncanonical AKT/ERK1/2 signaling via interaction with low-density lipoprotein receptor-related protein (LRP1). Neutralization of PAI-1 or inhibition of LRP1, AKT/ERK1/2, or SMAD3 signaling abolished DHH deficiency-induced EndoMT. DHH competitively inhibited PAI-1 binding to LRP1, thereby attenuating downstream pro-EndoMT signaling. Intriguingly, treatment with PAI-1 inhibitor TM5275 mitigated endothelial Dhh deficiency induced EndoMT in vivo. Of translational relevance, recombinant mouse DHH protein administration reduced atherosclerosis progression, stabilized plaque, and decreased the expression of EndoMT markers in ApoE knockout mice. CONCLUSIONSDesert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 signaling. The present study implicates endothelial DHH as a potential therapeutic target for atherosclerotic cardiovascular disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/729715v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@194c8a3org.highwire.dtl.DTLVardef@1004d52org.highwire.dtl.DTLVardef@d47c73org.highwire.dtl.DTLVardef@368866_HPS_FORMAT_FIGEXP M_FIG C_FIG Desert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 binding to LRP1 and downstream AKT/ERK, as well as SMAD2/3 signaling. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIDHH was identified as a flow-responsive resilience gene that is downregulated by disturbed flow in endothelial cells. C_LIO_LIEndothelial-specific deletion of Dhh promoted endothelial-to-mesenchymal transition (En-doMT) and atherosclerosis. C_LIO_LIDHH directly interacts with PAI-1 and preclude PAI-1 mediated pro-EndoMT signaling. C_LI What Are the Clinical Implications?O_LIDHH maintains endothelial homeostasis during atherosclerosis. C_LIO_LITargeting endothelial DHH-PAI-1 axis may represent a potential therapeutic strategy to reduce EndoMT and limit plaque progression. C_LIO_LILower circulating DHH level may serve as a potential biomarker of endothelial dysfunction and plaque vulnerability in atherosclerotic disease. C_LI

biochemistry↗

bioRxiv2026

Systematic In Silico Off-Target Assessment of siRNAs: Integrated Tissue-Specific Scoring and Cross-Species Preclinical Model Selection with TargetSureR

Small interfering RNAs (siRNAs) have become a transformative class of nucleic acid therapeutics for clinical disease treatment, yet sequence-dependent off-target silencing continues to pose a major safety barrier that hinders their preclinical refinement and large-scale translational application. Existing bioinformatics tools only support partial off-target evaluation, either focusing on basic sequence optimization or simple seed-region scanning, and fail to deliver systematic, multi-dimensional and reproducible safety assessment for siRNA lead screening. To fill this gap, we developed TargetSureR, a lightweight, modular and CRAN-compatible open-source R package dedicated to full-process siRNA off-target risk profiling. This tool accommodates dual sequence-based and precomputed position-based inputs, integrates GTEx multi-tissue expression data and curated cancer, adverse-event and immune gene panels, and establishes a seven-dimensional scoring framework to stratify off-target risks into four hierarchical tiers. It further enables tissue-specific safety characterization and quantitative cross-species model selection, with an Ensembl API fallback mechanism ensuring high transcript annotation resolution. Built purely in R with no external shell dependencies, TargetSureR provides a standardized, robust and user-friendly workflow for systematic siRNA preclinical safety evaluation, and is freely available at https://github.com/nishuai/TargetSureR.

bioinformatics↗

bioRxiv2026

Task-space dimensions guide human exploration in complex environments

Efficient exploration is essential for rapid learning in high-dimensional environments, where rewards depend on a sparse and unknown subset of task dimensions. Here, we developed a multidimensional value-learning task in which participants explored without explicit knowledge of the underlying structure. Across multiple task designs, participants consistently demonstrated successful learning under structural uncertainty. Behavioral analyses revealed that over half of participants adopted a structured exploration strategy--Full Dimension Scan (FDS)--with three key properties. First, participants systematically isolated and sampled one candidate dimension at a time, effectively reducing search complexity. Second, FDS was temporally persistent within dimensions while maintaining diverse sampling of feature values, enabling efficient local inference. Third, participants sequentially deployed FDS across dimensions, achieving broad coverage of the task space. Importantly, this strategy transferred across tasks: prior experience in lower-dimensional environments promoted stronger FDS use and improved performance in higher-dimensional settings. Consistent with these findings, a dimension-guided exploration model incorporating dimension-level attentional control best captured human behavior. Together, these results identify dimension-guided exploration as a core principle that transforms high-dimensional search into tractable, structured learning, providing new insight into adaptive behavior in complex environments.

animal behavior and cognition↗

bioRxiv2026

ISPpu10 is a structure-gated bridge RNA recombinase that drives safe, large-scale genomic plasticity

IS110 elements employ bridge RNA to direct target site recognition, yet whether additional layers of specificity exist beyond RNA-DNA base pairing is unknown. Here we identified ISPpu10, an IS110 element in Pseudomonas putida that is associated with >100-kb segmental amplifications during adaptive laboratory evolution. All insertions mapped to multiple identical copies of a single conserved intergenic sequence harboring a GC-rich 5' extension that forms a stem-loop. Systematic mismatch and compensatory substitution scanning revealed a sequence-structure dual-match logic: base pairing between the bridge RNA and target DNA serves as an RNA-guided match, whereas the target-encoded stem-loop provides an additional specificity determinant. Transplanting this stem-loop into Escherichia coli targets improved on-target integration and reduced genome-wide off-target insertion, establishing the stem-loop as a portable structural gate. These findings reveal a structural recognition layer beyond base-pairing, suggesting how bacteria reconcile transposition with genome integrity and offering a strategy for precise genome editing.

microbiology↗

bioRxiv2026

Multi-component functionalized Bifidobacterium longum hydrogel for multi-target integrated therapy of colitis-associated anxiety and depression

Inflammatory bowel diseases (IBDs) are frequently accompanied by anxiety and depression, largely driven by perturbed gut-brain axis signaling. However, current oral therapies remain constrained by the spatial and functional separation between intestinal inflammation and central nervous system dysfunction. Here, we present a comprehensive gut-brain dual region integrated therapeutic strategy based on functionalized Bifidobacterium longum hydrogel (INPs@BL@Gel), in which baicalin and tyrosine are coordinated with Fe(III) to form infinite coordination polymers (ICPs), coated with inulin, assembled onto Bifidobacterium longum (BL), and subsequently encapsulated within a pH- and matrix metalloproteinase-responsive silk fibroin-gelatin hydrogel. INPs@BL@Gel exhibits high drug-loading, effective gastric protection, inflammation-triggered release, and long-term intestinal colonization. Within the inflamed intestine, BL and components synergistically suppress inflammatory responses, restore gut microbiota homeostasis, and promote intestinal barrier repair through multi-target integrated therapy. Importantly, BL combined with components markedly enhances the production of beneficial neuroactive metabolites such as homovanillic acid and short-chain fatty acids, which integrated regulate neuroinflammation, preserve synaptic function, and facilitate blood-brain barrier repair via the gut-brain axis. In vivo studies demonstrate that INPs@BL@Gel not only exert potent therapeutic efficacy against colitis and effectively alleviate associated depression, but also reshape the gut microbiota and restore barrier integrity, achieving an remarkable comprehensive therapeutic effect. O_FIG O_LINKSMALLFIG WIDTH=158 HEIGHT=200 SRC="FIGDIR/small/710940v1_fig1a.gif" ALT="Figure 11"> View larger version (59K): org.highwire.dtl.DTLVardef@1a831f3org.highwire.dtl.DTLVardef@1676617org.highwire.dtl.DTLVardef@15f99c1org.highwire.dtl.DTLVardef@1677cc4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOScheme 1.C_FLOATNO (a) Schematic diagram of the design and preparation of functionalized Bifidobacterium longum hydrogel. (b) Exploration of the mechanism of INPs@BL@Gel in treating colitis-associated anxiety and depression through a dual-site multi-target synergistic strategy. C_FIG

pathology↗

bioRxiv2026

An omega glutathione S-transferase in Apis mellifera contributes to chemical adaptation through pesticide sequestration and antioxidant defense

The European honey bee (Apis mellifera L.) is a key agricultural pollinator frequently exposed to pesticide residues, yet the molecular basis of its chemical adaptation, particularly glutathione S-transferases (GSTs) involved in xenobiotic detoxification, remain incompletely understood. In this study, AmGSTO1 was structurally and functionally characterized to evaluate its role in agrochemical interaction and protection against oxidative stress. The crystal structure of AmGSTO1 in complex with glutathione revealed its 3D architecture and key active-site residues were identified by structural analysis and site-directed mutagenesis. Fluorescence binding assays demonstrated measurable affinity for multiple agrochemicals, including TCP, fenoprop, 2,4-D, tetramethrin, nicotine, and 3-phenoxybenzaldehyde. However, HPLC analysis showed no detectable substrate depletion, suggesting ligand binding to AmGSTO1 without catalytic turnover. AmGSTO1 exhibited antioxidant activity toward cumene hydroperoxide, hydrogen peroxide, and paraquat, as well as dehydroascorbate reductase activity. These findings indicate that AmGSTO1 may contribute to agrochemical tolerance through ligand sequestration and redox protection mechanisms.

biochemistry↗

bioRxiv2026

Sympathetic neurons control adaptive immunity in response to Streptococcus pneumoniae infection by regulating T cell and B cell effector function

Adaptive immunity in the lung must be rapidly mobilized to control bacterial pathogens, yet the neuroimmune signals that shape local B and T cell responses remain poorly defined. Here we identify a sympathetic-immune axis that regulates lung-resident memory B cells, antigen-specific IgG production, and protection against Streptococcus pneumoniae. Lung-targeted chemical sympathectomy reduced norepinephrine availability, diminished Tbet memory and resident-memory B cell populations, and markedly impaired S. pneumoniae-specific IgG, resulting in increased bacterial burden. Mice lacking Adrb1 & Adrb2-adrenergic receptors phenocopied these defects, and adoptive transfer of Adrb1/Adrb2-/- B cells into Ighm-/- hosts was sufficient to reduce IgG and worsen infection. Combined T cell depletion and B cell-intrinsic adrenergic receptor loss further impaired bacterial control and suppressed IFNgamma, indicating that norepinephrine stimulates T cell IFNgamma release and that norepinephrine and IFNgamma together drive optimal B cell IgG production. In vitro, norepinephrine enhanced T cell IFNgamma secretion, and norepinephrine plus IFNgamma synergistically increased IgG. These findings define norepinephrine as a key regulator of lung-resident humoral immunity and reveal a neuroimmune mechanism that promotes antibody-mediated bacterial clearance at the respiratory mucosa.

immunology↗

bioRxiv2026

Single-cell transcriptomic landscapes reveal cell-type-specific regulatory mechanisms of nutrient accumulation and transport in wheat grain

To elucidate the transcriptional regulatory mechanisms underlying wheat grain development, we constructed single-cell transcriptomic atlases of wheat grains at 4 and 8 days after pollination (DAP) using single-nucleus RNA sequencing. A total of 58,546 high-quality nuclei were clustered into 16 distinct cell populations representing all major seed tissues, including the embryo, aleurone layer, transfer cells, endosperm, inner pericarp, seed coat, and embryo surrounding region. Comparative analysis revealed a dynamic transcriptional reprogramming from growth-related pathways at DAP 4 to nutrient accumulation at DAP 8, which coincided with shifts in the expression of hormone signaling and organ development genes, as well as starch and storage protein genes. Pseudotime trajectory analysis identified two major differentiation branches, highlighting distinct roles in nutrient storage and support. Notably, the transcription factor TaMADS58 was found to regulate pericarp cell number while simultaneously enhancing protein content and processing quality. Concurrently, TaJEKLL, specifically expressed in nucellar projection cells, was demonstrated to influence nucellar projection development and nutrient transport. Natural variation in TaMADS58 and TaJEKLL revealed their potential to decouple yield from quality traits, offering promising applications for crop improvement. Collectively, this study provides a high-resolution single-cell resource for wheat seed biology and demonstrates that investigating gene expression with spatiotemporal precision at the single-cell level can facilitate the discovery of key genes for precisely regulating individual traits.

plant biology↗

bioRxiv2025

LISA: A Comprehensive R Package for Lentiviral Integration Site Analysis in Gene Therapy Safety Assessment

BackgroundGene therapy using integrating viral vectors has shown remarkable clinical success, but the random integration of vectors into the host genome poses potential safety concerns, particularly insertional mutagenesis. Common Integration Sites (CIS) near oncogenes significantly increase the risk of clonal expansion and malignant transformation. Current tools for integration site (IS) analysis lack comprehensive functionality for safety assessment, particularly in identifying risk-associated genomic regions and tracking clonal dynamics over time. ResultsWe developed LISA (Longitudinal Integration Site Analysis), a comprehensive R package specifically designed for gene therapy safety evaluation. LISA incorporates a novel approach that trains integration site profiles using cumulative curves derived from normal cell infusion samples and normal patient samples, with subsequent statistical testing to distinguish these normal samples from those with exceptional clonal expansion, thereby enabling effective identification of dominant clone formation. For longitudinal studies, LISA monitors fluctuations in clonal dynamics via Richness and Evenness metrics, and integrates this cumulative curve-based statistical testing approach into its early warning system to detect potentially dominant clones. Additionally, LISA features an optimized CIS detection algorithm with O (n log n) time complexity, achieved through chromosome-position encoding and a seed-site strategy, which facilitates efficient analysis of large-scale clinical datasets. The package also provides systematic functional annotations, including annotations for Safe Harbor regions, enhancer/promoter elements, and proximity to three curated gene sets: adverse event-associated genes (AE genes, n=36), cancer-related genes (n=980), and immune-related genes (n=2,485). Furthermore, it encompasses six categories of interactive visualizations and has been validated using real clinical data from gene therapy trials.

bioinformatics↗

bioRxiv2025

Stimuli-Expressed Protein Qubits for Quantum Quantification of Heavy Metals in Natural Water

Environmental heavy metal pollution poses a severe threat to ecological security and human health, necessitating the development of highly sensitive, specific, and rapid detection technologies. Traditional fluorescent biosensors are often constrained by high background interference and limited sensitivity, while single-target detection systems struggle to meet the demands of complex environmental monitoring. This study constructs a novel magnetically modulated photonic quantum biosensing system based on the CadC-T7 gene circuit, replacing the traditional fluorescent reporter gene EGFP with the magnetically modulated fluorescent protein MagLOV - a quantum biomaterial. To enhance its magnetic modulation performance, the mutant with the highest lock-in amplitude during the directed evolution (R10, MagLOV 2) was selected; Simultaneously, systematic parameter optimization was conducted to determine the optimal magnetic modulation frequency (0.05 Hz), the heavy metal stimulation duration (the 2-hour group exhibited the most significant intra-group variation), and the bacterial concentration at the onset of the heavy metal stimulation (controlled at OD600 = 1 to prevent fluorescence quenching due to culture turbidity). The system demonstrates excellent multi-analyte detection capabilities for lead chloride, lead nitrate, and cadmium chloride across a concentration range of 10-8 to 10-4 M. Compared to conventional steady-state photometric methods based on EGFP and MagLOV 2, the lock-in analysis of MagLOV 2 achieves detection sensitivities enhanced by 1[~]2 orders of magnitude, with detection limits as low as 2.4 nM for cadmium chloride, 4.8 nM for lead nitrate, and 9.9 nM for lead chloride. Langmuir isotherm fitting results demonstrate high quantitative accuracy (R2 > 0.950), with particularly outstanding fitting performance for cadmium chloride (R2 = 0.999) and lead nitrate (R2 = 0.995).

synthetic biology↗

bioRxiv2025

FAM19A4 Enhances Neutrophil Respiratory Burst via p38 MAPK in Lethal Sepsis

Sepsis causes high mortality and resource strain, with neutrophil-derived reactive oxygen species (ROS) contributing to excessive inflammation. The secretory protein FAM19A4 modulates ROS release, but its role in sepsis was unclear. We measured elevated FAM19A4 levels in septic patients and cecal ligation and puncture (CLP) mice, correlating with increased mortality. Fam19a4-/- mice subjected to CLP showed significantly improved survival and attenuated multiorgan injury without impaired peritoneal bacterial clearance or altered circulating neutrophil counts. Deficiency reduced the cell counts of neutrophil (Ly6G+) and macrophage (F4/80+) in lungs and liver, diminished systemic ROS production tracked by bioluminescence, and decreased neutrophil extracellular trap (NET) formation in serum and lung tissue. In vitro, FAM19A4 enhanced neutrophil phagocytosis and ROS generation but did not affect lipopolysaccharide-induced chemotaxis. Mechanistically, bulk RNA sequencing, western blotting, and the p38 inhibitor SB203580 demonstrated that FAM19A4 drives neutrophil ROS release specifically through p38 MAPK signaling activation. These results indicate that FAM19A4 is upregulated during sepsis and exacerbates outcomes by enhancing neutrophil ROS production via p38 MAPK, representing a promising therapeutic target for this condition.

molecular biology↗

bioRxiv2025

MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart

Hybridization-based spatial transcriptomics technologies have advanced our ability to map cellular and subcellular organization in complex tissues. However, existing methods remain constrained in gene coverage, multimodal compatibility, and scalability. Here, we present MERFISH+, an enhanced version of Multiplexed Error-Robust Fluorescence in Situ Hybridization (MERFISH), which integrates chemical probe anchoring in protective hydrogels with high-throughput microfluidics and microscopy. This optimized design supports robust and repeated hybridization cycles across an entire centimeter-scale tissue sample. MERFISH+ allowed to simultaneously quantify over 1,800 genes and resolve the 3D organization of chromatin loci and their associated epigenomic marks in developing human hearts. Using a generative integration framework for spatial multimodal data (Spateo-VI), we harmonized these MERFISH+ transcriptomic and chromatin data to reconstruct a 3D spatially-resolved multi-omic atlas of the developing human heart at subcellular resolution capturing 3.1 million cells across 34 distinct populations. This 3D atlas provides a holistic view of an entire organ enabling the characterization of 3D cellular neighborhoods and transcriptional gradients of substructures such as the descending arteries. Thus, MERFISH+ offers a robust, large-format platform for spatial multi-omics that enables high resolution mapping of gene expression at subcellular resolution and the characterization of cellular organization within 3D organs. One Sentence SummaryMERFISH+ is an spatial multi-omics platform that integrates hydrogel-based probe anchoring, automated high-throughput microfluidics, and large-format multimodal data production to enable comprehensive, subcellular resolution mapping of gene expression and chromatin organization across millions of cells within complex developing human organs. HighlightsO_LIMERFISH+ expands MERFISH capabilities to measure >1,800 genes and at whole-organ 3D imaging scale C_LIO_LICombines chemical probe anchoring with high-throughput volumetric microscopy and microfluidics C_LIO_LIGenerates a 3D molecular atlas of a developing human heart with > 3.1 million cells at subcellular resolution C_LIO_LIIntroduces Spateo-VI, a novel generative framework integrating 3D multimodal datasets C_LI

genomics↗

bioRxiv2025

Agro-STARR-seq enables in planta genome-wide enhancer discovery and AI-empowerd enhancer design

Comprehensive enhancer screening is essential for dissecting gene regulatory networks. However, methods for such screening remain limited in plants. We present Agro-STARR-seq, an in planta enhancer screening platform using Agrobacterium-mediated delivery of STARR-seq libraries into Nicotiana benthamiana leaves. In the Arabidopsis genome, we identified 14,715 sequences with enhancer activity, of which 91.59% were located outside of open chromatin regions. This largest in planta enhancer dataset to date enabled AI-assisted design of highly active synthetic enhancers. For the large N. benthamiana genome, we pre-processed the genomic DNA with an Assay for Transposase Accessible Chromatin (ATAC) procedure before the Agro-STARR-seq protocol,and found that only one-third of open chromatin exhibited enhancer activity, 76.00% of which showed no canonical H3K27ac histone marks. Footprinting analysis further enables systematic linkage of transcription factor (TF) binding to enhancer function. Overall, Agro-STARR-seq provides a novel platform for dissecting and engineering plant enhancers.

genomics↗

bioRxiv2025

MORC2 Mediates Transcriptional Regulation Through Liquid-Liquid Phase Separation and DNA Binding

MORC2 is a chromatin-associated ATPase essential for transcriptional silencing and genome stability, yet the biophysical principles governing its regulatory activity remain elusive. Here, we demonstrate that full-length MORC2 undergoes biomolecular condensation to form dynamic nuclear assemblies, a process fundamentally required for its repressor function. Endogenous MORC2 forms discrete, dynamic condensates in neurons from EGFP-MORC2 knock-in mice, supporting the physiological relevance of these assemblies in vivo. Mechanistically, a 3.1 [A] crystal structure of coiled-coil 3 (CC3) identifies a dimeric scaffold that serves as a structural hub, while multivalent sticker interactions between an intrinsically disordered region (IDR) and a newly defined IDR-binding domain (IBD) drive condensation. We show that DNA acts as a molecular scaffold that triggers MORC2 condensation, which in turn allosterically stimulates its ATPase activity. Critically, by employing a "killswitch" strategy to decouple assembly from internal fluidity, we reveal that only dynamic MORC2 condensates--not static aggregates or condensation-deficient mutants--can restore transcriptional repression in MORC2-knockout cells. Furthermore, pathogenic variants linked to CMT2Z and SMA differentially perturb these material properties and enzymatic turnover, providing a mechanistic link between condensate dysregulation and human neuropathies. Together, our findings establish a DNA-templated condensation mechanism for MORC2 and provide a molecular framework for understanding how the material state of chromatin-associated machinery dictates gene regulation and disease pathogenesis

cell biology↗

bioRxiv2025

Specific Pathogen Free Ten Gene-Edited Pig Donor for Xenotransplantation

Xenotransplantation has entered the clinical phase to fulfill the global organ shortage. However, recent clinical studies revealed that the xenograft from current gene-edited (GE) pigs still poses the risk of immune rejection, and biosafety concerns. In this study, we successfully constructed a large batch of 10- (GTKO/CMAHKO/ {beta}4GalNT2KO/hCD46/hCD55/hCD59/hTBM/hEPCR/hCD39/hCD47) GE cloned (GEC) donor pigs by utilizing gene editing and somatic cell cloning technology, and successfully obtained F1 generation. Phenotypic characterization of 10-GEC pigs showed the deletion of three xenoantigens along with expression of seven human transgenes in various tissues. Digital droplet polymerase chain reaction, and whole genome sequencing indicated 2 copies of hCD46/hCD55/hCD59/hTBM/hCD39 and 1 copy of hEPCR/hCD47 in pig genome without significant off-target and damage to the porcine own functional genes. The validation results showed that 10-GEC pigs effectively inhibited the attacks of human antibodies, complement, and macrophages on porcine endothelial cells and alleviated the coagulation abnormalities between pigs and humans. 10-GEC pigs were negative for all zoonotic pathogens (48) including cytomegalovirus, except streptococcal infections. Kidney, heart, and liver xenografts from these 10-GE pigs were transplanted to non-human primates (NHP), which started working normally without hyperacute rejection. Among them, the heart and liver transplant recipient died without resuscitation due to unexpected interruption of oxygen supply, while the 2 kidney transplant recipients survived for 23 and 16 days, respectively. Pathological analysis showed that 10-GE pig kidney xenografts showed mesenchymal congestion, and fibrosis, cellular hyperplasia, with minor antibody and complement deposition, and significantly reduced the infiltration of CD68+ macrophage. In summary, we successfully produced a group of specific pathogen free GEC donor pigs that effectively mitigated immune rejection upon multi-organ transplantation to NHP.

immunology↗