Biology subjects

Zhang, Q.

Publications and source records attributed to Zhang, Q..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Structural semantic evolutionary distance (SSED) unifies the selection of cancer driver genes across macroevolution and tumorigenesis.

The non-random, site-specific enrichment of somatic mutations in cancer driver genes (CDGs) suggests their emergence is governed by underlying evolutionary constraints. However, quantitative methods to define these constraints and their underlying principles remain underexplored. To address this, we introduce the Structural Semantic Evolutionary Distance (SSED), a metric leveraging the pretrained ESM-3 protein language model to quantify evolutionary divergence within a unified structural semantic space. Our analysis demonstrates that CDGs are subject to persistent structural semantic constraints across species, tolerating a significantly narrower range of structural semantic changes during evolution compared to non-CDGs. Crucially, clinically observed oncogenic mutations follow this same principle, favoring minimal structural perturbation as shaped by long-term gene evolution. Such mutations maintain core protein function while conferring a capacity for immune evasion, thereby driving clonal expansion. Guided by this "evolutionary constraint" framework, we successfully predicted and experimentally validated a previously uncharacterized oncogenic mutation, KRAS R135L, in bronchial epithelial cells. Furthermore, clinical cohort analysis demonstrated that SSED acts as an independent predictor of response to immune checkpoint blockade, offering information orthogonal to tumor mutational burden (TMB). This study unifies the evolutionary principles governing CDGs across macroevolutionary and microevolutionary (tumorigenesis) timescales, elucidates the balance between structural adaptability, functional conservation, and immune pressure, and identifies a novel predictive biomarker for cancer immunotherapy.

genetics↗

bioRxiv2025

Nuclear export governs TDP-43 phase transitions and cytoplasmic aggregation

RNA-binding protein TAR DNA-binding protein 43 (TDP-43) can form liquid-like, nuclear assemblies whose phase behavior is thought to influence its aggregation propensity and neurotoxic activity. The mechanism(s) that governs the liquid-to-solid phase transition of TDP-43 is poorly defined. Here we combined chemical and genome-wide genetic screenings to identify cellular factors that modulate the phase behavior of an RNA-binding defective TDP-43 mutant. Our screens uncovered multiple cellular processes including RNA splicing, protein translation, proteostasis imbalance and nuclear export as TDP-43 phase regulators. We also developed a semi-permeabilized cell system that partially recapitulates the TDP-43 phase transition in vitro, and showed that nuclear export inhibition reshapes the nuclear environment to favor RNA-dependent liquid-liquid phase separation (LLPS) of TDP-43, which mitigates its aggregation. Nuclear export inhibition in a brain organoid model bearing an ALS-associated mutation reduces pathogenic phospho-TDP-43 accumulation. These findings identify multiple modulators of TDP-43 phase transitions in a sensitized model system and establish a framework for further dissecting the link between nuclear transport and TDP-43 phase dynamics.

cell biology↗

bioRxiv2025

Enhancer/Enhanceosome/Super-enhancer and the promoter-proximate RNA Polymerase II (Pol II) pausing are coupled

Virus infection triggers the expression of IFN-x{beta}, which requires at least four groups of transcription factors and p300/CBP to form an enhanceosome. The promoter-proximal Pol II pausing regulation in metazoans includes the recruitment of CDK9 by JMJD6 and BRD4, the generation of a unique phosphorylation pattern of CTD of Pol II, the recruitment of JMJD5, and the cleavage of arginine methylated histone tails on the +1 nucleosome. We find that both BRD4 and p300/CBP control the activity of CDK9. It is likely that the BRD4 docking site on nucleosomes is generated by p300/CBP. We conclude that enhancer/enhanceosome/super-enhancer and Pol II pausing regulation are coupled and could be the unique universal mechanism that differentiates animals from unicellular organisms.

biochemistry↗

bioRxiv2025

Differential Alterations of Gut Microbiota in Girls with Isolated Obesity, Isolated Precocious Puberty, and Their Comorbidity

BackgroundChildhood obesity and precocious puberty (PP) are escalating public health concerns with a significant comorbidity. Emerging evidence implicates gut microbiota dysbiosis in both conditions, yet microbial associations with their co-occurrence remain unexplored. MethodsA total of 68 girls (18 normal, 25 PP-only, 18 obesity-only, and 7 obesity-PP comorbidity) were enrolled. 16S rRNA sequencing was applied to determine gut microbiota of girls. Microbial diversity, composition, and differential abundant taxa were analyzed. ResultsWhile overall microbial diversity and community structure were similar across groups, obesity-only subjects exhibited significantly increased microbial richness (Chao1 index, P<0.01 vs. all groups), characterized by a higher Firmicutes/Bacteroidota ratio (P<0.001 vs. normal/PP), increased Proteobacteria (P<0.001 vs. normal), and enrichment of genera including Blautia, Faecalibacterium, Roseburia, Anaerostipes, Haemophilus, and Lachnospiraceae_NK4A136_group (P<0.05 vs. other groups). PP-only subjects showed reduced Verrucomicrobiota (P<0.001 vs. normal/obesity) and elevated Escherichia_Shigella (P<0.05 vs. normal). Most strikingly, the obesity-PP comorbid group exhibited a unique gut microbiota profile characterized by a dramatic depletion of Firmicutes compared to the obesity-only group (P<0.001) and a remarkable nearly 100-fold increase in Verrucomicrobiota abundance (P<0.001 vs. other groups), suggesting a distinct microbial ecotype potentially contributing to the pathophysiology of this comorbidity. ConclusionThis study delineated unique gut microbiota alterations associated with isolated obesity, isolated PP, and their comorbidity in girls. The distinct dysbiotic pattern in comorbid obesity-PP suggested complex microbiota-host interactions, providing a new microbiological perspective for understanding the mechanism of comorbidity between obesity and precocious puberty.

microbiology↗

bioRxiv2025

Chemical Microenvironment of the Coral Gastrovascular Cavity and Its Associated Bacterial Diversity

Coral gastrovascular cavities (GVCs) host diverse microorganisms and, as semi-closed compartments, are characterized by elevated nutrient concentrations and pronounced diel fluctuations in oxygen (O2) and pH. However, their broader chemical microenvironment and associated microbial activities remain poorly understood. Here, we provide direct evidence for active anaerobic metabolism in the GVC by measuring hydrogen (H2), nitric oxide (NO), and nitrous oxide (N2O) production, indicative of microbial fermentation, nitrogen fixation and denitrification. Changes in GVC H2 concentrations after feeding suggest that feeding modulates substrate availability, which in turn influences microbial activity in this compartment. In bleached corals, the GVC remained consistently hypoxic and acidic, and anaerobic metabolic processes persisted across the diel cycle. These patterns suggest a shift in energy and nutrient cycling pathways within the bleached coral holobiont. Together, our findings identify the GVC as a dynamic site of microbial activity that may play an important role in holobiont carbon and nitrogen cycling, with potential implications for nutrient balance and coral resilience.

ecology↗

bioRxiv2025

IgG-Bridging-Seeded Synergistic Aggregation of SARS-CoV-2 Spikes Underlies Potent Neutralization by A Low-Affinity Antibody

Mechanistic studies of viral neutralization typically prioritize high-affinity antibodies, relegating low-affinity binders to the sidelines. We report P5-1C8, a Class 1 SARS-CoV-2 antibody that exemplifies this underexplored "low-affinity yet high-potency" phenotype, retaining strong neutralization of Omicron JN.1 despite markedly weakened trimer binding (KD = 225 nM; IC50 = 0.06 nM). Structural and biophysical analyses reveal that P5-1C8 engages WT and BA.1 spikes through canonical intra-spike bivalency, but with JN.1 it induces aggregation. Using virion-like nanoparticles displaying multiple spikes, we show that IgG remains bound with no detectable dissociation and triggers pronounced aggregation. Coarse-grained molecular dynamics delineate the stepwise pathway in which weak IgG-spike contacts seed aggregation via transient inter-spike bridging. Together, these findings establish the first mechanistic framework demonstrating how weak-binding antibodies can nonetheless achieve potent neutralization through higher-order aggregation, thereby expanding the conceptual landscape of antibody function and opening new directions for antibody evaluation and design. Graphical AbstractLow-affinity antibodies are frequently disregarded in discovery pipelines. This work reports P5-1C8, a Class 1 SARS-CoV-2 antibody with weak trimer binding (KD-to-IC50 > 3,700-fold) yet potent neutralization of Omicron JN.1. Structural, biophysical, functional and coarse-grained simulations collectively demonstrate that transient inter-spike IgG bridging seeds higher-order aggregation, which in turn drives neutralization and provides a mechanistic framework. O_FIG O_LINKSMALLFIG WIDTH=199 HEIGHT=200 SRC="FIGDIR/small/691454v1_ufig1.gif" ALT="Figure 1000"> View larger version (79K): org.highwire.dtl.DTLVardef@1d4f132org.highwire.dtl.DTLVardef@1274400org.highwire.dtl.DTLVardef@e186a6org.highwire.dtl.DTLVardef@4f1870_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

Genome-wide CRISPR screen reveals PEX11B as a host restriction factor against ORFV through membrane fluidity regulation

Host-pathogen interactions are shaped by cellular restriction factors that direct antiviral defenses. We built the first ovine genome-wide CRISPR knockout library in sheep testis (OA3.Ts) cells, targeting all protein-coding genes. Using this platform, we identified PEX11B, a peroxisomal membrane regulatory protein, as a strong restriction factor against orf virus (ORFV) infection. Removing PEX11B increased viral susceptibility and triggered severe cytopathic effects with membrane fusion and syncytia formation. Mechanistic studies showed that PEX11B knockout harmed peroxisomal integrity and disrupted lipid metabolism. This led to greater plasma membrane fluidity, creating a proviral environment that allowed more viral entry and replication. These results reveal a new antiviral function for PEX11B in blocking viral infection and underscore the importance of peroxisomal regulation in host-virus interactions.

microbiology↗

bioRxiv2025

Developmental Trajectories of Addition and Subtraction in Early School-aged Children

Mastering basic arithmetic lays the foundation for lifelong mathematical achievement, yet how the neural mechanisms underlying addition and subtraction calculations develop during childhood remain unclear. This study investigated the developmental trajectories of addition and subtraction calculations in school-aged children, and explored how arithmetic-specific neural responses in the right parieto-occipital region are related to age-related improvements in behavioral performance. Here, we recorded electroencephalography (EEG) signals from 115 typically developing children divided into three age groups (7-8-, 9-10-, and 11-12-year-olds) during an arithmetic task involving addition and subtraction calculations. We analyzed the P300 component from the original waveforms and the {Delta}P300 component from the difference waveforms, which were generated by subtracting the event-related potentials (ERPs) elicited by the first operand from those elicited by the second operand to isolate arithmetic-specific neural processes. The results revealed that, in both calculations, older children showed better behavioral performance (faster reaction time and larger PI) and greater right parieto-occipital {Delta}P300 amplitudes, with a key developmental stage at 11-12 years. Furthermore, all groups of children exhibited greater right parieto-occipital P300 and {Delta}P300 amplitudes in subtraction, whereas the smaller right parieto-occipital {Delta}P300 amplitudes in addition significantly mediated the relationship between age and PI. These findings reveal distinct patterns for addition and subtraction calculations over development, highlighting the right parieto-occipital {Delta}P300 amplitude as a neural marker of arithmetic performance, particularly for addition calculation.

neuroscience↗

bioRxiv2025

A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia

The basal ganglia are interconnected subcortical nuclei with complex topographical organization that orchestrate goal-directed behaviors and are implicated in neurodegenerative movement disorders. We generated a cellular-resolution, spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, sampling over one million cells in each species. By integrating spatial data with a cross-species, consensus snRNA-seq cell type taxonomy, this atlas reveals conserved principles of molecular organization within and across structures. The cellular architecture is complex but highly stereotyped, with gene expression gradients superimposed onto discrete compartments. Extensive spatial sampling illuminates 3D gradients of molecular organization in the striatum and reveals cell type-specific core and shell compartments in the primate internal globus pallidus, which is conserved with mouse. This unified, cross-species spatial transcriptomic atlas will be a foundational resource for characterizing the molecular and functional organization of the basal ganglia and their roles in health and disease.

neuroscience↗

bioRxiv2025

Spatial patterning of transcriptional and regulatory programs in the primate subcortex

Mammalian brain cell identity is shaped by intrinsic factors and external context. We present a spatially resolved transcriptomic and gene regulatory atlas of cell types across all subcortical regions in a primate, the common marmoset. Dense sampling and cross-species integration revealed spatially precise neuronal assemblies, including in complex midbrain and diencephalic structures. Chromatin accessibility and transcriptional identity are spatially tuned within and across subcortical structures; spatial gradients within hippocampal subfields are orchestrated by graded transcription factors acting through graded enhancers. The primate-expanded thalamic GABAergic population shares transcriptional and regulatory syntax with conserved midbrain populations, reflecting an evolutionary adaptation compared with rodents. Similar regional expression across cell types can arise by distinct regulatory architectures, as for telencephalic astrocytes and neurons. Conversely, distant cell types can share regulatory programs despite divergent identities: striatal GABAergic medium spiny neurons and telencephalic glutamatergic neurons share a postsynaptic regulatory program despite divergent lineage, region, and neurotransmitter identity.

neuroscience↗

bioRxiv2025

Engineering Apical Integrin-binding Cellular Patches to Directed Cell Reprogramming via Mechanical Remodeling

Engineering extracellular microenvironments to control stem cell fate remains a central challenge in regenerative medicine. Here, we develop ECM-mimetic cellular patches formed by the supramolecular assembly of laminin-derived, integrin-binding ligands. The resulting fibrillar networks exhibit well-defined molecular packing and nanoscale ligand distribution, enabling specific engagement of apical integrin {beta}1 on mesenchymal stem cells. This controlled interface converts molecular assembly into hierarchical mechanotransduction, coordinating cytoskeletal remodeling, nuclear deformation, and chromatin reorganization to drive neuronal reprogramming without genetic or chemical induction. Mechanistic studies reveal that the interplay between ligand assembly, spatial orientation, and network stability governs integrin activation and downstream transcriptional regulation These findings demonstrate how molecularly programmed assemblies can transform passive matrices into active, cell-instructive materials. This work establishes a framework for designing supramolecular systems that couple structural hierarchy with mechanotransductive control to direct stem cell fate and advance regenerative material strategies.

bioengineering↗

bioRxiv2025

Dissecting sequence determinants of DNA methylation and in silico perturbation

DNA methylation shapes cellular identity and genome function, yet the sequence logic that governs its establishment remains largely unresolved. Here we present MethylAI, a cross-species-pretrained and human-specialized deep learning framework that predicts single-CpG methylation states directly from genomic sequence with high fidelity. Through quantitative attribution, MethylAI uncovers intrinsic cis-regulatory principles embedded in DNA, revealing conserved transcription factor (TF) motifs whose influence extends beyond CpG composition. Activated motifs demarcate gene-body CpG islands, encode lineage-defining methylation states, and align with TF occupancy and diverse histone modifications, thereby linking sequence syntax to local chromatin regulation. CTCF perturbation experiments validated MethylAI-predicted methylation shifts at activated motifs, showing strong concordance with in silico perturbations. Mapping genetic variants onto methylation-linked active motifs further uncovered widespread connections to zinc-finger TF families, providing mechanistic insight into how noncoding variation contributes to human traits and diseases. By transforming DNA sequence into interpretable methylation grammar, MethylAI establishes a generalizable framework for decoding the regulatory architecture of the human epigenome.

genomics↗

bioRxiv2025

IRCAS: a novel end-to-end approach to identify, rectify and classify comprehensive alternative splicing events in a transcriptome without genome reference

Alternative splicing (AS) is a fundamental post-transcriptional mechanism that amplifies proteomic diversity and enables adaptive responses across eukaryotes. Current AS detection methods rely heavily on reference genomes, limiting their applicability to non-model organisms. Existing reference-free approaches suffer from inaccurate splice site prediction and treat detection and classification as separate processes, resulting in cascading errors. We present IRCAS, an integrated end-to-end framework for reference-free AS analysis, comprising three modules: identification, rectification, and classification. IRCAS employs colored de Bruijn graphs for AS detection, an attention-based CNN for splice site rectification, and a hybrid Graph Neural Network combining GAT and Transformer layers for classification. Evaluation across four species demonstrates substantial improvements: splice site accuracy increased to 92-96% versus 50-55% for existing methods, and end-to-end accuracy reached 83.4% compared to 41.2% for the previous best method. IRCAS establishes a new benchmark for reference-free AS detection in non-model organisms. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=167 SRC="FIGDIR/small/689457v1_fig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1162531org.highwire.dtl.DTLVardef@e3c2e2org.highwire.dtl.DTLVardef@10f9032org.highwire.dtl.DTLVardef@c3cb5e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig 1.C_FLOATNO Workflow for construction and application of IRCAS. IRCAS is composed of three parts: identification, rectification, classification. (A) Workflow for reference-free AS identification from a raw transcriptomic data. First, according to the input transcripts, we apply BLAST all versus all alignment for preliminary screen. Then we adopt the MkcDBGAS Graph construction strategy. A cDBG was constructed from two sequences using a specified k-mer size. Based on bubble topologies, bubbles were classified into 5 types: SNV-induced, four AS-induced, MX-induced, AL-induced, AF-induced. (B)Workflow for AS position offset rectification and reconstruction of cDBG. Input transcript pairs are converted into a single sequence that includes two virtual nucleotides denoting the splicing start and end sites. SUPPA, a reference-based method, is utilized to determine the true splicing sites. The sequence is encoded into an nx6 vector using one-hot encoding. The offset between the true and predicted splicing sites is calculated and encoded as the ground truth. An attention-based convolutional neural network (CNN) rectification model is trained on these data to predict the offset, enabling the reconstruction of the cDBG with corrected splicing positions. (C) Workflow for 4 types AS classification. For each cDBG, node features, edge features, and global features are extracted. These features are integrated into distinct layers of a graph attention network (GAT)-Transformer hybrid model. This architecture enables high-precision classification of four types of AS events. (D)Workflow for end-to-end application of IRCAS. Transcriptomic data from any species lacking a reference genome is processed by IRCAS, enabling the classification of seven AS types with high accuracy. C_FIG

bioinformatics↗

bioRxiv2025

Cycling Molecular Assemblies (CyMA) for Ultrasensitive Golgi Imaging

The Golgi apparatus is central to intracellular trafficking, yet its dynamic visualization remains constrained by probes that require high concentrations and long incubations. Here we present cycling molecular assemblies (CyMA), a design concept that harnesses endogenous dynamic enzymatic futile cycle to drive ultrasensitive imaging. The BODIPY-CyMA probe operates through reversible palmitoylation-depalmitoylation mediated by palmitoyl acyltransferases and thioesterases, establishing a nonequilibrium steady-state that actively concentrates the probe at the Golgi. This enzymatic cycling converts diffusion-limited localization into self-amplifying signal generation, enabling morphology imaging at concentrations as low as 100 pM and real-time tracking of Golgi dynamics within minutes at nanomolar levels. This probe requires minimal incubation time, exhibits negligible cytotoxicity, faithfully reports pharmacological Golgi disassembly, and functions in vivo in Drosophila larvae. BODIPY-CyMA exemplifies how coupling molecular self-assembly to endogenous enzymatic cycles affords a general strategy for constructing dynamic, non-perturbative probes for live cell and in vivo imaging.

biochemistry↗

bioRxiv2025

Yuanyang allele pairs enable engineered obligate co-inheritance for population replacement and suppression

Mendels law of segregation, which dictates independent assortment of alleles, is a cornerstone of genetics. Here, we present the Yuanyang allele pair (YYAP), an engineered underdominance gene drive system that enforces obligate co-dependency between homologous alleles via synthetic toxin-antitoxin circuits. This design produces a striking deviation from classical Mendelian segregation: YYAP alleles cannot segregate independently, reshaping inheritance outcomes without altering the physical mechanics of meiosis. In Drosophila melanogaster, optimized YYAP strain K711 exhibits >99% hemizygous lethality when crossed with wild type, while maintaining stable transmission and high fitness in transheterozygotes. Cage experiments demonstrate efficient population replacement, positioning YYAP as a confined, resistance-proof alternative to CRISPR homing gene drives. Release of only males represents a self-limiting suppression strategy that was also successful in cage experiments. By imposing a near-complete postzygotic incompatibility, YYAP establishes a programmable framework that not only supports pest management, but also enables modeling of reproductive isolation and allelic co-dependency, thereby creating opportunities to explore speciation and broader synthetic inheritance systems in ecology and evolution.

molecular biology↗

bioRxiv2025

Class-I myosin responds to change in membrane tension during clathrin-mediated endocytosis in human induced pluripotent stem cells

Clathrin-mediated endocytosis (CME) is an essential cellular process that needs to operate efficiently across a wide range of conditions. Internalization of the endocytic site involves forces generated by membrane-bound proteins and Arp2/3-mediated branched actin filament assembly to bend the plasma membrane (PM) from flat to omega-shaped. In mammalian CME, the requirement for a branched actin filament network varies depending on cell type and differences in membrane tension. However, how the actin network adapts to changes in load in order to ensure robustness of this process over a range of membrane tensions is not understood. Here, we combine live-cell imaging and super-resolution microscopy of genome-edited human induced pluripotent stem cells (hiPSCs) to investigate the role of the mammalian class-I myosin, Myosin1E (Myo1E), in load adaptation. Under normal conditions, sites that recruit Myo1E are rare and exhibit slow CME dynamics. However, as membrane tension increases and CME dynamics are slowed globally, Myo1E is recruited to more sites, likely to assemble more branched actin, resulting in increased force generation to rescue stalled sites and promote internalization. Loss of Myo1E results in increased Arp2/3 complex lifetime at CME sites under normal conditions, and at high membrane tension, these sites fail to recruit as many Arp2/3 molecules. We propose that Myo1E is recruited to CME sites that have stalled due to increased membrane tension, where it helps build a more effective branched actin network by generating force through motor activity and recruiting additional Arp2/3 complexes to rescue stalled sites. SignificanceFor mammalian cells to internalize extracellular cargo via clathrin-mediated endocytosis (CME), specific regions of the plasma membrane (PM) must bend from flat to inwardly curved, a process that requires force-generating proteins. One key component in generating this force during CME is the branched actin network, in which actin filaments polymerize against the plasma membrane. When PM tension increases, more force is required to generate curvature, prompting the assembly of actin and actin associated proteins to aid the process. We demonstrate that the class-I myosin motor, Myosin1E (Myo1E), becomes increasingly crucial as membrane tension rises, presumably to build a more effective branched actin network to facilitate internalization of slowed sites.

cell biology↗

bioRxiv2025

A human forebrain organoid model phenocopies dysregulated RNA and protein homeostasis in ALS/FTD-associated TDP-43 proteinopathies

TAR DNA-binding protein 43 (TDP-43) proteinopathy is a defining pathological feature of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), yet the downstream molecular events linking TDP-43 dysfunction to neurodegeneration remain incompletely understood. Here, we model TDP-43 proteinopathy by introducing the ALS/FTD-associated TARDBP K181E mutation into human induced pluripotent stem cells and differentiating them into three-dimensional forebrain organoids. Organoids carrying the K181E mutation exhibit spontaneous TDP-43 hyperphosphorylation, cytoplasmic p-TDP43 accumulation, RNA dysregulation, pro-inflammatory signaling, and activation of apoptotic pathways without TDP-43 overexpression or external stress. Single-cell transcriptomics and enhanced crosslinking immunoprecipitation reveal that the K181E mutation alters TDP-43 RNA-binding specificity, causing widespread RNA mis-splicing including cryptic exon inclusion. Among affected targets, we identify cryptic exon inclusion in the transcription factor PRDM2. PRDM2 cryptic exon-derived peptide immunoreactivity was detected in ALS spinal motor neurons and associated with p-TDP-43 pathology. These findings identify PRDM2 mis-splicing as a candidate downstream event linking TDP-43 dysfunction relevant to ALS and FTD. One sentence summaryHuman brain organoids reveal how mutant TDP-43 disrupts RNA processing and causes neuronal stress.

neuroscience↗

bioRxiv2025

Derivation, Characterizations, and Applications of Rabbit Haploid Embryonic Stem Cells

Haploid embryonic stem cells (haESCs), which contain a single set of chromosomes, provide powerful systems for investigating gene function and creating gene-edited animal models. haESCs have been derived from several mammalian species including human, mouse and rats, yet not from rabbits. Here, we report the derivation of parthenogenetic haESCs of rabbit (rbPhESCs) using an optimized culture medium. These cells maintain a stable haploid karyotype during long-term culture and own pluripotency features comparable to diploid embryonic stem cells derived from rabbit fertilized embryos. By integrating gene trapping cassette into ROSA26 locus, rbPhESCs offer an ideal platform for high-throughput functional genomic screening, as shown in haESCs from other mammals. Consistent with their parthenogenetic origin, rbPhESCs durably preserve maternal-specific imprinting patterns even after extended culture in serum-containing conditions, providing a valuable platform for generating disease models deficient in maternally expressed imprinted genes. Therefore, our findings expand the repertoire of mammalian haESCs and establish rbPhESCs as a valuable platform for genetic studies and biotechnological applications in rabbits.

cell biology↗