Biology subjects

Zhou, X.

Publications and source records attributed to Zhou, X..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Transcriptional Readthrough at Atf4 Locus Suppresses Rps19bp1 and Impairs Heart Development

BACKGROUNDActivating Transcription Factor 4 (ATF4) functions as a transcriptional regulator in various cell types and tissues under both physiological and pathological conditions. While previous studies have linked ATF4 activation with promoting cardiomyocyte (CM) death in dilated cardiomyopathy (DCM), atrial fibrillation, and heart failure, its role in developing CMs remains unexplored. METHODSWe generated multiple distinct CM-specific (Atf4cKO(e2/3/pA) and Atf4cKO(e2)) and global Atf4 knockout (Atf47del/7del and Atf41ins/1ins) mouse models targeting different Atf4 regions, as well as cardiomyocyte-specific deletion of Rps19bp1 to study cardiac phenotypes. Detailed morphological and molecular analyses were performed. RESULTSAtf4cKO(e2/3/pA) (targeting exon 2-3 including the polyadenylation signal (polyA)) mice exhibited severe cardiac defects and died before E17.5, likely due to ectopic activation of p53 signaling pathway resulting from Rps19bp1 downregulation, a potent suppressor of p53. Further investigation revealed that deleting the polyA signal of Atf4 in Atf4cKO(e2/3/pA) mice led to transcriptional readthrough, resulting in the formation of an Atf4-Cacna1i fusion transcript and Rps19bp1 downregulation. To avoid readthrough while abolishing ATF4 function, we introduced small indels into exon 3 of Atf4 in mice (Atf47del/7del and Atf41ins/1ins), which showed normal Rps19bp1 expression and cardiac morphology. Importantly, CM-specific deletion of Rps19bp1 recapitulated the cardiac defects and transcriptional change seen in Atf4cKO(e2/3/pA) mice. CONCLUSIONSWe found that the downregulation of Rps19bp1, not loss of ATF4 function, underlying the cardiac phenotypes in Atf4cKO(e2/3/pA) mice. The reduced expression of Rps19bp1 in Atf4cKO(e2/3/pA) mice is likely due to the unintentional deletion of Atf4 polyA signal and subsequent transcriptional readthrough, underscoring the essential role of RPS19BP1, not ATF4, in cardiac development. Consistent Rps19bp1 downregulation has been observed in other tissue-specific Atf4 knockout models utilizing the Atf4fl(e2/3/pA) allele, suggesting that previously reported Atf4 KO phenotypes may result from Atf4 transcriptional readthrough effects. These findings reveal a locus-dependent transcriptional interference mechanism and emphasize the importance of avoiding confounding cis effects in genetically engineered models. TRANSLATIONAL PERSPECTIVEOur findings clarify ATF4s role in heart development by showing that cardiac defects in cardiomyocyte-specific ATF4 knockout mice--using a widely employed floxed ATF4 line--result from unintended downregulation of RPS19BP1 caused by transcriptional readthrough. This shifts the focus from ATF4 to RPS19BP1, a key regulator of p53 activity, as a potential driver of cardiac developmental abnormalities. Clinically, these insights caution against misinterpretation of genetic knockout models and highlight RPS19BP1 as a promising target for congenital heart disease and related cardiac dysfunctions, with potential implications for future therapies.

genetics↗

bioRxiv2025

Leveraging Large Language Models for Redundancy-Aware Pathway Analysis and Deep Biological Interpretation

Extracting coherent, biologically meaningful insights from vast, complex multi-omics data remains challenging. Currently, pathway enrichment analysis serves as a cornerstone for the functional interpretation of such data. However, conventional approaches often suffer from extensive functional redundancy caused by shared molecular components and overlapping pathway definitions across databases. This redundancy can obscure key biological signals and compromise the interpretability of pathway enrichment results. Here, we present MAPA (Functional Module Identification and Annotation for Pathway Analysis Results Using Large Language Models [LLM]), an open-source computational framework that resolves redundancy and enhances pathway analysis result interpretation. MAPA computes functional similarity between pathways using LLM-based text embeddings, enabling comparison across different databases. It constructs pathway similarity networks and identifies functional modules via community detection algorithms. Crucially, MAPA employs LLMs for automated functional annotation, integrating Retrieval-Augmented Generation (RAG) to generate comprehensive and real-time biological summaries and reduce hallucinations. Benchmarking demonstrated MAPAs superior performance: the biotext embedding similarity showed a large effect size (Cliffs {delta} = 0.96) compared with the Jaccard index ({delta} = 0.73), and module identification achieved high accuracy (Adjusted Rand Index [ARI] = 0.95) versus existing methods (ARI = 0.23-0.33). Human expert evaluation confirmed that MAPAs annotations match expert-quality interpretations. Finally, a multi-omics aging case study illustrates that MAPA uncovers coherent functional modules and generates insights extending beyond conventional pathway analyses. Collectively, MAPA represents a significant advance in redundancy-aware pathway analysis, transforming pathway enrichment results from fragmented lists into biologically coherent narratives. By leveraging the capabilities of LLMs, MAPA offers researchers a robust, scalable tool for deriving deep mechanistic insights from complex and vast multi-omics datasets, marking a new direction for AI-driven bioinformatics.

bioinformatics↗

bioRxiv2025

First Whole-Genome Chikungunya Virus Sequence Detected in Mosquitoes during the 2025 Foshan Outbreak: Evidence of Field Vector Infection and Transmission Potential in China

BackgroundSince July 2025, an outbreak of mosquito-borne chikungunya fever occurred in Foshan City, Guangdong Province, China. This was the second outbreak in China following the one that occurred in Dongguan City, Guangdong Province, in 2010. Moreover, the intensity of this outbreak was significantly greater than that of the previous one. Updates to 23 August, more than 10,000 human cases had been reported. Here, we present the first full genome sequence of the chikungunya virus (CHIKV) derived from field-trapped mosquitoes during the outbreak. MethodsAdult Aedes albopictus were BG-trap captured from residences and parklands in three hotspot towns with high density of confirmed human cases. Mosquitoes were morphologically identified and pooled by species, sex and environment types. RNA was extracted, screened by CHIKV RT-qPCR, then positive pools underwent sanger and whole-genome sequencing for complete sequences. Lineage and mutational profiles were inferred by maximum likelihood phylogenetic and comparison against human and mosquito genomes. The distribution of amino acid site mutations in different protein coding regions was also analyzed. ResultThrough 11 days of collection using 10 BG-traps, 2,803 mosquitoes were captured. 1569 (55.97%) female Ae. albopictus were divided into 77 pools and 9.09% (7/77) of the pools tested positive for CHIKV. The local Ae. albopictus minimum infection rate (MIR, per 1000 females) was 4.46, while the MIR for residences in Lecong Town was the highest at 9.17. The MIR for parklands was slight higher than for residences (4.60 vs. 4.30). All the 5 Ae. albopictus-derived complete CHIKV genome clustered within ECSA-Indian Ocean lineage genotype, closely related to human-derived genomes on 2025 Reunion Island. Amino-acid mutations E1-A226V/E2-L210Q were detected in the strains, which enhanced adaptability to Ae. albopictus and increased the transmission capacity. Novel mutation observed on E1 and E2 were totally consist to the patient-derived CHIKV in 2025 Reunion Island. ConclusionsIt was the first mosquito-derived CHIKV whole-genome during the 2025 Foshan outbreak, filling a critical gap between human case and entomological surveillance. Ae. albopictus was confirmed as the primary vector during the outbreak. The current outbreak CHIKV strain with particular amino-acid mutations had adapted to Ae. albopictus transmission. Compared to previous Chikungunya outbreaks over the past decade, the Foshan outbreak occurred earlier (early July), in a larger urban area (with a population of over 9.5 million), and with abundant breeding sites for the vector mosquito Ae. albopictus. However, the outbreak was quickly brought under control, with daily case numbers consistently decreasing, which is closely linked to the strong vector control measures implemented by the Chinese government in the early stages of the outbreak. Moreover, this event once again underscores the necessity of early monitoring of vector mosquitoes and the importance of implementing highly effective vector intervention measures as soon as possible after an outbreak occurs.

microbiology↗

bioRxiv2025

Decoding the Redox-Driven Fate of Organic Micropollutants through Microbial Co-metabolic and ROS-Mediated Degradation in Wastewater

The uncontrolled release of organic micropollutants (OMPs) from wastewater treatment plants highlights a failure to synergize co-metabolic and reactive oxygen species (ROS)-driven biodegradation pathways. Here, we demonstrate that engineered redox cycling--dynamic fluctuations between oxic and anoxic conditions--fundamentally reshapes microbial metabolism and OMP reaction networks to dramatically enhance removal. Using an integrated multi-omics approach centered on paired mass distance (PMD) reactomics, we show that redox cycling increased the removal of 32 diverse OMPs from a baseline of 32% up to 67%. This enhancement was driven by a complete restructuring of degradation mechanisms: cycling stimulated microbial amino acid and fatty acid metabolism by up to 42%, which coupled to controlled ROS production where oxidative pathways (+15.995 Da) accounted for 47% of transformations under intermittent aeration. We mapped distinct "enzymatic fingerprints," with strong correlations (r > 0.7) linking Proteobacteria monooxygenases to oxidative reactions and Rhodobacteraceae dehydrogenases to reductive ones (+2.016 Da), revealing clear functional specialization. Ultimately, the redox regime dictates the entire OMP transformation network topology, shifting pathways from simple hydroxylation to complex, multi-step networks. This work provides a mechanistic framework establishing redox manipulation as a powerful strategy to synergistically activate degradation pathways, allowing existing infrastructure to meet stringent discharge regulations.

bioengineering↗

bioRxiv2025

Herbivorous insects independently evolved salivary effectors to regulate plant immunity by destabilizing the malectin-LRR RLP NtRLP4

Plants utilize on receptor-like proteins and receptor-like kinases (RLPs/RLKs) to perceive and respond to a wide variety of invading pathogens and insect herbivores. While the strategies employed by microbial pathogens to suppress plant immunity have been well characterized, it remains unclear how herbivorous insects counteract receptor-mediated defenses. Here, we show that salivary effectors evolve independently in whiteflies and planthoppers to dampen RLP4-mediated plant immunity. RLP4, as a leucine-rich repeat RLP (LRR-RLP), confers plant resistance against herbivorous insects by forming the RLP4/SOBIR1 complexes. In the whitefly Bemisia tabaci, BtRDP, the Aleyrodidae-specific salivary sheath protein, interacts with RLP4 from multiple plant species and promotes its ubiquitin-dependent degradation. Overexpression of NtRLP4 in transgenic plants exerts a detrimental effect on B. tabaci by exploiting the crosstalk between the salicylic acid (SA) and jasmonic acid (JA) pathways. Conversely, overexpression of BtRDP or silencing of NtRLP4 effectively alleviates such negative effects. In planthopper Nilaparvata lugens, the Delphacidae-restricted salivary protein NlSP104 also targets and promotes the degradation of OsRLP4 from rice plants. These findings reveal convergent evolution of salivary proteins in insects, and underscore the complex interactions between plants and herbivorous insects.

molecular biology↗

bioRxiv2025

Time-Resolved Crystallography Reveals the Mechanisms of GTP hydrolysis for N-RAS and the Oncogenic Mutants G12C, G12V and Q61L

The RAS family of small GTPases are molecular switches that convey downstream signals regulating cell proliferation, differentiation, and apoptosis. The signaling competent GTP-bound RAS transitions to its inactive GDP-bound form through {gamma}-phosphate hydrolysis. Oncogenic RAS mutations hamper GTP hydrolysis and are present in up to 30% of all human cancers. Structural studies of RAS proteins bound to non-hydrolysable GTP analogs have revealed snapshots of the enzyme in its possibly active form. Yet, the mechanism of GTP hydrolysis has not been structurally resolved. To visualize this reaction in real time, we performed time-resolved crystallographic experiments employing a photolabile caged-GTP substrate. Fifty-seven distinctive reaction intermediates were captured during hydrolysis of a live GTP for N-RAS, the oncogenic mutants G12C, G12V and Q61L; and Y32R, a fast hydrolytic mutant. The reaction mechanisms and rates for the native and each of the mutants differed significantly; however, they shared common elements: an initially catalytically-defective open state, which transitions into the closed Michaelis complex state with solvent-assisted O3B-P{gamma} bond lengthening and breaking, followed by the release of the Mg2+ stabilized PO3-/PO4-3 species and unfolding of the switch loops. Given the conserved nature of GTP- and ATP-ases active sites, this structural work lays the basis to understand the universal mechanism of {gamma}-phosphate hydrolysis. Furthermore, search for cryptic binding sites during GTP hydrolysis in G12C, G12V, and Q61L mutants reveals the presence of distinctive state-dependent binding pockets that could be targets for structure-based drug discovery of experimentally resolved intermediates states.

cancer biology↗

bioRxiv2025

A Tissue Proteolysis Activity Mapping and Substrate Discovery Platform for Identifying Novel Tumor-Activated Biosensors

Dysregulated extracellular proteolytic activity is a prominent hallmark of cancer and can thus be exploited for tumor detection and therapeutic development. However, the discovery of tumor-responsive probes has been hindered by the lack of methods capable of capturing proteolytic events directly in tissue samples. Here, we report PSurf, a platform that enables the identification of tissue-specific protease sensors with tissue specimens. Through differential selection of tumor-specific sequences over healthy tissue, PSurf identified context-specific tumor-activated probes that precisely distinguish metastatic lesions in lung tissue slices. Using these substrates, we engineered nanobody-targeted biosensors that release urinary reporters upon tumor-specific cleavage in vivo, enabling precise noninvasive tumor detection in a murine lung metastasis model. PSurf provides a foundation for developing conditionally activated agents through tissue-specific activity mapping and probe discovery.

bioengineering↗

bioRxiv2025

GPCR Antagonism via Antibody-Mediated Rewiring of Receptor Trafficking and Degradation

G-protein coupled receptors (GPCRs) represent one of the most important yet incompletely targeted classes of therapeutic proteins. Here, we report a novel strategy for functional GPCR antagonism through antibody-mediated endocytosis and lysosomal degradation. Our engineered bispecific antibodies, termed GPCR-TfR1 Targeting Chimeras (GTACs), achieve potent and selective downregulation of various GPCRs, including RXFP1 and CCR6, critical cancer and immune drug targets that are difficult to antagonize with conventional approaches. GTACs led to complete inhibition of receptor activity with over 100-fold greater potency than conventional antibody antagonists. Using four-color imaging, we elucidated the trafficking mechanism of both the target protein and TfR1 in living cells. The GTAC platform enables robust antagonism of signaling across diverse GPCR families and establishes induced endocytosis and lysosomal trafficking as a fundamentally new paradigm for therapeutic GPCR modulation.

bioengineering↗

bioRxiv2025

CIAdex: Single-Cell FTIR Spectral Fingerprinting for Cell Identity Verification and Aging Quantification in Therapeutic Cell Manufacturing

Ensuring the identity and optimal aging state of cell products is critical for the efficacy and safety of cell therapies. Despite rapid iterations, there remains an urgent need for robust and easy-to-implement tests to characterize cell products. Here, we present CIAdex (Cell Identification and Aging Index), an analytical framework that utilizes single-cell Fourier-transform infrared (FTIR) spectral fingerprints and machine learning to achieve precise label-free cell identity assessment and aging quantification. CIAdex employs a Feature Extraction Processor to automatically extract FTIR spectral variables corresponding to distinct cellular biomolecular features, enabling reliable distinction of lineage-, donor-, and batch-specific cell populations using linear discriminant analysis. Through application of the XGBoost algorithm, a quantitative aging index (trPDL/trPN) was further generated for tracking cellular aging dynamics along culture expansion. Notably, trPDL/trPN quantitatively represent subtle age-related shifts among different batches and drug-induced senescence or rejuvenation effects which are unmeasurable by existing methods. Together, our work demonstrates that CIAdex, by simultaneous label-free identity verification and aging quantification of cell populations, offers a transformative approach to interpret single-cell FTIR spectral fingerprints and provides novel metrics for quality control in cell manufacturing with significant potential for optimization and assurance of cell therapies safety and efficacy.

cell biology↗

bioRxiv2025

Human hippocampal ripples prioritise model-based learning

Humans often learn optimally, inferring the value of options they have never directly experienced by leveraging internal models of the world, a process known as model-based learning. Yet how the brain decides which unexperienced options to update first remains unclear. Here we recorded intracranial EEG from 34 epilepsy patients performing a reinforcement-learning task that required using task structure to infer the value of unvisited (non-local) paths. After each reward, brief hippocampal "ripple" events signalled which indirect experience was most valuable, thereby encoding that paths priority. Longer ripples carried the strongest priority signals, allowing the brain to update high-value, unvisited options first and thereby optimise learning. Ripple events also coincided with selective cortical reactivation of these high-priority paths, consistent with prioritised replay. Crucially, when hippocampal ripples were precisely synchronised with activity in the lateral frontopolar cortex (LFPC), individuals showed greater model-based learning: stronger ripple-LFPC coupling predicted more effective use of task structure and more accurate learning of non-local values. Our findings establish hippocampal ripple-centred prefrontal coordination as a fundamental mechanism that prioritises valuable experiences for model-based learning, explaining how the human brain learns so efficiently.

neuroscience↗

bioRxiv2025

MRI-based 3D Estimation of Skeletal Muscle Architecture and Strain during Contraction

Skeletal muscle generates forces that drive the motion of the human body. Three-dimensional (3D) quantification of whole-muscle architecture and strain, and their relationship during contraction is critical to understanding the mechanical function of skeletal muscle in health and disease. This has proven to be challenging, as brightness mode ultrasound is capable of measuring muscle architecture during contraction but cannot capture 3D changes in whole-muscle architecture, while Diffusion Tensor Imaging (DTI)-based tractography can measure 3D whole-muscle architecture but its use during contraction is precluded by long scan times (>5 minutes). In this study, we implement DTI-based tractography with an image registration-based approach, previously validated under passive deformation, to estimate 3D whole-muscle architecture of the tibialis anterior (TA) muscle during moderate intensity contractions (20-40% MVC). Moreover, this approach allows the measurement of whole-muscle strain during contraction, facilitating the evaluation of intramuscular relationships between architecture and strain. Our results show a decrease in the fiber-tract length, an increase in the pennation angle, and an increase in the fiber curvature of the TA during contraction. Intramuscular strain heterogeneity was observed between and within different regions of the muscle, with exploratory analyses suggesting that regional strain heterogeneity could be influenced by muscle architecture. Our results showcase the potential of MRI-based methods to obtain 3D estimates of whole-muscle architecture and strain during contraction, providing a breadth of new data that allows for new avenues of skeletal muscle biomechanical research.

bioengineering↗

bioRxiv2025

Membrane Tethering of Honeybee Antimicrobial Peptides in Drosophila Enhances Pathogen Defense at the Cost of Stress-Induced Host Vulnerability

Antimicrobial peptides (AMPs) represent a promising alternative to conventional antibiotics in combating multidrug-resistant pathogens, yet their clinical translation is hindered by proteolytic instability, cytotoxicity, and poor bioavailability. Here, we demonstrate that glycosylphosphatidylinositol (GPI)-mediated membrane tethering of honeybee defensin1 (Def1) in Drosophila melanogaster enhances its antimicrobial efficacy by [~]100-fold compared to secreted or untethered forms, while preserving physiological and behavioral integrity under baseline conditions. Using a genetically engineered Drosophila model, we expressed three Def1 variants: native (Def1), secreted (s-Def1), and membrane-tethered (t-Def1). Flies expressing t-Def1 exhibited superior bacterial clearance of Pseudomonas aeruginosa and improved survival post-infection, with no adverse effects on locomotion, courtship, or sleep architecture. However, under stress paradigms--including sleep deprivation and dextran sulfate sodium (DSS)-induced gut injury--t-Def1 exacerbated intestinal barrier dysfunction, as evidenced by elevated Smurf phenotype incidence, highlighting a trade-off between antimicrobial potency and epithelial vulnerability. Our work establishes Drosophila as a powerful platform for dissecting AMP mechanisms and engineering spatially targeted therapies, offering translational insights for pollinator health and human infectious disease management. These results advocate for iterative refinement of membrane-anchoring strategies to balance therapeutic efficacy with host safety, advancing the development of next-generation AMPs with minimized off-target effects.

biochemistry↗

bioRxiv2025

AlphaFlex: Accuracy modeling of protein multiple conformations via predicted flexible residues

Understanding protein conformational dynamics is critical for elucidating disease mechanisms and facilitating structure-based drug design. While AlphaFold2-based methods have advanced static structure prediction, modeling multiple conformation states with both accuracy and efficiency remains challenging. We present AlphaFlex, an innovative framework that integrates flexible residue prediction with a directed masking strategy for multiple sequence alignments. By selectively relaxing co-evolutionary constraints in dynamic regions, AlphaFlex enables accurate prediction of biologically relevant states while preserving structural fidelity. Benchmarking on 69 apo-holo pairs from the CoDNaS dataset, including enzymes, binding proteins, and chaperones, reveals AlphaFlexs superior performance in both flexible residue identification and multiple conformation prediction. Comparative analysis against AF-Cluster, AF2-conformations, and AlphaFlow demonstrates AlphaFlexs significant advantage, achieving the highest success rate (42%) in accurately predicting apo/holo structures (TM-score >0.95 for both states) while consistently outperforming these methods in reproducing both apo and holo conformations. Notably, AlphaFlex maintains robust performance for membrane proteins, resolving inward- and outward-facing conformations with equal fidelity. Case studies further reveal its unique ability to sample physically plausible intermediate states along transition pathways. These results establish AlphaFlex as a pivotal computational tool for mapping protein conformational landscapes, with promising potential to accelerate structure-based therapeutic development.

bioinformatics↗

bioRxiv2025

Buyang Huanwu Decoction Ameliorates Peripheral Nerve Injury by Promoting Cell Cycle through Activation of PI3K/AKT/mTOR/HIF-1α Pathway

BackgroundPeripheral nerve injury (PNI) can lead to partial or even total motor and sensory dysfunction, severely affecting the work and life of patients, but recovery of nerve function is often poor due to the complexity of the nerve repair and regeneration process. Cumulative evidence suggests the contribution of cell cycle regulation in repairing PNI injury, and p27KIP1 is a key molecule in regulating the cell cycle. ObjectiveThe aim of this study is to elucidate the repair mechanism of peripheral nerve injury (PNI) from the point of view of regulating cell cycle and to explore the therapeutic effect of Buyang Huanwu Decoction (BHD). To provide new strategies for the treatment of PNI and to explore valuable drugs initially. MethodsThe clamp injury model was chose as a PNI model and different doses of BHD extract were administered by gavage for 14 days. Limb motor function, sciatic nerve index and sciatic nerve pathology were assessed and p27Kip expression level was determined. The in vivo chemical composition of BHD extract was determined and drug targets were retrieved by TCMSP, STITCH and Swiss Target Prediction to predict the mechanism of BHD treatment for PNI using network pharmacology. Pathway-related proteins including P-PI3K, P-AKT, P-mTOR and HIF-1a were validated by western blotting assay. ResultsCompared with control rats, PNI rats had abnormal motor function, sciatic nerve damage and reduced p27Kip expression. Administration of BHD for 14 days significantly improved PNI in rats, which not only repaired sciatic nerve function, attenuated sciatic nerve pathology and inhibited p27Kip expression to regulate the cell cycle in PNI rats, but also activated the PI3K/AKT/mTOR/HIF-1a pathway. ConclusionThe above results suggest that PI3K/AKT/mTOR/HIF-1a mediated cell cycle regulation may be an important repair mechanism for PNI, and that BHD can improve PNI by accelerating the cell cycle to promote neural repair and regeneration.

cell biology↗

bioRxiv2025

A reference panel for linkage disequilibrium and genotype imputation using whole-genome sequencing data from 2,680 participants across India

India is the most populous country globally, yet genetic studies involving Indian individuals remain limited. The Indian population is composed of many founder groups and has a mixed genetic ancestry, including an ancestral component not observed anywhere outside of India. This presents a unique opportunity to uncover novel disease variants and develop more tailored medical interventions. To facilitate genetic research in India, a crucial first step is to create a foundational resource that serves as a benchmark for future population studies and methods development. To this end, we have constructed the largest and most nationally representative linkage disequilibrium and genotype imputation reference panels in India to date, using high-coverage whole-genome sequencing data of 2,680 Indian participants from the Longitudinal Aging Study in India-Harmonized Diagnostic Assessment of Dementia (LASI-DAD). As an LD reference panel, LASI-DAD includes 69.5 million variants, representing 170% and 213% increases relative to the 1000 Genomes Project (1000G) and TOP-LD panels, respectively. Besides serving as an LD lookup panel, LASI-DAD facilitates various statistical analyses that rely on precise LD estimates. In a polygenic risk score (PRS) analysis, LASI-DAD improved the predictive performance of PRS by 2.1% to 35.1% across traits and studies. As an imputation reference panel, LASI-DAD improved the imputation accuracy by 3% to 101% (mean = 38%) compared to the TOPMed panel (Version R3) and by 3% to 73% (mean = 27%) compared to the Genome Asia Pilot (GAsP) panel across different minor allele frequencies. The LASI-DAD reference panel is publicly available to benefit future studies.

genetics↗

bioRxiv2025

Accurate Protein-Protein Interactions Modeling through Physics-informed Geometric Invariant Learning

AlphaFold has set a new standard for predicting protein structures from primary sequences; however, it faces challenges with protein complexes across species, engineered proteins, and antigen-antibody, where co-evolutionary signals may be sparse or missing. Herein, we present ProTact, a SE(3)-invariant geometric graph neural network that integrates physics-informed geometric complementarity and trigonometric constraints as robust inductive biases to enhance protein-protein contact predictions. ProTact is applicable to both experimental and predicted monomer structures and utilizes a modulated key point matching algorithm to approximate accurate docking poses. Experimental evaluations demonstrate that ProTact consistently outperforms state-of-the-art sequence-based and structure-based methods on benchmark datasets, achieving notable relative improvements of 31.63% in Precision@10 for CASP 13 and 14 targets, and 31.94% for DIPS-Plus datasets. Moreover, when combined with AlphaFold3 as re-scoring functions, ProTact surpasses its default confidence scores, offering over 30.48% improvements in the low-MSA contexts. We anticipate that the proposed framework will advance our understanding of protein interactions, functions, and design.

bioinformatics↗

bioRxiv2025

Cryogenic Electron Tomography Redefines Herpesvirus Capsid Assembly Intermediates Inside the Cell Nucleus.

Herpesviruses encapsulate their double-stranded DNA (dsDNA) genomes within an icosahedral nucleocapsid formed in the infected cell nucleus. Four biochemically purified nucleocapsids have been characterized, but their roles in herpesvirus replication remain controversial. The status of the capsid vertex-specific component (CVSC), essential for capsid stability and dsDNA packaging and retention, is also unclear. By integrating cryogenic focused ion beam milling with electron tomography and subtomogram averaging, we derived atomic models for all protein components, including the CVSC, across different herpesvirus capsid types within infected cell nuclei. Focused classification of pentonal vertex densities revealed differences in CVSC occupancy between genome-filled capsids and capsids lacking dsDNA, highlighting structural heterogeneity and providing insight into distinct capsid assembly stages in situ. These intra-nuclear findings redefine the maturation model of herpesvirus capsid assembly, advancing the understanding of herpesvirus replication, and demonstrate the effectiveness of in situ electron imaging by studying virus assembly within host cells.

microbiology↗

bioRxiv2025

Prime assembly with linear DNA donors enables large genomic insertions

Targeted insertion of large DNA fragments has promising applications for genome engineering and gene therapy1,2. Twin prime editing (PE) guide RNAs (pegRNAs) have enabled relatively large insertions, but the efficiency remains low for insertions greater than 400 base pairs3-6. Here we describe a Prime Assembly (PA) approach for the insertion of large DNA donor fragments, whose ends are designed to overlap with the flaps generated by twinPE. We used PA to insert one, two, or three overlapping DNA fragments, with total insertion sizes ranging from 0.1 to 11 kilobase pairs. An inhibitor of non-homologous end joining (NHEJ) enhanced both the efficiency and precision of insertions. PA relies on DNA templates that are easily produced and does not require co-delivery of exogenous DNA-dependent DNA polymerases. Our study demonstrates that PA can initiate "Gibson-like" assembly in cells to generate gene insertions without double-stranded DNA breaks or recombinases.

biochemistry↗