Biology subjects

Ma, J.

Publications and source records attributed to Ma, J..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

A Generative Foundation Model for Antibody Design

Antibodies are indispensable components of the immune system, yet the design of high-affinity antibodies remains a time-consuming and experimentally intensive process. To address this challenge, we present IgGM, a novel generative foundation model designed to accelerate high-affinity antibody engineering. IgGM learns the complex relationships underlying the binding interactions between antigens and antibodies, as well as the mapping between antibody sequences and structures. By conditioning on different inputs, IgGM supports a wide range of antibody design tasks, including complex structure prediction, inverse design, affinity maturation, framework optimization, humanization, and de novo antibody design. It is compatible with both conventional antibodies and nanobodies, and allows user-defined CDR loop lengths for flexible design. To prioritize candidates, we introduce a frequency-based computational screening strategy that enhances design efficiency. Extensive evaluation through both in silico benchmarks and in vitro experiments across diverse antigens such as PD-L1, Protein A, TNF-, IL-33, SARS-CoV-2 RBD and its variants demonstrates that IgGM consistently generates antibodies or nanobodies with high measured affinity. These results underscore IgGMs versatility and effectiveness as a powerful tool for next-generation antibody discovery and optimization.

bioinformatics↗

bioRxiv2025

Visible Light-Controllable Surgical Hemostatic Adhesives Enabled by Vitamin B12-Stabilized Poly(α-Lipoic Acid)

Water-resistant adhesives are indispensable for biomedical applications, from surgical wound closure to internal hemostasis. While poly(-lipoic acid)-based adhesives show promise for their strong underwater adhesion, their clinical utility has been limited by uncontrolled polymerization-depolymerization dynamics. Here we present a visible light-controllable adhesive system enabled by a simple mix of -lipoic acid (LA) and vitamin B12 (i.e., adenosylcobalamin or AdoB12)--a photolabile compound--without resorting to any chemical modification. Benign visible light irradiation facilitates the cleavage of the C-Co bond and the subsequent formation of B12-thiolate complexes that stabilize LA polymers against depolymerization. The photoresponsive LA-AdoB12 adhesive system has proven highly effective in a wide range of surgical applications, achieving (1) strong bonding in porcine skin models in vitro, (2) reliable sealing of punctured organs (lung, heart and stomach) ex vivo, and (3) immediate hemostasis in active bleeding models such as topical, esophageal, and intestinal wounds in vivo. This work highlights a simple yet powerful strategy for creating visible light-controllable bioglues well-suited for diverse surgical applications.

bioengineering↗

bioRxiv2025

CCL5/CCR5 signaling modulates depression-relevant behavior, neuronal oscillations, and long-term depression of synaptic activity.

Major depressive disorder (MDD) is a debilitating disorder, often associated with perseverative thinking and anxiety. Localized reductions in pyramidal cell activity may contribute to associated symptoms, and effective antidepressant treatments typically enhance overall neuronal excitation. CCL5 is a chemokine that has been shown to reduce excitatory-neuronal activity, and is also increased with MDD and conditions that increase MDD risk. Here, we investigate the CCL5/CCR5 axis for its ability to modulate depression-relevant endpoints that are diminished in MDD, including neuronal oscillations, as well as biochemical and behavioral correlates of the disorder. In comparison to wildtype mice, CCR5 knockouts had increased gamma and theta power, and stronger theta/high-gamma phase amplitude coupling during dark-cycle EEG recordings. Compared to strain-matched wildtype mice, CCR5 knockouts also demonstrated reduced anxiety, increased sucrose preference, and improved associative memory. Proteomic analysis of the hippocampus showed that CCR5 knockouts had reduced levels of the GABA receptor alpha-4 subunit, which mediates tonic inhibition and restricts pyramidal cell plasticity. In complementary primary neuronal culture studies, CCL5 diminished GSK-3{beta} activity and impaired NMDA-dependent long-term depression (LTD), a form of plasticity that promotes cognitive flexibility. In addition, CCL5 signaling increased parvalbumin expression in GABAergic neurons through a CCR5-dependent manner. In combination with the ability of CCR5 to restrain gamma oscillation power and LTD, our data raise the possibility that CCL5/CCR5 signaling inhibits neuronal excitation through increased PV+ interneuron activity. Moreover, data are consistent with the possibility that CCR5 antagonists might share the ability of established antidepressants to both increase PC excitation and reduce PC inhibition. Significance StatementMajor depressive disorder (MDD) is a global leading cause of disability, and is associated with increased chemokine activation and inflammation. In this study, we investigate how the CCR5/CCL5 chemokine axis regulates behavioral and cognitive endpoints associated with MDD. This study aims to provide insight to how chemokine signaling underlies mood and behavioral symptoms of neuropsychiatric disorders. We hope this research supports further investigation of CCR5 antagonists for MDD and related mood and anxiety disorders.

neuroscience↗

bioRxiv2025

Crosslinking of Lipid Nanoparticles Enhances the Delivery Efficiency and Efficacy of mRNA Vaccines

Lipid nanoparticles (LNPs) have enabled the effective delivery of RNA therapeutics and mRNA vaccines. However, their broader applications are limited by the suboptimal stability and endosomal escape efficiency. Here, we present an easy-to-adopt post-assembly crosslinking approach to enhance the structural and functional stability of mRNA LNPs. By leveraging a series of cholesterol derivatives and crosslinking methods, we induce crosslinks of the lipid components following mRNA LNP assembly to form the crosslinked LNPs (cLNPs). We systematically evaluated crosslinking parameters and identified optimal conditions that enhance both the physical stability and transfection efficiency of cLNPs. Our findings demonstrate that cLNPs exhibit improved structural integrity under storage and lyophilization conditions, as well as increased extracellular stability and endosomal escape efficiency, resulting in improved performance of mRNA LNPs both in vitro and in vivo. This crosslinking strategy represents a critical advance in LNP engineering, enabling more resilient LNPs and broadening the applicability of LNP-based therapies for gene therapy and vaccine delivery. Our work lays the foundation for developing next-generation LNPs with superior stability and delivery efficiency, broadening the impact of RNA therapeutics and vaccines.

bioengineering↗

bioRxiv2025

Stress granule sequestration of OXPHOS gene transcripts exacerbates glycolytic restriction

Stress granules (SGs) are dynamic organelles formed under cellular stress and they are generally regarded as protective entities. Meanwhile, their role in pathogenesis is becoming increasingly recognized, but the underlying mechanisms remain elusive due to the diverse nature of both stress types and biological contexts. Here we investigate SG dynamics and temporal changes in bulk and SG-associated transcriptomes under different regimens that inhibit glycolysis. We subject cells to either single assaults of glucose depletion (GD) or 2-deoxy-D-glucose addition (2DG) or a combined treatment (GD+2DG). We find that SGs formed under these conditions exhibit distinct properties, including eIF2 phosphorylation dependency, mRNA composition, and capacity to disassembly. Our results show that SGs induced by GD+2DG uniquely trap oxidative phosphorylation (OXPHOS) gene transcripts, leading to mitochondrial dysfunction. We provide evidence suggesting that the persistency of SGs formed under GD+2DG treatment is interwoven with mitochondrial dysfunction resulting in heightened apoptosis, effects that can also be recreated under single assaults when combined with mitochondrial inhibition. Our findings suggest that SG formation induced by inhibiting a single metabolic pathway can widen its impact in intensifying cellular metabolic stress under specific conditions, providing mechanistic insights into the paradoxical dual nature of SGs in stress response and pathology.

cell biology↗

bioRxiv2025

Translational control of innate barrier defense by the gut microbiota

The intestinal epithelium is protected by a mucus barrier, infused with antimicrobial proteins, that restricts microbial access to host tissue. Because assembling this barrier is energetically costly, its production must be tightly regulated. Here, we show that the microbiota regulates the translation of key mucus barrier components, including the structural glycoprotein mucin 2 and the antimicrobial enzyme lysozyme. This process is initiated by microbial induction of histone deacetylase 5 (HDAC5) in secretory epithelial cells of the intestine. HDAC5 promotes deacetylation of 14-3-3 proteins, enabling activation of the energy sensing kinase mTOR which enhances translation of mucus and antimicrobial proteins. These findings reveal a mechanism by which the microbiota controls barrier immunity at the level of protein synthesis and suggest that the HDAC5-mTOR axis integrates microbial and energetic signals to regulate intestinal defense. One sentence summaryThe gut microbiota enhances translation of innate barrier defense proteins through HDAC5-mediated activation of mTORC1 signaling.

immunology↗

bioRxiv2025

A synaptic mechanism for encoding the learned value of action-derived safety

Motivated behavior is often framed in terms of biologically grounded outcomes, such as food or threat. Yet many motivated actions, like the pursuit of safety or agency, depend on outcomes that lack explicit sensory value and must instead be inferred from experience. Here, we identify a thalamostriatal circuit mechanism by which such internally constructed outcomes acquire motivational value. In mice performing an active avoidance task, neurons in the paraventricular thalamus (PVT) projecting to the nucleus accumbens (NAc) develop a safety-encoding signal that emerges following successful avoidance. This signal is experience-dependent and value-sensitive, diminishing upon devaluation of the instrumental contingency. Selective silencing of the PVT[->]NAc projection at safety onset disrupts avoidance persistence without impairing action-outcome learning, as confirmed by computational modeling of value updating based on prediction error. Mechanistically, PVT input recruits cholinergic interneurons (CINs) to modulate dopamine release and this influence depends on synaptic potentiation mediated by GluA2-lacking AMPA receptor insertion at PVT-CIN synapses. Disrupting this plasticity selectively impairs the avoidance response by blunting the motivational value of safety without affecting acquisition. These findings reveal how thalamic circuits assign value to abstract, internal outcomes, providing a framework for understanding how goals like safety are inferred, stabilized, and rendered behaviorally effective.

neuroscience↗

bioRxiv2025

DANCE 2.0: Transforming single-cell analysis from black box to transparent workflow

Preprocessing is a critical step in single-cell data analysis, yet current practices remain largely a black-box, trial-and-error process driven by user intuition, legacy defaults, and ad hoc heuristics. The optimal combination of steps such as normalization, gene selection, and dimensionality reduction varies across tasks, model architectures, and dataset characteristics, hindering reproducibility and method development. We present DANCE 2.0, an automated and interpretable preprocessing platform featuring two key modules: the Method-Aware Preprocessing (MAP) module, which discovers optimal pipelines for task-specific methods via hierarchical search, and the Dataset-Aware Preprocessing (DAP) module, which recommends pipelines for new datasets via similarity-based matching to a reference atlas. Together, MAP and DAP execute over 325,000 pipeline searches across six major tasks - clustering, cell type annotation, imputation, joint embedding, spatial domain identification, and cell type deconvolution - yielding robust and generalizable recommendations. MAP-recommended pipelines consistently outperform original method defaults, with substantial gains across all tasks. Beyond automation, DANCE 2.0 reveals interpretable preprocessing patterns across tasks, methods, and datasets, transforming preprocessing into a transparent, data-driven process. All resources are openly available at https://github.com/OmicsML/dance to support broad community adoption and future methodological advances.

bioinformatics↗

bioRxiv2025

Convergent Evolution of Sociality Causes Reduction of Mutation Rates in Spiders

Germline mutation rates influence the pace of molecular evolution, yet the roles of selection and life history in shaping their evolution remain to be determined. Comparative systems with replicated evolutionary transitions provide a unique opportunity to determine how changes in life history influence germline mutation rates. In the spider genus Stegodyphus, permanent sociality evolved independently three times within the past million years and is associated with obligate inbreeding, female-biased sex ratios, reduced fecundity, and sharply reduced effective population sizes. We sequenced 202 parent-offspring trios from 34 full-sibling families across three social and four closely related subsocial species and analysed quality-filtered trios in a phylogenetic comparative framework. Each independent transition to sociality was associated with an approximately 2-fold reduction in the de novo mutation rate in the germline. Phylogenetic analyses of synonymous branch lengths suggest that the mutation rates declined in parallel with the transitions to sociality. These rapid reductions in mutation rates in social lineages with small effective population sizes run counter to the drift-barrier hypothesis, which predicts that reduced selection efficacy would lead to higher mutation rates. We find no evidence that reduced mutation rates in the social species was favoured by selection for improving DNA repair efficiency, since there is no upregulation of DNA repair pathway genes in the ovaries of the social species. On the contrary, the mutation rate is reduced across mutational classes and in somatic tissue in social species compared with their subsocial counterparts. These patterns suggest that the reduction in mutation rate in social spiders is a consequence of convergent life history changes, including reduced body size and production of fewer, larger eggs. Our results highlight that the evolution of sociality, which entails major life history changes, can rapidly reshape fundamental evolutionary parameters, such as the germline mutation rate.

evolutionary biology↗

bioRxiv2025

BrainBeacon: A Cross-Species Foundation Model for Single-cell Resolved Brain Spatial Transcriptomics

The brains functional complexity emerges from spatiotemporal heterogeneity in molecular, cellular, and circuit organization, shaped by evolution, aging, and disease. Single-cell spatial transcriptomics provides a transformative framework to decode this complexity, resolving cell-type-specific expression patterns, region-specific regulation, evolutionary divergence, and disease-associated disruptions. Despite recent advances in spatial transcriptomics, a unified foundation model capturing cross-species, whole-brain cellular architecture remains lacking. Here, we introduce BrainBeacon, the first cross-species foundation model for whole-brain spatial transcriptomics. Trained on 133 million spatially resolved cells covering a total area of 210194 mm2 from human, macaque, marmoset and mouse brains profiled across five major platforms, BrainBeacon integrates gene expression rankings, spatial cellular organization, and evolutionarily conserved genetic relationships into a unified transformer-based architecture. A two-stage training strategy captures both intra-cellular transcriptional dependencies and inter-cellular spatial interactions, yielding biologically grounded and interpretable representations of brain structure. Subsequently, BrainBeacon enables cross-species alignment of brain cell types and anatomical regions, facilitating integrative analyses of conserved and divergent cellular architectures. Moreover, it uncovers spatial regulatory mechanisms of aging by predicting bidirectional perturbation responses between cells and their local niche. Together, BrainBeacon serves as a foundational cross-species model for whole-brain spatial transcriptomics, enabling virtual brain atlas construction, systematic in silico perturbation studies, and mechanistic insights into brain disease pathogenesis.

bioinformatics↗

bioRxiv2025

Thrombin-preconditioned Mesenchymal Stem Cell-Derived Exosomes For Wound Healing in vitro and in vivo

Background and ObjectivesThe skin is the largest organ of the human body, capable of protecting it from external harm. However, due to trauma, paralysis and other external factors, skin damage can occur, scars may form. Exosomes have regenerative functions and, as a cell-free therapy, show great potential for wound healing. In this study, we investigate that whether different umbilical cord mesenchymal stem cell exosomes (UCMSCs-Exos) can accelerate the healing of skin. MethodsIn our study, UCMSCs were cultured from newborns and Cultured with thrombin. Exosomes were isolated from mesenchymal stem cells culture supernatant by ultracentrifugation. The impact of exosomes on Hacat cell migration was evaluated in vitro. Additionally, the wound healing capacity of exosomes was evaluated in vivo using a mouse skin injury model. ResultsCompared to UCMSCs-Exos, T-UCMSCs-Exos significantly promoted cell proliferation and migration of cells. In vivo experiments demonstrated that T-UCMSCs-Exos can accelerate wound closure and enhance collagen maturation, promoting angiogenesis in the vascularized wound area. These results indicate that T-UCMSCs-Exos have a good potential for accelerating wound healing and minimizing scar formation. ConclusionsOur research indicate that thrombin pre-UCMSCs, the production of exosomes significantly increased. The prepared T-UCMSCs-Exo can accelerate skin wound healing during the process of skin injury repair, promote angiogenesis, and facilitate the reconstruction of epidermis and dermis as well as hair follicle regeneration. These findings demonstrate that T-UCMSCs-Exos for skin wounds are a promising cell-free therapy that can be applied in the treatment of skin injuries.

cell biology↗

bioRxiv2025

Decoding functional genes across species with annotation-independent machine learning

Dissecting the genetic basis of complex traits across species is a challenge for traditional low-throughput, species-specific methods. To overcome these limitations, we introduce a computational framework that integrates cross-species comparative genomics and machine learning to identify functional genes for shared phenotypes, independent of prior annotation. Our method links orthologous gene group (OG) profiles to specific traits, enabling the powerful discovery of functional genes across diverse evolutionary clades. For plant-arbuscular mycorrhizal symbiosis, a notoriously difficult system, our model pinpointed a regulatory network by identifying 27 core plant-AM symbiosis genes among its top 50 candidate OGs, including the critical receptor SYMRK. The approach also proved highly effective for identifying functional genes related to the tested vertebrate skeletal development and multiple bacterial traits. Most notably, for bacterial motility, our model not only identified 63 known motility genes from the top 100 candidate OGs (of which 78 are present in Escherichia coli) but also guided the experimental validation of three novel essential genes. This annotation-independent strategy represents a paradigm shift in functional genomics, offering a scalable and universal engine to decode the genetic architecture of complex traits and illuminate the vast functional dark matter across the tree of life.

genomics↗

bioRxiv2025

Buffer Valency Engineering Enables High-concentration and Shelf-stable DNA Transfection Particles for Viral Vector Production

Cost-effective and scalable production is critical for advancing the clinical translation of adeno-associated virus (AAV)-mediated gene therapy. The widely used transient transfection method using plasmid DNA (pDNA)-loaded transfection particles for AAV production faces technical challenges due to instability of the particles and the concentration limits for particle preparation, hindering reproducibility and scalability. Here, we report a streamlined and scalable strategy to generate shelf-stable, highly concentrated pDNA/poly(ethylenimine) (PEI) transfection particles. By incorporating trivalent citrate ions in the dilution buffers, we kinetically modulate electrostatic complexation to achieve uniform nanoparticle assembly and prevent aggregation at high concentrations. This enables a tenfold increase in pDNA concentration in stabilized transfection particles from a typical range of 10-20 g/mL to 200 g/mL, while reducing the required dosing volume from 5-10% to 0.5% of the cell culture medium. The particle assembly process is robust to changes in mixing scale and timing and is compatible with standard workflows. We demonstrate equivalent AAV production efficiencies to standard methods and consistent performance in various production scales, which confirms the practical utility of this assembly method in developing robust, scalable, and cost-effective AAV manufacturing processes.

biochemistry↗

bioRxiv2025

An Evaluation of Biomolecular Energetics Learned by AlphaFold

Deep learning has revolutionized protein structure prediction, with function prediction on the horizon1,2. Biomolecular properties, including structure and all aspects of function, emerge from atomic-level interactions and the probabilities of their formation3,4. Learning the physical rules that govern these probabilities allows models to deliver accurate structure predictions and may enable extrapolation beyond the training data--a capability needed to predict the many biologically important functional properties where comprehensive data are not readily attainable5. Current structure-based models follow a training logic primarily focused on matching atomic coordinates, rather than atomic interactions and their probabilities. It remains unknown whether the models have learned the physical rules that underlie atomic interactions, the extent of their knowledge, and the prediction errors that arise from limits to this knowledge. We found that state-of-the-art structure prediction models, AlphaFold2, AlphaFold3, and ESMFold, capture basic energetic principles but show pervasive biases in the conformational preferences of molecular interactions. These biases manifest as widespread prediction errors, including the misassignment of a large fraction of side-chain non-covalent interactions--[~]30% for the AlphaFold models and [~]60% for ESMFold--and an inability to reproduce experimentally derived conformational ensembles. More than half the errors made by AlphaFold2 and AlphaFold3 are in common, suggesting limitations not overcome by using different model architectures. Overall, our multifaceted, physics-grounded evaluation identified previously unknown, system-wide deficiencies in current structure prediction models. This framework is applicable to and needed for all biomolecular structure and function prediction models that deliver atomic-level structural information. The insights derived from these evaluations will allow researchers to judiciously apply current models and will guide the development of next-generation models to achieve accurate prediction of biomolecular function.

biophysics↗

bioRxiv2025

Temporal Dynamics of Urinary Extracellular Vesicle Excretion and Cargo in Healthy Subjects over 24 Hours

Urinary extracellular vesicles (uEVs) are promising non-invasive biomarkers of renal physiology and pathology, yet little is known about their temporal excretion patterns or optimal normalization strategies as urine concentrations vary significantly during the day. In this basic physiology study, we used a uniquely designed processing protocol of urine collection to characterize the variation of uEV excretion and cargo throughout a 24 hour period in healthy subjects. Thirteen healthy adults collected every individual void over 24 hours and these voids were independently analyzed along with a composite sample intended to recreate a 24 hour collection sample. uEVs were enriched by low-speed centrifugation with three low-ionic-strength washes to minimize uromodulin contamination. Size, concentration, morphology and cargo of uEVs were characterized with nanoparticle tracking analysis, cryo-electron microscopy, immunoblotting and single EV flow cytometry. We observed a stable urine creatinine excretion into the urine over the day. uEV concentrations varied up to 100-fold across the day between individuals with a decreasing trend over time with the result close to reaching statistical significance (p=0.06). uEV concentration was positively associated with urine creatinine, specific gravity, and TSG101, an EV marker. The association between urine flow and uEV excretion varied across the day. Most tested uEV cargo markers exhibited substantial within individual variation over the day without consistent trends in our healthy cohort. When grouped into predefined time periods to visualize temporal patterns, a transient dip at noon was observed, followed by a significant increase in the subsequent period, consistent with a pattern previously reported. These findings offer foundational insights into uEV excretion patterns over the course of a day in a healthy cohort and emphasize key methodological considerations essential for advancing uEV biomarker research.

physiology↗

bioRxiv2025

Lf2 is a knotted homeobox regulator that modulates leaflet number in soybean

Variation in leaf complexity modulates light capture and is a target for crop enhancement. Soybean typically has compound leaves with three leaflets each, but a spontaneous mutation, designated lf2, possesses seven leaflets, offering a means to dissect the molecular mechanisms specifying leaflet number and assess its potential for soybean improvement. However, the developmental and genetic bases of the lf2 mutation remain unknown. Here, we characterize the seven-leaflet phenotype and identify the mutation responsible for the phenotypic changes. Microscopic examination of leaf emergence sites revealed that the seven-leaflet phenotype arises in a two-step process: five leaflets form initially followed by secondary leaflet initiation at the margins of the central leaflet. Genetic mapping delineated lf2 to a [~]2.5 Mb region at the start of chromosome 11. Fortuitously, integration of pedigree analysis with comparative analysis of genomic sequences from the region pinpointed a 2-bp deletion in the coding sequence of a gene, which is homologous to the Arabidopsis KNAT7 encoding a KNOTTED1-LIKE HOMEOBOX 2 transcription factor, as the sole candidate for Lf2. The deletion is predicted to result in disruption of the putative DNA-binding homeodomain. Expression of the wild-type allele of the candidate gene in the seven-leaflet lf2 mutant restored the three-leaflet phenotype, while disruption of the wild-type allele through CRISPR-Cas9 editing induced extra leaflet formation. This study advances our understanding of leaflet formation in legumes and provides a template for utilizing compound leaf architecture to optimize photosynthetic efficiency and yield in soybean.

plant biology↗

bioRxiv2025

Ketone body driven lipid remodeling supports thermogenic adaptation to fasting

Metabolic adaptation to fasting may have conferred survival advantage to early humans and predicts weight gain caused by overnutrition in modern societies. Fasting suppresses brown adipose tissue (BAT) thermogenesis; however, it is unclear how BAT rewires cellular metabolism to balance between energy conservation and heat generation. Here, we report that BAT in mice under fasting and cold challenge consumed ketone bodies, specifically acetoacetate (AcAc). Ablating liver ketogenesis decreased, while enhancing hepatic AcAc output defended, body temperature in mice facing the dual challenge. Using stable isotope tracing in brown adipocytes in vitro combined with quantitative analysis of metabolic fluxes and lipidomics in BAT from genetic mouse models, we disentangled the two metabolic fates of AcAc - terminal oxidation in the mitochondria and lipid biosynthesis in the cytosol. Notably, AcAc-sourced carbon preferentially supported polyunsaturated fatty acid synthesis in BAT, linking to the positive impact of intermittent fasting on lipid profiles in both mice and humans. Therefore, ketone body utilization by thermogenic adipocytes contributes to metabolic resilience of mammals and can be targeted to optimize benefits of dietary regimens.

physiology↗

bioRxiv2025

LSH-mediated resolution of R-loops mitigates transcription-replication conflicts to preserve genomic stability in prostate cancer cells

Prostate cancer cells exhibit heightened transcriptional activity to sustain their aggressive phenotype, yet this creates DNA topological stress, leading to RNA: DNA hybrids (R-loops) and DNA damage that compromise genomic stability. LSH, an SNF2-family chromatin remodeler, is frequently dysregulated in cancers and linked to tumor progression, but its mechanistic role in genome maintenance remains unclear. Here, we demonstrate that LSH resolves R-loops in an ATP-dependent manner, mitigating transcription- replication (TR) conflicts in prostate cancer cells. LSH depletion caused R- loop accumulation due to reduced FANCD2 recruitment, exacerbating DNA damage and impairing Rad51 filament formation. Strikingly, LSH deficiency also increased R-loops at promoters of MYC and E2F target genes, stalling RNA polymerase II elongation and disrupting transcriptional programs critical for proliferation. Our findings reveal LSH is a key guardian of genome integrity, resolving R-loops to prevent TR conflicts and maintaining DNA repair fidelity. By linking LSH to R-loop resolution and transcriptional regulation, this study reveals its dual role in prostate cancer pathogenesis-- supporting malignant proliferation while safeguarding genomic stability. These insights nominate LSH as a potential therapeutic target to disrupt oncogenic transcription and induce synthetic lethality in prostate cancer.

cancer biology↗