Biology subjects

Liu, Z.

Publications and source records attributed to Liu, Z..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

Mdig shapes 3D chromatin architecture of immune checkpoint genes and limits metastasis of triple negative breast cancer cells

Despite decades of progress in metastasis research, the identity of bona fide metastasis-driving genes remains elusive. By shifting the focus from individual genes to the three-dimensional (3D) architecture of the genome, we identify the mineral dust-induced gene (mdig) as a chromatin-topology regulator that suppresses immune-checkpoint activation and metastasis in triple-negative breast cancer (TNBC). Re-expression of mdig in mdig-knockout (KO) cells markedly reduced liver metastasis, whereas mdig loss activated epithelial-mesenchymal transition (EMT), T-cell exhaustion, and antigen-presentation pathways. Across multiple cancer types, high mdig expression predicted improved responses to immune checkpoint blockade (ICB). Mechanistically, mdig depletion derepressed inhibitory checkpoint genes, including PD-L1, PD-L2, LGALS9, and PLXNB1/2, accompanied by increased H3K9me3 and H3K36me3 at these loci. Hi-C profiling revealed that mdig maintains topologically associating domains (TADs) and long-range repressive loops at checkpoint loci; loss of mdig disrupted these structures, enabling coordinated activation of immune-evasion programs. Genome-wide analyses showed extensive TAD remodeling in mdig KO cells, with pronounced alterations on chromosome X. Collectively, these findings position mdig as a key chromatin-architectural regulator of immune evasion and metastatic behavior, underscoring its potential as a biomarker for ICB responsiveness in TNBC and beyond. Significance statementMetastasis remains the leading cause of cancer mortality, yet bona fide metastasis-driving genes remain difficult to define. By examining three-dimensional genome architecture rather than individual gene function, we identify mdig as a chromatin-topology regulator that restrains immune evasion and metastasis in triple-negative breast cancer. Loss of mdig disrupts TAD structures and long-range repressive loops at immune-checkpoint loci, enabling coordinated activation of EMT, antigen-presentation, and T-cell-exhaustion programs. Restoring mdig expression markedly reduces liver metastasis, and high mdig levels across cancers predict improved responses to immune-checkpoint blockade. These findings establish mdig as a key regulator of chromatin organization and a potential biomarker for immunotherapy responsiveness.

cancer biology↗

bioRxiv2025

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

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

genomics↗

bioRxiv2025

Evolutionarily Conserved T-tubule-Mitochondria Contacts in Striated Muscle

The intricate architecture of skeletal muscle is essential for its contractile function, with the spatial organization of organelles such as T-tubules and mitochondria playing a crucial role in maintaining muscle performance and health1,2. T-tubules propagate electrical signals deep into muscle fibers to ensure synchronous contraction, while mitochondria provide the necessary energy for muscle contraction3-5. Previous studies have extensively documented the interactions between T-tubules and the sarcoplasmic reticulum (SR), which are essential for excitation-contraction coupling6,7. However, the detailed spatial relationship between T-tubules and mitochondria has remained relatively unexplored. In this study, we utilized zebrafish and mice as model organisms to investigate the contacts between T-tubules and mitochondria. Using array tomography, deep learning-based analysis, and advanced microscopy techniques, we discovered extensive membrane contact sites, termed T-tubule-Mitochondria (TTM) contacts. These contacts are evolutionarily conserved across vertebrates, including skeletal and cardiac muscles. Our findings reveal a previously unrecognized, intimate spatial coupling between T-tubules and mitochondria, with significant implications for muscle physiology and pathology. Understanding these TTM contacts could provide new insights into the mechanisms underlying muscle function and the development of muscle-related diseases.

cell biology↗

bioRxiv2025

IgE-producing cells on the move: CCR2 is a key regulator of IgE+plasma cell migration

BackgroundImmunoglobulin E (IgE) plays a fundamental role in the pathogenesis of allergic disease, including asthma. The IgE-producing plasma cells (PCs) are thought to persist indefinitely, providing a sustained source of allergen-specific IgE. Although these cells can accumulate in the bone marrow (BM), after prolonged allergen exposure, their frequency remains remarkably low, and the mechanisms that regulate their migration are poorly understood. ObjectiveTo investigate the chemokine receptor profile and the migration potential of the human IgE-producing cells. MethodsTonsil B cells were stimulated with IL-4 and anti-CD40 to induce class switching to IgE and IgG1. The chemokine receptor profile of IgE+ and IgG1+ switched cells was determined using flow cytometry and migration towards relevant chemokines was quantified using transwell chemotaxis assays. Chemokine expression was also validated by re-analysis of a published single cell RNA sequencing (scRNAseq) dataset of PCs isolated from nasal polyps (NP) of patients with allergic fungal rhinosinusitis. ResultsIgE PCs exhibit significantly reduced expression of the BM-homing chemokine receptor CXCR4 and impaired migration towards its ligand, CXCL12. While IgE+ PCs can upregulate CCR10 and respond to its ligand, CCL28, this behaviour is similar to IgG1+ PCs. Strikingly, however, IgE PCs selectively upregulate CCR2 and migrate robustly towards its ligand CCL2. Re-analysis of NP scRNAseq data confirmed that IgE PCs express significantly higher levels of CCR2 compared with PCs of all other isotypes. ConclusionsThese findings identify CCR2 as a key regulator of IgE PC migration and provide insights into their homing preferences that may shape the nature of the IgE responses.

immunology↗

bioRxiv2025

Metabolic, epigenetic and transcriptomic alterations in postnatal 16p11.2 deficient murine astrocytes

Autism Spectrum Disorders (ASD) are associated with metabolic dysregulation. While astrocytes are integral to cerebral metabolism, their molecular and functional changes in ASD are poorly known. Using early postnatal primary cortical astrocytes from a mouse model of 16p11.2 deletion ASD syndrome (16p11.2df/+ mice), we observed core molecular alterations with sex-specific profiles, suggesting divergent energetic pathways and epigenetic regulation. Targeted metabolomics revealed opposing phenotypes in male versus female 16p11.2df/+ astrocytes, particularly for alpha-ketoglutaric acid. Functionally, 16p11.2df/+astrocytes exhibited elevated phosphorylation in low glucose culture conditions, and reduced glycolysis in high glucose. Epigenetic profiling of male 16p11.2df/+astrocytes revealed differentially hydroxymethylated and methylated regions, with foci on chromosomes 3 and 13. Finally, bulk RNA sequencing in male and female mutant astrocytes indicated differential gene expression with profound sex differences, mostly affecting pathways related to cellular morphology. By establishing 16p11.2df/+ astroglial molecular signatures, this study refines our understanding of glial changes in ASD.

cell biology↗

bioRxiv2025

DeepDOX1: A Dual-Drive Framework Integrating Deep Learning and First-Principles Physics for Drug-Protein Affinity Prediction

In this work, we present DeepDOX1, a dual-drive drug-protein affinity (DPA) prediction tool features the tight integration of a concise AI architecture and a quantum mechanics based representation. The first-principle physics generated features incorporating the interactions between the drug and the protein pocket allows a relatively simple CNN model trained on a relatively small training set to exhibit exceptional generalization capabilities across extensive testing. Notably, DeepDOX1 outperforms popular AI models in the tests simulating real-world drug design scenario and a highly challenging test set featuring covalent ligands, halogenated ligands and metalloproteins. In addition, we designed a series of novel covalent inhibitors targeting the diabetes target hu-FBPase using DeepDOX1. Subsequent experimental validation including enzyme-level bioactivity assays and crystal structure determination confirmed the DeepDOX1s effectiveness in real-world drug design applications. It is conceivable that the combination of AI and first-principle QM might be one of the next breakthrough points of DPA prediction.

bioinformatics↗

bioRxiv2025

Immunotherapy with Pro-regenerative Macrophages from Embryonic Stem Cells Ameliorate Osteoarthritis via TNFAIP3-Mediated Chondroprotection

Immune cell-based therapies for osteoarthritis (OA) remains underexplored. Macrophages coordinate tissue repair, yet their functional heterogeneity and therapeutic applicability, particularly for designed stem cell-derived populations with tailored reparative properties are not fully delineated. Inspired by embryonic skeletal development as a paradigm of scarless regeneration, we identified a pro-regenerative macrophage population through a single-cell RNA atlas of developing skeletal tissues. We subsequently established a mechanically dynamic induction approach to efficiently generate pro-regenerative macrophages from human embryonic stem cells (hESCs), mimicking this developmental phenotype. In vitro, these macrophages mitigate cartilage degradation in OA explants and suppress pro-inflammatory, catabolic signaling in chondrocytes. Injection into murine OA joints robustly attenuates disease progression, reduces extracellular matrix breakdown, and resolves synovial inflammation, representing the first demonstration of immune cell-based therapy for OA. Mechanistically, these macrophages orchestrate chondroprotection not through broad immunosuppression, but by activating a TNFAIP3-dependent signaling hub that restrains inflammatory and catabolic responses in chondrocytes. This TNFAIP3 activation precisely reversed the OA-associated gene signature, suppressing catabolic mediators while enhancing reparative factors, thereby restoring the anabolic-catabolic balance. Our findings uncover a developmental blueprint for engineering pro-regenerative macrophages from stem cells and establish a pioneering targeted immune cell therapy that engages an intrinsic chondroprotective program, offering a transformative and translationally relevant strategy for OA treatment.

immunology↗

bioRxiv2025

Synchronized Latency Reversal and Immune Clearance by a Multifunctional Fusion Protein Enables HIV-1 Reservoir Reduction

Strategies that concurrently reactivate latent reservoirs and enhance immune-mediated clearance hold significant promise for achieving an HIV cure. Here, we developed hyperIL-15xsCD4-Fc (15xsCD4-Fc), a fusion protein that integrates latency reactivation, targeted immune engagement, and effector-mediated killing into a single molecule. This agent not only potently reverses HIV-1 latency in CD4+ T cells from people living with HIV-1 (PLWH) through coordinated IL-15 receptor signaling and sCD4-mediated HIV-1 envelope (Env) engagement, but also enhances antigen-specific CD8+ T cell response in PBMCs derived from PLWH. Furthermore, 15xsCD4-Fc enables Env-specific elimination of reactivated latently infected cells by NK cells while preventing off-target cytotoxicity. In PBMCs from PLWH, 15xsCD4-Fc reduced replication-competent HIV-1 DNA by 93.8%. In antiretroviral treated HIV-1-infected humanized mice, the molecule demonstrated both safety and efficacy in diminishing viral reservoir in lymphoid organs. This spatiotemporally coupled approach to reservoir exposure and immune recognition establishes a clinically viable strategy for clearing the HIV-1 reservoir. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/693434v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@8f8f0org.highwire.dtl.DTLVardef@10f63f7org.highwire.dtl.DTLVardef@16c1de2org.highwire.dtl.DTLVardef@11e1787_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Reinforcement learning enables single-cell foundation models to learn cellular differentiation

While single-cell foundation models excel at static representation learning and single-step perturbation prediction, their capacity to model and control dynamic, sequential cell state transitions remains underexplored. Here, we introduce Differentiation with Reinforcement Learning (DiRL), a framework that transforms foundation models into predictive environments for optimizing multi-step perturbation strategies. By formulating differentiation as a goal-conditioned sequential decision-making problem, DiRL trains agents to navigate the high-dimensional latent landscape of gene expression, learning policies that direct stem cells toward specific terminal fates. Evaluated on iPSC-derived organoid datasets, DiRL outperforms random perturbation baselines with a 69% win rate, with performance scaling systematically as the planning horizon increases. Beyond optimization, DiRL offers interpretable insights into the mechanics of cell fate transitions: the learned policies successfully recover known sequential regulators in Wnt and Hedgehog signaling pathways, while the value function from the critic model recapitulates biological pseudotime orderings comparable to established trajectory inference methods. These results demonstrate that coupling reinforcement learning with foundation models enables a paradigm shift from static embedding analysis to dynamic trajectory modeling, providing a powerful engine for discovering sequential perturbation strategies in regenerative medicine.

bioinformatics↗

bioRxiv2025

Lysosomal swelling triggers LRRK2 activity

LRRK2 is implicated in lysosomal functions, but the physiological upstream cues that engage endogenous LRRK2 activity are incompletely defined. Here we show that lysosomal swelling serves as a selective and reversible trigger for LRRK2-mediated Rab phosphorylation, without requiring membrane damage. Acute inhibition of PIKfyve, but not the general disruption of phosphoinositide signaling, induces the robust accumulation of phosphorylated Rabs across endolysosomal membranes. Rescue of swelling through pharmacological restoration of lysosomal ionic imbalances from PIKfyve inhibition suppresses LRRK2 activation without restoring lysosomal function. Mechanical lysosomal swelling from indigestible osmolyte uptake causes a dose-dependent increase in LRRK2-mediated Rab phosphorylation on both swollen and non-swollen lysosomes. Together, these findings identify LRRK2 as a sensor of lysosomal volume and mechanical stress, not specifically membrane damage or PIKfyve inhibition. As lysosomal swelling is a shared pathological feature across LRRK2-linked diseases, these results reframe LRRK2 as part of an endolysosomal surveillance system responsive to lysosomal distension.

neuroscience↗

bioRxiv2025

Retroreflective beam multiplexing enables high-throughput two-photon voltage imaging in vivo

Voltage imaging demands technical innovations to realize its full potential in neuroscience. Although two-photon microscopy is widely used in brain research, its imaging speed is insufficient for high-throughput voltage recordings. To overcome this limitation, we developed an all-optical beam multiplexing engine via retroreflection from two near-parallel mirrors. This approach integrates seamlessly with standard two-photon microscopes, enabling kilohertz-frame-rate imaging across a 16-fold expanded field of view while maintaining synaptic resolution. Operating at over 220 megapixels per second, it enables submillisecond imaging of dendritic propagation of action potentials and simultaneous voltage recording from more than 200 hippocampal neurons in head-fixed, behaving mice. This advancement unlocks new possibilities for large-scale, high-speed functional studies in neuroscience.

neuroscience↗

bioRxiv2025

MFAP5 Drives Elastic Fiber Disorganization to Promote Pulmonary Fibrosis

BACKGROUNDElastic fibers (EF) disorganization contributes to increased tissue stiffness and impaired lung function in pulmonary fibrosis (PF). However, the complex structural features of EF are difficult to capture using conventional histology. Moreover, the molecular mechanisms governing EF homeostasis during fibrosis remain poorly understood. METHODSA high-dimensional Elastic Fiber Algorithm (EFA) was developed to digitally quantify EF structural features in PF. Gene variation-rate analysis was performed to identify candidate regulators of EF homeostasis. Fibroblast-specific and pathological fibroblast-specific MFAP5 knockout mice were generated to assess the role of MFAP5 in PF rodent models. Bulk RNA sequencing was employed to investigate MFAP5-mediated fibroblast activation and signaling pathways. RESULTSEFA revealed profound EF disorganization in fibrotic lungs, capturing various architectural alterations. Gene variation-rate analysis identified MFAP5 as a candidate regulator of EF homeostasis, with upregulated expression in PF patients and mouse models. Fibroblast-specific deletion of MFAP5 significantly attenuated fibrosis, restored EF architecture, reduced collagen deposition, and improved pulmonary function in PF mouse models. MFAP5-positive fibroblasts displayed a dynamic shift toward pathological states during PF progression. Mechanistically, MFAP5 promoted fibroblast activation and ECM production via v{beta}3 integrin-mediated TGF{beta} signaling. CONCLUSIONSMFAP5 is a key orchestrator of EF remodeling and fibroblast activation in PF. Targeting MFAP5 restores EF homeostasis, reduces fibrotic severity, and represents a potential therapeutic strategy for PF.

molecular biology↗

bioRxiv2025

From genomic decay to functional advantage: Trait-based evidence for long-term host residency of a next-generation coral probiotic

A key bottleneck in microbiome engineering is ensuring the long-term host association of introduced microbes. Selecting probiotic candidates based on evolutionary genomic decay signatures of emerging host dependency offers a potential solution. The Ruegeria strain B4 of the population MC10, identified by such signatures, has shown persistent colonization in corals in a companion study. Whether this persistence translates into a measurable host benefit compared to other coral-associated Ruegeria strains, and which mechanisms underlie such benefit, remained unknown. Here we directly compare the probiotic efficacy of MC10-B4 against two sympatric Ruegeria strains isolated from the same coral colony and mucus compartment, controlling for host genotype and microenvironment. MC10-B4 inoculation significantly increased heat stress tolerance in the coral model cnidarian Aiptasia (Exaiptasia diaphana strain H2), outperforming both sympatric control strains. To understand the mechanistic basis of this probiotic efficacy, we characterized the functional profile of MC10 using an integrated multi-omics approach. The genome of MC10 is enriched in genes associated with host-interaction, including siderophore-mediated iron acquisition and exopolysaccharide biosynthesis, which were phenotypically confirmed by detectable iron scavenging and enhanced biofilm formation. Following exposure to coral tissue extract, MC10-B4 underwent a coordinated motility-to-sessility proteomic reprogramming, downregulating flagellar motor components while upregulating flagellin and biofilm regulators. This response was distinct from its sympatric relatives, which instead mounted broad upregulation of nutrient acquisition systems. MC10-B4s functional profile, particularly its sensitivity to oxidative stress, contrasts with the traits typically favored in conventional probiotic screens. Our results move beyond the descriptive identification of a coral probiotic by providing initial mechanistic insight into traits associated with long-term host association and improved thermal performance. These findings validate an evolution-guided approach that prioritizes innate colonization potential over pre-defined laboratory functionalities, informing the rational design of durable probiotics.

microbiology↗

bioRxiv2025

Acoustoluminescence in Transition Metal and Rare Earth Oxides Beyond 1800 nm for In Vivo Imaging

Acoustoluminescence (AL) is promising for molecular imaging in living tissue, but efficient acousto-optic conversion remains challenging due to the [~]108 times difference in quantum energy between phonons (1 MHz ultrasound) and photons (visible or near-infrared light). Here, we report AL in transition metal oxides (TMOs) and rare earth oxides (REOs) at wavelengths beyond 1800 nm in the short-wave infrared (SWIR) or near-infrared II (NIR-II, 1000-3000 nm) window, under ultrasound excitation at power densities 100-150-fold lower than those required for sonoluminescence in liquids. High-temperature N2/H2-mixed gas reduction was demonstrated as a safe and efficient method to regulate the AL spectra and brightness of TMOs and REOs. TMOs exhibited broadband NIR-II AL emission. Intrinsic emission peaks of rare earth ions and non-conventional luminescence were observed in the AL spectra of REOs under ultrasound excitation. NIR-II AL imaging enabled twice the penetration depth of fluorescence imaging. We developed a scanning focused ultrasound AL imaging system for in vivo tumor imaging through the intact hindlimb, achieving acoustic resolution and penetration depths exceeding one centimeter.

bioengineering↗

bioRxiv2025

Dynamic alterations of DNA methylation and transcriptome in adaptation to and recovery from the space environment

Space exploration presents tremendous health challenges. Here, we report time series of multi-omic and phenotypic profiles of seventeen astronauts from six China Manned Space missions with continuous spaceflight durations ranging from 13 to 180 days. We revealed a key role of DNA methylation regulation in reshaping gene expression patterns to adapt to the space environment. Long-duration spaceflight showed more alterations in epigenetic modifications correlated with alternative splicing and protein acetylation. During recovery, an "overrange rebound" phenomenon was observed, furthermore, a mathematical model was established to describe this implying important phenomenon. Moreover, we revealed the correlations between molecular alterations and phenotypic changes such as coagulation activation and bone intensity loss. Additionally, we performed ground-based simulation experiments to estimate the impacts of individual stressors in the space environment on DNA methylation. In summary, our study highlights the importance and complexity of epigenetic regulation in adaptation to and recovery from the space environment.

genomics↗

bioRxiv2025

Vagal volume receptors in the heart compensate for blood loss and posture change

Cranial nerves densely innervate the heart and vasculature, with sensory neurons reporting on blood pressure, respiratory gases, and tissue damage1. The roles of arterial baroreceptors in systemic physiology are well appreciated2, but the functions of vagal cardiac mechanoreceptors have been more difficult to parse, in part due to the closed-loop structure of the cardiovascular system. Here, we use genetic tools for isolated study of vagal mechanoreceptors in the heart, finding that they are acutely sensitive to circulating blood volume and play key roles in compensating for decreased filling of the heart that occurs in an upright posture and during hemorrhage. Vagal PIEZO2 neurons form characteristic end-net endings in the heart and display blood volume-dependent responses with every heartbeat that are timelocked to atrial and ventricular systole. Vagal PIEZO2 knockout eliminates heartbeatcoupled nerve activity, and compromises carotid blood pressure when mice on a tilttable are rotated to an upright position. Vagal PIEZO2 knockout mice also display a lethal failure to sustain blood pressure during trauma-induced blood loss. Together, these findings demonstrate an essential function for vagal cardiac mechanoreceptors in sustaining the constancy of blood circulation.

neuroscience↗

bioRxiv2025

Artemisinin-Conjugated Phototheranostic Probe for Golgi-Targeted H2O2 Detection and Side Effect Attenuation

Understanding the mechanism by which Artemisinin conjugated with phototheranostic probes for reducing side effects (AC-Pr-RSE) will guide endeavor to improve the therapeutic outcomes. Herein, the first report describes the application of a cytotoxic artemisinin derivative and N-methyliminodiacetic acid (MIDA) boronates conjugated with a naphthalimide fluorophore for the detection of H2O2 in the Golgi apparatus. A comparative analysis of the localization signals from the fluorescent artemisinin derivative and organelle-specific dyes uncovered that the Golgi apparatus functions as the primary site of its accumulation, which could efficiently enhance the intracellular reactive oxygen species (ROS) level and induce cell apoptosis. This work highlights the potential of AC-Pr-RSE study, which enables us to optimize the design of theranostic probes to improve their biological activities during oxidative stress.

biochemistry↗

bioRxiv2025

Strong genotype-by-genotype and genotype-by-environment interactions induced by antibiotic resistance mutations

The often parallel evolution of antibiotic resistance in different species offers a promising basis for predicting evolutionary change. However, the extent to which parallel genetic evolution is reflected at the phenotypic level remains unclear. We investigated how genetic background and temperature influence the fitness effects of homologous rifampicin resistance mutations in absence of antibiotics across two temperatures and three species (Escherichia coli, Acinetobacter baylyi and Lactiplantibacillus plantarum). We measured the effect of resistance mutations on two growth traits (maximum growth rate and maximum optical density) across all conditions and fit linear models to this data using Bayesian inference. Our model fits provide evidence for pervasive genetic interactions in both growth traits, including mutation by species (GxG), mutation by temperature (GxE), and GxGxE interactions. In particular, the effect of resistance mutations was strongly dependent on genomic background, to the extent that mutations often reduced growth in one species but increased it in another (sign epistasis). Similarly, the effect of mutations on growth was strongly influenced by temperature, with some mutations increasing growth at one but decreasing growth at the other temperature. Most notably, three resistance mutations induced strong heat sensitivity in A. baylyi. Our results reinforce previous studies that report strong epistatic and GxE effects of resistance mutations, indicating that in the absence of additional data and more mechanistic models, predicting fitness effects of resistance mutations across species and environments can be very challenging.

evolutionary biology↗