Biology subjects

Tao, H.

Publications and source records attributed to Tao, H..

At least 19 recordsLinked to original sources

bioRxiv2026

Matrix stiffness shapes immunometabolic states and response to PD-1 blockade in gastric cancer

The extracellular matrix of solid tumors exhibits spatially heterogeneous stiffness, yet how matrix stiffness shapes antitumor immunity in gastric cancer (GC) remains unclear. Here, we integrated anti-PD-1 clinical cohorts, GC specimens, single-cell and spatial transcriptomic analyses, a syngeneic mouse model, and tunable-stiffness hydrogels to clarify the immunological consequences of matrix stiffness. High matrix stiffness was associated with collagen accumulation and immune exclusion, while higher stiffness-associated transcriptional scores were related to poorer response to PD-1 blockade. Matrix softening markedly reshaped the immune microenvironment and enhanced the efficacy of PD-1 blockade. Mechanistically, stiff matrices promoted F-actin remodeling and YAP nuclear enrichment, driving LDHA-dependent glycolytic reprogramming in GC cells that further impaired the effector function of CD8 T cells. Intriguingly, matrix softening was accompanied by enhanced IFN-{gamma}-responsive PD-L1 expression in GC cells, consistent with adaptive immune resistance that may contribute to the limited antitumor effects of matrix softening alone. These findings suggest that matrix remodeling alleviates spatial and metabolic constraints on antitumor immunity, providing a preclinical rationale for combining matrix softening with PD-1 blockade in GC.

cancer biology↗

bioRxiv2026

Diacylglycerol Kinases Balance DAG Signaling to Control B Cell Maturation, Germinal Center Homeostasis, and Humoral Immunity

Diacylglycerol (DAG) is a critical second messenger downstream of the B-cell receptor (BCR), but how DAG signaling is regulated during B-cell development and humoral responses remains incompletely understood. Here, complementary gain- and loss-of-function approaches revealed stage-specific requirements for diacylglycerol kinase (DGK)-regulated signaling in B cells. Expression of the gain-of-function DGK{zeta} mutant DGK{zeta}{Delta}NLS had limited effects on early BM B-cell development but progressively impaired transitional and mature B-cell populations. DGK{zeta}{Delta}NLS attenuated BCR-induced ERK1/2 and mTOR signaling, activation, and proliferation and, when expressed in AID-expressing B cells, reduced GC B-cell survival and T-dependent IgG responses without detectably impairing GC B-cell proliferation in vivo. Conversely, combined DGK/{zeta} deficiency resulted in marked spontaneous GC B-cell expansion associated with enhanced ERK1/2, Akt, and S6 signaling and increased glucose uptake. Despite this steady-state GC expansion, DGK/{zeta}-deficient mice developed spontaneous autoreactivity and mounted impaired antigen-specific antibody responses. Thus, B-cell developmental stages exhibit differential sensitivity to altered DGK activity, and opposing perturbations of DGK-regulated signaling produce reciprocal effects on GC B-cell accumulation while both compromise productive humoral immunity. These findings identify DGKs as critical regulators that tune lipid signaling for B-cell maturation, GC homeostasis, and effective antibody responses.

immunology↗

bioRxiv2026

Large-scale dimensional behavioral profiling dissociates fear memory from locomotor confounds in mice: The necessity of baseline-normalized metrics

Fear conditioning is widely used to assess associative memory in mice, yet percent freezing conflates memory with baseline locomotor and anxiety-related traits. A systematic survey of recent studies (2020-2025) found that fewer than 1% statistically integrate locomotor activity into freezing analyses. Here, we address this gap using a large-scale dataset of >10,000 mice across >160 comparisons, including genetic mutations, pharmacological interventions and aging, tested in 15 standardized behavioral paradigms. Conventional freezing scores covaried strongly with general locomotor activity, obscuring memory-related phenotypes. Multiple factor analysis identified two principal behavioral dimensions, locomotor activity and learning/memory: conventional freezing aligned with the locomotor dimension, whereas freezing subtraction and the activity suppression ratio mapped onto the memory dimension and improved detection of synaptic plasticity phenotypes. These analyses show that baseline locomotor normalization is essential for interpreting fear conditioning as a memory assay and provide an open framework for selecting and reporting locomotor-normalized metrics.

neuroscience↗

bioRxiv2026

Mitochondrial degradation of metallothionein enables local zinc mobilization during zinc limitation

Zinc is an essential structural and enzymatic cofactor for roughly 10% of proteins, including transcription factors, metabolic enzymes, and cytoskeletal components. It also supports critical functions across organelles such as gene regulation in the nucleus, protein folding in the endoplasmic reticulum, and energy production and antioxidant defense in mitochondria. Despite these indispensable roles, the cellular mechanism that recycles zinc to maintain homeostasis during zinc deficiency remains poorly understood. Here, we identify a biphasic response to zinc limitation, which involves the rapid degradation of the zinc-storing metallothionein followed by the degradation, in an autophagy-dependent manner, of other zinc-binding proteins. We show that metallothionein is rapidly imported into the mitochondria to be degraded by the mitoprotease LONP1. Zinc starvation leads to severe mitochondrial dysfunction and metallothionein degradation allows local zinc release to alleviate nutrient stress. Our results reveal a non-canonical, mitochondria-mediated degradation pathway for a nutrient-storing protein that mobilizes zinc locally to maintain metabolic homeostasis and establish mitochondria as active hubs for nutrient recycling.

cell biology↗

bioRxiv2026

Comparative profiling of carnitine palmitoyltransferase 1 isoforms reveals vincamine as a selective carnitine palmitoyltransferase 1b inhibitor

Carnitine palmitoyltransferase 1 (CPT1) catalyzes the rate-limiting step of fatty acid oxidation and has emerged as a therapeutic target for metabolic diseases and cancer. CPT1 exists in three isoforms, CPT1a, CPT1b, and CPT1c, with distinct tissue distributions and enzymatic properties; however, limitations of previous platforms enabling parallel isoform comparison have undermined efforts to identify selective inhibitors that could minimize off-target effects. Here, we describe a DTNB-based enzyme activity assay adapted for high-throughput screening of CPT1b, the predominant isoform in cardiac and skeletal muscle. Mitochondrial extracts from Expi293F cells transfected with CPT1a or CPT1b expression plasmids served as sources of catalytically active enzymes. The assay was validated using three previously confirmed CPT1b inhibitors: (R)-(+)-etomoxir, perhexiline, and malonyl-CoA. We then generated side-by-side inhibitory profiles for both isoforms, identifying vincamine as a lead selective inhibitor of CPT1b. Furthermore, chlorpromazine, previously characterized only as a broad CPT1 inhibitor and subsequently shown to inhibit CPT1a, is demonstrated here to also inhibit CPT1b, expanding its known isoform profile. Together, these results establish a robust platform for comparative isoform profiling and demonstrate that selective modulation of CPT1b is achievable, with implications for targeted therapeutics in metabolic and oncological disease.

cell biology↗

bioRxiv2026

Vascularized Human Cardiac Organoids Reveal Endothelial-Cardiomyocyte Crosstalk and Mechanisms of Carfilzomib-Induced Cardiotoxicity

Human cardiac organoids (hCOs) provide a powerful platform for modeling heart development and disease, yet their lack of vasculature limits physiological relevance. Here, we generate vascularized human cardiac organoids (vhCOs) by assembling hCOs with blood vessel organoids, enabling the self-organized formation of unified tissues with extensive vascular networks and substantially enhanced cardiomyocyte (CM) maturation. Single-nucleus multiomic profiling reveals CM state resembling the 17-week human fetal heart, while endothelial cells (ECs) acquire cardiac-specific and arterial-like identities. Integrative cell-cell communication analyses and experimental validation identify CM-derived Laminin-2 as a driver of arterial EC specification, while reciprocal EFNB2 signaling from arterial ECs promotes CM maturation, uncovering bidirectional cardiac-vascular crosstalk. Modeling carfilzomib-induced cardiotoxicity in vhCOs reveals ATF4-dependent endoplasmic reticulum (ER) stress and IL8-mediated inflammatory responses that are blunted in non-vascularized hCOs. Pharmacological attenuation of ER stress alleviates carfilzomib-induced cardiotoxicity. Altogether, vhCOs provide a developmentally advanced and physiologically faithful human cardiac model.

cell biology↗

bioRxiv2026

TRACE: End-to-end temporal inference and annotation of animal behaviors from video

Quantitative analysis of animal behavior is fundamental to neuroscience and ethology but remains constrained by the scalability, subjectivity, and limited reproducibility of manual annotation. Many automated approaches infer behavior through intermediate representations such as pose trajectories, whereas direct video modeling retains motion, appearance, and context, but its accuracy and efficiency remain incompletely established. Here we introduce V-TRACE (Video-based Temporal Recognition and Annotation of Continuous Ethograms of Animal Behavior), an end-to-end platform with a graphical user interface for behavioral detection and annotation. V-TRACE combines transformer-based video encoders with a multi-scale temporal module to model behavioral dynamics across a broad range of durations. Its modular design supports interchangeable encoder architectures within a common detection pipeline to produce frame-resolved behavioral identities and derive temporal boundaries from continuous recordings. Across datasets spanning species and experimental contexts, V-TRACE demonstrates high accuracy and high-throughput inference, enabling scalable, efficient, and context-aware animal behavior analysis directly from video.

animal behavior and cognition↗

bioRxiv2025

Guidance receptor-mediated mechanocompliance of GBM cells facilitates immune-silent invasion

The lethality of glioblastoma (GBM) stems from diffuse infiltration and immune evasion, two hallmarks traditionally studied separately. Here, we identify as unifying mechanism how GBM cells utilize guidance receptors Plexin-D1 and Plexin-B2 to gain mechanocompliance, i.e., the ability to deform and remodel membrane/cytoskeleton during confined migration without triggering immune activation. We show that PLXND1 upregulation marks invasive fronts and predicts poor survival of glioma patients. Through live-cell imaging in microchannels, intracranial xenografts, single-nucleus transcriptomics, and lipidomics we demonstrate that Plexin-D1/B2 enable GBM cells to retract tumor microtubes (TMs), traverse constrictions, and escape microglial surveillance. Single and especially double deletion of PLXND1 and B2 resulted in TM overgrowth, membrane instability, and susceptibility to cell fragment shedding, leading to impaired migration and a shift to activation of tumor-associated myeloid cells. Our findings thus reveal a molecular strategy used by GBM cells to penetrate through interstitial space while escaping immune surveillance. SIGNIFICANCEPlexin-mediated mechanocompliance underlies the invasive yet immune-silent behavior of GBM cells, exposing a vulnerability that could be therapeutically exploited by forcing invading tumor cells into a mechanically fragile, immunogenic state.

cancer biology↗

bioRxiv2025

Cortical tension as a mechanical barrier to safeguard against premature differentiation during neurogenesis

Neuronal differentiation requires coordinated gene reprogramming and morphodynamic remodeling. How mechanical forces integrate with nuclear gene programs during neurogenesis remains unresolved. Here, we identify cortical tension as a mechanical barrier that safeguards against premature neuronal differentiation. Deletion of Plexin-B2, a guidance receptor controlling actomyosin contractility, lowers this barrier, enabling neurite outgrowth and accelerating neuronal lineage commitment. We show that coupling of extrinsic differentiation cues with intrinsic morphodynamics is essential for stabilizing neuronal fate and that cortical barrier and epigenetic barrier act in concert to regulate developmental timing. In cerebral organoids, Plexin-B2 ablation triggered premature cell-cycle exit and differentiation, resulting in progenitor pool depletion and neuroepithelial disorganization, phenotypes echoing intellectual disability in patients with rare pathogenic PLXNB2 variants. Our studies demonstrate that cortical tension functions as mechano-checkpoint that regulates the onset of neurogenesis. Lowering this barrier may provide a strategy to accelerate induced neuron generation and maturation for CNS disease modeling.

neuroscience↗

bioRxiv2025

Single cell resolved spatial immune repertoire unveils spatial heterogeneity of lymphoid aggregates in human immune disorders

Adaptive immunity, mediated by T and B cell responses, is essential for defending against infections and cancers while also being implicated in autoimmune diseases. Tracking T and B cell repertoires in situ at single-cell resolution is essential for understanding adaptive immune responses. To address the lack of tools for in situ single-cell T/BCR (XCR) sequencing, we developed Stereo-XCR-seq, an efficient strategy for retrieving and sequencing TCR and BCR from Stereo-seq cDNA libraries at subcellular resolution. Stereo-XCR-seq provides unbiased full-length XCR reads alongside spatial transcriptomics, enabling the identification of heterogeneous lymphoid aggregates with distinct clonal activities in cancers and inflammatory bowel disease (IBD). We identified plasma cell aggregates that differ from tertiary lymphoid structures (TLSs) in both transcriptomic profiles and clonal activities, with spatial positioning potentially mediating unique immune responses. Collectively, Stereo-XCR-seq enables in situ single-cell profiling of T and B cell clonal activities within tissue microenvironments, providing insights into lymphocyte adaption to environmental stimuli. This technology provides potential for advancing our understanding of tissue immunity and the development of therapeutic strategies for immune disorders.

immunology↗

bioRxiv2024

High-resolution mastigoneme structure reveals 5',5'-phosphodiesters stabilized glycan folding

Glycans play a crucial role in structure organization, energy metabolism, and signal transduction in living organisms. Compared with proteins and nucleic acids, glycans exhibit remarkable molecular heterogeneity, extensive conformational flexibility, and diverse linkages. These properties pose significant challenges for obtaining high-resolution structure of glycans. Here, we report a cryo-EM structure of the heavily glycosylated Chlamydomonas mastigoneme at 2.3-2.5 [A] resolutions. In addition to enabling analysis of accurate interactions for glycosyl packing, the high resolution map reveals an unprecedented 5,5-phosphodiester bond that links adjacent glycan chains attached to hydroxyproline (Hyp) residues n and n+3. Structural analysis reveals a secondary structural element for glycoconjugates, which we name the poly-Hyp (pHP) glycohelix. Our work represents an important advancement in deciphering glycan folding.

biochemistry↗

bioRxiv2024

DGKα and ζ Deficiency Causes Regulatory T-Cell Dysregulation, Destabilization, and Conversion to Pathogenic T-Follicular Helper Cells to Trigger IgG1-Predominant Autoimmunity

Regulatory T cells (Tregs) actively engage in immune suppression to prevent autoimmune diseases but also inhibit anti-tumor immunity. Although Tregs express a TCR repertoire with relatively high affinities to self, they are normally quite stable and their inflammatory programs are intrinsically suppressed. We report here that diacylglycerol (DAG) kinases (DGK) ( and ( are crucial for homeostasis, suppression of proinflammatory programs, and stability of Tregs and for enforcing their dependence on CD28 costimulatory signal. Treg-specific deficiency of both DGK( and ( derails signaling, metabolic, and transcriptional programs in Tregs to cause dysregulated phenotypic and functional properties and to unleash conversion to pathogenic exTregs, especially exTreg-T follicular helper (Tfh) 2 cells, leading to uncontrolled effector T cell differentiation, deregulated germinal center (GC) B-cell responses and IgG1/IgE predominant antibodies/autoantibodies, and multiorgan autoimmune diseases. Our data not only illustrate the crucial roles of DGKs in Tregs to maintain self-tolerance but also unveil a Treg-to-self-reactive-pathogenic-exTreg-Tfh-cell program that is suppressed by DGKs and that could exert broad pathogenic roles in autoimmune diseases if unchecked.

immunology↗

bioRxiv2024

Permissive and instructive Hox codes govern limb positioning

The positioning of limbs along the anterior-posterior axis varies widely across vertebrates. The mechanisms controlling this feature remain to be fully understood. For over 30 years, it has been speculated that Hox genes play a key role in this process but evidence supporting this hypothesis has been largely indirect. In this study, we employed loss- and gain-of-function Hox gene variants in chick embryos to address this issue. Using this approach, we found that Hox4/5 genes are necessary but insufficient for forelimb formation. Within the Hox4/5 expression domain, Hox6/7 genes are sufficient for reprogramming of neck lateral plate mesoderm to form an ectopic limb bud, thereby inducing forelimb formation anterior to the normal limb field. Our findings demonstrate that the forelimb program depends on the combinatorial actions of these Hox genes. We propose that during the evolutionary emergence of the neck, Hox4/5 provide permissive cues for forelimb formation throughout the neck region, while the final position of the forelimb is determined by the instructive cues of Hox6/7 in the lateral plate mesoderm. Impact statementElucidation of the Hox code defining forelimb positioning provides novel insights in lateral plate mesoderm patterning and the integration of vertebrate column structure and limb positioning.

developmental biology↗

bioRxiv2024

Single-cell dissection of prognostic architecture and immunotherapy response in Helicobacter pylori infection associated gastric cancer

Most of the gastric cancer (GC) worldwide are ascribed to Helicobacter pylori (H. pylori) infections, which have a detrimental effect on the immunotherapys efficacy. Comprehensively dissecting the key cell players and molecular pathways associated with cancer immunotherapies is critical for developing novel therapeutic strategies against H. pylori infection associated GC. We performed a comprehensive single-cell transcriptome analysis of nine GC with current H. pylori infection (HpGC), three GC with previous H. pylori infection (ex-HpGC), six GC without H. pylori infection (non-HpGC), and six healthy controls (HC). We also investigated key cell players and molecular pathways associated with GC immunotherapy outcomes. We revealed the molecular heterogeneity of different cell components in GC including epithelium, immune cells, and cancer-associated fibroblasts (CAFs) at the single-cell level. The malignant epithelium of HpGC exhibited high expression level of inflammatory and epithelial-mesenchymal transition (EMT) signature, HpGC and ex-HpGC were enriched with VEGFA+ angiogenic tumor-associated macrophages (Angio-TAM) and IL11+ inflammatory CAF (iCAF), characterized by high expression levels of NECTIN2 and VEGFA/B. Additionally, we found significant correlations between the abundance of iCAF with Angio-TAM and TIGIT+ suppressive T cells, and iCAF interacted with Angio-TAM through the VEGF and ANGPTL angiogenic pathways. We also developed an immune signature and angiogenic signature and demonstrated that the iCAF abundance and angiogenic signature could predict poor immunotherapy outcomes in GC. We revealed the transcriptome characteristics and heterogeneity of various cellular constituents of HpGC and demonstrated that a synergistic combination of immunotherapy and anti-angiogenic targeted therapy may be an effective therapeutic modality for HpGC.

cancer biology↗

bioRxiv2024

Multi-omics Reveals Immune Response and Metabolic Profiles during High-Altitude Mountaineering

The physiological perturbations induced by high-altitude exposure in mountain climbers, manifesting as metabolic and immunologic deviations, have been previously reported but are not fully understood. In this study, we obtained longitudinal multi-omic profiles of blood samples for healthy mountain climbers during two mountaineering stages (acclimatization and extreme altitude mountaineering). Our integrative assay included metabolomics and lipidomics profiling of plasma coupled with single-cell transcriptomic analysis of 375,722 immune cells. Longitudinal analysis revealed dynamic immune response profiles, during the acclimatization period, characterized by the downregulation of inflammatory responses in monocytes and classical dendritic cells (cDCs) and an increase in the proportion of cytotoxic CD8+ T cells with enhanced immune effector processes. In contrast, during extreme altitude mountaineering, the activation of inflammatory responses and impairment of T cell effector function were observed, concomitant with an increased cellular response to hypoxia and oxidative stress pathways. Furthermore, we found upregulated glycolysis and antioxidant gene expression during extreme altitude mountaineering, which was primarily orchestrated by HIF1A and NFE2L2, while decreased expression of these genes was observed in dysregulated plasmacytoid dendritic cells (pDCs). Finally, high-resolution plasma metabolic analysis revealed significant alterations in the metabolism of climbers, involving enhanced glutamine and fatty acid metabolism.

bioinformatics↗

bioRxiv2023

Targeting PKC alleviates iron overload in diabetes and hemochromatosis

Diabetes is one of the most prevalent chronic diseases worldwide. Iron overload increases the incidence of diabetes and aggravates diabetic complications that cause mortality. Reciprocally, diabetes potentially promotes body iron loading, but the mechanism remains not well understood. In this study, we demonstrated systemic iron excess and the upregulation of iron exporter ferroportin (Fpn) in the enterocytes and macrophages of multiple diabetic mouse models. Increased Fpn expression and iron efflux was also seen in the enterocytes of type 2 diabetic human patients. We further showed that protein kinase C (PKC), which is activated in hyperglycemia, was responsible for the sustained membrane expression of Fpn in physiological and in diabetic settings. For the first time, we identified that PKCs were novel binding proteins and positive regulators of Fpn. Mechanistically, hyperactive PKC promoted exocytotic membrane insertion while inhibited the endocytic trafficking of Fpn in the resting state. PKC also protected Fpn from internalization and degradation by its ligand hepcidin dependent on decreased ubiquitination and increased phosphorylation of Fpn. Importantly, the loss-of-function and pharmacological inhibition of PKC alleviated systemic iron overload in diabetes and hemochromatosis. Our study thus highlights PKC as a novel target in the control of systemic iron homeostasis.

cell biology↗

bioRxiv2023

Manipulation of Bacterial ROS Production Leads to Self-escalating DNA Damage and Resistance-resistant Lethality for Intracellular Mycobacteria

The high prevalence of drug resistance in mycobacteria calls for antimicrobial mechanisms that suppresses the development of resistance. As a structurally conserved multi-site bio-macromolecule, DNA is presumed to be an ideal candidate for such resistance-resistant drug target. However, survey of marketed and investigational DNA interactors indicates that they are not immune to resistance development. Here, we report our strategy to achieve real resistance-resistant DNA targeting by incurring "catastrophic" DNA damage with an organoruthenium-natural product hybrid. The dual-mode DNA damage, in the form of strong tri-valent binding and concomitant oxidative modification, is achieved by manipulating of bacterias native endogenous ROS production mechanism upon lethal stress (such as DNA binding). Such self-escalating DNA damage, together with precise targeting of intracellular bacteria via vacuole fusion, thus endows the hybrids resistance-resistant lethality against mycobacteria and in vivo efficacy in animal models.

microbiology↗

bioRxiv2023

Differences in Hepatocellular Iron Metabolism Underlie Sexual Dimorphism in Hepatocyte Ferroptosis

Males show higher incidence and severity than females in hepatic injury and many liver diseases, but the mechanisms are not well understood. Ferroptosis, an iron-mediated lipid peroxidation-dependent death, plays an important role in the pathogenesis of liver diseases. We determined whether hepatocyte ferroptosis displays gender difference, accounting for sexual dimorphism in liver diseases. Compared to female hepatocytes, male hepatocytes were much more vulnerable to ferroptosis by iron and pharmacological inducers including RSL3 and iFSP1. Male but not female hepatocytes exhibited significant increases in mitochondrial Fe2+ and mitochondrial ROS (mtROS) contents. Female hepatocytes showed a lower expression of iron importer transferrin receptor 1 (TfR1) and mitochondrial iron importer mitoferrin 1 (Mfrn1), but a higher expression of iron storage protein ferritin heavy chain 1 (FTH1). It is well known that TfR1 expression is positively correlated with ferroptosis. Herein, we showed that silencing FTH1 enhanced while knockdown of Mfrn1 decreased ferroptosis in HepG2 cells. Removing female hormones by ovariectomy (OVX) did not dampen but rather enhanced hepatocyte resistance to ferroptosis. Mechanistically, OVX potentiated the decrease in TfR1 and increase in FTH1 expression. OVX also increased FSP1 expression in ERK-dependent manner. Elevation in FSP1 suppressed mitochondrial Fe2+ accumulation and mtROS production, constituting a novel mechanism of FSP1-mediated inhibition of ferroptosis. In conclusion, differences in hepatocellular iron handling between male and female account, at least in part, for sexual dimorphism in induced ferroptosis of the hepatocytes.

cell biology↗