Biology subjects

Wang, H.

Publications and source records attributed to Wang, H..

At least 19 recordsLinked to original sources

bioRxiv2026

CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers

Cell- and tissue-type-specific DNA methylation markers provide epigenetic signatures of cellular identity and are widely used to infer cellular origin from bulk and single-cell methylomes. Existing resources mainly emphasize disease-associated biomarkers, methylome atlases, genomic annotations or RNA-based cell markers, leaving an unmet need for an integrated region-level resource dedicated to such markers. Here we present CellMethMarker (http://gu-zhanglab.hfcas.ac.cn/CellMethMarker), a curated database integrating 347,514 de novo markers derived from uniformly processed whole-genome and reduced-representation bisulfite sequencing datasets, 2,203,507 literature-derived marker records and harmonized metadata for 2,810 samples. CellMethMarker enables cell- and tissue-centered marker retrieval, coordinate-based search, genome-browser visualization, interactive methylation analysis and data download. In an independent single-cell methylome atlas, these markers recover the expected cell-type-associated methylation patterns, and a platform-matched reference built from them lowers the mean deconvolution error from 0.365 to 0.144. CellMethMarker therefore links region-level DNA methylation variation to cellular identity and supports methylome-based cell-type annotation and deconvolution.

bioinformatics↗

bioRxiv2026

Brain state locks silent memories in a trained fly connectome

Complete connectomes now exist for insect nervous systems, but whether a fixed wiring diagram can learn, and what its memories consist of, is unknown. Here, we trained a spiking model of the whole male Drosophila central nervous system, 167,106 neurons with fixed wiring, to plan moves and to remember a visual cue. Spikes write the cue into neuronal adaptation, which holds it silently until the next input reads it out. Cells that hold the trace are enriched for transcripts of a calcium-activated potassium channel in fly cell atlases. The learned readout recalls the trace only in the brain state of learning: the same trace evokes a different response at another delay, and a disease-like loss of potassium current rewrites the trace and changes how it is read. Learning in the new state is spared. Memory failure can arise from a change of state rather than a loss of storage.

neuroscience↗

bioRxiv2026

Stabilizing gas in aqueous liquids with metal-organic frameworks for persistent acoustic transduction

Gas is the most efficient mediator of acoustic energy owing to its high compressibility, yet its thermodynamic instability in aqueous environments makes it inherently transient, limiting sustained ultrasound-biological interfacing. Here, we show that gas can be stabilized, confined, and manipulated in the liquid phase to function as a persistent acoustic transducer. By trapping gas within designed microporous metal-organic framework (MOF) nanocrystals, interfacial forces establish a stable ternary-phase equilibrium that suppresses water intrusion and prevents gas collapse, enabling reversible, non-destructive oscillations under ultrasound stimulation and providing design principles for stabilizing gas in liquid environments. By leveraging high-resolution ultra-high-speed digital image correlation (DIC), we unveil the previously inaccessible spatiotemporal dynamics of confined gas oscillations within these nanotransducers under ultrasound stimulation, revealing localized amplification of the surrounding acoustic field and establishing a quantitative structure-function relationship for programmable acoustic transduction. These aqueous-phase gas nanotransducers exhibit sustained acoustic amplification over millions of excitation cycles and remain functional after prolonged storage (>2 years) under physiological conditions. In vitro and in vivo, this platform enables long-term ultrasound imaging and sustained, non-invasive neuromodulation by converting confined gas oscillations into persistent and amplified mechanical actuation. Our findings establish a generalizable design framework for stabilizing gas in liquid environments to achieve persistent and programmable acoustic transduction, thereby enabling sustained ultrasound-biological interfacing and opening opportunities for gas-based therapeutics.

bioengineering↗

bioRxiv2026

Susceptibility and cellular responses of COPD airway epithelium to cigarette smoke in stem cell-derived ALI models

Despite cigarette smoke being the chief driver of chronic obstructive pulmonary disease (COPD), numerous patients maintain their smoking habits by opting for low-yield or slim cigarettes under the misconception of diminished health risks. Differential effects of high-tar conventional versus low-tar slim cigarettes on COPD airway epithelium remain poorly defined. We established an air-liquid interface (ALI) model using patient-derived COPD airway epithelial stem cells and exposed cultures to high-tar conventional smoke (TC), low-tar slim smoke (SC), or filtered air (NC). Both regimens induced IL-1{beta} inflammation, ciliary structural changes, and oxidative stress, with TC eliciting stronger responses. Single-cell RNA sequencing resolved six epithelial populations. In ciliated cells, hdWGCNA showed NC modules associated with cilium organization and assembly, SC adaptive defense responses, and TC more extensive reprogramming of ciliary functional networks. Basal cells displayed stress-pathway activation, squamous metaplasia signatures, and developmental regression toward a stem-like state, with TC producing approximately 1.7-fold stronger regression than SC. Secretory cells exhibited identity erosion, antimicrobial program downregulation, and a shift toward keratinization and squamous-oriented programs, again more pronounced under TC. These findings indicate that high-tar conventional smoke exerts greater influence than low-tar slim smoke on COPD airway epithelium across inflammatory, structural, and lineage-specific molecular dimensions, providing high-resolution insight into cell-type-specific responses to continued smoke exposure.

cell biology↗

bioRxiv2026

Creator 1.0: Phylogeny-Guided Stagewise Pretraining for Plant Genome Foundation Models across 1,000 Species

Genomic language models have advanced DNA sequence analysis, but their applicability to plant-specific tasks and representation changes during pretraining remain poorly characterized. Here, we present Creator 1.0, a 2-billion-parameter parameter plant genome foundation model pretrained on 1,000 plant genomes using phylogeny-guided stagewise pretraining (PGSP). Training comprised 83 consecutive stages and produced 52 cumulative checkpoints associated with distinct plant orders. On GENEB, the stage 83 checkpoint ranked first among 46 models across 10 plant-related tasks, with a mean Matthews correlation coefficient (MCC) of 0.565, and fourth across all 100 tasks. Evaluation of 52 checkpoints on six plant lncRNA tasks identified different optimal stages under full-data, 10-shot and 1-shot settings, corresponding to stages 71, 72 and 29, respectively. Checkpoint performance varied across tasks, without consistent advantages for corresponding plant orders. These findings demonstrate the competitive performance of Creator 1.0 and highlight the potential of PGSP to provide task-adaptable checkpoints for plant genomic applications.

genomics↗

bioRxiv2026

Spatially enforced engagement of PD-1⁺ T cells with AXL⁺ cells reprograms the tumor microenvironment and overcomes anti-PD-1 resistance

Background: AXL overexpression promotes tumor-cell plasticity, local immune suppression, and resistance to PD-1 blockade. Conventional anti-AXL and anti-PD-1 antibodies combinations act independently and do not ensure physical proximity between PD-1+ T cells and AXL+ cells within the immunosuppressive tumor microenvironment. Methods: To address this limitation, we developed a non-tandem, tetravalent IgG bispecific antibody designed to simultaneously engage PD-1 and AXL (BiTE-AXL/PD-1). Its antitumor activity was evaluated using in vitro functional assays and humanized and immunocompetent head and neck squamous cell carcinoma (HNSCC) models and compared with the combination of monospecific anti-AXL and anti-PD-1 antibodies. Spatial multiplex imaging was used to characterize treatment-associated changes in the tumor microenvironment of an anti-PD-1-resistant murine model. Results: BiTE-AXL/PD-1 enhanced T-cell activation, promoted AXL-dependent tumor-T-cell conjugation, and increased tumor-cell killing in vitro, outperforming the combination of the two monospecific antibodies. In humanized and immunocompetent HNSCC models, BiTE treatment significantly delayed tumor growth compared with the antibody combination and was well tolerated, with no overt toxicity. Spatial multiplex imaging revealed a shift from a fibroblast-dominated microenvironment characterized by exhausted CD8+ T cells toward dendritic-cell- and CD8+ T-cell-enriched niches associated with antitumor immune activity. Conclusion: BiTE-AXL/PD-1 promotes physical proximity between PD-1+ T cells and AXL+ cells, enhances antitumor immune responses, and remodels the immunosuppressive tumor microenvironment. These findings support PD-1/AXL bispecific targeting as a promising therapeutic strategy to overcome resistance to PD-1 blockade in HNSCC.

cancer biology↗

bioRxiv2026

Xenograft supervision and joint methylation-fragment-end encoding define a reusable molecular scoring layer for cell-free tumor DNA

Circulating tumor DNA is often scarce in plasma, and regional methylation summaries can obscure informative differences between individual molecules. Here we present ctDNA-BERT, a Transformer that scores individual bisulfite reads without predefined differentially methylated regions by jointly encoding CpG methylation state, nucleotide context and the fragment 3' end. Xenografts provide molecule-level tumor supervision. The resulting frozen scorer supported tumor-fraction estimation in synthetic and patient-derived xenograft mixtures and enriched tumor-concordant methylation and chromatin-accessibility signals in independent hepatocellular carcinoma and stage III pan-cancer plasma without cohort-specific retraining. Features derived from selected reads discriminated stage I cancers from healthy controls in a retrospective cohort of 1,477 specimens, achieving an out-of-fold area under the receiver operating characteristic curve of 0.884. By separating molecular scoring from sample-level inference, ctDNA-BERT provides a reusable read-level scoring layer for cell-free DNA methylation analysis.

bioinformatics↗

bioRxiv2026

ESX-1 substrates ESAT-6 and CFP-10 limit cGAS-STING activation via DNA and Zn2+ restriction

ESX-1-mediated phagosomal permeabilization exposes mycobacterial DNA to cytosolic cGAS-STING surveillance, yet the response is not overwhelming, suggesting additional layers of control exist. Here we show that the ESX-1 substrates ESAT-6 and CFP-10 constrain cGAS activation through complementary biochemical mechanisms. Purified Mycobacterium tuberculosis CFP-10 is a metal-dependent, 5'-3' exonuclease-like enzyme that preferentially degrades linear DNA, limiting the availability of stimulatory ligand. By contrast, purified M. tuberculosis ESAT-6 binds Zn2+ and limits the Zn2+-dependent conditions required for cGAS activation. During M. marinum infection, loss of these substrates augmented interferon-associated responses. Wild-type alleles restored immune suppression, whereas DNA-processing-defective CFP-10 or Zn2+-binding-defective ESAT-6 variants did not. These genotype-dependent differences were largely abolished in cGas-/- and Sting-/- macrophages. The double mutant was attenuated in zebrafish and mice, and its enhanced immune activation and attenuation were markedly diminished in cGas-/- mice. Prior exposure to the mutant improved zebrafish survival following wild-type challenge. Thus, beyond enabling mycobacterial DNA access to the cytosol, ESX-1 deploys its substrates to constrain cGAS-STING signaling by controlling activating-ligand availability and the metal-dependent environment required for sensor activation.

microbiology↗

bioRxiv2026

Repetitive transcranial magnetic stimulation targeting motor cortical region induces cell-type-specific transcriptional reprogramming and behavioral recovery in non-human primate model of Rett syndrome

Rett syndrome (RTT), a severe neurodevelopmental disorder caused by mutations in the MECP2 gene, currently lacks effective treatments. The motor cortex is a pivotal hub in RTT and autism spectrum disorders, and its impairments contribute to motor, social, and cognitive deficits. Here we examined the effects of repetitive transcranial magnetic stimulation (rTMS) targeting motor area in non-human primate of RTT (MECP2-mutant monkey) and investigated neuromolecular basis underlying therapeutic effects. We identified a new treatment target, ventral premotor cortex (PMv), for RTT and found that following a 20-day rTMS course, several behavioral and functional connectivity measures showed directional changes. Neuroimaging analyses confirmed that rTMS induced reorganization of large-scale functional connectivity with enhanced functional integration between the somatomotor and the salience networks and normalized coupling between the motor cortex and both the thalamus and the anterior cingulate cortex. Notably, single-nucleus RNA sequencing revealed that rTMS triggered cell-type-specific transcriptional reprogramming: it rescued pathological hyperactivity of excitatory neurons by restoring the expression and regulatory networks of immediate early genes (e.g., FOS, EGR1) and corrected dysregulated intercellular signaling (e.g., NRG, WNT). These findings indicate that targeting motor cortical areas with brain stimulation may treat RTT, which warrants further clinical validation.

neuroscience↗

bioRxiv2026

A polysynaptic hypothalamuspelvic-ganglion circuit regulates prostate tumor growth via WNT3A

Brain-tumor communication is increasingly recognized. Peripheral autonomic nerves regulate prostate cancer progression, yet how the brain influences local nerve-tumor interactions remains unclear. We identify a polysynaptic circuit linking the hypothalamic paraventricular nucleus (PVN), dorsal motor nucleus of the vagus (DMV), major pelvic ganglion (MPG) and prostate tumor in mice. Although both nuclei were activated during tumor growth, PVN activity restrained, whereas DMV activity promoted tumor growth. MPG ablation abolished DMV-induced tumor promotion. Combining LMD with Smart-seq2 revealed transcriptional remodeling and increased Wnt3a expression in tumor-innervating, activated MPG neurons under upstream neural control. MPG explants released WNT3A, whose neutralization suppressed explant-induced cancer-cell proliferation. Together, our findings identify a polysynaptic PVN-DMV-MPG circuit that regulates prostate tumor growth and implicate WNT3A as a mediator of the pro-tumor effects of the MPG, highlighting the therapeutic potential of targeting the neural circuit and downstream molecular pathway.

cancer biology↗

bioRxiv2026

Shared and distinct immunometabolic states link to divergent pathology in cutaneous mycobacterial infections

Cutaneous mycobacterial infections provide a common tissue setting in which related intracellular pathogens elicit distinct pathological responses, but the innate immune basis of this divergence remains incompletely understood. Here, we combined single-cell profiling from 33 individuals with histological and functional analyses, examining healthy skin and lesions from multibacillary leprosy (MB), paucibacillary leprosy (PB), cutaneous tuberculosis (CTB) and Mycobacterium marinum infection (Mari). All infections showed lower mononuclear phagocyte and higher natural killer (NK) cell proportions within the CD45 compartment, alongside shared and infection-associated dendritic cell, macrophage and NK cell programs. CTB and Mari displayed broader macrophage antimicrobial signatures, whereas MB showed lipid-associated programs and attenuated interferon-associated effector expression across multiple macrophage subsets. Reduced expression of fructose-1,6-bisphosphatase 1 (FBP1) was associated with the absence of Langhans giant cells in MB, and pharmacological FBP1 inhibition nearly abolished fusion of macrophages. Compared with NK cells from Mari, MB NK cells showed reduced central carbon and oxidative metabolism signatures alongside increased lipid-associated programs. Functional experiments showed that inhibition of glucose utilization, disruption of mitochondrial function, or co-culture with foamy macrophages abundant in MB lesions reduced NK cell IFN-{gamma} production. These findings identify shared and distinct innate immune programs and suggest that their interplay with local metabolic environments shapes divergent pathology across cutaneous mycobacterial infections.

immunology↗

bioRxiv2026

Slow Ionic Dynamics Reshape Bistability in a Biophysical Mean-Field Model of Brain Activity

Brain states such as sleep, seizures, and resting wakefulness are often described in terms of transitions between distinct population states. Biophysically inspired mean-field models that couple neuronal firing statistics to slow ionic homeostasis provide a mechanistic bridge between detailed single-neuron physiology and macroscopic brain activity. Here we examine this issue in a biophysical mean-field model of cortical populations driven by potassium exchange and compare its dynamical repertoire with a matched spiking network across six physiological and pathological regimes. The fast subsystem contains a substantial region in which low- and high-activity fixed points coexist, but this conditional bistability is not inherited by the physiological resting branch of the complete slow-fast system. A generic fast-slow calculation identifies how feedback through a dynamical ionic variable changes the stability conditions of the fast subsystem, and an exact equilibrium reduction of the KIonEx-MF equations yields a single equilibrium on the physiological resting branch over the range examined. This resting state is excitable: perturbations generate intermittent synchronized events in both the mean-field and spiking-network descriptions. The results show how slow ionic dynamics can reshape conclusions drawn from a frozen fast subsystem and provide noise-driven excitability as an alternative route to spontaneous population transitions.

neuroscience↗

bioRxiv2026

Dynamics and activation of the Legionella Type IV secretion system

Legionella pneumophila uses the Dot/Icm type IV secretion system (T4SS) to translocate hundreds of effector proteins into host cells, yet how this transenvelope machine assembles and becomes secretion competent remains poorly understood. Here, using cryo-electron tomography and in situ single-particle cryo-electron microscopy, we resolve distinct structural and functional states of the native Dot/Icm T4SS. Unexpectedly, the T4SS predominantly occupies a resting state containing the outer membrane core complex but lacking the inner-membrane complex, including DotA. Recruitment of inner-membrane components establishes a fully assembled but secretion-inactive primed state. A 3.6 [A] cryo-EM structure of the DotO-DotI-DotJ-IcmT complex, integrated with in situ reconstructions, reveals how membrane-associated components organize DotO into a hexamer of dimers ATPase platform. Upon host contact, the T4SS undergoes extensive conformational remodeling while preserving its transenvelope scaffold. Activation involves dilation of the DotG outer membrane gate and transformation of the DotA-IcmX protochannel into an open translocation conduit that extends beyond the bacterial surface. Substrate-associated state exhibit further channel expansion, revealing structural plasticity associated with effector translocation. During macrophage infection, the extracellular conduit bridges the bacterial and host membranes, establishing a direct pathway for effector delivery. Together, our findings reveal a stepwise mechanism of Dot/Icm T4SS channel assembly and activation, in which coordinated remodeling of the secretion channel converts a resting apparatus into a host-engaged translocation machine.

microbiology↗

bioRxiv2026

Mechanism-Based Discovery of New TRIDs Targeting Ribosome Pockets

Approximately 10% of all human pathogenic mutations are nonsense mutations which give rise to premature termination codon (PTC) diseases, leading to an estimated 35 million people worldwide who harbor such mutations. To date, no approaches leading to medical treatments which increase PTC readthrough have received FDA approval. However, one well-tolerated translation readthrough inducing drug (TRID), ataluren, was conditionally approved for 11 years by the European Medicines Agency for treatment of nonsense mutation Duchenne Muscular Dystrophy. In recent work we have shown that ataluren increases readthrough indirectly, by exclusively inhibiting termination without directly affecting readthrough by suppressor aminoacyl-tRNAs (sup-aa-tRNAs). Based on the idea that this mode of action (MoA) might be the reason for the low toxicity of ataluren, we have discovered potential new TRIDs, which target pockets within the ribosome to which the termination factor eRF1 binds but sup-aa-tRNAs do not. These new TRIDs, dipeptide derivatives of eRF1 and some Sartans, mimic the MoA of ataluren. Three Sartans, which are angiotensin II receptor blockers and FDA-approved for treatment of hypertension, are significantly more potent than ataluren in our reconstituted in vitro readthrough assay. These compounds might be more effective than ataluren in treating some PTC diseases. We anticipate that further development of these lead compounds will lead to more general effectiveness, used both alone and in combination with other classes of readthrough inducers.

biochemistry↗

bioRxiv2026

Super-resolution imaging flow cytometry

Organelle architecture is a key determinant of cellular state. However, its heterogeneity remains difficult to quantify at population scale because conventional imaging flow cytometry is diffraction-limited. Here we present super-resolution imaging flow cytometry (SR-IFC), a high-throughput structured-illumination platform combining stroboscopic excitation, microfluidic hydrodynamic focusing and AI-assisted reconstruction. From three phase-shifted frames acquired along the flow axis, SR-IFC reconstructs images with approximately 118-nm isotropic in-plane resolution, about two-fold beyond the diffraction limit, at up to approximately 720 cells per second. In microbiology, SR-IFC resolves individual lipid droplets in nitrogen-starved Euglena gracilis and reveals spatial reorganization during lipid biogenesis missed by diffraction-limited imaging. In immunology, it maps activation-associated mitochondrial remodeling across primary human CD8+ T-cell differentiation, including a transient networked state. SR-IFC thus provides a broadly applicable platform for population-scale super-resolution phenotyping across diverse areas of biology.

bioengineering↗

bioRxiv2026

RiboGRAM learns multi-scale non-coding RNA grammar for structural and regulatory inference

Protein-coding sequences are read through the triplet genetic code, whereas the organization of molecular information within non-coding RNA sequences remains elusive. Here, we identify a non-coding RNA grammar defined by multi-scale motif usage and 5'-to-3' positional gradients, and develop RiboGRAM to learn this organization. Across nine organisms, non-coding RNAs showed scale-dependent divergence from coding sequences, with directional U-rich and AU-rich gradients. Integrating multi-scale sequence encoding with contextual modeling, RiboGRAM organized RNA families, revealing motif-associated and pair-like patterns across layers. Without structural supervision, non-coding RNA pretraining improved base-pair recovery over coding or messenger RNA pretraining, with representations supporting alignment-free diffusion-based 3D modeling of short RNAs. In human RNA-protein binding profiles, RiboGRAM identified position-resolved motif organization across protein targets and cell types, with sequence-preference shifts associated with reduced cross-cell transferability. Together, these results establish a learnable grammar of non-coding RNA sequence organization for structural and regulatory inference.

bioinformatics↗

bioRxiv2026

Microbial Reductive Dechlorination of Hexachlorobutadiene by Dehalococcoides

Hexachlorobutadiene (HCBD), a persistent organic pollutant (POP), poses a significant threat to ecological environments and human health. While anaerobic microbial transformation is a promising remediation strategy, the specific microorganisms and metabolic mechanisms involved have remained poorly understood. This study demonstrates the successful enrichment of an anaerobic microbial consortium from river sediment, with lactate as an electron donor, capable of transforming HCBD. Within 240 days, 62.5 mol of HCBD was sequentially dechlorinated through pentachlorobutadiene (PCBD), tetrachlorobutadiene (TeCBD), trichlorobutadiene (TCBD), and dichlorobutadiene (DCBD) to chlorobutadiene (CBD). Co-amendment with HCBD and trichloroethene (TCE) resulted in complete removal of both compounds. 16S rRNA gene sequencing and quantitative PCR showed enrichment of Dehalococcoides, linking its population growth to HCBD and TCE dechlorination. This study demonstrates that Dehalococcoides growth was associated with HCBD transformation in the enrichment cultures, broadens our understanding of the metabolic capabilities of Dehalococcoides, and identifies a candidate gene for this important environmental process, offering valuable insights for the bioremediation of sites contaminated with HCBD.

microbiology↗

bioRxiv2026

Indole-3-propionic acid nano-prodrugs sustain increased lymphoid exposure and alleviate experimental autoimmune arthritis

Chronic inflammatory diseases, including rheumatoid arthritis (RA), currently require sustained control of inflammation. Although long-acting therapies can reduce dosing frequency, those that rely on systemic immunosuppression may still compromise protective immunity. Microbiota-derived metabolites offer a complementary starting point for immune modulation through naturally occurring host-microbe signals. Indole-3-propionic acid (IPA), a gut microbial tryptophan metabolite naturally present in human circulation, has newly recognized immunoregulatory activity, yet its effects across disease contexts and its potential for therapeutic use remain incompletely defined. Here, we developed polymeric IPA nano-prodrugs (pIPANP) by conjugating IPA to a methacrylamide polymer through ester linkages and formulating the polymer into injectable nanoparticles. Following subcutaneous administration of fluorescently-labeled pIPANP, injection-site fluorescence remained detectable for at least 35 days, with labeled material detected in multiple lymph nodes. LC-MS/MS confirmed higher lymph-node IPA concentrations in mice treated with the pIPANPs compared to free IPA control at every sampled time point over 14 days. In collagen antibody-induced arthritis (CAIA), pIPANPs reduced clinical disease severity and paw swelling under both prophylaxis and therapeutic administration. pIPANP treatment increased the relative representation of CD11cCD103CD11b- cells with a conventional dendritic cell (cDC)1-associated phenotype and reduced costimulatory-marker frequencies in both CD11cCD103 and CD11cCD11b populations, most prominently in hock-draining lymph nodes. These changes were accompanied by increased PD-1 and IFN-{gamma} frequencies among CD4 and CD8 T cells. Fluorescent nanoparticle tracking showed preferential association with several myeloid populations, while single-cell profiling revealed divergent interferon-response signatures across splenic populations. These findings reveal arthritis-associated immunomodulatory activity of polymeric IPA and support its further development as a microbiome-inspired, long-acting approach to inflammatory arthritis.

bioengineering↗