Biology subjects

Liu, H.

Publications and source records attributed to Liu, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Cooperative Peripheral CB1 Inhibition by Extracellular Antibody Binding and Orthosteric Antagonism

The cannabinoid receptor CB1 is an important therapeutic target for obesity and metabolic disorders, yet centrally acting CB1 antagonists are limited by neuropsychiatric side effects. Although the anti-CB1 antibody Nimacimab has advanced to Phase 2 clinical trials for metabolic disorders, the molecular mechanisms underlying peripheral CB1 inhibition remain poorly understood. Here, we report cryo-EM structures of human CB1 bound to Nimacimab alone and in complex with the orthosteric antagonists Rimonabant and JD5037. Unlike previously characterized inhibitory GPCR antibodies that block ligand access through steric occlusion or directly engage orthosteric sites, Nimacimab functions through extracellular allosteric inhibition by stabilizing an inactive-like extracellular architecture of CB1. Antibody binding restricts extracellular conformational dynamics and allosterically stabilizes inactive-state signaling microswitches. Importantly, extracellular antibody engagement is structurally compatible with orthosteric antagonism and cooperatively enhances CB1 inhibition. Structural analysis further reveals how JD5037 remodels the extracellular vestibule to achieve peripheral-selective antagonism. Together, these findings establish extracellular allosteric inhibition as a distinct mechanism of GPCR regulation and provide a structural framework for the development of peripherally selective CB1 therapeutics.

pharmacology and toxicology↗

bioRxiv2026

Sequence-specific and programmable catalytic degradation of extracellular microRNAs by membrane-anchored DNA nanomachines

Extracellular microRNAs (miRNAs) contribute to metastasis through communication between tumour cells and their microenvironment, yet their sustained, sequence-selective depletion remains challenging. Here we report Programmable RNA-Intercepting Molecular Eraser (PRIME), a membrane-anchored DNA nanomachine that organizes miRNA recognition and catalytic degradation at the cell surface. A double-tetrahedral DNA scaffold positions a programmable recognition hairpin beside RNase H. Target binding generates an RNA/DNA hybrid for RNase H-mediated cleavage, and product release resets the hairpin for subsequent degradation cycles. Membrane-anchored PRIME depleted matched extracellular miRNAs by 70.6-89.4% across lung, breast and cervical cancer cell models. Multi-target PRIME (M-PRIME) inhibited migration by 71.3-96.0% in Transwell assays across these models. To evaluate its therapeutic potential, we established an orthotopic lung-tumour model and an early-intervention breast-cancer lung-colonization model in mice. Aptamer-directed M-PRIME combined with gemcitabine reduced pulmonary tumour burden by 74.5% in established lung tumours and 93.2% in the lung-colonization model. These effects were consistent with PRIME-mediated extracellular miRNA degradation, with circulating target miRNA levels reduced by 77.5-98.7% relative to gemcitabine alone. Together, these findings establish a programmable material strategy for sustained extracellular RNA depletion and support its potential to enhance chemotherapy in preclinical tumour models.

biochemistry↗

bioRxiv2026

NexuST: A Hierarchical Foundation Model for Spatial Transcriptomics

Spatial transcriptomics captures molecular states within cells and their organisation in tissue. However, integrating fine-grained gene information with spatial context at scale remains challenging for existing foundation models. Here we present NexuST, a hierarchical foundation model that repeatedly interleaves gene-level molecular modelling with cell-level spatial modelling, allowing the two levels to refine one another during end-to-end pretraining. For pretraining, we curated HumanST-46M, comprising 45.7 million human cells from 72 datasets across 11 organs and three imaging-based platforms. Across four held-out datasets totalling approximately 2.6 million cells, NexuST achieved state-of-the-art or competitive performance in cell-type annotation, region prediction, gene recovery and neighbourhood-composition prediction. We find that cell-intrinsic expression remains informative even for spatial tasks, as shown by an expression-only PCA baseline, while NexuST shows particularly strong gains where spatial context is essential. Overall, NexuST establishes a hierarchical framework that can serve as a general backbone for future spatial transcriptomics foundation models.

bioinformatics↗

bioRxiv2026

Agentic transcranial functional ultrasound imaging: @fUS

Functional ultrasound (fUS) imaging provides deep, wide-field access to brain function, but instrument cost and complex acquisition and analysis workflows restrict its wider adoption. Here we introduce @fUS, an agentic transcranial imaging platform with an open architecture that integrates purpose-built hardware with executable experimental skills and persistent structured memory. The system combines 128-channel, 16-bit acquisition at 125 MHz with GPU-based processing and enables functional imaging through the intact scalp and skull of mice, with approximately 100-m spatial resolution and 10-Hz temporal sampling, providing a basis for longitudinal studies without cranial-window surgery. Its agent connects scientific objectives to experimental design, direct instrument control and data analysis, retaining context across interactions and supporting inspectable workflows through text and hands-free voice control. Neuroscience trainees with limited engineering experience independently configured the system within 30 min. Agent-assisted exploration of whisker-stimulation datasets revealed low-frequency vascular changes beyond conventional response mapping, supported by complementary two-photon measurements of single-vessel diameter. By combining transcranial imaging with accessible instrument control and analysis, @fUS provides a foundation for wider adoption and larger, more diverse neuroscience datasets. More broadly, it offers a framework for scientific instruments in which measurement, computation and experimental reasoning are developed as parts of the same system.

bioengineering↗

bioRxiv2026

Restoring Aquaporin-4 alleviates molecular and motor phenotypes in zQ175 mouse model of Huntington disease

Huntington&'s disease (HD) is characterized by progressive accumulation of mutant huntingtin (mHTT), neurodegeneration and motor dysfunction. Increasing evidence implicates impaired glymphatic function and loss of perivascular aquaporin 4 (AQP4) polarization in HD, suggesting that defective brain waste clearance may contribute to disease pathogenesis. Whether restoration of AQP4&-mediated glymphatic transport can ameliorate HD pathology remains unknown. We tested whether genetic restoration of AQP4 improves glymphatic function and HD&-associated phenotypes in heterozygous zQ175 knock-in mice. At 2 months of age, premanifest zQ175 mice received a single retro-orbital injection of BBB-penetrant AAV9&-PHP.eB encoding the AQP4 (M1 isoform). Glymphatic transport was assessed by intracisternal injection of fluorescent BSA 647 and quantification of parenchymal influx and drainage to the deep cervical lymph nodes. Perivascular AQP4 localization, mHTT aggregation, gliosis, DARPP32 immunoreactivity, CSF neurofilament light chain (NfL) and total Tau, structural brain volumes by 11.7T MRI, and motor behavior were assessed longitudinally through 12 months of age. AAV9&-PHP.eB&-AQP4 produced widespread brain expression and restored perivascular AQP4 localization in the striatum and cortex of zQ175 mice. AQP4 overexpression significantly increased glymphatic tracer influx into brain parenchyma and BSA-647 drainage to the deep cervical lymph nodes. At 12 months, AQP4 restoration reduced CSF NfL and total Tau concentrations, mHTT aggregate number and mean aggregate size, and striatal Iba1 positive microglia and GFAP-positive astrocytes (P < 0.05). AQP4 overexpression also preserved striatal DARPP32 immunoreactivity and significantly attenuated striatal atrophy measured by MRI. Female zQ175 mice showed improved balance-beam performance and locomotor activity, while effects on motor performance in males did not reach statistical significance. AQP4 overexpression attenuated body-weight loss in both sexes. No detectable structural, behavioral or body-weight abnormalities were observed following sustained AQP4 overexpression in wild-type mice. In summary, restoration of AQP4 enhances glymphatic transport and is associated with reduced proteopathic, neuroinflammatory and neurodegenerative phenotypes in zQ175 HD mice. These findings provide proof-of-concept that impaired glymphatic function is a modifiable component of HD pathology and support AQP4&-mediated restoration of brain waste clearance pathways as a potential disease-modifying therapeutic strategy.

neuroscience↗

bioRxiv2026

The OxyR-Responsive TacAT Module Promotes Oxidative Stress Adaptation and In Vivo Fitness in K. pneumoniae

During infection, Klebsiella pneumoniae must withstand host-derived oxidative stress not only by detoxifying reactive oxygen species (ROS) but also by repairing oxidative damage to cellular physiology. How these detoxification and stress-adaptive responses are coordinated remains unclear. Here, we identify a plasmid-encoded tacAT locus as an OxyR-responsive regulatory module that supports peroxide tolerance and in vivo fitness in K. pneumoniae. Guided by the conservation of the OxyR DNA-binding domain and its consensus binding motif, we surveyed promoter-proximal regions of the K. pneumoniae CRK3022 chromosome and plasmids for candidate OxyR-responsive loci. This analysis identified tacAT, a putative type II toxin-antitoxin (TA) module, as the only plasmid-associated candidate. OxyR directly bound the tacAT promoter and contributed to tacAT induction during hydrogen peroxide (H?O?) stress. The TacAT complex exhibited DNA-binding and transcriptional regulatory activity, promoting the expression of genes linked to protein quality control and membrane/envelope homeostasis, including clpB, htpG, cadC, bhsA, and marA. Deletion of tacAT compromised survival under lethal peroxide challenge and attenuated bacterial dissemination, tissue pathology, and inflammatory responses in a murine bacteremia model. These findings define an OxyR-TacAT regulatory branch that connects peroxide sensing with stress-adaptive gene expression, revealing how a TA-associated module can be integrated into stress-adaptive programs during host-associated oxidative stress.

microbiology↗

bioRxiv2026

The hydrocup: a hollow electrospun scaffold for in vivo hydrogel-laden cell delivery

For regenerative medicine applications, transplanted cells are difficult to retain in a specific place to maximize the localized release of cytokines, which can positively modulate immune responses, angiogenesis and tissue regeneration. Here, we developed a hollow electrospun (ESP) scaffold with one open and one closed end to enclose a hydrogel laden with human mesenchymal stem cells (hMSCs); we termed this combination the hydrocup. hMSCs remained viable for 28 days in vitro and released functional cytokines similar to hMSCs in transplanted but non-enclosed hydrogels. The hydrocups remained intact and fixed in place for 6 weeks after subcutaneous implantation in rats, demonstrating in vivo compatibility. These results demonstrate that the hydrocup is the first, to our knowledge, cell-laden hydrogel delivery scaffold. This innovation could be developed for a wide variety of cell-based cytokine secretion or drug-laden hydrogel applications.

bioengineering↗

bioRxiv2026

Noninvasive tomography of tumor progression via dynamical changes of T-cells in surrounding microenvironment

Tumor progression is shaped by a continuous competition between malignant expansion and immune access within the surrounding microenvironment. Although spatial assays can reveal where T cells accumulate, most current approaches remain descriptive, treating immune organization as a static pattern and failing to infer the latent resistance structure that governs progression. Here we show that changes in peri-tumoral T-cell distribution can support noninvasive tomography of tumor progression. Using spatially resolved human breast tumor sections and controlled numerical experiments, we formulate immune-tumor interaction within a mean-field game framework in which T cells act as agents responding to a heterogeneous microenvironment while the tumor shapes an equivalent barrier field that restricts infiltration. This framework converts boundary enrichment, layered blocking and core penetration patterns into a constrained inference problem whose solution yields quantitative maps of immune exclusion, barrier strength and progression-associated internal states. Forward simulations show that barrier geometry reshapes immune-density equilibria, and inference experiments show that closely related barrier fields can be recovered from immune-density observations under controlled and tissue-shaped proxy settings. By linking observable T-cell redistribution to latent microenvironmental resistance, this approach establishes a route toward noninvasive, repeatable assessment of tumor progression without direct biopsy of the underlying barrier structure.

cancer biology↗

bioRxiv2026

Localized SARS-CoV-2 Infection Triggers a Tissue-Wide Antiviral Response and Functional Impairment of Olfactory Sensory Neurons

Olfactory dysfunction is a hallmark of COVID-19, yet the mechanisms by which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes widespread sensory impairment remain incompletely understood. We compared the olfactory epithelial tropism of multiple SARS-CoV-2 variants in a mouse model and observed that Alpha and Beta variants exhibited the greatest infectivity for the olfactory epithelium (OE), whereas Omicron rarely infected this tissue despite comparable pulmonary viral titers. We further defined the effects of SARS-CoV-2 on olfactory sensory neurons (OSNs) using immunohistochemistry, single-cell RNA sequencing, spatial gene expression characterization, and functional odor stimulation. The localized infection of sustentacular cells triggered a tissue-wide interferon-stimulated antiviral response that extended beyond infected regions for Alpha and Beta but was largely absent following Omicron infection. Mature OSNs transiently adopted an interferon-responsive state before exhibiting persistent downregulation of odorant signal transduction, mitochondrial, and activity-dependent gene pathways. Consistent with these transcriptional changes, odor stimulation failed to elicit normal activity-dependent gene expression during SARS-CoV-2 infection, indicating impaired neuronal function without widespread neuronal loss. Progressive accumulation of macrophages further indicated sustained inflammatory remodeling of the OE. Together, these findings demonstrate that SARS-CoV-2 infection initiates tissue-wide antiviral signaling in the OE that persistently disrupts OSN function, providing a mechanistic framework for COVID-19-associated anosmia.

neuroscience↗

bioRxiv2026

Maleic acid adjuvates BCG to induce CD4+CD8+ T cells and sterilize tuberculosis

Anti-tuberculosis (TB) immunity typically emphasizes CD4+ T and CD8+ T cells that only provide limited protection against Mycobacterium tuberculosis (Mtb) infection. The anti-TB function of CD4+CD8+ T cells remains unexplored, mostly due to the dogma that ThPOK and Runx3 antagonize each other to block their development and their scarcity. Here, we show that immunization of BCG (Bacillus Calmette-Gu&eacuterin) with Complete Freund's Adjuvant (CFA) markedly induced CD4+CD8+ T cells through the gut microbiota Clostridium butyricum or its metabolite maleic acid. Mtb-specific CD4+CD8+ T cells exhibited a broad T-cell receptor repertoire and sterilized Mtb infection by inducing SLAMF1 and neutrophil responses. Mechanistically, maleic acid interacted with PAK2 to promote STAT5 phosphorylation at Ser127, thus upregulating Ets1 expression. Direct binding of Ets1 to the Runx3 and ThPOK promoters orchestrated their expression to redirect the CD8+ T cell differentiation towards the CD4+CD8+ lineage. Moreover, immunization of BCG plus Clostridium butyricum or maleic acid sterilized Mtb infection in mouse models. These findings establish CD4+CD8+ T cells as superior immune effectors against Mtb, a concept that could fundamentally redirect the current paradigm for anti-TB vaccine development.

microbiology↗

bioRxiv2026

A fungal effector hijacks conserved plant GSK3-like kinases to reprogram host cell identity

Stable developmental programs normally resist reprogramming, yet pathogens can override these constraints to induce profound tissue and cellular remodeling. How microbial pathogens access conserved developmental signaling networks to reprogram host growth and differentiation remains poorly understood. Here, we show that the maize smut fungus Ustilago maydis deploys the effector Iag1 to reprogram host cell fate by targeting the conserved GSK3-like kinase BIN2. Iag1 contains a PPNT short interaction motif found also in plant viral effectors that mediates its association with BIN2 and related maize GSK3-like kinases and is essential for effector activity and full fungal virulence. This interaction attenuates BIN2-dependent signaling, reduces phosphorylation of the BIN2 substrate BES1, and triggers extensive transcriptional reprogramming consistent with coordinated perturbation of brassinosteroid, auxin, and other BIN2-regulated developmental pathways. These changes result in extensive epidermal developmental reprogramming, including loss of stomatal identity, altered cell division orientation, and aberrant cell expansion. Together, our findings identify GSK3-like kinases as conserved developmental signaling hubs that pathogens can exploit to unlock host developmental plasticity and suggest that short motifs provide an evolutionarily flexible strategy for targeting these central regulatory nodes.

plant biology↗

bioRxiv2026

Generation and application of human pluripotent stem cells derived peri-nervoids

Autologous nerve grafts remain the gold standard for peripheral nerve repair, but donor scarcity, donor-site morbidity and incomplete functional recovery limit their use. Schwann cells (SCs) drive autograft-mediated regeneration, yet their limited availability and expansion impede SC-based therapies. Here, we generated human pluripotent stem cell-derived SCs, motor neuron-enriched spinal cord organoids and nociceptive sensory neuron-enriched dorsal root ganglion organoids, and assembled them into a nerve-like construct termed the Peri-nervoid. Single-cell RNA sequencing revealed context-dependent SC plasticity: axonal co-culture promoted myelination, whereas axonal transection induced a repair phenotype resembling SC dedifferentiation during Wallerian degeneration. Following transplantation into 7-mm sciatic nerve defects in NSG mice, human SCs survived and remyelinated regenerating host axons, while axon-containing grafts enhanced regeneration relative to SC-only grafts. No abnormal proliferation, systemic toxicity or major-organ histopathology was detected. These findings position the Peri-nervoid as a scalable, developmentally inspired platform for developing engineered grafts for peripheral nerve repair.

bioengineering↗

bioRxiv2026

Genetic regulation of circulating metabolome in cattle

The circulating metabolome is a vital intermediate layer linking genetics to complex phenotypes, yet existing genome-wide studies-even in humans-rarely capture dynamic physiological contexts or cellular regulatory mechanisms. Here, we present the Cattle Metabolome Atlas (https://cattlema.farmgtex.org/), a comprehensive resource of 3,436 plasma metabolites and 4,851 serum metabolites from 4,651 animals with matched sequence-level genotypes across highly dynamic parity and lactation stages. We mapped 728 plasma and 622 serum metabolite quantitative trait loci (mQTL), revealing widespread context-dependent regulatory architectures. Integrating these mQTL with the multi-tissue expression quantitative trait loci (eQTL) and single-cell atlas of 59 tissues demonstrates that 74-79% of mQTL colocalize with eQTL across 29 tissues, prioritizing the liver as the primary systemic hub and resolving metabolic programs at single-cell resolution. Furthermore, we charted 538 causal gene-tissue-metabolite-trait cascades across 11 complex traits in cattle. Finally, cross-species analyses demonstrate partial evolutionary conservation of genetic metabolism between cattle and humans, establishing this atlas as a powerful asset for cattle genetics and genomics, selective breeding, and comparative biology.

genetics↗

bioRxiv2026

A native single-transcript TnpB architecture enables efficient virus-induced genome editing and visual screening of heritable progeny harboring phenotypically silent edits

TnpB are ultra-compact RNA-guided nucleases, yet most reported systems require separate expression of the nuclease and cognate reRNA, eroding their size advantage and restricting viral delivery in plants. Here we demonstrate that ISDra2 TnpB harnesses its native overlapping architecture in which the reRNA sequence resides within the 3' coding region of TnpB, processing its own mRNA to generate functional reRNA and enabling single-transcript genome editing in plants. Only a 7-bp conserved motif followed by a 16-20 bp spacer directly downstream of the coding sequence suffices for editing, requiring no exogenous ribozymes or independent guide promoters. This ultra-compact design enables simultaneous packaging of the editing system and an NbPDS silencing module into a single TRV vector, achieving robust editing in systemic Nicotiana benthamiana tissues and establishing a dual VIGE-VIGS strategy for direct visual selection of heritable, transgene-free edited progeny via distinct albino phenotypes, reducing laborious large-scale genotyping even for targets lacking inherent visible traits.

plant biology↗

bioRxiv2026

Computer vision-aided locomotor behavioral analysis identifies therapeutic motor signatures in a mouse model of Huntington disease

Huntington disease (HD) is a neurodegenerative disorder characterized by progressive motor dysfunction. Traditional open-field tests quantify spontaneous locomotor parameters; however, fine mouse motor signatures, particularly disease stage-specific changes in HD motor symptoms and pharmacodynamic responses to therapeutic treatments. Here, we employed a computer vision-aided behavioral flow analysis designed to quantify fine, HD-relevant motor dysfunction in the zQ175DN HD mouse model, ranging from early HD-like motor signatures to well-defined motor deficits. Markerless pose estimation and Keypoint-MoSeq segmented standard top-view open-field recordings into recurrent behavioral syllables, which were then organized into higher-order clusters and transition networks. Disease stage-dependent changes in syllable occurrence, syllable duration, behavioral-state composition, and transition structure were identified. These analyses are not possible with traditional open-field assays. Syllable-duration features provided the strongest genotype discrimination, and HD-like motor features were also characterized by hub remodeling and transition-network disorganization. These features were integrated into an HD motor dysfunction (HDMD) score based on age- or HD progress-matched wild-type (WT) -standardized absolute deviations. The HDMD score distinguished HD mice from WT across multiple symptomatic stages and correlated with HD pathology and disease severity. Effect-size and power analyses suggested improved efficiency for detecting potential therapeutic effects. This framework requires only standard top-view recordings and may also support retrospective analysis of existing open-field video datasets. Overall, the HDMD framework provides a practical strategy for identifying fine motor changes in HD mice, aiding study design and preclinical efficacy assessment in HD drug development.

neuroscience↗

bioRxiv2026

A Multi-Omics Study of Cognitive Resilience to Alzheimer's Disease

Alzheimers disease (AD) is the most severe form of dementia. While significant efforts have been made to identify AD risk factors and develop therapeutics, much less attention has been given to neurobiological factors and molecular signatures associated with cognitive resilience. Substantial evidence suggests that modifiable factors, such as physical and mental activity, may contribute to cognitive reserve and resilience. To this end, we developed a resilient cohort of paired genetics, transcriptomics and proteomics data from the prefrontal cortex of 282 cognitively normal older adults. We conducted extensive preprocessing and rigorous quality control (QC), including QC on sequence metrics and sample matching across multiomics. This cohort can be leveraged for identification of molecular signatures of cognitive resilience to AD and is freely shared with the research community.

genomics↗

bioRxiv2026

Constructing microbiome co-occurrence networks with confidence: A conditional, nonparametric, inference-based approach

Constructing microbial association networks is a common strategy for exploring relationships among taxa in microbiome studies. Although marginal correlation methods are easy to implement and allow formal inference, they can produce spurious edges driven by indirect associations through other taxa. Conditional graphical-modeling methods aim to recover direct associations, but many rely on Gaussian or linear assumptions and often provide limited uncertainty quantification. We propose a conditional, nonparametric approach based on the scaled expected conditional covariance (SEcov). SEcov measures population-level conditional association by residualizing each taxon with respect to the remaining taxa and scaling the resulting expected conditional covariance. The resulting estimator can incorporate flexible machine-learning methods for conditional-mean estimation and admits asymptotic normal inference, enabling p-values and confidence intervals for taxon-pair associations. We demonstrate through simulation studies that our proposed approach improves network recovery relative to other methods, and we illustrate the new method via construction of a co-occurrence network for the vaginal microbiome during pregnancy. IMPORTANCEHigh-throughput sequencing has made it possible to characterize microbial communities at large scale, and network analysis is widely used to summarize relationships among taxa. However, networks based on marginal correlations may include indirect associations, whereas many conditional graphical models rely on assumptions that may be difficult to justify for sparse, zero-inflated, compositional microbiome data. SEcov offers a practical alternative by estimating conditional associations nonparametrically and attaching inferential uncertainty to individual edges. This allows investigators to construct microbiome networks using statistically interpretable evidence for taxon-pair associations, rather than relying solely on arbitrary correlation cutoffs or regularization tuning parameters.

bioinformatics↗

bioRxiv2026

The MOS4-associated complex subunit MAC5A maintains meristem development by regulating transcription elongation in Arabidopsis

The precise coordination of co-transcriptional RNA processing with transcriptional elongation is essential for eukaryotic gene regulation, yet the machineries coupling these processes remain largely elusive. Here, we reveal a role for the spliceosome-associated MOS4-associated complex (MAC) in regulating plant development through the direct regulation of transcriptional elongation. We demonstrate that the MAC subunit MAC5A physically interacts with Elongator Protein 6 (ELP6), a core component of the transcriptional Elongator complex. Genetic analyses reveal that MAC5A and ELP6 function synergistically to regulate apical meristem activity. Importantly, the MAC5A-Elongator module is required for the efficient expression of the critical auxin efflux carrier PIN-FORMED1 (PIN1) by enhancing RNA Polymerase II (RNAPII) occupancy across the PIN1 locus. Furthermore, we show that this elongation-promoting function is not unique to MAC5A, as other core MAC components are similarly required for efficient transcription progression. Together, our findings uncover a splicing-elongation nexus where MAC5A likely acts as a molecular bridge between the spliceosome and the elongation polymerase. This functional coupling ensures the efficient transcription of key developmental regulators, providing a mechanistic framework for the coupling of RNA processing to transcription and suggesting a conserved principle of gene expression control across eukaryotes.

plant biology↗