Biology subjects

Liu, H.

Publications and source records attributed to Liu, H..

At least 289 records · Page 16Linked to original sources

bioRxiv2025

D-LMBmapX: Generalized Deep-Learning Pipeline for Automated Whole-brain Neural Circuitry Profiling Across Any Developmental Stages

Understanding whole-brain circuitry development is essential for uncovering the origins of disorders linked to abnormal neural wiring, yet progress has been limited by the lack of tools for accurate, comprehensive analysis. Brain development is highly dynamic and region-specific, with pronounced inter-individual variability during early stages, and no existing method achieves whole-brain profiling at arbitrary stages. The rapidly changing morphology of developing axons further complicates segmentation. Here, we present D-LMBmapX, a deep learning pipeline for automated whole-brain circuitry profiling across postnatal development. D-LMBmapX constructs sample-inferred atlases from flanking anchor stages, enabling accurate registration at any time point. By developing a foundation model for generalised axon and soma segmentation, it supports quantitative mesoscale developmental connectomics, demonstrated through spatial-temporal profiling of catecholaminergic projections. D-LMBmapX also enables robust cross-modality and cross-dimensional registration, including precise alignment of single 2D slices to 3D references, and offers generalizable strategies for 5D analysis of diverse biomedical spatial datasets.

neuroscience↗

bioRxiv2025

Global distribution of honeybee gut microbiome and pesticide-driven adaptations in opportunistic microbial species

Honeybees (Apis mellifera) rely on a specialized gut microbiome shaped by climate, flora, agrochemicals, and dietary supplements. Yet, how these factors alter microbiome composition and function remains unclear. We integrated 16S rRNA and shotgun metagenomics data from eight published studies across six regions, alongside newly generated 16S data from Armenia, to assess how environmental and agrochemical factors influence the honeybee gut microbiome. We also introduced a novel co-abundance and functional analysis pipeline to identify treatment-affected bacterial networks and associated pathways. We observed a stable core of six to twelve phylotypes in amplicon and metagenomic datasets respectively. However, we note significant geographic variation in relative abundances, likely reflecting differences in diet, climate, and local flora. Armenian data revealed distinct seasonal shifts, particularly elevated Commensalibacter in autumn and minor urban-rural differences. Pesticide treatments elicited varying responses: oxalic acid drove pronounced beta-diversity shifts; neonicotinoids had subtler effects, both primarily impacting opportunistic pathogens; and glyphosate disrupted core taxa with stronger effects in newly emerged bees under prolonged exposure. Co-abundance network analysis highlighted that the pesticide-associated community was enriched in adaptive pathways, including potential glyphosate degradation by Pseudomonas, biofilm formation, and aromatic amino acid synthesis. These findings reaffirm the stability of the honeybee core microbiome yet underscore that environmental and anthropogenic stressors induce distinct compositional and functional shifts. We emphasize the need for longitudinal metagenomic approaches that enable high-resolution functional profiling and co-abundance network analysis to clarify how these microbiome shifts impact bee health and colony sustainability.

microbiology↗

bioRxiv2025

Neutralizing antibodies elicited by Nipah virus G-head nanoparticle target diverse sites and inhibit receptor binding and fusion

Nipah virus (NiV) and Hendra virus (HeV), two highly pathogenic Henipaviruses (HNVs), pose a significant public health threat. The attachment glycoprotein (G) plays a crucial role in viral attachment and entry, making it an attractive target for vaccine and therapeutic antibody development. However, the antigenic landscape and neutralization sensitivity of the G protein remain poorly defined. Here, we systematically characterize 27 monoclonal antibodies (mAbs) elicited by NiV G head (GH) nanoparticle-immunized mice. Among these, 25 mAbs exhibit neutralizing activity against two major NiV strains, NiV-Malaysia and NiV-Bangladesh, with five mAbs also cross-inhibiting HeV infection. Although all mAbs target GH, they inhibit viral infection through distinct mechanisms, either by blocking receptor ephrin-B2 engagement with the G protein or by preventing viral membrane fusion. Notably, mAbs from two distinct groups conferred complete protection to hamsters against lethal NiV-Malaysia infection. Structural analysis of NiV GH in complex with four representative Fabs reveals four non-overlapping epitopes, including two novel antigenic sites and one shared protective epitope identified across species. Our study provides a comprehensive map of the antigenic determinants of NiV GH, elucidates the relationship between epitopes, neutralization mechanisms, and protection, and offers new insights and opportunities for antibody-based therapies and vaccine development. HighlightsMost mAbs induced in G head nanoparticle-immunized mice are potent neutralizers MAbs recognizing the G head block receptor binding or viral fusion Structural analysis shows mAbs target four distinct epitopes on G head protein Receptor competition site on G head is a shared protective antigenic site in human and multiple animals

immunology↗

bioRxiv2025

Machine Learning-Enhanced Extraction of Protein Signatures of Renal Cell Carcinoma from Proteomics Data

In this study, we generated label-free data-independent acquisition (DIA)-based liquid chromatography (LC)-mass spectrometry (MS) proteomics data from 261 renal cell carcinomas (RCC) and 195 normal adjacent tissues (NAT). The RCC tumors included 48 non-clear cell renal cell carcinomas (non-ccRCC) and 213 ccRCC. A total of 219,740 peptides and 11,943 protein groups were identified with 9,787 protein groups per sample on average. We adopted a comprehensive approach to select representative samples with different mutation sites, considering histopathological, immune, methylation, and non-negative matrix factorization (NMF)-based subtypes, along with clinical characteristics (gender, grade, and stage) to capture the complexity and diversity of ccRCC tumors. We used machine learning identified 55 protein signatures that distinguish RCC tumors from NATs. Furthermore, 39 protein signatures that differentiate different RCC tumor subtypes were also identified. Our findings offer an extensive perspective of the proteomic landscape in RCC, illuminating specific proteins that serve to distinguish RCC tumors from NATs and among various RCC tumor subtypes.

cancer biology↗

bioRxiv2025

Identifying regulators of aged fibroblast activation in 3D tissue models

Robust 3D tissue culture models to activate aged fibroblasts for cell-based therapies and identify regulators of such activation are still missing. In our previous study, we showed that aged fibroblasts can be activated simply through applying compressive force, without the need for exogenous factors, leading to increased migration. In this study, we develop a pipeline to evaluate the role of specific pharmacological inhibitors for transcription factor inference and cell migration involved in aged fibroblast activation. By integrating RNA-seq data with bioinformatic tools (prize collecting Steiner tree method and iRegulon) we inferred 15 candidates. In addition, we used cell migration and heterochromatin content as readouts for validating these candidates. Furthermore, we identified three potential master regulators of fibroblast activation and rejuvenation: FOXO1, STAT3, and PDK1. These findings offer valuable insights for future drug discovery, disease modeling, and regenerative medicine.

cell biology↗

bioRxiv2025

Filamented Light (FLight) Biofabrication of Mini-Tendon Models Show Tunable Matrix Confinement and Nuclear Morphology

One hallmark of healthy tendon tissue is the high confinement of tenocytes between tightly packed, highly aligned collagen fibers. During tendinopathy, this organization becomes dysregulated, leading to cells with round-shaped morphology and collagen fibers which exhibit crimping and misalignment. The elongated nuclei in healthy tendons are linked to matrix homeostasis through distinct mechanotransduction pathways, and it is believed that the loss of nuclear confinement could upregulate genes associated with abnormal matrix remodeling. Replicating the cell and nuclear morphology of healthy and diseased states of tendon, however, remains a significant challenge for engineered in vitro tendon models. Here we report on a high throughput biofabrication of mini-tendons that mimick the tendon core compartment based on the Filamented Light (FLight) approach. Each mini-tendon, with a length of 4 mm, was composed of parallel hydrogel microfilaments (2-5 {micro}m diameter) and microchannels (2-10 {micro}m diameter) that confined the cells. We generated four distinct matrices with varying stiffness (7-40 kPa) and microchannel dimensions. After 14 days of culture, 29% of tenocytes in the softest matrix with the largest microchannel diameter were aligned, exhibiting an average nuclear aspect ratio (nAR) of 2.1. In contrast, 84% of tenocytes in the stiffest matrix with the smallest microchannel diameter were highly aligned, with a mean nAR of 3.4. When tenocytes were cultured on the FLight hydrogels (2D) as opposed to within the hydrogels (3D), the mean nAR was less than 1.9, indicating that nuclear morphology is significantly more confined in 3D environments. By tuning the stiffness and microarchitecture of the FLight matrix, we demonstrated that mechanical confinement can be modulated to exert control over the extent of nuclear confinement. This high-throughput, tunable platform offers a promising approach for studying the mechanobiology of healthy and diseased tendons and for eventual testing of drug compounds against tendinopathy.

bioengineering↗

bioRxiv2025

Filamented Light (FLight) Bioprinting of Mini-Muscles with Self-Renewal Potential

The plasticity and regenerative capacity of skeletal muscle arise from quiescent stem cells activated upon overload, injury, or inflammation. Developing in vitro muscle models to study these properties could advance muscle disease modeling and pre-clinical evaluation. Here, we leverage Filamented Light (FLight) bioprinting as a high-throughput approach for producing mini-muscle tissues. Using Pax7-nGFP myoblasts, we bioprinted mini-muscles from pristine collagen-fibrinogen. The FLight hydrogel consisted of aligned microstructures which guided the formation of aligned myotubes. Mini-muscles demonstrated in vivo-like tissue organization, including highly aligned myotubes and a Pax7+ cell pool embedded in newly deposited laminin. Both spontaneous and electrically stimulated contractions were observed. Collagen-fibrinogen matrix was promising for maintenance of the Pax7+ cell pool. Damage from cardiotoxin-induced injury of the mini-muscles led to a massive proliferation of Pax7+ cells and restoration of the contractile properties. Notably, small molecules such as Repsox could enhance regeneration. FLight printed mini-muscles have potential for applications in muscle biology, exercise/atrophy, disease models, and drug screening.

bioengineering↗

bioRxiv2025

Size switchable DNA origami structure enabled by dynamic crossovers

DNA nanostructures are formed by many DNA double helices connected via crossovers. If multiple DNA double helices are connected by crossovers at different base positions (different rotational angles), these DNA double helices are stacked together to obtain desired two- or three-dimensional DNA structures. Here we inserted i-motif or hairpin motifs in crossover regions of one layer DNA origami structure and employed dynamic DNA element to implement size-switchablity between expansion and contraction. By changing pH or adding complementary strands to regulate interspacings between DNA double helixes, multiple crossover replacements realize the dynamic size changes between 68 nm and 150 nm as characterized by atomic force microscopy. We further demonstrated dynamic sizes changes enabled or inhibited FRET (fluorescence resonance energy transfer) signals between Cy3 and Cy5 and the controlled distances between protein molecules. The results reveal the feasibility of fabricating size-switchable DNA origami nanostructures via crossover redesign, demonstrating their potential in nano-engineering, proximity enabled chemical reacitons, as well as for biomedical applications.

bioengineering↗

bioRxiv2025

Single-cell Transcriptomics Unravel Stereocilia Degeneration as a Key Contributor to Age-related Vestibular Dysfunction in Mice and Humans

Age-related vestibular dysfunction (ARVD) is a prevalent, debilitating condition in the elderly. The etiology and molecular mechanisms are poorly understood. We focused on mechanosensitive hair cells (HCs) as they are vulnerable to aging. Using single-cell RNA-seq transcriptomes of young and old mouse vestibular HCs, we show that aging vestibular HCs display both universal molecular signatures, such as genomic instability, mitochondrial dysfunction, and impaired proteostasis, and cell type-specific changes associated with deterioration of hair bundles and mechanotransduction. In alignment with transcriptomic findings, imaging and electrophysiological recordings from aged vestibular sensory epithelia confirmed the degeneration of the hair bundles and a reduction in mechanotransduction. Importantly, this deterioration of hair bundles and vestibular function precedes HC loss, highlighting impaired mechanotransduction as a key contributor to ARVD. Furthermore, molecular and cellular changes associated with aging signatures are less pronounced in vestibular HCs than in cochlear HCs, underscoring tissue-specific age-related differences between the two sensory epithelia in the inner ear.

neuroscience↗

bioRxiv2025

GenomeOcean: An Efficient Genome Foundation Model Trained on Large-Scale Metagenomic Assemblies

Functional genomic sequences occupy an infinitesimal fraction of the astronomically large DNA sequence space, implying that evolution explores a low-dimensional manifold shaped by universal biochemical and evolutionary constraints. To investigate this underexplored Genomic Manifold Hypothesis using scalable, data-driven evidence, we developed GenomeOcean, a 4-billion-parameter generative model trained on 219 TB of diverse, co-assembled global environmental metagenomic data using an optimized transformer. The model captures both universal phylogenetic syntax and protein-coding fidelity. Furthermore, we validate the embeddings intrinsic low dimensionality. Crucially, comparisons with the independently trained Evo 2 model demonstrate a strong linear correspondence between their embedding spaces and convergent generative behaviors. These results suggest that the genomic manifold represents a fundamental biological principle, offering a unified framework for understanding evolutionary constraints and guiding synthetic biology.

bioinformatics↗

bioRxiv2025

Epithelial miR-149-5p up-regulation is associated with immune evasion in progressive bronchial premalignant lesions

The molecular drivers bronchial premalignant lesion progression to invasive lung squamous cell carcinoma are not well defined. Prior work profiling longitudinally collected bronchial premalignant lesion biopsies by RNA sequencing defined a proliferative subtype, enriched with bronchial dysplasia. We found that a gene co-expression module associated with interferon gamma signaling and antigen processing/presentation was down-regulated in progressive/persistent versus regressive lesions within the proliferative subtype, suggesting a functional impact of these genes on immune evasion. RNA from these same premalignant lesions was profiled by microRNA (miRNA) sequencing and a miRNA-gene network analysis identified hsa-miR-149-5p as a potential regulator of this antigen presentation gene co-expression module associated with lesion progression. hsa-miR-149-5p was found to be predominantly expressed in the epithelium and up-regulated in progressive/persistent versus regressive proliferative lesions while targets of this miRNA, the transcriptional coactivator of MHC-I gene expression, NLRC5, and the genes it regulates were down-regulated. MicroRNA in situ hybridization of hsa-miR-149-5p in tissue from adjacent fixed biopsies showed that hsa-miR-149-5p was increased in areas of bronchial dysplasia in progressive/persistent versus regressive lesions. Imaging mass cytometry showed that NLRC5 protein expression was decreased in progressive/persistent versus regressive lesions within areas of hyperplasia, metaplasia, and dysplasia. Additionally, basal cells with high versus low levels of NLRC5 were found to be in close spatial proximity to CD8 T cells, suggesting that these cells exhibit increased functional MHC-I gene expression in lesions with low hsa-miR-149-5p expression. Collectively, our data suggests a functional role for hsa-miR-149-5p in bronchial premalignant lesions and may serve as a therapeutic target for PML immunomodulation. STATEMENT OF SIGNIFICANCEIntegrative analysis across bronchial premalignant lesions has identified and localized a potential regulator of immune evasion in progressive/persistent lesions that could be a novel therapeutic target.

cancer biology↗

bioRxiv2025

Epidermal stem cell-derived extracellular vesicles induce fibroblasts mesenchymal-epidermal transition to alleviate hypertrophic scar via the miR-200s/ZEBs axis

Hypertrophic scar (HS) is a prevalent yet unresolved wound healing complication characterized by persistent hyperactive and proliferative fibroblasts, leading to excessive extracellular matrix (ECM) synthesis and collagen contraction. Our previous studies have identified epidermal stem cells (ESCs) as critical for wound healing and HS remodeling, with its extracellular vesicles (EVs) playing a vital role. However, the specific mechanisms remain unclear. In this study, we first discovered that ESC-EVs could effectively induce the mesenchymal-epidermal transition (MET) of HS fibroblasts (HSFs) and inhibit their biological activity. Furthermore, by next-generation sequencing and multiplexed CRISPR/Cas9 system, we elucidated that this therapeutic effect is mediated by the miR-200 family (miR-200s) encapsulated in ESC-EVs, which targeted and inhibited ZEB1 and ZEB2 in HSFs. This vital role and mechanism have been thoroughly validated in both in vitro cell experiments and in vivo rat tail HS (RHS) models. These findings not only shed light on a previously unidentified mechanism of ESC-EVs for HS, but also provide potential novel targets and strategies for its precise treatment.

cell biology↗

bioRxiv2025

Microbes under climatic refugia: Self-stabilizing subcommunity rank dynamics in large-river deltaic estuaries

Microorganisms, akin to macroorganisms, can be sheltered by climatic refugia, overlooked for optimism about microbial extinction. By categorizing microbial communities into ecologically distinct subcommunities, we conducted a two-year survey of large-river deltaic estuaries (LDEs) which are regarded as refugial hotspots, and established rank hierarchies to monitor temporal changes. We found that, consistent with macroecology, LDEs harbor distinct microbial community structures, with the abundance distribution of subcommunities exhibiting resilience against environmental perturbations, persisting on an annual cycle. In particular, while the evenness of subcommunity rank abundance curves fluctuates frequently, shifts in rank order are less dynamic but, once initiated, have a more pronounced impact on subsequent rank dynamics. Our results suggest that the microbial subcommunity rank structure in LDEs is both persistent and robust, aligning with classic patterns of species abundance distributions. This study emphasizes that, despite differences in their roles, the stable functioning of microbial rank systems is also fundamental to the refugial capacity of ecosystems and should be given equal importance.

ecology↗

bioRxiv2025

ca-circSCN8A promotes HPASMCs ferroptosis via LLPS initiated R-Loop

BACKGROUNDFerroptosis has been implicated in pulmonary hypertension. Chromatin-associated RNAs are linked to ferroptosis. However, their role in pulmonary vascular ferroptosis in PH is unexplored. METHODSBioinformatics, Sanger sequencing, RNase R and others were employed to identify differentially higher expression of ca-circSCN8A. Functional gain and loss assays were employed to unveil the role of ca-circSCN8A in hypoxia-induced redox-dependent ferroptosis in HPASMCs and PH mice model. Interaction between ca-circSCN8A and FUS was detected via RNA immunoprecipitation and pull-down assays. FRAP, CHIRP-qPCR, MDA, GSH and GSSG were conducted to explore the potential molecular mechanism. RESULTSca-circSCN8A was firstly identified and confirmed to be upregulated in PH. Upregulation of ca-circSCN8A can promote hypoxia induced ferroptosis in HPASMCs. Under hypoxic conditions, ca-circSCN8A promoted the lactylation of FUS by recruiting EP300, leading to formation of LLPS of ca-circSCN8A/FUS/EP300. LLPS maintained the stability of the R-Loop formed by ca-circSCN8A and ferroptosis related-gene SLC7A11 promoter that inhibit the transcription of the SLC7A11 gene, further result in the disruption of the redox balance and causes ferroptosis in HPASMCs. CONCLUSIONSca-circSCN8A recruits EP300 to promote the lactylation of FUS, thereby promoting LLPS formation of ca-circSCN8A/EP300/FUS. Further, the LLPS motivates ca-circSCN8A to form R-loop with its non-host SLC7A11 and participating in the regulation of hypoxic induced HPASMCs redox-dependent ferroptosis. This is the first confirmation that circRNAs forming R-loops with non-host genes regulated by LLPS. Our findings indicated that ca-circSCN8A plays an important role in ferroptosis of hypoxic induced HPASMCs and may be a potential target for the treatment of PH.

molecular biology↗

bioRxiv2025

Extracellular stiffness regulates site-specific lung development

Extracellular matrix (ECM) stiffness plays a crucial role in regulating cell fate and maturation, but its influence on lung development is limited known. Here we utilized stiffness-tunable gelatin methacryloyl (GelMA) hydrogels to investigate how ECM stiffness influences site-specific lung development in a stem cell-derived lung organoid model. We found increased stiffness promoted NKX2-1+ lung progenitor cells (LPCs) generation. In airway organoids (hAWOs), stiff hydrogels directed proximal airway differentiation enriched with goblet, ciliated, and basal cells; whereas the decreased stiffness favored emergence of secretory cells in the proximal-distal transition zone and distal airway. In alveolar organoids (hALOs), increased stiffness enhanced AT2 and AT1 cells transition. Moreover, infection assays with Omicron BA.1.1 and Delta variants recapitulated the proximal-to-distal tropism of SARS-CoV-2 in the lung. Transcriptomic sequencing revealed ECM stiffness regulates lung development via Hippo, TGF-{beta}, HIF and Wnt pathways. These findings advance mechanism understanding of ECM stiffness on lung development and provide a novel mechanical regulation for generating site-specific lung organoids.

cell biology↗

bioRxiv2025

HD2Net: A Deep Learning Framework for Simultaneous Denoising and Deaberration in Fluorescence Microscopy

Fluorescence microscopy is essential for biological research, offering high-contrast imaging of microscopic structures. However, the quality of these images is often compromised by optical aberrations and noise, particularly in low signal-to-noise ratio (SNR) conditions. While adaptive optics (AO) can correct aberrations, it requires costly hardware and slows down imaging; whereas current denoising approaches boost the SNR but leave out the aberration compensation. To address these limitations, we introduce HD2Net, a deep learning framework that enhances image quality by simultaneously denoising and suppressing the effect of aberrations without the need for additional hardware. Building on our previous work, HD2Net incorporates noise estimation and aberration removal modules, effectively restoring images degraded by noise and aberrations. Through comprehensive evaluation of synthetic phantoms and biological data, we demonstrate that HD2Net outperforms existing methods, significantly improving image resolution and contrast. This framework offers a promising solution for enhancing biological imaging, particularly in challenging aberrating and low-light conditions.

bioengineering↗

bioRxiv2024

The 1001G+ project: A curated collection of Arabidopsis thaliana long-read genome assemblies to advance plant research

Arabidopsis thaliana was the first plant for which a high-quality genome sequence became available. The publication of the first reference genome sequence almost 25 years ago was already accompanied by genome-wide data on sequence polymorphisms in another accession, or naturally occurring strain. Since then, inventories of genome-wide diversity have been generated at increasingly precise levels. High-density genotype data for A. thaliana, including those from the 1001 Genomes Project, were key to demonstrating the enormous power of GWAS in inbred populations of wild plants, and the comparison of intraspecific polymorphism with interspecific divergence has illuminated many aspects of plant genome evolution. Over the past decade, an increasing number of nearly complete genome sequences have been published for many more accessions. Here, we highlight the diversity of a curated collection of previously published and so far unpublished genome sequences assembled using different types of long reads, including PacBio Continuous Long Reads (CLR), PacBio High Fidelity (HiFi) reads, and Oxford Nanopore Technologies (ONT) reads. This 1001 Genomes Plus (1001G+) resource is being made available at http://1001genomes.org. We invite colleagues with yet unpublished genome assemblies from A. thaliana accessions to contribute to this effort.

genomics↗

bioRxiv2024

Comparative genomics of the sexually transmitted parasite Trichomonas vaginalis reveals relaxed and convergent evolution and genes involved in spillover from birds to humans

Trichomonas vaginalis is the causative agent of the venereal disease trichomoniasis which infects men and women globally and is associated with serious outcomes during pregnancy and cancers of the human reproductive tract. Trichomonads parasitize a range of hosts in addition to humans including birds, livestock, and domesticated animals. Recent genetic analysis of trichomonads recovered from columbid birds has provided evidence that these parasite species undergo frequent host-switching, and that a current epoch spillover event from columbids likely gave rise to T. vaginalis in humans. We undertook a comparative evolutionary genomics study of seven trichomonad species, generating chromosome-scale reference genomes for T. vaginalis and its avian sister species Trichomonas stableri, and assemblies of five other species that infect birds and mammals. Human-infecting trichomonad lineages have undergone recent and convergent genome size expansions compared to their avian sister species, and the major contributor to their increased genome size is increased repeat expansions, especially multicopy gene families and transposable elements, with genetic drift likely a driver due to relaxed selection. Trichomonads have independently host-switched twice from birds to humans, and genes implicated in the transition to the human host include those associated with host tissue adherence and phagocytosis, extracellular vesicles, and CAZyme virulence factors.

microbiology↗