Biology subjects

Dong, B.

Publications and source records attributed to Dong, B..

At least 19 recordsLinked to original sources

bioRxiv2026

LiverHomo: An Integrated and Interactive Human Liver Single-Cell Atlas with Protein Interaction and Cell-Cell Communication Networks

LiverHomo is an integrated cell atlas developed from publicly available human liver single-cell RNA sequencing (scRNA-seq) datasets spanning healthy and diverse liver disease contexts. While several single-cell resources for the human liver are available, LiverHomo provides broad disease coverage and extends transcriptomic exploration through the integration of protein-protein interaction (PPI) networks and cell-cell interactions. LiverHomo provides an interactive web portal (https://liverhomo.org) for exploring cellular composition, gene expression, differentially expressed genes, Gene Ontology annotations, cell-cell interactions, and context-specific PPI networks across diseases and cell types. To facilitate intuitive access to these multidimensional data, the portal incorporates Ask LiverHomo, a natural-language assistant that interprets user queries and directs users to relevant analyses and visualizations. Interactive histograms, violin plots, network visualizations, and metadata exploration enable users to examine the atlas at cellular, transcriptomic, and protein-interaction levels, while the underlying data are readily accessible for further analysis. Together, LiverHomo provides an integrated and accessible resource for investigating cellular and molecular alterations across human liver health and disease.

bioinformatics↗

bioRxiv2026

LiverDCP: A Disease-Cell-Protein Framework for Multi-scale Modeling of Disease Biology

Understanding how molecular interactions give rise to disease phenotypes across cellular contexts remains a central challenge in biomedical research. Here, we introduce a Disease-Cell-Protein (DCP) paradigm for modeling multi-scale disease biology, which jointly represents disease states, cellular composition, and protein interaction networks within a unified graph architecture. We instantiate this paradigm in the liver as LiverDCP by integrating LiverHomo, a harmonized single-cell atlas of liver diseases, with proteome-wide predicted protein-protein interactions to construct over 280 context-specific interactomes across diverse liver disease and cellular conditions. LiverDCP employs a multi-context representation learning strategy that enables joint training across hundreds of disease-cell environments, capturing shared interaction principles while preserving context-specific variation. LiverDCP incorporates pretrained protein sequence-derived features through a geometry-aware two-phase training scheme that preserves embedding structure while improving predictive performance. The resulting DCP protein embeddings reveal extensive rewiring of protein functional states across diseases, providing a transferable representation for downstream biomedical applications. Without GWAS supervision during representation learning, LiverDCP enables disease-risk gene classification and identifies cell types through which genetic risk may act. For therapeutic target discovery, LiverDCP recovers established Phase II+ MASH targets and prioritizes previously unrecognized candidates from the unannotated proteome, with 26 of the top 50 predictions showing independent PubMed evidence related to MASH biology. Context-specific interaction analysis further provides mechanistic hypotheses for less-characterized candidates. Together, these results establish DCP as a generalizable framework for connecting molecular interactions, cellular context, genetic risk, and therapeutic opportunities across complex diseases.

systems biology↗

bioRxiv2026

Single-section spatial hypoxia–cytotoxic associations do not consistently reproduce across breast cancer patients

Spatial transcriptomics can reveal localized tumor-immune relationships, but thousands of spots from one tissue section do not provide thousands of biological replicates. We evaluated the distinction between within-section association and patient-level reproducibility using public breast cancer datasets. In a 10x Genomics Visium discovery section containing 3,798 spots, hypoxia-related transcription was inversely associated with cytotoxic gene activity in neighboring spots (Spearman{rho} = -0.202). High-hypoxia spots also had lower neighborhood cytotoxic scores than low-hypoxia spots (rank-biserial effect = -0.286). We then tested the directional association in an independent HER2-positive cohort comprising 36 sections, 13,619 spots, and eight patients. Only 19 of 36 sections and five of eight patients showed negative associations. The median patient-level correlation was -0.043 and did not differ from zero in a one-sided exact Wilcoxon test (P = 0.473). Sensitivity analyses using alternative cytotoxic and hypoxia signatures, neighborhood sizes, and Kendall correlation did not support a consistent inverse patient-level effect. Thus, a strong single-section association did not consistently reproduce across patients. These results caution against interpreting spot-level spatial associations from one section as patient-level biological effects.

Cancer Biology↗

bioRxiv2026

Intermittent parathyroid hormone employs autonomous and non-autonomous mechanisms to drive osteogenesis from Ebf3-expressing skeletal progenitor cells

How systemic hormonal signals coordinate stem cell fate decisions in adult tissues remains incompletely understood. In bone marrow, Cxcl12-abundant reticular (CAR) cells, marked by Early B-cell Factor 3 (Ebf3) expression, are multipotent mesenchymal progenitors that maintain the hematopoietic stem cell niche and serves as a major osteoblast progenitor source during adult bone remodeling. Using inducible lineage tracing coupled with single-cell transcriptomics and conditional genetics in mice, we show that intermittent parathyroid hormone (iPTH; teriparatide) drives osteogenesis from CAR cells by simultaneously engaging cell-intrinsic and cell-extrinsic mechanisms. Directly, iPTH suppresses lineage-enforcing transcription factors Ebf3, Ebf1, and Foxc1, thereby destabilizing progenitor identity and priming CAR cells for osteogenic commitment. Simultaneously, iPTH stimulates osteoclastic bone resorption, releasing TGF{beta} which recruits these primed progenitors to bone surfaces, a process abolished by osteoclast depletion. Preventing CAR cell maturation via Sp7 deletion abrogates iPTH-induced bone gain, establishing these progenitors as essential mediators of bone anabolism. This coupled mechanism, in which intrinsic transcriptional priming converges with extrinsic niche remodeling, is conserved in human CAR cells from teriparatide-treated postmenopausal women, which show concordant suppression of EBF3 and FOXC1 and elevated TGF{beta}-responsive gene signatures. These findings reveal a general principle by which a systemic hormone orchestrates tissue remodeling through simultaneous reprogramming of progenitor identity and remodeling of the niche microenvironment.

physiology↗

bioRxiv2026

Liver-to-Atria Inflammatory Axis Driving Arrhythmia

BackgroundMetabolic dysfunction-associated steatohepatitis (MASH) is emerging as a risk factor of cardiometabolic diseases, including the atrial fibrillation (AF) - the most common sustained arrhythmia. Given that the liver is a major source of inflammatory mediators, lipids, and hepatokines under metabolic stress, we hypothesized that hepatocyte-derived factors in MASH may accelerate atrial remodeling and arrhythmogenesis. MethodsAnalysis of the Atherosclerosis Risk in Communities (ARIC) visit 5 cohort was performed to determine the association between the FIB-4 index - a classic indicator of liver fibrosis, and AF risk, with multivariable adjustment for common comorbidities. A murine model of MASH was induced using the GAN (Gubra-Amylin NASH) diet. Programmed intracardiac stimulation and echocardiography were performed to assess AF susceptibility and cardiac function. Calcium imaging, histology, flow cytometry, plasma proteomics, and single-nucleus RNA sequencing (snRNA-seq) analyses were employed to elucidate the role of recruited inflammatory macrophages via hepatocyte-derived osteopontin (OPN) in MASH-induced atrial remodeling. ResultsAnalysis of the ARIC cohort confirmed a higher cumulative incidence of AF and an elevated adjusted hazard ratio (HR) in patients with intermediate and high FIB-4 indices compared to individuals with low FIB-4 scores. MASH mice exhibited increased susceptibility to pacing-induced AF, accompanied by enhanced proarrhythmic calcium release events, atrial enlargement, and fibrosis, independent of ventricular dysfunction. Proteomics and snRNA-seq revealed that the hepatocyte-secreted OPN under MASH conditions promoted the differentiation and recruitment of TGFBR1+ inflammatory macrophages to the atria, leading to gasdermin D (GSDMD) activation - an effector of inflammasome signaling and consequent proarrhythmic atrial remodeling. Activation of the monocyte-derived pro-inflammatory TGFBR1+ macrophages was dependent on the OPN receptor CD44. Furthermore, the MASH-induced atrial fibroinflammatory milieu and enhanced AF susceptibility were mitigated through several strategies, including hepatocyte-specific Spp1 (encoding OPN) deletion, neutralization of circulating OPN, ablation of CD44 or GSDMD. ConclusionsThese findings establish a pathogenic role of the hepatokine osteopontin in driving activation and recruitment of TGFBR1+ inflammatory macrophages into the atria, leading to proarrhythmic atrial remodeling under MASH. Osteopontin-targeted therapy or GSDMD inhibition prevents AF, indicating a novel therapeutic strategy for liver disease-related atrial arrhythmogenesis. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIIn the ARIC cohort, metabolic dysfunction-associated steatohepatitis (MASH) is associated with increased risk of atrial fibrillation (AF) after adjusting for common comorbidities. Elevated levels of circulating osteopontin (encoded by SPP1) predict an increased risk of AF in patients with MASH-induced liver fibrosis. C_LIO_LIMASH enhances hepatocyte secretion of osteopontin, leading to expansion of myeloid cells and recruitment of inflammatory macrophages into atria. This liver-to-atrial inflammatory circuit promotes the development of a substrate conducive to AF, which can be attenuated by hepatocyte-specific Spp1 deletion or neutralizing anti-anti-osteopontin antibody treatment to eliminate the mediator, or ablation of inflammasome effector gasdermin D to correct the atrial response. C_LI What are the clinical implications?O_LIOsteopontin may serve as a biomarker for AF in MASH cohorts. C_LIO_LIAnti-osteopontin therapy through neutralizing antibodies may serve as a novel therapeutic strategy for liver disease-related atrial arrhythmia. C_LI

systems biology↗

bioRxiv2026

The endoderm cell trajectory of urochordate Styela clava reveals the dual developmental origin and evolution of digestive tract

The digestive system exhibits extensive diversity in developmental mechanisms and morphology across metazoans, yet the evolutionary origins underlying its organ differentiation remain unclear. Here, single-cell RNA sequencing was employed to investigate endodermal cell lineage specification during metamorphosis in the urochordate Styela clava, a newly established model for chordate evolution. By profiling 26,099 cells across five stages, we identified 21 major cell clusters and reconstructed the endodermal differentiation trajectories. Our analysis reveals two larval endodermal progenitor populations with distinct differentiation potentials. Pseudotime and RNA velocity analyses indicate that these progenitors give rise to stomach and intestinal lineages, respectively. Cross-species comparisons reveal putative homologous relationships between ascidian endodermal lineages and mouse definitive and visceral endodermal lineages, suggesting dual origins of digestive tract in chordates. We also identified conserved TGF-{beta} and FGF regulatory programs in digestive organ patterning and highlight earlier fate restriction of stomach and intestinal progenitors in ascidians compared to vertebrates. These findings provide insights into how chordate digestive organs evolved from ancestral endodermal patterning programs.

evolutionary biology↗

bioRxiv2026

Glucokinase links metabolism and lineage plasticity in neuroendocrine prostate cancer via interaction with AKT1

Cancer cells frequently rewire their metabolism to sustain growth and survival under stress. Despite the critical role of metabolic adaptation in tumorigenesis, how specific metabolic enzymes regulate lineage plasticity remains unclear. Here, through FDG-PET imaging and transcriptomic analyses, we reveal markedly elevated glucose uptake in neuroendocrine prostate cancer (NEPC) and identify glucokinase (GCK) as a MYCN-induced metabolic enzyme. Beyond its metabolic role, GCK is indispensable for maintaining the neuroendocrine lineage of prostate cancer cells by establishing a functional circuit with AKT1 through reciprocal regulation--AKT1 binds and phosphorylates GCK at S373, whereas GCK phosphorylates AKT1 at S473. Pharmacological disruption of this AKT1-GCK axis suppresses tumor growth in NEPC mouse models and patient-derived xenografts. Altogether, our findings uncover both the metabolic and noncanonical kinase functions of GCK and establish the AKT1-GCK axis as a key link between metabolic reprogramming and neuroendocrine lineage transition in prostate cancer.

cancer biology↗

bioRxiv2025

Identification of the protein precursor for thyroid hormone synthesis in the basal chordate ascidian Styela clava

Thyroid hormones (THs) play crucial roles in development, growth, and metabolism across the animal kingdom1,2. Although the mechanism of TH synthesis in vertebrates has been well described, it remains elusive in invertebrates due to the lack of identified orthologs of the thyroglobulin (TG), the protein precursor for TH synthesis3,4. Here, we identified a functional TG protein encompassing multiple TG type 1 (Tg1)-domains, encoded by the ScTg-like gene in proto-vertebrate ascidian Styela clava based on the immunoprecipitation-mass spectrometry combined with phylogenetic and expression pattern analyses. In vitro iodination experiments demonstrated that ScTG-like has the capacity to provide hormonogenic sites for TH synthesis. Furthermore, in vivo gene knockdown of ScTg-like revealed that the larval metamorphosis was significantly inhibited as a consequence of diminished TH levels, indicating that ScTg-like is responsible for the production of endogenous TH. Additionally, an invaginated follicle-like structure was first discovered at the central anterior of the larval trunk where both ScTG-like protein and THs were deposited, suggesting that this structure serves as the location for THs synthesis and storage, functionally similar to vertebrate thyroid follicles. Moreover, we analyzed the structural features of ScTG-like protein and detected the similarly organized Tg1-containing proteins in multiple bilaterian phyla, suggesting that endogenous TH synthesis may be an ancestral, possibly synapomorphic, trait of bilaterians. Our study is the first to identify the TH protein precursor outside vertebrates by providing the direct evidence of endogenous de novo TH synthesis, which offers insights into the evolution of TG protein and the emergence of a major vertebrate endocrine system.

evolutionary biology↗

bioRxiv2025

Interface-Sensitive Epi-Coherent Anti-Stokes Raman Scattering Microscopy for Imaging Cell Adhesion Dynamics

Studying cell adhesion dynamics is critical to understand how cells interact with the extracellular matrix and how they migrate. Conventional microscopy techniques for interfacial studies either lack chemical information or require fluorescence labeling. We found that homodyne epi-coherent anti-Stokes Raman scattering (epi-CARS) microscopy, when focused as interfaces, has intrinsic interfacial selectivity. The interference of the back-reflected nonresonant signals amplifies the contrast of cell adhesion areas, generating a distinctive negative contrast at attachment areas, which reflects the distance between the cell membrane and the substrate with tens of nanometers precision. The Epi-CARS configuration also provides high contrasts for cellular lipid droplets when applied in the inverted microscope configuration. Furthermore, by incorporating a pinhole into our confocal epi-CARS system, we can effectively reject out-of-focus reflections that degrade epi-CARS image quality, allowing us to amplify adhesion and lipid droplet contrasts for complex samples, such as cells. We applied this method to study cell-substrate adhesion dynamics of mitotic cells, revealing adhesion site splitting during mitosis and their outward development during postmitotic spreading. Furthermore, we found that after mitosis, the leading edges exhibited homogeneous adhesion regions with thicker water layers, whereas the retracting edges showed heterogeneous adhesion patterns with thinner layers at the contact sites.

biochemistry↗

bioRxiv2025

Fast Hyperspectral and Super-Resolved Mapping of Lipid Membrane Polarity with Single-Molecule Sensitivity

Cell membranes display nanoscale heterogeneity in lipid composition and organization that regulates vital biological processes yet remains challenging to resolve with conventional imaging. We introduce spectral phasor single molecule localization microscopy (SP-SMLM), a hyperspectral and super-resolution method that combines wavefront-like optical filtering with single molecule imaging for simultaneous spatial and spectral analysis. A lab-built three-channel imager with sine/cosine filters encodes emission spectra of single molecules into the phasor space, enabling high-throughput, high-SNR mapping of membrane polarity at sub-50 nm spatial and 15-sec temporal resolutions. Through simulation, we validate that the phasor angle correlates with the spectral mean for single dye molecules. When applied to Nile Red-stained COS-7 cells, SP-SMLM revealed organelle-specific polarity differences and dynamic remodeling of lipid composition within live cells. The methods hyperspectral capability, rapid acquisition, and compatibility with 2D/3D imaging platforms position SP-SMLM as a powerful tool for studying membrane heterogeneity and dynamics in live cells.

biophysics↗

bioRxiv2025

High Throughput Hyperspectral and Multiplexed Super-Resolution Fluorescence Imaging by SP-STORM

Simultaneous determination of spatial location and spectral color of single molecules at large molecular density with high throughput was achieved by combining single molecule photoswitching and in-hardware transformation based spectral phasor analysis. The method, named spectral phasor enabled stochastic optical reconstruction microscopy (SP-STORM), achieved simultaneous super-resolution imaging of five subcellular structures with minimum crosstalk for the first time. The high throughput feature of SP-STORM enables these subcellular structures to be readily resolved in about one minute, which is more than a magnitude faster than other multiplexing single molecule localization microscopy techniques. The concept of SP-STORM is also compatible with and can be readily applicable to other super-resolution microscopy.

biophysics↗

bioRxiv2025

Bidirectional translocation of actomyosin drives epithelial invagination in ascidian siphon tube morphogenesis

How epithelia perform a spatiotemporal heterogeneous force generating program to drive a sequential tissue morphogenesis remains unclear, particularly the underlying precise mechanical mechanisms. This study investigated dynamic actomyosin reorganization between apical and lateral membrane cortex regions during two sequentially invaginated stages during ascidian atrial siphon tube morphogenesis. At the initial invagination stage, the originally lateral-located actomyosin redistributed to the apical domains, while those actomyosin redistributed back to lateral domains at the accelerated invagination stage. Using genetic mutants to modulate myosin activities, the initial invagination was strengthened or abolished, indicating invagination is apical constriction dependent. Optogenetic inhibition of myosin activities in lateral domains after initial invagination stage blocked the further processes, suggesting lateral constriction of actomyosin is required for the accelerated invagination. Vertex model simulations uncovered a coupled mechanism underlying epithelial invagination driven by apicobasal tension imbalance and lateral contraction. We thus propose an actomyosin redistribution mechanical model: lateral actomyosin first redistributes apically to drive apical constriction and shape the initial invagination, then apical actomyosin redistributes laterally to promote lateral contractility and accelerate invagination. Our findings reveal a bidirectional reorganization of actomyosin network as a central mechanism driving epithelial invagination, providing insights on epithelial invagination and the organ morphogenesis during development.

developmental biology↗

bioRxiv2025

Modeling Post-Gastrula Development via Bidirectional Pluripotent Stem Cells

The absence of stem cells capable of efficiently generating both trophoblast and epiblast lineages has hindered precise recapitulation of embryonic development. Through high-content chemical screening, we established an AL medium to generate mouse and human bidirectional pluripotent stem cells (BPSCs) characterized by concurrent OCT4/CDX2 expression. Mouse BPSCs demonstrated high plastic differentiation into trophoblast, epiblast and primitive endoderm lineages in vitro within 48 hours without exogenous induction factors and efficiently contributed to the embryo and extraembryonic tissues in vivo. Mechanistically, hyperactivation of the Wnt signaling pathway breaks the early lineage differentiation barrier by initiating a Lef1-dependent bypass. Remarkably, BPSCs can efficiently generated E8.5 embryoids that completed gastrulation and displayed advanced features such as brain development, a closed neural tube, a beating heart, somite formation, and primordial germ cells. These findings highlight BPSCs as a powerful tool for investigating early lineage specification and post-gastrulation embryonic development, with potential applications across multiple species.

developmental biology↗

bioRxiv2025

UniCure: A Foundation Model for Predicting Personalized Cancer Therapy Response

Predicting drug efficacy across diverse patient contexts remains a major challenge in oncology, as models trained on cancer cell lines often fail to capture patient-specific biology. Emerging biological foundation models and patient-derived technologies offer a promising solution. Here, we present UniCure, the first pre-trained foundation model integrating both omics and chemical foundation models (UCE and Uni-mol) to predict transcriptomic responses to drugs across diverse cellular and tissue contexts, enabling personalized cancer therapy and drug prioritization at the individual level. Rather than encoder/decoder used in traditional models, UniCure utilizes parameter-efficient fine-tuning (PEFT) techniques for optimizing the training process, a novel FlexPert module for modeling flexible drug-cell interactions, and a Maximum Mean Discrepancy (MMD) loss for learning unpaired data. Trained on over 1.8 million perturbation RNA-seq profiles over 22,000 compounds, 166 cell types, and 24 tissues, UniCure achieves high accuracy in predicting both dose-dependent responses and drug combination effects, demonstrating strong generalization across bulk and single-cell transcriptomic data. In particular, fine-tuning on our patient-derived tumor-like clusters and real-world data of 800 profiles enables UniCure to generate individualized therapeutic predictions on patients tissue samples. In addition, UniCure enables patient stratification based on the predicted drug responses, providing a new way for subtyping patients. UniCures drug prioritization was validated across over 1000 patients from pan-cancer cohorts and supported by experiments of candidate therapeutics. By enabling the potential to screen millions of compounds per patient at scale, UniCure represents a biologically grounded tool that could advance personalized precision oncology and accelerate drug discovery.

bioinformatics↗

bioRxiv2025

OriGene: A Self-Evolving Virtual Disease Biologist Automating Therapeutic Target Discovery

Here, we present OriGene, a self-evolving multi-agent system that functions as a virtual disease biologist, systematically identifying original and mechanistically grounded therapeutic targets at scale. OriGenes architecture integrates over 600 specialized tools through a Model Context Protocol (MCP), enabling it to reason across diverse data modalities including genomics, protein networks, pharmacology, clinical records and literature evidence, to generate and prioritize target discovery hypotheses. We implemented a strategy combining a knowledge graph-based Tool RAG with an advanced agent selection mechanism to enable dynamic, context-aware tool deployment. Through a self-evolving framework, OriGene continuously integrates human and experimental feedback to iteratively refine its core thinking templates, tool composition, and analytical protocols, thereby enhancing both accuracy and adaptability over time. To comprehensively evaluate its performance, we established TRQA, an original benchmark comprising over 1,900 expert-level question-answer pairs spanning a wide range of diseases and target classes. OriGene consistently outperforms human experts, leading research agents, and state-of-the-art large language models in accuracy, recall, and robustness, particularly under conditions of data sparsity or noise. Critically, OriGene nominated previously underexplored therapeutic targets for liver (GPR160) and colorectal cancer (ARG2), which demonstrated significant anti-tumor activity in patient-derived organoid and tumor fragment models mirroring human clinical exposures. These findings demonstrate OriGenes potential as a scalable and adaptive platform for AI-driven discovery of mechanistically grounded therapeutic targets, offering a new paradigm to accelerate drug development.

bioinformatics↗

bioRxiv2025

The potential of 4-Methylumbelliferone to be repurposed for treating liver fibrosis

4-Methylumbelliferone (4-MU) is the active component of hymecromone, a choleretic and antispasmodic drug with an excellent safety profile. In rodent studies, high doses of 4-MU are also used to inhibit the production of hyaluronan (HA), a biomarker of liver fibrosis. Further, 4-MU shows excellent efficacy in inhibiting liver fibrosis of different etiologies in animal studies, eliciting interest in its repurposing for this condition. However, 4-MUs mechanism of action, and whether it inhibits liver fibrosis by impeding HA synthesis, remains unclear. Using several transgenic mouse models with HA overproduction or degradation in different types of liver cells, we found that both directions of perturbation reduced liver fibrosis levels. In addition, degrading HA via hyaluronidase PH20 overexpression impaired liver function manifested by increased serum aminotransferase (ALT) activity levels. These findings challenge both the role of HA modulation in 4-MUs action and the strategy of targeting HA to treat liver fibrosis. Additional mouse models also excluded the possibility that 4-MU modulates intestinal farnesoid X receptor (FXR) to inhibit liver fibrosis. Ablation of gut microbiota partially abolishes 4-MUs anti-liver fibrosis effect. However, the anti-liver fibrosis effect of 4-MU was lost in the lower-dose group, and the high doses effect in reducing ALT disappeared over time despite its liver fibrosis-reducing effect. Based on these findings, we argue that the lack of efficacy of 4-MU at a translatable dose and lack of a clear mechanism that allows further improvement of 4-MUs efficacy make 4-MU impractical for development as an anti-liver fibrosis treatment. HighlightsO_LI4-MU inhibits MASH fibrosis. C_LIO_LIBoth HA overproduction and digestion in the liver reduce liver fibrosis. C_LIO_LIIntestinal epithelial cell FXR is not required for 4-MU to reduce liver fibrosis. C_LIO_LIThe gut microbiota is partially responsible for 4-MUs antifibrotic effect in the liver. C_LIO_LI4-MU lacks the potential to be further developed into anti-liver fibrosis treatment. C_LI

molecular biology↗

bioRxiv2025

Enhancing Biomedical Optical Volumetric Imaging via Self-Supervised Orthogonal Learning

Optical volumetric imaging grapples with inherent noise problems arising from photon budget constraints, light scattering, and space-bandwidth product bottlenecks, all of which degrade structural fidelity and become even more pronounced than in planar imaging. While deep learning presents potential for denoising, supervised methods are hindered by the impracticality of paired dataset, and existing self-supervised approaches fail to fully exploit the intrinsic volumetric structural redundancy inherent to optical imaging. Here, we present a self-supervised Volumetric biomedicAL Imaging Denoiser (VALID) that leverages intrinsic three-dimensional spatial coherence for highly efficient volumetric denoising through a self-supervised orthogonal learning framework. VALID demonstrates robust denoising performance across diverse imaging modalities, including two- and three-photon microscopy, light-field microscopy, and optical coherence tomography, substantially enhancing structural fidelity in deep-tissue, multimodal, and dynamic imaging scenarios. By combining computational efficiency with zero-shot adaptability, VALID establishes a transformative approach to volumetric image enhancement with structure-aware precision.

neuroscience↗

bioRxiv2025

Label-Free Quantification of Apoptosis and Necrosis Using Stimulated Raman Scattering Microscopy

Recombinant proteins are critical for modern therapeutics and diagnostics, with Chinese hamster ovary (CHO) cells serving as the primary production platform. However, environmental and chemical stressors in bioreactors often trigger cell death, particularly apoptosis, posing a significant challenge to recombinant protein manufacturing. Rapid, label-free methods to monitor cell death are essential for ensuring better production quality. Stimulated Raman scattering (SRS) microscopy offers a powerful, label-free approach to measure lipid and protein compositions in live cells. We demonstrate that SRS microscopy enables rapid and reagent-free analysis of apoptotic and necrotic transitions. Our results show that apoptotic cells exhibit higher protein concentrations, while necrotic cells show an opposite trend. To enhance analysis, we developed a quantitative single-cell analysis pipeline that extracts chemotypic and phenotypic signatures of apoptosis and necrosis, enabling the identification of subpopulations with varied responses to stressors or treatments. Furthermore, the cell death analysis was successfully generalized to other stressors and cell types. This study highlights SRS microscopy as a robust and non-invasive tool for rapid monitoring of live cell apoptotic and necrotic transitions. Our method and findings hold potential for improving quality control in CHO cell-based biopharmaceutical production and for evaluating cell death in diverse biological contexts.

cell biology↗