Biology subjects

Yan, Y.

Publications and source records attributed to Yan, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

AI-enabled reconstruction of 3D spatial multi-omics at single-cell resolution

Three-dimensional (3D) spatial multi-omics provides unparalleled insights into biological activities, yet remains technically prohibitive. Here, we introduce Histo3D-MO, a hybrid experimental-computational pipeline for reconstructing single-cell-resolution 3D spatial multi-omics maps. Notably, Histo3D-MO integrates sparse, omics-disjoint spatial measurements with dense Hematoxylin and Eosin (H&E) histology through SPatial multi-Omics from h&E imaGEs (SPONGE), achieving cell-level 3D mapping across multiple omics layers. Validated using held-out slices, SPONGE substantially outperforms existing omics prediction methods. We further developed an algorithmic suite for 3D cell-type propagation and tissue-domain annotation, enabling whole-volume characterization of the tumor microenvironment. Applied to the in-house hepatocellular carcinoma data, Histo3D-MO revealed spatially organized patterns of translation efficiency, volumetric decoupling between malignant cells and monocytes, and depth-associated monocyte differentiation trajectories. Together, these results establish Histo3D-MO as a scalable framework for reconstructing single-cell-resolution 3D spatial multi-omics and interrogating tissue organization across complex biological systems.

bioinformatics↗

bioRxiv2026

The basal cell state maintains pancreatic cancers by controlling an immunosuppressive circuit

Intra-tumoral heterogeneity is a cardinal feature of solid tumors, yet how distinct cancer cell states functionally contribute to malignant and stromal diversity in situ remains poorly understood. Using mouse models to lineage-trace or genetically ablate the two predominant cancer cell states in autochthonous pancreatic ductal adenocarcinoma (PDAC), we discover that basal cancer cells are highly plastic, whereas classical cancer cells exhibit limited plasticity. Strikingly, ablation of the basal, but not the classical, state induced rapid and durable tumor collapse, driven by loss of immunosuppressive cancer-associated fibroblasts, macrophage repolarization, and reprogramming of the tumor cytokine milieu, culminating in tumor destruction by cytotoxic lymphocytes. Knockout of a single cytokine, GM-CSF, specifically in basal cells recapitulated macrophage repolarization and lymphocyte recruitment observed upon basal state ablation and shrank tumors. These results reveal the basal cell state controls an immunosuppressive cell circuit critical for PDAC maintenance, motivating therapeutic targeting of the basal cells.

cancer biology↗

bioRxiv2026

Genetically encoded systems for cytosolic activity recording and molecular archiving across time

Cellular functions are governed by dynamic changes in molecular abundance, state, activity, and interactions within the cytosol. Current molecular tape recorders leverage nuclear transcriptional programs in eukaryotic cells to provide scalable readout of gene regulation dynamics, but cytosolic activity, molecular abundance, and state remain inaccessible. Here, we introduce CyTRACE, a genetically encoded, scalable framework for cytosolic activity recording and molecular archiving across time. CyTRACE ventures beyond the cell nucleus, deploys cytosol-localized protein tape monomers as direct activity sensors and molecule catchers, and offers physiological sensitivity, spatiotemporal resolution, and programmability. Within this modular framework, CytoSense records protease and kinase signaling activities while CytoCatch archives cytosolic proteins, each with temporal continuity in single mammalian cells. CyTRACE thus opens cytosolic biology to scalable activity readout and molecular interrogation.

Synthetic Biology↗

bioRxiv2026

ANCHOR: haplotype-aware allelic and isoform inference from single-cell long-read RNA sequencing with de novo variant calling

Long-read RNA sequencing enables haplotype- and isoform-resolved allelic analysis of transcriptomes, yet extending this capability to single cells and distinct cell types remains computationally challenging due to sparse coverage, sequencing errors, incomplete variant information, and reference-biased transcript assignment. Here we present ANCHOR, a haplotype-aware framework for single-cell long-read RNA sequencing that performs de novo expressed-variant discovery, molecule-level haplotype assignment and isoform-resolved allelic quantification. ANCHOR combines a signed-graph variant caller, pair hidden Markov modelling and beta-binomial UMI aggregation to infer parental allele counts for genes and splice-resolved isoforms, without requiring a pre-existing phased genotype or deep learning. In human single-cell long-read RNA benchmarks, ANCHOR improved variant-calling performance over tested long-read RNA callers at single-cell and low-to-moderate coverage, and its beta-binomial model reduced depth-driven false positives in allele-specific expression testing. Applied to newly generated single-cell long-read RNA-seq data from reciprocal mouse crosses during gastrulation, ANCHOR resolved cell-type- and isoform-specific parent-of-origin imprinting and identified an antagonistic maternally biased Sgce isoform. ANCHOR provides a general framework for allele-and isoform-resolved analysis of diploid single-cell long-read transcriptomes.

bioinformatics↗

bioRxiv2026

Recipient cell identity governs intracellular transport and membrane interactions of extracellular vesicles across species

Extracellular vesicles (EVs) function as a natural communication system, enabling transfer of biomolecules between cells. Although EVs are produced by nearly all cell types and have shown promise as therapeutic agents, our understanding of how EVs from different cellular origins recognize recipient cells, are taken up, and processed intracellularly remains limited. In particular, it remains unclear whether intracellular EV behavior is primarily governed by EV-intrinsic properties or by the recipient-cell environment. Here, we systematically investigate the relative contributions of EV origin and recipient-cell identity to intracellular EV trafficking. By combining single-vesicle tracking with machine learning-based diffusion-state classification, we analyzed EVs derived from four distinct sources across three recipient cell types over three different time spans. This approach enabled characterization of dynamic transport behaviors, overcoming limitations of traditional ensemble-averaging methods. We observed recipient cell-dependent differences in intracellular trafficking patterns, ranging from relatively uniform and dynamic motion to more heterogeneous and confined behaviors, reflecting variability in intracellular transport environments. Despite these differences, EV origin had only a modest influence on intracellular dynamics following uptake. These findings suggest a model in which intracellular transport arises from an interplay between general EV-associated properties and cell-specific environment.

biophysics↗

bioRxiv2026

SciCore-Omics: a tri-modal foundation model unifying histology, spatial transcriptomics and language for spatial biology

Histomorphology and spatial transcriptomics capture complementary aspects of tissue biology, but their relationships remain difficult to extract, align, and interpret at scale. Existing foundation models typically connect histology, omics, or language only pairwise, which limits their capacity to jointly infer molecular states, decode spatial tissue organization, and generate biologically grounded explanations. Here, we show SciCore-Omics, the first tri-modal foundation model linking histology images, spatial transcriptomics, and biological language. We constructed a spatially paired image-gene-text dataset comprising 151,182 spots across multiple tissues and performed a three-stage progressive training of SciCore-Omics on this dataset. Across gene expression prediction and spatial domain recognition, SciCore-Omics achieved 23.6-80.9% relative gains in task-specific metrics over the strongest external baselines. It further showed robust zero-shot generalization in histopathology classification, outperforming GPT-5 by 6.16 percentage points in mean accuracy across four benchmarks. Expert evaluation in 10 breast cancer cases confirmed its H&E-only case-level molecular reasoning capability. Together, our method demonstrates that a tri-modal framework can effectively bridge histomorphology and molecular state, providing a more general and interpretable foundation model for computational pathology and omics analysis.

bioinformatics↗

bioRxiv2026

TRACE: a graph-based workflow for TCR-epitope prioritization and tumor-reactive T-cell identification

Accurate prioritization of T-cell receptor (TCR)-epitope interactions and identification of tumor-reactive T cells are important but difficult steps in immunotherapy-oriented bioinformatics workflows. Existing methods typically address these tasks separately and either model TCR-epitope pairs as independent observations or rely primarily on transcriptomic signatures. In this study, we present DUET (Dual Unified Evaluation of TCR-Epitopes and Tumor-reactive T cells), a graph-based computational workflow that unifies both applications within a single heterogeneous graph framework. The protocol represents TCRs, epitopes, and T cells as typed nodes connected by similarity and association edges, and combines pretrained sequence embeddings with edge-aware graph attention, Laplacian positional encoding, and bidirectional cross-domain attention. Applied to the IEDB and VDJdb benchmarks, DUET achieved AUROC/AUPR values of 0.937/0.922 and 0.992/0.990, respectively, outperforming five state-of-the-art algorithms. In addition, on a single-cell RNA-seq dataset, the workflow achieved an AUROC of 0.984 and an AUPR of 0.984, substantially exceeding transcriptomic signature-based baselines for tumor-reactive T-cell identification. Ablation analysis showed that Laplacian positional encoding provided the largest performance gain, particularly in sparse graph settings. These results suggest that heterogeneous graph modeling can serve as a practical protocol for integrating receptor sequence, antigen context, and cellular phenotype in computational immunology.

bioinformatics↗

bioRxiv2026

Dual histone methylation reader ZCWPW2 links histone methylation to initiation of meiotic recombination

Meiotic homologous recombination initiates with the formation of programmed DNA double-strand breaks (DSBs) by complexes comprising SPO11 and accessory proteins at discrete sites called recombination hotspots. In mammals, PRDM9-dependent H3K4me3 and H3K36me3 define recombination hotspots, but how these epigenetic characteristics determine the physiological DSB formation remains unknown. Here we show that dual histone methylation reader ZCWPW2 can recognize H3K4me3 and H3K36me3 marks in testis. The binding activity of ZCWPW2 to histone methylation is dependent on PRDM9 function. Moreover, we find the epigenetic writer-reader axis PRDM9-ZCWPW2 is essential for DSB formation at meiotic recombination hotspots, which may be partly explained by the finding that ZCWPW2 can physically interact with HORMAD1, IHO1, MEI4, and REC114. Finally, the absence of ZCWPW2 leads to disrupted chromosomal synapsis and recombination, thereby obstructing meiotic progression. Taken together, our findings provide new insights into how histone modifications and their associated regulatory proteins collectively regulate meiotic homologous recombination initiation.

cell biology↗

bioRxiv2026

Arthritis-Associated Inflammation Remodels Colonic O-Glycosylation

The gut-joint axis describes how impaired intestinal epithelial function and increased gut permeability allow luminal factors to enter circulation. This can drive inflammation in Rheumatoid Arthritis, a chronic condition affecting the joint with systemic features. What mechanisms contribute to disease persistence are, as yet, incompletely understood. In health, extensively Oglycosylated intestinal mucins are central to epithelial protection and immune homeostasis; however, whether mucin glycosylation is altered during arthritis has not been addressed. Here, we investigated whether arthritisassociated inflammation alters mucin Oglycosylation, potentially compromising intestinal barrier function. Using a collageninduced arthritis mouse model, we combined epithelial transcriptomics, mass spectrometry-based glycomics, and imaging approaches to profile intestinal glycosylation. We identified distinct glycan remodeling in the colon, characterized by reduced fucosylation, while the ileum remained largely unaffected. In vitro studies using 3D human epithelial cultures further demonstrated that inflammatory cues, particularly from TNFactivated stromal cells, are sufficient to reduce epithelial fucosylation. Together, these findings identify a stromal-inflammatory mechanism that disrupts mucin glycosylation during arthritis. Loss of colonic fucosylation emerges as a novel element of inflammatory arthritis, providing an additional mechanistic link between intestinal inflammation and fibroblast-dependent modulation of the tissue microenvironment.

immunology↗

bioRxiv2026

Simultaneous brain-wide single-cell recording resolves spatiotemporal memory architecture

Many fundamental mammalian brain functions emerge from the coordinated activity of cells distributed across large, brain-wide networks. To understand these processes in healthy and diseased states, ideally one would simultaneously measure and analyze single-cell activity at the brain-wide scale, an enduring challenge for live-measurement approaches that often face an inherent tradeoff between spatial resolution and scale. Here, we present GLOBE (sinGle-cell spatiotemporaL recOrding Brain-widE), a technology for brain-wide single-cell recording of cellular activity in vivo with spatiotemporal resolution, physiological sensitivity, and parallelization-accelerated readout. GLOBE leverages genetically encoded intracellular protein tape recorders and a high-throughput computational platform for integrated image and signal analysis. GLOBE records analog signal amplitudes across a continuous time axis, requires only standard light microscopy for in situ readout, and is compatible with expansion microscopy and RNA readouts. We applied GLOBE to simultaneously record transcriptional activity of the immediate early gene Fos in up to 219,703 neurons simultaneously across a single mouse brain over 5.5 continuous days, with a timestamp precision of 3.1-6.7 hours (median absolute error), a local recording density of 69-90% of neurons per imaging field of view, and a post-mortem imaging readout speed of 2.9 seconds per neuron on average. GLOBE resolves the brain-wide spatiotemporal structure of single-cell activity, revealing that Fos transcriptional dynamics associated with fear learning and memory retrieval are distributed across the brain with region-specific temporal heterogeneity, and that the variance of this structure scales down as the number of sampled cells increases. We envision GLOBE to have broad applications for dissecting and decoding physiological and pathological processes at the brain-wide scale.

neuroscience↗

bioRxiv2026

AlaRS-mediated lactylation shields PARP1 from ubiquitination to promote HNSCC progression

Abstract textMetabolic reprogramming in solid tumors causes massive lactate accumulation, yet how this drives oncogenesis remains incompletely understood. Here, we identify alanyl-tRNA synthetase (AlaRS) as a cellular lactyltransferase that promotes head and neck squamous cell carcinoma (HNSCC) progression. AlaRS directly catalyzes site-specific lactylation of the DNA repair protein PARP1 at lysines K249 and K667. Crucially, we uncover a competitive post-translational crosstalk wherein this lactylation directly antagonizes PARP1 ubiquitination. This "lactyl-shield" prevents proteasomal degradation, hyper-stabilizing the PARP1-Mortalin complex and sustaining tumor proliferation via p53/p21 dysregulation. To therapeutically exploit this mechanism, we identified chelerythrine (CHE) as a potent, selective inhibitor that directly binds the AlaRS catalytic center. CHE abrogates AlaRS lactyltransferase activity, destabilizes PARP1, and robustly suppresses HNSCC xenograft growth in vivo. These findings establish a novel metabolic-post-translational axis linking lactate accumulation to oncoprotein stabilization, providing a blueprint for targeting tRNA synthetase moonlighting functions in cancer.

molecular biology↗

bioRxiv2026

Allosteric Biosensors Unravel GTPase-Effector Feedback

Fluorescent biosensors that report protein conformation in vivo have been invaluable for understanding how the spatio-temporal dynamics of signaling controls cells. However, for GTPases these biosensors report the activated conformation using reagents that block the binding of downstream proteins, generating dominant negative effects and altering normal cell physiology. We present here a generalizable design to make GTPase biosensors (AlloRac1 and AlloCdc42), in which a circularly permuted fluorescent protein is inserted into a conserved loop allosterically connected to the effector binding site, generating activity-dependent fluorescence without blocking ligand interactions. The Rac1 biosensor showed that effector interactions led to increased Rac1 activation, indicating an auto-regulatory positive feedback made visible by the new biosensor design. This feedback regulated the kinetics and localization of Rac1 activity, including Rac1 activity gradients that controlled motility. Feedback was generated through Rac1 interaction with the effector Pak1, which led to further activation of Rac1 by the guanine exchange factor {beta}-Pix. The new biosensor approach enables quantitative imaging of previously obscure spatio-temporal dynamics in GTPase regulation.

cell biology↗

bioRxiv2026

Axonal swelling as a neuron-specific compartment to sequester and expel misfolded proteins

Neurons are long-lived, highly specialized cells with extended neurites, requiring precise control of misfolded proteins over time and space. Yet, where misfolded proteins are directed and how quality-control pathways adapt during aging are still unresolved. Here, we identify a neuron-specific quality-control compartment that emerges in neurites as aggresome function declines with age, which we call SolAS (Soluble Misfolded Proteins-induced Axonal Swellings). These structures not only sequester misfolded proteins but also facilitate their clearance via microvesicles and exophers. During aging, neurite SolAS and soma aggresomes function hierarchically to maintain proteostasis, with aggresomes acting as the primary sequestration sites in young neurons and SolAS taking over this role as their function declines with age. This transition is driven by a shift from a ubiquitin-dominant to a SUMO-dominant balance. Moreover, solid pathogenic amyloids, such as GA50, can be converted into soluble forms and sequestered into SolAS via SUMO fusion, thereby reducing neurotoxicity. Our findings identify a previously unrecognized neuronal quality-control pathway critical for proteostasis during aging.

neuroscience↗

bioRxiv2026

PARP1-mediated 5' flap dynamics facilitate Okazaki fragment maturation

Abstract/SummaryPrecise regulation of enzyme recruitment during Okazaki fragment maturation (OFM) is essential for faithful and efficient lagging-strand DNA synthesis. Emerging evidence suggests that PARP1 contributes to OFM yet its specific functions remain unclear. Here, we define context-dependent functions of PARP1 during OFM. Under physiological conditions, PARP1 co-localizes with PCNA in early S phase and restrains Pol {delta}-PCNA- mediated strand-displacement DNA synthesis, thereby preventing the formation of long 5' flaps, which is refractory to FEN1 cleavage. On the other hand, in LIG1-deficient cells, in which DNA nicks and unexpectedly long 5' flaps accumulate, PARP1 promotes the recruitment of LIG3 to catalyze OF ligation and DNA2 to facilitate long 5' flap processing. Collectively, our findings uncover previously unrecognized roles of PARP1 in regulating 5' flap dynamics to ensure efficient OFM and cell viability. HighlightsO_LIPARP1 plays context-dependent regulatory functions in Okazaki fragment maturation (OFM). C_LIO_LIPARP1 controls strand displacement DNA synthesis by the PCNA-Pol{delta} complex to dictate generation of short over long RNA-DNA flaps during canonic OFM. C_LIO_LIPARP1 senses unligated Okazaki fragments in DNA Ligase 1 deficient cells and suppresses unwanted conversion of DNA nicks into 5 flaps. C_LIO_LIProcessing of unligated nicks or flaps by DNA ligase 3 or DNA2, respectively in LIG1 deficient cells depends on PARP1. C_LIO_LIPARP1 inhibitors induce synthetic lethality with DNA ligase 1 or DNA2 inhibition. C_LI

molecular biology↗

bioRxiv2026

Task demands dynamically structure feature selection, routing, and integration in the human brain

AbstractFlexible visual categorization requires selecting task-relevant information from complex stimuli and transforming it through structured computations. Yet how task demands flexibly control these computations in the human brain remains unresolved. Dynamic faces provide a powerful test case, conveying stable identity through 3D shape and transient emotional expression through 4D movement. Using generative 4D face modelling, participant-specific MEG (N = 24), and information-theoretic analyses, we show that the brain implements a structured processing architecture. Task relevance first gates feature representations in occipital cortex, selectively sustaining relevant features while suppressing irrelevant ones. These features are then routed along pathway-specific channels--3D identity features to the ventral pathway and 4D emotion features to the lateral pathway. Finally, these inputs converge in temporal cortex, where identity and emotion features are synergistically integrated for learned identities. These results show how task demands dynamically structure feature selection, gating, routing, and integration, thereby constraining the computations that support flexible categorization.

neuroscience↗

bioRxiv2026

A Single-Cell Temporal Atlas of Mouse Nasal Embryonic Development

The mammals breathe and perceive odors through anatomically and functionally distinct respiratory and olfactory regions of the nose; however, how the early embryo endows this system remains largely unknown. Here, we present a temporal high-resolution single-cell RNA sequencing (scRNA-seq) atlas of mouse nasal development, comprising 183,247 cells collected from 20 embryos spanning embryonic day 10.5 (E10.5) to E18.5. We identified 7 major cell clusters and 52 molecularly defined subtypes, including previously unrecognized rare populations and niche-derived signaling components involved in progenitor cell maintenance. Lineage reconstruction of epithelial and mesenchymal compartments revealed dynamic cell fate transitions and highlighted candidate regulators of lineage specification, including Foxa1 as a regulator of nasal respiratory ciliated epithelium differentiation. Integration with adult nasal epithelium datasets further delineated transcriptional dynamics of olfactory stem cells. This study provides a molecular roadmap of nasal development and offers a valuable resource for future research into nasal biology and regenerative strategies.

developmental biology↗

bioRxiv2026

Clonal morphology-guided combination therapies overcome heterogeneity-driven drug tolerance

Tumor heterogeneity plays a critical role in tumor relapse and the development of drug resistance. Current personalized strategies, based on genetic profiling or bulk tumor drug sensitivity testing, offer limited clinical value as they overlook clonal heterogeneity. Here, through establishing primary tumor cell cultures from multiple metastatic sites, we observed that tumor cells exhibit high morphological plasticity and readily form distinct clonal morphologies during monoclonal expansion. Moreover, these heterogeneous clones displayed distinct tumorigenic and histological traits in orthotopic models, which may imply their differing clinical relevance in tumor progression. We also found that clonal morphological heterogeneity was exhibited by both established cell lines and primary lines derived from chemically induced tumor models. Subsequently, we analyzed the drug sensitivity profiles of tumor clones and identified clone-specific sensitive drugs. Despite limited in vitro synergy in pairwise combinations, both in vitro and in vivo assays confirmed their potent, clone-selective inhibition, suggesting rational drug combinations can precisely target distinct clonal populations. Taken together, Collectively, our findings propose that a heterogeneity-informed drug selection paradigm, enabled by rapid clonal morphology analysis of patient-derived cells, can be used to prevent recurrence and overcome resistance. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/703021v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1db607dorg.highwire.dtl.DTLVardef@19bbcd4org.highwire.dtl.DTLVardef@18a3355org.highwire.dtl.DTLVardef@304794_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITumor cells develop distinct morphologies during clonal expansion. C_LIO_LIDistinct morphologies serve as simple markers of tumor heterogeneity. C_LIO_LIDistinct clonal morphology defines a unique drug-response profile. C_LIO_LIClone-selective drug combinations combat heterogeneity-driven resistance. C_LI

cancer biology↗

bioRxiv2026

p62 protein pleomorphism confers tissue-specific function

Protein structure dictate function, and proteins often perform the same function in different cell/tissue-type environments. Here, we report that in Drosophila melanogaster, the broadly expressed protein p62/SQSTM1 instead performs mutually exclusive functions across tissues - autophagy in midgut and mitochondria-associated proteostasis in muscle. These functional differences arise from tissue-specific secondary and tertiary structures adopted by the same p62 polypeptide, rather than protein abundance, isoforms, post-translational modification, or binding-partner availability. The tissue-specific structures are cell autonomous and resistant to environmental perturbation. Deletion of a short intrinsically disordered region converts muscle p62 to a midgut-like structural and functional state, but this forced switch causes muscle dysfunction, linking tissue-specific physiology to alternative structural states of the same polypeptide. We posit that Drosophila p62 exemplifies a mechanism for tissue-specificity in which intrinsic structural plasticity and the physiochemical/molecular environment of a tissue enable a broadly expressed protein to adopt tissue-specific structure and function.

cell biology↗