Biology subjects

Xue, L.

Publications and source records attributed to Xue, L..

At least 19 recordsLinked to original sources

bioRxiv2026

A 21-Color Spectral Flow Cytometry Panel for Comprehensive Immunophenotyping of Rat Tissues and a Companion 9-Color T-Cell Functional Assay

Although rats are crucial translational research models due to their immunological homology and surgical feasibility, the scarcity of conjugated antibodies has hampered high-dimensional immune profiling. To bridge this gap, we created a synergistic two-panel method that uses full-spectral flow cytometry: a 21-color comprehensive immunophenotyping panel and a 9-color intracellular cytokine staining (ICS) panel. The 21-color panel navigates the limited fluorophore pool and maps innate and adaptive lineages at high resolution. While it can be used to profile neutrophils and monocytes in peripheral blood it reaches its full potential in lymphoid organs, allowing for the simultaneous evaluation of tissue-resident macrophages, dendritic cells, T cell differentiation (including Tregs), and APC function. Based on this phenotypic paradigm, the 9-color ICS panel dissects effector T cell activation and Th1/Th2/Th17 cytokine production. Furthermore, we reserved the PE color during panel creation, allowing for the use of antibodies and probes with PE or comparable fluorophores in conjunction with this panel, hence increasing overall flexibility. This combination technique, designed for rat peripheral blood, spleen, and lymph nodes, combines panoramic phenotyping with functional analysis, offering an adaptable foundation for complicated tissue microenvironments in tumor immunology, rheumatology, and autoimmunity research.

immunology↗

bioRxiv2026

Architectural trade-offs between environmental stability and genomic redundancy reveal divergent pneumoviral entry strategies

Human respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) exhibit distinct seasonal epidemiology, with RSV circulating in early autumn and hMPV peaking in midwinter, yet the structural basis for this niche partitioning remains undefined. Here, we integrate in situ cryo-electron tomography and functional virology to decode the architectural logic governing their entry dynamics. RSV employs a matrix (M)-regulated prefusion F (pre-F) organization, partitioning trimers into stabilizing hexagonal superlattices and fusion-competent pools to maintain superior thermotolerance. By contrast, hMPV compensates for its intrinsically unstable, monomeric pre-F with extreme ribonucleoprotein polyploidy, packaging [~]4-fold more genome equivalents to ensure productive infection. Fusion events localize exclusively to M-depleted, non-arrayed membrane regions, establishing a spatial checkpoint for activation. These findings reveal a conserved trade-off between environmental resilience and genomic redundancy that dictates divergent pneumoviral entry strategies, explaining their distinct seasonal ecological niches.

microbiology↗

bioRxiv2026

The overlooked role of muscle regeneration failure in post-implantation complications: a thorough investigation into mechanisms of recurrent urethral stricture

Bioresorbable collagen membranes rarely achieve complete organ regeneration, often necessitating secondary operations. In this study, urethral defects were modeled in 60 Chinchilla rabbits; 30 were reconstructed using collagen membrane patches. Histological, immunohistochemical and in situ PCR analyses were performed at multiple time points up to 270 days post-implantation to assess inflammatory (TGF-{beta}1, Wnt2, iNOS) and regenerative (collagen I/III, -SMA, E-cadherin) markers. A biopsy from a patient with recurrent urethral stricture was analyzed using the same methodology. At three months after implantation, the mucosal layer had recovered, however, the underlying muscle layer remained incompletely regenerated. The muscle bundles were surrounded by -SMA-positive myofibroblast-rich connective tissue with upregulated profibrotic markers. Comparable patterns of impaired muscle regeneration and high TGF-{beta}1 expression were found in the human specimen. Our findings suggest that while muscle layer regeneration is essential for structural restoration, it may also trigger a sustained profibrotic cascade.

bioengineering↗

bioRxiv2026

Learning Perturbation Effects Through Contrastive Alignment of Multimodal Biological Embeddings

Multimodal single-cell perturbation screens offer a scalable approach for characterizing the effects of genetic and chemical interventions on cellular state. However, most existing representation-learning methods are tailored to a single perturbation modality and fail to explicitly incorporate external semantic knowledge, which limits their ability to generalize across datasets and perturbation types. Here, we introduce PertOmni, a CLIP-style multimodal representation-learning framework that aligns transcriptomic perturbation signatures with text-derived embeddings of curated genes and compound descriptions, as well as image-derived embeddings from cell paintings. PertOmni jointly trains a shared transcriptomic encoder and dataset-specific text encoders using a masked contrastive objective that emphasizes within-cell-type discrimination while mitigating confounding effects arising from cell-type heterogeneity. We evaluate the produced joint embedding space on bi-directional retrieval, drug-gene interaction inference, and perturbation prediction across both small-molecule and CRISPRi perturbation datasets, and demonstrate consistent improvements over strong baseline methods.

bioinformatics↗

bioRxiv2026

Integrating Histology with Spatial Molecular Programs Using a Multimodal Foundation Model

Histopathological assessment remains central to cancer diagnosis and stratification, yet its mechanistic interpretation remains limited without molecular context. To address this, we developed SQUALL, a multimodal foundation model integrating histology with spatial molecular programs. For pretraining, we assembled histMol, a large-scale corpus of 1.76 billion paired histology-spatial transcriptomics spots/bins across 33 tissues and 12 platforms from 3,446 tissue sections. Following pretraining, SQUALL enables transcriptome-wide virtual biomarker profiling, prognostically relevant spatial niches discovery, and integrative disease progression modeling. Leveraging its multimodal embeddings, SQUALL identifies niches associated with tertiary lymphoid structure (TLS) maturation and ovarian cancer relapse, reconstructs molecular trajectories of breast cancer invasion across 325,112 spots, and uncovers underlying transcriptional programs. Applied to whole-slide images from 898 patients, SQUALL outperforms existing pathology foundation models in outcome prediction while enabling interpretable risk stratification. Together, these results establish spatially aligned multimodal pretraining as a new paradigm for extending molecular insights into pathology images.

bioinformatics↗

bioRxiv2026

Rhodopsin is a tunable capacitor buffering the toxic, desensitizing retinoids of the vertebrate eye

The eye is a marvel of evolution, but visual sensitivity introduces the risk of blinding photodamage. Here we reveal that the locus of sensitivity--the visual pigment rhodopsin --moonlights as a tunable mechanism of retinal photoprotection. Independent of signaling, light activated rhodopsin (R*) serves as an overflow capacitor buffering all-trans retinal (atRAL), a toxic and desensitizing retinoid agonist that accumulates as lipofuscin--a clinical marker of macular degeneration. Across mammals, R* stability reflects binding affinity and sequestration of atRAL (capacitance), thereby mitigating phototoxicity to a degree proportional to species photodamage risk, with human R* uniquely non-protective. A mouse model of defective atRAL clearance treated with a synthetic R* of unnaturally high atRAL capacitance preserved retinal function following light damage. This gene therapy also provided supra-physiological scotopic sensitivity despite being a signal-silent receptor, shielding neighboring dark-state receptors from agonist interference during regeneration, while also enhancing the signaling of endogenous R*. While the consensus human rhodopsin is not photoprotective, during recent evolution, mutations that protect against light damage emerged in high irradiance human environments and are now significantly associated with a 38% reduced risk of blindness and low vision. Together, our findings redefine rhodopsin as a tunable light buffer that can be leveraged to enhance photoreceptor function beyond natural limits.

biochemistry↗

bioRxiv2026

Paternal behavior is controlled by preoptic Trpc5 neurons

Male parenting behavior is highly conserved and activated only after offspring are born. Here we show that the behavioral switch from infanticide in virgin male mice to caregiving in wild-type sires is associated with enhanced expression and activation of Transient receptor potential channel 5 (Trpc5) in estrogen receptor (Esr1)-expressing neurons in the hypothalamic medial preoptic area (MPOA). While selective deletion of Trpc5 from Esr1MPOA neurons diminishes paternal behavior in sires, overexpression of Trpc5 in these neurons converts the otherwise infanticidal virgin males to exhibit care to pups. Mechanistically, Trpc5-dependent changes in neuronal excitability underlie fatherhood-associated Esr1MPOA neuron plasticity. Notably, Trpc5 overexpression also enhances escape behavior and elicits exploratory diving behavior, suggesting that these neurons control a broader adaptive parenting response in males. These findings establish a Trpc5-dependent MPOA neural signal as a critical regulator of paternal behavior.

neuroscience↗

bioRxiv2026

MSstatsResponse: Semi-parametric statistical model enhances detection of drug-protein interactions in chemoproteomics experiments

Chemoproteomics is a popular approach for the identification of small molecule-protein interactions in biological systems. Several chemoproteomics workflows leverage functionalized chemical probes and mass spectrometry to measure protein engagement through direct protein enrichment or competition using a range of small molecule concentrations. Statistical methods for analysis of such dose-response chemoproteomics datasets are limited. For example, existing methods rely on fixed curve shapes and are sensitive to experimental variation, particularly when the number of doses or replicates is limited. Here, we present MSstatsResponse, a semi-parametric statistical framework for analyzing chemoproteomic dose-response experiments that uses isotonic regression that does not require a fixed curve shape. This approach improves the accuracy and robustness of curve fitting, target identification, and half-response estimation across diverse experimental designs. We evaluate MSstatsResponse by generating a benchmark chemoproteomic dataset that profiled the competition between the kinase-binding probe XO44 and the drug Dasatinib using three mass spectrometry acquisition strategies: data-independent acquisition, tandem mass tag-based data-dependent acquisition, and selected reaction monitoring. We further evaluate the method on simulated datasets that vary the number of doses, number of replicates, and levels of noise, and demonstrate that MSstatsResponse consistently improves sensitivity, specificity, and reproducibility compared to existing methods, particularly in low-replicate and low-dose settings. MSstatsResponse is implemented as an open-source R/Bioconductor package that integrates with the MSstats ecosystem for quantitative proteomics. It provides a unified workflow for preprocessing, curve fitting, target identification, and experimental design, enabling researchers to select the number of doses and replicates appropriate to their experimental goals. The software and documentation are freely available at https://bioconductor.org/packages/MSstatsResponse.

bioinformatics↗

bioRxiv2026

Blood-brain barrier dysfunction predicts cognitive trajectory after ischemic stroke

Ischemic stroke doubles the risk of dementia.1-4 Stroke severity and location affect cognition early,5,6 but late dementia risk is not related to infarct characteristics, nor is it reduced by preventing additional strokes,3,6,7 and its mechanism is unknown. We identified a plasma proteomic signature of chronic stroke that was consistent with blood-brain barrier (BBB) dysfunction, including a 58% decrease in plasma levels of platelet-derived growth factor B and downregulation of its pathway compared to healthy controls. During 2 years of follow-up, the stroke-specific proteome was accentuated in stroke survivors who subsequently declined in the processing speed/executive function cognitive domain. To test BBB function, we performed dynamic contrast-enhanced MRI 6-9 months after stroke in an additional cohort and found 1.7-fold higher whole brain BBB leakage compared to controls. Finally, we compared autopsy tissue from people with infarcts and dementia at death to those with infarcts and no dementia. Those who died with dementia had dramatic loss of vascular mural cell coverage compared to those without dementia (median 0.7% vs. 27%). Thus, our proteomic, functional, and structural data implicate chronic BBB dysfunction in cognitive decline late after stroke, revealing potential proteomic and imaging biomarkers and, importantly, a novel target for intervention.

neuroscience↗

bioRxiv2026

THIK-1 channel mediates microglial glucose sensing and modulates AgRP neurons

Microglia play essential roles in maintaining energy homeostasis, and their dysfunction contributes to metabolic disease. Although high-fat diet (HFD) exposure induces microglial activation, the underlying mechanisms remain poorly defined. Here, we identified a previously unrecognized role for THIK-1 channel in mediating glucose sensing of microglia in arcuate nucleus of the hypothalamus (ARH), during HFD-induced obesity. Pharmacological inhibition of THIK-1 channel with tetrapentylammonium (TPA) suppresses feeding and attenuates body-weight gain in diet induced obese mice. Mechanistically, inhibition of agouti-related peptide (AgRP) neurons is indispensable for TPA-induced hypophagia. Moreover, THIK-1 inhibition promotes microglial phagocytosis of perineuronal nets (PNNs), leading to reduced AgRP neuronal activity and feeding suppression. Together, these findings establish THIK-1 as a critical glucose sensor in hypothalamic microglia and uncover a microglia-dependent pathway through which overnutrition modulates AgRP neuronal activity via PNN remodeling to regulate energy balance, highlighting THIK-1 as a potential therapeutic target for treatment of diet-induced obesity.

neuroscience↗

bioRxiv2026

AutoPELSA: an automated sample preparation system for proteome-wide identification of target proteins of diverse ligands

Protein-ligand interactions are fundamental to cellular function and drug discovery, and ligand-modification-free strategies have emerged as powerful tools for proteome-wide interrogation of these interactions. Among these, the peptide-centric local stability assay (PELSA) stands out for its high sensitivity. It uses a single digestion step to detect ligand-induced local stability shifts, enabling precise binding region localization and affinity estimation. However, manual PELSA workflows suffer from multiple labor-intensive steps that introduce variability and constrain throughput, limiting large-scale applications. To address these limitations, we developed AutoPELSA, an automated platform that streamlines the PELSA workflow including the limited proteolysis step and the following peptide separation step. AutoPELSA completes 96 samples in [~]4 h, enabling high-throughput analysis under native conditions. AutoPELSA reliably detected targets of both strong-affinity ligands (e.g., staurosporine, identifying 114 kinase targets) and low-affinity ligands, including -ketoglutarate (30 known targets). Furthermore, a mixed-ligand dose-response strategy enabled simultaneous determination of binding affinities for multiple ligand-protein interaction regions in a single experiment. Overall, AutoPELSA provides a scalable and modification-free platform for proteome-wide identification and affinity profiling of ligand-protein interactions.

molecular biology↗

bioRxiv2025

Structural and biochemical studies of human PP2A(B55) holoenzyme and ENSA protein complex

The serine/threonine protein phosphatase 2A (B55) holoenzyme (PP2A(B55)), a key cell cycle regulator, is tightly regulated by ENSA, whose phosphorylation at Ser67 inhibits PP2A(B55). The structural basis for how pENSA orchestrates this inhibition to govern mitotic progression remains unclear. In this study, we disapproved the previous hypothesis of direct ENSA-PP2A A subunit interaction, and showed that the ENSA-PP2A(B55) interaction requires the PP2A holoenzyme. We then determined cryo-EM structure of the PP2A(B55)-ENSAS67D complex at 3.03 [A] resolution, which reveals four distinct regions of ENSA, each engaging specific sites on the B55 or C subunits. The structure reveals an extended, inhibited conformation of the PP2A(B55) holoenzyme, which contrasts sharply with the contracted, active state of apo PP2A(B55). pENSA binding induces the C subunit to shift away from the B55 subunit, with the pS67-containing motif inserting into the catalytic site of C subunit and locking the PP2A(B55) holoenzyme in an inactive state. Our work also revealed novel ligand-binding surfaces on B55, and expanded definition of the short linear motif (SliM). Overall, our work provided novel insights into PP2A regulation during cell cycle, and offers new avenues for the discovery of specific PP2A(B55) inhibitors and modulators.

biophysics↗

bioRxiv2025

STING and VDAC inhibitors attenuate inflammation and ineffective erythropoiesis caused by an altered metabolome in the Nan (EKLF/E339D) mouse model of neonatal anemia

Erythroid Kruppel-like factor (EKLF/KLF1) is an essential transcriptional regulator of all aspects of erythropoiesis. The mouse neonatal anemia (Nan) mutation is driven by a semi-dominant mutation in one allele of the EKLF second Zn-finger at position E339D. RNA-seq analysis of Nan/+ erythroid cells showed that expression of numerous enzymes associated with metabolic pathways are changed as a result. We assessed and analyzed the effects of this dysregulation by mass spectrometry of embryonic and adult material. Our results show that mono-allelic expression of Nan-EKLF has profound impacts on erythroid cell metabolism: levels of amino acids, nucleotides, and metabolites are altered, more energy is needed for survival and proliferation, and glucose is taken up more rapidly. As a result, mitochondrial morphology is distorted, leading to VDAC1 oligomerization and mtDNA release to the cytosol. This activates the cGAS-STING signaling pathway and induces a type-I IFN response that drives inflammation. Use of STING or VDAC inhibitors alleviates these conditions both ex vivo and in vivo. Mechanistically, treatment restores normal erythroid cell divisions and differentiation, and decreases inflammatory pathways in the bone marrow. Our findings are likely directly relevant to the dyserythropoiesis observed in CDA type IV patients that carry a similar mutation.

molecular biology↗

bioRxiv2025

A global atlas of deep-sea cold seep viruses uncovers extensive genomic novelty, pervasive viral dark matter, and biotechnological potential

Cold seeps are globally distributed deep-sea ecosystems harboring diverse chemosynthetic microbial communities, yet their viral components remain poorly understood. Here, we establish the Global Cold Seep Virome, a comprehensive catalog of 191,937 species-level viral operational taxonomic units (vOTUs) and 2.44 million viral protein clusters reconstructed from 314 metagenomes spanning 18 cold seep sites worldwide. Most vOTUs are distinct from those in existing environmental viromes, suggesting that cold seeps harbor a largely unexplored viral reservoir. Host prediction suggests diverse viral associations with key prokaryotes, including anaerobic methanotrophic archaea. Protein annotation reveals that these viruses encode widespread uncharacterized proteins and viral hallmark proteins with divergent physicochemical properties, potentially contributing to their ecological adaptability. We also identify putative auxiliary metabolic genes, anti-defense genes, and lysins, and experimentally validate representative anti-defense proteins and lysins with strong activities. This resource expands current knowledge of deep-sea viral diversity and provides a foundation for studying virus-host interactions, testing biogeochemical hypotheses, and exploring biotechnological potential in cold seep ecosystems.

microbiology↗

bioRxiv2025

Mineralized Tissue-Targeting Expression System for Local Control of Gene Expression

Targeted control of gene expression in mineralized tissue would enable the use of nucleic acids to modulate the local microenvironment at diseased sites, ultimately promoting bone regeneration. Piperazine-linked bisphosphonate ionizable lipids provide a facile approach to targeting the transfection of mineralized tissue with lipid nanoparticles (LNPs). Here, we develop a Mineralized Tissue-Targeting Expression System (MiTEX) using bisphosphonate LNPs to locally target mineralized tissues by adsorption to mineral surfaces and bone graft materials. MiTEX demonstrated a significant increase in the adsorption of RNA onto hydroxyapatite substrates, which retained the ability to transfect bone mesenchymal cells via the adsorbed layer of mRNA LNPs. Bone graft scaffolds functionalized by adsorbed Cre mRNA-LNP were implanted to genetically label newly formed bone tissues in vivo. The surface affinity and adsorption of bisphosphonate lipids provided a local reservoir in mineralized tissues, sustaining the in vivo delivery of MiTEX. Furthermore, the targeted delivery of RNA therapeutics was demonstrated using STAT3 siRNA to modulate gene expression and proinflammatory cytokine release in ex vivo periodontal tissues. The design of this new RNA-functionalized delivery platform will promote the development of precision nucleic acid therapeutics for local anti-inflammatory treatments and bone regeneration at mineralized tissue interfaces.

bioengineering↗

bioRxiv2025

Anti-CD38-Targeted Piperazine-Derived Lipid Nanoparticles Overcome Hepatic Clearance for mRNA Delivery to Multiple Myeloma Cells In Vivo

Multiple myeloma (MM) is an incurable plasma cell malignancy characterized by clonal heterogeneity, immune evasion, and therapeutic resistance. Messenger RNA (mRNA) therapeutics offer programmable strategies to express therapeutic proteins and gene editors, but their efficacy is limited by poor extrahepatic delivery. To overcome these barriers, we developed a lipid nanoparticle (LNP) platform for targeted mRNA delivery to MM cells in vivo. Through combinatorial screening, we identified C16-O1, a piperazine-based ionizable lipid that efficiently transfects both CD138+ and therapy-resistant CD138-MM subclones. For tumor selectivity, LNPs were functionalized with an antibody fragment against CD38, a clinically validated MM antigen. Anti-CD38 LNPs reached the tumor-site and significantly reduced hepatic accumulation in murine xenografts. As an in vitro proof-of-concept, delivery of Cas9 mRNA and an IRF4-targeting guide RNA induced gene knockout, cell-cycle arrest, and lenalidomide sensitization. Together, these findings establish a robust framework for targeted mRNA delivery in MM and other hematologic malignancies.

bioengineering↗

bioRxiv2025

Comprehensive benchmarking of somatic single-nucleotide variant and indel detection at ultra-low allele fractions using short- and long-read data

Mosaic mutations in normal tissues occur at low variant allele fractions (VAFs), complicating detection. To benchmark strategies, the SMaHT Network created a cell-line mixture (1:49) and produced ultra-deep whole-genome sequencing using short and long reads (five centers, 180-500x each). We assembled a reference of 44,008 mosaic SNVs and 2,059 Indels, cross-validation between platforms to expose limits of short-read analysis. We also partitioned the genome by mappability to examine the impact of genomic context, added a negative reference set, and accounted for culture-derived mutations. When seven institutions applied eleven algorithms to mixture data, call sets were largely discordant across tools and replicates, partly reflecting stochastic presence of low-VAF mutations in biological replicants. For >2% VAF SNVs, sensitivity and precision approached [~]80% at [≥]300x, with little gain from additional sequencing. This work provides a comprehensive framework for reliable detection of low-VAF mutations in non-cancer tissues and a valuable resource for the community.

bioinformatics↗

bioRxiv2025

Class A PBPs reinforce the septal cell wall following initial synthesis by SEDS-bPBP pairs during bacterial cytokinesis

Bacterial cytokinesis requires the coordinated action of septal peptidoglycan (PG) synthases to ensure efficient and accurate septum formation. Two major types of synthases contribute: SEDS-bPBP and bifunctional class A PBPs (aPBPs). How their activities are organized in space and time has remained unclear. Using Deinococcus radiodurans, which often contains both constricting and closed septa in the same cell, we show that septal PG synthesis proceeds through distinct steps at different regions. Primary synthesis at the leading edge by SEDS-bPBP pairs drives constriction, whereas aPBPs act later at the lagging edge and in closed septa to thicken the wall, enhance cross-linking, and reinforce septal integrity. At the single-molecule level, both synthase types move directionally to perform processive PG synthesis at distinct sites. We also observed spatiotemporal separation of SEDS-bPBP and aPBP synthases in Staphylococcus aureus, suggesting that secondary septal PG synthesis is a conserved mechanism securing successful cytokinesis.

microbiology↗