Biology subjects

Lin, L.

Publications and source records attributed to Lin, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Recombinant SIRT1 expression and SIRT1 METTL3 interaction analysis with computational identification of phytochemical SIRT1 activators and inhibitors

Sirtuin 1 (SIRT1), a NAD{+/-}dependent histone deacetylase, regulates diverse biological processes including aging, stress response, and cancer progression. Owing to its dual roles in tumor suppression and promotion, selective modulators of SIRT1 have attracted considerable therapeutic interest. This study explored the interaction of SIRT1 with METTL3 and screened phytochemicals from Indian medicinal plants for potential SIRT1 activation or inhibition. Human SIRT1 (residues 183-665) was cloned, expressed in E. coli, purified, and validated by isothermal titration calorimetry (ITC) to confirm binding with METTL3. Computational approaches, including molecular docking, ADMET profiling, molecular dynamics (MD) simulations, MM-PBSA free energy estimation, and frontier molecular orbital (FMO) analysis, were employed to characterize ligand interactions. Docking revealed Catechin, Epicatechin, Kaempferol, and Bisdemethoxycurcumin as potent inhibitors, showing stronger binding than the reference inhibitor Selisistat by stabilizing the catalytic pocket via key hydrogen bonds and {pi}-{pi} stacking interactions. Among activators, Ginsenosides and Carnosol demonstrated higher affinities than resveratrol, binding the allosteric site through hydrophobic and electrostatic interactions. MD simulations highlighted Catechin and Ginsenosides as the most stable modulators, supported by reduced RMSD, compact Rg values, and favorable hydrogen bond occupancy. MM-PBSA confirmed their strong binding free energies, while ADMET analysis predicted favorable pharmacokinetic properties and low toxicity, particularly for Catechin and Ginsenosides. Overall, this study integrates expression and purification of the protein and computational modeling to identify phytochemicals as potential SIRT1 modulators and provides novel insights into the SIRT1-METTL3 regulatory axis. These findings highlight Catechin and Ginsenosides as promising scaffolds for therapeutic strategies targeting cancer and metabolic disorders.

molecular biology↗

bioRxiv2026

Spatially resolved host-fungal transcriptomics profiling by fungal-DBiT

Hosts and their associated fungi coexist within a shared tissue environment, engaging in dynamic interactions that influence immune regulation, tissue homeostasis, and disease progression. Dissecting these interactions requires spatially resolved and unbiased approaches capable of capturing gene expression from both host and fungal cells within intact tissue architecture. Here, we present fungal-DBiT, a spatial transcriptomic platform that enables simultaneous, high-resolution mapping of host and fungal RNAs, directly in tissue sections. Using fungal-DBiT, we profiled the spatial distribution of host and fungal transcripts in a fungal infection mouse model, and review pronounced spatial heterogeneity in fungal localization and activity, accompanied by region-specific host transcriptional responses. We further applied fungal-DBiT to intestinal tissues under physiological conditions, demonstrating its sensitivity in detecting low-abundance fungal species in the absence of overt inflammation. Together, these results demonstrate the ability of fungal-DBiT to resolve host-fungal interactions in situ and highlight its utility for studying mycobiome associated immune responses and disease processes with spatial precision.

microbiology↗

bioRxiv2026

Sex shapes capillary flows and oxygen extraction in the middle-aged mouse brain

Sex differences in brain aging are well documented, but their origin within the cerebrovascular hierarchy remains unclear. Here we show that cortical blood flow is higher in female than male mice at 15 months of age, at a point when an earlier sex difference in pulsatility and resistance indices has already converged, pial vessel diameter shows no difference between sexes, and estrogen levels are similar between sexes. Using an indicator-dilution and intravascular oxygen measurements using two-photon microscopy, we found that capillary transit-time heterogeneity (CTH) scales more steeply with mean transit time in females, consistent with a passively regulated capillary network, and that this is accompanied by reduced oxygen extraction fraction (OEF) without deficit in arterial oxygen delivery. Spatial transcriptomics reveals that sex differences are organized into distinct regional programs, most prominently in white matter, where a male-associated myelin and axonogenesis signature accompanies reduced white matter volume in females. These molecular and structural differences coincide with elevated hippocampal microglial reactivity and an altered spatial search strategy in females, without any detectable differences in circulating markers of stress, blood-brain barrier integrity, or immunity. Together, these findings indicate that sex differences in the aging brain are expressed at the level of capillary flow regulation and regional tissue programs rather than through bulk cerebral blood flow alone, and that elevated blood flow in females can mask, rather than reflect, adequate tissue oxygenation.

neuroscience↗

bioRxiv2026

SEEKER: A genome-scale library-on-library screening platform for deciphering T cell recognition of antigen

Decoding which antigens activate a given T cell receptor (TCR) is a central challenge in immunology. We present SEEKER, a functional genome-scale library-on-library screening platform built on three elements: a Jurkat-derived T-APC cell (TAPCell) that combinatorially expresses one TCR and one peptide-MHC drawn from separate libraries together with an NFAT activation reporter; encapsulation of single TAPCells in a thermos-reversible hydrogel for isolated clonal expansion, so recognition is read out as intraclonal activation; and dual-asymmetric PCR that links TCR- and pMHC-encoding sequences into a heritable unit, enabling progressive hit enrichment over screening rounds. SEEKER interrogates ~10^8 TCR-pMHC combinations per run without prior knowledge. Screening joint-infiltrating CD8+ T cells from HLA-B*27+ ankylosing spondylitis patients against proteome-wide libraries validated 53 TCR-peptide pairs, uncovered extensive cross-recognition of self and common viral epitopes, and revealed highly polyreactive T cells recognizing up to 80 autoantigens, implicating virus-triggered poly-autoreactivity in multi-organ autoimmune diseases.

immunology↗

bioRxiv2026

NexuST: A Hierarchical Foundation Model for Spatial Transcriptomics

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

bioinformatics↗

bioRxiv2026

Neuropeptides NLP-10 and FLP-18 stimulate lipid catabolism in chronically diet-restricted Caenorhabditis elegans

Neuropeptides mediate inter-tissue communication in energy metabolism, yet most remain functionally uncharacterized. Using C. elegans, we uncover a neuropeptide signaling cascade that drives lipid catabolism under chronic dietary restriction. We show that impaired pharyngeal function leads to dyspepsia and nutrient insufficiency, which activates a signaling axis comprising two peptide-receptor pairs, NLP-10-NPR-35 and FLP-18-NPR-4. This cascade originates in ADL sensory neurons, relays through multiple interneurons, and enhances triglyceride hydrolysis in the intestine. Genetic disruption of any component of this axis restores fat accumulation in diet-restricted mutants, whereas overexpression of individual components in well-fed animals is insufficient to drive fat mobilization. Importantly, the same neuropeptide axis is engaged in starved wild-type animals, indicating a general response toward energy deficit rather than mutant-specific effects. These findings reveal a conserved neuroendocrine circuit that senses internal energy shortage and orchestrates systemic metabolic adaptation, providing a conceptual framework for how neuropeptide networks integrate nutritional status with energy balance in animals.

neuroscience↗

bioRxiv2026

Uncertainty-Guided Decision-Making in Bumble Bees

The evolutionary origins of cognitive monitoring remain contested. Metacognition, the capacity to monitor one's own cognitive states, has long been linked to complex vertebrate brains, yet whether a miniature brain can evaluate the reliability of its internal representations is unknown. Here we demonstrate that bumble bees engage in uncertainty-guided decision-making. Bees dynamically adjusted opt-out choices according to perceptual difficulty, settling for a smaller guaranteed reward to avoid errors, and actively paid a reward cost to seek information under uncertainty. Without any retraining, bees transferred this 'opt-out-under-uncertainty' rule to novel tactile and working-memory tasks under an all-probe design. This strategy was stable across individuals and accurately captured by a confidence-based decision model. Our findings suggest that a brain of approximately one million neurons can support an abstract domain-general uncertainty-monitoring policy, indicating that the neural substrates for uncertainty-guided decision-making may be far more ancient and widely distributed than previously assumed.

animal behavior and cognition↗

bioRxiv2026

Dynamic Responses to an Inflammatory Challenge Distinguish Metabolic Health Across Lean and Obese Individuals

Inflammation is a key driver of cardiometabolic disease, yet it remains unclear whether systemic inflammatory markers can distinguish metabolically healthy from unhealthy individuals or capture the temporal dynamics of inflammation. Here, we combined systemic immune profiling with a cantharidin-induced peripheral blister model to investigate dynamic inflammatory regulation across metabolic phenotypes in metabolically healthy lean (MHL), metabolically unhealthy lean (MUL), metabolically healthy obese (MHO), and metabolically unhealthy obese (MUO) individuals. While systemic inflammation was elevated in obesity, differences between metabolically healthy and unhealthy groups were modest, with limited discrimination by plasma proteomics, circulating leukocyte phenotyping, and whole-blood transcriptomics. In contrast, the dynamic response to inflammatory challenge revealed pronounced differences at proteomic, cellular, and transcriptomic levels. Metabolically unhealthy individuals exhibited exaggerated early innate immune responses, impaired inflammatory resolution and tissue repair, reduced recruitment of reparative immune cells, and sustained T cell presence. Transcriptomic analyses further showed blunted dynamic gene regulation and defective epidermal barrier restoration. These findings indicate that metabolic health is better reflected in tissue-level inflammatory dynamics than in systemic measures.

immunology↗

bioRxiv2026

Sobetirome, a thyroid hormone receptor beta agonist, is a potential therapeutic agent for pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal disease with limited treatment options. Our group previously identified the antifibrotic potential of thyroid hormone, triiodothyronine (T3); however, clinical translation of thyroid hormone therapy is limited by its systemic adverse effects. In this study, we investigate whether sobetirome, a selective and well tolerated thyroid hormone receptor beta (THRB) agonist, offers antifibrotic benefits of thyroid hormone while minimizing systemic toxicity. Our study reveals that sobetirome, administered via intraperitoneal or inhalational routes, effectively mitigates bleomycin-induced pulmonary fibrosis in mice, with no evidence of toxicity. We identified that sobetirome restores mitochondrial homeostasis via activating the THRB-PPARGC1a axis. This protects alveolar type II epithelial cells from injury-induced apoptosis while selectively inducing apoptosis and metabolic reprogramming in apoptosis resistant IPF fibroblasts. Cell-specific deletion of Ppargc1a in either alveolar epithelial cells or fibroblasts abolishes sobetirome-mediated protection, establishing PPARGC1a as an essential mediator of therapeutic response. Importantly, sobetirome reverses fibrosis-associated transcriptional programs in human IPF lung tissue, reducing expression of key fibrosis-associated genes, including collagen I alpha 1 (COL1A1), collagen III alpha 1 (COL3A1), periostin (POSTN), cathepsin K (CTSK), and Chitinase 3 Like 1 (CHI3L1), while promoting extracellular matrix remodeling, epithelial restoration, and tissue homeostasis. Collectively, our findings identify THRB activation as a novel metabolic strategy for reversing pulmonary fibrosis. Across complementary in vitro, in vivo, and human ex vivo models, sobetirome restores mitochondrial function, modulates apoptotic pathways in pathogenic cells, and promotes fibrosis resolution, highlighting its potential as a lung-targeted therapeutic approach for IPF and other fibrotic lung diseases.

systems biology↗

bioRxiv2026

Membrane-gated SNARE zippering focuses energy for fusion

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) drive stagewise membrane fusion by zippering into membrane-bridging four-helix bundles. Yet the conformations underlying successive fusion stages and the coupling of folding energy to bilayer remodeling remain unclear. Using optical tweezers, we measured the intermediates, energetics, kinetics, and force dependence of individual synaptic SNARE complexes assembled in cis on single membranes and in trans between apposed membranes. Membrane-anchored cis-SNAREs assembled through N-terminal and cooperative C-terminal/linker-domain transitions, whereas their transmembrane domains showed little intrinsic dimerization. Syntaxin retained membrane-dependent helical continuity through its linker domain before zippering was complete. PIP2 strengthened but slowed late zippering. In trans, membrane repulsion arrested single trans-SNARE complexes in a half-zippered state. G{beta}{gamma} further clamped this intermediate and inhibited late zippering; G-GDP, but not G-GTP{gamma}S, relieved the clamp, revealing a nucleotide-dependent mechanism for GPCR-mediated inhibition of neurotransmitter release. Modeling suggests that cooperative late zippering, syntaxin linker helicity, and concerted action of multiple SNAREs focus folding energy released over a long distance onto short-range membrane apposition. Thus, mechanically gated SNARE zippering is regulated by membrane forces, lipids, and regulatory proteins.

cell biology↗

bioRxiv2026

STAT1 sets microglial neutral-lipid content independently of lipid-handling transcriptional programs

Inflammatory activation and lipid remodeling are linked features of microglial states, but how inflammatory transcription factors shape microglial lipid handling is unclear. Here we show that STAT1 sets neutral-lipid content in microglia through a route not predicted by lipid-handling transcription. Acute STAT1 depletion in primary microglia lowered neutral-lipid content while lipid-uptake and lipid-storage programs were induced, and interferon-{gamma} activation moved inflammatory transcription in the opposite direction yet lowered lipid content alike. Single-cell transcriptomic and chromatin profiling of Stat1- and Irf1-deficient mice showed that STAT1 and IRF1 organize overlapping inflammatory and lipid-handling programs, with genome-wide accessibility changes that did not predict transcriptional output at individual lipid-handling loci. Microglia co-expressing STAT1 and APOE recurred across Alzheimer's disease and multiple sclerosis datasets. Transcriptional program engagement is therefore separable from cellular lipid state, and lipid-handling gene expression cannot be read as a proxy for microglial lipid content.

neuroscience↗

bioRxiv2026

ETAP-CLF: an ESM3-based transformer attention framework for binary protein classification

Binary protein classification supports diverse tasks in computational biology, including pathway-membership inference and sequence-based candidate prioritization. Protein language models generate information-rich residue-level representations, but downstream classifiers commonly compress them using fixed pooling operations that may discard task-relevant sequence context. We present ETAP-CLF, a compact framework that combines pretrained per-residue ESM3 embeddings with lightweight transformer contextualization and learned attention pooling to classify variable-length proteins and generate residue-level attention scores. The ESM3 parameters remained frozen, and the same ETAP-CLF architecture and hyperparameter configuration were used across ferroptosis-, senescence-, and pyroptosis-associated protein prediction. ETAP-CLF achieved AUROCs of 0.98, 0.95 and 0.91 for these tasks, respectively. In the ferroptosis benchmark, ETAP-CLF outperformed the evaluated published models. These results demonstrate that a common downstream design can adapt to multiple process-associated classification tasks without fine-tuning the task-specific model architecture. ETAP-CLF provides a generalizable approach for sequence-based protein prioritization and a basis for broader evaluation across binary protein-classification problems.

bioinformatics↗

bioRxiv2026

Chromatin state shapes site-specific A-to-I RNA editing

Adenosine-to-inosine (A-to-I) RNA editing is a widespread post-transcriptional mechanism that diversifies the transcriptome. While ADAR enzymes catalyze this reaction, the upstream mechanisms that determine why individual adenosines are edited at markedly different efficiencies remain poorly understood. Here, we integrated multi-omics datasets from human cell lines and mouse embryonic tissues and developed machine learning models that distinguish high-and low-frequency editing sites based on local epigenetic features. Across species, tissues, and developmental stages, H3K36me3 consistently emerges as the strongest negative predictor of editing frequency, whereas the histone variant H2A.Z.1 shows a positive association. Functional validations in H2AFZ-knockdown cells reveal that H2A.Z.1 preferentially facilitates editing at high-frequency sites (76.3% of sites decreased, mean {Delta} =-0.07), whereas SETD2-knockout-mediated loss of H3K36me3 selectively derepresses editing at low-frequency sites (86.9% upregulated, [~]2.7-fold increase). These findings establish chromatin state as an upstream regulatory layer that modulates RNA editing independently of editing enzyme abundance and reveal opposing roles for H3K36me3 and H2A.Z.1 in shaping RNA editing landscapes. Together, our study provides a conceptual framework linking epigenetic regulation to post-transcriptional RNA modification, suggesting that chromatin-mediated regulation contributes to the establishment of site-specific RNA editing programs across mammalian genomes.

genetics↗

bioRxiv2026

EndoAge Atlas: Non-linear dynamics of endothelial aging reveal organ-specific vascular trajectories in mice

Aging is a complex and multifactorial condition that leads to a gradual decline in organ functions and subsequent vulnerability to various diseases. Although the hallmarks of aging are well studied, the linear models developed based on these paradigms repeatedly fall short in capturing the dynamic, non-linear, and tissue-specific changes that occur because of aging. Furthermore, multi-organ level studies in humans are limited by the constraints of tissue availability and other confounding variables. This emphasises the importance of animal models in executing systemic investigations of aging. As the universal regulator of vascular function, endothelial cells (ECs) act as the initial responders to aging cues and undergo profound molecular and functional changes over time. This remodelling of the ECs is considered the central driver of multiple age-associated diseases. However, the global and tissue-specific molecular trajectories of aging in ECs are yet to be well characterised. Here, we introduce EndoAge atlas, a single-nucleus RNA-sequencing atlas comprising approximately 1.3 million ECs from 32 sex-balanced C57BL/6 mice across eight tissues and five distinct age groups. This atlas identifies tissue-specific endothelial heterogeneity, age-associated gene programs with distinct functional signatures, and uncovers non-linear gene expression trajectories across organs. Collectively, the EndoAge atlas constitutes a comprehensive reference for vascular aging across mammalian tissues, providing a foundational platform for developing targeted therapeutic strategies for age-related diseases.

bioinformatics↗

bioRxiv2026

Electrophysiological features of signals recorded from white matter

Intracranial neurophysiology studies have typically ignored signals from electrodes located in white matter (WM), assuming that their information content is artifactual or related to nearby gray matter (GM). Here, we tested the electrophysiological and functional features of signals recorded from different WM locations. Signals were recorded from 19 patients undergoing intracranial monitoring for drug-resistant epilepsy by means of stereo-electroencephalography (sEEG). Each sEEG electrode was classified into WM or GM based on the surrounding tissue. We obtained recordings from a total of 1,717 sEEG electrode contacts, 36% in WM, while the patients were in awake resting state (5 minutes). For each sEEG electrode, we employed a model-based spectral decomposition to separate periodic and aperiodic components, and we computed signal complexity metrics. For a subset of participants, we computed WM structural information from diffusion-weighted magnetic resonance imaging and we evaluated functional signals during a cognitive control task. Our results show that signals recorded from WM have different spectral features and higher complexity than GM. Complexity correlates positively with fractional anisotropy, and modulations related to behavior during the task were detected in WM. Overall, this indicates that WM signals carry information that may reflect signal propagation across WM fiber tracts.

neuroscience↗

bioRxiv2026

Defining Quality Control Standards for Single-Cell Proteomics by Inter-Laboratory Benchmarking

Single-cell proteomics can quantify thousands of proteins from individual mammalian cells, yet the absence of community-wide quality control limits biological interpretability. Here, the HUPO Single Cell Initiative presents the first inter-laboratory single-cell proteomics benchmarking study across seven laboratories using standardized 384-well plates acquired on Orbitrap Astral and timsTOF Ultra2 instruments. Centralized analysis across six DIA software tools revealed that software choice impacts identification depth and quantitative accuracy more than instrument vendor. Multi-layered quality control enabled the detection of cell-leakage during sorting, LC misconfiguration, column degradation and site-specific pipetting failures. Inter-lab quantitative correlations were strongest between instruments of the same vendor relative to cross-platform comparisons. Sequential correction for plate identity and well position recovered clean cell-type separation for confident downstream differential expression analysis. This study provides a data-driven quality control framework spanning plate design to batch correction for reproducible single-cell proteomics across laboratories and platforms.

biochemistry↗

bioRxiv2026

Thymic Treg-derived T follicular regulatory cells prevent catastrophic humoral autoimmunity in response to TLR7-driven inflammation

T follicular regulatory cells (TFR) are a follicle-resident subset of regulatory T cells (TREG) that limit germinal center (GC) responses and enforce humoral tolerance. Although TFR are known to focus antibody responses to foreign antigens, how GC-specific regulation is maintained during inflammation remains unclear. Here, TLR7-driven inflammation unmasked a critical, non-redundant role for TFR in preserving immune tolerance. Selective loss of TFR caused severe autoimmunity and increased mortality, driven by inflammation-induced expansion of autoreactive B and T cell clones and epitope spreading. Autoreactivity resolved upon cessation of inflammation in TFR-sucicient mice but persisted in their absence. Mechanistically, TFR limited the establishment and expansion of spontaneous GCs in response to inflammation, and responding TFR displayed transcriptional, phenotypic, and clonal features of thymic TREG. This suggests that whereas TFH upregulate FoxP3 to shut down end-stage GCs, it is thymic TREG-derived TFR that safeguard GC integrity under inflammatory stress to prevent lethal autoimmunity.

immunology↗

bioRxiv2026

Inherent Biomechanical Properties of the Lung: In vivo-Ex vivo Comparisons in Mice

Mammalian lungs operate within a thoracic "cage" composed of parietal pleura, rib cage, skeletal muscle, and diaphragm, yet clinical ventilator metrics largely reflect the combined mechanics of lung and surrounding structures and the thoracic cage. We hypothesized that thoracic boundary conditions selectively alter measured lung biomechanics. We performed paired pulmonary function testing (FlexiVent) in C57BL6 mice of both sexes spanning development through adulthood, measuring quasi-static pressure-volume behavior and dynamic forced-oscillation parameters in vivo (supine, mechanically ventilated) and again ex vivo in the same lungs. In a subset, we additionally compared in vivo and ex vivo {micro}CT-derived lung volumes, including a pressure-fixed ex vivo protocol using snap freezing at controlled inflation pressure. Quasi-static pressure-volume curves were similar between conditions, with near-identity at higher pressures and only modest divergence at low pressures, consistent with thoracic structures primarily modulating recruitment/de-recruitment rather than intrinsic elastic recoil. Maximal volume at 30 cmH2O showed strong in vivo-ex vivo correlation and minimal bias, and static compliance and PV-loop hysteresis exhibited small biases relative to reported disease-model effect sizes. In contrast, dynamic mechanics demonstrated a clear in vivo elevation of tissue damping (G) with only modest change in tissue elastance (H) and little change in Newtonian resistance (Rn), producing a meaningful increase in hysteresivity ( = G/H). This dissociation implicates frequency-dependent mechanical heterogeneity (e.g., time-constant mismatch/pendelluft) imposed or amplified by nonuniform thoracic loading. Ex vivo {micro}CT enabled reliable whole-lung segmentation and correlated with ex vivo PFT volumes at matched pressures, whereas in vivo volumetry showed weaker agreement. These results indicate that thoracic structures contribute modest restriction but disproportionately increase dynamic dissipation and heterogeneity, suggesting that ex vivo functional testing and oscillometry-like metrics may better detect biomechanical changes inherent to lung parenchyma.

physiology↗