Biology subjects

Gao, L.

Publications and source records attributed to Gao, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Renal nutrient loss promotes metabolic health at the expense of increased vulnerability to acute kidney injury

Obesity is a major risk factor for interrelated cardiorenal metabolic diseases including type 2 diabetes, heart failure and chronic kidney disease (1-4). Although obesity develops when energy intake chronically exceeds energy expenditure, individuals vary markedly in the amount of adiposity and metabolic dysfunction that develop in response to comparable caloric excess. Controlled overfeeding studies demonstrate several-fold variation in weight gain between individuals (5), while susceptibility to metabolic dysfunction also differs substantially between populations (6), suggesting considerable variation in how excess nutrients are partitioned. Energy balance is conventionally considered in terms of intake and expenditure, yet energy-containing nutrients can also be eliminated from the body. The kidney is uniquely positioned to regulate this third component of energy balance by determining whether filtered metabolites are reabsorbed or excreted. The metabolic benefits of SGLT2 inhibition demonstrate that reducing renal nutrient reabsorption can favourably alter systemic metabolic function (7,8), but whether naturally occurring variation in renal nutrient conservation contributes to metabolic disease susceptibility remains unknown. Here, screening eleven genetically divergent mouse strains identified BXD34 mice as strikingly resistant to diet-induced obesity, ectopic lipid accumulation and insulin resistance despite increased caloric intake. Mechanistically, this protection was associated with widespread urinary nutrient loss accompanied by coordinated suppression of renal solute transport, but came at the cost of profound susceptibility to acute kidney injury. Together, these findings identify renal nutrient conservation as an underappreciated determinant of whole-body metabolism and reveal a renometabolic trade-off in which protection from obesity is achieved at the expense of renal resilience.

physiology↗

bioRxiv2026

Efficacy of postmenopausal estrogen replacement in SIV-infected female macaques on antiretroviral therapy.

The success of modern antiretroviral therapy (ART) has increased the life expectancy of people living with HIV to levels approaching that of uninfected individuals. For women living with HIV (WLWH), this means that more will survive to undergo menopause and experience the consequences of decreased ovarian hormone levels, particularly estrogen (E2). The recent change in federal guidance for use of postmenopausal hormone therapy is increasing demand for both E2-alone and E2+progestogen formulations to control adverse symptoms of menopause. The consequences and efficacy of hormone therapy in WLWH are thus an important issue for WLWH and their healthcare providers. The role of E2 replacement in postmenopausal WLWH is a significant issue because of its potential effects on control the viral reservoir and its demonstrated beneficial metabolic effects in uninfected postmenopausal women. To address these questions, we employed a novel nonhuman primate model of postmenopausal WLWH undergoing E2 replacement. Reproductively competent female rhesus macaques were infected with simian immunodeficiency virus (SIV) and then subjected to a daily ART regimen. After complete suppression of plasma viremia, all animals were ovariectomized (OVX) and then implanted with Silastic capsules containing either cholesterol vehicle or sufficient E2 to restore pre-OVX plasma levels. Plasma and cell-associated viral dynamics, immune responses, body composition, systemic and tissue-specific metabolic parameters, cytokine profiles, and parameters of bone health were followed longitudinally from baseline through 34 weeks of E2 deficiency or replacement. We found that E2 status did not significantly affect plasma or tissue viral dynamics or overall metabolic homeostasis. However, E2 replacement exerted beneficial effects on several aspects of bone health in spite of a chronic inflammatory state that persisted following effective ART suppression of the SIV reservoir. Our findings suggest that hormone therapy, specifically E2 replacement, offers benefit to WLWH, particularly with respect to bone loss.

physiology↗

bioRxiv2026

Atlas-scale single-cell analysis beyond in-memory paradigm with scAtlasPy

Single-cell atlases are rapidly outgrowing the memory capacity of standard workstations, challenging the in-memory paradigm underlying mainstream computational ecosystems. Here, scAtlasPy decouples scale of atlas from memory capacity by leveraging the disk-resident computing. It enables full-resolution analysis of a 100-million-cell atlas with only 42.9 GB peak memory, whereas state-of-the-art platforms are limited at 3 million cells with 512 GB memory. scAtlasPy achieves 137,745 cells/s, 10.4x faster than scDataset with 82.6% lower memory usage for random minibatch retrieval. Its extensible architecture offers a flexible platform for diverse atlas-scale analytical tasks, facilitating the discovery of complex cellular heterogeneity and functions in massive cell atlases.

bioinformatics↗

bioRxiv2026

In Vivo Screening for a Promising Antiparasitic Agent Against Neobenedenia melleni in Epinephelus fuscoguttatusfemale x E. lanceolatusmale and Identification of Its Potential Target

Monogenean ectoparasites, particularly Neobenedenia species, cause severe economic losses in mariculture. Here, ectoparasites isolated from cultured hybrid groupers (Epinephelus fuscoguttatus[female] x E. lanceolatus[male]) were confirmed as Neobenedenia melleni based on ITS1 phylogeny. In vivo screening of six structurally diverse compounds identified compound D (CAS No. 206111-37-7), a 5,6-dihydropyridine derivative, as the most effective antiparasitic agent, achieving 76.54% efficacy at 0.5 mg/L in a 90 min bath treatment. Dose-response assays demonstrated that 0.7 mg/L compound D achieved 95.23% antiparasitic efficacy without causing evident tissue damage or cytotoxicity to GF-1 cells. Ultrastructural observation by scanning electron microscopy revealed marked tegumental alterations, including deep fissures and extensive surface folding, in treated parasites. Molecular docking against ten candidate proteins identified {beta}-tubulin as the most favorable docking target, with a binding energy of -6.53 kcal/mol and three hydrogen-bond interactions, suggesting that {beta}-tubulin may be involved in the antiparasitic activity of compound D. Overall, these findings highlight compound D as a promising lead candidate for short-bath therapy against N. melleni and suggest that cytoskeletal disruption through {beta}-tubulin interaction represents a plausible mechanism of action.

zoology↗

bioRxiv2026

Computer-aided drug screening of anti-Neobenedenia melleni drugs based on annexin B1 in farmed pearl grouper

Monogenean capsalids of the genus Neobenedenia are widespread parasites of wild and farmed marine fish, and represent a great threat to the mariculture of grouper in China. Fishery drug development to screen and find effective compounds to control and prevent the disease is urgent needed, considering the vast production of grouper in China (294 ktons in 2025). Annexins have been discovered in Neobenedenia and other parasites, and marked differences between the parasite annexins and those of the hosts make them potentially attractive drug targets for anti-parasite therapeutics. Herein, we utilized computer-based drug discovery screens using unique Neobenedenia melleni annexin B1 and a database of 1,456,161 small molecules. The 3D structure of annexin B1 was firstly modeled by three different protein prediction tools, namely AlphaFold 3, SWISS-MODEL, and I-TASSER, of which the most accurate protein structure was used as the drug target for the following structure-based virtual screening. In vivo experimental validation of 11 compounds after molecular docking shows that abamectin (Aba) has the most effective anti-Neobenedenia bioactivity at the concentration of 0.16 mg/L as the initial screening concentration. Given its low toxicity to host grouper (24 LC50=0.254 mg/L), abamectin was chose for further investigation. A 24 h bath exposure successfully lowered the parasitic load in infected grouper, yielding an 24 h EC50 of 0.033 mg. To elucidate the anti-parasite mechanism, long-timescale molecular dynamics simulations (1000 ns) of annexin B1 and Aba was conducted, which allowed for atomic and molecular-level analysis of the essential protein motions involved in the interaction of annexin B1 and its substrate. The interaction profile between annexin B1 and abamectin was dominated by hydrophobic contacts and water bridges, involving residues TYR-210, GLU-214, GLU-244, and SER-247, which path a way for further drug optimization.

zoology↗

bioRxiv2026

NIR-II squeezed light-field microscopy enables high-speed volumetric imaging of deep-tissue dynamics in vivo

High-speed three-dimensional imaging in scattering biological tissues remains challenging because volumetric microscopy generally requires scanning, whereas snapshot light-field approaches divide limited detector pixels among multiple views. This constraint is particularly severe in the second near-infrared window (NIR-II), where InGaAs cameras have small sensor formats and high detector noise. Here we introduce NIR-II squeezed light-field microscopy (NIR-II SLIM), which optically rotates and compresses multiple perspective views before detection, allowing efficient use of camera pixels while retaining complementary spatial information for three-dimensional reconstruction. NIR-II SLIM acquires up to 600 volumes s-1 with a reconstructed lateral sampling grid of 512 x 512 pixels. We use this method for label-free imaging of cardiac dynamics in pigmented late-larval zebrafish, resolving chamber deformation and millisecond-scale atrioventricular-valve motion, and for NIR-II fluorescence imaging of vascular and lymphatic transport in mice. NIR-II SLIM provides a detector-efficient approach for high-speed volumetric imaging of rapid biological dynamics in scattering tissues.

bioengineering↗

bioRxiv2026

Tissue-resident memory B cells augment local anti-cancer immunity via IgA

Tissue-resident memory B cells (BRM) provide powerful localized protection against microbial infection in barrier tissues. It is unknown if analogous BRM populations survey solid tumors and contribute to anti-cancer immunity. We profiled B cells from patients with colorectal cancer and cutaneous basal cell carcinoma and identified a CD69+ memory B cell population consistent with a tissue-resident phenotype. Integrative analysis of transcriptomic datasets identified an optimized signature enriched across cancer types. Tumor infiltrating BRM-like cells preferentially exhibited autoreactivity and their signature correlated with patient outcomes and response to immunotherapy. Skin and lung targeted vaccination established localized BRM that provided IgA dependent organ specific protection upon tumor challenge in murine models. These findings establish BRM as an active component of anti-cancer immunity via preferential reactivity to tumor associated self-antigens.

immunology↗

bioRxiv2026

Knee Joint Biomechanics During Lunges at Different Tibial Angles and External Loads: A Musculoskeletal Analysis with Finite Element Insights

ObjectiveThis study investigates knee joint biomechanics during lunges under varying tibial angles and external loads using musculoskeletal modeling and finite element analysis. The goal is to provide a biomechanical basis for understanding knee loading patterns and optimizing sports training and rehabilitation. MethodsTwenty-six healthy young men performed lunges under tibial inclination angles relative to the ground (60{degrees} and 90{degrees}) and two external load conditions (bodyweight and an additional 98 N external load). Kinematic and kinetic data were captured using motion capture and force plates. Musculoskeletal models were used to estimate joint moments, range of motion, and stiffness, with data analyzed using two-way repeated-measures ANOVA. Finite element analysis was performed at 90{degrees} tibial angle to evaluate tissue stress and displacement. ResultsThe joint moment at a 60{degrees} tibial angle was much higher than at a 90{degrees}. External load showed significant effects on knee stiffness, with lower rotational stiffness in the horizontal plane (P < 0.001) and lower coronal plane stiffness at 90{degrees} (P = 0.012) under the 98 N external-load condition, indicating reduced resistance to angular displacement in these planes. Under the 90{degrees} tibial-angle condition with external load, peak stress and displacement were concentrated in the posterior horn of the meniscus, with a maximum displacement of 3.12 mm. ConclusionThe anterior tilt of the tibia increased sagittal-plane knee loading, while external load mainly reduced joint stiffness in the coronal and horizontal planes. Under the 90{degrees} loaded condition, the concentration of stress and displacement in the posterior horn of the meniscus suggests a mechanically unfavorable loading pattern rather than direct evidence of injury risk. These findings may provide useful biomechanical information for load management during lunge-based training and rehabilitation.

bioengineering↗

bioRxiv2026

A Generalized Spatial Progress Code for Navigation in the Medial Prefrontal Cortex

Goal-directed navigation requires an internal estimate of progress toward a desired outcome, yet how the brain constructs and represents such a signal remains unclear. Here, we designed a multi-route navigation paradigm with geometrically distinct paths and imaged medial prefrontal cortex (mPFC) activity as mice performed goal-directed route choice behavior. We found that a substantial fraction of mPFC neurons fired at consistent positions along a normalized start-to-goal axis, independent of path geometry, running direction, and task context. At the ensemble level, mPFC activity reliably decoded spatial progress but carried minimal information about path identity. This progress code emerged with task familiarity and required input from the hippocampal CA1. Inactivation of either mPFC or CA1[->]mPFC projection did not disrupt learned path preference but impaired navigational fluency in trained mice. These findings reveal a hippocampal-prefrontal mechanism for representing abstract, context-generalized spatial progress within a goal-directed navigational episode, supporting fluent navigation across variable routes.

neuroscience↗

bioRxiv2026

NLR from soybean Rsv1 locus confers broad-spectrum resistance to soybean mosaic virus G1-G7 strains by recognizing viral P3 protein

Nucleotide-binding leucine-rich repeat (NLR) immune receptor genes are of significant value in disease resistance breeding and the control of viral diseases. Soybean mosaic virus (SMV) poses a serious threat to soybean production and the Rsv1 locus in soybean cultivar Suweon 97 confers broad-spectrum resistance against SMV strains G1 to G7; however, this locus harbors no fewer than 18 NLR genes, and thus the broad-spectrum antiviral mechanisms underlying the Rsv1 locus remain poorly understood to date. Here, we established a rapid and highly efficient screening system for cloning NLR genes from soybean Rsv1 locus and identified a broad-spectrum antiviral NLR gene 13g184900 from this highly complicated locus. The NLR encoded by 13g184900 can recognize viral P3 protein from all SMV strains (G1-G7) and another potyvirus Bean common mosaic virus (BCMV). The coiled-coil (CC) domain of this NLR directly interacts with viral P3 protein. Additionally, we showed that this NLR originated from wild soybean accession in East China and has been introduced into several soybean cultivars during domestication. Collectively, we developed a high-throughput screening system for identifying NLR genes in soybean and our study provides new mechanistic perspective on how the Rsv1 locus mediates the broad-spectrum resistance to all SMV G1-G7 strains.

plant biology↗

bioRxiv2026

Lineage-specific evolution of LTR retrotransposons under natural selection drives genomic divergence in diploid Oryza species

LTR retrotransposons (LTR-RTs) are major drivers of plant genome evolution. However, the principles governing how natural selection shapes their lineage-specific dynamics across closely related species remain elusive. Here, we performed a comprehensive comparative analysis of LTR-RTs across 15 diploid Oryza species, representing all major genome types. We reconstructed the spatiotemporal distribution and evolutionary trajectories of LTR-RTs, revealing three distinct evolutionary patterns influenced by natural selection: lineage-specific expansion under purifying selection, balanced co-evolution under balancing selection, and lineage-specific retention under strong positive selection. We further demonstrated that species-specific LTR-RT families significantly contribute to highly diverged regions (HDRs) and non-aligned regions (NOTALs), drive segmental duplications, and influence genome size variation. Notably, the removal of LTR-RTs, particularly from medium-removal-rate families, is a key factor in genome size contraction. Our study provides a population-genetic perspective on LTR-RT evolution and highlights their critical role in shaping genomic divergence and adaptation in Oryza. Our findings provide a population-genetic framework for understanding how the co-evolutionary dynamics between TEs and their hosts shape genome architecture and adaptation in closely related species.

genomics↗

bioRxiv2026

ROS Impair Mitophagy via PARylation of PINK1

Mitophagy is the process of selective autophagic clearance of damaged mitochondria and is closely implicated in neurodegenerative disease. PTEN-induced kinase 1 (PINK1) and a RBR E3 ubiquitin-protein ligase (Parkin) constitute a positive feedback loop in mitophagy initiation. It is known that reactive oxygen species (ROS) modulate mitophagy, while the exact regulatory mechanism remains largely elusive. Here, we found that exogenously applied ROS effectively block mitophagy induced by acute mitochondrial damage agents, which could be reversed by antioxidants. Mechanistically, ROS activate poly(ADP-ribose) polymerase 1 (PARP1), and suppression of PARP1 eliminates the inhibitory effect of ROS on mitophagy. Notably, PARP1 directly interacts with PINK1 and mediates its PARylation at residue E417, thereby negatively regulating PINK1 function. Collectively, our study identifies PARylation as a new form of post-translational modification of PINK1 and reveals a novel mechanism underlying the regulatory role of ROS in mitophagy by PARP1 activation and PARylation of PINK1. In briefGao et al. demonstrate that exogenous ROS inhibit mitophagy. Mechanistically, ROS activate PARP1, which mediates PARylation of PINK1, a central regulator of mitophagy, leading to its functional impairment. This study reveals a novel regulatory mechanism of ROS on mitophagy through PARP1 activation and identifies PARylation as a novel form of post-translational modification of PINK1. HighlightsO_LIROS block PINK1-Parkin-mediated mitophagy. C_LIO_LIROS activate PARP1. C_LIO_LIPARP1 suppression eliminates the inhibitory effect of ROS on mitophagy. C_LIO_LIPARylation of PINK1 by PARP1 impairs its activity and mitophagy. C_LI

Cell Biology↗

bioRxiv2026

High-resolution image-projection fluorescence lifetime imaging microscopy

Fluorescence lifetime imaging microscopy (FLIM) provides molecular contrast that is largely independent of fluorophore concentration, yet it remains constrained by a persistent trade-off among acquisition speed, photon dose, and detector complexity. To address this challenge, we developed image-projection fluorescence lifetime imaging microscopy (IP-FLIM), an integrated optical and computational platform that enables high-resolution, component-resolved lifetime imaging using only a linear single-photon avalanche diode array. We validate IP-FLIM using fluorescent microbeads and bovine pulmonary artery endothelial cells, demonstrating up to 22.3x improvement in contrast-to-noise ratio and 72.3% reduction in background noise over conventional filtered back-projection reconstruction. By combining wide-field projection acquisition with computational k-space reconstruction, IP-FLIM provides a scalable route to fast, high-resolution multiplex lifetime imaging.

bioengineering↗

bioRxiv2026

OmicOS: A Comprehensive Omics Ecosystem Infrastructure and Agent System for the AI Era

Biology has accumulated a vast ecosystem of omics methods, but much of this ecosystem remains built for expert humans rather than scientific agents. Methods are scattered across Python packages, R/Bioconductor and CRAN workflows, command-line tools, incompatible data containers and implicit object states, making even routine analyses difficult for an AI system to choose, execute and verify reliably. Here we introduce OmicOS, a comprehensive omics ecosystem infrastructure and agent system that turns OmicVerse V2, an open-source omics community, into an executable foundation for agentic biology. OmicVerse V2 provides the community substrate: scalable AnnDataOOM-compatible rust backends, agent-friendly Python algorithms for single-cell, spatial, bulk and multi-omics analysis, interfaces to single-cell foundation models, and Python-native reconstructions of historically R-centred Bioconductor/CRAN-style workflows. OmicOS makes this substrate actionable by registering analytical functions as state-aware capability contracts, allowing agents to inspect live data objects, select valid methods, execute controlled workflows and record provenance. The result is not a fixed pipeline, but a programmable omics environment in which agents compose real analyses from verified community methods rather than inventing tools. Across external and purpose-built benchmarks, OmicOS ranked first among the evaluated systems, reaching 81.2% on BiomniBench. Adding OmicVerse to a minimal agent improved task completion by up to 34.2 percentage points with qwen-3.6-35b, and controlled ablations showed that the gains came from registry-grounded execution rather than from larger models, documentation retrieval or unrestricted tool exposure. The same infrastructure scaled to atlas-sized data, reproduced R-centred workflows in Python and converted external pathology software into agent-usable skills. In a discovery task starting from a whole-body spatial map and the term "Alzheimers disease", OmicOS composed a non-canonical workflow that integrated spatial expression, genetic association, eQTL and colocalization evidence to nominate a colon epithelial risk axis centred on PICALM, CD2AP and CR1. Together, OmicVerse and OmicOS define an open foundation for AI-era omics, showing how a community of biological methods can be transformed into a reliable, extensible and agent-operable system for discovery. HighlightO_LIOmicVerse 2.0 consolidates 694 methods spanning 11 omics domains into agent-callable high-level APIs. C_LIO_LIRebuildR automatically reconstructs and evolves R/Bioconductor methods as Python-native implementations under output-equivalence gates. C_LIO_LIOmicOS establishes a state-of-the-art omics agent harness, ranking first on general omics benchmarks across models and substantially improving the analytical capability of local open-source models. C_LIO_LICompositional use of ecosystem modules nominates a colon epithelial axis associated with Alzheimers disease risk. C_LIO_LIExternal algorithm packages supporting automatic iterative evolution can be integrated into the OmicOS ecosystem. C_LI

bioinformatics↗

bioRxiv2026

Evaluation of Alcohol, Tobacco, and HPVs Synergistic regulation of Head and Neck Squamous Cell Carcinoma Treatment Response to PD-L1 Checkpoint Inhibitor Treatment

Although immune checkpoint inhibitors targeting the programmed death-ligand 1 (PD-L1) axis have transformed the treatment of recurrent and metastatic head and neck squamous cell carcinoma (HNSCC), durable clinical responses remain limited to a minority of patients, and the determinants of treatment resistance remain incompletely understood. Human papillomavirus (HPV) infection, alcohol consumption, tobacco use, and are the three most prominent etiological risk factors for HNSCC; however, despite their well-established individual roles in disease development, the influence of their combined exposure on PD-L1 axis regulation and immunotherapy response remains largely unexplored. In this study, we analyzed multi-omic data from 498 primary HNSCC tumors in The Cancer Genome Atlas (TCGA), stratifying patients into seven subgroups reflecting all observed exposure combinations, with HPV status determined directly from RNA-sequencing reads using Pathoscope. Notably, PD-L1 (CD274) expression was significantly downregulated in the triple-exposure cohort (1.51-fold reduction, p < 0.05), along with reduced expression of the upstream regulator JAK2 (1.44-fold reduction, p < 0.05) being seen. Immune deconvolution suggested progressively greater immune infiltration with accumulating exposures, yet gene set enrichment analysis revealed concurrent downregulation of T cell activation, T cell differentiation, and NK cell-mediated immunity in the triple-exposure subgroup -- consistent with an inflamed but functionally suppressed tumor microenvironment. Preliminary integration with an independent single-cell RNA-sequencing dataset of HNSCC patients undergoing neoadjuvant PD-1/CTLA-4 blockade further suggested enrichment of granulocyte and regulatory T cell populations among non-responding patients. Survival differences between cohorts were also observed, likely reflecting biological heterogeneity driven by distinct etiologies and differences in clinical presentation across exposure groups. Together, these findings provide early insights into how multi-etiological exposure burden may shape PD-L1 axis dysregulation and immune microenvironment remodeling in HNSCC, with potential implications for patient stratification in checkpoint inhibitor therapy.

cancer biology↗

bioRxiv2026

Gut Microbiota-derived Acetate Safeguards the Colonic Epithelial Acetyl-CoA Reserve to Avert Colonic Senescence

Aging is a major driver of tissue senescence, but little is known about the development of age-unrelated tissue senescence. Here we show that nucleocytosolic acetyl-CoA deficiency in colon epithelial cells, caused by Acly ablation and bacterial depletion, triggers age-independent, p53-dependent colonic senescence leading to severe systemic inflammation. Acetate supplementation, acetate-producing bacterial transplantation, targeted depletion of senescent cells or treatment with lysine deacetylase inhibitors blocks colonic senescence and inflammatory injury. Spontaneous colonic senescence develops following simultaneous deletion of epithelial Acly and Acss2, confirming that microbe-derived acetate maintains the epithelial acetyl-CoA pool via ACSS2 to avert colonic senescence. Mechanistically, acetyl-CoA deficiency deprives a cohort of mitochondrial and nuclear proteins of acetylation, leading to increased oxidative stress and DNA repair stress that trigger cellular senescence. Among these proteins, ATP5F1A-K161 acetylation and H4-K5/8 acetylation are required to protect colonic epithelial cells from developing senescence. These observations unveil a previously unknown mechanism that governs colonic senescence.

physiology↗

bioRxiv2026

High Purity Differential Expression of Genes across Spatial Domains

Spatial transcriptomics maps gene expression within tissue architecture, offering deep insights into cellular function. A key yet overlooked phenomenon is the systematic imbalance in gene regulation within spatial domains, contrasting with traditional analyses. We define and validate this as a prevalent hallmark--High-Purity Differential Expression (HiP-DEP)--where genes in a domain shift predominantly in one direction (i.e., predominantly up- or downregulated). We introduce a Spatial Purity index to quantify it. Analysis of 190 diverse datasets across diverse tissues, diseases, and technologies revealed that spatial domains possess significantly higher purity than conventional bulk (p = 5.4 x 10-11) or single-cell data (p = 6.9 x 10-14), establishing HiP- DEP as a core hallmark of spatial biology. Using our HiP-DEP framework, we show its utility in: decoding core oncogenic regulation and its spatial gradient in breast cancer; uncovering hidden phenotypic divergence between morphologically similar Alzheimers plaques; and identifying active cellular communication niches in normal brain tissue. By shifting focus from individual genes to coordinated transcriptional programs, HiP-DEP provides a new paradigm for precision spatial omics analysis.

bioinformatics↗

bioRxiv2026

Inducible nitric oxide synthase (iNOS) regulates skin eschar lesions, bacterial persistence, and inflammatory resolution in mouse models of scrub typhus

Orientia tsutsugamushi (Ot) is an obligately intracellular bacterium that causes scrub typhus, a potentially severe infectious disease characterized by systemic inflammation and multiorgan dysfunction. We recently reported a protective role for IFN-{gamma} signaling in host defense against Ot infection; however, the underlying mechanisms remain obscure. Inducible nitric oxide synthase (iNOS, encoded by Nos2) is a key antimicrobial effector induced downstream of IFN-{gamma} signaling. Here, we used transgenic mouse models to further investigate the biological functions of iNOS. We first revealed the requirement of iNOS for the restriction of Ot growth in cultured bone marrow-derived macrophages. Using an intradermal mouse model, we found that while tissues of Nos2-/- and wild-type mice exhibited comparable bacterial burdens during acute infection phases, Nos2-/- mice developed eschar-like lesions similar to those observed in Ifngr1-/- mice, indicating a critical role for the IFN-{gamma}/iNOS axis in regulating skin pathology in scrub typhus. Notably, Nos2-/- mice displayed impaired bacterial clearance during the recovery phase (day 42), with persistent bacterial burdens in multiple organs accompanied by sustained immune activation and elevated inflammatory responses. Histopathological and biochemical analyses further revealed increased tissue damage and dysregulated physiological homeostasis in Nos2-/- mice during recovery. Mechanistically, iNOS deficiency resulted in heightened myeloid cell activation and prolonged expression of proinflammatory mediators, suggesting a dual contribution of iNOS in both antimicrobial defense and inflammation resolution. Collectively, these findings provide new insight into IFN-{gamma}-mediated defense mechanisms and imply the distinct roles of iNOS during different stages of scrub typhus. Author summaryScrub typhus is a potentially severe infectious disease caused by the bacterium Orientia tsutsugamushi (Ot), which is transmitted to humans through the bite of infected mites. Despite its global impact and expanding geographic distribution, the immune mechanisms that protect against this infection remain incompletely understood. In this study, we examined the role of inducible nitric oxide synthase (iNOS), an immune effector molecule that helps the host control infection. Using mouse models, we found that iNOS plays dual and stage-specific roles during Ot infection. Mice lacking iNOS developed dysregulated immune homeostasis during acute infection and exhibited skin lesions resembling the eschars observed in some patients with scrub typhus. In addition, these mice showed delayed bacterial clearance, prolonged inflammation, and increased tissue damage during the recovery phase. Our findings indicate that iNOS contributes not only to host antimicrobial defense but also to the control of excessive inflammation following infection. These results provide new insight into host defense mechanisms in scrub typhus and may help inform future therapeutic or preventive strategies.

immunology↗