Biology subjects

Fan, Y.

Publications and source records attributed to Fan, Y..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Patient-Calibrated Dynamical Modeling and Embedded Trend-Zone Predictive Control for Closed-Loop Deep Brain Stimulation in Parkinson's Disease

Closed-loop deep brain stimulation (cDBS) for Parkinsons disease requires control strategies that tolerate noisy sensing, patient-specific stimulation responses, medication-related fluctuations, and embedded hardware constraints. We developed a patient-calibrated minute-scale dynamical model of subthalamic beta activity and an embedded explicit trend-zone predictive controller, eTZPC. The model combined a basal-ganglia mechanistic prior with stimulation-amplitude and medication-cycle recordings from five patients, and incorporated individualized stimulation-{beta}STN maps, fast- and slow-timescale stimulation responses, levodopa-related modulation, background drift, and observation noise. eTZPC was designed to maintain {beta}STN activity within a patient-specific target zone under stimulation-amplitude, step-size, and quantization constraints. Compared with dual-threshold (DT) and proportional-integral-derivative (PID) controllers across four disturbance scenarios, eTZPC achieved target-zone regulation close to PID while reducing stimulation-switching burden toward the low-switching profile of DT. Ablation analyses identified distinct contributions of smoothing, trend prediction, patient-specific action modeling, and embedded explicit implementation. Parameter-mismatch tests showed that eTZPC was relatively robust to dynamic and disturbance-parameter deviations, but remained sensitive to errors in the steady-state stimulation-{beta}STN map. Patient-in-the-loop recordings in five patients further confirmed execution consistency and compliance with stimulation-boundary and step-size constraints. These findings support patient-calibrated dynamical modeling combined with low-complexity explicit control as a feasible framework for further embedded cDBS evaluation.

neuroscience↗

bioRxiv2026

AAV tools enable functional modulation and readout of central and peripheral nervous systems in spiny mice

Among mammals, spiny mice (Acomys spp.) exhibit the unique capacity to regenerate parts of their nervous system. Studying this phenomenon has the potential to reveal new targets that can slow or halt human neurodegenerative disorders. Unfortunately, research tools (e.g., transgenic lines, gene delivery vehicles) are lacking compared to those available for other rodent models. Here, we tested systemic adeno-associated viral vectors (AAVs) in Acomys dimidiatus and identified three promising candidates: X1.1, CAP-Mac, and MaCPNS1. Characterizing their tropism following intravenous delivery, we found that in the brain, MaCPNS1 and X1.1 primarily transduced astrocytes. In the peripheral nervous system, MaCPNS1 efficiently transduced dorsal root ganglia, axon bundles of the ear pinnae, and enteric neurons throughout the gastrointestinal tract. As a proof-of-concept, we used MaCPNS1 to chemogenetically modulate the activity of enteric neurons, successfully decreasing gastric motility in vivo and increasing colonic motility ex vivo. We expect these findings to enable functional studies of the uniquely regenerative nervous system of Acomys, which may in turn help advance neuroregenerative therapeutics for humans. Summary StatementIdentification of an AAV tool to efficiently deliver transgenes to the central and peripheral nervous systems of spiny mice enables functional studies of the nervous system in a mammalian model of regeneration.

neuroscience↗

bioRxiv2026

Still standing: persistence traits capture belowground plant functions beyond resource exploration and acquisition

Belowground plant trait research has predominantly focused on trade-offs in fine root traits via the root economics space. Yet, this fine root framework captures only a fraction of the functional strategies plants employ beneath the soil surface. Here, we broaden the perspective on belowground plant functioning by integrating traits related to root system extent, clonality and bud banks, using data from the new UNDERPLOT database. This integration links measurable traits to key belowground functions: resource acquisition, spatial exploration, and persistence. Our analysis shows that the fine root economics space explains less than 5% of the variation in traits related to root system extent, clonality, and bud banks. Instead, an expanded trait analysis reveals three significant dimensions, explaining 62% of total trait variation. The third dimension, represents an independent, persistence-related gradient, not captured by existing root economics frameworks. We propose that understanding belowground plant strategies requires embracing additional functional gradients. The strategy of persistence, in particular, varies significantly across growth forms and is a critical dimension of plant response to resource limitation and stress, becoming increasingly important as global change shifts disturbance regimes.

plant biology↗

bioRxiv2026

Contrast-induced changes in chemical exchange saturation transfer MRI differentiate tumor progression from pseudoprogression

Tumor pseudo-progression (PsP) refers to an initial increase in tumor size or the appearance of new lesions. These pseudo-progressive lesions are predominantly composed of infiltrative inflammatory cells, such as macrophages. This phenomenon commonly occurs in patients undergoing radiation therapy or immunotherapy and typically indicates a positive treatment response. However, it often leads to premature treatment cessation due to misinterpretation as disease progression. Non-invasive imaging biomarkers capable of distinguishing pseudo-progression from true progression would greatly aid in treatment decision-making. In our preliminary study, we explored the potential of gadoterate meglumine (Gd-DOTA, a macrocyclic Gd-contrast) in combination with amine chemical-exchange saturation transfer (amine-CEST) imaging to differentiate tumor from radiation necrosis by assessing Gd-DOTA uptake by infiltrating immune cells, such as macrophages. To evaluate whether amine-CEST, in combination with Gd-DOTA, can differentiate macrophages from cancer cells, we incubated them with Gd-DOTA for 30 minutes. Subsequently, the cells were processed, and amine-CEST imaging was performed on a 9.4 Tesla preclinical scanner. Upon treatment with Gd-DOTA, we did not observe a significant change in amine-CEST contrast in F98 cells compared with untreated cells, whereas treated macrophages exhibited a marked decrease ([~]40%) in amine-CEST signal compared with untreated macrophages. This reduction in signal was attributed to the uptake of Gd-DOTA by macrophages, which notably shortened water T1 relaxation, thereby quenching the amine-CEST signal. Conversely, cancer cells showed no appreciable change in the amine-CEST signal, indicating no Gd-DOTA uptake. Furthermore, to validate that T1 shortening influences amine-CEST signal, cancer cells were also treated with manganese chloride (MnCl2) for 30 minutes. The uptake of MnCl2 by cancer cells similarly induced T1 shortening, as observed in macrophages, resulting in a decrease in the amine-CEST signal from these cells. Next, we performed the amin-CEST imaging on F98 tumor-bearing rats and radiation necrotic rats. Post-injection with Gd-DOTA showed no appreciable change in the amine-CEST contrast in the tumor-bearing rat, whereas a significant decrease in contrast was observed in the radiation necrotic rat. This further demonstrates that no change in the amine-CEST contrast in tumor-bearing rats is due to cancer cells failing to take up Gd-DOTA. The decrease in amine-CEST contrast in radiation-treated rats reflects the uptake of Gd-DOTA by macrophages infiltrating the radiation-necrotic regions. This straightforward imaging approach holds promise for clinical translation. It offers a novel method for characterizing pseudo-progressive lesions and monitoring diverse treatment responses in cancer patients using standard clinical scanners.

cancer biology↗

bioRxiv2026

Droplet-compatible single-cell DNA methylation sequencing with PreTIC

Single-cell DNA methylation sequencing has remained technically specialized due to challenges of interfacing conversion chemistry with droplet microfluidics. We introduce pre-tagmentation in situ conversion (PreTIC), which enables whole-methylome profiling on a commercial droplet platform using off-the-shelf reagents. With PreTIC, we produce over 13,000 single-cell methylomes from fixed frozen cells in two days and resolve cell-specific epigenetic variation in human peripheral blood mononuclear cells.

genomics↗

bioRxiv2026

TIM3+ Tumor Associated M2 Macrophages Impair Antitumor T Cell Immunity and Promote Gastric Cancer Progression and Peritoneal Metastasis

Peritoneal metastases (PM) are the leading cause of cancer-related death in gastric cancer (GC) patients with survival typically < 9 months. Here, we demonstrate that TIM3 and its ligands are increased along the GC continuum and associated with poor survival. Integrated omics analyses and functional studies revealed highly enriched TIM3 in CD163+ tumor associated M2 immunosuppressive macrophages significantly promote tumor cell invasion and tumor growth in vivo, while TIM3 depletion in macrophages reduced tumor cell malignant attributes and increased T cell immunity from PBMCs or CD45+ immune cells of malignant ascites in co-culture system. By cytokine and kinase arrays, we discovered that depletion of TIM3 in macrophages reduced the production of notable secretome of cytokines/chemokines from M2 macrophages; and the protumor function of TIM3+ macrophages rely on the p90RSK1/2/CCL20 axis. Finally, we reveal that TIM3 blockage or genetic KO had superior antitumor activity in combination with anti-PD1 immunotherapy and mitomycin C (MMC) chemotherapy. Together, this study uncovers an important role for TIM3 in tumor associated M2 macrophages and underscores the potential of TIM3 blockage in GC patients with PM. Statement of significanceIn this study, we show TIM3 increases along GC continuum, and highly enriched on tumor associated M2 macrophages that fuel tumor growth; and suppress T cell function via p90RSK1/2/CCL20 axis. TIM3 depletion restores T-cell immunity and curbs tumor growth. TIM3 blockade combined with anti-PD1 and mitomycin C provide a novel therapeutic strategy for GC patients with PM.

immunology↗

bioRxiv2026

ARID1A deficiency unleashes centromeric RNA transcription to drive chromosomal instability and boosts PKMYT1 inhibitor efficacy via RNA sensing

Cancer gene-associated mutations and molecular hallmarks of chromosomal instability (CIN) are unexpectedly common in histologically normal cells and tissues. These emerging findings challenge the binary distinction between "normal" and "cancerous" cells and suggest that early tumorigenesis may commence against a background of widespread yet largely tolerated genomic instability. However, it remains largely unexplored how a cancer gene-associated mutation can initiate the development of CIN-like states in non-malignant cells and drive tumor evolution. ARID1A, a chromatin remodeling factor, was identified as the most frequently mutated gene in both gastric normal epithelium and tumors. This distinctive molecular convergence presents an opportunity to elucidate the mechanisms by which a cancer-associated gene facilitates the initiation of early CIN phenotypes and develop effective antitumor strategies. In the present study, using primary human gastric organoids, we employed optical genome mapping (OGM) and live-imaging technologies to demonstrate that ARID1A depletion induced a wide spectrum of structural variants (SVs), copy number variants (CNVs), and chromosomal segregation errors, characteristic features of CIN at a very early stage of gastric tumorigenesis. Mechanistically, ARID1A bound centromere repetitive satellite DNA (satDNA) sequences. Its SWI/SNF-associated chromatin remodeling activity was required for suppressing satDNA transcription and the production of -SatRNA, through restricting RNAPII elongation. Consequently, ARID1A depletion led to overexpression of -SatRNA, and a higher incidence of sister chromatid exchange (SCE), a sensitive indicator of CIN. Importantly, the elevated -SatRNA expression in ARID1A-deficient cells further established a dual therapeutic vulnerability for G2/M checkpoint blockade, such as PKMYT1 inhibitor (PKMYTi), by concurrently aggregating CIN-induced cell death and activating self-dsRNA sensing-mediated innate immune response. Notably, PKMYTi markedly promoted -SatRNA expression, aberrant release of these self-derived dsRNAs into the cytosol and a robust activation of the RIG/MDA5-MAVS-depenent type-I interferon response in ARID1A-depleted cells. As expected, PKMYTi potentiated the efficacy of immunotherapy in ARID1A-deficient gastric tumors. Together, our findings reveal that ARID1A deficiency unleashes centromeric -SatRNA transcription, which sets the molecular stage for tumor evolution and targeted therapy by coordinately inducing CIN and self-dsRNA-induced innate immune responses.

cancer biology↗

bioRxiv2026

Mapping developmental patterns of intrinsic timescale

Intrinsic timescale is a commonly used measure of spontaneous neural dynamics that quantifies the temporal window of processing of neuronal populations. Intrinsic timescale displays a hierarchical cortical organization across multiple species and imaging modalities, with shorter timescales in sensorimotor cortex compared to association cortex. However, less is known about how intrinsic timescale evolves during human brain development and whether its cortical maturation patterns generalize to independent developmental samples. Here we estimate the intrinsic timescale in two independent cross-sectional datasets of youth (HCPD: n=565; HBN: n=729; age range 8-22 years) and investigate its neurodevelopmental patterns. We find that developmental patterns in the intrinsic timescale follow a hierarchical pattern that recapitulates an axis spanning sensorimotor to association cortices (S-A axis). Our analysis of an independent healthy young adult dataset (HCPYA: n=973, age range 22-37 years) underscores the specificity of these developmental findings, suggesting that the intrinsic timescale develops along the S-A axis in youth and stabilizes in adulthood. Together, these results reveal convergence between major axes of cortical organization and development, highlighting intrinsic timescale as a principled marker of hierarchical brain maturation in youth.

neuroscience↗

bioRxiv2026

SPTBN2 promotes an immunosuppressive tumor microenvironment and cross-resistance to anti-cancer therapies

Immunosuppressive tumor microenvironment (TME) inactivates CD8+ cytotoxic lymphocytes (CTLs). Here, we identify SPTBN2 spectrin as a key immunosuppressive regulator induced in CTLs in response to nutritional deficit. In human pancreatic and colorectal cancers, SPTBN2 expression negatively correlated with CTL infiltration and patients survival. In TME of mouse pancreatic and colorectal adenocarcinomas, SPTBN2 inactivated intratumoral CTLs, stimulated tumor growth and conferred cross-resistance to anti-cancer therapies. SPTBN2 knockout protected CAR T-cells from trogocytosis and increased their memory state. SPTBN2 maintained levels of cell surface proteins such as BTLA that undermine CAR T-cell cytotoxicity and promote exhaustion. Re-expression of BTLA largely reversed phenotypes in SPTBN2-deficient CAR T-cells. In manufactured CAR T cells, SPTBN2 was associated with their clinical failure in pediatric patients with leukemia. Accordingly, ablation of SPTBN2 in CAR T-cells increased their cytotoxicity, in vivo persistence and therapeutic effects indicating that SPTBN2 can be targeted to increase the efficacy of anti-cancer therapies.

cancer biology↗

bioRxiv2026

Complete Genomes of Cultivated Gut Bacteria Reveal Mobile Genetic Element-Driven Functional Diversity with Therapeutic Implications

Cultivated bacterial isolates are essential for elucidating gut microbiota functions, yet reliance on fragmented draft genomes and limited mobile genetic element (MGE) annotation has constrained high-resolution analyses. Here, we present the Cultivated Complete Genome Reference (CCGR), a comprehensive compendium of 1,150 fully circularized human gut bacterial genomes. Overcoming draft limitations, CCGR achieves chromosome-scale resolution and reveals distinct evolutionary strategies shaping gene topological organization in response to bacterial growth. Furthermore, we decode the dynamic landscape of MGEs, demonstrating that broad-host-range phages follow strict positional patterns by integrating at conserved chromosomal hotspots flanked by nutrient transporter loci. Importantly, we provide mechanistic in vivo evidence that accessory genomic elements drive strain-level functional heterogeneity. Specifically, the plasmid-encoded scrK gene in Levilactobacillus brevis involved in fructose catabolism is required to mitigate fructose-diet-exacerbated colitis. Collectively, CCGR establishes a framework linking chromosomal architecture and MGEs to bacterial evolution and host health, enabling precise, strain-resolved functional investigations.

microbiology↗

bioRxiv2026

Single-cell atlas of pig-to-monkey kidney xenotransplantation reveals macrophage chimerism and an IFN-ε orchestrated graft protective immune niche

The clinical translation of xenotransplantation is constrained by an incomplete understanding of the cellular circuitry governing graft rejection versus adaptation under current immunosuppressive regimens. Here, we present a high-resolution single-cell atlas of pig-to-monkey kidney xenotransplantation in a preclinical model, capturing the early immune dynamics preceding graft loss. Our analysis reveals a landscape dominated by innate immunity, characterized by species-specific distribution of macrophages. We identify recipient-derived macrophage subsets (ACKR1+, FN1+, MARCO+, IDO1+) enriched for multiple immune checkpoint molecules, alongside donor-resident subpopulations (APOE+, CCL2+, IL-1A+) exhibiting pro-inflammatory pathogenic signatures, and leverage their transcriptional profiles to computationally predict candidate therapies (belatacept, abatacept, pexidartinib). Further analysis demonstrates that despite divergent differentiation trajectories, both recipient-derived and donor-resident macrophages converge toward hybrid M1/M2 states at their terminal stages. Notably, we uncover a graft-protective circuit orchestrated by epithelial-derived interferon-epsilon (IFN-{varepsilon}), which specifically engages multiple subsets including IDO1+ macrophages to establish a localized immune-tolerant niche. This study establishes the xenograft epithelium as an active participant in immune modulation via the IFN-{varepsilon} axis and reveals macrophage functional chimerism as a key actionable feature of cross-species immune responses.

genomics↗

bioRxiv2026

High-channel-count neural recording and stimulation platform with 5,376 simultaneous recording channels

Advancing neural interfaces requires large-scale, high-density recording technologies capable of capturing full-spectrum neural activity across cortical and subcortical regions. Here, we present a scalable approach to integrate neural electrodes with advanced application-specific integrated circuits (ASICs). Specifically, we custom-designed an ASIC with 5,376 simultaneous channels, each sampling at 20 kS/s and enabling >1.3 Gb/s total data streaming throughput. The ASIC incorporates in-pixel amplification, time-division multiplexed ADCs, and on-chip stimulation capabilities, ensuring precise signal acquisition with minimal power consumption while maintaining a low noise level of 5.5 {micro}Vrms. We further developed an interconnect strategy using gold bump bonding, which allows for high-density integration of the flexible probe and rigid chip. We demonstrate the capacity of this platform through the integration with a flexible ECoG array. The resulting device allows for the high-resolution mapping of in vivo field potentials on the cortical surfaces of rat brains, supported by the precise localization of evoked sensory activities. These results prove an effective approach towards highly integrated neural interfaces with applications in brain-computer interfaces, neuroprosthetics, and large-scale functional brain mapping.

bioengineering↗

bioRxiv2026

The intercellular transfer of extracellular vesicles markers CD63, CD9 and CD81 is spatially polarized and restricted to cell vicinity

Extracellular vesicles (EVs) are small lipid structures secreted by cells that originate from the cell surface (typically enriched in the tetraspanin (tspan) CD9) or from multivesicular bodies (typically enriched in the tspan CD63). Current methods for studying EVs involve concentrating and purifying EVs, without providing information about the distance or amount of EVs that may transfer from one cell to another. Here, we developed a coculture assay of human mammary MCF-7 cells to study the transfer of mCherry-CD81 or mCherry-CD9 from "donor" cells to a lawn of "acceptor" cells stained with cell tracker blue or green (CTB/CTG), non-transferrable fluorescent dyes. Using confocal fluorescence microscopy, we observed the presence of spots containing mCherry-CD81 or mCherry-CD9 outside donor cells, concentrated at short distance from donor cells and that overlapped with CTB signal, suggestive of their internalization in acceptor cells. Endogenous CD63, CD81 and CD9 also transferred more efficiently at short distances, even in the presence of a flow, as shown by immunostaining cocultures of wild type and KO CD-63, or -9, or -81 cells with antibodies directed against these tspans. Computation of the (x,y,z) coordinates of tspans-containing spots revealed a double polarized transfer: in (x,y), it distributed along a gradient that started from donor cells and decreased with the distance, and in (z), it was stronger in basal compared to upper planes, a (z) polarization that was affected by syntenin-1 depletion in donor cells. Simultaneous monitoring of CD9/CD81 transfer from into double CD81/CD9 KO cells showed that cells transferred more CD81 spots than of CD9. At the basal level, CD63 and CD81 spots were plasma membrane derived as they almost always contained CD9+, and resembled membranous remnants of migration. However, live cell imaging showed migration independent secretion of EVs in the extracellular space, in upper planes. Altogether, not only is our coculture assay suitable for the direct qualitative and quantitative study of EV-transfer, but it highlighted shared three-dimensional features of EV markers transfer between cells.

cell biology↗

bioRxiv2026

Critical assessment of intratumor and low-biomass microbiome using long-read sequencing

The detection of low-biomass microbial DNA in human tissues is often confounded by contamination, as demonstrated in the debates over the existence of microbiomes in the placenta, brain, blood, and tumors. Here we show that genomic DNA fragment length serves as a discriminator: while genuine microbiome genomes have long genomic DNA fragments, contaminant DNA is typically short. Using germ-free mouse tissues with bacterial spike-ins and human cell lines, we developed a metric that normalizes microbial read length to host read length. Across multiple human tumor and normal tissues, we found genuine microbiome signals are largely limited to tissues with natural microbial exposure (e.g., gastrointestinal tract, cervix, vagina, skin), while other tissues (e.g. kidney, brain, blood, and placenta) showed no evidence of resident microbiome. These findings support DNA fragment length as a metric for quality controlling low-biomass microbiome profiling, clarifying the debates and strengthen future studies of resident microbiome in tissues.

genomics↗

bioRxiv2026

Calcium directs actin assembly via allosteric activation of formin INF2

Calcium signals spatiotemporally orchestrate cytoskeletal dynamics, typically through Rho GTPase-mediated signaling cascades, yet the direct molecular transducers that convert local calcium transients into spatially controlled actin assembly have remained elusive. Here, we uncover a structure-based mechanism by which calcium-bound calmodulin (Ca2+-CaM) directly activates formin INF2 to drive actin assembly. We demonstrate that Ca2+-CaM binds to the diaphanous inhibitory domain (DID) of INF2 with nanomolar affinity, inducing allosteric conformational changes that sterically disrupt INF2 autoinhibition. The unexpected bipartite Ca2+-CaM binding interface on INF2 enables ultrasensitive decoding of local calcium microdomains, such as ER-mitochondrial contacts, where activated INF2 promotes actin polymerization to facilitate mitochondrial fission. We further show that the Charcot-Marie-Tooth disease-associated INF2 R91G mutation enhances Ca2+-CaM binding via optimized interfacial dynamics, suggesting a gain-of-function disease mechanism. Our work establishes the Ca2+-CaM-INF2 axis as a direct molecular transducer linking spatial calcium signals to actin-dependent organelle dynamics, defining a Rho-GTPase-independent paradigm for calcium-cytoskeleton communication, with broad implications for INF2-linked pathologies.

biochemistry↗

bioRxiv2025

PocketX: Preference Alignment for Protein Pockets Design through Group Relative Policy Optimization

Designing protein pockets that target specific ligands is crucial for drug discovery and enzyme engineering. Although deep generative models show promise in proposing high-quality pockets, they are usually trained purely to match the data distribution and therefore overlook key biophysical properties, such as binding affinity, expression, and solubility, that ultimately determine developability and success. We introduce PocketX, an online reinforcement learning framework that explicitly aligns a generative model with desired biophysical properties. The framework first trains a base model that co-designs pocket structures and sequences conditioned on a target ligand, and then fine-tunes this model with Group Relative Policy Optimization (GRPO) to reward the desired attributes. Because GRPO employs group-relative rewards, it produces lower-variance policy updates, resulting in more stable and efficient learning than competing alignment strategies. Evaluated on the CrossDocked2020 benchmark, PocketX surpasses existing methods in metrics such as binding energy and evolutionary plausibility. Ablation studies further show that GRPO outperforms alternative alignment strategies, including Direct Preference Optimization (DPO), confirming GRPOs effectiveness for biophysical property alignment.

bioinformatics↗

bioRxiv2025

Decoupling Efficacy from Toxicity: Engineering Spatial Control in AAV-Mediated Gene Therapy

Hepatotoxicity poses a critical safety challenge for AAV-mediated gene therapy. To mitigate this, we evaluated strategies to minimize off-target hepatic transduction using an antibody expression model. We compared (i) muscle-restricted wild-type AAV9 expression and (ii) a novel myotropic capsid variant, AAV.eM. In humanized B-NDG mice bearing Raji-Luc lymphomas, intravenous administration of AAV9-MHCK7 encoding an CD19CD3 bispecific T-cell engager failed to reduce tumor burden. Conversely AAV.eM-MHCK7-CD19CD3 substantially alleviated tumor burden and achieved lymphoma clearance. By leveraging tissue-specific microRNAs, precise restriction of AAV.eM-mediated transgene expression to skeletal or cardiac muscle was achieved. Incorporating a heart-specific miR-208a binding site into the transgenes 3UTR did not compromise therapeutic efficacy when delivered via AAV.eM-MHCK7. Intramuscular delivery of AAV9-MHCK7-CD19CD3 or AAV.eM-MHCK7-CD19CD3 both cleared Raji-Luc tumors at a dose of 5 x 1012 vg/kg, underscoring the advantage of localized and targeted rAAV delivery over systemic administration. Notably, only AAV.eM-MHCK7-CD19CD3 achieved tumor eradication at a tenfold lower intramuscular dose (5 x 1011 vg/kg), reducing manufacturing costs and risks of dose-dependent immunogenicity and toxicity. Our findings demonstrate that combining tissue-specific targeting--via engineered capsids or tissue-selective promoters--with local delivery robustly reduces off-target hepatic expression, providing a strategic framework for enhancing the safety of AAV-based gene therapies.

cancer biology↗

bioRxiv2025

Eosinophil-derived COX-2 protects against experimental colitis through the PGE2-IL-22 axis

Inflammatory bowel disease (IBD) is driven by a breakdown in immune regulation and epithelial barrier function, yet the contribution of eosinophils to this process has remained poorly defined and controversial. While eosinophils infiltrate the intestinal mucosa during both flares and remission, their role in shaping disease outcomes is unclear. Our RNA-seq analyses of colonic eosinophils isolated from dextran sulfate sodium (DSS)-treated mice revealed a significant upregulation of cyclooxygenase (Cox)-2 (gene name, Ptgs2). Eosinophil-specific deletion of Cox-2 (Ptgs2fl/fleoCre+/-) reduced IL-22 production and exacerbated DSS- and trinitrobenzene sulfonic acid (TNBS)-induced colitis, characterized by greater weight loss, higher disease activity, colon shortening, and epithelial injury. Administration of recombinant IL-22 reversed these phenotypes. Mechanistically, eosinophil-derived COX-2 enhanced IL-22 production by type 3 Innate lymphoid cells (ILC3s) through prostaglandin E2 (PGE2) signaling. Consistently, Ptgs2fl/fleoCre+/-mice exhibited reduced colonic PGE2 levels, while PGE2 analog treatment restored IL-22 production and mucosal protection. Our findings identify eosinophil-derived COX-2 and PGE2 as a critical regulator of IL-22 production during colitis, uncovering a previously unrecognized eosinophil-ILC3 crosstalk that safeguards the intestinal barrier and represents a promising therapeutic target in IBD. Significance StatementThe role of eosinophils in inflammatory bowel disease (IBD) has remained unresolved. We identify eosinophil-derived COX-2 as the main source of prostaglandin E2 (PGE2) in colitis, which drives IL-22 production by ILC3s to maintain epithelial protection. This discovery defines a protective eosinophil/PGE2/IL-22 circuit and reveals a therapeutic target to strengthen barrier defense in IBD.

immunology↗