Biology subjects

Gong, Y.

Publications and source records attributed to Gong, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Scalable methylome-transcriptome profiling resolves clonal organization in human hematopoiesis

Understanding human tissue maintenance and remodeling requires linking clonal ancestry to molecular state, yet scalable joint measurement remains challenging. Here, we introduce Droplet-MT and an integrated computational workflow for joint transcriptome and methylome profiling at ~10,000 cells per library. Methylation epimutations enable mutation-independent clonal reconstruction from high-coverage methylomes, while reference-based label transfer assigns cells to established clones at ~0.2% CpG coverage, reducing sequencing cost. Clone-aggregated somatic variants provide genetic annotation without additional single-cell genotyping. Across ~21,000 paired profiles from healthy blood and longitudinal acute myeloid leukemia, we resolved small and expanded clones with heterogeneous lineage output. In leukemia, the framework distinguished changes in malignant clonal abundance, state remodeling within persistent clones, and recovery of healthy polyclonal hematopoiesis. Malignant monocytes remained transcriptionally and epigenetically distinct from healthy and recovery-associated cells despite treatment-associated remodeling. Droplet-MT enables scalable analysis of human tissues by linking clonal organization with molecular state and retrospective genetic annotation.

genomics↗

bioRxiv2026

Autophagosome-tethering compounds selectively lower mutant ataxin-3 in preclinical models of spinocerebellar ataxia type 3

Spinocerebellar ataxia type 3 (SCA3) is most common subtype of autosomal dominant spinocerebellar ataxia worldwide and the most prevalent CAG expansion disorder in the east Asian population, but disease-modifying therapies remain unavailable. SCA3 is caused by the accumulation of polyglutamine- (polyQ-) expanded mutant ataxin-3 (mAtxn3), while the wild-type ataxin-3 (wtAtxn3) plays an important cellular role. Thus, allele-selective clearance of mAtxn3 without affecting wtAtxn3 is highly desired for SCA3 treatment. To achieve this goal, we tested previously reported compounds that have been shown to selectively degrade the Huntingtons disease causing mutant HTT protein by tethering the expanded polyQ to the autophagosome protein LC3. Here, we demonstrated that two of these compounds, AN2 and GW5074, selectively reduced both soluble and aggregated mAtxn3 with expanded polyQ (84Q), but not wtAtxn3, in both cellular and mouse models of SCA3. Mechanistically, both compounds lowered mAtxn3 by enhancing its autophagic degradation without obvious activation of global autophagy. At the molecular level, both compounds increased mAtxn3-LC3 interaction and colocalization to enhance the allele-selectively autophagic degradation of mAtxn3. Phenotypically, both compounds rescued cell viability and ATP content of SCA3 cellular models. In SCA3 patient pluripotent stem cells (iPSCs) derived cortical neurons, both compounds allele-selectively reduced mAtxn3 and partially rescued neurite shortening. Importantly, in a well-established SCA3 transgenic mouse model (MJD84.2), intracerebroventricular, intraperitoneal, and oral administration allele-selectively reduced mAtxn3 in multiple brain regions and rescued motor function deficits. Oral dosing achieved nanomolar cerebellar exposure and showed no overt liver, kidney, or glial toxicity over 28 days. Analyses of 1303 Chinese patients with SCA3 and ATXN3 constructs of different polyglutamine lengths further supported the compounds polyQ length-dependent activity with relative sparing of normal-length ataxin-3. Together, these findings provide preclinical proof of concept that utilizing orally available small molecule compounds to allele-selectively enhance mAtxn3 autophagic degradation for SCA3 treatment. One-sentence summarySmall-molecule autophagosome-tethering compounds selectively lower mutant ataxin-3 through an LC3- and autophagy-dependent mechanism and improve disease-related phenotypes in preclinical models of SCA3.

neuroscience↗

bioRxiv2026

Identifiable inverse optimal transport for single-cell state transitions

Signed effects of target-state programmes are unidentifiable in balanced optimal transport because fixed endpoint distributions make their contributions constant across feasible plans. We introduce UOT-IOT, a semi-relaxed inverse transport framework that restores measurable targetmass responses and provides a rank condition for local identifiability. It recovers coefficients inground-truth benchmarks (correlation 0.997 versus 0.081 for balanced transport), transfers frozen directions to six unseen samples with specificity controls, and achieves the lowest transition error against seven methods under matched evaluation conditions. GH-IOT separates shared directions from context and lineage-history offsets, revealing opposing history-associated effects. IFN/HLA is associated with patient treatment response, whereas EMT relates to drug sensitivity and perturbation-induced state changes. PERSIST-IOT improves future population-composition prediction in an independent experiment. Together, these modules distinguish current state,transition propensity and future population outcomes while supporting testable biological interpretations.

bioinformatics↗

bioRxiv2026

ctDNA Release Heterogeneity in Luminal Breast Cancer Revealed by Single-Cell Multi-Omics Spatial Analysis

Backgroud Breast cancer is a leading cause of cancer-related mortality, and HR+/HER2-; is the predominant subtype. Molecular pathology, including PIK3CA and ESR1 mutation, informs prognosis and treatment selection. Circulating tumor DNA (ctDNA) offers a non-invasive approach for cancer monitoring, but its clinical utility is limited by tissue plasma discordance, reflecting heterogeneous ctDNA release. The cellular and spatial determinants of this release remain poorly understood, particularly in HR+/HER2-; subtype, where heterogeneity across subclones complicates liquid biopsy interpretation. Results To identify the cellular and spatial determinants of ctDNA release, we developed scMASTER, integrating single-cell transcriptomes and mutations, spatial transcriptomics and matched tumor and plasma DNA sequencing. In ten patients with non-metastatic HR+/HER2- breast cancer, eight recurrent malignant epithelial states showed distinct ctDNA release potential. Antigen-presentation, stress, mitosis and mesenchymal-like states showed high release. PIK3CA and ESR1 mutations were linked to distinct functional states and altered ctDNA detectability. Three spatial architectures, EMT-enriched regions, intraductal luminal progenitors and avascular hypoxic zones, showed high release. Tumor-microenvironment interactions were bidirectional: anti-tumoral immunity correlated with reduced release, whereas immunomodulatory components correlated with increased release. A stratification model based on these features identified high-risk, immunosuppressed patients with poor prognosis, validated across external cohorts. Conclusions Our study establishes a single-cell spatial framework for decoding ctDNA release heterogeneity, linking tumor states, somatic mutations, spatial architecture, and immune interactions to ctDNA release. These findings provide mechanistic insights into tissue-plasma discordance, offer a biological rationale for interpreting ctDNA dynamics, refine patient risk stratification and liquid biopsy-based monitoring in HR+/HER2-; breast cancer.

cancer biology↗

bioRxiv2026

Transthyretin Contributes to Hippocampal Blood-Brain Barrier Recovery Following Intestinal Inflammation, with Reduced Expression in Alzheimer's Disease

Background: The blood-brain barrier (BBB) is increasingly recognized as an active immunoregulatory interface that responds dynamically to systemic inflammation. As intestinal inflammation can influence brain homeostasis through the gut-brain axis, the endogenous mechanisms that preserve BBB integrity during gut-derived inflammatory stress remain poorly understood. Methods and Results: We combined dextran sulfate sodium-induced colitis, fecal microbiota transplantation, aged mice, APP/PS1 mice, human Alzheimer's disease (AD) brain tissue, single-cell RNA sequencing, in vivo BBB permeability assays, and gain- and loss-of-function approaches to investigate adaptive neurovascular responses to gut inflammation and their mechanism in maintaining BBB integrity. Intestinal inflammation induced a region-specific adaptive response characterized by increased hippocampal vascular remodeling and partial restoration of BBB integrity following the initial inflammatory insult. Single-cell transcriptomic analysis identified a transthyretin (TTR)-enriched vascular-associated microglial state accompanying these neurovascular changes. Functional studies demonstrated that TTR contributes to maintaining BBB integrity by promoting endothelial homeostasis and limiting endothelial endocytosis, consistent with modulation of FcRn-associated transport pathways. This adaptive neurovascular response was progressively attenuated in aged mice and APP/PS1 mice and was accompanied by reduced vascular TTR expression in human AD brains. Conclusion: These findings identify TTR as a contributor of adaptive neurovascular homeostasis during gut-derived neuroinflammation. Impairment of this homeostatic response with aging and AD may contribute to persistent BBB dysfunction and chronic neuroinflammation, highlighting neurovascular resilience as a potential therapeutic target.

neuroscience↗

bioRxiv2026

BioIMA: a one-click desktop tool for standardized extraction of phenotypic traits from biological images

Standardized extraction of quantitative phenotypes from images is increasingly important across plant biology, from ecological and evolutionary studies to genetics, breeding, and functional genomics. However, as large image datasets are increasingly used for trait analysis, many biologically relevant traits, including size, shape, color, and spatial patterning, are still measured manually or using fragmented semi-automated workflows. These limitations reduce throughput, reproducibility, and accessibility, especially for researchers without computational expertise. Here, we present BioIMA, an open-source desktop tool for rapid and standardized phenotyping from biological images. BioIMA integrates foundation model-based segmentation with automated trait computation, allowing users to extract quantitative measurements from images through an intuitive graphical interface and without model training. To validate its performance, we quantified a set of knot morphological traits in two Populus species, as these measurements are typically time-consuming to perform manually. Automatic measurements showed strong agreement with manual ImageJ-based measurements (R2 > 0.95), while reducing per-image processing time by approximately 75% (from ~15 s to ~4 s). BioIMA was further applied to diverse plant datasets, including Helianthus and Rhododendron images with varying morphologies and background conditions. Although developed for plant phenotyping, BioIMA may also be extended to other biological samples where region-based size, shape, or color traits are of interest. By combining accessibility and standardization in a lightweight local application, BioIMA provides a practical community resource for image-based phenotyping in ecological and evolutionary studies.

bioinformatics↗

bioRxiv2026

Lineage recording reveals hijacked hepatic progenitor states as a common origin of HCC and ICC

HighlightsCERAMIC enables continuous and high-capacity lineage tracing of liver tumor initiation Fatty liver-associated hepatocytes acquire regenerative and premalignant cell states before malignant transformation Lineage reconstruction identifies Hep_Bi-zonal cells as the cellular origin of liver tumor initiation Transcriptional and regulatory programs distinguish tumor-fated hepatocytes from failed-to-transform lineages Peroxisomal metabolism is required for progenitor-state formation and liver tumor initiation Spatial remodeling identifies a macrophage niche associated with tumor-fated hepatocytes Dual ontogenies and functional specialization of lipid-associated macrophages shape the tumor-fated hepatocyte niche Fatty liver disease predisposes to primary liver cancer, yet the lineage routes and niche mechanisms that select rare tumor-fated hepatocytes remain unclear. Here we developed CERAMIC, a high-capacity CRISPR-Cas9 lineage recorder that co-recovers editing scars and transcriptomes from single cells, and applied it to an AKT/NRAS-driven model of MASLD-associated liver tumor initiation. Longitudinal lineage, single-cell and spatial analyses revealed a hierarchical trajectory in which bipotential bi-zonal hepatocytes (Hep_Bi-zonal), rather than pericentral-like hepatocytes (Hep_CVlike), generated regenerative and neoplastic hepatocyte progenitor states that progressed toward both hepatocellular carcinoma and intrahepatic cholangiocarcinoma lineages. Tumor-fated cells preferentially expanded along a remodeled midlobular-periportal axis and depended on ACOX1-mediated peroxisomal beta-oxidation to withstand lipotoxic and oxidative stress. Spatial and lineage analyses further identified a sequential lipid-associated macrophage niche, in which monocyte-derived LAMs engaged tumor-fated hepatocytes through an LGALS9-P4HB axis, and P4HB inhibition suppressed tumor expansion. These findings define liver tumor initiation as a lineage-restricted process licensed by peroxisomal metabolic adaptation and macrophage-derived niche signals.

cancer biology↗

bioRxiv2026

Organ-resolved endothelial regulatory programs link aging and metabolic overload to vascular immune remodeling

Systemic aging and metabolic overload remodel the vasculature; however, how endothelial cells integrate these stresses across organs remains unclear. Using multi-organ single-cell and spatial transcriptomics with functional validation, we mapped endothelial and hematopoietic responses in adipose tissue, skeletal muscle, liver, and heart. Organ-specific endothelial transcriptional features were relatively preserved, whereas chronic stress selectively reconfigured regulatory programs: aging induced a conserved Irf/Stat-centered endothelial program, while high-fat diet engaged organ-biased lipid and remodeling programs. Spatial analysis revealed perivascular niches centered on aging-associated interferon-stimulated endothelial activation, with neighboring immune and stromal cells expressing C3 and LRP1-associated signals. Rather than simply amplifying inflammation, these niches contained mechanisms that restrained IFN activation, as C3 depletion upregulated vascular IRF7 expression. In parallel, the IFN downstream effector BST2 promoted anti-inflammatory macrophage differentiation and suppressed atherosclerosis. These findings define vascular inflammaging as an organ-resolved niche process in which endothelial IFN activation is coupled to local inflammatory restraint. HighlightsO_LIAging induces a shared endothelial type I IFN program across organs. C_LIO_LIA high-fat diet triggers organ-biased endothelial remodeling programs. C_LIO_LIPerivascular interferon niches couple inflammation with local restraint. C_LIO_LIIFN-induced endothelial BST2 promotes CD200R-associated macrophage regulatory features. C_LI

cell biology↗

bioRxiv2026

Ciz1 safeguards Drosophila wing development by suppressing oxidative stress

Cell proliferation and fate specification are fundamental processes that ensure the generation of organs with proper size and patterning. Oxidative stress caused by accumulation of reactive oxygen species (ROS) can lead to cell cycle arrest, senescence, cell death and cell fate misspecification, thereby impairing normal development and contributing to many pathological processes. In this study, we identify Drosophila Ciz1 as a critical factor that safeguards epithelial homeostasis and development by preventing oxidative stress. Knockdown of Ciz1 in the Drosophila wing imaginal disc, an epithelial tissue that serves as the larval precursor of the adult wing, results in a small wing phenotype accompanied by thickened and ectopic veins. We further demonstrate that reduced Ciz1 expression leads to accumulation of donut-shaped mitochondria and elevated ROS levels. The increased oxidative stress subsequently suppresses proliferation via activation of JNK and promotes excessive vein formation by upregulating Rhomboid, a positive regulator of EGFR signaling. Interestingly, although Ciz1 is a zinc finger protein that predominantly localizes to the nucleus, neither its zinc finger motifs nor its nuclear localization is required for suppression of oxidative stress. Instead, the prion-like domain in its N-terminal part is essential for this activity. Our work identifies Ciz1 as an important factor in preventing oxidative stress and maintaining epithelial homeostasis.

Developmental Biology↗

bioRxiv2026

Buffered sweat microfluidics with AI-enabled translation for clinically actionable blood urea estimation and renal risk stratification

Kidney-function assessment relies on blood urea as a clinically informative metabolic marker; however, its dependence on venipuncture and centralised laboratory testing limits high-frequency monitoring and delays timely clinical intervention. Here, we report an integrated platform combining a wearable buffered microfluidic patch with a physiology-informed, data-driven calibration framework for real-time, non-invasive estimation of blood urea from microlitre-scale sweat volumes (4.79 L). By precisely regulating the release kinetics of internal buffer salts, the device stabilises the local reaction microenvironment, mitigating variability in sweat pH and flow to ensure reproducible measurement. The resulting signals are processed through an artificial intelligence (AI)-enabled analysis pipeline that integrates sweat urea with patient-specific physiological information to generate clinically interpretable outputs. In multicentre studies, sweat urea shows a strong association with blood urea across diverse cohorts, but with nonlinear and time-lagged relationships that limit direct use. The AI-enabled calibration model compensates for these effects, enabling high-fidelity estimation of blood urea (r = 0.945 versus gold-standard measurements) at clinically relevant concordance levels. The platform further identifies kidney injury with 89.1% accuracy and stratifies disease severity with 83.2% accuracy. Notably, these results demonstrate that the integration of physicochemical stabilisation and AI-enabled data-driven translation establishes sweat as a clinically actionable surrogate for renal monitoring, supporting population-level estimation and highlighting the potential for personalised longitudinal assessment, and enabling a scalable, non-invasive strategy for high-frequency kidney disease management.

biophysics↗

bioRxiv2026

Newly arisen indel governs a leaf shape polymorphism in the Ivy Leaf Morning Glory (Ipomoea hederacea)

Leaf shape varies widely across plant taxa and has repeatedly been shown to affect ecophysiology, interspecific interactions, and fitness. We used population genomics, genome wide association studies (GWAS), and comparative genomics to determine the genetic basis and evolutionary history of an uncharacterized Mendelian leaf shape polymorphism in Ipomoea hederacea. To do so, we assembled a reference genome and generated whole genome sequencing for 123 individuals from 55 populations. We identified a 117 kb indel that perfectly co-segregates with leaf shape by conducting a GWAS and assessing differences in coverage. Syntenic orthologs for genes on the indel were present in five other Ipomoea species with various leaf shapes, indicating the indel is a newly arisen deletion in I. hederacea despite similar leaf shape phenotypes in the other species. More broadly, these results illustrate how a range of leaf shape phenotypes can be produced by distinct genetic mechanisms even in closely related species. Although none of the genes on the indel itself are known leaf shape candidates, there are multiple leaf shape candidate genes in close proximity that are involved in the auxin biosynthesis pathway. Additionally, the genes within the indel have gene functions that could affect other potentially ecologically relevant traits that have previously been shown to be associated with leaf shape in I. hederacea. Therefore, the pleiotropic effects of the indel polymorphism can have important implications for understanding the ecological mechanisms influencing a well-documented leaf shape latitudinal cline in I. hederacea. Significance StatementIpomoea hederacea has been used to investigate the ecological and evolutionary effects of leaf shape because of a well-documented latitudinal leaf shape cline governed by an uncharacterized Mendelian polymorphism in this species. We identified a 117 kb indel that perfectly co-segregates with leaf shape in I. hederacea. The indel appears to be a distinct genetic mechanism than those governing similar leaf shapes in other closely related Ipomoea species. Additionally, possible pleiotropic effects of the indel on other traits has important implications for understanding the ecology and evolution of leaf shape variation in I. hederacea. Therefore, the results and the new genomic resources that we developed will facilitate future work understanding the genetic, developmental, and ecological mechanisms governing leaf shape variation.

plant biology↗

bioRxiv2026

Ultra-efficient High Resolution 3D Reconstruction of Spatial Omics Data with Neural Transcriptomic Field

Biological tissues are inherently three-dimensional (3D) ecosystems where spatial architecture dictates cellular function. While spatial omics technologies have revolutionized molecular profiling, they are largely restricted to isolated two-dimensional (2D) tissue sections. Existing computational methods attempting to reconstruct 3D volumes from sparse slices rely heavily on local slice-to-slice interpolation, struggling to balance high-fidelity reconstruction, noise reduction, and atlas-scale efficiency. Here, we present Neural Transcriptomic Field (NTF), a deep learning framework employing multi-resolution hash-grid encoding and implicit neural representations. Unlike interpolation-based approaches that merely bridge adjacent observations, NTF learns a global, continuous 3D representation of the tissue. By modeling the underlying latent biological patterns, NTF intrinsically decouples true molecular signals from technical artifacts, naturally enabling robust denoising and high-fidelity reconstructions. This global field paradigm shatters traditional scalability limits: NTF achieves up to a 1,000x speedup over existing methods, notably reconstructing a 100-million-cell scale 3D whole-mouse embryo atlas in under 15 minutes. Furthermore, NTF can generate super-resolved volumes from sparse input (e.g., utilizing only 10% of slices) and robustly extrapolating into unseen tissue regions. We demonstrate NTFs versatility across diverse transcriptomic and proteomic datasets, capturing complex spatiotemporal dynamics in Drosophila and mouse embryogenesis, and mapping intra-tumoral functional gradients in human breast cancer. Ultimately, NTF provides an unprecedentedly fast, scalable, and robust computational engine for constructing the next generation of comprehensive 3D tissue atlases.

bioinformatics↗

bioRxiv2026

Ferrous Iron Accumulation Is a Hallmark and Therapeutic Vulnerability of Therapy-Induced Senescence

Chemotherapy and radiation reduce tumor burden but leave behind residual cells that survive via therapy-induced senescence (TIS). These cells constitute a latent reservoir fueling recurrence, yet strategies for their selective elimination are lacking. Here, we identify lysosomal ferrous iron accumulation as a conserved hallmark and actionable vulnerability of TIS tumor cells. Across diverse models, senescent tumor cells exhibit marked hypersensitivity to ferroptosis induction. In breast cancer PDX models, sequential ferroptosis induction following chemotherapy significantly delays recurrence, while dual inhibition of GPX4 and FSP1 produces durable, often complete, eradication of residual tumors without overt toxicity. Mechanistically, activation of the TFEB-HO-1 axis in TIS tumor cells drives ferrous iron accumulation, thereby priming cells for ferroptosis. Together, these findings establish ferrous iron accumulation as a defining feature of TIS and position ferroptosis induction as a potent senolytic strategy to eliminate therapy-refractory residual disease. Statement of significanceSenescent tumor cells remaining after treatment can drive cancer recurrence yet remain poorly understood and therapeutically intractable. Here, we identify lysosomal ferrous iron accumulation as a universal hallmark of therapy-induced senescence and demonstrate that ferroptosis induction functions as an effective senolytic strategy. Our findings provide mechanistic and translational support for the "one-two punch" therapeutic paradigm.

cancer biology↗

bioRxiv2026

ParSeek: Accurate cryo-EM particle picking with a deep learning model trained on synthetic data

Accurate particle picking from noisy cryo-EM micrographs is essential for high-resolution reconstruction. Current deep learning methods rely on manually annotated data, which is labor-intensive, subjective, and limits particle recall under low signal-to-noise ratio (SNR). Here we introduce ParSeek, an automated picker trained entirely on synthetic data without human annotation. Synthetic micrographs are generated by projecting known 3D structures into realistic background patches that reproduce experimental noise. On seven public cryo-EM datasets, ParSeek outperformed Topaz and CryoSegNet on four datasets, achieving the highest F1-score (up to 0.82) and reaching 0.63 on a challenging membrane protein dataset. Density maps from ParSeek-picked particles showed cross-correlation coefficients up to 0.995 with the reference and a minimal resolution difference of 0.1 [A]. ParSeek also overcame severe orientation bias on an influenza dataset, yielding a reasonable reconstruction. Applied to three experimental datasets (an antibody-antigen complex and two GPCRs), ParSeek enabled reconstructions at 5.0 [A], 4.0 [A], and 2.8 [A], respectively. The 2.8 [A] map resolved side-chain densities and ligand flexibility. This study establishes a fully synthetic-data-driven strategy that eliminates manual annotation for training cryo-EM deep-learning models, paving the way for automated, unbiased particle picking.

molecular biology↗

bioRxiv2026

Compressive axial-integrated planar scanning (CAPS) microscopy for high-speed volumetric imaging of cardiac dynamics

Investigating cardiac dynamics, including contractile function and intracardiac flow, requires volumetric imaging capable of resolving whole-organ events at micrometer resolution and millisecond timescales. However, the limited readout bandwidth of detectors imposes fundamental trade-offs among spatial sampling, field of view, and achievable volume rates. Here we introduce compressive axial-integrated planar scanning (CAPS) microscopy, a computational imaging framework that combines rapid light-sheet scanning, detection-side axial multiplexing with model-based reconstruction to enhance detector bandwidth utilization for high-speed volumetric imaging. Using widely accessible optical sensors and components, CAPS achieves cellular-scale resolving power across heart chambers at 200 volumes per second with an effective detector pixel rate of 5.82 GHz, representing a [~]15-fold increase in spatiotemporal throughput relative to uncompressed volumetric acquisition. Coordinated high-speed encoding and computational reconstruction further mitigate rolling-shutter distortions in CMOS sensors while preserving frame rate and intrinsic optical sectioning. We demonstrate that CAPS enables beat-resolved imaging of single-cell cardiomyocyte kinematics, chamber-scale contractile dynamics, and intracardiac hemodynamics in zebrafish larvae under both healthy and pharmacologically perturbed conditions. Collectively, these advances establish CAPS as a powerful framework for quantitative, in vivo characterization of coordinated and disrupted cardiac dynamics at cellular resolution, supporting high-speed volumetric interrogation of organ-level function and disease progression.

bioengineering↗

bioRxiv2026

Therapeutic Potential of Hypoxia-Preconditioned hiPSC-Epicardial Cell-Derived Exosomes in Mice with Myocardial Infarction

BackgroundIt has been demonstrated that stem cell transplantation promotes healing of the infarcted heart through paracrine effects. However, the therapeutic potential of exosomes secreted by hiPSC-derived epicardial cells (hEP-Exos) for treating infarcted hearts remains unclear. Myocardial infarction (MI) can trigger EP activation, increasing EP paracrine function. Therefore, this study aims to determine and compare the cardioprotective effects of exosomes secreted by hEPs under normoxic (Exo-N) and hypoxic (Exo-H) conditions in MI mice and to explore the underlying mechanisms. MethodsTwo types of exosomes were collected by ultracentrifugation and delivered via intramyocardial injection in a murine MI model. The protective effects of Exo-N and Exo-H on the infarcted heart were assessed using echocardiography, histological examination, and immunofluorescence analysis. Additionally, microRNA sequencing, luciferase activity assays, and miRNA gain-and loss-of-function experiments were performed to identify enriched miRNAs and investigate their roles in different exosome populations. ResultsIn vitro, both Exo-N and Exo-H enhanced the migration and tube-formation capacities in human umbilical vein endothelial cells (HUVECs) and reduced the apoptosis in hiPSC-derived cardiomyocytes (hCMs) under oxygen-glucose deprivation (OGD), with Exo-H exhibiting a stronger effect. In vivo, both Exo-N and Exo-H significantly improved contractile function, reduced infarct size, and mitigated adverse remodeling in mouse hearts with MI, accompanied by increased cardiomyocyte survival and angiogenesis, with Exo-H showing superior efficacy. Mechanistically, miRNA sequencing revealed distinct cargo profiles between Exo-N and Exo-H. miR-214-3p was identified as a key mediator of the enhanced therapeutic potency of Exo-H. miR-214-3p promoted EC angiogenesis by suppressing vasohibin-1 and attenuated cardiomyocyte mitochondrial fission and apoptosis by suppressing mitochondrial elongation factor 2 (MIEF2). ConclusionsThis study demonstrates that administration of hEP-Exos, particularly Exo-H, provides robust cardioprotection by enhancing cardiomyocyte survival and angiogenesis, potentially mediated by miR-214-3p. These findings suggest that conditioned hEP-Exos could be a promising and effective acellular therapeutic option for treating MI.

cell biology↗

bioRxiv2026

Discovery of Selective Nrf2 Activators from Natural Products: AComputational Screening Approach to Minimize Off-Target Effects on PXR and CYP2D6

Nuclear factor erythroid 2-related factor 2 (Nrf2) is a central regulator of cellular antioxidant responses and a highly promising therapeutic target for a range of oxidative stress-related diseases. However, the clinical translation of Nrf2 activators has been hampered by significant off-target effects--notably unintended activation of the pregnane X receptor (PXR) and inhibition of cytochrome P450 2D6 (CYP2D6)--which can lead to dangerous drug-drug interactions and metabolic complications. To overcome this critical barrier, we conducted the first large-scale computational screening of 628,898 natural products from the COCONUT database, integrating molecular docking with a rigorous three-tier selectivity strategy designed to prioritize compounds that strongly bind KEAP1 (the primary Nrf2 repressor) while minimizing interactions with PXR and CYP2D6. Our innovative approach identified 10 ultraselective candidates that demonstrate potent KEAP1 affinity, negligible PXR engagement, and only moderate CYP2D6 binding--achieving up to 12.29-fold selectivity for Nrf2 pathway activation. These top hits are structurally novel, enriched in lipid-like and nucleoside-inspired scaffolds, and exhibit promising drug-like properties. By providing both a curated set of chemically diverse, selectivity-optimized leads and a publicly accessible screening dataset, this work establishes a new foundation for the rational development of safer, more precise Nrf2-targeted therapies, bridging a crucial gap between target potential and clinical viability. By prioritizing compounds with minimal off-target effects on PXR and CYP2D6, our approach offers a scalable template for reducing drug development failures and advancing safer therapeutics for oxidative stress-related diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/718057v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@13c6c79org.highwire.dtl.DTLVardef@1f5a078org.highwire.dtl.DTLVardef@fa4f4borg.highwire.dtl.DTLVardef@16bc881_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

bioinformatics↗

bioRxiv2026

End-to-end bimodal anti-counterfeiting by informational DNA nanoparticles

The superior stealth properties and high information density make DNA a sought-after candidate in the field of molecular steganography. Here, we developed the InfinMark end-to-end DNA steganography framework for anti-counterfeiting applications by combining the characteristics of both the Internet of Things (IoT) and DNA-of-Things (DoT). InfinMark includes five modules: Information Transcoding, Fingerprint Writing, Nano-encapsulation, Invisible Marking, and Multi-level Rapid Authentication. It ensures precise anti-counterfeiting information reading and writing through a dynamic DNA-compatible transcoding algorithm, achieves seamless embedding by developing scalable nanoparticle manufacture methods, and supports cross-scenario on-site verification, ultimately granting it comprehensive anti-counterfeiting capabilities spanning from source labeling to terminal tracing. By addressing the bottlenecks in IoT and DoT integration, lifecycle tracking, as well on-site product authentication, this research constructs a full-chain bimodal anti-counterfeiting system, thereby showcasing the practical application of informational DNA nanoparticles in various aspects of production and daily life.

synthetic biology↗