Biology subjects

Chen, D.

Publications and source records attributed to Chen, D..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Reactivating conflicting evaluative memories during sleep reduces decision ambivalence

Memory guides everyday evaluations and decision-making. Yet people often encounter inconsistent information about the same target, giving rise to conflicting evaluative memories and decision ambivalence. Decision ambivalence is not only aversive but also reduces confidence, increases hesitation, and leads to maladaptive choices. While sleep consolidates memories, its role in resolving these evaluative conflicts and shaping decision dynamics remains unknown. Here, we investigated how memory reactivation during sleep, a critical period for memory consolidation and transformation, would reconstruct conflicting evaluative memories and thus influence next-day decision ambivalence. In a valence reversal learning procedure, participants first encoded positive or negative cue-outcome associations (A-B) on Day 1, followed by learning A-C associations yet with opposite valences on Day 2 (i.e., Day 1 negative-to-Day 2 positive and Day 1 positive-to-Day 2 negative). During subsequent non-rapid eye movement (NREM) sleep on Day 2 night, half of the cues were re-presented to sleeping participants to reactivate the cue-associated memories. Upon waking up, participants completed post-sleep evaluation and memory tests. Our results showed that cueing reduced decision ambivalence, especially in the negative-to-positive condition, as evidenced by less curved mouse-tracking trajectories. Meanwhile, cueing promoted the integration of conflicting evaluative memories, again in the negative-to-positive condition. Critically, cueing-induced ambivalence reduction was evident only for items that were integrated after sleep. Electrophysiologically, stronger cue-elicited delta power during NREM sleep predicted next-day ambivalence reduction, while higher cue-elicited spindle probabilities were associated with better memory integration. Together, our findings suggest that memory reactivation during post-learning NREM sleep actively reorganizes conflicting memories, providing a mechanistic pathway through which offline memory reprocessing resolves waking decision ambivalence.

neuroscience↗

bioRxiv2026

Heat stress-induced condensation of G3BP1 in perinuclear P-bodies in C. elegans' germline

Stress granules (SGs) are essential subcellular assemblies that enable cells to adapt to environmental stress, and their dynamic assembly and disassembly are critical for maintaining cellular homeostasis and reproductive capacity. However, the function and regulation of stress granules in germline cells remain mysterious. In this study, we characterized the function of GTBP-1, the homolog of human G3BP1, in response to heat stress in Caenorhabditis elegans and elucidated its regulation in stress granule dynamics. gtbp-1 mutants exhibit pronounced temperature-dependent biodirectional reproductive characteristics. At lower temperatures, their brood size is higher than that of wild-type animals, whereas at 25 {degrees}C they are completely sterile. GTBP-1 is diffusely distributed at normal culturing temperatures but forms perinuclear stress granules upon heat shock in the germline. While the NTF2 domain is essential for germline stress granule formation, other domains, including the IDR, RRM and RGG, are required for the recovery phase after heat shock. GTBP-1 stress granules colocalize with the P-bodies, but not with other germ granules. The depletion of P-bodies prohibited the perinuclear GTBP-1 stress granule formation. A combination of forward genetic screening together with RNAi-based candidate screening identified the P body components, the RNA helicase LAF-1, the SUMO protein SMO-1, and the mTOR pathway effector RSKS-1(S6K) as key regulators of GTBP-1 germline stress granule formation. Together, this work revealed that germline stress granules may be subjected to multiple layers of regulations and GTBP-1 may safeguards reproductive homeostasis under temperature stress by coordinating germline stress granule condensation. Author SummaryReproduction is particularly vulnerable to environmental stress, yet germ cells must remain functional to ensure fertility. How germ cells protect themselves under stressful conditions is still not well understood. In this study, we used the nematode Caenorhabditis elegans to examine how germ cells respond to heat stress, focusing on GTBP-1, a conserved protein involved in stress granule formation. We found that GTBP-1 plays contrasting roles depending on temperature: under normal conditions it restrains reproduction, whereas under heat stress it becomes essential for maintaining fertility. When animals are exposed to elevated temperature, GTBP-1 rapidly forms granules around the nuclei of germ cells, these granules assemble at sites occupied by processing bodies, another type of RNA-containing structure, revealing a close spatial relationship between two stress-responsive compartments. We also found that this process is regulated by conserved factors involved in RNA regulation and nutrient-responsive signaling. Together, our findings show how germ cells reorganize RNA-protein assemblies to preserve reproductive capacity under stressful conditions.

genetics↗

bioRxiv2026

Neurocognitive deficits in controlling aversive memory among insomnia disorders

BackgroundInsomnia disorder is a common sleep disturbance characterized by adverse daytime cognitive and emotional impairments, such as repetitive negative thinking and increased psychological distress. Memory control, a key self-regulatory ability to control or inhibit unwanted thoughts and memories, plays an essential role in supporting cognitive functions and emotional well-being. Here, we delineate the neurocognitive mechanisms underlying memory control among individuals with insomnia. Methods41 participants meeting DSM-5 criteria for insomnia disorder and 40 healthy sleepers completed an emotional Think/No-Think task, during which participants either retrieved (Think) or suppressed the retrieval (No-Think) of aversive memories in response to memory cues while electroencephalograms were recorded. ResultsLinear mixed model analyses with age and depression scores as covariates showed that participants with insomnia exhibited impaired memory control abilities, as evidenced by reduced suppression-induced forgetting in memory recall when compared to healthy sleepers. Electrophysiologically, healthy sleepers showed enhanced right prefrontal theta power in retrieval suppression than in retrieval, indicating elevated needs of inhibitory control during memory control. In sharp contrast, this difference was absent among those with insomnia. Notably, the greater the severity of insomnia symptoms, the smaller the retrieval vs. retrieval suppression theta power differences across participants, linking inefficient top-down control of unwanted memories with low sleep qualities. ConclusionIndividuals with insomnia showed impaired memory control of aversive memories and aberrant electrophysiological activities during retrieval suppression. Future research shall investigate the causal relationship between memory control abilities and insomnia symptoms.

neuroscience↗

bioRxiv2026

AAV-Mediated Dual-Gene Therapy Restores Metabolic Function in Mice with Propionic Acidemi

Background and AimsPropionic acidemia (PA) is a rare autosomal recessive disorder caused by mutations in PCCA or PCCB, which encode the two subunits of propionyl-CoA carboxylase (PCC). PCC deficiency causes toxic metabolite accumulation and multi-organ damage. Current management, including dietary restriction, pharmacological support, and liver transplantation, does not restore enzymatic activity. We developed a dual-gene adeno-associated virus (AAV) therapy that delivers both PCC subunits to treat both PA subtypes. MethodsWe generated a clinically relevant PCCA-R73W knock-in mouse model and administered AAV8 vectors encoding native human PCCA and PCCB under the control of a liver-specific thyroxine-binding globulin promoter (AAV8-TBG-hPCCA-P2A-hPCCB). Metabolite levels and organ safety were longitudinally assessed. ResultsDual-gene therapy produced dose-dependent reductions in plasma C3/C2 ratio, 3-hydroxypropionic acid, 2-methylcitric acid, and propionylglycine, and significantly outperformed single-gene (PCCA-only) therapy. Neonatal facial-vein injection achieved metabolic correction comparable to or better than adult treatment. The longitudinal follow-up revealed sustained efficacy over a 16-week period, with no signs of hepatotoxicity or adverse effects. ConclusionsSingle-dose, dual-gene AAV therapy achieves sustained metabolic correction and demonstrates long-term safety in a clinically relevant PA model, supporting its translational potential for both type I and type II propionic acidemia.

genetics↗

bioRxiv2026

Exploration of the screening and regulatory mechanisms of biomarkers related to ac4C modification in laryngeal squamous cell carcinoma patients based on single-cell analysis and machine learning

BackgroundN4-acetylcytidine (ac4C) modification plays a critical role in cancer development. Exploring ac4C modification in laryngeal squamous cell carcinoma (LSCC) may help elucidate its pathogenesis. MethodsLSCC-related datasets were obtained from GEO. After preprocessing and annotating single-cell data, malignant cells were identified by CNV scoring and further divided into subpopulations. Malignant epithelial cells (MECs) were identified and subclustered based on ac4C-related gene activity. Prognostic genes were screened using Cox regression and machine-learning approaches, followed by validation in clinical samples using qPCR. The biological and immunological relevance of these genes was further explored through immune infiltration, immunotherapy response, and mutation analyses. ResultsThe 14,465 identified MECs were classified into five subgroups (MEC1-5), among which MEC3 showed the strongest association with the ac4C gene set. Machine-learning analysis of MEC3-derived genes yielded seven prognostic markers, including BARX1, FHL2, NXPH4, PKMYT1, TNFAIP8L1, CRLF1, and CENPP. qPCR confirmed their differential expression between tumor and adjacent normal tissues. These genes were significantly associated with alterations in the tumor immune microenvironment, with high-risk patients showing increased immune infiltration and immune activity. ConclusionSeven ac4C-related prognostic genes were identified that may contribute to LSCC progression by modulating the tumor immune microenvironment, providing potential therapeutic insights.

developmental biology↗

bioRxiv2026

Intravital single-molecule imaging reveals cytoskeletal turnover as a driver of membrane remodeling in live animals

Understanding how cells regulate plasma membrane architecture inside intact living organs in a live animal has been limited by the inability to directly measure molecular dynamics in vivo. Here we introduce intravital single-molecule microscopy (iSiMM), an imaging approach that enables tracking of individual, endogenously expressed cytoskeletal components at the plasma membrane in live mice. Applying iSiMM to murine acinar secretory cells, we identify discrete basolateral membrane domains built on deeply folded membrane infolds that function as a pre-existing membrane reservoir. Single-molecule measurements reveal continuous, regulated molecular turnover within these domains. Physiological stimulation accelerates cytoskeletal exchange promoting rapid membrane unfolding and cell expansion. Together, these findings establish iSiMM as a general strategy for probing molecular kinetics underlying dynamic cellular behaviors in intact organs. One-sentence summaryIntravital single-molecule microscopy enables direct measurement of molecular kinetics underlying dynamic cellular behaviors in intact living organs.

cell biology↗

bioRxiv2026

MYRF drives heterochronic miRNAs and LIN-42, and amplifies oscillatory programs for stage transitions

Larval development in C. elegans proceeds through discrete stages, yet the mechanisms that drive stage transitions remain incompletely defined. Here, we identify the transmembrane transcription factor MYRF as a master temporal regulator essential for larval progression. MYRF cleavage and nuclear accumulation oscillate across larval stages, peaking during mid-to-late intermolt phases. MYRF directly activates key heterochronic microRNAs--including lin-4, mir-48/241/84, and let-7--and amplifies the oscillatory gene network by promoting central regulators such as nhr-23. MYRF loss-of-function or acute depletion suppresses and flattens this network, causing developmental arrest during the late intermolt phase of each larval cycle and stalling molting, seam cell division, and vulval morphogenesis. Notably, MYRF oscillations precede and induce activation of lin-42/Period, which feeds back to repress myrf, sharpening oscillatory precision. Together, these findings establish MYRF as a central driver of larval stage transitions, coupling microRNA-conferred temporal identity with an amplifier-based logic that executes stage- and phase-specific developmental programs.

developmental biology↗

bioRxiv2026

DIA-based quantitative proteomics reveal the protective effects of quercetin against atopic dermatitis via attenuating inflammation and modulating immune response

Atopic dermatitis is a common inflammatory skin disorder characterised by recurrent eczematous lesions and intense itch. Quercetin is a naturally occurring flavonoid, exhibits antioxidant and anti-inflammatory properties. Previous studies have indicated its beneficial role in managing atopic dermatitis (AD); however, the precise underlying mechanism remains unclear. This study aimed to investigate the protective effects of quercetin against AD and to elucidate its potential mechanisms. We demonstrated that quercetin effectively suppressed the overexpression of pro-inflammatory effector factors--including interleukin (IL)-1{beta}, thymic stromal lymphopoietin (TSLP) and chemokine (C-X-C motif) ligand 1/10/11 (CXCL1/10/11)--in immortalized human keratinocytes (HaCaT) stimulated by TNF-/IFN-{gamma}. Proteomic analysis revealed 88 differentially expressed proteins, suggesting that quercetins therapeutic action involves multiple pathways. Notably, the NOD-like receptor signaling pathway was identified as a key factor. The key proteins related to this pathway including inhibitor of nuclear factor kappa B kinase epsilon (IKBKE), indoleamine 2,3-dioxygenase 1 (IDO1) and chemokine (C-X-C motif) ligand 9 (CXCL9) showed a significant decrease in expression levels after quercetin treatment. Collectively, these results demonstrate that quercetin alleviates AD symptoms by attenuating inflammatory responses, likely through inhibition of the NOD-like receptor signaling pathway.

pharmacology and toxicology↗

bioRxiv2025

SPARK: deciphering tumor-specific signaling networks through an integrative predictive model

While kinase-substrate associations (KSAs) are fundamental to cancer signaling, their rewiring patterns and functional roles across different cancers during cancer progression remain generally poorly characterized. Current predictive tools often fail to integrate three-dimensional structural constraints and cancer-specific dynamic information, limiting their biological relevance and translational potential. To address this, the present study constructs SPARK, a machine learning framework that integrates multi-modal features within cancer-specific contexts. These include data-driven features (such as phosphoproteomic co-expression, mutual information, protein-level abundance, and phosphosite-level abundance), knowledge-driven features (e.g., STRING protein-protein interactions), and structural features (ESM-2 embeddings compressed via an autoencoder). The training of the model was done with the adoption of the XGBoost classifier on data from eight CPTAC cancer cohorts. SPARK demonstrates strong predictive performance across different cancer types, with AUROC values ranging from 0.929 to 0.957 (mean: 0.944) in normal tissues and 0.941 to 0.958 (mean: 0.948) in tumor tissues. The accuracy of these predictions was further validated against experimentally determined kinase-substrate specificities. Using SPARKs predictions, tissue-specific phosphorylation signaling networks are systematically reconstructed. These SPARK-derived networks reveal distinct phosphorylation patterns and kinase activation landscapes across cancers while identifying several highly tissue-specific kinases as promising therapeutic targets. O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/692871v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@3023d0org.highwire.dtl.DTLVardef@7f4b8eorg.highwire.dtl.DTLVardef@139977dorg.highwire.dtl.DTLVardef@89446_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

bioinformatics↗

bioRxiv2025

Flexible parental care in a songbird correlates with sex-specific responses to seasonal phenology, mating opportunity and reproductive success

O_LISpecies with diverse parental care patterns often exhibit flexibility in response to environmental changes. Such changes can influence parental care decisions by altering the trade-offs between current and future reproduction. While previous studies have revealed correlations between specific social and ecological factors and parental care patterns, the joint effects of multiple factors could be rather complex and may result in different outcomes within and across populations, and between sexes. C_LIO_LIIn this study, we revealed parental care systems and their seasonal variations across three geographic populations in a polygamous species, the Chinese penduline tits (Remiz consobrinus), by monitoring breeding events over years. To investigate how local conditions (including social and ecological conditions) correlate with sex-specific parental care patterns, we compared breeding phenology and local conditions (including season length, mating opportunity and reproductive success) across the populations. C_LIO_LIStriking population differences in parental care strategies are found in this species: biparental care predominated in one population, whereas female-only care was more common in the other two. Our analyses reveal that, despite a large difference in season length, the time of egg-laying peaked similarly across the three populations. Female penduline tits determined the breeding phenology, which varies male mating opportunities dramatically over the season. For all populations, male Chinese penduline tits were more likely to desert the clutch when male mating opportunities were high. In contrast, females consistently provided care, regardless of variation in female mating opportunities. C_LIO_LIWe also found that fitness costs on the current brood resulting from offspring desertion differed across populations. This desertion cost on brood fitness matters more than achieving a high reproductive reward in driving the emergence of uniparental care, contrary to the theory that uniparental care only occurs when single parents can efficiently raise nestlings alone. C_LIO_LIOur study demonstrates that similar parental care patterns across populations could result from different underlying factor interactions and highlights the consistent sex-specific responses to local conditions in parental care. C_LI

ecology↗

bioRxiv2025

High-salt diet disturbs the physiological uterine endothelial junction remodeling during pregnancy

A high-salt diet (HSD) induced excessive sodium intake is a major risk factor for various diseases. However, its specific effects on uterine endothelial cell and pregnancy outcomes remain poorly understood. In this study, we demonstrated that HSD induces gestation specific hypertension and adverse pregnancy outcomes in murine models. The proper spiral artery remodeling, which involved the decidual vascular endothelia, is thought to be essential for normal regulation of gestational blood pressure. We explored the molecular basis for the adaptation of vascular endothelial cell based on the transcriptome data, and uncovered the significant changes for the cell junction in the endothelia during this process. Furthermore, it was revealed that HSD induced more salt accumulation in the uteri and triggered the disturbed vascular endothelium cytoskeletal remodeling, which was associated impaired trophoblast cell invasion and incorporation into the vascular wall. Overall, our study identifies unique roles of decidual endothelium for pregnancy vascular remodeling, and demonstrates that HSD disrupts physiological spiral artery remodeling through endothelial maladaptation, which may concurrently induce systemic endothelial damage in maternal systemic vascular.

physiology↗

bioRxiv2025

Longitudinal Imaging of the Premalignant Tumor Microenvironment Reveals Transient Myeloid States Predictive of Tumor Fate

The spontaneous regression of cancer lesions illustrates the power of immune surveillance; yet these transient events have largely escaped systematic analysis. Using longitudinal intravital microscopy in a carcinogen-induced model of head and neck cancer, we followed premalignant lesions within the same animals for 24 weeks at single-cell resolution. This strategy uncovered three trajectories: progression, stability, or regression, and enabled direct analysis of immune dynamics underlying each fate. Lesion outcome was determined by the spatial organization of myeloid-derived antigen-presenting cells: regressing lesions were characterized by dense clusters of myeloid-derived cells associated with CXCL9+/CXCL10+ expression and T cell recruitment, whereas progressing lesions displayed a scattered infiltration of these cells. Remarkably, transient myeloid clusters arose prior to any detectable lesion formation and marked regions that would later develop into premalignant lesions. These findings identify spatiotemporal myeloid organization as an early determinant of tumor fate and provide a mechanistic framework for predicting and intercepting cancer at its inception. Summary SentenceEarly myeloid architecture dictates cancer fate: dense CXCL9/CXCL10 clusters with T-cell enrichment accompany regression, whereas sparse infiltration predicts progression. Transient pre-lesional myeloid clusters emerge at future tumor sites, revealing immune organization as an early determinant of malignancy.

cancer biology↗

bioRxiv2025

Pan-cancer analysis reveals that tumor microbiomes generate specific epitopes through transcriptional reprogramming

The therapeutic promise of tumor microbial peptides faces a critical safety paradox: tumors and peritumor tissues harbor compositionally similar microbiomes, yet safe immunotherapy demands tumor-specific targeting. We performed comprehensive transcriptomic analysis of microbial communities from 1,868 tumor and peritumor samples across 11 cancer types. Although 88.5% of microbial species are present in both tissue types, tumor and peritumor tissues exhibit profound transcriptional divergence: only 34.1% of microbial genes are expressed in both tissue types, and merely 18.2% of predicted HLA-binding peptides overlap. This transcriptional divergence represents microbial transcriptional reprogramming (MTR) in tumor tissues, through which microbes activate distinct genomic regions while adapting to tumor microenvironmental pressures, thereby generating tumor-specific peptide repertoires. Using Microbial Transcriptional Reprogramming Index (MiTRI) to quantify MTR, we found that higher MiTRI values correlate with expanded immunogenic peptide repertoires. Mass spectrometry-based immunopeptidomics confirmed that 25% of naturally presented microbial peptides originate from MTR regions. Crucially, in microsatellite-stable colorectal cancer, neo-adjuvant therapy responders exhibited significantly higher MiTRI values. T cell receptors (TCRs) recognized MTR-derived epitopes at 2.10-fold higher rates than genome-wide epitopes, accounting for 79.1% of clonally expanded TCRs. These findings establish MTR as the principle that ensures the tumor-specificity and safety of micorbiome-directed immunotherapy.

cancer biology↗

bioRxiv2025

AEBP2-Directed H3K27me2 Defines a Specific Vulnerability in EZH2-mutant Lymphoma

The catalytic subunit of Polycomb Repressive Complex 2 (PRC2), EZH2, is recurrently mutated in 25% of diffuse large B-cell lymphomas (DLBCL), causing increased H3K27me3 and decreased H3K27me2 levels. EZH2 inhibitors provide clinical benefit, but resistance frequently develops, highlighting the need for alternative therapeutic targets. Here, we identify the PRC2 accessory protein AEBP2 as a specific genetic dependency in EZH2-mutant DLBCL. While AEBP2 acts through PRC2, its essential role is surprisingly independent of canonical H3K27me3-mediated gene silencing. Instead, AEBP2 functions within a PRC2.2 complex lacking JARID2, using its zinc-finger domains to sample intergenic chromatin to sustain H3K27me2. Notably, loss of AEBP2 or NSD2 caused contrasting changes in intergenic H3K27me2 levels, driving sensitivity or resistance to PRC2 inhibitors, respectively. Our findings identify AEBP2-PRC2.2-maintained intergenic H3K27me2 as a therapeutic vulnerability in EZH2-mutant DLBCL and highlight dysregulated H3K27me2 as an underappreciated form of PRC2 dysfunction in cancer, with important therapeutic implications.

cancer biology↗

bioRxiv2025

Dynamic Spiral Artery Remodeling in Early Human Pregnancy: An Analysis of Specimens Collected with a Standardized Protocol

Human uterine spiral artery remodeling (SAR) is a tightly regulated process involving complex interactions between interstitial and endovascular extravillous trophoblasts (iEVTs and enEVTs) and diverse maternal decidual cell populations. However, the intrinsic spatiotemporal dynamics of SAR in human placentation remain poorly understood, largely due to the limited availability of high-quality maternal-fetal interface specimens. Electively terminated early pregnancies offer a valuable resource for studying SAR in situ, yet inconsistent methods for distinguishing fragmented villous and decidual tissues have hindered reproducibility and interpretation. Herein we present a standardized protocol for the classification and characterization of high-quality maternal-fetal interface specimens from elective terminations by integrating stereomicroscopic evaluation with confirmation by immunohistochemistry and immunofluorescence microscopy. Combined with multiplex immunofluorescence imaging with cell-type- specific markers, this approach enabled precise spatial mapping and quantification of key morphological and cellular events in SAR from gestational weeks 5 to 10. Our analyses reveal that SAR initiates as early as week 5 with extraluminal recruitment of natural killer (NK) cells, followed by the formation of tightly packed EVT plugs within the lumens of spiral arteries in the decidua compacta; these plugs progressively extend deeper into the vessels and gradually loosen as gestation progresses. Notably, enEVTs appear to acquire NK cell-like phenotypes that may facilitate the displacement of endothelial and smooth muscle cells, promoting progressive vessel dilation. In summary, we provide a robust and reproducible method for assessing physiological SAR in early human pregnancy, supporting the adoption of our methodology in future studies of pathological SAR and related pregnancy disorders. Summary SentenceA standardized protocol for classifying maternal-fetal interface specimens from electively aborted materials at gestational weeks 5-10 was developed to quantify the spatiotemporal spiral artery remodeling dynamics in early human pregnancy. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=176 HEIGHT=200 SRC="FIGDIR/small/682615v2_ufig1.gif" ALT="Figure 1"> View larger version (66K): org.highwire.dtl.DTLVardef@ad6f1eorg.highwire.dtl.DTLVardef@5a3dcborg.highwire.dtl.DTLVardef@8f06b7org.highwire.dtl.DTLVardef@1f877_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2025

Network pharmacology, bioinformatics, molecular docking and experimental verification of the mechanism of HXZTS treatment on osteoarthritis synovium

BackgroundOsteoarthritis (OA) is a prevalent joint disease characterized by synovial inflammation and synovial fibroblast dysfunction. Elucidating the molecular mechanisms underlying synovial tissue impairment in OA is crucial for developing targeted therapeutic interventions. Huoxuezhitongsan (HXZTS), a traditional Chinese medicine formula, has shown promising therapeutic effects in treating OA, but its mechanisms of action on synovial tissue remain unclear. MethodThis study integrated network pharmacology, bioinformatics analysis, molecular docking, and experimental validation to elucidate the potential targets, pathways, and mechanisms by which HXZTS exert therapeutic effects on osteoarthritic synovial tissue. ResultsNetwork analysis identified 21 active ingredients and 111 common targets of HXZTS for OA, with key compounds like quercetin, {beta}-sitosterol, and stigmasterol. Enrichment analysis revealed HXZTS modulates inflammation through TNF, IL-17, and MAPK signaling pathways, oxidative stress, apoptosis, angiogenesis, and metabolic regulation. Molecular docking demonstrated strong binding affinities of HXZTS compounds with targets like AKT1, TNF, TP53, IL6, and VEGFA. RT-qPCR validation confirmed the downregulation of inflammatory mediators like IL6 and PTGS2, alongside the upregulation of genes associated with potential cartilage repair effects, such as MMP1 and MMP3, upon HXZTS treatment. ConclusionsHXZTS exerts therapeutic effects on osteoarthritic synovial tissue through a multifaceted mechanism involving modulation of inflammation, oxidative stress, apoptosis, angiogenesis, and metabolic regulation. These findings provide insights into the potential application of HXZTS as a complementary or alternative therapeutic approach for managing OA and a foundation for developing novel targeted therapies.

bioinformatics↗

bioRxiv2025

Non-integrating direct reprogramming generates therapeutic endothelial cells with sustained vascular regeneration capacity enhanced by nanomatrix delivery

RationaleDirect reprogramming of fibroblasts into endothelial cells (rECs) using ETV2 shows promise for vascular regeneration. However, current approaches using integrating viral vectors pose clinical translation barriers, and poor long-term cell survival limits therapeutic efficacy. ObjectiveTo develop a clinically compatible method for generating rECs using non-integrating adenoviral ETV2 (Ad-ETV2) and enhance their engraftment and therapeutic efficacy through peptide amphiphile (PA) nanomatrix encapsulation. Methods and ResultsHuman dermal fibroblasts were reprogrammed using Ad-ETV2 and characterized by flow cytometry, RNA sequencing, and functional assays. Therapeutic efficacy was evaluated in murine hindlimb ischemia with or without PA-RGDS encapsulation over 12 months. Ad-ETV2 induced robust endothelial gene expression (CDH5, KDR, PECAM1) within 6 days, with 40-50% reprogramming efficiency. KDR+ Ad-rECs demonstrated functional endothelial properties including Ac-LDL uptake, tube formation, and exceptional proangiogenic factor secretion (200-fold higher HGF than HUVECs). RNA sequencing revealed rapid transcriptional reprogramming with fibroblast gene suppression and endothelial/angiogenic gene activation. In hindlimb ischemia, Ad-rECs significantly enhanced blood flow recovery and capillary density versus controls. Long-term analysis revealed sustained vascular contribution through three mechanisms: direct incorporation, perivascular support, and vessel guidance, persisting throughout 12 months--the longest reported follow-up for reprogrammed cells. PA-RGDS encapsulation markedly improved cell retention; while 75% of cells were lost by 3 months, retention stabilized thereafter with minimal additional loss through 12 months. ConclusionsAdenoviral ETV2 delivery enables efficient generation of clinically compatible rECs without genomic integration. These cells demonstrate potent and sustained therapeutic efficacy through multiple vascular regeneration mechanisms. PA-RGDS encapsulation significantly enhances long-term engraftment, establishing this combined approach as a promising platform for treating ischemic cardiovascular diseases.

cell biology↗

bioRxiv2025

Single-vessel transcriptome map pathological landscapes and reveal NR2F2-mediated smooth muscle cell phenotype acquisition in capillary malformations

BackgroundCapillary malformation (CM) is a congenital vascular anomaly affecting the skin, mucosa, and brain, yet the understanding of its vascular pathogenesis remains limited. MethodsWe applied spatial whole-transcriptome profiling (GeoMx) and gene set enrichment analysis within CM lesions at single vasculature level. Differentially expressed genes were validated by immunofluorescence staining. Phosphoproteomics was profiled to uncover lesion- wide phosphorylation sites on proteins. Single-cell RNA sequencing was performed on CM- derived induced pluripotent stem cells (iPSCs) to determine differentiation trajectories of lesional vascular lineages. In silico gene perturbation was used to predict candidate genes for modulating vascular pathological progression, followed by functional validation in CM iPSC-derived endothelial cells (ECs) using a Tet-on system. ResultsA spatial transcriptomic atlas was constructed, and pathological landscape of individual CM vasculature was delineated. CM vessels exhibited hallmarks of endothelial-to-mesenchymal transition (EndMT), including disruption of adherens junctions (AJs), vascular identity transitions, and metabolic remodeling. Phosphoproteomics confirmed that differentially phosphorylated proteins were enriched in EndMT- and AJ-related pathways. Aberrant expression of venous transcriptional factor NR2F2 was observed in lesional ECs and correlated with progressive enlargement from capillaries to larger-caliber vessels containing multiple layers of smooth muscle cells (SMCs). In CM iPSCs, differentiation course yielded reduced ECs but increased SMCs. In silico knockout simulation predicted NR2F2 as a crucial regulator of facilitating SMC phenotype in CM. Consistently, enforced NR2F2 expression during iPSC differentiation suppressed endothelial markers while inducing SMC-associated genes. ConclusionsSingle CM vasculature displays pathological hallmarks characterized by EndMT and AJ disruption, leading to progressive vascular remodeling. NR2F2 functions as a central regulatory factor orchestrating the acquisition of the SMC phenotype, thereby representing a potential therapeutic target in CM.

pathology↗