👤 Kexin Ren

Atherosclerosis (AS) serves as the pathological foundation for numerous cardiovascular and cerebrovascular diseases and is highly comorbid with depression. The mechanisms underlying this co-morbidity are exceptionally complex, posing significant challenges to effective clinical treatment. Consequently, our study aims to explore the potential biomarkers and mechanisms involved in developing atherosclerosis co-depression disease. We performed differential expression analysis, protein-protein interaction analysis, Gene Ontology (GO) function enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis on co-differentiated genes using AS and depression-related datasets from the GEO database. Potential biomarkers were identified through ROC curve analysis. To evaluate the effectiveness of the model, we established an animal model of AS comorbid with depressive disorder and performed a series of assessments, including the sugar-water preference test, open field test, tail suspension test, lipid profile analysis, and pathological examination of aortic sections. Additionally, RNA sequencing analysis of brain tissue, Golgi staining, and detection of synaptic function-related proteins were performed in AS comorbid depressed mice. Finally, in vitro cellular experiments were conducted to further validate the molecular targets and underlying mechanisms. We identified 968 differentially expressed genes associated with AS and 472 differentially expressed genes associated with depression, with 30 genes co-differentially expressed. Protein-protein interaction (PPI) analysis revealed that CCR5, CCR2, NPY, and OPRM1 were strongly associated with AS co-depression, while ROC analysis indicated that Shank2, MDGA2, and S100B were diagnostic markers for AS with depression. Differentially expressed genes were closely associated with the chemokine signaling pathway, neuroactive ligand-receptor interaction, cytokine-cytokine receptor interaction, and taste transduction. Animal studies demonstrated that ApoE Our study identified seven candidate AS co-depression biomarkers and verified that inflammation-induced damage to synaptic plastic rows is an important mechanism of AS co-depression, providing new insights into the diagnosis and treatment of AS co-depression disorders. Show less

The integrity of blood-brain barrier (BBB) plays a pivotal role in the pathogenesis of Alzheimer's disease (AD) by regulating Aβ clearance and neurotoxic compound exclusion. Hyperlipidemia exacerbates AD by impairing the BBB function. Inclisiran, a PCSK9-targeting siRNA, reduces cholesterol levels; however, its neuroprotective effects remain unclear. Here, we report the novel discovery that Inclisiran attenuates AD-like changes through the PCSK9-ferroptosis axis in brain microvascular endothelial cells (BMECs). First, integrated bioinformatics analysis and experimental validation of cortical tissues from patients with AD and healthy controls revealed a coordinated upregulation of PCSK9 and β-amyloid (Aβ), accompanied by increased iron deposition and significant activation of the ferroptosis pathway. Interestingly, these changes are located in the BMECs of the blood-brain barrier rather than in the brain parenchyma. Second, in hyperlipidemic ApoE Show less

Aniridia, driven by PAX6 mutations, causes aniridia-associated keratopathy (AAK), a progressive condition linked to limbal stem cell deficiency. A major hurdle to developing targeted therapies for AAK is the incomplete understanding of the molecular abnormalities in affected corneas. To address this, we leveraged Pax6± (Pax6 het) mice, a model of AAK, and applied single-cell RNA sequencing (scRNA-seq) to profile the transcriptomic changes at a single-cell resolution. ScRNA-seq of corneal/limbal tissues of wild type (WT) and Pax6 het mice were conducted. Immunostaining was performed to examine the expression of specific markers for stem cells. ScRNA-seq identified a quiescent limbal epithelial stem cell (LESC)-like cell cluster and an early transient amplifying cell (eTAC)-like cluster. An increase in the cell numbers in these two clusters in the Pax6 het mouse corneas was observed. Immunostaining detected a marked increase in markers for these two clusters including Tmem176b, Apoe, and Krt15 in the corneal epithelium of Pax6 het mice, suggesting an increase of these LESC/eTA-like cells into the corneal epithelium. The Pax6 deficiency inhibited the expression of genes involved in cell proliferation in the eTAC-like cluster as well as the expression of genes related to corneal epithelial cell fate and differentiation compared with WT mice. Our single cell transcriptome of the limbus and cornea of Pax6 het mice indicates that AAK may be due to the increase of dysfunctional stem/eTACs with defects in committing to a corneal epithelial cell fate and differentiation. Show less

Atherosclerosis is a chronic inflammatory disease marked by lipid accumulation and immune cell infiltration in arterial walls. Macrophages contribute by internalizing oxidized low-density lipoprotein, forming foam cells, and driving inflammation. The ubiquitin-proteasome system regulates immune and inflammatory responses in atherosclerosis. This study investigated the protective role of TRIM31 (tripartite motif-containing 31), an E3 ubiquitin ligase, in macrophage lipid metabolism and inflammation through selective regulation of LOX-1 (lectin-like oxidized low-density lipoprotein receptor-1). Transcriptomic profiling, macrophage-specific TRIM31 was selectively upregulated in macrophages under oxidized low-density lipoprotein stimulation and in atherosclerosis plaques. Trim31 deficiency exacerbated plaque burden, foam cell formation, and inflammatory signaling (n=8 per group). Single-cell analysis revealed enrichment of lipid transport and inflammatory pathways in Trim31-deficient plaques. LOX-1 was identified as a key TRIM31 substrate. TRIM31 promoted K48-linked ubiquitination of LOX-1 at lysine 12, facilitating its degradation. The atheroprotective effects of Trim31 were abolished in TRIM31, an inducible, macrophage-enriched protective factor in atherosclerosis, restricts foam cell formation and inflammation by targeting LOX-1 for proteasomal degradation. These findings position TRIM31 as a promising therapeutic target for macrophage-driven atherogenesis. Show less

Most brain organoids derived from human induced pluripotent stem cells (iPSCs) lack microglia and thus immune function. Microglia-like cells (MGCs) can be differentiated from iPSCs, while the characteristics of isogenic MGC-containing brain organoids in modeling neurodegeneration and cell-cell communications have not been well investigated. In this study, iPSC-derived MGCs are co-cultured with isogenic forebrain cortical organoids (iFCo), which are stimulated with extracellular vesicles (EVs) of brain organoids differentiated from Alzheimer's disease (AD) patient-derived iPSCs (APOE ε4/ε4 and presenilin 1). The AD EV-stimulated co-culture organoids are treated with EVs from healthy MGCs or co-culture. Differential responses of the co-cultured organoids and the MGCs to AD EVs are demonstrated. The co-cultured organoids mitigated pro-inflammatory gene expressions. EVs from healthy MGCs or co-culture reduced the expression of IL-12β, iNOS, TREM2, and CASS4, which are associated with neural inflammation and degeneration, as well as showed regulation on genes involved in microglial activation and carbon metabolism. AD EV cargo analysis by proteomics and microRNA-sequencing revealed APOE and APP proteins and microRNAs regulated pathways such as mitophagy. This study paves the way for understanding the role of microglia and brain organoids in modeling neural degeneration and the development of EV-based cell-free therapeutics for AD treatment. Show less

Atherosclerosis (AS), a major cardiovascular disease driver, can be caused by high levels of serum cholesterol. Eggs are the main source for dietary cholesterol, and although epidemiological studies reported no association between egg intakes and cardiovascular diseases, dietary cholesterol intake is still restricted for individuals with dyslipidemia. This study evaluated the effects of egg yolk lipids isolated from low-cholesterol (LC) and normal eggs (NC) on the progression of AS using the ApoE Show less

Obesity is a well-established risk factor for asthma pathogenesis. However, the underlying mechanisms remain incompletely understood, and effective therapeutic interventions are currently lacking, making asthma management in obese individuals particularly challenging. Asthma is characterized by chronic airway inflammation, eosinophilic infiltration, and airway hyperresponsiveness (AHR). In this study, we investigated the novel role of fibroblast growth factor 21 (FGF21), a stress-inducible hepatokine with pleiotropic metabolic regulatory functions, in obesity-associated AHR using a diet-induced obesity mouse model (n = 10). Serum samples were collected from obese and lean asthma patients, along with relevant clinical indicators, including body mass index (BMI), forced expiratory volume in 1 second (FEV1%), and the FEV1/forced vital capacity (FVC) ratio, to facilitate the investigation. Moreover, diet-induced obese mice with innate AHR (male, n = 10) were employed to clarify the effects of FGF21 and FGF21-neutralizing antibody on obesity induced AHR. In vitro, LAD2 human mast cells and P815 murine mast cells activated by compound 48/80 were used to elucidate the underlying mechanisms. Our findings demonstrate that serum FGF21 levels exhibit reportedly elevated in participants with obesity and are associated with impaired pulmonary function. In diet-induced obese (DIO) mice, FGF21 levels were increased in both serum and bronchoalveolar lavage fluid (BALF). In vivo investigations demonstrate that administration of recombinant FGF21 exacerbated AHR in DIO mice, whereas FGF21-neutralizing antibody treatment ameliorated obesity-induced AHR and suppressed mast cell infiltration. Mechanistically, FGF21 was found to potentiate mast cell activation through cholesterol biosynthesis modulation. Crucially, pharmacological inhibition of FGFR1 abrogated FGF21-induced mast cell hyperactivity and cholesterol synthesis, indicating FGFR1-dependent signaling in this process. These findings may represent the FGF21/FGFR1 axis as a potential therapeutic target for obesity-related AHR and asthma. Show less

Fibroblast growth factor receptor 2 (FGFR2) has gained recognition as a compelling therapeutic target in oncology. We present LHQ766, a novel orally bioavailable FGFR2 inhibitor demonstrating exceptional potency and selectivity, through optimization of our previously reported FGFR2 inhibitor 7. The structures and purity of all target compounds were confirmed by Show less

A plethora of factors contribute to cognitive impairment in Alzheimer's disease (AD), including neuroinflammation, synaptic dysfunction and gene alteration. In search of transcription factors controlling dysregulated genes in AD, we identified that the histone demethylase PHF2 (KDM7C) was a top-ranking candidate. Significant upregulation of PHF2 was found in AD human postmortem tissues, iPSC-derived neurons from AD patients, and a familial AD mouse model (5xFAD). ChIP-seq analysis and quantitative PCR profiling with bidirectional manipulation of Phf2 revealed that Phf2 regulated many genes critically involved in inflammatory pathways and neurodegeneration, including Stat3, Nfkbia, Nfkb2, Tnfrsf1a, Fgfr1, IL6st, Notch2, and Csf1. Knockdown of Phf2 in 5xFAD mice reduced the expression of inflammatory genes, leading to the substantial reduction of microglia/astrocyte activation and the restoration of glutamatergic synaptic function. Behavioral studies showed that Phf2 knockdown in 5xFAD mice significantly improved performance in the Barnes maze test, indicating a mitigation of spatial memory deficits. Our findings have revealed the epigenetic enzyme PHF2 as a regulator of neuroinflammatory processes in AD, linking its activity to both gene expression and cognitive outcomes. It suggests that targeting PHF2 could be a novel therapeutic approach for AD and other brain disorders involving neuroinflammation. Show less

The high prevalence of cancer immunotherapy resistance, coupled with substantial tumor heterogeneity, underscores the urgent need for innovative therapeutic targets. A deeper understanding of immunoregulatory mechanisms would provide new targets and combination therapeutic strategies for tumor therapy. In this study, we demonstrate that HSD17B12 enhances anti-tumor immunity and represents a promising therapeutic target. Mechanistically, HSD17B12 promotes lysosome-dependent degradation of PD-L1 via the VAC14 and ESCRT complexes across various malignancies, regardless of its 3-ketoacyl-CoA reductase activity. HSD17B12-deficient cells displayed PD-L1 accumulation in both tumor cells and exosomes, reducing T cell-mediated cytotoxicity. Notably, we found a significant negative correlation between HSD17B12 and PD-L1 expression in colorectal cancer tissues. Furthermore, high HSD17B12 expression in CRC correlated with increased infiltration of cytotoxic T cells. Based on these findings, we designed a peptide, HSD-CC1-NPGY, which effectively reduces PD-L1 expression in cells and suppresses tumor growth in a mouse model. Overall, our results establish HSD17B12 as an important regulator of anti-tumor immunity and a promising therapeutic target for cancer treatment. Show less

Compared with non-left-behind children (NLBC), left-behind children (LBC) face a higher risk of academic stress, depression, and anxiety symptoms due to separation from their parents; however, the heterogeneity of academic stress profiles and their relationships with the symptom network remain insufficiently explored. To address this gap, a cross-sectional survey of 10,524 Chinese children compared LBC (n = 2487) and NLBC. Latent profile analysis (LPA) was first conducted to identify academic stress subgroups among LBC. Subsequently, depression-anxiety symptom networks were estimated using Ising and Gaussian graphical models (GGM), with edge weights derived from regularised logistic regression (Ising) and partial correlation (GGM). Simulated interventions were further evaluated via the NodeIdentifyR algorithm (NIRA). Overall, compared to NLBC, LBC exhibited higher levels of academic stress, depression, and anxiety (ps < 0.001, Cliff's δ = 0.076; Cohen's d = 0.067). LPA revealed three academic stress subgroups: moderate (31.44%), high (9.17%), and low (59.39%). The severity of depression and anxiety symptoms increased with the level of academic stress. The high stress subgroup displayed a sparse network with stronger edges (e.g., A1 'Sudden Fear'-A4 'Physical Symptoms', edge weight = 2.10) compared to moderate- and low-academic stress subgroups. Core nodes with the strongest expected influence were A8 ('Decision Hesitation', moderate subgroup), A2 ('Worry', high subgroup), and D1/D6 ('Sadness' and 'Failure', low subgroup). Simulated interventions indicated that alleviating A8 'Decision Hesitation' or A2 'Worry' most effectively reduced symptom risk (16.66%-30.76%), whereas D8 'Motor' and A7 'Early Departure' were associated with maximal symptom aggravation. Taken together, by integrating LPA-derived academic stress profiles with symptom network analysis, this study reveals distinct symptom associations across subgroups. In the high stress subgroup, symptom A2 ('Worry') is a core intervention target; in the low stress subgroup, A7 ('Early Departure') holds preventive potential. These findings underscore subgroup-specific interventions tailored to individual stress profiles. Show less

To examine associations between the 24-h composition of movement behaviors (sedentary behavior [SB], light physical activity [LPA], moderate-to-vigorous physical activity [MVPA], and sleep) and physical and mental health in older adults using compositional data analysis. Data came from 4,150 adults aged ≥ 60 in the 2015 China Health and Nutrition Survey. Multiple‑balance isometric log‑ratio regression and compositional isotemporal substitution models were used to assess relative associations and the effect of time reallocation. The 24‑hour geometric mean composition was 43.1% sleep, 30.6% SB, 21.8% LPA, and 4.5% MVPA. LPA was positively associated with physical (β = 0.062, Replacing sedentary time or sleep with LPA, even in small amounts, is associated with better physical and mental health in older adults, supporting integrated 24‑hour activity guidelines that emphasize light‑intensity movement. Show less

This study aimed to assess the childbirth readiness of women in their third trimester of pregnancy and to identify distinct readiness profiles using latent profile analysis (LPA). Additionally, it explored the factors influencing childbirth readiness in order to guide targeted interventions for improved maternal and neonatal outcomes. A cross-sectional study was conducted among women in their third trimester of pregnancy between May and November 2024. Eligible participants completed a general information questionnaire, the Childbirth Readiness Scale (CRS), the Childbirth Attitude Questionnaire (CAQ), and the Perceived Social Support Scale (PSSS). LPA identified three groups with distinct childbirth readiness levels: "Low Readiness - Childbirth Knowledge Deficit" (37.9%), "Moderate Readiness - Good Lifestyle Habits" (47.9%), and "High Readiness - Rich Health Knowledge" (14.2%). In addition, gestational age, previous childbirth history, adverse pregnancy outcomes, childbirth attitudes, and social support had different influences on women in different latent profiles of childbirth readiness. There was significant heterogeneity in childbirth readiness among women in their third trimester. Women with lower readiness-especially in childbirth knowledge-would greatly benefit from targeted educational programs, whereas those with moderate readiness levels would find enhanced emotional and psychological support most advantageous. These findings support the implementation of profile-based, personalized prenatal care strategies to improve childbirth preparedness and optimize maternal and neonatal outcomes. Show less

Reflective practice has emerged as a critical competency for psychiatric nurses, enabling them to critically evaluate and adapt their care approaches. Growing evidence suggests that reflective practice may serve as a key driver of high-quality caring behaviors, which are essential for establishing therapeutic relationships and improving outcomes in mental health settings. This study aimed to classify latent profiles of reflective practice among psychiatric nurses and examine their effects on caring behaviors. This cross-sectional study was conducted to recruit psychiatric nurses from ten mental health treatment centers across ten hospitals in Sichuan Province, China, between January and March 2024. Psychiatric nurses completed an online investigation encompassing the Reflective Practice Questionnaire and the Caring Behaviors Inventory (CBI). Latent profile analysis (LPA) and hierarchical regression analysis were employed to achieve the study objectives. A total of 346 psychiatry nurses were included in this study. The reflective practice of psychiatric nurses was classified into three subgroups in this study: "passive reflective participants" (n=48, 13.9%), "moderately balanced reflective practitioners" (n=175, 50.6%), and "high-achieving reflective leaders" (n=123, 35.5%). The hierarchical regression analysis revealed a significant positive association between distinct profiles of reflective practice and psychiatric nurses' caring behaviors (ΔR The identification of three distinct reflective practice profiles ("passive reflective participants", "moderately balanced reflective practitioners", and "high-achieving reflective leaders") provides a nuanced understanding of the reflective practice among psychiatry nurses. Targeted development programs, such as peer mentoring for the "passive" group and the "moderate" group, could be designed based on individual profile membership to optimize caring behaviors in psychiatric nursing. Show less

Peripheral artery disease (PAD) is a major manifestation of systemic atherosclerosis and affects vascular health in older adults. Dyslipidaemia contributes significantly to PAD, but the predictive value of composite lipid indices remains unclear. The non-high-density lipoprotein cholesterol (non-HDL-C) to high-density lipoprotein cholesterol (HDL-C) ratio (NHHR) reflects the balance between atherogenic and protective lipoproteins. This study aimed to explore the association between the NHHR and PAD among vascular surgery inpatients aged ≥50 years in Kunshan, China. This retrospective cross-sectional study included 3,532 patients (aged ≥ 50 years) hospitalized at the Affiliated Kunshan Hospital of Jiangsu University, Suzhou, from December 2017 to August 2024. NHHR, calculated as (total cholesterol - HDL-C)/HDL-C, was the exposure variable; PAD, defined as PAD-like symptoms with an ankle brachial index < 0.9, was the outcome. Covariates included age, sex, lipoprotein(a) level [Lp(a)], apolipoprotein A1 level (Apo A1), alanine aminotransferase (ALT) level, neutrophil count (NEUT), hypertension status, diabetes status, smoking status, and alcohol consumption status. Multivariate logistic regression, smooth curve fitting, and threshold analyses were performed. After adjustment for confounders, the NHHR was nonlinearly associated with PAD (OR = 0.77; 95% CI: 0.65-0.93; The NHHR was associated with the presence of PAD, with the evidence suggesting a nonlinear relationship and potential sex-specific differences. Given the retrospective cross-sectional design, this association does not support causal inference or strong predictive claims. The NHHR may help identify individuals who could benefit from further clinical evaluation for PAD, but prospective studies are needed to confirm its clinical relevance before its routine application. Show less

The pervasive nature of social media has given rise to the phenomenon of fear of missing out (FoMO), which poses significant challenges to the mental health of children. By drawing on an individual-centered approach, this study aims to provide a nuanced understanding of FoMO. We delved into the evolving nature of FoMO patterns among 541 Chinese primary school students within a one-year interval. Employing Latent Profile Analysis (LPA) and Random Intercept Latent Transition Analysis (RI-LTA), we uncovered three distinctive profiles of FoMO: Social Sentinels, Worry Warriors and Untroubled Buddies. To predict transitions between these profiles, we examined anxiety and mindfulness. We also investigated the relationship between two related outcomes and latent transitions. The results revealed that the Untroubled Buddies profile was relatively stable, while the Social Sentinels and Worry Warriors profiles showed more frequent transitions over time. Regarding the antecedents, our findings demonstrated that primary school students with high anxiety were more likely to be categorized under the Social Sentinels and Worry Warriors profiles, increasing their risk of transitioning from the Untroubled Buddies profile to the other two profiles over time. Regarding the associations with outcomes, significant differences emerged among the three profiles in terms of emotional and behavioral problems as well as depression at three measurement points. Identifying different FoMO profiles among primary school students and understanding the nature of transitions between these profiles have implications for developing targeted interventions to mitigate FoMO risks among primary school students, as well as preventing individuals from transitioning into profiles associated with higher risks of emotional and behavioral problems and depression. Show less

The polyphenols in grains are highly active, but some polyphenols in highland barley are in a bound form and have extremely low bioavailability. Fermentation by lactic acid bacteria (LAB) is capable of altering the functionality of foods. This research investigated the effects of fermentation with different LAB, such as Lactobacillus acidophilus (LAC), Lactobacillus casei (LCA), Lactobacillus rhamnosus (LRH), Lactobacillus plantarum (LPL), and Lactobacillus bulgaricus (LBU), on the hypoglycemic activity and mechanism of polyphenols in highland barley. The hypoglycemic activity of the fermentation products was measured by in vitro antioxidant, enzyme activity, and glucose consumption experiments. Untargeted metabolomic analysis used UHPLC-Q Exactive HF-X/MS to reveal distinct metabolic profiles among the fermented groups. Molecular docking and western blot experiments were conducted to elucidate the mechanism underlying the hypoglycemic effect of fermentation products. Polyphenolic antioxidant activity in highland barley and its inhibitory activities against α-glucosidase and α-amylase were increased after LAC fermentation. Furthermore, the fermented extracts improved glucose consumption in HepG2 cells. The content determination and metabolomic analysis showed that fermented highland barley polyphenols were increased, and 113 differential phenolic metabolites were identified and annotated, among which 44 exhibited a significant upregulation compared with raw highland barley polyphenols. At the molecular level, the polyphenol extract upregulated PI3K and phosphorylated Akt expression in HepG2 cells. Overall, the results indicate that fermentation by LAC biotransformed highland barley polyphenols into smaller molecules with improved hypoglycemic activities, thereby enhancing their bioavailability. Show less

Xinjiang Province possesses several local sheep breeds which are well known for their tender meat, delicious taste, and lack of odor. At present, the microbial composition in the gastrointestinal tract of Xinjiang sheep and its correlation with the lipid metabolism and meat flavor are still not investigated. This study investigated the community composition of intestinal microbiota and its relationship with lipid metabolism enzymes and volatile organic compounds (VOCs) in four breeds of Xinjiang sheep. Bacteroidetes and Firmicutes, known for their roles in carbohydrate fermentation and short-chain fatty acids (SCFAs) production, dominated the microbial communities across all breeds. The Hetian sheep had the highest number of operational taxonomic unit (OTU) species as well as higher lipid metabolism enzyme activities (acetyl-CoA carboxylase: 11907 ± 1075.12 U g The results revealed a link between the unique flavor profile of Xinjiang mutton and the composition of its intestinal microbiota. The intestinal microbiota directly modulates host lipid metabolism through the secretion of SCFAs, ultimately regulating lipid deposition and VOCs in mutton. © 2025 Society of Chemical Industry. Show less

Methotrexate (MTX) is a widely used chemotherapy drug, but its neurotoxicity can lead to cognitive impairments, particularly through effects on hippocampal function. Nevertheless, the underlying molecular mechanisms are not fully understood. Deciphering MTX-induced cognitive impairment-linked molecular mechanisms in cells of the hippocampus could uncover novel therapeutic targets. In this study, we established a mouse model of cognitive impairment induced by the chemotherapy drug MTX. We applied single-nucleus RNA sequencing (snRNA-seq) to analyze the transcriptomic alterations in hippocampal cells of mice following MTX treatment, with a focus on neuron-specific gene expression changes. MTX chemotherapy led to a decrease in excitatory neurons but an increase in inhibitory neurons, altering the excitatory-inhibitory balance of neural networks and thus mediate cognitive dysfunction. Furthermore, MTX significantly disrupted the transcriptional regulatory network and potential trajectory of GABAergic neurons. It enhanced the Nrg1-Erbb4 pathway while attenuating the Nrxn3-Lrrtm4 pathway, destabilizing trans-synaptic signaling and causing abnormalities in excitatory and inhibitory synaptic functions. These disruptions may ultimately lead to neural network imbalance and cognitive dysfunction. This study highlights the specific effects of MTX chemotherapy on hippocampal cellular function and provides valuable insights into the molecular mechanisms underlying cognitive deficits and potential therapeutic targets. Show less

Autophagy supports clear cell renal cell carcinoma (ccRCC) progression, yet its upstream regulatory mechanisms remain to be fully defined. Integrating bulk, single-cell, and spatial transcriptomics, we identify a regulatory axis wherein the transcription factor ZBED6 activates the expression of the autophagy-initiating kinase PIK3C3 via the repression of IGF2, thereby driving pro-tumorigenic autophagy. Spatial analysis confirms the co-localization of ZBED6 and PIK3C3 in tumor tissues. Using genes associated with this axis, we develop a six-gene prognostic signature that stratifies patients with distinct survival outcomes and differential responses to immunotherapy and targeted therapy. Functional assays show that ZBED6 promotes ccRCC cell proliferation, migration, and invasion. This work elucidates a pathway governing autophagy in ccRCC and provides a framework for prognostic assessment and precision therapy. Show less

Metabolic‒epigenetic crosstalk critically orchestrates hepatocellular carcinoma (HCC) pathogenesis. Deciphering the precise mechanism underlying epigenetic remodeling and metabolic reprogramming in HCC may lead to novel treatment paradigms, however, the key mechanisms remain elusive. RT-qPCR, western blotting and tissue microarrary Immunohistochemistry were used to detect the expression of RasGEF domain family member 1B (RASGEF1B) in HCC and normal liver tissues. Transcriptome sequencing and high-resolution untargeted metabolomics were integrated to identify the downstream regulatory mechanism through which RASGEF1B inhibited the HCC progression. Epigenetic regulation was investigated using methylation-specific PCR and luciferase reporter assays. Bioinformatic prediction and molecular docking suggested a functional interplay among RASGEF1B, ALDH7A1, and BMI1, which was experimentally confirmed through coimmunoprecipitation, GST pull-down, and immunofluorescence assays. Protein stability and ubiquitination status of ALDH7A1 were examined using cycloheximide, immunoprecipitation assay, and an in vitro reconstituted ubiquitination system. In this study, the antitumor role of RASGEF1B was confirmed in vitro and in vivo. Transcriptomic profiling revealed that RASGEF1B overexpression significantly reduced the snail family transcriptional repressor 1 (SNAI1), a master regulator of the epithelial-mesenchymal transition. Untargeted metabolomics revealed that RASGEF1B promoted SNAI1 DNA methylation through Betaine-mediated methionine metabolic reprogramming. Further analysis confirmed that RASGEF1B competitively protected the ALDH7A1 protein from BMI1-dependent ubiquitination, thereby elevating cellular Betaine levels in HCC. This study revealed that RASGEF1B inhibited SNAI1 to suppress HCC through metabolite‒epigenetic crosstalk. Our findings potentially offer a new perspective on the classical RAS signaling framework, uncovering a metabolic‒epigenetic axis as an innovative therapeutic approach for improving clinical outcomes in patients with HCC. [Image: see text] The online version contains supplementary material available at 10.1186/s12967-026-07785-z. Show less

Cellular senescence, characterized by permanent cell cycle arrest, significantly influences cancer development, immune regulation, and progression. However, the precise mechanisms by which senescence contributes to colorectal cancer prognosis remain to be fully elucidated. By integrating expression profiles of senescence-related and prognostic genes in colon adenocarcinoma (COAD) patients, we formulated and confirmed a nine-gene cellular senescence-related signature (CSRS) that integrates senescence-associated and prognosis-predictive genes using data from the CellAge, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). A cell senescence-related prognostic formula was developed as follows: CSRS = (CASP2 × 0.2098) + (CDKN2A × 0.1196) + (FOXD1 × 0.1472) + (ING5 × 0.3723) + (OXTR × 0.0786) + (PHGDH × 0.1408) + (SERPINE1 × 0.1127) + (SNAI1 × 0.1034) + (LIMK1 × 0.0747). In a multivariate Cox proportional hazards model, the CSRS score, age and TNM stage were all identified as significant independent indicators for overall survival, affirming their prognostic value in colorectal cancer. The CSRS-high group exhibited significantly up-regulated senescence-associated secretory phenotype (SASP) and immune cell infiltration, whereas the CSRS-low group showed an apparent better response to immune-checkpoint inhibitor therapy. Our findings suggest CSRS score and its constituent genes represent potential biomarkers for prognosis and immunotherapeutic benefit in COAD patients. Extending this nine-gene set into a broader senescence-associated panel should be a next step toward delivering truly individualized treatment plans. Show less

Wilms tumor (WT), the most common pediatric malignant renal tumor, shows high recurrence in high-risk subtypes due to chemoresistance. Tumor microenvironment (TME) remodeling, particularly M2-type tumor-associated macrophages (TAMs), contributes to chemoresistance, but underlying mechanisms remain unclear. This study explored TME-related chemoresistance mechanisms in WT and developed targeted therapeutic strategies. Clinical WT samples were analyzed for M2-type TAMs infiltration and SNRPC expression. Bioinformatics analysis of TARGET-WT data identified M2-associated genes. In vitro experiments (cell transfection, qRT-PCR, Western blot, co-culture, ChIP and dual-luciferase reporter assays) explored SNRPC’s role in regulating M2-type TAMs. Animal models (orthotopic tumor and lung metastasis) verified in vivo effects. A hybrid exosome nanosystem (DOX/siSNRPC@hEVs) was constructed and evaluated for efficacy and safety. Statistical analyses included t-test, ANOVA, and survival analysis. M2-type TAMs (CD68⁺CD163⁺) infiltration was higher in chemoresistant WT and associated with poor prognosis. SNRPC was overexpressed in chemoresistant WT, correlated with M2-type TAMs, and promoted tumor malignancy and M2-type TAMs polarization. Mechanistically, SNRPC activated NF-κB signaling, inducing CXCL17 upregulation to recruit M2-type TAMs, with partial CXCL17 release via migrasomes. DOX/siSNRPC@hEVs showed high targeting, reduced toxicity, inhibited tumor growth/metastasis, and reversed chemoresistance by reducing M2-type TAMs. The SNRPC-NF-κB-CXCL17-M2 TAMs axis drives WT chemoresistance. DOX/siSNRPC@hEVs effectively targets this axis, providing a novel strategy for high-risk WT. [Image: see text] The online version contains supplementary material available at 10.1186/s13046-026-03680-z. Show less

Leptin resistance limits anti-obesity efficacy. We identified a leptin-sensitizing mechanism through tirzepatide (TZP), a glucagon-like peptide-1 receptor (GLP-1R) and glucose-dependent insulinotropic polypeptide receptor (GIPR) dual-agonist. Our tirzepatide clinical trial revealed that circulating leptin levels at baseline correlated with weight loss efficacy in patients with obesity, suggesting leptin and tirzepatide could interact to achieve stronger effects on weight loss. Next, we utilized the diet-induced obesity (DIO) mice and demonstrated the synergistic effects of tirzepatide and leptin combination (TZP+Lep) on weight loss. TZP+Lep treatment further improved hepatic insulin sensitivity and upregulated thermogenetic gene expression in brown adipose tissue. Metabolic profiling under thermoneutrality revealed TZP+Lep treatment further reduced food intake and increased energy expenditure. Tirzepatide sensitized leptin signaling in hypothalamic pro-opiomelanocortin (POMC) and GLP-1R expressing neurons. TZP+Lep synergistically increased POMC neuronal firing by decreasing the inhibitory postsynaptic input. Together, our work showed combining tirzepatide and leptin as a potential way for better maintenance of metabolic homeostasis in obesity management. Show less

Ulcerative colitis (UC) is a prevalent chronic gastrointestinal disease. Gene plays an important role in UC pathogenesis. Therefore, we aim to identify UC susceptibility genes and specific cell types expressing these genes. We conducted a cross-tissue transcriptome-wide association study by integrating UC GWAS with 49 tissues gene expression matrix from the Genotype-Tissue Expression project. Subsequently, we employed Functional Summary-based Imputation to verify candidate genes within colon tissue. Conditional and Joint Analysis was utilized to filter out genes potentially influenced by linkage disequilibrium. Multimarker Analysis of Genomic Annotation was then applied to pinpoint genes relevant to UC. Validation of the selected genes was performed using Mendelian randomization. GeneMANIA analysis was conducted to elucidate biological functions of identified genes. Finally, single-cell RNA sequencing was employed to ascertain cell types in which these genes are enriched. The cross-tissue transcriptome-wide association study, Functional Summary-based Imputation and Multimarker Analysis of Genomic Annotation analyses identified a total of 5 genes, of which 3 genes, ADCY3, ITGB6, and MTMR3, were retained after Mendelian randomization. These genes were found to be implicated in several functional pathways, including the cyclic AMP metabolic process and phosphorus-oxygen lyase activity. Furthermore, we observed ADCY3 predominantly enriched in B cells, while ITGB6 and MTMR3 enriched in epithelial cells. Our study has identified 3 genes associated with UC susceptibility. These findings not only enhance our understanding of the genetic underpinnings of UC, but also offer novel avenues for exploring molecular mechanisms and potential therapeutic targets for UC. Show less

Short sleep duraiton is a putative risk for dementia, whereas midlife obesity is an well-known risk factor. Midlife short sleep and obesity share some biological changes such as inflammations or metabolic changes, but their combined impact is not yet fully understood. Our aim is to investigate the associations of short leep obesity with cognitive decline and dementia risk, and to investigate whether these associations are mediated by blood markers. This is an analysis of prospective cohort study of adults who were free of dementia, had data on sleep duration and BMI at baseline in 1997-1999, and were tracked for dementia diagnoses until 2023 via linkage to electronic health records. Participants will be divided into four groups: (1) the reference group (2) short sleep (2) short sleep (≤6 hours) and non-obese weight; (3) normal sleep and obesity (≥30kg/m Show less

The sea cucumber collagen contains a high content of hydrophobic amino acids, which play essential roles in various bioactivities. A total of 2647 unknown active peptide fragments (2-20 amino acids) were obtained via virtual enzymolysis from 16 known collagen sequences in Apostichopus japonicus. Then, the novel bifunctional hexapeptide (DCDPRL, 717.788 Da) with hypoglycemic and antioxidant activities was identified via molecular docking and pharmacokinetics. DCDPRL revealed strong radical scavenging capacity in vitro with IC Show less

G protein-coupled receptors (GPCRs) play key roles in physiology and are central targets for drug discovery and development, yet the design of protein agonists and antagonists has been challenging as GPCRs are integral membrane proteins and conformationally dynamic. Here we describe computational Show less

Growth traits are among the most important economic phenotypes targeted in the genetic improvement of beef cattle. To understand the genetic basis of growth traits in Huaxi cattle, we performed a genome-wide association study (GWAS) on body weight, eye muscle area, and back fat thickness across five developmental stages in a population of 202 Huaxi cattle. Additionally, publicly available RNA-seq data from the longissimus dorsi muscle of both young and adult cattle were analyzed to identify key genes and genetic markers associated with growth in Huaxi cattle. In total, 7.19 million high-quality variant loci (SNPs and INDELs) were identified across all samples. In the GWAS, the three multilocus models (FarmCPU, MLMM, and BLINK) outperformed the conventional single-locus models (CMLM, GLM, and MLM). Consequently, GWAS analysis was conducted using multilocus models, which identified 99 variant loci significantly associated with growth traits and annotated a total of 83 candidate genes (CDGs). Additionally, 23 of the 83 CDGs overlapped with significantly differentially expressed genes identified from public RNA-seq datasets of longissimus dorsi muscle between young and adult cattle. Furthermore, gene functional enrichment (KEGG and GO) analyses revealed that over 30% of the pathways and GO terms were associated with muscle development and fat deposition, crucial factors for beef production. Specifically, key genes identified included Show less