Biology Direct[JOURNAL]
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200 papers
Hypoxia and lactate metabolism-related gene COL5A3 promotes triple negative breast cancer progression via DDR1/FAK/PI3K/AKT pathway.
Shao QF, Wang ZY, Liang W … +3 more , Li YY, Zhu B, Chen WX
Biol Direct · 2026 Jun · PMID 42310796 · Full text
BACKGROUND: Triple-negative breast cancer (TNBC) is a highly aggressive subtype characterized by a lack of hormone receptors and specific molecular targets, leading to limited treatment options, high recurrence rates, an...
BACKGROUND: Triple-negative breast cancer (TNBC) is a highly aggressive subtype characterized by a lack of hormone receptors and specific molecular targets, leading to limited treatment options, high recurrence rates, and poor clinical prognosis. The Warburg effect in cancer cells generates a tumor microenvironment characterized by hypoxia, low glucose, and high lactate levels, which severely promotes chemoresistance, immune escape, and distant metastasis. Nevertheless, the prognostic significance of hypoxia and lactate metabolism-related genes in TNBC remains largely unclear, and more accurate prediction models are urgently needed. METHODS: Clinical information and gene expression profiles of patients with TNBC were obtained from online databases. LASSO and multivariate Cox regression analyses were used to establish the hypoxia and lactate metabolism-related prediction model, and the prognostic value was further validated using Kaplan-Meier plotter, receiver operating characteristic curves, and nomogram. Gene set enrichment analysis was performed to evaluate the pathways and molecular functions. Tumor mutation, microsatellite instability, RNA expression-based stemness scores, immune infiltration, and drug susceptibility analyses were performed to identify potential therapeutic targets. Single-cell transcriptome data were processed and quality-controlled using Seurat. Monocle2, CellChat, and ssGSEA analyses were used to investigate the relationship between COL5A3, malignant phenotype, and tumor microenvironment. A series of in vitro experiments was performed to evaluate the biological functions of hub gene COL5A3. RESULTS: Five genes, COL5A3, LRRC8D, IGFL1, SEPTIN3, and PEG10, were identified to establish the hypoxia and lactate metabolism-related risk score. TNBC patients divided into high-risk or low-risk groups according to the risk score exhibited substantial differences in survival outcome, tumor mutation, immune infiltration, and drug sensitivity. The constructed model showed strong predictive performance, with receiver operating characteristic curves showing area under the curve values of 0.82, 0.86, and 0.90 at 365, 1085, and 1825 days, respectively. Single-cell analysis showed that high COL5A3 expression was associated with greater proliferative capacity, drug resistance, and stemness. COL5A3 is also involved in regulating the interaction between TNBC cells and other cells in the tumor microenvironment. In vitro studies have indicated that COL5A3 could promote tumor proliferation, migration, invasion, and drug resistance via the DDR1/FAK/PI3K/AKT pathway in TNBC cells. OF-1 was initially identified as a candidate compound with potential therapeutic relevance for TNBC. CONCLUSION: A novel hypoxia and lactate metabolism-related gene signature could be used for prognosis prediction in TNBC patients, and the hub gene COL5A3 promotes TNBC progression via the DDR1/FAK/PI3K/AKT pathway. Further research is needed to explore the biological roles of these genes in TNBC to refine the therapeutic approaches.
Dissecting mitochondria-nucleus contact sites using SPLICS reveals a distributed and dynamic tethering network.
Deligiannopoulou A, Barazzuol L, Peggion C … +4 more , Poggio E, Campanella M, Brini M, Calì T
Biol Direct · 2026 Jun · PMID 42310781 · Full text
Mitochondria-nucleus contact sites (also known as nucleus-associated mitochondria, NAMs) are emerging as important platforms for inter-organelle communication; however, their molecular organisation and regulation remain...
Mitochondria-nucleus contact sites (also known as nucleus-associated mitochondria, NAMs) are emerging as important platforms for inter-organelle communication; however, their molecular organisation and regulation remain poorly understood. Here, we use split-GFP-based contact site sensors (SPLICS-P2A) to quantitatively dissect the contribution of candidate tethering proteins to the formation of short-range mitochondria-nucleus contacts in HeLa cells. Through systematic overexpression and downregulation approaches, we identify TOM70, MFN2, AKAP95, and the catalytic subunit of PKA as positive modulators of contact formation when individually overexpressed. In contrast, loss-of-function experiments reveal a selective role for TOM70, whose downregulation significantly reduces contact site abundance, whereas depletion of other candidates has limited effects. These results suggest that mitochondria-nucleus contacts are not maintained by single dominant tethers but instead rely on the coordinated contribution of multiple proteins. To further investigate cooperative mechanisms, we performed co-expression experiments. Among the combinations tested, TSPO in conjunction with either the regulatory or catalytic subunits of PKA significantly increased contact site formation, indicating that specific protein partnerships are required to establish functional tethering. Overall, our data support a model in which mitochondria-nucleus contact sites are heterogeneous and regulated by a network of interacting factors rather than a single structural component. These findings highlight the complexity of inter-organelle communication and underscore the importance of dissecting both individual and combinatorial roles of contact site components to understand their functional relevance.
ALDH1L2 suppresses ferroptosis-associated responses and reduces sunitinib sensitivity in renal cell carcinoma organoids.
Hu X, Yang J, Li D … +6 more , Deng M, Xie M, Zhan J, Yang C, Che X, Deng K
Biol Direct · 2026 Jun · PMID 42304489 · Full text
BACKGROUND: Sunitinib is an important therapeutic option for renal cell carcinoma (RCC), but reduced response to sunitinib still limits its clinical benefit. This study explored the mechanism underlying reduced sunitinib...
BACKGROUND: Sunitinib is an important therapeutic option for renal cell carcinoma (RCC), but reduced response to sunitinib still limits its clinical benefit. This study explored the mechanism underlying reduced sunitinib sensitivity in RCC and aimed to identify potential strategies to improve sunitinib response. METHODS: RCC organoids were established and characterized, and sunitinib-responsive genes were screened by transcriptomic analysis. Public datasets and clinical RCC samples were used to evaluate the clinical relevance of ALDH1L2. ALDH1L2 overexpression and knockdown were performed in RCC organoids to examine its effects on sunitinib sensitivity and ferroptosis-related changes. Organoid-derived xenograft models were used for in vivo validation. Molecular docking, cytotoxicity assays, CETSA, SPR, and functional experiments were used to screen and validate candidate compounds targeting ALDH1L2. RESULTS: Sunitinib inhibited RCC organoid growth, with IC50 values of approximately 8 μM. Transcriptomic analysis showed that ALDH1L2 was upregulated after sunitinib treatment. Clinical analyses indicated that ALDH1L2 was highly expressed in RCC tissues and was associated with poorer survival and advanced stage. In RCC organoids, ALDH1L2 overexpression attenuated sunitinib-induced ROS accumulation and ferroptosis-related changes, as reflected by changes in GPX4, SLC7A11, GSH/GSSG, NADP /NADPH, Fe, and MDA. In contrast, ALDH1L2 knockdown enhanced these changes and increased the sensitivity of RCC organoids to sunitinib. In organoid-derived xenograft models, ALDH1L2 overexpression reduced the antitumor effect of sunitinib and decreased tumor ROS accumulation. Erastin counteracted the protective effect of ALDH1L2 overexpression. Hederacolchiside A1 (HA-1) was identified as a candidate compound targeting ALDH1L2. HA-1 reduced ALDH1L2 protein abundance, altered its thermal stability, enhanced the inhibitory effect of sunitinib, and counteracted ALDH1L2-mediated sunitinib tolerance in RCC organoids. CONCLUSIONS: These findings suggest that ALDH1L2 contributes to reduced sunitinib sensitivity in RCC organoids by attenuating ferroptosis-related responses. HA-1 may improve the response of RCC organoids to sunitinib by targeting ALDH1L2, supporting further evaluation of this combination strategy.
Transcriptomic analysis of differential expression and correlation of coding and non-coding RNAs in urine from patients with idiopathic membranous nephropathy.
Li J, Zhou Z, Wu R … +1 more , Chen Q
Biol Direct · 2026 Jun · PMID 42304425 · Full text
BACKGROUND: The incidence rate of idiopathic membranous nephropathy (IMN) has been increasing, and its pathogenesis is still unclear. Exploring new diagnostic molecular markers and the molecular mechanisms of IMN. METHOD...
BACKGROUND: The incidence rate of idiopathic membranous nephropathy (IMN) has been increasing, and its pathogenesis is still unclear. Exploring new diagnostic molecular markers and the molecular mechanisms of IMN. METHODS: Fifteen healthy controls and fifteen IMN patients were recruited. Clinical baseline data of all participants, including age, gender, and body mass index (BMI), along with histopathological staging (Ehrenreich-Churg classification) and immunohistochemical staining results for phospholipase A2 receptor (PLA2R), were collected and analyzed. Meanwhile, peripheral blood and urine samples were obtained to detect renal function-related biochemical indicators, including serum creatinine (Scr), estimated glomerular filtration rate (eGFR), serum albumin, 24-hour urinary protein (24 h UPT), serum total cholesterol (TC), anti-PLA2R antibody titer, and serum immunoglobulin G (IgG). Urine samples (n = 10) were also used for high-throughput sequencing analysis. RESULTS: Serum albumin was significantly downregulated in the IMN group, while 24 h UPT, TC, anti-PLA2R Ab titer, and IgG were upregulated. MicroRNA (miRNA) transcriptomic analysis identified 34 differentially expressed (DE) miRNAs. Hsa-miR-576-3p, hsa-miR-766-5p, and NovelmiRNA-837 exhibited strong diagnostic potential via ROC curve analysis (AUC > 0.8). Sixty-four DE mRNAs were identified in IMN tissues, with enrichment in pathways such as Ribosome and MAPK signaling-fly. ENST00000481739 (RXRA) was upregulated in IMN, correlated with anti-PLA2R Ab titer, and exhibited diagnostic potential (AUC = 0.929). Thirty-five DE lncRNAs were identified in IMN, enriched in autophagy, mitophagy, and apoptosis pathways. TCONS_00180924, TCONS_00176280, TCONS_00208611 correlated significantly with TC, 24-h urinary protein, and anti-PLA2R Ab titer. CONCLUSIONS: This study provides a foundation for developing non-invasive diagnostic tools and targeted therapies for IMN.
EYA1 regulates CIITA phosphorylation to promote EYA1-CIITA-Runx2 complex formation and extracellular matrix integrity in osteoarthritis.
Nie G, Li Y, Zhao H … +4 more , Wang D, Zhang Y, Yang X, Wen X
Biol Direct · 2026 Jun · PMID 42304399 · Full text
BACKGROUND: Osteoarthritis (OA) involves progressive extracellular matrix (ECM) degradation in articular cartilage. We previously revealed that the mA demethylase ALKBH5 stabilizes Runx2 mRNA in chondrocytes via YTHDF1,...
BACKGROUND: Osteoarthritis (OA) involves progressive extracellular matrix (ECM) degradation in articular cartilage. We previously revealed that the mA demethylase ALKBH5 stabilizes Runx2 mRNA in chondrocytes via YTHDF1, thereby increasing MMP and ADAMTS expression, causing ECM degradation. However, the transcriptional co-regulators of Runx2 remain unidentified. METHODS: OA was induced in mice via injection of sodium monoiodoacetate (MIA). The histological architecture and proteoglycan content of the articular cartilage were evaluated using H&E and Safranin O-Fast Green staining, while subchondral bone microarchitecture was assessed by micro-computed tomography. Circulating proinflammatory cytokine levels were determined by ELISA. RESULTS: Immunoprecipitation and mass spectrometry analyses of articular cartilage from MIA-induced OA mice identified the transcriptional coactivator EYA1 (Eyes Absent Homolog 1) and CIITA (Class II Major Histocompatibility Complex Transactivator) as novel Runx2-interacting proteins. In vitro and in vivo experiments demonstrated that EYA1, CIITA, and Runx2 form a functional EYA1-CIITA-Runx2 complex that binds to the promoters of MMP and ADAMTS genes and activates their expression. Silencing any member of the complex significantly reduced transcription of these matrix-degrading enzymes. Furthermore, we identified EYA1 as a phosphatase that dephosphorylates CIITA at serine 782, a phosphorylation site targeted by Pim3 (provirus integration site for Moloney murine leukemia virus 3) under inflammatory conditions. CONCLUSION: Our findings uncover a previously unrecognized transcriptional mechanism in OA pathogenesis, in which EYA1 promotes ECM degradation by regulating CIITA dephosphorylation and assembling a transcriptional complex with CIITA and Runx2. Targeting this pathway may provide a promising therapeutic strategy for OA.
Single-cell multi-omics dissection of RevitalAge Markers uncovers age-dependent immunotherapy resistance and druggable targets in melanoma.
Zhou H, Wei B, Tan W … +6 more , Shi J, Ren C, Zhang J, Yang C, Zhao Z, Ning S
Biol Direct · 2026 Jun · PMID 42304383 · Full text
Aging-related molecular reprogramming profoundly influences melanoma progression and therapeutic sensitivity, yet underlying mechanisms remain poorly understood. We constructed a comprehensive multi-omics atlas integrati...
Aging-related molecular reprogramming profoundly influences melanoma progression and therapeutic sensitivity, yet underlying mechanisms remain poorly understood. We constructed a comprehensive multi-omics atlas integrating mutations, transcription, methylation, and copy number variations, utilizing the MOFA algorithm to uncover key age-driving factors. Among 20 factors, Factor6 exhibited significant negative age correlation and survival protection (HR = 0.95, P = 4.494e-05), defined as "RevitalAge Marker (RAM)". Integration of three single-cell RNA sequencing datasets revealed 4,796 RAM+ cells (predominantly endothelial cells and fibroblasts) exerting tumor-suppressive functions through VEGFA-VEGFR2 angiogenic pathways and mitochondrial ATP synthesis, while 7,229 RAM- cells (dominated by malignant cells) exhibited enhanced EMT, hypoxic adaptation, and MAPK signaling activation. RAM+ cells were governed by ZFP42 and IRF8 maintaining anti-tumor immunity, while RAM- cells controlled by ILF2 and ISL1 promoted metastasis and immune evasion, with RAM- malignant cells enriched in patients over 65 years and associated with immunotherapy resistance. Machine learning analysis of RAM-associated genes identified five core signatures (GPR143, ST3GAL4, RAB38, GMPR, FDFT1) demonstrating superior immunotherapy response prediction (AUC = 0.78-1.00). Drug sensitivity profiling revealed ST3GAL4 exhibited strong correlations with AZ628 (pan-RAF inhibitor) and RDEA119 (MEK inhibitor), which was further validated by molecular docking showing excellent binding affinities (binding energies: -8.7 and - 7.2 kcal/mol). This study provides structural evidence for targeted therapeutic strategies in ST3GAL4-overexpressing melanoma and establishes foundations for age-stratified immunotherapy.
Analysis and validation of abnormal signaling pathways and immune cell infiltration characteristics in digestive system cancers based on peroxisome-related genes.
Wen J, Wang Z, Luo S … +6 more , Aili A, Zou H, Niu S, Liu H, Fan W, Li J
Biol Direct · 2026 Jun · PMID 42298691 · Full text
BACKGROUND: Although emerging evidence suggests a role for peroxisomes in tumorigenesis, their functions in digestive cancers remain unclear. This study aims to investigate the association between peroxisomes and digesti...
BACKGROUND: Although emerging evidence suggests a role for peroxisomes in tumorigenesis, their functions in digestive cancers remain unclear. This study aims to investigate the association between peroxisomes and digestive tract tumors. METHODS: To systematically investigate peroxisomal functions in digestive cancers, we first constructed and validated tumor-specific prognostic signatures based on peroxisome-related genes (PRGs) through univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses. We then characterized the tumor immune microenvironment (TIME) with CIBERSORT, X-CELL, and EPIC algorithms, and identified tumor-specific and common signalings via Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA). Focusing on hepatocellular carcinoma (HCC), we experimentally validated peroxisome-related therapeutic responses by profiling signature genes in radioresistant cells and an orthotopic transarterial chemoembolization (TACE) rat model. PEX13 knockdown further assessed peroxisomal role in radiosensitivity and targeted therapy response. Clinical relevance of PEX13 was evaluated in HCC cohort. Single-cell RNA sequencing dataset and lipidomics further revealed peroxisomal mechanisms in HCC progression. Finally, peroxisomal function in colorectal cancer (CRC) was validated in vitro. RESULTS: Novel peroxisome-related prognostic signatures demonstrated strong predictive power in HCC, colon adenocarcinoma, rectal adenocarcinoma, pancreatic adenocarcinoma, gastric adenocarcinoma, esophageal adenocarcinoma, esophageal squamous cell carcinoma, and cholangiocarcinoma. High-risk patients displayed an immunosuppressive microenvironment, characterized by increased infiltration of regulatory T cells, M2 macrophages, Th2 cells, or cancer-associated fibroblasts, or Th1 cells' reduction. Peroxisomes engaged in several distinct yet convergent pathways, most notably "positive regulation of response to stimuli". HCC prognostic genes were dynamically regulated in response to therapeutic stimuli, including radiotherapy, targeted therapy, and TACE. Clinically, the expression of PEX13 was markedly upregulated in tumor tissues from therapy-resistant HCC patients. Mechanistically, peroxisomal dysfunction induced by silencing PEX13 in HCC or UBE2D2 in CRC may overcome therapeutic resistance (radiotherapy/ lenvatinib resistance in HCC, radioresistance in CRC) through reprogramming lipid metabolism. CONCLUSIONS: Peroxisomes act as pivotal regulators of digestive cancer progression by modulating signaling pathways, the TIME, therapeutic resistance, and lipid metabolism. Targeting peroxisomal function, particularly in high-risk subgroups of HCC and CRC, warrants further exploration as a promising therapeutic strategy.
USP20 as a key regulator of immunosuppression and a novel predictor of poor prognosis in lung adenocarcinoma.
Wang L, Qiao D, Gu R … +9 more , Zhang Q, Guo Y, Liu L, Zhu M, Fan Y, Zhang P, Lv Q, Yan J, Cang S
Biol Direct · 2026 Jun · PMID 42288924 · Full text
BACKGROUND: To systematically delineate the expression landscape, genetic alterations, prognostic value, and immunological relevance of ubiquitin-specific protease 20 (USP20) in lung adenocarcinoma (LUAD). By integrating...
BACKGROUND: To systematically delineate the expression landscape, genetic alterations, prognostic value, and immunological relevance of ubiquitin-specific protease 20 (USP20) in lung adenocarcinoma (LUAD). By integrating bulk and single-cell transcriptomic analyses, we aimed to identify the cellular sources of USP20 and clarify its potential roles in remodeling the tumor immune microenvironment (TME), thereby evaluating its utility as a prognostic biomarker and candidate immunotherapeutic target. METHODS: USP20 expression was profiled across The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and multiple Gene Expression Omnibus (GEO) cohorts. Prognostic significance was assessed using Kaplan-Meier analysis and Cox proportional hazards models. USP20 genetic alterations were interrogated via cBioPortal. Differentially expressed genes (DEGs) associated with USP20 were identified, followed by GO/KEGG enrichment and GSEA to infer biological functions. TME characteristics were evaluated using ESTIMATE and CIBERSORT, and associations with immune checkpoint molecules were examined. Consensus clustering was performed to define USP20-related molecular subtypes and compare their immune landscapes. Single-cell RNA-seq datasets (TISCH and GSE146100) were integrated to resolve USP20 expression across tumor and immune compartments. Finally, immunohistochemistry, multiplex immunofluorescence, flow cytometry, and in vitro/in vivo functional assays were conducted to validate the biological and immunoregulatory roles of USP20 in LUAD. RESULTS: USP20 was consistently upregulated in LUAD relative to normal lung tissues across independent cohorts. High USP20 expression was associated with inferior overall survival and remained an independent prognostic risk factor. Genetic profiling showed a low mutation rate of USP20, with copy number amplification as the predominant alteration. Functional analyses indicated that USP20-associated DEGs were enriched in immune-related programs, including T-cell activation, antigen processing and presentation, interferon signaling, and immune checkpoint regulation. High USP20 expression correlated with a distinct immune contexture, featuring reshaped immune cell composition, increased infiltration of immunosuppressive populations, and elevated expression of multiple immune checkpoint molecules. Consensus clustering further revealed USP20-related molecular subtypes with divergent immunosuppressive features and clinical outcomes. Single-cell analyses demonstrated heterogeneous and cell-type-specific USP20 expression across malignant and immune populations, supporting a context-dependent immunomodulatory role. Experimental validation confirmed that USP20 promotes LUAD cell proliferation and migration and is associated with immune dysregulation within the TME. CONCLUSIONS: USP20 is aberrantly overexpressed in LUAD and portends poor prognosis. USP20 may facilitate disease progression by shaping tumor-immune interactions, including immune infiltration patterns, T-cell activation/exhaustion states, and immune checkpoint signaling. USP20 and its related molecular subtypes may serve as prognostic biomarkers and potential indicators of immunotherapeutic responsiveness, offering insights for precision immunotherapy in LUAD.
A protocol for computational design of mRNA vaccines with high functionality and specificity.
Ramadan MA, ElGohary HM, Faraag AH … +1 more , Mysara M
Biol Direct · 2026 Jun · PMID 42288920 · Full text
The design of effective mRNA vaccines requires rigorous target selection, optimization, and validation to ensure stability, immunogenicity, specificity, and overall efficacy. A standardized protocol is needed to guide th...
The design of effective mRNA vaccines requires rigorous target selection, optimization, and validation to ensure stability, immunogenicity, specificity, and overall efficacy. A standardized protocol is needed to guide the process from gene selection to in silico optimization of the final vaccine construct. This protocol provides a comprehensive computational framework integrating all stages of mRNA vaccine design by defining the design space, essential criteria, and a step-by-step methodology. To demonstrate its applicability, the protocol is applied to the SARS-CoV-2 spike protein, targeting both the coding sequence (CDS) and multi-epitope vaccine construct (MEVC). It incorporates immunoinformatics-based epitope selection, population coverage analysis, codon adaptation index optimization, minimum free energy-based RNA secondary structure assessment, target accessibility into a unified computational development workflow. The resulting constructs exhibited strong predicted immunogenicity and broad population coverage, further supported by in silico cloning and immune simulation validation for the optimized MEVC, consistent with prior in vitro and preclinical findings. Collectively, this protocol establishes a standardized computational roadmap for the design of CDS and MEVC mRNA vaccines, facilitating the development of stable, immunogenic, and translationally efficient vaccines against a wide range of pathogens.
Autochthonous dengue transmission in Europe: epidemiology, mechanisms, and modelling insights.
Campinopoli G, Caro AD, D'Alise A … +5 more , Conventi F, McHugh TD, Melino G, Zumla A, Ippolito G
Biol Direct · 2026 Jun · PMID 42286757 · Full text
BACKGROUND: Dengue is the most rapidly expanding arboviral infection globally, with rising incidence and widening geographic distribution driven by urbanisation, climate change, vector expansion, and global mobility. Alt...
BACKGROUND: Dengue is the most rapidly expanding arboviral infection globally, with rising incidence and widening geographic distribution driven by urbanisation, climate change, vector expansion, and global mobility. Although traditionally confined to tropical and subtropical regions, dengue is increasingly emerging in temperate settings, including Europe. Recent outbreaks in Italy, Spain, and France, together with evidence of under-recognised transmission, indicate a transition from sporadic importation to recurrent autochthonous infection. This shift is facilitated by the establishment of Aedes albopictus, increasing climatic suitability, an increase in case importation from endemic areas and delays in clinical recognition and public health response. MAIN BODY: In non-endemic regions, dengue presents distinct challenges, including low population immunity, limited clinical awareness, and diagnostic constraints that may hinder early detection. While advances in vaccines, particularly TAK-003, and novel vector control strategies such as Wolbachia-based interventions offer new opportunities, their role in Europe remains context-specific and complementary to strengthened surveillance and preparedness systems. Modelling approaches provide valuable decision support but are constrained by data limitations in emerging settings. CONCLUSIONS: The emergence of dengue in Europe should be viewed as an early signal of broader changes in vector-borne disease dynamics. Proactive investment in integrated surveillance, diagnostics, vector control, and targeted vaccination strategies will be essential to mitigate future risk and prevent sustained transmission in non-endemic regions.
Rosavin alleviates COPD via inhibition of IL-17-enriched NET formation and NF-κB signaling.
Xiao G, Li J, Yuan L … +4 more , Huang W, Zhang S, Luo W, Yu C
Biol Direct · 2026 Jun · PMID 42286620 · Full text
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide and is characterized by persistent inflammation, microbiota dysbiosis, and excessive neutrophil extracellular trap (N...
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide and is characterized by persistent inflammation, microbiota dysbiosis, and excessive neutrophil extracellular trap (NET) formation. Rosavin, a natural phenylpropanoid glycoside, exhibits anti-inflammatory and immunomodulatory activities, but its therapeutic potential in COPD remains unclear. METHODS: A COPD rat model was induced by intratracheal lipopolysaccharide instillation combined with chronic passive cigarette smoke exposure. Rosavin (50 or 100 mg/kg) or the NF-κB inhibitor BAY 11-7082 (3 mg/kg) was administered for treatment. Pulmonary function tests (FEV1/FVC, PEF, and airway resistance), histopathological evaluation (HE and PAS staining), bronchoalveolar lavage fluid (BALF) inflammatory cell counts, ELISA-based cytokine assays, and oxidative stress markers (MDA, MPO, and SOD) were systematically assessed. NET formation was evaluated using MPO-DNA ELISA, Western blotting, and immunofluorescence for CitH3 and MPO/IL-17 colocalization. In addition, lung microbiota composition was analyzed by 16 S rRNA gene sequencing. Cigarette smoke extract (CSE)-stimulated BEAS-2B cells were used to assess the direct effects of Rosavin on NF-κB activation in vitro. RESULTS: Rosavin significantly inhibited NF-κB activation, improved lung function, and reduced structural damage, oxidative stress, and inflammatory cytokines in COPD rats. It also suppressed NET formation, including IL-17-enriched NETs, by downregulating MPO, NE, and CitH3. In BEAS-2B cells, Rosavin similarly reduced CSE-induced NF-κB activation and cytokine release. Microbiota profiling showed decreased diversity and enrichment of Fusobacterium nucleatum in COPD rats, whereas Rosavin restored beneficial taxa such as Lactobacillus spp. BAY 11-7082 produced comparable effects, supporting NF-κB inhibition as a key mechanism. CONCLUSION: Rosavin ameliorates COPD-associated pathology through integrated mechanisms involving NF-κB inhibition, reduction of IL-17-enriched NET formation, and modulation of lung microbiota composition. These findings identify Rosavin as a promising multi-target therapeutic candidate for COPD.
β3-adrenergic blockade targets fatty acid oxidation to induce ferroptotic vulnerability in pediatric T-ALL.
Banella C, Travaglini S, Carrozzo F … +12 more , Roveta A, Pegoraro F, Mattei G, Amato R, Ascone M, Luca F, Chinnici A, Marchi C, Chiocca E, Tondo A, Veltroni M, Calvani M
Biol Direct · 2026 Jun · PMID 42277944 · Full text
Pediatric T-cell acute lymphoblastic leukemia (T-ALL) accounts for approximately 15% of childhood ALL. It is associated with a high risk of relapse, with ~25% of patients failing conventional therapy. Resistance is drive...
Pediatric T-cell acute lymphoblastic leukemia (T-ALL) accounts for approximately 15% of childhood ALL. It is associated with a high risk of relapse, with ~25% of patients failing conventional therapy. Resistance is driven by pro-survival signaling, impaired apoptosis, and metabolic adaptations that sustain leukemic proliferation under stress. Herein, we investigate the role of β3-adrenergic receptor (β3-AR) antagonist SR59230A signaling in the metabolic reprogramming and therapeutic vulnerability of pediatric T-ALL. β3-AR expression and transcriptomic profiling following SR59230A exposure were assessed in T-ALL cell lines by RNA sequencing, followed by gene set enrichment analysis of Gene Ontology and Hallmark pathways. Metabolic alterations were validated by Seahorse analyses of mitochondrial respiration, glycolysis, fatty acid oxidation (FAO), and fuel dependency. Systemic iron metabolism was evaluated by ferritin and free iron quantification using COBAS8000. β3-AR was markedly upregulated in T-ALL cells compared with normal hematopoietic counterparts, identifying a selective metabolic vulnerability. Pharmacologic inhibition of β3-AR with SR59230A affected mitochondrial oxidative phosphorylation, predominantly complex I, and suppressed FAO. The metabolic collapse disrupted bioenergetic flexibility and triggered ferroptotic cell death. This was accompanied by modulation of ferritin and transferrin levels, suggesting their potential role as biomarkers of metabolic response. Importantly, β3-AR blockade sensitized T-ALL cells to oxidative phosphorylation inhibition, resulting in synergistic cytotoxicity in refractory models. Collectively, these findings identify β3-AR as a central regulator of metabolic plasticity in pediatric T-ALL highlighting metabolic and iron-dependent vulnerabilities as potential combined targets for high-risk disease.
FOXK1: a multifaceted regulator in metabolic reprogramming and disease progression.
He T, Ma G, Yuan G
Biol Direct · 2026 Jun · PMID 42271494 · Full text
Forkhead box K1 (FOXK1) is an important member of the FOX transcription factor family and functions as a signal-responsive regulator of cellular metabolism, proliferation, differentiation, and stress adaptation. FOXK1 ac...
Forkhead box K1 (FOXK1) is an important member of the FOX transcription factor family and functions as a signal-responsive regulator of cellular metabolism, proliferation, differentiation, and stress adaptation. FOXK1 activity is tightly controlled by a multilayered regulatory network, including genetic and epigenetic alterations, transcriptional regulation, non-coding RNAs, and diverse post-translational modifications. These regulatory networks collectively coordinate FOXK1 stability, subcellular localization, and transcriptional activity in a context-dependent manner. Disruption of this tightly balanced regulatory system can lead to sustained FOXK1 activation and contribute to disease pathogenesis.In cancer, FOXK1 predominantly functions as an oncogenic transcription factor that promotes metabolic reprogramming, maintenance of cancer stem cell properties, epithelial-mesenchymal transition, invasion, metastasis, vasculogenic mimicry, and therapeutic resistance. Beyond oncology, emerging evidence further implicates FOXK1 in metabolic disorders, inflammatory diseases, reproductive dysfunction, and neurological conditions, suggesting broader context-dependent pathological functions. Given its central role in multiple disease-associated signaling networks, FOXK1 has emerged as a potential therapeutic target. In this review, we systematically summarize the structural characteristics and regulatory mechanisms of FOXK1, and comprehensively discuss its roles in physiological and pathological processes. We further highlight current advances in FOXK1-targeted therapeutic strategies and address the key challenges for clinical translation. This review provides a conceptual framework for future therapeutic strategies and rational drug development targeting FOXK1.
From bone to beyond: osteoclasts dictate metastatic fate in lung adenocarcinoma via the OLFML3-DPPA2 stemness switch.
Qiu R, Xue Y, Deng Y … +2 more , Liu X, Du Y
Biol Direct · 2026 Jun · PMID 42271492 · Full text
The unfavorable prognosis of patients with bone metastasis of lung adenocarcinoma (LUAD) is largely due to both osteolytic destruction and tumor stem cell-mediated secondary metastasis. However, the mechanisms by which t...
The unfavorable prognosis of patients with bone metastasis of lung adenocarcinoma (LUAD) is largely due to both osteolytic destruction and tumor stem cell-mediated secondary metastasis. However, the mechanisms by which the bone microenvironment augments the stemness of LUAD cells remain inadequately understood. In this study, we developed a LUAD cell model with enhanced stemness, termed BM3, by subjecting the cells to three rounds of conditioning within the bone microenvironment. Our findings identified osteoclasts, rather than osteoblasts, as the principal stromal cells that facilitate the enhancement of stemness in BM3 cells. This facilitation was inhibited by the application of either a tumor necrosis factor-alpha (TNF-α) neutralizing antibody or an NF-κB inhibitor. Additionally, we established that the expression level of the secretory protein olfactomedin-like protein 3 (OLFML3) is positively associated with the stemness of BM3 cells and exerts a self-reinforcing effect on tumor cell stemness. Mechanistic analyses revealed that OLFML3 upregulates the pluripotency-associated factor developmental pluripotency-associated protein 2 (DPPA2), which subsequently promotes the expression of core stemness factors, including CD44, OCT4, and SOX2, thereby augmenting the stemness and metastatic potential of tumor cells. Clinical data suggest that serum OLFML3 may serve as a candidate biomarker for identifying LUAD patients with bone metastasis who are at increased risk of subsequent metastatic spread. Our study uncovers a novel mechanism in which osteoclasts within the bone microenvironment augment the stemness of LUAD cells via the TNF-α-NF-κB-OLFML3-DPPA2 signaling axis. This finding provides an essential theoretical foundation for developing strategies aimed at suppressing secondary dissemination following bone metastasis in LUAD.
Multi-omics reveals fibroblast subtypes with distinct roles in inflammatory bowel disease.
Guo X, Zhang M, Han J … +5 more , Li L, Xie Z, Zhang G, Zhang S, Zhou G
Biol Direct · 2026 Jun · PMID 42265813 · Full text
BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract involving complex interactions among epithelial, immune, and stromal components. Fibroblasts are key regulator...
BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract involving complex interactions among epithelial, immune, and stromal components. Fibroblasts are key regulators of intestinal inflammation and fibrosis, but their heterogeneity, distribution, and therapeutic potential remain unclear. METHODS: We systematically identified and characterized intestinal fibroblast subtypes in IBD while exploring the intercellular communication between fibroblasts and immune cells through the integration of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) analyses. Functional gene signatures derived from fibroblast subtypes were applied to bulk RNA-seq datasets to predict therapeutic responses using logistic regression and random forest models. Concurrently, pertinent findings were validated in the intestinal tissues and primary fibroblasts of patients with IBD using multiplex immunohistochemistry (mIHC), western blotting, and quantitative real-time PCR (qPCR). RESULTS: We identified 10 distinct stromal subpopulations comprising two fibroblast subtypes strongly associated with IBD pathology: ICAM1 inflammatory fibroblasts (iFibro_ICAM1) and FAP matrix-producing fibroblasts (mFibro_FAP). These subsets demonstrate distinct transcription factor activity, metabolic reprogramming, and spatial proximity to immune infiltrates, and they undergo remodeling within the inflammatory microenvironment of IBD. Pseudotime trajectory analysis suggested that the iFibro_ICAM1 subset potentially represents a precursor state. CellChat analysis revealed enhanced intercellular communication between fibroblast subsets and immune cells in ileal and colorectal IBD tissues. Furthermore, a machine learning model based on gene expression signatures derived from these fibroblasts effectively predicted poor therapeutic responses to anti-TNF treatments in patients with IBD. CONCLUSIONS: This study provides a comprehensive characterization of fibroblast heterogeneity in IBD, highlighting the crucial roles of inflammatory and fibrotic fibroblast subsets as key mediators of immune-stromal interactions and potential predictors of therapeutic responsiveness.
Piceatannol attenuates thoracic aortic aneurysm progression by targeting STK33.
Liu Y, Liu J, Shi R … +1 more , Tan L
Biol Direct · 2026 Jun · PMID 42265708 · Full text
BACKGROUND: Thoracic aortic aneurysm (TAA) is a life-threatening vascular condition with limitedpharmacological interventions. This study aimed to identify novel causaldruggable genes and therapeutic candidates for TAA....
BACKGROUND: Thoracic aortic aneurysm (TAA) is a life-threatening vascular condition with limitedpharmacological interventions. This study aimed to identify novel causaldruggable genes and therapeutic candidates for TAA. METHODS: We performed Mendelian randomization (MR) by integrating cis-expression quantitativetrait loci (eQTL) and genome-wide association studies (GWAS) data to identifycausal genes for TAA. Therapeutic candidates were predicted via the DrugSignatures Database (DSigDB) and prioritized using molecular docking. Theclinical relevance of the lead target, STK33, was assessed in human TAA tissuesusing immunohistochemistry (IHC). The therapeutic efficacy of piceatannol wasrigorously validated across three distinct platforms: Angiotensin II(AngII)-stimulated vascular smooth muscle cells (VSMCs), and two complementaryanimal models (BAPN-induced and AngII-infused TAA mice). RESULTS: MR analysis identified 31 druggable genes significantly associated with TAA risk.Integration with DSigDB and molecular docking pinpointed piceatannol as a potentcandidate targeting STK33. IHC staining revealed that STK33 expression wasmarkedly downregulated in human TAA tissues, a trend consistently observed inAngII-stimulated VSMCs and mouse TAA models. In vivo, piceatannol treatmentsignificantly reduced TAA incidence, mortality, and aortic dilation in bothBAPN-induced and AngII-induced mouse models. Mechanistically, piceatannoleffectively restored STK33 protein levels and attenuated the loss of VSMCcontractile markers (MYH11, α-SMA, and CNN1) both in vivo and invitro. These protective effects were largely abolished by STK33 knockdown,confirming a target-specific mechanism. CONCLUSIONS: Piceatannol attenuates TAA progression, potentially through targeting and stabilizing STK33 expression. By utilizing a multi-model validation strategy (two in vivo modelsand an in vitro cell model), our findings highlight the piceatannol-STK33 axisas a promising therapeutic candidate for TAA.
Comprehensive multi-omics pan-cancer analysis revealed that ANTXR1 is a potential biomarker for diagnosis and immunotherapy.
Qiu Y, Yu Z, Lai W … +4 more , Xu W, Yang J, Zhou S, Chen J
Biol Direct · 2026 Jun · PMID 42251445 · Full text
BACKGROUND: Anthrax toxin receptor 1 (ANTXR1, TEM8) has been implicated in tumor angiogenesis and progression, yet its pan-cancer immunological role remains incompletely defined. METHODS: We conducted an integrative pan-...
BACKGROUND: Anthrax toxin receptor 1 (ANTXR1, TEM8) has been implicated in tumor angiogenesis and progression, yet its pan-cancer immunological role remains incompletely defined. METHODS: We conducted an integrative pan-cancer analysis using multi-omics and clinical data from TCGA, GTEx, and public databases to evaluate the expression, prognostic and diagnostic value, genomic features, immune associations, and drug sensitivity of ANTXR1. Single-cell and spatial transcriptomic analyses were performed to define its cellular and spatial distribution. Functional roles were validated in gastric cancer (GC) using in vitro and in vivo models. RESULTS: ANTXR1 was aberrantly expressed across multiple tumor types and significantly associated with tumor stage and unfavorable prognosis, particularly in GC. Diagnostic analyses demonstrated high accuracy of ANTXR1 in several malignancies. Elevated ANTXR1 expression correlated with genomic instability, stromal enrichment, M2 macrophage infiltration, and reduced CD8⁺ T cell abundance, indicating an immunosuppressive tumor microenvironment. Single-cell and spatial analyses identified fibroblasts as the primary source of ANTXR1 with co-localization to extracellular matrix components. Functionally, ANTXR1 knockdown suppressed GC cells proliferation, migration, invasion, and tumor growth, inhibited M2 macrophage polarization, and enhanced CD8⁺ T cell activity, partly through PI3K/AKT pathway inhibition. CONCLUSION: ANTXR1 functions as a stromal-associated immunomodulatory driver of tumor progression and immune suppression, representing a promising biomarker and therapeutic target in stromal-rich cancers.
TRIM71 suppresses cervical cancer progression by inhibiting Nectin4-mediated Wnt/β-catenin signaling.
Liu T, Chen J, Dai B … +8 more , Du D, Chen M, Zhao N, Mai H, Fan H, Lin L, Liang Y, Yao S
Biol Direct · 2026 Jun · PMID 42237330 · Full text
BACKGROUND: Tripartite motif-containing 71 (TRIM71), an RNA-binding E3 ubiquitin ligase, plays essential roles in malignant progression, but its function in cervical cancer (CC) remains unclear. METHODS: TRIM71 expressio...
BACKGROUND: Tripartite motif-containing 71 (TRIM71), an RNA-binding E3 ubiquitin ligase, plays essential roles in malignant progression, but its function in cervical cancer (CC) remains unclear. METHODS: TRIM71 expression was assessed in CC cell lines and clinical specimens using qRT-PCR, Western blotting, and immunohistochemistry. The clinical significance of TRIM71 was evaluated through correlation analyses and survival models. Functional assays in vitro and xenograft models in vivo were used to determine the biological roles of TRIM71. RNA-sequencing, RIP-sequencing, luciferase reporter assays, actinomycin D decay assays, and co-immunoprecipitation assays were performed to elucidate underlying mechanisms. RESULTS: TRIM71 expression was significantly reduced in CC cell lines and tumor tissues, and its low expression correlated with aggressive clinicopathologic features and poorer survival, identifying it as an independent prognostic factor. Functionally, TRIM71 overexpression impaired CC cell proliferation, migration, invasion, and cytoskeletal remodeling, whereas TRIM71 loss enhanced these malignant behaviors. In vivo, TRIM71 suppressed tumor growth, lung metastasis, and angiogenesis. Transcriptome analysis and molecular assays showed that TRIM71 inhibited Wnt/β-catenin signaling and Epithelial-mesenchymal transition (EMT). RIP-seq revealed Nectin4 as a direct TRIM71 target. TRIM71 bound the Nectin4 3'-UTR and reduced its mRNA stability without affecting ubiquitination. Rescue experiments demonstrated that Nectin4 was essential for TRIM71-mediated repression of Wnt/β-catenin signaling, as Nectin4 restoration or pathway activation reversed TRIM71's inhibitory effects, whereas Nectin4 silencing or pathway inhibition negated the impact of TRIM71 knockout. CONCLUSIONS: TRIM71 may function as a tumor suppressor in CC by regulating Nectin4 expression and influencing Wnt/β-catenin signaling, EMT, tumor progression, and angiogenesis.
DNA methylation patterns re-establish during clonal expansion restoring cell-to-cell epialleles heterogeneity.
Costabile D, Russo M, Della Monica R … +8 more , Buonaiuto M, De Riso G, Sabbarese M, Catapano G, Cocozza S, Visconti R, Chiariotti L, Cuomo M
Biol Direct · 2026 Jun · PMID 42231478 · Full text
It is still debated whether the combination of methylated and unmethylated CpGs, defined as epialleles, is stably propagated during cell division or whether epiallele diversity can dynamically emerge over time. By analyz...
It is still debated whether the combination of methylated and unmethylated CpGs, defined as epialleles, is stably propagated during cell division or whether epiallele diversity can dynamically emerge over time. By analyzing epiallele profiles in putative single-cell-derived clones, we sought to track the behaviour of DNA methylation profiles through cell divisions to determine whether epialleles are faithfully copied from mother to daughter cells, or instead a heterogeneous epiallele population is generated, giving rise to cell-to-cell methylation variability. Our findings revealed that: i) clonal expansion did not result in the maintenance of a single dominant epiallele configuration; ii) expanding clones progressively re-established a broad repertoire of epialleles similar to that observed in the mixed population; iii) although the major epiallele structures were partially preserved, each clone displayed a distinct epiallele distribution characterized by differences in epiallele frequencies relative to the bulk population. Notably, these clone-specific epiallele distributions remained relatively stable as cell numbers increased during proliferation. Overall, our findings suggest that epiallele diversity reemerges during clonal expansion, consistent with the dynamic behavior of DNA methylation at individual CpG sites and cell-to-cell variability in DNA methylation patterns.
Deep learning-driven decoding of ubiquitination: from regulatory mechanisms to targeted protein degradation.
Zhang J, Xia B, Wang Z … +13 more , Wang Z, Sun Y, Wang H, Li X, Gao X, Zhao W, Li Y, Zhou F, Chen T, Shi Z, Lv J, Yang R, Zhang Y
Biol Direct · 2026 Jun · PMID 42226266 · Full text
BACKGROUND: Ubiquitination is a highly dynamic post-translational modification that plays central roles in protein homeostasis, signal transduction, immune regulation, and cell fate control. Through the coordinated actio...
BACKGROUND: Ubiquitination is a highly dynamic post-translational modification that plays central roles in protein homeostasis, signal transduction, immune regulation, and cell fate control. Through the coordinated actions of E3 ubiquitin ligases and deubiquitinating enzymes, ubiquitination shapes the ubiquitin-proteasome system and influences a wide range of physiological and pathological processes. Dysregulation of this system is closely associated with cancer, neurodegenerative disorders, immune dysfunction, and metabolic disease. However, a comprehensive understanding of ubiquitination remains limited because of incomplete annotation, context-dependent regulation, transient molecular interactions, and highly complex many-to-many regulatory networks. MAIN BODY: In this review, we summarize how deep learning is reshaping ubiquitination research at multiple levels. First, we outline the major deep learning architectures applied in this field, including convolutional neural networks, recurrent neural networks, Transformers, protein language models, graph neural networks, generative models, and reinforcement learning. Second, we review recent progress in predicting ubiquitination sites and ubiquitin chain-related features, with emphasis on sequence-based, structure-informed, and multimodal representation learning strategies. Third, we discuss how deep learning contributes to mechanistic decoding of ubiquitination specificity, including substrate recognition by E3 ubiquitin ligases and deubiquitinating enzymes, degron identification, and the organization of ubiquitination regulatory networks. Fourth, we highlight the translational relevance of these approaches in biomarker discovery, targeted protein degradation, molecular glue discovery, degrader optimization, and ubiquitin-centered therapeutic design. Collectively, these advances show that deep learning is not only improving predictive accuracy, but also enhancing mechanistic interpretability and enabling rational molecular design. CONCLUSION: Deep learning is driving ubiquitination research from descriptive prediction toward mechanistic understanding and therapeutic application. Future progress will depend on developing more interpretable models, integrating physiological context, and strengthening experimental validation. Such efforts will accelerate the translation of ubiquitin biology into clinically useful biomarkers, precision diagnostics, and targeted therapies.
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