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Transitions of cancer cells between distinct cell states, which are typically driven by transcription reprogramming, fuel tumor plasticity, metastasis, and therapeutic resistance. Whether the transitions between cell states can be therapeutically targeted remains unknown. Here, using the epithelial-to-mesenchymal transition (EMT) as a model, we show that the transcription reprogramming during a cell-state transition induces genomic instability through R-loops and transcription-replication conflicts, and the cell-state transition cannot occur without the ATR kinase, a key regulator of the replication stress response. ATR inhibition during EMT not only increases transcription- and replication-dependent genomic instability but also disrupts transcription reprogramming. Unexpectedly, ATR inhibition elevates R-loop-associated DNA damage at the SNAI1 gene, a key driver of the transcription reprogramming during EMT, triggering ATM- and Polycomb-mediated transcription repression of SNAI1. Beyond SNAI1, ATR also suppresses R-loops and antagonizes repressive chromatin at a subset of EMT genes. Importantly, inhibition of ATR in tumors undergoing EMT reduces tumor growth and metastasis, suggesting that ATR inhibition eliminates cancer cells in transition. Thus, during EMT, ATR not only protects genome integrity but also enables transcription reprogramming, revealing that ATR is a safeguard of cell-state transitions and a target to suppress tumor plasticity. Show less

Epithelial-to-mesenchymal transition (EMT) is essential for normal development and cancer progression. However, how nuclear Lamins regulate EMT is unclear. Here, we show that Lamin A/C modulates the epithelial-mesenchymal (E-M) plasticity of cells through its interaction with the chromatin organizer, EZH2. The overexpression of Lamin A reinforces an epithelial identity, while its depletion promotes a mesenchymal phenotype. This positions Lamin A/C as a crucial modulator of Epithelial-Mesenchymal plasticity. Furthermore, CDK1-mediated phosphorylation of Lamin A/C (Ser22) and EZH2 (Thr345) disrupts Lamin A/C-EZH2 interaction, destabilizing EZH2, with a concomitant decrease in the occupancy of the heterochromatin mark (H3K27me3) on the SNAI1, TWIST1, and ZEB1 promoters, thereby facilitating a transition towards mesenchymal transcriptional programs. Conversely, phosphodeficient Lamin A/C (S22A) and EZH2 (T345A) mutants restore epithelial identity, highlighting a regulatory role of the Lamin A/C-EZH2 axis in maintaining epithelial homeostasis. In vivo, xenograft assays in NOD-SCID mice reveal that while phosphorylated Lamin A/C or EZH2 promote tumor growth and metastasis, phospho-deficient mutants markedly suppress it. Lamin A/C-EZH2 interaction regulates the expression of E-M-associated transcription factors, highlighting the role of this interaction in modulating transcriptional plasticity, thereby serving as a potential therapeutic target for regulating metastasis in breast cancers. Show less

Discrete subaortic stenosis (DSS) is a congenital heart disease in which a fibrotic membrane forms below the aortic valve; the underlying cellular mechanisms are currently unknown. Since an elevated pressure gradient in the left ventricular outflow tract (LVOT) is a distinguishing feature of DSS, it is hypothesized that the membrane formation is caused by elevated wall shear stress applied to the endocardial endothelial cells (EECs) that line the LVOT, triggering fibrosis. To correlate shear stress to an EEC fibrotic phenotype, we applied fluid shear stress to EECs at physiological and pathological shear rates using a cone-and-plate device, designed to recapitulate physiological wall shear stress in a controlled in vitro environment. Controlled shear stress regimes were applied to EECs to replicate the conditions observed in DSS patients. We found that elevated shear stress triggered EEC alignment as well as endothelial-to-mesenchymal transformation (EndMT) signaling pathways driven by upregulation of SNAI1 gene expression. The EECs were then treated with a small molecule inhibitor of Snail1 protein, CYD19, to attempt to attenuate EndMT signaling, and subsequently subjected to pathological shear stress. The Snail1 inhibitor did downregulate selected markers of EndMT signaling, although only transiently. Interestingly, the application of shear stress had a greater effect on the EEC gene and protein expression than did the Snail1 inhibition. This investigation of EEC response to shear stress reveals the pronounced and complex effect of this mechanical stimulation on the EEC phenotype. Further study should reveal the mechanisms that drive fibrosis and the formation of the DSS membrane. Show less

Prostate cancer (PCa) is the most general cancer in men and is often linked with distant metastasis in its later stages. The caffeic acid (CA) derivative, N-(4-methoxyphenyl)methylcaffeamide (MPMCA), demonstrates superior liver-protective effects compared to CA. Nevertheless, the functions of MPMCA on prostate cancer metastasis remain unclear. Here, we demonstrate that MPMCA blocks migration and invasion in prostate cancer cells without affecting cell viability. By suppressing the production of mesenchymal markers Vimentin, N-cadherin and β-catenin and upregulating the production of the epithelial marker Zonula Occludens-1 (ZO-1), MPMCA also controls Epithelial-Mesenchymal Transition (EMT). The Phosphoinositide 3-kinase (PI3K), Protein kinase B (AKT) and mechanistic target of rapamycin (mTOR) pathway has been documented to regulate MPMCA-inhibited cell motility. Transfection with Snail and Slug cDNA reverses MPMCA's suppression of EMT, migration, and invasion in prostate cancer cells. Importantly, our in vivo data indicates that MPMCA reduces Snail and Slug expression and prostate cancer metastasis. Our evidence suggests that MPMCA is a novel therapeutic candidate for treating metastatic prostate cancer. Show less

The mechanisms by which the autosomal dominant disorder tuberous sclerosis complex (TSC) results in liver fibrosis remain poorly understood. KDM6A, a histone demethylase, has been implicated in the pathogenesis of fibrosis in multiple tissues. This study aimed to elucidate the molecular mechanism by which KDM6A contributed to TSC-associated fibrosis. We observed fibrogenesis, epithelial-mesenchymal transition (EMT) induction and upregulation of Kdm6a in vivo and in vitro upon Tsc1 or Tsc2 deficiency. Knockdown of Kdm6a attenuated both fibrosis and EMT phenotypes. Mechanistically, Kdm6a depletion reduced phosphorylation of ERK1/2 and downregulated Snai1 expression. Activation of the MAPK/ERK pathway with PMA restored EMT-related protein expression, confirming the functional involvement of this signaling axis. Furthermore, Tsc1 or Tsc2 deficiency promoted Kdm6a expression via the mTORC1 pathway, while Kdm6a knockdown conversely suppressed mTORC1 activity by reducing mTOR protein expression, suggesting a positive feedback loop between Kdm6a expression and mTORC1. These findings indicate that Kdm6a promotes fibrosis in TSC through the activation of the MAPK/ERK/SNAI1 signaling pathway. Moreover, the combination of mTORC1 and KDM6A inhibitors results in marked regression of fibrosis and liver lesions in TSC models, unveiling a potential treatment for TSC patients with inadequate response to mTORC1 inhibitors. Show less

Fuchs endothelial corneal dystrophy (FECD) results in the death of the nonproliferative endothelial cells of the posterior corneal surface, leading to corneal swelling, clouding, and potential blindness. Few studies have suggested the potential role of transcription factors in the endothelial to mesenchymal transition (EnMT) during disease progression. This study aimed to evaluate the expression of selected transcription factors in the corneal endothelium of FECD patients to understand their role in disease pathogenesis. This is a prospective, pilot, case-control study for studying the gene expression in patients with FECD. Transcription factors ZEB1, TCF4, smad proteins (SMAD3, SMAD4), zinc finger proteins SNAI1 and SNAI2, lymphoid enhancer binding factor 1 (LEF1), N-cadherin (CDH2), claudin 10 (CLDN10), and nuclear factor (erythroid-derived 2)-like 2 (NFE2L2/NRF2), which are involved in the EnMT, were selected for the study. Fourteen FECD endothelia were compared with 15 control endothelia for the gene expression analyses using quantitative real-time PCR. Significant differential expressions were seen in the levels of SMAD3 (P = 0.0251) in moderate cases compared to control tissues. Further, TCF4 and NFE2L2 showed significantly different expressions among the moderate and severe cases (P = 0.0262 and P = 0.0350, respectively), with expressions decreasing with severity, indicating their possible role in disease progression. Our pilot study on transcription factor gene expressions in FECD patients' tissue samples suggests NRF2 and TCF4 to play an important role in the disease pathogenesis and progression. 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

Schizophrenia (SCZ) is a complex psychiatric disorder, and its pathogenic mechanisms are not yet fully understood. The identification of reliable blood biomarkers and molecular subtypes for early diagnosis and effective therapy remains a significant challenge. To address this issue, we utilized a combination of bioinformatics and machine learning (ML) to identify potential biomarkers for SCZ. Our approach involved the integration of 12 different ML algorithms to develop a diagnostic signature based on data from several datasets, including GSE18312, GSE27383, GSE38485, GSE54913, and GSE165604. A nomogram was constructed using these datasets for potential clinical applications. In addition, clustering analysis was performed on SCZ patients using consensus clustering and non-negative matrix factorization (NMF) algorithms. We further evaluated subtype differences in biological functions and immune cells through various methods, such as gene set enrichment analysis (GSEA), gene set variation analysis (GSVA), Proteomaps, and IOBR analyses. Our results identified a diagnostic signature composed of 16 genes (APBB2, CLCN1, SYDE1, PAX5, SNAI1, DAZL, UNC93B1, PLAGL2, HS3ST1, ITPKB, PILRA, BTLA, SWAP70, AZI2, ADM, and AVPR2), which demonstrated robust performance in diagnosing SCZ across eight different datasets. A nomogram based on these genes was created, providing clinical benefits for SCZ patients. Among the identified genes, AZI2 was found to be the most critical, influencing inflammation and immunity. We also identified potential chemical compounds that could target these 16 genes. Unsupervised clustering and NMF algorithms revealed two distinct subtypes of SCZ, each associated with unique immune cell profiles, biological functions, and protein expression levels. In conclusion, this study not only developed a diagnostic signature and a novel nomogram for SCZ but also provided new insights into the subtypes of SCZ. These findings may pave the way for personalized diagnosis and treatment strategies for SCZ patients. Show less

Thoracic aortic dissection (TAD) is a life-threatening acute vascular condition with high morbidity and mortality. Endothelial cells (ECs) are critical for maintaining vascular homeostasis, yet the role of endothelial-to-mesenchymal transition (EndoMT), a key cell-fate process in vascular development and disease, in TAD remains poorly defined. Furthermore, the functional role of PDK4 (pyruvate dehydrogenase kinase 4) as a driver of this pathological cell-fate transition has not been elucidated. To delineate the mechanistic contribution of EndoMT to TAD, we integrated transcriptomic profiling and immunofluorescence analysis in human aortic specimens and a β-aminopropionitrile-induced murine model. Following the identification of PDK4 as a critical downstream effector of EndoMT signaling via RNA-sequencing and chromatin immunoprecipitation assays, its functional role was validated using conditional EC-specific knockout mice and adeno-associated virus-mediated endothelial gene modulation. Serum samples were collected, and ELISA was used to measure levels of endothelial injury markers for assessing EC-dysfunction. In addition, therapeutic potential was assessed using dichloroacetate, a small-molecule PDK4 inhibitor. A robust activation of the EndoMT gene program was observed in both human TAD specimens and murine aortic tissues, characterized by the loss of endothelial identity and acquisition of mesenchymal traits. Transcriptomic screening pinpointed PDK4 as a critical mediator upregulated during EndoMT. Mechanistically, we demonstrated that the transcription factor Our findings demonstrate that the pathological EndoMT program is activated in ECs by PDK4, which aggravates TAD development in β-aminopropionitrile-induced mouse models, highlighting PDK4 as a promising therapeutic target for TAD. Show less

The annual ~36,000 prostate cancer (PCa) deaths represent a large clinical unmet need and a call for deeper understanding of PCa metastasis. Epithelial-mesenchymal-transition (EMT) has been used to model metastatic behaviors in numerous cancers including PCa. One hallmark of EMT is cell cycle suppression, but how EMT impacts PCa proliferation remains unclear primarily due to the lack of appropriate models. We transiently induced Snail1 (SNAI1) expression, an EMT driver expressed in PCa, at physiological levels in three PCa cells lines, C4-2B, 22Rv1, and DU145. We used RNA-seq, ChIP-Seq, bioinformatics, qRT-PCR, shRNA, and immunoblotting to identify mechanisms of Snail1-driven inhibition of proliferation. Snail1 suppressed proliferation and G2/M cell cycle progression, without affecting cell death. Mechanistically, Snail1 upregulated expression of CEBPγ, ERG1, FOXO1, cyclin G1, p21, stress genes SESN3 and SOD3, apoptotic programmers Puma, Bax, and Noxa, and senescence-related laminB1, and downregulated Ki67, cyclins A2 and B2. ChIP-Seq data identified Snail1 direct binding to p21, cyclin B2 and G1, EGR1, and CEPBγ promoters. EGR1 induced FOXO1, and EGR1 was required for Snail1-induced SOD3 and Puma, and suppression of Caspase 3 to prevent apoptosis. The EGR1/FOXO1 axis induced BAX, Noxa, and SESN3. CEBPγ was required for Snail1 induction of Lamin B1 to block Snail1-induced senescence. We identified three new major downstream targets of Snail1 that improve our understanding of the role of EMT in limiting stress signaling, apoptosis, and senescence during cell cycle suppression to create a vulnerability for therapeutic targeting. Show less

Three-dimensional (3D) spheroid models are increasingly used to emulate the tumour microenvironment for preclinical drug screening. This study aimed to optimise and assess spheroid formation from MDA-MB-468 triple-negative breast cancer (TNBC) cells using hanging drop, liquid overlay, and rigid scaffold methods under normal oxygen (NOC) and low oxygen (LOC) culture conditions. Spheroids were generated and characterised using bright-field microscopy with AnaSP morphometrics (sphericity, solidity, and perimeter). Gene expression of Epithelial-Mesenchymal Transition (EMT), stemness, and hypoxia/angiogenesis markers (CD44, HIF1A, VEGFA, TWIST1, SNAI1, and NES) was quantified using qPCR. The optimised model was further evaluated using field-emission scanning electron microscopy (FE-SEM) and Hoechst fluorescence. A workflow combining hanging-drop pre-aggregation with ultra-low attachment (ULA) or agarose-coated plates under NOC produced consistent, compact spheroids. Scaffold cultures formed rapidly but showed size variability under NOC and LOC. Across methods, spheroids were less compact, and gene expression patterns deviated from expected hypoxic responses. Spheroids cultivated under normoxic conditions demonstrated enhanced structural integrity and transcriptional fidelity. Nonetheless, the study identified that the most compact and resilient spheroids were achieved through the use of hanging-drop pre-aggregation combined with ULA-plates under NOC. The enhanced structural integrity and transcriptional fidelity observed in these spheroids make them valuable models for studying cancer biology and drug responses. The online version contains supplementary material available at 10.1007/s11033-026-11451-4. Show less

Perfluorooctane sulfonate (PFOS), a pervasive and persistent environmental pollutant, has been epidemiologically linked to thyroid disorders, but its toxic effects on papillary thyroid carcinoma (PTC) remain unclear. This study provides the clinical evidence that PFOS accumulates at significantly higher levels in human PTC tumor tissues compared to adjacent normal tissues (p = 0.037), indicating tissue-specific bioaccumulation. To investigate its health impact, we modeled chronic environmental exposure by treating human PTC cells with low, environmentally relevant concentrations of PFOS (0.01, 0.05 μM). Chronic exposure markedly enhanced malignant phenotypes, including proliferation, migration, and invasion. Mechanistically, PFOS activated the PI3K/AKT/mTOR signaling pathway, which subsequently drove epithelial-mesenchymal transition (EMT), as evidenced by upregulation of β-catenin and SNAI1, and increased expression of matrix metalloproteinase (MMP-2 and MMP-9). These pro-tumor effects were partially reversed by the pharmacological inhibitor BEZ235, which targets PI3K/mTOR. In vivo validation using a mouse xenograft model confirmed that PFOS exposure promotes tumor growth and upregulates the same pathway and effector molecules. This study provides integrated clinical and experimental evidence that PFOS exposure at environmentally relevant concentrations promotes PTC progression by inducing PI3K/AKT/mTOR-mediated EMT and associated enzyme secretion. These findings offer crucial experimental insight into the toxic role of PFOS as an environmental contaminant in thyroid tumors and underscore the urgent need for enhanced environmental health risk assessment and regulatory action. Show less

Acute lymphoblastic leukemia (ALL) is a genetically heterogeneous disease where current clinical practice guidelines remain focused on traditional cytogenetic markers. Despite recent advances demonstrating excellent diagnostic accuracy for gene expression signatures, a discontinuity exists between biomarker validation and clinical implementation. This study aimed to develop and validate a multiparametric gene expression signature using digital PCR (dPCR) to accurately diagnose pediatric ALL, with potential utility for monitoring measurable residual disease (MRD). We analyzed 130 bone marrow aspirates from pediatric patients from four clinical groups: non-leukemia, MRD-negative, MRD-positive and leukemia characterized by immunophenotype. Gene expression of an 8-gene panel ( Show less

Prostate cancer is the second most commonly diagnosed cancer worldwide. Although androgen deprivation therapy initially demonstrates clinical benefit, disease relapse with more aggressive phenotypes frequently occurs. The acidic tumor microenvironment in solid tumors may alter drug responsiveness. This study investigates how extracellular pH influences the cytotoxic effects of bicalutamide in human prostate cancer cell lines. PC3 and LNCaP cells were exposed to bicalutamide at varying concentrations at pH 7.4 and pH 6.8. IC50 values were determined using the MTT assay. Cell migration, apoptosis, and cell cycle distribution were evaluated by wound-healing assay, annexin V/PI staining, and DNA content analysis, respectively. The expression of Bicalutamide (140 μg/mL) reduced PC3 cell viability to 39.62% at pH 7.4 compared with 51.36% at pH 6.8. In LNCaP cells, viability declined to 33.64% at pH 7.4% and 56.09% at pH 6.8. Treated PC3 cells exhibited significantly greater migration at pH 6.8 ( The efficacy of bicalutamide in prostate cancer cells is significantly influenced by extracellular pH. The drug exerts stronger cytotoxic, antimigratory, and proapoptotic effects at physiological pH (7.4) compared with acidic conditions (6.8). Show less

Preeclampsia (PE), a severe hypertensive disorder of pregnancy, is associated with circadian rhythm disruption, but the underlying placental molecular networks remain poorly understood. This study aimed to identify key hub genes, regulatory pathways, and novel biomarkers at the intersection of Early-Onset PE (EOPE) and the placental circadian clock. The placental transcriptomic dataset GSE114691 (20 EOPE vs. 20 gestational age-matched preterm controls) was analyzed to identify differentially expressed circadian genes (DECGs). Hub genes were prioritized via protein-protein interaction (PPI) networks. Hub gene expression was validated using effect size (Cohen's d) analysis, and diagnostic performance was evaluated using Receiver Operating Characteristic (ROC) curve analysis. An upstream TF-miRNA co-regulatory network and drug-gene interactions were also analyzed. This pipeline identified 33 DECGs and 10 central hub genes (TGFB1, SPP1, ENG, CD63, SNAI1, GPT2, APLN, EZR, NTRK2, and GLUD1), all significantly dysregulated in EOPE. Crucially, analysis of the core clock machinery revealed a specific uncoupling of the regulatory feedback loop. ROC analysis revealed exceptional diagnostic potential. Notably, NTRK2 emerged as a novel, near-perfect classifier (Area Under the Curve [AUC] = 0.99), outperforming the established marker ENG (AUC = 0.97). Upstream analysis identified key transcription factors (FOXC1, GATA2), and drug-gene analysis revealed clinically relevant interactions between TGFB1 and the chronotherapeutic agents melatonin and aspirin. This study provides a systems-level map of the disrupted placental circadian network in EOPE. Our findings suggest that circadian misalignment is a central feature of placental pathology, offering a molecular rationale for developing novel chronotherapeutic strategies. Show less

Luminal breast cancer (LBC) is the most common subtype of breast cancer affecting women worldwide. Although luminal breast cancer typically has a better prognosis, it mostly responds poorly to neoadjuvant chemotherapy. Non-coding RNAs, especially long non-coding RNAs and microRNAs are crucial in regulating biological processes that contribute to breast cancer development. MALAT1, a long non-coding RNA, is pivotal in the progression of breast cancer. Epithelial-mesenchymal transition (EMT) is critical for cell movement during embryonic development. Clarifying this role could pave various avenues for developing innovative strategies for combating this subtype of malignancy. The present study aimed to investigate the expression profiles and clinical relevance of MALAT1 level and EMT-related miRNAs (miR-17-5p, miR-20a-5p, miR-93-5p, miR-135b-5p, and miR-146a-5p) alongside EMT markers (E-cadherin, N-cadherin, vimentin, fibronectin, twist, SNAI1, Slug, ZEB1, and ZEB2) in LBC patients. Fresh tissues were collected from fifty patients and twenty noncancerous controls. Differential expression of the markers was evaluated using qRT-PCR assay. Spearman Rho test assessed the relationship between the expression levels. Linear regression test evaluated the correlation between the parameters and various clinico-pathological features. Our results revealed an overall upregulation of MALAT1 in breast cancer tissues although this increase did not reach statistical significance. Overexpression of miR-20a-5p, miR-135b, and ZEB2 was reported, whereas miR146a-5p, ZEB1 and Vimentin levels were suppressed. Correlation analysis demonstrated that miR-20a-5p was positively correlated with SNAI1, E-cadherin, N-cadherin and Slug also it was significantly associated with family history and tumor laterality. Our findings suggest that miR-20a-5p plays an oncogenic role in luminal breast cancer by promoting EMT, while MALAT1 may contribute to disease progression through indirect regulatory mechanisms. Finally, MALAT1 and miR-20a-5p might serve as potential therapeutic and prognostic targets in LBC. Show less

Gastric cancer remains a leading cause of cancer mortality worldwide, largely due to its high metastatic potential driven by epithelial-mesenchymal transition (EMT). Here, we identify Deltex E3 ubiquitin ligase 3L (DTX3L) as a previously unrecognized tumor suppressor in gastric cancer. DTX3L expression is markedly reduced in metastatic and mesenchymal-type gastric cancers and positively correlates with favorable patient prognosis. Functional analyses in cell lines, organoids and animal models demonstrate that DTX3L depletion promotes gastric cancer cell migration, invasion, stem-like properties and metastasis, whereas its overexpression exhibits opposite effects. Mechanistically, DTX3L acts as an E3 ubiquitin ligase that directly interacts with and ubiquitinates SNAI1, a master EMT regulator, leading to its GSK-3β dependent proteasomal degradation. Loss of DTX3L stabilizes SNAI1 and enhances EMT and stem-like phenotypes. Moreover, we uncover that TGF-β1-induced miR-135b-5p downregulates DTX3L, forming a regulatory axis that promotes EMT. Collectively, our findings reveal a novel DTX3L-SNAI1 signaling pathway governing EMT and metastasis in gastric cancer, providing mechanistic insight and suggesting DTX3L as a potential prognostic biomarker and therapeutic target. Show less

Copyright: © 2026 Adeyika et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Aberrant DNA methylation changes lead to abnormal gene expression that contributes to the development and progression of prostate cancer (PCa). Inquiry of genome-wide DNA methylation dataset, we identified the homeodomain pancreatic and duodenal homeobox 1 (PDX1) gene as differentially hypermethylated in PCa compared to normal prostate tissues. Immunohistochemical analysis of matched PCa and normal prostate tissues using tissue microarray showed a significant 2.33-fold (p = 0.0001) higher PDX1 protein expression in the PCa compared to the normal prostate tissues. In PCa cell lines (PC-3 and LNCaP) engineered to stably overexpress or knockdown PDX1, the ectopic PDX1 expression significantly enhanced cell proliferation and migration, whereas PDX1 knockdown suppressed these phenotypic processes. Quantitative RT-PCR and Western blot analysis demonstrated that PDX1 overexpression was associated with increased expression of key metabolic regulators; INSR, IGF1R, CXCR4, CDH2, TWIST1, and SNAI1, whereas there is decreased expression of ESR2, and TNFα. Conversely, PDX1 knockdown led to the opposite effect in expression profiles of these metabolites. Notably, these effects were more pronounced under high-glucose conditions compared to low-glucose environments. Overall, our findings suggest that PDX1 plays a tumor-promoting role in human PCa cells by influencing expression of metabolites in insulin, inflammatory, and epithelial-mesenchymal transition (EMT) signaling pathways. Given its potential role in metabolic regulation, full insights into the function of PDX1 in PCa could contribute to improved treatment and prevention strategies, particularly for men with PCa and comorbidities such as obesity and diabetes. Show less

Epithelial-mesenchymal transition (EMT) plays a critical role in tumor progression; however, the underlying molecular mechanisms of EMT in papillary thyroid carcinoma (PTC) remain incompletely understood. This study aimed to investigate EMT-related mechanisms in PTC using an integrative approach combining single-cell RNA sequencing and machine learning. Differentially expressed genes (DEGs) between PTC and normal thyroid tissues were identified, and EMT-related candidate genes were obtained by intersecting DEGs with EMT-related genes (EMT-RGs). Prognostic genes were screened using univariate Cox regression, and a risk model was constructed based on 101 machine learning algorithm combinations. Patients were stratified into high- and low-risk groups (HRG and LRG) according to risk scores, and the model was validated in an internal cohort. Additional analyses included nomogram construction, immune infiltration profiling, tumor mutational burden (TMB) assessment, drug sensitivity prediction, and molecular regulatory network analysis. Prognostic gene expression was further validated in vitro. Eight EMT-related prognostic genes (TYRO3, E2F1, TNFSF15, TGFBR3, PTX3, FHL2, SNAI1, and WT1) were identified. Patients in the HRG exhibited significantly poorer overall survival than those in the LRG. The nomogram showed good predictive accuracy for survival estimation. Immune infiltration analysis revealed significant differences between risk groups across six immune-related features. Splice site-related mutations were predominantly observed in the LRG but were absent in the HRG. Drug sensitivity analysis indicated higher sensitivity to BIRB.0796 in the LRG, whereas ABT-263, AG-014699, BX-795, and DMOG were more effective in the HRG. Single-cell analysis identified fibroblasts as key cell populations, with FHL2, PTX3, and TGFBR3 showing increased activity during critical differentiation stages. In vitro experiments confirmed expression patterns consistent with bioinformatics findings. This study identifies eight EMT-related prognostic genes in PTC and highlights their potential value as biomarkers for prognostic evaluation and therapeutic stratification. Show less

Primary Sjögren's disease (pSjD) is a chronic autoimmune disease. Clinically, sialography and lip gland biopsy in patients with pSjD show characteristic ductal dilations. However, the roles of the immune responses in ductal dilation remain unknown. We show that Th2 cells and their core cytokine IL-4 promote salivary duct dilatation in human and experimental SjD. Specifically, striated duct dilation is accompanied by periductal lymphocyte infiltration, which is correlated with increased IL-4 levels. In vivo, IL-4 neutralization reduced ductal dilation. Mechanistically, IL-4 induces the formation of cyst-like structures in cultured embryonic submandibular glands of mice. At the molecular level, IL-4 activates SHH signaling pathway in striated duct epithelial cells, upregulating SNAI1 and suppressing Cadherin 1 expression. This process disrupts interepithelial adhesion, leading to ductal dilation. Thus, IL-4 drives salivary gland ductal dilation that interferes with salivary gland function in SjD. Our findings should have implications for a potential therapeutic target in clinical pSjD. Show less

While the epithelial-mesenchymal transition (EMT) is known to promote cancer stemness and metastasis, a hybrid partial EMT (p-EMT) state has recently been identified. This study examined the influence of HCT 116 cells were infected with Show less

Colorectal cancer (CRC) is a highly aggressive malignancy prone to liver metastasis, which significantly worsens prognosis of patients. Autophagy supports tumor cell survival by meeting metabolic demands and evading programmed cell death. This study aimed to develop a prognostic risk signature for CRC patients by integrating autophagy- and metastasis-related genes and to investigate its association with the tumor immune microenvironment and implications for immunotherapy. Weighted gene co-expression network analysis (WGCNA) identified candidate genes related to autophagy and liver metastasis. Univariate Cox and LASSO regression analyses were employed to develop a risk signature in the TCGA cohort, which was subsequently validated using an independent GEO cohort. Functional enrichment, immune infiltration, the heterogeneity and dynamics of macrophages and A prognostic risk signature incorporating six biomarkers ( In our study, we developed and validated a novel autophagy- and liver metastasis-associated prognostic signature for CRC. The risk signature effectively predicts alterations in the tumor immune microenvironment, immunotherapy, chemotherapy sensitivity and intercellular communication across different risk groups. Importantly, our findings reveal that autophagy and liver metastasis synergistically foster an immunosuppressive microenvironment, highlighting a potential target for therapeutic intervention. Show less

Snail (SNAI1), a central transcription factor driving epithelial-mesenchymal transition (EMT), is pivotal in cancer metastasis and tissue remodeling. Owing to its labile nature, Snail activity is tightly controlled by post-translational modifications that dictate its stability. Here this review summarizes how the ubiquitin-proteasome system orchestrates Snail degradation through coordinated phosphorylation and ubiquitination, mediated by diverse E3 ligases and regulated by kinases, acetyltransferases and deubiquitinases. These mechanisms dynamically adjust Snail levels in both the cytoplasm and nucleus, thereby modulating EMT outcomes. In parallel, emerging studies reveal that chaperone-mediated autophagy (CMA) provides an additional layer of regulation. Through recognition of KFERQ-like motifs, CMA selectively directs cytoplasmic Snail to lysosomes for LAMP2A-dependent degradation, functioning as a quality control system. Impairment of CMA leads to nuclear accumulation of Snail, enhancing its EMT-inducing and prometastatic potential. Together, the ubiquitin-proteasome system and CMA represent complementary, context-dependent axes that maintain Snail homeostasis. Their disruption facilitates EMT activation and metastatic progression. By integrating recent findings, this review highlights the dual degradative control of Snail and its implications for cancer biology, providing a conceptual framework for therapeutic approaches aimed at restoring degradative balance and limiting metastasis. Show less

To investigate whether vaccinia-related kinase 1 (VRK1) mediates transforming growth factor-beta2 (TGF-β2)-caused epithelial-mesenchymal transition (EMT) and inflammatory responses in retinal pigment epithelial (RPE) cells through regulating snail family transcriptional repressor 1 (SNAI1), and to validate its role in a proliferative vitreoretinopathy (PVR) mouse model. Human RPE cell line ARPE-19 cells were treated with TGF-β2 to construct an EMT model. Western blot detected VRK1 level. The effects of VRK1 on SNAI1 expression and biological behavior of ARPE-19 cells were detected by immunofluorescence, ELISA, Transwell, and scratch assay, and the interaction between VRK1 and SNAI1 was confirmed through immunoprecipitation. A PVR mouse model was constructed, and the effects of VRK1 or/and SNAI1 on retinal damage were assessed by pathologic staining. Inflammatory factors and EMT-related proteins were assessed with ELISA and Western blot. VRK1 was upregulated in ARPE-19 cells after TGF-β2 treatment. Overexpression of VRK1 increased cell viability, promoted cell migration and EMT, and the levels of inflammatory factors. Silencing of VRK1 reversed the above indexes. There was a direct interaction between VRK1 and SNAI1, and overexpresssion SNAI1 weakened the impacts of silencing of VRK1. In PVR mice, silencing of VRK1 ameliorated retinal structural damage, decreased proinflammatory factor levels, and suppressed SNAI1 and mesenchymal marker expression. SNAI1 overexpression antagonized the protective effects of silencing VRK1 and exacerbated EMT and inflammatory responses. VRK1 plays a key role in retinal structural and inflammatory damage in PVR mice by regulating SNAI1 and mediating TGF-β2-caused EMT and inflammatory responses in RPE cells. Show less

Mutations in BMP4 have been associated with malformations of the urinary tract in human patients. Genetic studies in mice have shown that these defects are linked to the expression of Bmp4 in the mesenchymal primordium of the ureter, where it acts as a critical signal for coordinated cytodifferentiation of the mesenchymal and epithelial tissues. Here, we used unbiased transcriptional profiling of ureters with genetic depletion of Bmp4 and pharmacological inhibition of BMP4 signaling to decipher the gene regulatory network controlled by BMP4 in the early ureter, focusing on transcription factors as possible drivers of cytodifferentiation. We show that in Bmp4-deficient ureters, expression of Grhl3, Msx2, Pparg, Trp63 and Foxa1 in the epithelial compartment, and of Gata6, Hopx, Id2, Id4, Myocd, Snai1 and Tbx18 in the mesenchymal primordium is reduced. Expression of Msx2, Pparg, Gata6, Id genes, Tbx18 and Snai1 requires direct BMP4 signaling input, whereas reduced expression of the other genes is likely due to secondary changes, including increased retinoic acid signaling. Conditional gene targeting of Smad4 revealed that BMP4-dependent activation of transcription factor genes is mediated in part by SMAD effectors in both ureteral tissues. Thus, our work links BMP4 (signaling) to known transcriptional regulators of ureteral cytodifferentiation and uncovers additional factors that may be relevant to this program. Show less

The development of resistance to anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors and a poor response to immune checkpoint inhibitors (ICIs) remain challenges in ALK-rearranged non-small cell lung cancer (NSCLC). We performed immune-related gene expression profiling (irGEP) for ALK-rearranged NSCLC to assess the characteristics of the tumor microenvironment and explore potential therapeutic avenues. This study analyzed tumor samples from the ALCURE trial, a prospective observational study examining the efficacy of and mechanisms of resistance to alectinib in patients with ALK-rearranged NSCLC. The irGEP analysis was performed with a panel encompassing 750 immune-related genes. Tumor samples from 52 of the 249 ALCURE trial patients were analyzed. Tumors with high CD8A expression showed upregulation of SNAI1 and downregulation of CDH1, with these genes encoding an epithelial-mesenchymal transition (EMT)-related transcription factor and E-cadherin, respectively, suggestive of EMT progression in these tumors. Tumors with high CD8A expression also manifested downregulation of genes related to tumor angiogenesis, including ANGPT2 (angiopoietin-2) and FLT1 (VEGF receptor 1), suggestive of a quiescent angiogenic state that may facilitate the recruitment of CD8 CD8 Show less

Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignancies due to its aggressive nature and resistance to therapy. The epithelial-mesenchymal transition (EMT) drives cancer progression, regulated by transcription factors (TFs) such as SNAI1, SNAI2, ZEB1, ZEB2, and TWIST. This study evaluates EMT-TF expression in PDAC and its clinical relevance. PDAC tissues from 45 patients were analyzed using qRT-PCR and Western blot. Clinical features and survival outcomes were statistically examined for correlations with EMT-TF levels. mRNA levels of SNAI1 (16.4-fold, p = 0.02), SNAI2 (21.8-fold, p = 0.028), ZEB1 (17.2-fold, p = 0.037) were significantly elevated in PDAC tissues compared to healthy controls. TWIST showed 3.75-fold increase in PDAC tissue; however, this elevation was not significant (p = 0.124). Corresponding protein-level increases were observed for Snail1/Slug and Zeb1. High SNAI1 expression correlated with peripancreatic invasion (p = 0.026) while ZEB1 overexpression was significantly associated with shorter survival (15.2 vs. 33.3 months, p = 0.037) and remained an independent prognostic factor in multivariate analysis. ZEB2 mRNA was reduced, however, protein levels were elevated. TWIST mRNA overexpression was not reflected at the protein level. Overexpression of EMT transcription factors SNAI1 and ZEB1 reflect more aggressive histopathological patterns of PDAC. The strong correlation of SNAI1 expression with the expression of other EMT-TFs highlights its' role in peripancreatic invasion, as well as impact on overall survival and may serve as an argument defining the leading role of SNAI1 in this context. Show less