Search Results (108)

Background/Objectives: Oral squamous cell carcinoma (OSCC) commonly arises from oral potentially malignant disorders (OPMDs), yet reliable molecular biomarkers that predict malignant transformation remain scarce. Because epithelial carcinogenesis follows similar multistep trajectories across multiple organs, pan-cancer transcriptional analyses may reveal conserved pathways relevant to early oral tumorigenesis. This study aimed to identify shared transcriptional signatures across carcinomas and evaluate their applicability to precancerous-to-carcinoma progression. Methods: Bulk RNA-seq data from five carcinomas (lung, colon, breast, prostate, and head and neck squamous cell carcinoma, HNSCC) were obtained from TCGA to identify shared differentially expressed genes (DEGs) (|log₂FC| ≥ 2; FDR < 0.05). Functional enrichment, clustering, and gene–pathway network analyses characterized conserved biological processes. Independent GEO datasets containing premalignant and malignant samples, including OPMD and OSCC cohorts, were examined to assess early-stage relevance. Results: A conserved 45-gene signature was identified, enriched for transcriptional regulation, chromatin organization, and RNA polymerase II-mediated processes. Regulatory hubs, including ZIC5, MYBL2, ONECUT2, POU4F1, and PDX1, and strong upregulation of cancer-testis antigens (MAGEA3, MAGEA6, MAGEC2) were notable. Integration with premalignant datasets revealed 13 genes consistently dysregulated across early lesions, involving pathways such as cell differentiation, apoptosis, and lipid transport. Several genes remained altered from normal tissue through OPMD to OSCC, supporting their potential as stable biomarkers. Conclusions: This study identifies conserved transcriptional programs shared across epithelial cancers and detectable in OPMDs. These findings highlight promising biomarker and regulatory candidates for improving early detection and risk stratification of oral precancer, addressing a critical unmet need in OSCC prevention and clinical management. Full article

Tuft cells (TCs) are rare chemosensory epithelial cells that regulate mucosal homeostasis in multiple organs, but their role in salivary gland (SG) biology remains poorly defined. This study aimed to define TC structure in mice submandibular glands (SMGs), determine how TC loss affects gland organization and function, and evaluate whether TC abundance in human minor SGs is associated with Sjögren’s disease (SjD) features. Specifically, TC ultrastructure and ductal localization were characterized in female and male C57BL/6J mouse SMGs by transmission electron microscopy and immunostaining. Wild-type and C57BL/6J-Pou2f3^-/- (TC-deficient mouse strain) SMGs were analyzed by histology and bulk RNA-seq, and salivary function was assessed by saliva flow and proteomics. Human minor SG biopsies from SjD and non-Sjögren sicca (nSjD) patients were analyzed by immunostaining and Poisson regression. In mice SMGs, TCs showed conserved ultrastructural features and localization in both sexes. TC loss was associated with marked sex-biased transcriptome remodeling, morphological disruption, and altered saliva quantity and quality. In humans, TC counts differed between nSjD and SjD groups and were associated with salivary flow, serologic status, and histopathologic features. These findings support a role for TCs in SG epithelial integrity and suggest TC abundance as a candidate biomarker of SG dysfunction. Full article

Background: HER2-low breast cancer is a biologically heterogeneous subgroup in which hormone receptor (HR) expression critically shapes prognosis and treatment, but the underlying regulatory mechanisms remain unclear. MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression and may contribute to HR heterogeneity. This study aimed to identify deregulated miRNAs and associated gene networks distinguishing HER2-low/HR-positive from HER2-low/HR-negative tumors, elucidating the molecular mechanisms underlying this divergence. Methods: Differential expression analyses of miRNAs and genes were performed using Wilcoxon tests and DESeq2 (|log₂FC| > 1; FDR-adjusted p-value < 0.05). Survival analyses were conducted using Cox proportional hazards models to evaluate the individual miRNAs and miRNA signature. Functional enrichment analyses, including GO, KEGG and Reactome pathways, were performed. Correlation analysis and the miRNA target prediction were integrated to identify regulatory interactions. Results: Comparisons between HER2-low/HR-positive and HER2-low/HR-negative tumors identified 165 significantly deregulated miRNAs and 170 strongly deregulated genes. Intersection analysis highlighted miR-9-5p, miR-532-5p and miR-576-5p as specifically associated with HR-negative status. Survival analyses showed non-significant trends for the overall survival and progression-free interval. Functional enrichment analysis revealed hormone-related pathways in HR-positive tumors and immune, inflammatory and proliferative pathways in HR-negative tumors. Integrative correlation and target prediction analyses identified two miRNA–mRNA regulatory axes, miR-576-5p/TGFBI and miR-9-5p/POU2F2. Conclusions: Our study demonstrated that HER2-low breast cancer exhibits distinct miRNA and gene expression profiles, which highlight different transcriptomic profiles according to HR status for the first time. Specific miRNA–gene networks may drive transcriptional heterogeneity, serving as potential biomarkers for stratification and as therapeutic targets. These findings provide insight into the molecular basis of HER2-low tumor diversity and support future development of HR-directed therapeutic strategies. Full article

Background: Gamma-aminobutyric acid (GABA), the principal inhibitory neurotransmitter in the central nervous system (CNS), is also a potent modulator of peripheral endocrine function. We previously demonstrated that dietary GABA supplementation improves growth and fatty acid metabolism in male mice while elevating pituitary growth hormone (GH). However, the mechanisms by which GABA regulates the somatotropic axis remain unclear. Methods: Adolescent mice (3–4 weeks old) were treated with or without GABA in drinking water. Cultured pituitaries and GH3 somatotroph-derived cells were exposed to GABA, Picrotoxin, or STO-609, and protein expression was analyzed by Western blot. Results: GABA treatment increased Pit-1 (POU1F1) protein levels among males in vivo (ctrl: 0.55 ± 0.11; GABA: 1.46 ± 0.16; p = 0.0034) and ex vivo (ctrl: 0.66 ± 0.03; GABA: 1.46 ± 0.14; p = 0.0013), as well as in GH3 cells (ctrl: 1.36 ± 0.12; GABA: 3.05 ± 0.12; p < 0.0001). GH expression was also increased by GABA treatment in ex vivo pituitaries (ctrl: 1.62 ± 0.06; GABA: 1.84 ± 0.01; p = 0.0115) and GH3 cells (ctrl: 0.34 ± 0.08; GABA: 1.35 ± 0.13; p = 0.0006). Mechanistically, GABA, via the GABA_A receptor (GABA_AR), enhanced CaMKK2 pathway activity, as evidenced by increased phosphorylation of CaMKIV (ctrl: 0.86 ± 0.07; GABA: 1.12 ± 0.07; p = 0.0378) and AKT (ctrl: 0.89 ± 0.08; GABA: 1.75 ± 0.23; p = 0.0122). Inhibition of GABA_ARs by picrotoxin (PTX) markedly reduced Pit-1 (GABA: 2.73 ± 0.29; GABA + PTX: 1.76 ± 0.21; p = 0.0351) and GH expression (GABA: 0.17 ± 0.02; GABA + PTX: 0.05 ± 0.02; p = 0.0052). Treatment with CaMKK2 inhibitor STO-609 reduced basal Pit-1 (ctrl: 1.76 ± 0.09; STO-609: 1.25 ± 0.12; p = 0.0157) and GH levels (ctrl: 1.18 ± 0.10; STO-609: 0.50 ± 0.04; p = 0.0006). Ghrelin receptor activation by anamorelin (ANA) increased Pit-1 (ctrl: 0.83 ± 0.8; ANA: 1.59 ± 0.28; p = 0.0425) and GH (ctrl: 0.27 ± 0.03; ANA: 0.66 ± 0.16; p = 0.0497) through a CaMKK2-independent pathway but required basal GABA_AR activity for maximal effect. Conclusions: These findings identify GABA as a modulator of somatotroph hormone expression through a CaMKK2/CaMKIV-dependent cascade and reveal a previously unrecognized interplay whereby the basal GABAergic tone promotes Pit-1 expression, thereby positively regulating ghrelin receptor signaling. This study provides new insights on the cellular mechanisms behind GABA-induced GH synthesis, which may reveal new strategies for modulating the somatotropic axis and help contextualize the variety of reported physiological and cognitive effects of GABA supplementation. Full article

The Wnt/β-catenin signaling pathway is involved in regulating the pluripotency of mammalian stem cells. Fine-tuning of Wnt/β-catenin modulates the transition of naïve, formative or primed states with distinct lineage bias. However, its specific function in large domestic animals such as bovines remains unclear. Here we systematically investigated the role of Wnt/β-catenin signaling and its key effector TCF1 in bovine expanded pluripotent stem cells (bEPSCs) using a combination of small molecules (CHIR99021, XAV939, IWR-1, iCRT3). The results showed that prolonged Wnt/β-catenin activation with CHIR99021 induced morphological changes and downregulated the expression of core pluripotency genes POU5F1 (OCT4) and SOX2 in bEPSCs, while the existence of Wnt/β-catenin inhibitors XAV939 and IWR-1 upregulated these two genes. Knockdown of TCF1, a major nuclear effector of CTNNB1 (β-catenin), reduced the expression of pluripotency genes (POU5F1, SOX2) and key Wnt/β-catenin components (TCF3, LEF1 and CTNNB1). Combined treatment with CHIR99021 and the canonical β-catenin/TCF inhibitor iCRT3 resulted in the overactivation of Wnt/β-catenin signaling, and promoted the expression of core pluripotency genes, revealing extensive rewiring of the Wnt/β-catenin pathway in bovines. Consistent with these findings, global transcriptomics revealed that CHIR99021 combined with iCRT3 enhanced the expression of key pluripotency-related genes and further activated Wnt/β-catenin signaling target genes while simultaneously suppressing mitogenic pathways such as PI3K-Akt and MAPK signaling. Transcriptome profiling also demonstrated that this combination drives bEPSCs toward a hybrid naïve/formative pluripotency state. Together, these results demonstrate that Wnt/β-catenin signaling homeostasis is critical for bovine pluripotency regulation, which provides a foundation for refining livestock stem cell culture conditions and understanding the evolution of pluripotency networks. Full article

Short-term hypothermic storage at 4 °C represents a promising non-freezing alternative for transporting bovine embryos and synchronizing assisted reproductive procedures. However, chilling induces oxidative stress, mitochondrial dysfunction, and apoptosis, which markedly impair post-preservation embryonic viability. Glutathione (GSH), a key intracellular antioxidant, may mitigate these damaging effects, yet its protective mechanisms during bovine blastocyst hypothermic preservation remain unclear. Here, we investigated the impact of exogenous GSH supplementation on the survival, hatching ability, cellular integrity, mitochondrial function, and developmental potential of bovine blastocysts preserved at 4 °C for seven days. Optimization experiments revealed that 4 mM GSH provided the highest post-chilling survival and hatching rates. Using DCFH-DA, TUNEL, and γ-H2AX staining, we demonstrated that 4 °C preservation significantly increased intracellular reactive oxygen species (ROS), DNA fragmentation, and apoptosis. GSH supplementation markedly alleviated oxidative injury, reduced apoptotic cell ratio, and decreased DNA double-strand breaks. MitoTracker and JC-1 staining indicated severe chilling-induced mitochondrial suppression, including decreased mitochondrial activity and membrane potential (ΔΨm), which were largely restored by GSH. Gene expression analyses further revealed that chilling downregulated antioxidant genes (SOD2, GPX1, TFAM, NRF2), pluripotency markers (POU5F1, NANOG), and IFNT, while upregulating apoptotic genes (BAX, CASP3). GSH effectively reversed these alterations and normalized the BAX/BCL2 ratio. Moreover, SOX2/CDX2 immunostaining, total cell number, and ICM/TE ratio confirmed improved embryonic structural integrity and developmental competence. Collectively, our findings demonstrate that exogenous GSH protects bovine blastocysts from chilling injury by suppressing ROS accumulation, stabilizing mitochondrial function, reducing apoptosis, and restoring developmental potential. This study provides a mechanistic foundation for improving 4 °C embryo storage strategies in bovine reproductive biotechnology. Full article

Cervical cancer remains a significant global health burden, with chemoradioresistance representing a major obstacle to successful treatment. To elucidate the mechanisms underlying this resistance, we established a unique pair of isogenic primary cervical cancer cell lines, AdMer35 and AdMer43, obtained from a patient with squamous cell carcinoma of the cervix before and after radiation therapy. The aim of our study was to characterize the transcriptomic and cellular heterogeneity of these cells. We conducted an in-depth comparative analysis using single-cell RNA sequencing. Analysis of this paired, patient-derived isogenic model suggests that chemoradioresistance can arise through coordinated multilevel cellular adaptations. Resistant AdMer43 cells demonstrated transcriptional reprogramming, with the upregulation of embryonic stemness factors (HOX, POU5F1, SOX2), a shift in extracellular matrix from fibrillar to non-fibrillar collagens, and activation of inflammatory pathways. We identified and characterized critical cell-state dynamics: resistant cells exhibited a remodeled ecosystem with a metabolically reprogrammed senescent-like cell population showing an enhanced pro-tumorigenic communication via EREG, SEMA3C, BMP, and WNT pathways. Furthermore, we identified a progenitor-like cell population with a minimal CNV burden, potentially serving as a reservoir for tumor persistence. These findings offer novel insights for developing targeted strategies to eliminate resistant cell pools and improve cervical cancer outcomes. Full article

Mutations in the POU1F1 gene cause defects in the expression of the genes encoding thyroid-stimulating hormone (TSH)-β subunit, growth hormone (GH), and prolactin (PRL). Here, we characterized 15 missense and nonsense mutations. Protein stability was reduced in the P14L, P24L, F135C, K145X, F233S and E250X mutants. Transactivation by 15 mutants in the TSHβ promoter was moderately correlated with that of the PRL promoter. Based on their transcriptional activity, we classified them into three groups: group I, equivalent to the wild type; group II, partial; and group III, substantially lost. A review of case reports on four patients with group II mutations revealed that TSH deficiency manifested after recombinant GH therapy. A transcription factor, GATA2, is the main activator in the TSHβ gene, while POU1F1 protects its function from inhibition by the suppressor region (SR). We found that the SR is critical for the pathogenesis of TSH deficiency. The transactivation of the TSHβ promoter by the K216E mutant was equivalent to that of wild-type POU1F1; however, that of the PRL promoter was low, while the opposite was found in the R271W mutant. The functional property of K216E suggests that the interaction of POU1F1 with GATA2 may not always be necessary for the activation of the TSHβ promoter. Full article

Schizophrenia is a highly polygenic and clinically heterogeneous disorder. In this paper, we first review layer-specific evidence across genetics, epigenetics, transcriptomics, proteomics, and patient-derived induced pluripotent stem cell (iPSC) models, then integrate cross-layer findings. Genetics research identifies widespread risk architecture. Hundreds of loci from common, rare, and CNV analyses. Epigenetics reveals disease-associated DNA methylation and histone-mark changes. These occur at neuronally active enhancers and promoters, together with chromatin contacts that link non-coding risk to target genes. Transcriptomics show broad differential expression, isoform-level dysregulation, and disrupted co-expression modules. These alterations span synaptic signaling, mitochondrial bioenergetics, and immune programs. Proteomics demonstrates coordinated decreases in postsynaptic scaffold and mitochondrial respiratory-chain proteins in cortex, with complementary inflammatory signatures in serum/plasma. iPSC models recapitulate disease-relevant phenotypes: including fewer synaptic puncta and excitatory postsynaptic currents, electrophysiological immaturity, oxidative stress, and progenitor vulnerability. These same models show partial rescue under targeted perturbations. Integration across layers highlights convergent pathways repeatedly supported by ≥3 independent data types: synaptic signaling, immune/complement regulation, mitochondrial/energetic function, neurodevelopmental programs and cell-adhesion complexes. Within these axes, several cross-layer convergence genes/proteins (e.g., DLG4/PSD-95, C4A, RELN, NRXN1/NLGN1, OXPHOS subunits, POU3F2/BRN2, PTN) recur across cohorts and modalities. Framing results through cross-layer and shared-pathway convergence organizes heterogeneous evidence and prioritizes targets for mechanistic dissection, biomarker development, and translational follow-up. Full article

Small Cell Lung Cancer (SCLC) is an aggressive neuroendocrine malignancy representing approximately 15% of all lung cancers. Characterized by rapid progression, early metastasis, and high circulating tumor cell burden, SCLC has a poor prognosis. Although initial responses to chemotherapy, radiotherapy, and immunotherapy are common, relapse due to acquired resistance is nearly inevitable. Molecular studies have identified four transcription factor–driven subtypes—ASCL1, NEUROD1, POU2F3, and YAP1—each with distinct biological traits and therapeutic vulnerabilities. However, clinical classification remains largely homogeneous, limiting precision treatment strategies. Immunotherapy has modestly improved survival, as demonstrated in trials like IMpower133, CASPIAN, and ADRIATIC. Yet only a small subset of patients—approximately 12%—achieve long-term survival beyond five years. Understanding the biological and immunological profiles of these exceptional responders is critical. Future research should prioritize comprehensive biomarker integration, including PD-L1, TMB, DLL3, CD3, and emerging targets. Novel agents such as tarlatamab (DLL3-targeting) and ifinatamab deruxtecan (B7-H3–targeting) have shown encouraging efficacy in early-phase trials, though predictive markers remain elusive. A multi-dimensional approach combining tissue, blood, and immune profiling is essential to advance precision oncology in SCLC and improve patient selection for emerging therapies. Full article

As an interspecies hybrid inheriting genetic material from horse and donkey lineages, mules provide a unique model for studying allele-specific regulatory dynamics. Here, we isolated adult fibroblasts (AFs) and placental fibroblasts (PFs) from mule tissues and reprogrammed them into induced pluripotent stem cells (iPSCs). Intriguingly, placental fibroblast-derived iPSCs (mpiPSCs) exhibited reduced reprogramming efficiency compared to adult fibroblast-derived iPSCs (maiPSCs). Through allele-specific expression (ASE) analysis, we systematically dissected transcriptional biases in parental cell types and their reprogrammed counterparts, revealing conserved preferential expression of asinine alleles in core pluripotency regulators (e.g., POU5F1/OCT4, SOX2, NANOG) across both cell lineages. Strikingly, mpiPSCs displayed stronger asinine allele dominance than maiPSCs, suggesting tissue-specific parental genomic imprinting. Mechanistic exploration implicated PI3K-AKT signaling as a potential pathway mediating the reprogramming inefficiency in placental fibroblasts. By integrating transcriptomic profiling with ASE technology, this study uncovers allele selection hierarchies during somatic cell reprogramming in hybrids and establishes a framework for understanding how parental genomic conflicts shape pluripotency establishment. These findings advance interspecies iPSC research by delineating allele-specific regulatory networks and providing insights into the molecular constraints of hybrid cellular reprogramming. Full article

Background/Objectives: Acinar-to-ductal metaplasia (ADM) refers to the dedifferentiation or transdifferentiation of pancreatic acinar cells. Recently, ADM has received considerable attention as a potential precursor of pancreatic tumours. Previous studies in mouse models identified tuft cells, chemosensory epithelial cells, in ADM and pancreatic intraepithelial neoplasia (PanIN), both considered precursor lesions of pancreatic ductal adenocarcinoma (PDAC), but not in PDAC. We examined the presence of tuft cells in human ADM and PanIN. Methods: We analysed tissue samples from 29 patients (16 women, 13 men; median age 74 years) who underwent surgical resection for pancreatic tumours. Immunohistochemical staining for the tuft cell marker, POU2F3, was used to detect tuft cells in ADM and PanIN lesions. Results: ADM was present in all patients. POU2F3-positive tuft cells were observed in 46.4% of ADM lesions (327/705) but not in normal pancreatic acini. The number of POU2F3-positive tuft cells per PanIN area were significantly higher in low-grade PanIN (median, 2 cells; range, 0–20 positive cells) than in high-grade PanIN (median, 0 cell; range 0–4 positive cells) (p = 0.0050). The percentage of POU2F3-positive tuft cells per total cells in low-grade PanIN lesions (median, 1.1%; range 0–2.5%) was also significantly higher than that in high-grade PanIN lesions (median, 0%; range 0–1.1%) (p = 0.0044). Conclusions: Our results suggest that tuft cells emerge in human pancreatic acini during ADM, possibly as part of tissue repair following injury. Full article

Background/Objectives: Response to immune checkpoint inhibitors (ICIs) is associated with several biological pathways, including tumor immunogenicity and antitumor immunity. Identifying host factors involved in these pathways may guide personalized ICI treatment. Methods: We describe the application of chromatin conformation assays to blood from patients with advanced urothelial carcinoma from the phase 3 JAVELIN Bladder 100 trial (NCT02603432). This trial demonstrated a significant survival benefit with avelumab maintenance plus best supportive care (BSC) vs. BSC alone following non-progression with platinum-based chemotherapy as first-line therapy. Blood-based chromatin conformation markers (CCMs) were screened for associations with high/low immune effector gene expression in tumors and for interactions with outcomes and tumor mutation burden. Results: Candidate CCMs included genes involved in several immune response pathways, such as POU2F2, which encodes a transcription factor that regulates B-cell maturation. Conclusions: Our findings suggest that polygenic host factors may affect response to ICIs and support further investigation of chromatin conformation assays. Full article

The possibilities of small-cell lung cancer (SCLC) therapy were strictly limited for years, leading to high patient mortality rates. New approaches to SCLC treatment are being proposed, including chemoimmunotherapy. However, biomarkers enabling appropriate personalization of therapy in SCLC patients have not been identified yet. Even though molecular subtyping (ASCL1, NEUROD1, POU2F3, and YAP1) seems pivotal in the management of SCLC, expression of other genes might be potentially valuable during patients’ stratification. Due to their crucial role in tumorigenesis and SCLC invasiveness, benefits arising from MET and SLFN11 gene evaluation are suggested. Our study was designed to evaluate the relationship between the mRNA expression of these genes and chemoimmunotherapy efficacy in SCLC patients. A total of 35 patients with extensive-stage SCLC (ES-SCLC) treated with first-line chemoimmunotherapy were involved in the study. mRNA expression of MET and SLFN11 genes was evaluated using the RT-qPCR technique in FFPE tissue collected from all patients. Molecular results were correlated with clinicopathological features and outcome of disease (OS, PFS). We detected SLFN11 expression in 60% (21 of 35) of the samples. SLFN11 expression was higher in patients with longer PFS (p = 0.05) and with the T4 feature in the TNM scale (p = 0.08). MET mRNA was expressed in all FFPE tissues. We observed that risk of progression and death was higher in patients with higher expression of MET mRNA (p = 0.06 and p = 0.04, respectively). Our study showed that MET and SLFN11 expression might serve as additional biomarkers for prediction of chemoimmunotherapy efficacy in ES-SCLC patients. Full article

Zygotic genome activation (ZGA) marks the critical transition from reliance on maternal transcripts to the initiation of embryonic transcription early in development. Despite extensive characterization in model species, the regulatory framework of ZGA in sheep remains poorly defined. Here, we applied single-cell RNA sequencing (Smart-seq2) to in vivo- and in vitro-derived sheep embryos at the 8-, 16-, and 32-cell stages. Differential expression analysis revealed 114, 1628, and 1465 genes altered in the 8- vs. 16-, 16- vs. 32-, and 8- vs. 32-cell transitions, respectively, with the core pluripotency factors SOX2, NANOG, POU5F1, and KLF4 upregulated during major ZGA. To uncover coordinated regulatory modules, we constructed a weighted gene co-expression network using WGCNA, identifying the MEred module as most tightly correlated with developmental progression (r = 0.48, p = 8.6 × 10⁻¹⁴). The integration of MERed genes into the STRING v11 protein–protein interaction network furnished a high-confidence scaffold for community detection. Louvain partitioning delineated two discrete communities: Community 0 was enriched in ER–Golgi vesicle-mediated transport, transmembrane transport, and cytoskeletal dynamics, suggesting roles in membrane protein processing, secretion, and early signaling; Community 1 was enriched in G2/M cell-cycle transition and RNA splicing/processing, indicating a coordinated network for accurate post-ZGA cell division and transcript maturation. Together, these integrated analyses reveal a modular regulatory architecture underlying sheep ZGA and provide a framework for dissecting early embryonic development in this species. Full article