Search Results (3,468)

Background/Objectives: MSS-CRC comprises a heterogeneous group of tumors generally considered “immune cold” due to limited neoantigen generation and T-cell exclusion or inactivation. Current evidence indicates that the composition of T and B immune cells within the tumor microenvironment represents a prognostically relevant factor, significantly associated with both tumor expression profiles and molecular subtypes. Methods: We conducted an exploratory analysis to identify prognostically relevant immune cell components in this group of tumors and to investigate corresponding differences in RNA-based bulk expression and high-resolution spatial transcriptomic profiles. Results: A total of 254 localized mismatch repair-proficient colorectal cancer cases were evaluated. Our findings revealed PD-L1 expression as a robust independent prognostic biomarker associated with favorable outcomes in this specific population. Bulk RNA expression analysis showed that PD-L1-negative tumors exhibited an expression profile consistent with abundant cancer-associated fibroblast infiltration, increased matrix stiffness, and impaired immune activation—features consistent with tumor progression and poorer clinical outcomes. In contrast, PD-L1-positive tumors displayed stromal programs enriched in immune activation and controlled remodeling, consistent with an immunologically active microenvironment. Spatial transcriptomics added an additional layer of evidence, revealing that epithelial to mesenchymal transition-related programs can dominate stromal niches in PD-L1-negative tumors, particularly within macrophage-enriched stromal regions. Conclusions: Our observations suggest an association between PD-L1 expression on immune cells and immune-activated versus mesenchymal-dominant states, potentially occurring within macrophage-enriched stromal niches. These results provide insight into the biological mechanisms underlying disease progression and highlight tumor-associated macrophages as a potential therapeutic target to overcome immune resistance, particularly in PD-L1-negative MSS-CRC tumors. Full article

Influenza A virus (IAV) surveillance in swine relies heavily on molecular detection, yet RNA stability in diagnostic specimens such as oral fluids can be rapidly compromised when cold-chain conditions are not maintained. This pilot study evaluated the ability of four molecular-grade carbohydrates (20% trehalose, sorbitol, sucrose, and mannitol) and two commercial nucleic acid stabilizers (PrimeStore^® MTM and RNAlater^®) to preserve RT-qPCR-detectable IAV RNA in swine oral fluids exposed to field-relevant stress conditions. Oral fluid samples collected from pigs experimentally infected with H1N2 (Study 1: n = 150; DPIs 2, 3, 4) or with H1N2 and H3N2 (Study 2: n = 58; DPI 5) were subjected to storage at 25 °C for up to 144 h (Study 1) or 2, 5, 10, or 15 freeze–thaw cycles (Study 2), with DPIs (Study 1) or subtypes (Study 2) serving as biological replicates, given the limited sample size. IAV detection was quantified as efficiency standardized Cq values (ECq) and analyzed using a linear mixed-effects model. Overall, both carbohydrates (trehalose, sorbitol, sucrose) and commercial stabilizers maintained higher ECq values than untreated oral fluids under both thermal and freeze–thaw stress conditions. Due to the limited sample size, these findings should be interpreted cautiously, yet they demonstrate the potential utility of carbohydrates as a low-cost, non-inactivating alternative for stabilizing IAV RNA in field-collected oral fluids. Full article

Background/Objectives: AP-2δ, encoded by TFAP2D, is one of the least characterized members of the AP-2 transcription factor family, although available evidence suggests biologically relevant roles in lung cancer that have not yet been thoroughly examined. The aim of the present study was to provide an integrated characterization of AP-2δ/TFAP2D in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Methods: LUAD and LUSC data were obtained from The Cancer Genome Atlas. The analysis comprised the expression profiling of AP-2δ target genes, survival-guided TFAP2D stratification, clinical profiling, differential expression and intersection analyses, methylation-derived chromatin compartment profiling, TFAP2D-associated cofactor rewiring, and genome-wide enrichment of AP-2δ targets. In parallel, pocket prioritization was performed using an AlphaFold model of AP-2δ with cross-tool consensus mapping. Results: TFAP2D stratification delineated biologically-distinct states in both histological subtypes (LUAD and LUSC). AP-2δ target genes showed subtype-specific expression patterns and functional organization. The consistent survival association was observed for progression-free interval rather than uniformly across all endpoints. Clinical profiling was more closely associated with molecular subtype composition than broad clinicopathological differences. Differential expression analyses identified both shared and histology-dependent programs associated with TFAP2D. In the chromatin-compartment analysis, LUSC showed a broader and more coherent footprint, whereas LUAD displayed more selective cofactor rewiring. Structure-based analysis prioritized a small set of reproducible candidate pockets concentrated within ordered regions of the TF_AP-2 domain. Conclusions: AP-2δ marks biologically meaningful but histologically non-uniform regulatory states in lung cancer. These findings provide an integrated framework for understanding TFAP2D-dependent regulation in LUAD and LUSC, highlighting AP-2δ as a candidate for future mechanistic and translational investigation. Full article

Hepatitis E virus (HEV) is a zoonotic pathogen of global concern that circulates in both domestic and wild swine populations. Understanding its presence and dynamics in wildlife reservoirs is crucial for assessing spillover risks and designing One Health surveillance strategies. This study investigated the occurrence, genetic diversity, and evolutionary relationships of HEV in wild boars from mainland Portugal. A total of 120 animals from seven districts were tested, with HEV RNA detected in four cases (3.3%), all from the Évora district near the Spanish border. One positive sample was successfully sequenced, and phylogenetic analysis based on the complete genome classified it within the HEV-3m subtype, clustering with predominantly human-derived sequences from Spain and France, which highlights its zoonotic potential. A second phylogenetic analysis based on a partial genomic fragment, including sequences from domestic pigs in Portugal, revealed the co-circulation of subtypes 3e, 3f, and 3m without clear spatial or temporal patterns. Phylogeographic analysis suggested that the identified strain was most likely introduced from Spain, supporting the hypothesis of cross-border transmission through wild boar movement. No recombination events were detected in the sequence obtained in this study. These findings provide the first molecular evidence of HEV-3m circulation in wild boars in Portugal, offering valuable insight into the HEV strain circulation in European wildlife populations. The zoonotic potential of HEV and the likelihood of interspecies transmission highlight the need for coordinated cross-border surveillance and integrated One Health strategies. Full article

Objectives: The mechanism of action of genes related to lactate metabolism in papillary thyroid carcinoma (PTC) is still unclear. In this study, key genes that play a role in PTC were selected from the known genes related to lactate metabolism, and their roles in promoting lactate metabolism in PTC cells were investigated. Methods: Through bioinformatics analysis and cell experiments, the roles of the relevant genes in lactate metabolism and their roles in the occurrence and development of PTC were verified. Results: Through bioinformatics analysis, 12 candidate genes were obtained. Through qRT-PCR experiments, it was confirmed that the expressions of TIMP1 and DPP4 were higher in thyroid papillary carcinoma than in normal PTC cells. By inhibiting the expression of TIMP1 and DPP4 using siRNA, the invasion and proliferation abilities of PTC could be reduced. Compared with normal thyroid cells, the contents of lactic acid and LDHA in PTC cells were higher. Knocking down the expression of TIMP1 and DPP4 would reduce the lactate production ability of PTC cells, and TIMP1 and DPP4 promoted the accumulation of lactate in PTC cells.Conclusions: In this study, by screening the differentially expressed lactate metabolism genes in PTC, different prognostic subtypes were constructed based on the molecular expression patterns. Multi-group student’s t-tests were conducted on the differential signaling pathways and tumor immune regulation of the prognostic subtypes, and a PTC prognosis prediction model was constructed. It was further confirmed that the lactate metabolism genes TIMP1 and DPP4 are highly expressed in PTC and can regulate the proliferation, invasion, metastasis and lactate metabolism of PTC cells. Full article

Breast cancer is classified into distinct molecular subtypes, including Luminal A, Luminal B, HER2-enriched, Basal-like, and Claudin-low. While traditional studies mostly use 2D cell cultures, 3D models better mimic in vivo tumor conditions. In this study, we generated and characterized 3D spheroids from breast cancer cell lines representing different molecular subtypes. Morphologically, spheroids were either compact (MCF-7/AZ, T47D, BT474, MDA-IBC-3, BT-20, SUM149PT) or loosely adhered (MDA-MB-468, SK-BR-3, MDA-MB-231), while retaining key parental subtype biomarkers. Cell viability decreased with increasing spheroid size, but apoptotic cCasp3 staining was restricted to Basal-like spheroids. Compact spheroids expressed E- and/or P-cadherin, indicating epithelial or epithelial–mesenchymal transition (EMT) hybrid traits, while loose spheroids showed vimentin expression linked to a mesenchymal phenotype. Overall, EMT status, rather than molecular subtype, primarily determined spheroid morphology. In conclusion, EMT-associated features, rather than intrinsic molecular subtype, may contribute to 3D spheroid architecture of breast cancer cell lines. Full article

Heterotopic ossification (HO), the pathological formation of mature bone in non-skeletal soft tissues (e.g., muscles, tendons), severely impairs patient mobility and quality of life. Despite decades of research, systematic analysis of signaling networks across HO subtypes (acquired traumatic HO, hereditary Fibrodysplasia Ossificans Progressiva (FOP), Progressive Osseous Heteroplasia (POH)) remains insufficient, and clinical therapies suffer from high recurrence and severe side effects. This review synthesizes recent advances in HO pathogenesis: FOP involves gain-of-function activin A receptor type I (ACVR1) mutations (mostly R206H), disrupting bone morphogenetic protein (BMP)/Activin A signaling; POH arises from paternal guanine nucleotide-binding protein, alpha-stimulating activity polypeptide (GNAS) loss-of-function mutations, derepressing Hedgehog signaling via reduced cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) activity; tHO features trauma-induced inflammation/hypoxia activating BMP/transforming growth factor–beta (TGF-β) pathways. Key signaling crosstalk (e.g., BMP-Yes-associated protein (YAP)-Indian hedgehog (IHH)) is integrated, and novel therapies (ACVR1 inhibitors, Activin A antibodies, retinoic acid receptor gamma (RARγ) agonists, adeno-associated virus (AAV)-mediated ACVR1 silencing) are highlighted, with emphasis on subtype-specific efficacy. A stratified, mechanism-based HO management framework is proposed, aiming to accelerate precision therapy development and advance understanding of aberrant tissue regeneration. Full article

Background/Objectives: Diffuse large B-cell lymphoma (DLBCL) is molecularly heterogeneous, and approximately 30-50% of patients fail to achieve cure with standard R-CHOP. Genotype-directed first-line therapy may improve outcomes by targeting subtype-specific oncogenic pathways. This study evaluated the feasibility, efficacy, and safety of a molecularly adapted R-CHOP-X strategy with two-year follow-up. Methods: In this single-center, prospective, non-randomized study conducted between September 2023 and the data cut-off (16 September 2025), 43 adults with newly diagnosed DLBCL (excluding high-grade B-cell lymphoma, primary immune-privileged, and primary mediastinal large B-cell lymphomas) underwent tumor genotyping using the LymphGen classification after targeted sequencing: a 19-gene Sanger panel (Cohort 1, n = 35) or an expanded 60-gene panel (Cohort 2, n = 8; proof-of-concept). All patients received one initial cycle of R-CHOP as bridge therapy pending molecular profiling results, followed by five cycles of R-CHOP-X, with the additional agent (vorinostat, acalabrutinib, decitabine, or lenalidomide) selected according to molecular subtype. Response was assessed by PET/CT per Lugano criteria; adverse events were graded per NCI CTCAE v5.0. Results: The overall study population was predominantly high-risk: 72% had an IPI of 3–5, 58% had stage III–IV disease, and 67% exhibited a non-GCB immunophenotype. Expansion from the 19-gene to the 60-gene panel reduced unclassifiable (NOS) cases from 34% to 12%. The overall response rate was 100% (43/43); complete response among patients completing therapy was 100% (35/35). At two years, overall survival was 92% (95% CI 83–100%) and progression-free survival was 94% (95% CI 86–100%). Two early relapses occurred (NOS and N1 subtypes), both resulting in death. Grade 3–4 neutropenia, thrombocytopenia, and anemia occurred in 26%, 12%, and 7% of patients, respectively; no dose reductions or treatment discontinuations were recorded. Conclusions: Molecularly adapted R-CHOP-X is feasible and associated with high response rates and favorable two-year survival in newly diagnosed DLBCL, comparing favorably with historical R-CHOP outcomes in high-risk populations. Expanded genomic panels substantially improve molecular classifiability. These findings warrant validation in larger, multicenter, randomized clinical trials. Full article

Background: This study investigates the role of N6-methyladenosine (m6A) regulators in osteoporosis (OP) and their interplay with the immune microenvironment, aiming to identify potential m6A-related biomarkers for OP risk assessment and treatment. Methods: Transcriptomic data from GEO datasets were analyzed for differential expression of 22 m6A regulators and immune infiltration patterns. Consensus clustering and m6Ascore grouping defined molecular subtypes, while machine learning algorithms identified potential biomarkers, leading to the construction and validation of a nomogram. Experimental validation involved peripheral blood monocytes (PBMCs) transcriptome sequencing and Western blot of bone tissue. Results: FTO, HNRNPC, and METTL4 were upregulated, while CBLL1 and YTHDF2 were downregulated in OP, with two distinct m6A modification patterns and immune phenotypes identified. METTL4, HIRA, MATN4, and YTHDF2 were selected as potential biomarkers, and the nomogram demonstrated favorable predictive performance in training and external datasets. Single-cell RNA sequencing confirmed the cellular distribution of these biomarkers. HIRA heterogeneity in Marrow Mesenchymal Stem Cells (BMSCs) was associated with distinct cell–cell communication patterns. Transcriptome sequencing confirmed HIRA RNA downregulation in OP PBMCs, and Western blot verified decreased HIRA protein in OP bone tissue. Conclusions: This study establishes a potential m6A-related biomarker signature for OP and provides multi-level experimental evidence that HIRA is a consistently downregulated biomarker, linking epigenetic modification to immune dysregulation in osteoporosis. Full article

Background: Pancreatic adenocarcinoma (PAAD) is a highly malignant cancer posing severe clinical challenges. Although the dual role of pyroptosis in tumor progression is increasingly recognized, the prognostic value of its molecular heterogeneity in PAAD remains underexplored. Methods: We integrated multi-omics data and applied interpretable machine learning to construct a predictive framework centered on pyroptosis heterogeneity. Using non-negative matrix factorization (NMF) on pyroptosis-related genes (PRGs), patients were classified into distinct molecular subtypes. Evaluating 117 machine learning combinations, we employed random survival forest (RSF) to build the final model, followed by comprehensive internal and external validation. SHapley Additive exPlanations (SHAP) analysis provided global and local interpretability. Clinical potential was assessed via nomogram, drug sensitivity prediction, single-cell analysis, and immunohistochemical validation. Results: We identified two biologically distinct pyroptosis subtypes and developed a ten-gene pyroptosis subtype-associated gene signature (PSAGS). PSAGS demonstrated robust performance across training, test, and multiple external validation cohorts, outperforming most published models. Multivariate analysis confirmed its independent prognostic value, and a PSAGS-based nomogram exhibited clinical utility. PSAGS-stratified subgroups showed differential responses to immunotherapy, chemotherapy, and targeted agents. Single-cell analysis revealed cell type-specific links between PSAGS scores and pyroptosis activity, indicating that high-PSAGS malignant cells foster an immunosuppressive microenvironment through extracellular matrix (ECM)-mediated signaling. Protein-level validation confirmed upregulation of signature genes in PAAD tissues. Conclusions: This work presents a biologically reliable prognostic model for personalized PAAD management and elucidates how pyroptosis heterogeneity drives tumor progression through cellular interactions. Full article

Background: Many studies evaluating central nervous system (CNS) metastases in breast cancer (BC) combine germline BRCA1 and BRCA2 pathogenic variant carriers, limiting gene-specific interpretation. We evaluated gene-specific overall survival (OS) after CNS metastasis and time to CNS involvement. Methods: We retrospectively identified BC patients with confirmed CNS metastases (1995–2022) from the Medical University of Vienna and the kConFab consortium. Germline status was classified as gBRCA1 PV, gBRCA2 PV, or non-carrier. Primary endpoint was OS from CNS metastasis diagnosis; secondary endpoint was CNS metastasis-free interval from primary BC diagnosis. Kaplan–Meier/log-rank tests were used for group comparisons. Multivariable Cox models assessed OS in complete cases, stratified by molecular subtype and adjusted for prognostic factors. Sensitivity analyses included subtype-adjusted and time-period models. Results: Among 115 patients (gBRCA1 n = 32, gBRCA2 n = 18, and non-carriers n = 65), median OS differed by germline status (p = 0.019): 20.0 months (95% CI 6.7–60.0) for gBRCA2 versus 7.1 months (95% CI 3.7–10.0) for gBRCA1 and 7.6 months (95% CI 3.4–12.0) for non-carriers. In subtype-stratified analyses, gBRCA1 showed similar mortality to non-carriers (HR 0.90, 95% CI 0.49–1.64, p = 0.730), while gBRCA2 showed a lower but non-significant hazard (HR 0.48, 95% CI 0.18–1.25, p = 0.131). Median CNS metastasis-free interval was longer for gBRCA2 (8.4 years) versus gBRCA1 (3.0 years) and non-carriers (3.1 years; p = 0.020). Sensitivity analyses were consistent. Conclusions: gBRCA2 carriers demonstrated longer unadjusted OS after CNS metastasis and a longer CNS metastasis-free interval compared with gBRCA1 carriers and non-carriers. However, these associations were attenuated and not statistically significant after adjustment, and should therefore be interpreted as hypothesis-generating. These findings supports further investigation of gene-specific CNS disease trajectories in larger cohorts. Full article

Recent years have seen growing interest in the relationship between the heart and kidney disease, resulting in the general term cardiorenal syndrome (CRS) being coined for disorders involving both the heart and kidneys. However, no accurate animal model exists that can replicate the specific cardiorenal associations characteristic of the human CRS subtype. Preclinical studies published between 1990 and 2024 were identified from online electronic databases. These were reviewed and subjected to meta-analysis according to PRISMA, with the quality assessed using the SYRCLE tool. In total, the review and analysis included 251 papers discussing the rodent presentation of cardiorenal associations, expressed by various hemodynamic, echocardiographic and histopathologic parameters, and selected molecular hallmarks. A wide spectrum of invasive and non-invasive animal approaches has been proposed for CRS. Numerous approaches evoked cardiorenal impairments by elevating systemic pressure. Among the “one-hit” models, Dahl/SS and ISO-HF most commonly resulted in cardiac and renal alterations mimicking CRS-2, while DOCA-salt or STZ were the most likely to elicit cardiac injury in progression of renal failure. The clinical relevance of “two-hit” animal models of cardiorenal associations merits another study. Full article

Background: Ceramide (Cer) dysregulation in content and composition is linked to various skin conditions, particularly sensitive and dry skin. Existing ceramide quantification methods often lack efficiency, sensitivity, or comprehensive analytical capabilities. This study aimed to adopt an optimized LC-MS/MS platform to ensure the acquisition of reliable and accurate ceramide quantitative data, thereby providing robust methodological support for an in-depth investigation of the differences in ceramide profiles among different dry skin subtypes. Methods: Stratum corneum samples were collected via tape stripping from 93 adult female volunteers, who were stratified into sensitive dry skin, non-sensitive dry skin, and normal skin groups based on clinical assessments. Cer metabolomics was analyzed via targeted metabolomics using liquid chromatography–tandem mass spectrometry (LC-MS/MS). Results: Quantitative analysis of ceramide content in different groups revealed significantly elevated levels of ultra-long-chain ceramides and the atypical Cer (d17:1/24:0) in the SD group, alongside relatively lower levels of shorter-chain ceramides. The NSD group, in contrast, was predominantly enriched in shorter-chain ceramides. Statistical analysis showed statistically significant differences in the levels of Cer (d18:1/24:0), Cer (d18:1/24:1), and Cer (d17:1/24:0) between the SD group and the N group. The UPLC-MS/MS method exhibits a wide linear range and high recovery. Conclusions: This method offers a reliable tool for the quantitative analysis of ceramides in dermatological, physiological, and pathological research. The findings not only underscore the profound heterogeneity in lipid metabolism underlying different dry skin subtypes but also provide a molecular rationale linking aberrant ceramide chain lengths to compromised barrier integrity and heightened inflammatory susceptibility. The partially validated analytical platform and the specific ceramide signatures revealed herein offer valuable tools and insights for advancing the mechanistic understanding, diagnosis, and targeted intervention of sensitive dry skin. Full article

Objective: Optic pathway glioma (OPG) diagnosed in adults represents a rare and understudied tumor subtype. While pediatric OPGs are typically benign and associated with NF1 and RAS/MAPK pathway dysregulation, less is known about the clinical characteristics and prognostic drivers of OPGs in adults. Methods: A systematic review was conducted in accordance with PRISMA guidelines across multiple databases. Studies reporting patient-level data and follow-up for patients diagnosed with optic pathway glioma at age ≥ 18 years were included. Results: Ninety-six studies comprising 149 adult patients were analyzed. Median patient age was 47 years (range: 18–90), and 51.0% of tumors were high-grade (WHO grade 3–4). Increasing age at diagnosis was significantly correlated with higher WHO grade (ρ = 0.600, p < 0.001), and optic tract involvement was associated with high-grade disease (χ² = 8.08, p = 0.004; ϕ = 0.26). Median follow-up was 12 months, with 74 patients alive and 75 deceased at last follow-up. WHO grade was strongly associated with overall survival (log-rank p < 0.0001), with 24-month survival ranging from 96.9% for grade 1 tumors to 11.3% for grade 4 tumors. Compared with observation or steroid-only management, both surgical and non-surgical oncologic treatments were associated with longer observed survival, although no significant difference was observed between active treatment modalities. Conclusions: Optic pathway gliomas in adults exhibit a multimodal biologic distribution, encompassing both indolent low-grade tumors and aggressive high-grade malignancies. Survival outcomes appear to be primarily driven by tumor biology, with age and anatomic involvement correlating with tumor grade. Prospective, multicenter studies with comprehensive molecular profiling are needed to refine prognostic stratification and guide evidence-based management of this rare disease. Full article

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer defined by the absence of estrogen and progesterone receptors, as well as the lack of human epidermal growth factor 2 receptor overexpression. TNBC is associated with early onset, high metastatic potential, therapeutic resistance, and poor clinical outcomes exacerbated by the limited availability of effective targeted therapies. Advances in multi-omics profiling have further stratified TNBC into distinct molecular subtypes, each exhibiting unique genomic, epigenomic, and immune-related features that influence therapeutic responsiveness. This review explores the interplay between TNBC molecular heterogeneity, immune evasion mechanisms, and epigenetic regulation. TNBC demonstrates variable immunogenicity, with tumor-infiltrating lymphocytes serving as important prognostic and predictive biomarkers. However, immune escape commonly occurs through tumor microenvironment remodeling, T-cell exhaustion, cancer stem cell enrichment, and immune checkpoint pathways activation. Although immune checkpoint inhibitors have improved outcomes in selected patients, particularly in combination with chemotherapy, primary and acquired therapeutic resistance remain a significant challenge. Emerging evidence highlights the central role of epigenetic mechanisms in regulating immune-related gene expression and shaping the tumor immune microenvironment. Epigenetic silencing of antigen presentation machinery, interferon signaling pathways, and chemokine expression contributes to immune evasion and immunotherapy resistance. Importantly, pharmacological modulation of epigenetic regulators can restore immune recognition and induce “viral mimicry” through reactivation of endogenous retroelements, thereby enhancing antitumor immunity. Collectively, this review underscores the therapeutic potential of integrating epigenetic therapies with immunotherapy and chemotherapy to overcome immune resistance in TNBC. A deeper understanding of epigenetic-immune interactions may facilitate the development of more precise and effective treatment strategies tailored to TNBC molecular subtypes. Full article