Search Results (471)

Telomerase reverse transcriptase (TERT) plays a key role in tumorigenesis by maintaining telomere length, promoting chromosomal stability, and enabling cells to evade replicative senescence. TERT promoter mutations have been detected in various types of tumor; however, their prevalence in ameloblastoma has not been verified. This study aimed to determine the frequency of TERT promoter mutations in ameloblastoma. This retrospective study included formalin-fixed, paraffin-embedded (FFPE) tissue specimens and corresponding medical records from patients who underwent surgical treatment for jaw ameloblastoma at the Department of Oral and Maxillofacial Surgery, Kyungpook National University (Daegu, Republic of Korea) between January 2011 and December 2024. Clinical data were reviewed through January 2026. Of the 49 patients included, genomic DNA was extracted from two 5 μm thick FFPE tissue sections using the PANAMAX™ FFPE Plus DNA Extraction Kit (HLB PANAGENE, Daejeon, Republic of Korea), according to the manufacturer’s instructions. Hotspot TERT promoter mutations (C228T and C250T) were analyzed using the PNAClamp™ TERT Mutation Detection Kit (HLB PANAGENE, Daejeon, Republic of Korea). From a total of 73 TERT promoter mutation analyses performed in 49 patients, one of the recurrent cases harbored both C228T and C250T hotspot mutations. In the non-recurrent group, one case exhibited a C250T mutation. These findings indicate that TERT promoter mutations are rare in ameloblastoma. Full article

Seasonal influenza A evolves quickly through mutations in haemagglutinin (HA) and neuraminidase (NA), which can reduce vaccine match and lower protection. Many sequence-only models do not link codon-level mutations to three-dimensional (3D) protein context and long-term evolutionary signals within one scoring framework. This study presents TRIAD-Influenza (TRIAD: Token–Residue–Integrated Architecture for Drift), a multi-view transformer that combines (i) codon- and residue-level sequence representations, (ii) structure-derived residue interaction features from predicted HA/NA models, and (iii) an embedding-space phylogeny that captures cluster and drift context. The pipeline curates more than $3\times {10}^5$ paired HA/NA coding sequences from the NCBI Virus resource (2010–2024) using strict quality control and codon-aware alignment and predicts 3D structures for nearly all unique HA and NA proteins to build contact graphs and surface/stability descriptors. TRIAD-Influenza outputs a continuous, structure-aware risk score for each HA/NA pair and produces interpretable mutation hotspot maps using gradient saliency and a contact-weighted mutation risk index (CMRI). On rolling-origin temporal cross-validation and for a temporally held-out internal test window with strong class imbalance (∼3.4% high-risk), the model shows strong ranking performance (AUROC $\approx 0.89$; AUPRC $\approx 0.44$; Brier score $=0.069$) while operating at surveillance speed (median latency $\approx 1.6$ ms per HA/NA pair). External validation on independent GISAID/Nextstrain cohorts (2023–2024; 5000 isolates) preserves discrimination (AUROC $\approx 0.85$–$0.86$). Predicted risk scores correlate with experimental haemagglutination inhibition (HI) antigenic distances (Spearman $\rho$ up to ≈0.82 at the virus-aggregated level), and CMRI hotspots enrich known epitope and deep mutational scanning escape residues (odds ratios $\approx 2.7$–$3.6$). Overall, token–residue–phylogeny coupling enables rapid, structure-aware prioritisation of emerging influenza A HA/NA sequences and delivers compact hotspot maps for expert review and targeted experiments. Full article

Oral squamous cell carcinoma (OSCC) is a prevalent form of head and neck cancer that typically develops on the lip or within the oral cavity. Although there have been advances in early detection and treatment, the prognosis for patients, particularly those with advanced-stage disease, remains poor. Liquid biopsy, particularly through the analysis of cell-free DNA (cfDNA) in plasma and urine, has emerged as a promising tool for non-invasive cancer detection and monitoring. This study assessed cfDNA concentration dynamics in plasma and urine samples from 32 OSCC patients, with 5 undergoing genomic characterization by targeted next-generation sequencing (NGS). CfDNA levels were higher in patients compared to healthy controls and showed transient increases following treatment initiation, likely reflecting tumor cell death, followed by a gradual return to baseline. However, cfDNA concentrations were not significantly associated with tumor stage, recurrence, or progression-free survival. Targeted NGS analysis revealed a heterogeneous mutational landscape, identifying 76 variants across tumor tissue and initial cfDNA, with 30.3% shared between both sources. Recurrent hotspot mutations were detected in several important genes, including TP53, PIK3CA, KRAS, APC, and FBXW7. Urine cfDNA also captured several mutations absent from plasma or tissue, supporting its complementary value. These findings demonstrate that cfDNA analysis can dynamically reflect treatment response and capture tumor heterogeneity in OSCC. While informative, cfDNA quantification alone offers limited prognostic reliability, reinforcing the need for a multidimensional approach that includes genomic and clinical evaluation. Overall, this study supports the potential of liquid biopsy as a real-time, non-invasive tool for molecular monitoring and personalized management of OSCC patients. Full article

Pancreatic cancer (PC) is a highly aggressive malignancy characterized by limited opportunities for early diagnosis and poor clinical outcomes, underscoring the need for minimally invasive biomarkers to improve detection and patient stratification. Given emerging evidence that mitochondrial DNA (mtDNA) alterations reflect cancer-related biological processes, this study investigated whether blood-derived mtDNA profiles could provide clinically relevant information in PC. In this exploratory study, whole-blood mtDNA from 33 PC patients and 10 healthy individuals were analyzed using next-generation sequencing to assess single-nucleotide variants (SNVs), allele frequencies, and mtDNA copy number. A total of 252 unique mtDNA SNVs were identified, including variants exclusive to PC patients, variants unique to controls, and variants shared between groups. While the overall SNV burden did not differ significantly between groups, PC patients showed distinct mutation distributions and allele frequency patterns, with cancer-exclusive variants occurring predominantly at low allele frequencies. Mutation hotspots were observed in the ND5, COI, and D-loop regions, implicating genes involved in oxidative phosphorylation and mtDNA maintenance. Although mtDNA copy number did not differ significantly between groups, greater variability was observed among PC patients and was associated with differences in survival outcomes. Overall, these findings indicate that blood-based mtDNA profiling captures biologically relevant variation associated with PC and supports further development of integrated mtDNA-based approaches for improved risk assessment and patient stratification. Full article

Papillary thyroid cancer (PTC) is the most common endocrine malignancy with especially high incidence in Middle Eastern populations. While classical hereditary syndromes explain a minority of cases, the broader germline landscape of non-syndromic PTC remains unclear. Whole-exome sequencing was performed on 245 unselected Saudi PTC patients to identify germline pathogenic or likely pathogenic variants (PVs/LPVs) in cancer predisposition genes. Clinical and molecular characteristics, and family history were integrated to assess phenotypic correlations. Eleven patients (4.5%) harbored germline PVs/LPVs in cancer susceptibility genes including STK11, TP53, BRCA1, BRCA2, FANCA, SLX4, RAD50, MSH6, POLD1 and NF1. Four patients (36.4%) carried PVs/LPVs in canonical FA pathway genes; this increased to five patients (45.5%) when RAD50 was included. Two unrelated patients harbored the same STK11 variant (p.R304Q) without classical Peutz–Jeghers syndrome features. A TP53 hotspot mutation (p.R175H) was identified in a patient with a personal history of gastric cancer, a malignancy associated with Li–Fraumeni syndrome. Notably, the BRCA1 PV detected matches a known Saudi founder mutation in hereditary breast cancer, now observed in PTC. Most germline positive cases lacked syndromic manifestations, underscoring limitations of phenotype or family history-driven genetic testing strategies. These findings suggest that a small subset of non-syndromic PTC cases may carry germline PVs/LPVs in cancer predisposition genes, highlighting the need for broader genetic screening frameworks. Unbiased whole-exome analysis in unselected cohorts can uncover under-recognized genetic risk and guide screening strategies to address the unique hereditary landscape of thyroid cancer in underrepresented populations. Full article

STT3A encodes the catalytic subunit of the oligosaccharyltransferase A (OST-A) complex and is classically linked to severe autosomal-recessive congenital disorder of glycosylation (CDG). To define the distinct autosomal-dominant disorder, we reviewed all published cases and integrated three previously unpublished individuals from the CDG natural history study. Across 21 individuals, abnormal transferrin glycosylation was present in nearly all individuals (20/21), and subtle facial dysmorphism was common (18/21). Neurodevelopmental involvement was frequent, including motor delay (13/21), learning difficulties (13/21), speech delay (12/21), and intellectual disability (10/21). Musculoskeletal manifestations were also common, including skeletal abnormalities (12/21), short stature (11/21), muscle cramps (8/21), and early-onset osteoarthritis in adults (6/21). Less frequent features included congenital heart defects (5/21) and coagulation factor deficiency (5/21). Importantly, the newly reported individuals expand dominant STT3A-CDG with previously unreported features, including anorectal malformation, morbid obesity, and clinically significant bleeding diathesis with von Willebrand factor and factor VIII deficiency. Biochemical signatures ranged from classic type I transferrin patterns to subtle or atypical abnormalities, emphasizing that near-normal transferrin testing does not exclude the diagnosis. Variants clustered in conserved catalytic regions, with recurrent p.Arg405 across de novo, inherited, and mosaic cases supporting a mutational hotspot and likely dominant-negative mechanism. Full article

Over 70 mutations in the transforming growth factor beta-induced (TGFBI) gene are associated with corneal dystrophies that impair vision. The R555W hotspot mutation is a major cause of granular corneal dystrophy type 1 (GCD1). Here, we evaluated the technical feasibility of CRISPR/Cas9-mediated editing of the R555W mutation in peripheral blood mononuclear cells (PBMCs) obtained from a patient with GCD1. Three single guide RNAs (sgRNA1–3) and matched single-stranded oligodeoxynucleotide donors (ssODN1–3) were designed and co-transfected into PBMCs. Transfected cells were enriched by flow cytometric sorting, with GFP-positive cells representing approximately 2–4% of the total electroporated population. Editing outcomes were initially screened using high-resolution melting (HRM) analysis, and the sgRNA3–ssODN3 combination identified as the most promising candidate was subsequently validated by next-generation sequencing (NGS). Sequencing revealed a homology-directed repair efficiency of 98.2% among GFP-positive sorted cells, demonstrating efficient and precise genome editing within the enriched population. Because PBMCs are not disease-relevant corneal epithelial cells and only genomic endpoints were assessed, the clinical applicability of this study is limited and the work should be considered a technical proof-of-concept. This framework supports optimization of CRISPR-based strategies prior to studies in biologically relevant corneal models. Full article

Cervical small-cell neuroendocrine carcinoma (SCNEC) is a rare cervical cancer with high metastatic potential and is frequently associated with high-risk human papillomavirus (HPV) infection. Because of its low incidence, SCNEC remains understudied and treatment options are limited, posing major therapeutic challenges. This study aimed to characterize SCNEC at the molecular and functional levels to support more informed therapeutic strategies. Organoids and spheroids were generated from a cervical SCNEC biopsy, and a matched organoid-derived xenograft was established in immunodeficient mice. Model fidelity was evaluated by histopathology and immunohistochemistry. HPV status was assessed by p16 immunostaining and HPV18 PCR, and viral–host integration sites were inferred using whole-exome sequencing (WES) junction reads. WES was also used to compare shared somatic variants and copy-number alterations across the patient tumor, organoid, and xenograft. Drug responses were assessed in organoids and spheroids following exposure to a panel of chemotherapeutic agents and a targeted inhibitor. Organoids exhibited robust growth, morphologic maturation, and efficient recovery after cryopreservation. The organoids and matched xenografts faithfully recapitulated SCNEC, with preserved neuroendocrine differentiation (CD56, synaptophysin, and NSE positivity), a high Ki-67 proliferative index (>80%), and strong p16 expression. HPV18 status was conserved across the primary tumor, organoids, and xenografts, with an integration site at chr8 (8q24.21) associated with increased MYC expression. WES revealed strong cross-model concordance, including 26 shared somatic variants with a canonical PIK3CA hotspot mutation (p.E542K) and conserved oncogenic copy-number gains of PIK3CA, TERT, and MYC, as well as copy number loss of TP53. Functional assays showed dose-dependent loss of viability following exposure to conventional cytotoxic agents or an mTOR pathway inhibitor. This study presents the first integrated molecular and functional analyses of patient tumors and matched organoid and xenograft models in cervical SCNEC. These models offer robust resources for mechanistic studies and may enable precision therapeutic strategies for this rare malignancy. Full article

Background: Metabolic enzymes catalyze biochemical pathways that sustain cellular metabolism. Their activity, stability, and molecular interactions are extensively regulated by post-translational modifications (PTMs). However, an integrated systems-level understanding of how diverse PTMs are organized across the human metabolic network remains poorly defined. Methods: We integrated experimentally reported PTM annotations from PhosphoSitePlus, dbPTM, and the quantitative PTM database (qPTM), and identified 29 distinct PTM types present across the 771 human metabolic enzymes. PTM features were quantitatively characterized at multiple levels, including sequence- and composition-based metrics (modification density and PTM potentiality rate), recurrence- and co-occurrence-based features (predominant sites, hotspot regions and PTM crosstalk), and functional-context annotations (protein-region localization and mutation overlap). These integrated features were subsequently used for unsupervised clustering to evaluate higher-order organizational patterns. Results: The analysis revealed that PTMs are unevenly distributed across metabolic enzymes, with phosphorylation, acetylation, ubiquitination, and methylation representing the most prevalent and recurrent regulatory modifications. Clustering segregated enzymes into two regulatory groups: (i) a PTM-enriched regulatory group characterized by high PTM density, frequent hotspot and crosstalk regions, and enrichment of rate-limiting enzymes, and (ii) a broad metabolic group with comparatively sparse PTM regulation. This non-uniform organization reflects the preferential accumulation of multiple regulatory PTMs on enzymes occupying key control points in central metabolic pathways, thereby forming a discrete regulatory subnetwork within metabolism. Conclusions: This study presents a systems-level, multi-PTM atlas of human metabolic enzymes and provides a quantitative framework for prioritizing PTM-regulated enzymes and pathways relevant to signaling–metabolism integration and disease-associated metabolic regulation. Full article

Background/Objectives: The tumor suppressor gene TP53 is one of the most frequently mutated genes in human cancers, with alterations predominantly affecting its DNA-binding domain (DBD). However, the mutational landscape and functional consequences of TP53 variants remain poorly characterized in African populations. This study aimed to characterize mutations in exons 5–6 of TP53 in oral cavity cancer (OCC), prostate cancer (PC), and breast cancer (BC) in a Senegalese population, and to assess their structural effects, functional consequences, and impact on protein–protein interactions with BCL-2. Methods: Seventy-eight archived tumor DNA samples from Senegalese patients with OCC, PC, and BC were analyzed. Variants were annotated using COSMIC and dbSNP databases. Functional impact was evaluated with PolyPhen-2. Structural stability changes ($\Delta \Delta G$) were predicted using FoldX, conformational dynamics ($\Delta \Delta S_{vib}$) were assessed with ENCoM, and effects on the p53–BCL-2 interaction were analyzed using DDMut-PPI. Statistical analyses were also performed. Results: BC exhibited the highest TP53 mutation frequency, whereas OCC showed greater mutational diversity. Exon-level analysis revealed a significant enrichment of exon 6 mutations in BC. Structural analyses indicated that exon 5 mutations across all cancers and mutations in OCC were predominantly destabilizing and associated with loss-of-function effects. In contrast, recurrent exon 6 mutations in PC and BC, particularly V217L and V218M, were predicted to stabilize the p53 structure. Conformational dynamics differences between exons were significant only in PC. All analyzed mutations were predicted to stabilize the p53–BCL-2 interaction. Conclusions: This integrative in silico study identified cancer and exon-specific TP53 mutation patterns in a Senegalese population, highlighting exon 6 as a context-dependent hotspot with potential oncogenic implication in PC and BC. Despite its computational nature, the study provides valuable insights that merit further investigation. Full article

Aflatoxin B₁ (AFB₁) produced by Aspergillus flavus poses severe food safety risks. Competitive exclusion using atoxigenic A. flavus strains offers a promising biological control approach to managing agricultural contamination by reducing populations of toxigenic strains and aflatoxin levels. However, reliable identification of atoxigenic strains remains challenging, and the mechanisms underlying competitive interactions between toxigenic and atoxigenic strains require clarification for effective implementation. Therefore, this study systematically analysed A. flavus strains for aflatoxin gene clusters and AFB₁ production to address these critical gaps. Our analysis revealed that atoxigenic strains had intron losses and high-impact mutations in several genes, particularly aflL and aflLa, which affect aflatoxin biosynthesis. Key genes norA/aflE, verA/aflN, and omtA/aflP emerged as mutation hotspots, sometimes causing false-negative PCR results that complicate strain identification. Also, AFB₁ production was inversely related to spore concentration on MEA medium, with fewer spores resulting in higher toxin levels. Interaction tests demonstrated that toxigenic and atoxigenic strains exhibited morphological changes only when co-cultured without physical separation, suggesting that this was mediated by diffusible molecules. Furthermore, differences in the levels of linoleic acid reduction products distinguished toxigenic from atoxigenic strains. These findings thus illuminate the complex genetic and metabolic factors influencing aflatoxin production and fungal interactions. Full article

Background/Objectives: Metaplastic breast carcinoma (MpBC) is a rare and aggressive malignancy characterized by significant histological heterogeneity and limited response to standard chemotherapy. Due to its morphological diversity, MpBC often presents diagnostic challenges and can overlap with other mesenchymal tumors. This study aimed to characterize the genomic landscape of MpBC using a nationwide Japanese database and to explore the molecular basis of its diagnostic ambiguities and therapeutic responses. Methods: We retrospectively analyzed genomic and clinical data from 123 MpBC cases registered in the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) database. To evaluate diagnostic boundaries, genomic profiles of histological mimickers, including 19 cases of angiosarcoma and eight cases of myoepithelial carcinoma, were also examined. Furthermore, an exploratory single-cell RNA-sequencing analysis was performed on 3274 cells from independent MpBC datasets to investigate cellular heterogeneity and potential lineage plasticity. Results: TP53 (73.2%) and PIK3CA (46.0%) were the most prevalent genomic alterations in the MpBC cohort. Exploratory analysis suggested that PIK3CA mutations may be associated with an improved disease control rate in patients receiving taxane-based therapy (p = 0.028). Comparisons with mimickers identified distinctive molecular signatures, such as MED12 and HRAS hotspot mutations, across entities. Single-cell transcriptomics identified a distinct subpopulation (7.02% of malignant cells) co-expressing epithelial and phyllodes-like signatures. Conclusions: These findings suggest that MpBC harbors hybrid malignant cell populations that may contribute to its complex morphological diversity. While the therapeutic associations are based on a limited cohort and require prospective validation, the integration of comprehensive genomic and single-cell profiling provides an exploratory framework that may potentially enhance diagnostic accuracy in the future. However, these associations remain preliminary and require prospective validation to confirm their clinical utility. Full article

Pathological USH2A mutations cause Usher syndrome type II, characterized by progressive retinitis pigmentosa and hearing and balance impairment. This study aims to investigate the cellular mechanisms underlying USH2A-related retinal degeneration using human induced pluripotent stem cell (hiPSC)-derived retinal organoids. The introduction of a homozygous nonsense mutation in the USH2A hotspot exon-13 resulted in normal photoreceptor development but loss of ciliary localization of usherin long form B and its interacting proteins, ADGRV1 and whirlin. Notably, single-cell RNA sequencing revealed unexpected significant transcriptional changes in Müller glial cells (MGCs), suggestive of disruptions in the translation, innate immune response, and endolysosomal system. These findings suggest that, while photoreceptor cells are mildly affected by the exon-13 USH2A mutation, MGCs exhibit major transcriptional changes, potentially contributing to the disease progression and therefore shedding light on potential alternative therapeutic targets. Full article

Background: Epidermal growth factor receptor (EGFR) is a transmembrane tyrosine kinase that is frequently post-translationally modified by glycosylation. In cancer, EGFR amplifications and hotspot mutations such as L858R that promote proliferation have been detected in a significant fraction of non-small cell lung carcinomas and breast adenocarcinomas. Analyses of disruptions to glycosylation pathways in cancer cells identified EGFR glycosylation at residue N361 as one of the most heavily impacted sites. Methods: We stably expressed a glycosylation-deficient mutant EGFR, N361A, with or without the oncogenic EGFR mutation L858R in cells. Proximity ligation assays were employed to study the effects of the glycosylation mutant on the co-localization of EGFR and HER2. The effects of the glycosylation-deficient mutant on the efficacy of agonists, such as EGF and amphiregulin, or antagonists, such as osimertinib and necitumumab, were defined using cell viability assays and immunoblots. Results: N361A increased the membrane localization and co-localization of EGFR with its binding partner HER2. The glycosylation-deficient mutation decreased cell proliferation, including proliferative responses to EGFR ligands. The mutant cells demonstrated reduced sensitivity to inhibition using the antibody inhibitor necitumumab, which inhibits EGFR by binding the extracellular domain. Conclusions: Disruption of glycosylation at N361, located near the ligand binding and dimerization regions, created a dominant negative form of EGFR, which non-productively co-localized with HER2, resulting in a blockage in proliferation. These findings underline the critical relevance of post-translational glycosylation modifications on EGFR function. Full article

Chronic Kidney Disease (CKD) and Colorectal Cancer (CRC) share a profound epidemiological link, supported by Mendelian randomization studies suggesting causality. This review articulates a refined Gut–Kidney Axis, focusing on the pathophysiology of indole-derived uremic toxins. CKD-induced dysbiosis drives hepatic synthesis and systemic accumulation of indoxyl sulfate, which is proposed to promote carcinogenesis via Aryl Hydrocarbon Receptor (AhR) and Akt signaling, ultimately upregulating c-Myc and EGFR. We propose a two-compartment model: while systemic indoxyl sulfate reflects the total gut indole pool (mainly from planktonic bacteria), adherent bacteria like Fusobacterium nucleatum may create high-concentration indole hotspots within the tumor microenvironment. Clinically, we advocate for protein-independent DNA methylation biomarkers (SEPT9, SDC2) to avoid renal confounding. Furthermore, we propose a novel diagnostic panel integrating serum indoxyl sulfate (systemic load) and urinary indoxyl sulfate (gut production) to guide therapy. Therapeutically, targeting upstream drivers (AhR/Akt) may bypass resistance to anti-EGFR therapies in KRAS-mutated tumors. We also discuss the repurposing of the oral adsorbent AST-120 and emerging bacteriophage therapies as strategies to disrupt this oncogenic axis. This review offers a comprehensive framework for stratified management of CKD-associated CRC. Full article