Search Results (498)

The long-term efficacy of vector control programs is seriously hampered by the evolution of insecticide resistance. In this scenario, assessing the distribution, frequency, and drivers of resistance spread is crucial to planning effective control programs. Here, we addressed these issues in the mosquito Culex pipiens, focusing on the Emilia-Romagna region (Italy), a known hotspot of diflubenzuron (DFB) resistance. First, Cx. pipiens larvae were screened for point mutations conferring DFB resistance to capture the distribution and frequency of resistance-associated alleles across the region. To this end, a fragment of the chitin synthase 1 gene spanning the mutated site was sequenced. Then, by using population genomics, we investigated the vector population structure in this area. Our findings revealed that resistance-associated alleles maintain a focal geographic distribution in the region, with higher mutation frequencies in the central-eastern than in the western provinces. Also, we observed that the populations of Cx. pipiens are a highly homogeneous gene pool and can be interconnected across the region, highlighting the risk of resistance alleles spread across Emilia-Romagna. Overall, this study stresses the importance of systematically surveying resistance-associated alleles and their integration with population genomic data to gain relevant information for resistance management. Full article

Central nervous system histiocytic sarcoma is exceedingly uncommon, particularly with intramedullary spinal cord involvement. We describe a 27-year-old man presenting with motor weakness and radiating pain. MRI revealed a homogeneously enhancing intramedullary mass at the C2–3 level with diffuse leptomeningeal dissemination, raising suspicion for a disseminated neoplastic process. Histopathology demonstrated pleomorphic large histiocyte-like cells with strong CD163, CD68, and lysozyme expression, confirming histiocytic sarcoma. Targeted next-generation sequencing detected a TP53 hotspot mutation (p.Arg273His), classified as a Tier II variant according to the joint AMP/ASCO/CAP guidelines, while additional variants were of uncertain clinical significance. This case highlights the rare intramedullary presentation of histiocytic sarcoma with leptomeningeal dissemination and emphasizes the importance of radiologic–pathologic correlation for accurate diagnosis. Full article

Bovine coronavirus (BCoV) is a key pathogen causing calf diarrhea and bovine respiratory diseases, bringing sustained economic losses to the cattle industry. As an RNA virus, BCoV possesses high mutation and recombination capacities, leading to prominent genomic genetic diversity. The genome contains hypervariable and conserved regions, with the S (especially S1), HE and Open Reading Frame (ORF4) genes serving as major variation hotspots linked to viral antigenicity, tissue tropism shift and immune evasion. Host immune pressure drives strong positive selection on S protein antigenic variation. This review discusses existing research limitations and proposes future directions including genomic surveillance, reverse genetics verification and broad-spectrum vaccine development to support BCoV prevention and control. Full article

Background: Fibroblast Growth Factor Receptor 3 (FGFR3) mutations are common and clinically relevant alterations in bladder cancer, with implications for diagnosis, monitoring, and patient selection for targeted therapies. Tissue-based testing is often limited by sample availability, invasiveness, and the need for repeated sampling. This study aimed to develop and analytically validate a sensitive double drop-off droplet digital polymerase chain reaction (ddPCR) assay for simultaneous detection of four FGFR3 hotspot mutations in tissue and liquid biopsy samples. Methods: The assay targeted four FGFR3 mutations (S249C, R248C, Y373C, G370C) using reference probes that generate a constant fluorescence signal and wild-type-specific drop-off probes that lose binding when a mutation is present, thereby distinguishing wild-type double-positive droplets from mutant droplets with reduced drop-off fluorescence. Analytical validation was performed using synthetic mutant oligonucleotides, wild-type genomic DNA, and cell-free DNA (cfDNA) from healthy donors (HDs). Specificity, limit of blank (LOB), limit of detection (LOD), and assay precision were evaluated. Performance was compared with next-generation sequencing (NGS) in formalin-fixed paraffin-embedded (FFPE) tissue DNA. FGFR3 mutations were also assessed in matched plasma and urinary cfDNA from bladder cancer patients. Results: The assay demonstrated clear cluster separation, no cross-reactivity, and reliable detection of all mutations down to 0.2% mutant allele frequency (MAF). Strong agreement was observed with a mutation-specific singleplex ddPCR assay for S249C. Concordance with NGS in tissue DNA was 74.2%, with ddPCR identifying additional low-abundance mutations not reported by NGS. FGFR3 mutations were detected in plasma and urinary cfDNA, with complete concordance between matched plasma and urine samples. Conclusions: This ddPCR assay provides a rapid, sensitive, and cost-effective method for detecting clinically relevant FGFR3 mutations and may complement sequencing-based approaches for molecular monitoring using tissue, plasma, and urine specimens. Full article

Background: Mechanosensitive ion channels PIEZO1 and PIEZO2 are key mediators of mechanotransduction, which converts physical forces into cellular signals involved in proprioception, touch, vascular function, and other physiological processes. Mutations in human PIEZO proteins are linked to various diseases, such as hereditary xerocytosis, lymphatic dysplasia, and proprioceptive dysfunction. However, the role of intrinsic disorder in the regulation of these proteins and their susceptibility for disease-associated mutations remains unclear. Methods: We analyzed canonical human PIEZO1 and PIEZO2 protein sequences using machine learning, neural network, and energy-based disorder predictors, together with the prediction of disorder-mediated binding regions, phase separation propensity, interaction networks, evolutionary conservation, clinically annotated human variants, and peptide structural modeling. Results: Both proteins showed moderate intrinsic disorder, with PIEZO2 having slightly greater disorder propensity and higher predicted phase separation potential. Intrinsically disordered regions frequently overlapped binding-prone segments and post-translational modification sites, supporting regulatory functions. Evolutionary comparisons showed strong conservation of PIEZO proteins, while selected disordered regions retained disorder propensity despite greater sequence variability. Disease-causing variants mainly affected the ordered regions of both proteins, whereas disordered regions contained proportionally more benign variants and relatively few pathogenic mutations. The modeling of mutations within disordered hotspots showed altered local conformational tendencies, indicating that some disease variants may disrupt dynamic interaction interfaces rather than global structure. Interaction network analysis linked both proteins to enriched mechanotransduction, ion transport, and cytoskeletal pathways. Conclusions: Overall, our findings identify intrinsic disorder as an underappreciated feature of PIEZO channel biology and provide a framework for interpreting PIEZO-associated channelopathies. PIEZO proteins also perfectly illustrate the proteoform concept, where one gene yields a highly diverse kit of mechanosensitive molecular tools. While humans only have two primary PIEZO genes (PIEZO1 and PIEZO2), the body generates a vast array of functional variations. Full article

Background and Clinical Significance: Steroid cell tumours of the ovary, not otherwise specified (SCT-NOSs), are rare sex cord–stromal neoplasms with a poorly characterised molecular landscape, in which only exceptional CTNNB1 mutations have so far been reported and no recurrent driver alteration is firmly established. A better characterisation of their molecular spectrum has clinical significance for accurate diagnostic categorisation of ovarian sex cord–stromal tumours and for the identification of potentially targetable pathway alterations in this rare entity. Case Presentation: We report two consecutive SCT-NOSs of the right ovary, retrieved from the archives of the Department of Pathology of the Hôpital Universitaire de Bruxelles and of Curepath. Both underwent comprehensive sex cord–stromal and differential immunohistochemistry and targeted next-generation sequencing on a 168-gene panel with a mean coverage of 2690× (Case 1) and a 17-gene panel (Case 2) (MGI DNBSEQ-T7 for Case 1; Ion GeneStudio S5 for Case 2). A 56-year-old post-menopausal woman (Case 1) and a 50-year-old immunosuppressed woman with a history of renal transplantation and lymphoma (Case 2) both presented with rapidly progressive virilisation. The two right ovarian tumours (20 to 25 mm, no Reinke crystals) displayed an unambiguous sex cord–stromal immunophenotype (α-inhibin, calretinin, SF-1 and Melan-A positive; CD10, WT1, EMA, AE1/AE3 and PAX8 negative), with aberrant nuclear and cytoplasmic β-catenin staining. Sequencing identified a pathogenic CTNNB1 c.133T>C p.(Ser45Pro) variant in Case 1 and a pathogenic CTNNB1 c.95A>T p.(Asp32Val) variant in Case 2, with wild-type FOXL2 in both. Conclusions: Three of the four molecularly characterised CTNNB1-mutated SCT-NOSs converge on the two principal GSK-3β phosphorylation residues of β-catenin, identifying Wnt/β-catenin-pathway dysregulation as a potentially recurrent event and providing additional evidence for the involvement of the Wnt/β-catenin pathway in an emerging molecular subset of SCT-NOS. In a tumour with the canonical sex cord–stromal immunophenotype, an exon 3 CTNNB1 hotspot mutation should not be regarded as evidence against the diagnosis of SCT-NOS and may help define a distinct molecular subset. Full article

Antifungal resistance in filamentous fungi has emerged as a major threat to global public health, posing a serious challenge particularly to immunocompromised populations. This review provides a systematic overview of the molecular mechanisms, diagnostic approaches, and clinical therapeutic strategies for antifungal resistance in filamentous fungi, with a focus on Aspergillus fumigatus, Fusarium spp., Mucorales, and Scedosporium spp./Lomentospora prolificans. Resistance mechanisms can be broadly categorized as intrinsic resistance and acquired resistance. Intrinsic resistance arises from species-specific genetic traits, such as structural differences in target sites, constitutive overexpression of efflux pumps, and metabolic pathway redundancy. Acquired resistance develops under drug pressure through target gene mutations (e.g., hotspot mutations and promoter tandem repeats in CYP51A), efflux pump overexpression, biofilm formation, and epigenetic regulation. For diagnosis, conventional culture and antifungal susceptibility testing remain the gold standard; however, molecular techniques—including MALDI-TOF MS, targeted resistance gene PCR, and metagenomics—are substantially improving detection efficiency. Therapeutic strategies should be stratified based on antifungal susceptibility testing results and species identification. Precision dosing guided by therapeutic drug monitoring, combination therapy, and the introduction of novel agents (including isavuconazole, rezafungin, fosmanogepix, and olorofim) are progressively improving clinical outcomes. Looking ahead, global surveillance and multisectoral collaboration are essential to deepen our understanding of resistance evolution, accelerate the clinical translation of novel diagnostic and therapeutic tools, and curb the global spread of resistance. Full article

Background/Objectives: B-cell receptor (BCR) signalling is implicated in Burkitt lymphoma (BL) lymphomagenesis, although its activation may differ across biological and epidemiological settings. While surface IgM is the predominant immunoglobulin isotype of BCR in BL, cases expressing IgA transcripts or lacking detectable surface immunoglobulin (sIg) expression have been reported, suggesting a more complex pattern of sIg expression than previously recognized. This study aimed to evaluate sIg heavy-chain expression by immunohistochemistry in a relatively large series of BL cases from endemic and sporadic settings and to investigate the mutational landscape of surface immunoglobulin-undetectable (sIg-UND) cases. Methods: sIg heavy-chain expression was assessed by immunohistochemistry in 55 formalin-fixed paraffin-embedded BL samples. Targeted next-generation sequencing was performed on four sIg-UND cases using an Illumina capture-based custom panel covering 74 lymphoma-related genes. KRAS and NRAS hotspot mutations were additionally assessed by real-time PCR. Results: Overall, 41/55 cases showed IgM expression, including 31 IgM-positive and 10 IgM+/UND cases, whereas 8/55 cases showed IgA expression (IgA+/UND). IgA-expressing cases were significantly enriched at mucosal sites, particularly the oral cavity and gastrointestinal tract, consistent with the relevance of these anatomical sites to mucosal IgA production. Six cases lacked detectable sIg expression, showing negativity for all tested immunoglobulin heavy chains in more than 90% of neoplastic cells. Four sIg-UND cases were available for sequencing. These cases harbored mutations affecting genes commonly altered in BL, together with alterations in genes less commonly represented in recurrent BL series, such as MEF2B, CREBBP, PRDM1, PIM1, ARID3A, HIST1H1B, and HIST1H1C. Conclusions: Our study provides a systematic immunohistochemical characterization of surface immunoglobulin heavy-chain expression in a relatively large series of endemic and sporadic BL. We identified a subset of IgA-expressing BL cases enriched at mucosal sites, whereas rarer cases lacked detectable surface immunoglobulin expression. The mutational profile of sIg-UND cases highlights alterations affecting genes involved in epigenetic regulation, chromatin organization, and B-cell differentiation, which may contribute to the biological heterogeneity of these cases. No KRAS or NRAS hotspot mutations were detected in the four sequenced sIg-UND cases, as assessed by targeted NGS and real-time PCR. Further functional studies are needed to clarify the biological and clinical significance of sIg-UND BL cases and to determine the functional relevance of the identified alterations. Full article

Intratumor heterogeneity (ITH) of premalignant colorectal lesions is an important area of research for understanding the diverse biological behavior of colorectal cancer (CRC). Accurate assessment of ITH depends substantially on the sampling strategy used. We present a novel methodological approach termed whole tumor heterogeneity topography (WTHT) and compare it with three previously described sampling strategies: whole tumor homogenization, macrodissection of selected tumor regions, and multisampling. A cohort of 184 advanced precancerous colorectal lesions was processed into paraffin blocks, and the entire tumor mass was systematically divided into equally sized samples (~10 mm³). DNA was isolated from each sample separately and analyzed for hotspot mutations in APC, KRAS, BRAF, PIK3CA, and TP53. ITH was quantified using mutation variance and a newly introduced Heterogeneity Grade (HG). Results obtained by WTHT were statistically and graphically compared with three other modeled sampling strategies. Significant differences were observed among the analyzed sampling approaches. Macrodissection showed the greatest deviation from WTHT, indicating substantial sampling bias, whereas multisampling produced the closest results. WTHT enabled precise quantification and spatial mapping of mutational clones across the entire lesion. WTHT combined with HG provides a robust and reproducible framework for comprehensive assessment of ITH in colorectal adenomas. Full article

Background/Aim: Fibroblast growth factor receptor 4 (FGFR4) is a tyrosine kinase involved in cell growth, proliferation, and angiogenesis. While FGFR1–3 are well studied in cancer, FGFR4 remains relatively understudied, and the distribution of its mutations across cancers and patient populations is not well defined. Materials and Methods: A retrospective pan-cancer analysis was performed using the AACR Project GENIE v12 database via cBioPortal. Tumors with somatic FGFR4 mutations were included, excluding copy number alterations and structural variants. Mutations were grouped by hotspot (amino acid 401) and major protein domains. Comparative analyses assessed cancer type distribution, demographics, mutation burden, and co-occurring genomic alterations using chi-square testing with multiple comparison correction. Results: A total of 4565 tumor samples (4283 patients) were analyzed. FGFR4 alterations were observed across diverse malignancies, most commonly non-small cell lung cancer, colorectal cancer, and melanoma. Mutations clustered primarily in the tyrosine kinase and immunoglobulin I-set domains, with no significant variation in distribution across cancer types. Sex was not associated with the mutation group, while race and ethnicity showed significant differences. The FGFR4 hotspot 401 group demonstrated a higher mutation burden, driven by a subset of hypermutated tumors, and showed enrichment for co-occurring alterations in chromatin remodeling, DNA repair, tumor suppressor, and receptor tyrosine kinase genes; however, sensitivity analyses indicated this association was largely attributable to mutation burden rather than a mutation-specific effect. Domain-based mutation groups had lower mutation burdens and fewer co-alterations. Conclusions: FGFR4 alterations occur across a broad range of cancers with consistent domain-level patterns. The hotspot 401 mutation shows a higher mutation burden and co-alteration frequency driven largely by a subset of hypermutated tumors, rather than acting as an isolated driver. Full article

Background: Gastric adenocarcinomas constitute a histologically and genomically heterogeneous group of cancers. The genomic classification of gastric cancers in four groups by The Cancer Genome Atlas (TCGA) has defined a framework for pathogenic discoveries. One of the groups is associated with infection by the gamma herpes virus Epstein–Barr virus (EBV) and represents a distinct subset of gastric cancers with potential therapeutic opportunities. Methods: The EBV-associated cancers from the TCGA gastric cancer cohort were analyzed to determine specific mutational and mRNA expression profiles that set these cancers apart from other gastric cancer subtypes. The cBioportal for Cancer Genomics site was used for downloading and analyzing the primary data. Results: EBV-associated cancers represented about 7% of the cohort. Mutations in the catalytic alpha subunit of PI3K kinase, PIK3CA, and the epigenetic modifiers ARID1A and BCOR were common. PIK3CA mutations were observed in 80% of EBV-associated cancers and frequently affected the hotspot codons E542 and E545. The few cases without PIK3CA mutations displayed frequent alterations in ERBB2 or in the regulatory unit of PI3K. EBV-associated cancers did not display excess cytidine to thymine (C>T) transitions compared with other gastric cancer genomic subtypes, as would be expected from the high genome methylation caused by the virus. In contrast, an increased rate of T to G (T>G) transversions was observed in EBV-associated cancers. Translesion polymerase eta (POLH), which produces a signature characterized by a preponderance of T>G, was up-regulated in EBV-associated gastric cancers and may be a contributing factor in this increase, up-regulated by wild-type p53 and over-expression of transcription factor IRF1. Conclusions: The data presented here suggest that mutagenesis in the EBV-associated gastric cancers is not a direct consequence of the virus-derived hypermethylation. Up-regulation of kinase PI3K and its pathway is a prerequisite for EBV transformation, and epigenetic alterations are frequently present, suggesting therapeutic avenues. Full article

Coronaviruses encode a variety of non-structural proteins (NSPs) that collectively mediate viral genome replication, transcription and remodeling of the host cellular microenvironment. As a highly conserved transmembrane protein, non-structural protein 6 (NSP6) predominantly localizes to the endoplasmic reticulum. Through interactions with other viral proteins and host factors, NSP6 participates in multiple pivotal processes, including the formation and stabilization of double-membrane vesicles (DMVs), reprogramming of lipid metabolism, blockade of autophagic flux, and evasion of innate immunity. Recent advances in structural biology and research on virus–host interactions have further elucidated the essential roles of NSP6 throughout the viral life cycle. Mutations in NSP6 are closely associated with viral adaptability, transmissibility and pathogenicity. Herein, we comprehensively review the latest advances on the molecular structure, biological functions and mutation hotspots of coronavirus NSP6, as well as its implications for antiviral research. This review aims to provide a theoretical basis for further dissecting the pathogenic mechanisms of coronaviruses and developing broad-spectrum antiviral drugs. Full article

Background: Comprehensive genomic profiling (CGP) via next-generation sequencing (NGS) is pivotal for precision oncology, yet many laboratories face challenges with incomplete genomic coverage, complex bioinformatics workflows, and limited integration of key biomarkers. Methods: We evaluated the analytical performance and clinical utility of a CGP assay using 119 tumor samples representing 18 types of cancer, previously analyzed with an orthogonal NGS panel. Concordance was assessed across 81 genes, covering 176 single-nucleotide variants (SNVs), eight copy number variations (CNVs), four deletions, one duplication, and four gene fusions. Limit of detection (LOD) studies employed AcroMetrix Mutant Hotspot Control and SeraSeq Lung and Brain CNV Mix. Microsatellite instability (MSI) and tumor mutational burden (TMB) were quantified. Inter- and intra-run reproducibility were evaluated to assess precision. Results: The CGP assay demonstrated high analytical performance, with >99% sensitivity, 100% specificity, and complete accuracy for variant detection. LOD studies revealed robust detection of SNVs at ≤5% variant allele frequencies (VAF) and CNVs at three copies. MSI and TMB results were consistent with clinical expectations, showing minimal bias compared to the orthogonal panel. Inter- and intra-run testing confirmed 100% reproducibility, indicating strong assay precision. Post-sequencing variant reporting was streamlined using the iCare platform, enabling direct FASTQ-to-report generation without intermediate bioinformatic steps. Conclusions: These findings support the present assay’s clinical utility in personalized oncology assessment. Full article

Herpes simplex virus 1 (HSV-1) is a rare cause of acute hepatitis, especially in patients with chronic immunosuppression. We performed whole-genome HSV-1 sequencing with a metagenomics approach on peripheral blood samples from an Italian case of fatal acute liver failure with high circulating HSV-1 (1,129,900,000 copies/mL), followed by phylogenetic analysis. After multiple sequence alignment, a final dataset of 182 whole-genome sequences was selected. The sequenced HSV-1 strain belonged to a phylogenetic clade isolated in Florida in 2002 (OQ724868.1). A characterization of single nucleotide polymorphisms and indels was performed to determine their effects on the viral genome: only one variant, classified as an indel, was detected with a high impact effect (c.905_906insGTTTT) in the UL49A gene, which is known to encode a membrane protein regulating virion morphogenesis, replication and assembly. In addition, this study also detected variants in other genes involved in crucial steps of the HSV-1 life cycle, like alpha-regulation (US7), capsid transport (UL36) and viral polymerase function (UL30). In conclusion, the results of this variant analysis confirmed that in HSV-1 hepatitis, some viral regions may be hotspots for adaptive mutations with a substantial impact on viral replication or immune evasion. Full article

Primary pulmonary adenocarcinoma in dogs is rare, and effective systemic therapies remain limited. To evaluate the molecular basis of potential precision oncology approaches, hotspot mutations in HER2, BRAF, KRAS, and PIK3CA were analyzed in 20 surgically resected canine pulmonary adenocarcinomas and three canine pulmonary adenocarcinoma cell lines. HER2 V659E and BRAF V595E mutations were each detected in 3/20 cases (15%), while KRAS G12V was detected in 1/20 cases (5%). No PIK3CA hotspot mutations were identified. The BRAF V595E mutation was additionally detected in the AZACL2 cell line. Functional analysis demonstrated increased sensitivity of AZACL2 cells to the BRAF inhibitor dabrafenib and MEK inhibitors including trametinib, compared with BRAF wild-type cell lines. These findings support MAPK pathway dependency in BRAF-mutant canine pulmonary adenocarcinoma. The mutation spectrum was broadly consistent with previous reports, suggesting a conserved molecular landscape across geographic regions. Collectively, these data identify BRAF and HER2 alterations as clinically relevant candidates for molecular diagnostics and targeted therapy in canine pulmonary adenocarcinoma. Full article