Search Results (7,357)

Colorectal cancer (CRC) develops through both conventional adenoma–carcinoma and serrated neoplasia pathways, yet noninvasive screening still under-detects the advanced precursor lesions that enable true cancer prevention. Stool-based screening reduces CRC mortality, but its preventive impact remains constrained by limited detection of advanced precancerous lesions (APLs), including advanced adenomas and sessile serrated lesions. Next-generation multitarget stool DNA assays (mt-sDNA; e.g., Cologuard Plus) have established high sensitivity for CRC and specificity approaching 94%, leaving improved APL detection as the principal opportunity for innovation. This review presents a consensus framework for a multi-omic stool screening paradigm that integrates host epigenetic markers (DNA methylation) with gut microbiome features using artificial intelligence (AI). Multi-omics capture complementary layers of early tumor biology: epithelial shedding and field effects reflected in host methylation signals together with luminal ecological and inflammatory changes represented by microbial features. Evidence from cross-cohort microbiome studies indicates that microbial signatures provide an additive—rather than standalone—axis of information for CRC and its precursor lesions. Because microbiome-based models are highly susceptible to batch effects arising from collection devices, extraction chemistry, sequencing platforms, and bioinformatic pipelines, practical mitigation strategies are outlined, including harmonized pre-analytics, batch-aware study design, leakage-resistant validation, and computational harmonization. A translational roadmap linking analytical validity, locked-model development, and prospective colonoscopy-verified clinical validation is proposed, aligned with TRIPOD + AI, STARD, PROBAST-AI, SPIRIT-AI, CONSORT-AI, and DECIDE-AI reporting standards. Scenario modeling using BLUE-C prevalence estimates suggests that improving APL sensitivity from approximately 43% to 55–65% at ~94% specificity could translate to detecting roughly 13–23 additional advanced precancerous lesions per 1000 individuals screened, highlighting the potential prevention impact of a multi-omic approach. This framework aims to guide developers and clinical investigators toward next-generation stool tests capable of materially improving precursor-lesion detection while maintaining clinically acceptable specificity. Full article

Background/Objectives: MYO7A is known to be the genetic cause of Usher syndrome type 1, as well as autosomal dominant and autosomal recessive non-syndromic hearing loss. In general, autosomal dominant MYO7A-associated hearing loss shows progressive high-frequency, sloping hearing loss. However, several variants are associated with low-frequency hearing loss. MYO7A-associated low-frequency hearing loss is relatively rare, and the clinical details remain unclear. Methods: A total of 18,475 Japanese patients with hearing loss were recruited. Targeted massively parallel sequencing of 158 deafness-related genes was performed, and individuals with variants related to MYO7A-associated low-frequency hearing loss were identified. Results: Among 18,475 hearing loss patients, we identified 60 patients from 44 unrelated families carrying five variants (p.[Asn140Lys; Glu1835Gln], p.Leu479Pro, p.Leu656Val, p.Gly660Arg, and p.Arg668His) for MYO7A-associated low-frequency hearing loss. Patients identified in this study initially showed postlingual-onset mild-to-moderate low-frequency hearing loss; however, high-frequency hearing also deteriorated after the fourth decade, eventually leading to moderate-to-severe flat-type hearing loss. In addition, we performed haplotype analysis for the recurrent variant c.1436T>C:p.Leu479Pro identified in this study and found that this variant is a founder mutation in the Japanese population. Conclusions: In this study, we were able to clarify the specific features of MYO7A-related low-frequency hearing loss in a significant number of patients. In particular, we clarified the details of hearing deterioration at each frequency. Our findings will be useful for providing more appropriate treatment and follow-up for MYO7A-associated low-frequency hearing loss. Full article

Rapeseed (Brassica napus L.) faces escalating threats from abiotic and biotic stresses, notably blackleg caused by Leptosphaeria maculans. Due to limited chemical control efficacy and stringent GMO regulations, marker-assisted selection (MAS) leveraging natural genetic variation has become an indispensable strategy for crop improvement. This study identified novel molecular markers for blackleg resistance by integrating genome-wide association study (GWAS) results with high-throughput genotyping by Diversity Arrays Technology sequencing. Phenotypic screening across the population demonstrated a wide spectrum of disease severity (scores 0–6), confirming the segregation of key resistance genes. The DArTseq platform identified nearly 104,000 markers, comprising 61% SilicoDArTs and 39% SNPs. Among the 33 most significant markers associated with resistance (p < 0.01), 76% were SilicoDArTs. Transcriptomic data further validated these findings, revealing 13 marker-linked genes expressed during infection, seven of which exhibited significant differential expression. Comprehensive functional annotation of Arabidopsis thaliana orthologs associated these genes with diverse cellular and plant-wide processes, particularly during stress responses. Collectively, these findings emphasize the complex polygenic nature of blackleg resistance and provide robust genomic tools for the accelerated breeding of resilient B. napus cultivars. Full article

Background and Objectives: Melanoma is the leading cause of skin cancer-related mortality due to its high propensity for early metastasis, although survival rates have improved with the advent of targeted and immune-based therapies. Accurate detection of targetable mutations and assessment of tumor mutational burden are essential for informed therapeutic decision-making. Mutation profiling is routinely performed using next-generation sequencing (NGS). The Oncomine Focus Assay (OFA) detects common alterations in 52 genes across various tumor entities, whereas MelArray is a melanoma-specific NGS panel covering mutations in 190 melanoma-relevant genes and providing a genome-wide copy number analysis. Moreover, tumor mutational burden is being assessed. Materials and Methods: In this retrospective study, we analyzed the phenotypic characteristics of 100 patients with cutaneous melanoma who underwent NGS testing using either OFA or MelArray. The aims were to compare the diagnostic yield of the two panels and to investigate potential associations between mutational profiles and clinicopathological features of melanoma. Results: Tumor location, ulceration, and Breslow thickness showed significant correlations with the melanoma subtypes. BRAF mutations were the most frequent driver alterations across all cutaneous melanoma subtypes; however, no significant correlation between specific driver mutations and phenotypic characteristics was identified. MelArray detected a notably high number of alterations in the TERT promoter and CDKN2A genes, which were not captured by OFA and are of potential therapeutic relevance. Conclusions: In conclusion, MelArray enables a more comprehensive molecular characterization of cutaneous melanoma compared with a small generic cancer panel and may support more personalized therapeutic decision-making. Full article

Background: Deletion of the MTAP gene at chromosome 9p21.3 defines a therapeutically actionable molecular subset of cancers due to synthetic lethal vulnerability to PRMT5 and MAT2A inhibition. The real-world prevalence and genomic context of MTAP deletion in diverse solid tumors remain incompletely characterized. Methods: We retrospectively analyzed 579 solid tumor specimens subjected to next-generation sequencing-based copy-number profiling. The prevalence of MTAP deletion and its co-occurrence with CDKN2A and CDKN2B were evaluated, and genomic deletion patterns across chromosome 9 were systematically assessed. Results: MTAP deletion was detected in 14 cases (2.4%, 95% confidence interval [CI], 1.45–4.02%), with enrichment in sarcoma, pancreatic cancer, and urothelial carcinoma. Concurrent CDKN2A loss was observed in 92.9% of MTAP-deleted tumors, and 64.3% showed additional CDKN2B loss, indicating a coordinated focal deletion event at 9p21.3. Statistical analyses confirmed strong genomic associations between MTAP and neighboring tumor suppressor genes. Across the full cohort, deletion frequency peaked at the 9p21 locus, and among MTAP-deleted tumors, co-deletion frequency decreased with increasing genomic distance. All MTAP-deleted tumors were microsatellite stable and low tumor mutational burden (TMB-low). Conclusions: Our findings demonstrate that MTAP deletion is an infrequent but genomically coherent event in solid tumors, characterized by a canonical 9p21 co-deletion pattern. This real-world analysis underscores the importance of comprehensive genomic profiling to identify patients who may benefit from emerging MTAP-directed therapies. Full article

Background and Objectives: Reliable tools for evaluating tumor biology and forecasting clinical outcomes in recurrent hepatocellular carcinoma (HCC) remain scarce, and molecular characterization through genetic profiling is equally limited in this setting. This investigation explores whether serum tumor marker expression patterns correlate with genomic mutation profiles, and whether such correlations may facilitate more accurate prediction of tumor biology and patient prognosis in recurrent HCC. Materials and Methods: We analyzed a cohort of 20 patients who underwent curative-intent resection for both primary and recurrent HCC. Tumor specimens collected at the time of each operation were subjected to targeted next-generation sequencing for mutation profiling. Based on pre-operative serum levels of AFP (alpha-fetoprotein) and PIVKA-II (Protein Induced by Vitamin K Absence or Antagonist-II) measured before each surgery, patients were stratified into four biomarker subgroups. Those who maintained the same biomarker subgroup at both operations were designated the ‘serum concordant group’, whereas those who transitioned between subgroups were classified as the ‘serum discordant group’. Clinical characteristics and mutation data were subsequently compared between these two classifications. Results: The interval from primary surgery to disease recurrence was significantly shorter in the serum concordant group relative to the serum discordant group (mean 11.16 ± 1.86 vs. 44.8 ± 9.45 months, p < 0.001). Additionally, disease-free survival following reoperation was significantly inferior in the concordant group compared with the discordant group (p = 0.039). Regarding mutational patterns, the concordant group demonstrated shared gene mutations between primary and recurrent lesions, while the discordant group exhibited divergent mutational landscapes across both timepoints. Conclusions: The concordance or discordance of serum tumor marker profiles between primary and recurrent HCC lesions may serve as a clinically accessible surrogate for underlying tumor biology and prognostic stratification. These results are preliminary and hypothesis-generating. Further studies in larger, independent cohorts are warranted to confirm the observed associations. Full article

Background/Objectives: To analyze possible epigenetic changes (miRNA) in systemic lupus erythematosus (SLE) patients on a Mediterranean diet (MD) supplemented with extra virgin olive oil (EVOO). Methods: Fifteen SLE patients with medium/high MD adherence were randomized into an intervention group (IG) (daily supplementation of 40 mL of EVOO for 24 weeks) or to a control group (CG). miRNA profiles from blood peripheral cells were analyzed pre-/post-intervention using next-generation sequencing. Differential expression analysis was performed by DESeq2 in R to determine changes in the log2FC. Functional enrichment analysis was performed using GeneCodis 4. Results: EVOO supplementation resulted in changes in the expression of 16 miRNAs in the IG. Compared to the CG, two miRNAs showed upregulation (miR-451a, miR-1307-5p) while five showed downregulation (miR-193b-50, miR-134-5p, miR1287-5p, miR-124-3p, miR-654-3p). miR-124-3p, which has been proposed to be an SLE biomarker, showed the lowest relative expression after EVOO supplementation (L2FC −3.36; p_unadj = 0.025), whereas miR-1307-5p (L2FC 1.115 p_unadj = 0.02) and miR-451a (L2FC 0.77 p_unadj = 0.036) showed the highest relative abundance. The functional enrichment analysis showed that Th1 and Th2 cell differentiation and the complement/coagulation cascades were among the top ten most significantly enriched pathways. Conclusions: Our data suggest that MD supplementation with EVOO leads to changes in the profile of miRNAs in SLE patients, potentially impacting disease pathogenesis. Further research is needed to validate these preliminary findings and the mechanisms by which EVOO modifies miRNA expression in the context of this disease. Full article

Recent high annual losses of honey bee (Apis mellifera) colonies, averaging 40% in the United States from 2008 to 2025, are concerning for beekeepers, growers, policy makers, and scientists. Viruses, the most abundant group of honey bee pathogens, impact honey bee fitness and contribute to colony losses. Several studies have utilized next-generation sequencing (NGS) technologies to discover new honey beeinfecting viruses and expand our understanding of the honey bee virome. Herein, we examined the viromes of honey bees obtained from longitudinally monitored, commercially managed colonies that experienced population decline (average ~44%) during the 2022–2023 beekeeping season. We hypothesized new viruses or virus genome variants may be associated with these declines. To test this hypothesis, we sequenced RNA obtained from virus-augmented honey bee samples from representative colonies managed by four beekeeping operations in California. We discovered three undescribed partitivirus-like sequences that were prevalent and abundant in all beekeeping operations, a new Lake Sinai virus, and a sequence variant of acute bee paralysis virus. In addition, we re-sequenced the genomes of 16 previously characterized bee and/or Varroa destructor mite infecting viruses and two previously described, but not well-characterized, partitivirus-like sequences (i.e., Apis mellifera associated partiti-like virus 1 and Hubeipartiti-like virus 34). Virus abundance was greater in libraries representing colonies that died during the monitoring period. Full article

Introduction: Advanced-stage high-grade serous ovarian cancer (HGSC) is a disease that is difficult to manage due to its heterogeneous clinical behavior. No reliable prediction of response to chemotherapy is currently available and the overall survival rate remains poor. Herein, we sought to determine the molecular mechanisms by which microRNAs (miRNAs) confer chemoresistance in ovarian cancer and demonstrate the efficacy of targeting miRNAs to sensitize HGSC to cisplatin treatment. Methods: Next-generation miRNA sequencing was performed using microdissected HGSC specimens to identify an miRNA signature for intrinsic chemoresistance, and miR-625-3p was selected for further study. The effects of miR-625-3p on cisplatin sensitivity were evaluated using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assays and cell death enzyme-linked immunosorbent assay. Transcriptome profiling analysis, online prediction algorithms, and reporter assays were used to demonstrate SSX2IP as the direct gene target of miR-625-3p. Cell death enzyme-linked immunosorbent assays, mass spectrometry, and high-speed confocal microscopy were used to determine the roles of SSX2IP in mediating the effects of miR-625-3p in cisplatin sensitivity via the extracellular vesicle (EV) secretion of cisplatin. Results: An miRNA signature for intrinsic chemoresistance was identified. Amongst all the downregulated miRNAs in the chemo-refractory samples, only miR-625-3p was associated with poorer overall survival and progression-free survival rates. Further functional studies showed that the overexpression of miR-625-3p significantly decreased cisplatin resistance in ovarian cancer cells both in vitro and in vivo. SSX2IP (Synovial Sarcoma, X Breakpoint 2 Interacting Protein) was confirmed to be the direct gene target of miR-625-3p and its upregulation abrogated miR-625-3p-mediated cisplatin resistance by enhancing the EV export of cisplatin in ovarian cancer cells. Conclusions: These findings provide a new paradigm for intrinsic cisplatin resistance acquisition by HGSC cells, which will be crucial for developing new treatment strategies for ovarian cancer based on the upregulation of miR-625-3p or downregulation of SSX2IP to enhance cisplatin sensitivity and improve patient survival rates. Full article

The transition from Sanger to next-generation sequencing (NGS) for HIV-1 drug resistance testing offers enhanced sensitivity but also introduces bioinformatic variability. This study evaluated four strategies: the commercial Exatype platform, the academic Stanford HIVdb-NGS, the open-source Quasitools (HyDRA) suite, and a custom de novo assembly workflow, iLunaR. Using 85 clinical HIV-1 pol MiSeq sequencing datasets, concordance was assessed at a 2% mutation detection threshold. A majority consensus standard defined true presence if a mutation was detected by at least three pipelines and supported by Sanger sequencing. While the datasets were successfully processed by all pipelines, discordances emerged in detecting low-abundance mutations and a specific case of structural mutation. iLunaR achieved perfect agreement (Cohen’s kappa = 1.000; 95% CI: 1.000–1.000). Quasitools demonstrated the lowest agreement (Cohen’s kappa = 0.901; 95% CI: 0.807–0.995) due to consistent reporting of mutations at lower abundance levels and aligner-induced reference bias misclassifying a deletion as a point mutation. Exatype (Cohen’s kappa = 0.951; 95% CI: 0.884–1.000) and Stanford (Cohen’s kappa = 0.926; 95% CI: 0.846–1.000) exhibited specific failures, including an omitted integrase mutation and codon translation errors, respectively. These findings confirm that bioinformatic algorithm choice remains a critical clinical variable despite NGS advancements in HIV-1 drug resistance testing. Full article

Background/Objectives: Tissue-agnostic therapy has transformed oncology by enabling treatment selection based on molecular alterations rather than tumor origin. Since 2017, nine U.S. Food and Drug Administration approvals across six biomarker classes have defined this paradigm. Thoracic and head and neck (H&N) cancers have been underrepresented in the registrational evidence supporting these approvals. This review systematically evaluated biomarker representation, histologic distribution, and clinical applicability of tissue-agnostic therapies in thoracic and H&N malignancies. Methods: A narrative systematic review was conducted using PubMed, ClinicalTrials.gov, and regulatory documents for all tissue-agnostic approvals between January 2017 and October 2025. Data were extracted from pivotal trials, including total enrollment, objective response rate (ORR), histologic distribution, and thoracic/H&N representation. Emerging biomarkers and resistance mechanisms were assessed from phase I–III studies and basket trials. Results: Nine tissue-agnostic approvals encompassing six biomarkers were identified: MSI-H/dMMR, TMB-High, NTRK, RET, BRAF V600E, and HER2 (IHC 3+). Across pivotal datasets (3800 patients), thoracic and H&N cancers accounted for fewer than 8% (n = 290) of enrolled patients. Thoracic representation was dominated by non-small-cell lung cancer (NSCLC) in RET, NTRK, and HER2 programs (150 patients, 4%), while small-cell lung, mesothelioma, and thymic carcinomas contributed <1% combined. H&N cancers comprised 140 patients (3–4%), primarily secretory salivary carcinoma in NTRK trials (n = 12–20), thyroid carcinoma in BRAF (n = 36) and RET (n = 45) programs, and rare HER2-positive salivary duct carcinomas. Conventional HNSCC and sinonasal cancers were limited to 1–2 cases per trial. Only two of nine trials (22%) reported prespecified CNS endpoints, and RNA-based fusion testing was employed in <40%, underscoring diagnostic variability and limited applicability. Conclusions: Although tissue-agnostic therapy has expanded the reach of precision oncology, thoracic and H&N cancers remain underrepresented in registrational evidence. Most approvals rely on single-arm basket studies with small, heterogeneous subsets that preclude histology-specific conclusions. Future research should prioritize histology-enriched trial designs, standardized molecular diagnostics, and real-world validation to establish reliable, equitable standards of care for these underrepresented malignancies. Full article

Background: Tumor mutational burden (TMB) is an FDA-approved biomarker for immune checkpoint inhibitor (ICI) therapy. However, its predictive value varies among tumor types and molecular contexts. We investigated whether a very high TMB identifies a biologically distinct subset and whether a higher cutoff provides additional clinical insights beyond the conventional high TMB threshold. Methods: We analyzed 133 patients with advanced solid tumors and TMB ≥ 10 mutations/Mb (mut/Mb) who underwent tumor genomic profiling using a 523-gene DNA/RNA next-generation sequencing panel. Tumors were stratified into prespecified TMB categories: 10–20 mut/Mb (TMB-H) and >20 mut/Mb (TMB-VH). The clinical characteristics, ICI outcomes (in the treated subset), and pathway-level genomic features were compared between groups. Results: TMB-VH was observed in 42/133 (31.6%) patients and spanned more than 20 tumor types. MSI was markedly more prevalent in TMB-VH than in TMB-H tumors (38.1% vs. 2.2%; Fisher’s exact p = 8.9 × 10⁻⁸). Pathway-level comparisons did not identify statistically significant differences after false discovery rate correction (all q > 0.05), and the observed patterns were descriptive in nature. In the ICI-treated subset with complete follow-up, objective response did not differ according to the TMB group. Overall survival (OS) was also similar between groups, whether measured from metastatic diagnosis (log-rank p = 0.937) or from ICI initiation (log-rank p = 0.814), although OS was numerically longer in the TMB-VH group in both analyses without reaching statistical significance. Conclusions: In this cohort study, TMB-VH was strongly associated with MSI but not independently associated with improved ICI outcomes. Larger multicenter cohorts are needed to validate pathway-oriented patterns and clarify the clinical utility of extreme TMB thresholds across various histologies. Integrating the functional context (e.g., MSI status, gene-level context, and pathway-level features) with TMB magnitude may enable more robust, tumor-aware biomarker models for immunotherapy selection. Full article

Background: Non-classical MHC class I molecules MICA and MICB are stress-inducible NKG2D ligands that contribute to immune surveillance, non-HLA antibody formation, and alloreactivity in solid organ and hematopoietic stem cell transplantation; population-level data for Southern Europe remain limited. Methods: High-resolution MICA and MICB genotyping was performed in 1364 unrelated individuals from southern Portugal using a hybrid-capture next-generation sequencing workflow, and allele calls were analyzed with standard population-genetic metrics (allele and genotype frequencies, heterozygosity, Hardy–Weinsberg equilibrium, and LD-like D, D′, r²) and multilocus allele presence/absence encodings explored by k-means clustering, spectral clustering, principal component analysis, t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection. Results: Forty-two MICA and twenty-two MICB alleles were identified; MICA*002:01, MICA*004:01, MICA*008:01, MICA*008:04 and MICB*002:01, MICB*004:01, MICB*005:02, MICB*008:01 were most frequent, and most individuals carried at least two distinct MICA and two distinct MICB allotypes. Co-occurrence and LD-like analyses revealed conserved MICA–MICB combinations, including a strong association between MICA*009:02 and MICB*005:06, while unsupervised analyses identified partially overlapping multilocus genotype backgrounds and recurrent four-allele constellations. Conclusions: These findings provide a detailed non-classical MHC reference for southern Portugal and a multilocus framework to support interpretation of non-HLA antibodies and MICA/MICB-aware donor evaluation in selected clinical scenarios, as well as the development of machine learning-based immunologic risk models. Full article

Invasive fungal diseases (IFDs) represent an escalating global health threat, compounded by the rapid emergence of antifungal resistance (AFR). This review synthesizes the contemporary landscape of AFR from clinical and microbiological perspectives, providing actionable insights for clinical practitioners. We examine the epidemiology of critical pathogens, including Candidozyma auris, clonal Candida parapsilosis, azole-resistant Aspergillus fumigatus, and dissect the underlying molecular mechanisms, from genetic mutations in ERG11 and cyp51A to novel emerging epigenetic and adaptive strategies. We critically appraise the diagnostic gap between phenotypic testing and clinical urgency, highlighting the role of rapid molecular assays and next-generation sequencing. Finally, we evaluate evidence-based therapeutic strategies, including the integration of novel agents such as rezafungin, ibrexafungerp, olorofim, and fosmanogepix), while emphasizing the imperative of antifungal stewardship, infection prevention and control in mitigating resistance, and “One-Health” interventions. Full article

Background: Once considered a sterile organ, the human stomach is now known to harbor a diverse microbial community that may influence both gastric homeostasis and disease. While extensive research has been conducted worldwide, regional variation in the gastric microbiome remains insufficiently characterized. This study aimed to describe the gastric antrum microbiome of Helicobacter pylori-negative Greek adults using 16S rRNA next-generation sequencing (NGS). Methods: Samples of gastric biopsies were obtained from patients undergoing gastroscopy at a tertiary hospital in Greece. H. pylori infection was excluded through a combination of bacterial culture and patient medical history. The final study group consisted of 9 subjects. Following DNA extraction, the 16S rRNA gene was sequenced on the Ion Torrent™ platform. Bioinformatic processing and statistical analyses were performed using the phyloseq, vegan, and ggplot2 R packages. Microbial composition, relative abundance, and alpha diversity (Shannon and Inverse Simpson indices) were evaluated at the genus level. Results: The gastric microbiome comprised 19 phyla, 150 families, 213 genera, and 391 species. The predominant phyla were Proteobacteria (36.92%), Firmicutes (34.21%), and Bacteroidetes (12.97%). The most prevalent families were Streptococcaceae, Helicobacteraceae, Prevotellaceae, and Pasteurellaceae. At the genus level, Streptococcus (21.71%), Helicobacter (18.39%), and Prevotella (9.99%) accounted for nearly half of the total relative abundance. Alpha diversity indices indicated moderate richness and evenness across samples. Conclusions: The gastric antrum microbiome of H. pylori-negative Greek individuals exhibits substantial taxonomic diversity dominated by Proteobacteria and Firmicutes. The microbial community structure aligns closely with profiles reported in other global populations. These findings provide a reference baseline for future comparative analyses involving H. pylori-positive individuals to better understand microbiome shifts associated with colonization and gastric disease. Full article