Search Results (285)

Background/Objectives: Tumor suppressor genes are often inactivated by genetic and epigenetic mechanisms. However, whether genetic alterations of these genes, including CDKN2A/P16, are coupled with epigenetic changes in cancer development and progression is unknown. Methods: Freshly frozen gastric carcinoma (GC) samples, paired noncancer surgical margin (SM) samples, white blood cell (WBC) samples, and clinicopathological information were collected from 200 patients. The copy number (CN) of the CDKN2A/P16 gene in these samples was determined by a P16-Light assay and normalized to that in white blood cells (WBCs). The DNA methylation level of the P16 promoter in GC and SM samples was determined by a 115 bp P16-specific MethyLight assay. Results: Both the P16 copy number and the DNA methylation level were significantly lower in GC samples than in SM samples (median, 1.94 vs. 2.14, p < 0.001 for P16 CN; 0.0004 vs. 0.0013, p = 0.002 for P16 methylation) and were associated with GC metastasis. The normalized P16 copy number was significantly lower in GCs without vs. with P16 methylation (p = 0.007). Similarly, more P16 somatic copy number deletions (SCNdel) were detected in GCs without vs. with P16 methylation (38.6% vs. 24.1%, p = 0.027). Conclusions: Somatic P16 copy number variations are closely coupled with P16 promoter DNA methylation during GC development. SCNdel and promoter DNA methylation complementarily inactivate P16 in GC development and promote GC metastasis. Full article

Hereditary breast cancer (BC) remains unexplained in a substantial proportion of families who test negative for BRCA1/2 and other known susceptibility genes. To contribute to the genomic characterization of these unresolved cases, we generated a whole-genome sequencing (WGS) dataset from six women belonging to two unrelated high-risk families, each comprising three sisters diagnosed with BC. All participants had previously received negative results in conventional multigene panel testing. WGS was performed on peripheral blood DNA using the Illumina NovaSeq platform, followed by variant calling against GRCh38 and the comprehensive annotation of single-nucleotide variants, indels, and structural variants. For each family, we identified shared ClinVar-annotated variants, rare exonic or splice-site alterations, and intronic variants located within a curated set of 286 cancer-related genes. The dataset includes per-patient VCF files, copy number variation annotations, and family-level variant summaries. Raw and processed data are publicly available through the Sequence Read Archive and Zenodo. This resource supports variant reinterpretation, exploration of regulatory and intronic regions, and methodological benchmarking in the study of familial BC beyond established susceptibility genes. Full article

Bladder cancer (BCa) is a major global urinary tract malignancy characterized by high incidence, frequent recurrence, and significant mortality. Early diagnosis is crucial for improving prognosis and minimizing invasive procedures; however, current standard techniques, cystoscopy and urine cytology, are limited by invasiveness, cost, low sensitivity, and subjectivity. This has spurred the development of non-invasive diagnostic strategies based on urine analysis. This review highlights five emerging approaches: AI-augmented urine cytology, genomic biomarker assays (e.g., PCR and NGS for mutations and copy-number variations), DNA methylation profiling, RNA biomarkers (mRNA, miRNA, lncRNA), and protein/peptide/metabolite detection utilizing ELISA, SERS, nanozymes, and mass spectrometry. We assess the diagnostic accuracy, innovations, and clinical potential of each, while addressing persisting issues such as lack of standardization, high costs, and insufficient sensitivity for early-stage lesions. Future directions include integrating multi-omics data with AI, advancing point-of-care devices, and conducting large-scale multicenter trials. Together, these developments promise to shift BCa management toward molecular-based early detection, enabling more precise, non-invasive, and personalized patient care. 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

Early detection of bladder cancer poses a major challenge for liquid biopsy due to limited tumor burden and low abundance of tumor-derived DNA. In such low-signal settings, detection sensitivity critically depends on both biofluid selection and effective integration of weak, distributed molecular signals. We analyzed Enzymatic Methyl-seq (EM-seq) data on 41 matched urine–plasma pairs, which demonstrated that urine samples exhibited significantly higher tumor fractions and greater concordance with tissue methylation profiles than plasma. Based on this observation, we developed a urine-based bladder cancer detection framework using EM-seq. We profiled 143 urine samples (68 bladder cancer and 75 healthy controls) and 14 bladder cancer tissues. Methylation markers (113,052 regions) were identified by comparing cancer tissues (n = 14) with urine from healthy individuals (n = 14). Using XGBoost, possible features and their combinations were evaluated, with the combination of methylation and copy number variations (CNV) yielding the best performance as the final ensemble model. When evaluated on an independent test set, the model achieved 91.9% sensitivity at 80% specificity, with an area under the curve (AUC) of 0.932 for bladder cancer detection and 0.928 for non-muscle invasive bladder cancer (NMIBC) detection. Notably, the model successfully detected four of seven mutation-negative cases, demonstrating complementary value to mutation-based approaches. Full article

Several receptors have received considerable attention as therapeutic targets in gastric cancer (GC), and numerous receptor inhibitors have been developed. However, the development of novel gastric cancer therapeutics is time-consuming. Therefore, this study aimed to identify drugs effective against gastric cancer from existing anticancer agents originally developed for other malignancies. In this study, the cancer-related genomic profiles of 286 genes were analyzed in 14 gastric cancer cell lines using targeted DNA sequencing, and these cell lines were utilized as models to evaluate the efficacy of 35 anticancer drugs. The 14 cell lines were assessed for 286 gene alterations, copy number variations, amplification of 14 gastric cancer-related therapeutic targets, and sensitivity to 35 drugs. p-MET and MET were overexpressed in the SNU5, SNU620, MKN45, and Hs746T cell lines, while p-EGFR was overexpressed in the NCI-N87 cell line. FGFR2 overexpression was observed in the Kato III and SNU16 cell lines. TGFβR1 was overexpressed in the MKN7 cell line. HER2 and CDK12 were overexpressed in the NCI-N87 and MKN7 cell lines. PD-L1 overexpression was detected in the Hs746T and MKN7 cell lines. CD44 was overexpressed in the SNU5 and Hs746T cell lines and CLDN18 overexpression was observed in the MKN7 cell line. Well-characterized gastric cancer cell lines are essential for drug development research. This study provides a framework for selecting cell lines that are responsive to each of the 35 anticancer drugs and elucidating their underlying therapeutic mechanisms through follow-up studies. Ultimately, clinical studies are required to confirm the therapeutic efficacy of the selected drugs. Full article

Background: Advances in genome-wide DNA-based technologies have fundamentally transformed prenatal genetic diagnostics, enabling detection of clinically significant submicroscopic chromosomal abnormalities that are not identifiable by conventional cytogenetic methods. These developments have important implications for the diagnosis and management of pregnancies complicated by fetal structural abnormalities, as they enable more accurate etiological diagnosis, improved prognostic assessment, and more informed clinical decision-making and reproductive counselling. Methods: This narrative review synthesizes contemporary international evidence on prenatal genetic diagnostic approaches, including conventional karyotyping, chromosomal microarray analysis (CMA), and genome-wide sequencing technologies. The review focuses on diagnostic performance, clinical utility, ethical considerations, and implementation within diverse healthcare systems. Results: Accumulating evidence demonstrates that genome-wide approaches—particularly CMA and sequencing-based methods—provide a higher diagnostic yield in fetuses with structural anomalies, with an incremental yield of approximately 3–5% over conventional karyotyping. This is mainly due to their ability to detect pathogenic copy number variants below the cytogenetic resolution of karyotyping. These technologies improve etiological insight, enhance genotype–phenotype correlation, and support more precise prognostication and reproductive counselling, especially in pregnancies with fetal structural anomalies. Emerging sequencing platforms further expand the diagnostic spectrum by integrating copy number and sequence-level variant detection. Conclusions: Genome-wide Copy Number Variation (CNV) analysis represents a critical component of contemporary prenatal diagnostics and should be integrated into invasive prenatal testing pathways in accordance with international recommendations. Genome-wide approaches need robust counselling frameworks and equitable health policy implementation to spread. The expense, lack of required experience, and variation in healthcare infrastructure across locations make widespread deployment difficult. Full article

Human papillomavirus (HPV) infection is a leading cause of cervical cancer and a significant contributor to anogenital and oropharyngeal malignancies worldwide. While the oncogenic functions of HPV oncoproteins E6 and E7 in disrupting nuclear tumor suppressor pathways are well established, their influence on mitochondrial biology has only recently emerged as a critical facet of HPV-driven carcinogenesis. This review synthesizes current evidence on the qualitative and quantitative alterations of mitochondrial DNA (mtDNA) and their functional consequences in HPV-associated cancers. We discuss how E6 and E7 modulate mitochondrial dynamics, bioenergetics, and redox balance, contributing to metabolic reprogramming, resistance to apoptosis, and adaptation to tumor microenvironmental stress. We also examine the clinical significance of mtDNA mutations, deletions, and copy number variations as potential biomarkers for diagnosis, prognosis, and therapy response. Advances in multi-omics approaches, high-throughput sequencing, and patient-derived organoid models have accelerated the exploration of mitochondria as therapeutic targets. Integrating mitochondrial profiling into HPV-related cancer research holds promise for identifying novel metabolic vulnerabilities and guiding the development of mitochondria-directed treatment strategies. Full article

Background/Objectives: Segmental duplications (SDs) are major drivers of genome evolution and structural variation in primates, particularly within acrocentric chromosomes, where rDNA arrays and duplicated sequences are densely clustered. However, the evolutionary dynamics of rDNA-linked SDs across great ape lineages have remained poorly characterized due to longstanding technical limitations in genome assembly. Here, we investigate the organization, copy number variation, and evolutionary conservation of acrocentric SDs in great apes by integrating fluorescence in situ hybridization (FISH) with comparative analyses of telomere-to-telomere (T2T) genome assemblies. Methods: Using eight human-derived fosmid probes targeting SD-enriched regions flanking rDNA arrays, we analyzed multiple individuals from chimpanzee, bonobo, gorilla, and both Bornean and Sumatran orangutans. Results: Our FISH analyses revealed extensive lineage-specific variation in SD copy number and chromosomal distribution, with pronounced heteromorphism in African great apes, particularly gorillas, and more conserved patterns in orangutans. Several SDs showed fixed duplications across species, while others exhibited high levels of polymorphism and individual-specific organization. Conclusions: Comparison with T2T assemblies confirmed consistent genomic localization for a subset of probes, whereas others displayed partial discordance, highlighting the persistent challenges in resolving highly repetitive and structurally dynamic regions even with state-of-the-art assemblies. Genome-wide analyses further revealed species-specific enrichment of SDs on rDNA-bearing chromosomes, with chimpanzees and bonobos showing higher proportions than gorillas, and contrasting patterns between the two orangutan species. Overall, our results demonstrate that rDNA-linked SDs represent highly dynamic genomic compartments that have undergone differential expansion and remodeling during great ape evolution. These regions contribute substantially to inter- and intra-species structural variation and provide a mechanistic substrate for lineage-specific genome evolution, underscoring the importance of integrating cytogenetic and T2T-based approaches to fully capture the complexity of duplicated genomic landscapes. Full article

Mitochondria are the energy factories of a cell and mitochondrial morphology, quantity, membrane potential, and DNA copy number can change depending on metabolic requirements and/or genetic defects. Different mutations in mitochondrial DNA might affect mitochondrial morphology and membrane potential differently. In this study we investigated mitochondrial morphology and membrane potential in vitro in mesoangioblast-derived human myotubes harboring a pathogenic mtDNA mutation and analyzed mitochondrial behavior following fusion with healthy mesoangioblasts. Myotubes were differentiated in vitro from mesoangioblasts obtained from two mitochondrial myopathy patients, M02 (96% m.3271T>C) and M11 (73% m.3291T>C), and from a functionally healthy male control, M06 (3% m.3243A>G). On day 5 of differentiation, healthy male mesoangioblasts (mM06) were added to mutant myotube cultures to allow cell fusion. On day 11, mitochondrial morphology and membrane potential were assessed by three-dimensional live-cell imaging using spinning disk confocal microscopy with tetramethylrhodamine methyl ester (TMRM). Following live imaging, cells were fixed and subjected to Y-chromosome fluorescence in situ hybridization (FISH), enabling identification and retrospective analysis of hybrid (i.e., fused with male control mesoangioblasts) and non-hybrid (i.e., not fused with these control mesoangioblasts) myotubes within the same imaging fields. Quantitative image analysis at the level of individual myotubes revealed that, when normalized to sarcoplasmic volume, mitochondrial volume, object number, and membrane potential did not differ between mutant and control myotubes despite heteroplasmy levels exceeding 70%. Fusion of healthy mM06 mesoangioblasts did not impair myotube formation and resulted in redistribution of mitochondrial content without an increase in mitochondrial object number, consistent with integration of donor mitochondria into the existing mitochondrial network. Across conditions, mitochondrial parameters were strongly influenced by myotube size, underscoring the importance of accounting for biological variation when quantifying mitochondrial features. Together, these findings demonstrate that high mtDNA mutation loads do not necessarily alter mitochondrial morphology or membrane potential under standard in vitro differentiation conditions and provide mechanistic insight into mitochondrial behavior following mesoangioblast fusion in human myotubes. Fusion of healthy mesoangioblasts supports integration of donor mitochondria into the existing network without compromising myogenesis, consistent with mitochondrial mixing rather than replacement. Full article

Despite the introduction of novel therapeutic options, the prognosis of advanced endometrial cancer remains poor. In recent years, increasing attention has been directed toward the molecular characterization of endometrial cancer. However, data specifically focusing on advanced-stage disease are still limited. In our single-center, retrospective, exploratory study with a limited sample size, we analyzed 32 patients with advanced or recurrent endometrial cancer treated at the Modena Cancer Center. Comprehensive molecular profiling was performed to assess DNA mutations, copy number variations, and RNA expression. We characterized the molecular landscape of this cohort, evaluated selected genomic alterations across predefined clinical subgroups, and explored their association with overall survival. Consistent with previous reports, a high prevalence of PTEN and PIK3CA mutations were observed. Patients experiencing relapse more than six months after diagnosis were more likely to harbor CTNNB1 mutations. KRAS mutations were more frequently detected in younger patients and in those with endometrioid histology, whereas PPP2R1A and TP53 mutations were enriched in tumors with non-endometrioid histology. Notably, CTNNB1 mutations were associated with a favorable prognostic impact, while KRAS mutations correlated with poorer overall survival. Our findings underscore the need for further investigation into the molecular landscape of advanced endometrial cancer, particularly in the context of therapeutic implications. Combinatorial treatment strategies targeting specific molecular alterations, such as KRAS, in combination with other targeted agents or therapeutic approaches, warrant further exploration. Full article

Background/Objectives: Detecting copy number variations (CNVs) from next-generation sequencing (NGS) is challenging, particularly in targeted sequencing panels, especially for cell-free DNA (cfDNA), where the signal is weak and noise is high. Methods: We present BayesCNV, a Bayesian hierarchical model for gene-level copy ratio estimation from targeted amplicon read depths compared to a CNV-neutral reference sample. The model provides posterior uncertainty for each gene and supports interpretable calling based on effect size and posterior confidence. The model also provides a principled quality-control strategy based on the marginal log likelihood of each sample, with low values indicating low confidence in the calls. BayesCNV uses thermodynamic integration, a technique to reliably estimate this quantity. We benchmark our method against two publicly available CNV callers using Seracare^® reference samples with known CNVs on the OncoReveal^® Core Lbx panel. Results: Our method achieves a sensitivity of 0.87 and specificity of 0.996, dramatically outperforming two competitor methods, IonCopy and DeviCNV. In a separate FFPE dataset using the OncoReveal^® Essential Lbx panel, we show that the marginal log likelihood cleanly separates, degraded from high-quality samples, even when conventional sequencing QC metrics do not. Conclusions: BayesCNV provides accurate and interpretable gene-level CNV estimates and uncertainty quantification, along with an evidence-based quality control metric that improves robustness in targeted cfDNA workflows. Full article

Carpione rhabdovirus (CAPRV) is an emerging virus within the family Rhabdoviridae, posing potential threats to aquaculture species such as golden pompano (Trachinotus anak). However, since the 21st century, and for CAPRV strains isolated from marine fish, only a single CAPRV2023 sequence has previously been available in public databases, with no additional sequences reported. Because the virus undergoes genetic variation, relying on this single sequence likely introduced mismatches or off-target risks in earlier detection assay designs. Notably, the previously developed two-step N-targeting detection assay was designed based solely on that single CAPRV2023 sequence. Consequently, this study involved determining and analyzing the N gene sequences from CAPRV isolates gathered from 2023 to 2025, with the aim of pinpointing conserved regions for assay development, and sequence comparisons subsequently verified the existence of mismatches in the primer–probe binding sites of the previous assay. Since quantitative assays in aquatic virology often define copy numbers utilizing either plasmid DNA templates or RNA templates produced via in vitro transcription, which may lead to variations in amplification kinetics and sensitivity, this study compared both standards to ensure reliable quantification across different nucleic acid types. Based on these findings, a one-step TaqMan quantitative PCR (qPCR) assay was developed and validated using dual nucleic acid standards, namely plasmid DNA and in vitro–transcribed RNA. Compared with conventional two-step qPCR, the one-step format combines cDNA synthesis and subsequent DNA amplification in a single sealed tube, thereby effectively preventing cross-contamination, simplifying the workflow, and improving detection efficiency. The assay exhibited strong linearity (R² > 0.99) and consistent amplification efficiencies between 90% and 110%, demonstrating excellent quantitative performance. The detection limits were 2 copies per reaction for plasmid DNA and 20 copies for in vitro–transcribed RNA templates. No cross-reactivity was observed with other aquatic pathogens, and the assay showed strong repeatability and reproducibility (coefficients of variation below 2.0%), providing a sensitive and reliable tool for epidemiological surveillance and the analysis of CAPRV distribution in marine aquaculture systems of southern China. Full article

Intra-tumor heterogeneity (ITH) is a compounding factor for cancer prognoses and treatment. Single-cell DNA sequencing (scDNA-seq) provides cellular resolution of the variations in a cell and has been widely used to study cancer progression and the responses to drugs and treatments. While low-coverage scDNA-seq technologies typically provide a large number of cells, accurate cell clustering is essential for effectively characterizing the ITH. The existing cell clustering methods are typically based on either single-nucleotide variations (SNV) or copy number alterations (CNA), without leveraging both signals together. Since both SNVs and CNAs are indicative of cell subclonality, in this paper, we designed a robust cell-clustering tool that integrates both signals using a graph autoencoder. Our model co-trains the graph autoencoder and a graph convolutional network (GCN) to guarantee meaningful clustering results and to prevent all cells from collapsing into a single cluster. Given the low-dimensional embedding generated by the autoencoder, we adopted a Gaussian mixture model (GMM) to further cluster the cells. We evaluated our method on eight simulated datasets and a real cancer sample. Our results demonstrate that our method consistently achieved higher V-measure scores compared to SBMClone, an SNV-based method, and a K-means method that relies solely on CNA signals. These findings highlight the advantage of integrating both SNV and CNA signals within a graph autoencoder framework for accurate cell clustering. Full article

Background and Objectives: Although beaded filament structural protein 1 (BFSP1) may be involved in oncogenic mechanisms, its clinical relevance and functional role in liver hepatocellular carcinoma (LIHC) remain unclear. This study examined the prognostic significance, regulatory mechanisms, and potential therapeutic implications of BFSP1 in LIHC. Materials and Methods: Comprehensive bioinformatics analysis was performed across multiple platforms using datasets derived from The Cancer Genome Atlas. Differential gene expression, DNA methylation, copy number variation, immune cell infiltration, drug sensitivity, and co-expression networks were systematically examined. Functional enrichment analyses of protein–protein and gene–gene interaction networks were conducted using STRING and GeneMANIA. Additionally, short interfering RNA-mediated knockdown and wound-healing assays were performed in HepG2 cells to evaluate BFSP1 function in vitro. Results: The results showed that BFSP1 mRNA expression was significantly upregulated in tissues from LIHC patients. Elevated BFSP1 levels were associated with poorer prognostic patterns, which were further supported by detailed clinicopathological subgroup analyses. Furthermore, BFSP1 expression was correlated with promoter hypomethylation and associated with patterns of tumor-infiltrating immune cells, including specific immune cell subtypes such as M1 and M2 macrophages. Integrative analyses revealed strong associations between BFSP1 and drug sensitivity, as well as a regulatory network encompassing genes involved in the cell cycle, DNA repair, and metabolic processes. Functional knockdown of BFSP1 significantly reduced HepG2 cell migration in vitro, as assessed by wound healing assay, with decreased wound closure at 24 h (11.0% vs. 16.5%) and 48 h (7.4% vs. 12.5%) compared with the control (p < 0.05, n = 6 biological replicates). Conclusions: In conclusion, these findings suggest that BFSP1 functions as a multifaceted prognostic biomarker and a potential therapeutic target for LIHC. Full article