Search Results (8,373)

Background/Objectives: The therapeutic landscape of advanced or metastatic urothelial carcinoma (UC) has shifted from platinum chemotherapy to precision immuno-oncology. Immune checkpoint inhibitors (ICIs)—pembrolizumab, nivolumab, and avelumab—show efficacy across platinum-refractory, maintenance, and adjuvant settings, yet benefit is limited to subsets, underscoring the need for biomarkers. Antibody–drug conjugates (ADCs), notably enfortumab vedotin(EV), and targeted agents such as FGFR inhibitors further expand options. This review synthesizes current evidence and emerging paradigms to guide combinations and sequencing. Methods: We performed a narrative synthesis of peer-reviewed trials (emphasizing pivotal phase III studies), key translational investigations, and contemporary guidelines on ICIs, ADCs, HER2-directed therapies, FGFR inhibitors, molecular subtyping, and genomic profiling in UC, integrating efficacy signals, biomarker associations, and practical implications for sequencing. Results: ICIs now occupy multiple settings, but heterogeneous benefit highlights the importance of molecularly informed selection. EV alone and with pembrolizumab has produced unprecedented first-line activity, prompting a strategic shift. Molecular subtyping and genomic profiling delineate phenotypes with variable immune responsiveness and targetable vulnerabilities, enabling rational combinations and refined sequencing. Ongoing trials are evaluating next-generation ADCs, HER2-directed approaches, and dual checkpoint blockade to achieve durable, personalized disease control. Conclusions: Management of locally advanced or metastatic UC is converging on precision immuno-oncology, wherein biomarker-driven selection, molecular subtyping, and thoughtful sequencing of ICIs, ADCs, and targeted agents are central to optimizing outcomes. Active trials and translational advances are expected to refine personalized strategies and embed molecular guidance into routine care. Full article

Introduction: Klebsiella variicola, a member of Klebsiella pneumoniae complex, has emerged as an opportunistic pathogen for human infection; however, antimicrobial resistance and hypervirulent characteristics of K. variicola have rarely been investigated in South Korea. Methods: We analyzed 76 clinical K. variicola isolates collected from 12 hospitals between September 2022 and October 2023. Bacterial identification was performed by MALDI-TOF MS. Antimicrobial susceptibility was tested by disk diffusion tests. Resistance determinants and virulence traits were investigated, and whole-genome sequencing was performed for hypermucoviscous or carbapenem-resistant K. variicola isolates. Results: Most (89.5%, 68/76) were susceptible to all 18 antimicrobials tested in this study, and 3 isolates harbored bla_CTX-M-15. One isolate carried bla_KPC-2 on its IncX3 plasmid, which is closely related to carbapenem-resistant K. pneumoniae plasmids. Capsular typing revealed 51 wzi allelic types. Ten isolates showed mucoid phenotype, mainly with KL60 and KL61. Conclusions: This study reveals relatively low resistance rates in K. variicola strains but the presence of multidrug-resistant and hypermucoviscous K. variicola strains. In addition, the evidence of interspecies dissemination of bla_KPC-2 highlights the need for continuous genomic surveillance. Full article

Background/Objectives: Lyme disease diagnosis remains challenging due to the limitations of current methods. While PCR-based assays are widely used, their sensitivity can be affected by sample type and the inhibition of host DNA. This study aimed to evaluate the feasibility and sensitivity of a CRISPR/Cas12-based detection system for Borrelia burgdorferi sensu lato, comparing its performance with real-time PCR. Methods: DNA from three Borrelia genospecies (B. burgdorferi, B. garinii, and B. afzelii) was amplified targeting the OspA gene. Detection was performed using a Cas12/crRNA system with a fluorescent ssDNA reporter. Sensitivity assays were conducted on serial dilutions of Borrelia DNA, with and without human genomic DNA, and results were compared with qPCR. Results: Direct detection of Borrelia DNA without amplification was not feasible. However, when combined with PCR, the Cas12/crRNA system reliably detected as few as 5 genome copies per reaction. End-point PCR extended to 60 cycles improved detection robustness for B. garinii and B. afzelii, although sensitivity decreased in the presence of human genomic DNA. Conclusions: The Cas12/crRNA-based system offers a sensitive and accessible alternative to qPCR, especially in settings lacking real-time PCR instrumentation. Future developments may include integration with isothermal amplification and microfluidic platforms to enhance direct detection capabilities. Full article

Background: Seminoma is a malignant germ cell tumor that most commonly involves the testicles but may involve the mediastinum, the retroperitoneum, and other extra-gonadal sites as well. This study aims to investigate the somatic genomic landscape of seminoma. Methods: Data for a retrospective observational analysis of seminoma was acquired from the American Association for Cancer Research (AACR) Project Genomics Evidence Neoplasia Information Exchange (GENIE) with clinical and genomic data from 2017 and beyond. Using the R and R Studio software (R 4.5.0), analyses for common somatic mutations and copy number alterations were run with a statistical significance of p < 0.05. Results: The most mutated genes included KIT (22.6%), KRAS (17.1%), and MTOR (5.1%), with significant copy number alterations in CDKN1B (17.2%), KRAS (14.7%), CCND2 (10.3%), and H3F3C (9.8%). These suggest involvement within the KIT/RAS/MAPK and PI3K/AKT/mTOR (PAM) pathways for seminoma development. A novel finding within comparative evaluation of PMS1 and AMER1 mutations were found in Black individuals. Additionally, our findings were consistent with a lower testicular cancer rate among individuals with African ancestry than European ancestry. BRD4 mutations were found only in metastatic samples while KMT2C, STAG2, ALK, AXL, and EGFR were only found in primary samples, suggesting a possible association. Conclusions: This study provided a comprehensive molecular and genetic profiling of seminoma including key genetic alterations, affected pathways, and potential therapeutic strategies. Moreover, overlap between pathways and gene mutations provides the potential for alternative treatment options for seminoma via multiple pathways. Full article

(1) Background: The BMP/GDF (Bone Morphogenetic Protein/Growth Differentiation Factor) subfamily (Decapentaplegic-Vg1-related, DVR) within the transforming growth factor beta (TGF-β) superfamily plays critical roles in governing biological developmental processes and physiological functions. (2) Methods: In this study, we systematically investigated the DVR gene family in hexaploid Qihe gibel carp (Carassius gibelio var. Qihe) through comprehensive genomic identification, phylogenetic analysis, chromosome mapping, and cis-regulatory element prediction. The experimental design for gene expression analysis involved collecting samples from multiple tissues (brain, muscle, liver, kidney, etc.) and different developmental stages (20, 45, and 60 days post hatching, dph) to examine the expression patterns of four GDF8 genes using quantitative real-time PCR (qRT-PCR). (3) Results: We identified 50 DVR members in Qihe gibel carp. Phylogenetic analysis classified the 50 DVR family members into 20 distinct protein types, with 29 BMPs (Bone Morphogenetic Proteins) and 21 GDFs (Growth Differentiation Factors) identified. All 50 DVR proteins of Qihe gibel carp have similar TGF-β domains except for four BMP1 proteins. Chromosomal localization revealed widespread distribution of DVR members across 36 chromosomes, a pattern potentially linked to the hexaploid genome of Qihe gibel carp. Genes within the same subgroup exhibited conserved intron–exon architectures and similar intron numbers; syntenic conservation within subgroups may reflect functional constraints after polyploidization, implying evolutionary pressure to maintain functional domains. Through spatiotemporal expression profiling, we uncovered functional divergence among four GDF8 (myostatin) paralogs: GDF8-1 and GDF8-2 were predominantly expressed in brain and muscle tissues (dorsal and caudal), while GDF8-3 and GDF8-4 showed hepatic, cerebral, and renal specificity. Intriguingly, all paralogs exhibited a gradual upregulation during late development (20–60 days post hatching, dph), with peak expression staggered between 45 dph (GDF8-1/2) and 60 dph (GDF8-3/4). (4) Conclusions: These findings suggest that GDF8 plays a critical regulatory role in the growth and development of Qihe gibel carp. Collectively, these results provide a foundation for further investigations into the functional roles of the DVR gene family during the ontogenetic development of this species. Full article

Background/Objectives: Despite the growing understanding of the relationship between the genome and nutrition, clearly defined and evidence-based clinical guidelines remain insufficient. The objective of this review was to identify and compile all available European guidelines related to the impact of genetic predisposition on nutritional recommendations in the field of gastroenterology. Methods: A review of guidelines and position papers issued by four European organisations [the European Crohn’s and Colitis Organisation (ECCO), the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN), the European Society for Clinical Nutrition and Metabolism (ESPEN), and United European Gastroenterology (UEG)] was conducted for the past ten years. Results: Out of 5196 recommendations and statements extracted from 124 manuscripts, only 13 highlighted a link between genetic predisposition and dietary factors in clinical gastroenterology. From the available guidelines, there is no clear trend indicating an increased focus on genetic background and its association with nutrition in recent years. Conclusions: There is a critical opportunity for European organisations to develop an evidence-based information framework, guided by clinical protocols, in order to integrate the large volume of genetic data into clinical practice and personalised care of individuals with gastrointestinal disorders. Full article

Background: G-quadruplexes (G4s) are non-canonical higher-order nucleic acid structures that form at guanine-rich motifs, with features spanning both secondary and tertiary structural levels. These dynamic structures play pivotal roles in diverse cellular processes. Endogenous G4s (eG4s) function through their dynamically formed structures, prompting the hypothesis that their thermostability, as a key structural property, may critically influence their functionality. This study investigates the relationship between G4 stability and other functional genomic signals within eG4 regions and examines its broader impact on chromatin organization and transcriptional regulation. Methods: We developed a mapping strategy to associate in vitro-derived thermostability metrics and multi-omics functional signals with eG4 regions. A stability-centric analytical framework combining correlation analysis and causal inference using the Bayesian networks was applied to decipher causal relationships between G4 stability and the other related signals. We further analyzed the association between the stability of transcription start site (TSS)-proximal eG4s and the biological functions of their downstream genes. Results: Our analyses demonstrate that G4 thermostability exerts causal effects on epigenetic states and transcription factor binding, thereby influencing chromatin and transcription regulation. We further show distinct network architectures for G4-binding versus non-binding transcription factors. Additionally, we find that TSS-proximal eG4s are enriched in genes involved in core proliferation and stress-response pathways, suggesting that eG4s may serve as regulatory elements facilitating rapid stress responses through genome-wide coordination. Conclusions: These findings establish thermostability—though measured in vitro—as an intrinsic property that shapes eG4 functionality. Our study not only provides novel insights into the functional relevance of G4 thermostability but also introduces a generalizable framework for high-throughput G4 data interpretation, significantly advancing the functional decoding of eG4s across biological contexts. Full article

Background/Objectives: Next-generation sequencing (NGS)-based molecular profiling has revolutionized personalized medicine and unlocked new treatment options for cancer patients. Clinical guideline bodies agree that patients diagnosed with HR+/HER2− metastatic breast cancer (mBC) may benefit from comprehensive somatic genomic profiling to identify candidates for established targeted therapies and clinical trials, yet many patients are not receiving it due to a lack of widespread access to NGS. Methods: To better understand the perceived barriers (if any) to NGS tests in mBC, a study was conducted across multiple stakeholders including medical oncologists, nurses, physician assistants, lab directors, pathologists, payers, and patients. Results: This study revealed that despite the awareness and recognition of the value proposition of NGS-based molecular profiling in mBC, inconsistent payer coverage, high out of pocket costs for patients, and challenges in managing reimbursement and prior authorization processes can lead to suboptimal utilization of NGS, which can subsequently lead to suboptimal treatment decisions where approved therapies exist. Interestingly, many payers (33%) were not aware of the current somatic biomarker testing recommendations from NCCN guidelines. As a result, payers identified the lack of clear clinical guidelines (74% ranked as top 3), the lack of internal consensus on which NGS tests to cover (45%), and the absence of internal expertise on NGS (39%) as the primary hurdles for broader NGS access. Conclusions: The results suggest that widespread HCP and payer education on clinical guidelines (e.g., NCCN) and utility for targeted therapy selection is crucial for enhanced adoption of NGS-based molecular profiling in mBC. Full article

Preimplantation genetic testing for monogenic disorders (PGT-M) is a powerful tool for identifying genetic disorders prior to gestation. For hemoglobinopathies like thalassemias and sickle cell disease, PGT-M offers a preventative strategy to ensure that only embryos deemed genetically healthy are transferred. A comprehensive review of 22 original articles explores and summarizes the existing evidence on PGT-M techniques in hemoglobinopathies. The review focuses on key aspects such as accuracy, benefits, and drawbacks related to various hemoglobinopathies. Given the limited quantity of DNA obtained from an embryo biopsy, whole genome amplification (WGA) is a critical step for amplifying the sample. One of the available methods of WGA, multiple displacement amplification (MDA) is one of the most widely adopted method with acceptable allele drop-out (ADO) rates for hemoglobinopathies compared with traditional methods. Dealing with ADO constitutes a primary technical obstacle in PGT-M. The failure to amplify one allele in single-cell analysis is a major factor limiting the overall diagnostic accuracy of the procedure. To mitigate this issue, PCR-based and next-generation sequencing (NGS)-based approaches are employed. These methods incorporate linkage analysis with genetic markers such as short tandem repeats (STRs) or single-nucleotide polymorphisms (SNPs) to reduce the risk of incorrect interpretations from ADO and enhance the proportion of conclusive results. A future direction for PGT-M that involves the development of non-invasive methods (niPGT) will be included and discussed. Full article

Backgroud. Kocuria are widespread Gram-positive bacteria. Although they are traditionally classified as non-pathogenic, recent studies have shown that they can cause problems in various fields, from livestock and aquaculture to medicine. This has led to an increased need to understand their antibiotic resistance mechanisms in order to combat them. Methods. To study the determinants of Kocuria antibiotic resistance, we used bioinformatics methods. To identify antibiotic resistance genes, we retrieved the complete genome sequences of Kocuria strains from the RefSeq database and screened them for antibiotic resistance determinants with different mechanisms of action. We also studied Kocuria strains in more detail: we sequenced whole genomes of K. carniphila 988, K. rhizophila 155, K. rosea 394 and K. rosea 397, and, in addition to bioinformatics studies, and tested five strains for their ability to grow in the presence of antibiotics. Results. For these five strains, the presence of antibiotic resistance genes in their genomes correlated well with the observed resistance to the corresponding antibiotics: all 5 studied strains have a high level of resistance to chloramphenicol, in addition, K. carniphila 988 is highly resistant to azithromycin and avilamycin. Conclusions. Therefore, it has been demonstrated that antibiotic resistance genes are present in many Kocuria genomes and these genes are functional in the strains we have studied. Full article

Background/Objectives: Legionella micdadei is a clinically significant species within the Legionella genus, requiring accurate detection methods, surveillance, and precise clinical diagnosis. Our objective was to develop a sensitive polymerase chain reaction (PCR) assay specific for L. micdadei to detect its presence in environmental specimens. Methods: We targeted the 23S–5S intergenic spacer region, which can differentiate Legionella spp. We tested the detection of L. micdadei with 20 strains and determined the limit of detection with 2 strains. We verified assay specificity with 17 strains of other Legionella spp., 62 strains of other bacterial and fungal genera, and three human DNA specimens. We evaluated intra- and inter-run precision. We tested 15 environmental specimens (water, swabs of water faucets, mulch, and soil) by PCR. Results: The PCR assay demonstrated 100% analytical specificity (no cross-reactivity with non-targeted species), 100% inclusivity (detection of all L. micdadei strains), and high precision, with a coefficient of variation ≤ 2% across replicates. The limit of detection was estimated at 5 genomic DNA copies per reaction. We detected L. micdadei in environmental specimens. Conclusions: This PCR assay enables accurate detection of L. micdadei and is not subject to competition with other Legionella spp., thereby addressing limitations of current broad-spectrum Legionella approaches. The evaluation supports its application in environmental detection for surveillance. Full article

Background: Cardiovascular diseases remain a leading cause of death worldwide, yet the prevalence of pathogenic and likely pathogenic genetic variants associated with them is still underassessed in some populations. This study aimed to assess the frequency and geographic distribution of such variants within a representative sample of the Russian population. Additionally, it explored potential links between genotype and phenotype in a cohort of long-lived adults. Methods: We analyzed whole-genome sequencing data from 75,144 adults and 2,872 individuals aged 90 and older. Variants within 37 ACMG v3.1 genes were examined using InterVar, focusing on nonsynonymous variants and indels across exons and splicing sites. Variants were grouped based on ClinVar (as of 24 April 2023) annotations, with most subjected to manual review to confirm their significance. Results: Among the adult participants, 3,817 (5.1%) carried at least one of the variants under consideration. Of these, 141 (0.19%) carried pathogenic, 580 (0.77%) likely pathogenic, and 3,127 (4.16%) variants of uncertain significance. Variants not registered in ClinVar were found in 1,782 individuals (2.37%). Notably, one participant with cardiomyopathy carried a heterozygous TTN variant. In the long-lived cohort, 15 variants were classified as pathogenic or likely pathogenic, alongside 72 uncertain variants; overall, 19 individuals (0.66%) carried pathogenic or likely pathogenic variants. No significant difference was observed in variant frequency between the adult and long-lived groups. Conclusions: This study provided essential insights into the prevalence and geographic distribution of cardiovascular disease-related variants in Russia, laying the foundation for targeted genetic screening disease prevention strategies within this population. Full article

Background/Objectives: Uterine leiomyomas (ULs) and breast fibroadenomas (FAs) are the most common benign tumors in women, both arising in hormone-responsive mesenchymal tissues and often co-occurring during reproductive years. Despite their shared hormonal sensitivity and frequent MED12 mutations, their downstream molecular evolution remains poorly characterized. This study aimed to investigate whether ULs and FAs, though initiated by similar genetic alterations, diverge in their oncogenic trajectories, thereby addressing the molecular basis for their distinct clinical behaviors. Methods: We performed whole-exome sequencing (WES) on 15 uterine leiomyomas and 7 publicly available fibroadenomas with matched normal controls to compare somatic mutations, copy number alterations (CNAs), and mutational signatures. All UL samples were derived from Korean patients who underwent surgical treatment at a tertiary hospital between 2017 and 2019. Somatic variants were analyzed using MuTect2 and Strelka2. FACETS was used to estimate copy number changes in individual samples, and GISTIC2 to identify recurrent and statistically significant copy number alterations across patient cohorts. Mutational processes were inferred using SigProfiler. Microsatellite instability status was determined with MSIsensor2. The study was approved by the Institutional Review Board (UC17SNSI0092). Results: Comparative whole-exome sequencing of 15 ULs and 7 FAs from matched tumor-normal samples in an East Asian cohort confirmed both tumor types harbor identical MED12 p.G44D mutations, establishing shared molecular initiation. However, post-initiation evolution diverged dramatically: ULs exhibited chromosomal instability with 15 copy number amplifications, 6 of which affected oncogenes, but relatively modest point mutations. In contrast, FAs remained chromosomally stable but hypermutated, harboring 1.47× more variants than ULs despite lower tumor purity. Notably, one histologically benign FA harbored multiple loss-of-function mutations plus an EGFR gain-of-function mutation typically associated with malignant breast cancer, challenging traditional benign-malignant classifications. Conclusions: Despite sharing a common initiating mutation in MED12, ULs and FAs evolve through fundamentally distinct genomic pathways. UL evolves through chromosomal instability, whereas FA evolves through a mutator phenotype, with important implications for understanding tumor biology and molecular-based risk stratification. These findings support a paradigm of tissue-specific oncogenic evolution and underscore the potential clinical utility of genomic profiling in distinguishing benign tumors with atypical molecular features. Full article

Background/Objectives: The aims of this study are to define the roles of the neurotrophic tyrosine receptor kinase genes NTRK1, NTRK2 and NTRK3 (NTRK1/2/3) in CRC and to determine the clinicopathological, molecular, cancer signalling and potential predictive significances of NTRK1/2/3 expression in CRC, irrespective of NTRK gene fusion. Methods: Standard statistical tests in SPSS were utilised to interrogate the associations and correlations between NTRK1/2/3 expression and clinicopathological, molecular and genomic features in two CRC cohorts. NTRK1/2/3 expression deregulation was also investigated using correlation and regression analyses. Furthermore, gene set enrichment analysis (GSEA) and pathway/drug ontology enrichment analysis (POEA/DOEA) were utilised to interrogate the enrichment of cancer signalling pathways, as well as NTRK and other tyrosine kinase inhibitor response in the CRC cohorts. Results: Whilst NTRK1 expression was higher in the CRC subset with microsatellite instability, NTRK2/3 expression was preferentially overexpressed in the microsatellite stable subsets. Moreover, there was differential NTRK1/2/3 expression with respect to clinicopathological and molecular/genomic indices. In addition, this study demonstrated that NTRK1/2/3 expression was deregulated by a combination of copy number alterations (NTRK2), aberrant methylation (NTRK1/2/3) and potentially and cryptic gene fusion (NTRK3). Furthermore, GSEA and POEA demonstrated that NTRK1/2/3-high CRC subsets exhibited enrichment of and cross-talks among the NTRK signalling pathways, as well as of known cancer signalling pathways. The GSEA and DOEA showed that NTRK signalling was enriched for kinase inhibitors responses, representing evidence that NTRK1/2/3 expression may serve as biomarkers for multiple kinase inhibitors, including entrectinib—the tissue-agnostic kinase inhibitor for cancers with NTRK gene fusions. Conclusions: The results demonstrated that fusion-negative NTRK signalling may be active in CRC and may contribute to the molecular pathogenesis and biology of the disease. The results also demonstrated that the NTRK1/2/3 expression may be predictive multiple kinase inhibitors. Full article

Invertase, a core catalyst in sugar metabolism, irreversibly hydrolyzes sucrose into hexoses, establishing the fundamental biochemical pathway for carbon allocation in plants and playing pivotal roles in plant growth development, fruit quality regulation, and stress response. In the present study, we identified a total of 25 invertase genes from the kiwifruit (Actinidia chinensis cv Hongyang) genome and systematically analyzed the physicochemical properties, chromosomal localization, genomic features, and gene evolution patterns of the AcINV family. The evaluation of selection pressure indices robustly demonstrated that the INV family underwent purification selection during domestication. Furthermore, based on the correlation between gene expression levels during the post-harvest ripening stage of kiwifruit and soluble sugar content, we identified the potential gene AcCWINV4 as being associated with sugar accumulation. Furthermore, virus-induced gene silencing (VIGS) of AcCWINV4 confirmed its functional role in fruit sugar accumulation and plant response to cold stress. This study provides critical theoretical support for breeding cold-tolerant and high-quality kiwifruit varieties using molecular biological methods. Full article