Search Results (911)

Background/Objectives: Immune aging has been associated with survival outcomes in patients with lung adenocarcinoma (LUAD), but its relevance within the tumor microenvironment (TME) remains unclear. Methods: Clinical, RNA-sequencing, and somatic mutation data from the TCGA LUAD cohort were analyzed. Immune aging score within the TME was quantified using a predefined blood-driven 121-gene immune aging signature (IAS-121), and patients were categorized into the lowest versus the highest IAS-121 tertiles. Immune cell composition in the TME was inferred using xCell. Overall survival (OS) was evaluated using Kaplan–Meier analysis, Cox proportional hazards models adjusted for age, sex, tumor stage, smoking status, and EGFR mutation status, and restricted cubic spline analysis to examine the dose–response relationship between IAS-121 and mortality risk. Sensitivity analyses comparing the highest versus lowest quartiles or higher than median versus lower than median of IAS-121 were performed. Two independent LUAD cohorts (GSE68465 and GSE50081) were employed for validation. Results: A total of 518 patients with LUAD from the TCGA cohort were analyzed. Restricted cubic spline analysis showed a linear association between IAS-121 and OS. Patients in the highest IAS-121 tertile showed significantly better survival than those in the lowest tertile in both the TCGA cohort (p < 0.001) and the external validation cohorts (p = 0.003). In multivariable-adjusted Cox models, the lowest IAS-121 tertile was associated with worse survival in TCGA (adjusted HR 1.87, 95% CI 1.20–2.92) and in the pooled external cohorts (adjusted HR 1.57, 95% CI 1.02–2.43). Subgroup analyses showed generally consistent associations across clinical strata. Tumors with higher IAS-121 exhibited lower CD8⁺ and CD4⁺ naïve T-cell enrichment but higher neutrophil infiltration. Conclusions: Immune aging within TME is associated with poorer survival in LUAD. Given this study is hypothesis-generating, further investigations integrating tissue- and blood-based measures of immune aging are warranted to clarify its clinical and biological implications. Full article

Background: Cellular senescence is a key regulatory mechanism in tumor initiation and progression, influencing cancer development through modulation of the cell cycle, the immune microenvironment, and inflammatory responses. However, the molecular characteristics and potential clinical value of senescence-related genes in lung adenocarcinoma (LUAD) have not been systematically elucidated. This study aimed to comprehensively characterize the expression patterns, molecular subtypes, and prognostic significance of cellular senescence-related genes in LUAD, and to identify key regulatory determinants. Methods: Transcriptomic data of cellular senescence-related genes were obtained from The Cancer Genome Atlas (TCGA) cohort, and integrated analyses were performed to characterize their mutational landscape, copy number variations, and differential expression profiles. Senescence-related molecular subtypes were established using consensus clustering, followed by gene set variation analysis (GSVA) for pathway enrichment and immune infiltration analyses. A prognostic risk model was subsequently constructed using LASSO-penalized Cox regression, and its predictive performance was systematically evaluated. Candidate key regulators were further prioritized through bioinformatic screening, identifying FOLR1 as a hub gene. The biological function of FOLR1 was validated by qRT–PCR, Western blotting, assessment in clinical specimens, and a subcutaneous xenograft tumor model in mice. Results: Cellular senescence-related genes in LUAD exhibited a high frequency of somatic mutations and copy number alterations, accompanied by marked transcriptional dysregulation. Based on the expression profiles of these genes, LUAD patients could be stratified into three distinct molecular subtypes with significantly different clinical outcomes. These subtypes displayed pronounced heterogeneity in pathway enrichment patterns and immune cell infiltration. The subsequently developed prognostic signature demonstrated robust predictive performance in both the training and validation cohorts. Functional assays showed that FOLR1 was significantly downregulated in LUAD tissues and cell lines; FOLR1 knockdown promoted tumor cell proliferation, whereas restoration of its expression or pharmacological intervention markedly suppressed tumor progression. Consistently, in vivo xenograft experiments further corroborated the tumor-suppressive role of FOLR1 in lung adenocarcinoma. Conclusions: This study systematically delineated the molecular landscape of cellular senescence-related genes in LUAD and elucidated their associations with the tumor immune microenvironment and patient prognosis. Moreover, FOLR1 was identified as a potential tumor suppressor and therapeutic target. These findings provide a theoretical basis for senescence-informed molecular stratification and the development of precision treatment strategies in lung adenocarcinoma. Full article

Achromobacter spp. are opportunistic pathogens in people with cystic fibrosis (PwCF), yet the role of the upper airways in their persistence and adaptation remains poorly understood. We investigated whether the sinonasal compartment may act as reservoir and evolutionary niche for Achromobacter spp. during airway infection. Twenty-two isolates obtained from paired nasal lavage and sputum samples of seven PwCF were analysed by whole-genome sequencing. Within each PwCF, identical clone types were detected in both airway compartments, supporting bacterial exchange between upper and lower airways. Despite clonal relatedness, substantial genomic diversification was observed between paired isolates. Genomic signatures indicative of elevated mutation rates were detected in a high number of isolates (73%) and in both airway compartments, highlighting widespread genomic diversification across the respiratory tract. Mobilome analysis revealed compartment-specific variations in insertion sequences, prophages, and integrative elements, suggesting genome plasticity. Additionally, mutation in an aspartate kinase gene was consistently associated with loss of biofilm formation in vitro, highlighting a potential link between this pathway and biofilm phenotype. Overall, our findings indicate that upper and lower airways represent interconnected but partially independent ecological niches where Achromobacter populations can diverge during colonization, supporting the view that both compartments contribute to their persistence and evolution in CF airways. Full article

Background: Among primary intracranial neoplasms in adults, glioblastoma multiforme stands out for both its prevalence and its exceptionally invasive character. Uric acid-related genes (UARGs) may enhance tumor cell invasiveness and drug resistance by promoting oxidative stress responses. This study aimed to elucidate uric acid-driven mechanisms in glioblastoma, focusing on risk stratification and therapeutic vulnerability. Methods: Transcriptomic profiles of GBM were retrieved from TCGA and GEO repositories, followed by performing differentially expressed analysis, univariate Cox and LASSO regression, in order to screen prognostic UARGs and construct a risk model. Then, prognostic analyses were expanded by performing immune microenvironment analysis, drug sensitivity analysis, tumor mutation analysis, independent prognostic analysis, and nomogram construction. Additionally, dataset GSE162631 was interrogated to pinpoint pivotal cell subsets and to map intercellular communication as well as pseudo-time analysis. Results: A risk model incorporating six prognostic UARGs (TIMP1, PLAUR, CTSB, KLF10, RARRES2, and PTPRN) was constructed and identified as a favorable prognostic signature. Resting dendritic cells and drugs (including acetalax and trametinib) were found to be associated with GBM patients’ risk stratification. Low-risk patients showed relatively higher mutation rates of PTEN and TP53. A nomogram was developed based on RARRES2 and PTPRN, which exhibited favorable predictive performance for GBM prognosis. Furthermore, scRNA-seq profiling identified dendritic cells (DCs), macrophages, and T cells as key populations in the tumor microenvironment. Intercellular communication inference indicated relatively strong DCs-macrophage crosstalk, and pseudo-time analysis linked prognostic UARG expression to the differentiation trajectory of critical cell subsets. Conclusions: This study identified uric acid-related genes as potential independent indicators of clinical outcomes in glioblastoma progression. A novel prognostic UARG-associated signature was developed and validated, which showed potential in predicting GBM patient outcomes. Full article

Background/Objectives: X-linked Alport syndrome (XLAS) arises from pathogenic variants in COL4A5. Truncating variants are generally classified as severe, but whether clinically meaningful heterogeneity exists within this group remains unclear. This study aimed to establish a novel Col4a5 knock-in mouse model based on a clinical variant and to determine whether truncating mutation position influences disease severity. Methods: A de novo COL4A5 frameshift variant, c.2440delG, was identified in a patient with severe early-onset XLAS. A Col4a5-G814fs knock-in mouse was generated by CRISPR/Cas9 on the C57BL/6J inbred mouse strain background and compared with the established Col4a5-G5X nonsense model using survival analysis, serial functional measurements, kidney histopathology, transmission electron microscopy, and RNA sequencing. Results: The Col4a5-G814fs knock-in mouse was successfully generated and showed loss of glomerular α5(IV) collagen chain expression. Compared with G5X mice, G814fs mice exhibited shorter survival (median 141 vs. 161.5 days, p = 0.0004), earlier onset of proteinuria, and more severe kidney functional decline. By 16 weeks, G814fs mice also showed more severe glomerular basement membrane abnormalities and more extensive glomerulosclerosis. RNA sequencing revealed a shared inflammatory gene signature in both models, together with selective upregulation of genes related to the PPAR signaling pathway and fatty acid metabolism in G814fs kidneys. Conclusions: This study reports a novel de novo COL4A5 frameshift variant and establishes the first Col4a5-G814fs knock-in mouse model. Direct comparison with the G5X model shows that distinct truncating COL4A5 mutations can be associated with substantially different disease severity, providing a useful platform for future mechanistic and therapeutic studies in XLAS. Full article

Background: Glutaric acidemia type 1 (GA1) is an autosomal recessive neurometabolic disorder caused by pathogenic variants in glutaryl-CoA dehydrogenase (GCDH), with variable clinical severity despite early biochemical detectability. Population-specific mutational spectra and genotype–phenotype correlations remain insufficiently defined in infantile-onset disease. Therefore, this study aimed to define the GCDH variant spectrum in GA1 patients with mild hepatopathy and assess genotype–phenotype correlations. Methods: We performed integrated clinical, biochemical, and molecular characterization of 15 unrelated patients with infantile-onset GA1. Whole-exome sequencing (WES) was performed for all participants, and the resulting data were compared with the reference sequence of the GCDH gene. Results: All patients presented within the first 6 months of life with macrocephaly, seizures, dystonia, and feeding difficulties. Neurological impairment and mild hepatopathy were variably observed, and one patient developed an acute encephalopathic crisis. Six homozygous GCDH variants were identified, predominantly missense. A common variant, c.541G>C (p.Glu181Gln), accounted for 73.3% of cases and defined a consistent phenotype of early macrocephaly and movement disorder with frequent mild hepatic involvement, suggesting regional enrichment and raising the possibility of a founder effect that warrants confirmation in future haplotype studies. A truncating variant, c.382C>T (p.Arg128Ter), was associated with severe early encephalopathy. Exon 6 represented a mutational hotspot. Biochemically, all patients showed elevated urinary glutaric and 3-hydroxyglutaric acids, increased glutarylcarnitine, and low-to-normal free carnitine, with higher metabolite levels in clinically more severe cases. All variants were pathogenic or likely pathogenic and extremely rare in population databases. Conclusions: This cohort reveals a striking predominance of the GCDH c.541G>C variant and establishes a clear biochemical signature with genotype-associated clinical patterns in infantile-onset GA1. These findings support a population-specific mutational spectrum, refine genotype–phenotype correlations, and underscore the importance of early molecular diagnosis to guide targeted neurological and hepatic monitoring as well as regional screening strategies. Full article

Background/Objectives: Bud sports (somatic mutations) offer a quick way to develop new bougainvillea varieties by altering specific traits while keeping the desirable genetic background of the original cultivar. However, we still lack a comprehensive understanding of their genomic architecture and the molecular mechanisms behind their formation. This study aimed to characterize the population genomic characteristics of bud sports derived from the commercial variety Bougainvillea × buttiana ‘Miss Manila’. Methods: We employed genotyping by sequencing (GBS) on 39 accessions, including 27 bud sports and 12 conventional varieties. Population genomic analyses, such as principal component analysis (PCA), phylogenetic reconstruction, ADMIXTURE, and diversity statistics (π, He, Tajima’s D), were performed on 64,810 high-quality SNPs. Genome-wide scans for differentiation (FST) and selective sweeps (XP-CLR) were also conducted. Results: Bud sports showed significantly lower genetic diversity (π and He) than conventional varieties, which matches their clonal origin. PCA, phylogenetic, and ADMIXTURE analyses (optimal K = 4) revealed clear genetic differentiation and distinct population structures between the two groups. The bud sport population possessed fewer private alleles and a less negative Tajima’s D value. Genomic scans identified regions under selection in bud sports, with functional annotation pointed to genes involved in ubiquitin-mediated proteolysis and RNA transport. Notably, Bou_119143 (UDP-rhamnose rhamnosyltransferase 1) showed a high mutation frequency specifically in bud sports. Conclusions: We provide the first population-genomic evidence that bud sports of ‘Miss Manila’ are genetically distinct clonal lineages, shaped by somatic mutation and selection. These findings support bud sports as efficient sources for germplasm innovation. The identified genomic regions and candidate genes lay a foundation for future marker-assisted selection and molecular breeding in bougainvillea. Full article

Spinocerebellar Ataxia type 2 (SCA2) and Amyotrophic Lateral Sclerosis type 13 (ALS13) are triggered by polyglutamine expansion in Ataxin-2 (ATXN2). To understand these neurodegenerative disorders at the molecular level, the brains of 10-month-old Atxn2-CAG100-knockin mice were analyzed as microglial, astroglial and neuronal fractions via global RNA sequencing. Data were validated by comparison with the spinal cord oligonucleotide microarray profile or filtered by RNA-seq consistency. Here, we show that the mutation causes a massive inflammatory response in microglia and a reciprocal loss of neuronal transcripts in glial fractions, suggesting severe synapse loss. Beyond these general neurodegenerative signs, we identify pathognomonic changes in the machinery for protein translation and RNA splicing. Glial fractions showed upregulation of Gpnmb (to 2082%), Cst7, Clec7a, Axl, Csf1, Lgals3, Lgals3bp, Slc11a1, and Usp18 as an unspecific neuroinflammatory signature, versus downregulation of axonal Nefh (to <19%), and synaptic Scn4b, Camk2b, Rab15, and Grin1 mRNAs correlating with circuit disconnection. In all fractions, reductions in Kif5a, Rph3a, and Cplx1 were noted versus disease-specific inductions of ribosomal subunits, presumably mirroring the partial loss-of-function of ATXN2 as RNA translation modulator. Selective accumulations of embryonic factors Rnu1b2 and Eef1a1 versus downregulation of adult Eef1a2 specify the mutation impact on splicing and translation elongation. As a potential underpinning of toxic gain-of-function, the proteostasis transcript Rnf213 appeared increased in astroglial and microglial fractions. These transcriptome data suggest altered ribosomal and spliceosome machinery, with massive microgliosis versus mild astrogliosis, at the core of SCA2 and ALS13. Full article

Carcinoma showing thymus-like differentiation (CASTLE) is a rare malignancy arising in the thyroid or neck, with an uncertain cellular origin that complicates both diagnosis and treatment. To better understand its molecular underpinnings and identify potential therapeutic avenues, we conducted integrated whole-exome and transcriptome sequencing on six CASTLE and six thymic carcinoma samples. Whole-exome sequencing (WES) was performed on all 12 samples, while RNA sequencing was successful for 1 CASTLE and 6 thymic carcinoma samples. Our analysis included somatic mutation profiling, mutational signature deconvolution, differential gene expression, and characterization of tumor microenvironment for the cases with available data, with comparisons to genomic data from other thyroid cancers. CASTLE tumors demonstrated a higher median tumor mutational burden than thymic carcinoma and lacked the common BRAF and RAS mutations typically found in thyroid cancers. They harbored alterations in genes such as TRHDE, cilia-associated genes (ANKS6, CFAP46, DNAH6), and Wnt signaling components (TRRAP, BCL9L), as well as mutational signatures suggestive of mismatch repair deficiency and oxidative damage. MSIsensor-pro analysis of the WES data provided support for the potential for mismatch repair deficiency in a subset of CASTLE samples. Exploratory transcriptomic analysis from a single CASTLE case showed downregulation of thyroid follicular markers and an “immune-hot”, lymphocyte-rich microenvironment, closely resembling that of thymic carcinoma. While these findings require validation in larger cohorts, they support a thymic origin for CASTLE and establish its molecular distinction from follicular-derived thyroid cancers. The immunogenic tumor landscape suggests that immune checkpoint inhibitors, particularly those targeting PD-1/PD-L1, may be a promising therapeutic strategy, alongside emerging targets for precision oncology. Full article

Anti-analysis techniques, also known as evasive techniques, enable Windows malware to detect and evade dynamic inspection environments, undermining the effectiveness of virtual-machine and sandbox-based inspection. Despite extensive prior research, no unified classification has been paired with a large-scale empirical evaluation of static detection capabilities for these behaviors. This paper addresses this gap by presenting a comprehensive classification and detection framework. We consolidate 94 anti-analysis techniques from academic, community, and threat-intelligence sources into nine mechanistic categories and derive corresponding YARA rules for static identification. In total, 82 YARA signatures were authored or refined and evaluated on 459,508 malware and 92,508 goodware samples. After iterative refinement using precision thresholds, 42 rules achieved high accuracy (≥75%), 16 showed moderate precision (50–75%), and 24 were discarded due to unreliability. The results indicate strong static detectability for firmware- and BIOS-based checks, but limited precision for timing-based evasions, which frequently overlap with benign behavior. Although YARA provides broad coverage of observable artifacts, its static nature limits detection under obfuscation or runtime mutation; our measurements therefore represent conservative estimates of technique prevalence. All validated rules are released in an open-source repository to support reproducibility, improve incident-response workflows, and strengthen prevention and mitigation against real-world threats. Future work will explore hybrid validation, container-evasion extensions, and forensic attribution based on signature co-occurrence patterns. Full article

Adult acute lymphoblastic leukemia (ALL) is a highly heterogeneous hematologic malignancy where treatment response and relapse risk do not exclusively rely on the identification of genetic lesions but also on dynamic biological states sustained by specific transcriptional and epigenetic programs. Although the integrated application of multi-omics approaches has significantly expanded our knowledge of oncogenic dependencies, cellular plasticity, and mechanisms of therapeutic resistance, its systematic translation into the clinical practice of adult ALL is yet to become a reality. The aim of this review is to provide a critical and focused synthesis on how the integration of genomics, transcriptomics, and epigenetics enables the interpretation of disease biological behaviors and may guide personalized therapeutic strategies while simultaneously addressing the major limitations that hinder clinical implementation. Genomics allows for the identification of driver events and pharmacologically actionable vulnerabilities, whereas transcriptomics, including single-cell analyses, reveals functional states associated with clonal persistence, glucocorticoid resistance, and therapeutic adaptation, even in the absence of new mutations. In parallel, epigenetic signatures emerge as key elements in stabilizing oncogenic programs and resistant phenotypes, contributing to the biological plasticity of leukemic cells and representing potentially reversible therapeutic targets. Taken together, multi-omics signatures provide an integrated functional readout of adult ALL and support a dynamic precision-medicine model. However, adaptive therapeutic decisions aimed at relapse prevention require the full integration of these approaches through standardized strategies, longitudinal studies, and a sustainable implementation of molecular profiling and minimal residual disease monitoring. Full article

Background: Familial prostate cancer (PCa) accounts for nearly 20% of all PCa cases and is associated with increased genetic susceptibility and earlier disease onset. However, early detection and risk stratification in genetically predisposed individuals remain challenging. Circulating cell-free DNA (cfDNA) provides a minimally invasive source of tumor-derived genomic and epigenomic information. Integrating multi-omic cfDNA analyses may enhance the discovery of biomarkers relevant to familial PCa biology. Methods: We conducted a pilot feasibility study employing whole-genome, strand-specific sequencing of cfDNA from eight patients with familial PCa. A unified analytical pipeline was used to jointly profile genomic alterations and epigenomic features. Variant calling, methylation mapping, and allele-specific methylation (ASM) analysis were performed to identify somatic mutations, characterize epigenetic dysregulation, and explore potential interactions between genetic and epigenetic mechanisms. Results: Sequencing revealed 18,878 genetic variants, including 2276 potentially pathogenic alterations. We identified 26 recurrent high-impact mutations, such as stop-gain and start-loss variants, in genes including MUC4, MCM9, and SKA3. Epigenomic profiling demonstrated widespread gene-specific hypermethylation, consistent with transcriptional repression in these loci. ASM events were detected in TTC22, TEX51, WDR89, LAIR2, and SKA3, suggesting coordinated interactions between somatic variation and epigenetic regulation in familial PCa. Conclusions: This proof-of-concept study highlights the feasibility and potential of integrating whole-genome and epigenome profiling of cfDNA to decode the molecular architecture of familial prostate cancer. By jointly capturing genomic alterations and epigenetic signatures, including allele-specific methylation, this multi-omic liquid biopsy approach supports a high-resolution exploration of biologically relevant molecular features. Moreover, this integrated profiling strategy provides a minimally invasive and clinically scalable tool that may substantially improve risk assessment. These findings offer a promising foundation for future validation studies in larger cohorts, with the aim of advancing multi-omic cfDNA analysis as a next-generation technology in the field of precision oncologic epigenetics. Full article

Feline panleukopenia virus (FPV) is a major feline pathogen, but canine-derived FPV variants have recently been identified. Here, we compared the pathogenicity of a canine-derived FPV strain in cats with that of a lethal feline-derived FPV strain and evaluated the evolutionary significance of its NS1 mutations. Kittens infected with the canine-derived strain developed only mild, self-limiting diarrhea without fever or mortality, whereas those infected with the feline-derived strain developed severe disease and reached humane endpoints by 9 dpi. The canine-derived strain caused prolonged fecal shedding from 6 to 38 dpi but only low tissue viral loads (10¹–10³ copies/g), while the feline-derived strain reached markedly higher loads (10³–10⁶ copies/g), particularly in the ileum, jejunum, and lungs. Viral DNA levels in the lungs, ileum, caecum, and rectum were significantly higher in the feline-derived group. Sequence analysis identified four NS1 mutations, 115I, 132L, 247Q, and 595Q, which showed stepwise evolutionary accumulation and signatures of positive selection. These findings indicate that canine-derived FPV retains infectivity in cats but exhibits attenuated pathogenicity and reduced replication fitness, highlighting NS1 as a potential determinant of host adaptation. Full article

Background: Follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL) exhibit substantial heterogeneity, reflecting the diversity of the germinal center (GC). Histologic transformation of FL to DLBCL is associated with poor prognosis, yet robust biomarkers predicting transformation remain limited. Methods: We integrated single-cell DNA sequencing, single-cell RNA sequencing, and spatial transcriptomics in diagnostic lymph-node biopsies from non-transformed FL (ntFL), transformed FL (tFL), and DLBCL to characterize clonal states and immune niches in GC lymphomas. T-cell signatures associated with transformation were evaluated in an independently published single-cell FL dataset. Results: Transcriptional profiling revealed similarities between tFL and DLBCL, consistent with a GC-related malignant program. The tFL microenvironment showed enrichment of exhausted CD4⁺ regulatory and CD8⁺ effector T cells, together with CD4⁺ follicular helper T cells (Tfh) displaying an adhesion-related phenotype. Spatial analysis suggested increased proximity of exhausted/immunosuppressive T cells and enhanced Tfh-B-cell interactions in tFL compared with ntFL. These immune signatures were also observed in an external cohort and were associated with early transformation. In addition, clonal hematopoiesis-associated mutations were detected in microenvironmental cells across samples, suggesting a potential contribution to the lymphoma microenvironment. Conclusions: This work demonstrates the feasibility of integrating single-cell and spatial analyses in GC lymphomas and provides a framework for investigating tumor heterogeneity and immune organization. These findings may inform future studies on biomarker development and the rational design of immunotherapies. Full article

Lumpy skin disease virus (LSDV) is a large DNA capripoxvirus that causes LSD, a disease that has major economic impact. Since 1989, several sporadic outbreaks were reported in Israel, with the latest outbreaks in 2012, 2019 and 2023. Although considered genetically stable, LSDV shows a high degree of genetic recombination events and genetic variations. In particular, in-frame nonsense mutations were suggested to act as one of the main evolutionary drivers of outbreaks. Whole-genome sequencing of LSDV isolates from the 2019 and 2023 outbreaks was used for genomic analysis using various bioinformatics tools to characterize the genomic evolution, recombination events and micro-evolutionary forces shaping LSDV in Israel by comparing isolates. Comparative genomic analysis revealed substantial nucleotide substitutions in the 2019 and 2023 isolates relative to the 2012 isolate. Specifically, increased nucleotide mismatches, inter-genic deletion, enhanced APOBEC editing signatures and elevated codon usage. Additionally, numerous mutations were recognized, leading to structural disruptions in specific viral proteins and possible RNA instability. In conclusion, this analysis supports that nucleotide substitutions, codon selection pressure and APOBEC-associated editing had driven local microevolution of LSDV during the years between outbreaks despite the absence of clinical indications and major vaccination campaigns. Furthermore, genomic evidences of recombination events between the 2012 and 2019 isolates suggests that these processes may have contributed to the emergence of the variant identified during the 2023 outbreak. Full article