Search Results (2,103)

Bartter syndrome (BS) represents a group of rare, autosomal recessive renal tubular disorders characterized by hypokalemic hypochloremic metabolic alkalosis, secondary hyperaldosteronism, and normal to low blood pressure. The underlying pathophysiology is primarily driven by defects in critical ion transport proteins or channels localized within the thick ascending limb of the loop of Henle, leading to impaired salt reabsorption. Recent advances in molecular genetics have refined the classification of Bartter syndrome. Current evidence supports SLC12A1, KCNJ1, CLCNKB, BSND, and MAGED2 as the core disease genes within the contemporary BS spectrum, with MAGED2 causing a distinct X-linked transient antenatal form. In contrast, gain-of-function CASR variants, historically labeled “type V Bartter syndrome”, are now more appropriately described as CaSR-associated Bartter-like phenotypes within the broader spectrum of disorders of calcium homeostasis. Despite significant progress, two primary research limitations remain. First, fully elucidating genotype–phenotype correlations and overcoming diagnostic complexities continues to be highly challenging due to substantial phenotypic overlap and genetic heterogeneity. Compounding these diagnostic hurdles is the equally critical challenge of understanding mutation-driven pathogenic mechanisms to develop viable clinical interventions. This review systematically summarizes the current molecular genetic landscape of BS to address these gaps. We highlight the relationships between specific genetic variants and clinical manifestations, delve into molecular pathophysiology including protein misfolding and trafficking defects, and explore emerging therapeutic approaches such as molecular chaperones. By integrating genetic and clinical data, this work aims to provide a comprehensive framework to facilitate precise diagnosis and individualized treatment strategies, ultimately advancing precision medicine in the management of Bartter syndrome. Full article

Background: The STAG1 gene has been related to a poorly known form of intellectual disability, known as Intellectual Developmental Disorder, Autosomal Dominant 47 (MRD47). Functionally, MRD47 is part of the Cohesinopathies, a small family of rare genetic disorders caused by defective cohesin complex, whose activity is essential for sister chromatid cohesion and therefore for chromatin organization. Chromatin state modulation is an entangled process finely modulated by a large number of actors that, if altered, give rise to the so-called Chromatinopathies. The clinical and biological overlap among these families of conditions on one hand poses significant challenges during diagnostic definition, and, on the other, may help delineate more accurate management guidelines. Methods: Starting from the report of a novel pathogenic variant in the STAG1 gene, we performed a retrospective clinical and molecular review of all previously reported patients affected by this rare disorder. Once clinical and photographic data of all published patients were collected, we used Face2Gene deep learning technology to analyze STAG1 facial phenotype, comparing it to both Chromatinopathy and Cohesinopathy profiles. Results: Our clinical and molecular re-evaluation of reported cases confirms MRD47 as a mainly neurodevelopmental disorder. Through artificial intelligence technology, we were able to first create the gestaltic profile of MRD47. Face2Gene analyses of this composite phenotype, although limited by the tool’s analysis modalities, demonstrates the strong overlap of STAG1 disorder with Chromatinopathies. Conclusions: The present literature review, together with gestaltic analyses of the STAG1-related phenotype, underscores the strong resemblance of MRD47 to epigenetic machinery disorders. The present case brings to light once more the biological and phenotypical entanglement of Cohesinopathies and Chromatinopathies, hinting at STAG1 as the joining chain. Full article

Background: Antimicrobial resistance is a One Health problem driven by the intricate interactions across human, animal, and environmental interfaces that enable microbial exchange and movement of mobile genetic elements encoding resistance and virulence. This study investigated the genomic epidemiology of ESBL and non-ESBL Escherichia coli across One Health interfaces in Oman. Methods: This prospective cross-sectional study analyzed 295 non-duplicate Escherichia coli isolates derived from 104 clinical, 173 animal [diseased (123) and healthy (50)], 14 sewage and four water sources. Antimicrobial susceptibility testing was performed phenotypically, and a representative subset of 50 ESBL and non-ESBL Escherichia coli from the three interfaces underwent whole genome sequencing to determine MLST, phylogroups, resistance genes, virulence determinants and plasmid replicons. Results: ESBL prevalence was highest in human isolates (73%), followed by sewage (28.6%) and animals (16.3% diseased; 8% healthy). blaCTX-M-15 predominated in humans, whereas blaCTX-M-55 dominated in animals and sewage, suggesting ecological partitioning with partial overlap. Quinolone resistance was lowest in the animal interface. Sewage isolates harbored the most complex resistome, including rmtB and plasmid-mediated quinolone resistance genes. MLST analysis revealed high diversity in human isolates, including globally recognized ExPEC lineages (ST10, ST38, ST73, ST127, ST131), while ST224 dominated in animals with evidence of possible spillover to humans. ST167 was confined to sewage, consistent with environmental maintenance of high-risk clones. Phylogroup structuring showed predominance of A, B2 and D among human isolates and A, B1, and E among animal and sewage isolates. Virulence profiling demonstrated broader virulome diversity in humans, but shared core determinants (fimH, sitA, traT) across all domains. IncFIB(AP001918) was the dominant plasmid replicon, particularly among ESBL isolates, underscoring its role in horizontal gene dissemination. Alarmingly, mutation in pmrB (V161G) was identified in a healthy animal isolate, pointing to a need for greater colistin restriction in animal husbandry. Conclusions: This study highlights plasmid-mediated resistance and shared virulence determinants linking reservoirs; although AMR profile was quite distinct across the three interfaces, human isolates demonstrated greater resistance than animal isolates, suggesting healthcare-driven AMR in Oman. Continued integrated genomic surveillance is essential to monitor gene flow and inform coordinated antimicrobial stewardship strategies. Full article

Citrus genomes as storehouses of genetic information of immense commercial utility remain untapped for the improvement of fruit quality traits and other production-related stresses. With the rapid expansion of transcriptomic datasets, integrative meta-analysis has further aided in uncovering interspecies molecular mechanisms associated with fruit quality development. In this study, we performed a cross-project RNA-Seq meta-analysis, integrating multiple publicly available BioProjects encompassing diverse citrus species, viz., Citrus sinensis, C. reticulata, C. maxima, C. clementina, C. japonica, and C. papeda, known to dominate the morphogenetic evolution of the citrus industry. High-throughput RNA-Seq data were processed using various bioinformatics tools. A total of 15 interspecies comparisons identified 676 unique DEGs, enriched in pathways related to secondary juice yield and processing quality traits. We also established that domestication aided in metabolism, oxidative stress responses, phenylpropanoid and flavonoid biosynthesis, and hormone-mediated signaling. Multivariate analyses (PCA and heatmap visualization) highlighted distinct yet overlapping expression patterns across these citrus species. By combining differential expression, co-expression network analysis and QTL-GWAS integration, we identified 19 high-confidence candidate genes responsible for transcriptomic variation associated with measurable fruit quality traits. Genes such as LOC102612823 and LOC102607495, which co-localized with seed number QTLs on chromosome 1, represented strong candidates regulating reproductive development and seed formation, the traits that directly influence fruit texture and market acceptability. Genes linked to juice content QTLs, including LOC102611137 and LOC102612553 on chromosome 5, suggested their roles in metabolic regulations behind juice accumulation. These loci provided definitive breeding clues for enhancing the reshaping of citrus fruit transcriptomes while retaining key ancestral regulatory components. Full article

Plant viruses pose serious threats to global crop production, and members of the genus Tobamovirus are particularly problematic due to their environmental stability, efficient mechanical transmission and rapid global spread. Tomato brown rugose fruit virus (ToBRFV) has emerged as one of the most damaging tobamovirus affecting tomato, a crop of major economic importance worldwide. ToBRFV has been reported in more than 45 countries, including Portugal. However, to date, no peer-reviewed molecular characterization of local isolates has been published, and official records classify its presence in Portugal as transient. This study confirms the occurrence of ToBRFV and provides the first comprehensive genomic and phylogenetic characterization of local virus isolates in Portugal. RNA-seq generated 192,852,438 reads, of which 103,882,115 (58.9%) mapped to ToBRFV, allowing reconstruction of a complete 6393 nt viral genome. A second full-length consensus sequence was independently obtained from the same composite sample using an overlapping Sanger sequencing strategy, differing by only two SNPs. Comparative genomic, functional, structural, and phylogenetic analysis revealed low diversity, with most variation located in replicase-coding regions, while movement and coat protein genes remained highly conserved. Nucleotide-based phylogenies resolved geographically structured clades, although the Portuguese sequences formed a strongly supported subclade with a Chinese isolate. These findings support recent global dissemination of ToBRFV and reinforce the importance of integrated surveillance and genomic monitoring for effective virus management. Full article

Reproductive genetic carrier screening (RGCS) is recommended preconceptionally or early pregnancy to identify the risk of autosomal recessive (AR) disorders in healthy couples. Data on shared carrier status at the couple’s level remains limited in Eastern Europe. This study presents the first couple-based RGCS analysis in Western Romania. We retrospectively analyzed RGCS results from 247 couples with no known consanguinity at the time of evaluation (494 apparently unrelated individuals, aged 22–52 years), assessed at a single genetic center between 2020–2024. Next-generation sequencing was performed using an expanded panel targeting 302 genes, including 300 genes associated with AR onset disorders. This analysis was accompanied by both pre- and post-test genetic counseling. The prevalence of individual and shared carrier status and reproductive risk was assessed. Pathogenic or likely pathogenic (PLP) variants were identified in the study cohort, with an overall couple carrier frequency of 64.37%. Shared carrier status for PLP variants in the same gene was identified in 17.4%, including three couples carrying pathogenic variants in two shared genes. Additionally, 46.96% of couples carried pathogenic variants in different genes without overlapping. The most frequently shared genes with PLP variants were HFE, CFTR, SMN1, BTD, and COL7A1; 14 additional shared genes with PLP variants were associated with severe, early-onset disorders. Forty-three couples were deemed high risk for AR conditions. Their reproductive choices varied, including in vitro fertilization or proceeding with pregnancy with or without prenatal testing. Couple-based RGCS revealed a substantial burden of shared AR carrier status in Western Romania, supporting the implementation of population-level screening programs to improve reproductive risk assessment and informed decision-making. Full article

The degradation of plastic waste leads to the release of numerous chemical additives, including phthalate plasticizers, which have been implicated in the pathogenesis of metabolic disorders. Di (2-ethylhexyl) phthalate (DEHP) is a widely used plasticizer whose primary metabolite, mono (2-ethyl-5-carboxypentyl) phthalate (MECPP), has been associated with multiple metabolic diseases. In this study, we applied an integrated approach combining network toxicology and molecular docking to systematically investigate the potential mechanistic role of MECPP in metabolic dysregulation. Our strategy included multi-platform target prediction, disease gene association analysis, functional enrichment, protein–protein interaction network construction, and molecular docking analysis. The results suggested that MECPP may be associated with six common core targets, including BCL2, BCL2L1, MAPK14, MMP2, MMP9, and TNFRSF1A, which are mainly involved in apoptosis, inflammatory regulation, and extracellular matrix remodeling. Pathway enrichment analysis further indicated the potential involvement of several disease-overlapping pathways, including insulin resistance, neuroactive ligand–receptor interaction, efferocytosis, advanced glycation end product–receptor for advanced glycation end product (AGE–RAGE) signaling, phospholipase D signaling, and renin secretion. Overall, these findings suggest that MECPP may contribute to metabolic dysregulation through overlapping molecular mechanisms across multiple diseases. This study provides a computational basis for future experimental validation and environmental risk assessment. Full article

Aging is a regulated process marked by the accumulation of senescent cells, which remain viable but no longer divide. Senescent cells contribute to age-associated phenotypes and diseases, including osteoarthritis, dementia, and cancer, but their scarcity and heterogeneity have limited study. Here, we developed a fluorescence-guided high-resolution spatial transcriptomic profiling approach to precisely locate and profile p21-reporter-positive cells in aged liver. This method enabled unbiased detection of a p21-associated, senescence-enriched cell population and revealed its diverse cellular identities, including hepatocytes, macrophages, neutrophils, and plasma cells. Our analysis further showed that activated macrophages and hepatic stellate cells were more likely to exhibit a p21 positive (p21⁺) state than their resting counterparts. Transcriptomic profiling of p21-expressing cells indicated heterogeneous senescence-associated secretory phenotype (SASP) programs, with distinct inflammatory and remodeling signatures across cell identities and their spatial positions. In parallel, we identified an aggregation of interferon-stimulated gene (ISG)-expressing cells with limited overlap with p21 positivity, suggesting a distinct aging-associated stress program. Taken together, our fluorescence-guided spatial transcriptomic framework enables high-resolution, single-cell mapping of senescence in situ, delineating both senescent cell type specificity and cell identity–independent senescence programs, thereby advancing a more comprehensive understanding of regulatory mechanisms underlying aging. Full article

(1) Objective. To conduct a comparative bioinformatics analysis of the transcriptomic profiles of peri-implantitis and periodontitis to identify common and specific molecular signatures underlying their pathogenesis, as well as molecular parallels with atherosclerosis. (2) Methods: We used datasets from the Gene Expression Omnibus (GEO) database: dataset GSE223924 (30 gingival tissue samples from patients with peri-implantitis, periodontitis, and healthy subjects) and GSE100927 (atherosclerotic and control tissue; n = 104). Differentially expressed genes (DEGs) were identified based on the criteria: |logFC| > 1 and FDR < 0.05. To quantitatively assess the relative abundance of immune cells, we used the xCell deconvolution algorithm. (3) Results: In the peri-implantitis group, 3669 DEGs with upregulated expression and 3106 with downregulated expression were identified; in the periodontitis group, 1968 and 1250 DEGs, respectively. Functional analysis of the upregulated DEGs revealed activation of inflammatory processes, cell adhesion, and angiogenesis in both diseases. Key differences lay in the activation of adaptive immune mechanisms in peri-implantitis (enrichment of the “graft rejection” and “T-cell receptor signaling”) and innate immunity in periodontitis (enrichment of the “lipopolysaccharide response” and “Toll-like receptors (TLR) signaling” pathways). Analysis of downregulated DEGs revealed more profound disruptions in cytoskeletal organization and epithelial differentiation in periodontitis, as well as suppression of xenobiotic and lipid metabolism in both diseases. xCell deconvolution confirmed a significant increase in B cells, neutrophils, monocytes, M1 macrophages, and dendritic cells in peri-implantitis, and also revealed a trend toward an increase in these cells in periodontitis (p > 0.05), which is consistent with the activation of TLR signaling. In periodontitis, a significant increase in M2 macrophages and a decrease in Th1 cells were observed. Comparison with atherosclerosis revealed 272 common DEGs with peri-implantitis and 173 common DEGs with periodontitis. Functional analysis of the common genes confirmed their role in leukocyte transendothelial migration, cytokine production, and the “Lipids and Atherosclerosis” pathway. (4) Conclusions: Functional analysis and immune deconvolution consistently demonstrate that peri-implantitis is characterized by statistically significant activation of both adaptive and innate immunity, whereas in periodontitis, the activation of innate immunity manifests primarily at the level of signaling pathways. The significant overlap found between the transcriptional profiles of both diseases and atherosclerosis may indicate the presence of common pathogenetic links. Full article

Transposable elements (TEs) are major contributors to genome plasticity and can reshape gene regulation through stress-responsive activation and the formation of TE-gene chimeric transcripts. Although therapeutic stress is known to perturb transcriptional networks in cancer cells, its impact on canonical TE transcription and TE-gene chimera formation in esophageal squamous cell carcinoma (ESCC) remains poorly defined. To address this, we performed a comprehensive transcriptome-wide analysis of TE expression and TE-gene chimeric transcripts in KYSE150 ESCC cells following combined 125I radiation and carfilzomib treatment. The TE analysis showed 148 dysregulated TEs, characterized by ERV1 LTR element enrichment and distinct treatment-control sample separation, indicating structured remodeling of the TE transcriptome. We identified 301 significant TE-gene chimeric events, indicating category-specific remodeling with an increase in TE-initiated and TE-exonic chimeras and a decrease in TE-terminal events. The TE families that underwent the most transcriptional changes were not those that drove chimeric events, indicating that global TE activation does not passively cause chimera remodeling. The gene repression was strongly associated with chimeric transcripts, and gene expression changes were negatively correlated with chimerism frequency. SPANXN1, IL1RL1, and RSAD2, strongly downregulated genes, produced novel TE-derived isoforms and were high-potential functional candidates. Epigenetic context analysis showed considerable overlap between exonized chimeras and candidate cis-regulatory elements, suggesting a potential association with regulatory genomic contexts. Pathway enrichment analysis showed synchronized transcriptomic reprogramming and cell cycle and DNA repair pathway activation and autophagy inhibition. In esophageal cancer cells, concurrent genotoxic and proteotoxic stress causes complex TE remodeling, linking traditional TE transcriptional alterations to structured TE-gene chimera development and stress-related transcriptome reprogramming. Full article

Background: Pine wilt disease (PWD), caused by the pine wood nematode (PWN, Bursaphelenchus xylophilus), is a devastating forest disease. It has been reported in five provincial-level regions in Southwest China (Chongqing, Guizhou, Sichuan, Yunnan, and Tibet), threatening local pine forest ecosystems. Methods: To unravel the population genetic variation and population differentiation of PWN isolates in this region, we purified eighty-one isolates for whole-genome resequencing and bioinformatics analysis, identifying candidate genes associated with runs of homozygosity (ROH). Results: Population structure analysis clustered the 81 isolates into three distinct genetic groups (Groups 1, 2, and 3). Notably, Group 1 exhibited fewer and shorter ROH segments compared to Groups 2 and 3, indicating higher genetic diversity and a different inbreeding history. Functional annotation of genes overlapping ROH regions revealed that Group 1 contained a subset of the genes identified in Groups 2 and 3, primarily enriched in specific molecular function categories. Conclusions: The PWN populations in Southwest China exhibit genetic differentiation, forming three distinct groups. Group 1 shows a reduced ROH burden and lower inbreeding levels, whereas Groups 2 and 3 display more extensive ROH patterns that may reflect historical demographic processes or potential adaptive selection. The differential distribution of ROH-associated genes across groups suggests possible variation in historical demographic processes and could suggest possible directional selection. These findings contribute to understanding the population history and genomic characteristics of PWN in Southwest China, providing insights that could support disease management strategies. Full article

Ovarian cancer (OC) remains one of the deadliest gynecological malignancies, largely due to late diagnosis and the emergence of resistance to platinum–based chemotherapy. Long non–coding RNAs (lncRNAs) have recently emerged as key regulators of tumor progression and therapeutic adaptation. In this study, we performed integrative transcriptomic profiling of patient–derived TCGA ovarian tumor samples and carboplatin–resistant A2780 (CBDCA–R–A2780) cells to identify lncRNAs whose dysregulation overlaps between a cell–line resistance model and patient tumors. Our analyses revealed extensive transcriptional remodeling across both datasets, with MNX1–AS1 consistently emerging as a strongly deregulated transcript. Differential expression analysis showed robust upregulation of MNX1–AS1 in resistant cells and tumor tissues, accompanied by correlations with epithelial–mesenchymal transition (EMT)–related transcription factors such as FOXA1 and SNAI2 and inverse associations with epithelial markers including CDH1. Computational predictions using RIblast identified specific MNX1–AS1 binding regions with candidate miRNAs and mRNAs, prioritizing EMT–related transcripts (e.g., SNAI2, FOXA1, ZEB1) with favorable hybridization energies for future validation. Additional prioritized interactors included genes linked to stress response (IER2, FOSB) and invasion (MMP11, MMP1). Because A2780 has been discussed as an endometrioid–like/non–serous ovarian cancer model, mechanistic inferences primarily apply to this in vitro context, while TCGA analyses provide associative support rather than mechanistic validation. Collectively, these findings highlight MNX1–AS1 as a candidate regulator associated with transcriptional reprogramming in OC and a promising prognostic biomarker warranting further functional testing. Full article

Endometriosis and endometrial cancer are distinct gynecological conditions that share overlapping biological mechanisms with implications for clinical management. Endometriosis is a chronic, benign disorder characterized by the ectopic implantation of functional tissue lining the uterus, primarily affecting women of reproductive age. It commonly causes chronic pelvic pain, dysmenorrhea, dyspareunia, and infertility. The disease is marked by persistent inflammation, hormonal dysregulation, and alterations in cellular signaling, which mirror some neoplastic processes despite lacking malignant potential. Endometrial cancer is a malignant tumor of the uterine lining, most frequently diagnosed in postmenopausal women. Its incidence is rising due to aging, obesity, and prolonged estrogen exposure. Epidemiological studies suggest a modest increase in endometrial cancer risk among women with endometriosis. However, detection bias and metabolic confounders may influence this association. Both conditions share estrogen dependence, chronic inflammatory microenvironments, and dysregulated pathways such as PI3K/AKT/mTOR. Somatic mutations in genes, including PTEN and ARID1A, further underline molecular intersections. Clinical management is tailored to disease type and severity. Endometriosis therapy emphasizes stepwise hormonal treatment, multidisciplinary pain management, and surgery when indicated. Endometrial cancer management relies on staging, with particular emphasis on molecular classification and histopathology to guide surgery, radiotherapy, chemotherapy, hormone therapy, and immunotherapy in advanced cases. Emerging noninvasive biomarkers and precision medicine strategies may enhance diagnosis, monitoring, and targeted treatment in both conditions. Understanding their shared and divergent mechanisms aids risk stratification, individualized therapy, and improved quality of life. Further prospective studies are needed to optimize patient-specific management and translate mechanistic insights into clinical practice. Full article

Ongoing urbanization continuously reshapes water quality, habitat structure, and biological communities in river ecosystems; however, its impacts on host-associated microbial communities remain poorly documented. The fish gut microbiota, a critical interface between the aquatic environment and host physiology, is widely recognized as an integrative indicator of both environmental change and host ecological traits. This study established a continuous urbanization gradient along Shanghai’s Suzhou River, spanning from suburban areas through the outer and inner ring roads to the city center. Five common wild fish species (Coilia nasus, Hemiculter bleekeri, Culter alburnus, Acheilognathus macropterus, and Pseudorasbora parva) were collected, and their gut microbiota were characterized via high-throughput 16S rRNA gene sequencing. Significant variation in OTU richness, alpha diversity, and community structure was observed across urbanization gradients and among fish species. Principal coordinate analysis revealed that samples from suburban areas were structurally distinct from those collected in other zones, whereas inner-ring and urban-core areas exhibited substantial compositional overlap. Taxonomic analysis revealed that Firmicutes and Pseudomonadota dominated all samples; however, their relative abundances and genus-level composition varied considerably among fish species and across the urbanization gradient. PICRUSt-based functional prediction indicated that metabolic pathways predominated, particularly those involved in global and overview maps, carbohydrate metabolism, amino acid metabolism, energy metabolism, and metabolism of cofactors and vitamins. Collectively, these findings demonstrate that fish gut microbial communities exhibit spatial structuring along the urbanization gradient, with species-specific responses linked to ecological traits. This study provides valuable data on host-associated microbial communities in urban rivers and offers a reference for incorporating microbial indicators into urban water ecological assessments. Full article

Circadian clocks generate daily rhythms of gene expression that influence physiology, disease, and responses to therapeutics, yet how circadian transcription differs between juvenile and adult organisms remains unresolved. Here, we used genome-wide eXcision Repair sequencing (XR-seq) to quantify transcription-coupled repair as an indirect, high-sensitivity measure of transcription. We profiled the brain, liver, kidney, and testis from juvenile and adult C57BL6/J mice across a 24 h cycle and show that XR-seq enables sensitive circadian transcription mapping. In all organs except the testis, rhythmic transcription phases clustered near dawn and dusk. While core clock gene rhythms are largely preserved between juveniles and adults, rhythms of many clock-controlled genes differ markedly by age. Rhythmic genes are strongly organ-specific yet their overlap between ages is limited, indicating substantial developmental changes in circadian control. Together, these data provide a multi-organ map of juvenile versus adult circadian transcription and indicate that adult therapeutic schedules may not translate to juveniles. Full article