Search Results (65,507)

Uracil−DNA glycosylases (UNGs) are DNA repair enzymes responsible for the removal of uracil, a canonical RNA nucleobase, from DNA, where it appears through cytosine deamination or incorporation from the cellular dUTP pool. While human and Escherichia coli UNGs have been extensively investigated, much less is known about their plant counterparts, of which UNGs from Arabidopsis thaliana are the only studied examples. Here, we show that in sugar beet (Beta vulgaris L.), an important crop species, cold and salt stress induce the expression of the UNG gene (BvUNG) and modulate the level of the uracil-excising activity in the roots. Purified recombinant BvUNG efficiently removes uracil from DNA both in vitro and in an E. coli reporter strain but does not excise 5-hydroxyuracil, 5,6-dihydrouracil, or 5-hydroxymethyluracil. The activity is abolished by Ugi, a protein UNG inhibitor from PBS1 bacteriophage, and by a mutation of a conserved active site His residue. Structural modeling shows the presence of a disordered N-tail prone to undergo phase separation, followed by a long α helix oriented differently from its counterpart in human UNG. Overall, BvUNG is a functional uracil–DNA glycosylase that might participate in the response to abiotic stress. Full article

Alzheimer’s disease (AD) and major depressive disorder (MDD) are prevalent central nervous system (CNS) disorders that share overlapping symptoms but differ in underlying molecular mechanisms. Distinguishing these mechanisms is essential for developing targeted diagnostic and therapeutic strategies. In this study, we integrated multi-tissue transcriptomic datasets from brain and peripheral samples to identify differentially expressed microRNAs (miRNAs) in AD and MDD. Functional enrichment analyses (KEGG, GO) revealed that dysregulated miRNAs in AD were associated with MAPK, PI3K–Akt, Ras, and PD-1/PD-L1 signaling, pathways linked to synaptic plasticity, neuroinflammation, and immune regulation. In contrast, MDD-associated miRNAs showed enrichment in Hippo signaling and ubiquitin-mediated proteolysis, implicating altered neurogenesis and protein homeostasis. Network analysis highlighted key disease- and tissue-specific miRNAs, notably hsa-miR-1202 and hsa-miR-24-3p, with potential roles in neuronal survival and molecular network regulation. These findings suggest that miRNAs may serve as non-invasive biomarkers for diagnosis, prognosis, and treatment monitoring in both disorders. While therapeutic targeting of miRNAs offers promise, challenges such as blood–brain barrier penetration and tissue-specific delivery remain. This integrative approach provides a translational framework for advancing miRNA-based strategies in CNS disease research. Full article

Hepatitis B virus (HBV) remains a major global health challenge, with over 296 million people chronically infected worldwide. Despite the availability of antiviral therapies, a functional cure is rarely achieved, highlighting the need for novel therapeutic strategies. RNA 5-methylcytosine (m⁵C) is a pivotal epitranscriptomic mark implicated in RNA stability, transport, and translation. Emerging evidence shows that m⁵C is conserved within HBV RNA and plays critical roles in the viral life cycle. This review provides a comprehensive overview of the molecular mechanisms governing m⁵C deposition and recognition, summarizes recent advances in m⁵C biology, and highlights the emerging role of epitranscriptomic m⁵C regulation in HBV infection. We discuss the identification of HBV-specific m⁵C sites, the functions of key regulatory enzymes, and their interplay in viral RNA stabilization and evasion of innate immune responses. Interplay between m⁵C and other RNA modifications—particularly N6-methyladenosine (m⁶A)—is examined alongside virus-specific m⁵C regulation in EV71, HIV, HCV, EBV, and SARS-CoV-2. Potential links between m⁵C dysregulation and HBV-induced hepatocarcinogenesis are outlined, and emerging therapeutic strategies targeting the m⁵C machinery are highlighted. Together, these insights position the epitranscriptomic landscape as a promising avenue for innovative antiviral strategies. Full article

Background: Aberrant hepatic lipid metabolism is a key predisposing factor for dairy cow ketosis, with genetic factors playing a pivotal role in disease pathogenesis. However, systematic screening and functional validation of candidate genes for bovine ketosis remain limited. In this study, we aimed to identify genetic markers associated with clinical ketosis and explore their potential functional mechanisms underlying disease susceptibility. Methods: We conducted simplified genome sequencing (SuperGBS), genome-wide association studies (GWAS), and Sanger sequencing on Chinese Holstein cows, both healthy and with ketosis. Results: We reported that mitogen-activated protein kinase 1 (MAPK1) was significantly associated with clinical ketosis. Further investigation revealed concurrent upregulation of MAPK1 protein and disrupted hepatic lipid homeostasis in hepatocytes from in vivo and in vitro models. Critically, siRNA-mediated knockdown of MAPK1 reversed lipid metabolism processes and reduced lipid accumulation in β-Hydroxybutyric acid (BHB)-exposed bovine hepatocytes, thereby establishing MAPK1 activation as a driver of lipotoxicity in dairy cow ketosis. Additionally, we identified that supplementation of fibroblast growth factor 21 (FGF21) fusion protein not only reduced MAPK1 expression but also normalized hepatic lipid metabolism in BHB-exposed bovine hepatocytes. Conclusions: FGF21–MAPK1 imbalance is a reason for hepatic lipid metabolic dysfunction, providing a potential intervention approach to mitigate dairy cows’ ketosis. Full article

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterised by cognitive decline, synaptic loss, and multifaceted pathology involving amyloid-β (Aβ) aggregation, tau hyperphosphorylation, neuroinflammation, and impaired proteostasis. In recent years, biologic therapies, such as monoclonal antibodies, vaccines, antisense oligonucleotides (ASOs), and gene therapies, have gained prominence as promising disease-modifying strategies. In this review, we provide a comprehensive synthesis of current biologic approaches under clinical evaluation for AD. Drawing on data curated from ClinicalTrials.gov (as of 2025), we systematically summarise the molecular targets, therapeutic modalities, mechanisms of action, trial phases, and sponsors of over 60 biologic agents. These include Aβ-directed antibodies targeting distinct conformers such as protofibrils, pyroglutamate-modified species, and soluble oligomers; tau-targeted immunotherapies and RNA-based interventions; and emerging platforms focused on neuroimmune modulation, peptide hormones, and microbiota-based strategies. Gene and RNA therapeutics, particularly ASOs and small interfering RNAs (siRNAs) delivered intrathecally or via lipid nanoparticles, are also reviewed for their potential to modulate intracellular targets with high specificity. We also analyse the historical landscape of biologic candidates that failed to reach approval, discussing key reasons for trial discontinuation, including lack of clinical efficacy, safety concerns (e.g., amyloid-related imaging abnormalities), or inadequate biomarker responses. These cases offer crucial insights for refining future drug design. Looking ahead, we highlight major challenges and evolving perspectives in AD biologic therapy: expanding therapeutic targets beyond Aβ and tau, overcoming delivery barriers to the brain, designing prevention-oriented and genetically stratified trials, and navigating regulatory and ethical considerations. Together, these efforts signal a paradigm shift in AD drug development, from symptomatic treatment to mechanism-based precision biologics. By integrating real-time clinical trial data with mechanistic insight, this review aims to inform both translational research and therapeutic innovation in AD. Full article

Biomolecular condensates (BCs), formed through liquid–liquid phase separation (LLPS), are membraneless compartments that dynamically regulate key cellular processes. Beyond their canonical roles in energy metabolism and apoptosis, Mitochondria harbor distinct BCs, including mitochondrial RNA granules (MRGs), nucleoids, and degradasomes, that coordinate RNA processing, genome maintenance, and protein homeostasis. These structures rely heavily on proteins with intrinsically disordered regions (IDRs), which facilitate the transient and multivalent interactions necessary for LLPS. In this review, we explore the composition and function of mitochondrial BCs and their emerging involvement in neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Amyotrophic lateral sclerosis, and Huntington’s disease. We provide computational evidence identifying IDR-containing proteins within the mitochondrial proteome and demonstrate their enrichment in BC-related functions. Many of these proteins are also implicated in mitochondrial stress responses, apoptosis, and pathways associated with neurodegeneration. Moreover, the evolutionary conservation of phase-separating proteins from bacteria to mitochondria underscores the ancient origin of LLPS-mediated compartmentalization. Comparative analysis reveals functional parallels between mitochondrial and prokaryotic IDPs, supporting the use of bacterial models to study mitochondrial condensates. Overall, this review underscores the critical role of mitochondrial BCs in health and disease and highlights the potential of targeting LLPS mechanisms in the development of therapeutic strategies. Full article

Molecular diagnoses of Entamoeba histolytica and Strongyloides stercoralis in human samples are becoming increasingly common. To contribute to the ongoing standardization of molecular diagnostic approaches targeting these parasites, we compared three published E. histolytica- and S. stercoralis-specific real-time PCR assays in test comparisons without a reference standard. Latent class analysis (LCA) was used to calculate diagnostic accuracy estimations for the three compared assays per parameter. The comparison was conducted using stool samples from Ghanaian individuals. In the course of the assessment of 873 stool samples, the number of detected positive PCR results ranged from 10 to 15 for S. stercoralis and from 4 to 54 for E. histolytica depending on the applied assay. Diagnostic accuracy estimates of real-time PCR sensitivity for S. stercoralis and E. histolytica ranged from 89% to 100% and from 75% to 100%, respectively; diagnostic estimates of specificity ranged from 99% to 100% and from 94% to 100%, respectively. Diagnostic accuracy-adjusted prevalence estimates were 1.2% for S. stercoralis and 0.5% for E. histolytica. High cycle threshold values of real-time PCR > 35 showed a particularly reduced likeliness of reproducibility when applying competitor real-time PCR assays. There were no clear-cut differences in terms of diagnostic accuracy favoring either small-subunit ribosomal ribonucleic acid (SSU rRNA) gene sequences or the S. stercoralis dispersed repetitive sequence for S. stercoralis PCR. The same applied to the comparison of real-time PCRs targeting SSU rRNA gene sequences and the SSU rRNA episomal repeat sequence (SREPH) of E. histolytica. In conclusion, interchangeability of the compared real-time PCR assays was higher for the assessed S. stercoralis assays compared with the assessed E. histolytica assays. Regional diagnostic accuracy testing seems advisable before literature-adapted assays for rare tropical pathogens like S. stercoralis and E. histolytica are applied in different study regions. Full article

Intrauterine growth restriction (IUGR) severely hinders the development of the livestock industry and impacts economic efficiency. MicroRNAs (miRNAs) participate in the epigenetic regulation of animal growth and development. Using IUGR pigs as a model, this study analyzed transcriptomic data from IUGR piglets to investigate the miRNA-mRNA regulatory network in their testes. Compared with NBW pigs, IUGR pigs exhibited reduced testicular volume, decreased weight, and abnormal testicular development. A total of 4945 differentially expressed mRNAs and 53 differentially expressed miRNAs were identified in IUGR testicular tissues, including 1748 downregulated and 3197 upregulated mRNAs, as well as 41 upregulated and 12 downregulated miRNAs. The integrated analysis of differentially expressed genes, miRNA target genes, and the miRNA-mRNA network revealed that IUGR may impair testicular development by disrupting cell cycle progression and apoptotic pathways, thereby hindering normal testicular cell growth. Furthermore, analysis of the miRNA-mRNA network indicated that miRNAs such as ssc-miR-23a, ssc-miR-29c, ssc-miR-193a-3p, and ssc-miR-574-3p could serve as potential marker miRNAs for IUGR testes, while YWHAZ, YWHAB, and PPP2CA may function as core target genes within this regulatory network. In conclusion, this study enhances our understanding of male reproduction in IUGR pigs and provides a theoretical foundation for preventing and treating IUGR-induced male reproductive disorders. Full article

Background: Data on the use of dolutegravir (DTG) plus boosted darunavir (DRV/b) in people with 4-class drug-resistant HIV (4DR-PWH) are limited. This study assessed the virological effectiveness of DTG + DRV/b in this population using real-world data from the PRESTIGIO Registry. Methods: We compared three regimen groups: dual DTG + DRV/b (DODA), DTG + DRV/b plus an additional antiretroviral drug (DODA + Other), and regimens excluding DTG + DRV/b (NO-DODA). Virological failure (VF) was defined as ≥2 HIV-RNA values ≥ 50 copies/mL or 1 ≥ 1000 copies/mL. Mixed-effects logistic regression was used to assess VF, adjusting for antiretroviral therapy (ART) duration, age, number of fully active drugs, sex at birth, and nadir CD4+. Individuals could switch regimens during follow-up. Results: Among 249 4DR-PWH (median follow-up: 8.7 years), 844 ART regimens were analyzed: 72 (8.5%) DODA, 264 (31.3%) DODA + Other, and 508 (60.2%) NO-DODA. Compared to NO-DODA, the odds of VF were 77% and 35.9% lower with DODA and DODA + Other, respectively. Notably, in the DODA group, DTG and DRV/b were fully active in only 63.9% and 47.2% of the cases, respectively. Conclusions: DTG + DRV/b regimens were associated with a significantly lower risk of virological failure, even when drug activity was partial. This strategy remains a valuable option for managing multi-drug-resistant HIV. Full article

Cisplatin resistance remains a major therapeutic challenge in oral squamous cell carcinoma (OSCC), leading to treatment failure and poor outcomes. This study aimed to generate and characterize cisplatin-resistant OSCC models to elucidate resistance mechanisms. Two resistant OSCC cell lines (SCC-9R and HSC-3R) were developed through gradual dose escalation. Parental and resistant cells were analyzed via RNA-seq and gene set enrichment analysis, and validated through RT-qPCR, Western blot, immunofluorescence, and gelatin zymography. Functional assays, including 2D and 3D migration and invasion models, assessed phenotypic changes. A multi-omics analysis revealed molecular alterations in resistant cells, including 305 differentially expressed genes (DEGs) in HSC-3R (187 upregulated) and 782 in SCC-9R (298 upregulated) versus parental lines, with enrichment for extracellular matrix organization (p < 0.001) and consistent epithelial–mesenchymal transition (EMT) activation (p < 0.001), demonstrated by the upregulation of ZEB1, ZEB2, Vimentin, and TWIST1, and E-cadherin suppression. Functional validation confirmed an aggressive phenotype, including increased migration (p < 0.05), invasion (p < 0.01), and elevated MMP-2 (p < 0.01) and MMP-9 (p < 0.001) activity. Findings were verified in 3D spheroid models. Overall, cisplatin resistance in OSCC involves EMT, inflammatory signaling, and metabolic adaptation. The consistency of these features across both models supports the robustness of this in vitro system and reveals targets for therapeutic intervention. Full article

Parkinson’s disease (PD) is characterized by the progressive loss of dopaminergic neurons in the substantia nigra, and key pathways such as neuroinflammation, oxidative stress, and autophagy are believed to significantly contribute to the mechanisms of neurodegeneration. Calpain activation plays a critical role in neuroinflammation and neurodegeneration, as demonstrated by its impact on microglial activation, reactive oxygen species (ROS) production, and neuronal survival. In this study, we investigated the effects of calpain inhibition using calpeptin (CP) and calpain-2-specific inhibitors in cellular and murine models of neuroinflammation and PD. In BV2 microglial cells, LPS-induced production of pro-inflammatory cytokines (TNF-α, IL-6) and chemokines (MCP-1, IP-10) were significantly reduced by CP treatment with a concomitant decrease in ROS generation. Similarly, in VSC-4.1 motoneuron cells, calpain inhibition attenuated IFN-γ-induced ROS production and improved cell viability, demonstrating its neuroprotective effects. Moreover, in a murine MPTP model of PD, calpain inhibition reduced astrogliosis, ROCK2 expression, and levels of inflammatory cytokines (TNF-α, IL-1β, IL-6, IL-7, and IL12p70) and chemokines (MCP-1 and IP-10) in the dorsal striatum and plasma. The specific role of calpain-2 in immune modulation was further highlighted in human microglia, SV-40 cells. With respect to immune modulation in these cells, siRNA-mediated knockdown of calpain-2, but not calpain-1, significantly reduced antigen presentation to CD4+ T cells. Thus, calpain-2 is likely involved in regulating antigen presentation and activation of inflammatory CD4+ T cells. These findings underscore the therapeutic potential of calpain-2 inhibition in mitigating neuroinflammation and neurodegeneration, particularly in PD, by targeting microglial activation, ROS production, and neuronal survival pathways. Full article

Background: Reactive oxygen species (ROS) generated due to mitochondrial dysfunction are one of the primary causes of the initiation and progression of senescence. Although reducing mitochondrial ROS production is known as an effective strategy for the treatment of aging, effective components that reduce mitochondrial ROS production or effective treatments that utilize them have not yet been developed. Methods: Screening of plant-generated secondary metabolites to overcome ROS-mediated stress found that ε-viniferin, a dimer of resveratrol, effectively reduces mitochondrial ROS production. Results: ε-viniferin induced efficient electron transport and reduced mitochondrial ROS, a consequence of inefficient electron transport. In addition, ε-viniferin acted as a senolytic that selectively eliminates senescent fibroblasts, thereby restoring mitochondrial function and senescence-associated phenotypes. RNA sequencing analysis revealed that regulator of G protein signaling 16 (RGS16) was an important gene for ε-viniferin-mediated senescence rejuvenation. Upregulation of RGS16 showed similar effects as ε-viniferin in reducing mitochondrial ROS production and restoring mitochondrial function. Conclusions: This study discovered a novel mechanism by which ε-viniferin rejuvenates senescence by lowering ROS production in mitochondria. The novel mechanism will serve as a basis for developing therapeutics that regulate mitochondrial ROS production to treat aging. Full article

Cellular senescence is a fundamental hallmark of aging, contributing to tissue dysfunction and chronic disease through the senescence-associated secretory phenotype (SASP). The SASP encompasses a diverse and dynamic collection of secreted cytokines, chemokines, growth factors, and proteases that vary depending on cell type, senescence trigger, and microenvironmental context. Accurate quantification of SASP components is critical to understanding the mechanisms linking senescence to pathology and for advancing senotherapeutic strategies. However, measuring the SASP presents significant technical and biological challenges due to its complexity, heterogeneity, and context dependence. This review provides a comprehensive overview of the principal methodologies used to measure SASP components across different biological levels—transcriptional, translational, and functional—and sample types, including cell cultures, tissues, and systemic fluids. We discuss the advantages and limitations of widely used RNA-level techniques (e.g., qRT-PCR, RNA sequencing, in situ hybridization), protein-level assays (e.g., ELISA, Western blotting, mass spectrometry, Luminex, MSD), and spatial detection methods (e.g., immunohistochemistry, immunofluorescence). By organizing current SASP detection strategies by molecular level and sample source, this review highlights the importance of multiparametric approaches to capture the full spectrum of senescent cell activity. We also identify key methodological gaps and propose directions for refining SASP biomarker discovery in aging and disease research. Full article

Metabolically healthy (MHO) and unhealthy obesity (MUO) exhibit distinct molecular genetic mechanisms underlying metabolic disorders. Studying gene and microRNA expression in subcutaneous adipose tissue (SAT) may reveal key pathogenetic differences between these phenotypes. We compared the expression of genes (ADIPOQ, HIF1A, CCL2) and microRNAs (miR-142-3p, miR-155, miR-378) in SAT between MHO and MUO patients and assessed their association with metabolic parameters. The study included 39 obese patients (19 MHO, 20 MUO) and 10 healthy controls. SAT biopsies were analyzed using real-time PCR. Correlations with clinical and metabolic markers were evaluated. Obese patients showed decreased ADIPOQ (p = 0.039) and miR-142 (p = 0.008) expression and increased CCL2 (p = 0.004), miR-155 (p = 0.017), and miR-378 (p = 0.04) expression compared to the controls. MUO patients exhibited higher HIF1A expression (p = 0.03) and strong correlations between CCL2 and dyslipidemia (total cholesterol, triglycerides)/dysglycemia (fasting glucose) (r = 0.45, p = 0.03; r = 0.52, p = 0.01; r = 0.63, p = 0.001, respectively). miR-142 negatively correlated with fibrosis markers, while miR-378 was linked to insulin resistance. The differential gene and microRNA expression highlights the role of inflammation, hypoxia, and fibrosis in MUO pathogenesis. miR-142-3p, miR-155, and miR-378 may serve as potential biomarkers for metabolic risk stratification and therapeutic targets. Full article

Ulcerative colitis (UC) is associated with an elevated risk of colorectal cancer (CRC), driven by chronic inflammation and a distinct inflammation–dysplasia–carcinoma pathway. Conventional surveillance relies on colonoscopy and histologic assessment, but flat, multifocal dysplasia and sampling limitations challenge early detection. Tissue-based biomarkers offer promise in improving risk stratification and identifying patients at high risk for UC-associated CRC (UC-CRC). This review explores key categories of tissue biomarkers with potential clinical utility, including genetic mutations, epigenetic alterations, microRNA expression profiles, and markers of genomic instability such as telomere shortening, copy number variants, and aneuploidy. Many of these molecular alterations precede histologic dysplasia and reflect a “field effect,” suggesting their potential role in early cancer detection. Despite compelling associations between these biomarkers and neoplastic progression, most lack prospective validation and are not yet ready for routine clinical use. Future research should prioritize the development of integrated biomarker panels and validate their predictive accuracy in longitudinal UC cohorts. Molecular profiling may ultimately enable personalized, risk-adapted surveillance strategies that improve early detection while minimizing unnecessary interventions. Full article