Search Results (1,798)

Ovarian endometriosis (OE) is a chronic, inflammatory gynecological disorder associated with sterility and an elevated risk of ovarian cancer. Despite its high prevalence, the complex molecular mechanisms governing OE pathogenesis remain poorly investigated. We conducted a comprehensive histopathological and molecular investigation of OE in a cohort of 188 Saudi women (88 patients with OE and 100 healthy controls) using histopathological, qRT-PCR, immunostaining, and Western blot techniques. Histopathological analysis confirmed significant stromal fibrosis and chronic inflammation in endometriotic lesions. Gene expression profiling revealed a pro-proliferative, anti-apoptotic signature, marked by the upregulation of PTTG1 and the downregulation of TNFRSF10D, CDK4, and CDKN1A. Interestingly, we identified a post-transcriptional regulatory paradox in the inflammatory response: while IL-6 mRNA was significantly upregulated, its corresponding protein level was downregulated, suggesting a novel, tightly controlled mechanism to limit excessive local inflammation. Besides the increased autophagic activity and decreased Ubiquitin mRNA levels, epigenetic dysregulation was prominent, characterized by the upregulation of DNA methyltransferase DNMT3B and the downregulation of the histone variant H3.1. These findings elucidate novel molecular pathways underlying OE pathogenesis as evidenced by a post-transcriptional paradox in IL-6 expression, and uncover key dysregulations spanning cell proliferation, apoptosis, inflammation, autophagy, and epigenetic regulation. Full article

Neutrophil extracellular traps (NETs) contribute to innate immunity in sepsis, but their diagnostic value in neonates is unclear. We evaluated whether circulating NET-associated biomarkers discriminate septic from non-infected neonates. In this prospective observational study 96 neonates (≥34 weeks gestational age) with clinical suspicion of infection were enrolled (36 sepsis, 60 controls). Serum cell-free DNA (cfDNA), myeloperoxidase–DNA complexes (MPO-DNA), neutrophil elastase–DNA complexes (NE-DNA), and citrullinated histone H3 (H3cit) were measured alongside CRP and IL-6 at days 1, 3, and 5. Diagnostic performance was assessed by receiver operating characteristic (ROC) analysis with bootstrap confidence intervals. CRP (AUC 0.75, 95% CI 0.66–0.85) and IL-6 (AUC 0.73, 95% CI 0.61–0.83) showed the best diagnostic performance. cfDNA demonstrated moderate discrimination (AUC 0.72, 95% CI 0.60–0.84) but was only transiently elevated at day 1. MPO-DNA (AUC 0.47), NE-DNA (AUC 0.44), and H3cit (AUC 0.47) performed no better than chance. Within the sepsis group, MPO-DNA and NE-DNA at day 3 strongly correlated with the immature-to-total neutrophil ratio (ρ = 0.76 and 0.72), suggesting these markers reflect neutrophil degranulation rather than NET formation. NET-associated biomarkers do not improve diagnostic accuracy for neonatal sepsis beyond CRP and IL-6. These findings support the concept that neonatal innate immune responses differ fundamentally from adult patterns. Full article

Background/Objectives: Epigenetic regulation plays a fundamental role in controlling the spatiotemporal expression of genes in plants under stressful environmental conditions. While LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is known to be involved in histone modification, its function in regulating the biosynthesis of specialized metabolites, particularly monoterpenoid indole alkaloids (MIAs) in Catharanthus roseus, remains elusive. Methods: CrLHP1 was identified by mining the C. roseus proteome and characterized through sequence alignment, phylogenetic analysis, and conserved domain assessment. Virus-induced gene silencing (VIGS) was employed to suppress CrLHP1 expression, after which the transcript levels of jasmonic acid (JA)-responsive genes and key MIA biosynthetic genes, as well as the accumulation of vindoline and catharanthine, were analyzed. Furthermore, deep learning-based protein structure prediction (AlphaFold3) and yeast two-hybrid (Y2H) assays were conducted to explore protein-protein interactions. Results: CrLHP1 was confirmed as the ortholog of Arabidopsis thaliana LHP1 (AtLHP1). Exposure to 75 μM MeJA upregulated MIA upstream pathway genes while downregulating CrLHP1 transcription. Silencing CrLHP1 significantly upregulated JA-responsive and MIA biosynthetic genes, leading to enhanced catharanthine accumulation. Additionally, the structural prediction and Y2H assays revealed a physical interaction between CrLHP1 and CrJAZ1. Conclusions: These findings suggest that CrLHP1 negatively regulates MIA biosynthesis, potentially by modulating JA signal transduction through interaction with CrJAZ1. This study provides new insights into the possible epigenetic mechanisms governing alkaloid production in C. roseus. Full article

Cyclin-dependent kinase 1 (CDK1) is frequently upregulated in multiple cancers and plays a central role in cell cycle progression and tumorigenesis. However, whether CDK1 directly regulates the histone acetyltransferase KAT8 (also known as MOF) in non-small cell lung cancer (NSCLC) remains unclear. Here, we identify CDK1 as a kinase that directly interacts with and phosphorylates KAT8 at serine 348 (S348) and threonine 418 (T418). Mechanistically, CDK1-mediated phosphorylation, particularly at S348, enhances the interaction between KAT8 and MSL1, thereby stabilizing the MSL complex and promoting KAT8-dependent acetylation of histone H4 at lysine 16 (H4K16). Functionally, the phosphorylation-deficient mutant KAT8-S348A exhibits impaired MSL complex assembly, reduced H4K16 acetylation, and decreased NSCLC cell proliferation both in vitro and in vivo. Pharmacological inhibition of CDK1 using RO-3306 suppresses KAT8 phosphorylation and H4K16 acetylation, leading to significant tumor growth inhibition. Notably, this effect is partially rescued by re-expression of wild-type KAT8 but not by the S348A mutant, supporting a phosphorylation-dependent mechanism. Collectively, these findings define a CDK1–KAT8 signaling axis that promotes NSCLC proliferation through epigenetic regulation and suggest that targeting CDK1-dependent KAT8 phosphorylation may represent a potential therapeutic strategy for lung cancer. Full article

Background and objectives: The PWWP domain of lens epithelium-derived growth factor p75 (LEDGF/p75) mediates chromatin engagement through recognition of histone H3 lysine 36 di- and trimethylation (H3K36me2/3) and nucleosomal DNA. LEDGF/p75 plays a role in multiple human diseases. In particular, its interaction with HIV-1 integrase enables viral genome integration. However, the LEDGF PWWP domain remains difficult to target with small molecules as it lacks optimally shaped binding pockets. Here, we report the generation of high-affinity nanobodies (Nbs) to investigate the structure and function of this domain. Methods: Camelids were immunized with recombinant LEDGF PWWP domain, and immune phage display libraries were screened for affinity. Selected Nbs were recombinantly expressed in E. coli and purified. Their interaction with the PWWP domain of LEDGF and its close homolog HRP-2 was characterized using size-exclusion chromatography and surface plasmon resonance. Structural characterization of the Nbs was performed using X-ray crystallography. Functional effects on chromatin engagement were evaluated using an AlphaScreen assay. Results: Nine sequence-distinct Nbs were identified, seven of which were confirmed to bind the LEDGF PWWP domain with nanomolar affinities. Five Nbs also bound the HRP-2 domain, consistent with conserved functional surfaces, while two showed reduced affinity. The crystal structures of two Nbs (NbC03 and NbH10) confirmed there were canonical immunoglobulin folds, while the latter additionally revealed a domain-swapped dimer. Moreover, NbH10 dose-dependently inhibited the interaction between full-length LEDGF/p75 and H3K36me3-modified nucleosomes in vitro. Conclusions: This work establishes a validated panel of Nbs targeting the LEDGF PWWP domain and identifies one Nb capable of functionally disrupting the LEDGF–chromatin interaction. These Nbs serve as valuable tools for functional studies and structure-based drug design. Full article

Postnatal loss of cardiac regenerative capacity coincides with profound remodeling of signaling, structural, and metabolic programs in the developing heart. Here, we profiled Insulin growth factor (IGF)/Fibrobrast growth factor (FGF)/insulin receptors (InsR), Ras/Raf/MEK/ERK pathway components, cytoskeletal markers, and cell-cycle/metabolic proteins in mouse whole-heart tissue at P3, P7, P14, P28, and adulthood. IGF-1R- and IGF-2R-associated signals declined sharply during maturation, whereas InsR changed more modestly. FGFR1-derived immunoreactive species showed a transient early postnatal increase before marked reduction at later stages. These receptor-associated changes paralleled strong decreases in B-Raf, MEK1, and MEK2, together with pronounced loss of MEK1/2 activation-loop phosphorylation. MEK1 Thr292 phosphorylation also declined markedly, identifying a previously unrecognized developmental phosphorylation pattern. Structural maturation was accompanied by stable Actn2 expression, downregulation of immature cytoskeletal markers, increased cytochrome c and myoglobin, and significant loss of Aurora B and phospho-histone H3 in adult hearts. Together, these findings describe a coordinated postnatal maturation program in which signaling, cytoskeletal remodeling, metabolism, and proliferative withdrawal change in parallel. These data are consistent with reduced MAPK pathway activity during maturation and highlighting this signaling as node associated with closure of the neonatal regenerative window. Full article

The ubiquitously transcribed tetratricopeptide repeat Y-linked gene (UTY/KDM6C), a catalytically impaired histone demethylase encoded on the Y chromosome, has garnered increasing attention for its emerging roles in tumorigenesis and cancer progression. Despite high sequence homology with its X-linked paralog UTX/KDM6A, UTY exhibits markedly reduced or absent H3K27me3 demethylase activity due to critical amino acid substitutions in its Jumonji C domain. Consequently, UTY primarily functions through non-enzymatic mechanisms, acting as a scaffold in chromatin-remodelling complexes like COMPASS and SWI/SNF, or mediating protein–protein interactions that regulate transcriptional programs independent of demethylation. This aligns with epigenetic dysregulation in cancers, where imbalances in repressive H3K27me3 and active H3K4me either drive tumour suppressor silencing or oncogene activation. Unlike frequently mutated UTX in cancers such as breast, renal cell carcinoma, and acute myeloid leukaemia, UTY’s contributions in cancer are less defined, constrained by male-specific expression. Emerging evidence suggests UTY as a context-dependent tumour suppressor in AML and squamous-like pancreatic ductal adenocarcinoma. While direct functional validation remains limited in several cancer types, UTY is increasingly implicated as a potential tumour suppressor in haematological malignancies and prostate cancer. Therapeutically targeting UTY’s scaffold functions shows promise for male-specific cancers and merits future investigation. Full article

Background and Aims: Understanding regulatory interactions between hepatitis B virus (HBV) and host factors is essential for the development of next generation host-directed antiviral therapies and the achievement of a functional HBV cure. Here, we investigated HBV-induced alterations in host gene expression in primary human hepatocytes (PHH) to identify host factors exploited by the virus for replication and persistence. Whole-transcriptome sequencing (WTS) of HBV-infected PHH identified host pathways with potential roles in the HBV life cycle. RNA interference-based functional screening of dysregulated candidate genes identified cyclin L1 (CCNL1) as a key host factor. RNAi-mediated knockdown of CCNL1 reduced HBV gene expression, including hepatitis B surface antigen (HBsAg). Mechanistically, CCNL1 regulates phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII) at serine 2 (S2), consistent with a role in transcriptional regulation. CCNL1 knockdown further reduced the binding of total and phospho- (Ser2/Ser5) RNAPII, pan-acetylated histone H3 (H3ac), and H3K27ac to HBV covalently closed circular DNA (cccDNA), indicating impaired cccDNA-dependent transcription. In addition, CCNL1 expression was elevated in chronic hepatitis B patients compared with those with resolved infection. Collectively, these data demonstrate that CCNL1 promotes HBV transcription and replication through modulation of RNAPII phosphorylation and chromatin-associated transcriptional activity, identifying CCNL1 as a potential host susceptibility factor for HBV. Importance: Hepatitis B virus infection remains a major threat to human health in areas with high prevalence. There is need to fully understand the complex interactions between the virus and human host factors/processes to support ongoing efforts to develop anti-HBV therapies that can be used with existing therapies to achieve a better cure. HBV relies on host cellular factors and biological processes to establish and maintain efficient infection, making host–virus interactions attractive targets for therapeutic intervention. Thus, identifying host factors that support and/or restrict HBV infection is essential for understanding the molecular basis of chronic HBV infection and for developing host-targeting anti-HBV drugs. This study identifies cyclin L1 (CCNL1) as a host susceptibility factor that promotes HBV transcription and replication through regulation of RNA polymerase II activity and or post-transcriptional mechanisms. Full article

Background/Objectives: Immune evasion remains a critical barrier to effective hepatocellular carcinoma (HCC) therapy. Lactate dehydrogenase A (LDHA) drives lactate accumulation and histone lysine lactylation (Kla), reshaping the immunosuppressive microenvironment, while bromodomain-containing protein 4 (BRD4) sustains B7-H3 transcription via super-enhancer occupancy. Despite their synergistic roles in the lactate–Kla–B7-H3 immunosuppressive axis, no dual-target inhibitor simultaneously engaging both proteins has been reported. This study aimed to discover dual LDHA/BRD4 inhibitors from natural product libraries using an integrated AI-driven computational pipeline. Methods: We established a multi-tier virtual screening cascade comprising Lipinski/QED drug-likeness filtration, DiffDock-based AI docking, QuickVina binding energy validation, PLIP interaction profiling, 200 ns all-atom molecular dynamics simulations, MM-GBSA binding free energy calculations, and density functional theory analysis. Natural product libraries from COCONUT and CMNPD databases (84,730 compounds post-filtration) were screened against both targets. Results: High-throughput DiffDock screening identified 11 dual-target hits, from which CNP0038114.1 and CMNPD16582 emerged as prioritized lead candidates. All four protein–ligand complexes maintained structural stability throughout MD simulations, with MM-GBSA binding free energies ranging from −27.24 to −32.45 kcal/mol, predominantly driven by van der Waals interactions. DFT calculations revealed distinct electronic profiles: CNP0038114.1 exhibited a narrow HOMO–LUMO gap (2.718 eV) favoring charge-transfer reactivity, whereas CMNPD16582 displayed a larger gap (4.822 eV), suggesting superior chemical stability. Conclusions: This computational study furnishes two novel natural product leads for targeting the lactate–Kla–B7-H3 immunosuppressive axis in HCC, establishing a generalizable AI-driven workflow for dual-target inhibitor discovery. Full article

We present a neonatal case of Wiedemann–Steiner syndrome (WSS) with a de novo, previously reported KMT2A missense variant (c.3464G>A; p.Cys1155Tyr; NM_001197104.2), and provide a focused literature review of this specific variant. WSS (OMIM#605130) is a rare neurodevelopmental disorder caused by heterozygous variants in the KMT2A gene, which encodes a histone H3 lysine K4 (H3K4) methyltransferase involved in transcriptional regulation. Clinically, the syndrome is characterized by developmental delay, distinctive facial features, short stature, hypertrichosis, and neurological manifestations such as hypotonia and seizures. In this single-patient report, we describe additional clinical findings, including interstitial lung disease and hypertrophic pyloric stenosis requiring surgical intervention. These may represent rare manifestations of WSS that require confirmation in further reports before a formal expansion of the phenotypic spectrum can be established. Most pathogenic KMT2A variants arise de novo and are typically nonsense or frameshift; however, missense variants have also been reported and may have complex functional consequences. Haploinsufficiency is considered the primary pathogenic mechanism, leading to the disruption of chromatin modification and transcriptional regulation. While emerging genotype–phenotype correlations are being identified, considerable variability remains. Given the single-patient nature of this study, these observations should be considered hypothesis-generating and require confirmation in additional cases. Full article

Histone demethylases regulate epigenetic modifications and DNA damage repair in fungal pathogens, yet their specific functions in Magnaporthe oryzae remain poorly understood. This study identifies MoRph1, a JmjC domain-containing histone demethylase that interacts with the COMPASS complex. Targeted deletion of MoRph1 resulted in significantly reduced vegetative growth, impaired conidiation, and defective appressorium formation. The mutant displayed compromised appressorial turgor pressure due to delayed degradation of glycogen and lipid reserves, leading to inefficient host penetration and attenuated virulence on rice and barley. MoRph1 localized to the nucleus, and its absence caused increased nuclear abnormalities under DNA damage stress, suggesting impaired genome stability maintenance. Biochemical analysis confirmed that MoRph1 specifically demethylates histone H3 lysine 36 trimethylation. Transcriptome analysis revealed altered expression of genes associated with DNA replication, mismatch repair, and oxidative stress response. These results establish MoRph1 as a crucial epigenetic regulator coordinating fungal development, infection structure function, energy mobilization, and DNA damage repair. This study underscores the importance of chromatin-level regulation in fungal pathogenicity and provides a foundation for future evaluation of MoRph1 as a potential antifungal target. Full article

Neurodevelopmental disorders (NDDs) are characterized by remarkable phenotypic heterogeneity, in which individuals harboring mutations in the same gene display divergent clinical manifestations, ranging from mild cognitive impairment to severe neurodevelopmental deficits. Advances in neurogenetics and neurogenomics have rapidly expanded the catalog of genes associated with NDDs and have provided unprecedented insight into the genetic architecture of these conditions. However, how identical or similar genetic variants give rise to such diverse phenotypic outcomes remains largely unknown. Ubiquitin-mediated protein regulation is a central mechanism controlling diverse processes essential for neural development, including chromatin regulation, transcriptional dynamics, protein turnover, and synaptic function. Importantly, ubiquitination is a multilayered regulatory process governed by multiple determinants, including the availability of ubiquitination sites on substrates, the activity of ubiquitin ligases, the opposing actions of deubiquitinases, and priming post-translational modifications such as phosphorylation or acetylation. These regulatory layers create a dynamic ubiquitination landscape that may vary across individuals, cell types, developmental stages, and environmental contexts. In this review, we discuss how insights from neurogenetics and neurogenomics can be integrated with knowledge of ubiquitin signaling to better understand the molecular basis of phenotypic heterogeneity in NDDs. We propose that differential ubiquitination represents an important mechanistic framework through which genetic variation is translated into diverse molecular and cellular outcomes. Understanding the interplay between neurogenetic variation and ubiquitin-dependent regulatory networks may provide new perspectives on disease mechanisms and inform future therapeutic strategies for neurodevelopmental disorders. Full article

Background: Adipogenesis is governed by a complex interplay between transcriptional regulation and epigenetic remodeling. While many transcriptional pathways have been well characterized, less is known about how chromatin-level regulation shapes the timing of gene expression, particularly in large animal models such as pigs. In this study, we investigated histone modification patterns associated with four key adipogenic transcription factor genes—PPARG, GATA2, CEBPA, and CEBPB—in porcine mesenchymal stem cells (MSCs) undergoing adipogenic differentiation. Methods: Using RT-qPCR and ChIP-qPCR, we profiled gene transcription levels and epigenetic marks, including promoter- and exon-specific enrichment of the activating histone marks H3K9ac and H4K8ac, as well as the repressive mark H4K20me3, across six time points (day 0, 2, 4, 6, 8, and 10). Results: Although PPARG and GATA2 are located in close proximity on porcine chromosome 13, they exhibited distinct histone modification profiles. PPARG showed progressive promoter acetylation (H4K8ac) accompanied by transcriptional activation, whereas GATA2 displayed decreased exon acetylation (H3K9ac) associated with declining expression. In contrast, the H4K20me3 profile was similar for both genes, suggesting no direct association with their transcriptional activity. Interestingly, CEBPA (chromosome 6) and CEBPB (chromosome 17) exhibited temporally distinct histone modification patterns consistent with their roles in intermediate and early stages of adipogenic differentiation, respectively. Increased enrichment of the H3K9ac mark preceded the rise in transcript levels of the analyzed genes. Promoter regions showed higher enrichment of H4K8ac compared with exonic regions. A higher level of H4K20me3 was also observed for CEBPA and CEBPB than for PPARG and GATA2, which appeared to be more related to chromosomal localization than to direct transcriptional regulation. Conclusions: Together, these results reveal complex interactions between transcriptional dynamics and selected histone modifications that depend on both the gene analyzed and the stage of adipocyte differentiation. This study provides new insights into the epigenetic regulation of porcine adipogenesis and highlights chromatin context as an additional layer influencing transcriptional control. Full article

Background: Fertility preservation aims to maintain reproductive potential in patients undergoing potentially gonadotoxic treatments, increasingly relying on centralized cryobanks requiring ovarian tissue transport. Ovarian tissue cryopreservation is a widely implemented, evidence-based procedure for young women (age 18–35) with a regular ovarian reserve. The ovaries of patients are typically transported overnight to a centralized cryobank for freezing and storage, using a certified hypothermic organ preservation solution such as histidine-tryptophan-ketoglutarate (HTK) at 4–8 °C. The molecular effects of transport on ovarian tissue remain unclear. Methods: In this prospective study of 36 breast cancer patients, we compared whole-transcriptome RNA (RNA-seq) expression in 18 frozen–thawed ovarian biopsies after overnight hypothermic transport followed by slow-freezing versus 18 direct slow-freezing within ≤2 h under FertiPROTEKT-standard conditions. Results: The RNA-seq analysis identified 6 significantly upregulated genes (Bonferroni < 0.05, fold change > 1.5), including histone H2B and mitochondrial NADH dehydrogenase subunit 6 (MT-ND6). The small number of differentially expressed genes suggests only limited transcriptional changes between the two transport conditions. H2B upregulation was confirmed by qPCR, while MT-ND6 showed only moderate levels in RNA-seq but remained stable in qPCR. Immunohistochemical analysis confirmed protein presence and localization in formalin-fixed tissue from four samples, constituting, to our knowledge, the first report of MT-ND6 protein expression in human ovarian tissue. Conclusions: Overall, these results are consistent with subtle changes in chromatin organization and mitochondrial energy metabolism. Since RNA-seq revealed only modest differences in gene expression, with no appreciable up- or downregulation of apoptosis- or damage-related genes after ≤24 h, this indicates tissue stability under the studied combined conditions (transport + cryopreservation). These findings are consistent with the feasibility of the workflow under the studied conditions of centralized ovarian tissue cryobanking combined with overnight transportation and hypothermic HTK solution. Full article

Vitiligo is characterized by epidermal melanocyte destruction, with autoreactive CD8⁺ T cells playing a central pathogenic role, yet the mechanisms driving their hyperactivation remain unclear. Lactate has emerged as a key immunometabolite that functions as both a signaling molecule and an epigenetic modulator via protein lactylation. Nevertheless, the role of lactate in vitiligo pathogenesis has not been explored. Here, we report that serum lactate levels are significantly elevated in vitiligo patients and correlate positively with disease activity. In a mouse model, lactate administration accelerated vitiligo progression, accompanied by increased CD8⁺ T cell infiltration and melanocyte destruction in lesional skin. In vitro, lactate enhanced CD8⁺ T cell effector molecule expression (granzyme B, perforin, IFN-γ, CD107a) and cytotoxic function. Mechanistically, lactate increased global protein lactylation in CD8⁺ T cells, with marked enrichment at histone H3 lysine 9 (H3K9). H3K9 lactylation (H3K9la) was associated with enhanced chromatin accessibility and transcriptional activation of effector genes, as revealed by RNA sequencing and CUT&Tag analyses. Pharmacological inhibition of lactate production or lactylation abrogated these effects. Collectively, our findings identify lactate as a critical driver of CD8⁺ T cell pathogenicity in vitiligo through H3K9la-mediated epigenetic reprogramming, highlighting lactate metabolism and lactylation as potential therapeutic targets. Full article