Search Results (411)

Estrogen-related receptor beta (ESRRB) is thought to be an orphan receptor that functions as a transcription factor, pioneer factor, and mitotic bookmarker to regulate cell stemness, pluripotency, and differentiation. This study (1) investigates whether calcium and cadmium activation of ESRRB regulates signaling pathways of stemness and pluripotency, (2) explores the transcriptomic and biological alterations of metal activation of ESRRB, and (3) reveals the underlying mechanisms by which metals activate ESRRB. In HEK293T cells, treatment with calcium and cadmium increased the expression of ESRRB-regulated genes that was blocked by an ESRRB antagonist. In the breast cancer cell line MDA-MB-453, treatment with calcium, cadmium, or a synthetic agonist also increased the expression of ESRRB-regulated genes that was blocked by the antagonist, enhanced ESRRB nuclear localization, increased the recruitment of RNA polymerase 2 to estrogen-related receptor response elements (ERRE), enhanced cell stemness and proliferation pathways, and induced the expression of estrogen receptor alpha (ESR1 or Erα). Mutational analysis and molecular docking identified potential metal interaction sites within ESRRB’s ligand-binding domain. Together, these results suggest calcium acts as a natural ligand for ESRRB and cadmium, which mimics calcium, activate ESRRB to mediate cell stemness and pluripotency. Full article

Osteoporosis is a systemic skeletal disease that severely impairs the health of the elderly population. The interaction between the receptor activator of the NF-κB ligand (RANKL) and its receptor RANK is critical for osteoclast differentiation and function. Therefore, targeting the RANKL/RANK interaction represents a promising strategy for osteoporosis. In this study, we employed a newly established yeast two-hybrid system based on RANKL/RANK interaction and identified IMB-R38, a novel benzamide compound that dose-dependently blocked RANKL/RANK interaction by inhibiting the growth of AH109 cells harboring pAD-RANKL/pBD-RANK plasmids in quadruple-dropout medium. IMB-R38 significantly suppressed osteoclast differentiation, disrupted F-actin ring formation, and downregulated the expression of osteoclast-specific genes, including NFATc1 and MMP9 in RANKL-induced RAW264.7 macrophages. IMB-R38 also promoted osteoblast differentiation by upregulating the expression of osteogenic genes. Importantly, in a dexamethasone (DXM)-induced osteoporotic zebrafish model, IMB-R38 significantly increased bone mineralization, with anti-osteoporosis efficacy superior to that of alendronate sodium (Alen). RT-qPCR assays showed that IMB-R38 significantly upregulated the mRNA expression of osteogenesis genes (Bmp2, Runx2a, Runx2b, Sp7, Alp, and Oc) while markedly downregulating that of the osteoclastogenesis genes (Mmp9, Mmp13, and Mmp2) compared with the DXM group. Mechanistically, an SPR assay confirmed that IMB-R38 directly binds with RANK but not RANKL to disrupt RANKL/RANK interaction. Furthermore, Asp168 of RANK was identified as a key amino acid that mediates both RANKL interaction and IMB-R38 binding. The inhibition of RANKL/RANK by IMB-R38 suppressed JNK phosphorylation and, consequently, osteoclast differentiation and function. Collectively, our findings identify IMB-R38 as a novel RANKL/RANK inhibitor with therapeutic potential for osteoporosis through its regulation of bone metabolism. Full article

Multiple sclerosis (MS), the most prevalent chronic inflammatory, demyelinating and neurodegenerative disease of the central nervous system in young adults, exhibits marked sexual dimorphism, with a 3:1 female-to-male ratio, but more severe symptoms and greater neurological damage in males. Increasing attention has focused on identifying circulating molecules that reflect inflammatory activity within the central nervous system and could clarify the mechanisms underlying MS. Pleiotrophin (PTN), a cytokine implicated in autoimmune and neurological diseases, is significantly elevated in patients with relapsing-remitting MS (RRMS). To explore the potential contribution of PTN and its receptors to neuroinflammatory signaling, we quantified the mRNA expression of PTN receptors in peripheral blood mononuclear cells from RRMS patients compared to untreated RRMS patients and healthy control subjects. We further performed an in silico molecular docking and molecular dynamics analysis to assess the possible functional significance of PTN-receptor interactions. Our results show a significant overexpression of integrin subunit beta-3 (ITGB3) mRNA in peripheral blood mononuclear cells from RRMS patients compared to healthy control subjects. Molecular docking shows that PTN could binds to the metal ion-dependent adhesion site domain of ITGB3 via Mg²⁺/Ca²⁺-mediated stabilization and has a higher binding affinity than fibrinogen, the canonical endogenous ligand. These findings suggest that ITGB3 could be a dynamically regulated integrin receptor in RRMS that may participate in PTN-driven neuroinflammatory pathways in peripheral blood immune cells, influenced by disease stage, sex, and immunotherapy. While our results support the biological plausibility of PTN–ITGB3 engagement, they remain hypothesis-generating and require functional validation. The integration of molecular expression data and computational modeling underscores the potential involvement of ITGB3 as a possible participant in MS and warrants further investigation of its clinical and mechanistic role. Full article

The cannabinoid receptor type 2 (CB₂) is increasingly recognized as a crucial regulator of neuroimmune balance in the brain. In addition to its well-established role in immunity, the CB₂ receptor has been identified in specific populations of neurons and glial cells throughout various brain regions, and its expression is dynamically increased during inflammatory and neuropathological conditions, positioning it as a potential non-psychoactive target for modifying neurological diseases. The expression of the CB₂ gene (CNR2) is finely tuned by epigenetic processes, including promoter CpG methylation, histone modifications, and non-coding RNAs, which regulate receptor availability and signaling preferences in response to stress, inflammation, and environmental factors. CB₂ signaling interacts with TRP channels (such as TRPV1), nuclear receptors (PPARγ), and orphan G Protein-Coupled Receptors (GPCRs, including GPR55 and GPR18) within the endocannabinoidome (eCBome), influencing microglial characteristics, cytokine production, and synaptic activity. We review how these interconnected mechanisms affect neurodegenerative and neuropsychiatric disorders, underscore the species- and cell-type-specificities that pose challenges for translation, and explore emerging strategies, including selective agonists, positive allosteric modulators, and biased ligands, that leverage the signaling adaptability of the CB₂ receptor while reducing central effects mediated by the CB₁ receptor. This focus on the neuro-centric perspective repositions the CB₂ receptor as an epigenetically informed, context-dependent hub within the eCBome, making it a promising candidate for precision therapies in conditions featuring neuroinflammation. Full article

(1) Background: After HBV infection, viral transcripts and host RNA form a multi-layered interwoven regulatory network. However, a comprehensive map encompassing mRNA, miRNA, lncRNA, and circRNA is still lacking. This absence complicates the systematic explanation of the molecular mechanisms driving immune escape and metabolic reprogramming during the persistent infection stage. (2) Methods: In this study, we established a mouse model of chronic HBV infection and analyzed the differential expression of mRNA, miRNA, lncRNA, and circRNA through whole transcriptome sequencing (WTS). We constructed a competing endogenous RNA (ceRNA) network to systematically evaluate the overall impact of HBV on the host’s immune-metabolic pathways. (3) Results: RNA sequencing results indicated that HBV infection significantly up-regulated 194 mRNAs, 18 miRNAs, 184 lncRNAs, and 28 circRNAs, while down-regulating 42, 16, 122, and 31 corresponding transcripts, respectively. The differentially expressed genes were primarily enriched in pathways related to metabolism, immunity/inflammation, and signal transduction-ligand receptor interactions. Furthermore, the competitive endogenous RNA networks of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA constructed on this basis further identified miR-185-3p as a key core node. (4) Conclusions: In this study, based on whole transcriptome data, the gene expression profiles of rcccDNA/Ad-infected Alb-Cre transgenic mice (chronic HBV infection model) and normal Alb-Cre mice were systematically compared, and the core regulatory factor miR-185-3p of key differentially expressed genes was screened. The microRNA is expected to provide a new target for the precise treatment of chronic hepatitis B by targeted intervention of viral replication and high liver inflammation. Full article

Background: Intratumour heterogeneity (ITH) is one of the key characteristics of cancer and is closely associated with patient prognosis, treatment resistance, and tumor metastasis. Nevertheless, the study of ITH in hepatocellular carcinoma (HCC) remains limited. Methods: The present study elucidated the influence of ITH on the tumor microenvironment (TME) in HCC. We applied Non-negative Matrix Factorization (NMF) analysis to a cohort of 78 single-cell RNA sequencing (scRNA-seq) HCC samples to systematically characterize ITH. Furthermore, by integrating spatial transcriptomics (ST) data from five HCC patients, we comprehensively analyzed the spatial organization and functional properties of distinct niches within HCC. We conducted a detailed analysis of the cell-type co-localization relationships within the TME and constructed a comprehensive atlas of HCC spatial organization. Results: We observed a co-localization relationship between hypoxia tumor cells, plasmalemma vesicle-associated protein (PLVAP⁺) endothelial cells (EC), and vascular endothelial growth factor A (VEGFA⁺) cancer-associated fibroblasts (CAF), suggesting a key role for hypoxia tumor cells in VEGFA⁺ CAF transformation and tumor angiogenesis. We identified a unique boundary region enriched with dendritic cells1 (DC1), interferon-expressing tumor cells, lymphatic EC, C–X–C Motif Chemokine Ligand 10 (CXCL10⁺) macrophages (Mac), and secreted phosphoprotein 1 (SPP1⁺) Mac located between the tumor-infiltrating immune cells and tumor regions. Furthermore, we found that CXCL10⁺ Mac and SPP1⁺ Mac, despite co-localizing in the boundary region, exhibit distinct functions, which may be attributed to their unique spatial locations, with the former being closer to the immune-infiltrated region and the latter more proximal to the tumor area. Conclusions: Our study highlights the critical role of spatial interactions between tumor cells and the microenvironment in HCC. The findings offer new insights into ITH and underscore the importance of spatial organization in understanding cancer biology and designing future precision therapies. Full article

Food wanting in honeybees is closely associated with the neurotransmitter dopamine; however, the regulatory role of non-coding RNAs in this process remains unclear. In this study, using the honeybee (Apis mellifera) as a model organism, we systematically investigated the molecular network and functional mechanisms by which long non-coding RNAs (lncRNAs) regulate the dopaminergic signaling pathway to mediate food wanting. By establishing two appetite-state models, fed honeybees (FB) and starved honeybees (SB), and combining brain dopamine quantification with behavioral assays, we found that dopamine levels in the honeybee brain were significantly elevated during starvation. Using transcriptome sequencing, we identified 1146 lncRNAs in the honeybee brain, among which 174 were differentially expressed long noncoding RNAs (DElncRNAs) between the two states, predominantly upregulated. Cis- and trans-acting analyses revealed that these DElncRNAs could target multiple genes involved in neural signal transmission, synaptic function, and dopaminergic pathways. KEGG enrichment analysis showed that their target genes were significantly enriched in pathways such as taste transduction, dopaminergic synapse, and neuroactive ligand–receptor interaction. Furthermore, a ceRNA network revealed that several DElncRNAs may regulate dopamine synthesis genes, including DOPA decarboxylase (Ddc), by competing for dopamine-associated miRNAs such as miR-375-3p, influencing food wanting in honeybees. Overall, our findings provide a foundation for uncovering the potential regulatory mechanisms of DElncRNAs in honeybee food wanting and offer new insights into the connection between neural regulation and behavioral manifestation in insects. Full article

Acne vulgaris is a prevalent inflammatory disease of the pilosebaceous unit in which Cutibacterium acnes (C. acnes) contributes to lesion initiation and persistence, supporting antibacterial interventions as a component of clinical management. Given the essential role of the 50S large ribosomal subunit—particularly 23S rRNA sites in the peptidyl transferase center and nascent peptide exit tunnel—in C. acnes protein synthesis and viability, targeting the 50S offers an effective path to lead discovery for acne treatment. Here, we present an integrated computational–experimental workflow to identify anti-C. acnes candidates from a 186,659-compound natural product library. Curated 50S/23S ligands trained and validated two ML-QSAR regression models built on different molecular fingerprints (MACCS keys and PubChem 2D) to predict anti-C. acnes activity and rapidly triage the library. Compounds were further screened by ADMET filtering and structure-based docking to 23S rRNA pockets, followed by cluster and interaction analysis. Among six experimental hits, three compounds exhibited MICs against C. acnes of ≤8 μg/mL, with tripterin, a pentacyclic triterpenoid, being the most potent (0.5–2 μg/mL across two acne-relevant strains). Collectively, these results indicate that a 50S ribosomal-focused, multistage computational screening workflow, integrated with in vitro assays, efficiently prioritizes compounds with quantifiable anti-C. acnes activity across a broad range of natural products. Full article

Interest in non-canonical DNA structures continues to grow, in part fueled by the recent discovery of a new structure, G-triplex DNA. Originally proposed as folding intermediates for G-quadruplex DNA, G-triplex DNA has more recently been shown to form from truncated G-quadruplex sequence oligonucleotides and other, specifically designed sequences. In this review, we provide the first, comprehensive survey of G-triplex DNA and RNA, covering the literature up to 2024. We include reports of G-triplex DNA from bulk solution and single-molecule approaches, the structural characterization of G-triplex DNA, and the breadth of oligonucleotide sequences that have been reported to form these structures. The formation of G-triplex RNA structures is also reviewed. The evolving understanding of sequence and environmental effects on G-triplex formation are presented together with challenges due to structural polymorphism and competing formation of multimeric G-quadruplex structures. Hints of the biological relevance of G-triplexes are provided by reports of protein recognition of these structures and their effects on DNA replication in vitro. Interaction of G-triplex DNA with a variety of ligands has been reported, although the search for selective ligands that can distinguish G-triplex from G-quadruplex is on-going. The vast majority of publications in the area have focused on the utilization of G-triplex in biosensing applications, which has shown some advantages compared to G-quadruplex-based systems. These results highlight the potential utility of G-triplex structures in a variety of domains and show its promise in applications in biotechnology, medicine, and research. Full article

This study aimed to evaluate the individual and combined effects of dandelion extract and akebia extract on growth, inflammation, and gut microbiota in weaned rabbits. Using a two-factor randomized design, 120 rabbits (1.219 kg ± 0.077 kg, 35 days of age) were divided into four groups (10 replicates/group). Growth metrics (feed intake, fecal score, weight gain) and biological samples (blood, liver, jejunal/ileal mucosa, digesta) were analyzed over 28 days. Key results indicated that combined dandelion and akebia supplementation significantly increased daily weight gain during the first week (p < 0.05). Dandelion alone reduced liver Immunoglobulin G (IgG) and jejunal interleukin 6 (IL-6) (p < 0.05). Akebia supplementation decreased serum immunoglobulin A (IgA)/IL-6, liver interleukin 1β (IL-1β)/IL-6/IgG, and jejunal IL-1β/IL-6/IgG/IgA (p < 0.05). Gene expression revealed dandelion downregulated liver interferon-γ (IFN-γ)/interleukin 10 (IL-10) and jejunal IL-1β/interleukin 10 (TNF-α) (p < 0.05), while akebia suppressed hepatic C-C Motif Chemokine Ligand 3 (CCL3)/C-X-C Motif Chemokine Ligand 10 (CXCL10)/IFN-γ/IL-1β and mucosal IL-1β/IFN-γ (p < 0.05). A significant interaction effect (p < 0.05) between dandelion and akebia reduced ileal IL-6/IL-10/TNF-α and jejunal CXCL10/IL-10 mRNA expression. Akebia also increased cecal microbial diversity and the abundance of Oxalibacilli and Sutterella while reducing Firmicutes abundance (p < 0.05). In conclusion, both extracts modulated immunity and attenuated inflammatory responses through modulation of immunoglobulins, cytokines, and chemokines. Their combination demonstrated synergistic anti-inflammatory effects, alongside beneficial shifts in gut microbiota composition. Full article

This study systematically assessed the regulatory effects of Yunnan Lufeng aromatic vinegar (LFAV) on the intestinal microbiota composition, short-chain fatty acids, and cecal metabolites in mice. 16S rRNA high-throughput sequencing revealed that LFAV intervention significantly altered gut microbiota diversity; the M-L group exhibited 19.98% unique operational taxonomic units, while both Chao1 (496.63 ± 42.14) and Shannon indices (6.68 ± 0.32) increased by 37.46% and 3.25%, respectively, compared to the blank group, indicating enhanced microbiota richness. Species composition analysis demonstrated that the relative abundance of Firmicutes reached 75.4% in the M-L group, a 24.4% increase over the B group, whereas Bacteroidetes abundance decreased to 8.2%. GC-MS analysis detected peak butyric acid levels in the M-L group. Untargeted metabolomics identified 520 metabolites, of which 60 were significant differential metabolites. Cluster heatmap and Z-score analyses demonstrated that LFAV intervention significantly modulated mouse metabolites. KEGG pathway enrichment analysis indicated the upregulation of pathways including neuroactive ligand–receptor interactions and renin secretion. Pearson correlation analysis showed a strong positive correlation (p < 0.01) between Lactobacillus and acetic acid/butyric acid; concurrently, increased Lactobacillus proliferation and elevated butyric acid levels were observed in the M-L and M-M groups. These findings suggest that LFAV intervention promotes the proliferation of beneficial bacteria, which may improve intestinal health. Collectively, LFAV significantly modified gut microbiota structure and metabolites in mice, highlighting its potential as a natural prebiotic or functional food ingredient and providing a scientific basis for developing functional vinegar products. Full article

Since forkhead box P3 (FOXP3) is a hallmark of regulatory T (Treg) cells, the expansion of FOXP3⁺ adult T-cell leukemia/lymphoma (ATL) cells is believed to contribute to immune suppression and the pathogenesis of ATL. However, the mechanisms underlying the expansion of FOXP3⁺ ATL cells remain unclear. OX40, a co-stimulatory molecule, is expressed in ATL cells, and OX40 signaling has been shown to promote the differentiation and proliferation of Treg cells in mouse models. To investigate the mechanisms driving the expansion of FOXP3⁺ ATL cells, we examined the expression of OX40 and its ligand, OX40L. Our findings revealed that OX40 expression was elevated in patients with ATL and with a high frequency of FOXP3⁺ ATL cells. Flow cytometric analysis of peripheral blood mononuclear cells (PBMCs) from patients with acute ATL cultured for 18 h demonstrated that FOXP3⁻ and FOXP3⁺ cells predominantly expressed OX40L and OX40, respectively. Furthermore, small interfering RNA-mediated FOXP3 knockdown in HTLV-1-infected cell lines increased OX40L expression. These results suggest that interactions between FOXP3⁻ OX40L⁺ cells and FOXP3⁺ OX40⁺ cells may promote the proliferation of FOXP3⁺ ATL cells. Full article

G-quadruplexes (G4s) are four-stranded DNA or RNA structures formed by guanine-rich sequences. They occur in functional regions of the genomic material, including the promoter part of genes, regulatory region, and telomeric threads. G4s play a key role in various biological processes, including transcription, replication, and telomere maintenance. Guanidine-containing derivatives can bind to G-quadruplexes, either by intercalating into the structure or by interacting with the grooves or loops. The binding can stabilize the G-quadruplex, potentially affecting its biological function. In this paper, the ability of guanidinium-containing hordatines to interact with G4 was evaluated. Analogues lacking the guanidinium group or showing the benzofuran system instead of the dihydrobenzofuran core were prepared and tested as well. NMR titration and docking calculations were used to probe the binding of the compounds to G4 of c-MYC oncogene. Spectroscopic analyses were consistent with a significant interaction of benzofurans 3 and 4 at the 5′-end and 3′-end tetrads and with the formation of ligand/G-quadruplex complexes with a 2:1 stoichiometry. The resulting data were supported by docking simulations. Cytotoxic activity was evaluated on a model of U2OS osteosarcoma (ATCC HTB-96) and breast cancer (MDA-MB-231) cell lines, further highlighting the key role of the guanidinium fragment and the benzofuran core in the G-quadruplex stabilization. Full article

Background/Objectives: Seasonal reproduction in mammals is primarily regulated by the hypothalamic–pituitary–ovarian (HPO) axis, yet its molecular mechanisms in subterranean rodents living in light-restricted environments remain poorly understood. This study aimed to characterize the transcriptional regulation of the HPO axis during seasonal estrus in the Manchurian zokor (Myospalax psilurus, M. psilurus), a fossorial rodent exhibiting distinct breeding cycles despite perpetual darkness. Methods: Hypothalamic, pituitary, and ovarian tissues were collected from female zokors during estrus and anestrus (n = 5 per group). RNA sequencing was performed, followed by de novo transcriptome assembly and bioinformatic analyses. Differentially expressed genes (DEGs) were identified using edgeR, and functional enrichment was assessed via GO and KEGG analyses. Key DEGs were validated by RT-qPCR. Results: A total of 513, 292, and 138 DEGs were identified in the hypothalamus, pituitary, and ovary, respectively. GO analysis highlighted enrichment in G-protein-coupled receptor signaling, oxidation–reduction processes, and calcium ion binding. KEGG pathway analysis revealed significant enrichment of the neuroactive ligand–receptor interaction pathway across all three tissues. Key candidate genes included Trh and Mc3r in the hypothalamus, Pitx2 and NR4A2 in the pituitary, and PTGER2 and Sphk1 in the ovary. Conclusions: This study provides the first comprehensive transcriptomic profile of the HPO axis in Manchurian zokors during seasonal estrus. The neuroactive ligand–receptor interaction pathway appears central to reproductive regulation, and several tissue-specific genes were identified as potential regulators of seasonal breeding. These findings enhance our understanding of reproductive adaptation in subterranean mammals and offer a foundation for further functional studies. Full article

Human immunodeficiency virus (HIV-1) and SARS-CoV-2 continue to co-burden global health, motivating discovery of broad-spectrum small molecules. Conessine, a steroidal alkaloid, has reported membrane-active and antimicrobial properties but remains underexplored as a dual antiviral chemotype. To interrogate conessine’s multi-target antiviral potential against key enzymatic and entry determinants of HIV-1 and SARS-CoV-2 and to benchmark performance versus approved comparators. Eight targets were modeled: HIV-1 reverse transcriptase (RT, 3V81), protease (PR, 1HVR), integrase (IN, 3LPT), gp120–gp41 trimer (4NCO); and SARS-CoV-2 main protease (M^pro, 6LU7), papain-like protease (PL^pro, 6W9C), RNA-dependent RNA polymerase (RdRp, 7BV2), spike RBD (6M0J). Ligands (conessine; positive controls: dolutegravir for HIV-1, nirmatrelvir for SARS-CoV-2) were prepared with standard protonation, minimized, and docked using AutoDock Vina v 1.2.0exhaustiveness 4; 20 poses). Binding modes were profiled in 2D/3D. Protocol robustness was verified by re-docking co-crystallized ligands (RMSD ≤ 2.0 Å). Atomistic MD (explicit TIP3P, OPLS4, 300 K/1 atm, NPT; 50–100 ns) assessed pose stability (RMSD/RMSF), pocket compaction (Rg, volume), and interaction persistence; MM/GBSA provided qualitative energy decomposition. ADMET was predicted in silico. Conessine showed coherent, hydrophobically anchored binding across both viral panels. Best docking scores (kcal·mol⁻¹) were: HIV-1—PR −6.910, RT −6.672, IN −5.733; SARS-CoV-2—spike RBD −7.025, M^pro −5.745, RdRp −5.737, PL^pro −5.024. Interaction maps were dominated by alkyl/π-alkyl packing to catalytic corridors (e.g., PR Ile50/Val82, RT Tyr181/Val106; M^pro His41/Met49; RBD L455/F486/Y489) with occasional carbon-/water-mediated H-bonds guiding orientation. MD sustained low ligand RMSD (typically ≤1.6–2.2 Å) and damped RMSF at catalytic loops, indicating pocket rigidification; MM/GBSA trends (≈ −30 to −40 kcal·mol⁻¹, dispersion-driven) supported persistent nonpolar stabilization. Benchmarks behaved as expected: dolutegravir bound strongly to IN (−6.070) and PR (−7.319) with stable MD; nirmatrelvir was specific for M^pro and displayed weaker, discontinuous engagement at PL^pro/RdRp/RBD under identical settings. ADMET suggested conessine has excellent permeability/BBB access (high logP), but liabilities include poor aqueous solubility, predicted hERG risk, and CYP2D6 substrate dependence.Conessine operates as a hydrophobic, multi-target wedge with the most favorable computed engagement at HIV-1 PR/RT and the SARS-CoV-2 spike RBD, while maintaining stable poses at M^pro and RdRp. The scaffold merits medicinal-chemistry optimization to improve solubility and de-risk cardiotoxicity/CYP interactions, followed by biochemical and cell-based validation against prioritized targets. Full article