Search Results (4,731)

N6-methyladenosine (m⁶A) is a reversible RNA modification that dynamically regulates gene expression by modulating RNA stability, splicing, nuclear export, translation, and maturation—thereby orchestrating organismal development. In birds, including geese, the liver is a multi-functional organ central to metabolic regulation. Studies on the dynamic patterns of RNA m⁶A modifications during healthy liver growth and development remain limited. Here, we performed integrative methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) on liver tissues from geese at three biologically defined stages: post-hatch day 0 (0 week, P), fast growth (10 weeks, F), and sexual maturation (30 weeks, S). The level of m⁶A modification in total RNA extracted from liver tissues was higher in P than in F samples. Compared with other groups, the S group recorded the lowest m⁶A modification. In addition, 1641, 668, and 558 m⁶A peaks were differentially modified in the P, F, and S groups, respectively. The m⁶A peaks in the liver of the three groups were mainly enriched in the coding sequence and 3′ untranslated region. Moreover, integrated multi-omics analysis (MeRIP-seq and RNA-seq), combined with protein–protein interaction networks analysis, identified CDK1 as a core cell cycle regulator and IGF2BP3—a well-established m⁶A reader—as a consistently differentially expressed gene across all developmental stages. The m⁶A-regulated cell cycle, p53 signaling pathway, and pyrimidine metabolism pathway were identified in liver tissue as novel potential targets for controlling geese growth and metabolism. Together, these findings shed light on the dynamic regulation of RNA methylation during distinct growth phases in geese and advance our understanding of epigenetic mechanisms underlying poultry liver development. Full article

Epilepsy affects more than 50 million individuals worldwide, and approximately one-third of patients remain refractory to existing antiseizure medications. Advances in gene therapy and genome editing have opened new possibilities for disease-modifying interventions that directly target the molecular and circuit-level mechanisms underlying epileptogenesis. Recent progress in central nervous system tropic viral vectors, non-viral delivery systems, and programmable genome-editing technologies has enabled precise manipulation of neuronal and glial function in preclinical epilepsy models. Strategies range from restoration of haploinsufficient genes implicated in monogenic epilepsies, such as SCN1A in Dravet syndrome, to modulation of neuronal excitability through engineered ion channels, neuropeptides, and astrocyte-based approaches. In parallel, CRISPR-derived platforms, including transcriptional activation and repression systems, base editing, and prime editing, offer new avenues for regulating gene expression in post-mitotic neurons without introducing double-strand DNA breaks. Despite these advances, significant translational challenges remain, including efficient and cell-type-specific delivery, long-term safety, and the risk of network-level side effects in the epileptic brain. This review critically examines recent gene therapy and genome-editing approaches for epilepsy, highlights key technological and biological barriers to clinical translation, and discusses emerging strategies that may enable durable and targeted treatments for drug-resistant epilepsies. Full article

Osteoarthritis (OA) is a multifactorial disease characterized by inflammation, extracellular matrix remodeling, and joint degeneration, and it still lacks disease-modifying treatments. Here, we applied an ex vivo OA model based on transwell co-cultures of cartilage and synovial membrane explants harvested from OA patients to compare the effects of adipose-derived stem/stromal cell (ASC) conditioned medium (CM) with dexamethasone (DEX), a clinically used corticosteroid. Explants were treated for 48 h with 100 nM DEX, CM derived from 5 × 10⁵ ASCs, or left untreated. Outcomes included gene and protein expression of key mediators, metalloprotease and aggrecanase activities, and nitric oxide release. DEX significantly reduced inflammatory markers (e.g., PTGS, IL-1β, and IDO) and VEGF expression in both tissues, while CM did not elicit consistent anti-inflammatory effects. Regarding matrix remodeling, both treatments reduced metalloprotease activity, with DEX modulating MMP3 and MMP13 expression in both tissues and CM reducing only MMP3 expression in cartilage while presenting high levels of TIMP-1. These results confirm the robustness of the model, demonstrated by reproducible responses to DEX and its high-throughput potential, and underscore the need for mechanistic studies to optimize novel biotherapeutics. Full article

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related deaths worldwide, arising from profound metabolic reprogramming and widespread epigenetic dysregulation. However, the role of epigenetic aberrations in modulating metabolic reprogramming and the interplay between cis-regulatory elements (CREs), such as promoters, enhancers and super-enhancers, and metabolic adaptation have not been systematically summarized. Therefore, this review aims to integrate current evidence to elucidate the mechanisms of how cis-regulatory elements (CREs) drive oncogenic and metabolic signals in HCC progression. For instance, enhancers and super-enhancers transcriptionally activate key metabolic genes involved in aerobic glycolysis (GLUT1, HK2, PKM2, LDHA), de novo lipogenesis (ACLY, FASN, ACC), glutaminolysis (SLC1A5, GLS), and nucleotide synthesis. Meanwhile, many metabolic intermediates, including acetyl-CoA, succinyl-CoA and lactate, act as cofactors or substrates for epigenetic modifiers, creating bidirectional feedback loops that reinforce CRE-driven malignant phenotypes. Therefore, aberrant CREs acts as “metabolic switches” that sense and respond to various metabolic conditions to sustain HCC growth. Consequently, targeted intervention against oncogenic CREs, such as super-enhancers or their co-activators, to disrupt CRE-mediated metabolic vulnerabilities, has emerged as a highly promising new paradigm for precision therapy in HCC. Full article

Mesoporous bioactive glass (MBG) has been extensively studied in bone regeneration due to its excellent bioactivity and osteoconductive properties. Here, we prepared amino-modified MBG (MBG-NH₂) adsorbed osteopontin (OPN) to form MBG-NH₂/OPN composites, enabling the sustained release of OPN and enhancing osteoblast differentiation and mineralization capacity. Interestingly, we observed that MBG-NH₂ promotes the formation of osteoid deposits and calcium deposition in vitro. Furthermore, we also found that MBG-NH₂/OPN significantly enhances cell adhesion, differentiation, and mineralization. Consistent with these observations, we found the expression of the osteoblast-specific marker gene increased, including bone morphogenetic protein 2 (Bmp2) and Collagen I. Intriguingly, we also found that MBG-NH₂/OPN promotes osteoblast differentiation and mineralization through activating the extracellular regulated protein kinases1/2 (Erk1/2) signaling pathway. We concluded that MBG-NH₂/OPN enhances osteoblast differentiation and mineralization through the Erk1/2 pathway. These findings indicate that MBG-NH₂/OPN is a new potential biomaterial for bone regeneration. Full article

Hypertrophic cardiomyopathy (HCM), the most common inherited cardiomyopathy, represents a paradigmatic condition for precision cardiovascular medicine. Once regarded as a monogenic autosomal dominant disorder driven by rare sarcomeric variants, HCM is now recognized as a genetically complex disease characterized by incomplete penetrance, variable expressivity, and heterogeneous clinical trajectories. This review summarizes current evidence on the evolving genetic architecture of HCM, emphasizing the predominant role of definitively validated sarcomeric genes, particularly MYBPC3 and MYH7, and the clinical value of gene panel expansion. Phenotypic variability reflects interactions among variant classes, gene-specific mechanisms, and modifying factors. Differences between missense and truncating variants, haploinsufficiency and poison-peptide effects, allelic imbalance, and age-dependent penetrance contribute to diverse disease expression. Emerging data further support oligogenic inheritance and polygenic modulation, with genome-wide association studies and polygenic risk scores elucidating their contribution to disease susceptibility and variability, especially in genotype-negative patients and carriers of rare variants. We also address genes with emerging evidence and underrecognized pathogenic mechanisms, including deep intronic and splice-altering variants that may explain part of the missing heritability. The importance of distinguishing phenocopies is highlighted, advocating for phenotype-anchored diagnostic pathways integrating clinical assessment, multimodality imaging, and targeted genetic testing. Overall, contemporary data support a targeted, gene-validity-driven approach to genetic testing, where molecular findings primarily inform diagnosis and cascade screening, while risk stratification remains phenotype-led and longitudinal. Future progress will depend on integrative models combining rare variants, polygenic background, imaging, and biomarkers to translate genetic complexity into actionable precision care. Full article

PAX3 plays a vital role in regulating proper growth, migration, differentiation, and survival during development of normal tissues, including those derived from the embryonic neural crest. PAX3 is a transcription factor with two separate DNA-binding domains and can positively (and less frequently, negatively) regulate gene expression. The levels of PAX3 can be modified by upstream molecular pathways, and its subsequent downstream functions are regulated through a wide range of protein interactions and posttranscriptional modifications. PAX3 direct downstream target genes are other transcription regulators and factors that modulate cellular proliferation, lineage specificity, migration, and survival. The pathways that PAX3 regulates during development may be recycled and subverted during disease progression, for example, during cancer progression, growth, and metastasis. Indeed, PAX3 is overexpressed in several cancers, including melanoma, neuroblastoma, and rhabdomyosarcoma. While there is still much that is unknown about the mechanisms by which PAX3 controls such a wide array of key cellular functions, a great deal of progress has been made to advance our understanding of this critical and multi-faceted factor. Full article

Acidic chitinase (Chia) degrades chitin, a structural polysaccharide in insect exoskeletons, and plays important roles in omnivorous and insectivorous mammals and birds. In birds, gene duplications have generated multiple Chia paralogs with functional divergence, but the molecular basis for this diversification remains unclear. Here, we characterized three chicken Chia paralogs (Chia1–3) and identified distinct pH-dependent enzymatic profiles. Chia1 is enzymatically inactive but was captured by chitin-affinity resin despite lacking a canonical chitin-binding domain, suggesting residual substrate interaction through the catalytic domain or a non-catalytic role. Chia2 exhibits maximal activity at pH 2.0, whereas Chia3 peaks at pH 5.0 and displays broader activity. Exon swapping and site-directed mutagenesis identified residues 104 (Ala in Chia2, Asp in Chia3) and 269 (His vs. Asn) as key contributors to pH-dependent activity differences. Reciprocal substitutions shifted pH profiles accordingly. Structural modeling and computational pKa predictions suggested that D213 and residue 269 may function as a pKa-regulating module influencing catalytic ionization. Comparative sequence analysis revealed lineage-specific conservation of these residues, consistent with adaptive divergence. Our findings show that limited amino acid substitutions can markedly modify pH-dependent enzymatic activity, providing mechanistic insight into how local residue variation contributes to the functional diversification of duplicated genes. Full article

Sensitive quantitative detection of breast cancer gene synthetic sequences is crucial for related biosensing research. To address the limitations of traditional sensors for detecting ultra-low concentrations, this study developed a novel fiber-optic biosensor by combining nanomaterial sensitization with nanoparticle signal amplification strategies. A fiber optic sensor based on single-mode fiber-thin-core fiber-multimode fiber-single-mode fiber structure was fabricated and functionalized with black phosphorus (BP) nano-interface. The Au@cDNA complex was prepared by covalently immobilizing sulfhydryl-modified complementary DNA (cDNA) on the surface of gold nanoparticles (AuNPs). The complex specifically hybridized with the probe DNA (pDNA) immobilized on the surface of the sensor. The experimental results show that this sensor has a sensitivity of 0.793 nm/lgM and a detection limit of 20.27 fM in the concentration range of 100 fM to 100 nM. Specifically, the BP-functionalized sensor exhibits superior dynamic range, higher sensitivity, and lower detection limits for detecting Au@cDNA. The synergistic effect of interfacial sensitization by BP and signal amplification by AuNPs significantly enhances detection performance, providing a promising platform for ultra-sensitive biosensing applications. Full article

Background: Cervical carcinoma remains a widespread cancer worldwide, primarily caused by persistent infection with high-risk human papillomavirus (HPV). HPV types 16 and 18 account for approximately 70% of cervical cancer cases. Although prophylactic HPV vaccines are commercially available, their high cost and reliance on expensive expression platforms limit their accessibility in developing countries. Objectives: This study aimed to develop a cost-effective, plant-based HPV vaccine candidate by expressing capsomeric HPV-16 and HPV-18 L1 antigens in Brassica oleracea (broccoli). Methods: Modified L1 from HPV types 16 and 18 were designed to retain capsomeric assembly and fused with heat-labile enterotoxin B subunit (LTB). Immunoinformatics analyses were used to assess antigenicity, epitope distribution, and structural characteristics. Codon-optimized genes were cloned using Gateway^® technology and expressed in broccoli via Agrobacterium-mediated transformation. Transgenic plants were validated by PCR and qRT-PCR. Protein accumulation was quantified, and immunogenicity was evaluated in mice. Results: PCR and qRT-PCR confirmed the stable integration of two copies of the LTB-L1 transgenes in broccoli plants. Western blotting detected L1 protein at ~56.5 kDa, indicating the cleavage of the LTB-L1 fusion protein. The correct folding of L1 capsomeres was verified by antigen-capture ELISA. The recombinant proteins accumulated to approximately 0.33% and 0.35% of total soluble protein for HPV-16 and HPV-18, respectively. The immunization of mice with transgenic L1 induced significant humoral immune responses, comparable to those elicited by purified VLPs. Conclusions: The results demonstrate broccoli as a promising platform for the expression of immunogenic HPV L1 capsomeres and highlight its potential for the development of affordable, plant-based HPV vaccines. Full article

Background/Objectives: The large size of commonly used regulatory elements such as the cytomegalovirus (CMV) immediate-early promoter imposes a significant burden on the already restricted payload capacity of first-generation adenoviral vectors, potentially hindering the development of multi-antigen vaccine candidates. To address this limitation, we have engineered a panel of novel, small, semi-synthetic promoters designed to leverage the changes in transcriptomic milieu following adenoviral vector entry. Methods: Eight synthetic enhancer modules (SE1–SE8) were designed in silico, each composed of transcription factor binding sites (TFBSs) previously found in host genes that are upregulated during early adenoviral infection. These synthetic enhancers were coupled with a minimal CMV core promoter to generate a panel of compact semi-synthetic promoters (cSE1–cSE8), and their activity was evaluated in the context of ChAdOx1 viral vectors expressing GFP or a modified Plasmodium falciparum circumsporozoite (CSN) antigen. Promoter performance was characterised in vitro via flow cytometry, RT-qPCR, and Western blotting, and in vivo by quantifying antigen-specific T-cell (IFN-γ ELISpot) and IgG antibody (ELISA) responses in BALB/c mice. Results: In vitro characterisation revealed a wide range of promoter activity across the panel, with cSE3 and cSE5 driving transgene expression levels comparable to the benchmark CMV promoters despite their markedly reduced genomic footprint. In vivo, ChAdOx1 vectors incorporating cSE3 and cSE5 elicited potent antigen-specific T-cell and IgG responses that were comparable to those induced by the larger CMV control promoters. Conclusions: We have successfully developed semi-synthetic promoters that match the potency of the much larger, frequently used CMV promoters whilst simultaneously reducing genomic footprint. These novel regulatory elements will facilitate the design of next-generation vaccines, particularly those requiring large antigens or multi-antigen cassettes. Full article

Endoplasmatic reticulum (ER) stress is an imbalance between the load of unfolded proteins and the ability of cellular mechanisms to handle it. Under the influence of this stress, cells activate the unfolded protein response (UPR). The molecular mechanisms of ER stress have been repeatedly linked to metabolic and inflammatory diseases, such as obesity and allergic inflammation. The aim of our study was to investigate if the allergic inflammation in adipocytes affects the expression of UPR pathway genes and Ormdl3 and whether miRNA-665 can modify inflammatory response in adipocytes. We isolated rat preadipocytes and treated them with IL-13 to induce allergic inflammation. Later, we transfected them with miRNA-665 inhibitor. RNA was isolated from adipocytes and analyzed by qPCR. From cell culture medium, we performed an LDH assay and ELISA for secreted IL-6 and TNFα proteins. A comparison between control cells and IL-13-treated cells showed significant differences in the expression of most of the studied UPR pathway genes, Ormdl3 and Bax. Comparing the IL-13-treated cells after miR-665 transfection with non-transfected ones, we observe significant differences only in Ire1α gene. Our research suggests that allergic inflammation induces an adaptive UPR in adipocytes and miR-665 may selectively modify this response, triggering the IRE1/XBP1 axis. Full article

Duchenne muscular dystrophy (DMD) is a severe X-linked neuromuscular disorder caused by loss-of-function mutations in the dystrophin gene, leading to progressive muscle degeneration, motor decline, respiratory compromise, and cardiomyopathy. Diagnosis typically occurs in early childhood following recognition of motor delays, markedly elevated creatine kinase, and confirmatory genetic testing. Over the past decade, the therapeutic landscape for DMD has expanded substantially, evolving from exclusively supportive care to patient-centric multifaceted treatment paradigms, including corticosteroids, mutation-specific therapies, small molecule disease-modifying approaches, and gene replacement strategies. Despite these advances, no currently available therapy restores full-length dystrophin or completely halts disease progression. This review provides a clinically oriented comprehensive overview of currently Food and Drug Administration (FDA)-approved medications for DMD, with particular emphasis on corticosteroids, exon-skipping therapies, nonsense mutation readthrough agents, recently approved gene therapy, and select ongoing gene therapy trials. We summarize mechanisms of action, clinical efficacy, safety considerations, regulatory status, and highlight the challenges of integrating these therapies into longitudinal care. Through illustrative clinical vignettes, we highlight the real-world complexity of treatment selection, shared decision-making, and longitudinal care planning in contemporary DMD management. Full article

Background/Objectives: Xu Chunfu’s Modified Xianglian Pill (XXLP) has been used for centuries in Chinese medicine to treat “diarrhea” and “dysentery,” conditions analogous to modern ulcerative colitis (UC). However, the scientific basis for its efficacy and mechanisms remains unclear. Methods: The chemical composition of XXLP was analyzed via UPLC-ESI-MS/MS. A colitis mouse model was established using DSS, and the therapeutic effects were assessed based on body weight, disease activity index (DAI), colon length, and histopathology. Inflammatory cytokines were measured using ELISA. Proteomic analysis and molecular docking identified key targets, which were validated using LPS-induced HT-29 cells via Western blot (WB), qRT-PCR, immunofluorescence (IF), and transmission electron microscopy (TEM). Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Results: Analysis of XXLP led to the detection of 373 compounds. XXLP significantly improved colitis symptoms, including weight loss and colon shortening, and reduced the concentrations of inflammatory markers IL-1β, IL-18, TNF-α, and IL-6. Proteomics and molecular docking identified NADPH oxidase 2 (NOX2) as a key target of XXLP intervention in mice with colitis. qRT-PCR, WB, IF, and TEM results further confirmed that XXLP effectively suppressed the expression of NOX2 and its associated protein levels. Sequencing analysis of 16S rRNA showed that XXLP significantly increased the relative abundance of beneficial bacterial genera (Muribaculaceae and Ruminococcaceae) while markedly reducing the levels of harmful bacteria (Enterobacteriaceae). Correlation analysis revealed that specific microorganisms were correlated with NOX2-related protein expression and severity of colonic inflammation. Conclusions: XXLP effectively alleviates colitis by suppressing inflammatory responses. Its mechanism involves regulating the NOX2/ROS/mitochondria/NLRP3 axis and altering gut microbiota composition, providing novel insights for colitis treatment. Full article

Diet is a major, modifiable determinant of cardiometabolic, cancer, and inflammatory disease risk, yet individuals frequently exhibit substantial heterogeneity in metabolic and clinical responses to similar dietary exposures. Genetic susceptibility and its interplay with diet plausibly contribute to this variability, motivating gene–diet (G×D) interaction research and the broader ambition of precision nutrition. Translation has lagged, however, because interaction effects are typically modest, context-dependent, and difficult to reproduce, particularly in the presence of pervasive dietary measurement error, heterogeneous exposure definitions, and stringent multiplicity correction. A methodologically oriented synthesis is presented across eight domains of contemporary G×D epidemiology: classical regression interaction models; efficient study designs; dietary assessment and measurement error; dietary patterns, mixtures, and non-linear modeling; genome-wide and polygenic approaches; causal inference frameworks; multi-omics integration; and machine learning. Central concepts include the recognition that “interaction” is a scale-dependent estimand and that transparent reporting of coding choices and effect-modification metrics—including additive interaction when relevant for public health interpretation—is essential. Credible inference further depends on high-quality, harmonized dietary phenotyping with explicit energy adjustment and, where feasible, biomarker calibration, alongside robust control of population structure and gene–diet correlation using ancestry adjustment, mixed models, and family-based designs. Genome-wide and polygenic risk-based approaches expand discovery potential but require disciplined multiplicity strategies, discovery-replication workflows, and explicit evaluation of portability and equity across ancestries. Causal inference methods can strengthen etiologic interpretation when assumptions are defensible and sensitivity analyses are routinely implemented. Multi-omics and machine learning may enhance mechanistic and predictive insight, but only under rigorous quality control, validation, and reproducible pipelines. Overall, harmonized measurement, clear estimands, multi-ancestry replication, and integrated evidence pipelines are pivotal for producing robust and actionable G×D evidence. Full article