Search Results (19,657)

Background/Objectives: This study aimed to evaluate the serum activating transcription factor 4 (ATF4) and toll-like receptor 4 (TLR4) levels in patients with metabolic dysfunction–associated steatotic liver disease (MASLD), and to explain the mechanism in the inflammatory and fibrogenic signaling pathways that are thought to play a role in the development of MASLD through these parameters. Methods: Eighty-eight patients with MASLD and 88 age-sex matched healthy controls were included in this study. Serum ATF4 and TLR4 concentrations were measured using an ELISA method. Results: Both TLR4 (p = 0.010) and ATF4 (p < 0.001) levels were higher in the MASLD group. In this group, TLR4 showed a negative correlation with age. ROC analysis indicated that an ATF4 value of 1.305 or above identified MASLD with 93.2% sensitivity and 85.2% specificity (AUC = 0.968, p < 0.001). For TLR4, a cut-off of 343.5 yielded a sensitivity of 54.5% and a specificity of 70.5% (AUC = 0.613, p = 0.01), indicating limited discriminative ability. Conclusions: Patients with MASLD had higher serum TLR4 and ATF4 levels, consistent with their involvement in inflammatory and fibrotic pathways. ATF4 showed strong diagnostic performance and may serve as a useful non-invasive marker for early MASLD. When evaluated together with TLR4, it may provide complementary information regarding inflammatory pathway activation. Full article

Lateral Organ Boundaries Domain (LBD) proteins are plant-specific transcription factors characterized by a typical N-terminal LOB domain and are critical for plant growth, development, and stress response. Currently, LBD genes have been investigated in various plant species, but they have yet to be identified in Neolamarckia cadamba, known as a ‘miracle tree’ for its fast growth and acknowledged for its potential medicinal value in tropical and subtropical areas of Asia. In this study, a total of 65 NcLBD members were identified in N. cadamba by whole-genome bioinformatics analysis. Phylogenetic analysis revealed their classification into two clades with seven distinct groups, and their uneven distribution across 18 chromosomes, along with 6 tandem repeats and 58 segmental duplications. Furthermore, enrichment analysis of transcription factor binding motifs within NcLBD promoters identified the MYB-related and WRKY families exhibited the most significant enrichment in the NcLBD promoter. Protein interaction network analysis revealed potential interactions among NcLBD proteins, as well as their interactions with various transcription factors. RNA-seq and qRT-PCR analyses of NcLBDs transcript levels showed distinct expression patterns both across various tissues and under different hormone and abiotic stress conditions. Specifically, NcLBD3, NcLBD37, and NcLBD47 were highly expressed in vascular cells and induced by abiotic stress, including cold, drought, and salt, suggesting their significant role in the processes. In summary, our genome-wide analysis comprehensively identified and characterized LBD gene family in N. cadamba, laying a solid foundation for further elucidating the biological functions of NcLBD genes. Full article

Cervical cancer remains a significant global health burden, with chemoradioresistance representing a major obstacle to successful treatment. To elucidate the mechanisms underlying this resistance, we established a unique pair of isogenic primary cervical cancer cell lines, AdMer35 and AdMer43, obtained from a patient with squamous cell carcinoma of the cervix before and after radiation therapy. The aim of our study was to characterize the transcriptomic and cellular heterogeneity of these cells. We conducted an in-depth comparative analysis using single-cell RNA sequencing. Analysis of this paired, patient-derived isogenic model suggests that chemoradioresistance can arise through coordinated multilevel cellular adaptations. Resistant AdMer43 cells demonstrated transcriptional reprogramming, with the upregulation of embryonic stemness factors (HOX, POU5F1, SOX2), a shift in extracellular matrix from fibrillar to non-fibrillar collagens, and activation of inflammatory pathways. We identified and characterized critical cell-state dynamics: resistant cells exhibited a remodeled ecosystem with a metabolically reprogrammed senescent-like cell population showing an enhanced pro-tumorigenic communication via EREG, SEMA3C, BMP, and WNT pathways. Furthermore, we identified a progenitor-like cell population with a minimal CNV burden, potentially serving as a reservoir for tumor persistence. These findings offer novel insights for developing targeted strategies to eliminate resistant cell pools and improve cervical cancer outcomes. Full article

The mesenchymal–epithelial transition (MET) receptor is a tyrosine kinase activated by its sole known ligand, hepatocyte growth factor (HGF). MET signaling regulates key cellular processes, including proliferation, survival, migration, motility, and angiogenesis. Dysregulation and hyperactivation of this pathway are implicated in multiple malignancies, including lung, breast, colorectal, and gastrointestinal cancers. In non–small cell lung cancer (NSCLC), aberrant activation of the MET proto-oncogene contributes to 1% of known oncogenic drivers and is associated with poor clinical outcomes. Several mechanisms can induce MET hyperactivation, including MET gene amplification, transcriptional upregulation of MET or HGF, MET fusion genes, and MET exon 14 skipping mutations. Furthermore, MET pathway activation represents a frequent mechanism of acquired resistance to EGFR- and ALK-targeted tyrosine kinase inhibitors (TKIs) in EGFR- and ALK-driven NSCLCs. Although MET has long been recognized as a promising therapeutic target in NSCLC, the clinical efficacy of MET-targeted therapies has historically lagged behind that of EGFR and ALK inhibitors. Encouragingly, several MET TKIs such as capmatinib, tepotinib, and savolitinib have been approved for the treatment of MET exon 14 skipping mutations. They have also demonstrated potential in overcoming MET-driven resistance to EGFR TKIs or ALK TKIs. On 14 May 2025, the U.S. Food and Drug Administration granted accelerated approval to telisotuzumab vedotin-tllv for adult patients with locally advanced or metastatic non-squamous NSCLC whose tumors exhibit high c-Met protein overexpression and who have already received prior systemic therapy. In this review, we summarize the structure and physiological role of the MET receptor, the molecular mechanisms underlying aberrant MET activation, its contribution to acquired resistance against targeted therapies, and emerging strategies for effectively targeting MET alterations in NSCLC. Full article

BST2 has emerged as a multifunctional molecule that bridges antiviral defense, membrane architecture, and tumor immunity. Originally characterized as an interferon-inducible restriction factor that tethers virions to the plasma membrane, BST2 is now recognized as an oncogenic driver and immunoregulatory hub in diverse malignancies. In cancer, BST2 expression is frequently upregulated through promoter hypomethylation and transcriptional activation. Functionally, BST2 promotes proliferation, epithelial–mesenchymal transition, anoikis resistance, and chemoresistance, whereas its loss sensitizes tumor cells to proteotoxic and metabolic stresses. Beyond tumor cells, BST2 modulates the tumor microenvironment by promoting M2 macrophage infiltration, dendritic cell exhaustion, and natural killer (NK)-cell resistance, thereby contributing to immune evasion. Elevated BST2 expression correlates with poor prognosis in glioblastoma, breast, nasopharyngeal, and pancreatic cancers, and it serves as a circulating biomarker within small extracellular vesicles. In conclusion, BST2 is a dual-function molecule that integrates oncogenic signaling and immune regulation, making it an attractive diagnostic and therapeutic target for hematological and solid tumors. Full article

Melanin produced in melanocytes contributes to photoprotection, oxidative stress reduction, immune regulation, and epidermal homeostasis, while its dysregulation underlies diverse pigmentary disorders. Natural products modulate melanogenesis by regulating tyrosinase activity, intracellular signaling pathways such as extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) and cyclicAMP/protein kinase A/cAMP response element-binding protein (cAMP/PKA/CREB), and cellular redox balance. Anti-melanogenic effects have been reported for various fruit-derived phytochemicals, ginseng-based metabolites, and plant polyphenols, which act through direct enzymatic inhibition, suppression of melanoenic signaling, modulation of melanosome dynamics, and antioxidant or anti-inflammatory activities. Advances in delivery systems, including nano- and microencapsulation platforms, further enhance the stability and topical bioavailability of these compounds. In contrast, certain methoxylated flavonoids and phenolic constituents can stimulate pigmentation by sustaining melanogenic signaling and promoting microphthalmia-associated transcription factor (MITF)-driven transcription, emphasizing the context-dependent and bidirectional influence of natural substances on pigmentation outcomes. Collectively, these findings highlight the therapeutic potential of natural product-based modulators of melanogenesis while underscoring the need for mechanistic clarification, safety evaluation, and translational studies to ensure effective and controlled pigmentation management. This review summarizes the biological functions of melanin and examines natural strategies for regulating pigmentation. Full article

Background. The genus Streptomyces is known for its capability to produce a wide range of bioactive secondary metabolites. The enzymes required for their synthesis are encoded within biosynthetic gene clusters (BGCs), whose expression can be influenced by various physical and nutritional factors. Among these nutritional factors, it is worth highlighting carbon catabolic repression (CCR), which prevents the formation of secondary metabolites. It has been shown that transcriptional factors, in turn, regulated by glucose or by the enzyme glucose kinase (Glk), may be involved in this mechanism. It was shown that the expression of some transcriptional factors is regulated by glucose availability and that the enzyme glucose kinase (Glk) may play a role in this process. One of the transcriptional factors most upregulated in the presence of glucose/agar in Streptomyces coelicolor M145 is SCO7424, a member of the MarR family of transcriptional regulators. However, its influence on antibiotic synthesis has never been studied. Objective. In this work, we evaluated the effect of SCO7424 overexpression on the synthesis of actinorhodin (ACT) and undecylprodigiosin (RED), and its impact on growth and glucose consumption. Methods. A copy of the sco7424 gene was cloned into the pIJ702 plasmid, which was then transformed into a wild-type strain of S. coelicolor M145. Growth and antibiotic production were evaluated in the strain with two copies of sco7424 and in the wild-type strain. We also evaluated the expression of the probable target genes by quantitative RT-PCR. Results. We found that overexpression of sco7424 negatively impacts growth, glucose consumption kinetics, and the expression of specific regulators of the ACT and RED biosynthetic pathways, resulting in reduced ACT and RED production. Understanding the function of the regulatory cascades regulated by this family of regulators is crucial for boosting the yields of valuable metabolites produced by industrial strains. Full article

Background: Osteoarthritis (OA) is a prevalent degenerative joint disease often causing functional disability. Current therapies provide only temporary relief and can cause adverse effects that frequently result in pain and disability. Current pharmacological options offer only temporary symptom relief and may cause adverse effects. Piper sarmentosum (PS), a plant traditionally used for its medicinal properties, has demonstrated antioxidant and anti-inflammatory activities that may counteract OA-related degeneration. This study provides preliminary insight into the therapeutic potential of PS aqueous extract in human OA chondrocytes. Methods: Compounds in the PS aqueous extract were profiled using liquid chromatography–tandem mass spectrometry (LC-MS/MS). Primary human OA chondrocytes (HOCs) were treated with 0.5, 2, and 4 µg/mL of PS aqueous extract for 72 h. Key OA-related parameters were assessed, including anabolic markers (sulfated glycosaminoglycan (sGAG), collagen type II (COL II), aggrecan core protein (ACP), SRY-box transcription factor 9 (SOX9)), catabolic markers (matrix metalloproteinase (MMP) 1, MMP13, cyclooxygenase 2 (COX2)), oxidative stress (nitric oxide (NO) production, inducible NO synthase (iNOS) expression), and inflammatory responses (interleukin (IL) 6). Gene expression was quantified using qPCR, and protein levels were evaluated using the colorimetric method, immunocytochemistry, and Western blot. Results: A total of 101 compounds were identified in the extract, including vitexin, pterostilbene, and glutathione—bioactives known for antioxidant, anti-inflammatory, and chondroprotective functions. PS-treated chondrocytes maintain healthy polygonal morphology. PS aqueous extract significantly enhanced anabolic gene expression (COL2A1, ACP, SOX9) and sGAG production, while concurrently suppressing COX2 expression and NO synthesis. Additionally, PS aqueous extract reduced COX2 and iNOS protein levels, indicating inhibition of the NO signaling pathway. Catabolic activity was attenuated, and inflammatory responses were partially reduced. Conclusions: PS aqueous extract exhibits promising chondroprotective, antioxidant, and anti-inflammatory effects in human OA chondrocytes, largely through the suppression of NO-mediated catabolic signaling. The presence of multiple bioactive compounds supports its mechanistic potential. These findings highlight PS aqueous extract as a potential therapeutic candidate for OA management. Further ex vivo and in vivo studies are warranted to validate its efficacy and clarify its mechanism in joint-tissue environments. Full article

Disease-specific diversity in RNA transcripts stems from RNA splicing, ribosomal abnormalities, and other factors. However, the mechanisms underlying the regulation of rRNA expression in the nucleolus and mRNA expression in the cytoplasm during cancer and neuronal differentiation remain largely unknown. In this article, we review current knowledge and discuss the regulatory mechanisms of rRNA and mRNA expression in human diseases using the splicing model of PUF60 (poly(U) binding splicing factor 60)—also known as FUSE-binding protein-interacting repressor (FIR) (FUBP1-interacting repressor), RoBPI, SIAHBP1, and VRJS (Gene ID: 22827). Noncoding RNAs, much like coding RNAs, have been found to be translated into proteins with significant physiological functions. Splicing is also involved in dominant ORF RNAs implicated in the expression of both noncoding and coding RNAs. Here, we analyze recent findings regarding gene splicing, ribosome formation, and the determination of selected ORFs (dominant ORFs) in a system modeled on FIR splicing in two databases (RefSeq and ENSEMBL). rRNA transcription affects ribosomes, whereas mRNA expression and splicing affect the intracellular proteome. Our objective is to develop efficient methods for identifying biomarkers for disease diagnosis and therapeutic targets. In the field of cancer treatment, therapeutic drugs targeting intracellular signaling have proven effective. Full article

Schima superba, belonging to the genus Schima of Theaceae, is a common large tree in evergreen broad-leaved forests in subtropical regions of China. As one of the largest transcription factor families in plants, MYB transcription factors play an important role in plant stress response by specifically binding to cis-acting elements in different gene promoter regions to accurately regulate gene expression. However, there are few studies on MYB transcription factors in S. superba. The MYB transcription factor family of S. superba was found and examined in this study using the genomic and transcriptome data of the S. superba. A set of 220 MYB transcription factors was identified from S. superba and classified into four subfamilies. These transcription factors were unevenly distributed on 18 chromosomes of S. superba. The conserved domains of the same subfamily members are highly similar to the conserved motifs. The collinearity analysis between species showed that there were few orthologous genes located on chromosome 18 of S. superba. Numerous elements linked to phytohormone response, stress adaptation, and growth control can be found in the promoter regions of the S. superba MYB transcription factor family, according to an analysis of the promoter cis-acting elements. Verification via qRT-PCR showed that among 15 SsMYBs genes tested, SsMYB24 expression peaked at 96 h of drought stress, followed by a rapid downregulation upon rewatering to initial levels. This expression pattern aligned with the transcriptome data. This study is helpful to further identify the function of SsMYB transcription factors and provide a new molecular mechanism for improving drought tolerance of S. superba. Full article

Forkhead box protein O1 (Foxo1) is an insulin-suppressed transcription factor that governs multiple biological processes, including cell proliferation, apoptosis, autophagy, mitochondrial function, and energy metabolism. Over the past 25 years, Foxo1 has evolved from a liner insulin effector to a pleiotropic integrator of systemic metabolic stress during obesity and aging. Foxo1 integrates hormonal signals with energy balance and plays a central role in glucose and lipid metabolism, organ homeostasis, and immune responses. Given its pleiotropic functions, therapeutic targeting of Foxo1 pathway will require a nuanced, context-specific approach. Here, we reviewed key advances in Foxo1 studies over the past 25 years, including multi-hormonal control of Foxo1 activity, Foxo1-mediated inter-organ crosstalk, immune modulation, and contributions to aging-associated pathologies. Understanding the regulation of Foxo1 and its pleiotropic function across multiple tissues will advance insight into the pathogenesis of metabolic diseases and promote the translation potential of Foxo1 signaling manipulation for the treatment of metabolic disorders, including insulin resistance and type 2 diabetes. Full article

Antimicrobial resistance (AMR) is one of the major health threats of the 21st century and demands innovative sources of bioactive compounds. In 2019, infections caused by resistant bacteria directly accounted for 1.27 million deaths and contributed to an additional 4.95 million associated deaths, underscoring the urgency of exploring new strategies. Among emerging alternatives, specialized plant metabolites stand out, as their biosynthesis is enhanced under biotic or abiotic stress. These stimuli increase reactive oxygen species (ROS), activate cascades regulated by mitogen-activated protein kinases (MAPKs), and trigger defense-related hormonal pathways involving salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA), which in turn regulate transcription factors and biosynthetic modules, promoting the accumulation of compounds with antimicrobial activity. In this review, we synthesize recent literature (2020–2025) with emphasis on studies that report quantitative activity metrics. We integrate evidence linking stress physiology and metabolite production, summarize mechanisms of action, and propose a conceptual multi-omics pipeline, synthesized from current best practices, that combines RNA sequencing and LC/GC-MS-based metabolomics with bioinformatic tools to prioritize candidates with antimicrobial potential. We discuss elicitation strategies and green extraction, highlight bryophytes (e.g., Pseudocrossidium replicatum) as a differentiated chemical source, and explore citrus Huanglongbing (HLB) as a translational case study. We conclude that integrating stress physiology, multi-omics, and functional validation can accelerate the transition of stress-induced metabolites toward more sustainable and scalable medical and agricultural applications. Full article

Background: Pituitary neuroendocrine tumours (PitNETs) are clinically and biologically heterogeneous neoplasms that remain challenging to diagnose, prognosticate, and treat. Although recent WHO classifications using transcription-factor-based markers have refined pathological categorisation, histopathology alone still fails to predict tumour behaviour or support individualised therapy. Objective: This systematic review aimed to evaluate how machine learning (ML) and knowledge extraction approaches can complement pathology by integrating multi-dimensional omics datasets to generate predictive and clinically meaningful insights in PitNETs. Methods: The review followed the PRISMA 2020 statement for systematic reviews. Searches were conducted in PubMed, Google Scholar, arXiv, and SciSpace up to June 2025 to identify omics studies applying ML or computational data integration in PitNETs. Eligible studies included original research using genomic, transcriptomic, epigenomic, proteomic, or liquid biopsy data. Data extraction covered study design, ML methodology, data accessibility, and clinical annotation. Study quality and validation strategies were also assessed. Results: A total of 726 records were identified. After the reviewing process, 98 studies met inclusion criteria. PitNET research employed unsupervised clustering or regularised regression methods reflecting their suitability for high-dimensional omics datasets and the limited sample sizes. In contrast, deep learning approaches were rarely implemented, primarily due to the scarcity of large, clinically annotated cohorts required to train such models effectively. To support future research and model development, we compiled a comprehensive catalogue of all publicly available PitNET omics resources, facilitating reuse, methodological benchmarking, and integrative analyses. Conclusions: Although omics research in PitNETs is increasing, the lack of standardised, clinically annotated datasets remains a major obstacle to the development and deployment of robust predictive models. Coordinated efforts in data sharing and clinical harmonisation are required to unlock its full potential. Full article

Transforming growth factor β (TGF-β) superfamily members are critical in teleost sex determination and differentiation. Tgfb2b is an important TGF-β ligand gene exhibiting dominant expression in the ovary of Chinese tongue sole (Cynoglossus semilaevis), yet its function in sex regulation remains unclear. In the present study, the gene expression pattern, transcriptional regulation, and knockdown effect were examined. Its expression persisted and showed a gradual increase throughout ovarian development from 3 months to 1.5 years post-hatching. In situ hybridization (ISH) revealed that the gene was distributed across oocytes at stages I–III, while scarcely detectable in the testis. The transcriptional factors CCAAT/enhancer binding protein α (C/EBPα) and Jun proto-oncogene AP-1 transcription factor subunit (c-Jun) could repress the activity of tgfb2b promoter. In vitro knockdown of tgfb2b in C. semilaevis ovarian cells led to downregulation of its downstream genes (e.g., smad1 and smad2) as well as other sex-related genes (e.g., foxl2 and esr2b). Moreover, multi-omics analysis indicated that, in C. semilaevis gonads, a miRNA named novel-m0083-3p showed an opposite expression pattern with tgfb2b and might have a binding site with the gene. By dual-luciferase assay, tgfb2b was validated to be directly targeted and suppressed by the miRNA. These results demonstrate that tgfb2b plays a significant role in ovarian differentiation and development. Further functional and molecular studies on the interplay between tgfb2b and the foxl2–cyp19a–esr axis will help elucidate the regulatory network underlying sex development in teleost. Full article

Nucleated erythroid cells (NECs) have emerged as active participants in immune responses in addition to their canonical oxygen transport function. The subpopulations and immune heterogeneity of chick erythroid cells (ch-ECs) upon infection have not been fully characterized. Single-cell RNA sequencing (scRNA-seq) was used to profile ch-ECs in chicks infected with avian pathogenic Escherichia coli (APEC). Unsupervised clustering uncovered ten distinct ch-EC subpopulations (C1–C10), with significant compositional shifts between infected and control groups. Pseudotime analysis revealed a developmental continuum: C1, C3, C5, and C9 as early progenitors; C2, C4, C6, C7, and C10 as mature erythroid cells; and C8 as a naive population. We revealed 62 immune-related genes, including protein kinases and heat shock proteins, and subpopulation-specific differentially expressed genes (DEGs) linked to immune functions. SCENIC analysis revealed Fos, Srf, and Stat3 as key transcription factors with elevated regulon activity and specificity following infection. Subpopulations C2, C4, C6, and C7, which exhibited marked abundance changes, were scrutinized for immune relevance through integrated multi-omics analysis. Immune-related genes including FOS, AKAP9, HS6ST1, GAB3, TFRC, HSPA8, HSP90AA1, and DNAJB6 were identified. Enrichment analysis indicated activation of the MHC class I antigen presentation pathway, while pathways such as Mitogen-Activated Protein Kinase (MAPK) signaling, NOD-like receptor (NLR) signaling, and the heat shock response were found to be suppressed. In conclusion, this study delineates the immune gene repertoire and signaling networks of ch-ECs during APEC infection, offering new perspectives on NEC immunoregulatory functions. Full article