Search Results (1,053)

Plants must continuously balance the trade-offs between growth and defense, a constraint that is exacerbated by biotic and abiotic stresses, particularly when they occur together. Ethylene (ET) serves as a central, integrative regulatory node controlling this by linking developmental programs to stress-responsive signaling networks. Advances at the molecular and systems levels have revealed that ET mediates the redistribution of metabolic resources via coordinated regulation of its synthesis, perception, and downstream signaling. The ETR (Ethylene Receptor)-CTR1 (Constitutive Triple Response 1)-EIN2 (Ethylene Insensitive 2)-EIN3(Ethylene Insensitive 3) signaling module lies at the core of this network, integrating multiple hormonal pathways. Through dynamic crosstalk with jasmonic acid (JA), salicylic acid (SA), abscisic acid (ABA), auxin (AUX), and gibberellins (GA), ET enables the fine-tuned coordination of growth inhibition, immune activation, and stress acclimation in response to environmental fluctuations. Processes such as induced systemic resistance, programmed cell death, and architectural plasticity further reinforce this regulatory framework, with ethylene-responsive transcription factors, including ERFs (ethylene responsive factor gene family) and WRKYs, acting as critical convergence points. Emerging insights into ACC (1-aminocyclopropane-1-carboxylic acid) -dependent signaling, chromatin remodeling, and tissue-specific regulation expand the functional scope of ET beyond traditional hormone paradigms. At the same time, the ability of pathogens to manipulate ET signaling underscores its dual role in both promoting immunity and facilitating susceptibility. By integrating molecular, physiological, and ecological perspectives, this review highlights ET as a central coordinator of plant stress resilience and growth optimization, providing a unifying framework for understanding how plants adapt to complex and dynamic environments. Full article

Tree peony (Paeonia suffruticosa Andr.) is a traditional ornamental plant of high economic and cultural value, but its flower longevity is often limited by petal water loss. Cuticular wax serves as an essential barrier against non-stomatal water loss, and the AP2/EREBP (APETALA2/Ethylene-Responsive Element Binding Protein) transcription factor family is known to regulate wax biosynthesis. However, little information is available on the roles of AP2/EREBP genes in petal cuticle formation in tree peony. In this study, we performed transcriptome sequencing on petals of the tree peony cultivar ‘Bai Wang Shi Zi’ at three developmental stages (early, middle, and late). Using the assembled transcriptomic data, we identified 29 high-confidence AP2/EREBP family members, which were phylogenetically classified into AP2, ERF, and DREB subfamilies. Expression profiling revealed that 18 of these genes exhibited stage-specific expression patterns during petal development. Among them, two homologs of Arabidopsis SHN1 (SHINE 1) and WRI3 (WRINKLED 3), designated PsSHN1 and PsWRI3, showed peak expression at the middle stage. By co-expression analysis and phylogenetic comparison, three downstream candidate genes were identified and named PsCER2, PsKAS1, and PsLTPG1, based on their homology with known wax-related genes. Dual-luciferase reporter assays indicated that PsSHN1 and PsWRI3 can activate the promoters of PsCER2, PsKAS1, and PsLTPG1, suggesting a possible cooperative regulation of cuticle formation. Collectively, our findings provide promising candidate genes for prolonging floral lifespan by improving petal cuticular wax accumulation, and lay a preliminary foundation for molecular breeding and quality improvement of tree peony and other ornamental flowers. Full article

Background/Objectives: Clear cell renal cell carcinoma (ccRCC) is the most prevalent and biologically aggressive subtype of renal cell carcinoma, characterized by pronounced immunogenicity and extensive remodeling of the tumor microenvironment. Chronic inflammation and dysregulated cytokine signaling contribute substantially to tumor progression. Signal transducer and activator of transcription 3 (STAT3) represents a central molecular hub integrating cytokine- and hypoxia-driven pathways. This review aims to summarize current evidence on the cytokine–STAT3 signaling axis in ccRCC and to evaluate its translational relevance for biomarker development. Methods: A narrative review of the literature was conducted using PubMed, Scopus, and Web of Science databases. Experimental, translational, and clinical studies addressing cytokine signaling, STAT3 activation, tumor microenvironment interactions, and biomarker development in ccRCC were evaluated. Particular attention was given to studies analyzing cytokine profiles in tumor tissue, plasma, and urine, as well as their associations with STAT3 activation and clinicopathological parameters. Results: Accumulating evidence indicates that ccRCC exhibits a complex, compartment-specific cytokine signature involving interleukins, chemokines, and tumor necrosis factor (TNF)-related cytokines. Among these mediators, IL-6, IL-8, and selected chemokines such as CXCL10 appear particularly relevant due to their associations with tumor progression, immune modulation, and clinical outcome. Many of these mediators converge on persistent STAT3 activation, which promotes tumor cell survival, angiogenesis, immune suppression, and metastatic potential. Tissue-based analyses demonstrate correlations between altered cytokine expression and STAT3 activation, while urinary cytokine profiles reflect tumor-associated inflammatory processes in a non-invasive manner. Plasma cytokines appear to capture broader systemic inflammatory responses. Conclusions: The cytokine–STAT3 axis represents a biologically plausible signaling network associated with tumor progression and immune modulation in ccRCC. By integrating evidence from cytokine profiling in tumor tissue, plasma, and urine with current knowledge of STAT3 signaling, this review highlights the importance of compartment-specific inflammatory signatures in understanding ccRCC biology and their potential relevance for biomarker discovery. Integrative approaches combining cytokine profiling with functional assessment of STAT3 activation may improve disease characterization and support the development of diagnostic and prognostic biomarkers, although rigorous clinical validation remains necessary. Full article

Inflammaging is defined as chronic low-grade inflammation associated with aging and is increasingly recognized as a dynamic and mechanistically driven biological process rather than a state adequately described by circulating biomarkers alone. Traditional inflammatory markers alone, including interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and C-reactive Protein (CRP), fail to capture the complexity, tissue specificity, and causal architecture of inflammaging. Recent experimental evidence has demonstrated that diverse upstream drivers, including immunosenescence, gut microbiome dysbiosis, metabolic dysfunction, and cellular senescence, converge on a limited number of central inflammatory hubs, including nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), NOD-like receptor family pyrin domain containing 3 (NLRP3) inflammasome, GMP–AMP synthase–stimulator of interferon genes (cGAS–STING), Janus kinase/signal transducer and activator of transcription (JAK/STAT), and p38 mitogen-activated protein kinase (p38 MAPK) signaling. These mechanistic nodes represent promising therapeutic targets, potentially modifiable biological processes, and support the emerging concept of ‘druggable inflammaging’, whereby senotherapeutics, inflammasome inhibitors, innate immune modulators, and metabolic interventions may actively modify aging-associated inflammatory biology rather than simply monitor it through biomarkers. This review highlights a paradigm shift from biomarker-based assessment toward mechanism-based intervention, where inflammaging can be characterized as a modifiable biological process and a central target for precision pharmacological strategies in aging-related diseases. Full article

D-box binding protein (DBP) is a high-amplitude proline- and acidic amino acid-rich basic leucine zipper (PAR bZIP) transcription factor that functions as a key circadian output regulator downstream of the core molecular clock. Although DBP is widely recognized as a clock-controlled gene, its broader role in converting circadian timing into tissue-specific physiological programs remains incompletely integrated. In this review, we synthesize current evidence supporting DBP as a context-dependent D-box-centered regulatory node. We first summarize the upstream mechanisms that establish rhythmic Dbp expression, including CLOCK–BMAL1-dependent transcription, promoter-level amplification, signaling-dependent modulation, and post-translational control of DBP stability. We then discuss how DBP, together with related PAR bZIP activators and the opposing repressor E4 promoter-binding protein 4/nuclear factor interleukin 3 regulated (E4BP4/NFIL3), regulates D-box-mediated transcriptional output. Finally, we examine tissue-selective DBP functions in hepatic metabolism, pancreatic β-cell secretory competence, neural and behavioral regulation, reproductive neuroendocrine timing, and T helper 9 (Th9)-associated antitumor immunity. Across these systems, DBP does not act as a universal circadian effector; rather, its function depends on chromatin accessibility, cofactor availability, competing transcription factors, and local signaling context. We also highlight the current limits of human translational evidence and propose that DBP-centered signatures may be useful for interpreting circadian output failure in disease. Overall, DBP provides a mechanistically informative framework for understanding how circadian time is transformed into organ-specific physiological function and pathological vulnerability. Full article

Nuclear factor erythroid 2-related factor 2 (NRF2) has traditionally been framed as a Kelch-like ECH-associated protein 1 (KEAP1)-regulated stress-response transcription factor, but three observations now require a broader framework: NRF2 turnover is controlled by parallel E3 ligase systems; transcriptional output can be limited by coactivator assembly despite unchanged NRF2 abundance; and NRF2 activation can be beneficial or harmful depending on disease context, as illustrated by lung cancer models in which NRF2 paradoxically promotes metastasis through BTB and CNC homology 1 (BACH1) stabilization. We synthesize these observations into an NRF2 partner-code framework in which NRF2 acts as a context-dependent transcriptional platform assembled through four partly independent modules: a degradation module (KEAP1; β-transducin repeat-containing protein, β-TrCP; HMG-CoA reductase degradation protein 1/synoviolin 1, Hrd1/SYVN1; WD repeat-containing protein 23/DDB1- and CUL4-associated factor 11, WDR23/DCAF11); a cytoplasmic scaffold module (p62/sequestosome 1, p62/SQSTM1; IQ motif-containing GTPase-activating protein 1, IQGAP1; type I phosphatidylinositol 4-phosphate 5-kinase γ/heat shock protein 27, PIPKIγ–HSP27; peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, PIN1; peptidyl-prolyl isomerase A/cyclophilin A, PPIA); a nuclear coactivator module at Neh4/5 (CREB-binding protein/p300, CBP/p300; receptor-associated coactivator 3/steroid receptor coactivator 3, RAC3/SRC-3; protein arginine methyltransferase 1/coactivator-associated arginine methyltransferase 1, PRMT1/CARM1; Mediator complex subunit 16, MED16); and a DNA/chromatin module at Neh1 (small musculoaponeurotic fibrosarcoma [Maf] proteins, BACH1, and chromodomain helicase DNA-binding protein 6, CHD6). Mapping 22 partners onto the Neh-domain architecture identifies approximately 25 pharmacologically addressable interfaces, stratified into four translational tiers. The framework reframes NRF2 pharmacology around one principle: the most actionable target is often a partner rather than NRF2 itself, with disease context dictating the direction of modulation. We close with five testable hypotheses and a partner-code decision matrix linking disease, biomarker, and candidate target. Full article

Early-life factors influence adult-brain vulnerability to sporadic Alzheimer’s disease (AD), but the underlying molecular mechanisms are unknown. In this study, we performed an integrated analysis of mitogen-activated protein kinases (MAPK) pathways’ (ERK1/2, JNK, and p38 MAPK) activity in the hippocampus and prefrontal cortex of OXYS rats (a model of sporadic AD) on postnatal days 3 and 10 (P3 and P10): critical periods of brain maturation. Wistar rats (healthy controls) showed extensive developmental transcriptional remodeling of all MAPK pathways. OXYS rats exhibited alterations, most pronounced in the prefrontal cortex at P3, with the JNK pathway showing the greatest divergence. At the protein level, OXYS rats failed to show the normal age-related increase in hippocampal ERK1/2 phosphorylation and in JNK1/2 levels in both regions, indicating developmental signaling deficits. p38 MAPK remained stable among Wistar and OXYS rats. Thus, delayed brain maturation, which contributes to accelerated brain aging and neurodegeneration in OXYS rats, occurs simultaneously with alterations in MAPK signaling. These aberrations potentially are able to increase brain susceptibility to age-related pathologies later in life. Full article

Splicing factor 3b1 (SF3B1), a component of U2 small nuclear ribonucleoprotein (U2 snRNP), has been known for its essential roles in pre-mRNA splicing and alternative splicing. Here we show that knocking down (KD) of SF3B1 broadly induced a significant reduction in mRNA expression in the genome. One of the genes whose expression is reduced by SF3B1 KD is methyl-transferase-like 3 (METTL3), a writer of N6-methyladenosine (m⁶A). We demonstrate that expression of both METTL3 mRNA and protein is affected by SF3B1 KD, which further decreases the m⁶A RNA expression level. m⁶A-seq indicates that SF3B1 KD affects m⁶A distribution within multiple genes in the genome. In addition, a high proportion of hypo-methylation events by SF3B1 KD (~70%) are overlapped in METTL3 KD cells, and a conserved m⁶A motif is observed in the hypo-methylated regions as in SF3B1 KD cells, suggesting the m⁶A decrease by SF3B1 is a direct effect of the reduced METTL3 expression. Furthermore, RT-qPCR using unlabeled RNA and 5-Bromouridine (BrU)-labeled nascent RNA and actinomycin D treatment demonstrates that transcription of METTL3 is significantly reduced but the mRNA decay rate is not altered, suggesting that METTL3 expression is altered at the transcription level. We further show that SF3B1 interacts with RNA polymerase (Pol) II in the RNA independent manner, further indicating the involvement of SF3B1 in transcription. Lastly, we demonstrate that the transcription inactive H3K27me3 on the METTL3 promoter was significantly increased whereas transcription active H3K4me3 was not changed by SF3B1 KD. Taken together, we conclude that reduced SF3B1 expression suppresses the transcription of METTL3 and inhibits m⁶A RNA expression. Full article

Succinate, a tricarboxylic acid (TCA) cycle intermediate, is the essential signal molecule that links metabolic signals and inflammation. Dietary succinate supplementation has been reported to prevent obesity induced by a high-fat diet (HFD). However, the underlying mechanism remains elusive. Here, we found that dietary succinate elevated the serum succinate levels. Meanwhile, we found succinate increased methyltransferaselike 3 (METTL3) protein expression in brown adipocytes, thereby elevating N⁶-methyladenosine (m⁶A) levels in Hypoxia-inducible factor1-alpha (Hif1a) mRNA. Hif1a mRNA is recognized by the m⁶A-binding protein YTH domain-containing family protein 1 (YTHDF1), facilitating HIF1A protein expression. HIF1A activates the transcription of thermogenic genes, ultimately increasing brown adipose energy expenditure. Together, our research provided new insights into the effect of succinate on m⁶A modification in brown adipose tissue thermogenesis. Full article

Legume–rhizobium symbiosis represents a crucial biological nitrogen fixation system. The AP2/ERF transcription factor ERN1 plays a vital role in nodulation of model legumes; however, its function in peanut (Arachis hypogaea), a typical crack-entry infection legume, remains unclear. To explore this, we performed transcriptome sequencing of peanut roots at 3 days post-inoculation (dpi) with rhizobium. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that differentially expressed genes (DEGs) were mainly enriched in DNA-binding transcription factor activity, plant–pathogen interaction, and plant hormone signal transduction pathways. The most strongly up-regulated gene was AhERN1, which was highly expressed in peanut roots and nodules. Subcellular localization indicated that AhERN1 was a nuclear-localized protein, and yeast transcriptional activation assays confirmed that AhERN1 functions as a transcriptional activator relying on its C-terminal domain. Furthermore, hairy root overexpression of AhERN1 significantly increased the number of peanut nodules. Collectively, these results reveal that AhERN1 acts as a positive regulator to promote rhizobium-induced nodule development in peanut, providing new insights into the regulatory mechanism of nodulation in dalbergoid legumes. Full article

Peste des petits ruminants (PPR) is a highly contagious transboundary disease that affects small ruminants and impacts livestock production and trade. This study investigated the seroprevalence and associated risk factors of PPR in sheep, goats, camels, and wild ruminants in Bahrain. A total of 1240 sheep, 1224 goats, 100 camels, and 38 wild ruminants were tested using competitive ELISA. The individual seroprevalence rates were 26% in sheep and 25.5% in goats, with flock/herd-level prevalences of 22.7% and 29.6%, respectively. No antibodies were detected in camels or wild ruminants. The highest seroprevalence was observed in the Northern governorate. The identified risk factors included geographic location, age (<12 months for goats), sex (male for goats), and health status (weak animals). At the flock/herd level, large flock size and semi-intensive farming increased the likelihood of seropositivity. In addition, a 2023–2024 surveillance campaign tested 1044 young, locally born lambs and kids across all governorates. All animals were found to be negative for PPR according to a competitive enzyme-linked immunosorbent assay (cELISA) and a reverse transcription polymerase chain reaction (RT-PCR) test, confirming the absence of antibodies and active virus circulation in the population. These findings support the classification of Bahrain at Progressive Control Pathway for PPR (PCP-PPR) Level 3 status and emphasize the importance of continued surveillance and regional cooperation to mitigate the spread of diseases. Full article

Background: Cold stress is a major abiotic factor limiting rice growth and yield. Elucidating the molecular mechanisms underlying cold tolerance is therefore of great significance for variety improvement. This study focused on the cold-tolerant variety QJ10 and the cold-sensitive variety DHX2, systematically comparing their physiological and transcriptomic differences under cold stress and identifying genes and modules associated with the cold stress response. Methods: After 0, 3, 5, and 7 days of treatment at 4 °C, we measured leaf MDA and Pro contents, as well as SOD and POD activities. We performed multi-time-point transcriptome sequencing using RNA-seq, and conducted data mining and validation through differential expression analysis, Mfuzz trend clustering, WGCNA co-expression network analysis, GENIE3 regulatory network prediction, and qRT-PCR. Results: Compared with DHX2, QJ10 exhibited lower MDA levels and higher levels of Pro, SOD, and POD under cold stress. Transcriptome analysis identified a total of 13,599 differentially expressed genes. Trend clustering revealed that QJ10 primarily maintained genes associated with growth, development, and basal metabolism, whereas DHX2 tended to activate defense responses. WGCNA identified the MEturquoise module, which showed significant positive correlations with both cold treatment duration and the activities of SOD and POD. Genes in this module were significantly enriched in pathways such as carbon metabolism, photosynthesis, and ion transport. Twelve key transcription factors were identified, nine of which were highly expressed at the late stage of cold stress in QJ10. GENIE3 further predicted seven key regulatory factors centered on OsNAC2, OsLBD, and OsARF19; the expression patterns of these factors were validated by qRT-PCR and were consistent with the transcriptomic results. Conclusions: This study revealed that the cold tolerance of QJ10 is associated with enhanced antioxidant capacity, upregulation of genes related to carbon metabolism, and the induced expression of specific transcription factors. The key transcription factors identified here provide candidate genes for studying the molecular mechanisms of cold tolerance in rice. However, their regulatory functions require further experimental validation. Full article

Low back pain is closely associated with intervertebral disc (IVD) degeneration, in which inflammation and neovascularization within the annulus fibrosus (AF) contribute to pain generation. Platelet-derived growth factor (PDGF)-BB plays a crucial role in tissue repair and cellular homeostasis, but its role in AF cell biology remains poorly understood. To investigate the effects of PDGF-BB on human AF cells, healthy and degenerated AF cells were treated with PDGF-BB for 3 or 5 days, followed by bulk RNA sequencing. Functional enrichment of differentially expressed genes, transcription factor activity analysis, and protein–protein interaction network analysis was performed. Publicly available single-cell RNA-seq data were used to compare the transcriptomic profiles of native healthy and degenerated AF samples. In addition, TNF-α stimulation was conducted to validate the anti-inflammatory effects of PDGF-BB. Our findings suggest that PDGF-BB induced both common and context-dependent transcriptional responses in healthy and degenerated AF cells. In healthy AF cells, PDGF-BB consistently upregulated genes associated with cell cycle and developmental growth. In degenerated AF cells, PDGF-BB also induced these responses, while additionally it downregulated the genes related to extracellular matrix remodeling and collagen degradation. Meanwhile, PDGF-BB showed common effects in both healthy and degenerated cells by modulating the expression of genes within G protein-coupled receptor (GPCR) networks that are linked to complement, inflammation, and neurotransmitter signaling. In addition, PDGF-BB also suppressed the expression of genes involved in inflammatory-neurogenic signaling, including nerve growth factor (NGF), C-X-C motif chemokine ligand 12 (CXCL12), and apolipoprotein E (APOE). To relate these PDGF-BB induced responses to disc degeneration, we reanalyzed publicly available single-cell RNA-seq datasets from native human AF tissues and found that NGF-positive cells showed increased tumor necrosis factor (TNF)-α signaling activity. When AF cells were stimulated with TNF-α, PDGF-BB treatment significantly inhibited the expression of NGF, endothelin-1 (EDN1), and interleukin 6 (IL6) under both baseline and TNF-α-stimulated conditions. These results suggest that PDGF-BB modulates gene expression associated with inflammatory and neurogenic signaling as well as ECM remodeling in human AF cells, providing a transcriptomic insight into the PDGF-BB’s function in AF biology. Full article

Antiretroviral therapy (ART) effectively suppresses HIV-1 replication but does not purge the latent HIV-1 reservoir. Strategies aimed at HIV-1 latency reversal and subsequent elimination of infected cells are being explored. Targeting the inhibitor of apoptosis proteins (IAP) and DEAD-box polypeptide 3 (DDX3) RNA helicase reduces the HIV-1 reservoir ex vivo. However, the mechanisms driving apoptosis of HIV-1 infected cells remain unclear. Here, we uncovered the mechanism regarding HIV-1 transcriptional activation and induction of apoptosis specific for HIV-1 infected cells using an acute in vitro infection model. Inhibition of IAP by second mitochondrial-derived activator of caspases mimetic (SMACm; AZD5582) resulted in activation of non-canonical NF-κB pathway (RelB/p52) that induced HIV-1 transcription, confirming previous reports, whereas inhibition of DDX3 sensitized HIV-1 infected cells for apoptosis (DDX3i; FH1321). Transcriptome analysis revealed that HIV-1 actively suppressed apoptosis-related genes in HIV-1 infected cells. SMACm treatment resulted in a broad induction of these genes irrespective of infection. Notably, DDX3 inhibition specifically restored the expression of the majority of HIV-1 suppressed genes, and when combined with SMACm, restored almost all HIV-1 downregulated genes, thereby rendering HIV-1 infected cells sensitive to apoptosis. Thus, our data strongly suggest that inhibition of host factors IAP and DDX3 not only induces activation of HIV-1 transcription but also restores HIV-1 suppressed apoptotic processes in infected cells. Full article

Chronic inflammation is a well-established risk factor for cancer progression. This review aims to determine how persistent inflammatory signaling reshapes the tissue microenvironment to favor tumor cell proliferation, survival, and progression. It also discusses the role of cytokines such as IL-6 and TGF-β, reactive oxygen species (ROS), and the transcription factors NF-κB and STAT3 in inflammation and in the tumor microenvironment. Sustained activation of these pathways promotes genomic instability, loss of tumor suppressor gene function, enhanced oncogene expression, and resistance to apoptosis, collectively facilitating malignant transformation and tumor development. The key novelty of this review lies in integrating these interconnected networks with new evidence to clarify how they drive cancer initiation and progression. Furthermore, we discuss the therapeutic potential of plant-derived bioactive compounds, with a particular emphasis on curcumin. Curcumin exhibits significant anti-inflammatory and anticancer effects through inhibition of NF-κB and STAT3 signaling and its downstream targets, thereby attenuating inflammation-driven tumorigenesis. However, its clinical application is limited by poor bioavailability. Finally, this review highlights current strategies to overcome these limitations and future directions for optimizing curcumin-based interventions in inflammation-associated diseases. Full article