Search Results (706)

Renal cell carcinoma (RCC) represents the most frequent kidney malignancy and remains a major clinical challenge due to its often silent onset, high metastatic potential, and limited responsiveness to conventional chemotherapy. Increasing evidence indicates that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are key regulators of RCC tumorigenesis, progression, and therapy resistance. Rather than providing a purely descriptive overview, this review focuses on emerging mechanistic paradigms through which ncRNAs actively shape tumor behavior and therapeutic response in RCC. This review summarizes current knowledge on the biological and clinical relevance of ncRNAs in RCC, highlighting their dual roles as oncogenic drivers or tumor suppressors through the modulation of pathways involved in proliferation, apoptosis, angiogenesis, invasion, immune evasion, metabolic reprogramming, and ferroptosis. Particular emphasis is placed on mechanistically defined ncRNA regulatory axes controlling ferroptosis, autophagy, metabolic reprogramming, and immune escape, as well as on ncRNA-mediated intercellular communication via extracellular vesicles, which promotes the dissemination of resistance to targeted therapies. The review also addresses ncRNA-based diagnostic and prognostic applications, including miRNA signatures capable of discriminating RCC subtypes and circulating ncRNAs as minimally invasive biomarkers. Moreover, the manuscript discusses ncRNA-mediated mechanisms of resistance to targeted therapies such as sunitinib, sorafenib, and axitinib, emphasizing regulatory networks involving miRNA targets, lncRNA–miRNA sponging, RNA-binding proteins, extracellular vesicle transfer, and epigenetic modulation. Emerging therapeutic opportunities are also addressed, including strategies aimed at inhibiting oncogenic ncRNAs or restoring tumor-suppressive ncRNAs to enhance drug sensitivity and improve patient stratification. Full article

Epigenetic dysregulation is a central driver of cancer progression, therapeutic resistance, and phenotypic plasticity. Among epigenetic mechanisms, microRNAs (miRNAs) and DNA methyltransferases (DNMTs) engage in reciprocal regulatory interactions that extend beyond transient gene control. Emerging evidence indicates that DNMT–miRNA feedback loops function as epigenetic memory units, stabilizing malignant cell states and enabling durable phenotypic inheritance even after removal of initiating stimuli under conditions shaped by persistent redox and stress signaling cues. In this review, we synthesize mechanistic, computational, and translational studies demonstrating how double-negative DNMT–miRNA feedback architectures generate bistable regulatory circuits that lock cancer cells into epithelial–mesenchymal transition, stem-like, and therapy-resistant states through redox-sensitive regulatory thresholds rather than static epigenetic alterations. This framework provides a unifying explanation for why transient environmental or therapeutic cues can induce long-lasting epigenetic reprogramming and why conventional single-target epigenetic inhibitors often fail to achieve durable clinical responses. Building on this concept, we propose that herbal medicines and plant-derived phytochemicals act as epigenetic reset signals capable of destabilizing pathological epigenetic attractor states encoded by DNMT–miRNA memory circuits by modulating intracellular redox balance and redox-responsive signaling pathways. Owing to their multi-component and systems-level regulatory properties, herbal interventions modulate miRNA expression, DNMT activity, and upstream stress-responsive pathways in a coordinated manner, facilitating transitions from memory-dominated states toward renewed epigenetic plasticity. We further discuss the translational implications of combining miRNA-based therapies with herbal medicine as a strategy for epigenetic reprogramming rather than transient suppression within a redox-guided therapeutic framework. Finally, we address key challenges and clinical feasibility considerations, including delivery, heterogeneity, and safety, and outline future directions for biomarker-guided and systems-informed epigenetic therapies that incorporate redox state as a functional determinant of epigenetic responsiveness. By reframing DNMT–miRNA interactions through the lens of epigenetic memory, this review highlights miRNA–herbal combination strategies as a forward-looking approach for overcoming therapeutic resistance and achieving durable reprogramming in cancer through selective manipulation of redox-sensitive epigenetic signaling circuits. Full article

For decades, immunology has followed a clear paradigm: immunological memory resides only within the adaptive immunity, as a unique property of lymphocytes giving the host the ability to recognize specific antigens and offer long-term protection. However, this raises an important question: how valid is this belief in light of new evidence? The discovery of trained immunity shows that innate immune cells can also develop lasting functional changes. This finding prompts a profound reconsideration of the traditional framework. Trained immunity is a functional reprogramming of the innate immune cells driven by long-term epigenetic and metabolic reprogramming, resulting in enhanced responses upon subsequent exposure to the same pathogen or even to unrelated stimuli. The presence of pattern recognition receptors (PRRs) on innate immune cells already suggested a certain level of specificity in this compartment thanks to the engagement of a PRR by a pathogen-associated molecular pattern (PAMP) inducing memory-like properties in the responding cell. While such partial specificity can enhance protection, it may also amplify aberrant inflammatory circuits, thereby contributing to the initiation or worsening of autoimmune and chronic inflammatory diseases. This dual nature of trained immunity raises important questions for the field: is trained immunity ultimately harmful or beneficial in autoimmunity, and can its mechanisms be harnessed therapeutically rather than pathologically? The present Perspective will address these issues by examining recent findings that reveal the specificity, pathogenic potential, and translational opportunities in given examples of autoimmune diseases (ADs). Full article

Antiepileptic drugs (AEDs) are primarily indicated for controlling epileptic seizures. However, accumulating clinical evidence suggests that their benefits in patients with central nervous system (CNS) tumors extend beyond seizure management. Emerging evidence indicates that AEDs possess direct antitumor activity independent of their antiepileptic effects, highlighting a promising novel direction for CNS tumor therapy. This review elucidates the multifaceted antitumor mechanisms of classic (e.g., valproic acid and levetiracetam) and novel (e.g., cannabidiol) AEDs, including their impacts on metabolic reprogramming, epigenetic regulation, endoplasmic reticulum stress and unfolded protein response (ERS-UPR), ion homeostasis, and the tumor immune microenvironment (TIME) to provide new insights and a theoretical basis for developing multitarget therapeutic strategies. Full article

Metabolic reprogramming and epigenetic remodeling are critical features of tumorigenesis. The process of metabolic reprogramming causes metabolites like Succinyl-CoA to accumulate. Succinylation, which depends on succinyl-CoA as the direct donor group, plays a crucial role in regulating cancer metabolism. This involves the transfer of the succinyl group to the lysine residues of substrate proteins resulting in the alteration of the conformation and function of the proteins, modulating several signaling pathways, many of them involved in metabolism. There is growing evidence that succinylation can alter the activity and stability of metabolic enzymes and reshape metabolic networks. Furthermore, it precisely regulates gene expression through the epigenetic modification mechanisms of the histones and non-histone proteins. Lysine succinylation is thus a crucial hub linking tumor metabolic reprogramming and epigenetic remodeling. This review systematically summarizes the dynamic regulatory mechanisms of lysine succinylation and its critical roles in tumor metabolic reprogramming and epigenetic regulation. In the end, we discuss the crosstalk between succinylation and other post-translational modifications (PTMs) as well as recent advances in cancer therapies targeting succinylation. Full article

Glioblastoma (GBM) is a highly aggressive and therapy-resistant brain tumor, necessitating innovative multi-target strategies. Natural compounds like the triterpenoid Alisol B from Alisma orientale hold promise due to their polypharmacological potential, yet their system-level mechanisms are unclear. Using an integrated multi-omics approach (transcriptomics, proteomics, lysine acetyl-proteomics) in resistant GBM cells and validating findings in vitro and in AB strain zebrafish (Danio rerio) xenografts, we found that Alisol B induces endoplasmic reticulum stress and G2/M arrest, initiated by extensive lysine acetylation reprogramming on histones and metabolic enzymes (e.g., FASN, FDFT1). This epigenetic rewiring leads to disrupted cholesterol biosynthesis, characterized by transcriptional activation of the mevalonate pathway alongside post-transcriptional suppression of terminal enzymes (DHCR7, CYP51A1), suggestive of toxic intermediate accumulation. Alisol B also downregulated the oncogenic axis (BIRC5-FOXM1-ITGA4) and SCD5. This study delineates Alisol B’s novel multi-mechanistic action through concurrent epigenetic rewiring, metabolic dysfunction induction, and survival network dismantling. Our work elucidates the molecular pharmacology of a natural compound and provides a framework for developing polypharmacological therapies against resistant cancers, exemplifying natural products as tools to reveal new therapeutic paradigms. Full article

Human preimplantation embryo arrest (PREMBA) represents a significant clinical hurdle in assisted reproductive technology (ART), in which approximately 10% of in vitro fertilized (IVF) embryos arrest at the cleavage stages. Whole-exome sequencing (WES) studies have discovered numerous genetic mutations associated with preimplantation embryo arrest. These mutations often disrupt critical biological milestones such as maternal mRNA clearance (BTG4, ZFP36L2, ZAR1), subcortical maternal complex (TLE6, PADI6, OOEP, NLRP2, NLRP5, NLRP7, KHDC3L), DNA double-strand break formation and homologous recombination (REC114, TOP6BL, MEI1, MEI4, TRIP13), spindle assembly (TUBB8 and TUBA4A) and cell cycle and checkpoints (FBXO43, MOS, CHEK1, TRIP13, CDC20), as well as nuclear transport and translational regulation (KPNA7, DDOST). However, the cause of most clinical cases remains genetically unexplained. Studies investigating these unexplained arrests have uncovered widespread multi-omics abnormalities, including transcriptional arrest, DNA hypermethylation, higher chromatin accessibility, aberrant histone modification, chromosomal aneuploidy and senescent-like states. This review provides a comprehensive overview of the molecular mechanisms underlying PREMBA, categorized into those that are attributable to known genetic mutations and those with unexplained reasons. Full article

Background: DNMT3B is frequently overexpressed in molecular subsets of acute myeloid leukemia (AML) and is associated with poor prognosis. Unlike DNMT3A, DNMT3B is rarely mutated, suggesting dysregulation through epigenetic mechanisms. The regulatory basis and downstream consequences of DNMT3B overexpression in AML remain incompletely defined. Methods: We integrated analyses of BeatAML, TCGA, and BLUEPRINT cohorts with multi-omic profiling (RNA-seq, DNA methylation, ATAC-seq, and proteomics) in DNMT3B-high AML models. Nanaomycin A (NanA) was used as a DNMT3B-directed functional probe to interrogate cis-regulatory remodeling, transcriptional circuitry, and apoptotic dependencies. Results: DNMT3B overexpression was linked to enhancer-associated chromatin activation rather than recurrent genetic mutation, particularly in CEBPA- and NPM1-mutant AML. NanA exposure produced focal epigenomic remodeling, including 6900 differentially methylated CpGs, with 268 CpGs located within regions of altered chromatin accessibility. These changes were accompanied by coordinated transcriptomic and proteomic reprogramming enriched for cell-cycle, checkpoint, and stress-response pathways. Functionally, DNMT3B perturbation induced redistribution of cell-cycle phases with increased S-phase fraction and progressive apoptosis. Transcriptional profiling demonstrated induction of BH3-only sensitizers (NOXA, PUMA), repression of BCL2, and compensatory upregulation of MCL1 and BCL-XL, collectively reshaping apoptotic dependency. Combined DNMT3B perturbation and BCL2 inhibition produced cooperative cytotoxicity in DNMT3B-high AML models. Conclusion: DNMT3B functions as a context-dependent epigenetic regulator linking enhancer-associated chromatin organization with proliferative control and apoptotic resistance in AML. DNMT3B-directed epigenetic perturbation remodels cis-regulatory circuitry and is associated with increased venetoclax responsiveness, supporting DNMT3B-governed networks as a candidate co-targeting axis in high-risk AML. Full article

Aging is a progressive degenerative process characterized by the depletion of tissue stem cell reserves, organ atrophy, sarcopenia, and an impaired capacity to respond to physiological stress and injury. These changes lead to a reduction in both overall life expectancy and disease-free lifespan. Since aging represents a major risk factor for numerous diseases, including neurodegenerative, cardiovascular, and metabolic disorders, recent research has increasingly focused on identifying effective intervention strategies to promote “healthy aging” by slowing down the aging process as much as possible. At the molecular level, multiple factors contribute to cellular aging and, consequently, to the onset of senescence. These include mitochondrial dysfunction, defective DNA repair mechanisms, epigenetic reprogramming, and chronic low-grade inflammation. Among the mechanisms driving cellular senescence, oxidative stress is recognized as a key contributor to the loss of replicative capacity. When reactive oxygen species (ROS) levels exceed a critical threshold, they can damage essential macromolecules, including DNA. Therefore, ROS and oxidative stress represent crucial therapeutic targets to be considered in strategies aimed at counteracting cellular senescence. Based on these causal factors, several strategies have been identified that target modifiable lifestyle determinants, with a primary focus on nutrition and nutraceutical interventions. In this context, the present review aims to critically analyze scientific evidence regarding nutritional approaches designed to slow down the aging process, including their effects at the molecular level. Specifically, these strategies aim to reduce inflammation, preserve mitochondrial function to modulate ROS production, and protect macromolecules from oxidative stress. Full article

Colorectal cancer (CRC) is traditionally considered a “cold tumor” characterized by low immunogenicity and limited responsiveness to immune checkpoint inhibitors (ICIs). However, recent findings reveal that cytotoxic modalities can reprogram this immunologically inert landscape. This review integrates these evolving concepts to guide the optimization of future treatments. Radiotherapy induces extensive DNA double-strand breaks, which may generate de novo mutations through error-prone repair while simultaneously exposing cryptic antigens via increased transcriptional instability, alternative splicing, and enhanced proteasomal processing. Chemoradiation also amplifies epigenetic and epitranscriptomic sources of neoepitope diversity, including RNA editing and stress-induced splicing alterations, expanding the immunopeptidome beyond canonical mutation-driven neoantigens. These changes collectively enhance antigen presentation and facilitate T-cell priming. Chemotherapy further reduces immunosuppressive cell populations and promotes dendritic cell activation, creating a permissive milieu for subsequent immune engagement. Clinically, the VOLTAGE studies demonstrated that long-course chemoradiotherapy can sensitize even mismatch repair–proficient rectal cancers to PD-1 blockade, yielding clinically meaningful pathological responses. In contrast, mismatch repair–deficient rectal tumors may respond completely to ICIs alone. Short-course radiotherapy combined with chemotherapy and ICIs has also shown encouraging activity in the setting of total neoadjuvant therapy. Collectively, these findings support a paradigm in which radiotherapy, chemotherapy, and epigenetic/epitranscriptomic alterations—including RNA editing—act as potent modulators of tumor antigenicity. By expanding the neoantigen repertoire and reshaping the tumor microenvironment, these strategies can transform CRC from a cold tumor into one that is increasingly responsive to immunotherapy. Full article

Chronic inflammation associated with obesity drives metabolic dysfunctions and induces immune cell maintenance. Adipose tissue macrophages (ATMs), the predominant immune population within adipose depots, exhibit substantial heterogeneity and serve as central pathological mediators in obesity-induced adipose inflammation and metabolic dysregulation. In this review, we highlight the reprogramming of ATMs’ metabolic pathways, including glucose and lipid homeostasis associated with obesity, with a focus on chronic metabolic inflammation. Additionally, we discuss underlying mechanisms supporting ATMs remodeling in obesity, including transcriptional control and epigenetic regulation. Full article

Metabolic reprogramming is a defining feature of breast cancer, enabling tumor cells to sustain rapid proliferation, survive under stress, and resist therapy. Key pathways including glycolysis, glutaminolysis, lipid metabolism, and one-carbon metabolism, play central roles in meeting the energetic and biosynthetic demands of malignant cells. Enhanced glycolytic flux supports ATP generation and lactate production, while glutamine metabolism fuels the tricarboxylic acid cycle and provides nitrogen for nucleotide synthesis. Lipid metabolic pathways, particularly fatty acid synthesis, contribute to membrane biogenesis and signaling, and one-carbon metabolism driven by serine and glycine supplies methyl groups for epigenetic regulation and nucleotide production. These metabolic adaptations not only promote tumor growth but also create vulnerabilities that can be exploited therapeutically. Inhibiting these pathways has shown promise in preclinical models; however, challenges such as metabolic plasticity, tumor heterogeneity, and potential toxicity in normal tissues underscore the need for biomarker-driven strategies and rational combination therapies. Herein, we describe current knowledge of the role of these pathways in breast cancer progression, highlighting the role of key enzymes in promoting breast cancer tumor cell growth and in breast cancer prognoses. Full article

Phthalate esters (PAEs), ubiquitous plastic additives, have emerged as persistent contaminants in aquatic ecosystems, yet their propagation from molecular initiating events to ecosystem-level collapse remains poorly integrated. This review synthesizes current knowledge on the source-to-sink dynamics of PAEs, revealing a critical paradox in their bioaccumulation patterns: unlike classical persistent organic pollutants, high molecular weight PAEs exhibit distinct trophic dilution rather than biomagnification along food webs, driven by metabolic biotransformation in higher trophic organisms. Despite this dilution, PAEs trigger a bottom-up toxicity cascade. Driven by molecular initiating events, PAEs induce a range of adverse effects at the individual level, including immunotoxicity, neurotoxicity, endocrine disruption, metabolic dysfunction, and trans-trophic oxidative stress. Crucially, prolonged exposure drives epigenetic reprogramming, which reduces reproductive output, thereby threatening long-term population recruitment. These individual and population deficits could escalate into higher ecological consequences, specifically by diminishing benthic biological control over phytoplankton, dampening energy transfer efficiency, and simplifying community structure, thereby posing a potential threat to primary productivity and aquatic ecosystem sustainability. Despite recent advances, critical knowledge gaps remain, particularly regarding their cascading impacts on ecosystem services, as well as synergistic interactions between PAEs and other contaminants. In order to validate laboratory results with actual ecological risk assessments, future research should incorporate multi-scale models and quantitative adverse outcome Pathways as well as their synergistic interactions between PAEs and other contaminants, and advanced in vitro systems such as organoids. Resolving these issues is essential to reducing the risks that PAEs pose to aquatic environments. Full article

Breast cancer is a highly heterogeneous malignancy, characterized by diverse genetic, epigenetic, and phenotypic variations, as well as by metabolic reprogramming and oxidative stress. Lipid peroxidation bioactive product 4-hydroxynonenal (4-HNE) plays a significant role in the development and progression of cancer. In this study, we quantified circulating 4-HNE-modified proteins and performed comprehensive untargeted metabolomic profiling of the patients’ plasma using LC-ESI-QTOF-MS and GC-EI-QMS, aiming to investigate systemic metabolic pathways associated with oxidative damage in breast cancer. Significantly elevated levels of 4-HNE-modified proteins were detected in breast cancer patients compared to healthy controls, accompanied by distinct metabolomic signatures enriched in lipid metabolism. Several metabolites, including specific long-chain fatty acids, exhibited significant correlations with circulating 4-HNE-modified proteins, suggesting an interaction between lipid peroxidation-driven protein modification and breast cancer-associated metabolic reprogramming. Overall, this study provides evidence of associations between systemic 4-HNE-mediated protein modification and altered metabolic profiles in breast cancer, highlighting oxidative stress–related metabolites as potential biomarkers and pointing to redox-metabolic crosstalk in breast cancer patients. Full article

Cadmium (Cd) contamination of agricultural soils threatens crop productivity and food safety by disrupting physiological and molecular processes in plants. Increasing evidence indicates that epigenetic regulation, including DNA methylation, histone modifications, and emerging epitranscriptomic marks such as RNA methylation, plays a crucial role in coordinating plant responses to Cd stress. In parallel, plant-associated microbiomes have emerged as influential modulators of metal uptake, antioxidant capacity, hormone signaling, and stress resilience. Yet the mechanisms by which microbiome-derived signals intersect with host chromatin and transcriptome regulation under Cd exposure remain poorly understood. This review synthesizes current knowledge on plant epigenetic responses to Cd stress and critically examines how microbial metabolites, phytohormones, and redox-active compounds shape plant regulatory networks. Network-based ecological studies reveal that increased microbial community complexity and cooperative interactions are consistently associated with reduced Cd accumulation and enhanced plant performance, suggesting that microbial organization itself may represent an additional regulatory layer influencing plant responses. Despite compelling conceptual links, direct experimental evidence connecting microbiome signals to stable epigenetic or epitranscriptomic reprogramming under Cd stress remains limited. To date, only limited experimental studies have demonstrated causal relationships between microbial cues and host DNA or RNA methylation dynamics in Cd-exposed plants, highlighting clear mechanistic potential while also underscoring remaining knowledge gaps. By integrating physiological, ecological, and chromatin-level perspectives, this review identifies key unanswered questions and outlines future research directions to establish causal links between microbial community dynamics, epigenetic regulation, and long-term Cd stress adaptation in plants. Full article