Search Results (496)

Metabolic and cardiometabolic diseases are closely associated with mitochondrial dysfunction and redox imbalance. Ubiquinol–cytochrome c reductase core protein 2 (UQCRC2), a non-catalytic structural core subunit of mitochondrial respiratory chain Complex III, is increasingly recognized as a regulator of Complex III integrity, electron transfer, oxidative phosphorylation, and mitochondrial redox homeostasis. Under metabolic stress, reduced expression or functional impairment of UQCRC2 may promote electron leakage, mitochondrial reactive oxygen species (mtROS) generation, lipid peroxidation, impaired antioxidant defense, and disrupted glucose–lipid metabolism. These alterations may contribute to insulin resistance (IR), metabolic dysfunction-associated steatotic liver disease (MASLD), obesity, and cardiovascular disease (CVD). This review summarizes current evidence linking UQCRC2 dysfunction to mitochondrial bioenergetic failure, oxidative stress, inflammatory signaling, and cardiometabolic injury. We further discuss redox-regulatory pathways, including Nrf2, AMPK–SIRT1–PGC-1α, glutathione metabolism, and mitophagy, as well as pharmacological agents and natural compounds that may modulate UQCRC2-related mitochondrial responses. Collectively, these findings highlight UQCRC2 as a redox-sensitive mitochondrial node linking Complex III dysfunction to cardiometabolic injury and targeted redox-based interventions. Full article

Background: Bacterial adaptation to environmental and chemical stress involves coordinated, system-level responses collectively described as perturbome. Understanding conserved elements within core perturbomes may reveal strategic vulnerabilities for antimicrobial development. Methods: In this study, we implemented an integrative framework combining functional and comparative genomics, drug–target interactions and molecular docking to prioritize conserved stress-response targets in Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus. Results: A total of 147 genes from previously defined core perturbomes were analyzed through interactome reconstruction and functional enrichment. Interactome and functional analyses revealed significant connectivity and functional clustering, primarily associated with molecule biosynthesis, translation, transcriptional regulation, and energy metabolism. Orthology-based comparative genomics identified six conserved orthogroups shared across at least two species, representing key stress-adaptive nodes including fatty acid synthesis initiation, metabolic stress buffering, transcription termination (Rho), ATP synthesis, peptidoglycan remodeling, and UDP-glucose-mediated envelope biosynthesis. Drug–target interaction analyses suggested that these conserved proteins are modulated by enzymatic inhibitors, metabolite analogs, or active-site competitors. Structural and docking analyses focused on a selected protein, FabF (β-ketoacyl-ACP synthase II) and confirmed catalytically coherent binding of cerulenin within the active site, with high concordance between experimentally resolved and AlphaFold-predicted structures, supporting the reliability of structure-based prioritization. Conclusions: Overall, the results demonstrate that bacterial stress responses converge on evolutionarily conserved metabolic and regulatory elements essential for homeostasis and tolerance to perturbations, being the first work integrating core perturbome data from different microorganisms. The proposed perturbome-informed framework provides a rational strategy to identify robust, broad-spectrum antimicrobial targets and highlights opportunities for drug repurposing and future experimental validation. Full article

The pathological mechanism of autism spectrum disorder (ASD) exhibits dual heterogeneity: abnormal local energy metabolism and brain-wide high-order topological failure. To synergistically characterize these complex signals captured by advanced neuroimaging sensors, we propose the Quantum-Enhanced Graph Convolutional Wide Residual Network (QG-WRN), a modality-specific, decoupled parallel dual-stream architecture. In the classical branch, to accurately capture the spatial distribution of local metabolic abnormalities, we employ a wide residual network (WRN) to extract amplitude of low-frequency fluctuation (ALFF) features, leveraging its expanded feature channels to effectively mine regional neurodynamic properties. Furthermore, to overcome the representational bottlenecks of classical linear operators in parsing hidden, long-range network connections, we introduce quantum computing, exploiting its exponentially expansive state space and intrinsic low-parameter regularization mechanism. Guided by these properties, the quantum branch utilizes a variational quantum graph convolutional (QGCN) module—featuring a trainable circular encoding strategy and a hardware-efficient 4-qubit configuration—with a 2-layer nested message passing structure to process the functional connectivity (FC) matrix, harnessing quantum interference in Hilbert space to parse complex topology while effectively mitigating overfitting on small-sample medical data. A unified training scheme achieves full-dimensional fusion of node activity and topology. Achieving 68.49% accuracy, our method outperforms 10 classic and recent new baselines, providing a powerful computational intelligence tool for sensor-based ASD clinical diagnosis. Furthermore, interpretability analysis successfully maps core disease hubs to standard AAL116 atlas coordinates, providing a powerful tool for computationally aided ASD diagnosis. Full article

Endometriosis is increasingly recognized as a chronic systemic disorder extending beyond the classical estrogen-dependent paradigm, integrating metabolic, immune, fibrotic, and nociceptive pathways that sustain lesion persistence and refractory pelvic pain. We propose a mechanistic, translational hypothesis in which tirzepatide, a dual glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) receptor agonist, may modulate four interconnected pathological axes of refractory endometriosis—Warburg-type metabolic reprogramming with lactate accumulation, peritoneal immune dysfunction, NF-κB/NLRP3/TGF-β1-driven inflammatory–fibrotic remodeling, and persistent nociceptive sensitization—through three convergent molecular nodes: AMPK-associated signaling, GLP-1 receptor activity in peritoneal macrophages and spinal microglia, and the NF-κB/NLRP3/TGF-β1 axis. Particular emphasis is placed on the concept of “peritoneal incretin deficiency”, characterized by reduced peritoneal GLP-1 concentrations and increased expression of incretin-degrading proteases. This concept currently rests on a single, non-replicated case–control study, and the broader mechanistic chain is supported largely by indirect evidence extrapolated from adjacent inflammatory, metabolic, and neuroimmune disease models rather than by endometriosis-specific data. Direct experimental or clinical validation in endometriosis-specific models is currently absent. Accordingly, this article represents a hypothesis-generating framework rather than evidence of established efficacy, or a clinical treatment recommendation, intended to guide future mechanistic and prospective clinical investigation of incretin-based modulation as a potential adjunctive strategy in refractory endometriosis. Full article

Background/Objectives: Ultra-processed foods (UPFs) are increasingly recognized as dietary exposures associated with cardiometabolic, hepatic, and neurocognitive outcomes. However, UPFs are often treated mainly as nutrient-poor foods, whereas their processing-related features may perturb gut–liver–brain communication. This review examines whether metabolic dysfunction-associated steatotic liver disease (MASLD) can be conceptualized as a hepatic metabolic amplifier linking UPF exposure to cognitive aging. Methods: We conducted a structured narrative search of PubMed/MEDLINE, Web of Science Core Collection, and Scopus from January 2010 to 11 May 2026 across four evidence modules: UPFs and MASLD/NAFLD; UPFs and cognitive aging or dementia; UPFs and gut–liver–brain mechanisms; and MASLD/NAFLD and cognitive aging. Representative studies were prioritized according to direct relevance to the proposed axis, study design, exposure and outcome validity, mechanistic specificity, and contribution to major evidence gaps. Results: Observational and mechanistic evidence links higher UPF consumption with liver steatosis, MASLD/NAFLD-related outcomes, cognitive decline, cognitive impairment, stroke, and dementia-related outcomes, although causality remains incompletely established and residual confounding is important. Candidate pathways include food-matrix disruption, rapid eating, displacement of microbial substrates, selected additives and processing-derived compounds, intestinal barrier dysfunction, metabolic endotoxemia, bile acid signaling, hepatic lipotoxicity, systemic inflammation, vascular dysfunction, and neuroimmune activation. Many pathways overlap with general cardiometabolic dysfunction; the processing-centered contribution lies in positioning industrial formulation as an upstream exposure and MASLD as a hepatic node that may amplify gut-derived and metabolic signals relevant to brain aging. Conclusions: A processing-centered gut–liver–brain framework integrates UPFs, MASLD, and cognitive aging as linked metabolic-aging phenomena. Future studies should test UPF substitution using liver imaging, microbiome profiling, metabolomics, bile acid and inflammatory biomarkers, neuroimaging, and cognitive assessment. Full article

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

LRRK1 is essential for osteoclast-mediated bone resorption, and loss of LRRK1 function causes osteopetrosis in mice and humans. However, the mechanisms by which LRRK1 regulates osteoclast activity remain incompletely defined. We previously identified that phosphorylation of OSTM1 at threonine 328 and serine 329 was compromised in LRRK1-deficient osteoclasts. To test the role for OSTM1 phosphorylation in LRRK1 regulation of osteoclast functions, we expressed a phosphomimetic OSTM1 variant in LRRK1-null osteoclasts. Overexpression of phosphomimetic, but not a dephosphomimetic variant, partially restored resorptive activity in LRRK1-deficient osteoclasts in vitro. To test OSTM1’s role in rescuing defective bone resorption in Lrrk1-null mice, we generated Ostm1-T328E/S329D knock-in (KI) mice and crossed them onto the Lrrk1-deficient background. Ostm1-T328E/S329D KI mice displayed normal skeletal development and bone remodeling. When crossed to the Lrrk1-deficient background, OSTM1-T328E/S329D expression increased osteoclast resorptive activity and bone formation and partially improved trabecular architecture, although bone volume remained unchanged. These findings demonstrate that OSTM1 phosphorylation contributes to LRRK1-dependent regulation of osteoclast function and identify the LRRK1–OSTM1 pathway as a mechanistic node controlling bone resorption. Our work provides new insight into the molecular basis of LRRK1-mediated osteoclast function and highlights OSTM1 phosphorylation as a potential therapeutic target for metabolic bone diseases. Full article

The vertebrate mitochondrial genome (mitogenome) is a small, circular DNA molecule typically ~16–17 kb in length, encoding 37 genes that are essential for the electron transport chain, the mechanism that drives mostly all the ATP synthesis in cells. Owing to its central role in energy metabolism, its structure is highly conserved across vertebrate lineages in both the number and relative position of each gene in the genome. Nevertheless, different variations have been found in several teleost lineages, including antarctic fishes (Nototheniidae), gadiforms, hatchetfishes (Sternoptychidae), and Batrachoidiformes. The explanation for these phenomena remains unknown yet may reflect shifts in functional constraints and can provide insights into lineage-specific and/or coevolutionary processes. This raises the possibility that mitogenome structure is related to habitat selection, potentially reflecting environmental influences on energetic regulation. To further test this hypothesis, we studied more than 400 teleost species across all major teleost lineages. The mitogenome sequences were downloaded from NCBI and annotated using two independent algorithms (MITOZ and MITOS) and then compared with a reference (Danio rerio) to find any deviation from the standard structure. Similarly, ecological data was downloaded from FishBase using the R Package “rfishbase” 5.0.3. Two independent ancestral reconstruction analyses were carried out for both traits, “Mitogenome” and “Habitat”, using a reference evolutionary tree for teleosts to unravel both evolutionary histories. The possible association between mitogenome and habitat was then assessed using a suite of phylogenetic comparative methods, including Pagel’s correlation test (corHMM) to evaluate whether both traits evolved in a correlated fashion, branch-level co-transition analysis to identify lineages where structural changes and habitat shifts co-occurred, and node-by-node comparisons of ancestral state probabilities across the phylogeny. Preliminary results suggest a correlation between some deep-sea environments and a modified mitogenome structure, with structural deviations tending to cluster in lineages inhabiting greater depths. These exploratory findings raise the possibility that changes in mitogenome architecture may be linked to adaptations in energetic metabolism required for life in extreme low-energy environments. Further analyses are underway to clarify the functional significance of these genomic changes and their relationship to ecological and metabolic pressures in teleost evolution. Full article

Cancer stem cells (CSCs) constitute a resilient tumor subpopulation responsible for multidrug resistance, metastasis, and clinical relapse. A cardinal hallmark of these cells is profound metabolic plasticity. This dynamic defense mechanism facilitates rapid shifts between glycolysis, oxidative phosphorylation (OXPHOS), and alternative nutrient catabolism, enabling CSCs to bypass microenvironmental constraints. This review delineates how glycolytic adaptation functions as a primary driver of therapy resistance within the CSC niche. We dissect the regulatory triad controlling these metabolic shifts, which includes rate-limiting enzymes, epigenetic and epitranscriptomic remodeling, and master transcription factors. Glycolytic reprogramming transcends bioenergetics by acting as a metabolic signaling node. It integrates with the epithelial–mesenchymal transition (EMT) program, autophagic pathways, and the immunosuppressive tumor microenvironment (TME) to fortify CSC survival. We appraise emerging therapeutic interventions targeting these metabolic vulnerabilities. Strategies focus on optimizing small-molecule inhibitors, nanotechnology-enabled delivery systems, and immunometabolic combination regimens. This review establishes a conceptual framework for precision interventions aimed at disrupting CSC plasticity, overcoming therapeutic resistance, and preventing tumor recurrence. Full article

The innate–adaptive immune interface is a decisive control point determining whether therapeutic interventions induce durable protection, antitumor immunity, inflammatory, or immune tolerance. Many immunotherapies fail in translation because immunity is often treated as a single-output system rather than a spatially and temporally organized network shaped by tissue context, antigen-presenting cell fate, biomolecular conditioning, and metabolic state. This review introduces the immunoscape framework as a nanobiotechnology-oriented model for linking immune-state mapping with controllable translational variables, including delivery route, release kinetics, first-contact immune cells, lymphatic routing, biomolecular corona identity, antigen-presenting cell fate, and safety-gate assessment. Unlike systems immunology, which primarily describes immune networks, or conventional immune engineering, which often focuses on selected payloads, targets, or platforms, the immunoscape framework provides a design layer for predicting context-dependent immune outcomes. We discuss two converging strategies for reprogramming this interface: natural biologics, including beta-glucans, polyphenols, microbial metabolites, and extracellular vesicles; and smart nanomaterials, including lipid nanoparticles, biomimetic vesicles, lymph node-targeted platforms, and stimulus-responsive nanoarchitectures. We further propose translational design rules to guide clinically realistic immune-reprogramming nanomedicines for cancer, infectious, inflammatory, and regenerative applications. Full article

Background/Objectives: Immune checkpoints are critical regulatory pathways that maintain peripheral tolerance and prevent autoimmunity. Among these, the programmed death-1/programmed death-ligand 1 (PD-1/PD-L1) axis serves as a major inhibitory pathway that terminates T cell responses. While protein-based checkpoint blockade (ICB) targeting this axis has revolutionized clinical cancer therapy, its clinical efficacy is frequently limited by low response rates, immune-related adverse events (irAEs), and the emergence of adaptive resistance. To break through these bottlenecks, genetic interruption has emerged as a high-precision alternative to modulate the PD-1/PD-L1 pathway at the nucleotide level. Methods: A comprehensive systematic review of literature was performed across major databases (PubMed, Web of Science), with a focus on high quality studies published up to 2026. Results: Direct genomic disruption via CRISPR/Cas9 and post-transcriptional silencing through RNA interference can effectively neutralize inhibitory signaling at its source. Recent advances demonstrate that targeting upstream regulatory nodes—including metabolic checkpoints (e.g., lactate metabolism) and biophysical mechanisms (e.g., liquid–liquid phase separation)—provides superior transcriptional control over PD-L1. Furthermore, engineering CAR-T cells with multiplex gene editing (e.g., TCR/B2M/PD-1 knockout) or localized scFv secretion significantly enhances antitumor potency while reducing systemic toxicity. Innovations in organ-targeted lipid nanoparticles and stimuli-responsive biomimetic carriers further address the delivery barriers in solid tumors. Conclusions: Gene therapy provides a high-precision platform for PD-1/PD-L1 modulation, offering a viable strategy to overcome adaptive resistance. Future clinical application depends on the refinement of safer editing tools, such as base editing, and the standardization of intelligent delivery systems to ensure controllable and scalable cancer immunotherapy. Full article

Anaplastic thyroid carcinoma (ATC) represents the most aggressive thyroid malignancy, characterized by rapid progression, therapeutic resistance, and poor prognosis. Conventional treatments remain largely ineffective, highlighting the need for novel therapies. Metabolic reprogramming, particularly the Warburg effect (WE), has emerged as a promising area of investigation. This review synthesizes current evidence on the role of WE in ATC and PDTC, integrating data from molecular profiling, preclinical studies, and emerging therapeutic strategies. Oncogenic alterations frequently observed in ATC, including mutations in BRAF, RAS, TP53, and activation of PI3K/AKT/mTOR and HIF-1α signaling, converge to promote glycolytic reprogramming. This metabolic shift supports tumor proliferation, immune evasion, and metastasis through increased glucose uptake, lactate production, and microenvironmental remodeling. Key metabolic nodes, including glucose transporters, hexokinase, and monocarboxylate transporters, are regarded as promising targets. Preclinical studies suggest that pharmacological inhibition of these pathways reduces tumor growth, enhances radiosensitivity, and improves response to targeted therapies. Future efforts should focus on combination therapies, biomarker-driven patient stratification, and the development of targeted delivery systems to overcome toxicity and resistance. A deeper understanding of tumor metabolic heterogeneity will be essential for translating these approaches into clinical practice. 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

Background: Soil mulching is a widely adopted agricultural practice known to regulate soil microclimate and enhance crop productivity; yet the biochemical mechanisms by which intact plastic and biodegradable mulch films influence soil nitrogen (N) cycling at the metabolic pathway level remain largely unexplored. Understanding these nitrogen transformation pathways is critical for assessing the long-term impacts of mulching materials on soil microbial communities, soil health, and sustainable agricultural management. This study focuses on the biochemical effects of intact mulch film application on soil N metabolism. Methods: N cycle-related soil metabolites were profiled using GC–MS/MS and MALDI TOF/TOF MS and then integrated with multivariate statistical modelling and pathway-level metabolic network perturbation analysis to compare conventional plastic and biodegradable plastic mulch film application against unmulched controls. Results: A panel of 62 KEGG-annotated N-cycle metabolites was profiled, and material-dependent metabolome separation was confirmed by OPLS-DA (R²Y 0.893–0.956; Q² 0.546–0.786). Both mulching materials significantly perturbed soil N-metabolite pools but differed in terms of pathway identity, magnitude, and directionality. Conventional plastic mulching caused the greatest disruption—near-complete suppression of N-storage and stress-adaptation pools (NES of −1.16; impact score of 10.01) and severe impairment of aspartate-centred metabolism—with L-aspartate identified as a critical stoichiometric hub. Biodegradable mulching material imposed a distinct profile dominated by inhibition of branched-chain amino acid catabolism and lysine degradation, with L-pipecolate as a treatment-specific critical impact node. Conclusions: These findings support that mulching material choice is a primary determinant of soil N-cycling biochemistry. The observed metabolite-level perturbations are suggestive of potential consequences for nitrogen retention. Though this inference is based on metabolite pool size differences and network topology metrics rather than directly measured process rates, it should therefore be interpreted with appropriate caution. Full article