Search Results (240)

Mechanobiology plays a pivotal role in skeletal development and bone remodeling. Mechanical signals such as matrix stiffness, fluid shear stress, and hydrostatic pressure activate the Runt-related transcription factor 2 (RUNX2) bone-specific transcription factor through pathways including the mitogen-activated protein kinase (MAPK) signaling cascade and yes-associated protein (YAP)/transcriptional co-activator with PDZ-binding motif (TAZ) effectors. RUNX2 itself affects chromatin remodeling and nuclear architecture via Lamin A/C and Nesprin 1, thereby directing osteogenic differentiation. Thus, RUNX2 acts both as a mechanosensor and mechanoregulator, whereas RUNX2’s mechanosensitivity has been leveraged as a target to achieve bone regeneration. Notably, post-translational modifications and epigenetic alterations can orchestrate this regulation, integrating metabolic and circadian signals. However, due to RUNX2’s nuclear localization, its targeting remains a challenging issue. To this end, indirect targeting, through mammalian/mechanistic target of rapamycin complex 1 (mTORC1) or microRNAs (miRNAs), offers new strategies to employ biomechanics in an attempt to intervene with bone diseases driven by mechanical cues or degeneration, and ultimately repair and regenerate the damaged tissues. Herein we critically elaborate upon molecular aspects of RUNX2 regulation towards exploitation at the clinical level. Full article

Post-translational modifications (PTMs) are crucial chemical alterations occurring on proteins post-synthesis, impacting various cellular processes. During viral infections, PTMs are shown to play a multitude of roles in viral replication, host interaction, and immune evasion. Thus, these modifications can influence infectivity, with direct impact on the anti-viral host immune responses and potentially viral adaptation across species. This field is still scarcely explored, whilst understanding PTMs is not only important to advance the knowledge of virus pathology but also potentially to provide insights for vaccine development. In this review, we attempt to summarize the latest findings mainly published over the last 10 years, focusing on the roles of PTMs involved in virus infection and anti-viral immune responses, in the context of relevant human respiratory infections: influenza A virus (IAV), respiratory syncytial virus (RSV), and SARS-CoV-2. We decided to concentrate on these three viruses because they currently represent a global health problem due to recurrent outbreaks and pandemic potential. A deeper characterization of the PTMs may help in understanding virus–host interaction with possible implications on curative strategies. Further, we will report on cutting-edge technologies to study in vitro virus infection in different cellular-based systems. In particular, we describe and discuss the application of 2D and 3D lung organoid cell-culture systems as in vitro models to mimic respiratory environments and to study the PTMs in a controlled setting. Finally, we will discuss the importance of PTMs in the context of next-generation vaccine design, especially for their potential role to offer effective protection against respiratory viruses. Full article

In animals and humans, nutrients influence signaling cascades, transcriptional programs, chromatin dynamics, and mitochondrial function, collectively shaping traits related to growth, immunity, reproduction, and stress resilience. This review synthesizes evidence supporting nutrient-mediated regulation of DNA methylation, histone modifications, non-coding RNAs, and mitochondrial biogenesis, and emphasizes their integration within metabolic and developmental pathways. Recent advances in epigenome-wide association studies (EWAS), single-cell multi-omics, and systems biology approaches have revealed how diet composition and timing can reprogram gene networks, sometimes across generations. Particular attention is given to central metabolic regulators (e.g., PPARs, mTOR) and to interactions among methyl donors, fatty acids, vitamins, and trace elements that maintain genomic stability and metabolic homeostasis. Nutrigenetic evidence further shows how genetic polymorphisms (SNPs) in loci such as IGF-1, MSTN, PPARs, and FASN alter nutrient responsiveness and influence traits like feed efficiency, body composition, and egg quality, information that can be exploited via marker-assisted or genomic selection. Mitochondrial DNA integrity and oxidative capacity are key determinants of feed conversion and energy efficiency, while dietary antioxidants and mitochondria-targeted nutrients help preserve bioenergetic function. The gut microbiome acts as a co-regulator of host gene expression through metabolite-mediated epigenetic effects, linking diet, microbial metabolites (e.g., SCFAs), and host genomic responses via the gut–liver axis. Emerging tools such as whole-genome and transcriptome sequencing, EWAS, integrated multi-omics, and CRISPR-based functional studies are transforming the field and enabling DNA-informed precision nutrition. Integrating genetic, epigenetic, and molecular data will enable genotype-specific feeding strategies, maternal and early-life programming, and predictive models that enhance productivity, health, and sustainability in poultry production. Translating these molecular insights into practice offers pathways to enhance animal welfare, reduce environmental impact, and shift nutrition from empirical feeding toward mechanistically informed precision approaches. Full article

Valine-glutamine motif proteins (VQ), plant-specific transcriptional co-regulators harboring the conserved FxxhVQxhTG motif, play pivotal roles in coordinating plant stress adaptation through dynamic interactions with WRKY transcription factors (WRKY), mitogen-activated protein kinases (MAPKs) cascades, and hormone signaling pathways. Evolutionary analyses reveal the characteristics of their evolutionary protection and ancient origin, with lineage-specific expansion via genome duplication events. Structurally, compact genes lacking introns and the presence of intrinsic disordered regions (IDRs) facilitate rapid stress responses and versatile protein interactions. Functionally, VQ proteins orchestrate abiotic stress tolerance (e.g., drought, salinity, temperature extremes) by modulating reactive oxygen species (ROS) homeostasis, osmotic balance, and abscisic acid/salicylic acid (ABA/SA)-mediated signaling. Concurrently, they enhance biotic stress resistance via pathogen-responsive WRKY-VQ modules that regulate defense gene expression and hormone crosstalk. Despite advances, challenges persist in deciphering post-translational modifications, tissue-specific functions, and cross-stress integration mechanisms. Harnessing CRISPR-based editing and multi-omics approaches will accelerate the exploitation of VQ genes for developing climate-resilient crops. This review synthesizes the molecular architecture, evolutionary dynamics, and multifunctional regulatory networks of VQ proteins, providing a roadmap for their utilization in sustainable agriculture. Full article

Poly (lactic-co-glycolic acid) (PLGA) is a widely used copolymer with applications across medical, pharmaceutical, and other industrial fields. Its biodegradability and biocompatibility make it one of the most versatile polymers for nanoscale drug delivery. The present review addresses current knowledge and recent advances in PLGA-based co-delivery nanoformulations with a special reference to design strategies, functional mechanisms, and translational potential. Conventional and advanced fabrication methods, the structural design of PLGA-based nanocarriers, approaches to scale-up and reproducibility, classification of co-delivery types, mechanisms governing drug release, surface modification and functionalization are all discussed. Special attention is given to PLGA-based co-delivery systems, encompassing drug–drug, drug–gene, gene–gene and multi-modal combinations, supported by recent studies demonstrating synergistic therapeutic outcomes. The review also examines clinical translation efforts and the regulatory landscape for PLGA-based nanocarriers. Unlike most existing reviews that typically focus either on PLGA fundamentals or on co-delivery approaches in isolation, this article bridges these domains by providing an integrated, comparative analysis of PLGA-based co-delivery systems and elucidating a critical gap in linking design strategies with translational requirements. In addition, by emphasising the relevance of PLGA-based co-delivery for combination therapies, particularly in cancer and other complex diseases, the review highlights the strong clinical and translational potential of these platforms. Key challenges, such as reproducibility, large-scale manufacturing, and complex regulatory pathways, are discussed alongside emerging trends and future perspectives. Taken together, this review positions PLGA-based co-delivery strategies as a critical driver for advancing precision therapeutics and shaping the future landscape of nanomedicine. Full article

Individuals with rheumatoid arthritis (RA) face increased cardiovascular mortality due to heart failure (HF) complications. Post-translational modifications, such as citrullination (CIT) and malondialdehyde–acetaldehyde (MAA) adduction, are implicated in RA pathogenesis. However, their role in RA-associated HF is not well understood. This study examines the deposition of MAA and CIT in cardiac tissues of RA-HF patients and investigates how MAA and CIT adducts on fibrinogen (FIB-MAA-CIT) drive crosstalk between macrophages and endothelial cells in vitro. We demonstrated elevated MAA and CIT adducts, strong perivascular MAA-CIT co-localization, and increased perivascular collagen deposition in the myocardium of RA-HF patients compared to non-RA HF controls. Treating human coronary artery endothelial cells (HCAECs) with FIB-MAA-CIT induced upregulation of inflammatory markers including MCP-1, IL-6, ICAM-1, and VCAM-1 compared to unmodified FIB. This response was amplified when HCAECs were treated with cell culture media obtained from FIB-MAA-CIT-stimulated macrophages. FIB-MAA-CIT activation of macrophages engaged NF-κB and p38 signaling pathways and inhibition of these pathways reduced FIB-MAA-CIT-mediated macrophage cytokine secretion and subsequent HCAEC responses. In summary, our findings support a novel mechanism by which endogenously modified proteins drive macrophage–endothelial cell crosstalk, promoting myocardial inflammation. Targeting these post-translational modifications may present novel therapeutic strategies to mitigate HF in RA. Full article

Methacrylyl-CoA is a key metabolic intermediate in the valine catabolic pathway. Its accumulation has been found to be cytotoxic and associated with pathological conditions. Nevertheless, detailed biological effects of methacrylyl-CoA and methacrylate in human physiology and pathology are poorly understood. We propose that the electrophilicity of the alkene bond in the methacrylyl group can react with the cysteine residues in proteins resulting in an unexplored protein post-translational modification (PTM), cysteine S-2-carboxypropylation (C2cp). To test and validate this mechanistic hypothesis, we experimentally detected and profiled S-2-carboxypropylated proteins from the complex cellular proteome with the design and application of a bioorthogonal chemical probe, N-propargyl methacrylamide. We tested the probe in different mammalian cell models and demonstrated its versatility and sensitivity to protein cysteine S-2-carboxypropylation. We established quantitative chemical proteomics for global and site-specific profiling of protein S-2-carboxypropylation, which successfully identified 403 S-2-carboxypropylated proteins and 120 cysteine modification sites from HEK293T cells. Through bioinformatic analysis, we found that C2cp-modified proteins were involved in a variety of critical cellular functions including translation, RNA splicing, and protein folding. Our chemoproteomic studies demonstrating the proteome-wide distribution of cysteine S-2-carboxypropylation provide a new biochemical mechanism for the functional investigation of methacrylyl-CoA and understanding valine-related metabolic disorders. Full article

Type-I protein prenylation, the post-translational modification of CaaX motif-containing proteins, relies on two substrates: the target protein and a mevalonate-derived prenyl diphosphate co-substrate, either farnesyl diphosphate (FPP) or geranylgeranyl diphosphate (GGPP). Two enzymes, protein farnesyltransferase and type-I geranylgeranyltransferase, recognize and bind both co-substrates. Modifying potentially hundreds of distinct protein targets within a constrained timeframe poses a major regulatory challenge for the cell. However, the mechanisms controlling prenyltransferase activity, including substrate availability, enzyme specificity, and catalytic efficiency, remain poorly understood, particularly in plants. Plant prenylation systems exhibit distinctive features. The diversity of prenyl diphosphate donors is expanded by the plastidial methylerythritol phosphate pathway, which supplements the mevalonate pathway and may provide alternative prenyl groups beyond the canonical FPP and GGPP. Additionally, many CaaX-containing proteins are plant-specific, and post-transcriptional modifications generate multiple prenylatable isoforms, increasing substrate complexity. In this review, we examine the diversification of both prenyl diphosphate donors and protein substrates in plants, hypothesizing that such diversification may illuminate key mechanisms underlying the cellular regulation of protein prenylation. Full article

Background: Pancreatic ductal adenocarcinoma (PDAC) exhibits marked resistance to immunotherapy. Beyond its characteristically low tumor mutational burden, post-translational modifications (PTMs) remodel the immunopeptidome and promote immune escape through reversible, enzyme-driven programs. Subject Matter: We synthesize evidence that aberrant glycosylation, O-GlcNAcylation, phosphorylation, and citrullination constitute core determinants of antigen visibility operating within spatially discrete tumor niches and a desmoplastic stroma. In hypoxic regions, HIF-linked hexosamine metabolism and OGT activity stabilize immune checkpoints and attenuate antigen processing; at tumor margins, sialylated mucins engage inhibitory Siglec receptors on innate and adaptive lymphocytes; within the stroma, PAD4-dependent NET formation enforces T cell exclusion. We also delineate technical barriers to discovering PTM antigens labile chemistry, low stoichiometry, and method-embedded biases and outline practical solutions: ETD/EThcD/AI-ETD fragmentation, PTM-aware database searching and machine-learning models, and autologous validation in patient-derived organoid–T cell co-cultures. Finally, we highlight therapeutic strategies that either immunize against PTM neoepitopes or inhibit PTM machinery (e.g., PAD4, OGT, ST6GAL1), with stromal remodeling as an enabling adjunct. Conclusions: PTM biology, spatial omics, and patient sample models can uncover targetable niches and speed up PDAC vaccination, TCR, and enzyme-directed treatment development. Full article

ATPase family AAA domain-containing protein 2 (ATAD2) has been recognized as a key oncogene that regulates chromatin remodeling, transcription, and cancer progression. As a member of the bromodomain (BRD) family, ATAD2 plays a crucial role in epigenetic modifications and is associated with multiple malignancies. Despite being considered an undruggable target in the past, crystallography and computational modeling have significantly accelerated ATAD2 drug discovery and development. This review provides a comprehensive overview of the structural features, functional roles, and biological significance of ATAD2, particularly in the context of cancer. We present an in-depth overview of different molecular strategies reported in the literature to suppress ATAD2 expression, including genetic and pharmacological approaches, and discuss their mechanistic and therapeutic implications. Particular emphasis is given to recent efforts in developing small-molecule inhibitors, detailing their binding interactions, therapeutic potential, and challenges in clinical translation. In addition, we performed alanine scanning calculations on molecular dynamics (MD)-simulated trajectories derived from protein–ligand complexes based on X-ray co-crystal structures containing three distinct ligands with different binding modes. This analysis provided critical insights into the binding interface of BRD-ATAD2, enhancing our understanding of its ligand interactions. Furthermore, we examine the emerging roles of ATAD2 in mediating resistance to cancer therapies, underscoring its potential as a target for overcoming drug resistance. By integrating structural insights, mechanistic studies, drug discovery efforts, and the challenges of developing ATAD2-targeted cancer therapies, this review emphasizes the need for further research to optimize ATAD2 inhibition strategies and explore its full therapeutic potential in oncology. Full article

The recent SARS-CoV-2 pandemic has highlighted the need for quickly adaptable technologies in vaccine manufacturing. This can be achieved through virus-like particles (VLPs) as presentation platforms for target antigens. In this study, we investigated the purification of VLPs of the Hepatitis B Core antigen (HBc) and the SplitCore (SplCo) technology. The outer surface protein C (OspC) of Borrelia burgdorferi was genetically fused to HBc and its N-terminal SplCo protein. Product solubility in E. coli increased from 40% for HBc-OspC to 90% for SplCo-OspC. This could not be reproduced with similar SARS-CoV-2 receptor-binding domain fusions due to inclusion body formation. Hydrophobicity was found to be significantly lowered for the OspC fusions, in particular for the SplCo variant. Pre-purified samples were generated by precipitating soluble cell lysate. Subsequently, solubilized precipitates were subjected to anion exchange chromatography (AEX), and the elution fractions obtained contained VLPs, albeit with low purity. The VLPs were also disassembled prior to AEX for dissociative purification, but a subsequent reassembly could not be achieved for both fusion variants. A novel HBc variant was constructed for post-translational modification via click-chemistry. The solubility and hydrophobicity of this HBc variant remained high, but native AEX resulted in complete product loss. By contrast, a yield of 84% VLPs was obtained for the modified HBc after dissociative AEX. The surface-exposed azide group on the particles, introduced for click-chemistry, enabled coupling to fluorophores without compromising VLP stability. Conjugation efficiencies of up to 59% were obtained. These results suggest the potential of combining HBc and click-chemistry for future applications, e.g., the presentation of immunogenic epitopes or antigens. This underlines that for every antigen, both the optimal scaffold-decoration strategy and the subsequent manufacturing process should be carefully selected. Full article

The aberrant activation of glycolysis plays a pivotal role in the progression of liver diseases. Pyruvate kinase M2 (PKM2), one of the rate-limiting enzymes of glycolysis, not only regulates cellular metabolism but also translocates to the nucleus in its dimeric form, acting as a co-factor to modulate gene transcription. To further explore the regulatory mechanisms of PKM2, this review outlines the effects of post-translational modifications on PKM2’s structure, activity, and localization, and discusses the integrative role of PKM2 in epigenetics and metabolism, providing a foundation for the development of PKM2 regulators. Due to PKM2’s distinct biochemical properties, targeting PKM2 with specific regulators may offer a promising therapeutic strategy for the treatment of liver diseases. Full article

Hydrogen sulfide (H₂S), nitric oxide (NO), and carbon monoxide (CO) are now recognized as key gasotranmitters that regulate vascular function, contributing to vasodilation, angiogenesis, inflammation control, and oxidative balance. Initially regarded as toxic gases, they are produced on demand by specific enzymes, including cystathionine γ-lyase (CSE), endothelial nitric oxide synthase (eNOS), and heme oxygenase-1 (HO-1). Their activity is tightly controlled by redox-sensitive pathways. Reactive oxygen species (ROS), particularly superoxide and hydrogen peroxide, modulate gasotransmitter biosynthesis at the transcriptional and post-translational levels. Moreover, ROS affect gasotransmitter availability through oxidative modifications, including thiol persulfidation, nitrosative signaling, and carbonylation. This redox regulation ensures a tightly coordinated response to environmental and metabolic cues within the vascular system. This review synthesizes the current understanding of redox–gasotransmitter interactions, highlighting how ROS modulate the vascular roles of H₂S, NO, and CO. Understanding these interactions provides critical insights into the pathogenesis of cardiovascular diseases and offers potential redox-targeted therapies. Full article

The liver orchestrates metabolic homeostasis through dynamic post-translational modifications. β-hydroxybutyrylation (Kbhb), a ketone body-driven modification, regulates epigenetics and metabolism in humans and mice but remains unexplored in livestock. Here, we characterize the porcine hepatic β-hydroxybutyrylome using high-resolution mass spectrometry, identifying 4982 Kbhb sites on 2122 proteins—the largest dataset to date. β-hydroxybutyrylation predominantly targets non-histone proteins (99.68%), with enrichment in fatty acid β-oxidation, TCA cycle, and oxidative phosphorylation pathways. Subcellular localization revealed cytoplasmic (38.1%), mitochondrial (18.1%), and nuclear (15.3%) dominance, reflecting BHB-CoA synthesis sites. Motif analysis identified conserved leucine, phenylalanine, and valine residues at modified lysines, suggesting enzyme-substrate specificity. β-hydroxybutyrate treatment elevated global Kbhb levels, increasing TCA intermediates (e.g., α-ketoglutarate, +9.56-fold) while reducing acetyl-CoA, indicating enhanced mitochondrial flux. Cross-species comparisons showed tissue-specific Kbhb distribution (nuclear in human cells vs. mitochondrial in mice), highlighting metabolic adaptations. This study establishes pigs as a model for Kbhb research, linking it to energy regulation and providing insights into metabolic reprogramming. Full article

The complex pathological mechanisms of atherosclerosis (AS) involve lipid metabolism disorders, inflammatory responses, and plaque instability, resulting in significant challenges to effective clinical management. Current therapeutic approaches, such as statins and stent implantation, suffer from issues including single-target action, notable side effects, and the risk of restenosis. Nanoparticle-based drug delivery systems have demonstrated considerable promise by enabling the codelivery of multiple agents directly to atherosclerotic lesions, thereby improving therapeutic efficacy and minimizing systemic toxicity. Among various nanomaterials, organic nanoparticles have recently emerged as a research hotspot in the field of AS treatment due to their excellent biocompatibility, degradability, and potential for targeted modification. This review systematically summarizes the recent advances and emerging trends in the application of organic nanoparticles for AS treatment, employing bibliometric analysis to delineate research frontiers. We employed bibliometric tools to analyze 1999 articles on organic nanocarriers for AS therapy indexed in the Web of Science Core Collection. The analysis included co-occurrence and clustering techniques to explore influential keywords and key contributors. Temporal analysis was applied to identify emerging research hotspots and track the evolution of this field. The literature reveals three major current focal areas: (1) the development of engineered biomimetic organic nanoparticles; (2) the design of multifunctional polymer-based organic nanocarriers; and (3) the innovation of organic-coated stents. This article not only provides a comprehensive overview of cutting-edge organic nanotechnologies for AS therapy, but also critically discusses the challenges in clinical translation, offering insights into future directions for the development of safe, effective, and personalized nanomedicine strategies against AS. Full article