It was recently shown that vertebrates, ranging from fish to primitive mammals, possess type IV IFN (IFNυ). However, their precise function and elaborate signaling remains unknown. In this study, CaIFNυ was identified from Carassius gibelio and its transcriptional regulation and signaling was further investigated. Firstly, CaIFNυ displays significant differences in the distribution, magnitude, and kinetics of its antiviral properties compared with CaIFNa1, a typical type I IFN from C. gibelio. Secondly, IRF1/3/7 differentially activated CaIFNυ through homo- or heteroprotein complexes in a dose-dependent fashion and NF-κB (p65) was the most effective stimulator. Thirdly, CaIFNυ initiates the antiviral ISGs through the JAK-STAT as well as MAPK and PI3K signaling pathways by binding to the extra-cellular region of CaCRFB4 and CaCRFB12. Taken together, these findings reveal that CaIFNυ belonges to an antiviral cytokine lineage which is distinct from CaIFNa1.

BackgroundCellular senescence is a fundamental process leading to organismal aging and age-related diseases. Alterations accompanying cellular senescence concern, among others, nucleus architecture, chromatin structure, DNA damage and gene expression. Some changes are universal for all types of senescence, but some characteristics are typical for a given senescence inductor or cell type. The aim of the study was to analyze senescence-associated alterations in chromatin modifications and look for differences depending on senescence type (replicative, RS and stress-induced premature senescence, SIPS) in vascular smooth muscle cells (VSMCs) in vitro. The alterations were compared with those observed in VSMCs derived from atherosclerotic plaques (ex vivo) and, to assess their universality, with those in senescent fibroblasts.MethodsWe investigated the level and distribution of HP1α and H3 modifications that are markers of hetero- and euchromatin (H3K9me3, H3K27me3, H3K4me3, H3K9Ac - WB and IF), alterations in the transcriptomic profile (DNA microarray, qPCR), H3K4me3, H3K9me3 and HP1α protein distribution in the genome (ChIP-seq), and expression of enzymes involved in histone post-translational modifications (DNA microarray, qPCR, WB, IF).ResultsOur results have shown that the decline in H3K4me3 and H3K9me3 modifications and in HP1α is a universal hallmark of senescence in all tested cell and senescence types, although the extent of the change depends on the senescence inductor. The distribution of H3K4me3 and H3K9me3 in the genome of VSMCs depends on the senescence type, and the transcriptomic analysis identified genes and processes specific to each type.ConclusionsWe characterized senescence and cell type-dependent changes in chromatin-associated proteins and enzymes involved in histone H3 decoration which, in consequence, impact senescence-associated gene expression. We can conclude that certain similar alterations occur in senescent VSMCs ex vivo, although inter-individual differences usually obscure them. Our results clearly showed that differences existed not only between young and senescent cells but also between SIPS and RS ones. The subtle differences between various SIPS types suggest that various stressors activate the same cellular mechanisms. This study can serve as a starting point to search for factors that may be used to distinguish between SIPS and RS, which in turn could be helpful in defining conditions responsible for accelerated aging.

BackgroundCardiomyocyte proteostasis and calcium homeostasis are critical for maintaining cardiac function, with their dysregulation contributing to cardiac hypertrophy and heart failure. The Tripartite Motif Protein 24 (TRIM24), a well-characterized chromatin reader and transcriptional regulator in cancer, has recently emerged as a potential player in cardiac biology. However, its precise role in cardiomyocytes remains unclear. Using molecular, structural and functional approaches, this study investigates the impact of TRIM24 on cardiomyocyte function and gene regulation.MethodsTo dissect the molecular and functional role of TRIM24, we conducted RNA-sequencing (RNA-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) in neonatal rat ventricular cardiomyocytes (NRVCMs) to identify TRIM24-regulated pathways and transcriptional targets. Super-resolution microscopy and proteomics analysis were employed to examine its influence on chromatin organization and calcium-handling protein distribution. Calcium imaging and cardiomyocyte contractility assays were performed in both NRVCMs and human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) to assess functional effects. Additionally, NFAT activity was assessed to investigate its role in TRIM24-mediated hypertrophic signaling.ResultsThrough RNA-seq and ChIP-seq, we identified TRIM24 as a bidirectional transcriptional regulator, predominantly acting as a repressor but also exhibiting context-dependent activation of genes involved in e.g. cytoskeletal organization and calcium signaling. ChIP-seq identified TRIM24 binding at the NFATc4 locus, validated by motif analysis, while functional studies revealed that TRIM24 regulates NFATc4 protein levels and activity, enhancing upon overexpression and reducing upon knockdown. Furthermore, TRIM24 overexpression altered the expression and organization of Ryanodine Receptor 2 (RyR2), Sarcoplasmic/endoplasmic Reticulum Ca2+ ATPase 2a (SERCA2a), and Calsequestrin 1 (CASQ1), leading to calcium-handling defects. Super-resolution microscopy revealed a loss of chromatin organization and altered clustering of calcium-handling proteins. Despite a reduction in SERCA2a levels, TRIM24 activated the PI3K-AKT/PLN pathway, increasing phospholamban phosphorylation and compensatory calcium reuptake. In functional assays, TRIM24 overexpression increased beating frequency and calcium cycling in both NRVCMs and iPSC-CMs.ConclusionOur findings establish TRIM24 as a novel regulator of chromatin remodeling and cardiomyocyte transcription, directly influencing calcium homeostasis and contractility, with potential implications for cardiac disease.

The primary epigenetic alteration in the development of prostate cancer (PC) is aberrant methylation of the promoter region of tumor suppressor genes. Maintaining DNA methylation activity requires ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1). Through its SET and RING-associated (SRA) domain, UHRF1 identifies methylated cytosine-phosphate-guanine sequences and binds DNA methyltransferase 1 (DNMT1) directly to replicated DNA foci. Nevertheless, the modality used by UHRF1 to regulate gene networks in PC cells precisely and efficiently is unknown. Research has indicated that epigenetic modification is significantly influenced by the phase separation of epigenetic regulators. Thus, the purpose of this work was to find out if UHRF1 phase separation is a mechanism for PC cells to inherit DNA methylation in a stable manner. We evaluated the correlation between UHRF1 expression level and PC development, as well as used PC cell lines to study the mechanism of UHRF1 phase separation driving the progression of PC. The results of this study demonstrated that UHRF1 formed phase-separated droplets by its SRA motif and intrinsically disordered region 3. Furthermore, UHRF1 formed nuclear condensates at the promoter region of multiple cancer-related genes and recruited DNMT1 to allow epigenetic gene silencing that led to malignant proliferation of PC cells. These results revealed that phase separation of UHRF1 is crucial for PC pathogenesis.

Aging is an irreversible physiological process that progresses with age, leading to structural disorders and dysfunctions of organs, thereby increasing the risk of chronic diseases such as neurodegenerative diseases, diabetes, hypertension, and cancer. Both organismal and cellular aging are accompanied by the accumulation of damaged organelles and macromolecules, which not only disrupt the metabolic homeostasis of the organism but also trigger the immune response required for physiological repair. Therefore, metabolic remodeling or chronic inflammation induced by damaged tissues, cells, or biomolecules is considered a critical biological factor in the organismal aging process. Notably, mitochondria are essential bioenergetic organelles that regulate both catabolism and anabolism and can respond to specific energy demands and growth repair needs. Additionally, mitochondrial components and metabolites can regulate cellular processes through damage-associated molecular patterns (DAMPs) and participate in inflammatory responses. Furthermore, the accumulation of prolonged, low-grade chronic inflammation can induce immune cell senescence and disrupt immune system function, thereby establishing a vicious cycle of mitochondrial dysfunction, inflammation, and senescence. In this review, we first outline the basic structure of mitochondria and their essential biological functions in cells. We then focus on the effects of mitochondrial metabolites, metabolic remodeling, chronic inflammation, and immune responsesthat are regulated by mitochondrial stress signaling in cellular senescence. Finally, we analyze the various inflammatory responses, metabolites, and the senescence-associated secretory phenotypes (SASP) mediated by mitochondrial dysfunction and their role in senescence-related diseases. Additionally, we analyze the crosstalk between mitochondrial dysfunction-mediated inflammation, metabolites, the SASP, and cellular senescence in age-related diseases. Finally, we propose potential strategies for targeting mitochondria to regulate metabolic remodeling or chronic inflammation through interventions such as dietary restriction or exercise, with the aim of delaying senescence. This reviewprovide a theoretical foundation for organismal antiaging strategies.

The concurrent occurrence and exacerbation of multiple diseases, including geriatric diseases and chronic diseases, impose a heavy burden on human health and medical expenses. Clarifying the common mechanisms of related multifarious diseases and developing preventive and therapeutic strategies with synergistic effects for multiple diseases are of great significance in alleviating the burden on the medical system and reducing patients' burden of drug metabolism. Recent studies have revealed that gut microbiota disorders and intestinal barrier damage, which consequently cause metabolic and immunological disorders, may be a common pathological basis underlying various intestinal-related diseases. In this review, we focus on the intestinal barrier function, summarizing the multi-target interactions and common mechanisms involved in diseases related to the gut such as ulcerative colitis, colorectal cancer, and type 2 diabetes. We identified gut microbe-based strategies, including probiotics, prebiotics, synbiotics, postbiotics, as well as potential targets in faecal microbiota transplant and berberine. The common mechanisms and key targets in the treatment of these diseases mainly include increasing the abundance of beneficial genera Bifidobacterium and Lactobacillus, increasing the levels of Short Chain Fatty Acids, restoring the intestinal mechanical barrier, and suppressing gut inflammation infiltration. We aim to provide a crucial basis and direction for the development of novel drugs with therapeutic effects for multiple diseases, thereby alleviating the patients' burden of medication and enhancing the efficacy of treatment.

Helicobacter pylori (H. pylori) associated gastritis, marked by chronic gastric inflammation, heightens gastric cancer risk by fostering a malignancy-prone microenvironment. Disruption of the biorhythm contribute to the onset of various gastrointestinal disorders, such as gastric dyspepsia, gastric ulcers, and cancer. We aimed to investigate the functional roles and regulatory mechanisms of key biorhythm molecules in H. pylori associated gastritis. We investigated biorhythm gene expression in H. pylori-infected human gastric tissues and found significant impact on NFIL3 expression. Animal studies confirmed that H. pylori controls NFIL3 biorhythm. Clinical samples indicated a correlation between NFIL3 and gastritis severity, suggesting a regulatory role. Then, we found that H. pylori disrupt NFIL3 expression rhythm in gastric epithelial cells (GECs) through the CagA-activated ERK-SP1 pathway. Additionally, cytokines IL1β and TNFα enhance this disruption. RNA-seq and Gene set enrichment analysis (GSEA) indicated that NFIL3 positively regulates the inflammatory response during H. pylori infection. Our research highlights the crucial role of the biorhythm molecule NFIL3 in H. pylori associated gastritis. Modulating biorhythm molecules could be a promising therapeutic approach to manage disease progression, given their impact on gastrointestinal pathology.

BackgroundExtracellular vesicles (EVs), such as exosomes, have been extensively discovered for their function in various diseases and potential therapeutic properties. In this review, we aimed to describe the therapeutic roles of functionalized exosomes in cancer and regenerative medicine.MethodsIn this review study, we studied numerous articles over the past two decades published on the application of exosomes in different diseases, as well as on perspectives and challenges in this field.ResultsRecent advancements have shown that exosomes can be used as a drug delivery system. However, this approach faces challenges such as low efficiency and non-targeting effects. Different methods, including genetic, chemical, and physical modifications, are used to functionalize exosome surfaces to address these limitations. In some cases, a combination of modification methods has been used to produce smart exosomes. Different therapeutic agents have been inserted on exosome surfaces by different modification methods. These functionalized exosomes can effectively deliver therapeutic agents to target cells. A growing body of evidence shows that functionalized exosomes are promising for cancer therapy and regenerative medicine. They can not only effectively deliver therapeutic agents to cancer cells, inhibiting tumorigenesis, but also efficiently contribute to tissue repair and regeneration by increasing cell proliferation and angiogenesis. In this review, we discuss different modification methods used to functionalize exosomes and related studies. In addition, we describe the application of functionalized exosomes in cancer and regeneration, along with challenges and perspectives.ConclusionsAlthough functionalized exosomes show promising results, further studies are essential for the clinical translation of these exosomes.

The emergence of multidrug-resistant bacteria (MDR), particularly in cytosolic methicillin-resistant Staphylococcus aureus (MRSA) are causing substantial infections and posing an urgent global threat to public health. The era of antibiotic resistant has hindered the development of antibiotics that solely target bacteria, highlighting the need for alternative therapeutic strategies. Host-acting therapies are emerging as a dominant approach to address the shortage of novel antibiotics and prevent novel-resistant bacteria. Herein, we explored the modes of action of five flavonoids that combat cytosolic MRSA through host-acting antibacterial effects. Both in vitro and in vivo models demonstrated the efficacy of flavonoids in combating cytosolic MRSA lung infections. Transcriptomic and proteomic analyses revealed that the antibacterial targets of these flavonoids are linked to the phagosome pathway. Mechanistic studies further showed that flavonoids enhance lysosomal acidification, identifying it as a viable target for host-acting antibacterial drugs. These findings suggest that flavonoid treatments represent a promising host-acting therapeutic strategy for combating cytosolic MRSA infections.

The JAK-STAT pathway is an essential signaling mechanism that initiates immune responses against pathogen infections. The intrinsic homeostatic regulation of JAK-STAT signaling is critical for maintaining immune homeostasis. Previous studies have shown that aberrant activation of the invertebrate JAK-STAT pathway leads to inflammation-like symptoms. Understanding the homeostatic mechanisms of this pathway in invertebrates is of significant interest. Pacific white shrimp (Penaeus vannamei) is one of the most extensively studied invertebrates in immune system research. In this study, we demonstrate that the shrimp microRNA-34 (miR-34) attenuates JAK-STAT pathway activation by targeting JAK, thereby inhibiting STAT phosphorylation and nuclear translocation. Interestingly, miR-34 expression is directly regulated by STAT, forming a negative feedback regulatory loop in the JAK-STAT pathway. Disrupting this loop results in excessive JAK-STAT pathway activation and immune overactivation, exacerbating inflammation caused by Vibrio parahaemolyticus infection in shrimp. This study provides new insights into the regulatory mechanism of the JAK-STAT pathway and its roles in maintaining immune homeostasis in invertebrates.