AP-1 function and regulation

KCa3.1 upregulation mediated by Ang II-induced JNK/AP-1 activation contributes to atrial fibrosis

Atrial fibrillation is strongly associated with an increased risk of embolism, stroke, and heart failure. Current therapeutic approaches often have limited efficacy, and controlling atrial fibrosis remains a critical objective for upstream therapies. The specific mechanisms driving atrial fibrosis remain incompletely understood. The intermediate-conductance calcium-activated potassium channel KCa3.1 has been implicated in promoting fibroblast activation in various fibrotic diseases. This study investigates the role of angiotensin II (Ang II) in regulating KCa3.1, as well as its involvement in the pathogenesis of atrial fibrosis and the underlying signaling mechanisms. In a rat model, chronic Ang II infusion for 4 weeks induced atrial fibrosis, which was significantly attenuated by TRAM-34, a specific KCa3.1 channel blocker. In cultured rat atrial fibroblasts, Ang II treatment promoted fibroblast differentiation, proliferation, migration and collagen production, effects that were suppressed by TRAM-34 and KCa3.1 knockdown. Overexpression of KCa3.1 in fibroblasts further confirmed its pro-fibrotic role. Mechanistically, Ang II upregulated KCa3.1 expression and current density by activating the JNK/AP-1 signaling pathway. This involved phosphorylation of JNK, c-Jun, and c-Fos, leading to the formation of c-Jun/c-Fos heterodimers that directly bound to the KCa3.1 promoter to enhance its transcription. Together, these findings demonstrate that KCa3.1 mediates fibroblast activation and atrial fibrosis through the JNK/AP-1 pathway.

Imbalanced redox dynamics induce fibroblast senescence leading to impaired stem cell pools and skin aging

Skin function depends on a meticulously regulated dynamic interaction of distinct skin compartments such as the epidermis and dermis. Adaptive responses at the molecular and cellular level are essential for these interactions - and if dysregulated - drive skin aging and other pathologies. After defining the role of redox homeodynamics in physiology and aging pathology, we focus on the redox distress-dependent aging of dermal fibroblasts including their progenitors. We here discuss the prime role of senescent fibroblasts in the control of their own endogenous niche and stem cell niches for epidermal stem cells, hair follicle stem cells, adipocyte precursors and muscle stem cells. We here review that redox imbalance induced reduction in Insulin-like Growth Factor-1 drives skin aging by the depletion of stem cell pools. This IGF-1 reduction is mediated via the redox-sensitive transcription factor JunB and also by the redox-dependent changes in sphingolipid-metabolism, among others. In addition, we will discuss the changes in the extracellular matrix of the skin affecting cellular senescence and the skin integrity and function in aging. The aim is a deeper understanding of the two main redox-dependent hubs such as JunB-induced depletion of IGF-1, and the sphingolipid-mediated remodeling of the cell membrane with its impact on IGF-1, fibroblast heterogeneity, function, senescence and plasticity in skin aging.

Long-lasting expression of FosB/ΔFosB immunoreactivity following acute stress in the paraventricular and supraoptic nuclei of the rat hypothalamus

We examined expression profiles of FosB/∆FosB immunoreactivity and fosB gene transcripts in the paraventricular nucleus of the hypothalamus (PVH) and the supraoptic nucleus (SON) of rats following acute surgical stress (SS) and restraint stress (RS) and compared them with those of c-Fos immunoreactivity and c-fos mRNA. Following SS, the number of FosB/ΔFosB-ir cells markedly increased, the time course of which was slow-onset and long-lasting, in contrast with rapid-onset and short-lived c-Fos expression. Characteristically long-lasting FosB/ΔFosB expression was also observed following RS. On the other hand, fosB mRNA was short-lived, and its time course not much different from that of c-fos mRNA; thus, the long-lasting expression of FosB/∆FosB immunoreactivity may be attributed to the longer half-life of FosB proteins, and not to the persistent expression of fosB gene transcripts. Following SS, FosB/ΔFosB immunoreactivity was present mainly in PVH corticotropin-releasing factor (CRF) neurons and SON vasopressin (AVP) neurons, while c-Fos immunoreactivity in either PVH CRF neurons, or AVP and oxytocin neurons in PVH and SON. Following RS, FosB/ΔfosB- and c-Fos expression was almost restricted to PVH CRF neurons. The present study raises the possibility that FosB proteins in discrete populations of hypothalamic neuroendocrine neurons may play roles in forming adaptability to and/or resilience against stress, which takes longer than the acute phase response.

Effects of Astraflavonoid A and Astraside C from the Aerial Part of Astragalus membranaceus on TNF-α-Induced Human Dermal Fibroblasts

The present study investigates the anti-skin-aging properties and bioactive compounds of the aerial parts of Astragalus membranaceus, which are typically discarded as agricultural waste. Liquid chromatography-mass spectrometry analysis identified flavonoid glycosides as the major constituents of the aerial parts of A. membranaceus extract. Two principal flavonoids, astraflavonoid A (1) and astraside C (2), were isolated using repetitive chromatography. Compounds 1 and 2 demonstrated antioxidative properties, reducing reactive oxygen species and matrix metalloproteinase-1 levels in human dermal fibroblasts upon stimulation with TNF-α. Specifically, astraside C (2) inhibited the expression of pro-inflammatory cytokines interleukin-6 and interleukin-8, whereas astraflavonoid A (1) did not affect their expression. Additionally, the expression of inflammatory mediators such as nuclear factor kappa B and cyclooxygenase-2 (COX-2) was increased by 1, whereas it was suppressed by 2. Furthermore, in silico molecular docking experiments confirmed that compound 2 effectively binds to COX-2. These findings suggest that the aerial parts of A. membranaceus contain bioactive flavonol glycosides with promising anti-skin-aging properties, offering valuable use as agricultural byproducts.

Molecular characterization, expression pattern and the function of TRAF2 from blood parrot Amphilophus citrinellus ×Vieja melanura response to LPS stimulation

Tumor necrosis factor receptor-associated factor (TRAF) family is a critical signal transduction protein, and plays important roles in cell growth, apoptosis, and immune response, etc. In this study, molecular characteristics, expression patterns, and the role of TRAF2 in blood parrot Vieja synspila ♀ × Amphilophus citrinellus ♂, an important ornamental fish, were explored response to lipopolysaccharide (LPS) challenge. The full length of blood parrot TRAF2 was 2725 bp, with an open reading frame (ORF) of 1551 bp encoding 516 amino acids, and a molecular weight of 58.58 kDa. Blood parrot TRAF2 contained four conserved domains: RING, TRAF-type zinc finger, TRAF_BIRC3_bd, and MATH (Meprin and TRAF-C homology). Analysis of phylogenetic relationships showed that TRAF2 were conserved in different species, indicating that its role might be similar. Blood parrot TRAF2 mRNA could be detected in all of the tissues examined, and was distributed in both the cytoplasm and nucleus. The expression of blood parrot TRAF2 was up-regulated during LPS challenge. Overexpression of TRAF2 could significantly inhibit the activities of nuclear factor κB (NF-κB) and activated protein 1 (AP-1), and reduce the ratio of Bax/Bcl-2. This study indicated that the TRAF2 might play important roles in organisms during pathogen infection.

Multimeric transcription factor BCL11A utilizes two zinc-finger tandem arrays to bind clustered short sequence motifs

BCL11A, a transcription factor, is vital for hematopoiesis, including B and T cell maturation and the fetal-to-adult hemoglobin switch. Mutations in BCL11A are linked to neurodevelopmental disorders. BCL11A contains two DNA-binding zinc-finger arrays, low-affinity ZF2-3 and high-affinity ZF4-6, separated by a 300-amino-acid linker. ZF2-3 and ZF4-5 share 73% identity, including five out of six DNA base-interacting residues. These arrays bind similar short sequence motifs in clusters, with the linker enabling a broader binding span. Crystallographic structures of ZF4-6, in complex with oligonucleotides from the β-globin locus region, reveal DNA sequence recognition by residues Asn756 (ZF4), Lys784 and Arg787 (ZF5). A Lys784-to-Thr mutation, linked to a neurodevelopmental disorder with persistent fetal globin expression, reduces DNA binding over 10-fold but gains interaction with a variable base pair. BCL11A isoforms may form oligomers, enhancing chromatin occupancy and repressor functions by allowing multiple copies of both low- and high-affinity ZF arrays to bind DNA. These distinctive properties, apparently conserved among vertebrates, provide essential functional flexibility to this crucial regulator.

Investigation of c-Fos/c-Jun Signaling Pathways in Periostracum Cicadae's Inhibition of EMT in Gastric Tissue

Background/Objectives: Periostracum Cicadae (PC) is commonly used to treat chronic atrophic gastritis (CAG), but its underlying mechanisms are unclear. We investigated the therapeutic effects, active ingredients and molecular mechanisms of PC on CAG. Methods: We analyzed the components in the serum extract of PC by UHPLC-Q-Orbitrap-MS/MS. Then, we used rat and cell models to assess the impact of PC on CAG and employed network pharmacology and bioinformatics to predict key targets and active ingredients. Finally, we confirmed hub targets through experiments and molecular docking. Results: A total of 22 components were identified in the PC extract-containing serum using UHPLC-Q-Orbitrap MS/MS. Network pharmacology combined with molecular docking revealed that the protective effect was primarily mediated by three compounds: (Z)-akuammidine, chicoric acid, and columbianadin. And we revealed that c-Fos/c-Jun signaling pathways were crucial in therapy. PC extract-containing serum inhibited the vitality, migration, invasion, and multiplication of MC cells (model cells for CAG), induced apoptosis, and caused G0/G1 phase cell cycle arrest. The expression level of tumor necrosis factor-alpha (TNF-α), interleukin-6 (IL-6), interleukin-1 beta (IL-1β) and gastrin 17 (G17) in the serum of CAG rats increased, while the expression level of pepsinogen I (PG I) and pepsinogen II (PG II) decreased. After 12 weeks of PC administration, these conditions were significantly improved. PC not only reduced the levels of antigen KI-67 (Ki67) and tumor protein p53 (P53) but also enhanced SRY-box Transcription Factor (SOX2). Simultaneously, PC down-regulated the expression of N-cadherin and Vimentin while up-regulating that of E-cadherin. Conclusions: PC inhibited epithelial-mesenchymal transition (EMT) via the c-Fos/c-Jun signaling pathway, thereby providing therapeutic benefits for CAG. Our study elucidates the mechanisms and material basis of PC in treating CAG, providing experimental evidence to support its clinical application.

Identifying periphery biomarkers of first-episode drug-naïve patients with schizophrenia using machine-learning-based strategies

Schizophrenia is a complex mental disorder. Accurate diagnosis and classification of schizophrenia has always been a major challenge in clinic due to the lack of biomarkers. Therefore, identifying molecular biomarkers, particularly in the peripheral blood, is of great significance. This study aimed to identify immune-related molecular biomarkers of schizophrenia in peripheral blood. Eighty-four Peripheral blood leukocytes of first-episode drug-naïve (FEDN) patients with schizophrenia and 97 healthy controls were collected and examined using high-throughput RNA-sequencing. Differentially-expressed genes (DEGs) were analysed. Weighted correlation network analysis (WGCNA) was employed to identify schizophrenia-associated module genes. The CIBERSORT algorithm was adopted to analyse immune cell proportions. Then, machine-learning algorithms including random forest, LASSO, and SVM-RFE were employed to screen immune-related predictive genes of schizophrenia. The RNA-seq analyses revealed 734 DEGs. Further machine-learning-based bioinformatic analyses screened out three immune-related predictive genes of schizophrenia (FOSB, NUP43, and H3C1), all of which were correlated with neutrophils and natural killer cells resting. Lastly, external GEO datasets were used to verify the performance of the machine-learning models with these predictive genes. In conclusion, by analysing the peripheral mRNA expression profiles of FEDN patients with schizophrenia, this study identified three predictive genes that could be potential molecular biomarkers for schizophrenia.

Ultradeep Phosphoproteomics for Assessing Protein Kinase Inhibitor Selectivity on a Proteome Scale

The selectivity of protein kinase inhibitors (PKIs) remains a major challenge in drug discovery. In this study, we present an ultradeep phosphoproteomics approach for assessing PKI selectivity and elucidating mechanisms of action using Zanubrutinib as a model. Two complementary phosphoproteomics strategies were employed: phosphopeptides enriched with Zr4+-IMAC in combination with TiO2 beads were analyzed using data-independent acquisition (DIA), while tyrosine phosphopeptides enriched with SH2-Superbinder were analyzed via data-dependent acquisition (DDA). The comprehensive phosphoproteomic analysis identified that 97 and 316 phosphosites were significantly altered upon Zanubrutinib stimulation in the DDA and DIA data sets, respectively. Bioinformatics analysis of these phosphoproteins provided a detailed selectivity profile of Zanubrutinib, offering insights into its mechanism of action at the molecular level. Compared to existing methods, our approach is more comprehensive, has higher throughput, and is more precise─not only for PKI selectivity assessment but also for broader cell signaling research.

WDR26 depletion alters chromatin accessibility and gene expression profiles in mammalian cells

WD-repeat containing protein 26 (WDR26) is an essential component of the CTLH E3 ligase complex. Mutations in WDR26 lead to Skraban-Deardorff, an intellectual disability syndrome with clinical features resembling other disorders arising from defects in transcriptional regulation and chromatin structure. However, the role of WDR26 and its associated CTLH complex in regulating chromatin or transcription has not been elucidated. Here, we assessed how loss of WDR26 affects chromatin accessibility and gene expression. Transcriptome analysis of WDR26 knockout HeLa cells revealed over 2000 differentially expressed genes, while ATAC-Seq analysis showed over 32,000 differentially accessible chromatin regions, the majority mapping to intergenic and intronic regions and 13 % mapping to promoters. Above all, we found that WDR26 loss affected expression of genes regulated by AP-1 and NF-1 transcription factors and resulted in dramatic changes in their chromatin accessibility. Overall, our analyses implicate WDR26 and the CTLH complex in chromatin regulation.

Nitroxidative Stress, Cell-Signaling Pathways, and Manganese Porphyrins: Therapeutic Potential in Neuropathic Pain

Neuropathic pain, a debilitating condition arising from somatosensory system damage, significantly impacts quality of life, leading to anxiety, self-mutilation, and depression. Oxidative and nitrosative stress, an imbalance between reactive oxygen and nitrogen species (ROS/RNS) and antioxidant defenses, plays a crucial role in its pathophysiology. While reactive species are essential for physiological functions, excessive levels can cause cellular component damage, leading to neuronal dysfunction and pain. This review highlights the complex interactions between reactive species, antioxidant systems, cell signaling, and neuropathic pain. We discuss the physiological roles of ROS/RNS and the detrimental effects of oxidative and nitrosative stress. Furthermore, we explore the potential of manganese porphyrins, compounds with antioxidant properties, as promising therapeutic agents to mitigate oxidative stress and alleviate neuropathic pain by targeting key cellular pathways involved in pain. Further research is needed to fully understand their therapeutic potential in managing neuropathic pain in human and non-human animals.

Kaempferol Mitigates Pseudomonas aeruginosa-Induced Acute Lung Inflammation Through Suppressing GSK3β/JNK/c-Jun Signaling Pathway and NF-κB Activation

Background: Pseudomonas aeruginosa, one of the common bacterial pathogens causing nosocomial pneumonia, is characterized as highly pathogenic and multidrug-resistant. Kaempferol (KP), a natural flavonoid, has been shown to exhibit effectiveness in treating infection-induced lung injury. Methods: We applied network pharmacology to explore the underlying mechanisms of KP in treating P. aeruginosa pneumonia and further validated them through a mouse model of acute bacterial lung infection and an in vitro macrophage infection model. Results: The in vivo studies demonstrated that treatment with KP suppressed the production of proinflammatory cytokines, including TNF, IL-1β, IL-6, and MIP-2, and attenuated the neutrophil infiltration and lesions in lungs, leading to an increased survival rate of mice. Further studies revealed that KP treatment enhanced the phosphorylation of GSK3β at Ser9 and diminished the phosphorylation of JNK, c-Jun, and NF-κB p65 in lungs in comparison to the mice without drug treatment. Consistently, the in vitro studies showed that pretreatment with KP reduced the activation of GSK3β, JNK, c-Jun, and NF-κB p65 and decreased the levels of the proinflammatory cytokines in macrophages during P. aeruginosa infection. Conclusions: KP reduced the production of proinflammatory cytokines by inhibiting GSK3β/JNK/c-Jun signaling pathways and NF-κB activation, which effectively mitigated the P. aeruginosa-induced acute lung inflammation and injury, and elevated the survival rates of mice.

CTCF/RAD21 organize the ground state of chromatin-nuclear speckle association

Recent findings indicate that nuclear speckles, a distinct type of nuclear body, interact with certain chromatin regions in a ground state. Here, we report that the chromatin structural factors CTCF and cohesin are required for full ground-state association between DNA and nuclear speckles. We identified a putative speckle-targeting motif (STM) within cohesin subunit RAD21 and demonstrated that the STM is required for chromatin-nuclear speckle association, disruption of which also impaired induction of speckle-associated genes. Depletion of the cohesin-releasing factor WAPL, which stabilizes cohesin on chromatin, resulted in reinforcement of DNA-speckle contacts and enhanced inducibility of speckle-associated genes. Additionally, we observed disruption of chromatin-nuclear speckle association in patient-derived cells with Cornelia de Lange syndrome, a congenital neurodevelopmental disorder involving defective cohesin pathways. In summary, our findings reveal a mechanism for establishing the ground state of chromatin-speckle association and promoting gene inducibility, with relevance to human disease.

Proteomic meta-analysis unveils new frontiers for biomarkers research in pancreatic carcinoma

Pancreatic carcinoma (PC) is the sixth leading cause of cancer death in both sexes in 2022, responsible for almost 5% of all cancer deaths worldwide; it is characterized by a poor prognosis since most patients present with an unresectable and metastatic tumor. To date, the decreasing trend in mortality rates related to the most common cancers has contributed to making pancreatic cancer a serious public health problem. In the last few years, scientific research has led to many advances in diagnostic approaches, perioperative management, radiotherapy techniques, and systemic therapies for advanced disease, but only with modest incremental progress in PC patient outcomes. Most of the causes of this high mortality are, unfortunately, late diagnosis and an important therapeutic resistance; for this reason, the most recent high-throughput proteomics technologies focus on the identification of novel biomarkers and molecular profiling to generate new insights in the study of PC, to improve diagnosis and prognosis and to monitor the therapies progress. In this work, we present and discuss the integration of results from different revised studies on protein biomarkers in a global proteomic meta-analysis to understand which path to pursue scientific research. In particular, cancer signaling, inflammatory response, and cell migration and signaling have emerged as the main pathways described in PC, as well as scavenging of free radicals and metabolic alteration concurrently highlighted new research insights on this disease. Interestingly, from the study of upstream regulators, some were found to be shared by collecting data relating to both biological fluid and tissue biomarkers, side by side: specifically, TNF, LPS, p38-MAPK, AGT, miR-323-5p, and miR-34a-5p. By integrating many biological components with their interactions and environmental relationships, it's possible to achieve an in-depth description of the pathological condition in PC and define correlations between concomitant symptoms and tumor genesis and progression. In conclusion, our work may represent a strategy to combine the results from different studies on various biological samples in a more comprehensive way.

Exploring the mechanism of action of Lobetyolin in the treatment of allergic rhinitis based on network pharmacology and molecular docking

Lobetyolin (LBT) is an important active ingredient in the traditional medicinal plant Codonopsis pilosula (Franch.) Nannf. However, the pharmacological targets and mechanisms of action of LBT against allergic rhinitis (AR) are not known. The aim of this study was to evaluate the possible functional role and potential mechanism of LBT as an anti-AR treatment through a combination of network pharmacology and molecular docking. The disease database and target screening database were used to find potential targets for screening LBT for the treatment of AR. Further network visualization analysis, gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis were performed for potential targets. Finally, we performed some molecular docking with LBT and core targets to verify their relevant effects. The results revealed that a total of 64 target genes were obtained for LBT for AR. The top 10 targets with the highest enrichment scores were tumor necrosis factor, epidermal growth factor receptor, matrix metalloproteinase 9, recombinant toll-like receptor 4, erb-b2 receptor tyrosine kinase 2, JUN protooncogene, C-X-C motif chemokine receptor 4, HSP90AA1, kinase insert domain receptor, and matrix metalloproteinase 2. Gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that multiple signaling pathways are involved in LBT for AR. Molecular docking results showed that LBT binds strongly to the target proteins matrix metalloproteinase 2, matrix metalloproteinase 9, tumor necrosis factor, JUN protooncogene, and epidermal growth factor receptor through intermolecular forces. This study reveals for the first time the pharmacological targets and related pathways of LBT for the treatment of AR, indicating that LBT can intervene in the intrinsic molecular mechanism of AR through multiple targets and pathways.

Pancreatic endocrine and exocrine signaling and crosstalk in physiological and pathological status

The pancreas, an organ with dual functions, regulates blood glucose levels through the endocrine system by secreting hormones such as insulin and glucagon. It also aids digestion through the exocrine system by secreting digestive enzymes. Complex interactions and signaling mechanisms between the endocrine and exocrine functions of the pancreas play a crucial role in maintaining metabolic homeostasis and overall health. Compelling evidence indicates direct and indirect crosstalk between the endocrine and exocrine parts, influencing the development of diseases affecting both. From a developmental perspective, the exocrine and endocrine parts share the same origin-the "tip-trunk" domain. In certain circumstances, pancreatic exocrine cells may transdifferentiate into endocrine-like cells, such as insulin-secreting cells. Additionally, several pancreatic diseases, including pancreatic cancer, pancreatitis, and diabetes, exhibit potential relevance to both endocrine and exocrine functions. Endocrine cells may communicate with exocrine cells directly through cytokines or indirectly by regulating the immune microenvironment. This crosstalk affects the onset and progression of these diseases. This review summarizes the history and milestones of findings related to the exocrine and endocrine pancreas, their embryonic development, phenotypic transformations, signaling roles in health and disease, the endocrine-exocrine crosstalk from the perspective of diseases, and potential therapeutic targets. Elucidating the regulatory mechanisms of pancreatic endocrine and exocrine signaling and provide novel insights for the understanding and treatment of diseases.

Rapamycin enhances CAR-T control of HIV replication and reservoir elimination in vivo

Chimeric antigen receptor (CAR) T cell therapy shows promise for various diseases. Our studies in humanized mice and nonhuman primates demonstrate that hematopoietic stem cells (HSCs) modified with anti-HIV CAR achieve lifelong engraftment, providing functional antiviral CAR-T cells that reduce viral rebound after antiretroviral therapy (ART) withdrawal. However, T cell exhaustion due to chronic immune activation remains a key obstacle to sustained CAR-T efficacy, necessitating additional measures to achieve functional cure. We recently showed that low-dose rapamycin treatment reduced inflammation and improved anti-HIV T cell function in HIV-infected humanized mice. Here, we report that rapamycin improved CAR-T cell function both in vitro and in vivo. In vitro treatment with rapamycin enhanced CAR-T cell mitochondrial respiration and cytotoxicity. In vivo treatment with low-dose rapamycin in HIV-infected, CAR-HSC mice decreased chronic inflammation, prevented exhaustion of CAR-T cells, and improved CAR-T control of viral replication. RNA-sequencing analysis of CAR-T cells from humanized mice showed that rapamycin downregulated multiple checkpoint inhibitors and upregulated key survival genes. Mice treated with CAR-HSCs and rapamycin had delayed viral rebound after ART and reduced HIV reservoir compared with those treated with CAR-HSCs alone. These findings suggest that HSC-based anti-HIV CAR-T cells combined with rapamycin treatment are a promising approach for treating persistent inflammation and improving immune control of HIV replication.

Fenofibrate Reduces Ischemic Cerebral Edema via the Suppression of Aquaporin-4

The study aimed to investigate the neuroprotective effects of fenofibrate (FENO), a triglyceride-lowering drug, in rats with cerebral ischemia. An ischemic cerebral edema model was established in rats, and an oxygen-glucose deprivation/reoxygenation (OGD/R) model was created in astrocytes. Neurological deficits were quantified using a standardized deficit score. Protein expression levels were assessed through immunohistochemical staining, western blot analysis, and enzyme-linked immunosorbent assays (ELISA). Gene expression was determined using real-time polymerase chain reaction (RT-PCR), while luciferase activity was measured using a commercially available kit. We found that FENO significantly reduced infarct volume and neurological deficits in rats subjected to middle cerebral artery occlusion (MCAO). Additionally, FENO inhibited increased brain water content and upregulated the expression of aquaporin-4 (AQP4), a protein associated with cerebral edema, in the ischemic hemisphere. Furthermore, FENO suppressed the inflammatory response in cortical tissue by reducing the expression of cytokines such as interleukin-6 (IL-6), monocyte chemoattractant protein-1 (MCP-1), and tumor necrosis factor-alpha (TNF-α). It also increased the expression of myeloperoxidase (MPO) and promoted activation of astrocytes by increasing glial fibrillary acidic protein (GFAP). In vitro experiments further demonstrated that FENO reduced the expression of AQP4 against OGD/R in primary rat astrocytes. FENO also inhibited the activation of p38 by reducing its phosphorylation. Correspondingly, FENO suppressed the activation of activator protein 1 (AP-1) by reducing the levels of c-Jun and c-Fos, as well as the luciferase activity of AP-1. These effects were enhanced by the p38 specific inhibitor SB203580. Notably, the presence of the AP-1 specific inhibitor T5224 further promoted the effects of FENO in suppressing the expression of AQP4, implicating that the inhibitory effects of FENO on AQP4 expression are mediated by the p38/AP-1 signaling pathway. These findings suggest that FENO may have potential therapeutic benefits in stroke by targeting the p38/AP-1 signaling pathway and reducing AQP4 expression, thereby alleviating cerebral edema and inflammation.

Transcription factors in the development and treatment of immune disorders

Immune function is highly controlled at the transcriptional level by the binding of transcription factors (TFs) to promoter and enhancer elements. Several TF families play major roles in immune gene expression, including NF-κB, STAT, IRF, AP-1, NRs, and NFAT, which trigger anti-pathogen responses, promote cell differentiation, and maintain immune system homeostasis. Aberrant expression, activation, or sequence of isoforms and variants of these TFs can result in autoimmune and inflammatory diseases as well as hematological and solid tumor cancers. For this reason, TFs have become attractive drug targets, even though most were previously deemed "undruggable" due to their lack of small molecule binding pockets and the presence of intrinsically disordered regions. However, several aspects of TF structure and function can be targeted for therapeutic intervention, such as ligand-binding domains, protein-protein interactions between TFs and with cofactors, TF-DNA binding, TF stability, upstream signaling pathways, and TF expression. In this review, we provide an overview of each of the important TF families, how they function in immunity, and some related diseases they are involved in. Additionally, we discuss the ways of targeting TFs with drugs along with recent research developments in these areas and their clinical applications, followed by the advantages and disadvantages of targeting TFs for the treatment of immune disorders.

The role of BATF in immune cell differentiation and autoimmune diseases

As a member of the Activator Protein-1 (AP-1) transcription factor family, the Basic Leucine Zipper Transcription Factor (BATF) mediates multiple biological functions of immune cells through its involvement in protein interactions and binding to DNA. Recent studies have demonstrated that BATF not only plays pivotal roles in innate and adaptive immune responses but also acts as a crucial factor in the differentiation and function of various immune cells. Lines of evidence indicate that BATF is associated with the onset and progression of allergic diseases, graft-versus-host disease, tumors, and autoimmune diseases. This review summarizes the roles of BATF in the development and function of innate and adaptive immune cells, as well as its immunoregulatory effects in the development of autoimmune diseases, which may enhance the current understanding of the pathogenesis of autoimmune diseases and facilitate the development of new therapeutic strategies.

VEGFA, MYC, and JUN are abnormally elevated in the synovial tissue of patients with advanced osteoarthritis

Osteoarthritis (OA), affecting > 500 million people worldwide, profoundly affects the quality of life and ability to work. The mitogen-activated protein kinase (MAPK) signaling pathway plays an essential role in OA. To address the lack of studies focused on synovial cells in OA, we evaluated the expression patterns and roles of the MAPK signaling pathway components in OA synovial tissues using bioinformatics. The JUN, MYC, and VEGFA expression levels were significantly higher in the synovial tissues of patients with OA than in control tissues. These loci were closely related to abnormal proliferation, inflammation, and angiogenesis in the synovial tissues of patients with OA. We speculate that Myc and VEGFA activate the p38-MAPK signaling pathway to further activate Jun, thereby promoting abnormal inflammation, proliferation, and angiogenesis in OA synovial tissue. The high MYC, JUN, and VEGFA expression was positively correlated with the patients' K-L score, pain time, and synovial score. Furthermore, the high p38-MAPK and P-p38-MAPK expression confirmed that the abnormal expression and activation of the MAPK signaling pathway occurred in the synovial tissue of patients with OA. Our findings may provide a new direction for the clinical diagnosis and treatment of OA and insights into its pathogenesis.

Deciphering the influence of AP1M2 in modulating hepatocellular carcinoma growth and Mobility through JNK/ErK signaling pathway control

BACKGROUND

Hepatocellular Carcinoma (HCC) is the most common digestive system malignancy, with unclear pathogenesis and low survival rates. AP1M2 is associated with tumor progression, but its role and molecular mechanisms in HCC remain poorly understood and require further investigation.

METHODS

We utilized the Gene Expression Omnibus (GEO) and Expression Analysis Interactive Hub (XENA) databases to assess AP1M2 mRNA expression levels in HCC patients. Additionally, we employed the Cancer Genome Atlas (TCGA) database to identify pathways associated with both AP1M2 and HCC development. To evaluate the effect of AP1M2 on HCC cell proliferation and migration, we employed various techniques including EdU, CCK-8, Colony formation assay, and Transwell assays. Furthermore, Western blot analysis was conducted to examine the signaling pathways influenced by AP1M2.

RESULTS

AP1M2 expression was significantly increased at the mRNA level in HCC tissues(P<0.001). Importantly, overall survival (OS) analysis confirmed the association between higher AP1M2 expression and a poorer prognosis in HCC patients compared to those with lower AP1M2 expression (P<0.019).Multivariate Cox regression analysis showed that AP1M2 was an independent prognostic factor and a valid predictor for HCC patients. Furthermore, GSEA results indicated differential enrichment of lipid, metal metabolism, and coagulation processes in HCC samples demonstrating a high AP1M2 expression phenotype. In vitro experiments supported these findings by demonstrating that AP1M2 promotes HCC cell proliferation and migration, while activating the JNK/ERK pathway.

CONCLUSION

Our findings indicate that AP1M2 expression may serve as a potential molecular marker indicating a poor prognosis for HCC patients. Furthermore, we have demonstrated that AP1M2 significantly influences HCC cell proliferation and migration, with the JNK/ERK signaling pathway playing a key role in AP1M2-mediated regulation in the context of HCC.

Novel therapeutic targets for atherosclerosis: Targeting the FOSB-MECP2-Commd1 pathway

Atherosclerosis (AS) is a systemic disease and represents the primary underlying pathology of cardiovascular diseases. In this study, we aim to elucidate the roles of FBJ osteosarcoma oncogene B (FOSB) in AS development. ApoE-/- mice were used and fed a high-fat diet to establish an AS model. We observed elevated expression of FOSB in aortic tissues, which was associated with increased lipid deposition, macrophage recruitment. Knockdown of FOSB mitigated these AS-related pathological changes, and decreased the levels of TNF-α, IL-6 and IL-1β in aortic tissues and ox-LDL-induced RAW264.7 cells. Further investigations revealed that FOSB enhances the transcriptional activity of MECP2 by binding to its promoter region. MECP2 was found to be upregulated in aortic tissues and ox-LDL-induced RAW264.7 cells, exacerbating ox-LDL-induced cellular damage. Additionally, our study identifies Commd1 as a downstream target of MECP2. Overexpression of Commd1 reduced levels of TNF-α and IL-6, alleviating ox-LDL-induced inflammation and lipid deposition. In summary, our findings unveil a complex molecular interplay involving FOSB, MECP2, and Commd1 in AS pathogenesis. This study not only enhances our understanding of AS molecular mechanisms but also proposes potential therapeutic targets for its treatment.

Spatial tumor immune heterogeneity facilitates subtype co-existence and therapy response in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) displays a high degree of spatial subtype heterogeneity and co-existence, linked to a diverse microenvironment and worse clinical outcome. However, the underlying mechanisms remain unclear. Here, by combining preclinical models, multi-center clinical, transcriptomic, proteomic, and patient bioimaging data, we identify an interplay between neoplastic intrinsic AP1 transcription factor dichotomy and extrinsic macrophages driving subtype co-existence and an immunosuppressive microenvironment. ATAC-, ChIP-, and RNA-seq analyses reveal that JUNB/AP1- and HDAC-mediated epigenetic programs repress pro-inflammatory signatures in tumor cells, antagonizing cJUN/AP1 signaling, favoring a therapy-responsive classical neoplastic state. This dichotomous regulation is amplified via regional TNF-α+ macrophages, which associates with a reactive phenotype and reduced CD8+ T cell infiltration in patients. Consequently, combined preclinical anti-TNF-α immunotherapy and chemotherapy reduces macrophages and promotes CD3+/CD8+ T cell infiltration in basal-like PDAC, improving survival. Hence, tumor cell-intrinsic epigenetic programs, together with extrinsic microenvironmental cues, facilitate intratumoral subtype heterogeneity and disease progression.

Identification of molecular and cellular infection response biomarkers associated with anthrax infection through comparative analysis of gene expression data

Bacillus anthracis, a gram-positive bacillus capable of forming spores, causes anthrax in mammals, including humans, and is recognized as a potential biological weapon agent. The diagnosis of anthrax is challenging due to variable symptoms resulting from exposure and infection severity. Despite the availability of a licensed vaccines, their limited long-term efficacy underscores the inadequacy of current human anthrax vaccines, highlighting the urgent need for next-generation alternatives. Our study aimed to identify molecular biomarkers and essential biological pathways for the early detection and accurate diagnosis of human anthrax infection. Using a comparative analysis of Bacillus anthracis gene expression data from the Gene Expression Omnibus (GEO) database, this cost-effective approach enables the identification of shared differentially expressed genes (DEGs) across separate microarray datasets without additional hybridization. Three microarray datasets (GSE34407, GSE14390, and GSE12131) of B. anthracis-infected human cell lines were analyzed via the GEO2R tool to identify shared DEGs. We identified 241 common DEGs (70 upregulated and 171 downregulated) from cell lines treated similarly to lethal toxins. Additionally, 10 common DEGs (5 upregulated and 5 downregulated) were identified across different treatments (lethal toxins and spores) and cell lines. Network meta-analysis identified JUN and GATAD2A as the top hub genes for overexpression, and NEDD4L and GULP1 for underexpression. Furthermore, prognostic analysis and SNP detection of the two identified upregulated hub genes were carried out in conjunction with machine learning classification models, with SVM yielding the best classification accuracy of 87.5 %. Our comparative analysis of Bacillus anthracis infection revealed striking similarities in gene expression 241 profiles across diverse datasets, despite variations in treatments and cell lines. These findings underscore how anthrax infection activates shared genes across different cell types, emphasizing this approach in the discovery of novel gene markers. These markers offer insights into pathogenesis and may lead to more effective therapeutic strategies. By identifying these genetic indicators, we can advance the development of precise immunotherapies, potentially enhancing vaccine efficacy and treatment outcomes.

Notch signaling mediates between two pattern-forming processes during head regeneration in Hydra

Hydra head regeneration consists of hypostome/organizer and tentacle development, and involves Notch and Wnt/β-catenin signaling. Notch inhibition blocks hypostome/organizer regeneration, but not the appearance of the tentacle tissue. β-Catenin inhibition blocks tentacle, but not hypostome/organizer regeneration. Gene expression analyses during head regeneration revealed the Notch-promoting expression of HyWnt3, HyBMP2/4, and the transcriptional repressor genes CnGsc, Sp5, and HyHes, while blocking HyBMP5/8b and the c-fos-related gene HyKayak β-Catenin promotes the expression of the tentacle specification factor HyAlx, but not of HyWnt3 This suggests HyWnt3 and HyBMP4 as parts of a hypostome/organizer gene module, and BMP5/8, HyAlx, and β-catenin as parts of a tentacle gene module. Notch then functions as an inhibitor of tentacle production to allow regeneration of a hypostome/head organizer. HyKayak is a candidate target gene for HvNotch-induced repressor genes. Inhibiting HyKayak attenuated the expression of HyWnt3 Polyps of Craspedacusta do not have tentacles and thus after head removal only regenerate a hypostome structure. Notch signaling was not needed for head regeneration in Craspedacusta, corroborating the idea of its requirement during Hydra head regeneration to harmonize two co-operating pattern-forming processes.

Transcriptional regulation in the absence of inositol trisphosphate receptor calcium signaling

The activation of IP3 receptor (IP3R) Ca2+ channels generates agonist-mediated Ca2+ signals that are critical for the regulation of a wide range of biological processes. It is therefore surprising that CRISPR induced loss of all three IP3R isoforms (TKO) in HEK293 and HeLa cell lines yields cells that can survive, grow and divide, albeit more slowly than wild-type cells. In an effort to understand the adaptive mechanisms involved, we have examined the activity of key Ca2+ dependent transcription factors (NFAT, CREB and AP-1) and signaling pathways using luciferase-reporter assays, phosphoprotein immunoblots and whole genome transcriptomic studies. In addition, the diacylglycerol arm of the signaling pathway was investigated with protein kinase C (PKC) inhibitors and siRNA knockdown. The data showed that agonist-mediated NFAT activation was lost but CREB activation was maintained in IP3R TKO cells. Under base-line conditions transcriptome analysis indicated the differential expression of 828 and 311 genes in IP3R TKO HEK293 or HeLa cells, respectively, with only 18 genes being in common. Three main adaptations in TKO cells were identified in this study: 1) increased basal activity of NFAT, CREB and AP-1; 2) an increased reliance on Ca2+- insensitive PKC isoforms; and 3) increased production of reactive oxygen species and upregulation of antioxidant defense enzymes. We suggest that whereas wild-type cells rely on a Ca2+ and DAG signal to respond to stimuli, the TKO cells utilize the adaptations to allow key signaling pathways (e.g., PKC, Ras/MAPK, CREB) to transition to the activated state using a DAG signal alone.

Developmental exposures to common environmental pollutants result in long-term Reprogramming of hypothalamic-pituitary axis in mice

Humans are exposed to a range of endocrine disrupting chemicals (EDCs). Many studies demonstrate that exposures to EDCs during critical windows of development can permanently affect endocrine health outcomes. Most experimental studies address changes in secretion of hormones produced by gonads, thyroid gland and adrenals, and little is known about the ability of EDCs to produce long-term changes in the hypothalamic-pituitary (HP) control axes. Here, we examined the long-term effects of three common EDCs on male mouse HP gene expression, following developmental exposures. Pregnant mice were exposed to 0.2 mg/ml solutions of bisphenol S (BPS), 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), or 3,3',5,5'-tetrabromobisphenol A (TBBPA) from pregnancy day 8 through lactation day 21 (weaning day). Male offspring were left untreated until postnatal day 140, where pituitaries and hypothalami were collected. Pituitaries were assed for gene expression via RNA sequencing, while specific genes were assessed for expression in hypothalami via RT-qPCR. Differential expression, as well as gene enrichment and pathway analysis, indicated that all three chemicals induced long-term changes, (mostly suppression) in pituitary genes involved in its endocrine function. BPS and BDE-47 produced effects overlapping significantly at the level of effected genes and pathways. All three chemicals altered pathways of gonad and liver HP axes, while BPS altered HP-adrenal and BDE-47 altered HP-thyroid pathways specifically. All three chemicals reduced expression of immune genes in the pituitaries. Targeted gene expression in the hypothalamus indicates down regulation of hypothalamic endocrine control genes by BPS and BDE-47 groups, concordant with changes in the pituitary, suggesting that these chemicals suppress overall HP endocrine function. Interestingly, all three chemicals altered pituitary genes of GPCR-mediated intracellular signaling molecules, key signalers common to many pituitary responses to hormones. The results of this study show that developmental exposures to common EDCs have long-term impacts on hormonal feedback control at the hypothalamic-pituitary level.

New opportunities to overcome T cell dysfunction: the role of transcription factors and how to target them

Immune checkpoint blockade (ICB) therapies, which block inhibitory receptors on T cells, can be efficacious in reinvigorating dysfunctional T cell responses. However, most cancers do not respond to these therapies and even in those that respond, tumors can acquire resistance. New strategies are needed to rescue and recruit T cell responses across patient populations and disease states. In this review, we define mechanisms of T cell dysfunction, focusing on key transcription factor (TF) networks. We discuss the complex and sometimes contradictory roles of core TFs in both T cell function and dysfunction. Finally, we review strategies to target TFs using small molecule modulators, which represent a challenging but highly promising opportunity to tune the T cell response toward sustained immunity.

MicroRNA-146a-5p protects retinal ganglion cells through reducing neuroinflammation in experimental glaucoma

Neuroinflammation plays important roles in retinal ganglion cell (RGC) degeneration in glaucoma. MicroRNA-146 (miR-146) has been shown to regulate inflammatory response in neurodegenerative diseases. In this study, whether and how miR-146 could affect RGC injury in chronic ocular hypertension (COH) experimental glaucoma were investigated. We showed that in the members of miR-146 family only miR-146a-5p expression was upregulated in COH retinas. The upregulation of miR-146a-5p was observed in the activated microglia and Müller cells both in primary cultured conditions and in COH retinas, but mainly occurred in microglia. Overexpression of miR-146a-5p in COH retinas reduced the levels pro-inflammatory cytokines and upregulated the levels of anti-inflammatory cytokines, which were further confirmed in the activated primary cultured microglia. Transfection of miR-146a-5p mimic increased the percentage of anti-inflammatory phenotype in the activated BV2 microglia, while transfection of miR-146a-5p inhibitor resulted in the opposite effects. Transfection of miR-146a-5p mimic/agomir inhibited the levels of interleukin-1 receptor associated kinase (IRAK1) and TNF receptor associated factor 6 (TRAF6) and phosphorylated NF-κB subunit p65. Dual luciferase reporter gene assay confirmed that miR-146a-5p could directly target IRAK1 and TRAF6. Moreover, downregulation of IRAK1 and TRAF6 by siRNA techniques or blocking NF-κB by SN50 in cultured microglia reversed the miR-146a-5p inhibitor-induced changes of inflammatory cytokines. In COH retinas, overexpression of miR-146a-5p reduced RGC apoptosis, increased RGC survival, and partially rescued the amplitudes of photopic negative response. Our results demonstrate that overexpression of miR-146a-5p attenuates RGC injury in glaucoma by reducing neuroinflammation through downregulating IRAK1/TRAF6/NF-κB signaling pathway in microglia.

Characterization, expression and functional analysis of Hsp40 during LPS challenge in blood parrot Amphilophus citrinellus ×Vieja melanura

Heat shock protein 40 belonging to heat shock protein family plays an important role in the immune responses of organisms. In this study, the full length cDNA of Hsp40 was 2426 bp including a 1368 bp open reading frame (ORF) encoding 455 amino acids with a molecular weight of 49.16 kDa and a theoretical isoelectric point of 9.34 in blood parrot Vieja synspila ♀ × Amphilophus citrinellus ♂, an important ornamental fish in China. It had three conserved domains DnaJ, CRR and DnaJ_C. Phylogenetic analysis showed that the sequence of Hsp40 among species was conserved, and the blood parrot Hsp40 was closely related to Neolamprologus brichardi. Blood parrot Hsp40 mRNA could be detected in all of the tissues examined and mainly distributed in the cytoplasm. The expression of Hsp40 was upregulated during lipopolysaccharide (LPS) challenge. Upregulated Hsp40 inhibited the activity of nuclear factor κB (NF-κB) and activated protein 1 (AP-1) and reduced the ratio of Bax/Bcl-2 mRNA expression. This study provides a theoretical basis for further exploring the role of Hsp40 gene in the anti-bacterial immunity of blood parrot.

Involvement of Human Cellular Proteins and Structures in Realization of the HIV Life Cycle: A Comprehensive Review, 2024

Human immunodeficiency virus (HIV) continues to be a global health challenge, with over 38 million people infected by the end of 2022. HIV-1, the predominant strain, primarily targets and depletes CD4+ T cells, leading to immunodeficiency and subsequent vulnerability to opportunistic infections. Despite the progress made in antiretroviral therapy (ART), drug resistance and treatment-related toxicity necessitate novel therapeutic strategies. This review delves into the intricate interplay between HIV-1 and host cellular proteins throughout the viral life cycle, highlighting key host factors that facilitate viral entry, replication, integration, and immune evasion. A focus is placed on actual findings regarding the preintegration complex, nuclear import, and the role of cellular cofactors such as FEZ1, BICD2, and NPC components in viral transport and genome integration. Additionally, the mechanisms of immune evasion via HIV-1 proteins Nef and Vpu, and their interaction with host MHC molecules and interferon signaling pathways, are explored. By examining these host-virus interactions, this review underscores the importance of host-targeted therapies in complementing ART, with a particular emphasis on the potential of genetic research and host protein stability in developing innovative treatments for HIV/AIDS.

Octahydroindolizine alkaloid Homocrepidine A from Dendrobium crepidatum attenuate P. acnes-induced inflammatory in vitro and in vivo

ETHNOPHARMACOLOGICAL RELEVANCE

Dendrobium crepidatum Lindl. ex Paxton is a perennial epiphyte of Dendrobium genus, distributed in southern China, and utilized as the traditional Chinese medicine "Shihu" in Yunnan Province. Due to its heat-clearing and detoxicating properties, it is formulated as the "XiaoCuoWan" as recorded in the China Pharmacopoeia, and specially used to treat chronic skin inflammatory diseases, such as acne.

AIM OF THE STUDY

This research aimed to estimate impact of the octahydroindoline alkaloid Homocrepidine A (HCA), isolated from D. crepidatum, on acne inflammation using both human THP-1 cells and mouse models. Furthermore, the potential anti-inflammatory mechanism of HCA has been analyzed through molecular biology methods and computer simulation.

MATERIALS AND METHODS

THP-1 cells and mouse models induced by live Propionibacterium acnes (P. acnes) were employed to evaluate the anti-inflammatory properties of crude extract of D. crepidatum (DCE) and HCA. ELISA was utilized to detect the release of inflammatory cytokines in both cellular and murine ear tissues. RNAseq was used to screen the pathways associated with HCA-mediated inflammatory inhibition, while Western blot, RT-qPCR, and immunofluorescence were utilized to detect the expression of relevant proteins. Additionally, molecular docking simulations and cellular thermal shift assays were employed to confirm the target of HCA.

RESULTS

Our research shows that DCE and HCA can effectively alleviate acne inflammation. HCA inhibits TLR2 expression by interacting with amino acid residues in the TIR domain of hTLR2, including Pro-681, Asn-688, Trp-684, and Ile-685. Moreover, HCA disrupts inflammatory signal transduction mediated by MAPK and NF-κB pathways through MyD88-dependent pathway. Additionally, HCA treatment facilitates Nrf2 nuclear translocation and upregulates HO-1 expression, thereby inhibiting NLRP3 inflammasomes activation. In vivo experiments further revealed that HCA markedly attenuated erythema and swelling caused by P. acnes in mice ears, while also decreasing the expression of pro-inflammatory cytokines IL-1β and IL-8.

CONCLUSIONS

Our research highlights the protective effects of D. crepidatum and its bioactive compound HCA against acne inflammation, marking the first exploration of its potential in this context. The discoveries indicate that HCA treatment may represent a promising functional approach for acne therapy.

A tissue bandage for pelvic ganglia injury

Neurogenic bladder often occurs after pelvic ganglia injury. Its symptoms, like severe urinary retention and incontinence, have a significant impact on individuals' quality of life. Unfortunately, there are currently no effective treatments available for this type of injury. Here, we designed a fiber-enhanced tissue bandage for injured pelvic ganglia. Tight junctions formed in tissue bandages create a mini tissue structure that enhances resistance in an in vivo environment and delivers growth factors to support the healing of ganglia. Strength fibers are similar to clinical bandages and guarantee ease of handling. Furthermore, tissue bandages can be stored at low temperatures over 5 months without compromising cell viability, meeting the requirements for clinical products. A tissue bandage was applied to a male rat with a bilateral major pelvic ganglia crush injury. Compared to the severe neurogenic bladder symptoms observed in the injury and scaffold groups, tissue bandages significantly improved bladder function. We found that tissue bandage increases resistance to mechanical injury by boosting the expression of cytoskeletal proteins within the major pelvic ganglia. Overall, tissue bandages show promise as a practical therapeutic approach for ganglia repair, offering hope for developing more effective treatments for this thorny condition.

Comparative Analysis of Hepatic Gene Expression Profiles in Murine and Porcine Sepsis Models

Sepsis remains a huge unmet medical need for which no approved drugs, besides antibiotics, are on the market. Despite the clinical impact of sepsis, its molecular mechanism remains inadequately understood. Recent insights have shown that profound hepatic transcriptional reprogramming, leading to fatal metabolic abnormalities, might open a new avenue to treat sepsis. Translation of experimental results from rodents to larger animal models of higher relevance for human physiology, such as pigs, is critical and needs exploration. We performed a comparative analysis of the transcriptome profiles in murine and porcine livers using the following sepsis models: cecal ligation and puncture (CLP) in mice and fecal instillation (FI) in pigs, both of which induce polymicrobial septic peritonitis, and lipopolysaccharide (LPS)-induced endotoxemia in pigs, inducing sterile inflammation. Using bulk RNA sequencing, Metascape pathway analysis, and HOMER transcription factor motif analysis, we were able to identify key genes and pathways affected in septic livers. Conserved upregulated pathways in murine CLP and porcine LPS and FI generally comprise typical inflammatory pathways, except for ER stress, which was only found in the murine CLP model. Conserved pathways downregulated in sepsis comprise almost exclusively metabolic pathways such as monocarboxylic acid, steroid, biological oxidation, and small-molecule catabolism. Even though the upregulated inflammatory pathways were equally induced in the two porcine models, the porcine FI model more closely resembles the metabolic dysfunction observed in the CLP liver compared to the porcine LPS model. This comprehensive comparison focusing on the hepatic responses in mouse CLP versus LPS or FI in pigs shows that the two porcine sepsis models generally resemble quite well the mouse CLP model, with a typical inflammatory signature amongst the upregulated genes and metabolic dysfunction amongst the downregulated genes. The hepatic ER stress observed in the murine model could not be replicated in the porcine models. When studying metabolic dysfunction in the liver upon sepsis, the porcine FI model more closely resembles the mouse CLP model compared to the porcine LPS model.

Transcriptome and RNA sequencing analysis of H9C2 cells exposed to diesel particulate matter

Although air pollution has been classified as a risk factor for heart disease, the underlying mechanisms remain nebulous. Therefore, this study investigated the effect of diesel particulate matter (DPM) exposure on cardiomyocytes and identified differentially expressed genes (DEGs) induced by DPM. DPM treatment decreased H9C2 cell viability and increased cytotoxicity. Ten genes showed statistically significant differential expression following treatment with DPM at 25 and 100 μg/ml for 3 h. A total of 273 genes showed statistically significant differential expression following treatment with DPM at 25 and 100 μg/ml for 24 h. Signaling pathway analysis revealed that the DEGs were related to the 'reactive oxygens species,' 'IL-17,' and 'fluid shear stress and atherosclerosis' signaling pathways. Hmox1, Fos, and Fosb genes were significantly upregulated among the selected DEGs. This study identified DPM-induced DEGs and verified the selected genes using qRT-PCR and western blotting. The findings provide insights into the molecular events in cardiomyocytes following exposure to DPM.

The Metallothionein System in Tetrahymena thermophila Is Iron-Inducible

Metallothioneins are multifunctional proteins implicated in various cellular processes. They have been used as biomarkers of heavy metal exposure and contamination due to their intrinsic ability to bind heavy metals and their transcriptional response to both physiological and noxious metal ions such as cadmium (Cd) and mercury (Hg). In this study, we aimed to clarify the role of iron and reactive oxygen species (ROSs) in the induction of the metallothionein system (Mtt) in the ciliate protozoan Tetrahymena thermophila. We investigated the relative mRNA abundances of the metallothionein genes Mtt1, Mtt2/4, and Mtt5, revealing for the first time their responsiveness to iron exposure. Furthermore, by using inhibitors of superoxide dismutase (SOD) and catalase (CAT), alone or in combination with iron, we highlighted the roles of superoxide ion and endogenous hydrogen peroxide, as well as the complex interplay between the metal and ROSs. These results enhance our understanding of the metallothionein system in ciliates and suggest that ROSs may be a primary evolutionary driver for the selection of these proteins in nature.

Transcriptome-Wide Profiling of Nascent RNA in Neurons with Enriched H3K27ac Signal Elevates eRNA Identification Efficiency

Growing evidence suggests that activity-dependent gene expression is crucial for neuronal plasticity and behavioral experience. Enhancer RNAs (eRNAs), a class of long noncoding RNAs, play a key role in these processes. However, eRNAs are highly dynamic and are often present at lower levels than their corresponding mRNAs, making them difficult to detect using total RNA-seq techniques. Nascent RNA sequencing, which separates nascent RNAs from the steady-state RNA population, has been shown to increase the ability to detect activity-induced eRNAs with a higher signal-to-noise ratio. However, there is a lack of bioinformatic tools or pipelines for detecting eRNAs utilizing nascent RNA-seq and other multiomics data sets. In this study, we addressed this gap by developing a novel bioinformatic framework, e-finder, for finding eRNAs and have made it available to the scientific community. Additionally, we reanalyzed our previous nascent RNA sequencing data and compared them with total RNA-seq data to identify activity-regulated RNAs in neuronal cell populations. Using H3K27 acetylome data, we characterized activity-dependent eRNAs that drive the transcriptional activity of the target genes. Our analysis identified a subset of eRNAs involved in mediating synapse organization, which showed increased activity-dependent transcription after the potassium chloride stimulation. Notably, our data suggest that nascent RNA-seq with an enriched H3K27ac signal exhibits high resolution to identify potential eRNAs in response to membrane depolarization. Our findings uncover the role of the eRNA-mediated gene activation network in neuronal systems, providing new insights into the molecular processes characterizing neurological diseases.

Loss of ARID3A perturbs intestinal epithelial proliferation-differentiation ratio and regeneration

Intestinal stem cells at the crypt divide and give rise to progenitor cells that proliferate and differentiate into various mature cell types in the transit-amplifying (TA) zone. Here, we showed that the transcription factor ARID3A regulates intestinal epithelial cell proliferation and differentiation at the TA progenitors. ARID3A forms an expression gradient from the villus tip to the upper crypt mediated by TGF-β and WNT. Intestinal-specific deletion of Arid3a reduces crypt proliferation, predominantly in TA cells. Bulk and single-cell transcriptomic analysis shows increased enterocyte and reduced secretory differentiation in the Arid3a cKO intestine, accompanied by enriched upper-villus gene signatures of both cell lineages. We find that the enhanced epithelial differentiation in the Arid3a-deficient intestine is caused by increased binding and transcription of HNF1 and HNF4. Finally, we show that loss of Arid3a impairs irradiation-induced regeneration with sustained cell death and reprogramming. Our findings imply that Arid3a functions to fine-tune the proliferation-differentiation dynamics at the TA progenitors, which are essential for injury-induced regeneration.

The construction of a prognostic model by apoptosis-related genes to predict survival, immune landscape, and medication in cholangiocarcinoma

BACKGROUND

Cholangiocarcinoma (CCA) is a highly aggressive and invasive malignant tumor of the bile duct, with a poor prognosis and a high mortality rate. Currently, there is a lack of effective targeted treatment methods and reliable biomarkers for prognosis.

METHODS

We downloaded RNA-seq and clinical data of CCA from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases as training and test sets. The apoptosis-related genes were obtained from the Molecular Signatures Database (MsigDB) database. We used univariate/multivariate Cox regression and Lasso regression analyses to construct a riskscore prognostic model. Based on the median riskscore, we clustered the patients into high-risk (HR) and low-risk (LR) groups. We carried out Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) in HR and LR groups. The single sample gene set enrichment analysis (ssGSEA) was employed to analyze the immune infiltration of the HR and LR groups. The CellMiner database was utilized to predict drugs and perform molecular docking on drugs and target proteins.

RESULTS

We identified 8 genes with prognostic significance to construct a prognostic model. Results of GO and KEGG demonstrated that DEGs were mainly enriched in biological functions such as fatty acid metabolic processes and pathways such as the cAMP signaling pathway. Results of ssGSEA uncovered that immune cells such as DCs and Macrophages in the HR group, as well as immune functions such as Check-point and Parainflammation, were considerably higher than those in the LR group. Drug sensitivity prediction and results of molecular docking revealed that Rigosertib targeted the prognostic genes MAP3K1. HYPOTHEMYCIN and AMG900 effectively targeted JUN.

CONCLUSION

Our project suggested that the prognostic model with apoptotic features can effectively predict prognosis in CCA patients, proffering prognostic biomarkers and potential therapeutic targets for CCA patients.

A large-scale cancer-specific protein-DNA interaction network

Cancer development and progression are generally associated with gene dysregulation, often resulting from changes in the transcription factor (TF) sequence or expression. Identifying key TFs involved in cancer gene regulation provides a framework for potential new therapeutics. This study presents a large-scale cancer gene TF-DNA interaction network, as well as an extensive promoter clone resource for future studies. Highly connected TFs bind to promoters of genes associated with either good or poor cancer prognosis, suggesting that strategies aimed at shifting gene expression balance between these two prognostic groups may be inherently complex. However, we identified potential for oncogene-targeted therapeutics, with half of the tested oncogenes being potentially repressed by influencing specific activators or bifunctional TFs. Finally, we investigate the role of intrinsically disordered regions within the key cancer-related TF ESR1 in DNA binding and transcriptional activity, and found that these regions can have complex trade-offs in TF function. Altogether, our study broadens our knowledge of the TFs involved in cancer gene regulation and provides a valuable resource for future studies and therapeutics.

The enhancer RNA, AANCR, regulates APOE expression in astrocytes and microglia

Enhancers, critical regulatory elements within the human genome, are often transcribed into enhancer RNAs. The dysregulation of enhancers leads to diseases collectively termed enhanceropathies. While it is known that enhancers play a role in diseases by regulating gene expression, the specific mechanisms by which individual enhancers cause diseases are not well understood. Studies of individual enhancers are needed to fill this gap. This study delves into the role of APOE-activating noncoding RNA, AANCR, in the central nervous system, elucidating its function as a genetic modifier in Alzheimer's Disease. We employed RNA interference, RNaseH-mediated degradation, and single-molecule RNA fluorescence in situ hybridization to demonstrate that mere transcription of AANCR is insufficient; rather, its transcripts are crucial for promoting APOE expression. Our findings revealed that AANCR is induced by ATM-mediated ERK phosphorylation and subsequent AP-1 transcription factor activation. Once activated, AANCR enhances APOE expression, which in turn imparts an inflammatory phenotype to astrocytes. These findings demonstrate that AANCR is a key enhancer RNA in some cell types within the nervous system, pivotal for regulating APOE expression and influencing inflammatory responses, underscoring its potential as a therapeutic target in neurodegenerative diseases.

Kumujan B suppresses TNF-α-induced inflammatory response and alleviates experimental colitis in mice

Treatments of inflammatory bowel disease (IBD) are diverse, but their efficacy is limited, and it is therefore urgent to find better therapies. Controlling mucosal inflammation is a must in IBD drug treatment. The occurrence of anti-tumor necrosis factor α (TNF-α) monoclonal antibodies has provided a safer and more efficacious therapy. However, this kind of treatment still faces failure in the form of loss of response. β-Carboline alkaloids own an anti-inflammatory pharmacological activity. While Kumujan B contains β-carboline, its biological activity remains unknown. In this study, we attempted to determine the anti-inflammatory effects of Kumujan B using both the TNF-α- induced in vitro inflammation and DSS-induced in vivo murine IBD models. Our data show that Kumujan B attenuated the expression of interleukin 1β (IL-1β) and interleukin 6 (IL-6) induced by TNF-α in mouse peritoneal macrophages. Kumujan B suppressed c-Jun N-terminal protein kinases (JNK) signaling, especially c-Jun, for anti-inflammatory response. Furthermore, Kumujan B promoted K11-linked ubiquitination and degradation of c-Jun through the proteasome pathway. In an in vivo study, Kumujan B inhibited the expression of IL-1β, IL-6, and TNF-α and improved the colon barrier function in dextran sulfate sodium salt (DSS)-induced experimental mice colitis. Kumujan B exhibited in vivo and in vitro anti-inflammatory effects, making it a potential therapeutic candidate for treating IBD.

Molecular mechanism analysis of nontuberculous mycobacteria infection in patients with cystic fibrosis

Aim: This study aims to explore the molecular mechanisms of cystic fibrosis (CF) complicated with nontuberculous mycobacteria (NTM) infection. Materials & methods: Expression profiles of CF with NTM-infected patients were downloaded from GEO database. Intersection analysis yielded 78 genes associated with CF with NTM infection. The protein-protein interaction (PPI) network and the functions of hub genes were investigated. Results: Five hub genes (PIK3R1, IL1A, CXCR4, ACTN1, PFN1) were identified, which were primarily enriched in actin-related biological processes and pathways. Transcription factors RELA, JUN, NFKB1 and FOS that regulated hub genes modulated IL1A expression, while 21 other transcription factors regulated CXCR4 expression. Conclusion: In summary, this study may provide new insights into the mechanisms of CF with NTM infection.

The hormonal control of parturition

Parturition is a complex physiological process that must occur in a reliable manner and at an appropriate gestation stage to ensure a healthy newborn and mother. To this end, hormones that affect the function of the gravid uterus, especially progesterone (P4), 17β-estradiol (E2), oxytocin (OT), and prostaglandins (PGs), play pivotal roles. P4 via the nuclear P4 receptor (PR) promotes uterine quiescence and for most of pregnancy exerts a dominant block to labor. Loss of the P4 block to parturition in association with a gain in prolabor actions of E2 are key transitions in the hormonal cascade leading to parturition. P4 withdrawal can occur through various mechanisms depending on species and physiological context. Parturition in most species involves inflammation within the uterine tissues and especially at the maternal-fetal interface. Local PGs and other inflammatory mediators may initiate parturition by inducing P4 withdrawal. Withdrawal of the P4 block is coordinated with increased E2 actions to enhance uterotonic signals mediated by OT and PGs to promote uterine contractions, cervix softening, and membrane rupture, i.e., labor. This review examines recent advances in research to understand the hormonal control of parturition, with focus on the roles of P4, E2, PGs, OT, inflammatory cytokines, and placental peptide hormones together with evolutionary biology of and implications for clinical management of human parturition.

FOS+ Macrophages Promote Chronic Rejection of Cardiac Transplantation

OBJECTIVES

Chronic rejection remains the leading cause of progressive decline in graft function. Accumulating evidence indicates that macrophages participate in chronic rejection dependent on CD40-CD40L. The FOS family members are critical in inflammatory and immune responses. However, the mechanisms underlying the role of FOS family members in chronic rejection remain unclear. In this study, we aimed to elucidate the role and underlying mechanisms of FOS-positive macrophages regulated by CD40 that mediate chronic allograft rejection.

MATERIALS AND METHODS

We downloaded publicly accessible chronic rejection kidney transplant single-cell sequencing datasets from the gene expression omnibus database. Differentially expressed genes between the CD40hi and CD40low macrophage chronic rejection groups were analyzed. We established a chronic rejection mouse model by using CTLA-4-Ig. We treated bone marrow-derived macrophages with an anti-CD40 antibody. We assessed expression of the FOS family by flow cytometry, real-time quantitative polymerase chain reaction, Western blotting, and immunofluorescence. We identified altered signaling pathways by using RNA sequencing analysis. We detected DNA specifically bound to transcription factors by using ChIP-sequencing, with detection of the degree of graft fibrosis and survival.

RESULTS

FOS was highly expressed on CD40hi macrophages in patients with chronic transplantrejection. Mechanistically, we showed that CD40 activated NF-κB2 translocation into the nucleus to upregulate c-Fos and FosB expression, thus promoting chronic rejection of cardiac transplant.We showed thatNF-κB2 regulated c-Fos and FosB expression by binding to the c-fos and fosb promoter regions. Inhibition of c-Fos/activator protein-1 decreased graft fibrosis and prolonged graft survival.

CONCLUSIONS

CD40 may activate transcription factor NF-κB2 translocation into the nucleus of macrophages to upregulate c-Fos and FosB expression, thus promoting chronic rejection of cardiac transplant. Inhibition of c-Fos/activator protein-1 decreased grafts fibrosis and prolonged graft survival.

Pathways to therapy resistance: The sheltering effect of the bone marrow microenvironment to multiple myeloma cells

Multiple Myeloma (MM) is a malignant expansion of plasma cells in the bone marrow (BM), resulting in a disease characterized by symptoms of end organ damage from light chain secretion, crowding of the BM, and bone lesions. Although the past two decades have been characterized by numerous novel therapies emerging, the disease remains incurable due to intrinsic or acquired drug resistance. A major player in MM's drug resistance arises from its intimate relationship with the BM microenvironment (BMME). Through stress-inducing conditions, soluble messengers, and physical adhesion to BM elements, the BMME activates numerous pathways in the myeloma cell. This not only propagates myeloma progression through survival and growth signals, but also specific mechanisms to circumvent therapeutic actions. In this review, we provide an overview of the BMME, the role of individual components in MM survival, and various therapy-specific resistance mechanisms reported in the literature.

Progress in the Study of Fra-2 in Respiratory Diseases

Fos-related antigen-2 (Fra-2) is a member of the activating protein-1 (AP-1) family of transcription factors. It is involved in controlling cell growth and differentiation by regulating the production of the extracellular matrix (ECM) and coordinating the balance of signals within and outside the cell. Fra-2 is not only closely related to bone development, metabolism, and immune system and eye development but also in the progression of respiratory conditions like lung tumors, asthma, pulmonary fibrosis, and chronic obstructive pulmonary disease (COPD). The increased expression and activation of Fra-2 in various lung diseases has been shown in several studies. However, the specific molecular mechanisms through which Fra-2 affects the development of respiratory diseases are not yet understood. The purpose of this research is to summarize and delineate advancements in the study of the involvement of transcription factor Fra-2 in disorders related to the respiratory system.

Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer

Gastric cancer (GC) is the fifth most common cancer worldwide and is a heterogeneous disease. Among GC subtypes, the mesenchymal phenotype (Mes-like) is more invasive than the epithelial phenotype (Epi-like). Although gene expression of the epithelial-to-mesenchymal transition (EMT) has been studied, the regulatory landscape shaping this process is not fully understood. Here we use ATAC-seq and RNA-seq data from a compendium of GC cell lines and primary tumors to detect drivers of regulatory state changes and their transcriptional responses. Using the ATAC-seq data, we developed a machine learning approach to determine the transcription factors (TFs) regulating the subtypes of GC. We identified TFs driving the mesenchymal (RUNX2, ZEB1, SNAI2, AP-1 dimer) and the epithelial (GATA4, GATA6, KLF5, HNF4A, FOXA2, GRHL2) states in GC. We identified DNA copy number alterations associated with dysregulation of these TFs, specifically deletion of GATA4 and amplification of MAPK9 Comparisons with bulk and single-cell RNA-seq data sets identified activation toward fibroblast-like epigenomic and expression signatures in Mes-like GC. The activation of this mesenchymal fibrotic program is associated with differentially accessible DNA cis-regulatory elements flanking upregulated mesenchymal genes. These findings establish a map of TF activity in GC and highlight the role of copy number driven alterations in shaping epigenomic regulatory programs as potential drivers of GC heterogeneity and progression.

GSG2 promotes progression of human endometrial cancer by regulating PD-1/PD-L1 expression via PI3K-AKT pathway

Cell cycle dysregulation leading to uncontrolled growth is a primary characteristic of malignancy. GSG2, a mitosis-related kinase, affects the normal cell cycle by interfering with the normal dissociation of centromere cohesion, and its overexpression has been shown to play an important role in cancer cells. Here, we investigated the function of GSG2 as a tumor promoter in endometrial carcinoma and its relationship with the immunological microenvironment. We used immunohistochemistry to identify a correlation between the development and prognosis of GSG2 and endometrial cancer. Cell and animal experiments confirmed that GSG2 has a protumorigenic phenotype in endometrial cancer cell lines. Furthermore, using GeneChip analysis and a tumor-immune coculture model, we observed a link between GSG2 expression and the composition of the immune microenvironment. Therefore, we concluded that the activation of the PI3K/AKT pathway by GSG2 may impact DNA repair, disrupt the cell cycle, and regulate the immune response, all of which could increase the ability of EC cells to proliferate malignantly. Consequently, it is anticipated that GSG2 will be a viable therapeutic target in endometrial carcinoma.