AP-1 in cell proliferation and survival

Recent research advances of c-fos in regulating cell senescence

c-fos is an immediate early gene (IEG) that forms a heterodimeric activator protein-1 (AP-1) complex with c-Jun. Following stimulation by a variety of factors, it changes the expression of genes and participates in cellular growth, proliferation, differentiation, and apoptosis. Previous studies have reported that c-fos is linked to cellular senescence and is involved in aging-related signaling pathways or damage repair processes. However, there are limited studies related to this topic. This review summarizes the findings of the connection between c-fos and cellular senescence, including the regulatory role of c-fos in the senescence of stem cells and various kinds of somatic cells. In addition, we discussed the involvement of c-fos in the cellular senescence process and related signaling pathways, as well as the importance of regulating DNA damage repair. The current studies have demonstrated that c-fos has important roles in inhibiting stem cell senescence. They can pave the way for a more thorough examination of the aging process and the regeneration of stem cells and provide new therapeutic strategies for aging-related diseases.

Starvation activates ECM-remodeling gene transcription and putative enhancers in fibroblasts despite inducing quiescence

Depletion of growth factors and nutrients induces cellular quiescence, which often accompanies transcriptional silencing and chromatin compaction. Paradoxically, such depletion occurs in pathological microenvironments in which fibroblasts are activated to orchestrate tissue remodeling. The relationship between fibroblast activation and growth factor and nutrient depletion remains unclear. Here, we report that serum depletion in cell culture, a model for growth factor and nutrient depletions, extensively activates transcription in fibroblasts despite inducing quiescence. Activated genes were enriched for extracellular matrix (ECM) structural components and proteases. ECM-related transcription accompanied the activation of putative distal enhancers but not promoters. The activated putative enhancers were enriched for non-coding variants associated with inflammatory bowel disease (IBD) risk, suggesting an alteration in the ECM-remodeling gene regulatory network in IBD. This study implicates nutrient and growth factor depletion in activating the ECM-remodeling gene program in fibroblasts, challenging the prevailing view linking such depletion to transcriptional dormancy.

Updated insights on ASK1 signaling: mechanisms, regulation, and therapeutic potential in diseases

Apoptosis signal-regulating kinase 1 (ASK1) is a serine-threonine kinase, that is a member of the mitogen-activated protein kinase kinase (MAP3K) family, which is expressed or incorporated in nucleated cells which leads to the activation of multiple mitogen-activated protein kinases (MAPK) to regulate cell stress, tumour necrosis factor-α (TNF-α) ligand, lipopolysaccharides and apoptosis. ASK1 gets activated by the ROS, oxidative stress, endoplasmic stress (ER) and various inflammatory cytokines. Dysregulation of ASK1 can lead to various diseases like neurodegenerative disease, cardiovascular disease, cancer, and various other metabolic diseases such as diabetes. This review summarizes ASK1's structure, its family, regulation, and its dual role in disease, highlighting its therapeutic potential for oxidative stress and inflammation-driven conditions while emphasizing the need for further clinical research. Inhibition of ASK1 demonstrates promising potential in treating fibrosis and various other diseases. We also discuss the dual role of ASK1 in both cancer initiation and suppression. Additionally, we explore ASK1 as a therapeutic target in diseases driven by oxidative stress and inflammation, emphasizing the need for further research to support its clinical translation.

Increased matrix stiffness promotes fibrogenesis of hepatic stellate cells through AP-1-induced chromatin priming

Matrix stiffness has significant effects on cell behavior, however, less is known regarding the epigenomic and transcriptional regulation underling the effect of matrix stiffness on cells. In this study, we use an in vitro system to assess the phenotypic shifts of hepatic stellate cells (HSCs) following changes in matrix stiffness, and integrate multi-omics with imaging and biochemical assays to investigate the molecular mechanisms. We show that cells cultured on a stiff matrix display more accessible chromatin sites, which consist of primed chromatin regions that become more accessible prior to the upregulation of nearby genes. These regions are enriched in fibrosis-associated genes that function in cytoskeletal organization and response to mechanical stimulus. We also identify activation of p-JUN in response to the stiff matrix and promoting phenotypic shifts. The identified chromatin accessibility-dependent effect of matrix stiffness may be responsible for various fibrotic diseases and provide insight into intervening approaches.

The Activation of the CCND1 Promoter by AP-1 and SOX Transcription Factors in PC3 Prostate Cancer Cells Can Be Prevented by Anacardic Acid Analogs

Targeting more than one in nine men before age 70, prostate cancer is the most common type of cancer in men. The increased levels of cyclins, leading to activation of cyclin-dependent kinases (CDKs), play a critical role in the increased proliferation of prostate cancer cells. In this study, the regulation of the cyclin D1 (CCND1) promoter activity by activator protein-1 (AP-1) and SRY-related HMG-box (SOX) transcription factors has been characterized in PC3 prostate cancer cells. The SOX and AP-1 transcription factors can cooperate to activate the CCND1 promoter in PC3 prostate cancer cells and such cooperation can be enhanced by protein kinase A (PKA) and/or mitogen-activated protein kinase kinase 1 (ERK kinase 1, MAP2K1) signaling pathways. Moreover, anacardic acid analogs have been assessed for their potential in reducing cell viability and CCND1 promoter activity. The anacardic acid analog 8b, obtained from γ-resorcylic acid, reduces the viability and proliferation of PC3 cells by decreasing CCND1 promoter activity. The effect of analog 8b, which perfectly mimics the structure of anacardic acid, can be attributed to the inhibition of the activities of the transcription factors SOX and AP-1, which are important regulators of CCND1 promoter activity in prostate cancer cells.

FOS as a biomarker for myocardial infarction treatment with Deng's Yangxin Decoction: a systems biology-based analysis

Background

Deng's Yangxin Decoction (DYX) is a Chinese herbal formula used in clinical practice to treat patients with myocardial infarction (MI). However, its underlying mechanism remains unclear.

Objective

This study aims to explore potential biomarkers and associated mechanisms of DYX for MI.

Methods

Therapeutic targets for DYX were obtained based on the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform, Traditional Chinese Medicine Integrated Database, and UniProt databases. Key targets were screened using topological analysis. Differentially expressed genes (DEGs) between MI patients and controls were obtained using open-source datasets. Weighted gene co-expression network analysis (WGCNA) was utilized to screen MI-related genes in the expression array. Hub biomarkers were determined by intersecting DEGs, protein-protein interaction networks, and WGCNA results. Molecular docking validated interactions between DYX components and hub biomarkers. Immune infiltration was assessed via CIBERSORT. Single-cell RNA sequencing analyzed hub biomarker expression in coronary plaques.

Results

FOS was a core biomarker for DYX for MI. Molecular docking confirmed strong binding affinities between quercetin/baicalein and FOS. In addition, high expression of FOS was associated with immune infiltration of neutrophils, activated mast cells, activated dendritic cells, monocytes, and NK cells. FOS was also found to be expressed at high levels in mast and dendritic cells, monocytes, and some T cells in coronary plaques.

Conclusion

FOS is a target of DYX for the treatment of MI, and the mechanism of action may be related to the modulation of immune infiltration.

Vacuum Ultraviolet (VUV)-Induced Physicochemical Engineering of Titanium: Enhanced Fibroblast Activity, Redox System, and Glycosaminoglycan Binding for Soft Tissue Integration

Bacterial invasion at the titanium-tissue interface causes peri-implant inflammation, posing challenges for implants in orthopedics, maxillofacial prosthetics, and dentistry. This study hypothesized that titanium surface decarbonization improves soft tissue cell adhesion and growth. One-minute vacuum ultraviolet (VUV) light treatment at 172 nm reduced surface carbon from 60% to 29% without altering surface topography, making surfaces hydrophilic and hydro-attractive. Human fibroblasts attached to VUV-treated surfaces 2-4 times more frequently than untreated surfaces, with an even greater increase on tilted and curved surfaces. Fibroblast proliferation rose 2-6 times, with an expedited G1-to-S phase transition. Cell retention under dislodging forces increased 2-5 times on VUV-treated surfaces. RNA sequencing showed upregulation of extracellular matrix production, growth factors, cell cycle progression, antioxidant defenses, and proteoglycan/glycosaminoglycan (GAG)-binding, alongside downregulation of the inflammatory response on VUV-treated titanium surfaces. An oxidative stress test showed minimal adverse effects from hydrogen peroxide on cells on VUV-treated surfaces, attributed to increased intracellular glutathione reserves. Enhanced adhesion on VUV-treated titanium was negated by treating the cells with GAG-cleaving enzymes. These findings demonstrate that VUV-mediated decarbonization enhances fibroblast attachment, proliferation, and adhesion by fostering homeostatic cellular phenotypes involving proteoglycan/GAG interactions and antioxidant defense, offering a strategy to improve the soft tissue sealing around titanium implants.

Nuclear Import Defects Drive Cell Cycle Dysregulation in Neurodegeneration

Neurodegenerative diseases (NDDs) and other age-related disorders have been classically defined by a set of key pathological hallmarks. Two of these hallmarks, cell cycle dysregulation (CCD) and nucleocytoplasmic transport (NCT) defects, have long been debated as being either causal or consequential in the pathology of accelerated aging. Specifically, aberrant cell cycle activation in post-mitotic neurons has been shown to trigger neuronal cell death pathways and cellular senescence. Additionally, NCT has been observed to be progressively dysregulated during aging and in neurodegeneration, where the increased subcellular redistribution of nuclear proteins, such as TAR DNA-Binding Protein-43 (TDP-43), to the cytoplasm is a primary driver of disease. However, the functional significance of NCT defects as either a causal mechanism or consequence of pathology, and how the redistribution of cell cycle machinery contributes to neurodegeneration, remains unclear. Here, we describe that pharmacological inhibition of importin-β nuclear import is capable of perturbing cell cycle machinery both in mitotic neuronal cell lines and post-mitotic primary neurons in vitro. Our NemfR86S mouse model of motor neuron disease, characterized by nuclear import defects, further recapitulates the hallmarks of CCD we observed in mitotic cell lines and in post-mitotic primary neurons in vitro, and in spinal motor neurons in vivo. The observed CCD is consistent with the transcriptional and phenotypical dysregulation commonly associated with neuronal cell death and senescence-like features in NDDs. Together, this evidence suggests that impairment of nuclear import pathways resulting in CCD may be a common driver of pathology in neurodegeneration.

c-Jun regulates postpartum β-cell apoptosis and survival downstream of prolactin signaling

Pregnancy and postpartum states drive dynamic expansion and regression of maternal β-cell mass. Little is known about what regulates postpartum regression. We recently profiled murine islets from late gestation and early postpartum to identify regulators of β-cell apoptosis or survival. One hit was c-Jun, a transcription factor which regulates proliferation, apoptosis, and survival in various tissues. Here, we examine c-Jun regulation and function during gestation and postpartum and in murine and human islets. To examine the regulation of c-Jun within β-cells we used a mouse genetic model lacking β-cell prolactin receptor (PRLR) and stimulation of human and murine cultured islets with recombinant prolactin. Knockdown of c-Jun in MIN6 cells was accomplished using siRNA and lentiviral-shRNA, or in islets using pharmacologic inhibitors. We found that c-Jun expression in β-cells is temporally restricted to late gestation and early postpartum and requires PRLR signaling. Moreover, c-Jun expression was mutually exclusive with apoptotic β-cells identified by TUNEL staining. Prolactin treatment induces c-Jun expression downstream of MAPK/ERK signaling in both murine and human islets. Inhibition of c-Jun blocks prolactin-mediated survival of β-cells following pro-apoptotic stress, via the pro-survival factors Bcl2l1 (Bcl-xL) and Birc5 (Survivin). Finally, islets from pregnant donors exhibit increased c-Jun expression in β-cells, while absent in β-cells from donors with gestational diabetes (GDM). Together, our findings indicate that c-Jun contributes to pro-survival effects of lactogens downstream of PRLR/MAPK signaling in β-cells. c-Jun regulation is conserved in human islets and pregnancy and dysregulated in GDM.

Hydrogen Peroxide Modulates the Timely Activation of Jun and Erk in Schwann Cells at the Injury Site and Is Required for Motor Axon Regeneration

Peripheral nervous system (PNS) neurons, including motor neurons (MNs), possess a remarkable ability to regenerate and reinnervate target muscles following nerve injury. This process is orchestrated by a combination of intrinsic neuronal properties and extrinsic factors, with Schwann cells (SCs) playing a central role. Upon injury, SCs transition into a repair phenotype that allows axonal regeneration through molecular signaling and structural guidance. However, the identity of the SCs' reprogramming factors is only partially known. We previously identified hydrogen peroxide (H2O2) as an early and key driver of nerve repair, inducing gene expression rewiring in SCs to support nerve re-growth. In this study, we quantitatively assessed the role of H2O2 in the activation of key pro-regenerative signaling pathways in SCs following sciatic nerve compression, specifically the extracellular signal-regulated kinase 1/2 (ERK1/2) and c-Jun, which are essential for functional nerve recovery. Notably, we found that H2O2 neutralization does not impact degeneration, but it significantly affects the regenerative response. Collectively, our findings establish H2O2 as a promising regulator of the Schwann cell injury response at the injury site, linking oxidative signaling to the molecular mechanisms governing nerve regeneration.

The oncoprotein DEK controls growth-regulated gene expression by enhancing the DNA-binding activity of basic leucine zipper transcription factors

Overexpression of the oncogenic protein DEK is associated with a poor prognosis in various cancers. However, the molecular mechanisms by which DEK promotes cancer development and malignant transformation remain unclear. Previous studies have shown that DEK interacts with transcription factors, such as AP-2a and C/EBPα, and enhances their transcriptional activity. We hypothesized that DEK promotes cancer cell phenotypes by regulating transcription factors. We analyzed the interaction between DEK and the transcription factors to evaluate this hypothesis. We found that DEK binds to the basic regions within the basic leucine zipper (bZIP)- and basic helix-loop-helix leucine zipper (bHLH-ZIP)- transcription factors. Interestingly, DEK enhanced the DNA-binding capacity of two bZIP transcription factors, C/EBPα and ATF3, in vitro without being a component of the transcription factor-DNA complex. We performed DEK knockdown in lung adenocarcinoma A549 cells and examined the global transcriptome changes to determine the biological significance of the interaction between DEK and transcription factors. We found that diverse genes regulating cell growth and amino acid metabolism, which may potentially be regulated by c-Jun, a subunit of the bZIP transcription factor AP1, and c-Myc, a bHLH-ZIP transcription factor, were decreased by DEK knockdown. Consistent with these transcriptome changes, the cell growth, colony formation, and cell migration abilities of A549 cells were decreased by DEK knockdown. These results suggest that DEK promotes cancer cell malignancy by regulating the functions of the bZIP and bHLH-ZIP transcription factors.

Cyclin-dependent kinase 4 and 6 inhibitors in breast cancer treatment

Breast cancer is the second largest cancer in the world, and it has highest mortality rate in women worldwide. The aberrant activation of the cyclin-dependent kinase 4 and 6 (CDK4/6) pathway plays an important role in uncontrolled breast cancer cell proliferation. Therefore, targeting CDK4/6 to improve overall survival rates has been a strong interest in breast cancer therapeutics. Till date, four CDK4/6 inhibitors have been developed and approved for hormone receptor-positive and human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer therapies with great success. However, acquired resistance to CDK4/6 inhibitors has emerged and limits their effectiveness in breast cancer. In this review, we systematically discussed the mechanisms of resistance to CDK4/6 inhibitors including the cell cycle-specific and cell cycle-nonspecific mechanisms. Also, we analyzed combination strategies with other signaling inhibitors in clinical and preclinical settings that further expand the clinical application of CDK4/6 inhibitors in future breast cancer therapies.

The inhibitory effect of Astragalus flavone extract on hyperuricemia and its underlying molecular mechanism by targeting JNK/AP-1/NLRP3/IL-1β signaling pathway

BACKGROUND

Hyperuricemia (HUA) is a metabolic disease disturbing human health caused by the overproduction or underexcretion of uric acid (UA). Astragalus is the root of Astragalus membranaceus (Fisch.) Bunge, has notable regulatory effect on chronic nephritis, proteinuria and spontaneous sweating, suggesting it could be a potential anti-HUA agent. However, limited research has been conducted on its anti-HUA effect and mechanism.

METHODS

The present study performed untargeted and plasma metabolomics of Astragalus extract to identify the main constituents that can be absorbed and exert effect in mice, and further investigated the underlying mechanism by enzyme activity assay, Western Blotting and molecular docking.

RESULTS

The results showed that Astragalus flavone extract inhibited UA synthesis by binding to XOD to hinder substrate binding and inhibiting xanthine oxidase (XOD) protein expression, inhibited JNK/AP-1/NLRP3/IL-1β signaling pathway to alleviate prolonged HUA-induced inflammation and abnormal UA metabolism, and protected the kidney by reducing serum renal function index and improving renal tissue atrophy, fibrosis and tubular dilatation both in vitro and in vivo. Besides, glycitein and isoformononet were identified as the main flavones in Astragalus extract absorbed into the bloodstream of mice, isoformononetin was found to inhibit UA synthesis by direct binding to XOD, and glycitein was found to interact with c-Jun to facilitate UA excretion and inhibit inflammation.

CONCLUSION

This paper represents the pioneering investigation that firstly identifying two flavonoids of Astragalus extract that can be absorbed to fight against HUA, and elucidating their diverse molecular mechanism by targeting JNK/AP-1/NLRP3/IL-1β signaling pathway, UA metabolism and kidney protection.

An Intracellular Peptide Library Screening Platform Identifies Irreversible Covalent Transcription Factor Inhibitors

The development of an intracellular peptide library screening platform is described to identify covalent transcription factor (TF) antagonists. The Transcription Block Survival (TBS) assay and subsequent hit refinement previously produced potent but reversible antagonists of the oncogenic TF cJun. TBS moves beyond a target binding readout to ensure loss of TF function by blocking TF-DNA binding. Here, the TBS methodology is significantly expanded to identify covalent and highly selective inhibitors. A 131,072-member library is probed containing a Cys option at nine positions within a non-reducing cell line. This identified a single Cys residue with the appropriate geometry for disulphide bond formation with cJun C269 in its DNA binding domain. The selection of a unique Cys in the antagonist indicates both target shutdown and concomitant disulphide formation in a single step, resulting in increased potency. Substituting Cys with an electrophile generates an irreversible yet highly selective covalent cJun inhibitor capable of penetrating human melanoma cells in culture and depleting oncogenic cJun levels to inhibit cell viability, with enhanced efficacy compared to a previous cJun-targeting peptide. This enhanced covalent-TBS screening pipeline provides a robust approach to profile target protein surfaces for ligandable cysteines, producing covalent and selective antagonists with appropriately positioned warheads.

Sex differences in DNMT3A-mutant clonal hematopoiesis and the effects of estrogen

Blood cancers are generally more common in males, and the prevalence of most mutations that drive clonal hematopoiesis and myeloid malignancies is higher in males. In contrast, hematopoietic DNMT3A mutations are more common in females. Among ∼450,000 participants in the UK Biobank, the prevalence of DNMT3A mutations and copy-number abnormalities is higher in females than males. In a murine model, Dnmt3a-mutant hematopoietic stem cells (HSCs) from unperturbed female mice had increased stemness gene expression compared to male and wild-type (WT) mice. Estrogen regulates HSCs, and we found that Dnmt3a mutations maintain stemness in the setting of estrogen-induced proliferative stress. Dnmt3a-mutant myeloid cells outcompeted WT cells under chronic estrogen treatment, an effect that was dependent on cell-intrinsic estrogen receptor alpha activity. Our studies indicate that estrogen might contribute to the female predominance of DNMT3A-mutant clonal hematopoiesis.

Major Oxidative and Antioxidant Mechanisms During Heat Stress-Induced Oxidative Stress in Chickens

Heat stress (HS) is one of the most important stressors in chickens, and its adverse effects are primarily caused by disturbing the redox homeostasis. An increase in electron leakage from the mitochondrial electron transport chain is the major source of free radical production under HS, which triggers other enzymatic systems to generate more radicals. As a defense mechanism, cells have enzymatic and non-enzymatic antioxidant systems that work cooperatively against free radicals. The generation of free radicals, particularly the reactive oxygen species (ROS) and reactive nitrogen species (RNS), under HS condition outweighs the cellular antioxidant capacity, resulting in oxidative damage to macromolecules, including lipids, carbohydrates, proteins, and DNA. Understanding these detrimental oxidative processes and protective defense mechanisms is important in developing mitigation strategies against HS. This review summarizes the current understanding of major oxidative and antioxidant systems and their molecular mechanisms in generating or neutralizing the ROS/RNS. Importantly, this review explores the potential mechanisms that lead to the development of oxidative stress in heat-stressed chickens, highlighting their unique behavioral and physiological responses against thermal stress. Further, we summarize the major findings associated with these oxidative and antioxidant mechanisms in chickens.

Epidermal Resident Memory T Cell Fitness Requires Antigen Encounter in the Skin

CD8 + tissue resident memory T cells (T RM ) develop from effectors that seed peripheral tissues where they persist providing defense against subsequent challenges. T RM persistence requires autocrine TGFβ transactivated by integrins expressed on keratinocytes. T RM precursors that encounter antigen in the epidermis during development outcompete bystander T RM for TGFβ resulting in enhanced persistence. ScRNA-seq analysis of epidermal T RM revealed that local antigen experience in the skin resulted in an enhanced differentiation signature in comparison with bystanders. Upon recall, T RM displayed greater proliferation dictated by affinity of antigen experienced during epidermal development. Finally, local antigen experienced T RM differentially expressed TGFβRIII, which increases avidity of the TGFβRI/II receptor complex for TGFβ. Selective ablation of Tgfbr3 reduced local antigen experienced T RM capacity to persist, rendering them phenotypically like bystander T RM . Thus, antigen driven TCR signaling in the epidermis during T RM differentiation results in a lower TGFβ requirement for persistence and increased proliferative capacity that together enhance epidermal T RM fitness.

Various Cellular Components and Its Signaling Cascades Through the Involvement of Signaling Messengers in Keratinocyte Differentiation

Skin is a highly differentiated tissue, in which various signaling molecules play critical roles in the differentiation and proliferation of keratinocytes. Among these, the second messenger calcium and its gradient across skin layers are pivotal in regulating keratinocyte differentiation. Additionally, a diverse array of cellular signaling molecules has been identified as essential for promoting keratinocyte differentiation, thereby maintaining skin integrity and barrier function. The barrier function of the skin provides essential protection against exogenous stimuli and pathogens while maintaining structural stability. The homeostatic processes of skin differentiation are modulated by these second messengers and various signaling molecules. Thus, this review highlights the components associated with keratinocyte differentiation and their biological and pathophysiological roles, as well as redox-sensitive differentiation factors in the modulation of skin homeostasis. This review aims to enhance our understanding of skin physiology and provide insights that may facilitate the development of novel therapeutic strategies for skin diseases.

Single-Cell Multiomics Analysis of Early Wound Response Programs in the Mouse Corneal Epithelium

Purpose

Wound healing is crucial for restoring homeostasis in living organisms. Although wound response mechanisms have been studied extensively, the gene regulatory programs involved remain to be elucidated. Here, we used single-cell RNA sequencing (RNA-seq) and ATAC sequencing (ATAC-seq) analysis to profile the regulatory landscape of mouse corneal epithelium in early wound response.

Methods

We used our previously published single-cell data sets of homeostatic adult mouse corneal epithelium as the unwounded group. The wounded group data sets were obtained by sequencing the epithelium after an annular epithelial wound. Following the integration of the relevant data sets, the Seurat and ArchR packages were employed for single-cell RNA-seq and single-cell ATAC-seq data processing and downstream analysis, respectively. The Monocle 2 was used for pseudo-time analysis, CellChat for intercellular communication analysis, and pySCENIC for analyzing transcription factors. The expression of key genes was validated via immunofluorescence staining and quantitative real-time PCR.

Results

Our data show that the number of cell type-specific genes decreases and the number of common transcriptional responses increases in early wound response. Concurrently, we find that the chromatin accessibility landscape undergoes significant changes across all epithelial cell types and that the wound-induced open regions are similarly distributed across the genome. Motif enrichment analysis shows that Fosl1/AP-1 binding site is highly enriched among the opened regions. However, by assessing the correlation between changes in chromatin accessibility and gene expression, we observe that only a small subset of wound-induced genes shows a high correlation with the accessibility of nearby chromatin.

Conclusions

Our study provides a detailed single-cell landscape for transcriptomic and epigenetic changes in mouse corneal epithelium during early wound response, which improved our understanding of the mechanisms of wound healing.

Deficiency of ATF2 retards senescence induced by replication stress and pamidronate in mouse jaw bone marrow stem cells

The aging process is associated with a loss of bone mass and an accumulation of senescent cells, which is under epigenetic control. Morphological and molecular analysis revealed a notable reduction in bone mass and alveolar crest height in aged mice, accompanied by increased levels of senescent mouse jaw bone marrow stem cells (mJBMSCs). To investigate whether specific transcription factors are involved, assay for transposase-accessible chromatin with sequencing (ATAC-seq) was performed on mJBMSCs isolated from 2-, 4-, 8-, and 20-month-old mice. In 20-month-old mJBMSCs, increased chromatin accessibility was observed alongside elevated expression of activating transcription factor 2 (ATF2) in both cells and alveolar bone. Silencing Atf2 in mJBMSCs failed to reverse physiological aging, but delayed replication stress and pamidronate (PAM) induced senescence. The analysis of ATAC-seq and RNA sequencing indicated that the differentially expressed genes upregulated by PAM but downregulated by ATF2 deficiency were related to some key biological processes, including negative regulation of cell proliferation, inflammatory response, adipogenesis, and cellular senescence. The dual-luciferase assay was conducted to demonstrate that ATF2 enhances Cdkn2a transcription by binding to its promoter region. Our findings suggest significant chromatin alterations in aged mJBMSCs, positioning ATF2 as a potential target for combating externally induced senescence.

Granulosa cell expression of Fos is critical for regulating ovulatory gene expressions in the mouse ovary

A previous study showed that female Fos null mice fail to ovulate even when given gonadotropins, suggesting that ovarian expression of Fos is critical for successful ovulation. However, the expression of FOS and function of FOS have not been determined in the mouse ovary. FOS, a member of the Fos family (Fos, Fosb, Fosl1, and Fosl2), functions as a transcription factor by forming a heterodimer complex with a member of Jun family (Jun, Junb, and Jund). This study demonstrated rapid increases in Fos, along with other Fos and Jun family members, after hCG administration in the ovary of immature PMSG-primed mice and after the LH surge in naturally cycling animals. ChIP-seq analysis identified 1965 FOS-binding genes in granulosa cells collected at 3 h post-hCG, including Pgr, Ptgs2, Tnfiap6, and Edn2, genes known to be involved in the ovulatory process. When super-ovulation was induced, the number of oocytes released was significantly reduced in Esr2cre/+-driven granulosa cell-specific Fos knockout (gcFosKO) mice. This reduction was accompanied by lower expressions of Pgr, Ptgs2, Ptgs1, and Edn2 in preovulatory follicles of gcFosKO mice compared to those in control littermates. In addition, gcFosKO mice showed a trend toward a decreased average litter size. Together, the present study indicates that the preovulatory induction of Fos expression is crucial for increasing the expression of key ovulatory genes, yet the role of FOS may be partially substituted by other Fos and Jun family members induced in the preovulatory follicle in the gcFosKO mouse ovary.

c-Jun regulates postpartum β-cell apoptosis and survival downstream of prolactin signaling

Objective

Pregnancy and postpartum states drive dynamic expansion and regression of maternal β-cell mass. Little is known about what regulates postpartum regression. We recently profiled murine islets at different time points from late gestation to early postpartum to identify regulators of β-cell apoptosis or survival. One hit was c-Jun, a transcription factor which regulates proliferation, apoptosis, and survival in various tissues and cells. Here, we examine c-Jun regulation and function during gestation and postpartum and in murine and human islets.

Methods

To examine regulation of c-Jun within β-cells we used a mouse genetic model lacking β-cell prolactin receptor (PRLR) and stimulation of cultured islets with recombinant prolactin. We used chemical inhibitors of signal transduction pathways to examine signaling downstream of PRLR. TUNEL was used to detect endogenous or dexamethasone-induced apoptosis. Q-PCR, Western blotting, and immunostaining were used to assess gene and protein expression. Knockdown of c-Jun in MIN6 cells was accomplished using siRNA and lentiviral-shRNA. We examined both murine and human islets and tissues.

Results

We found that expression of c-Jun transcript in murine β-cells is temporally restricted to late gestation and early postpartum and requires prolactin signaling. Moreover, c-Jun protein expression was mutually exclusive with apoptotic β-cells identified by TUNEL staining. In both murine and human islets, prolactin treatment is sufficient to induce c-Jun expression and downstream MAPK/ERK signaling. Pharmacologic inhibition of c-Jun blocks prolactin-mediated survival of β-cells following pro-apoptotic stress, including failure to upregulate pro-survival factors Bcl2l1 (Bcl-xL) and Birc5 (Survivin). Finally, human islets during pregnancy also exhibit increased c-Jun expression in β-cells, but c-Jun induction is absent in β-cells from pregnant donors with gestational diabetes (GDM).

Conclusions

c-Jun contributes to pro-survival effects of lactogens downstream of PRLR / MAPK signaling in β-cells. c-Jun regulation is conserved in human islets and pregnancy and dysregulated in GDM.

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.

Effector T cells under hypoxia have an altered transcriptome similar to tumor-stressed T cells found in non-responsive melanoma patients

BACKGROUND

In the tumor microenvironment (TME), hypoxia stands as a significant factor that modulates immune responses, especially those driven by T cells. As T cell-based therapies often fail to work in solid tumors, this study aims to investigate the effects of hypoxia on T cell topo-distribution in the TME, gene expression association with T cell states, and clinical responses in melanoma.

METHODS

To generate detailed information on tumor oxygenation and T cell accessibility, we used mathematical modeling of human melanoma tissue microarrays that incorporate oxygen supply from vessels, intratumoral diffusion, and cellular uptake. We created tumor maps and derived plots showing the fraction of CD4 and CD8 T cells against the distance to the nearest vessel and oxygen pressure. To assess their function and transcriptional changes caused by hypoxia, effector T cells were generated and cultured under hypoxia (0.5% oxygen) or normoxia (21% oxygen). The T cell hypoxia-transcriptional signature was compared against datasets from msigDB, iATLAS (clinical trials of melanoma patients treated with immune checkpoint inhibitors (ICIs)), ORIEN AVATAR (real-world melanoma patients treated with ICIs), and a single-cell atlas of tumor-infiltrating lymphocytes.

RESULTS

We made three specific observations: (1) in melanoma T cells preferentially accumulated in oxygenated areas close to blood vessels (50-100 µm from the vasculature in the regions of high oxygen availability) but not in hypoxic areas far from blood vessels. (2) Our analysis confirmed that under hypoxia, T cell functions were significantly reduced compared with normoxic conditions and accompanied by a unique gene signature. Furthermore, this hypoxic gene signature was prevalent in resting and non-activated T cells. Notably and clinically relevant, the hypoxic T cell gene set was found to correlate with reduced overall survival and reduced progression-free survival in melanoma patients, which was more pronounced in non-responder patients undergoing ICI therapy. (3) Finally, compared with a single-cell atlas of tumor-infiltrating T cells, our hypoxia signature aligned with a population of cells at a state termed stress response state (TSTR).

CONCLUSIONS

Our study highlights the critical role of hypoxia in shaping T cell distribution and its correlation with clinical outcomes in melanoma. We revealed a preferential accumulation of T cells in oxygenated areas. Moreover, hypoxic T cells develop a distinct hypoxic gene signature prevalent in resting, non-activated T cells and TSTR that was also associated with poorer outcomes, particularly pronounced among non-responders to ICIs.

Comparative single-cell multiome identifies evolutionary changes in neural progenitor cells during primate brain development

Understanding the cellular and genetic mechanisms driving human-specific features of cortical development remains a challenge. We generated a cell-type resolved atlas of transcriptome and chromatin accessibility in the developing macaque and mouse prefrontal cortex (PFC). Comparing with published human data, our findings demonstrate that although the cortex cellular composition is overall conserved across species, progenitor cells show significant evolutionary divergence in cellular properties. Specifically, human neural progenitors exhibit extensive transcriptional rewiring in growth factor and extracellular matrix (ECM) pathways. Expression of the human-specific progenitor marker ITGA2 in the fetal mouse cortex increases the progenitor proliferation and the proportion of upper-layer neurons. These transcriptional divergences are primarily driven by altered activity in the distal regulatory elements. The chromatin regions with human-gained accessibility are enriched with human-specific sequence changes and polymorphisms linked to intelligence and neuropsychiatric disorders. Our results identify evolutionary changes in neural progenitors and putative gene regulatory mechanisms shaping primate brain evolution.

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.

Cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6i): Mechanisms of resistance and where to find them

CDK4/6 inhibitors (CDK4/6i) have significantly impacted on the treatment of HR + HER2 negative (HER2-) metastatic breast cancer (BC) when combined with endocrine therapy. Nonetheless, despite significant research efforts, the mechanisms of de novo and acquired resistance to CDK4/6i have not yet been fully elucidated, highlighting the need for a deeper understanding of these process. Additionally, the importance of dissecting CDK4/6i resistance from endocrine resistance for personalized treatment is increasingly recognized. Liquid biopsy has emerged as a minimally invasive tool for identifying circulating biomarkers of resistance through the integration of multiparametric and dynamic assessments that encompass ctDNA, CTCs, exosomes, and epigenetic ctDNA alterations, representing a promising perspective for the clinical characterization of treatment resistance and guiding post-progression strategies to improve patient outcomes. Aim of this review is summarize potential mechanisms of CDK4/6i resistance, along with the advantages of using liquid biopsy to identify resistance biomarkers in HR+/HER2- MBC patients treated with CDK 4/6 inhibitors.

Nuclear Import Defects Drive Cell Cycle Dysregulation in Neurodegeneration

Neurodegenerative diseases (NDDs) and other age-related disorders have been classically defined by a set of key pathological hallmarks. Two of these hallmarks, cell cycle dysregulation (CCD) and nucleocytoplasmic transport (NCT) defects, have long been debated as being either causal or consequential in the pathology of accelerated aging. Specifically, aberrant cell cycle activation in post-mitotic neurons has been shown to trigger neuronal cell death pathways and cellular senescence. Additionally, NCT has been observed to be progressively dysregulated during aging and in neurodegeneration, where the increased subcellular redistribution of nuclear proteins such as TAR DNA-Binding Protein-43 (TDP43) to the cytoplasm is a primary driver of many NDDs. However, the functional significance of NCT defects as either a primary driver or consequence of pathology, and how the redistribution of cell cycle machinery contributes to neurodegeneration, remains unclear. Here, we describe that pharmacological inhibition of importin-β nuclear import is capable of perturbing cell cycle machinery both in mitotic neuronal cell lines and post-mitotic primary neurons in vitro. Our Nemf R86S mouse model of motor neuron disease, characterized by nuclear import defects, further recapitulates the hallmarks of CCD in mitotic cell lines and in post-mitotic primary neurons in vitro, and in spinal motor neurons in vivo. The observed CCD is consistent with the transcriptional and phenotypical dysregulation observed in neuronal cell death and cellular senescence in NDDs. Together, this evidence suggests that impairment of nuclear import pathways resulting in CCD may be a common driver of pathology in neurodegeneration.

Advances in the relationship between AP-1 and tumorigenesis, development and therapy resistance

Activating protein 1 (AP-1) is a transcription factor composed of several protein families, Jun proteins and Fos proteins are the components of AP-1. AP-1 is involved in various cellular processes, such as proliferation, differentiation, apoptosis and inflammation. For tumor cells, AP-1 is considered to be a driver whose activity is associated with dysfunction and the onset, development, invasion, and migration of cancer. In addition, AP-1 has been reported to be involved in the drug resistance and radiation resistance of tumor cells during the treatment process. Therefore, AP-1 is a potential target for cancer therapy. At present, a number of inhibitors targeting AP-1 have been developed and have shown certain anti-cancer effects. However, due to the complex structure and function of AP-1, different structures of AP-1 show different effects in different tumor cells, and more studies are needed to reveal its mechanism of action. This article introduces the relationship between AP-1 and tumor development, summarize the current studies and developments of AP-1 related drugs, and provide the future development values of AP-1.

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.

A KSHV RNA-binding protein promotes FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation

Kaposi's sarcoma-associated herpesvirus (KSHV) encodes an RNA-binding protein ORF57 in lytic infection. Using an optimized CLIP-seq in this report, we identified ORF57-bound transcripts from 544 host protein-coding genes. By comparing with the RNA-seq profiles from BCBL-1 cells with latent and lytic KSHV infection and from HEK293T cells with and without ORF57 expression, we identified FOS RNA as one of the major ORF57-specific RNA targets. FOS dimerizes with JUN as a transcription factor AP-1 involved in cell proliferation, differentiation, and transformation. Knockout of the ORF57 gene from the KSHV genome led BAC16-iSLK cells incapable of FOS expression in KSHV lytic infection. The dysfunctional KSHV genome in FOS expression could be rescued by Lenti-ORF57 virus infection. ORF57 protein does not regulate FOS translation but binds to the 13-nt RNA motif near the FOS RNA 5' end and prolongs FOS mRNA half-life 7.7 times longer than it is in the absence of ORF57. This binding of ORF57 to FOS RNA is likely competitive to the binding of host nuclease AEN (ISG20L1) of which physiological RNase activity remains unknown. KSHV infection inhibits the expression of AEN, but not exosomal RNA helicase MTR4. FOS expression mediated by ORF57 inhibits AEN transcription through FOS binding to AEN promoter but transactivates RGS2, a regulator of G-protein-coupled receptors. FOS binds a conserved AP-1 site in the RGS2 promoter and enhances RGS2 expression to phosphorylate AKT. Altogether, we have discovered that KSHV ORF57 specifically binds and stabilizes FOS RNA to increase FOS expression, thereby disturbing host gene expression and inducing pathogenesis during KSHV lytic infection.IMPORTANCEWe discovered that FOS, a heterodimer component of oncogenic transcription factor AP-1, is highly elevated in KSHV-infected cells by expression of a viral lytic RNA-binding protein, ORF57, which binds a 13-nt RNA motif near the FOS RNA 5' end to prolong FOS RNA half-life. This binding of ORF57 to FOS RNA is competitive to the binding of host RNA destabilizer(s). KSHV infection inhibits expression of host nuclease AEN, but not MTR4. FOS inhibits AEN transcription by binding to the AEN promoter but transactivates RGS2 by binding to a conserved AP-1 site in the RGS2 promoter, thereby enhancing RGS2 expression and phosphorylation of AKT. Thus, KSHV lytic infection controls the expression of a subset of genes for signaling, cell cycle progression, and proliferation to potentially contribute to viral oncogenesis.

Transcriptomic Insights into Post-Spawning Death and Muscle Atrophy in Ayu (Plecoglossus altivelis)

In semelparous species like the ayu (Plecoglossus altivelis), spawning is followed by rapid physiological decline and death; yet, the underlying molecular mechanisms remain largely unexplored. This study examines transcriptomic changes in ayu skeletal muscle before and after spawning, with a focus on key genes and pathways contributing to muscle atrophy and metabolic dysfunction. Through RNA sequencing and DEG analysis, we identified over 3000 DEGs, and GSEA and KEGG pathway analysis revealed significant downregulation of energy metabolism and protein degradation. In post-spawning ayu, a rapid decrease in body weight was observed, accompanied by a decline in the expression of myosin heavy chain genes, which are major muscle protein genes, and gene expression changes indicative of muscle atrophy. Decreased expression of AP-1 transcription factors associated with muscle development and aging was also evident. PPI network analysis identified carbohydrate catabolism protein gapdh may be the key factor that led to muscle atrophy and accelerated aging in ayu. Our study revealed that after spawning, the ayu muscle tissue undergoes strong metabolic disorders and cellular stress responses, providing special insights into the mechanisms through the post-spawning death of ayu.

Multi-omics analysis reveals distinct gene regulatory mechanisms between primary and organoid-derived human hepatocytes

Hepatic organoid cultures are a powerful model to study liver development and diseases in vitro. However, hepatocyte-like cells differentiated from these organoids remain immature compared to primary human hepatocytes (PHHs), which are the benchmark in the field. Here, we applied integrative single-cell transcriptome and chromatin accessibility analysis to reveal gene regulatory mechanisms underlying these differences. We found that, in mature human hepatocytes, activator protein 1 (AP-1) factors co-occupy regulatory regions with hepatocyte-specific transcription factors, including HNF4A, suggesting their potential cooperation in governing hepatic gene expression. Comparative analysis identified distinct transcription factor sets that are specifically active in either PHHs or intrahepatic cholangiocyte organoid (ICO)-derived human hepatocytes. ELF3 was one of the factors uniquely expressed in ICO-derived hepatocytes, and its expression negatively correlated with hepatic marker gene expression. Functional analysis further revealed that ELF3 depletion increased the expression of key hepatic markers in ICO-derived hepatocytes. Our integrative analysis provides insights into the transcriptional regulatory networks of PHHs and hepatic organoids, thereby informing future strategies for developing improved hepatic models.

Effects of lysine and methionine on mRNA expression of candidate transcription factors by primary bovine mammary epithelial cells

It has been established that essential amino acids (EAA) regulate protein synthesis in mammary epithelial cells by rapidly altering the phosphorylation state of translation factors. However, the long-term transcriptional response to EAA supply has been investigated much less. Eight transcription factors were selected as candidate mediators of EAA effects on mammary cell function via the amino acid response (ATF4, ATF6), mitogen-activated protein kinase (JUN, FOS, EGR1), and mechanistic target of rapamycin complex 1 (MYC, HIF1A, SREBF1). The objective was to determine if and when expression of these candidate genes was affected in primary cultures of bovine mammary epithelial cells more than 24 h after imposing an EAA deficiency, and to evaluate effects of EAA deficiency on protein synthesis, endoplasmic reticulum size, cell proliferation, and lipogenesis. Differentiated cells were cultured in 1 of 3 treatment media representing normal physiological concentrations of all amino acids (CTL), low lysine (LK), or low methionine (LM) for 24, 40, 48, or 60 h. Both LK and LM suppressed protein synthesis and activated ATF4 expression, indicating the classic amino acid response pathway had been triggered. However, there was no effect of LK or LM on endoplasmic reticulum size, possibly related to elevated ATF6 expression on LM. Expression of early response genes JUN, FOS, EGR1 and MYC was not elevated by EAA deficiency but LM decreased EGR1 expression. LM also increased expression of HIF1A. The EGR1 and HIF1A expression results are consistent with the decrease in cell proliferation rate observed. Variable responses in SREBF1 expression to LK and LM at different timepoints may have contributed to a lack of effect on lipogenesis rates. These findings indicate that EAA deficiency may inhibit mammary protein synthesis and cell proliferation through transcription factors.

Collagen signaling and matrix stiffness regulate multipotency in glandular epithelial stem cells in mice

Glandular epithelia, including mammary gland (MG) and prostate, are composed of luminal and basal cells. During embryonic development, glandular epithelia arise from multipotent stem cells (SCs) that are replaced after birth by unipotent basal and unipotent luminal SCs. Different conditions, such as basal cell transplantation, luminal cell ablation, and oncogene expression can reinduce adult basal SC (BaSCs) multipotency in different glandular epithelia. The mechanisms regulating the reactivation of multipotency are incompletely understood. Here, we have found that Collagen I expression is commonly upregulated in BaSCs across the different multipotent conditions. Increasing collagen concentration or stiffness of the extracellular matrix (ECM) promotes BaSC multipotency in MG and prostate organoids. Single cell RNA-seq of MG organoids in stiff conditions have uncovered the importance of β1 integrin/FAK/AP-1 axis in the regulation of BaSC multipotency. Altogether our study uncovers the key role of Collagen signaling and ECM stiffness in the regulation of multipotency in glandular epithelia.

Network Pharmacology Combined with Bioinformatics Analysis to Texplore the Potential Mechanism of Phellodendri Chinensis Cortex Against Bladder Cancer

The pharmacological mechanism of Phellodendri Chinensis cortex (PCC) against diseases, especially bladder cancer (BC), has never been reported systematically. This study was designed to explore potential mechanism of PCC in treatment of BC. First, we used network pharmacology to discover the potential mechanism of Phellodendri Chinensis cortex and phellodendrine against bladder cancer. Then, we used bioinformatics analysis to verify the correlation between gene expression analysis, survival analysis and common targets. Finally, molecular docking was used to calculate the binding energies of phellodendrine and common targets.A total of 264 targets for PCC were predicted, and 391 BC-related targets were obtained from 4 databases. There were 54 potential targets, 315 biological processes, and 120 signaling pathways involved for PCC against BC. The CDKN2A expression increased and the ESR1, JUN, IL6, AR, and PTGS2 levels decreased in BC according to Gene Expression Profiling Interactive Analysis version 2. The high expression of JUN, MYC, EGFR, and EGF and low expression of VEGFA and PPARG were associated with short overall survival (OS). The high expression of AKT1, EGFR, and EGF and low expression of IL1β were associated with poor disease-free survival (DFS). The search of the intersection of phellodendrine and BC targets yielded 11 common targets, 50 biological processes, and 13 signaling pathways involved. High AURKA and FASN and low ESR1, JUN, ABCB1, and PTGS1 were expressed in BC. The high expression of FASN, ABCC1, PTGS1, JUN, and PIK3CA was associated with short OS, the high expression of PIK3CA and ABCC1 was associated with poor DFS prognosis. Phellodendrine showed a better binding affinity for PTGS2 protein with a docking score of -7.183 and a MM-GBSA result of -46.47 kcal/mol. This study revealed potential mechanism of PCC and phellodendrine against BC through network pharmacology and bioinformatics.

FRA1 controls acinar cell plasticity during murine KrasG12D-induced pancreatic acinar to ductal metaplasia

Acinar cells have been proposed as a cell-of-origin for pancreatic ductal adenocarcinoma (PDAC) after undergoing acinar-to-ductal metaplasia (ADM). ADM can be triggered by pancreatitis, causing acinar cells to de-differentiate to a ductal-like state. We identify FRA1 (gene name Fosl1) as the most active transcription factor during KrasG12D acute pancreatitis-mediated injury, and we have elucidated a functional role of FRA1 by generating an acinar-specific Fosl1 knockout mouse expressing KrasG12D. Using a gene regulatory network and pseudotime trajectory inferred from single-nuclei ATAC-seq and bulk RNA sequencing (RNA-seq), we hypothesized a regulatory model of the acinar-ADM-pancreatic intraepithelial neoplasia (PanIN) continuum and experimentally validated that Fosl1 knockout mice are delayed in the onset of ADM and neoplastic transformation. Our study also identifies that pro-inflammatory cytokines, such as granulocyte colony stimulating factor (G-CSF), can regulate FRA1 activity to modulate ADM. Our findings identify that FRA1 is a mediator of acinar cell plasticity and is critical for acinar cell de-differentiation and transformation.

Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation

Aberrant DNA methylation contributes to gene expression deregulation in cancer. However, these alterations' precise regulatory role and clinical implications are still not fully understood. In this study, we performed expression-methylation Quantitative Trait Loci (emQTL) analysis to identify deregulated cancer-driving transcriptional networks linked to CpG demethylation pan-cancer. By analyzing 33 cancer types from The Cancer Genome Atlas, we identified and confirmed significant correlations between CpG methylation and gene expression (emQTL) in cis and trans, both across and within cancer types. Bipartite network analysis of the emQTL revealed groups of CpGs and genes related to important biological processes involved in carcinogenesis including proliferation, metabolism and hormone-signaling. These bipartite communities were characterized by loss of enhancer methylation in specific transcription factor binding regions (TFBRs) and the CpGs were topologically linked to upregulated genes through chromatin loops. Penalized Cox regression analysis showed a significant prognostic impact of the pan-cancer emQTL in many cancer types. Taken together, our integrative pan-cancer analysis reveals a common architecture where hallmark cancer-driving functions are affected by the loss of enhancer methylation and may be epigenetically regulated.

A spatiotemporal molecular atlas of mouse spinal cord injury identifies a distinct astrocyte subpopulation and therapeutic potential of IGFBP2

Spinal cord injury (SCI) triggers a cascade of intricate molecular and cellular changes that determine the outcome. In this study, we resolve the spatiotemporal organization of the injured mouse spinal cord and quantitatively assess in situ cell-cell communication following SCI. By analyzing existing single-cell RNA sequencing datasets alongside our spatial data, we delineate a subpopulation of Igfbp2-expressing astrocytes that migrate from the white matter (WM) to gray matter (GM) and become reactive upon SCI, termed Astro-GMii. Further, Igfbp2 upregulation promotes astrocyte migration, proliferation, and reactivity, and the secreted IGFBP2 protein fosters neurite outgrowth. Finally, we show that IGFBP2 significantly reduces neuronal loss and remarkably improves the functional recovery in a mouse model of SCI in vivo. Together, this study not only provides a comprehensive molecular atlas of SCI but also exemplifies how this rich resource can be applied to endow cells and genes with functional insight and therapeutic potential.

EF24, a Curcumin Analog, Reverses Interleukin-18-Induced miR-30a or miR-342-Dependent TRAF3IP2 Expression, RECK Suppression, and the Proinflammatory Phenotype of Human Aortic Smooth Muscle Cells

Curcumin, a polyphenolic compound derived from the widely used spice Curcuma longa, has shown anti-atherosclerotic effects in animal models and cultured vascular cells. Inflammation is a major contributor to atherosclerosis development and progression. We previously reported that the induction of the proinflammatory molecule TRAF3IP2 (TRAF3 Interacting Protein 2) or inhibition of the matrix metallopeptidase (MMP) regulator RECK (REversion Inducing Cysteine Rich Protein with Kazal Motifs) contributes to pro-oxidant, proinflammatory, pro-mitogenic and pro-migratory effects in response to external stimuli in vascular smooth muscle cells. Here we hypothesized that EF24, a curcumin analog with a better bioavailability and bioactivity profile, reverses interleukin (IL)-18-induced TRAF3IP2 induction, RECK suppression and the proinflammatory phenotype of primary human aortic smooth muscle cells (ASMC). The exposure of ASMC to functionally active recombinant human IL-18 (10 ng/mL) upregulated TRAF3IP2 mRNA and protein expression, but markedly suppressed RECK in a time-dependent manner. Further investigations revealed that IL-18 inhibited both miR-30a and miR-342 in a p38 MAPK- and JNK-dependent manner, and while miR-30a mimic blunted IL-18-induced TRAF3IP2 expression, miR-342 mimic restored RECK expression. Further, IL-18 induced ASMC migration, proliferation and proinflammatory phenotype switching, and these effects were attenuated by TRAF3IP2 silencing, and the forced expression of RECK or EF24. Together, these results suggest that the curcumin analog EF24, either alone or as an adjunctive therapy, has the potential to delay the development and progression of atherosclerosis and other vascular inflammatory and proliferative diseases by differentially regulating TRAF3IP2 and RECK expression in ASMC.

Anisodamine (654-1/654-2) ameliorates septic kidney injury in rats by inhibiting inflammation and apoptosis

Introduction

To investigate the protective effects of anisodamine (654-1/654-2) against acute kidney injury (AKI) in LPS-induced septic shock rats and explore its molecular mechanisms.

Methods

56 rats were randomly divided into 8 groups: control, LPS, LPS + 654-1, and LPS + 654-2 (1.25, 2.5 and 5 mg/kg). The model was evaluated by monitoring MAP, HR, and plasma LD levels. ELISA and biochemical assay kits were used to measure the levels of inflammatory cytokines (IL-1β, IL-6, and TNF-α) and kidney injury markers (BUN and CRE). Additionally, RNA-seq and bioinformatic analysis were performed to explore the mechanism of action of 654-1/654-2, and verification was conducted by western blotting and RT-PCR.

Results

654-1/654-2 significantly restored the levels of MAP, HR, and plasma LD in septic shock rats. Furthermore, 654-1/654-2 (5 mg/kg) effectively ameliorated LPS-induced kidney structural damage and exhibited a dose-dependent reduction in levels of inflammatory cytokines and kidney injury markers. In addition, RNA-seq, WB, and RT-PCR analyses revealed that 654-1/654-2 exerted its effects by inhibiting the expressions of the NF-κB and MAPK pathways and activating the Pi3K/Akt/Bcl-2 signaling pathway, thereby mitigating AKI.

Discussion

This study suggested that 654-1/654-2 could alleviate AKI in septic shock rats by improving inflammation invasion and cell apoptosis. Notably, 654-1/654-2 collectively suppressed inflammation response through the p38/JNK/AP-1/NF-κB pathway. Additionally, 654-1 promotes survival signaling via the Pi3K/Akt/Bcl-2 pathway, whereas 654-2 reduces apoptosis through the P53/Bax pathway. These findings provided a theoretical basis for the clinical application of 654-1/654-2 in treating organ damage caused by septic shock.

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.

Nutrient starvation activates ECM remodeling gene enhancers associated with inflammatory bowel disease risk in fibroblasts

Nutrient deprivation induces a reversible cell cycle arrest state termed quiescence, which often accompanies transcriptional silencing and chromatin compaction. Paradoxically, nutrient deprivation is associated with activated fibroblast states in pathological microenvironments in which fibroblasts drive extracellular matrix (ECM) remodeling to alter tissue environments. The relationship between nutrient deprivation and fibroblast activation remains unclear. Here, we report that serum deprivation extensively activates transcription of ECM remodeling genes in cultured fibroblasts, despite the induction of quiescence. Starvation-induced transcriptional activation accompanied large-scale histone acetylation of putative distal enhancers, but not promoters. The starvation-activated putative enhancers were enriched for non-coding genetic risk variants associated with inflammatory bowel disease (IBD), suggesting that the starvation-activated gene regulatory network may contribute to fibroblast activation in IBD. Indeed, the starvation-activated gene PLAU, encoding uPA serine protease for plasminogen and ECM, was upregulated in inflammatory fibroblasts in the intestines of IBD patients. Furthermore, the starvation-activated putative enhancer at PLAU, which harbors an IBD risk variant, gained chromatin accessibility in IBD patient fibroblasts. This study implicates nutrient deprivation in transcriptional activation of ECM remodeling genes in fibroblasts and suggests nutrient deprivation as a potential mechanism for pathological fibroblast activation in IBD.

Comparison of Proliferating Cell Nuclear Antigen (PCNA) Expression among Nasal Polyp and Chronic Rhinosinusitis

BACKGROUND AND OBJECTIVE

Chronic rhinosinusitis is a common inflammatory disorder in sinonasal mucosa that could be developed with or without nasal polyps. Cellular proliferation is suggested as a possible mechanism of nasal polyp development. However, conducted studies in this context are limited. So, the present study's aim is the comparison of proliferating cell nuclear antigen (PCNA) expression in nasal polyps and chronic rhinosinusitis.

MATERIALS AND METHODS

In this cross-sectional study, 70 nasal polyp and 60 chronic rhinosinusitis samples from patients referred to Mostafa Khomeini Hospital, Tehran from 2017 to 2022 were immunohistochemically stained by PCNA marker. The percentage of PCNA nuclear expression was determined in two groups and its association with the type of pathological lesion and the patient's age and sex was analyzed by SPSS statistic software version 24 statistical software (IBM Statistics, USA).

RESULTS

The mean percentage expression of PCNA in nasal polyp and chronic rhinosinusitis samples was 16.55 ± 13.66 and 17.58 ± 12.68 respectively (ranging from 0 to 57 in both groups) however, there was no significant statistical difference between the two groups (p = 0.479). No relationship was found between PCNA expression with age and sex in none of the chronic rhinosinusitis and nasal polyp groups.

CONCLUSION

Proliferative activity of the nasal epithelial cell is similar in chronic rhinosinusitis with and without nasal polyps and it is considered that the increase of epithelial cell proliferative activity probably has no role in nasal polyp development in patients with chronic rhinosinusitis.

Verbascoside: comprehensive review of a phenylethanoid macromolecule and its journey from nature to bench

Polyphenolic compounds are among the most widely researched compounds for various therapeutic applications. However, naturally occurring phenylethanoid glycosides are least explored under this class of compounds. One such phenylethanoid glycoside, verbascoside (Vb), abundantly found among 200 species of 23 families, has gained recent attention due to its wide-spectrum therapeutic properties such as antioxidant, antimicrobial, anti-inflammatory, neuroprotective, cardioprotective, skin-protective, and anti-cancer. Despite having multiple therapeutic benefits, due to its large size, the compound has poor bioavailability for oral and topical applications. To meet these limitations, current research on Vb focuses on delivering it through nanoformulations. Presently, most developed formulations are liposome based for various applications, such as corneal epithelial wound healing, anti-neuropathic, anti-wrinkle, anti-hyperalgesia, atopic dermatitis, alopecia, and cutaneous wound healing. Multiple studies have confirmed the least acute and sub-acute toxicity for Vb. Few clinical studies have been performed for the therapeutic application of Vb to manage COVID-19, nephropathy, platelet aggregation, chronic primary glomerulonephritis, and acute hepatitis. Recent studies have shown the immense therapeutic potential of Vb in wound healing, dermatitis, neuroprotection, and anti-cancer activities, which creates a need for developing novel formulations for their respective uses. Long-term toxicity studies and techniques for scaling up Vb production by biotechnological approaches should be emphasized.

Ferroptosis-Related Genes in IgA Nephropathy: Screening for Potential Targets of the Mechanism

Aims: Exploring key genes and potential molecular pathways of ferroptosis in immunoglobulin A nephropathy (IgAN). Methods: The IgAN datasets and ferroptosis-related genes (FRGs) were obtained in the Gene Expression Omnibus (GEO) and FerrDb database. Differentially expressed genes (DEGs) were identified using R software and intersected with FRGs to obtain differentially expressed FRGs (DE-FRGs). After that, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis (PEA) and Gene Ontology (GO) functional annotation were performed on DE-FRGs. In the Search Tool for the Retrieval of Interacting Genes (STRING) website, we construct a protein-protein interaction (PPI) network. The PPI network was further investigated with screening hub genes with Cytoscape software. The core genes were then subjected to gene set enrichment analysis (GSEA). Finally, the samples were analyzed for immune infiltration in R, and the correlation between hub genes and immune cells was analyzed. Results: A total of 347 DEGs were identified. CD44, CDO1, CYBB, IL1B, RRM2, AKR1C1, activated transcription factor-3 (ATF3), CDKN1A, GDF15, JUN, MGST1, MIOX, MT1G, NR4A1, PDK4, TNFAIP3, and ZFP36 were determined as DE-FRGs. JUN, IL1B, and ATF3 were then screened as hub genes. GSEA and immune infiltration analysis revealed that the hub genes were closely associated with immune inflammatory responses such as NOD-like receptor signaling, IL-17 signaling, and TNF signaling. Conclusions: Our results show that JUN and ATF3 are possibly critical genes in the process of IgAN ferroptosis and may be related with immune cell infiltration.

EWS-FLI1 and Activator Protein-1 (AP-1) Reciprocally Regulate Extracellular-Matrix Proteins in Ewing sarcoma Cells

Ribonucleotide reductase (RNR) is the rate-limiting enzyme in the synthesis of deoxyribonucleotides and the target of multiple chemotherapy drugs, including gemcitabine. We previously identified that inhibition of RNR in Ewing sarcoma tumors upregulates the expression levels of multiple members of the activator protein-1 (AP-1) transcription factor family, including c-Jun and c-Fos, and downregulates the expression of c-Myc. However, the broader functions and downstream targets of AP-1, which are highly context- and cell-dependent, are unknown in Ewing sarcoma tumors. Consequently, in this work, we used genetically defined models, transcriptome profiling, and gene-set -enrichment analysis to identify that AP-1 and EWS-FLI1, the driver oncogene in most Ewing sarcoma tumors, reciprocally regulate the expression of multiple extracellular-matrix proteins, including fibronectins, integrins, and collagens. AP-1 expression in Ewing sarcoma cells also drives, concurrent with these perturbations in gene and protein expression, changes in cell morphology and phenotype. We also identified that EWS-FLI1 dysregulates the expression of multiple AP-1 proteins, aligning with previous reports demonstrating genetic and physical interactions between EWS-FLI1 and AP-1. Overall, these results provide novel insights into the distinct, EWS-FLI1-dependent features of Ewing sarcoma tumors and identify a novel, reciprocal regulation of extracellular-matrix components by EWS-FLI1 and AP-1.

Molecular dynamics simulation in tissue engineering

Introduction

In tissue engineering, the interaction among three primary elements, namely cells, material scaffolds, and stimuli, plays a pivotal role in determining the fate of cells and the formation of new tissue. Understanding the characteristics of these components and their interplay through various methodologies can significantly enhance the efficiency of the designed tissue engineering system. In silico methods, such as molecular dynamics (MD) simulation, use mathematical calculations to investigate molecular properties and can overcome the limitations of laboratory methods in delivering adequate molecular-level information.

Methods

The studies that used molecular dynamics simulation, either alone or in combination with other techniques, have been reviewed in this paper.

Results

The review explores the use of molecular dynamics simulations in studying substrate formation mechanism and its optimization. It highlights MD simulations' role in predicting biomolecule binding strength, understanding substrate properties' impact on biological activity, and factors influencing cell attachment and proliferation. Despite limited studies, MD simulations are considered a reliable tool for identifying ideal substrates for cell proliferation. The review also touches on MD simulations' contribution to cell differentiation studies, emphasizing their role in designing engineered extracellular matrix for desired cell fates.

Conclusion

Molecular dynamics simulation as a non-laboratory tool has many capabilities in providing basic and practical information about the behavior of the molecular components of the cell as well as the interaction of the cell and its components with the surrounding environment. Using this information along with other information obtained from laboratory tools can ultimately lead to the advancement of tissue engineering through the development of more appropriate and efficient methods.

METTL3 restricts RIPK1-dependent cell death via the ATF3-cFLIP axis in the intestinal epithelium

Intestinal epithelial cells (IECs) are pivotal for maintaining intestinal homeostasis through self-renewal, proliferation, differentiation, and regulated cell death. While apoptosis and necroptosis are recognized as distinct pathways, their intricate interplay remains elusive. In this study, we report that Mettl3-mediated m6A modification maintains intestinal homeostasis by impeding epithelial cell death. Mettl3 knockout induces both apoptosis and necroptosis in IECs. Targeting different modes of cell death with specific inhibitors unveils that RIPK1 kinase activity is critical for the cell death triggered by Mettl3 knockout. Mechanistically, this occurs via the m6A-mediated transcriptional regulation of Atf3, a transcription factor that directly binds to Cflar, the gene encoding the anti-cell death protein cFLIP. cFLIP inhibits RIPK1 activity, thereby suppressing downstream apoptotic and necroptotic signaling. Together, these findings delineate the essential role of the METTL3-ATF3-cFLIP axis in homeostatic regulation of the intestinal epithelium by blocking RIPK1 activity.