To maintain genome stability, the coordinated actions of multiple proteins and protein complexes, which are collectively known as genome guardians, are required. In prokaryotes, one such 20-member genome guardian family known as the single-stranded DNA binding protein (SSB) interactome exists. Proteins within this essential family contain oligonucleotide/oligosaccharide-binding folds (OB-fold). These structurally conserved OB-folds bind to the intrinsically disordered linkers characteristic of SSB protein C-termini, resulting in partner regulation. The mechanism of binding employed is similar to that utilized by Src homology 3 domain (SH3) proteins in eukaryotes. Binding requires the interaction of conserved PXXP motifs in the SSB linker with the OB-fold in the partner. A second region of SSB C-termini, an 8–10 stretch of predominantly acidic amino acids functions to maintain the linker domain in a biologically active conformation, while simultaneously preventing it from adhering to the OB-folds of the SSB tetramer from which it emanates. In addition, this acidic domain also functions as a secondary binding site docking with a distal site in the partner, stabilizing the linker/OB-fold interactions. The interaction of an SSB with its partner proteins is genus-specific and results in the loading of partners onto the genome at various stages of the cell cycle thereby maintaining genome stability.
Mesenchymal stem cells (MSCs) are widely utilized in tissue repair, anti-inflammatory treatment, and cell therapy due to their remarkable multidirectional differentiation potential, immunosuppressive capabilities, and low immunogenicity. However, the regulatory mechanisms underlying their functions are intricate, and epigenetic modifications are a significant contributing factor. N6-methyladenosine (m6A) modification affects the proliferation, differentiation, and immunomodulation of MSCs by regulating the stability, transport, and translation of RNA. Studies have shown that m6A modification promotes osteogenic differentiation through the bone morphogehetic protein/small mothers against decapentaplegic (BMP/Smad) and wingless-related integration site/β-catenin (Wnt/β-catenin) pathways. It also enhances the anti-inflammatory effect of MSCs by modulating immune cell polarization and the release of inflammatory mediators. Moreover, exosomes secreted by MSCs contribute to immunomodulation and the response to cancer treatment by regulating the m6A modification of genes in target cells. “Writers” of m6A, such as methyltransferase-like 3 (METTL3) and METTL14, and “erasers”, such as fat mass and obesity-associated protein (FTO) and alkB homolog 5 (ALKBH5), are crucial in regulating the functions of MSCs. Targeting m6A modification via the clinical application of MSCs may represent a new cancer treatment strategy. Therefore, a comprehensive investigation of the m6A regulatory mechanism is essential. This review provides theoretical and technical support for the clinical use of MSCs, facilitating the development of more effective therapeutic strategies.
The tumor microenvironment (TME) plays a fundamental role in tumor progression. Cancer cells interact with their surroundings to establish a supportive niche through structural changes and paracrine signaling. Cells around transformed tumor cells contribute to cancer development, while infiltrating immune cells in this aggressive TME often become exhausted. Solid tumors, especially the most invasive types such as pancreatic ductal adenocarcinoma, are notably stiff mechanically, with cross-linking enzymes significantly affecting the survival of cancer cells in both primary tumors and metastatic sites. In this review, we highlight recent key contributions to the field, focusing on single-cell sequencing of stromal cells, which are increasingly seen as highly heterogeneous yet classifiable into distinct subtypes. These new insights enable the development of effective co-treatment approaches that could significantly enhance current and novel therapies against the most aggressive cancers.
The oxidation of lipids, notably of polyunsaturated fatty acids (PUFAs), under oxidative stress is a self-catalyzed chain reaction that generates reactive aldehydes, among which 4-hydroxynonenal (4-HNE) is considered to act as a second messenger of free radicals. The pleiotropic effects of 4-HNE, which include the regulation of cellular antioxidant capacities, proliferation, differentiation, and apoptosis, are concentration-dependent as they depend on cell type. Therefore, 4-HNE has important roles in various pathophysiological processes and the pathogenesis of acute and chronic diseases, especially degenerative and malignant diseases. Before 4-HNE was recognized as a signaling molecule, it was known to be the cytotoxic mediator of oxidative stress, acting even if lipid peroxidation was not present, because it remains bound to proteins, changing their structure and function. Research in this field has revealed several novel modes of activities of 4-HNE associated with cell death, including not only apoptosis/programmed cell death and necrosis but also ferroptosis, autophagy, pyroptosis, necroptosis, parthanatos, oxeiptosis and cuproptosis. This review shortly summarizes these findings, aiming to encourage further research in the field that might open new ways to use 4-HNE as the bioactive factor for targeted cell death, in particular cancer cells.
Cancer continues to be a significant global health issue, influenced by genetic mutations and external factors like carcinogenic exposure, lifestyle choices, and chronic inflammation. The myelocytomatosis (MYC) oncogene family, including c-MYC, MYCN, and MYCL, is essential in the development, progression, and metastasis of various cancers such as breast, colorectal, osteosarcoma, and neuroblastoma. Beyond its well-known roles in cell growth and metabolism, MYC significantly shapes the tumor immune microenvironment (TIME) by altering immune cell dynamics, antigen presentation, and checkpoint expression. It contributes to immune evasion by upregulating checkpoints such as programmed death-ligand 1 (PD-L1) and cluster of differentiation (CD)47, suppressing antigen-presenting major histocompatibility complex (MHC) molecules, and promoting the recruitment of suppressive immune cells such as regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs). While direct targeting of MYC has proven challenging, recent advances in therapeutic strategies, including MYC-MYC-associated factor X (MAX) dimerization inhibitors, bromodomain and extra terminal domain (BET) and cyclin dependent kinase (CDK) inhibitors, synthetic lethality approaches, and epigenetic modulators, have shown promising results in preclinical and early clinical settings. This review discusses MYC’s comprehensive impact on TIME and examines the promising therapeutic strategies of MYC inhibition in enhancing the effectiveness of immunotherapies, supported by recent preclinical and clinical findings.
Autophagy is a highly conserved cellular degradation and recycling process essential for maintaining cellular homeostasis. However, autophagic activity declines with age, contributing to the accumulation of damaged organelles and protein aggregates. The decline in autophagic activity is considered a primary hallmark of aging, as it contributes to cellular dysfunction and the onset of age-associated diseases, including neurodegenerative disorders and metabolic dysfunction. Sustaining autophagy with age requires transcriptional regulation, which may become impaired with age. In this review, we summarize current understanding of transcriptional regulation of autophagy during aging, with a specific focus on transcription factor EB (TFEB) and forkhead box O (FOXO) transcription factors. We integrate mechanistic insights from both mammalian systems and model organisms to highlight how their regulatory activity declines with age through changes in expression, post-translational modifications, nuclear transport, and transcriptional efficiency. We further explore pharmacological and lifestyle interventions aimed at restoring autophagic function to mitigate cellular decline. Given the pivotal role of autophagy in promoting cellular resilience and disease prevention, targeting autophagy-regulating transcription factors holds promise as a therapeutic strategy to counteract age-related functional decline and extend healthspan.
Aging is an inevitable reality that every individual has to face. People look forward to intervene and slow down this process, for example, skin anti-aging cosmetic and therapeutic treatments are commercially available in a variety of methods, such as skin tightening and dermal fillers, but these approaches do not fundamentally change the aging state of senescent cells. Fortunately, macrophages possess the capability to promote tissue repair and regeneration, induce angiogenesis, and improve the tissue microenvironment, making their application in the field of skin anti-aging potentially possible. In this review article, we unveiled the features of aged skin, including a reduction in the extracellular matrix, a decrease in vascular density, diminished defense capabilities, and increased inflammation. We then summarized the possible anti-aging functions of macrophages in this field, such as anti-inflammation, immunoregulation, promotion of angiogenesis, and regeneration. We also suggested potential strategies for utilizing macrophages in anti-aging therapies, including recruiting macrophages to the skin, supplying induced macrophages, and regulating macrophage activity. In conclusion, macrophages may play a role in cell therapy for skin anti-aging, though their potential efficacy and mechanisms need to be further explored.
Epilepsy is one of the most common neurological disorders in both children and adults, characterized by significant clinical heterogeneity and dynamic natural course. The pathophysiological roles of astrocytes in epilepsy have been increasingly recognized. Fluid biomarkers derived from astrocytes are actively studied in epileptic disorders, although their use remains limited in clinical practice. This review aims to compile and analyze clinical and experimental findings concerning astrocytic biomarkers in epilepsy and related conditions, with a focus on glial fibrillary acidic protein (GFAP) and S100 calcium-binding protein B (S100B). Herein we examine their roles in assessing seizure burden and temporal dynamics, explore their potential in distinguishing epileptic from psychogenic non-epileptic seizures, and discuss their therapeutic, prognostic, and mechanistic implications in the context of epileptic disorders.
Single-cell RNA sequencing (scRNA-seq) technology, also known as single-cell transcriptome sequencing, has become a key tool in biology and medicine, enabling deeper insights into cellular diversity and disease mechanisms. Since 2009 when scRNA-seq technology was first introduced, many technologies have been developed and improved, with a wide range of applications in haematopoietic malignancies, solid tumours, and other fields. These technologies have been used by researchers to map transcriptomes, study intra- and inter-cellular heterogeneity, investigate tumour microenvironments, analyse specific cellular subpopulations, and assist in clinical studies. This review categorises scRNA-seq on the basis of different single-cell amplification techniques, provides an overview of the principles of currently commonly used scRNA-seq techniques, discusses the application of scRNA-seq in the context of haematopoietic malignancies, and will hopefully play a role in the future development of single-cell sequencing technologies.
Excessive inflammatory responses in sepsis result in multiorgan dysfunction, with the majority of these responses being modulated by the activity of a disintegrin and metalloproteinase 10 (ADAM10). Due to the widespread distribution of ADAM10 and its numerous substrates, therapies targeting ADAM10 will have a range of physiological effects, including modulating inflammation, but may also cause toxic side effects. Precise therapeutic targets for regulating ADAM10 in specific diseases are needed. In several studies, tetraspanin family members have been identified as regulators of specific proteins, including ADAM10. In various cell types, the identical tetraspanin exhibits distinct effects on the regulation of ADAM10, indicating that tetraspanins possess cell-specific roles in modulating ADAM10. Furthermore, the interaction of diverse tetraspanins with ADAM10 results in the cleavage of various substrates. In this review, we provide a summary of the diverse tetraspanins that are currently recognized to interact with ADAM10 to identify potential new targets for regulating ADAM10 in sepsis.
The deiodinase enzymes are the gatekeepers of the peripheral Thyroid Hormone (TH) metabolism since they catalyze the activation of the prohormone Thyroxine (T4) into the active Triiodothyronine (T3), as well as their inactivation into metabolically inactive forms. Type I and Type II Deiodinases, Type I Deiodinase (D1) and D2, respectively, catalyze the T4-to-T3 conversion, while Type III Deiodinase, D3, terminates the THs action converting T4 into reverse T3 (rT3) and T3 into T2. Deiodinases are sensitive rate-limiting components within the hormonal axis and their enzymatic dysregulation is a common occurrence in several pathological conditions, including cancer. As a result, these enzymes are a potential source of interest for the development of pharmacological compounds exhibiting modulatory effects. The current arsenal of inhibitors for these enzymes is still limited. To date, a significant challenge in the development of deiodinases’ inhibitors is the achievement of enzyme selectivity and tissue specificity without disrupting TH regulation in the surrounding healthy tissues. Furthermore, deiodinases were shown to be potent regulators of the neoplastic processes, and their expression is altered in tumors, predisposing to increased aggressiveness and progression toward metastasis. However, especially in the cancer context, this design is complicated by the spatial and temporal heterogeneity of deiodinases expression, expressed as inter-tumoral variability across different cancer types, intra-tumoral variability among distinct tumor regions or cell populations within the same tumor type, and dynamic changes over time. Nevertheless, deiodinases’ inhibitors hold promise as a novel class of cancer therapeutics. Here, we proposed an overview of the actual knowledge of deiodinases’ inhibitors, highlighting their potentials and limitations. Future research should focus on identifying the most effective inhibitors, refining delivery mechanisms, and optimizing treatment regimens to minimize side effects while maximizing therapeutic efficacy.
Acquired resistance limits the therapeutic efficacy of osimertinib in lung adenocarcinoma (LUAD). Redox homeostasis is crucial for LUAD progression. However, how redox imbalance interacts with the tumor microenvironment (TME) to drive osimertinib resistance (OR) remains unclear.
The single-cell RNA sequencing (scRNA-seq) data GSE243562 were combined with the Cancer Genome Atlas (TCGA)-LUAD transcriptomes to map the TME cell population heterogeneity in osimertinib-resistant LUAD. Through univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regularization, a prognostic signature founded on redox-related genes (RRGs) was built. Therapeutic compounds targeting these signature genes were prioritized by molecular docking. Their expression patterns were subsequently validated in vitro.
Cancer-associated fibroblasts (CAFs) were central hubs in the TME of osimertinib-resistant LUAD, exhibiting enhanced intercellular communication. Computational profiling identified 10 differentially expressed RRGs, predominantly enriched in CAFs. Using a six-gene signature comprising AGER, CYP2J2, FMO2, HSPA1B, SOD3, and VASN, we categorized LUAD patients into separate risk categories. High-risk patients showed significantly reduced survival, an immunosuppressive status, and a higher tumor mutation burden (p < 0.05). The overexpression of these six genes was confirmed in OR cells. Critically, inhibiting SOD3 restored osimertinib sensitivity in vitro (p < 0.05). Clinically, SOD3 expression was lower in patients sensitive to third-generation epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs) than in those with resistant disease.
Targeting CAFs represents a promising strategy to overcome osimertinib resistance. Our six-gene redox signature offers a clinical framework for patient risk stratification and novel therapeutic strategy design. Future work will explore these targets to develop new treatments for LUAD.
Severe fever with thrombocytopenia syndrome (SFTS), caused by Dabie bandavirus (DBV) infection, is characterized by early cytokine storm as a primary pathological feature, although the precise mechanisms remain unclear. Low-density neutrophils (LDNs) are elevated in the peripheral blood of patients with autoimmune or infectious diseases and are closely associated with inflammatory damage and disease severity. However, the pathogenic contribution of LDNs to the progression of SFTS is largely unexplored. This study employed single-cell RNA sequencing (scRNA-seq) to profile the transcriptomic characteristics of LDNs during the acute phase of SFTS, aiming to reveal their compositional and functional heterogeneity following DBV infection, explore their role in the cytokine storm, and further understand their impact on disease progression.
Cells were isolated from 13 acute-phase SFTS patients with varying disease severity and 3 healthy controls using density gradient centrifugation, followed by preparation of single-cell suspensions for 3′-end scRNA-seq. Sequencing data were processed using the Seurat pipeline, including dimensionality reduction, clustering, cell-type annotation, and visualization with Uniform Manifold Approximation and Projection (UMAP). Low-density granulocytes (LDGs) and their subclusters were identified using canonical gene markers. Functional enrichment of differentially expressed genes (DEGs) was analyzed by high-dimensional Weighted Gene Co-expression Network Analysis (hdWGCNA), Gene Ontology (GO), AddModuleScore, single-sample Gene Set Enrichment Analysis (ssGSEA), and immune-related Gene Set Enrichment Analysis (irGSEA), while cellular interactions were explored using CellCall.
1. Compositional heterogeneity: The proportion of LDNs in peripheral blood increased in SFTS patients with greater disease severity during the acute phase. 2. Functional heterogeneity: (1) LDN subclusters showed functional diversity but consistently displayed pro-inflammatory or anti-infective properties. (2) With intensification of the systemic inflammatory response, the expression of multiple cytokine genes (e.g., IL6, IL8, TNFA) and gene sets of the inflammatory pathway (e.g., TNFA-SIGNALING-VIA-NFKB, INFLAMMATORY-RESPONSE) were significantly upregulated in LDNs. Concurrently, the expression of gene sets of type I interferon response pathway (e.g., INTERFERON-ALPHA-RESPONSE, INTERFERON-GAMMA-RESPONSE) and genes of interferon-induced antiviral proteins (e.g., EIF2AK2, OAS1, MX1) were also elevated. (3) In severe cases, glucocorticoid therapy downregulated expression of these inflammatory genes, demonstrating anti-inflammatory effects but potentially increasing infection risk.
This study revealed an increased proportion and heightened pro-inflammatory activity of LDNs during the acute phase of SFTS, closely correlating with disease severity. These findings suggest that LDNs may serve as potential early-warning biomarkers for predicting severe progression in patients with SFTS.
Upon activation, hepatic stellate cells (HSCs) can convert into fibroblasts and increase the production of extracellular matrix, a major cause of liver fibrosis (LF) and a growing health issue worldwide. Other mechanisms by which HSCs may induce fibrosis remain to be explored, and the role of cell dynamic gene expression in liver fibrogenesis is not well understood. In this study, analysis by single-cell transcriptome sequencing (scRNA-seq) was used to explore the potential effects of HSCs in a bile duct ligation (BDL)-induced mouse model of LF, followed by the identification of novel targets for clinical diagnosis. Methods: Liver tissue collected from BDL and sham-operated C57BL/6J mice was used for scRNA-seq. To systematically dissect the molecular and cellular events following fibrosis, the scRNA-seq data was analyzed for differential gene expression, KEGG, pseudotime trajectory, and cellular communication. Morphological changes in the BDL and sham livers were examined by hematoxylin and eosin (H&E) staining, Masson’s trichrome staining, fiber staining, and Sirius red staining. Results: The scRNA-seq analysis performed on the BDL and sham groups revealed the gene expression of 20,764 cells across 27 cell types. Antioxidant levels declined markedly in HSCs from BDL mice, leading to a more pronounced occurrence of ferroptosis. We also found evidence suggesting that elevated apelin signaling and platelet activation in HSCs contributed to the increased synthesis of extracellular matrix and collagen fibers. The large accumulation of immune cells in the liver of BDL mice induces different outcomes for HSCs. Conclusion: The results of this study provide further insight into the cellular and molecular alterations that occur within a specific subset of HSCs during LF, offering valuable information on potential targets for therapeutic intervention.
Myocardial ischemia-reperfusion (I/R) injury represents the major obstacle to achieving successful therapeutic outcomes in acute myocardial infarction patients. Fat mass and obesity-associated protein (Fto), an N6-methyladenosine (m6A) RNA demethylase, has been shown to protect cardiomyocytes against oxygen-glucose deprivation/reperfusion-mediated injury by regulating annexin A1 (Anxa1) expression in vitro. The present study aims to confirm the cardioprotective role of the Fto/Anxa1 axis using in vivo myocardial I/R injury models.
Wild-type (WT) and Anxa1 knockout (KO) mice underwent 30-min left coronary artery ligation and 2-h reperfusion after intramyocardial delivery of recombinant adeno-associated virus serotype 9 encoding Fto (adFto) or a control vector (adnull). The effects of Fto overexpression on cardiac function, fibrosis, apoptosis, and inflammatory response were examined using echocardiography, Masson’s trichrome staining, western blot analysis, enzyme-linked immunosorbent assay, and immunohistochemical staining. m6A-RNA immunoprecipitation-quantitative polymerase chain reaction quantified Anxa1 mRNA methylation.
Fto overexpression by adFto significantly improved cardiac function, reduced serum creatine kinase-myocardial band and troponin T levels, and alleviated cardiac fibrosis in I/R-injured WT mice. Mechanistically, Fto weakened I/R-induced global m6A levels and decreased m6A enrichment on Anxa1 mRNA, thereby enhancing Anxa1 expression. In Anxa1 KO mice, adFto did not confer functional or molecular benefit.
Fto enhances Anxa1 and mitigates myocardial I/R injury with suppression of nucleotide-binding oligomerization domain-, leucine-rich repeat-, and pyrin domain- containing receptor 3 (Nlrp3)-inflammasome signaling in vivo, identifying the Fto-Anxa1 axis as a mechanistic contributor and potential therapeutic target.
Esophageal squamous cell carcinoma (ESCC) develops through a multistage process in which normal epithelium transitions into intraepithelial neoplasia and ultimately into invasive carcinoma. Elucidating the molecular changes and functional roles of key genes during this progression is critical for understanding the mechanisms underlying this malignant transformation.
Transcriptomic profiles of 12 normal esophageal tissues, 5 intraepithelial neoplasia tissues, and 7 ESCC tissues were analyzed via microarray. Stage-specific transcriptomic changes were systematically compared to delineate the phenotypic evolution that occurs during carcinogenesis, with a particular focus on identifying pivotal genes that regulate the precancerous-to-malignant transition. The candidate gene LINC01605 was further examined via the following approaches: (1) bioinformatics-based characterization of its tumor-associated functions using Genotype-Tissue Expression Project (GTEx) normal tissue and The Cancer Genome Atlas Program (TCGA) ESCC transcriptome; (2) functional validation in ESCC cell lines in which the gene was silenced or overexpressed in vitro; and (3) mechanistic exploration of RNA-binding partners via streptavidin bead-based RNA pull-down assays.
Multistage transcriptomic analysis revealed the progressive acquisition of cancer hallmarks during ESCC development. The transition from precancerous lesions to invasive carcinoma was characterized by epithelial dedifferentiation, extracellular matrix remodeling, and angiogenesis. LINC01605, which is a long noncoding RNA (lncRNA), was downregulated during this transition. GTEx revealed that LINC01605 was specifically expressed in the squamous epithelium of the esophagus and that its expression was negatively correlated with histological grade in the TCGA-ESCC dataset. Samples with high LINC01605 expression and those with low LINC01605 expression in the TCGA dataset exhibited significant functional differences in epithelial cell differentiation, proliferation, and migration, as well as in the extracellular matrix. Knocking down LINC01605 increased proliferation and migration in both the normal immortalized esophageal epithelial cell line NE3 and the ESCC cell line KYSE180. Conversely, the overexpression of LINC01605 isoforms suppressed these malignant phenotypes. RNA pull-down revealed potential interactions between LINC01605 and aurora kinase B (AURKB), which are components of the chromosomal passenger complex (CPC), suggesting its involvement in regulating the cell cycle.
LINC01605 functions as a tumor suppressor in ESCC by maintaining squamous cell differentiation and inhibiting proliferation and migration. LINC01605 downregulation facilitates malignant transformation during esophageal carcinogenesis.
Bone cancer pain (BCP) related neuronal damage is associated with ferroptosis, a regulated cell death dependent on iron. The noble gas argon is known to have neuroprotective effects, reducing neuroinflammation and enhancing neuronal recovery. However, its potential role in alleviating BCP through the modulation of neuronal ferroptosis remains unexplored.
Ferroptosis was induced by Erastin in SH-SY5Y human neuroblastoma cells. Plasmids were used to overexpress or knock down toll-like receptor (TLR) 2 and cyclooxygenase-2 (COX-2). The effects of argon treatment were evaluated in SH-SY5Y cells in which TLR2 and COX-2 expression was manipulated using viability assays, oxidative stress markers (reactive oxygen species (ROS), malondialdehyde (MDA), and glutathione (GSH)), and ferroptosis-related proteins (acyl-CoA synthetase long-chain family member 4 (ACSL4), glutathione peroxidase 4 (GPX4), and solute carrier family 7 member 11 (SLC7A11)). In vivo, a murine BCP model was developed by injecting Lewis lung carcinoma cells into the femoral cavity. Pain behaviors were analyzed, and spinal cord ferroptosis features were evaluated using histology, immunofluorescence, and transmission electron microscopy (TEM).
In vitro experiments showed that argon treatment restored SH-SY5Y cell viability after Erastin exposure, suppressed ROS and MDA production, and boosted GSH levels. It also downregulated ACSL4 and upregulated GPX4 and SLC7A11. In vivo, argon improved pain behaviors, reduced tumor burden, preserved neuronal integrity, and mitigated ferroptosis-induced damage to the spinal cords of BCP model mice. Argon also significantly suppressed TLR2 and COX-2 expression, disrupting the ferroptosis and inflammation cascades. However, overexpression of TLR2 or COX-2 reversed these protective effects, confirming the pivotal role of the TLR2-COX-2 axis in neuronal ferroptosis and pain modulation.
These findings demonstrate that argon effectively mitigates neuronal ferroptosis and alleviates BCP by downregulating the TLR2-COX-2 pathway, highlighting its therapeutic potential for conditions involving ferroptosis, such as cancer-related pain and neurodegenerative diseases.
Notch1 signaling regulates innate immune-mediated inflammation in acute liver injury (ALI). However, the precise mechanism by which Notch1 governs macrophage polarization during ALI remains poorly understood.
Wild-type (WT) mice received DAPT (10 mg/kg) prior to acetaminophen (APAP)-induced ALI. In parallel, bone marrow-derived macrophages (BMMs) were pretreated with either the β-catenin inhibitor XAV939 or the activator SKL2001, exposed to DAPT, and then challenged with lipopolysaccharide (LPS). Liver injury and inflammation were evaluated by hematoxylin and eosin (H&E) staining, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, immunohistochemistry, immunofluorescence, quantitative real-time PCR (RT-PCR), and western blotting.
Unexpectedly, DAPT treatment exacerbated APAP-induced liver injury (AILI), resulting in more severe hepatocellular damage and inflammation than in controls. DAPT-treated macrophages exhibited enhanced pro-inflammatory cytokines expression and a shift toward an M1-like phenotype. Mechanistically, the β-catenin/glycogen synthase kinase 3 beta (GSK3β) signaling pathway emerged as a pivotal regulator of macrophage polarization.
Notch1 inhibition unexpectedly worsens AILI by amplifying macrophage-driven pro-inflammatory responses via β-catenin signaling. These findings highlight the Notch1–β-catenin axis as a key regulator of hepatic macrophage function and a potential therapeutic target for sterile liver inflammation.
To evaluate cysteine dioxygenase 1 (CDO1) gene promoter methylation in circulating tumor DNA as a biomarker for the early diagnosis of lung cancer.
Data up to June 5, 2025, across electronic databases (PubMed, Embase, Web of Science, and the China National Knowledge Infrastructure) were searched. The quality assessment tool for diagnostic accuracy studies-2 (QUADAS-2) checklist was used to assess the risk of bias in the incorporated studies. A random-effects model was employed to generate summary statistics for diagnostic accuracy, which included pooled sensitivity and specificity estimates, the diagnostic odds ratio (DOR), and a summary receiver operating characteristic curve. An exploration of heterogeneity sources was undertaken using meta-regression, followed by a sensitivity analysis to test the consistency of the results. Finally, Deek’s funnel plot was generated to estimate publication bias, and the clinical feasibility was evaluated using Fagan’s nomogram.
Seven relevant studies were included in this meta-analysis. No major concerns regarding the quality risk of the included studies were observed. The pooled diagnostic sensitivity, specificity, and DOR values of the CDO1 promoter methylation for lung cancer were 0.63 (95% CI: 0.60–0.67), 0.78 (95% CI: 0.74–0.82), and 5.96 (95% CI: 4.06–8.74), respectively, and the area under curve was 0.7423. Statistical heterogeneity was observed in sensitivity (I2 = 73%, p < 0.1), specificity (I2 = 79.5%, p < 0.1), and DOR (I2 = 42.9%, p < 0.1); however, variables such as the region, sample source, sample size, and detection method did not significantly affect heterogeneity (p > 0.05). The results were robust as the DOR was not overly influenced by the deletion of any single study. No publication bias was observed in this study (p = 0.74). Additionally, under a pre-test probability of 20%, the positive post-test probability of CDO1 promoter methylation in lung cancer was predicted to be 42%. PROSPERO CRD420251131665, https://www.crd.york.ac.uk/PROSPERO/view/CRD420251131665.
The detection of CDO1 promoter methylation in biofluids represents a promising tool for the early diagnosis of lung cancer. Future studies should focus on improving detection methodologies and investigating combinational strategies with high accuracy.
Oncogenic FGFR4 signalling represents an attractive therapeutic target across multiple cancers, yet treatment resistance almost uniformly occurs. A critical mechanism steering resistance is a rapid and complex reprogramming of kinase signalling networks, called the adaptive bypass response. Capturing this dynamic rewiring to pinpoint, on a molecular level, the right combinatorial drug for the right FGFR4-driven cancer patient at the right time, will be key to achieving sustained tumour responses. But how can one accurately capture this process across different cancer types exhibiting contrasting levels of FGFR4 signalling pathway components and network behaviours? A recent study by Shin et al. delivers a technically elegant and biologically grounded exploration of the adaptive signalling landscape to tackle this, revealing cell context-dependent combinatorial strategies.
Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy with a high incidence of thrombosis. Coagulation factor 3 (F3) plays a key role in initiating the coagulation pathway. This study identified cell subpopulations that highly express F3 and explored their potential roles in PDAC.
This study evaluated 1837 patients with PDAC from two cancer hospitals between November 1, 2023, and November 30, 2024. The analyses included assessing coagulation and fibrinolysis indicators, and employing single-cell sequencing technology to examine the tumor microenvironment in freshly resected PDAC tissues. Findings were validated using the Gene Expression Omnibus database.
Over half of the patients (54.98%) with PDAC showed abnormal coagulation indicators. F3 mRNA and protein levels were higher in PDAC tissues than in normal tissues. This high F3 expression in PDAC was associated with a poor prognosis (p < 0.01). Analysis of 33,300 cells from freshly resected PDAC tissues showed high F3 expression in cancer-associated fibroblasts (CAFs) and ductal cells. Subsequent subtype analysis indicated that ductal cell 1 (tumor cells) and inflammatory CAFs (iCAFs) exhibited high F3 expression. Pseudotime trajectory analysis showed that iCAFs were prevalent in the earlier part of the pseudotime pathway. Notably, pathways associated with inflammation, phosphoinositide 3-kinase/Akt signaling, and coagulation and complement were significantly enriched in iCAFs. In addition, the interaction between iCAFs and tumor cells was regulated by growth factor receptor–ligand pairings. “GSE212966” and “GSE197177” data confirmed these results.
The high expression of F3 in specific iCAF subtypes suggests a role in PDAC hypercoagulability and tumor progression. Targeting these iCAF subtypes could provide potential strategies for treating PDAC.
Bladder cancer (BCa) is a highly heterogeneous malignancy, and precision treatment remains challenging. Identifying molecular biomarkers and risk factors is essential for improving prognosis and therapeutic strategies.
We integrated expression quantitative trait loci (eQTL) data with Mendelian randomization (MR) analysis to identify candidate risk genes associated with BCa. Subsequently, a prognostic risk model was developed using machine learning methods to explore its correlation with molecular features, immune cell infiltration, and ferroptosis-related pathways. Based on these findings, the Tripartite Motif Containing 59 (TRIM59) protein was selected for further experimental validation. The functional role of TRIM59 in BCa progression was further investigated using MTT assays in BCa cell lines. Additionally, western blotting (WB) was conducted to confirm the potential association between TRIM59 expression and ferroptosis regulation.
The risk model identified distinct signaling pathways that differentiate the high-risk and low-risk BCa groups. The low-risk group demonstrated greater infiltration of CD8+ T cells. Conversely, the high-risk group exhibited enhanced immune evasion, as evidenced by increased infiltration of macrophages and fibroblasts. Furthermore, TRIM59 exerts a regulatory influence on ferroptosis progression in BCa by modulating key genes involved in this process, including Solute Carrier Family 7 Member 11 (SLC7A11), Glutathione Peroxidase 4 (GPX4), and Acyl-CoA Synthetase Long Chain Family Member 4 (ACSL4).
Our integrative approach highlights the potential of genomic and immune microenvironment data in developing personalized risk models for BCa, offering insights into individualized treatment strategies. Importantly, TRIM59 is involved in ferroptosis resistance in BCa. These findings have potential implications for identifying diagnostic biomarkers and therapeutic targets for BCa treatment.
Endogenous and exogenous H2S can influence the virulence of bacteria and their susceptibility to antibiotics and oxidative stress. Escherichia coli and Bacillus subtilis, when grown in minimal medium with sulfate as the sole sulfur source, produce H2S when treated with cystine or under stress conditions, including exposure to chloramphenicol and ciprofloxacin. However, it is unknown whether Mycobacterium smegmatis is capable of producing sulfide under these conditions and how this production affects cell physiology.
Real-time monitoring of dissolved oxygen (dO2), pH, extracellular K+, and sulfide was performed directly in culture flasks using selective electrodes. Changes in the level of low molecular weight (LMW) thiols were recorded using spectrophotometric methods and high performance liquid chromatography (HPLC).
Sudden addition of cystine or chloramphenicol to growing M. smegmatis cultures increased the intracellular level of cysteine and induced its homeostasis mechanisms, which include the export of excess cysteine from cells and its incorporation into mycothiol (MSH), along with desulfurization with H2S formation. Ciprofloxacin also increased intracellular cysteine concentration and sulfide production but did not induce cysteine release. Both antibiotics inhibited growth and respiration, whereas cystine transiently increased respiration and glucose uptake in M. smegmatis, in contrast to E. coli, which showed a transient inhibition of these processes.
The mechanisms of cysteine homeostasis under the action of antibiotics in M. smegmatis are similar to those in E. coli and B. subtilis, indicating the universal nature of stress response. The opposing effects of cystine-derived H2S on physiological parameters in M. smegmatis and E. coli may be important factors contributing to their susceptibility to antibiotics.
Steroid hormones are widely used as anti-allergic drugs because of their potent anti-inflammatory properties and ability to suppress histamine release by 60–80%. Ursodeoxycholic acid (UDCA; 3α,7β-dihydroxy-5β-cholan-24-oic acid), used to treat liver disease, exerts immunosuppressive effects by binding to glucocorticoid receptors and inhibiting histamine release from mast cells. In contrast, other bile acids, such as chenodeoxycholic acid (CDCA; 3α,7α-dihydroxy-5β-cholan-24-oic acid) and deoxycholic acid (DCA; 3α,12α-dihydroxy-5β-cholan-24-oic acid), have been reported to promote histamine release. The mechanisms underlying these divergent effects remain unclear, raising questions regarding structural differences, receptor interactions, and downstream signaling. To address this knowledge gap, we examined the effects of several bile acids and C24 bile alcohols on the degranulation of rat basophilic leukemia (RBL-2H3) cells, a model for mast cell activation.
The effects of bile acids and alcohols on degranulation were tested in stimulated RBL-2H3 cells; furthermore, whether they affected store-operated calcium (SOC) channel-mediated Ca2+ entry—a critical step in mast cell degranulation—was investigated. To identify molecular targets, biotinylated bile acids were immobilized on magnetic beads and incubated with lipid raft fractions from RBL-2H3 cells to capture the interacting proteins.
All tested bile acids and alcohols significantly suppressed RBL-2H3 cell degranulation, thereby correlating with reduced extracellular Ca2+ influx via SOC channels. Further analysis revealed interference by Orai1, a key subunit of calcium release-activated calcium (CRAC) channels. This interaction appears to be mediated by the steroidal structures of the bile acids and alcohols.
These findings demonstrate that bile acids and alcohols inhibit SOC-mediated Ca2+ entry by directly interacting with Orai1, thereby blocking mast cell degranulation. Although the concentrations required for this effect were near cytotoxic levels owing to detergent-like properties, the results uncovered a novel molecular interaction between steroid structures and Orai1. This mechanistic insight provides a foundation for the development of targeted small molecule modulators of Orai1-mediated calcium entry, offering potential therapeutic strategies for allergic and inflammatory disorders.
Mitochondrial dynamics—the balance between fission, fusion, and mitophagy—are essential for maintaining cellular homeostasis and are increasingly implicated in the pathogenesis of Alzheimer’s disease (AD).
Here, we investigated the effects of targeted modulation of mitochondrial fission and fusion on mitochondrial morphology and metabolic status in primary hippocampal cultures derived from 5xFAD transgenic mice. Mitochondrial dynamics were modulated using the fission inhibitor Mitochondrial Division Inhibitor 1 (Mdivi-1), the fusion promoter mitochondrial fusion promoter M1 (MFP M1), and exogenous zinc as a fission activator. We evaluated mitochondrial morphology, lipofuscin accumulation, beta-amyloid (Aβ42) levels, and reactive oxygen species (ROS). The general condition of the cultures was assessed morphologically using neuronal and astrocytic markers.
Modulating mitochondrial dynamics altered mitochondrial morphology, decreased Aβ42, lipofuscin, and ROS levels, and improved cellular organization. Treatments with MFP and Mdivi-1 promoted mitochondrial hyperfusion without complete network integration and were associated with reduced astrogliosis and increased neuronal density. In contrast, zinc induced dose-dependent mitochondrial fragmentation and astrocytic clasmatodendrosis, with lower concentrations enhancing Aβ clearance and higher concentrations inducing toxicity.
Mitochondrial fusion and fission significantly influence lipofuscin and amyloid accumulation in 5xFAD cultures, underscoring their potential as therapeutic targets in neurodegenerative diseases. We propose that mitochondrial morphology acts as a key regulator of both cellular homeostasis and disease pathology.
Aortic dissection (AD) is a high-mortality cardiovascular emergency with unclear pathophysiological mechanisms. This study investigated S100 calcium-binding protein A9 (S100A9) as a therapeutic target for AD and explored its underlying mechanisms.
Proteomic analysis compared aortic tissues from patients with acute type A and matched non-dissected vascular tissues from the same patients. An AD model was induced in wild-type and S100A9 knockout mice via β-aminopropionitrile (BAPN). Survival, aortic diameter, and S100A9 expression were quantified. Furthermore, single-cell RNA sequencing was used to analyze cell populations and mitochondrial pathways in AD mice treated with an S100A9 inhibitor. Finally, the effect of S100A9 on mitochondrial function was investigated in Tohoku Hospital Pediatrics-1 (THP-1) cells.
Proteomics identified that S100A9 is significantly upregulated in AD tissue. Furthermore, S100a9 knockout (S100a9 KO) mice conferred protection against AD-induced mortality and aortic dilation. Single-cell RNA analysis revealed that S100A9 is predominantly expressed within the granulocyte population. S100A9 inhibition activated mitochondrial oxidative phosphorylation pathways and upregulated mtDNA-encoded gene expression. Human tissue mRNA levels confirmed decreased mtDNA in AD. Moreover, recombinant human S100A9 and angiotensin-II treatment in THP-1 cells reduced mitochondrial membrane potential and increased oxidative stress.
S100A9 is a potential contributor to AD pathogenesis. Inhibition of S100A9 might be a promising therapeutic target for AD.
Despite the enormous theoretical progress, there is currently no effective treatment for the cytokine storm (CS) in COVID-19 and Influenza, which is due to hyperactivation of NOD-like receptor protein 3 inflammasome (NLRP3-I). According to our research, the only way to prevent or interrupt the CS is to administer high but safe doses of colchicine, which inhibits NLRP3-I/CS.
Thyroid cancer progression involves cell-state plasticity in the form of epithelial–mesenchymal transition (EMT), and defects in DNA damage response (DDR), both of which are linked to metastasis and treatment failure. The role of pituitary tumor transforming 1 interacting protein (PTTG1IP/PBF) in these processes remains insufficiently defined.
Transcriptomes from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) (GSE138042) datasets were analyzed to prioritize EMT-associated genes and to assess correlations with EMT regulators, junction markers, and matrix metalloproteinases. PTTG1IP expression was measured by quantitative real‐time reverse transcriptase PCR (qRT-PCR) in thyroid cancer cell lines and normal thyroid HTori-3 cells. Cell viability (Cell Counting Kit-8 (CCK-8)) and apoptosis (terminal deoxynucleotidyl transferase dUTP nick end labeling, TUNEL) assays were performed following shRNA knockdown of PTTG1IP. The PTTG1IP–CTTN association was examined by co-immunoprecipitation and immunofluorescence. Chromatin immunoprecipitation (ChIP)-qPCR was used to investigate PTTG1IP occupancy at DDR gene promoters. Radiosensitivity was evaluated by loss of cell viability, flow-cytometric cell death, and phosphorylated H2AX (p-H2AX) immunofluorescence after irradiation.
PTTG1IP emerged as a top EMT-linked candidate across cohorts, with elevated mRNA and protein expression in thyroid cancers and cell lines. Silencing of PTTG1IP reduced viability and increased apoptosis in human thyroid cancer cell lines TPC-1 and KTC-1. PTTG1IP expression aligned with canonical EMT transcription factors and with DDR genes. Biochemically, PTTG1IP formed an endogenous complex with cortactin (CTTN) and co-localized in cancer cells. Mechanistically, PTTG1IP occupied the BRCA1, BRCA2, RAD51, RAD51-associated protein 1 (RAD51AP1), and ATM serine/threonine kinase (ATM) promoters. Functionally, depletion of PTTG1IP led to increased radiation-induced DNA damage and cell death, resulting in a greater post-irradiation loss of viability.
PTTG1IP is a multifunctional node in thyroid cancer, coupling cytoskeletal programs with DDR control, and supporting cell growth and treatment tolerance. The targeting of PTTG1IP, particularly to enhance radiosensitivity, may provide a novel therapeutic strategy for thyroid cancer.
Phosphatidylserine synthase 1 (PTDSS1) is a crucial enzyme involved in phospholipid synthesis. However, its role in the metabolic regulation of lung cancer remains unclear. This study hypothesized that PTDSS1 promotes lung cancer progression by regulating metabolic reprogramming through nuclear–mitochondrial crosstalk.
PTDSS1’s expression levels in lung cancer tissues and their correlation with patient prognosis were evaluated through bioinformatics analysis and immunohistochemistry. In vitro functional experiments, including cell proliferation, migration, invasion, and colony formation, were performed using PTDSS1-overexpressing lung cancer cell lines. Cellular glycolysis and mitochondrial oxidative phosphorylation levels were determined. PTDSS1’s subcellular localization was investigated through cellular fractionation and immunofluorescence. Its regulatory interaction with pyruvate kinase M2 (PKM2) was examined. Expression levels of metabolism-related genes and mitochondrial dynamics markers were analyzed by qRT-PCR and Western blot.
PTDSS1 was significantly overexpressed in lung cancer tissues. High PTDSS1 expression correlated with poor patient prognosis. PTDSS1 enhanced lung cancer cell proliferation, migration, and invasion capabilities. Metabolically, PTDSS1 promoted aerobic glycolysis. Mitochondrial oxidative phosphorylation was suppressed. Nuclear-localized PTDSS1 showed enhanced effectiveness in driving glycolysis and malignant progression. Mechanistically, PTDSS1 may accelerate glycolysis through PKM2 regulation. It may drive lung cancer progression through PKM2-mediated nuclear–mitochondrial homeostatic crosstalk.
PTDSS1 functions as a multifunctional oncogene. It drives lung cancer progression through PKM2-mediated nuclear–mitochondrial homeostatic crosstalk. PTDSS1 represents a potential prognostic biomarker and therapeutic target.
Cervical cancer remains a major cause of cancer-related death among women worldwide. Despite advances in treatment, prognosis remains poor for many patients due to tumor heterogeneity. DNA methylation, an epigenetic modification, is known to influence tumor development, but its role in defining molecular subtypes and prognostic stratification in cervical cancer remains inadequately understood.
We analyzed DNA methylation profiles from 287 cervical cancer samples obtained from the UCSC Xena database. Univariate and multivariate Cox regression analyses were applied to identify prognostic CpG sites, as these models allow evaluation of individual and combined effects of methylation sites on patient survival. Consensus clustering was performed to define robust molecular subtypes based on methylation patterns, providing insights into tumor heterogeneity. Differentially methylated regions were identified using the Quantitative Differentially Methylated Regions (QDMR) software, an entropy-based tool validated for detecting subtype-specific methylation markers. A Bayesian classifier was constructed and validated in training and test cohorts to evaluate the predictive accuracy of these markers for subtype classification. Additionally, immune cell infiltration was estimated using computational algorithms to assess tumor microenvironment differences, and chemosensitivity was predicted to explore potential clinical implications of the methylation subtypes.
Four distinct methylation-based subtypes differed in methylation patterns, histological types, clinical stages, and metastatic status. A total of 501 subtype-specific methylation sites were identified. The Bayesian classifier demonstrated strong predictive performance, with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.824 based on 10-fold cross-validation, indicating high classification accuracy and robustness. The immune microenvironment composition varied markedly among subtypes. Notably, Cluster 1 had elevated infiltration of central memory CD8+ and effector memory CD4+ T cells, whereas Cluster 4 exhibited reduced immune activation and the lowest immune checkpoint expression. These findings indicate subtype-specific differences in potential responsiveness to immunotherapy.
These DNA methylation-driven subtypes highlight the heterogeneity of cervical cancer and offer new insights for personalized therapy.