This review provides a comprehensive analysis of recent advancements in elucidating the molecular mechanisms underlying human immunodeficiency virus (HIV)-1 entry, focusing on the intricate interplay between the viral envelope glycoproteins (Env) and host cell receptors. We detail how structural insights into glycoprotein (gp)120-Cluster of Differentiation 4 (CD4)/coreceptor interactions and gp41-mediated membrane fusion inform therapeutic interventions, including fusion inhibitors and broadly neutralizing antibodies (bnAbs). The HIV-1 Env trimer undergoes a series of highly coordinated conformational transitions from a metastable prefusion state to a stable postfusion structure. CD4 engagement induces allosteric remodeling of gp120, unveiling coreceptor (C-C chemokine receptor type 5 (CCR5)/C-X-C chemokine receptor type 4 (CXCR4)) binding sites and priming gp41 activation. Fusion peptide insertion, six-helix bundle formation, and membrane merger are critical targets for inhibitors like T20 (enfuvirtide). Comparative analyses with other viruses reveal conserved fusion mechanisms despite distinct activation triggers, offering broader insights for antiviral development. By integrating structural biology, virology, and translational research, this review highlights how the mechanistic dissection of viral entry informs the design of next-generation therapeutics. We highlight strategies to disrupt Env-receptor interactions, block fusion intermediates, and harness cross-viral principles to counteract drug resistance and refine vaccine approaches. These insights not only deepen our understanding of HIV-1 pathogenesis but also drive the innovation of novel antiviral strategies.
Liver cancer, particularly hepatocellular carcinoma (HCC), represents a global health challenge. The tumor microenvironment (TME) plays a pivotal role in the progression and therapeutic resistance of HCC. Interventional therapies have emerged as pivotal modalities in the treatment of liver cancer, especially in cases that are unsuitable for surgical resection. The evolution of these techniques has been markedly enhanced by the integration of artificial intelligence (AI), which has the potential to increase precision, improve outcomes, and personalize patient care. This review covers modern interventional therapies for liver cancer, highlighting recent advances in minimally invasive procedures. It describes the intricate liver TME and emphasizes the importance of characterizing its diversity and identifying therapeutic targets. Additionally, we discuss how AI can decipher TME complexities, predict responses, categorize patients, and personalize treatments. By elucidating connections between the TME, therapeutic interventions, and AI, this review aims to improve the management and care of patients with liver cancer.
Clonal hematopoiesis (CH) is characterized by the expansion of hematopoietic stem and progenitor cells harboring somatic mutations, which confers an increased risk of hematologic malignancies and cardiovascular disease. Among CH-associated mutations, mutations affecting splicing factors (SFs), including splicing factor 3b subunit 1 (SF3B1), serine/arginine-rich splicing factor 2 (SRSF2), U2 small nuclear RNA auxiliary factor 1 (U2AF1), and zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2 (ZRSR2), play a unique role in promoting clonal expansion and leukemogenesis. In this review, we summarize recent findings on the role of SF mutations in CH progression, their interplay with other mutations (e.g., DNA methyltransferase 3 alpha (DNMT3A), ten-eleven translocation methylcytosine dioxygenase 2 (TET2) and isocitrate dehydrogenase 2 (IDH2)), and their impact on hematopoietic homeostasis. Epidemiological studies have demonstrated that SF-mutant CH exhibits an accelerated clonal expansion compared to other CH clones. Furthermore, murine models suggest that SF mutations alone do not inherently confer a growth advantage for clonal expansion but rather enhance disease phenotypes when co-existing with epigenetic mutations, such as IDH2 and TET2. These findings suggest that SF mutations contribute to CH expansion and malignant transformation through a synergistic interplay with other mutations and external factors such as inflammation. Given the clinical significance of SF mutations, ongoing research is focused on developing targeted therapies that modulate aberrant RNA splicing and prevent CH-driven leukemogenesis. Understanding the mechanisms underlying mutant spliceosome-mediated CH expansion may provide novel insights into early detection, risk stratification, and therapeutic interventions in hematologic malignancies.
Glutamate excitotoxicity is one of the key factors in the pathophysiology of the secondary injury cascade following traumatic brain injury (TBI) and spinal cord injury (SCI). These neurotraumatic conditions remain major causes of long-term disability and mortality worldwide, yet therapeutic options remain limited. Excessive glutamate release after neurotrauma leads to the overactivation of glutamate receptors, triggering calcium influx and the activation of destructive enzymes and signaling pathways that drive progressive neuronal death and tissue degeneration. This review examines the molecular mechanisms of glutamate-mediated excitotoxicity in neurotrauma, particularly focusing on TBI and SCI, and evaluates current and emerging therapeutic strategies aimed at modulating glutamate levels, receptor activity, and downstream signaling pathways. Particular attention is given to glutamate receptor antagonists, agents enhancing glutamate clearance, and neuroprotective compounds. A critical analysis of preclinical successes versus clinical failures reveals key translational barriers, including narrow therapeutic windows, patient heterogeneity, poor drug penetration across the blood-brain barrier, and adverse off-target effects. Delayed treatment relative to the peak of excitotoxic activity has also limited clinical efficacy. This review highlights the importance of understanding the temporal dynamics of glutamate toxicity and the necessity for precisely timed, stratified therapeutic interventions. This work contributes to the broader scientific effort to develop more effective neuroprotective therapies by identifying the mechanistic underpinnings and translational challenges of anti-excitotoxic strategies. Given the global burden of TBI and SCI, advancing targeted interventions for glutamate excitotoxicity holds significant promise for improving neurological outcomes and quality of life for affected individuals.
Systemic lupus erythematosus (SLE) is a chronic autoimmune disorder characterized by immune system dysfunction, the production of autoantibodies, and multi-organ inflammation. Lupus nephritis (LN) is one of the most severe complications of this condition. Approximately 60% of patients with SLE develop LN, which leads to both increased morbidity and mortality. Furthermore, LN has the potential to progress to end-stage renal disease. Macrophages, key components of the innate immune system, are involved in the pathophysiology of LN through immune complex clearance, antigen presentation, regulation of inflammation, and tissue repair. Macrophage polarization into pro-inflammatory (M1) versus anti-inflammatory (M2) functional phenotypes is a component of LN disease progression. M1 macrophages are responsible for supporting pro-inflammatory immunity and promoting tissue damage, whereas M2 macrophages are necessary for tissue repair and resolution of inflammation. However, dysregulated M2 function may exacerbate the pathogenesis of LN, indicating the complex role of macrophages in LN. Novel therapeutic approaches associated with the mechanisms of macrophage polarization and/or macrophage signaling pathways have emerged as therapeutic targets to modify the progression of LN. Furthermore, proinflammatory cytokines enhance renal inflammation and autoimmunity; alternatively, anti-inflammatory cytokines play a dual role in LN, contributing positively and negatively to the disease process. The purpose of this review is to investigate the role of macrophages in the pathogenesis of LN and highlight macrophage-targeted therapies or biomarkers as diagnostic tools and new therapeutic avenues to improve long-term outcomes for patients.
The nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3 (NLRP3) inflammasome is a multiprotein complex fundamental for the secretion of pro-inflammatory cytokines during the innate immune response. NLRP3 dysregulation is implicated in the pathogenesis of several diseases, such as inflammatory bowel disease, arthritis, cancer, Alzheimer’s disease, and type 2 diabetes. The pharmacological modulation of NLRP3 by several compounds, which are fully described in this review, represents an important strategy to regulate inflammatory processes. Moreover, NLRP3 is also involved in drug-related adverse reactions, and its pharmacological modulation represents a rapid strategy to mitigate such adverse effects, as reported in this study. NLRP3 inflammasome activation is tightly regulated by post-transcriptional modifications and epigenetic factors, such as long non-coding RNAs (lncRNAs) and DNA methylation, as well as other interacting regulators. Recently, different studies have revealed the importance of NLRP3 levels in predicting drug response. In particular, the methylation of the NLRP3 promoter, which is associated with the inflammasome expression level, emerged as a new promising pharmacoepigenetic biomarker for the glucocorticoid therapy response in several inflammatory disease conditions.
Epidemiological data show a strong connection between type 2 diabetes mellitus (T2DM) and metabolic-associated fatty liver disease (MAFLD). In recent years, the prevalence of both conditions has been rising simultaneously. When T2DM and MAFLD occur together, patients face a significantly higher risk of glucose and lipid metabolic disorders, with fatty liver more likely to progress to fibrosis or even malignancy. The underlying mechanisms are complex, involving multiple factors such as inflammatory responses, insulin resistance (IR), and cellular aging. Ferroptosis, a newly identified form of programmed cell death characterized by iron accumulation and lipid peroxidation, plays a crucial role in the development of T2DM and MAFLD, drawing significant attention. Current research suggests that ferroptosis contributes to the progression of these two diseases. However, the exact mechanisms of ferroptosis in T2DM-related MAFLD remain unclear. This review summarizes recent advances in ferroptosis research related to T2DM and MAFLD and highlights several potential therapeutic drugs and compounds targeting ferroptosis, aiming to provide a theoretical basis for their clinical application. Additionally, intracellular iron overload, elevated reactive oxygen species levels, and lipid peroxidation are closely associated with ferroptosis. Studies have shown that certain antidiabetic medications (e.g., metformin, pioglitazone, and liraglutide) may slow the progression of MAFLD by inhibiting ferroptosis. Furthermore, experimental studies targeting FerroTerminator1 (FOT1) have demonstrated promising therapeutic value for MAFLD and insulin resistance, suggesting that targeting ferroptosis could be an effective strategy for treating T2DM-related MAFLD.
Ionizing radiations (IRs), commonly used in both diagnostic imaging and cancer therapy, generate reactive oxygen species (ROS) and free radicals, causing significant DNA damage that can lead to genetic mutations, cell death, and tissue injury in both normal and tumor tissues. In response to the oxidative stress, the nuclear factor erythroid 2-related factor 2 (NRF2) is activated to induce target genes involved in antioxidant and detoxifying pathways, thereby playing a pivotal role in protecting cells from IR-induced oxidative damage. In clinical diagnostics, IR exposure from imaging techniques can result in DNA damage, inflammation, and increased risk of IR-induced pathologies, including cancer. NRF2 activation in response to these diagnostic exposures can help to protect normal tissues from damage by boosting antioxidant defenses. In radiotherapy, IR induces DNA damage to kill malignant cells, although it may also harm surrounding healthy tissue. Cancer cells exploit NRF2 activation to resist IR-induced cell damage, thereby maintaining redox balance and protecting themselves from oxidative stress. In that case, NRF2 inhibition could sensitize cancer cells to IR effects by disrupting their antioxidant defense, leading to increased ROS accumulation, enhanced DNA damage, and greater cell death. This review will summarize the role of NRF2 in mediating the response to IR in both healthy and cancerous cells, with a focus on its effects in clinical diagnostic and radiotherapy.
As an evolutionarily conserved timekeeping system, the circadian clock orchestrates physiological adaptations to diurnal environmental cues through transcriptional-translational feedback loops (TTFLs). Accumulating evidence reveals that circadian regulation governs immunological processes, with the immune system—a critical host defense mechanism—exhibiting robust circadian rhythmicity in functional organization. This review synthesizes recent advances in circadian modulation of pathogen-host interactions, immune cell trafficking, effector functions, circadian light hygiene—gut immune crosstalk, and tumor immunobiology. We examine the bidirectional crosstalk between circadian oscillators and immune pathways while addressing the clinical implications for immune-related pathologies. Significantly, we advocate chrono-immunotherapy as a transformative paradigm that leverages circadian principles to optimize therapeutic timing, enhancing efficacy while minimizing adverse effects. Future research directions aimed at elucidating mechanistic foundations and accelerating clinical translation are outlined. A comprehensive understanding of circadian-immune system dynamics not only provides fundamental insights into biological regulation but also establishes a chronobiological framework for precision medicine in immune-mediated disorders.
Despite extensive research, the systemic biological mechanisms underlying exercise-induced physiological adaptations remain incompletely understood. While animal models (e.g., rodents, non-human primates) have been instrumental in elucidating exercise-mediated benefits in aging and disease, interspecies differences in genomics, epigenetics, and metabolic regulation limit their translational relevance. The advent of induced pluripotent stem cell (iPSC)-derived 3D organoids revolutionizes exercise biology research by enabling human-specific modeling of tissue architecture and donor genomic/epigenetic profiles. This review highlights three transformative strategies: (1) Athlete-derived organoids preserving exercise-induced epigenetic memory to study muscle/neural adaptations; (2) Engineered systems integrating optogenetics and microfluidics to simulate mechanical forces (e.g., muscle contraction) and systemic signals (e.g., cytokines); (3) multi-omics mapping revealing exercise-responsive pathways like mitochondrial biogenesis. Collectively, these patient-specific models bridge pathophysiology with high-throughput screening, advancing precision medicine—from personalized training regimens to therapies counteracting sedentary-related diseases.
Research on the molecular progression of esophageal squamous dysplasia to cancer remains limited. The majority of prior studies have focused on morphological precancerous lesions sampled adjacent to tumors, and have relied primarily on the analysis of data from whole-exome sequencing.
To investigate the development of esophageal squamous cell carcinoma (ESCC), whole genome analysis was conducted on 13 precancerous tissues and 15 ESCC tissues. Field effects were avoided by using biopsies of squamous dysplasia from patients without concurrent tumor, thereby allowing study of molecular alterations associated with the true precancerous state.
Our results revealed frequent copy number alterations (CNAs) and structural variants (SVs) in esophageal squamous dysplasia. These changes were also detected in ESCC, indicating that genomic instability markers such as CNAs and SVs occur at an early stage and persist throughout ESCC evolution. The detection of TP53 mutations and CASP8 deletions in both premalignant lesions and ESCC suggests they may be early driving events during esophageal carcinogenesis. Mutations in MUC5B were observed in 7.7% of precancerous lesions and 6.7% of ESCC. Moreover, these mutations were associated with a higher tumor mutational burden (TMB) and an immune “hot” tumor microenvironment. Apolipoprotein B mRNA-editing catalytic polypeptide-like (APOBEC) enzyme-associated mutational signatures were exclusively identified in ESCC and may further exacerbate genomic instability in the more advanced stages of tumorigenesis. Significantly higher ploidy alterations levels were detected in ESCC compared to squamous dysplasia. Moreover, the cohort that underwent local recurrence of dysplasia within two years had significantly elevated ploidy alterations levels compared to those with no long-term recurrence. These results indicate that elevated levels of aneuploidy and genomic instability were associated with tumor progression and local recurrence of dysplasia.
Mutations in TP53 and MUC5B, as well as deletion of CASP8, may be early driver events in carcinogenesis and could precede the emergence of the APOBEC mutation signature. Moreover, ploidy alterations confer a selective advantage to genomically unstable cells, thereby promoting their progression toward malignant transformation. Collectively, our results demonstrate that genomic instability is prevalent in precancerous lesions and intensifies during the late stages of tumor progression. Cells with a certain level of genomic instability appear to possess a competitive advantage for malignant transformation.
The tumor microenvironment, especially the extracellular matrix (ECM), plays a critical role in cancer initiation and progression, although its underlying mechanisms remain incompletely understood. Conventional therapies (such as chemotherapy, surgery, and radiotherapy) often produce unsatisfactory outcomes. Immunotherapy, while showing limited clinical success to date, holds considerable promise. Growing evidence indicates that the biophysical properties of the ECM interact with immune cells, contributing to mechanisms of immunotherapy resistance in cancer. Alterations in these ECM properties can impair immune cell infiltration and function, thereby diminishing the effectiveness of immunotherapeutic approaches. This review explores how the biophysical features of the ECM and their crosstalk with tumor immune evasion pathways highlight the potential of ECM-targeted immunotherapy as an innovative strategy for cancer treatment.
Congenital heart disease (CHD) is characterized by structural and functional anomalies of the heart and major blood vessels present at birth. It is recognized as the most common congenital defect. Epidemiological studies highlight the substantial contribution of genetic factors to CHD pathogenesis. In our previous study, RNA polymerase II subunit I (POLR2I protein) was identified as a candidate genetic contributor to CHD. However, its functional role remains largely unexplored.
First, we performed bioinformatics analyses to evaluate the evolutionary conservation of the POLR2I protein across vertebrate species. The amino acid sequence similarity of the POLR2I protein exceeds 90% in different vertebrates, suggesting a correlation between their species. Quantitative real-time PCR (qRT-PCR) revealed significantly elevated polr2i gene expression during early embryonic stages and in adult zebrafish organs, including the heart, eyes, and brain. Morpholino oligonucleotide (MO)-mediated gene editing was used to downregulate the polr2i gene in zebrafish, and rescue experiments were performed by co-injecting capped polr2i gene mRNA. Transgenic zebrafish labeled with specific fluorescent protein facilitated detailed studies of cardiac and vascular development, myocardial mitochondrial quality, and embryonic asymmetry, respectively. Hemoglobin staining with o-Dianisidine assessed red blood cell accumulation.
Knocking down the polr2i gene through MO significantly disrupted developmental trajectories, as evidenced by reduced body size, axial curvature, enlarged yolk sacs, and elevated malformation and mortality rates. Rescue experiments confirmed the specificity of these phenotypes to polr2i gene loss. Affected embryos displayed elongated heart tubes with reduced overlap between chambers and significant pericardial edema, indicating severe cardiac malformations or functional impairments. Measured volume per beat, ejection fraction, and cardiac output decreased substantially. Furthermore, expression levels of critical cardiovascular markers were markedly reduced. Angiogenic processes were also disrupted, as evidenced by the reduced formation of intersegmental vessels and the caudal vein plexus. Impaired mitochondrial quality in myocardial cells was observed post-knockdown, along with notable defects in the left-right asymmetry of the heart, liver, and pancreas.
Knockdown of the polr2i gene not only impairs cardiac structure and function but also disrupts the normal developmental asymmetry of multiple organs. These findings enhance our understanding of polr2i gene’s role in CHD and underscore its potential as a therapeutic target.
Macrophage infiltration is prevalent in lung cancer tissues, significantly influencing disease progression and clinical outcomes. Lung squamous cell carcinoma (LUSC) is often diagnosed at advanced stages, resulting in poor prognosis. Identifying effective diagnostic biomarkers, particularly those associated with macrophage infiltration, is crucial for early detection and improved treatment outcomes. This study aims to identify diagnostic markers specifically linked to M1 macrophages in LUSC.
Differential gene expression analysis and immune cell infiltration assessment were conducted using the limma and CIBERSORT packages. The WGCNA algorithm was then applied to identify genes in modules related to M1 macrophages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to investigate the biological functions of M1 macrophage-related differentially expressed genes (DEGs). To identify M1 macrophage-associated biomarkers in LUSC, a diagnostic model was developed using four machine learning algorithms, with validation through nomogram visualization, calibration curves, and external datasets. Finally, immunohistochemical staining was performed to further confirm the expression of hub genes and the predictive accuracy of M1 macrophage-related biomarkers in LUSC.
A total of 143 M1 macrophage-related DEGs were identified, which were involved in regulating immune response pathways. The support vector machine (SVM) model based on these genes demonstrated exceptional performance, with area under the curve (AUC) values of 0.995 in the training cohort and 1.000 in three external validation datasets. Immunohistochemical analysis further confirmed the diagnostic accuracy of Matrix metalloproteinase-7 (MMP7), Reticulon-1 (RTN1), Zinc finger protein ZIC 2 (ZIC2), Killer cell lectin-like receptor subfamily B member 1 (KLRB1), and C-X-C motif chemokine 13 (CXCL13), yielding an AUC of 0.992. These results highlight the strong diagnostic capability of the 5 hub genes in LUSC.
The study highlights the pivotal role of M1 macrophage-related DEGs in LUSC tumorigenesis. The newly identified 5 hub genes provide a highly accurate diagnostic tool for LUSC, offering potential improvements for both diagnostic and therapeutic strategies.
Osteosarcoma (OS) is a highly aggressive primary bone malignancy with a prominent propensity for metastasis. The identification of the key molecular drivers for OS progression is paramount to developing effective therapies. Although kinesin family member 18A (KIF18A) has previously been suggested to play a role as a potential oncogene in the development and metastatic progression of several types of cancer, little is known about its exact functional role in OS.
OS datasets were retrieved from the GSE126209 database and the TARGET dataset, with a focus on expression data of kinesin family genes. Differential expression analysis of these genes was conducted using R, comparing tumor tissues to paired adjacent non-tumor tissues, as well as between metastatic and non-metastatic cases. In order to illuminate the functional mechanism, pathway enrichment analysis was executed through Gene Set Enrichment Analysis (GSEA), and the tumor immune microenvironment composition was analyzed comprehensively using the CIBERSORT algorithm. Functional experiments were conducted to investigate the effects of OS KIF18A on cell behaviors. In vivo experiments were used to identify the function of KIF18A on tumor growth. In addition, drug sensitivity profiling and analysis of the lncRNA-mediated regulatory network were implemented to seek possible therapeutic relevance.
Analysis of the kinesin family gene expression in the GSE126209 OS dataset revealed that KIF18A is markedly upregulated in tumor tissues compared to normal counterparts. Further analysis of the TARGET database indicated that elevated KIF18A expression is associated with metastatic OS, a finding that was validated using clinical samples from OS patients. Our functional assay indicated that KIF18A increased proliferation, invasion, and migration activity of OS cells in vitro and inhibited apoptosis. In line with this, the knockdown of KIF18A remarkably suppressed tumor growth in OS xenograft models in vivo. Pathway enrichment analysis revealed dysregulation of several key signaling pathways associated with KIF18A expression, providing mechanistic insights into its oncogenic role. Immune profiling indicated that high KIF18A expression was linked to an immunosuppressive tumor microenvironment. Furthermore, drug sensitivity analysis indicated that lower KIF18A expression was associated with a higher sensitivity to lapatinib. Additionally, a set of lncRNAs associated with KIF18A expression was identified, implicating potential regulatory networks involved in OS progression.
This study reveals that KIF18A is upregulated in OS, particularly in metastatic cases, and is linked to poor clinical outcomes. Functional experiments confirm that KIF18A promotes proliferation, migration, and invasion of OS cells while suppressing apoptosis. In vivo experiments reveal that KIF18A knockdown strongly inhibits tumor growth. KIF18A expression correlates with dysregulation of key oncogenic pathways, an immunosuppressive microenvironment, and potential immunotherapy resistance. These results highlight KIF18A’s role as a pivotal oncogene in OS progression and suggest its promise as both a prognostic biomarker and a therapeutic target.
Acute lung injury (ALI) triggered by sepsis continues to pose a significant difficulty in clinical practice. Due to its anti-inflammatory and antioxidant activities, calcitonin is considered a potential therapeutic option in sepsis.
Bioinformatics analysis was performed using the GSE89376 and GSE67652 datasets. Serum levels of CD3D and NLR family pyrin domain containing 3 (NLRP3) inflammasome, as well as high-mobility group box 1 (HMGB1)/myeloid differentiation primary response gene 88 (MyD88)/nuclear factor-κB (NF-κB) pathway components, were evaluated in sepsis/ALI patients. The effects of calcitonin and CD3D knockdown on human pulmonary microvascular endothelial cells (hPMECs) activated by lipopolysaccharide (LPS) were investigated in vitro. Experimental assays, including quantitative real-time polymerase chain reaction (qRT-PCR), Cell Counting Kit-8 (CCK-8) assay, western blotting (WB), enzyme-linked immunosorbent assay (ELISA), and flow cytometry, were used to assess cell viability, apoptosis, cell cycle, and oxidative stress markers.
CD3D was identified as a key sepsis/ALI-associated hub gene and correlated with NF-κB pathway activation in patients. CD3D silencing in hPMECs effectively suppressed LPS-induced inflammation, oxidative stress, apoptosis, and G1 phase arrest by downregulating the expression of NLRP3, phosphorylation (p)-NF-κB, MyD88, and HMGB1. Calcitonin alone mitigated LPS-induced injury in a dose-dependent way and further enhanced the protective impacts of CD3D knockdown. Co-treatment resulted in synergistic inhibition of interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α, a reduction in oxidative markers, restoration of antioxidant capacity (superoxide dismutase (SOD) and glutathione (GSH)), improved endothelial cell viability, and attenuation of apoptosis. Notably, combined treatment more robustly suppressed the HMGB1/MyD88/NF-κB pathway than either intervention alone.
CD3D exacerbates sepsis-induced ALI by potentiating the HMGB1/MyD88/NF-κB pathway and NLRP3 inflammasome, driving inflammation and oxidative stress. Combined CD3D knockdown and calcitonin treatment offers a novel synergistic therapeutic strategy for mitigating pulmonary endothelial injury in sepsis.
Faust Akl et al. revealed in Nature a paradigm-shifting mechanism distinct from myeloid-driven immunosuppression, whereby glioblastoma induces T-cell apoptosis via tumor-derived IL-11, prompting astrocytes to reprogram into immunosuppressive tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)+ effectors, thereby establishing astrocytes as active immunomodulators. Therapeutically, herpes simplex virus type 1 (HSV-1) (anti-TRAIL) achieves a dual therapeutic effect, offering novel strategies to overcome glioblastoma (GBM)’s evasion tactics.
Bladder outlet obstruction (BOO) frequently accompanies benign prostate hyperplasia (BPH) in aging males and often leads to bladder fibrosis, a secondary pathological change that contributes to bladder dysfunction. The role of Cathepsin S (CTSS), a cysteine protease associated with immune responses, in this process remains to be fully elucidated.
Bladder tissues from BOO model mice were analyzed using microarray profiling, followed by Gene Ontology (GO) and pathway enrichment analyses. Candidate genes, including CTSS, C-X-C Motif Chemokine Ligand 17 (CXCL17), and Angiopoietin Like 7 (ANGPTL7), were identified. CTSS was selected for further investigation based on its association with fibrotic processes. The functional role of CTSS in smooth muscle cell hypertrophy and fibrosis was verified both in vivo and in vitro. A co-culture system of smooth muscle cells and monocyte–macrophages was used to explore the underlying mechanism.
Microarray and bioinformatic analysis identified CTSS as a key candidate gene associated with immune response in BOO-induced bladder fibrosis. CTSS expression was upregulated in BOO bladders and was demonstrated to promote smooth muscle cell hypertrophy and fibrotic changes. Mechanistically, CTSS mediated proteolytic cleavage of the interleukin-6 receptor (IL-6R) on immune cells, generating soluble IL-6R (sIL-6R). This process facilitated IL-6 trans-signaling, which in turn promoted smooth muscle cell hypertrophy and exacerbated bladder fibrosis.
These findings indicate that CTSS contributes to BOO-induced bladder dysfunction and fibrosis by activating IL-6 trans-signaling through cleavage of IL-6R. CTSS may represent a potential therapeutic target for mitigating bladder fibrosis in BPH.
Resistance to anoikis is a critical mechanism that enables metastatic dissemination. Abrogation of this cellular safeguard is therefore a hallmark of aggressive cancer progression. Despite the importance of anoikis, there are still few biomarkers among anoikis-related genes (ARGs) that could aid in the prognostication of bladder cancer (BC) patients and potentially serve as drug targets.
This study leveraged bioinformatics analyses of publicly available BC datasets to evaluate the association between differentially expressed ARGs and patient prognosis. Least Absolute Shrinkage and Selection Operator (LASSO) regression analysis was employed to build a novel prognostic signature model for BC based on ARGs. This model was also used to predict the response of BC to anticancer drugs. Additionally, immunohistochemistry was used to assess expression of the key gene, MYC, in BC samples obtained from patients undergoing surgery and from those receiving immune checkpoint inhibitor (ICI) therapy.
The ARG-based signature, developed and validated through the analysis of public databases, was an independent predictor of patient outcomes. Furthermore, it effectively stratified patients into two cohorts (high- and low-risk), allowing investigation of differential drug sensitivities. The risk stratification model identified 10 ARGs (IGF1, CALR, E2F1, MYC, PLK1, SATB1, FASN, ID2, RAC3, and GKN1) as potential therapeutic vulnerabilities. Notably, MYC was identified as a central hub gene within the ARG signature. Elevated MYC expression was strongly associated with worse prognosis in muscle-invasive bladder cancer (MIBC), and with a diminished response to immunotherapy.
This work demonstrated significant prognostic value for the ARG-based model. Specific ARGs could function as crucial biomarkers for patient outcome, while simultaneously offering new avenues for therapeutic intervention.
Primary liver cancer (PLC) exhibits a high incidence and mortality rate. Early diagnosis and effective treatment are crucial for improving patient survival rates. This study aims to identify biomarkers of hepatitis B-related liver cancer and establish a new method for molecular subtype classification based on differential metabolite-related regulatory gene expression profiles.
This study collected sterile midstream urine samples from patients with hepatitis B-related liver cancer who had not received standardized systematic antiviral therapy or anticancer therapy, as well as from healthy controls. Potential biomarkers were identified through liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based metabolomics, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis performed on the differential metabolites. Gene expression data of 371 hepatocellular carcinoma (HCC) samples in The Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) database were clustered using gene annotations for differential metabolites derived from the Human Metabolome Database (HMDB). The Kaplan-Meier (KM) survival curve was employed to assess the prognosis of different HCC molecular subtypes. Expression differences of subtype-specific genes and their enrichment in Hallmark, KEGG and Gene Ontology (GO) pathways were analyzed. The Tumor Immune Dysfunction and Exclusion (TIDE) scoring tool was used to evaluate the subtypes’ response to immunotherapy. Sensitivity to sorafenib was also compared across the different subtypes.
A total of 53 differential metabolites were identified (p < 0.01), which were significantly enriched in seven metabolic pathways (p < 0.05). Three potential biomarkers were discovered: Suberic acid, 2′-O-methylcytidine, and 3′-Sialyllactose. Regulatory genes associated with these differential metabolites clustered HCC samples from the TCGA-LIHC database into two molecular subtypes (C1 and C2). KM survival analysis indicated that patients in the C2 subtype exhibited higher overall survival compared to those in C1. Differential genes between the two subtypes were significantly enriched in Hallmark, KEGG and GO pathways. The TIDE scoring tool revealed a higher likelihood of immune escape in C1 subtype patients. Molecular targeted drug analysis suggested that sorafenib may be more effective in patients with the C1 subtype.
Suberic acid, 2′-O-methylcytidine, and 3′-Sialyllactose hold promise as metabolic biomarkers for hepatitis B-related liver cancer. Understanding the diversity of the human liver cancer gene expression profile from a metabolomic perspective has potential applications for developing novel clinical treatment strategies.
Since its introduction in 2008, sorafenib has remained the standard first-line systemic treatment for advanced hepatocellular carcinoma (HCC). Nevertheless, its clinical benefits are often compromised by the rapid emergence of drug resistance. This study explores the molecular mechanisms underlying sorafenib resistance, with particular emphasis on the involvement of connective tissue growth factor (CCN2/CTGF) in the regulation of c-Met signaling pathways.
We began by evaluating CCN2 expression levels in HCC tissue samples via immunohistochemistry and analyzing their correlation with clinicopathological characteristics. To functionally characterize CCN2, we established stable HCC cell lines with either knockdown or overexpression of the gene using lentiviral transduction. The effects of CCN2 on cellular proliferation and drug resistance were evaluated using cell counting kit-8 (CCK-8) and colony formation assays. To elucidate the downstream signaling mechanisms, a tyrosine kinase PCR array was employed to identify expression changes within the tyrosine kinase superfamily after CCN2 knockdown. Further investigation into the molecular mechanism by which CCN2 promotes sorafenib resistance was conducted using real-time quantitative PCR (RT-qPCR), western blotting, and immunofluorescence. Finally, the therapeutic potential of co-targeting CCN2 and sorafenib was validated in a nude mouse xenograft tumor model.
Our results establish that CCN2 overexpression significantly enhances HCC proliferation, while also inducing resistance to sorafenib. Mechanistically, we identified that CCN2 binds to integrin αV, triggering focal adhesion kinase (FAK) phosphorylation, which in turn promotes yes-associated protein (YAP) nuclear translocation and leads to the transcriptional upregulation of c-Met. This proposed signaling axis was consistently supported by tyrosine kinase PCR array, co-immunoprecipitation, and western blot analyses. Ultimately, in vivo experiments confirmed that simultaneously targeting CCN2 and administering sorafenib produces a synergistic effect, markedly inhibiting tumor growth and restoring therapeutic sensitivity.
These results not only elucidate a novel CCN2/FAK/YAP/c-Met axis in sorafenib resistance but also provide a mechanistic rationale for dual-targeting strategies to improve outcomes in advanced HCC.
Sepsis is a life-threatening condition characterized by a dysregulated host response to infection, often leading to multiorgan dysfunction. Despite their clinical importance, early diagnostic biomarkers that reflect organ-specific damage remain inadequately characterized.
Targeted metabolomic profiling of amino acids, organic acids, fatty acids, nucleosides, and kynurenine pathway metabolites was performed on lung, kidney, spleen, and liver tissues obtained from a lipopolysaccharide-induced mouse model of sepsis, using liquid chromatography-tandem mass spectrometry and gas chromatography-tandem mass spectrometry. Univariate and multivariate statistical analyses (principal component analysis and partial least squares discriminant analysis) were performed to identify potential biomarkers, followed by pathway analysis to elucidate their biological relevance.
Twenty-nine metabolites were significantly altered across the four tissues, exhibiting organ-specific metabolic signatures. Tyrosine, epinephrine, 5-hydroxytryptophan, and kynurenic acid in the kidney; serine, 4-hydroxyproline, normetanephrine, xanthosine, uridine, adenosine, succinic acid, cis-aconitic acid, linoleic acid, and eicosadienoic acid in the spleen; alanine, α-aminobutyric acid, ornithine, uridine, adenosine, 5′-deoxy-5′-methylthioadenosine, succinic acid, and cis-aconitic acid in the lung; and α-aminobutyric acid, pipecolic acid, uridine, inosine, adenosine, glycolic acid, and oxaloacetic acid in the liver were identified as potential biomarkers reflecting organ-specific dysfunction in sepsis.
This study highlights the distinct organ-specific metabolic alterations in sepsis and identifies candidate biomarkers that may reflect early organ dysfunction. These findings provide a foundation for the development of precise diagnostic and medical strategies for sepsis.
Myocardial fibrosis is a key pathological driver of Hypertrophic Cardiomyopathy (HCM), contributing to adverse remodeling and poor prognosis. The transforming growth factor-β1/Smad3 (TGF-β1/Smad3) signaling cascade plays a central role in fibrogenesis; however, effective antifibrotic therapies remain limited. Astragalus polysaccharide (APS), a bioactive constituent of Astragalus membranaceus, has demonstrated cardioprotective potential. Nevertheless, the mechanisms underlying its effects in HCM-associated fibrosis remain unknown.
Pressure overload induced HCM was established in C57BL/6J mice using transverse aortic constriction (TAC), and animals were randomized to control, TAC, low-dose APS (50 mg/kg/day), or high-dose APS (100 mg/kg/day) groups. Cardiac function was evaluated by echocardiography, while myocardial hypertrophy and fibrosis were assessed by morphometry, Masson’s staining, and collagen I (Col-I) expression analysis. Parallel in vitro studies employed angiotensin II stimulated (Ang II-stimulated) H9C2 cardiomyocytes, with or without the TGF-β1/Smad3 agonist SRI-011381, to explore mechanistic pathways.
TAC induced marked cardiac dysfunction, ventricular dilation, and extensive fibrosis, accompanied by upregulation of TGF-β1, phosphorylated Smad3, and Col-I expression (all p < 0.05). APS treatment dose-dependently preserved systolic function, attenuated collagen deposition, and suppressed activation of the TGF-β1/Smad3 axis, with the strongest effects observed in the high-dose group. In vitro, APS significantly inhibited Ang II induced hypertrophy and fibrotic protein expression; these effects were abrogated by SRI-011381, confirming pathway specificity.
APS exerts cardioprotective and antifibrotic effects in HCM by inhibiting the TGF-β1/Smad3 signaling pathway. These findings highlight APS as a promising therapeutic candidate for targeting myocardial fibrosis and improving outcomes in HCM.
Small ubiquitin-related modifier protein (SUMO)ylation is a reversible post-translational modification of proteins. SENP5, a SUMO-specific protease, plays key roles in a wide range of cellular processes. This study aims to investigate the potential involvement of SENP5 in lipopolysaccharide (LPS)-induced acute lung injury (ALI).
First, we established LPS-treated human normal lung epithelial cells (BEAS-2B) and a lung injury mouse model. SENP5 expression was then analyzed in vivo and in vitro using quantitative real-time PCR (qRT-PCR), Western blot, hematoxylin–eosin (H&E) staining, and immunohistochemistry. Then, CCK-8 assay and flow cytometry were employed to assess inflammatory response and apoptosis following SENP5 knockdown in LPS-induced BEAS-2B cells. Next, H&E, immunohistochemistry, and survival analysis were conducted to investigate apoptosis and proliferation in SENP5 conditional knockout (cKO) mice. Finally, RNA sequencing was used to screen for differentially expressed genes in SENP5 knockdown BEAS-2B cells. Downstream molecules and signaling pathways were analyzed using Western blot and qRT-PCR.
SENP5 was notably upregulated in both LPS-induced BEAS-2B cells and the lung injury mouse model. In vitro, SENP5 knockdown markedly exacerbated the LPS-induced suppression of BEAS-2B cell viability and promoted inflammatory response and apoptosis. Besides, the conditional knockout of SENP5 significantly increased apoptosis and inhibited proliferation in the lungs of mice. RNA sequencing indicated SENP5 deficiency inhibited solute carrier family 7 member 5/mechanistic target of rapamycin (SLC7A5/mTOR) signaling in LPS-induced BEAS-2B cells. Therefore, we confirmed that SENP5 might exert a protective effect against LPS-induced lung injury by inhibiting apoptosis of lung epithelial cells through the SLC7A5/mTOR signaling pathway.
SENP5 might play a protective role in LPS-induced lung injury by inhibiting apoptosis of lung epithelial cells through the SLC7A5/mTOR signaling pathway.
The C-X-C motif chemokine receptor 3 (CXCR3) antagonist AMG 487 has been shown to alleviate acute lung injury (ALI) in mice. Other CXCR3 antagonists, including NBI-74330, TAK-779, and SCH 546738, exhibit anti-inflammatory effects in various diseases, including apical periodontitis, arthritis, and acute respiratory distress syndrome (ARDS). However, with the exception of AMG 487, the roles of these antagonists in ALI remain poorly understood. Macrophages can differentiate into various phenotypes and play a crucial role in the progression of inflammatory and autoimmune diseases.
In this study, we demonstrate that the CXCR3 agonist C-X-C motif chemokine ligand 10 (CXCL10) enhances macrophage efferocytosis and polarizes inflammatory macrophages toward the M1 phenotype, thereby exacerbating ALI in mice. Conversely, nine CXCR3 antagonists were found to inhibit macrophage efferocytosis and promote the polarization of inflammatory macrophages toward the M2 phenotype, resulting in the alleviation of ALI in mice. Subsequently, molecular docking techniques were employed to analyze interactions between nine CXCR3 antagonists and the CXCR3 protein, with the aim of screening for superior antagonist structures and designing more effective compound configurations targeting the CXCL10-CXCR3 axis. Notably, TAK-779 exhibited the most stable binding affinity to the CXCR3 protein. Furthermore, two newly modified compounds—TAK-779 from imidazolium 1 and TAK-779, 2745583—demonstrated enhanced efficacy compared to the original TAK-779 compound.
All nine CXCR3 antagonists were shown to influence macrophage function to varying degrees and confer protective effects against ALI. These finding suggest that comparative evaluation of CXCR3 antagonists and the discovery of novel compounds may provide new therapeutic targets for the treatment of inflammatory diseases.
Charles Darwin hypothesized that evolution is based on adaptations to a changing environment, and that organisms that developed even slightly favorable variations would ultimately be most likely to survive. This concept is clearly reflected in the life cycles of pathogenic species. While modern antibiotics, antiviral agents, and vaccines can successfully eliminate many pathogens and prevent infections, only susceptible strains are affected. Bacteria and viruses that can adapt and develop resistance mechanisms will survive and thrive in the absence of ongoing competition. We build on this framework by considering the evolutionary impact of microbial-mediated adaptations experienced by the host. For example, intracellular mitochondria, largely believed to be descendants of symbiotic ancestral bacteria, can be specifically targeted by viral pathogens. Taken one step further, we hypothesize that Darwinian theory may also apply to atoms and molecules, which are not “alive” by any conventional definition, but interact with one another and self-assemble according to the principles of thermodynamics that promote stability in defined environments. Building on these foundations, our hypotheses and conceptual framework will facilitate further exploration into the evolution of microbial mechanisms that modulate behavior, shape the development of the immune system, and promote host evolution.
Ankyrin G (ANK3), belonging to the ankyrin family, contributes to cellular structural integrity by linking the cytoskeleton to the plasma membrane. Abnormal ANK3 expression has been reported across several human malignancies, yet the regulatory mechanisms involved are still poorly understood. The process of dividing introns into several steps is referred to as recursive splicing (RS). RS can control the quality of transcripts produced by regulating the retention of the RS-exon. Hundreds of annotated RS-exons in human mRNAs are attributed to the inhibition of RS by the exon junction complex (EJC).
In this study, we demonstrated that ANK3 is reduced in hepatocellular carcinoma (HCC) and suppresses HCC metastasis. We then analyzed the multiple splicing methods of ANK3, confirming that RS exists in ANK3 transcript variant 4 (ANK3-TV4) and that RS was weakened in HCC.
Mechanistically, ANK3 inhibited HCC metastasis, which may be partly attributed to inhibition of the Wnt pathway. ANK3 binds to E-cadherin via its N-terminal ankyrin repeat domain to regulate E-cadherin expression. ANK3 knockdown activates the Wnt pathway, downregulates E-cadherin expression, and promotes its degradation. Conversely, ANK3-TV4 overexpression inhibited the Wnt signaling pathway, upregulated E-cadherin protein expression, and inhibited E-cadherin degradation. RBM8A, a core EJC factor, regulates the RS of ANK3-TV4.
Knockdown of RBM8A promoted RS of ANK3-TV4 and upregulated its expression. We investigate the role of RS in HCC, providing a novel therapeutic perspective and identifying potential targets for intervention.
As a major contributor to cancer-associated deaths, advanced colorectal cancer (CRC) has a constrained range of effective treatment options. The short isoform of bromodomain-containing protein 4 (BRD4-S) has recently been implicated as a potential oncogenic driver; however, its regulatory mechanisms and functional role in CRC remain incompletely understood.
BRD4-S expression, regulation, and function in CRC were investigated through bioinformatics analyses of the Cancer Genome Atlas (TCGA) datasets, in vitro studies using CRC cell lines (HT29, SW620), and in vivo xenograft models in nude mice. Experimental approaches included quantitative real-time PCR (qRT-PCR), Western blotting, co-immunoprecipitation, RNA immunoprecipitation, immunofluorescence, colony formation, Cell Counting Kit-8 (CCK-8), and scratch assays. Gene enrichment and interaction analyses were performed to identify relevant pathways and molecular partners.
BRD4-S was markedly upregulated in CRC tissues and cell lines, and elevated BRD4-S expression correlated with poorer patient survival. Silencing BRD4-S, but not BRD4-L, significantly impaired CRC cell proliferation, migration, and tumor growth in vivo. Mechanistically, the RNA helicase DEAD-box helicase 27 (DDX27) interacted with Serine and Arginine Rich Splicing Factor 6 (SRSF6) to promote alternative splicing of BRD4 pre-mRNA toward the BRD4-S isoform. Inhibition of SRSF6 phosphorylation suppressed BRD4-S production and blocked activation of the mitogen-activated protein kinase (MAPK)/extracellular regulated protein kinases ERK signaling pathway, identified as a key downstream effector of BRD4-S.
This study defines a novel DDX27–SRSF6–BRD4-S–MAPK/ERK signaling axis that drives CRC progression. These findings underscore the therapeutic potential of targeting BRD4 isoform switching and its regulatory splicing machinery in CRC.
The Ralstonia solanacearum species complex (RSSC) is a group of destructive plant-pathogenic bacteria that targets a wide range of economically important crops across the globe, including tomato, pepper, and tobacco. Extensive research on this plant pathogen is essential due to the severe losses it inflicts on agricultural production.
We isolated strain MLY158 from diseased tobacco, identifying it as Ralstonia pseudosolanacearum. The strain was characterized genomically by biochemical profiling, genome sequencing, compositional and functional annotation, and comparative genomics.
MLY158 was capable of utilizing D-glucose (dGLU), sucrose (SAC), and D-trehalose dihydrate (dTRE). The genome had a total size of 5.88 MB and consisted of a circular chromosome and a circular megaplasmid. It contained 5485 coding genes and had a GC content of 67.50%. Comparative genomic results revealed that MLY158 is closely related to R. pseudosolanacearum strain GMI1000 (average nucleotide identity (ANI) value of 99.03%). MLY158 has 527 special genes and 13 homologous genes of species-specific gene families. The primary differences between MLY158 and genomes from other strains are located in the phage protein region and show characteristics of high genomic uniqueness.
Complete genome sequence analysis of MLY158 has contributed important information regarding the genome of the bacterial wilt disease pathogen R. pseudosolanacearum. This work provides useful references for future research into molecular disease control strategies and disease-resistant breeding.
In recent years, neuroglia has become a therapeutic target for neurodegenerative diseases. Despite the recognition of a variety of microglial morphologies associated with the neuroinflammatory process that involve diverse functionalities for this glial type, it is still unknown its beneficial or harmful role to the surrounding tissue.
The study presented here proposes a novel approach to the neurodegenerative progression based on the reliability of its results due to the use of a natural model. Morphological alterations in microglia were assessed in cerebellar samples from prion-affected individuals at different stages of the natural disease (pre-clinical, clinical and terminal).
Immunohistochemical profiles confirmed that the abundance and morphology of the cells were found irrespective of the stage of the disease. Only an evident association of dystrophic pattern with advanced stages of the neurodegenerative process of scrapie was consistently demonstrated.
Overall, we conclude that the observations described here support a potential failure of microglial cells that could perhaps lead to their inability to perform some of their physiological functions, maybe due to a senescent state. Gaining insight into the multifaceted roles of neuroglia in central nervous system (CNS) diseases is of critical importance in knowledge and understanding of CNS disease pathogenesis, but also in generating novel therapeutic strategies.