Cytoscape Automation: empowering workflow-based network analysis

An integrative approach to identifying NPC1 as a susceptibility gene for gestational diabetes mellitus

OBJECTIVE

The objective of this study was to identify a novel gene and its potential mechanisms associated with susceptibility to gestational diabetes mellitus (GDM) through an integrative approach.

METHODS

We analyzed data from genome-wide association studies (GWAS) of GDM in the FinnGen R11 dataset (16,802 GDM cases and 237,816 controls) and Genotype Tissue Expression v8 expression quantitative trait locus data. We used summary-data-based Mendelian randomization to determine associations between transcript levels and phenotypes, transcriptome-wide association studies to provide insights into gene-trait associations, multi-marker analysis of genomic annotation to perform gene-based analysis, genome-wide complex trait analysis-multivariate set-based association test-combo to determine gene prioritization, and polygenic priority scores to prioritize the causal genes to screen candidate genes. Subsequent Mendelian randomization analysis was performed to infer causality between the candidate genes and GDM and phenome-wide association study (PheWAS) analysis was used to explore the associations between selected genes and other characteristics. Furthermore, to gain a deeper understanding of the functional implications of these susceptibility genes, GeneMANIA analysis was used to determine the fundamental biological functions of the therapeutic targets and protein-protein interaction network analysis was performed to identify intracellular protein interactions.

RESULTS

We identified two novel susceptibility genes associated with GDM: NPC1 and KIAA1191. Magnetic resonance imaging revealed a strong correlation between NPC1 expression levels and a lower incidence of GDM (odds ratio: 0.922, 95% confidence interval: 0.866-0.981, p = 0.011). PheWAS at the gene level indicated that NPC1 was not associated with any other trait. The biological significance of this gene was evidenced by its strong association with sterol metabolism.

CONCLUSION

Our study identified NPC1 as a novel gene whose predicted expression level is linked to a reduced risk of GDM, providing new insights into the genetic framework of this disease.

An immunocompetent mouse model revealed that congenital Zika virus infection disrupted hippocampal function by activating autophagy

Congenital Zika virus (ZIKV) infection significantly affects neurological development in infants and subsequently induces neurodevelopmental abnormality symptoms; however, the potential mechanism is still unknown. Therefore, in order to effectively intervene in neurodevelopmental abnormalities in infected infants, it is necessary to identify the main brain regions affected by congenital infection. In this study, we constructed a congenital ZIKV-infected murine model using immunocompetent human STAT2 knock-in mice, which presented long-term neurodevelopmental abnormalities with abnormal neurodevelopmental symptoms. We found that the hippocampus, which regulates cognitive behaviour and processes spatial information and navigation, was the main brain region affected by congenital infection and that hippocampal cells were more prone to autophagy during the growth period of these mice at the transcriptional and pathological levels. These findings highlighted that congenital ZIKV infection could interrupt hippocampal function by activating autophagy, thus providing a theoretical basis for the clinical treatment of congenital ZIKV-infected infants.

Transcriptome responses to single and combined stressors in seagrass populations from pristine and impacted sites reveal local adaptive features and core stress-response genes

In their natural habitats, seagrasses face multiple abiotic stressors, which can often occur simultaneously. However, most studies have only focused on growth and physiological responses to single stressors. Here, we examined transcriptome responses of the tropical seagrass Halophila stipulacea collected from a northern Gulf of Aqaba pristine site and an anthropogenically-impacted site, grown in a mesocosm, and exposed to ecologically-relevant, single and combined, thermal and excess nutrient stressors. Growth of plants from the impacted site was more tolerant to stress than plants from the pristine site. The combined thermal and nutrient stressor elicited greater transcriptome reprogramming than the single stressors in both populations and induced the expression of a combination-specific set of genes involved in stress responses. Furthermore, thermal stress exerted a dominant influence upon the transcriptome response to the combined stressor. Transcriptomes of plants from the impacted site displayed reduced responsiveness to stress, the presence of genes exhibiting a "stress-ready" mode of expression under all stressors, and increased resilience (recovery to control transcriptomes). We also identified core stress-response genes that could be leveraged as early indicators of stress in the field. Overall, our data suggest that environmental conditions in seagrass habitats can drive local molecular adaptation, and that the response of seagrasses to combined stressors associated with climate change and coastal anthropogenic stressors cannot be predicted from the response to single stressors.

Identification of potential biomarkers in cardiovascular calcification based on bioinformatics combined with single-cell RNA-seq and multiple machine learning analysis

BACKGROUND

The molecular and genetic mechanisms underlying vascular calcification remain unclear. This study aimed to determine the differences in calcification marker-related gene expression in macrophages.

METHODS

The expression profiling datasets GSE104140 and GSE235995 were analysed to identify differentially expressed genes (DEGs) between fibroatheroma with calcification and diffuse intimal thickening. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, Weighted Gene Co-expression Network Analysis (WGCNA), and Gene Set Enrichment Analysis (GSEA) were performed to assess functional characteristics. Hub genes were identified through a protein-protein interaction (PPI) network and machine learning approaches. Single-cell RNA sequencing data (GSE159677) validated the expression of calcification-related genes in macrophages, while Mendelian randomization analysis explored their potential causal relationship with coronary calcification. Further validation was conducted using enzyme-linked immunosorbent assay (ELISA) on coronary calcification samples and immunohistochemistry in ApoE-/- mice. Intravascular ultrasound was performed to assess coronary calcification severity.

RESULTS AND CONCLUSIONS

Two key biomarkers, ITGAX and MYD88, were identified as diagnostic indicators of cardiovascular calcification. Both biomarkers were significantly upregulated in calcified samples and were strongly associated with immune processes. Single-cell RNA sequencing confirmed their high expression in multiple immune cell types. Additionally, molecular docking analysis revealed that retinoic acid interacted with both biomarkers, suggesting potential therapeutic relevance. Immunohistochemical and ELISA analyses further validated their elevated expression in calcified samples. These findings provide novel insights into the molecular mechanisms of vascular calcification and highlight potential diagnostic and therapeutic targets.

Effective data visualization strategies in untargeted metabolomics

Covering: 2014 to 2023 for metabolomics, 2002 to 2023 for information visualizationLC-MS/MS-based untargeted metabolomics is a rapidly developing research field spawning increasing numbers of computational metabolomics tools assisting researchers with their complex data processing, analysis, and interpretation tasks. In this article, we review the entire untargeted metabolomics workflow from the perspective of information visualization, visual analytics and visual data integration. Data visualization is a crucial step at every stage of the metabolomics workflow, where it provides core components of data inspection, evaluation, and sharing capabilities. However, due to the large number of available data analysis tools and corresponding visualization components, it is hard for both users and developers to get an overview of what is already available and which tools are suitable for their analysis. In addition, there is little cross-pollination between the fields of data visualization and metabolomics, leaving visual tools to be designed in a secondary and mostly ad hoc fashion. With this review, we aim to bridge the gap between the fields of untargeted metabolomics and data visualization. First, we introduce data visualization to the untargeted metabolomics field as a topic worthy of its own dedicated research, and provide a primer on cutting-edge visualization research into data visualization for both researchers as well as developers active in metabolomics. We extend this primer with a discussion of best practices for data visualization as they have emerged from data visualization studies. Second, we provide a practical roadmap to the visual tool landscape and its use within the untargeted metabolomics field. Here, for several computational analysis stages within the untargeted metabolomics workflow, we provide an overview of commonly used visual strategies with practical examples. In this context, we will also outline promising areas for further research and development. We end the review with a set of recommendations for developers and users on how to make the best use of visualizations for more effective and transparent communication of results.

Exploring the pharmacokinetic, toxicity and anti-arthritic activity of bioactive polyphenols to mitigate the HIF-regulated angiogenic-pannus growth in rheumatoid arthritis

Current therapies for rheumatoid arthritis, including anti-inflammatory agents and immunomodulators, primarily target common inflammatory mechanisms. However, the efficacy of most bioactive compounds claimed to possess anti-arthritic properties remains mechanistically unproven, particularly against progressive conditions like pannus development. This study investigates the pharmacokinetics, toxicity, and impact of reported anti-arthritic polyphenols on HIF-regulated pannus development in rheumatoid arthritis through in silico and in vitro approaches. Eighty bioactive compounds with documented anti-arthritic properties were selected from the literature and subjected to sequential evaluation of pharmacodynamic and pharmacokinetic activity. The study identified five promising candidates qualified to perform in vivo toxicity and in vitro biochemical assays. Toxicity testing using Galleria mellonella larvae indicated dose-dependent effects on the midgut, with no mortality observed at doses up to 2000 mg/kg body weight. In vitro assays, including antioxidant and anti-inflammatory evaluations, further validated the therapeutic potential of these compounds. Compounds that satisfied all predictive criteria were subjected to molecular interaction analysis against hub-gene targets implicated in HIF-regulated angiogenesis in rheumatoid arthritis. RA-associated proteins were identified from NCBI-GEO and DisGeNET (GWAS) databases. Functional annotation and protein-protein interaction analysis identified IL-6, IL-1β, HIF-1α, PPARG, and TIMP1 as key hub targets. Molecular docking using PyRx revealed the binding affinities of the selected bioactive compounds against these targets. These findings suggest that the screened bioactive polyphenols exhibit low toxicity and hold potential as regulators of HIF-mediated angiogenesis in rheumatoid arthritis, offering a novel therapeutic approach for progressive disease management.

Purine nucleoside phosphorylase dominates Influenza A virus replication and host hyperinflammation through purine salvage

Influenza A virus (IAV) poses a significant threat to human health. The outcome of IAV results from the viral-host interaction, with the underlying molecular mechanisms largely unknown. By integrating the plasma proteomics data of the IAV-infected patients into the viral-inflammation protein-protein interaction (VI-PPI) network created in this study, purine nucleoside phosphorylase (PNP), the critical enzyme in purine salvage, was identified as a potential hub gene that connected the different stages of IAV infection. Extended survival rates and reduced pulmonary inflammatory lesions were observed in alveolar epithelial cell (AEC)-specific PNP conditional knockout mice upon H1N1 infection. Mechanistically, PB1-F2 of IAV was revealed as a novel viral transcriptional factor to bind to the TATA box of PNP promoter, leading to enhanced purine salvage in H1N1-challenged AECs. The activation of PNP-mediated purine salvage was verified in IAV-infected patients and A549 cells. PNP knockdown elicited a purine metabolic shift from augmented salvage pathway to de novo synthesis, constraining both viral infection and pro-inflammatory signaling through APRT-AICAR-AMPK activation. Moreover, durdihydroartemisinin (DHA), predicted by VI-PPI as a novel PNP inhibitor, exerted beneficial effects on the survival and weight gain of H1N1-challenged mice via its direct binding to PNP. To reveal for the first time, we found that PNP, activated by IAV, plays a hub role within H1N1-host interaction, simultaneously modulating viral replication and hyperinflammation through purine salvage. Our study sheds new light on a "two-for-one" strategy by targeting purine salvage in combating IAV-related pathology, suggesting PNP as a potential novel anti-influenza host target.

Integrated transcriptomics and lipidomics reveal mechanisms regulating lipids formation and accumulation in oil body during walnut seed development

BACKGROUND

Through combined analysis of the transcriptomics and lipidomics of walnut, the possible molecular mechanism of lipid formation and accumulation in oil bodies was revealed.

CONCLUSION

The formation and accumulation of lipids are critical determinants of nut quality, with walnut storing lipids primarily in oil bodies (OBs). Currently, there is still a lack of systematic research on the formation and accumulation of lipids in walnut OBs (WOBs). Therefore, this study integrated lipidomics and transcriptomics to comprehensively identify the changes in WOBs and walnut kernels at 60, 74, 88, 102, 116, and 130 days after pollination (DAP). The results showed that fatty acid content in walnut kernels and WOBs had opposite trends, especially oleic, linoleic, and linolenic. Principal component analysis of the samples and cluster analysis of differentially expressed genes (DEGs) showed that the total samples were divided into three main groups: 60-74, 88-102, and 116-130 DAP. RNA sequencing generated 33,918 unigenes (14,995 DEGs), including 228 DEGs highly related to lipid metabolism, in 18 cDNA libraries prepared from walnut kernel. These genes were mainly involved in metabolic pathways such as pyruvate metabolism, glycerophospholipid metabolism, glycerolipid metabolism, and fatty acid biosynthesis during lipid synthesis. On the other hand, the expression levels of ACC, KASII, SAD, FAD2, FAD3, and PDAT genes were downregulated at 88-130 DAP compared with 60-74 DAP, which might be the key genes regulating the reduction of free fatty acid content in WOBs. In addition, 21 FAD genes were identified, including seven SAD genes, three FAD2 genes, five FAD3 genes, one FAD5 gene, one FAD6 gene, and four FAD7/8 genes. These genes were closely related to the synthesis of unsaturated fatty acids in WOBs, especially FAD2 and FAD3. The findings offered valuable insights into the dynamic changes in lipids and genetic resources and provided a foundation for walnut quality improvement.

Single cell analysis and bioinformatics reveal pyroptosis mechanisms in hepatocellular carcinoma

BACKGROUND

Hepatocellular carcinoma (HCC) is the third leading cause of cancer related death, and its molecular mechanisms have not been fully elucidated. This study aims to elucidate the molecular mechanisms linking pyroptosis and immune microenvironment changes in HCC, with a focus on macrophage polarization and inflammatory responses.

METHODS

Selected gene expression profiles from the Gene Expression Omnibus database, established protein-protein interaction (PPI) networks, and performed functional enrichment analysis using databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG). The expression of relevant hub genes was verified by immunohistochemistry, real-time quantitative PCR, and Western Blot based on clinical tissues. Single-cell identification of HCC cell types and malignant cells, trajectory analysis, and intercellular signal communication further analyzed the molecular mechanisms between immune cells and liver cells. Bioinformatics combined with single-cell analysis to elucidate the immune pyroptosis molecular mechanism that underlay the development of HCC.

RESULTS

Molecular biology has identified six pyroptosis hub genes in HCC. The key hub genes of immune pyroptosis were validated through immunohistochemistry and in vitro experiments. Enrichment analysis shows that intersecting genes are enriched in immune responses, chemokine mediated signaling pathways, and inflammatory responses. InferCNV and copyKAT accurately predict that malignant cells distribute in HCC tissues, and their main malignant cells may be hepatocytes, endothelium and epithelial cells. Cell trajectory analysis found that monocyte, macrophage polarization could play a first role in HCC. The cellular clustering of single cells revealed the infiltration of immune cells, especially the polarization of macrophages, which plays an important role. Immunohistochemistry suggests that hub genes such as HMGB1, CYCS, GSDMD, IL-1β, NLRP3, and IL18 are the link between macrophage polarization and pyroptosis during HCC development.

CONCLUSIONS

In summary, the main molecular mechanisms underlying the pathogenesis of HCC are related to immune cell infiltration, particularly macrophage infiltration polarization that promotes the secretion of inflammatory factors leading to hepatocyte pyroptosis. These findings provide novel insights into the macrophage-driven pyroptosis pathways in HCC, potentially paving the way for new immunotherapeutic strategies.

Investigation of cognitive enhancements and mechanisms of kinsenoside in APP/PS1 mice through network pharmacology, in vivo experiments, and machine learning

AIMS

To investigate the therapeutic effects of kinsenoside on cognitive dysfunction in APP/PS1 transgenic mice and to explore its potential targets.

MATERIALS AND METHODS

Network pharmacology was employed to identify targets of kinsenoside in Alzheimer's disease (AD). The Morris water maze test was conducted to assess the therapeutic effects of kinsenoside on cognitive dysfunction in APP/PS1 transgenic mice, and immunofluorescence was used to evaluate the impact of kinsenoside on amyloid-beta (Aβ) pathology and brain lymphatic structure and function. The Raybiotech GSM-CAA-4000 protein chip was used to detect changes in inflammatory factors. Graph convolutional network (GCN) analysis was applied to analyze and identify core targets from the protein chip results, which were then intersected with the network pharmacology findings, followed by molecular docking and molecular dynamics simulations.

RESULTS

Network pharmacology analysis indicated that kinsenoside inhibits inflammation and oxidative stress signaling pathways involved in AD. The maximum neighborhood connectivity (MNC) algorithm identified HSP90AA1, HSP90AB1, PIK3CA, STAT3, IL6, and IFNγ as potential targets. In vivo mouse experiments demonstrated that kinsenoside has the ability to reduce Aβ plaque deposition and expand meningeal lymphatic vessels(mLVs), improving the glymphatic system drainage, which ultimately leads to improved cognitive function. This beneficial effect may be related to the inhibition of IFNγ by kinsenoside.

CONCLUSION

Based on preclinical data, kinsenoside shows promising potential in the treatment of AD.

Identification of polychlorinated biphenyls (PCBs) and PCB metabolites associated with changes in the gut microbiome of female mice exposed to an environmental PCB mixture

Polychlorinated biphenyls (PCBs) are neurotoxic hazardous materials that may cause toxicity via the gut-liver-brain axis. This study investigated PCB × microbiome interactions in adult female mice exposed orally to an environmental PCB mixture. Female mice (6-week-old) were exposed daily for 7 weeks to peanut butter containing 0, 0.1, 1, or 6 mg/kg/day of PCBs. Twenty hours after the final exposure, the cecal content was collected to characterize the microbiome composition and predicted function. PCB and its metabolites in feces were analyzed using gas chromatography-tandem mass spectrometry (GC-MS/MS), while cecal content was assessed with liquid chromatography-high resolution mass spectrometry (LC-HRMS). PCB exposure influenced the abundance of microbial taxa and predicted functions within the cecal content. Complex PCB and metabolite mixtures were detected in the gastrointestinal tract. Network analysis revealed associations between specific parent PCBs and metabolites with changes in the abundance of bacteria in the gastrointestinal tract. These findings demonstrate that individual PCBs and their metabolites significantly influence the abundance of specific bacteria in the gastrointestinal tract following oral PCB exposure. These findings inform further research targeting the microbiome to attenuate the adverse health outcomes of PCB exposure.

Carposphere microbiota alters grape volatiles and shapes the wine grape typicality

While specific environments are known to shape plant metabolomes and the makeup of their associated microbiome, it is as yet unclear whether carposphere microbiota contribute to the characteristics of grape fruit flavor of a particular wine region. Here, carposphere microbiomes and berry transcriptomes and metabolomes of three grape cultivars growing at six geographic sites were analyzed. The composition of the carposphere microbiome was determined mainly by environmental conditions, rather than grape genotype. Bacterial microbiota likely contributed to grape volatile profiles. Particularly, candidate operational taxonomic units (OTUs) in genus Sphingomonas were highly correlated with grape C6 aldehyde volatiles (also called green leaf volatiles, GLVs), which contribute to a fresh taste. Furthermore, a core set of expressed genes was enriched in lipid metabolism, which is responsible for bacterial colonization and C6 aldehyde volatile synthesis activation. Finally, a similar grape volatile profile was observed after inoculating the berry skin of two grape cultivars with Sphingomonas sp., thus providing evidence for the hypothetical microbe-metabolite relationship. These results provide novel insight into how the environment-microbiome-plant quality (E × Mi × Q) interaction may shape berry flavor and thereby typicality, serving as a foundation for decision-making in vineyard microbial management.

Transcriptome-derived evidence reveals the regulatory network in the skeletal muscle of the fast-growth mstnb-/- male tilapia

Myostatin (Mstn) negatively regulates muscle growth and Mstn deficiency induced "double-skeletal muscle" development in vertebrates, including tilapias. In this study, we performed a transcriptomic analysis of skeletal muscle from both wild-type and mstnb-/- males to investigate the molecular mechanisms underlying skeletal muscle hypertrophy in mstnb-/- mutants. We identified 4697 differentially expressed genes (DEGs), 113 differentially expressed long non-coding RNAs (DE lncRNAs), 211 differentially expressed circular RNAs (DE circRNAs), and 98 differentially expressed microRNAs (DE miRNAs). The DEGs were significantly enriched in proteasome and ubiquitin-mediated proteolysis pathways. Cis- and trans-targeting genes of DE lncRNAs were also notably enriched in the above two pathways. The putative host genes of DE circRNAs linked to myofibrils, contractile fibers, and so on. Additionally, DE miRNAs were associated with ubiquitin-mediated proteolysis and key signaling pathways, including AMPK, FoxO, and mTOR. Furthermore, the core competing endogenous RNA (ceRNA) network was constructed comprising 31 DEGs, 37 DE miRNAs, 14 DE circRNAs, and 45 DE lncRNAs. The key roles of ubiquitin-proteasome system were highlighted in the ceRNA network. Taken together, this study provides a novel perspective on muscle mass increase in Mstn mutants through the repression of protein degradation and facilitates our understanding of the molecular mechanisms of skeletal muscle hypertrophy in fish.

M2 macrophage-derived exosome facilitates aerobic glycolysis and osteogenic differentiation of hPDLSCs by regulating TRIM26-induced PKM ubiquitination

BACKGROUND

Our previous findings revealed that exosomes derived from M2-polarized macrophages enhance the osteogenic differentiation of human periodontal ligament stem cells (hPDLSCs), and identified key microRNAs (miRNAs) using high-throughput miRNA sequencing. Therefore, the present study aimed to elucidate the role and underlying molecular mechanism by which exosomes derived from M2 macrophages mediate the osteogenic differentiation of hPDLSCs.

METHODS

Following lentiviral-mediated modulation of miR-6879-5p in both hPDLSCs and M2 macrophage-derived exosomes, RT-qPCR, western blotting, and Alizarin Red staining were applied to assess alterations in osteogenic markers, including ALP, OCN, Collagen I, and RUNX2, as well as mineralized nodule formation in hPDLSCs. Immunoprecipitation-mass spectrometry (IP-MS) was employed to identify proteins interacting with miR-6879-5p target genes in hPDLSCs.

RESULTS

Knockdown of miR-6879-5p in the exosomes reduced the expression of osteogenic markers and inhibited calcified nodule formation in hPDLSCs. Overexpression of TRIM26 attenuated the osteogenic differentiation of hPDLSCs, an effect that was reversed by miR-6879-5p overexpression. IP-MS identified 410 TRIM26-interacting proteins in hPDLSCs. These proteins were associated with ubiquitination, aerobic glycolysis, and amino acid metabolism. The hub proteins in the TRIM26-associated PPI network included RPL and RPS family proteins, as well as glycolysis-associated proteins. CO-IP confirmed an interaction between TRIM26 and PKM, and showed that TRIM26 increased PKM ubiquitination. Overexpression of PKM rescued TRIM26-mediated suppression of osteogenic marker expression and mineralized nodule formation in hPDLSCs.

CONCLUSION

miR-6879-5p carried by M2 macrophage-derived exosomes promotes osteogenic differentiation and aerobic glycolysis in hPDLSCs via modulating TRIM26-mediated ubiquitination of PKM.

Therapeutic role of Crateva religiosa in diabetic nephropathy: Insights into key signaling pathways

Crateva religiosa, a plant used in traditional medicine, is valued for its bioactive properties. Traditional approaches are more accepted worldwide as a cost effective alternatives being used in network pharmacology to explore the complex interactions of drug targets among molecular pathways. The study investigated the potential of Crateva religiosa's phytoconstituents using meticulous computational analysis and empirical confirmation. The IMPPAT, GeneCards and DisGeNET data bases were used to obtain the active moieties and disease targets respectively. Crateva phytoconstituent's DN-target network and protein-protein interaction (PPI) network were developed and analyzed using the STRING online platform and Cytoscape software. GO and KEGG analyses were conducted using the g: profiler databases while the process of molecular docking involved the use of MOE software. The screening process identified dillapiole (CR-C1), beta ionone (CR-C2) 10-epi-γ-eudesmol (CR-C3), cis/trans linalool oxide (CR-C4/5) and nerolidol (CR-C6), as potential active phytoconstituents of C. religiosa and AKT1, PPARG, PTGS2, EGFR, ESR1, JAK2, MAPK1, PARP1, GSK3B, and PPARA as matching targets in DN. The enrichment analysis revealed that the common targets were primarily linked to inflammatory response, oxidative stress, immunological modulation, and cell death. The main signal pathways suggested were PI3K-Akt, AGE-RAGE, and IL-17. Moreover, molecular docking analysis determined that the AKT1, PPARG and PTGS2 are the essential targets that had a good affinity for their respective active molecules.

Astragali radix - Curcumae rhizoma herb pair suppresses hepatocellular carcinoma through EGFR/AKT/mTOR pathway and induces lipid peroxidation-related ferroptosis via HIF-1α/HO-1/GPX4 axis

ETHNOPHARMACOLOGICAL RELEVANCE

The Astragali Radix - Curcumae Rhizoma herb pair (ACHP) originated from the famous traditional Chinese medicine text "YiXueZhongZhongCanXiLu", in which the two herbs were paired to form Chinese herbal compounds commonly used clinically for digestive system tumors, such as hepatocellular carcinoma (HCC). Although ACHP has been inherited for thousands of years in China, its mechanism against HCC remains unclear.

AIM OF THE STUDY

The study aims to evaluate the effect and explore the mechanism of ACHP against HCC.

METHODS

The efficacy and safety of ACHP against HCC in vivo were evaluated by tumor volume, organ index, H&E staining, hepatic and renal factors. The serum metabolites of ACHP were identified by UPLC-Q-TOF-MS/MS. The key targets and potential mechanisms of ACHP against HCC were screened by transcriptomics, network pharmacology and molecular docking. The effect and induction of ferroptosis of ACHP-containing serum on HCC in vitro was evaluated by MTT, colony formation assay and specific detection kits. The expression of ferroptosis-related proteins and pathways in vivo was detected by immunohistochemistry.

RESULTS

ACHP significantly inhibited tumor proliferation compared to the two herbs used separately, and showed a favorable safety profile. A total of 75 serum metabolites were identified in both positive and negative ion modes. Transcriptomics results revealed that ferroptosis played a key role in the anti-HCC process of ACHP. Network pharmacology and molecular docking results suggested that the anti-HCC effect of ACHP may be related to EGFR/AKT/mTOR pathway and HIF-1α/HO-1/GPX4 axis. In vitro and in vivo experiments further demonstrated that ACHP suppressed oncogenic signaling via the EGFR/AKT/mTOR pathway while inducing lipid peroxidation-related ferroptosis through HIF-1α/HO-1/GPX4 axis, thereby inhibiting HepG2 cells proliferation and HCC mice tumor growth.

CONCLUSION

ACHP exerts its effects by suppressing oncogenic signaling through the EGFR/AKT/mTOR pathway and inducing lipid peroxidation-related ferroptosis in HCC via the HIF-1α/HO-1/GPX4 axis. This systematic investigation establishes a coherent pharmacological chain from compound identification to mechanism verification, highlighting ACHP's therapeutic potential as a ferroptosis inducer targeting oncogenic signaling networks in HCC.

Bladder cancer biomarker analysis and drugtarget prediction based on pyroptosis-related genes

BACKGROUND

Bladder cancer (BC) is a common and lethal condition that presents a considerable risk to public health. Studies have demonstrated that inflammation is pivotal in the onset and advancement of BC. Pyroptosis is a type of programmed cell death distinguished by inflammatory reactions associated with innate immunity. Inhibiting inflammatory cytokine production and modulating pyroptosis-related pathways may provide a potential treatment approach for BC. We predicted and validated the Pyroptosis-related genes and potential biomarkers associated with BC, ultimately predicting therapeutic drugs based on the hub gene targets.

METHODS

The gene expression profiles for BC were acquired from the Gene Expression Omnibus (GEO) database. Bioinformatics analysis identified gene expression differences associated with pyroptosis in BC. The differently regulated pyroptosis-related genes were validated, and enrichment studies of specific biological processes and associated signaling pathways in BC were performed. Immune infiltration analysis and single-cell analysis were conducted to clarify the immune infiltration characteristics in BC. Therapeutic agents were forecasted based on critical gene targets.

RESULTS

In BC, 27 differentially expressed pyroptosis-related genes were discovered, with CASP8, NLRP3, CASP3, IL18, TP53, GSDME, IL1A, PYCARD, CYCS, and CASP9 recognized as key genes. Enrichment analysis revealed that the occurrence of pyroptosis was primarily associated with inflammation, activation of immune responses, and apoptosis. Additionally, data validation demonstrated that CASP8, NLRP3, CASP3, IL18, TP53, CYCS, and CASP9 were involved in the regulation of pyroptosis. The results of immune infiltration and single-cell analyses further validated that B-cells-memory, T-cells_CD8, T-cells_follicular-helper, Macrophages-M1, Dendritic_cells_activated, and Mast_cells_resting play significant roles in the immune processes of BC. The drug targeting predictions for pivotal genes identified Triethyl phosphate, Regorafenib, Ponatinib, Lenvatinib, Nintedanib, and Quercetin as potential key drugs or compounds for the treatment of BC.

CONCLUSION

This study elucidated the relationship between the development of BC and mechanisms of cellular senescence, apoptosis, and immunity. It clarified the roles of 27 genes associated with cellular senescence in BC and predicted that Triethyl phosphate, Regorafenib, Ponatinib, Lenvatinib, Nintedanib, and Quercetin may be key drugs or compounds for the treatment of BC.

PDE3A as a Therapeutic Target for the Modulation of Compartmentalised Cyclic Nucleotide-Dependent Signalling

Phosphodiesterase 3A (PDE3A) hydrolyses cAMP, adjusting cAMP signalling pathways with temporal and spatial accuracy. PDE3A contributes to the control of cAMP in several cellular compartments, including the plasma membrane, the cytosol, or membrane-limited organelles such as the nucleus and the sarcoplasmic reticulum. Through this ability and its expression in various cell types, it regulates a variety of cellular processes like contractility of muscle cells, gene expression, differentiation and proliferation. Dysregulated cAMP signalling causes or is associated with diseases. The therapeutic potential of PDE3A is, however, limited by the lack of specific modulators. Emerging approaches to targeting PDE3A centre on specifically addressing its catalytic domain or its cellular localisation. This review highlights the growing knowledge of PDE3A's functions in cellular signalling and therapeutic opportunities, opening the door to more fully utilise its potential for the treatment of disease.

Prediction of secreted uncharacterized protein structures from Beauveria bassiana ARSEF 2860 unravels novel toxins-like families

Insecticides are toxic substances used to control a wide variety of agricultural insect pests. Most of these are chemicals in nature, and their increasing residues in soil, water, and fruits contribute to environmental pollution, chronic human illnesses, and the emergence of insecticide resistance phenomenon. In the context of a green environment, bioinsecticide metabolites, including proteins, are a safe alternative that mostly has selective toxicity to insects. Thus, this study aimed to predict and identify new toxin-like families through uncharacterized secreted proteins from one of the most potent entomopathogenic fungi, Beauveria bassiana ARSEF 2860, which was selected as a model. In this work, a total of 2483 amino acid sequences of uncharacterized proteins (Ups) were retrieved from the RefSeq database. Among these, 365 UPs were identified as secreted proteins using the SignalP web server. We implemented the integration of well-designed bioinformatic tools to characterize and anticipate their homologous similarities at the sequence (InterPro) and structural (AlphaFold2) levels. The structural function annotation of these proteins was predicted using DeepFRI. With 269 successfully predicted folds, we identified new putative families with pathogenesis functions related to toxins like Janus-faced atracotoxins (insecticidal spider toxin), Cry toxins (commercial insecticide from Bacillus thuringiensis), ARTs-like toxins, and other insecticidal toxins. Furthermore, some proteins that are not homologous to any known experimental data were functionally predicted as cation metal ion binding (Zn, Na, and Co) with potential toxicity. Collectively, computational structural genomics can be used to study host-pathogen interactions and predict novel families.

Mendelian randomization analysis reveals the potential of the IKZF1 gene as a therapeutic target in colorectal cancer

INTRODUCTION

Colorectal cancer (CRC) is a global health burden, highlighting the urgent need for the discovery of new biomarkers and therapeutic targets. This study integrates genetic epidemiology methods, such as Mendelian randomization (MR), with GWAS data to predict treatment efficacy and identify novel CRC therapeutic targets.

METHODS

We utilized cis-eQTL data from the eQTLGen consortium and CRC GWAS data from the IEU Open GWAS database. MR analysis was conducted via the R package TwoSampleMR. Bayesian colocalization analysis was applied to identify shared genetic effects between CRC risk factors and potential therapeutic targets. Phenome-wide association study (PheWAS), protein-protein interaction (PPI) network construction, and enrichment analyses were performed to elucidate the functional profiles of the targets. Molecular docking and dynamics simulations were employed to evaluate the therapeutic potential of the identified targets.

RESULTS

MR analysis identified 60 genes associated with CRC risk. Our analysis identified IKZF1 as a significant therapeutic target through colocalization analysis. The PheWAS results revealed no significant genomic correlations for IKZF1, suggesting its potential as a specific therapeutic target. PPI and enrichment analyses highlighted the role of IKZF1 in epigenetic regulation and transcriptional control. Molecular docking and dynamics simulations confirmed the strong binding affinities of potential drugs with IKZF1.

CONCLUSION

This study identified IKZF1 as a promising therapeutic target for CRC through MR and colocalization analyses. The target's association with immune modulation and epigenetic mechanisms, supported by molecular docking and dynamics simulations, positions IKZF1 as a key player in advancing precision CRC therapies, warranting further clinical investigation.

Microbiome and fragmentation pattern of blood cell-free DNA and fecal metagenome enhance colorectal cancer micro-dysbiosis and diagnosis analysis: a proof-of-concept study

Colorectal cancer (CRC) is the third most common cancer, and it can be prevented by performing early screening. As a hallmark of cancer, the human microbiome plays important roles in the occurrence and development of CRC. Recently, the blood microbiome has been proposed as an effective diagnostic tool for various diseases, yet its performance on CRC deserves further exploration. In this study, 133 human feces and 120 blood samples are collected, including healthy individuals, adenoma patients, and CRC patients. The blood cfDNA and fecal genome are subjected to shotgun metagenome sequencing. After removing human sequences, the microbial sequences in blood are analyzed. Based on the differential microbes and functions, random forest (RF) models are constructed for adenoma and CRC diagnosis. The results show that alterations of blood microbial signatures can be captured under low coverage (even at 3×). RF diagnostic models based on blood microbial markers achieve high area under the curve (AUC) values for adenoma patients (0.8849) and CRC patients (0.9824). When the fragmentation pattern is combined with microbial and KEGG markers, higher AUC values are obtained. Furthermore, compared to the blood microbiome, the fecal microbiome shows a different community composition, whereas their changes in KEGG pathways are similar. Pathogenic bacteria Fusobacterium nucleatum (F. nucleatum) in feces increased gradually from the healthy group to the adenoma and CRC groups. Additionally, F. nucleatum in feces and blood shows a positive correlation in CRC patients. Cumulatively, the integration of blood microbiome and fragmentation pattern is promising for CRC diagnosis.IMPORTANCEThe cell-free DNA of the human microbiome can enter the blood and can be used for cancer diagnosis, whereas its diagnostic potential in colorectal cancer and association with gut microbiome has not been explored. The microbial sequences in blood account for less than 1% of the total sequences. The blood microbial composition, KEGG functions, and fragmentation pattern are different among healthy individuals, adenoma patients, and CRC patients. Machine learning models based on these differential characteristics achieve high diagnostic accuracy, especially when they are integrated with fragmentation patterns. The great difference between fecal and blood microbiomes indicates that microbial sequences in blood may originate from various organs. Therefore, this study provides new insights into the community composition and functions of the blood microbiome of CRC and proposes an effective non-invasive diagnostic tool.

MicroRNA-486: a dual-function biomarker for diagnosis and tumor immune microenvironment characterization in non-small cell lung cancer

BACKGROUND

This investigation evaluates the clinical significance and molecular mechanisms of microRNA-486 (miR-486) as a potential biomarker in non-small cell lung cancer (NSCLC) through an integrative analytical approach.

METHODS

We conducted systematic search and meta-analysis of diagnostic studies from major biomedical databases from inception through April 04, 2025, followed by comprehensive bioinformatics interrogation. Protein-protein interaction (PPI) networks were constructed using STRING to identify key hub genes regulated by miR-486. Validation of hub genes employed TCGA datasets, while immune infiltration analysis utilized TIMER2.0 platform.

RESULTS

The meta-analysis indicated that miR-486, both individually and in combination, could be effective biomarkers for NSCLC detection. Afterwards, functional enrichment analyses of miR-486 target genes highlighted significant ontology terms and pathways crucial to the initiation and progression of NSCLC. PPI networks revealed key proteins and modules that participate in multiple essential pathways associated with NSCLC pathogenesis. Furthermore, the identified hub genes were validated for differential expression in cancerous versus normal tissues, suggesting their potential diagnostic utility, while subsequent survival analyses confirmed their prognostic value through significant associations with overall survival. Notably, these hub genes were found to be significantly associated with immune infiltration levels, immune microenvironment scores, and immune-related proteins in NSCLC.

CONCLUSIONS

This dual-modality investigation establishes miR-486 as a multi-functional biomarker in NSCLC, demonstrating both diagnostic utility and immunoregulatory potential through tumor microenvironment modulation.

Investigating the Genetic Links Between Immune Cell Profiles and Bladder Cancer: A Multidisciplinary Bioinformatics Approach

Background: Bladder cancer (BC) is a common malignancy in the urinary system, with an increasing incidence rate. Immune cell infiltration within the tumor microenvironment (TME) plays a crucial role in BC progression and treatment response. However, the immune cell composition of the TME presents a significant challenge to the effectiveness of current therapeutic strategies. Methods: We performed bidirectional Mendelian randomization (MR) analysis to investigate the impact of immune cells on BC risk. Single nucleotide polymorphisms (SNPs) related to immune cells were annotated, and candidate genes associated with BC risk were identified. Differential expression analysis identified immune-related differentially expressed genes (iDEGs), and a protein-protein interaction (PPI) network along with functional enrichment analysis were conducted to explore their roles in tumor development. Machine learning-based feature selection was applied to identify potential biomarkers and therapeutic targets. Results: MR analysis revealed eight immune cell subtypes significantly associated with BC. Using SNPs linked to these immune cells, 129 candidate genes were identified through the SNPense tool and cross-referenced with differentially expressed genes in BC, resulting in identification of 28 iDEGs. Machine learning identified five potential diagnostic biomarkers (COLEC12, TMCC1, CEP55, KLK3, COL4A1) with an AUC of 0.903, which are implicated in immune modulation and cancer progression. Conclusions: This study provides new insights into immune mechanisms in BC and identifies promising biomarkers for early diagnosis and therapeutic intervention.

Functional metabolomics revealed pyroglutamic acid may play a key role in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and irreversible respiratory disease with poor survival rates. Despite significant research efforts, IPF still lacks a curative treatment. Excessive epithelial-mesenchymal transition (EMT) contributes to approximately one-third of fibroblasts in pulmonary fibrosis and plays a critical role in IPF pathogenesis. Identifying factors that regulate EMT is essential for developing effective therapeutic strategies for IPF. In this study, functional metabolomics revealed significant alterations in multiple metabolites in transforming growth factor-beta 1 (TGF-β1)-induced A549 cells, with pyroglutamic acid and 5-oxoprolinase (OPLAH) being identified as the most critical factors. Cellular experiments demonstrated that pyroglutamic acid effectively inhibited TGF-β1-induced EMT in A549 cells. Mechanistically, pyroglutamic acid inhibited IPF by suppressing EMT through the inhibition of Smad2/3 expression in TGF-β1-induced A549 cells. Bioinformatics analysis further elucidated the pyroglutamate is a potential metabolite that inhibits EMT. In addition, this study is the first to highlight the pivotal role of pyroglutamic acid and OPLAH in regulating EMT in IPF, offering novel insights into the metabolic mechanisms involved in IPF inhibition and providing a foundation for developing innovative therapeutic approaches for IPF.

Integrative network and computational toxicology reveal the molecular mechanisms in PFOA-induced spermatogenic disorder

Perfluorooctanoic acid (PFOA), a widely used industrial chemical, poses significant environmental and biological toxicity, particularly affecting reproductive health. This study aimed to integrate network toxicology, machine learning, and molecular dynamics simulations (MDS) to uncover the molecular mechanisms of PFOA-induced spermatogenic toxicity. Toxicity profiling using admetSAR revealed that PFOA exhibited pronounced reproductive toxicity and a strong binding affinity to nuclear receptors, including estrogen, androgen, and PPAR gamma. By integrating PFOA targets derived from toxicology databases with differentially expressed genes associated with non-obstructive azoospermia, we pinpointed 256 differentially expressed spermatogenic toxicity targets from an initial pool of 4311 potential PFOA targets. Gene ontology (GO) and KEGG pathway enrichment analyses highlighted biological processes, such as spermatogenesis and cell cycle regulation, along with pathways related to cell division and intercellular communication. Protein-protein interaction networks and machine learning algorithms (LASSO, SVM-RFE, RF) pinpointed five core genes-RAD51, KIF15, PTTG1, BIRC5, and CDC25C-that serve as potential diagnostic biomarkers. Molecular docking revealed strong binding affinities between PFOA and these proteins, with RAD51 showing the highest binding stability (-8.467 kcal/mol). Furthermore, MDS confirmed stable interactions, with low RMSD, RMSF, and Rg values, indicating structural stability. In vivo studies showed that PFOA exposure (1 and 5 mg/kg) caused testicular damage in mice in a dose-dependent manner, with significant downregulation of core target proteins; in vitro experiments demonstrated a concentration-dependent reduction in GC1 cell viability and substantial alterations in its gene expression. This study highlights the critical roles of these mechanisms through which PFOA disrupts spermatogenesis, emphasizing core biomarkers that may serve as therapeutic targets. Our findings contribute insights into the reproductive toxicity of PFOA and similar environmental pollutants, offering a basis for developing strategies to protect male fertility.

Dusp14-Mediated Dephosphorylation of MLKL Protects Against Cardiomyocyte Necroptosis in Hypothyroidism-Induced Heart Failure

BACKGROUND

Hypothyroidism leads to multiple organ dysfunction, with the heart the most affected. However, the pathologic mechanism of hypothyroidism-induced heart failure remains to be completely elucidated. Thyroid hormone replacement therapy enhances myocardium systolic function but increases the occurrence of arrythmias. There is an urgent need to explore these mechanisms in detail and to discover and develop drugs that can target and manage heart failure in patients with hypothyroidism.

METHODS

In this study, a mouse model of hypothyroidism-induced heart failure was established through the administration of propylthiouracil. Dusp14 knockout mice were generated, and adeno-associated virus-mediated cardiomyocyte-specific overexpression of Dusp14 (dual specificity phosphatase 14) was used in combination with related cellular experiments to investigate the protective effects of Dusp14 on hypothyroidism-induced heart failure. Further analyses confirmed the crucial involvement of necroptosis in the pathogenesis of hypothyroidism-induced heart failure, and demonstrated the protective role of Dusp14 in modulating necroptosis. In addition, a novel small molecule compound that effectively regulates Dusp14 activity in vitro was identified through molecular docking, providing a potential therapeutic avenue.

RESULTS

Dusp14 regulates necroptosis and mitigates hypothyroidism-induced heart failure. Myocardial tissue sections from mice in the hypothyroidism group showed positive Evans blue dye staining, and the serum levels of the myocardial injury marker lactate dehydrogenase were significantly higher compared with the euthyroid group (n=8). In addition, phosphorylation levels of the necroptosis marker MLKL (mixed lineage kinase domain-like protein) were significantly elevated, indicating the activation of necroptosis (n=8). These findings suggest that myocardial necroptosis is activated during hypothyroidism. Myocardial-specific overexpression of Dusp14 reduced myocardial necroptosis and improved myocardial contractile function in hypothyroid mice (n=8). In contrast, Dusp14 knockout exacerbated myocardial contractile dysfunction and necroptosis in these mice (n=5-7). These results indicate that Dusp14 alleviates hypothyroidism-induced heart failure by inhibiting necroptosis. P077-0472, a small molecule compound, was identified as an activator of Dusp14, which could inhibit cardiomyocyte necroptosis from hypothyroidism (n=6).

CONCLUSIONS

Dusp14 inhibits cardiomyocyte necroptosis from hypothyroidism and consequently rescues damaged cardiomyocytes. P077-0472, a novel small molecule compound that activates the dephosphorylation function of Dusp14, could inhibit cardiomyocyte necroptosis from hypothyroidism.

Cystathionine γ-lyase is an essential biocontrol-positive regulator of Trichoderma gamsii strain TC788

Some Trichoderma strains have been widely used in agriculture due to their biological control functions against plant pathogens. However, only a few intracellular biocontrol-related factors of them were explored. In this study, T. gamsii strain TC788 was discovered possessing comprehensive antagonistic capacity to the fungal phytopathogen Rhizoctonia solani causing damping-off disease of pepper, in which cystathionine γ-lyase is proved to be an essential biocontrol positive regulator as evidenced by combined analyses of transcriptome and proteome, proteins interaction network, and gene homologous recombination. Overexpression of cystathionine γ-lyase significantly up-regulated expression levels of six pathway proteins and enzyme activities of secreted proteins associated with biocontrol. It also increased contents of cysteine and hydrogen sulfide in enriched pathway of cysteine and methionine metabolism, and improved concentration of the main volatile organic compound, 6‑pentyl‑2H‑pyran‑2‑one, by 4.18 times. Pot experiments further confirmed that overexpressed strain of TC788 enhanced inhibiting ability against R. solani, promoted growth indicators, and induced systemic resistance of pepper seedlings compared with wild type strain. This work provides theoretical bases of biocontrol effects performed by strain TC788 against the phytopathogen, and explores preliminarily interaction between the strain and pepper plant.

Genome-wide Mendelian randomization study identifies therapeutic targets for diabetic microangiopathy

AIMS

This study aims to identify potential therapeutic targets for diabetic microangiopathy by integrating genome-wide association studies (GWAS) and Mendelian randomization (MR) analyses.

METHODS

A comprehensive analysis of GWAS datasets on diabetic microangiopathy was conducted by using two-sample MR to determine the causal effects of blood-expressed druggable genes at both the transcriptional and protein levels. Co-localization analysis was conducted to validate gene-trait associations, while phenome-wide association studies (PheWAS) explored broader phenotypic implications. Additionally, protein-protein interaction (PPI) networks were constructed to elucidate gene interactions and molecular docking was conducted to determine therapeutic druggability.

RESULTS

Nine candidate therapeutic targets (PSORS1C3, HLA-C, RAMP1, CTSG, SREBF1, BTN3A2, PPA1, PRKD2, and PPIG) were identified, with co-localization analysis confirming their involvement in diabetic microangiopathy. Among them, HLA-C exhibited associations with additional traits, suggesting the specificity of the remaining targets. Functional enrichment analysis indicated a predominant involvement of immune-related pathways, underscoring their relevance to the pathogenesis of diabetic microangiopathy. Furthermore, molecular docking studies revealed strong binding affinities.

CONCLUSIONS

This study provides compelling genetic evidence supporting the role of immune-related druggable genes in diabetic microangiopathy and identifies novel therapeutic targets for intervention.

Identification and validation of shared biomarkers and drug repurposing in psoriasis and Crohn's disease: integrating bioinformatics, machine learning, and experimental approaches

Background

Psoriasis and Crohn's disease (CD) are chronic inflammatory diseases that involve complex immune-mediated mechanisms. Despite clinical overlap and shared genetic predispositions, the molecular pathways connecting these diseases remain incompletely understood. The present study seeks to identify shared biomarkers and therapeutic targets for psoriasis and CD.

Methods

Differentially expressed genes (DEGs) were identified from publicly available transcriptomic datasets related to psoriasis and CD. Simultaneously, weighted gene co-expression network analysis (WGCNA) was performed to identify gene modules associated with the clinical traits of psoriasis and CD. Subsequently, biomarkers were prioritized from shared key genes by integrating protein-protein interaction (PPI) networks with machine learning models. Gene Set Enrichment Analysis (GSEA), along with Gene Ontology (GO) and KEGG pathway analyses, were performed to determine the biological significance of the identified genes. Immune infiltration analysis underscored the involvement of hub genes in immune regulation, while single-cell transcriptomic analysis revealed the cellular localization of these hub genes. Additional targeted molecular biology experiments validated the shared biomarkers. DSigDB predictions were employed to identify potential therapeutic compounds. Molecular docking simulations were performed to assess the binding affinity of the drugs to key target proteins. Finally, additional in vitro experiments were conducted to validate the therapeutic effects of the identified compounds.

Results

The study identified KIF4A, DLGAP5, NCAPG, CCNB1, and CEP55 as key regulatory molecules and shared biomarkers for both diseases. GSEA and pathway analysis highlighted the importance of cell cycle regulation and immune response pathways in the comorbidities of psoriasis and CD. Immune infiltration analysis emphasized the role of hub genes in immune regulation. Furthermore, DSigDB predictions and molecular docking simulations indicated strong therapeutic potential for Etoposide, Lucanthone, and Piroxicam, with Etoposide showing the highest affinity for key targets. In cellular models, Etoposide demonstrated promising therapeutic effects by significantly downregulating the expression of psoriasis-related keratinocytes marker genes (KRT6, KRT16) and CD-related inflammatory cytokines (IL6, IL8, TNF-α), highlighting its potential in treating psoriasis and CD.

Discussion

This study integrates bioinformatics, machine learning, and molecular validation to identify the shared molecular mechanisms of psoriasis and CD, uncovering novel biomarkers and potential combined therapeutic candidates. These findings provide valuable insights into potential treatment strategies for these diseases.

Construction and Identification of Inflammation-Related TF-mRNA-miRNA Coexpression Network and Immune Infiltration in Parkinson's Disease

Background: Parkinson's disease (PD) is the second most common neurodegenerative disease worldwide. Inflammation, marked by the infiltration of inflammatory mediators and the proliferation of inflammatory cells, is closely linked to PD. This study aims to identify and validate inflammation-related biomarkers in PD and construct a TF-mRNA-miRNA coexpression network through bioinformatics analysis. Methods: The PD-associated dataset GSE7621 and inflammation-related genes were downloaded from the GEO Database and GeneCards platform to obtain inflammation-related differential expression genes (IRDEGs). The key IRDEGs were generated by PPI network analysis. The gene expression levels of the key IRDEGs were validated by blood samples from PD patients using QPCR analysis. We utilized the ENCODE, hTFtarget, CHEA, miRWALK, and miRDB databases to obtain upstream and downstream molecular network models for constructing the TF-mRNA-miRNA interaction network of the key IRDEGs. Finally, based on CIBERSORT algorithm, the associations between IRDEs and immune cell infiltration were investigated. Results: A total of four key IRDEGs (CXCR4, LEP, SLC18A2, and TAC1) were screened and validated. Through biological function analysis, key-related pathways and coexpression networks of PD were identified. These genes may be closely related to the onset of PD. Additionally, we found that increased CD4 T-cell infiltration might be associated with the occurrence of PD. Conclusions: We identified four potential inflammation-related treatment target and constructed a TF-mRNA-miRNA regulatory network. This information provides an initial basis for understanding the complex PD regulatory mechanisms.

Hepatoprotective effects of wine-steamed Schisandra sphenanthera fruit in alleviating APAP-induced liver injury via the gut-liver axis

Drug-induced liver injury (DILI) is a common adverse drug reaction that can result in liver injury, particularly in cases of paracetamol (APAP) abuse. Schisandra sphenanthera Rehd. et Wils. has attracted attention due to its hepatoprotective properties, and the underlying mechanism is unclear. In this study, a mouse model of APAP-induced liver injury was employed to evaluate network pharmacology analysis, histopathological analysis, the gut microbiota, and fecal metabolome to investigate the mechanism by which S. sphenanthera fruit extract (SFE) alleviates DILI. Network pharmacology indicated that the SFE can attenuate APAP-induced liver injury via key targets, including MAPK3 and CASP3. Furthermore, SFE effectively alleviated APAP-induced oxidative stress (MDA, SOD, and GSH) and inflammation (IL-6, TNF-α, and IL-1β). Further analysis of gut microbiota and fecal metabolites revealed that SFE promoted the growth of Bacteroidales and Erysipelotrichales, and decreased the growth of Lactobacillales, leading to increased production of tryptophan metabolites. Correlation analysis showed that the increase in gut microbiota by SFE was positively correlated with improved antioxidant ability and improved liver and gut function. In conclusion, SFE pretreatment can alleviate APAP-induced liver injury by targeting the gut-liver axis, and provides a valuable reference for the clinical use of SFE in the prevention or treatment of DILI.

Exploring the reproductive exposure risks of phthalates and organophosphates in atmospheric particulate matter based on quantitative structure-activity relationships and network toxicology models

Minimal study focused on the association between mixed pollutants in atmospheric particulate matter (PM2.5) and their reproductive health risks. Utilizing a novel quantitative structure-activity relationship (QSAR) integrated machine learning algorithms, we evaluated the mixed reproductive health risks associated with phthalates (PAEs) and organophosphates (OPEs) exposure by assessing the affinities of these compounds binding to estrogen receptors (ER) and androgen receptors (AR). The mixed toxicity equivalent factor (TEFmix) and mixed toxicity equivalent quantity (TEQmix) by the QSAR model were all smaller than the sum TEF and TEQ of individual PAEs and OPEs, which may be due to the antagonistic effect of PAEs and OPEs monomers on reproductive toxicity. Based on network toxicology approach, a total of 590 potential targets associated with PAEs and OPEs affecting sex hormones were initially identified, with an additional 50 core targets, including AR and ER. Di-2-ethylhexyl phthalate (DEHP), triphenyl phosphate (TPHP) and mono-(2-ethylhexyl) phthalate (MEHP) were key components to disrupt AR and ER signaling pathway, and was confirmed by molecular docking analysis. In addition to ER and AR, serine/threonine kinase 1 (AKT1) and heat shock protein 90α family A member 1 (HSP90AA1) might be key targets for reproductive toxicity, which have hardly mentioned before. Our study provided precious information on the mixed reproductive exposure risk of PAEs and OPEs in PM2.5, and innovatively explored the potential mechanisms of PAEs and OPEs affecting human reproductive health using network toxicology.

Genomic Exploration of Nonalcoholic Fatty Liver Disease: Insights From Gene Expression and Variation in Morbidly Obese Individuals

Nonalcoholic fatty liver disease (NAFLD) is a common liver condition resulting from metabolic syndrome characterized by fat accumulation in the liver. It is often associated with obesity and diabetes, contributing to hepatic steatosis in liver cells. The prevalence of NAFLD is increasing globally, with 32% of the adult population affected. Genetic modifiers, such as single nucleotide polymorphisms, can increase susceptibility to the disease. Gene expression analysis and genetic variation can help identify disease-causing pathways and reveal biomarkers involved in NAFLD. This study employed integrative bioinformatics analysis, including bulk RNA-seq and single-cell RNA-seq, to explore differentially expressed genes and their genetic variants in NAFLD vs. control and NAFLD vs. cirrhosis, highlighting genes influencing NAFLD progression. Moreover, this study identified AKR1D1, LIPC, UGT2B17, DGAT2, and SERPINE1 implicated in metabolic, immune, and lipid functions while being overexpressed in both hepatocyte cells among obese patients identified and validated through Liver Cell Atlas, highlighting their pivotal role in the pathogenesis of the disease in obese patients through perturbed hepatocytes. Furthermore, novel pathogenic variants of AKR1D1, LIPC, and SERPINE1, associated with congenital bile acid synthesis defects, abnormal circulating lipid concentrations, and plasminogen activator inhibitor type 1 deficiency conditions, were identified. Conclusively, this integrative multiomics study highlights the novel pathogenic variants of AKR1D1, LIPC, and SERPINE1 in metabolic, immune, and lipid pathways that are highly expressed among hepatocytes in obese patients while possibly carrying pathogenic mutations that may be associated with NAFLD, emphasizing their potential as novel targets for therapeutic strategies and biomarker development in early diagnosis and treatment before the onset of cirrhosis or hepatocellular carcinoma.

Focusing on spinal stenosis: emerging discoveries concerning Alendronate-induced risks and genetic drug targets

BACKGROUND

Spinal stenosis is a common disease in clinical practice, and drug use is one of its potential predisposing factors. Alendronate, a widely used clinical drug for osteoporosis treatment, has the potential to trigger spinal stenosis. Based on the real world, this study aims to deeply investigate the association between spinal stenosis and alendronate, and to explore novel drug targets against spinal stenosis at the genetic level.

METHODS

Alendronate patient data from the FDA Adverse Event Reporting System (FAERS) from Q1 2004 to Q4 2024 were included in the study, and four pharmacovigilance analytic methods and Bonferroni corrected P-values were applied to the baseline data, and subgroups of data were analyzed. Complementarily, Weibull distribution were applied to further parse the data. Meanwhile, in order to explore therapeutic targets against spinal stenosis, Mendelian randomization analyses were carried out based on eQTLGen consortium data as well as genome-wide association study (GWAS) data from two large independent cohorts. Subsequently, the medicinal value of the identified drug targets was verified by drug prediction and molecular docking techniques.

RESULTS

Pharmacovigilance analysis showed a strong positive signal between alendronate and spinal stenosis, especially in females and older patients. Fourteen significant drug targets were identified. Their medicinal value was verified by drug prediction and molecular docking, obtaining four protein-drug docking model structures.

CONCLUSIONS

This study reveals an alendronate-spinal stenosis association, offering insights for clinical prevention. It also identifies new genetic drug targets, opening new treatment pathways for spinal stenosis.

TRIAL REGISTRATION

Not applicable.

De Novo Protein Synthesis Occurs Through the Cytoplasmic Translation Machinery in Mammalian Spermatozoa

The current hypothesis suggests that translation occurs in capacitated spermatozoa through mitochondrial ribosomes. Mitochondrial translation has several particularities, which rise some questions about how mitochondrial ribosomes can ensure sperm translation activity. Here, we aimed to elucidate if cytoplasmic translation occurs in mammalian spermatozoa. A bioinformatic workflow was performed to identify translation-related proteins in human spermatozoa and their association with cytoplasmic translation. The surface sensing of translation (SUnSET) method was used to measure translation activity in capacitated human and bovine spermatozoa. Two translation inhibitors, cycloheximide (CHX, cytoplasmic) and D-chloramphenicol (D-CP, mitochondrial) were used to identify which ribosomes were active in sperm. To spot newly synthesized proteins, puromycin-peptides were immunoprecipitated and analysed by mass spectrometry. A second approach was performed using translation inhibitors and analysing the sperm proteome by mass spectrometry. Bioinformatic analysis revealed that human spermatozoa possess 510 translation proteins, which were enriched for cytoplasmic mRNA translation. CHX decreased translation activity in mammalian sperm, whereas no effect was observed after D-CP treatment. Nine proteins were immunoprecipitated and identified as newly synthesized in capacitated bovine spermatozoa. CHX and D-CP decreased the level of 22 proteins that were replaced, or de novo translated during capacitation. New proteins were associated with relevant processes for sperm physiology. Both translation inhibitors decreased sperm rapid progressive motility and increased sperm immotility. Our results proved sperm translation occurs through cytoplasmic translation machinery in capacitated bovine and human spermatozoa. These results also support that sperm translation is required during capacitation to produce relevant proteins for sperm functions.

Analysis of differential transcriptome expression reveals that ISG15 provides support for embryo development by promoting angiogenesis in porcine mesometrium

Mesometrium is the "gateway" through which the endometrium exchanges nutrients and substances with the outside world due to blood vessels entering endometrium across mesometrium. Therefore, dissecting the transcription atlas of the mesometrium will be a great help in understanding the role of mesometrium during implantation. In this study, we collected samples from the mesometrium and adjacent endometrium on the 12th day of estrous cycle and pregnancy. Transcription atlas of mesometrium and adjacent endometrium revealed that genes such as ISG15, which are related to the pathway of response to Interferon α and γ, were significantly enriched. The result of immunohistochemistry demonstrated that the core genes within these pathways were mainly located in the vascular endothelial cells both the endometrium and mesometrium. ISG15 interferon assay revealed the down-regulation of ISG15 induced proliferation, migration and tube formation. Taken together, we concluded that down-regulation of genes related to response of interferons promoted angiogenesis in the mesometrium and adjacent endometrium, allowing mesometrium to play an essential supportive role in pregnancy.

Transcriptomic analysis reveals the function of m6A regulators in aged cochlea

OBJECTIVE

Presbycusis is a prevalent health issue among the elderly. Previous studies have shown mechanisms related to this condition, but the underlying mechanisms of presbycusis remain elusive. N6-methyladenosine (m6A) modification in regulating gene expression and cellular functions has been implicated in the development of various diseases. Nevertheless, the potential role of m6A regulators in presbycusis is still unclear. In this study, we aim to determine the expression of m6A regulators in the cochleae of young and old mice, and to investigate their potential role in aging.

METHODS

We sequenced the transcriptome from the cochleae of six young (2-mo) and six old mice (24-mo) bioinformatics analysis. Differential expression analysis and downstream functional analysis was performed to identify m6A regulators. Association of m6A regulators with protein-protein interaction and transcription factor-miRNA networks were constructed to explore their regulatory mechanisms.

RESULTS

ALKBH5 and YTHDC1 were found upregulated in the aged cochleae. They were strongly correlated with immune-related pathways, immune molecular subtypes, and immune infiltration levels in old mice, suggesting their potential involvement in immune-related mechanisms of presbycusis. Receiver Operating Characteristic (ROC) curve analysis demonstrated the high diagnostic potential molecules of AlkB Homolog 5 (ALKBH5) and YTHDC1.

CONCLUSION

This study has established a molecular foundation and introduce a novel perspective on the role of m6A regulators in presbycusis, emphasizing ALKBH5 and YTHDC1 as potential markers.

LEVEL OF EVIDENCE

Acknowledging methodological similarities with Level 3 (non-randomized controlled cohort or case-control studies) in clinical research, we reference Level 3 as a comparative framework, while recognizing the distinct differences between clinical and animal research settings.

Metabolomic profiles in allergic rhinitis: A systematic review and meta-analysis

BACKGROUND

Allergic rhinitis (AR) is a prevalent chronic inflammatory condition that significantly affects patient quality of life and poses a substantial public health burden. Recent advancements in metabolomics have facilitated a deeper understanding of the metabolic pathways involved in AR, offering potential for new biomarkers and therapeutic targets.

OBJECTIVE

To conduct a systematic review and meta-analysis of clinical studies summarizing the metabolomic profiles of AR to gain deeper insights into the metabolic changes and pathologic processes underlying AR.

METHODS

A comprehensive literature search was conducted across PubMed, Embase, Scopus, and Web of Science databases up to October 2024. A qualitative review of the screened studies was performed, followed by meta-analyses of metabolites reported in at least 2 studies. High-impact targets, pathways, and their associations were identified using bioinformatic analyses.

RESULTS

A total of 21 studies, encompassing 84 metabolites associated with AR, met the inclusion criteria. There were 7 metabolites that consistently exhibited up-regulation in AR across multiple studies and were included in the meta-analysis. Pathway enrichment analyses revealed significant involvement of pathways such as "valine, leucine, and isoleucine biosynthesis" and "linoleic acid metabolism" in AR pathogenesis. The metabolite-pathway-gene network analysis highlighted key functional connections between metabolites, pathways, and immune response genes.

CONCLUSION

This comprehensive analysis indicates that differential metabolites may play pivotal roles in AR pathogenesis, offering potential biomarkers and therapeutic targets. Further studies are necessary to validate these findings and elucidate the complex metabolic pathways involved in AR.

Elimination of intracellular microbes using drug combination therapy and unveiling survival mechanism of host cells upon microbial invasion

Intracellular microbes are actively present in various tumor types in low biomass and play a major role in metastasis. Eliminating intracellular microbes on a cellular level with precision remains a challenge. To address this issue, we designed a screening pipeline to characterize intracellular microbes and their interaction with host cells. We used host and microbial in vitro lab-based constant and reproducible model, host as (mammalian cancer HeLa), and microbial strain as (Escherichia coli 25922). To study the pharmacological impact on intracellular bacterial load, we used antibiotics (ampicillin, roxithromycin, and ciprofloxacin) and chemotherapy drugs (doxorubicin and cisplatin) as external stimuli for both host and microbes. We found that increasing pharmacological stress does not increase microbial load inside the host cells. Eliminations of intracellular bacteria was done by using permutation orthogonal arrays (POA), whereby we acquired optimal drug combination in particular sequence of drugs, which reduced 90%-95% of the intracellular microbial load. Proteomic analysis revealed that upon invasion of Escherichia coli 25922, HeLa cells enriched ATP production pathways to activate intermediate filaments, which should be investigated closely via in vivo models.

Identification of ferroptosis-related genes and potential drugs in osteoarthritis

BACKGROUND

Osteoarthritis (OA) is a common chronic degenerative joint disease in orthopedics, and ferroptosis is a newly identified mode of cell death present in OA. Inhibition of inflammatory cytokine expression and modulation of chondrocyte ferroptosis related pathways may be novel strategies for the treatment of OA. The purpose of this work was to uncover prospective biomarkers and molecular processes of ferroptosis in OA, as well as to better understand the molecular mechanisms of ferroptosis in OA treated with resveratrol.

MATERIAL AND METHODS

We obtained OA gene expression profiles from the Gene Expression Omnibus (GEO) database. OA-expressed ferroptosis-related genes were identified using Genecards data, differential gene analysis, and weighted gene co-expression network analysis. Enrichment analysis was utilized to identify signaling pathways and molecular mechanisms linked with ferroptosis in OA, while immune infiltration analysis indicated immune cell infiltration in OA. The action targets of resveratrol were taken from the TCM database to determine the therapeutic targets of resveratrol for the treatment of OA. To validate the molecular process, molecular docking was performed using the therapeutic targets' enrichment analysis. Finally, in vitro investigations confirmed the molecular mechanism of ferroptosis in resveratrol-treated OA.

RESULTS

Bioinformatic analysis identified 462 OA ferroptosis gene sets, with GPX4, TFRC, SLC7A11, EGFR, and IL1B serving as significant hub genes. Enrichment analysis revealed that ferroptosis was also linked to animal mitophagy, the FoxO signaling pathway, the Toll-like receptor signaling pathway, the PI3K-Akt signaling pathway, inflammation, immune response activation, and cellular autophagy. The immune infiltration data revealed that T_cells_CD4_memory_resting, T_cells_CD4_memory_activated, NK_cells_activated, and Mast_cells_activated were considerably infiltrated in OA. Resveratrol ameliorated OA via modulating autophagy and ferroptosis via GPX4, TFRC, SLC7A11, EGFR, and IL1B, according to a mechanistic study.

CONCLUSION

We discovered the mechanism of GPX4, TFRC, SLC7A11, and EGFR, IL1B ferroptosis-related genes in OA, and preliminary evidence suggests that resveratrol improves OA by regulating ferroptosis and immunological processes, which may give a new route for OA treatment.

Based on single-cell and transcriptome data, ferroptosis and the immunological landscape in osteosarcoma were discovered

Ferroptosis has been demonstrated to have a significant role in osteosarcoma (OS), a highly aggressive and invasive malignant bone tumor. Nevertheless, the precise molecular mechanism underlying OS remains unknown. Understanding the makeup of the immune microenvironment in OS is crucial for its therapy, as the disease grows in the highly specialized, complex, and dynamic bone microenvironment. Resveratrol (Res) possesses anti-inflammatory, immunomodulatory, chemopreventive, antioxidant, and anticancer properties, it is unknown if it can modify ferroptosis to prevent OS. This time, using single-cell analysis and other bioinformatic studies, we will clarify the targets and composition of the immunological microenvironment of the ferroptosis process in OS, as well as the role of certain transcription factors in it. Ultimately, network pharmacology and vitro experiment have led to the initial identification of the molecular processes governing ferroptosis in OS, which are regulated by Res. The findings suggested the potential use of ALB, EGFR, GPX4, IL6, STAT3, and PTEN as OS prognostic and diagnostic biomarkers. Chondroblastic, myeloid cells, osteoblastic OS, CD4 + T, NK, CD8 + T, B cells, M1 macrophages, Chondro_Proli, etc. made up the majority of the immunological microenvironment of OS. The entire cellular trajectory demonstrates that immune cells infiltrating during the early stages of OS are mostly CD4 + T, NK, CD8 + T, B_cell, and M1 macrophages. This affects the development of myeloid cells and chondroblastic cells, which ultimately leads to the progression of highly malignant chondro cells to OS. Numerous pathways allow transcription factors including BCLAF1, MAF, SP1, TCF12, KLF11, and KMT2D to contribute to the development of tumors. Finally, by interacting with the aforementioned targets, cells, Res is thought to impede the evolution of OS. In conclusion, ferroptosis and alterations in the immunological milieu are significant factors in the development of OS, and Res may one day be employed as a therapeutic drug to treat OS.

Proteomics and lipidomics of human umbilical cord mesenchymal stem cells exposed to ionizing radiation

OBJECTIVES

Mesenchymal stem cell (MSC)-based therapies exhibit beneficial effects on various forms of tissue damage, including ionizing radiation-induced lesions. However, whether ionizing radiation affects the functions of human umbilical cord mesenchymal stem cells (hucMSCs) remains unclear. This study aimed to investigate the effect and possible mechanisms of ionizing radiation on the proliferation and differentiation of hucMSCs.

METHODS

The hucMSCs were divided into the 1 Gy group (exposure to a single dose (1 Gy) of X-ray radiation (1 Gy/min) for 14 days) and control (without radiation treatment) group. The proliferation, apoptosis, and adipogenic and osteogenic differentiation abilities of hucMSCs in the two groups were evaluated. Moreover, the lipidomics and proteomics analyses were conducted to explore crucial lipids and proteins by which ionizing radiation affected the functions of hucMSCs. In addition, the effects of BYSL on radiation-treated hucMSCs were explore, as well as the involved potential mechanisms.

RESULTS

X-ray radiation treatment inhibited proliferation, promoted apoptosis, and decreased adipogenic and osteogenic differentiation abilities of hucMSCs. Key lipids, such as triglyceride (TG) and phosphatidylcholine (PC), and hub proteins (BYSL, MRTO4, and RRP9) exhibited significant differences between the 1 Gy group and control group. Moreover, BYSL, MRTO4, and RRP9 were significantly correlated with TG and PC. BYSL overexpression evidently promoted the cell proliferation, adipogenic and osteogenic differentiation abilities of radiation-treated hucMSCs, as well as the protein expression levels of p-GSK-3β/GSK-3β and β-catenin, while suppressed cell apoptosis. However, the GSK-3β inhibitor (1-Az) treatment reversed the protein expression levels of p-GSK-3β/GSK-3β, β-catenin and BYSL, as well as the cell proliferation, apoptosis, adipogenic and osteogenic differentiation abilities of radiation-treated hucMSCs.

CONCLUSIONS

Our findings reveal that the proliferation and differentiation of hucMSCs are suppressed by radiation, which may be associated with the changes of key lipids (TG and PC) and proteins (BYSL, MRTO4, and RRP9). Furthermore, BYSL promotes adipogenic and osteogenic differentiation abilities of radiation-treated hucMSCs via GSK-3β/β-catenin pathway. These findings help explain the response of hucMSCs to radiation and have clinical implications for improving the outcomes of MSC-based therapies after radiotherapy.

Gene editing, metabolomics, network pharmacology strategies to explore terpenoid content and anti-TMV activity in NtSPS1 knockout Nicotiana tabacum

The content of terpenoids in tobacco can alter its resistance to TMV. NtSPS1, a pivotal structural gene in tobacco, is capable to regulate the terpenoid content. In this study, we investigated the effect of NtSPS1 knockout in HD on the content of terpenoids and the anti-TMV activity of this mutant using gene editing, widely targeted metabolomics, network pharmacology, and molecular docking. 48 terpenoids (six up-regulated and five down-regulated) in NtSPS1 knockout tobacco compared with WT leaves. Notably, solanesol was remarkable downregulation which was lowered by fourfold and compounds 1 (log2FC = 18.2), 8 (log2FC = 16.7) were significant upregulation between the mutants and wild-type line leaves. The 46 terpenoid's target network encompassed 150 nodes, 509 edges and their underlying mechanisms in the therapeutic management of TMV are discussed. Furthermore, the network pharmacology and molecular docking revealed that compounds 16, 18, 23, 27, and 36 exhibited significant affinity in their respective interactions. Ultimately, five compounds were assayed for their anti-TMV effects, noteworthily, compounds 36 showed potential anti-TMV activity. Above all, we adopted a multifaceted approach to gain a comprehensive understanding of the terpenoid content and anti-TMV properties in NtSPS1 knockout HD. It enlightens the therapeutic potential of NtSPS1 knockout tobacco and it is helpful to find undescribed anti-TMV activity inhibitors, as well as searching for new anti-TMV candidates from the mutants.

Identification of Hub Genes for Dexmedetomidine Alleviation of Limb Ischemia-Reperfusion-Induced Lung Injury in Rats by Transcriptomic

Background

Limb ischemia-reperfusion (LIR), a prevalent clinical condition, frequently precipitates acute lung injury (ALI). Dexmedetomidine (DEX), a selective alpha2-adrenergic receptor agonist, mitigates LIR-induced ALI. However, its underlying mechanisms remain incompletely elucidated. This study aimed to identify hub genes implicated in DEX-mediated protection against LIR-ALI in rats.

Methods

Sprague-Dawley rats were allocated into five groups (n = 3 per group): Sham (femoral artery exposure without occlusion), LIR, LIR + DEX, LIR + Inhibitor, and LIR + DEX + Inhibitor. LIR was induced by clamping the femoral arteries for 3 hours, followed by reperfusion. DEX (50 μg/kg) or Atipamezole (alpha2-receptor inhibitor, 250 μg/kg) was administered prior to ischemia. Lung injury was evaluated via hematoxylin-eosin staining, wet/dry ratio assessment, and quantification of IL-1beta, TNF-alpha, malondialdehyde (MDA), and superoxide dismutase (SOD) levels. RNA sequencing was performed to identify differentially expressed genes (DEGs), followed by functional enrichment analysis, protein-protein interaction (PPI) network construction, and hub gene identification. Gene-gene interaction (GGI) networks were established. Polymerase chain reaction (PCR) and enzyme linked immunosorbent assay (ELISA) validation was conducted.

Results

LIR induced severe lung injury and inflammation, both of which were attenuated by DEX pretreatment. RNA sequencing identified 2,302 DEGs1, 471 DEGs2, 340 DEGs3, and 1,407 DEGs4. After intersection and subtraction analyses, 255 DEX-associated DEGs (DEGs-Dex) and 290 inhibitor-associated DEGs (DEGs-In) were identified, with enrichment in Wnt/PI3K-Akt signaling (DEX) and glycerolipid/butanoate metabolism (In). Nine Hub-Dex genes and four Hub-In genes were identified, among which Selp and Tars1 exhibited a strong positive correlation (correlation = 0.55, P < 0.05). Six hub genes (Tars1, Atf4, Ep300, Sphk1, AABR07051376.1, and Mmp9) were validated.

Conclusion

Six hub genes associated with DEX-mediated protection against LIR-ALI were identified, providing mechanistic insights and potential therapeutic targets for intervention.

Unveiling the role of phages in shaping the periodontal microbial ecosystem

The oral microbiome comprises various species and plays a crucial role in maintaining the oral ecosystem and host health. Phages are an important component of the periodontal microbiome, yet our understanding of periodontal phages remains limited. Here, we investigated oral periodontal phages using various advanced bioinformatics tools based on genomes of key periodontitis pathogens. Prophages were found to encode various auxiliary genes that potentially enhance host survival and pathogenicity, including genes involved in carbohydrate metabolism, antibiotic resistance, and immune modulation. We observed cross-species transmission among prophages with a complex network of phage-bacteria interactions. Our findings suggest that prophages play a crucial role in shaping the periodontal microbial ecosystem, influencing microbial community dynamics and the progression of periodontitis.IMPORTANCEIn the context of periodontitis, the ecological dynamics of the microbiome are largely driven by interactions between bacteria and their phages. While the impact of prophages on regulating oral pathogens has been increasingly recognized, their role in modulating periodontal disease remains underexplored. This study reveals that prophages within key periodontitis pathogens contribute significantly to virulence factor dissemination, antibiotic resistance, and host metabolism. By influencing the metabolic capabilities and survival strategies of their bacterial hosts, prophages may act as critical regulators of microbial communities in the oral cavity. Understanding these prophage-mediated interactions is essential not only for unraveling the mechanisms of periodontal disease progression but also for developing innovative therapeutic approaches that target the microbial ecosystem at the genetic level. These insights emphasize the need for more comprehensive studies on the ecological risks posed by prophages in shaping microbial pathogenicity and resistance.

Identification and validation of the inflammatory response-related LncRNAs as diagnostic biomarkers for acute ischemic stroke

Ischemic stroke is one of the leading causes of deaths and disability, which is linked to inflammation. In this study, we aimed to identify inflammation-related lncRNAs as diagnostic biomarkers of acute ischemic stroke (AIS). A competing endogenous RNAs (ceRNA) network was established through whole transcriptome analysis. Gene expression datasets from the GEO database were analyzed to identify differentially expressed genes (DEGs), miRNAs and lncRNAs. Inflammation-related DEGs were determined through the intersection of the DEGs of the inflammation-related gene set from Genecards. Multiple databases like lncBase and Targetscan were analyzed to establish a ceRNA network. Several hub genes and sub-networks were obtained from a protein to protein (PPI) network. In addition, the candidate lncRNAs derived from the subnetwork were validated using mice MCAO model and clinical samples. Finally, a network comprising 20 lncRNAs, 26 miRNAs, and 43 inflammatory genes was analyzed, leading to the identification of MALAT1, SNHG8, and GAS5 as potential diagnostic biomarkers. Knockdown of MALAT1 and GAS5 resulted in decreased neurological severity score and inflammation response in mice MCAO model, indicating that these genes were significant diagnostic biomarkers for distinguishing AIS from healthy controls. These findings show that circulating MALAT1 and GAS5 have the potential to serve as clinical diagnostic biomarkers of AIS associated with inflammation.

Pseudomonas aeruginosa Quorum Signals; Associations with Virulence, and Impact of Therapeutic Gamma Radiation Doses

Quorum sensing (QS) signals are the fundamental regulators of P. aeruginosa cellular machinery. From this perspective, this study aimed to analyze a pathogenic Pseudomonas aeruginosa isolate quorum signals profile prior and following exposure to therapeutic gamma radiation doses, and associate them with their virulence. Analysis of quorum signals was conducted utilizing GC-Mass spectroscopy and CFM-ID 4.0 mass spectra prediction webserver. The correlation between these signals and P. aeruginosa virulence was investigated through in vitro and computational methods. The isolates pyocyanin, biosurfactant, and biofilm productions were quantified before and after gamma irradiation and the STRING-DB were used to scrutinize the QS synthesizing proteins interactions. Further, the Cytoscape software statistically analyzed the QS proteins-proteins interaction networks. The study reported the recovery of acyl-homoserine lactones (C2, C4, C6, and C12-HSLs) and fatty acid signals (DSFs) from the P. aeruginosa isolate ethyl acetate extract and proposed the potential isolation of longer-chain HSLs (> C12-HSLs). New functional associations were identified for QS synthesizing proteins, which involve spermidine, fatty acids, and siderophores biosynthesis. The irradiated P. aeruginosa extracts GC-MS chromatograms exhibited notable changes in the retention times of QS signals and their mass spectra with the retrieval of different forms of fatty acids esters. Additionally, irradiated P. aeruginosa demonstrated a modest increase in the production of both biofilms and biosurfactants. This finding indicated that changes in quorum signals profile post irradiation boosted P. aeruginosa virulence mechanisms, which may potentially lead to an exacerbation of infection pathogenesis following the application of therapeutic gamma radiation doses.

Exploring the link between Di-2-ethylhexyl phthalate (DEHP) exposure and muscle mass: A systematic investigation utilizing NHANES data analysis, network toxicology and molecular docking approaches

Sarcopenia is a syndrome characterized by a progressive, widespread decline in muscle mass and strength. DEHP, a plasticizer involved in daily life and widely used, has been found in various everyday items and causes developmental dysregulation, reproductive impairments, tumorigenesis, and transgenerational disease. However, much remains to be discovered regarding the association between exposure to this environmental toxin and sarcopenia, as well as the toxic targets and molecular mechanisms. This research elucidated the relationship between contact with DEHP and the development of sarcopenia by integrating NHANES data analysis, network toxicology, and molecular docking. 3199 adults were enrolled, and multiple linear regressions were performed to reveal a significant negative correlation between lnDEHP and ALMBMI. Eighty-eight targets associated with DEHP and sarcopenia were identified. Subsequent STRING and Cytoscape screening stressed 20 key targets, including CASP3, BCL2, MMP9, BCL2L1, APP, and CTSS. GO and KEGG enrichment analyses revealed that these targets are involved in ligand-receptor interactions, apoptosis, and calcium signaling pathways. Molecular docking simulations using CB-dock confirmed the high-affinity binding interactions between DEHP and these key targets. This study validated the relationship between DEHP exposure and muscle mass. Further, it provided a theoretical basis for investigating the molecular mechanisms of DEHP exposure-induced skeletal muscle toxicity.

Effects of naphthoquinone scaffold-derived compounds on head and neck squamous cell carcinoma based on network pharmacology and molecular docking

OBJECTIVES

This study aimed to analyze the effects of naphthoquinone scaffold-derived compounds on head and neck squamous cell carcinoma (HNSCC) using network pharmacology and molecular docking.

METHODS

We screened candidate compounds from the ASINEX database and evaluated their drug likeness and toxicity. They identified 80 compounds with naphthalenone structures, focusing on 1,4-naphthoquinone and 1,2-naphthoquinone scaffolds. The possible targets of these compounds were predicted using databases like SwissTargetPrediction and Similarity Ensemble Approach Database (SEA).

RESULTS

The common targets between the compounds and HNSCC were identified, yielding 65 overlapping targets. A protein-protein interaction (PPI) network was constructed, and 20 hub genes were identified based on centrality metrics. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these compounds' protective effects against HNSCC are associated with cancer-related pathways, such as those in cancer and proteoglycans in cancer. Molecular docking was performed to evaluate the binding affinity between the compounds and hub genes. The results showed that the compounds had strong binding affinities with key targets like MET and TYK2, with binding energies < -5 kcal/mol.

CONCLUSIONS

The study suggests that naphthoquinone derivatives could serve as novel chemotherapy agents for HNSCC, warranting further research for clinical application.

lncRNA PAN3-AS1 Modulates Cilium Assemble Signaling Pathway Through Regulation of RPGR as a Potential MS Diagnostic Biomarker: Integrated Systems Biology Investigation

Multiple sclerosis (MS), an autoimmune condition of the central nervous system (CNS), can lead to demyelination and axonal degeneration in the brain and spinal cord, which can cause progressive neurologic disability. MS symptoms include dysautonomia and progressive decline in motor abilities. In this investigation, we performed an integrated bioinformatics and experimental approach to find the expression level and interaction of a novel long non-coding RNA (lncRNA), PAN3-AS1, in MS samples. Microarray analysis was performed by R Studio using GEOquery and limma packages. lncRNA-mRNA RNA interaction analysis was performed using the lncRRIsearch database. Pathway enrichment analysis was performed by KEGG and Reactome online software through the Enrichr database. Protein-protein interaction analysis was performed by STRING online software. Gene ontology (GO) analysis was performed by Enrichr database. Based on microarray analysis, lncRNA PAN3-AS1 has a significantly low expression in MS samples compared to the control (logFC - 1.2, adj. P. Val 0.03). qRT-PCR results approved bioinformatics analyses. ROC analysis revealed that PAN3-AS1 could be considered a potential diagnostic biomarker of MS. Based on lncRNA-mRNA interaction analysis, lncRNA PAN3-AS1 regulates the expression level of RPGR. RPGR and its protein interactome regulate the cilium assembly, chaperon-mediated autophagy, and microarray biogenesis. lncRNA PAN3-AS1, as a significant low-expressed lncRNA in MS samples, could be a potential diagnostic MS biomarker. PAN3-AS1 might regulate the expression level of cilium assembly and chaperon-mediated autophagy. Dysregulation of PAN3-AS1 might affect the expression of RPGR and its protein interactome.