The lack of a sufficient number of validated miRNA targets severely hampers the understanding of their biological function. Even for the well-studied miR-155-5p, there are only 239 experimentally validated targets out of 42,554 predicted targets. For a more complete assessment of the immune-related miR-155 targetome, we used an inverse correlation of time-resolved mRNA profiles and miR-155-5p expression of early CD4+ T cell activation to predict immune-related target genes. Using a high-throughput miRNA interaction reporter (HiTmIR) assay we examined 90 target genes and confirmed 80 genes as direct targets of miR-155-5p. Our study increases the current number of verified miR-155-5p targets approximately threefold and exemplifies a method for verifying miRNA targetomes as a prerequisite for the analysis of miRNA-regulated cellular networks.

Multiple myeloma (MM) is a hematological malignancy with the proliferation of malignant plasma cells. Numerous studies have highlighted the critical role of ferroptosis in MM. However, how to use ferroptosis-related genes (FRGs) for prognostic prediction and treatment guidance in MM remains unknown.

By analysis of GEO databases, the prognostic gene was identified and a therapeutic strategy for MM patients based on FRGs was explored. A total of 12 FRGs were identified, utilizing the STRING database and Cytoscape software, and the PPI networks were constructed to identify hub genes and further functional enrichment analyses. Based on the aforementioned data, this study analyzed the expression of RUVBL2 in MM patients by qRT-PCR and Western blotting. To validate the functional role of RUVBL2 in the MM cells, cellular experiments were ultimately conducted.

The analysis highlighted six hub genes, including TP53, MCM5, TLR4, RUVBL2, GCLM and ITGA6, and functional enrichment analyses indicating enrichment in DNA replication, regulation of apoptotic signaling pathway and PI3K/AKT signaling pathway. Prognostic analysis indicated that TP53, RUVBL2, and MCM5 are associated with MM prognosis, with RUVBL2 displaying a notable area under the curve (AUC) of 0.823 in ROC analysis. The study first determined that RUVBL2 is highly expressed in MM, siRUVBL2-mediated deletion of RUVBL2 inhibited proliferation, promoted apoptosis and increased the sensitivity of BTZ in MM cells, and also overcame BTZ resistance in CD138+ primary cells from MM patients.

Our study first suggested that RUVBL2 may be regarded as potential therapeutic targets and prognostic value in MM.

The gut microbiota is a crucial link between diet and cardiovascular disease (CVD). Using fecal metaproteomics, a method that concurrently captures human gut and microbiome proteins, we determined the crosstalk between gut microbiome, diet, gut health, and CVD. Traditional CVD risk factors (age, BMI, sex, blood pressure) explained < 10% of the proteome variance. However, unsupervised human protein-based clustering analysis revealed two distinct CVD risk clusters (low-risk and high-risk) with different blood pressure (by 9 mmHg) and sex-dependent dietary potassium and fiber intake. In the human proteome, the low-risk group had lower angiotensin-converting enzymes, inflammatory proteins associated with neutrophil extracellular trap formation and auto-immune diseases. In the microbial proteome, the low-risk group had higher expression of phosphate acetyltransferase that produces SCFAs, particularly in fiber-fermenting bacteria. This model identified severity across phenotypes in heart failure patients and long-term risk of cardiovascular events in a large population-based cohort. These findings underscore multifactorial gut-to-host mechanisms that may underlie risk factors for CVD.

The Coronavirus Disease 2019 (COVID-19) pandemic has led to numerous cases of co-infection with SARS-CoV-2 and other viruses, including Kaposi's sarcoma-associated herpesvirus (KSHV), worldwide. This co-infection has increased patient mortality due to the lack of efficient bi-targeted drugs. Cambogin, a bioactive natural product, has been shown to effectively induce regression of KSHV-latently infected tumours in xenograft mice models; however, its impact on SARS-CoV-2 infection remains unclear. Here, we report that Cambogin targets 46 host genes commonly affected by both SARS-CoV-2 and KSHV infections, as identified through bioinformatics analysis. These genes are related with 14 key upstream signalling pathways, particularly those involved in inflammation regulation, protein phosphorylation, metabolic processes, and cellular stress response. Within the transcriptional factor (TF)-miRNA co-regulatory network, ten out of 46 hub-target genes are closely linked to Cambogin and KSHV/SARS-CoV-2. Importantly, Cambogin not only efficiently blocks the replication and virion production of SARS-CoV-2 in vitro and in vivo by reducing the expression of EGFR and Cyclin A2, but also simultaneously inhibits both SARS-CoV-2 infection and the growth of KSHV-induced tumours in vivo using a murine xenograft model. These findings provide an alternative strategy for the potential use of Cambogin in the treatment of SARS-CoV-2 patients, particularly those with KSHV co-infection.

JOURNAL/nrgr/04.03/01300535-202508000-00026/figure1/v/2024-09-30T120553Z/r/image-tiff Interferon regulatory factor 7 plays a crucial role in the innate immune response. However, whether interferon regulatory factor 7-mediated signaling contributes to Parkinson's disease remains unknown. Here we report that interferon regulatory factor 7 is markedly up-regulated in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse model of Parkinson's disease and co-localizes with microglial cells. Both the selective cyclic guanosine monophosphate adenosine monophosphate synthase inhibitor RU.521 and the stimulator of interferon genes inhibitor H151 effectively suppressed interferon regulatory factor 7 activation in BV2 microglia exposed to 1-methyl-4-phenylpyridinium and inhibited transformation of mouse BV2 microglia into the neurotoxic M1 phenotype. In addition, siRNA-mediated knockdown of interferon regulatory factor 7 expression in BV2 microglia reduced the expression of inducible nitric oxide synthase, tumor necrosis factor α, CD16, CD32, and CD86 and increased the expression of the anti-inflammatory markers ARG1 and YM1. Taken together, our findings indicate that the cyclic guanosine monophosphate adenosine monophosphate synthase-stimulator of interferon genes-interferon regulatory factor 7 pathway plays a crucial role in the pathogenesis of Parkinson's disease.

JOURNAL/nrgr/04.03/01300535-202507000-00024/figure1/v/2024-09-09T124005Z/r/image-tiff Differentiation of oligodendrocyte progenitor cells into mature myelin-forming oligodendrocytes contributes to remyelination. Failure of remyelination due to oligodendrocyte progenitor cell death can result in severe nerve damage. Ferroptosis is an iron-dependent form of regulated cell death caused by membrane rupture induced by lipid peroxidation, and plays an important role in the pathological process of ischemic stroke. However, there are few studies on oligodendrocyte progenitor cell ferroptosis. We analyzed transcriptome sequencing data from GEO databases and identified a role of ferroptosis in oligodendrocyte progenitor cell death and myelin injury after cerebral ischemia. Bioinformatics analysis suggested that perilipin-2 (PLIN2) was involved in oligodendrocyte progenitor cell ferroptosis. PLIN2 is a lipid storage protein and a marker of hypoxia-sensitive lipid droplet accumulation. For further investigation, we established a mouse model of cerebral ischemia/reperfusion. We found significant myelin damage after cerebral ischemia, as well as oligodendrocyte progenitor cell death and increased lipid peroxidation levels around the infarct area. The ferroptosis inhibitor, ferrostatin-1, rescued oligodendrocyte progenitor cell death and subsequent myelin injury. We also found increased PLIN2 levels in the peri-infarct area that co-localized with oligodendrocyte progenitor cells. Plin2 knockdown rescued demyelination and improved neurological deficits. Our findings suggest that targeting PLIN2 to regulate oligodendrocyte progenitor cell ferroptosis may be a potential therapeutic strategy for rescuing myelin damage after cerebral ischemia.

Type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD) have similar clinical characteristics in the brain and islet, as well as an increased incidence with ageing and familial susceptibility. Therefore, in recent years there has been a great desire for research that elucidates how anti-diabetic drugs affect AD. This work attempts to first elucidate the possible mechanism of action of DPP-IV inhibitors in the treatment of AD by employing techniques from network pharmacology, molecular docking, molecular dynamic simulation, principal component analysis, and MM/PBSA. A total of 463 targets were identified from the SwissTargetPrediction and 784 targets were identified from the SuperPred databases. 79 common targets were screened using the PPI network. The GO and KEGG analyses indicated that the activity of DPP-IV against AD potentially involves the hsa04080 neuroactive ligand-receptor interaction signalling pathway, which contains 17 proteins, including CHRM2, CHRM3, CHRNB1, CHRNB4, CHRM1, PTGER2, CHRM4, CHRM5, TACR2, HTR2C, TACR1, F2, GABRG2, MC4R, HTR7, CHRNG, and DRD3. Molecular docking demonstrated that sitagliptin had the greatest binding affinity of -10.7 kcal/mol and established hydrogen bonds with the Asp103, Ser107, and Asn404 residues in the active site of the CHRM2 protein. Molecular dynamic simulation, PCA, and MM/PBSA were performed for the complex of sitagliptin with the above-mentioned proteins, which revealed a stable complex throughout the simulation. The work identifies the active component and possible molecular mechanism of sitagliptin in the treatment of AD and provides a theoretical foundation for future fundamental research and practical implementation.

Glioblastoma multiforme (GBM) is the most frequent type of primary malignant brain tumor. This study utilized Mendelian randomization (MR) analysis to explore the causal link between proteins in plasma and cerebrospinal fluid and GBM.

This study aimed to identify proteins in both plasma and cerebrospinal fluid (CSF) that could serve as potential therapeutic targets for GBM.

We employed previously published protein quantitative trait loci (pQTL) data from CSF and plasma as the exposure data, alongside aggregated Genome-Wide Association Study (GWAS) data on GBM for our MR analysis. Furthermore, we conducted Bayesian co-localization analysis and examined the protein-protein interaction (PPI) networks of CSF and plasma proteins related to GBM risk.

MR identified three key proteins linked to GBM risk: ribophorin I (RPN1) in plasma, von Willebrand factor (vWF) and macrophage-stimulating protein (MSP). in CSF. Elevated RPN1 and MSP were associated with decreased GBM risk, while increased vWF was linked to higher risk. External validation confirmed that RPN1 served as a key protein in GBM development. Bayesian co-localization showed a 10.35 % probability of a shared causal variant between RPN1 and GBM. Protein-protein interaction analysis further highlighted related proteins for RPN1.

In summary, the plasma protein RPN1 and the CSF proteins vWF and MSP are causally associated with the risk of GBM. Further research is needed to clarify the roles of these candidate proteins in GBM. Notably, RPN1 may serve as a potential therapeutic target for GBM. Future clinical studies on GBM treatment could explore drugs targeting RPN1.

Aquaporins (AQPs) are specialized membrane proteins that create selective water channels, facilitating the transport of water across cell membranes and playing a vital role in maintaining water balance and regulating osmotic pressure in aquatic animals. This study identified 9 aquaporin genes from the genome of R. philippinarum, and a comprehensive analysis was conducted on their gene structure, phylogenetic relationships, protein structure, and chromosome localization. RNA-seq data analysis revealed that aquaporin genes were differentially expressed at different developmental stages, in tissue distribution, and in response to salinity stress. In addition, qPCR results revealed that the expression levels of aquaporin genes (AQP1, AQP4d, and AQP3) were significantly elevated in response to both acute low and high salinity stress, suggesting their important role in osmotic pressure regulation in R. philippinarum. This study's results offer an important reference for further investigations into the regulation of osmotic pressure and salinity adaptation of aquaporin in R. philippinarum.

The escalating prevalence of Type-2 diabetes mellitus (T2DM) poses a significant global health challenge. Utilizing integrative proteomic analysis, this study aimed to identify a panel of potential protein markers for T2DM, enhancing diagnostic accuracy and paving the way for personalized treatment strategies.

Proteome profiles from two independent cohorts were integrated: cohort 1 composed of 10 T2DM patients and 10 healthy controls (HC), and cohort 2 comprising 87 T2DM patients and 60 healthy controls. Differential expression analysis, functional enrichment analysis, receiver operating characteristic (ROC) analysis, and classification error matrix analysis were employed.

Comparative proteomic analysis identified the differential expressed proteins (DEPs) and changes in biological pathways associated with T2DM. Further combined analysis refined a group of protein panel (including CA1, S100A6, and DDT), which were significantly increased in T2DM in both two cohorts. ROC analysis revealed the area under curve (AUC) values of 0.94 for CA1, 0.87 for S100A6, and 0.97 for DDT; the combined model achieved an AUC reaching 1. Classification error matrix analysis demonstrated the combined model could reach an accuracy of 1 and 0.875 in the 60% training set and 40% testing set.

This study incorporates different cohorts of T2DM, and refines the potential markers for T2DM with high accuracy, offering more reliable markers for clinical translation.

The online version contains supplementary material available at 10.1007/s40200-025-01562-3.

As an important member of global aquaculture, oysters (Crassostrea gigas) have significant economic value. With the development of commercial aquaculture, the frequent occurrence of diseases caused by Vibrio alginolyticus has become a hindrance to high-density aquaculture. Gill tissue, as an important component of immune system of the oysters, plays the key point in the face of invasion by foreign substances. Compared to the diploid oyster, the triploid oyster presents a higher growth rate and lower growth investment, making it a more ideal model for studying oyster immune defense. In this study, triploid oysters were as the research subject, and gill tissues attacked by V. alginolyticus were sequenced. By analyzing samples from different time points, 1746 DEGs were obtained. The KEGG and GO functional enrichment analysis showed that gill tissues mainly participate in immune function through the PIK3-Akt signaling pathway and the MAPK signaling pathway. The protein interaction network revealed three genes (CASP8, CASP9 and PIK3CA) that play core roles in immune defense by analyzing the interaction relationship between genes. Finally, qRT-PCR verified the expression of key genes. This study provides a more effective scientific basis for disease prevention and control of oysters and other bivalve shellfish, and helps to promote the sustainable development of aquaculture.

The aim of this study is to employ network pharmacology to identify potential therapeutic targets for Ganoderma lucidum in the treatment of optic atrophy, and elucidate the underlying pharmacological mechanism.

This study is mainly divided into two parts. In the first part, the chemical composition and Target of Ganoderma lucidum compound were predicted by TCMSP and Swiss Target Prediction, and the crossover gene between OA and Ganoderma lucidum target gene was screened based on GeneCards and OMIM database. Then, the target genes were enriched and the main pathways of action were analyzed to discover the possible mechanism of action for the treatment of optic atrophy. Finally, the selected core compounds and core targets were interfaced to understand the main binding patterns and affinity. The second part mainly verifies whether Ganoderma lucidum polysaccharide has protective effect on RGC. Firstly, CCK8 method was used to detect the proliferation and virulence analysis of RGC-5 cells with different concentrations of Ganoderma lucidum polysaccharide, and then RGC-5 cells were cultured in subgroups for 12 h, and then put into anaerobic encapsulation to make molds. After 24 h of continuous culture, cells were removed and collected for subsequent RT-PCR and WB detection.

Through screening target genes of Ganoderma lucidum and OA, 85 potential therapeutic targets were obtained by intersection. Through PPI network analysis of 85 potential targets, it was found that the degree values of TP53, TNF, CASP3, IL6, EGFR, MTOR, ESR1 and other targets were higher. (+)-Ganoderic acid Mf, (+)-Methyl ganolucidate A, epoxyganoderiol A, Ergosta-4,7, 22-Trien-3, 6-Dione and other compounds play a key role in the whole network. It may be the key compound of ganoderma lucidum in treating OA. Through enrichment pathway analysis, it was found that the number of genes was enriched in AGE-RAGE signaling pathway, cAMP signaling pathway, inflammation and cancer pathways, and the structure of TP53, TNF, CASP3, and IL6 binding to the above compounds was stable and the binding activity was high.

The findings suggest that Ganoderma lucidum may exert its therapeutic effects on optic atrophy by targeting TP53, TNF, CASP3, and IL6. Additionally, it may also be involved in the AGE-RAGE signaling pathway and cAMP signaling pathway. These results provide reference for the clinical application of ganoderma lucidum in the treatment of OA.

Caspases (CASPs) are attractive targets for cancer therapy. Many prognostic models based on gene signatures include genes from the CASPs family in diffuse glioma. CASP3, CASP4 and CASP6 in glioma have been studied individually. However, specialized comprehensive analysis of the roles of CASPs family in glioma is lacking. Therefore, this study utilized bioinformatics methods to investigate this issue. CASP1-10 expressionlevels were significantly up-regulated in LGG and GBM and glioma, and varied significantly across different clinical subgroups of glioma and LGG and various cell types, and most of CASP1-10 members showed significant differences in recurrence status of LGG. 10 signatures (CASP1-10) were associated with poor overall survival (OS) in glioma and LGG and GBM. However, pan-cancer survival analysis showed that CASP1-10 were associated with the prognosis of LGG, but not GBM. CASP1-10 were related to poor prognosis of glioma and LGG, except for CASP9, which was the opposite of a protective factor. CASP1-10 were independent prognostic factors for OS in glioma and LGG, except for CASP5, and also for recurrence-free survival (RFS) in LGG. Most of CASP1-10 were also independent prognostic factors for disease-specific survival (DSS) and progression-free interval (PFI) and had diagnostic value in glioma and LGG. Genetic alterations of CASP1-10 genes set were associated with poor prognosis in LGG. CASP1-10 were involved in immune infiltration and programmed cell death in glioma and LGG and GBM, and might promote the apoptosis of immune cells. Compared to GBM, CASP1-10 had a more significant impact on the prognosis, cancer-related pathways, and immune infiltration in LGG, indicating that CASP1-10 might play important roles in the recurrence and progression of LGG, and might be promising therapeutic targets for LGG. Therefore, it is speculated that natural caspase inhibitor p35 may be a promising drug for the treatment of glioma, especially for LGG.

The current understanding of glioma pathogenesis is limited by the lack of comprehensive insights into the metabolic reprogramming associated with isocitrate dehydrogenase (IDH) mutations. This study aims to contribute a step to this gap by investigating the role of energy metabolism-related genes in glioma. Our objective is to identify key molecular markers that could serve as prognostic markers and potential therapeutic targets for more effective treatment strategies in IDH-mutant glioma patients.

We conducted an in-depth analysis of gene expression data from TCGA, CGGA, and GEO databases, employing Weighted Gene Co-expression Network Analysis (WGCNA) and differential gene expression analysis to pinpoint candidate genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to elucidate the biological pathways implicated by these genes. Protein-Protein Interaction (PPI) and Gene Multiple Association Network Integration Algorithm (GeneMANIA) networks were constructed to map gene interactions, and survival analysis and Cox regression models were utilized to assess the prognostic value of the identified genes. Additionally, CIBERSORT was used to evaluate immune cell infiltration in the tumor microenvironment.

Our findings identified SPHKAP as a gene significantly downregulated in glioma tissues compared to control samples. Specifically, low SPHKAP expression was associated with a poorer prognosis of patients with IDH-mutant glioma and linked to the expression of key enzymes involved in energy metabolism. Meanwhile, in IDH-mutant gliomas, reduced SPHKAP expression was correlated with increased macrophage infiltration, enhanced T cell response, and upregulation of immune checkpoint genes, highlighting its role as an independent prognostic marker.

This study reveals the differential expression of SPHKAP in glioma, suggesting its potential as a prognostic marker for IDH-mutant gliomas, providing information for future studies aimed at developing targeted therapies for glioma patients.

Attention-deficit/hyperactivity disorder (ADHD) is a heterogeneous neurodevelopmental condition with a high prevalence of co-occurring conditions, contributing to increased difficulty in long-term management. Genome-wide association studies have identified variants shared between ADHD and co-occurring psychiatric disorders; however, the genetic mechanisms are not fully understood. We integrated gene expression and spatial organization data into a two-sample Mendelian randomization study for putatively causal ADHD genes in fetal and adult cortical tissues. We identified four genes putatively causal for ADHD in cortical tissues (fetal: ST3GAL3, PTPRF, PIDD1; adult: ST3GAL3, TIE1). Protein-protein interaction databases seeded with the causal ADHD genes identified biological pathways linking these genes with conditions (e.g., rheumatoid arthritis) and biomarkers (e.g., lymphocyte counts) known to be associated with ADHD, but without previously shown genetic relationships. The analysis was repeated on adult liver tissue, where putatively causal ADHD gene ST3GAL3 was linked to cholesterol traits. This analysis provides insight into the tissue-dependent temporal relationships between ADHD, co-occurring traits, and biomarkers. Importantly, it delivers evidence for the genetic interplay between co-occurring conditions, both previously studied and unstudied, with ADHD.

Alzheimer's disease (AD) is a neurodegenerative disorder with a higher risk incidence in females than in males, and there are also differences in AD pathophysiology between sexes. The role of sex in the pathogenesis of AD may be crucial, yet the cellular and molecular basis remains unclear. Here, we performed a comprehensive analysis using four public transcriptome datasets of AD patients and age-matched control individuals in prefrontal cortex, including bulk transcriptome (295 females and 402 males) and single-nucleus RNA sequencing (snRNA-seq) data (224 females and 219 males). We found that the transcriptomic profile in female control was similar to those in AD. To characterize the key features associated with both the pathogenesis of AD and sex difference, we identified a co-expressed gene module that positively correlated with AD, sex, and aging, and was also enriched with immune-associated pathways. Using snRNA-seq datasets, we found that microglia (MG), a resident immune cell in the brain, demonstrated substantial differences in several aspects between sexes, such as an elevated proportion of activated MG, altered transcriptomic profile and cell-cell interaction between MG and other brain cell types in female control. Additionally, genes upregulated in female MG, such as TLR2, MERTK, SPP1, SLA, ACSL1, and FKBP5, had high confidence to be identified as biomarkers to distinguish AD status, and these genes also interacted with some approved drugs for treatment of AD. These findings underscore the altered immune response in female is associated with sex difference in susceptibility to AD, and the necessity of considering sex factors when developing AD biomarkers and therapeutic strategies, providing a scientific basis for further in-depth studies on sex differences in AD.

Behavioral variant of Frontotemporal Dementia (bvFTD) and Bipolar Disorder (BD) share overlapping symptoms, complicating diagnosis. BvFTD, especially linked to C9orf72 expansions, often mimics BD, highlighting the need for reliable biomarkers. This study aimed to differentiate bvFTD from BD using miRNA profiles in neural-enriched extracellular vesicles (NEVs). A cohort of 100 subjects was analyzed: 40 bvFTD (20 sporadic, 20 C9orf72 carriers), 40 BD, and 20 healthy controls. NEVs were isolated from plasma and profiled using real-time PCR. Among 754 miRNAs, 11 were significantly deregulated in bvFTD and BD. MiR-152-5p was downregulated in sporadic bvFTD, while let-7b, let-7e, miR-18b, and miR-142-5p were altered in C9orf72 carriers. BD patients showed distinct patterns in miR-331-5p, miR-335, and miR-345 compared to bvFTD. Bioinformatics analyses revealed that let-7e, let-7b, miR-18b, and miR-142-5p share common long non-coding RNA (lncRNA) targets, including XIST, NEAT1, and OIP5-AS1, suggesting their involvement in molecular networks relevant to C9orf72-related bvFTD. These miRNA signatures can differentiate bvFTD from BD, especially in C9orf72-related cases, and offer insights into disease pathways. Further research is needed to validate these findings and explore their clinical application.

Plasma proteins play critical roles in a series of biological processes and represent a major source of translational biomarkers and drug targets. In this study, we performed Mendelian randomization (MR) to explore potential causal associations of protein quantitative trait loci (pQTL, n = 54,219) with major depressive disorder (MDD) using summary statistics from the PGC (n = 143,265) and further replicated in FinnGen cohort (n = 406,986). Subsequently, gene expression quantitative trait loci (eQTL) of identified proteins were leveraged to validate the primary findings in both PGC and FinnGen cohorts. We implemented reverse causality detection using bidirectional MR analysis, Steiger test, Bayesian co-localization and phenotype scanning to further strengthen the MR findings. In primary analyses, MR analysis revealed 2 plasma protein significantly associated with MDD risk at Bonferroni correction (P < 3.720 × 10-5), including butyrophilin subfamily 2 member A1 (BTN2A1, OR = 0.860; 95 % CI, 0.825-0.895; P = 1.79 × 10-5) and butyrophilin subfamily 3 member A2 (BTN3A2, OR = 1.071; 95 % CI, 1.056-1.086; P = 3.89 × 10-6). Both the identified proteins had no reverse causality. Bayesian co-localization indicated that BTN2A1 (coloc.abf-PPH4 = 0.620) and BTN3A2 (coloc.abf-PPH4 = 0.872) exhibited a shared variant with MDD, a finding that was subsequently validated by HEIDI test. In the replication stage, BTN2A1 and BTN3A2 were successfully validated in the FinnGen cohort. This study genetically determined BTN2A1 and BTN3A2 were associated with MDD and these findings may have clinical implications for MDD prevention.

Chemoresistance is a key obstacle in the long-term survival of patients with locally and advanced lung adenocarcinoma (LUAD). This study used bioinformatic analysis to reveal the chemoresistance of gene-neutrophil extracellular traps (NETs) associated with LUAD. RNA sequencing data and LUAD expression patterns were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, respectively. The GeneCards database was used to identify NETosis-related genes (NRGs). To identify hub genes with significant and consistent expression, differential analysis was performed using the TCGA-LUAD and GEO datasets. LUAD subtypes were determined based on these hub genes, followed by prognostic analysis. Immunological scoring and infiltration analysis were conducted using NETosis scores (N-scores) derived from the TCGA-LUAD dataset. A clinical prognostic model was established and analyzed, and its clinical applications explored. Twenty-two hub genes were identified, and consensus clustering was used to identify two subgroups based on their expression levels. The Kaplan-Meier (KM) curves demonstrated statistically significant differences in prognosis between the two LUAD subtypes. Based on the median score, patients were further divided into high and low N-score groups, and KM curves showed that the N-scores were more precise at predicting the prognosis of patients with LUAD for overall survival (OS). Immunological infiltration analysis revealed significant differences in the abundances of 10 immune cell infiltrates between the high and low N-score groups. Risk scores indicated significant differences in prognosis between the two extreme score groups. The risk scores for the prognostic model also indicated significant differences between the two groups. The results provide new insights into NETosis-related differentially expressed genes (NRDEGs) associated with chemotherapy resistance in patients with LUAD. The established prognostic model is promising and could help with clinical applications to evaluate patient survival and therapeutic efficiency.

Idiopathic pulmonary fibrosis (IPF) is a worsening fibrotic condition characterized by a short survival rate and limited treatment options. This study evaluates the potential anti-fibrotic properties of Schisandrin B (Sch B) through network pharmacology and experimental validation. A mouse model of bleomycin-induced pulmonary fibrosis was established, and the modeled mice were treated with Sch B at three doses (20 mg/kg/day, 40 mg/kg/day, and 80 mg/kg/day). A fibrotic model was developed in NIH/3T3 cells by treating them with TGF-β (10 ng/mL) and administering Sch B at various concentrations (10, 20, and 40 µM). The results revealed that Sch B treatment delayed the development of bleomycin-induced pulmonary fibrosis and substantially decreased the transcription levels of collagen I and α-SMA in TGF-β-induced fibroblasts. Core targets were screened with protein-protein interaction network analysis, molecular complex detection (MCODE), and CytoHubba plugin. The application of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and molecular docking highlighted the significance of the HIF-1α signaling pathway in the potential mechanism of Sch B in IPF therapy. Western blot, PCR, and immunofluorescence were performed to validate the effects of Sch B on HIF-1α. In vivo and in vitro, Sch B administration reduced HIF-1α expression. These outcomes provide valuable insights into the potential mechanism by which Sch B delays IPF development, with HIF-1α potentially serving as a key target. However, further investigation is warranted to assess the safety and efficacy of Sch B in clinical settings.

This study was designed to investigate the role of Ligustrum lucidum Ait and Ecliptae Herba on premature ovarian failure (POF) and the underlying mechanisms. In the POF mouse model constructed using cyclophosphamide (CTX), Ligustrum lucidum Ait and Ecliptae Herba increased ovarian index and estradiol (E2) levels and curtailed motility and follicle-stimulating hormone (FSH). Ligustrum lucidum Ait and Ecliptae Herba alleviated ovarian pathological damage in POF mice and promoted the expression of ovarian CD31 and Vascular Endothelial Growth Factor A (VEGFA). Through high-performance liquid chromatography-mass spectrometry (HPLC-MS) and network pharmacology, Specnuezhenide and ecliptasaponin A were identified as the key components of Ligustrum lucidum Ait and Ecliptae Herba in anti-POF action. The important target associated with these components is Estrogen Receptor (ESR) 1. Molecular docking and in vitro experiments showed that Specnuezhenide and ecliptasaponin A can both bind to the ESR protein; knocking down ESR1 inhibited the anti-apoptotic effect of Specnuezhenide and ecliptasaponin A on CTX-induced POF cells. In conclusion, the key components of Ligustrum lucidum Ait and Ecliptae Herba that alleviate POF are Specnuezhenide and ecliptasaponin A, which improve the condition by upregulating ESR1.

Fatigue is commonly marked by reduced endurance and impaired function, often linked to overexertion and chronic conditions. Quinoa (Chenopodium quinoa Willd.), with its rich amino acids and resilience to harsh conditions, offers a novel strategy for combating fatigue. This study explored the antifatigue effects of quinoa protein (QPro) and its hydrolysate (QPH) in weight-loaded swimming mice. After 4 weeks of oral administration, QPro and QPH significantly prolonged swimming duration, reduced serum fatigue biomarkers (lactic acid, urea nitrogen, lactate dehydrogenase, creatine kinase), and elevated glycogen reserves in the liver and muscle. RT-qPCR analysis indicated that QPH activated hepatic gluconeogenesis via G6Pase and PEPCK signaling and enhanced mitochondrial function through PGC-1α/NRF1/TFAM signaling in muscle. Additionally, QPro and QPH boosted antioxidant defenses by improving antioxidant enzyme activity, reducing malondialdehyde through the Nrf2/HO-1 pathway, and suppressing inflammation by reducing TNF-α and IL-6 levels. Network pharmacology identified 31 key targets involved in energy metabolism and inflammation, providing novel insights into the molecular mechanisms underlying the antifatigue properties of quinoa peptides. These findings highlight the potential of QPro and QPH as natural and bioactive ingredients in functional foods for enhancing endurance and mitigating fatigue.

Traditional drug discovery approach is based on one drug-one target, that is associated with very lengthy timelines, high costs and very low success rates. Network pharmacology (NP) is a novel method of drug designing, that is based on a multiple-target approach. NP integrates systems such as biology, pharmacology and computational techniques to address the limitations of traditional methods of drug discovery. With help of mapping biological networks, it provides deep insights into biological molecules' interactions and enhances our understanding to the mechanism of drugs, polypharmacology and disease etiology. This review explores the theoretical framework of network pharmacology, discussing the principles and methodologies that enable the construction of drug-target and disease-gene networks. It highlights how data mining, bioinformatics tools and computational models are utilised to predict drug behaviour, repurpose existing drugs and identify novel therapeutic targets. Applications of network pharmacology in the treatment of complex diseases-such as cancer, neurodegenerative disorders, cardiovascular diseases and infectious diseases-are extensively covered, demonstrating its potential to identify multi-target drugs for multifaceted disease mechanisms. Despite the promising results, NP faces challenges due to incomplete and quality of biological data, computational complexities and biological system redundancy. It also faces regulatory challenges in drug approval, demanding revision in regulatory guidelines towards multi-target therapies. Advancements in AI and machine learning, dynamic network modelling and global collaboration can further enhance the efficacy of network pharmacology. This integrative approach has the potential to revolutionise drug discovery, offering new solutions for personalised medicine, drug repurposing and tackling the complexities of modern diseases.

Amyloid-proteinopathy is observed in type 2 diabetes, where Islet amyloid polypeptide is secreted atypically and impedes cellular homeostasis. The thiazolidinediones family is reported to influence amyloid-beta aggregations. However, research on drug-based stimulation of insulin signaling to alleviate Islet amyloid aggregations is lacking. To understand the impact of pioglitazone on islet amyloid aggregation, we conducted an in vivo and in silico analysis. For in vivo analysis, we generated a transgenic Drosophila harboring the preproform of human Islet amyloid polypeptide (IAPP) that can be ectopically expressed in a spatio-temporal manner. We show that the unprocessed form of IAPP also has the propensity to form aggregates and cause degeneration. Pioglitazone feeding effectively reduces the burden of Islet amyloid aggregations in the larval brain. In silico analysis shows that there is a higher protein-ligand binding energy for IAPP with pioglitazone than amyloid-beta. These results suggests that pioglitazone might be repurposed as a drug to cure islet amyloidogenesis.

Mammalian aging is reportedly driven by the loss of epigenetic information; however, its impact on skeletal muscle aging remains unclear. This study shows that aging mouse skeletal muscle exhibits increased DNA methylation, and overexpression of DNA methyltransferase 3a (Dnmt3a) induces an aging-like phenotype. Muscle-specific Dnmt3a overexpression leads to an increase in central nucleus-positive myofibers, predominantly in fast-twitch fibers, a shift toward slow-twitch fibers, elevated inflammatory and senescence markers, mitochondrial OXPHOS complex I reduction, and decreased basal autophagy. Dnmt3a overexpression resulted in reduced muscle mass and strength and impaired endurance exercise capacity with age, accompanied by an enhanced inflammatory signature. In addition, Dnmt3a overexpression reduced not only sensitivity to starvation-induced muscle atrophy but also the restorability from muscle atrophy. These findings suggest that increased DNA methylation disrupts skeletal muscle homeostasis, promotes an aging-like phenotype, and reduces muscle metabolic elasticity.

Loneliness and social isolation are serious yet underappreciated public health problems, with their genetic underpinnings remaining largely unknown. We aimed to explore the role of protein-coding variants in the manifestation of loneliness and social isolation.

We conducted the first exome-wide association analysis on loneliness and social isolation, utilizing 336,115 participants of white-British ancestry for loneliness and 346,115 for social isolation. Sensitivity analyses were performed to validate the genetic findings. We estimated the genetic burden heritability of loneliness and social isolation and provided biological insights into them.

We identified six novel risk genes (ANKRD12, RIPOR2, PTEN, ARL8B, NF1, and PIMREG) associated with loneliness and two (EDARADD and GIGYF1) with social isolation through analysis of rare coding variants. Brain-wide association analysis uncovered 47 associations between identified genes and brain structure phenotypes, many of which are critical for social processing and interaction. Phenome-wide association analysis established significant links between these genes and phenotypes across five categories, mostly blood biomarkers and cognitive measures.

The measurements of loneliness and social isolation in UK Biobank are brief for these multi-layer social factors, some relevant aspects may be missed.

Our study revealed 13 risk genes associated with loneliness and 6 with social isolation, with the majority being novel discoveries. These findings advance our understanding of the genetic basis of these two traits. The study provides a foundation for future studies aimed at exploring the functional mechanisms of these genes and their potential implications for public health interventions targeting loneliness and social isolation.

Tetralogy of Fallot (TOF) is the most common cyanotic heart defect in neonates. While there is compelling evidence of genetic contribution to the etiology of TOF, the contribution of noncoding variants to the development of the defect remains unexplored. Potentially damaging noncoding de novo variants (NC DNVs) were detected from 141 Chinese nonsyndromic TOF trios (CHN-TOF) and compared with those detected in the Pediatric Cardiac Genomics Consortium (PCGC). Bioinformatic analyses on noncoding and previously detected coding DNVs were performed to identify developmental pathways affected in TOF. Chinese but not PCGC-TOF patients showed a notably increased burden of putative damaging NC DNVs (n = 249). In Chinese, NC and coding DNVs were predominantly associated with cardiomyocyte differentiation and with chamber/valve/aorta development, respectively, producing a combined enrichment in NOTCH signaling (p = 1.1 × 10-6) and outflow tract morphogenesis (p = 2.2 × 10-5). Genes with NC DNVs (e.g., EFNB2, HEY2, and PITX2) interacted with NOTCH1 and FLT4 in a tight STRING protein-protein interaction (PPI) network. During the in vitro cardiac differentiation process, these noncoding candidate genes, which harbored potentially damaging regulatory NC DNVs, exhibited co-expression with NOTCH signaling genes and demonstrated dysregulated gene expression at various differentiation stages following NOTCH1 downregulation. In summary, our findings highlight a significant contribution of NC DNVs to TOF and suggest the presence of population genetic heterogeneity. Integrative analyses implicate dysregulation of NOTCH signaling, with converging influences from both coding and noncoding variants, in TOF within the Chinese population.

Human cells consist of a complex hierarchy of components, many of which remain unexplored1,2. Here we construct a global map of human subcellular architecture through joint measurement of biophysical interactions and immunofluorescence images for over 5,100 proteins in U2OS osteosarcoma cells. Self-supervised multimodal data integration resolves 275 molecular assemblies spanning the range of 10-8 to 10-5 m, which we validate systematically using whole-cell size-exclusion chromatography and annotate using large language models3. We explore key applications in structural biology, yielding structures for 111 heterodimeric complexes and an expanded Rag-Ragulator assembly. The map assigns unexpected functions to 975 proteins, including roles for C18orf21 in RNA processing and DPP9 in interferon signalling, and identifies assemblies with multiple localizations or cell type specificity. It decodes paediatric cancer genomes4, identifying 21 recurrently mutated assemblies and implicating 102 validated new cancer proteins. The associated Cell Visualization Portal and Mapping Toolkit provide a reference platform for structural and functional cell biology.

Emerging evidence suggests that the function and position of organelles are pivotal for tumor cell dissemination. Among them, lysosomes stand out as they integrate metabolic sensing with gene regulation and secretion of proteases. Yet, how their function is linked to their position and how this controls metastasis remains elusive. Here, we analyze lysosome subcellular distribution in patient-derived melanoma cells and patient biopsies and show that lysosome spreading scales with melanoma aggressiveness. Peripheral lysosomes promote matrix degradation and cell invasion which is directly linked to the lysosomal and cell transcriptional programs. Using chemo-genetical control of lysosome positioning, we demonstrate that perinuclear clustering impairs lysosome secretion, matrix degradation and invasion. Impairing lysosome spreading significantly reduces invasive outgrowth in two in vivo models, mouse and zebrafish. Our study provides a direct demonstration that lysosome positioning controls cell invasion, illustrating the importance of organelle adaptation in carcinogenesis and suggesting its potential utility for diagnosis of metastatic melanoma.

Wenweishu (WWS) is a traditional Chinese medicine compound formulated for chronic atrophic gastritis (CAG) treatment by warming the stomach and alleviating pain. However, its pharmacological mechanisms remain underexplored.

This study investigated the therapeutic effects and potential mechanisms of WWS on CAG with spleen-stomach cold deficiency syndrome (SSCDS).

To achieve this, an SSCDS-CAG rat model and a human gastric mucosal epithelial cells (GES-1) cell model were established using multi-factor modeling and N-Methyl-N'-nitro-N-nitrosoguanidine (MNNG) induction, respectively. WWS's effects on gastric injury were evaluated through pathology, inflammation, serum biomarkers, and apoptosis. Additionally, MNNG's effects on GES-1 cells were analyzed. Network pharmacology, involving protein-protein interaction networks, GO/KEGG enrichment, and molecular docking, was employed to predict WWS's potential targets and mechanisms in SSCDS-CAG. Mechanistic insights were further validated using immunohistochemistry, quantitative reverse transcription polymerase chain reaction, and western blotting.

In vivo results showed that WWS alleviated symptoms in SSCDS-CAG rats, lowering symptom scores and improving gastric histopathology. It modulated serum biomarkers and reduced inflammation and apoptosis in both in vivo and in vitro studies. Network pharmacology results revealed 263 overlapping targets between WWS and SSCDS-CAG, associated with apoptosis, inflammation, and the PI3K/AKT pathway. Molecular docking revealed strong binding affinity between the core target and active WWS components. In SSCDS-CAG rats and GES-1 cells, WWS inhibited PI3K/AKT phosphorylation, increased PTEN expression, and regulated Bcl-2, Bax, and cleaved caspase-3 levels.

WWS reduces inflammation and apoptosis in multi-factor CAG rats and MNNG-induced GES-1 cells by modulating the PTEN/PI3K/AKT signaling pathway and apoptosis-related proteins.

Rhizome of Gastrodia elata Blume (RGE) is a valuable traditional Chinese Medicine (TCM) in the clinical practice. The Compendium of Materia Medica records that RGE has the effect of flatting liver wind out. It has sedative, analgesic, hypnotic, anticonvulsant, anti-hypertensive, anti-myocardial ischemia, anti-arrhythmic and anti-platelet aggregation effects. RGE is often used to relieve and treat vertigo, headache, hypertension, convulsions, and epilepsy in TCM clinic for thousands of years. Accumulated evidences have suggested that hypertension disease is related to the renin-angiotensin-aldosterone system (RAAS) disturbance. However, the potential pharmacodynamic components and anti-hypertensive mechanisms of RGE are unclear now.

The active component and mechanism of RGE in treating hypertension were elucidated to strengthen the quality control and development of anti-hypertensive drugs.

The anti-hypertensive active components of RGE were analyzed by multi-dimensional qualitative analysis method including ethanol extract, in-vitro intestinal absorption, in-vivo plasma. The ultra high performance liquid chromatography-mass spectrometry (UPLC-Q-Exactive MS/MS) analysis technology was adopted to identify these components. Network pharmacology was applied to predicted anti-hypertensive active components, target proteins and pathways. Molecular docking was used to evaluate the potential molecular binding modes between 68 components and nine proteins. Spontaneously hypertensive rats (SHR) model was adopted to evaluate the activity of reducing systolic and diastolic blood pressure (SBP and DBP). Levels of renin, angiotcnsin II (Ang II) and aldosterone (ALD) in serum were determined by Elisa kit. Immunohistochemical were adopted to compare the changes of Ang II receptor 1 (AT1R) protein levels in SHR model and RGE groups.

The multi-dimensional components qualitative analysis method of RGE was established. The results showed that 79, 70 and 30 components were identified in RGE ethanol extract, in-vitro intestinal absorption and in-vivo plasma, respectively. These components were mainly parishins, nucleosides, amino acids, phenolic acids, flavonoids, organic acids et al. Network pharmacology results showed that anti-hypertensive active components were nucleosides and organic acids. It was speculated that RGE could exert its anti-hypertensive effect by regulating aldosterone-regulated sodium reabsorption, renin-angiotensin system pathways and related target proteins. Molecular docking results showed that 21 components including parishins, nucleosides and phenolic acids were potential active components of anti-hypertensive. Taking together, parishin A, B, E, C, D, adenosine, N6-(4-hydroxybenzyl) adenosine, guanosine, ferulic acid were the main anti-hypertensive active components of RGE. Pharmacodynamic results showed that RGE (0.7 g·kg-1) at low dosage could reduce SBP and DBP of SHR in vivo. Meanwhile, RGE (1.4 g·kg-1) markedly reduced the contents of renin, angiotcnsin II and ALD (p < 0.05) of SHR. Immunohistochemical data demonstrated that RGE (0.7 g·kg-1) could downregulate the protein expression of AT1R. In general, RGE can significantly reduce blood pressure of SHR by regulating RAAS.

The multi-dimensional components qualitative analysis combining network pharmacology and molecular docking technology provide a new perspective for discovering potential anti-hypertensive components of RGE. RGE possess anti-hypertensive activity by regulating multiple targets of RAAS. Thus, it has the potential to develop into the novel raw material of anti-hypertensive drugs.

Acute respiratory distress syndrome (ARDS) is characterized by severe respiratory failure and significant inflammation, leading to vascular and epithelial cell damage. The absence of effective pharmacologic treatments underscores the need for novel therapeutic approaches. Telocytes (TCs), a newly identified type of interstitial cells, have shown potential in tissue repair and angiogenesis, particularly through the release of exosomal microRNAs (miRNAs). Exosomes were isolated from LPS (lipopolysaccharide)-stimulated TCs and characterized using western blotting and nanoparticle tracking analysis. The role of exosomal miR-221 in angiogenesis was assessed through tube formation, migration, and proliferation assays in mouse vascular endothelial cells (MVECs). The JAK/STAT pathway's involvement in miR-221 regulation was determined using western blotting and qRT-PCR. A dual-luciferase assay confirmed E2F2 as a direct target of miR-221. ARDS mouse model was established via LPS instillation, and the therapeutic effects of TCs-derived exosomes were evaluated by histopathological scoring, cytokine analysis, and endothelial barrier integrity assays. Our findings demonstrated that exosomes from LPS-stimulated TCs significantly promoted angiogenesis, proliferation, and migration in MVECs. These effects were mediated by miR-221, which downregulated E2F2 expression, an important regulator of endothelial cell functions. The JAK/STAT pathway played a crucial role in miR-221 production, with pathway inhibition reducing miR-221 levels and attenuating its pro-angiogenic effects. In vivo, TCs-derived exosomes reduced lung inflammation and tissue damage in ARDS mice, effects that were reversed by miR-221 inhibition. These results suggested that TCs-derived exosomes promoted angiogenesis and alleviated ARDS through the JAK/STAT-miR-221-E2F2 axis.

Rhizomes of Drynaria quercifolia have long been traditionally used to manage rheumatic pain. However, there is limited research supporting this traditional practice and insufficient evidence demonstrating the molecular mechanisms of action of plant-derived bioactives in rheumatoid arthritis (RA). The current study aims to identify the effective components in Drynaria quercifolia methanol rhizome extract (DME) and their probable pharmacological mechanisms in alleviating Rheumatoid Arthritis (RA) using network-pharmacology, molecular docking, molecular-dynamics simulations, and gene expression-based validation. Gas chromatography-mass spectrometry (GC-MS) based screening identified 41 volatile phytocomponents from DME having drug-like potentiality. Network pharmacology-based screening revealed 117 therapeutic targets for RA of which 11 have been identified as core targets. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that key target genes were mostly enriched in the inflammatory response associated with multiple signalling pathways. Molecular docking and molecular dynamics studies revealed that key target proteins like serine/threonine-protein kinase (AKT1), peroxisome proliferator-activated receptor alpha (PPARA), and peroxisome proliferator-activated receptor gamma (PPARG), exhibited strong binding affinity and stable interactions with multiple phytocomponents present in DME. For experimental verification FCA (Freund's complete adjuvant)-induced chronic arthritis model employed for further molecular investigation. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) results validated that DME significantly (p ≤ 0.05) regulate the expression of key identified target genes AKT and PPARG in experimental RA model. Moreover, this study further confirmed that DME significantly (p ≤ 0.05) downregulated pro-inflammatory mediators like COX-2, IL-6 and TNF-α at gene and protein levels and also normalized (p ≤ 0.05) different oxidative stress parameters in both the low and high dose groups of DME-treated arthritic animals. In conclusion, the network-based in silico approach indicated that the phytocomponents present in DME probably act in a synergistic way to modulate key identified targets associated with RA, which was further validated by experimental studies. Therefore, DME could be a potential alternative in immunomodulatory therapies to combat RA and related chronic inflammatory conditions.