Current Medicinal Chemistry - Online First

The objective of the present study was to explore the bi-directional causal relationship between IPF and diabetes (type 1 diabetes and type 2 diabetes)/diabetic nephropathy/glycemic traits [fasting glucose and glycated hemoglobin (HbA1c)]/fasting blood insulin through MR analysis.

A bi-directional two-sample Mendelian randomization (MR) study design was adopted to evaluate the causal relationship between IPF and diabetes (type 1 diabetes and type 2 diabetes), diabetic complications (diabetic nephropathy) and glycemic traits [fasting blood glucose, glycated hemoglobin (HbA1c), fasting insulin] in a European population. Genome-wide association study summary data was obtained. The inverse variance weighted (IVW) method with a fixed-effects model was used to estimate the primary causal effects. The causal effects are represented by reporting odds ratios (OR) and their corresponding 95% confidence intervals (CI). The robustness of results was assessed using the MR-Egger and Weighted Median methods.

In the forward MR analysis, the IVW method revealed a significant causal effect of IPF on type 2 diabetes (OR=1.031, 95% CI: 1.011-1.052). Similar estimates were obtained through the Weighted Median method. However, no significant causal effects were observed on type 1 diabetes, diabetic nephropathy, fasting blood glucose, HbA1c, and fasting insulin, respectively (p>0.05). We performed the reverse MR analysis using similar methods to the forward MR approach. MR analysis only showed a significant causal association of fasting insulin with IPF risk, with an OR of 3.576 (95% CI: 1.958-6.531).

Genetically determined IPF was linked to an elevated risk of type 2 diabetes. The inverse MR analysis indicated that there was no causal impact of genetically predicted type 2 diabetes on the IPF risk.

Genetically predicted fasting blood insulin was found to be positively associated with IPF risk.

Osteoporosis (OP) and aortic stenosis (AS) are highly prevalent age-related disorders that frequently coexist. Epidemiological studies suggest a pathological link between OP and AS beyond age, yet the molecular mechanisms underlying this bone-vascular axis remain poorly defined. This study aimed to identify shared genes and pathways contributing to the comorbidity of OP and AS.

Publicly available AS and OP transcriptomic datasets were retrieved from the GEO database. Weighted gene co-expression network analysis (WGCNA) and differential gene expression (DEG) analysis were conducted to identify disease-associated genes. Candidate hub genes were screened through protein-protein interaction (PPI) network analysis using twelve network topology algorithms. High-confidence genes were obtained by intersecting candidates with AS-related genes from the Comparative Toxicogenomics Database (CTD). Independent cohorts were used to validate candidate genes, and least absolute shrinkage and selection operator (LASSO) regression was performed to assess their diagnostic potential.

WGCNA revealed 665 shared genes enriched in immune and inflammatory processes, cell adhesion, and glycosaminoglycan biosynthesis. PPI network analysis identified 32 candidate hub genes, and integration with CTD yielded 15 high-confidence genes. Validation across independent datasets confirmed dysregulated expression of CD4, GZMB, and SDC1 in both AS and OP samples. ROC analysis demonstrated high diagnostic accuracy of these genes, with a combined AUC of 0.94.

These findings highlight immune and inflammatory pathways as convergent mechanisms driving both AS and OP. The hub genes CD4, GZMB, and SDC1 participate in immune regulation and extracellular matrix remodeling, suggesting their involvement in the shared pathogenesis of skeletal and cardiovascular degeneration.

Integrative bioinformatics identified CD4, GZMB, and SDC1 as key genes linking OP and AS, providing potential biomarkers and therapeutic targets for managing these age-related comorbidities.

This study aimed to explore potential causal relationships between mitochondria-related genes and irritable bowel syndrome (IBS) using integrative multi-omics analysis.

Genome-wide association study data for IBS (1,480 cases and 454,868 controls) were integrated with mitochondrial gene data from DNA methylation quantitative trait loci, blood expression quantitative trait loci, and protein quantitative trait loci. Molecular trait associations with IBS were assessed through summary-based Mendelian randomization and co-localization analyses. Steiger filtering analysis was applied to identify causal directions, and candidate genes were independently replicated by two-sample MR in the FinnGen R11 cohort.

Three primary genes supported by multi-omics evidence—CASP3, GATM, and PDK1—were identified. Increased CASP3 methylation, expression, and protein were positively associated with IBS risk, indicating pro-apoptotic and pro-inflammatory mechanisms, whereas elevated GATM expression and protein were negatively associated, consistent with a protective role via creatine-mediated energy homeostasis.

Additionally, 19 genes were classified as secondary evidence genes and 5 as tertiary evidence genes. Among these, genes such as ACAD10 and MSRA were validated using FinnGen data.

This study represents the first application of multi-omics techniques to elucidate the relationship between mitochondrial genes and IBS. The findings indicate multiple candidate pathogenic genes and highlight the role of mitochondrial dysfunction in IBS pathogenesis. These findings offer new opportunities for the discovery of IBS biomarkers and the development of therapeutic strategies.

Clostridium difficile infection (CDI) is a serious global health concern characterized by toxin-induced colonic damage, ranging from diarrhea to life-threatening conditions. Despite improved diagnostics and treatments, recurrence rates of up to 30% underscore persistent gaps in effective disease management.

CDI pathogenesis is driven by the disruption of the gut microbiota, often due to broad-spectrum antibiotic use. Risk factors such as advanced age, hospitalization, IBD, and immunosuppression increase the severity and recurrence of the infection. The hypervirulent ribotype 027 strain has been associated with increased mortality and treatment resistance, necessitating targeted therapies.

Emerging treatments such as FMT and monoclonal antibodies show promise for CDI management, with FDA approvals marking progress in microbiome restoration. However, hurdles remain in safety, regulation, and donor screening. Advances in diagnostic and scoring tools have aided in the detection and treatment, but differentiating between colonization and infection remains a challenge. Preventive measures and novel agents such as bacteriocins and bacteriophages offer targeted, microbiome-sparing strategies.

Despite recent advances, CDI management remains challenging because of diagnostic uncertainty and frequent recurrences. Innovative treatments such as FMT and monoclonal antibodies are promising but face limitations in safety, access, and cost. Preventive strategies and decision tools help, yet distinguishing colonization from infection remains difficult, underscoring the need for ongoing and multidisciplinary innovation.

This review highlights current approaches to CDI diagnosis, treatment, and prevention, stressing the urgent need for innovative strategies to reduce recurrence. Targeted research and policy efforts are vital to improving outcomes and quality of life for those affected.

Ischemic Stroke (IS) represents the most prevalent subtype of cerebrovascular disease, characterized by complex pathophysiological mechanisms that remain inadequately characterized, particularly concerning mitochondrial dysfunctions. These mitochondrial impairments are increasingly recognized as contributory factors in IS pathogenesis, emphasizing the need for further investigation into the underlying molecular mechanisms involved.

In this study, we integrated transcriptomic datasets from the Gene Expression Omnibus (GEO) with the comprehensive MitoCarta3.0 mitochondrial proteome inventory to elucidate the role of dysregulated Mitochondrial-Related Genes (MRGs) in IS. We employed an advanced bioinformatics and machine learning pipeline, incorporating differential expression profiling alongside network-based prioritization using CytoHubba. Rigorous feature selection was conducted through LASSO regression, Support Vector Machine (SVM), and Random Forest (RF) algorithms to derive a robust core MRG signature. Our methodology included training and validation cohorts to construct diagnostic models, which were critically evaluated via Receiver Operating Characteristic (ROC) curves, nomograms, and calibration analyses.

Our analysis identified a seven-gene signature comprising DNAJA3, ACSL1, HSDL2, ECHDC2, ECHDC3, ALDH2, and PDK4, which demonstrated significant correlation with activated CD8⁺ T-cell and natural killer cell infiltration. Furthermore, integrative network analyses revealed intricate regulatory interactions among MRGs, microRNAs, and transcription factors. Notably, drug-target predictions indicated Bezafibrate as a promising therapeutic agent for modulating mitochondrial homeostasis in the context of IS.

These findings offer a novel framework for ischemic stroke diagnosis and therapy, yet their computational derivation underscores the need for thorough experimental validation of MRGs and drug candidates, along with the integration of diverse clinical data to confirm their real-world applicability.

Our findings underscore mitochondrial dysfunction not only as a critical factor in IS pathogenesis but also as a viable therapeutic target. The identified MRG signature presents potential for clinical application in diagnostic and pharmacological strategies aimed at ameliorating ischemic injury. This study highlights the translational significance of systems biology approaches within cerebrovascular medicine, warranting further mechanistic exploration of mitochondrial-immune interactions in stroke pathology.

Gliomas are aggressive brain tumors with a poor prognosis and high recurrence. Oridonin, a traditional Chinese medicine, has shown potential in treating various cancers, but its role in glioma treatment, especially in modulating Epithelial-Mesenchymal Transition (EMT), remains underexplored.

We identified 371 potential target genes of Oridonin using various bioinformatics databases. Enrichment analyses, including Differential Expression Analysis, Gene Set Enrichment Analysis (GSEA), and Weighted Gene Co-expression Network Analysis (WGCNA), were performed to link these targets to glioma characteristics. in vitro experiments validated Oridonin's impact on EMT-related gene expression in glioma cells.

Enrichment analyses identified 19 common genes between Oridonin and glioma targets, with 12 EMT-related core genes. KEGG enrichment highlighted PI3K-Akt, MAPK pathways, and glioma pathways, while DO enrichment included high-grade gliomas. CCK8 assay showed Oridonin IC50 values of 6.92 μM for H4 and 10.54 μM for SW1783 glioma cell lines. WB results indicated increased E-Cadherin and decreased Vimentin, N-Cadherin, and Snail expression after Oridonin treatment. PPI network and single-cell transcriptome analyses identified key genes linked to glioma progression and immune cell infiltration.

Oridonin may inhibit glioma progression by targeting EMT-related pathways like PI3K-Akt and MAPK. The upregulation of E-Cadherin and downregulation of Vimentin, N-Cadherin, and Snail suggest a reversal of the EMT process. Future work should validate these effects in vivo and explore Oridonin's ability to cross the blood-brain barrier.

Oridonin may provide a novel therapeutic approach for glioma by targeting EMT-related pathways, offering a foundation for further clinical investigation.

Neuroinflammation, primarily mediated by activated microglia, is a significant contributor to neurodegenerative diseases, such as Alzheimer's and Parkinson's disease. Quercetin (QCT), a dietary flavonoid, has demonstrated anti-inflammatory and neuroprotective properties; however, the detailed molecular mechanisms behind these effects remain unclear. This study aimed to investigate the anti-inflammatory actions of QCT, particularly focusing on its potential to suppress the activation of microglia and subsequent neuroinflammation.

BV2 microglial cells were stimulated with lipopolysaccharide (LPS) to induce an inflammatory response and were subsequently treated with various concentrations of QCT. Cell viability was assessed using the MTT assay. Levels of pro-inflammatory cytokines (IL-6, TNF-α) and nitric oxide (NO) were quantified through ELISA and Griess reaction methods, respectively. Western blot analysis was conducted to examine inducible nitric oxide synthase (iNOS), NF-κB, IκBα, and phosphorylated IκBα protein expressions. In silico approaches, including protein-protein interaction (PPI) network analysis and molecular docking, were employed to explore potential molecular mechanisms involving NF-κB signaling pathways.

Treatment with QCT significantly reduced the secretion of IL-6 (96%) and TNF-α (87%), as well as NO production (42%), in a dose-dependent manner. Western blot results demonstrated a marked reduction in iNOS expression and inhibition of NF-κB activation through reduced phosphorylation of IκBα following QCT treatment. Molecular docking indicated a strong binding affinity between QCT and IKKβ, suggesting inhibition of the NF-κB pathway.

The findings indicated QCT to exert potent anti-inflammatory effects in LPS-stimulated BV2 cells by modulating key proteins involved in the NF-κB signaling pathway. Specifically, the docking results implied QCT’s direct interaction with the catalytic subunit IKKβ, inhibiting IκBα phosphorylation and subsequent NF-κB activation. The results have been found to be consistent with previous literature, reinforcing QCT's role in reducing neuroinflammation through specific molecular targets and pathways. Further in vivo studies are necessary to validate the findings.

Quercetin effectively suppressed neuroinflammation in microglial cells through inhibition of the NF-κB signaling pathway, reducing levels of critical pro-inflammatory mediators. The outcomes have highlighted the potential of quercetin as a preventive nutraceutical for neurodegenerative diseases, necessitating future in vivo investigations to confirm its therapeutic efficacy.

The causality between thyroid disorders and Gastroesophageal Reflux Disease (GERD) remains to be deciphered. This two-sample Mendelian Randomization (MR) study was performed to elucidate the causal association between GERD and thyroid diseases and functions.

Summary statistics for GERD were retrieved from a published GWAS dataset deposited in the Integrative Epidemiology Unit OpenGWAS database. Thyroid hormone level data were obtained from the ThyroidOmics Consortium, and genetic variants associated with thyroid disorders were sourced from the FinnGen Project. MR statistical analyses used the Inverse Variance Weighted (IVW) algorithm, followed by various sensitivity and reliability analyses. Odds Ratio (OR) and beta coefficient (β) with 95% Confidence Interval (CI) were estimated for categorical and continuous outcomes, respectively. The significant causal association was determined based on a Bonferroni-corrected threshold of p-value < 0.0021 (calculated as 0.05/24 trait pairs).

The findings of MR analysis tend to favor the causality of GERD for hyperthyroidism (IVW: OR = 1.517, 95% CI: 1.164 to 1.978, p = 2.04E-03) but not the other thyroid disorders. The reverse MR estimates suggested that thyroid disorders may not affect the susceptibility of GERD. Moreover, genetic proxied GERD was significantly negatively associated with circulating Thyroid Stimulating Hormone (TSH) level (IVW: β = -0.048, 95% CI: -0.078 to -0.019, p = 1.17E-03), whereas the causality of this enteropathy on Free Triiodothyronine (FT3), Free Thyroxine (FT4), Total Triiodothyronine (TT3), FT3/FT4 ratio, and TT3/FT4 ratio (and vice versa) is unfounded.

This MR study indicates that the genetic liability to GERD is significantly detrimental to hyperthyroidism risk and the homeostasis of TSH.

The findings suggest that effective GERD management could mitigate hyperthyroidism risk.