Identification and cross-validation of autophagy-related genes in cardioembolic stroke

Exploration of the shared gene signatures and molecular mechanisms between cardioembolic stroke and ischemic stroke

Introduction

This study aimed to investigate the shared molecular mechanisms underlying cardioembolic stroke (CS) and ischemic stroke (IS) using integrated bioinformatics analysis.

Methods

Microarray datasets for the CS (GSE58294, blood samples from CS and controls) and IS (GSE16561, blood from IS and controls; GSE22255, peripheral blood mononuclear cells from IS and matched controls) were acquired from the Gene Expression Omnibus database. Differential expression analysis and weighted gene co-expression network analysis were utilized to identify shared genes between the two diseases. Protein-protein interaction (PPI) network and topology analyses were conducted to identify the core shared genes. Three machine learning algorithms were employed to detect biomarkers from the core shared genes, and the diagnostic value of the hub genes was evaluated by establishing a predictive nomogram. Immune infiltration was evaluated using single-sample gene set enrichment analysis (ssGSEA), and pathways were analyzed with gene set enrichment analysis.

Results

There were 125 shared up-regulated genes and 2 shared down-regulated between CS and IS, which were mainly involved in immune inflammatory response-related biological functions. The Maximum Clique Centrality algorithm identified 25 core shared genes in the PPI network constructed using the shared genes. ABCA1, CLEC4E, and IRS2 were identified as biomarkers for both CS and IS and performed well in predicting the onset risk of CS and IS. All three biomarkers were highly expressed in both CS and IS compared to their corresponding controls. These biomarkers significantly correlated with neutrophil infiltration and autophagy activation in both CS and IS. Particularly, all three biomarkers were associated with the activation of neutrophil extracellular trap formation, but only in the IS.

Conclusion

ABCA1, CLEC4E, and IRS2 were identified as potential key biomarkers and therapeutic targets for CS and IS. Autophagy and neutrophil infiltration may represent the common mechanisms linking these two diseases.

Macrophage Membrane Coated Manganese Dioxide Nanoparticles Loaded with Rapamycin Alleviate Intestinal Ischemia-Reperfusion Injury by Reducing Oxidative Stress and Enhancing Autophagy

Background

Intestinal ischemia-reperfusion (I/R) injury is a common and severe clinical issue. With high morbidity and mortality, it burdens patients and the healthcare system. Despite the efforts in medical research, current treatment options are unsatisfactory, urging novel therapeutic strategies. Oxidative stress and dysregulated autophagy play pivotal roles in the pathogenesis of I/R injury, damaging intestinal tissues and disrupting normal functions. The aim of this study is to fabricate macrophage membrane-coated manganese dioxide nanospheres loaded with rapamycin [Ma@(MnO₂+RAPA)] for alleviating intestinal I/R injury.

Methods

We engineered honeycomb MnO2 nanospheres coated with a macrophage membrane to act as a drug delivery system, encapsulating RAPA. In vitro OGD/R model in IEC-6 cells and in vivo mouse I/R injury models were used. Targeting ability was evaluated through in-vivo imaging system. Effects on cell viability, reactive oxygen species (ROS) levels, oxygen generation, inflammatory factors, apoptosis, autophagy, and biocompatibility were detected by methods such as MTT assay, fluorescence microscopy, ELISA kit, TUNEL assay, Western blotting and histological analysis.

Results

In this study, Ma@(MnO₂+RAPA) efficiently deliver RAPA to damaged tissues and exhibited good ROS-responsive release. Our data showed that Ma@(MnO₂+RAPA) reduced ROS, increased O₂, inhibited inflammation, and promoted autophagy while reducing apoptosis in IEC-6 cells. In a mouse I/R model, Ma@(MnO₂+RAPA) significantly reduced Chiu's score, improved tight conjunction proteins, decreased apoptosis, reduced levels of inflammatory cytokines and oxidative stress. RAPA released from the Ma@(MnO₂+RAPA), enhanced the expression of autophagy-regulated proteins p62, Beclin-1, and LC3II. The biocompatibility and safety of Ma@(MnO₂+RAPA) were confirmed through histological analysis and biochemical detection in mice.

Conclusion

Our results demonstrated that Ma@(MnO₂+RAPA) alleviated intestinal I/R injury by reducing oxidative stress, promoting autophagy, and inhibiting inflammation. This study offers a potential therapeutic strategy for the treatment of intestinal ischemia-reperfusion injury.

Ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry-characterized extract of Aerides odorata Lour alleviates paracetamol-induced hepatotoxicity in animal model evidenced by biochemical, molecular, and computational studies

BACKGROUND

Many kinds of orchids have significant health benefits although adequate research on their biological functions is yet to be carried out. This study investigated the paracetamol-induced liver damage-protecting effect of epiphytic Aerides odorata methanol extract (AODE).

METHODS

The protective effects of AODE were studied by analyzing its effect on liver function parameters, messenger RNA (mRNA) expression, and tissue histopathological architecture. The results were confirmed by ligand-receptor interaction of molecular docking and multitarget interaction of network pharmacological analyses.

RESULTS

AODE significantly (p < 0.05) minimized the dose-dependent increase in acid phosphatase, aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, γ-glutamyl transferase, lactate dehydrogenase, and total bilirubin compared to the reference drug silymarin. Malondialdehyde level decreased, and the antioxidant genes catalase (CAT), superoxide dismutase (SOD), β-actin, paraoxonase-1 (PON1), and phosphofructokinase-1 (PFK-1) were upregulated in AODE-treated paracetamol-intoxicated rats. A total of 376 compounds comprising phenols and flavonoids were identified using ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (UPLC-qTOF-MS). The online toxicity assessment using SwissADME and admetSAR exhibited drug-like, nontoxic, and potential pharmacological properties. Additionally, in silico analysis showed that isoacteoside, one of the identified compounds, exhibited the best docking score (-11.42) with the liver protein human pituitary adenylate cyclase-1 (Protein Data Bank ID: 3N94). Furthermore, network pharmacology analysis identified the top 10 hub genes, namely AKT1 (protein kinase B), CTNNB1 (catenin beta-1), SRC (proto-oncogene c-Src), TNF (tumor necrosis factor), EGFR (epidermal growth factor receptor), HSP90AA1 (heat shock protein 90α), MAPK3 (mitogen-activated protein kinase 3), STAT3 (signal transducer and activator of transcription 3), CASP3 (caspase protein), and ESR1 (estrogen receptor 1), which are responsible for hepatoprotective activity.

CONCLUSION

The findings demonstrate that AODE could be a novel hepatoprotective target in drug-induced liver damage with a further single compound-based animal study.

CDK5R1, GSE1, HSPG2 and WDFY3 as indirect epigenetic-sensitive genes in atrial fibrillation

BACKGROUND

Although mounting evidence supports that aberrant DNA methylation occurs in the hearts of patients with atrial fibrillation (AF), noninvasive epigenetic characterization of AF has not yet been defined.

METHODS

We investigated DNA methylome changes in peripheral blood CD4+ T cells isolated from 10 patients with AF relative to 11 healthy subjects (HS) who were enrolled in the DIANA clinical trial (NCT04371809) via reduced-representation bisulfite sequencing (RRBS).

RESULTS

An atrial-specific PPI network revealed 18 hub differentially methylated genes (DMGs), wherein ROC curve analysis revealed reasonable diagnostic performance of DNA methylation levels found within CDK5R1 (AUC = 0.76; p = 0.049), HSPG2 (AUC = 0.77; p = 0.038), WDFY3 (AUC = 0.78; p = 0.029), USP49 (AUC = 0.76; p = 0.049), GSE1 (AUC = 0.76; p = 0.049), AIFM1 (AUC = 0.76; p = 0.041), CDK5RAP2 (AUC = 0.81; p = 0.017), COL4A1 (AUC = 0.86; p < 0.001), SEPT8 (AUC = 0.90; p < 0.001), PFDN1 (AUC = 0.90; p < 0.01) and ACOT7 (AUC = 0.78; p = 0.032). Transcriptional profiling of the hub DMGs provided a significant overexpression of PSDM6 (p = 0.004), TFRC (p = 0.01), CDK5R1 (p < 0.001), HSPG2 (p = 0.01), WDFY3 (p < 0.001), USP49 (p = 0.004) and GSE1 (p = 0.021) in AF patients vs HS.

CONCLUSIONS

CDK5R1, GSE1, HSPG2 and WDFY3 resulted the best discriminatory genes both at methylation and gene expression level. Our results provide several candidate diagnostic biomarkers with the potential to advance precision medicine in AF.