TLR2 and CASP7 as the biomarkers associated with non-alcoholic fatty liver disease and chronic kidney disease

Multiomics Analysis and Machine Learning-based Identification of Molecular Signatures for Diagnostic Classification in Liver Disease Types Along the Microbiota-gut-liver Axis

Background

Liver disease, responsible for around two million deaths annually, remains a pressing global health challenge. Microbial interactions within the microbiota-gut-liver axis play a substantial role in the pathogenesis of various liver conditions, including early chronic liver disease (eCLD), chronic liver disease (CLD), acute liver failure (ALF), acute-on-chronic liver failure (ACLF), non-alcoholic fatty liver disease (NAFLD), steatohepatitis, and cirrhosis. This study aimed to identify key molecular signatures involved in liver disease progression by analyzing transcriptomic and gut microbiome data, and to evaluate their diagnostic utility using machine learning models.

Methods

Transcriptomic analysis identified differentially expressed genes (DEGs) that, when integrated with regulatory elements microRNAs, transcription factors, receptors, and the gut microbiome highlight disease-specific molecular interactions. To assess the diagnostic potential of these molecular signatures, a two-step analysis involving principal component analysis (PCA) and Random Forest classification was conducted, achieving accuracies of 75% for ALF and 89% for NAFLD. Additionally, machine learning algorithms, including K-neighbors, multi-layer perceptron (MLP), decision tree, Random Forest, logistic regression, gradient boosting, CatBoost, Extreme Gradient Boosting (XGB), and Light Gradient Boosting Machine (LGBM), were applied to gene expression data for ALF and NAFLD.

Results

Key genes including CLDN14, EGFR, GSK3B, MYC, and TJP2, alongside regulatory miRNAs let-7a-5p, miR-124-3p, and miR-195-5p and transcription factors NFKB1 and SP1 may be suggested as critical to liver disease progression. Additionally, gut microbiota members, Dictyostelium discoideum and Eikenella might be novel candidates associated with liver disease, highlighting the importance of the gut-liver axis. The Random Forest model reached 75% accuracy and 83% area under the curve for ALF, while NAFLD classification achieved 100% accuracy, precision, recall, and area under the curve underscoring robust diagnostic potential.

Conclusion

This study establishes a solid foundation for further research and therapeutic advancement by identifying key biomolecules and pathways critical to liver disease. Additional experimental validation is needed to confirm clinical applicability.

Macrophage inhibition in the alleviation of nonalcoholic steatohepatitis caused by bariatric surgery

The incidence of nonalcoholic steatohepatitis (NASH) is increasing worldwide, and effective treatment is urgently needed. To understand the molecular mechanisms behind the effectiveness of bariatric surgery in treating NASH, we integrated single-cell and bulk RNA sequencing data to identify the role of liver macrophage polarization in alleviating NASH and screen possible drugs for treatment. Analysis revealed that bariatric surgery alleviates NASH by inhibiting liver M1 macrophage polarization with 12 differentially expressed M1 macrophage-related genes. Additionally, 56 potentially effective drugs were predicted for NASH treatment. These findings shed light on the effectiveness of bariatric surgery in treating NASH and offer potential drug candidates for further exploration.

LC-HRMS profiling of Dendrobium huoshanense aqueous extract and its therapeutic effects on nonalcoholic fatty liver disease in mice through the TLR2-NF-κB and AMPK-SREBP1-SIRT1 signaling pathways

Dendrobium huoshanense (DH) belongs to the Dendrobium genus of the Orchidaceae family and is a herbaceous plant that protects the liver and nourishes the Yin according to traditional Chinese Medicine (TCM) theory. This research aimed to determine the therapeutic effect and mechanisms of DH on a nonalcoholic fatty liver disease (NAFLD) mouse model and its chemical composition. For pharmacological research, the pathological damage and lipid accumulation in liver tissues were evaluated using HE and oil red staining, respectively. The differential proteins between the model and DHH groups were screened using 4D label-free quantitative proteomics, and the proteomic results were verified using Western blot. The potential mechanism was validated by metabolomic analysis. The main active ingredients in a DH aqueous extract were identified using UHPLC-Q Exactive HF HRMS. Pathological staining results showed that DH can reverse liver pathological damage and lipid accumulation in the NAFLD model. Quantitative proteomics revealed that the differential proteins were mainly associated with liver lipid deposition (LAL, AMPK, TM7SF2, SBCAD, and SIRT1), insulin resistance (GYS1, GYS2, PYGL, FoxO1, and PPAR-γ), and inflammation (TLR2 and MAPKAPK). Western blot verified the above-mentioned results. Metabolomic analysis also indicated that the DH aqueous extract ameliorated NAFLD in mice by affecting cholesterol metabolism and AMPK signaling pathway, proving its significant therapeutic effects on the NAFLD model. Sixty-five compounds were identified from DH aqueous extract by analyzing the precise molecular weight and MS/MS fragmentation pathway. The pharmacological mechanism of DH in treating NAFLD mainly involved the TLR2-NF-κB and AMPK-SREBP1-SIRT1 signaling pathways.

Bacteroides fragilis aggravates high-fat diet-induced non-alcoholic fatty liver disease by regulating lipid metabolism and remodeling gut microbiota

Gut microbiota dysbiosis is a prominent determinant that significantly contributes to the disruption of lipid metabolism. Consequently, it is essential to the occurrence and development of non-alcoholic fatty liver disease (NAFLD). Nevertheless, the connection between diet and symbiotic gut microbiota in the progression of NAFLD remains uncertain. The purpose of this study was to explore the role of supplementing commensal Bacteroides fragilis (B. fragilis) on lipid metabolism, gut microbiota, and metabolites in high-fat diet (HFD)-fed mice, elucidating the impact of gut microbiota and metabolites on the development of NAFLD. Our study revealed that supplementation with B. fragilis exacerbated both weight gain and obesity in mice. B. fragilis exacerbated blood glucose levels and liver dysfunction in mice. Furthermore, an increase in liver lipid accumulation and the upregulation of genes correlated with lipid metabolism were observed in mice. Under an HFD, supplementation of commensal B. fragilis resulted in alterations in the gut microbiota, notably a significant increase in Desulfovibrionaceae, which led to elevated endotoxin levels and thereby influenced the progression of NAFLD. It was interesting that the simultaneous examination of gut microbiota metabolites revealed a more pronounced impact of diet on short-chain fatty acids. This study represented the pioneering investigation into the impact of B. fragilis on NAFLD. Our findings demonstrated that B. fragilis induced dysregulation in the intestinal microbiota, leading to elevated levels of lipopolysaccharide and dysfunction in glucose and lipid metabolism, thereby exacerbating NAFLD.IMPORTANCESome intestinal symbiotic microbes are involved in the occurrence of the metabolic disorders. Our study investigated the impact of supplementing commensal Bacteroides fragilis on host metabolism in high-fat diet-fed mice. Research results indicated that adding a specific bacterial strain to the complex intestinal microecology can worsen metabolic conditions. This effect mainly affects the structural diversity of intestinal microorganisms, the increase in harmful bacteria in the gut, and the elevation of endotoxin levels, blood glucose, and lipid metabolism, thereby impacting the progression of non-alcoholic fatty liver disease (NAFLD). Understanding the principles that govern the establishment of microbial communities comprising multiple species is crucial for preventing or repairing dysfunctions in these communities, thereby enhancing host health and facilitating disease treatment. This study demonstrated that gut microbiota dysbiosis could contribute to metabolic dysfunction and provides new insights into how to promote gut microbiota in the prevention and therapy of NAFLD.