Bioinformatics analysis to obtain critical genes regulated in subcutaneous adipose tissue after bariatric surgery

Chen, Shuai; Jiang, Yicheng; Qi, Xiaoyang; Song, Peng; Tang, Liming; Liu, Hanyang

doi:10.1080/21623945.2022.2115212

Cited by 9 publications

(9 citation statements)

References 56 publications

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“…The gene MXRA5 encodes the matrix remodeling-associated protein 5, which has been linked to several biological processes, including extracellular matrix remodeling, cell adhesion, and immune responses. MXRA5 has been found to be upregulated in the adipose tissue of obese individuals and to be associated with in ammation and insulin resistance [41]. For CFH and FCGR3B, the exact roles in adipose tissue biology or TED are not well understood.…”

Section: Discussionmentioning

confidence: 99%

Interaction between N6-methyladenosine and autophagy in the immune infiltration and subtype classification of thyroid eye disease

Zhao

Gong

Chen

2023

Preprint

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Background:Thyroid eye disease (TED) is a chronic inflammatory autoimmune disease with a complex etiology. N6-methyladenosine (m6A) modification and autophagy were confirmed separately to be involved in the TED process. Increased evidence has shown that m6A is critical in regulating autophagy in various diseases. However, there is limited knowledge about the interactive effects of m6A modification and autophagy in TED. Our research aimed to investigate the effects of m6A modification and autophagy interactivity in TED. Results: We first identified dysregulation of five m6A regulators and 44 ARGs in TED patients compared to healthy controls. After correlation analysis, overlapping with the validated target genes from the RM2target database, and verification in our samples, FTO and BNIP3 were considered biomarkers for TED. Subsequently, based on dysregulated m6A regulators and ARGs separately, we classified 27 TED patients into two clusters, and the immune infiltration characteristics of clusters were further evaluated. Cluster-related differentially expressed genes were identified, and the enriched biological functions and pathways were elucidated. In addition, using two machine learning algorithms, we created a prediction model for TED patients with different molecular clusters. The nomogram, calibration curve, and decision curve analysis were performed to assess the performance of the predictive model. Conclusions: This study revealed that an interactive effect between FTO and BNIP3, suppressed FTO might downregulate the expression of BNIP3 in an m6A-dependent manner, inhibiting the autophagy and subsequently promoting the TED process. In addition, we constructed a nomogram model in predicting the TED. These results provide new insights into understanding the mechanism of TED.

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Section: Discussionmentioning

confidence: 99%

Interaction between N6-methyladenosine and autophagy in the immune infiltration and subtype classification of thyroid eye disease

Zhao

Gong

Chen

2023

Preprint

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“…Two microarray datasets regarding liver tissues after BS were retrieved in the GEO database ( Table 1 ). GSE83452 and GSE106737 were merged via the R packets in SilicoMerging [ 26 ], and then, the empirical Bayesian methods were used to adjust the batch effects. By using the limma V3.42.0 packets with a standard of |log(fold change, FC)| > 1.5, DEGs in postoperative liver tissue samples were figured out.…”

Section: Methodsmentioning

confidence: 99%

“…Then, we fix the cells with 4% polymethanol for 30 min. A microscope was used to observe and photograph the stained cells after washing them three times with PBS and staining them with Oil Red O for 30 min [ 26 ].…”

Section: Methodsmentioning

confidence: 99%

“…Zhang et al acquired the differential genes in liver tissue after BS from the GEO database and obtained LCP1, a key gene that regulates liver inflammation through WGCNA and PPI networks [ 21 ]. Chen et al analyzed the data on BS influencing the subcutaneous adipose tissue transcriptome expression in GEO databases and obtained key genes that regulate fat differentiation through WGCNA, SVM-RFE algorithms, and LASSO logistic regression and verified them [ 26 ].…”

Section: Introductionmentioning

confidence: 99%

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Screening of Biomarkers in Liver Tissue after Bariatric Surgery Based on WGCNA and SVM-RFE Algorithms

et al. 2023

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As the most common chronic liver disease around the world, nonalcoholic fatty liver disease (NAFLD) has a close connection with obesity, diabetes, and metabolic syndrome. Bariatric surgery (BS) is considered to be the most effective treatment for NAFLD. However, the regulatory mechanism of hepatic lipid metabolism after BS remains poorly elucidated. By analyzing two transcriptome datasets regarding liver tissues after BS, namely, GSE83452 and GSE106737, we acquired 110 differentially expressed genes (DEGs). By further analysis of DEGs in terms of the weighted gene coexpression network analysis (WGCNA) and support vector machine-recursive feature elimination (SVM-RFE) algorithms, we identified four crucial genes participating in the regulation of hepatic lipid metabolism: SRGN, THEMIS2, SGK1, and FPR3. In addition, the results of gene set enrichment analysis (GSEA) showed that BS can activate immune-related regulatory pathways and change immune cell infiltration levels. Finally, through cellular level studies, we found that the silencing of SRGN affects the expression of SREBP-1, SIRT1, and FAS during adipogenesis in the liver and the formation of lipid droplets in the liver. In summary, the immune system in the liver is activated after BS, and SRGN participates in the regulation of hepatic lipid metabolism.

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“…The least absolute shrinkage and selection operation and SVM-RFE algorithms were used to obtain key DEFRGs to diagnose PCOS based on the "glmnet" and "e1071" R packages (21). The LASSO algorithm was used to adjust the optimal value of the penalty parameter (λ) using a 10-fold cross-validation.…”

Section: Construction and Evaluation Of Lasso And Svm-rfe Modelsmentioning

confidence: 99%

Relationships of ferroptosis-related genes with the pathogenesis in polycystic ovary syndrome

Lin

Jin²,

He³

et al. 2023

Front. Med.

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BackgroundNumerous studies have suggested that ferroptosis plays a significant role in the development of polycystic ovary syndrome (PCOS), but the mechanism remains unclear.MethodsIn this study, we explored the role of ferroptosis-related genes in the pathogenesis of PCOS using a comprehensive bioinformatics method. First, we downloaded several Gene Expression Omnibus (GEO) datasets and combined them into a meta-GEO dataset. Differential expression analysis was performed to screen for significant ferroptosis-related genes between the normal and PCOS samples. The least absolute shrinkage selection operator regression and support vector machine–recursive feature elimination were used to select the best signs to construct a PCOS diagnostic model. Receiver operating characteristic curve analysis and decision curve analysis were applied to test the performance of the model. Finally, a ceRNA network-related ferroptosis gene was constructed.ResultsFive genes, namely, NOX1, ACVR1B, PHF21A, FTL, and GALNT14, were identified from 10 differentially expressed ferroptosis-related genes to construct a PCOS diagnostic model. Finally, a ceRNA network including 117 lncRNAs, 67 miRNAs, and five ferroptosis-related genes was constructed.ConclusionOur study identified five ferroptosis-related genes that may be involved in the pathogenesis of PCOS, which may provide a novel perspective for the clinical diagnosis and treatment of PCOS.

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Bioinformatics analysis to obtain critical genes regulated in subcutaneous adipose tissue after bariatric surgery

Cited by 9 publications

References 56 publications

Interaction between N6-methyladenosine and autophagy in the immune infiltration and subtype classification of thyroid eye disease

Interaction between N6-methyladenosine and autophagy in the immune infiltration and subtype classification of thyroid eye disease

Screening of Biomarkers in Liver Tissue after Bariatric Surgery Based on WGCNA and SVM-RFE Algorithms

Relationships of ferroptosis-related genes with the pathogenesis in polycystic ovary syndrome

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