Identification of Ferroptosis-Related Genes in Heart Failure Induced by Transverse Aortic Constriction.

Gu JJ ，Du TJ ，Zhang LN ，Zhou J ，Gu X ，Zhu Y ... -  《Journal of Inflammation Research》

Expression profiles and functions of ferroptosis-related genes in intimal hyperplasia induced by carotid artery ligation in mice.

Intimal hyperplasia (IH) is a prominent pathological event that occurs during in-stent restenosis and atherosclerosis. Ferroptosis, characterized by iron-dependent and lipid peroxidation, has become the recent focus of studies on the occurrence and progress of cardiovascular diseases. However, there are few studies on ferroptosis and IH. Therefore, we aimed to identify and validate ferroptosis-related markers in IH to explore new possibilities for IH diagnosis and treatment. The IH microarray dataset (GSE182291) was downloaded from the Gene Expression Omnibus (GEO) database and ferroptosis-related genes (FRGs) were obtained from the FerrDb databases. The differentially expressed genes (DEGs) were analyzed using the GEO2R. Overlapping was performed to identify the ferroptosis-related DEGs among the DEGs and FRGs. Then, clustering, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) analyses were performed. Subsequently, the hub genes were identified using Cytoscape and hub gene-transcription factors and hub gene-microRNA networks were constructed. Finally, real-time qPCR (RT-qPCR) and immunohistochemistry (IHC) were used to verify the mRNA and protein levels of the hub FRGs in IH. Thirty-four FRGs showing significantly different expression were identified from a total of 1,197 DEGs 2 days after ligation; 31 FRGs were selected from a total of 1,556 DEGs 14 days after ligation. The GO and KEGG analyses revealed that these 34 ferroptosis-related DEGs identified 2 days after ligation were mainly enriched in the basolateral plasma membrane, ferroptosis, lipid and atherosclerosis, and IL-17 signaling pathways. The 31 ferroptosis-related DEGs in endometrial hyperplasia identified 14 days after ligation were mainly enriched in response to oxidative stress, ferroptosis, tumor necrosis factor signaling pathway, and lipid and atherosclerosis. Five hub FRGs (Il1b, Ptgs2, Cybb, Cd44, and Tfrc) were identified using PPI networks; four hub FRGs (Il1b, Ptgs2, Cybb, and Cd44) were validated to be upregulated 2 and 14 days after ligation using RT-qPCR and show significantly different expression 14 days after ligation via IHC. Our findings verify the expression of hub DEGs related to ferroptosis in IH and elucidate the potential relationship between ferroptosis and IH, providing more evidence about the vital role of ferroptosis in IH.

Zhang L ，Li W ，Shi B ，Zhang X ，Gong K ... -  《Frontiers in Genetics》

Identification and validation of ferroptosis-related gene signature in intervertebral disc degeneration.

Lower back pain (LBP) is a leading cause of disability in the elderly and intervertebral disc degeneration (IDD) is the major contributor to LBP. Ferroptosis is a newly discovered programmed cell death, characterized by iron-dependent lethal lipid peroxidation. Growing evidence has shown that ferroptosis plays important roles in various human diseases. However, the underlying mechanism of ferroptosis in IDD remains elusive. This study is aimed to uncover the key roles of ferroptosis in the pathogenesis and progression of IDD comprehensively. To investigate the ferroptosis related differentially expressed genes (FRDEGs) in IDD, we analyzed the microarray data from the Gene Expression Omnibus (GEO) database. Then we performed functional enrichment analysis and protein-protein interaction (PPI) network analysis, and screened out the hub FRDEGs. To further evaluate the predictive value of these hub FRDEGs, we performed ROC analysis based on the GSE124272 dataset. A total of 80 FRDEGs were identified, including 20 downregulated and 60 upregulated FRDEGs. The FRDEGs were primarily involved in the biological processes of response to chemical, and response to stress. KEGG pathway enrichment analysis showed that the FRDEGs were mainly involved in ferroptosis, TNF signaling pathway, HIF-1 signaling pathway, NOD-like receptor signaling pathway, and IL-17 signaling pathway. Ten hub OSRDEGs were obtained according to the PPI analysis, including HMOX1, KEAP1, MAPK1, HSPA5, TXNRD1, IL6, PPARA, JUN, HIF1A, DUSP1. The ROC analysis and RT-qPCR validation results suggested that most of the hub FRDEGs might be potential signature genes for IDD. This study reveals that ferroptosis might provide promising strategy for the diagnosis and treatment of IDD.

Xiang Q ，Zhao Y ，Li W 《Frontiers in Endocrinology》

Identification of hub genes associated with oxidative stress in heart failure and their correlation with immune infiltration using bioinformatics analysis.

Both oxidative stress and the immune response are associated with heart failure (HF). In this study, our aim was to identify the hub genes associated with oxidative stress andimmune infiltration of HF by bioinformatics analysis and experimental verification. The expression profile of GSE36074 was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were screened by GEO2R. The genes related to oxidative stress were extracted from GeneCards websites. Then, the functional enrichment analysis of oxidative stress-related DEGs (OSRDEGs) was performed using DAVID. In addition, we constructed a protein-protein interaction (PPI) network using the STRING database and screened for hub genes with Cytoscape software. We also used CIBERSORTx to analyze immune infiltration in mice heart tissues between the TAC and Sham groups and explored the correlation between immune cells and hub genes. Finally, the hub genes were carried out using reverse transcription quantitative PCR (RT-qPCR), immunohistochemistry (IHC) and western blot. A total of 136 OSRDEGs were found in GSE36074. Enrichment analysis revealed that these OSRDEGs were enriched in the mitochondrion, HIF-1, FoxO, MAPK and TNF signaling pathway. The five hub genes (Mapk14, Hif1a, Myc, Hsp90ab1, and Hsp90aa1) were screened by the cytoHubba plugin. The correlation analysis between immune cells and hub genes showed that Mapk14 was positively correlated with Th2 Cells, while Hif1a and Hsp90ab1exhibited a negative correlation with Th2 Cells; Myc exhibited a negative correlation with Monocytes; whereas, Hsp90aa1 was negatively correlated with NK Resting. Finally, five hub genes were validated by RT-qPCR, IHC and western blot. Mapk14, Hif1a, Myc, Hsp90ab1, and Hsp90aa1 are hub genes of HF and may play a critical role in the oxidative stress of HF. This study may provide new targets for the treatment of HF, and the potential immunotherapies are worthy of further study.

Gu J ，Zhang LN ，Gu X ，Zhu Y ... -  《PeerJ》

Identification of potential ferroptosis key genes and immune infiltration in rheumatoid arthritis by integrated bioinformatics analysis.

Ferroptosis is of vital importance in the development of Rheumatoid arthritis (RA). The purpose of this project is to clarify the potential ferroptosis-related genes, pathways, and immune infiltration in RA by bioinformatics analysis. We acquired ferroptosis-related genes (FRGs) from Ferroptosis database (FerrDb). We obtained the Gene dataset of RA (GSE55235) from the Gene Expression Omnibus (GEO) Database, screened the differentially expressed genes (DEGs) in RA and control samples, and then took the intersection of it and FRGs. Aiming to construct the protein-protein interaction (PPI) networks of the FRGs-DEGs, STRING database and Cytoscape software 3.7.0 would be used. Furthermore, hub genes were identified by CytoNCA, a Cytoscape plug-in. The gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment of FRGs-DEGs were performed. We identified 34 FRGs-DEGs, including 7 upregulated and 27 downregulated genes by taking the intersection of the FRGs and DEGs. PPI analysis identified a total of 3 hub genes(VEGFA, PTGS2, and JUN). GO enrichment analyses and KEGG Pathway enrichment displayed that the FRGs-DEGs are involved in the response to oxidative stress and corticosteroid, heme binding, FoxO-signal pathway. Results of immune infiltration displayed that increased infiltration of T cells, while Macrophages M2 less may be related to the occurrence of RA. The hub genes involved in ferroptosis in RA may be VEGFA, PTGS2, and JUN, which are mainly involved in FoxO-signal pathway. T cell, Mac, and plasma cells may be involved in the regulation of RA-joints-synovial-inflammation.

Fan Y ，Li Y ，Fu X ，Peng J ，Chen Y ，Chen T ，Zhang D ... -  《Heliyon》