For lncRNA, circRNA and mRNA sequencing of thyroid-associated ophthalmopathy patients and normal people
Ontology highlight
ABSTRACT: We identified the differentially expressed mRNAs and lncRNAs/circRNAs of the case group and the control group through high-throughput sequencing technology, performed a functional enrichment analysis of the differentially expressed genes, and used protein-protein interaction (PPI) analysis to identify the hub genes. A novel ceRNA network was successfully established, and the network components may serve as promising diagnostic biomarkers or therapeutic targets for thyroid-associated ophthalmopathy in the future.
Project description:We measured the expression level of tRFs and mRNAs in thyroid-associated ophthalmopathy patients through high-throughput sequencing technology and verified the expression by quantitative real-time PCR. Then, the possible biological regulation and potential clinical significance of target genes of differentially expressed tRFs were assessed.
Project description:Our study aimed to investigate the differentially expressed lncRNA and circRNAs and their potential roles in orbital adipose/connective tissue from patients with thyroid-associated ophthalmopathy (TAO).
Project description:Thyroid-associated ophthalmopathy (TAO) is a complex eye and orbital disorder that is uniquely linked to Graves’ hyperthyroidism (GH). A popular explanation for the development of orbital inflammation in these patients is autoimmunity against the TSH-receptor expressed in orbital preadipocytes. However, this has not been proven and alternative hypotheses should be entertained. We have shown recently that antibodies against highly purified rabbit skeletal muscle calsequestrin are sensitive and specific markers of eye muscle inflammation in patients with thyroid autoimmunity. Keywords: disease state comparison In the study presented here, RNA from thyroid tissue of hyperthyroid patients with (n=10) and without (n=8) symptoms of ophthalmopathy was compared across 20,589 genes.
Project description:Purpose:The purpose of this study is to investigate the potential mechanisms that triggering the onset of constrictive pericarditis and to screen hub genes that exert impact on pathogenesis of patients with constrictive pericarditis. Methods: We screened differentially expressed genes with the data obtained from RNA-seq on CP samples and matched normal samples. Functional annotation analysis and protein-protein interaction (PPI) network were performed to investigate the potential key pathways and genes that play significant roles in CP. Furthermore, the ceRNA network was established and the Gene Set Enrichment Analysis (GSEA) was executed to dig key circRNAs. Results: Following the identification of differentially expressed genes, functional annotation analysis was conducted, suggesting that differentially expressed mRNAs (DEMs) were mainly involved in inflammatory response related pathways. The top 11 genes with the highest degree were extracted from PPI network. A total of 377 predicted regulatory relationships among the differentially expressed genes were found and the ceRNA network was established. Finally, GSEA was conducted on the circRNAs and the key biological pathways were identified. Conclusion: Our study is the pioneering research to analyze the pathogenesis of CP with integrated informatics and we have identified several hub genes, which reveals that the generation of CP is closely related to inflammation and fibrosis.
Project description:Purpose:The purpose of this study is to investigate the potential mechanisms that triggering the onset of constrictive pericarditis and to screen hub genes that exert impact on pathogenesis of patients with constrictive pericarditis. Methods: We screened differentially expressed genes with the data obtained from RNA-seq on CP samples and matched normal samples. Functional annotation analysis and protein-protein interaction (PPI) network were performed to investigate the potential key pathways and genes that play significant roles in CP. Furthermore, the ceRNA network was established and the Gene Set Enrichment Analysis (GSEA) was executed to dig key circRNAs. Results: Following the identification of differentially expressed genes, functional annotation analysis was conducted, suggesting that differentially expressed mRNAs (DEMs) were mainly involved in inflammatory response related pathways. The top 11 genes with the highest degree were extracted from PPI network. A total of 377 predicted regulatory relationships among the differentially expressed genes were found and the ceRNA network was established. Finally, GSEA was conducted on the circRNAs and the key biological pathways were identified. Conclusion: Our study is the pioneering research to analyze the pathogenesis of CP with integrated informatics and we have identified several hub genes, which reveals that the generation of CP is closely related to inflammation and fibrosis.
Project description:This study aimed to identify the crucial molecules and explore the function of noncoding RNAs and related pathways in IDD. We randomly selected 3 samples each from an IDD and a spinal cord injury group (control) for RNA-sequencing. We identified 463 differentially-expressed long noncoding RNAs (lncRNAs), 47 differentially-expressed microRNAs (miRNAs), and 1,334 differentially-expressed mRNAs in IDD. Three hundred fifty-eight lncRNAs as cis-regulators could potentially target 865 genes. Protein–protein interaction (PPI) network analysis confirmed that IL-6, VEGFA, IGF1, MMP9, CXCL8, FGF2, IL1B, CCND1, ITGAM, PTPRC, FOS and PTGS2 were hub genes. We built a competing endogenous RNA (ceRNA) network and identified lncRNA XIST–hsa-miR-4775–PLA2G7 and lncRNA XIST–hsa-miR-424-5p–AMOT/TGFBR3 ceRNA axes.
Project description:Purpose: Immunoglobulin A nephropathy (IgAN) is immune-mediated primary glomerulonephritis, which is the most common reason leading to renal failure worldwide, the exact pathogenesis of IgAN is not well defined. Accumulating evidence indicates that circular RNAs (circRNAs) play crucial roles in the immune disease by involving in the competing endogenous RNA (ceRNA) network mechanism. At present, the studies of the circRNA profiles and circRNA-associated ceRNA networks in the IgAN are still scarce. This study aimed to elucidate the potential roles of circRNA, microRNA (miRNA), and messenger RNA (mRNA) ceRNA network in peripheral blood mononuclear cells (PBMCs) of IgAN. Methods: CircRNA sequencing was used to identify the differential expressed circRNAs (DEcircRNAs) of PBMCs in IgAN and healthy controls. A circRNA-miRNA-mRNA ceRNA network was constructed to further investigate the mechanisms of IgAN. Results: A total of 145 circRNAs were differentially expressed in IgAN compared with controls (|log2 (FC)|>1 and P-value <0.05). Combined with the data from GSE73953 and GSE25590 in GEO database, a ceRNA network was constructed which contained 16 DEcircRNAs, 72 differential expressed mRNAs (DEmRNAs) and 11 differential expressed miRNAs (DEmiRNAs). Conclusion: Our study identified a novel circRNA-mediated ceRNA regulatory network mechanisms in the pathogenesis of IgAN.
Project description:Primary Sjögren’s syndrome (pSS) is a chronic autoimmune disease characterized by abnormal immune cell activation. This study aimed to investigate differentially expressed long non-coding RNA (lncRNA) in peripheral blood mononuclear cells (PBMCs) in patients with pSS to identify lncRNAs that affect pSS pathogenesis. Transcriptome sequencing detected 38096 lncRNAs and 50869 mRNAs in PBMCs from patients with pSS and healthy individuals. The differentially expressed mRNAs underwent functional enrichment analysis. A protein interaction relationship (PPI) and ceRNA network was constructed. LncRNA expression in patients with pSS and controls was determined using RT-PCR. 1180 lncRNAs and 640 mRNAs were differentially expressed in pSS patients (fold change > 2 in healthy persons). The PPI network was constructed with 640 mRNAs and a ceRNA network with four key lncRNAs (GABPB1-AS1, PSMA3-AS1, LINC00847 and SNHG1). A co-expression relationship was found between GABPB1-AS1 and several upregulated mRNAs (IFI44, IFI44L, IFI6, and EPSTI1). RT-PCR revealed that GABPB1-AS1 and PSMA3-AS1 were significantly upregulated 3.0- and 1.4-fold in the pSS group, respectively. In patients with pSS, the GABPB1-AS1 expression level was positively correlated with B cell and IgG levels. GABPB1-AS1 expression levels are positively correlated with B cell levels and may be involved in the pathogenesis of pSS.