Response to programmed cell death protein 1 antibody in patients with Epstein-Barr virus-associated intrahepatic cholangiocarcinoma.

AIM: Epstein-Barr virus-associated intrahepatic cholangiocarcinoma (EBVaICC) has a distinct genomic profile and increased CD3+ and CD8+ T cells infiltration. However, the efficacy of immunotherapy in EBVaICC remains largely unknown. This study aimed to assess the efficacy of programmed cell death protein 1 (PD-1) antibody therapy in EBVaICC. METHODS: Patients with metastatic biliary tract cancer (BTC) diagnosed at Sun Yat-sen University Cancer Center from January 2016 to December 2021 were identified. In situ hybridisation was performed to detect EBV. Overall survival (OS) and progression-free survival (PFS) were measured. RESULTS: A total of 698 patients with metastatic BTC were identified, of whom 39 (5.6%) had EBVaICC. Among the 136 patients who were not administered PD-1 antibody, the OS was similar between patients with EBVaICC and EBV-negative ICC (median OS 12.5 versus 9.5 months, respectively; P = 0.692). For the 205 patients who were administered PD-1 antibody, patients with EBVaICC had significantly longer OS than patients with EBV-negative ICC (median OS 24.9 versus 11.9 months, respectively; P = 0.004). Seventeen patients with EBVaICC were administered PD-1 antibody. Eight patients (47%) achieved a partial response, and 17 patients achieved disease control. The median PFS was 17.5 months. CONCLUSIONS: This study identified a clinically actionable subset of patients with EBVaICC with a promising response to the PD-1 antibody.

Identification of biomarkers, pathways and potential therapeutic agents for salt-sensitive hypertension using RNA-seq.

Background: Salt-sensitive hypertension (SSH) is a common type of essential hypertension in China. In recent years, although an increasing number of researches have focused on SSH, few studies have been researched on patients with SSH. The objective of this study was to explore the genes and pathways linked with SSH using RNA-sequencing (RNA-seq). Materials and methods: We used RNA-seq to analyze the transcriptome of peripheral blood mononuclear cells (PBMCs) of five SSH patients and five SRH patients. Next, we analyzed the differentially expressed genes (DEGs) using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Gene Set Enrichment (GSEA) enrichment analysis. Then, Cytoscape was used to construct the protein-protein interaction (PPI) network and the hub genes. Finally, CMAP analysis found that several small molecular compounds could reverse the altered DEGs. Results: A total of 431 DEGs were found in the PBMC samples, including 294 up-regulated and 137 down-regulated genes. Functional enrichment analysis found significant enrichment in immune-related associations such as inflammation, chemokine, and cytokine-cytokine receptor interaction. The hub genes of the two modules were IL-6, IL-1A, CCL2, CCL3L3, and BUB1. In addition, we identified two small molecular compounds (iopromide and iloprost) that potentially interacted with DEGs. Conclusion: This study suggests some potential biomarkers for the diagnosis of SSH. It provides new insights into SSH diagnosis and possible future clinical treatment.

Identification of circRNA-miRNA-mRNA Regulatory Network and Autophagy Interaction Network in Atrial Fibrillation Based on Bioinformatics Analysis.

BACKGROUND: Circular RNA (circRNA) has been receiving increased attention in the research of atrial fibrillation (AF). Our study aims to find potential circRNAs and identify the circRNA-miRNA-mRNA regulatory network in AF based on bioinformatics analysis. METHODS: GSE129409 was retrieved from the Gene Expression Omnibus (GEO) database, and we used R software to analyze the differentially expressed circRNAs (DECs). Subsequently, we used several bioinformatics methods to obtain the target miRNAs and the target genes. Next, we performed Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the target genes. Then, we used Cytoscape 3.8.2 software to visualize and construct the circRNA-miRNA-mRNA regulatory network, the protein-protein interaction (PPI) network, and the autophagy-related genes network. RESULTS: We identified a total of 21 DECs, including 6 upregulated DECs and 15 downregulated DECs. After further analysis, we obtained a circRNA-miRNA-mRNA regulatory network consisting of 11 DECs, 9 target miRNAs and 410 target genes, and a PPI network. Finally, the potential novel genes of autophagy in AF were revealed by bioinformatics analysis. CONCLUSION: This study could explore the potential role of circRNA, autophagy-related genes and construct the circRNA-miRNA-mRNA regulation network in AF.

lncRNA KCNQ1OT1 may function as a competitive endogenous RNA in atrial fibrillation by sponging miR­223­3p.

Atrial fibrillation (AF) is one of the most common forms of cardiac arrhythmia. Novel evidence has indicated that a competing endogenous RNA (ceRNA) mechanism may occur in AF. The present study aimed to identify differentially expressed microRNAs (miRNAs/miRs) in AF and predict their targeting long non­coding RNAs (lncRNAs) to identify a potential ceRNA network involved in AF using bioinformatics analysis. The GSE68475 microarray dataset was downloaded from the Gene Expression Omnibus database and differentially expressed miRNAs in AF were obtained. In addition, right atrial appendage (RAA) tissues from patients with AF were collected to determine the expression levels of the miRNAs identified following bioinformatics analysis using reverse transcription­quantitative PCR (n=8 per group). Subsequently, Gene Ontology (GO) functional term and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway enrichment analyses of the target genes of differentially expressed miRNAs of interest were performed. The potential upstream lncRNAs targeting the identified miRNAs were predicted using bioinformatics analysis. A dual luciferase reporter assay was used to verify the existence of a targeted relationship between the differentially expressed miRNA and lncRNA of interest. The results identified 43 differentially expressed miRNAs, including 23 upregulated miRNAs. The trends in the expression levels of miR­223­3p were inconsistent between the microarray data and those recorded in the RAA tissues from patients with persistent AF. Therefore, miR­223­3p was selected as the miRNA of interest for further investigations. The target gene of miR­233­3p was found to be enriched in 57 GO terms and 21 KEGG signaling pathways. According to the bioinformatics prediction, 69 lncRNAs targeting miR­223­3p were identified, including the lncRNA growth arrest­specific transcript 5, lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) and lncRNA MYC­induced long non­coding RNA. The results from dual luciferase assay confirmed that miR­223­3p was a direct target of KCNQ1OT1. A ceRNA regulatory relationship may exist between KCNQ1OT1 and miR­223­3p in AF, providing therefore a novel potential research target for further studies.

Identification of key immune-related genes and immune infiltration in atrial fibrillation with valvular heart disease based on bioinformatics analysis.

BACKGROUND: Atrial fibrillation (AF) is the most common persistent arrhythmia. Valvular heart disease (VHD) and AF frequently coexist. In our study, from performing bioinformatics analysis, we sought to identify immune-related genes (IRGs) and explore the role of immune cell infiltration in AF-VHD in depth, aiming at investigating the potential molecular mechanism and developing new therapeutic targets for AF, including AF-VHD. METHODS: The gene expression of the GSE41177 and GSE79768 datasets were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were analyzed via the limma package in Bioconductor with R software. Differentially expressed immune-related genes (DEIRGs) were selected via combination ImmPort database with DEGs, and the enrichment function and pathway analysis were explored. A protein-protein interaction (PPI) network was built with a Search Tool for the Retrieval of Interacting Genes/Proteins plugin in Cytoscape. The CIBERSORT algorithm was used to evaluate immune infiltration in the left atrial (LA) tissues between AF-VHD and sinus rhythm (SR) patients. Finally, a correlation analysis between key DEIRGs and infiltrating immune cells was performed. RESULTS: A total of 130 DEIRGs were detected. Enrichment function of DEIRGs demonstrated that they are significant in immune and inflammatory responses. The key DEIRGs assessed by the PPI network and involved in both the immune and inflammatory responses were the C-X-C motif chemokine ligand (CXCL) 1, pro-platelet basic protein (PPBP), CXCL12, and C-C motif chemokine ligand 4 (CCL4). The immune infiltration findings indicated that, compared with the LA tissues from SR patients, the tissues from AF-VHD patients contained a higher proportion of gamma delta T cells, but a lower proportion of CD8 and regulatory T cells. The results of correlation analysis demonstrated that CXCL1 was positively correlated with activated mast cells and significantly negatively correlated with resting mast cells. PPBP, CXCL12, and CCL4 were positively correlated with the infiltration of various immune cells, such as neutrophils, plasma cells, and resting dendritic cells. CONCLUSIONS: The key immune-related genes and the differences in immune infiltration in LA tissues play an essential role in the occurrence and progression of AF-VHD.

Long Noncoding RNA HOTAIR Functions as a Competitive Endogenous RNA to Regulate Connexin43 Remodeling in Atrial Fibrillation by Sponging MicroRNA-613.

Several studies have indicated that long noncoding RNAs (lncRNAs)-HOX transcript antisense RNA (HOTAIR) is involved in some cardiovascular diseases by regulating gene expression as a competitive endogenous RNA (ceRNA). GJA1 encoding Cx43 is one potential target gene of microRNA-613 (miR-613). Meanwhile, there is a potential target regulatory relationship between HOTAIR and miR-613. The present study is aimed at investigating whether HOTAIR functions as a ceRNA to regulate the Cx43 expression in atrial fibrillation (AF) by sponging miR-613. The expressions of HOTAIR, miR-613, and Cx43 were detected in the right atrial appendages of 45 patients with heart valve disease, including 23 patients with chronic AF. The HOTAIR overexpressed and underexpressed HL-1 cell model were constructed to confirm the effect of HOTAIR on Cx43. Then, the Cx43 expression was detected to testify the interplay between HOTAIR and miR-613 after cotransfecting HOTAIR and miR-613. Furthermore, luciferase assays were performed to verify that HOTAIR could regulate Cx43 remolding as a ceRNA by sponging miR-613. The expression of HOTAIR and Cx43 was significantly downregulated in chronic AF group. HOTAIR regulated positively the Cx43 expression in HL-1 cells. The upregulated effect of HOTAIR on the Cx43 expression could be remarkably attenuated by miR-613. Moreover, the inhibitory effect of miR-613 on the Cx43 expression could be obviously mitigated by HOTAIR. At last, luciferase assays confirmed HOTAIR functioned as a ceRNA in the Cx43 expression by sponging miR-613. Our study suggests that HOTAIR, functioning as a ceRNA by sponging miR-613, is an important contributor to Cx43 remolding in AF.