Identification of potential biomarkers associated with CD4+ T cell infiltration in myocardial ischemia-reperfusion injury using bioinformation analysis.

Background: Myocardial ischemia-reperfusion injury (MIRI) is often part of clinical events such as cardiac arrest, resuscitation, and reperfusion after coronary artery occlusion. Recently, more and more studies have shown that the immune microenvironment is an integral part of ischemia-reperfusion injury (IRI), and CD4+ T-cell infiltration plays an important role, but there are no relevant molecular targets for clinical diagnosis and treatment. Methods: The transcriptome data and matched group information were retrieved from the Gene Expression Omnibus (GEO) database. The ImmuCellAI-mouse (Immune Cell Abundance Identifier for mouse) algorithm was used to calculate each symbol's CD4+ T cell infiltration score. The time period with the greatest change in the degree of CD4+ T cell infiltration [ischemia-reperfusion 6 hours (IR6h)-ischemia-reperfusion 24 hours (IR24h)] was selected for the next analysis. Weighted gene co-expression network analysis (WGCNA) and differential expression analysis were performed to screen out CD4+ T cell-related genes and from which the gene CLEC5A was screened for the highest correlation with CD4+ T cell infiltration. The potential regulatory mechanism of CD4+ T cells in MIRI was discussed through various enrichment analysis. Finally, we analyzed the expression and molecular function (MF) of CLEC5A and its related genes in MIRI. Results: A total of 406 CD4+ T cell-related genes were obtained by intersecting the results of WGCNA and differential expression analysis. Functional enrichment analysis indicated that the CD4+ T cell-related genes were mainly involved in chemokine signaling pathway and cell cycle. By constructing a protein-protein interaction (PPI) network, a total of 12 hub genes were identified as candidate genes for further analysis. Through the correlation analysis between the 12 candidate genes found in the PPI network and CD4+ T cell infiltration fraction, we determined the core gene CLEC5A. Finally, a gene interaction network was constructed to decipher the biological functions of CLEC5A using GeneMANIA. Conclusions: In this study, RNA sequencing (RNA-Seq) data at different time points after reperfusion were subjected to a series of bioinformatics methods such as PPI network, WGCNA module, etc., and CLEC5A, a pivotal gene associated with CD4+ T-cells, was found, which may serve as a new target for diagnosis or treatment.

Identification of a potential bioinformatics-based biomarker in keloids and its correlation with immune infiltration.

Keloid formation is a pathological consequence resulting from cutaneous irritation and injury, primarily attributed to excessive collagen matrix deposition and fibrous tissue proliferation. Chronic inflammation, left uncontrolled over an extended period, also stands as a substantial contributing factor. The precise mechanisms underlying keloid formation remain unclear. Therefore, this study aimed to identify key genes for diagnostic purposes. To achieve this, we used two Gene Expression Omnibus (GEO) data sets to identify differentially expressed genes. We identified one particular gene, homeobox C9 (HOXC9), using a thorough strategy involving two algorithms (least absolute shrinkage and selection operator and support vector machine-recursive feature elimination) and weighted gene co-expression network analysis. We then assessed its expression in normal and keloid tissues. In addition, we explored its temporal expression patterns via Mfuzz time clustering analysis. In our comprehensive analysis, we observed that immune infiltration, as well as cell proliferation, are crucial to keloid formation. Thus, we investigated immune cell infiltration in the keloid and normal groups, as well as the correlation between HOXC9 and these immune cells. It was found that HOXC9 was closely associated with the immune microenvironment of keloids. This shows that HOXC9 can serve as a potential biomarker and therapeutic target for keloids.

Identification of lysosomal genes associated with prognosis in lung adenocarcinoma.

Background: Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer, representing 40% of all cases of this tumor. Despite immense improvements in understanding the molecular basis, diagnosis, and treatment of LUAD, its recurrence rate is still high. Methods: RNA-seq data from The Cancer Genome Atlas (TCGA) LUAD cohort were download from Genomic Data Commons Portal. The GSE13213 dataset from Gene Expression Omnibus (GEO) was used for external validation. Differential prognostic lysosome-related genes (LRGs) were identified by overlapping survival-related genes obtained via univariate Cox regression analysis with differentially expressed genes (DEGs). The prognostic model was built using Kaplan-Meier curves and least absolute shrinkage and selection operator (LASSO) analyses. In addition, univariate and multivariate Cox analyses were employed to identify independent prognostic factors. The responses of patients to immune checkpoint inhibitors (ICIs) were further predicted. The pRRophetic package and rank-sum test were used to compute the half maximal inhibitory concentrations (IC50) of 56 chemotherapeutic drugs and their differential effects in the low- and high-risk groups. Moreover, quantitative real-time polymerase chain reaction, Western blot, and human protein atlas (HPA) database were used to verify the expression of the four prognostic biomarkers in LUAD. Results: Of the nine candidate differential prognostic LRGs, GATA2, TFAP2A, LMBRD1, and KRT8 were selected as prognostic biomarkers. The prediction of the risk model was validated to be reliable. Cox independent prognostic analysis revealed that risk score and stage were independent prognostic factors in LUAD. Furthermore, the nomogram and calibration curves of the independent prognostic factors performed well. Differential analysis of ICIs revealed CD276, ICOS, PDCD1LG2, CD27, TNFRSF18, TNFSF9, ENTPD1, and NT5E to be expressed differently in the low- and high-risk groups. The IC50 values of 12 chemotherapeutic drugs, including epothilone.B, JNK.inhibitor.VIII, and AKT.inhibitor.VIII, significantly differed between the two risk groups. KRT8 and TFAP2A were highly expressed, while GATA2 and LMBRD1 were poorly expressed in LUAD cell lines. In addition, KRT8 and TFAP2A were highly expressed, while GATA2 and LMBRD1 were poorly expressed in tumor tissues. Conclusions: Four key prognostic biomarkers-GATA2, TFAP2A, LMBRD1, and KRT8-were used to construct a significant prognostic model for LUAD patients.

Exploration of the shared genes and signaling pathways between lung adenocarcinoma and idiopathic pulmonary fibrosis.

Background: Idiopathic pulmonary fibrosis (IPF), a type of interstitial lung disease (ILD), is a chronic disease with an unknown etiology. The occurrence of lung cancer (LC) is one of the main causes of death in patients with IPF. However, the pathogenesis driving these malignant transformations remains unclear; therefore, this study aimed to identify the shared genes and functional pathways associated with both disease conditions. Methods: Data were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. To identify overlapping genes in both diseases, the "limma" package in R software and weighted gene coexpression network analysis (WGCNA) were used. Venn diagrams were used to obtain the shared genes. The diagnostic value of the shared genes was assessed using receiver operating characteristic (ROC) curve analysis. Gene Ontology (GO) term enrichment was performed on the shared genes between lung adenocarcinoma (LUAD) and IPF, and the genes were also functionally enriched using Metascape. A protein-protein interaction (PPI) network was created using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database. Finally, the link between shared genes and common antineoplastic medicines was investigated using the CellMiner database. Results: The coexpression modules associated with LUAD and IPF were discovered using WGCNA, and 148 genes were found to overlap. In addition, 74 upregulated and 130 downregulated overlapping genes were obtained via differential gene analysis. Functional analysis of the genes revealed that these genes are primarily engaged in extracellular matrix (ECM) pathways. Furthermore, COL1A2, POSTN, COL5A1, CXCL13, CYP24A1, CXCL14, and BMP2 were identified as potential biomarkers in patients with LUAD secondary to IPF showing good diagnostic values. Conclusions: ECM-related mechanisms may be the underlying link between LC and IPF. A total of 7 shared genes were identified as potential diagnostic markers and therapeutic targets for LUAD and IPF.

Identification of a polycomb group-related gene signature for predicting prognosis and immunotherapy efficacy in lung adenocarcinoma.

Background: Several studies have reported the role of polycomb group (PcG) genes in human cancers; however, their role in lung adenocarcinoma (LUAD) is unknown. Methods: Firstly, consensus clustering analysis was used to identify PcG patterns among the 633 LUAD samples in the training dataset. The PcG patterns were then compared in terms of the overall survival (OS), signaling pathway activation, and immune cell infiltration. The PcG-related gene score (PcGScore) was developed using Univariate Cox regression and the least absolute shrinkage and selection operator (LASSO) algorithm to estimate the prognostic value and treatment sensitivity of LUAD. Finally, the prognostic ability of the model was validated using a validation dataset. Results: Two PcG patterns were obtained by consensus clustering analysis, and the two patterns showed significant differences in prognosis, immune cell infiltration, and signaling pathways. Both the univariate and multivariate Cox regression analyses confirmed that the PcGScore was a reliable and independent predictor of LUAD (P<0.001). The high- and low-PCGScore groups showed significant differences in the prognosis, clinical outcomes, genetic variation, immune cell infiltration, and immunotherapeutic and chemotherapeutic effects. Lastly, the PcGScore demonstrated exceptional accuracy in predicting the OS of the LUAD patients in a validation dataset (P<0.001). Conclusions: The study indicated that the PcGScore could serve as a novel biomarker to predict prognosis, clinical outcomes, and treatment sensitivity for LUAD patients.

Cx43 overexpression reduce the incidence of obstructive sleep apnea associated atrial fibrillation via the CaMK⠡γ/HIF-1 axis.

BACKGROUND: Previous studies by our group have demonstrated chronic intermittent hypoxia (CIH) can decrease connexin 43 (Cx43) protein expression and thus increase atrial fibrillation (AF) inducibility. Cardiac sympathetic denervation (CSD) can reduce AF and increase Cx43 expression, however, the underlying molecular mechanisms and signaling pathways are still unclear. METHODS AND RESULTS: An obstructive sleep apnea (OSA) rat model in vivo experiments and CIH H9c2 cells model in vitro experiments were used to figure out the roles and underlying mechanisms of Cx43 on OSA-associated AF. In this study, we examined the expression of Cx43, CaMKⅡγ, Bax, Caspase 3, HIF-1 Bcl-2, Tunel, and CPB/p300, to discover the association between proteins and the mechanism of regulatory changes. The downstream proteins of Cx43 were calculated by gene sequencing and data analysis. We found Cx43 expression was significantly downregulated after CIH exposure in rat and H9c2 cells. Active caspase-3 and Bax at CIH+8 h group are high, but decreased at OE+8 h group. The Bcl-2 expression was higher in the N and OE+8 h group than CIH+8 h group. TUNEL-positive cells from the CIH+8 h group was markedly higher. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated Cx43 overexpression inhibited the CaMKIIγ expression, and CaMKIIγ was involved in the HIF-1 signaling pathway. In addition, we also found Cx43 overexpression remarkably decreased the HIF-1 protein and p300 mRNA expression, which inhibits the CaMKIIγ/HIF-1 signaling pathway. CONCLUSIONS: Taken together, these results suggested Cx43 overexpression inhibits the expression of calcium/calmodulin dependent protein CaMKⅡγ via the Cx43/CaMKIIγ/HIF-1 axis, which finally reduces the myocardial apoptosis and incidence of AF.

Analysis of prognostic model based on immunotherapy related genes in lung adenocarcinoma.

Lung cancer is one of the most common malignant tumors, and ranks high in the list of mortality due to cancers. Lung adenocarcinoma (LUAD) is the most common subtype of lung cancer. Despite progress in the diagnosis and treatment of lung cancer, the prognosis of these patients remains dismal. Therefore, it is crucial to identify the predictors and treatment targets of lung cancer to provide appropriate treatments and improve patient prognosis. In this study, the gene modules related to immunotherapy were screened by weighted gene co-expression network analysis (WGCNA). Using unsupervised clustering, patients in The Cancer Genome Atlas (TCGA) were divided into three clusters based on the gene expression. Next, gene clustering was performed on the prognosis-related differential genes, and a six-gene prognosis model (comprising PLK1, HMMR, ANLN, SLC2A1, SFTPB, and CYP4B1) was constructed using least absolute shrinkage and selection operator (LASSO) analysis. Patients with LUAD were divided into two groups: high-risk and low-risk. Significant differences were found in the survival, immune cell infiltration, Tumor mutational burden (TMB), immune checkpoints, and immune microenvironment between the high- and low-risk groups. Finally, the accuracy of the prognostic model was verified in the Gene Expression Omnibus (GEO) dataset in patients with LUAD (GSE30219, GSE31210, GSE50081, GSE72094).

Histone acetylation modification regulator-mediated tumor microenvironment infiltration characteristics and prognostic model of lung adenocarcinoma patients.

Background: The incidence rate of lung adenocarcinoma (LUAD) is rapidly increasing. Recent studies have reported that histone acetylation modification plays an important role in the occurrence and development of tumors. However, the potential role of modification of histone acetylation modification in the development of tumor immune microenvironment is still unclear. Methods: In this study, we comprehensively evaluated the acetylation modification patterns of LUAD samples obtained from various different databases based on 36 histone modification regulators, and constructed a prognostic model based on The Cancer Genome Atlas (TCGA) LUAD cohort using the Cox regression method. The close relationship between histone acetylation and tumor immune characteristics was further studied, including immune infiltration, immune escape and immunotherapy. Finally, we combined three cohort (GSE30219, GSE72094 and GSE50081) from Gene Expression Omnibus (GEO) database to verify the above results. Results: We analyzed the expression, mutation and interaction of 36 histone acetylation regulated genes. After Univariate Cox regression analysis and least absolute shrinkage and selection operator regression (LASSO), 5 genes (KAT2B, SIRT2, HDAC5, KAT8, HDAC2) were screened to establish the prognosis model and calculate the risk score. Then, patients in the TCGA cohort were divided into high- and low-risk groups based on the risk scores. Further analysis indicated that patients in the high-risk group exhibited significantly reduced overall survival (OS) compared with those in the low-risk group. The high- and low-risk groups exhibited significant differences in terms of tumor immune characteristics, such as immune infiltration, immune escape and immunotherapy. The high-risk group had lower immune score, less immune cell infiltration and higher clinical stage. Moreover, multivariate analysis revealed that this prognostic model might be a powerful prognostic predictor for LUAD. In addition, drugs sensitive for this classification were identified. Finally, the efficacy of the prognostic model was validated by cohort (GSE30219, GSE72094 and GSE50081) from GEO database. Conclusions: Our study provided a robust signature for predicting changing prognosis of patients with LUAD. Thus, it appears to be a potentially useful prognostic tool. Moreover, the important relationship between histone acetylation and tumor immune microenvironment was revealed.

AP3S1 is a Novel Prognostic Biomarker and Correlated With an Immunosuppressive Tumor Microenvironment in Pan-Cancer.

Background: Adaptor-related protein complex 3, sigma one subunit (AP3S1) is one of the encoding subunits of the adaptor complex AP-3. However, its role in various tumor types and relationship with the tumor immune microenvironment (TIME) remains unclear. Methods: AP3S1 expression was analyzed using datasets from The Cancer Genome Atlas, Genotype-Tissue Expression, UALCAN, and HPA databases. Then, we performed a systematic analysis of the genetic alterations, clinical features, and prognostic value of AP3S1 in pan-cancer. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to identify the signaling pathways associated with AP3S1. The correlation between immune cell infiltration and AP3S1 expression was analyzed using immune cell infiltration data from the ImmuCellAI, TIMER2, and a previous study. Finally, we analyzed the association of AP3S1 with tumor mutational burden (TMB), microsatellite instability (MSI), and immune-related genes. Results: We found AP3S1 overexpression in most tumors and a significant association with low survival rates. GSEA and GSVA results show that AP3S1 is involved in tumor progression and associated with immune pathways in different tumor types. We also found that AP3S1 expression was positively correlated with the level of infiltration of immunosuppressive cells (tumor-associated macrophages, cancer-associated fibroblasts, Tregs) and negatively correlated with immune killer cells, including NK cells and CD8+ T cells, in pan-cancer. The expression of AP3S1 could affect TMB and MSI in various cancers. In addition, AP3S1 was positively correlated with most immunosuppressive genes, including PD-1, PD-L1, CTLA4, LAG3 and TIGIT in most cancer types. Conclusion: Our study reveals that AP3S1 is a potential pan-cancer oncogene and plays an essential role in tumorigenesis and cancer immunity. Elevated expression of AP3S1 indicates an immunosuppressive microenvironment and can be used as a potential prognostic biomarker and a target for immunotherapy.