单基因生信文章每日见刊监控2021-4-26

2021-4-26

文章1

MYD88 Is a Potential Prognostic Gene and Immune Signature of Tumor Microenvironment for Gliomas

发表杂志：Frontiers in Oncology

影子因子：4.831；即时影响因子：6.02

摘要：

The CIBERSORT and ESTIMATE were used to figure out the composition of TME in 698 glioma cases from The Cancer Genome Atlas (TCGA) database. Differential expression analysis identified 2103 genes between the high and the low-score group. Then the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, univariate Cox regression analysis, and protein–protein interaction (PPI) network construction were conducted based on these genes. MYD88 was identified as the key gene by the combination univariate Cox and PPI analysis. Furthermore, MYD88 expression was significantly associated with the overall survival and WHO grade of glioma patients. The genes in the high-expression MYD88 group were mainly in immune-related pathways in the Gene Set Enrichment Analysis (GSEA). We found that macrophage M2 accounted for the largest portion with an average of 27.6% in the glioma TIICs and was associated with high expression of MYD88. The results were verified in CGGA database and clinical cases in our hospital. Furthermore, we also found the MYD88 expression was higher in IDH1 wild types. The methylation rate was lower in high grade gliomas.

文章2

Correlation of Tim-3 expression with chemokine levels for predicting the prognosis of patients with glioblastoma

发表杂志：J Neuroimmunol

影子因子：3.125；即时影响因子：3.35

摘要：

Glioblastoma (GBM) immunotherapy, which blocks the checkpoint inhibitor molecule T cell immunoglobulin domain and mucin domain-3 (Tim-3), has potential therapeutic applications. However, not all patients do benefit from the targeted therapy. This study aimed to explore Tim-3 expression correlated chemokine profiles and immune cell infiltration and investigate their potential as prognostic markers of glioblastoma (GBM) immunotherapy. We analyzed transcriptional data of GBM from TCGA database, to measure Tim-3 expression by R package DESeq2 analysis and observed differentially expressed genes in GBM samples with high Tim-3 expression levels. We also probed the relative gene enrichment pathways. Tim-3 expression was evident in biological processes including the recruitment of immune cells. We also identified some chemokines related to Tim-3 expression. The expression levels of CCL18, CXCL13 and CCL7 were significantly higher in GBM tissues with high Tim-3 expression than in GBM tissues with low Tim-3 expression. In addition, exploring the relationship between immune cell infiltration and Tim-3 expression suggested that Tim-3 expression was positively related to significant immune cell infiltration.

文章3

Prognostic Power of a Chaperonin Containing TCP-1 Subunit Genes Panel for Hepatocellular Carcinoma

发表杂志：Frontiers in Genetics

影子因子：3.258；即时影响因子：4.41

摘要：

Chaperonin containing TCP-1 (T-complex protein 1) (CCT) is a large molecular weight complex that contains nine subunits (TCP1, CCT2, CCT3, CCT4, CCT5, CCT6A, CCT6B, CCT7, CCT8). This study aimed to reveal key genes which encode CCT subunits for prognosis and establish prognostic gene signatures based on CCT subunit genes. The data was downloaded from The Cancer Genome Atlas, International Cancer Genome Consortium and Gene Expression Omnibus. CCT subunit gene expression levels between tumor and normal tissues were compared. Corresponding Kaplan-Meier analysis displayed a distinct separation in the overall survival of CCT subunit genes. Correlation analysis, protein-protein interaction network, Gene Ontology analysis, immune cells infiltration analysis, and transcription factor network were performed. A nomogram was constructed for the prediction of prognosis. Based on multivariate Cox regression analysis and shrinkage and selection method for linear regression model, a three-gene signature comprising CCT4, CCT6A, and CCT6B was constructed in the training set and significantly associated with prognosis as an independent prognostic factor. The prognostic value of the signature was then validated in the validation and testing set. Nomogram including the signature showed some clinical benefit for overall survival prediction. In all, we built a novel three-gene signature and nomogram from CCT subunit genes to predict the prognosis of hepatocellular carcinoma, which may support the medical decision for HCC therapy.