Identification of key gene modules and hub genes of human mantle cell lymphoma by coexpression network analysis

Abstract

Purpose Mantle cell lymphoma (MCL) is a rare and aggressive subtype of non-Hodgkin lymphoma that is incurable with standard therapies. The use of gene expression analysis has been of interest, recently, to detect biomarkers for cancer. There is a great need for systemic coexpression network analysis of MCL and this study aims to establish a gene coexpression network to forecast key genes related to the pathogenesis and prognosis of MCL. Methods The microarray dataset GSE93291 was downloaded from the Gene Expression Omnibus database. We systematically identified coexpression modules using the weighted gene coexpression network analysis method (WGCNA). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis were performed on the modules deemed important. The protein–protein interaction networks were constructed and visualized using Cytoscape software on the basis of the STRING website; the hub genes in the top weighted network were identified. Survival data were analyzed using the Kaplan–Meier method and were compared using the log-rank test. Results Seven coexpression modules consisting of different genes were applied to 5,000 genes in the 121 human MCL samples using WGCNA software. GO and KEGG enrichment analysis identified the blue module as one of the most important modules; the most critical pathways identified were the ribosome, oxidative phosphorylation and proteasome pathways. The hub genes in the top weighted network were regarded as real hub genes (IL2RB, CD3D, RPL26L1, POLR2K, KIF11, CDC20, CCNB1, CCNA2, PUF60, SNRNP70, AKT1 and PRPF40A). Survival analysis revealed that seven genes (KIF11, CDC20, CCNB1, CCNA2, PRPF40A, CD3D and PUF60) were associated with overall survival time (p < 0.05). Conclusions The blue module may play a vital role in the pathogenesis of MCL. Five real hub genes (KIF11, CDC20, CCNB1, CCNA2 and PUF60) were identified as potential prognostic biomarkers as well as therapeutic targets with clinical utility for MCL.

CHN1 is a Novel Prognostic Marker for Diffuse Large B-Cell Lymphoma

“…CD3D, CLU, ICOS, KLRB1 and LAT appear to be prognostic factors in a range of malignancies, such as B-NHL, 19 , 20 colorectal cancer, 21 , 22 ovarian cancer, 23 bladder cancer, 24 breast cancer, 25 , 26 cervical cancer, 27 and lung cancer, 28–31 and play important roles in lymphoma development. 32–36 Of note, the role and prognostic value of CHN1 in B-NHL have never been reported before, so we focused our attention on CHN1 in this study.…”

“…Kaplan-Meier curves showed that the high expression of these genes was correlated with a prolonged survival time in both GSE10846 (Figure 3A-F, p < 0.05) and GSE117556 (Figure 3G-L, p < 0.05). CD3D, CLU, ICOS, KLRB1 and LAT appear to be prognostic factors in a range of malignancies, such as B-NHL, 19,20 colorectal cancer, 21,22 ovarian cancer, 23 bladder cancer, 24 breast cancer, 25,26 cervical cancer, 27 and lung cancer, [28][29][30][31] and play important roles in lymphoma development. [32][33][34][35][36] Of note, the role and prognostic value of CHN1 in B-NHL have never been reported before, so we focused our attention on CHN1 in this study.…”

Identification of Key Pathways and Genes Related to the Development of Hair Follicle Cycle in Cashmere Goats

“…The genes with similar expression patterns were summarized in the same module by the module eigengenes (MEs) [ 36 ]. The modules with more than 75% similarity were merged by using the default tree height cut of 0.25: MEDISSTHRES=0.25 in WGCNA [ 36 , 37 ].…”

CDC20 in and out of mitosis: a prognostic factor and therapeutic target in hematological malignancies

“…Combination of proTAME with Apcin, doxorubicin and venetoclax show synergic effects. [ 124 , 125 ] MDS CDC20 over-expression in high-risk patients Shorter RFS and inferior OS [ 126 – 128 ] MM CDC20 over-expression in cell lines and high-risk patients Inferior OS proTAME treatment induced G2/M arrest and increased apoptosis. Combination with etoposide and doxorubicin, vincristine or melphalan potentiated proTAME effect.…”