Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma

Abstract

Background Hepatocellular carcinoma (HCC) is considered to be a malignant tumor with a high incidence and a high mortality. Accurate prognostic models are urgently needed. The present study was aimed at screening the critical genes for prognosis of HCC. Methods The GSE25097, GSE14520, GSE36376 and GSE76427 datasets were obtained from Gene Expression Omnibus (GEO). We used GEO2R to screen differentially expressed genes (DEGs). A protein-protein interaction network of the DEGs was constructed by Cytoscape in order to find hub genes by module analysis. The Metascape was performed to discover biological functions and pathway enrichment of DEGs. MCODE components were calculated to construct a module complex of DEGs. Then, gene set enrichment analysis (GSEA) was used for gene enrichment analysis. ONCOMINE was employed to assess the mRNA expression levels of key genes in HCC, and the survival analysis was conducted using the array from The Cancer Genome Atlas (TCGA) of HCC. Then, the LASSO Cox regression model was performed to establish and identify the prognostic gene signature. We validated the prognostic value of the gene signature in the TCGA cohort. Results We screened out 10 hub genes which were all up-regulated in HCC tissue. They mainly enrich in mitotic cell cycle process. The GSEA results showed that these data sets had good enrichment score and significance in the cell cycle pathway. Each candidate gene may be an indicator of prognostic factors in the development of HCC. However, hub genes expression was weekly associated with overall survival in HCC patients. LASSO Cox regression analysis validated a five-gene signature (including CDC20, CCNB2, NCAPG, ASPM and NUSAP1). These results suggest that five-gene signature model may provide clues for clinical prognostic biomarker of HCC.

The SNHG1-Centered ceRNA Network Regulates Cell Cycle and Is a Potential Prognostic Biomarker for Hepatocellular Carcinoma

“…Variation in gene expression patterns is a common feature in cancer tissues, and the expression pattern in cancer tissues has prognostic significance (Yang et al 2021). The present study systematically analyzed DEGs between HCC and adjacent normal tissues by mining the TCGA data and identified a total of 1000 DEGs.…”

“…Variations in gene expression patterns have been shown to be associated with the pathogenesis of HCC and to have prognostic significance (Yang et al 2021). Serum alphafetoprotein (AFP) is the most commonly applied molecular marker for screening, diagnosis, and treatment of HCC (Pinero et al 2020).…”

Identification and verification of novel immune-related ferroptosis signature with excellent prognostic predictive and clinical guidance value in hepatocellular carcinoma

“…We obtained GSE36376 cohort (193 HCC and 240 adjacent normal tissues), GSE14520 cohort (247 HCC and 241 adjacent normal tissues), GSE25097 cohort (268 HCC and 243 adjacent normal tissues) and GSE10143 cohort (80 HCC tissues) from GEO. LIRI cohort (273 HCC and 203 adjacent normal tissues), the last external cohort, was obtained from the ICGC ( Liu et al, 2019 ; Yang et al, 2021b ; Jin et al, 2022 ; Li et al, 2022 ). ImmPort ( immport.org/home ) and InnateDB ( innatedb.ca/ ) databases provided 2,660 immune-related genes (IRGs), while FerrDb ( zhounan.org/ferrdb ) database shared 259 ferroptosis-related genes (FRGs) for us.…”