Identification of BRIP1, NSMCE2, ANAPC7, RAD18 and TTL from chromosome segregation gene set associated with hepatocellular carcinoma

Cancer Genet. 2022 Nov;268-269:28-36. doi: 10.1016/j.cancergen.2022.09.003. Epub 2022 Sep 9.

Abstract

Introduction: Hepatocellular carcinoma is one of the most frequent cancers with high mortality rate worldwide.

Methods: TCGA LIHC HTseq counts were analyzed. GSEA was performed with GO BP gene sets. GO analysis was performed with differentially expressed genes. The subset of genes contributing most of the enrichment result of GO_BP_CHROMOSOME_SEGREGATION of GSEA were identified. Five genes have been selected in this subset of genes for further analysis. A microarray data set, GSE112790, was analyzed as a validation data set. Survival analysis was performed.

Results: According to GSEA and GO analysis several gene sets and processes related to chromosome segregation were enriched in LIHC. GO_BP_CHROMOSOME_SEGREGATION gene set from GSEA had the highest size of the genes contributing most of the enrichment. Five genes in this gene set; BRIP1, NSMCE2, ANAPC7, RAD18 and TTL, whose expressions and prognostic values have not been studied in hepatocellular carcinoma in detail, have been selected for further analyses. Expression of these five genes were identified as significantly upregulated in LIHC RNA-seq and HCC microarray data set. Survival analysis showed that high expression of the five genes was associated with poor overall survival in HCC patients.

Conclusion: Selected genes were upregulated and had prognostic value in HCC.

Keywords: Chromosome segregation; GEO; GSEA; LIHC.

MeSH terms

  • Apc7 Subunit, Anaphase-Promoting Complex-Cyclosome
  • Carcinoma, Hepatocellular* / metabolism
  • Chromosome Segregation
  • DNA-Binding Proteins / genetics
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Humans
  • Ligases / genetics
  • Ligases / metabolism
  • Liver Neoplasms* / metabolism
  • Ubiquitin-Protein Ligases / genetics

Substances

  • Apc7 Subunit, Anaphase-Promoting Complex-Cyclosome
  • RAD18 protein, human
  • DNA-Binding Proteins
  • Ubiquitin-Protein Ligases
  • NSMCE2 protein, human
  • Ligases