Insights into significant pathways and gene interaction networks in peripheral blood mononuclear cells for early diagnosis of hepatocellular carcinoma.

BACKGROUND

Early diagnosis of hepatocellular cancer (HCC) significantly helps improve patient survival. However, high specific and sensitive tests for screening patients with early stage of HCC are not yet available. Novel HCC biomarkers based on gene expression profiles of peripheral blood mononuclear cells (PBMCs) might change the situation. Recently, a three gene-based signature for the non-invasive detection of early HCC was reported.

OBJECTIVE

To compare the differences in global gene expression profiles in PBMCs of healthy individuals and HCC patients, with a specific aim to uncover the significantly altered biological pathways and important hub genes.

MATERIALS AND METHODS

Two groups of data were extracted from Affymetrix microarray expression dataset GSE49515. One group had 10 PBMCs samples from healthy control individuals, and the other had 10 PBMCs samples from patients with HCC. Gene expression profiles of both groups were analyzed and compared. Furthermore, ribonucleic acid (RNA) levels of seven of the identified differentially expressed genes (DEGs) were further confirmed by quantitative reverse transcription polymerase chain reaction (QRT-PCR).

RESULTS

Significant differences were uncovered in gene expression profiles in PBMCs of healthy individuals and HCC patients. Three hundred and seventy-five up-regulated and 169 down-regulated DEGs were identified. Three hundred and eighty-seven gene ontology (GO) biological processes and 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were over-represented by the identified DEGs.

CONCLUSIONS

Using identified DEGs, significantly changed biological processes such as nucleic acid metabolic process and KEGG pathways such as cytokine-cytokine receptor interaction in PBMCs of HCC patients were identified. In addition, several important hub genes, for example, CUL4A, and interleukin (IL) 8 were also uncovered.