Comparison of transcriptome characteristics of human tumor cell lines with identical backgrounds from different sources / 国际药学研究杂志

ABSTRACT

Objective To understand the influence of different conditions to the potential phenotypes of cells, through the transcriptome sequencing and analysis for two cancer cell lines with identical genetic background from different sources, so as to provide an experimental basis for rigorous cell model-based drug screening. Methods Human cervical cancer (HeLa) cell and human liver cancer (HepG2) cell lines, newly introduced from ATCC (HeLa-ATCC and HepG2-ATCC) and a previously laboratory-stored (HeLa-PLS and HepG2-PLS) cell lines were used in the present study. The second generation high-throughput sequencing platform Illumina Novoseq was used for transcriptome sequencing, and the Gene Ontology (GO) function and pathway enrichment analysis based on the GO data base and the Kyoto Encyclopedia of Genes and Genomes (KEGG) data base, fusion gene analysis and analysis of mutation sites were performed for the differentially expressed genes (DEG). Meanwhile, the sequencing and analytical work was also performed for evaluating the effect of different culture times on the transcriptome of the ATCC-sourced HeLa cells. Results Total 7366 and 8786 DEGs in the HeLa and HepG2 cell lines were found between the HeLa-ATCC and HeLa-PLS cells and between the HepG2-ATCC and HepG2-PLS cells, respectively, HeLa and HepG2 cells, which were classified into 519 and 778 metabolic pathways by the GO function and pathway enrichment analysis, respectively. The DEGs in the HeLa cells were mainly enriched in the extracellular matrix tissues, metabolic pathways, cancer signaling pathways, cytokines and their interaction systems with receptors. The DEGs in the HepG2 cells were mainly enriched in the extracellular matrix tissues, neural active ligands and their interaction systems with receptors, cancer signaling pathways and mitogen-activated protein kinase (MAPK) signaling pathways. The cancer signaling pathway was attenuated in the HeLa-PLS cell line, while the cancer signaling pathway was enhanced in the HepG2-PLS cell line, accompanied with changes in the neuroactive factor-receptor binding activity and cytokine-receptor binding activity. On the other hand, significant changes on the genes related to the ion channels, the cell membrane receptors, such as G protein-coupled receptors, and the intracellular calcium signaling pathways found in the HeLa-ATCC cells within 6-24 hours after the cells were fully adhered. Conclusion Compared with the HeLa-ATCC and HepG2-ATCC cells, the transcriptome of the HeLa-PLS and HepG2-PLS cells showed significant changes, involving a wide range of cellular functions. Cell transcriptome sequencing might likely provide useful informations for understanding cell identity and controlling experimental conditions for drug screening and evaluation.