Genomic features reveal the clonal evolution in human hepatocellular carcinoma cell lines MHCC97 with stepwise metastatic potentials

Abstract Beckground：The series of human Metastatic Hepatocellular Carcinoma (MHCC) cell lines MHCC97 with a continuously enlarged metastatic capabilities have been widely used as a metastatic model in cancer research. However, their genomic features have not been thoroughly investigated so far. This study aims to reveal the genetic events that could drive metastatic clonal evolution through uncovering their genomic aberrations, together with methylomic and transcriptomic alteration.Results： We investigated the karyotypes on MHCC97L and HCCLM6 HCC cell lines with lower and the highest metastatic capability respectively, and interrogated their complete repertoire of genomic features by performing whole genome sequencing (WGS), whole exome sequencing (WES) and single-nucleotide polymorphism (SNP) genotyping. Mutations including single nucleotide variant (SNV), copy number variation (CNV) and structural variant (SV) were called. In addition, the methylome profiles were analyzed via Illumina Infinium HumanMethylation450 Bead Chip and the transcriptome profiles were analyzed via RNA sequencing (RNA-Seq). The karyotypic examination revealed that MHCC97L cells are more heterogenous than the HCCLM6 cells. The clonal analysis on the two cell lines revealed that a minor subclone with the mutations predisposed to metastatic potential within the MHCC97L become the dominant one within the HCCLM6 cell population. The amplification of CAV1, CAV2 and MET, together with STAT1 deep deletion and DELC1 promoter hypermethylation could be the earlier key drivers occurred in the MHCC97L cells. Subsequently, extra CCL4, CCL26 and TWIST2 amplification, along with the c.1061T>G in SMAD5 and c.1373A>G in RNF169 mutations and deregulatory promoter methylation in the HCCLM6 cells, aggravate the metastatic capability.Conclusions： Our results revealed that HCCLM6 cells might be derived from a minor subclone within the MHCC97L cell population, where the genetic events, including MET, CAV1 and CAV2 amplification, together with the extra mutations, amplification and deregulatory promoter methylation of some genes, drive the clonal expansion and evolution of those cells with the metastatic capability.