Exploring molecular basis of therapy response in patient derived primary liver cancer cell lines

Primary liver cancers (PLCs) rank among the most lethal solid cancers worldwide due to lack of effective biomarkers for early detection and limited treatment options in advanced stages. While cell lines have been of significant impact for cancer research over the last decades, development of in vitro models that closely recapitulate phenotypic and molecular diversity of the primary cancers is urgently needed to improve the outcome of patients.

Long-term cultures of 7 primary liver cancer cell lines of hepatocellular and cholangiocellular origin were established using defined culture conditions. Morphological and histological characteristics of obtained cell lines and xenograft tumors were analyzed and compared to original tumors. Time course analyses of transcriptomic and genomic changes were performed using next-generation sequencing (NGS). Key oncogenic alterations were identified by targeted NGS and cell lines carrying potentially actionable mutations were treated with corresponding specific inhibitors.

Newly patient-derived cell lines (PDCL) fully resembled morphological features of the primary cancers in vitro and in vivo. Transcriptome profiles of the PDCL showed high concordance with the primaries and remained stable for 30 passages. Next-generation sequencing approaches confirmed that key oncogenic mutations such as TP53, KRAS, CTNNB1 as well as potentially actionable mutations (e.g. MET, cKIT, KDR) were highly conserved in the PDCL during long-term cultivation. Integrative genomic and transcriptomic approaches demonstrate the utility of PDCL as a representative model for distinct prognostic subpopulations of liver cancer patients. Moreover, the PDCL could be effectively used for therapeutic testing after long-term passaging. Specific targeting of detected actionable mutations, such as MET and cKIT, confirmed a superior response and sustained sensitivity to specific inhibition in comparison to non-mutated control cells. Interestingly, we also observed a progressive increase in genomic diversity during early passages (P30) which further remained stable after long-term passaging (P100). Therapeutically these changes did not affect response to actionable mutation as well as classic chemotherapeutics.

Together, our integrative analysis demonstrates that the use of newly established cell lines represents a sophisticated model to discover relevant molecular subgroups and to test drug sensitivity by exploring precision medicine approaches.