Newly established gastrointestinal cancer cell lines retain the genomic and immunophenotypic landscape of their parental cancers

Daniela Hirsch,Felix Rueckert,Thomas Ried,Christian Sauer,Stephanie Witt,Steffen Seyfried,Tobias Staib,Timo Gaiser,David Fiedler

doi:10.1038/s41598-020-74797-0

Abstract

Human cancer cell lines are frequently used as model systems to study molecular mechanisms and genetic changes in cancer. However, the model is repeatedly criticized for its lack of proximity to original patient tumors. Therefore, understanding to what extent cell lines cultured under artificial conditions reflect the phenotypic and genomic profiles of their corresponding parental tumors is crucial when analyzing their biological properties. To directly compare molecular alterations between patient tumors and derived cell lines, we have established new cancer cell lines from four patients with gastrointestinal tumors. Tumor entities comprised esophageal cancer, colon cancer, rectal cancer and pancreatic cancer. Phenotype and genotype of both patient tumors and derived low-passage cell lines were characterized by immunohistochemistry (22 different antibodies), array-based comparative genomic hybridization and targeted next generation sequencing (48-gene panel). The immunophenotype was highly consistent between patient tumors and derived cell lines; the expression of most markers in cell lines was concordant with the respective parental tumor and characteristic for the respective tumor entities in general. The chromosomal aberration patterns of the parental tumors were largely maintained in the cell lines and the distribution of gains and losses was typical for the respective cancer entity, despite a few distinct differences. Cancer gene mutations (e.g., KRAS, TP53) and microsatellite status were also preserved in the respective cell line derivates. In conclusion, the four examined newly established cell lines exhibited a phenotype and genotype closely recapitulating their parental tumor. Hence, newly established cancer cell lines may be useful models for further pharmacogenomic studies.

Highlights

Human cancer cell lines are frequently used as model systems to study molecular mechanisms and genetic changes in cancer
A culture context dependent genomic evolution when propagating tumor cells outside their host environment cannot be denied[11,12]. This is corroborated by more recent findings from Ben-Uri et al, showing that during patient-derived xenograft (PDX) passaging particular copy number alterations (CNAs) were acquired that differed from the ones seen in patients, while certain CNAs characteristic for and recurrently observed in patient tumors gradually disappeared during PDX passaging such as the gain of chromosome arm 8q in breast c ancers[13]
Data from single cell cloning showed single cell derived clones of established CRC cell lines select for but cannot fully maintain the genotype of the parental cell population[16]. All these findings highlight the critical role of culture conditions, prolonged passaging and the degree of genomic instability in shaping the evolution of cancer cell lines genomes and phenotypes away from patient tumors. This underlines the need for the establishment of new patient-derived models such as patient-derived cell lines (PDCLs), PDXs or patient-derived organoids (PDOs), which may better reflect the biologic properties of the tumors they were derived from

Summary

Introduction

Human cancer cell lines are frequently used as model systems to study molecular mechanisms and genetic changes in cancer. Data from single cell cloning showed single cell derived clones of established CRC cell lines select for but cannot fully maintain the genotype of the parental cell population[16] All these findings highlight the critical role of culture conditions, prolonged passaging and the degree of genomic instability in shaping the evolution of cancer cell lines genomes and phenotypes away from patient tumors. We performed a direct side-by-side comparison with the respective parental tumors to determine to what extent the newly established low-passage cell lines reflect the phenotypic, genomic and genetic characteristics of the tumor from which they have been derived To this end, both parental tumors and corresponding derived cell lines were analyzed by immunohistochemistry, array comparative hybridization (aCGH) and targeted generation sequencing (TruSeq Amplicon 48-gene panel). This allowed us to assess how faithfully newly established PDCLs model their tumors of origin

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