Abstract 4387: The clonal composition of colorectal cancer cell lines is defined by the maintenance of specific genomic imbalances, not by ongoing chromosomal instability
Authors: Wangsa Darawalee , Schiefer Madison , Bronder Daniel , Padilla-Nash Hesed , Torres Irianna , Warner Lidia , Hu Yue , Gertz E Michael , Schwartz Russell , Schäffer Alejandro A. , Hirsch Daniela , Gaiser Timo , Meyer Rüdiger , Camps Jordi , Heselmeyer-Haddad Kerstin , Ried Thomas 
Published: July 2017

Tumor type specific genomic imbalances are the defining feature of carcinomas. It remains elusive to which extent intratumor heterogeneity and the clonal composition of cancer cell populations influences the genetic makeup and the phenotype of tumors. Many studies aimed at understanding the idiosyncrasies of cancer rely on the analysis of cell lines derived from primary tumors. In an attempt to decipher patterns of chromosomal heterogeneity we analyzed the widely used colorectal cancer cell lines DLD-1, HCT116, H508, SW620, HT-29 and SW480 using FISH and gene expression profiling. First, we applied a four color probe set that targets the oncogenes EGFR, CCND1, CDX2 and TERC and enumerated 200 metaphase spread, which included chromosome counts, and 5,000 interphase cells. Not surprisingly, the mismatch repair deficient cell lines DLD-1 and HCT116 were the most stable, whereas the aneuploid cell lines displayed a higher degree of instability. These results prompted us to apply our recently developed multiplex interphase FISH approach that allows copy number analysis of 12 gene loci in individual cells to 11 single cell derived clones from both HT-29 and SW480. SW480 was considerably more instable than HT-29. The parental lines consisted of major clones, which were propagated in the single cell derived lines. These analyses were complemented by gene expression profiling of the single cell derived clones and the parental cell lines using the Nanostring technology which measures expression levels of 770 cancer-associated genes. The SW480 clones separated into two distinct clusters that reflect discrete ploidy levels that were also present in the parental line. We then explored whether mutations of the BRAF (HT-29) and KRAS (SW480) genes observed in the parental lines were maintained in the derived clones; this was the case in all instances. Finally, we reconstructed phylogenetic trees of tumor evolution using a specifically developed algorithm, termed FISHTrees.

Our meticulous analysis of the clonal composition of these colorectal cancer models shows that, despite a certain degree of chromosomal instability, specific genomic imbalances are maintained. The results challenge the concept of ongoing chromosomal instability in cancer cell populations. This suggests a karyotype evolution that is driven by the necessity to arrive at a different plateau of chromosomal copy number as the driving force of carcinogenesis.

Citation Format: Darawalee Wangsa, Madison Schiefer, Daniel Bronder, Hesed Padilla-Nash, Irianna Torres, Lidia Warner, Yue Hu, E Michael Gertz, Russell Schwartz, Alejandro A. Schäffer, Daniela Hirsch, Timo Gaiser, Rüdiger Meyer, Jordi Camps, Kerstin Heselmeyer-Haddad, Thomas Ried. The clonal composition of colorectal cancer cell lines is defined by the maintenance of specific genomic imbalances, not by ongoing chromosomal instability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4387. doi:10.1158/1538-7445.AM2017-4387