Abstract 977: 3D-models of patient-derived colon tumors for the identification of genetic factors important in the regulation of cancer stem cells
Authors: Regan Joseph L. , Schumacher Dirk , Staudte Stephanie , Boehnke Karsten , Keilholz Ulrich , Haybaeck Johannes , Lehrach Hans , Henderson David , Schaefer Reinhold , Regenbrecht Christian R. , Mumberg Dominik , Lange Martin 
Published: August 2015

Abstract
Colon cancer is a heterogeneous tumour entity. Growing evidence supports a subpopulation of cancer stem cells (CSCs) as both the drivers of tumour growth and the source of relapse following treatment. Elucidation of the cellular heterogeneity within a tumour would therefore facilitate better characterization of patient subtypes and lead to more personalized and effective treatments. Here, as part of the OncoTrack* consortium, we report the use of a Matrigel-based 3D in vitro model for the identification of genetic factors important in the regulation of CSCs.
The identity and frequency of CSCs within each patient-derived culture model was determined by separating cells using fluorescence assisted cell sorting (FACS) based on expression of previously defined markers of colon CSCs (ALDH+ CD44+ CD166+). Isolated subpopulations of cells are functionally tested for CSC properties in vitro (limiting dilution serial passage and population dynamics analysis) and in vivo (limiting dilution serial xenotransplantation). These studies reveal ALDH+ colon cancer cells to be highly enriched for CSCs and demonstrate large levels of variation in CSC frequency between patients.
To identify genes and pathways that could be used to specifically target CSC function, ALDH+ tumour cell subpopulations were subjected to genome-wide analyses using next-generation sequencing for detailed characterization at the level of the transcriptome and methylome. To date, genes important in the regulation of normal stem cells and CSCs, such as BMI1, EPHB2 and the WNT signalling pathway, were found to be highly expressed in CSCs. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) mediated gene technology was used to knock out genes of interest and their role in regulating CSC function was confirmed using established functional assays.
These studies provide insight into the relationship between variable tumour composition and the variable response of tumours to treatment. Ultimately, these studies will facilitate the more accurate classification and personalized treatment of colon tumours.
*The research leading to these results has received funding from the European Union's Seventh Framework Program (FP7/2007-2013) for the Innovative Medicine Initiative under grant agreement n°115234.
Citation Format: Joseph L. Regan, Dirk Schumacher, Stephanie Staudte, Karsten Boehnke, Ulrich Keilholz, Johannes Haybaeck, Hans Lehrach, David Henderson, Reinhold Schaefer, Christian R. Regenbrecht, Dominik Mumberg, Martin Lange. 3D-models of patient-derived colon tumors for the identification of genetic factors important in the regulation of cancer stem cells. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 977. doi:10.1158/1538-7445.AM2015-977