Gene expression profiling of PDX-derived lung squamous carcinoma cells (TUM622) grown in 2D vs. 3D culture

Tumorigenesis depends on intricate interactions between genetically altered tumor cells and their surrounding tumor microenvironment (TME). Investigation of tumor cell-TME interactions could be greatly facilitated by models that mimic human disease on both the genotypic and phenotypic levels. Three dimensional (3D) cultures represent an important means to study the impact of tumor cell-TME interactions on specific aspects of neoplastic phenotypes. Here, we developed a novel 3D culture system (termed TUM622) derived from a patient-derived xenograft (PDX) of a lung squamous carcinoma (LUSC) that was grown in extracellular matrix (Damelin et al, Cancer Research; 71(12) June 15, 2011). Single TUM622 cells established acinar-like structures with proper apical-basal polarity, remained non-motile and demonstrated heterogeneous expression of stem-like and differentiation markers similar to the original PDX model and patient tumor, but nonetheless exhibited hyperplasia. Transcriptional profiling and gene set enrichment analysis (GSEA) revealed many similarities to the established acinar models, as well as modulation of the Wnt signaling pathway and stem cell signatures. These results demonstrate that the tumor microenvironment significantly influences the plasticity of NSCLC tumor cells. In order to gain a better understanding of the cell intrinsic mechanisms regulating TUM622 acinar morphogenesis in 3D, we performed transcriptional profiling of TUM622 cells collected from 2D and 3D cultures.We identified genes that vary more than 1.5-fold with reproducible changes among the biological replicates (p < 0.05) and found a total of 9227 genes differentially expressed, indicating that changing culture conditions from 2D to 3D exerts a major influence on gene expression in TUM622 cells. A total of 6 samples, including a triplicate of TUM622 cells in 2D culture and a triplicate of TUM622 cells in 3D culture were harvested by FACS (EpCAM+ cells) and then used for gene expression profiling with the human U133+2 GeneChip