A new 3D culture system to identify disease-relevant genes in colorectal cancer [Microarray expression]

It is increasingly appreciated that properties of cultured epithelial cells differ dramatically in 2D compared to 3D, and the latter more faithfully recapitulates in vivo behavior. By studying a battery of human colorectal cancer (CRC) cell lines in type-1 collagen, we have found that HCA-7 cells form colonies with two distinctive and persistent morphological and functional properties. We observed predominantly single-layered polarized cysts (cystic colonies, CC) and a smaller fraction displaying disorganized solid masses (spiky colonies, SC) that were highly invasive in vivo. Despite overall genomic similarity, CC and SC exhibited distinct and dynamic patterns of gene expression in 3D. In type-1 collagen culture, a human colorectal cancer cell line, HCA-7, forms colonies with two distinct morphologies, cystic colonies (CC) and spiky colonies (SC). CC and SC were isolated and grown in 3D collagen in 12-well dishes using 50,000 cells/ml. On day 5, 10, or 15, total RNA was extracted from the middle and microarray analysis was performed in Affymatrix 133 Plus 2.0 array. So there were total of six samples performed (SC1 Day 5, 10, 15 and CC3 day 5, 10, 15)