Anna Asplund
Uppsala University
Sweden
Title: Global expression analysis of cell lines; what can we learn about in vitro growth?
Biography
Biography: Anna Asplund
Abstract
Enormous amounts of money and time is spent on research performed on cell lines. In December 2013 a new version of the Human cell line atlas was released, featuring complete transcriptomic profiling of 43 human cell lines of diverse cellular origin. In addition, in situ protein profiles with IHC images, generated using well validated antibodies, are available for approximately 5500 gene products. With transcriptomic data additionally available from 27 different tissues, comparisons between diverse sets of both tissues and cell lines has allowed us to identify principle differences in gene expression between in vivo and in vitro growth. The analysis reveals that approximately 32% of the protein coding genes are expressed in all samples, both tissues and cell lines, and are likely to perform “housekeeping” functions. For the remaining 68%, tissues show a greater level of expression of genes involved in regulation of communication, while cell lines more abundantly express genes involved in mitosis. Hierarchical clustering reveals that, as expected, all cell lines cluster together, and not with their respective tissue counterparts. However, if only genes displaying a specific expression in a subset of tissues or cell lines are included in the analysis, the clustering appears quite different. In addition, global transcriptome analysis of colorectal cancer cell line CaCo2 reveals a greater level of resemblance to colon tissue if cultured in 3D compared to in 2D. The expression of colorectal specific genes appears to be retained in 3D, while lost in 2D. Major differences are also seen in morphology.