Cancer Cell Line Encyclopedia Expanded to Include RPPA Analysis Data

IN ONCYTE nitrocellulose film slides

The Cancer Cell Line Encyclopedia is a collaborative project started in 2008 with the goal to characterize, from a genetic and pharmacological standpoint, a large panel of human cancer models. The idea was to develop data linking genetic profiles to pharmacological outcomes that can translate into personalized therapeutic regimens and accelerate cancer research. The dataset has been expanded, as reported in a recent Nature publication, to include “genetic, RNA splicing, DNA methylation, histone H3 modification, microRNA expression, and reverse-phase protein array (RPPA) data for 1,072 cell lines from various lineages and ethnicities”. RPPA analysis was conducted by arraying serially diluted cell lysates on ONCYTE® nitrocellulose substrates using an Aushon 2470 Arrayer. The arrayed content was then probed with a primary antibody specific to cancer biomarkers and subsequently detected using a biotin-conjugated secondary antibody. Comparison between RPPA and RNA sequencing data revealed discrepancies in expression levels of MSH6 in 16 colorectal cell lines, suggesting a linkage between truncating mutations of MSH2 and loss of MSH6 protein, two proteins involved in DNA repair. ONCYTE® nitrocellulose films are the substrates of choice for RPPA analysis.  The superior binding capacity of ONCYTE films translates into high assay sensitivity, without compromising data reproducibility.

Read more here:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697103/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320027/

All the CCLE processed datasets are available at the CCLE portal (www.broadinstitute.org/ccle) and DepMap portal (http://www.depmap.org)